Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic.

Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
46545 T C TCAATCACTCCATTCATCGAGCTAATGCTCGACGAAACCTTGTTGGATCCGTGGCAAAAGCT[T/C]AGTGAATGGTTCAAAAGCGAAGAGCCTTCCACTGCCTTTGAACTGTTCCATAAAACATTC
47677 C T AACTATAAAGTCCTTGACTTTTGCATTATAGCTAATACCCGGGAAACAAGTTTTAGTATCACAT[C/T]TTTTAGTGAAAACAAAGCCAGGTGAACACCTGAAACAACGAGGGCACCTACCTATGCTCTT
48799 A G AAAATGGCATTCGAGAGCAGCAATGCTGAAGTGAGCGACCGTGGTCTGTTTGGCTCCGGCAAA[A/G]AGGGCGAAGCCAAGAACGAAGAGGAAGATTTGGTTGCCGGAGTCGAAAGTCAGAAGGTCGACGAATC
48917 G T ATAAGCGGAGAAAGGAGCAAGGAGGAGGAAGAGAAGAGCGACAAGTGGCACAGGGTAGAACG[G/T]AGCAGTGGGAAGTTCATGAGGAGGTTCAGGCTGCCTGAAAACGCAAAGATGGATGAGGTGAAGGCAGC
49539 T C GCCTACTGGATCGTCAATCGCAGGGCAATCAAATTACAAATAAATCCTAAAATCAATTTCTAGGGTT[T/C]AAAATGTCAGGAAGAGGGAAAGGAGGTAAAGGTCTTGGAAAGGGAGGAGCCAAGCGTCATCGTAA
49865 T C TTCTTCACTTGCTCCTTCGGCACAGTCACGGTGAGAACTCCATTCTCCATTGCAGCCTTCACCTCAT[T/C]CATCTTCGCATTTTCAGGCAGTCTAAACCTCCTCATGAATCTCCCACTGCTCCTTTCTATCCTGTG
50217 A G ATTGGTCACGTGCTTCTGGTGCTTATCGCGCTAAGTATTTACGGGCTATTGCCGCTAAGGTGACGGAGAA[A/G]AAACCTTTATTGGCTAAGCTAGAATCACTTGATTGTGGGAAACCTTTAGATGAAGCAGCATGGGA
50217 A G ATTGGTCACGTGCTTCTGGTGCTTATCGCGCTAAGTATTTACGGGCTATTGCCGCTAAGGTGACGGAGAAAAA[A/G]CCTTTATTGGCTAAGCTAGAATCACTTGATTGTGGGAAACCTTTAGATGAAGCAGCATGGGA
50447 G A ACTGCTTCGGTGCCTGCTGGTGCTTGGGTCAGCAACACCACGGCATAAGCCAGTGCAAACAC[G/A]GTAATCAGTGGCGACGATGCTTTCATGTTTCCAATTCTTCTACCTCTTCTATCTTTTGTTTACTTTGGTTGTTG
50665 G C GTTTAATGTTTACTGCTTTATTTTGGTATGAATGAAAAACATGGCTTCTATGAAAATCCCTGT[G/C]CTGTGTACTCACGAATTAGACTAGTTGAAATGAGAAGAAATAAATCTGATCTTATTTTTAAAAAAAAAAAAAA
50949 A G TATTACTGGTCACTCCACCCGGTATACATTGATGGCAGCGGTCGAATTATATGCGAAGGC[A/G]TGGCAAAATTGTACCGCTACAACGTCCAGGACAAGAGCTTGGAAATTTATCCTGTTAGCCAAAAAGTTGAAGGGGTA
50949 A T TATTACTGGTCACTCCACCCGGTATACATTGATGGCAGCGGTCGAATTATATGCGAAGGCATGGCAAA[A/T]TTGTACCGCTACAACGTCCAGGACAAGAGCTTGGAAATTTATCCTGTTAGCCAAAAAGTTGAAGGGGTA
51157 T A GACTTCTTCCTGGGTCCGCTTGGGCCCTTTCTACCTGCAACTCCCTTCTTCGATTTTCCGCC[T/A]GCCTCCATTGTTTCGAATTTGAGCTTCTAAATTAAATCTAGGGTTTCCTGAACGGATTTGGGGAGAAAGGCGATTG
51399 C T GAATCAGAAAGAGAAAGAGTAACAGTCCCATCCTCAGCAGCAGTCACATTTCCAAGGTCACCAGCATGGCGGTT[C/T]TCATCCTCAGGTGCCCCATGTTCCTTTCCAACAGGATTGAAGTGAGGACCAGTAGACATGCATCC
51461 T G ATTCCTTTCTTAGTTGCGCATTTGAGAGATGATCATAAGGTCGACATGCACACTGGTTGCACCTTCAATCACCG[T/G]TATGTTAAGTCCAATCCTAGAGAGGTCGAGAATGCCACTTGGATGCTTACGGTATTCAACTGTTT
51461 T C ATTCCTTTCTTAGTTGCGCATTTGAGAGATGATCATAAGGTCGACATGCACACTGGTTGCACCTTCAATCACCGTTA[T/C]GTTAAGTCCAATCCTAGAGAGGTCGAGAATGCCACTTGGATGCTTACGGTATTCAACTGTTT
51511 C G AGCATGAGCGGATACATATGGTTACAAATGGATCAAGCACCTCTCCCAACCCAACCACCACACACCA[C/G]CACACACGCTAAGGCGATTGATCAGGGCGTATGAGGTTTGAGATGAGCATTCTCAGATACTTCATCAGGAGG
52179 A T GATTCTATCATCATTATTATGTCTACAACGGGTACTTAGCGTATATCCTATGTAGCAACTTTATTTTGTGTT[A/T]GTTCGACGTGATTTGATTTAAACACATTTGTAGCAAGTTTTATGATAATTTGATCATGATATTCATTCTA
52179 C G GATTCTATCATCATTATTATGTCTACAACGGGTACTTAGCGTATATCCTATGTAGCAACTTTATTTTGTGTTAGTT[C/G]GACGTGATTTGATTTAAACACATTTGTAGCAAGTTTTATGATAATTTGATCATGATATTCATTCTA
52261 C T GGGTGGCTTGCTGAAGGGTTGATCGATGATTGCTGAATTTAACACTTCTTTCATCTACCAAATGGCAGGAT[C/T]GATCGATGATTCATAAGGATTCTTCATACAAACTTAATTCCTTCAAATCTTTAGAGGCCATCATTTGTTGTG
52455 T G AAAAAACTATGGCGCTTGGTAACCCATGAACCCATCGGTTTCCACTTGTAAATGGTTATGTAGAAC[T/G]TAAATGGAAAATGTAGATTCAATGATCAAACCGAATATCCAACCAAGTTTCCAGATATGTAGCTTTTTTGCTATTCTG
52455 A C AAAAAACTATGGCGCTTGGTAACCCATGAACCCATCGGTTTCCACTTGTAAATGGTTATGTAGAACTTAA[A/C]TGGAAAATGTAGATTCAATGATCAAACCGAATATCCAACCAAGTTTCCAGATATGTAGCTTTTTTGCTATTCTG
52523 A C GCTTTTCCAGCCCCACAAAAATCGGCAAGTTCATCAATACCCTCATCCAAGCACGCTGTGCTATC[A/C]ACATCAAAGCAAACTGCATCTGCCTTACGCCAAATATCTAGCACCTCTTTAGTGGGTAGCGTATTATCAAATTTGGTAG
52775 C A TCTTCTTTTACAAACAGGTTGTATAATTTCAGCTCGACGAGCGCGGTGGACCCGACGCTGAGCTCGGCGTACGCCA[C/A]GCTGCTGCAGGCGGTGTGTCCGAACACAACTGCGAATGTGAAGGTTGATTTGGATTTGGTGACGCCGAA
52877 A G GCCCGTGCCCACAGCTCCAACATTGCCTGGGCCTGTGCCCACAGTACCGACACCGTCCGTGCCTACAGTTCC[A/G]ACACTACCAATGCCTCCCGTACCGGAAATCCCTAAGATACCTGCCCCGCCTACAATACCTCCCATCCCTACTCC
53047 C T TTCTGGAAATGTTGACGGCGACTGAAGGAGGGGAGGCGTCGGAGGCGGCGAGGTCGTAGGTGTAGGGGGTGAGGAGGGAGTTGA[C/T]GGAGAAGACGCTGACGTTGTAAGGGAAGTTGCGGACGAGGGAAAGGATGGTGGCGTTGGAGGA
53071 G A ACCAAATGAAAGCTTCATTGCTACATCCACTCACCCAGTTCCCAGTACTAACAAAACGCACT[G/A]CCAAGAAAATAAAACCCAGAAGGGACTGAAAAAGACAACGGCGATAATTCATAGAGATCAACGGATGCACAACCTTCTAAAGAAT
53185 G T AGGGAATCTTCTTAATCAGTGACAGTTTAATACGGTACATTGTTCATGGAATATTAGAGCAAATTATTACAAGTGGAAATAA[G/T]ATTCTCAATGTTGAGACACCTATATCACACATATAGCACTGTGCTTATACATCGATACAGATAAA
53471 A G AAAAAAATAAAAGAAGTACAAAGCAAATAATGGCATCCCTCTCCTCTCTATGCTCACCCACACTTTCAAACTCTTT[A/G]ACATCAAAGCCAAAATCAAACCCATTCAGATCATGCTCCAAATCTAAACTCACCATCTCCTGCTCTTCTTCC
53693 G A AGGCAAGGAAGGACTCTTTATGGGTTTGGTGGTTAAAACTCCTACTGTTTGATCATGATTACTTTTGGCAATTTC[G/A]TGGTTTAGTTGTTTCTGAGGAAGCATTCGTCATGTGTTTATTCTGCAATTGAATTTCATTATTGGAGTTGAAAAA
53693 T C AGGCAAGGAAGGACTCTTTATGGGTTTGGTGGTTAAAACTCCTACTGTTTGATCATGATTACTTTTGGCAATTTCGTGG[T/C]TTAGTTGTTTCTGAGGAAGCATTCGTCATGTGTTTATTCTGCAATTGAATTTCATTATTGGAGTTGAAAAA
53771 G T CTTCTTCCTCTGAATCCACCACCGCCTCTTGGAGGTCTCATTTTGCGATGTAACTAAAAAGACCGAATTTAGAATATAGTGGC[G/T]GAGGAATTATGATGGACGAGAACAAACGGCCTTATATAGCAGATCGATATTAGCCAGTAGGCCAACA
53797 T C AACCACACCTCTTCTCCGATGGCTAACCTTGCCAAGTGACGCTATGAGCCTACGCCACCTCCCTATTGACCA[T/C]TGAAGTTGAGTTTCTACTTCCCCCATCGAACCAAAACCTTTCACCTTTTTCTCGCTGCCTTGGCACTCTCTCCCCTCG
53797 T C AACCACACCTCTTCTCCGATGGCTAACCTTGCCAAGTGACGCTATGAGCCTACGCCACCTCCCTATTGACCATTGAAG[T/C]TGAGTTTCTACTTCCCCCATCGAACCAAAACCTTTCACCTTTTTCTCGCTGCCTTGGCACTCTCTCCCCTCG
53797 T C AACCACACCTCTTCTCCGATGGCTAACCTTGCCAAGTGACGCTATGAGCCTACGCCACCTCCCTATTGACCATTGAAGT[T/C]GAGTTTCTACTTCCCCCATCGAACCAAAACCTTTCACCTTTTTCTCGCTGCCTTGGCACTCTCTCCCCTCG
54029 C T GCGGGTTTTGCAGCCAAAAGAGCATTGACAAAAGCTCCAATATTCTCTCGTAAAATCTCTTCAGAAAAATTTGCCTT[C/T]CCAAGACCCACATGGACATTAGCAGTTTTATCGTTTTTAAAATCAATACGACCACATTTTGCTGCTTTAACAGC
54029 A T GCGGGTTTTGCAGCCAAAAGAGCATTGACAAAAGCTCCAATATTCTCTCGTAAAATCTCTTCAGAAAAATTTGCCTTCCCAAG[A/T]CCCACATGGACATTAGCAGTTTTATCGTTTTTAAAATCAATACGACCACATTTTGCTGCTTTAACAGC
54067 C A GGGTCTGGAAGCTGATTCTGGGGCAGTTGCTAAAGTCATATTGGAAGACTGCGCTGATCAGTTTGA[C/A]GGGGTTAAGTCTTTGGTGGAAGTGGCTGGAGTTACTGGGAAGATTGCCAAGGAGATCAGGAAAGCTTTTCCAGGTATCAAGTGCAC
54067 A G GGGTCTGGAAGCTGATTCTGGGGCAGTTGCTAAAGTCATATTGGAAGACTGCGCTGATCAGTTTGACGGGGTTAAGTCTTTGGTGGA[A/G]GTGGCTGGAGTTACTGGGAAGATTGCCAAGGAGATCAGGAAAGCTTTTCCAGGTATCAAGTGCAC
54073 G T CCCATCATAACAACAGAATCGCCTCTAAGCCCCTTGCGAATGTTCTGTAGCTGATTTGATCCAACATTATCGGCAATAGCGAT[G/T]AGTACTTGACTATACTCCTCGAGCATTTTGCACAGCCTTTCATCGTACTTTCCTTTTCTGGAACTTTGT
54253 G A TATTTTGCATCGAATAATTTTTATATGATGGGAAATTATCCTGACAAATTTTTGTTATAGAGATGTAGTTCTCTAATATTATTGT[G/A]TTGTTTCTCACTCTGAGCTTGTTGCTCAAACAGTTATACTGTACCGTGGCTGGATTATCTTGGTTTAA
54355 C G ACATAGTACGTATTTTCCTATTTACAATTTTTTAAGGGCAAAACGTAATAAGATAACTCGCCTGCGTGCACGTGAA[C/G]GTGCTGGTCGAGTCATCGTATGCATAACTGTACGCCTGCGGACAAGCGGTTTTGAAGATGTTGGCGTATTTCGAGGG
54383 A T GATGCACCTTTAACTATGACCATTTGGAGACTGCTTAACGCCAGCAGTGTAGATTGGGTGCTTTGGTACAAG[A/T]TAGAAATCAGTAATTCTGTCTCATCTTCACTAAATTTCTGGTCACTCCACCCAGTATGCATTGATGGCAGCGGTCGAATTA
54393 A C GTTTGGGCTCAAACGAAAGCACTTCATTCTTCAAATCATAGGAAACGTGGAAATTCTGTGTCTGTATGTTACCTAATATTGA[A/C]GAAATACCCCGCGATTCTGAAACCGTGAAACAGTACAAGTTTGTATCGTCATCCTTGATTAGGTAATTGCT
54393 G A GTTTGGGCTCAAACGAAAGCACTTCATTCTTCAAATCATAGGAAACGTGGAAATTCTGTGTCTGTATGTTACCTAATATTGAAGAAATACCCC[G/A]CGATTCTGAAACCGTGAAACAGTACAAGTTTGTATCGTCATCCTTGATTAGGTAATTGCT
54543 T C AAAAAAGTACTGGACACATACAAAGGTTTCGAGAACCTTAACACCTTAGTTGACGTAGGAGG[T/C]GGAGTTGGAGGTACCATCAAATTGATTGTTAAGAAGCATCCTTATTTGAAGGGAATCAATTTCGATCTCCCTCATGTTATATCTGAGGCAGA
54543 T A AAAAAAGTACTGGACACATACAAAGGTTTCGAGAACCTTAACACCTTAGTTGACGTAGGAGGTGGAGTTGGAGG[T/A]ACCATCAAATTGATTGTTAAGAAGCATCCTTATTTGAAGGGAATCAATTTCGATCTCCCTCATGTTATATCTGAGGCAGA
54571 G A CAAGACATCGAATTCATGGATCTTTGCACTATCTTCTCCTCTCTAAAATCCCAGCCAACCTATCTTCTT[G/A]TTCTCTCAATCCTCGGCATCATCACGTTCACAAAGGTCTCATTCAAGCTTCTTTTATGGGTTTACGTCACATTCCTACGCCCCGG
54635 C A AATAAGTAGTGCAGAGCGAAATATACAACCAACAAACATACAGAAGTTTGAAGACCAAGAAGAAGAATGATATCC[C/A]TTCAATCCTCAGCTGCAATGGCAACCCCTCTACTTCATCTTCATAGAAGAAGAAATCAACATACCAAACTCAACAGGCT
54817 C T CTAAAACAAACGAACCCAGACTGTGTAGTCGCCGGCCTATTCCTGCCGTGGATCCACAATGTCGC[C/T]TCCAAGCTCAACGTCCCCAGCTTAGACTTCCATTCCTCCAACTTCACTTCCAACTGTATGTCCCACACTGTAGAACTCCACAACCTCCTC
54817 C G CTAAAACAAACGAACCCAGACTGTGTAGTCGCCGGCCTATTCCTGCCGTGGATCCACAATGTCGCCTC[C/G]AAGCTCAACGTCCCCAGCTTAGACTTCCATTCCTCCAACTTCACTTCCAACTGTATGTCCCACACTGTAGAACTCCACAACCTCCTC
54817 A G CTAAAACAAACGAACCCAGACTGTGTAGTCGCCGGCCTATTCCTGCCGTGGATCCACAATGTCGCCTCC[A/G]AGCTCAACGTCCCCAGCTTAGACTTCCATTCCTCCAACTTCACTTCCAACTGTATGTCCCACACTGTAGAACTCCACAACCTCCTC
54817 G A CTAAAACAAACGAACCCAGACTGTGTAGTCGCCGGCCTATTCCTGCCGTGGATCCACAATGTCGCCTCCAAGCTCAAC[G/A]TCCCCAGCTTAGACTTCCATTCCTCCAACTTCACTTCCAACTGTATGTCCCACACTGTAGAACTCCACAACCTCCTC
54817 A G CTAAAACAAACGAACCCAGACTGTGTAGTCGCCGGCCTATTCCTGCCGTGGATCCACAATGTCGCCTCCAAGCTCAACGTCCCCAGCTT[A/G]GACTTCCATTCCTCCAACTTCACTTCCAACTGTATGTCCCACACTGTAGAACTCCACAACCTCCTC
54877 T C GACATGCCCGGCGTCAAGCCAGGCGACGTCAGCGTGCGCATCGAGGACGACAACGTCCTGGTCATAAACGGAGAGAGGAAGAGGGAAGC[T/C]GCGGAGGAGGGGATGAAGTACTTGAGAATGGAGAGGAGAATGGGGGAGTTTATGAGGAAGTTCGTTT
54877 G A GACATGCCCGGCGTCAAGCCAGGCGACGTCAGCGTGCGCATCGAGGACGACAACGTCCTGGTCATAAACGGAGAGAGGAAGAGGGAAGCTGC[G/A]GAGGAGGGGATGAAGTACTTGAGAATGGAGAGGAGAATGGGGGAGTTTATGAGGAAGTTCGTTT
55479 C T AAACCCCCGACAAAATAAAAACAAGAGAAATGATTAAACATCCCAATTAATTTCTTGACAGCAAGACTTATGGGCAA[C/T]CCAAATCAACCAGACACAAACCTTCGCCTCAAAATGAAGGCTTTTAACCTCCAAATCCGTAGAGAGTCCTTCCCTGCCTCTT
55671 C T TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAG[C/T]TCTGAAGACGCATCGAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55671 C T TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCT[C/T]TGAAGACGCATCGAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55671 C A TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCTCTGAAGA[C/A]GCATCGAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55671 A T TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCTCTGAAGACGC[A/T]TCGAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55671 T C TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCTCTGAAGACGCA[T/C]CGAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
55671 C G TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCTCTGAAGACGCAT[C/G]GAGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55671 G A TGGTTCAGTGAAGAAGACCTTCAAGCATATGCGGATCTTTATCAGAAATCCGGTTTCAAGTATCCACTACAAGTTCCATACAGAGCTCTGAAGACGCATC[G/A]AGAAGATGTTGATCTGAGCTCGGCTCCCAAAGTTGAAGTTCCAACTTTGCTGATAATGGG
55725 A G CAGTTTAATTTCTTCCTTCAAACGAATCAAGCAAATATGTCTTGCTGTGGCGGTAACTGTGGCTGCGGATCATCCTGCAAGTGCGGAA[A/G]CGGATGCGGAGGATGTAAGATGTACGGTGATGTTGGTGAGGAGAGAAGCAGCATGACTACGACTTCGATTCT
55729 G A TGGAGGTAGGCCAGGCGTTGGTTCAGGTCCCGCTGGATGCCGTTGAGCCGTTGGATCACGGCACGGCCAAGGGATAGAGGGTCTGATTCGT[G/A]GGCCTCCAGGTGGTCGATGGCAGGTGATATGCGGATTGCGGTCCGGTCCGGTCCAATAGCATTGGAAAT
55809 C T GATGCTCGGATAACCTTCACCGGAATGATTGACTACGGACTGAGCCTAGGCTTCACGTATGTAG[C/T]CGTACAACAGCAGACGTTACCCAATAGGCATGGGAACGACAGATAGCAGATGGACAACATGGCCATGGCAAAATACATAAATTCTCAAGCCACTGTT
55879 T C ATGCATAGTAAATTGAAATCTAGACCATGACCACATCAGATCTTGATTCTAAACCCACATTAAGCCCTTT[T/C]ACCTCTGATCCTCCTTGCAAGTTGAATGTCCTTGGGCATGATGATAACTCTCTTAGCATGAATGTCACAAAAATTAGTGTCCTCAAACAAA
55879 T C ATGCATAGTAAATTGAAATCTAGACCATGACCACATCAGATCTTGATTCTAAACCCACATTAAGCCCTTTTACCTCTGATCCTCCTTGCAAG[T/C]TGAATGTCCTTGGGCATGATGATAACTCTCTTAGCATGAATGTCACAAAAATTAGTGTCCTCAAACAAA
55925 A G GTTGTCAGCAAGCTTTCGGATTCGGTCAAGGCAGAGGTCAACGATCTCTTTGCCAATGGTATAGTGGCCACGGGCAAAGTTATTAGCAGC[A/G]TCCTCCTTCCCACTAATAAGCTGTTCAGGATGAAATAGCTGGCGGTAAGTTCCAGTTCTGACTTCATCAAT
55925 C G GTTGTCAGCAAGCTTTCGGATTCGGTCAAGGCAGAGGTCAACGATCTCTTTGCCAATGGTATAGTGGCCACGGGCAAAGTTATTAGCAGCATCCTCCTT[C/G]CCACTAATAAGCTGTTCAGGATGAAATAGCTGGCGGTAAGTTCCAGTTCTGACTTCATCAAT
55975 T C GGGTTTGGTTTATGAAGAAGATCGATGTTTTTAGTCTCCTCACTGTGGTCCATGTTCGCTACCTTA[T/C]CATCCATCGACCTCATTTCTTCTTTCCACTTGAACTCACCTCCAAGCTAAAGCCTGCATTTTGAGAGATTTTCTTGTTATCCAGTAGGCCAACAG
56071 A C TAAAAATGGAAGAAAGAGGAGCTGTAGACAGGGGCGGATTCGGTAGAGGCTTTGGTCGCGGACG[A/C]GACCGCGGGCGTGACCGACGAGGAGGTCGGCGTGGACGCCGTGATGACGGTGGAAAAGAGGAATGGGTTCCAGTCACCAAGCTCGGTCGCCTCGTGAA
56089 A G TTCAACATAGATGATGAAGGACGGGCAGAGAAACAACAGTGTGCTGTTGCCGCTTCAAATATCATTAGGAATTTCTC[A/G]TTTATGCCAGAAAATGAGACAATCATGGCTCAACATAGGCATTGCGTGGAAACAGTATTTCAGTGTGTTGAAGATCAGCATACAG
56089 C T TCAACATAGATGATGAAGGACGGGCAGAGAAACAACAGTGTGCTGTTGCCGCTTCAAATATCATTAGGAATTTCTCATTTATGCCAGAAAATGAGACAAT[C/T]ATGGCTCAACATAGGCATTGCGTGGAAACAGTATTTCAGTGTGTTGAAGATCAGCATACAG
56135 C T GATGCTTCTGTGTCAAAAGGTCCAAGAAATAGCAGCGAGTACTTGCAGAAATTGCTGCCT[C/T]ACTTACTAGATGTGCTTGTGGACAATTGTTCGTCAAAAGGCGGTGTTCATGTAGGTTACTATAGACAAGAACATGATCGAAACAACATGAACAATACCAA
56187 A G CAACCATTATTTTTGGTGCTGATGTAACCCATCCTCATCCTGGCGAGGATTCTAGTCCATCAATTGCAGCTGTTGTTGCTTCCCAAGATTGGCCAGAGGT[A/G]ACCAAATATGCTGGGTTGGTAAGTGCACAAGCACATCGCCAGGAACTCATACAAGATTTATAT
56309 G A CCCTTCAGGGAGAGGCCGCACATGTGGGACACGTCGAACAGGCTACCGTTGGCGCGGCAGTTCAAGGTGGAGTCGATGAT[G/A]GAATCCTTGTACTGGATCGGCATCGACCAACCGGCGAAAGGGACCATCTTTCCACCGTGGGATACGTGGAAGTCGTGGAGGAC
56449 C A TTTTTTTTTTTTAAACAAAATGCCATAATGCATAAAACAAAAGCTATGATCACATTTTTCA[C/A]CTTCAACCATCAAACAACACTGCGAACAAAAACTGGACAGAAAACAAACTAGACATTGACATGCTTTGATCCTCATCGCCATATAGGAAGTATATCAGAA
56449 C T TTTTTTTTTTTTAAACAAAATGCCATAATGCATAAAACAAAAGCTATGATCACATTTTTCACCTTCAACCATCAAA[C/T]AACACTGCGAACAAAAACTGGACAGAAAACAAACTAGACATTGACATGCTTTGATCCTCATCGCCATATAGGAAGTATATCAGAATGA
56449 C T TTTTTTTTTTTTAAACAAAATGCCATAATGCATAAAACAAAAGCTATGATCACATTTTTCACCTTCAACCATCAAACAACA[C/T]TGCGAACAAAAACTGGACAGAAAACAAACTAGACATTGACATGCTTTGATCCTCATCGCCATATAGGAAGTATATCAGAATGA
56629 C T CATGTGATGTTGTTTGCAAGCGTGAGCATCTGTTCCAGTTCTGGAGGTCTCATATTCATAGGCCCATGGTGTTAGTTGGACCTAG[C/T]CTTGGTGCTGCTGTTGCAATTGATTTTGCAGCTTGCCATCCTGAAGCGGTGGCAAAATTGGTTCTAATTGATGCTAGTGT
56705 G A GCTGAATATCCTTGGGCATTATAGTGACCCGTTTGGCATGGATTGCACAGAGGTTAGTGTCCTCGAAGAGTCCAACCAAGTAGGCCTCAGCGGCTTCCTG[G/A]AGTGCCAGAACAGCATGGCTCTGGAAACGCAGATCAGTCTTGAAATCCTGTGCAATTTCCC
56773 T G CAAGAAACAATGAGTGAGGAAATTGAGCACTCATTTCTGGACATTAATGGCCTCAAGCTTCACATAGC[T/G]CAAACTGGCAAAGGAGAGAAGGGGACAGTAGTATTCTTACATGGATTTCCAGAAATATGGTACACATGGAGGTATCAAATGCAGGCAGTTGCAAAAGC
56773 G A CAAGAAACAATGAGTGAGGAAATTGAGCACTCATTTCTGGACATTAATGGCCTCAAGCTTCACATAGCTCAAACTGGCAAAGGAGAGAAGGG[G/A]ACAGTAGTATTCTTACATGGATTTCCAGAAATATGGTACACATGGAGGTATCAAATGCAGGCAGTTGCAAAAGC
56801 T C GATCTGATGTATGCAAAGAGGGCGTTTGTGCATTGGTATGTTGGCGAAGGGATGGAGGAAGGGGAGTTCAGCGAGGCCAGGGAGGA[T/C]TTGGCTGCCCTCGAGAAGGACTATGAGGAGGTAGGGGCGGAGAGTGCCGAAGGGGATGAAGGTGATGACGGTGAGGAGTA
56905 G A ATAGATTTAGTATTCCATAACAATGGATGCTTTATCAACCACTACACATCAAATTCCATCTCTCATTCCAAAATC[G/A]TCGGTTTCAAACACCGCCAATAACAACAGCAAACTTCTTATAAATCCCGCATCATCAAACGCGTACCACCCTCTGTCAACTAACAATTCCCC
57061 A G GCATTTGTATTTAGGGGAAAGAAACAATTATGTTTTGTTATTTGTCATATCTGTCATTTTCGTACTTTGTTTGGTTGGTGTG[A/G]TAATGTACTCTGTGGTCCGAGTGATAATAATTGGTAATACATGATTATAAATGGGTGTACTGAATTCAAATTATTCTGAATGGTT
57061 C A GCATTTGTATTTAGGGGAAAGAAACAATTATGTTTTGTTATTTGTCATATCTGTCATTTTCGTACTTTGTTTGGTTGGTGTGATAATGTACT[C/A]TGTGGTCCGAGTGATAATAATTGGTAATACATGATTATAAATGGGTGTACTGAATTCAAATTATTCTGAATGGTT
57061 T C GCATTTGTATTTAGGGGAAAGAAACAATTATGTTTTGTTATTTGTCATATCTGTCATTTTCGTACTTTGTTTGGTTGGTGTGATAATGTACTC[T/C]GTGGTCCGAGTGATAATAATTGGTAATACATGATTATAAATGGGTGTACTGAATTCAAATTATTCTGAATGGTT
57065 A G CAATAAGTTTAAGAAGAACAAAAATTCATCCAAGAAAGAGCAGTCTTCTCAGAAAGGAGGGA[A/G]CACATCGCATGAAGCAACAGGCAACGAGTGGCTGCAATCAGGCCAATGCCCGATAGCGAAGTCCTACAGAGCAGTAAGCTCCGTCCTCCCCTTGGTAGCA
57207 G A CCCTCCCCCTATCCCGCTATAAAAATCCGTTCCCTTCTCCCATCCTCAAAAAACCTCACCGTCCGAC[G/A]GTCCCTCTCCAGTGACGGTGGAGGAGGAATCGGAAACGGAGGCGCCGGTAGATTTCCCGGAGGAGGTGGCGGGGATCACGATGGAGACGGCGCCAACAAA
57207 T G CCCTCCCCCTATCCCGCTATAAAAATCCGTTCCCTTCTCCCATCCTCAAAAAACCTCACCGTCCGACGGTCCCTC[T/G]CCAGTGACGGTGGAGGAGGAATCGGAAACGGAGGCGCCGGTAGATTTCCCGGAGGAGGTGGCGGGGATCACGATGGAGACGGCGCCAACAAAA
57219 C T TTACTGATCAATGGCGCTCCAGGCTACATTTTCCCCTTCAGCGCTATCTGCTCACAAAGAGGGCAAGAAAAGTGTGAAAGATTCCATTTTCTTTGGAGCT[C/T]CTCTCTTTGAGCATGTCAAGTCTAGTTTCAGCCCTTCTCCTAACAGAAACAAGAGGACAAG
57223 C T TGGATTTTGGCTTTGACATTGTCGATGGTGTCCGAACTCTCTACTTCAAGAGTGATGGTTTTACCAGT[C/T]AGAGTTTTAACAAAGATTTGCATCTTGAAGAAAAGTTACGAAAATTGGTGGAGCTTGCGAGGGACTAGCGATTTCAAAGAACTTCCAGTAGGCCAACAGT
57223 A G TGGATTTTGGCTTTGACATTGTCGATGGTGTCCGAACTCTCTACTTCAAGAGTGATGGTTTTACCAGTCAG[A/G]GTTTTAACAAAGATTTGCATCTTGAAGAAAAGTTACGAAAATTGGTGGAGCTTGCGAGGGACTAGCGATTTCAAAGAACTTCCAGTAGGCCAACAGT
57223 G T GGCTTTGACATTGTCGATGGTGTCCGAACTCTCTACTTCAAGAGTGATGGTTTTACCAGTCAGAGTTTTAACAAAGATTTGCATCTTGAAGAAAAGTTAC[G/T]AAAATTGGTGGAGCTTGCGAGGGACTAGCGATTTCAAAGAACTTCCAGTAGGCCAACAGT
57257 C T GACAGCTTTCGGGTTTACCCCGATGTCTGCGGTAAACCCGTCCTTCCCGTAGGCCTTCTCCCTCCACCGGAG[C/T]CCGTCGAGAATCAGGAGGGTGATCAGATCGTGCGGTGGCTGAGCAACAAAAAGGCCAGATCTGTAGTGTACATTTCTTTTGGAAGCGAAACGGGCTT
57313 G A GCAGAGGCCACTGTTCCGCATGATACGCTCGCATCAGCTTGTGGAGTTGCCACTGCTATGA[G/A]TGCGATTGCTACCATGGCGCAGATGATCAATGAGTAGCAAGACATTTTCCTCTTTCTCTTATATTTGATTTTTGATGCTTAATAATGAGTGAGTCCAGTA
57313 C T GCAGAGGCCACTGTTCCGCATGATACGCTCGCATCAGCTTGTGGAGTTGCCACTGCTATGAGTGCGATTG[C/T]TACCATGGCGCAGATGATCAATGAGTAGCAAGACATTTTCCTCTTTCTCTTATATTTGATTTTTGATGCTTAATAATGAGTGAGTCCAGTAGGCCAACA
57319 A G CCCAGGAAAATTTCCCCCGAAACGATCCCCACATAACAAAAAAATGATTGTAATCTACACATCATAAATCCTTAAAATTGGGTCAATCA[A/G]CCTCAGTGTAATTATTAATATGGTATATTTATGGTAACCATACCACATCAATGGTCCTGCATGATTAAATTAAAGCCCAA
57385 C T ATATGAAAGGCAAGGACTTCGCATTTAGACTTAATAGTATTCAGACATGGGTCAGCGCAGCATTGACAGATGATGACACATGTATGGATGGATTTTCCAA[C/T]AAATCCATGGATGGCAAGATCAAGACAATTGTCAGAGGCCGCGTTTTGAATGTGGCTCAG
57525 G C CTGAGCAATATCAACATTCCGCTTATCGTTACGAAAAATCGTCAGAATCTCCCAAAGATCCACA[G/C]GCGTCCCCGATCTCCGAACAAGCTCCAAACAACGAGCAGCAAGCTGTCTCGTATGGTCGGTCACCCACGAGCTGGCACGCTCTGCCTGTCTGCGCCTAGA
57525 C T CTGAGCAATATCAACATTCCGCTTATCGTTACGAAAAATCGTCAGAATCTCCCAAAGATCCACAGGCGTCCCCGATCT[C/T]CGAACAAGCTCCAAACAACGAGCAGCAAGCTGTCTCGTATGGTCGGTCACCCACGAGCTGGCACGCTCTGCCTGTCTGCGCCTAGAGGGCTG
57655 G A TTTCGGGGGTCCATACAAACTCATTTTGAGGGTCGAGCAGTAGGGTCAACTTATCCATCTGAGTCTGATCAAAA[G/A]CGTGCGTGACTGGGTCGATGTAAGCTGCGTATATTCGCACATGTCGAGTAACGCTGCTTAACCATTGACCTCCGTATTCCCTGCTCATGTTTTTACT
57655 G A TTTCGGGGGTCCATACAAACTCATTTTGAGGGTCGAGCAGTAGGGTCAACTTATCCATCTGAGTCTGATCAAAAGCGTGCGTGACTGG[G/A]TCGATGTAAGCTGCGTATATTCGCACATGTCGAGTAACGCTGCTTAACCATTGACCTCCGTATTCCCTGCTCATGTTTTTACT
57791 T C ATCAACACTACCACCAAGTTAATAGAATGGATCCATACAAACACCTTCAAATCACAGTCAACCATGGCGCAACGTCCCTAACACGCCA[T/C]AGCGTCCTACCCGTCTCCTCCACAAACTCCGACCCCAACCTCCCAACCATCTCCAAAGACATCCCTCTCACCACCGCCGACACC
57791 G A ATCAACACTACCACCAAGTTAATAGAATGGATCCATACAAACACCTTCAAATCACAGTCAACCATGGCGCAACGTCCCTAACACGCCATAGC[G/A]TCCTACCCGTCTCCTCCACAAACTCCGACCCCAACCTCCCAACCATCTCCAAAGACATCCCTCTCACCACCGCCGACACC
57815 G A ATCTATCAATCTAGCACGTAATAATAAATAAAATAGGAGGGAGAAGAAGAAGAGGAACTGATTGATTAATTCATATCA[G/A]TTGATCAGTTATGGCGAACGGATCTGCGATTCCTTTTCTTCTTGTTCTTTCTTTTCTAGCTGCGATGCAACTGCTGCAGGTGTTTGCAGTAAAA
57847 T C AATTCTTCAGAATCGTCGGAGACTTTATCGTAGGGTTTGTGAGTCTCGAGATTGTCGTGCACGCAGGAGGCGAAGATTCCATGGCCGTAGAAGA[T/C]GATACGAGGGACGTTTAGTTTGATAGCGGTGTCGGAGATCCAGTGGAACATGTAGTCGGCGACGATGCAATCGGGGCG
57847 A G ATTCTTCAGAATCGTCGGAGACTTTATCGTAGGGTTTGTGAGTCTCGAGATTGTCGTGCACGCAGGAGGCGAAGATTCCATGGCCGTAGAAGATGATACG[A/G]GGGACGTTTAGTTTGATAGCGGTGTCGGAGATCCAGTGGAACATGTAGTCGGCGACGATGCAATCGGGGCG
57859 G C TTCTTCTGATGTGATGATAGCTCGGAACTAGCTTTGTTGACGCTTGCCAGAACACAGTGGGTTTTGGATCG[G/C]AGCCCTATTGCTGCCGACCCTTGTTTCACTGCTTCCATAGCGTACTCGACTTGGAACAGTCGTCCAGCCGGCGACCATGTTGTGACGTCAGTGTCGTACT
57931 T C TATCTTGGGATTTGTCTTGGCATGCAAACTGCGGTTATAGAGTTCGCACGTTCAGTTCTTAACATGCATGA[T/C]GCAAACAGCACTGAATTTGACGTTGAAACTACAAATCCTTGTGTCATTTTCATGCCAGAGGGATCCAAAACTCATATGGGAGGAACAATGCGACTTGGAT
57945 T C TCTGAGAAACCCCAGCCAAGAATATCAATCGCCCATGTCTCTAATCCCACATCCTGAAGCAA[T/C]GGATATGTGTACCTCCATTCCAAAACTGAACTGTCAAAACCGTGAAGGAGAACAATAGGCTCAGATCCTAGTTTCTTGCTTGGCAATGGCTTTATACAGC
57945 C T TCTGAGAAACCCCAGCCAAGAATATCAATCGCCCATGTCTCTAATCCCACATCCTGAAGCAATGGATATGTGTA[C/T]CTCCATTCCAAAACTGAACTGTCAAAACCGTGAAGGAGAACAATAGGCTCAGATCCTAGTTTCTTGCTTGGCAATGGCTTTATACAGCTGCTCATGAT
57945 G A AGAAACCCCAGCCAAGAATATCAATCGCCCATGTCTCTAATCCCACATCCTGAAGCAATGGATATGTGTACCTCCATTCCAAAACTGAACTGTCAAAACC[G/A]TGAAGGAGAACAATAGGCTCAGATCCTAGTTTCTTGCTTGGCAATGGCTTTATACAGCTGCTCATGAT
57987 C A AATGGAAACGTTATGCAATCGACTGGGAGCATGATGCAGTCACCTCAACCACATTACAAC[C/A]AGCCTCCACTGATGATGCCTCCACAACAGTACCAGAAGATGCCACCTCCTGCTGCAGCCATGTGGGTACAGCAGCCGTCCCATATCCCTCCTCCAGTTCC
57987 A T AATGGAAACGTTATGCAATCGACTGGGAGCATGATGCAGTCACCTCAACCACATTACAACCAGCCTCCACTGATGATGCCTCCACAACAGT[A/T]CCAGAAGATGCCACCTCCTGCTGCAGCCATGTGGGTACAGCAGCCGTCCCATATCCCTCCTCCAGTTCCTCAGGCTCCAATG
57993 G A GCGTAGAGCTCATTCCATTTGTACTGGGTATTAATCGTTGTGGCATTTACAGCTTTGAATCGGATCGTGTTCAG[G/A]TACTTAAACCTCGAAAATCAATATCTAAGACCAATATTTTACATTGTCGAATCATAATGGAAGCGAAGAAGAAGAAGAGAAGCAGGACAAAAGAAAATT
58005 C T TTAGCTTCCCAGAAATAAACATCGGTGTGGCAAAGTGAAGTGAAAAGGATCTTAATTCGAACTTCATTAGC[C/T]TGAGGTGGTGCCACCTCCACTTCTTCCATCACAAGAGGCTTGCCCGCCTCCCATGAAACCGCAGCTTTGCACTTGATGACCTGACCAGCTGTGCTAGACA
58005 C G TTAGCTTCCCAGAAATAAACATCGGTGTGGCAAAGTGAAGTGAAAAGGATCTTAATTCGAACTTCATTAGCCTGAGGTGGTGCCACCTCCACTTCTTC[C/G]ATCACAAGAGGCTTGCCCGCCTCCCATGAAACCGCAGCTTTGCACTTGATGACCTGACCAGCTGTGCTAGACATC
58065 A G AAATTAGACGATAAACCAAATACCGTAATGGTAATCATCTCATACCAAAGGGGTTACATGAGATCCAATCCAATTTCGAACATTTAACACAGAATTTCAC[A/G]ACACAGATCCGTAAATAAACTAAACATTAACCGCCGAAACCATAAAGGGTCCTTCCCTGACGCTT
58065 A T TTAGACGATAAACCAAATACCGTAATGGTAATCATCTCATACCAAAGGGGTTACATGAGATCCAATCCAATTTCGAACATTTAACACAGAATTTCACAAC[A/T]CAGATCCGTAAATAAACTAAACATTAACCGCCGAAACCATAAAGGGTCCTTCCCTGACGCTT
58243 C G AAAAAAGTGGTGACTTCATCGGATTGACTTCCCTTCGATTTCAAGCATTTCCGAGCATCCAGCAAT[C/G]GAGCATCCAGCGATCGAGGACTCCAATTTCGAGCATCTCGAGATTAATCCTGGTGGATTAGAGTTTCTACTGATCATTAAAGTTTAAAACCAGTACGAAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
58385 A AC ACACCAGAAAAGACACAAAACCCAGAGACAAAACTAACACAAGAATCCACCAACATACACCAACACCCAAAAAATTCCACCTGACAAA[A/AC]GCCAGACAACGCCGGAGAAAAAGTTCACTAAGCAATGAATCGGAACAGAAACGTACGGTTACCTTGCGTTGCAAATTATAGGAAAGA
58427 C T GAACTTTTGATCAGGAAGCTTCCGTTCCAGAGACTGGTTCGCGAAATCGCTCAAGATTTCAAGACCGATTTGAGGTTCCAGAGCTCCGC[C/T]GTTTCTGCTCTGCAAGAGGCGTCTGAGGCGTATTTGGTTGGTCTCTTCGAGGATACTAATCTGTGCGCTATTCATGCTAAGAGAGT
58427 T G GAACTTTTGATCAGGAAGCTTCCGTTCCAGAGACTGGTTCGCGAAATCGCTCAAGATTTCAAGACCGATTTGAGGTTCCAGAGCTCCGCCGTTTC[T/G]GCTCTGCAAGAGGCGTCTGAGGCGTATTTGGTTGGTCTCTTCGAGGATACTAATCTGTGCGCTATTCATGCTAAGAGAGT
58427 G T AACTTTTGATCAGGAAGCTTCCGTTCCAGAGACTGGTTCGCGAAATCGCTCAAGATTTCAAGACCGATTTGAGGTTCCAGAGCTCCGCCGTTTCTGCTCT[G/T]CAAGAGGCGTCTGAGGCGTATTTGGTTGGTCTCTTCGAGGATACTAATCTGTGCGCTATTCATGCTAAGAGAGT
58441 C T TCCTTCCAGAGGGATTTTACGTAGCAAGATGGAGGGAACCTGGAAGAGCGGAGGCAGATTTTGGACGATTTGATGTGAAGACTGTTGTACGGAACGTTTA[C/T]ATACTATTTTCGAGCTCCGAGATCCCCATTGCGAAGGATGCAAATCAGGAGATAATGGATCTTGTAGATCC
58479 C G GATCCTACAAAAACCCCATCACAACCCAACTGCATCATCAGTGCCGCATCTGCCGGAGTAGCCACCC[C/G]ACCTGCAGCAAATTGCACGACAGGCAACCTTCCCAACTGCTTAGTCTGCATCACCAAATCATATGGCGCAGCAATTTTCTTTGCGAAGGTAAACACCTCA
58479 T C GATCCTACAAAAACCCCATCACAACCCAACTGCATCATCAGTGCCGCATCTGCCGGAGTAGCCACCCCACCTGCAGCAAA[T/C]TGCACGACAGGCAACCTTCCCAACTGCTTAGTCTGCATCACCAAATCATATGGCGCAGCAATTTTCTTTGCGAAGGTAAACACCTCATCATCATC
58479 G A GATCCTACAAAAACCCCATCACAACCCAACTGCATCATCAGTGCCGCATCTGCCGGAGTAGCCACCCCACCTGCAGCAAATTGCAC[G/A]ACAGGCAACCTTCCCAACTGCTTAGTCTGCATCACCAAATCATATGGCGCAGCAATTTTCTTTGCGAAGGTAAACACCTCATCATCATC
58557 G A TTCTTGGAGCTGGGATTTACAGAGAGCTGAGAGAATATGGTTTGGAGATTGGCTGAGGAGAATGGAATCGAAGTTGCTGCTTGTCGAGA[G/A]AGAAAGGTAGGCCCAAAGCCTGCTGTGGTTCTCATGAAATGCATGGTGACTTTTGTGCCTGGTAACATGTCTTTTTCTAGCACTGCT
58595 G A CACTGTTGGCCTACTGGAACACTAAATAATAGAATGGATCCATCCAAATACCTTCAATTCACACCCAACCATGACGCAACGTCCCTAAC[G/A]CGCCACATCCCGCCCGTCTCCCCCGCAAACTCCGACCCCGACCTCCCGACCATCTCTAAAGACGTCCCTCTCACAACCGCCGACACC
58595 C A CACTGTTGGCCTACTGGAACACTAAATAATAGAATGGATCCATCCAAATACCTTCAATTCACACCCAACCATGACGCAACGTCCCTAACGCGC[C/A]ACATCCCGCCCGTCTCCCCCGCAAACTCCGACCCCGACCTCCCGACCATCTCTAAAGACGTCCCTCTCACAACCGCCGACACC
58645 G A TTCTGCAGCTGAATTTCTTGGTATTTACGAAGTCCCCTTAGCAGCATACTCTATTTAAAATCAAACAATTTTTTCAAACACTAACATCTG[G/A]CCTTATAAGAGACCTCTCCTGTGTGCTGAGATTAAGGAAGTTCGGCCAACCGATTCCAAAATGCGACTAAACGCGACTTTAACAGG
58705 G A TGAATAGTTTAATGAAGAAGCACACCTGGAAGCAATGCGGCCGAAACTTCGACAACAGCCGAGCTCTCGATGGACAC[G/A]TGCGTTCTCATTTGCTGGGCAACATCAGACGAGGGCATAAGCTATTAAGTTTATAAATTTGCACAAAATCACGACCAATAAACTCTAGCGATTCAATCAC
58705 G C TGAATAGTTTAATGAAGAAGCACACCTGGAAGCAATGCGGCCGAAACTTCGACAACAGCCGAGCTCTCGATGGACACGTGC[G/C]TTCTCATTTGCTGGGCAACATCAGACGAGGGCATAAGCTATTAAGTTTATAAATTTGCACAAAATCACGACCAATAAACTCTAGCGATTCAATCAC
58705 A G TGAATAGTTTAATGAAGAAGCACACCTGGAAGCAATGCGGCCGAAACTTCGACAACAGCCGAGCTCTCGATGGACACGTGCGTTCTC[A/G]TTTGCTGGGCAACATCAGACGAGGGCATAAGCTATTAAGTTTATAAATTTGCACAAAATCACGACCAATAAACTCTAGCGATTCAATCAC
58705 T C TGAATAGTTTAATGAAGAAGCACACCTGGAAGCAATGCGGCCGAAACTTCGACAACAGCCGAGCTCTCGATGGACACGTGCGTTCTCA[T/C]TTGCTGGGCAACATCAGACGAGGGCATAAGCTATTAAGTTTATAAATTTGCACAAAATCACGACCAATAAACTCTAGCGATTCAATCAC
58705 G A TGAATAGTTTAATGAAGAAGCACACCTGGAAGCAATGCGGCCGAAACTTCGACAACAGCCGAGCTCTCGATGGACACGTGCGTTCTCATTTGCT[G/A]GGCAACATCAGACGAGGGCATAAGCTATTAAGTTTATAAATTTGCACAAAATCACGACCAATAAACTCTAGCGATTCAATCAC
58717 C T TGGCGAAGTTGTCGGTCATTCCTGTTAGGAGAGGATACTGGGGGAACAAGATTGGAAAGGTGCATACTGTTCCATGCAAGGTGACTGGGAAGTG[C/T]GGTAGTGTTACTGTGAGAATGGTGCCAGCTCCAAGAGGGTCGGGGATTGTGGCTGCTAGGGTGCCAAAGAAGGTGCTACAGTT
58813 T C CTAGTAGGTGGAAGTACCAGAATTCCAAAGGTTCAACAACTATTGAAGGATTTCTTTGAGGGAAAAGAGCC[T/C]AACAAGGGAGTGAACCCCGACGAAGCTGTTGCTTATGGTGCCGCTGTTCAGGGTGGCATTCTCAGTGGGGAAGGCGGTGATGAAACCAAAGATATCCTTC
58829 G C GTTGTAATATGCCGATCTCAGTTGTGCTGATTTTGATTGCCCTAGTGATAACCTCTTCTTTTTCCTCAACAAACCTTCAACGAATTACCTCAGTCTGCGA[G/C]TGGGCAAGGGGCAGCAATCTCCAAGCAGCCAAACAGGGAAGCGAGAGGCAGAGGCGTAGAGCGAGTATGCGCTCAAT
58925 C G GTTTGGTAAATTAGAATTTGGATGCACCTGGTGGACTAGTACTCCTACTTGCTGGTTGCGTGGAAAATACAGTG[C/G]GAGAATCAGGGGATCCCTGCAAAATGGAGAGTTCGAATACAGATGACAGCAAAAGCTACAACGAAATCGACGGCGTCGGTAACGGTGATAACTTCGGCGA
58961 C T CGTACACAGCGCTGGAGTTGGAGACGTTACAGACACAAGTTTCGATGAGGATGAAACAGATGGCATTAGTTCATGGAGGCT[C/T]ATTATCAATATCAATTTCACCGCTCTTGTTGACTGCACTCGTATTGCGATTCAAACAATGAGAAAACTGAAGAAGCCTGGTGCTGTGATGAACATGG
58985 A G GGACCGTTGATGGTGGTTTGCAGACACACTTTTGCCAGGATGAATTAAGATCGTCCAAAGCTAATGACATTACGAAAAGAGTGGTCGGCCACACCGTTCC[A/G]GTTCTCCATGGCGAGACATTTTCATTGAGAATACTGGTTGATCATTCTATTGTGGAGAGTTTTGC
59083 A C ACTTAGTGGTAGGGGGAGGCGGAGTAGTTGGAGCTGGTGGAGTACATGCAACATGTGTAGAGGAGACAATAGAAAACAGAAGGTTAAGGGCAAGGAGTGC[A/C]GCTATGCATGCAAGTGAGTTTGCCATTTTTATTTGGGGATTATGTTTACTGTCCAGTAGGCC
59087 A G GTGAAGTAAAGGTTCATGGCCTGCAAAAAGCCGAGCTCCTCCAAAGCAGCACAGGCATACATGCCCTGAGCACGTCCTAC[A/G]CGCTCCGACTCCGCCTCCGGTCCTGCCGTCAGCATATCGTCCATCATCGTTATCACTCCAAAAACCGGAAATGAAAAAGCAGAATTATTGTTGGAAACA
59123 T C AGGTACAACAAGAAACCCACCATTACTTCGAGGGAGATCCAGACTTCTGTCCGTCTTGTTCTGCCTGGCGAACT[T/C]GCAAAGCACGCTGTCTCTGAAGGCACTAAGGCGGTGACCAAGTTCACCAGCACCTGATTCGATTCCTGATCTATTTCTAGTTTGTTTTCTTTTACTTTTT
59123 C T AGGTACAACAAGAAACCCACCATTACTTCGAGGGAGATCCAGACTTCTGTCCGTCTTGTTCTGCCTGGCGAACTTGCAAAGCA[C/T]GCTGTCTCTGAAGGCACTAAGGCGGTGACCAAGTTCACCAGCACCTGATTCGATTCCTGATCTATTTCTAGTTTGTTTTCTTTTACTTTTTCTGTT
59175 G T TACCCCATCAGCATAAATTGGTTTCGGCCGAAAATGGAAAGTGGAGTTAATGGAGACCTCGATCCTTCTCCATGAAGAATCATCGTTCAC[G/T]GTTAGTACGTAACATTCTGAGACAGTCTCATCAGCCATTACCAACAGAACAACTTTATATCTTAGGGTTTTTAGATCGAAACCAAAACCC
59301 C CA GAATAACAGAAGAACGCCAATACATGTTAATAACGAGTGCTGGAATACATAAATAACACCGCAACCAAGATTGGGTGCTTACAACACAAATTCAT[C/CA]AAAAGGAACACCGACAACAACAATAATAGTCTAGTACATTCTTCAAAAGGGAGCAGCATATATAAAGATGCTCCTTTATTCTCAAC
59341 C T AGAGAAAACGTGGTGAAAGTGACGATAAGATGGCTATGCTCATTGACCTAATGCACGAGAGACAGATGAAAAAATCTCGGA[C/T]GCACTCTGATAGTCCTAATACGGGTACTAGCGTGGAATCAACGGGAAGTTCTACAACTTATGCAAATACGGTAGCTCGTATGCAACGTCTTGGAGCAACG
59397 G A AGTATGGGTGAACTGCTCTCAACCCTGCTTCACACAAGCGCCTTGGGGAGGAAACAAACGTAGTGGTTTCGGACGTGA[G/A]CTTGGTGAATGGGGTCTTGAAAACTACTTAAGCGTGAAGCAGGTGACCGAGTATGTGTCAAGCGAGCCATGGGGATGGTACCCTGCTCCTTCCAAACTCT
59397 T A GGTGAACTGCTCTCAACCCTGCTTCACACAAGCGCCTTGGGGAGGAAACAAACGTAGTGGTTTCGGACGTGAGCTTGGTGAATGGGGTCTTGAAAACTAC[T/A]TAAGCGTGAAGCAGGTGACCGAGTATGTGTCAAGCGAGCCATGGGGATGGTACCCTGCTCCTTCCAAACTCTAAA
59397 C T ACTGCTCTCAACCCTGCTTCACACAAGCGCCTTGGGGAGGAAACAAACGTAGTGGTTTCGGACGTGAGCTTGGTGAATGGGGTCTTGAAAACTACTTAAG[C/T]GTGAAGCAGGTGACCGAGTATGTGTCAAGCGAGCCATGGGGATGGTACCCTGCTCCTTCCAAACTCTAAA
59417 C T GGCACTGCATACACGTTCTTCACACCGGCAAACTCCAAGCATTCGAAGAAACTGGTTAACATTCTGGAAGGAGC[C/T]GGACAGATGGTCACTCCTGAACTGGCTCTAATGGCCAGGTCATCAGGCAACGGTAAAGGTTCTGGAAACAATTTCAGATCAAGAGGATGGGGCTATGGCA
59437 A G TTTCTTGGAACTTCTACTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCT[A/G]AAGCTCCTCTTGACAAAGTTTGTGTCCTTAGTTGCGGCATTTCTACTGGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGC
59437 C T TTTCTTGGAACTTCTACTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCTAAAGCTCCTCTTGA[C/T]AAAGTTTGTGTCCTTAGTTGCGGCATTTCTACTGGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGCTGTTTTTGGACT
59437 C T TTTCTTGGAACTTCTACTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCTAAAGCTCCTCTTGACAAAGTTTGTGT[C/T]CTTAGTTGCGGCATTTCTACTGGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGCTGTTTTTGGACT
59437 T A TTTCTTGGAACTTCTACTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCTAAAGCTCCTCTTGACAAAGTTTGTGTCCT[T/A]AGTTGCGGCATTTCTACTGGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGCTGTTTTTGGACT
59437 A G AACTTCTACTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCTAAAGCTCCTCTTGACAAAGTTTGTGTCCTTAGTTGCGGC[A/G]TTTCTACTGGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGCTGTTTTTGGACT
59437 T C CTTTTAGTGAATATACAGTTGTGCATGCCGGTTGTATCGCAAAGATCAATCCTAAAGCTCCTCTTGACAAAGTTTGTGTCCTTAGTTGCGGCATTTCTAC[T/C]GGACTTGGTGCTGCATTGAATGTTGCAAAACCAGCAAAGGGGTCGACTGTGGCTGTTTTTGGACT
59523 T C CCAACACCAGTTGGACCTAAAACAAAACGACCCAGTAGGCTGCTGTGGTCTACCAAGTCCAGCCCTTGATCTGAGAACAGC[T/C]TCAGCCACCGCATCAACTGCCATATCCTGGCCAACCACTCTCTTGTGCAGCCTCTCCGCCAAACCAATCAGTCTTTCCTTTTCATTCTGGCCCAGTCTTG
59557 T C ATCAACAGGGACAAAGCCATTATGAACAGAAGCCTTAACAGCATCAAGCACCAACTGTGTCTTCCTCGTCAA[T/C]TCAGGCCACTTAACCTCTGGCGCCATTCCATTACTCTTAATATCTCCAACCAACCTCGAAAACTCAGCAACCATCCTAGCCTCCTGAGGCAGCTCGGTGT
59567 T C GGCATCTTTAAGAGCGGGGACCCAGCGAAGAGGGCTAGGGCGATTGTGCAGGCAGTTACTCATTATAG[T/C]GATCCGGATATTCTTGCCGATGTTAGCTGTGGGCTTGGGGAGGCTATGGTTGGGATCAATTTGAATGATGCAAAGGTTGAGAGGTTTGCTGCACGTTCGG
59567 T C GGCATCTTTAAGAGCGGGGACCCAGCGAAGAGGGCTAGGGCGATTGTGCAGGCAGTTACTCATTATAGTGATCCGGA[T/C]ATTCTTGCCGATGTTAGCTGTGGGCTTGGGGAGGCTATGGTTGGGATCAATTTGAATGATGCAAAGGTTGAGAGGTTTGCTGCACGTTCGGAATGATGAG
59607 C T TAGAGGGCTTGCAGACAAACGCCACGACCAAGAATACCAAACTTATCTGATAAATAGCAACAAGTAGGAAGTTCATGTCATCGTGTTATTGTATTTCTGT[C/T]GTATTTATGTTTGTATTTTCTTTTGTGTAATGAAATGTAGTCATTTTGTTCAAAAAAAAAA
59613 G A AGTTCAAAGATTACAGACCTTCACAATCCTCGCCACCTGCTAAGTCTAGCTCTGCACCTAAGAAGGTAGAGCAAGGGCCTACCAAAACTCCTTTGTCTGC[G/A]CCATCAAGGCCTCAAGAAGCCAAGAGTGTTAAAGACCGTGTATTTGCTAGTCCTCTTGCAAGAAAATTGGC
59755 C T AAATTTTACGTCTGCGCCACTCGCAGCAGCAAGAATCTACTTATCTTGACTCCTGATGCCTCTGAGCCCTCCGCCTGACCATAC[C/T]AAAACTTATTTCGCTGGTGCTATCGGGATCTGCATCGCTCTTTGTCTGTATACGTTGACTCGTTCTACCTTGCCACCCGTTGGTGATAACATACACAGTT
59755 C T TCGCAGCAGCAAGAATCTACTTATCTTGACTCCTGATGCCTCTGAGCCCTCCGCCTGACCATACCAAAACTTATTTCGCTGGTGCTATCGGGATCTGCAT[C/T]GCTCTTTGTCTGTATACGTTGACTCGTTCTACCTTGCCACCCGTTGGTGATAACATACACAGTT
59767 C T TTCATAAAACATGTACTTCCGATAAATTGAGTACTAATTTTATCTAGATTTGAAGCGGTGA[C/T]GGCACTTCAGATGGAATAACAGGAAGATGCCCTTTCTCTTGAAGGCTTTTCACGGTCTCGTAAAGAGTCTGCGAGGTTGGGGTAAACTGCAGTCCCAAAT
59767 C A GTACTTCCGATAAATTGAGTACTAATTTTATCTAGATTTGAAGCGGTGACGGCACTTCAGATGGAATAACAGGAAGATGCCCTTTCTCTTGAAGGCTTTT[C/A]ACGGTCTCGTAAAGAGTCTGCGAGGTTGGGGTAAACTGCAGTCCCAAATCTTTCAATCGCTGATTCGAAATT
59825 C T GTTAGTACGAACTGGGCACATAAAATGCCGTACACCTTGCGGATAAAACCCCATCGAAGCTCGTTTTCGCCATGGCTAAGACCCGGATACAGCGTCGATC[C/T]GTCGCCTGCCTCCAAGTCAAAGTTCTCAAGCTTAGTAAATTTACTCATTTTTTGACAATT
59829 T G ACGTGCTGGAAGAAGAAAAATGCGGCAATTTCCATTGTCATATCCAAGTCAGATGCCGTCAGCACCGCCACTGATGCCATCCTCAACTCTGTTACC[T/G]CTTTGGTCTTTCTCTCACAATGACGAGCTTCTGCTCGCCATGGAAGAGTCGCAACTCGAAGAAAAGTGGAATGAAATCAGAAAAACAA
59829 T A ACGTGCTGGAAGAAGAAAAATGCGGCAATTTCCATTGTCATATCCAAGTCAGATGCCGTCAGCACCGCCACTGATGCCATCCTCAACTCTGTTACCTCT[T/A]TGGTCTTTCTCTCACAATGACGAGCTTCTGCTCGCCATGGAAGAGTCGCAACTCGAAGAAAAGTGGAATGAAATCAGAAAAACAA
59849 G A AAGATTGCATGGTTTCATCCCTGGCATGATGATGACTAACACATAAGACTTCAGCAGCTTATTTACGCATGCTGGAGTTGAGGTCACTGCACTTGCGTC[G/A]CACGCACATGCTGGTTGGTGCGATGAACTTCTTATCATGTTTGTCAGGATGGTCCAAGAGGTGGTGTAGAGTTGCCATTAGCATA
59917 A T GGACGGTGGGTACGCAGGCCCAAGAACTCCAAGCGAAACCGCAGTCGACACTTTGATTTTATCCGTAAGCCC[A/T]GCGCCGCCCAAAGCGTTTATGATGTTTGACATTGCGCCCAGCACGTACTGAGCTTGCGCTCCGGGTATGACTTCGTTGCCTACCGCGATGTACTTGAAGG
59917 T C GGACGGTGGGTACGCAGGCCCAAGAACTCCAAGCGAAACCGCAGTCGACACTTTGATTTTATCCGTAAGCCCAGCGCCGCCCAAAGCGTTTATGATGTT[T/C]GACATTGCGCCCAGCACGTACTGAGCTTGCGCTCCGGGTATGACTTCGTTGCCTACCGCGATGTACTTGAAGGAGACGGATGGGTA
59917 G A GCAGGCCCAAGAACTCCAAGCGAAACCGCAGTCGACACTTTGATTTTATCCGTAAGCCCAGCGCCGCCCAAAGCGTTTATGATGTTTGACATTGCGCCCA[G/A]CACGTACTGAGCTTGCGCTCCGGGTATGACTTCGTTGCCTACCGCGATGTACTTGAAGGAGACGGATGGGTA
60073 C G CCCAACCAATCTCTCACCTCATCGCCACTCCTCACCTCTCCTTCTCCTTCCACTCCTTCCATTAAATACCTCCATTCTCACTTCCCACGTTTTTCTTCTT[C/G]CAGTTCAAACAACCTCAAACACGATGAGAGGATCCCTCCTATCCCGCCTCGCCCGCCACCACCGCCGCCATTTCGCTACATC
60243 C G GGGGAGCCATTCATTAATGGAGAAGCGGTACCTTACCATCCAAAGTACCATGAAGAGTGG[C/G]TTCGCAATAATGCTCGTGCTAACGAGAGGTCACGTCGCAATGACCGTCCTCGTAATTTCGACAGGTCGAGGAACTTTGAGAGAAGAGGAGAAATGCGTTC
60247 A C AAAAAAGTACAATTGTCCCCATAAGGGCAGCCTTCTTCAGTGAAGAACTTCTTACAGTGTCTGCCTTTGTTGTAGGACCTCTGCCCTTCACCAG[A/C]AGCTGTATCTACGGTCAGTATAGGGATATGATGCTCTTCTCTTGTTTCAACCGACTCTTCATTTGCGGCCACAATCTCCTGCCAGTTGGGAGG
60257 G A CAAGGAGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTC[G/A]TCAGGTTCATCAGGCTGCGGTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACA
60257 A G CAAGGAGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTC[A/G]GGTTCATCAGGCTGCGGTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
60257 G A CAAGGAGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCA[G/A]GTTCATCAGGCTGCGGTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACA
60257 G A CAAGGAGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCAGGTTCATCA[G/A]GCTGCGGTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACA
60257 G A CAAGGAGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCAGGTTCATCAG[G/A]CTGCGGTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACA
60257 G C AGGCAGAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCAGGTTCATCAGGCTGC[G/C]GTGCCGCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACAG
60257 C T GAGTGAAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCAGGTTCATCAGGCTGCGGTGC[C/T]GCTTCGAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACAG
60257 C T AAGACTGATTGGACCAAAGCTCCCTTTACTGCTTACTATAGAAACTTCAACGCCAATGCCTGCATCTGGTCGTCAGGTTCATCAGGCTGCGGTGCCGCTT[C/T]GAAACCAATGTTGTCAACAGCTTCAGGCGCAGCAGATTGGTATAACCATGAGTTGGATTCAATGAGTTACAG
60289 A G TTGTAGGTTTCAATTGATTTCGCCTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGC[A/G]GGGAGCTTCTTCTCGGCTCGGGGCTTCTTGCCAGCTGGTGTTTTCTCGGCAGCGGTCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGG
60289 T A TTGTAGGTTTCAATTGATTTCGCCTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGC[T/A]CGGGGCTTCTTGCCAGCTGGTGTTTTCTCGGCAGCGGTCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAA
60289 G A TTGTAGGTTTCAATTGATTTCGCCTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGCTCGGGGCTTCTT[G/A]CCAGCTGGTGTTTTCTCGGCAGCGGTCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAAA
60289 A G TGTAGGTTTCAATTGATTTCGCCTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGCTCGGGGCTTCTTGCC[A/G]GCTGGTGTTTTCTCGGCAGCGGTCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAAA
60289 G C ATTTCGCCTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGCTCGGGGCTTCTTGCCAGCTGGTGTTTTCTC[G/C]GCAGCGGTCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAAA
60289 G A CTTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGCTCGGGGCTTCTTGCCAGCTGGTGTTTTCTCGGCAGCG[G/A]TCTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAAA
60289 T C TTTCGCTTCTTCTTTTTGTCGGCAGCTGCGGACGAGTCTTTGGCAGGGAGCTTCTTCTCGGCTCGGGGCTTCTTGCCAGCTGGTGTTTTCTCGGCAGCGG[T/C]CTTCTTTTCTTCTTCAGGCTTCTTCTCAGCGGGCTTTTTCTCGGCTTTGGGTGCCATGGCAAA
60343 C G ACCTCCACCACCTTCTTCGGCACAAACCTGAAACTGGCCTTTTCGGGCGTCGTCCCTGTGAGCACTTTCATCATGTGTT[C/G]GCAGCCCGGCGGGCCGTGGAACCACCATTCCAGGTCCGGTGCCAGGAGCTCCACCACCGTGTCCGTCTCTTTATTTGCCAGCCTCGCATATAGTGATTCC
60363 C T TTACATTTTCCAAACTTCACCATCATTTTTTACATGAAAGGACTAACAAACCCAAGTTCAAACATAACTAATGAAACGCATTATAATAAAAACCAACCAA[C/T]CGAACCCATTACCGAAATCAGAACCAAATCAAACCCTCTCACCTCTAATCCTCCTTGCAAGCTGAAT
60541 A G TCTTATGATAAGAACATTGAAGACGAGGTGCGGCCAGTTGTGGTGCCGGATTTTGTGATCGAATCGGACTCGGACAAATACTGGTGCCC[A/G]CATCCTCAAACCGGTGTTTTTGGGCCAGCGGATCCCTCTTTTGGTGCTGGTGCGAGTGCTGATCATGTTGGTGCTCGGTCCTCTGATGGTGCTGCTT
60543 G A GATTTACGCACCTTCTTCACTTTAGGCTTCACCGCCCCTGTCACCTTCTTTTTAGCCGGAGTTACCTTTGCCTTAGATGGAGCAGCTTTCTTCTTAGC[G/A]GGTGCAGCCTTAGCCTTTGCCGGAGCTGCCTTCTTGGCCACAGCCTTCACCTTCTTCGCTGGCGCGGTTTTTGATTTGGTGGCCTTCTTCT
60565 A G GGAGGGCTTAAGCTGCATAGAAGCTTAAGCTGCATAGAAGCTTATTAGCGACGGATGTGCTGTGCATCAAAGAGGCAACATC[A/G]GGTTCAGCTGTTTATGTATATTGTCCATGTATATATGGGGTATGTCAATTGTCAGCCGTGATACCAGCATATTACGAAATCTGTTTCTAGTGTGTTTCAA
60615 C G GCTTCTTGATCCCATATCCAACAGCAACCAACTTAGATGCACCCCAAAATAGACCGGGCATTTCAACGCTGCGAACAGCCTCCTCGAGCTTCTTCATGTC[C/G]GTCTCATCATCCCACGGTTTCACATCAAGAAGAACAGATGATTTCCCACTCTCTTTCTTCTT
60669 G A CAAAACTGACCCATCACATCCCTCTACAAAGCAATCATGAAAATGCATTCTTAGAAGGCCAGCAGCAAGA[G/A]TAGGATCATCACTCAAAGCTTGATTAACAGTGTTCCTCACAATCATCTCTGCAAATGGACATCTCAGTATGTAGTACCCCATGGACAGAGCTTCCACTTT
60727 T A AAAGCAGTCGACAAATGCAAAAGGAAACTTCGTGGTTTCATCGCTGAGAAGAACTGTGCTCCCTTGATTCTCCGATTAGCGTGGCATTCGGCAGGGACTT[T/A]CGATGTAAATACGAAAACAGGAGGACCTTTTGGGACAATAAAACACCCTGCTGAACTAGCACA
60751 T C TAGCCCAAAAGCAAACCGAATCATGCACACATACAAATCATATAAGACACAGAACAAAGGAAAGCT[T/C]TAGGCACATAGTCGACTAGCAATCTGAAGATTCGATCATAAACCAATTCTGCAATCCAAGTTTACCAACGCAGACAGAGCTTATCACACAGAGAAAACCT
60795 G A GTGAGTTGCAATTTCATTAGATGGTAACTAAATTGCAGTGATGCACCTAATTTAGTGAAGCACCTATGTAGTAAAACATCTCAACTCAGCAATATGTACA[G/A]CTCTTCCAGGGACAGCAATAAATACTTCATCGTAAAAAGCATGGCTTGATCTGTTCTTCATTTTGCAAAGCAGGCTA
60943 C T TTCATCCAATCCCGTCGAAGACTATCATATTTGTTTCGGATTTTGCTTTCGTCAATCGGTACGATGTCCGGAATGGTTTCTATGGCATCATTGAACTTT[C/T]CTGCAATCACTTTATGCACACCTTTTTTGTTGCTGCCACAAGCACCGTATGCATCAACAGAACATTGCAGCATAATCTGAGTTGCAGTAAA
60961 T C TTGAACCTAATCGAGTACCTACTGCGGGAAAACAATTCAGACAGTGCCATCATAAACGAACTGGGGTTCCCGCG[T/C]CTAATGATGCACCTGGTGTTAAGTGAGGACTCCAGTGTGCGAGAAGCGGCTCTTGGGTCTCTCCTCCAGCTCACCAACAACCAGCCATCTACTACATCAA
60973 T C TTGGCCCGCTAGCAGTCAGGTTGGTTCTGATGGACCGGGCCTGGTTCAAGGACCAGTCAACTTGAATTGTGGGTCCACCAGGGATAGGGCCTGAGACTTT[T/C]TGCTGGGAGTTTCTGTAGTGGAGGACAGCCGTGCTTGATAGGATTTTGGTGGTGAAACGAGTGG
61005 A G TCAAAATCCTTCTTTTTATAAGCAGCATTCCCTGCTTCCTTTTGCTTCTGCGCCTCCTTTTTCCTCTCCTTCTTCTCCTTCTCCGTCTCATCCATC[A/G]CCTCTTCTTCCATAGGCTCTGGCACAGCCTCTTCTTTCTTCTTCTCTTGCTCCTTCTCATTCACACTCTCGCTTTCTTTTTCCTTCTCTTTAGATTC
61009 T C CTTTTTGGGAGCAGCTGCTTTTTGCCGAATGGAAGCGAAAATCTGGCTTGGAATTTACCGACACTTCCATTGA[T/C]TGCAGCATTGTTGCTGACAATGTTTGTGTTGCCTAGAAAACTGCTGCATGTTGCTGCTGCTGCGGTGGCCATTTGAGTTTTGTTTCTGTTGAGAAAATAG
61027 A C ATTAACGCTGTGTGCACCCATCTTGGTTGTGTTGTGCCATTCAATAGCGCTGAAAACAAATTCAT[A/C]TGCCCCTGCCATGGTTCTCAGTACAACAATCAAGGAAAGGTTGTCAGAGGGCCAGCACCTTTGTCACTGGCATTGGCTCATGCTGATATTGACGATGGCA
61027 T C ATTAACGCTGTGTGCACCCATCTTGGTTGTGTTGTGCCATTCAATAGCGCTGAAAACAAATTCATATGCCCCTGCCATGG[T/C]TCTCAGTACAACAATCAAGGAAAGGTTGTCAGAGGGCCAGCACCTTTGTCACTGGCATTGGCTCATGCTGATATTGACGATGGCAAGGTTATTTTTGTGC
61027 C T ATTAACGCTGTGTGCACCCATCTTGGTTGTGTTGTGCCATTCAATAGCGCTGAAAACAAATTCATATGCCCCTGCCATGGTTCTCAGTACAA[C/T]AATCAAGGAAAGGTTGTCAGAGGGCCAGCACCTTTGTCACTGGCATTGGCTCATGCTGATATTGACGATGGCAAGGTTATTTTTGTGCCATGGACC
61027 A T ATCTTGGTTGTGTTGTGCCATTCAATAGCGCTGAAAACAAATTCATATGCCCCTGCCATGGTTCTCAGTACAACAATCAAGGAAAGGTTGTCAGAGGGCC[A/T]GCACCTTTGTCACTGGCATTGGCTCATGCTGATATTGACGATGGCAAGGTTATTTTTGTGCCATGGACCGAAAC
61055 G A ATATGAGGAATACGATAAAGGACGAGAAGATAGGAGGGAAGTTGGGCGGAGAAGACAAGAAGAAGATAGAGGATGCCATAGATGAGGCCATCAAGTGGTT[G/A]GATGCGAATCAGCTTGGTGAAGTGGACGAGTTTGAAGACAAGATGAAGGAACTGGAGTCGATATGCAATCCGATCATAGCA
61123 G A GACTGAGTCGACTGAGCCATCAGGAACCTCAACTGCAGCATTTGAACTGAAGTCAGTGCATAAA[G/A]CCGGCGCATGGACAGGTGAGGCAGGGTAAAGAACAACATTATAAAAGGCAGGACCAAGACGGGCAGAGTGAGAAGACAGCGGACACACAAGAAACGGCAA
61123 C T GACTGAGTCGACTGAGCCATCAGGAACCTCAACTGCAGCATTTGAACTGAAGTCAGTGCATAAAGC[C/T]GGCGCATGGACAGGTGAGGCAGGGTAAAGAACAACATTATAAAAGGCAGGACCAAGACGGGCAGAGTGAGAAGACAGCGGACACACAAGAAACGGCAAGA
61123 G A GACTGAGTCGACTGAGCCATCAGGAACCTCAACTGCAGCATTTGAACTGAAGTCAGTGCATAAAGCCG[G/A]CGCATGGACAGGTGAGGCAGGGTAAAGAACAACATTATAAAAGGCAGGACCAAGACGGGCAGAGTGAGAAGACAGCGGACACACAAGAAACGGCAAGAGC
61123 T C GACTGAGTCGACTGAGCCATCAGGAACCTCAACTGCAGCATTTGAACTGAAGTCAGTGCATAAAGCCGGCGCATGGACAGG[T/C]GAGGCAGGGTAAAGAACAACATTATAAAAGGCAGGACCAAGACGGGCAGAGTGAGAAGACAGCGGACACACAAGAAACGGCAAGAGCCTTACCATCTCAC
61123 C T GACTGAGTCGACTGAGCCATCAGGAACCTCAACTGCAGCATTTGAACTGAAGTCAGTGCATAAAGCCGGCGCATGGACAGGTGAGG[C/T]AGGGTAAAGAACAACATTATAAAAGGCAGGACCAAGACGGGCAGAGTGAGAAGACAGCGGACACACAAGAAACGGCAAGAGCCTTACCATCTCACTA
61127 T C TTTTTCCAGTTAGTGAATCATGGAATAGATCTGGAACTTCTAAAGAAGGTCAAGAAAGTGAG[T/C]TCTGATTGTTATAAAATGGAGAGGGAGATTTTGTTTAATAAATCAAGGCCAGTTAACACAGTAAATGAAGCTGTCAAGAATGGAAGCATGGAGAAGAAAC
61127 T C TTTTTCCAGTTAGTGAATCATGGAATAGATCTGGAACTTCTAAAGAAGGTCAAGAAAGTGAGTTCTGATTG[T/C]TATAAAATGGAGAGGGAGATTTTGTTTAATAAATCAAGGCCAGTTAACACAGTAAATGAAGCTGTCAAGAATGGAAGCATGGAGAAGAAACTGGATGATT
61127 A G AGTTAGTGAATCATGGAATAGATCTGGAACTTCTAAAGAAGGTCAAGAAAGTGAGTTCTGATTGTTATAAAATGGAGAGGGAGATTTTGTTTAATAAATC[A/G]AGGCCAGTTAACACAGTAAATGAAGCTGTCAAGAATGGAAGCATGGAGAAGAAACTGGATGATTTTGACTGGGAGGATGTGTTCT
61127 A G TGAATCATGGAATAGATCTGGAACTTCTAAAGAAGGTCAAGAAAGTGAGTTCTGATTGTTATAAAATGGAGAGGGAGATTTTGTTTAATAAATCAAGGCC[A/G]GTTAACACAGTAAATGAAGCTGTCAAGAATGGAAGCATGGAGAAGAAACTGGATGATTTTGACTGGGAGGATGTGTTCTT
61147 A C CATTCCTTCGCTTCTTCCCTTCCACATAAACCCAATTTCAGAGTAAAAAATTACAATGCACACCTTCCTCTCACTGCAGCTCACGTT[A/C]TCTCTCCCAATTCTCTTATTCTCCTTCGCTTCCGCCCGCATTCCCGGCGTCTTTACCGGCGGTCCATGGCAGTCAGCCCACGCCACTTTTTACGGCGGCA
61241 GT G GCACCATACCATGGGCTGCCTGATGATGATACTGGCTTTTTCACGGTCTTTCTCATGGTGAATTTTCCATTGCCCATGAGCTCAGAACCAGAG[GT/G]TTTTGGGACGGTTTTACTCTGGTTCCGGCTAAGGCTGGTGAAGAGAGAGCCATTGTGGATGCCATTTTATTGAAGAGGTGAATTGAACTGAAG
61241 G T TGATGATGATACTGGCTTTTTCACGGTCTTTCTCATGGTGAATTTTCCATTGCCCATGAGCTCAGAACCAGAGGTTTTGGGACGGTTTTACTCTGGTTCC[G/T]GCTAAGGCTGGTGAAGAGAGAGCCATTGTGGATGCCATTTTATTGAAGAGGTGAATTGAACTGAAGTTTGTGAT
61251 G C GGTTTTTGTTTCTTAGAAGATTGGATTACAGAGAAAATGCTACGGAGATGGCTGAGGGGTGTGTGGCCG[G/C]GAAGCCTGGTGGGGTTGCGGTGTTAAAGCTGGGCAGTTGTGGCACGCGCGCGCACAGGCAGAGTAGCTTCGCCGTTTTCTCTCTCTTCCATTGATGCTGG
61251 G T GGTTTTTGTTTCTTAGAAGATTGGATTACAGAGAAAATGCTACGGAGATGGCTGAGGGGTGTGTGGCCGGGAAGCCTGGTGG[G/T]GTTGCGGTGTTAAAGCTGGGCAGTTGTGGCACGCGCGCGCACAGGCAGAGTAGCTTCGCCGTTTTCTCTCTCTTCCATTGATGCTGGTGGTCAGTGTTTG
61251 T C GGTTTTTGTTTCTTAGAAGATTGGATTACAGAGAAAATGCTACGGAGATGGCTGAGGGGTGTGTGGCCGGGAAGCCTGGTGGGGTTGCGGTGT[T/C]AAAGCTGGGCAGTTGTGGCACGCGCGCGCACAGGCAGAGTAGCTTCGCCGTTTTCTCTCTCTTCCATTGATGCTGGTGGTCAGTGTTTGGCT
61251 C T AAGATTGGATTACAGAGAAAATGCTACGGAGATGGCTGAGGGGTGTGTGGCCGGGAAGCCTGGTGGGGTTGCGGTGTTAAAGCTGGGCAGTTGTGGCACG[C/T]GCGCGCACAGGCAGAGTAGCTTCGCCGTTTTCTCTCTCTTCCATTGATGCTGGTGGTCAGTGTTTGGCTAATTTGCCT
61391 T C AAAATATATGCCTTTATAGGGAAATTAAATCCAAATCCATCAGCCATGATTAAATACGCAATTTAATTTTAGCCTAAACCGAAAGATAATATCCATTAAT[T/C]CAAGCTTTCAAATTAACACCACGGATTACATAACAGAAAGCCACAGATTAAACACACGATTTTAAAATTAACCGCCAAAGCCATAAAGA
61457 A G TGTGGCCTTTTTTTTTGTAATTTAAACTAAAAGTGTTGGATTACTTTGTTTTGTTTTGAGGAAACATCAGGACCGATTCCTGTGATAC[A/G]TTCAAAAGCCAAGCCATTACTTAGTTTTCTCCATCTTCATTACACTGCTCCGTTCTGTCCCCAGTTTCTCACCATTTCTTCAAGTTTCCAGGAATACACA
61457 T C AAAAGTGTTGGATTACTTTGTTTTGTTTTGAGGAAACATCAGGACCGATTCCTGTGATACATTCAAAAGCCAAGCCATTACTTAGTTTTCTCCATCTTCA[T/C]TACACTGCTCCGTTCTGTCCCCAGTTTCTCACCATTTCTTCAAGTTTCCAGGAATACACAGCCGCTAC
61727 A G GTCATCAACCTCAGTTGCCTATTTGCTATTCCTGCACTCATCAACTGTCATTCTCATTCTCAGATCAAATGGCAACAACCGTGGTGGAAGCAGCTCCAGT[A/G]GCAGCAGTCGAAAGCGTAGCACCAGTGATTGCTGAGGAAGCGAAGATCGAACCCGAGGCAGCTGCTGTTGAGTTAGCTGCAGCTCC
61727 A T AACCTCAGTTGCCTATTTGCTATTCCTGCACTCATCAACTGTCATTCTCATTCTCAGATCAAATGGCAACAACCGTGGTGGAAGCAGCTCCAGTAGCAGC[A/T]GTCGAAAGCGTAGCACCAGTGATTGCTGAGGAAGCGAAGATCGAACCCGAGGCAGCTGCTGTTGAGTTAGCTGCAGCTCCAGCTGC
61789 A T TTTTTTTTTTTTTTGAGCAAACAACGCACTGAAATTTCATTCAAAGAACACCCCCAACAAAAAT[A/T]AAACTAAACTCCCAACGCCCTGTTTTTACATAAGCCATCGCATCTTCCACAAACCCAAAAGCTAAATTAAAATACCCTAAAAACAACATAATCTAAGCTC
61789 G C TTTTTTTTTTGAGCAAACAACGCACTGAAATTTCATTCAAAGAACACCCCCAACAAAAATAAAACTAAACTCCCAACGCCCTGTTTTTACATAAGCCATC[G/C]CATCTTCCACAAACCCAAAAGCTAAATTAAAATACCCTAAAAACAACATAATCTAAGCTCTCTCGCCTCTGATCCTTCTAGCAAGCTGCAT
61831 A C GAGGAGGCAGTGCATGTCGACAACTAGCTCCTACACTGCTGACAAGGCCGATACCCCAAACATCAGCAGC[A/C]AGGTTCGATTAATGCAGCCATTAAGAGACCGACTTGCCATCATATCGGGTGCGTCGGGCGGGATAGGATCCGAAATATGCACCCACCTTCACTCCATGGG
61831 G C GCTCCTACACTGCTGACAAGGCCGATACCCCAAACATCAGCAGCAAGGTTCGATTAATGCAGCCATTAAGAGACCGACTTGCCATCATATCGGGTGCGTC[G/C]GGCGGGATAGGATCCGAAATATGCACCCACCTTCACTCCATGGGAGCAAAGTTAGTTATCAGCTACTTGGGGG
61857 C T AAGATCCCCACATAATACTCAGGCCCAACTGAACTCGATACGATGGCATGATTCTCATCAATCAGCTC[C/T]TCCAAATTTCCAACGCTCATCGGAGTACCTCTAATCTCATCCACCTTCGTCCGATCCTCCTCGTTCTTCTCCTCGTTAGGCTTCAACCTCTCCTGATTCC
61857 A G AGATCCCCACATAATACTCAGGCCCAACTGAACTCGATACGATGGCATGATTCTCATCAATCAGCTCCTCCAAATTTCCAACGCTCATCGGAGTACCTCT[A/G]ATCTCATCCACCTTCGTCCGATCCTCCTCGTTCTTCTCCTCGTTAGGCTTCAACCTCTCCTGATTCCCCACAAACTCCTCTTCCATCAATAG
61863 G A CAAAAATTGCACGGAGGCAGCCATCGACCTGGATCCTCCACGTTACGTTTGCAAAGACATGAGCTTCCACAGCTGCCAGACCAGGTGCAGCATTATCTGA[G/A]CCCTTTCTCTGACCAGTCTCAGTGCATGGGTTCCTATGCTGAAGCTATATATTTTATCTCATATATGTATTTGTATCATGAGCAGCAT
61919 A G AGTTTGATTCGTGGAGATGGGGTTCAAGATGTGATTATAACCGGAAATAATGGAACAATCGACGGGCAAGGTGATGTTTGGTGGACAATGTGGCACCGGA[A/G]AACCCTTCGTTTTACTAGACCTCATCTTTTGGAATTCCTGCATTCTTCCGATATCATTATCTCTAATCTTGTTTTCATGGATTC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
62005 T A TTCTTCTTCTTATCTACTTTCGCTGACGAGTCTTTGGCGGCAGGAAGCTTTTTCTCCGCTTTGGGCTTTTTACCAGCTGGAGATTTCTC[T/A]GCGACGGGCTTCTTTTCAGCTTTGGGCGCCATTGCAAAATTAGGGTTTCTGAATTGGGATTTGGTTGTCAGACGAAGACGGGGACAGTTGATCGATCCAG
62005 T C TTCTTCTTCTTATCTACTTTCGCTGACGAGTCTTTGGCGGCAGGAAGCTTTTTCTCCGCTTTGGGCTTTTTACCAGCTGGAGATTTCTCTGCGACGGGC[T/C]TCTTTTCAGCTTTGGGCGCCATTGCAAAATTAGGGTTTCTGAATTGGGATTTGGTTGTCAGACGAAGACGGGGACAGTTGATCGATCCAG
62005 T G GCAGGAAGCTTTTTCTCCGCTTTGGGCTTTTTACCAGCTGGAGATTTCTCTGCGACGGGCTTCTTTTCAGCTTTGGGCGCCATTGCAAAATTAGGGTTTC[T/G]GAATTGGGATTTGGTTGTCAGACGAAGACGGGGACAGTTGATCGATCCAGTAGGCCAACAG
62041 G A TCAAATTAATGGTTAAATTTGGTATATCAGGTTATTATGCTTTAGACGATGTGAGGTTGACACCATATAGGTGTTATTTTGTGTGTCTTGAATCTGATAT[G/A]CGTTTTGTAGTCTCATTGTTTGAGTTTGAATAAATTAACTGTTTGAATCAAAAAAAAAAAAA
62059 A T ACGCAGCTTTCGCGGCTGGAAAATTCAACGACGCGGTAAAGCATTTTACCGACGCCATAGCACTGTCCCCTACCAACCACGTCCTCT[A/T]CTCAAACCGGTCCGCAGCCTACGCCTCTCTGAATCGCTTTTCCGATGCTCTTTCTGATGCTAAGAAAACGGTCGAGCTAAACCCTAACTGGGCCAAAGGC
62059 C T ACGCAGCTTTCGCGGCTGGAAAATTCAACGACGCGGTAAAGCATTTTACCGACGCCATAGCACTGTCCCCTACCAACCACGTCCTCTACTCAAA[C/T]CGGTCCGCAGCCTACGCCTCTCTGAATCGCTTTTCCGATGCTCTTTCTGATGCTAAGAAAACGGTCGAGCTAAACCCTAACTGGGCCAAAGGCT
62059 T C AGCATTTTACCGACGCCATAGCACTGTCCCCTACCAACCACGTCCTCTACTCAAACCGGTCCGCAGCCTACGCCTCTCTGAATCGCTTTTCCGATGCTCT[T/C]TCTGATGCTAAGAAAACGGTCGAGCTAAACCCTAACTGGGCCAAAGGCTACAGCCGCCTTGG
62073 G C TGATAAGTATGTATGTAGGGTATATGTTGTCACTGCTTGCGTCTTGTGTCATGTTGTCTGCTATCTGGTAATGTAATAAGAGGCGATATATTATTCTATA[G/C]TATAATAATAGCTCGCCTTTTGTGTGTCTCCTATGTTGTAACTTGTACACTAGTTTCATTTCATTATGAATTATTAATGTAT
62109 A G CCTTTCTTTCATCACCACATACATGAATATTCGCATCCCCAACATGCATACCCAATGAATTTAACAATAAATACCACACTACTGCTTGTTTTAACTTAAA[A/G]GTATATTAGGATTATCTAAGAAGAAACTACTGAAGATCATTTTTCTTCCACTTTACCTTCTCATCATCTACAGTCTCAA
62159 A G CTGCGGTAGTAGGGAGGAGAGTACGATCTGGACCTGCATCTGCCGTAGTAAGGGGAATATGACCTCTCCCTATCTGATGAATAATAGTCAGGTGTCATGT[A/G]CCTGCTGCTGCCCCGTCTCCCTCTTGGCGAGGGACTACGTGAACTTCCTCGTCCACTTTTCAACCCAAG
62177 A G CAACCAGCAAACAGTGCCAAATAAGCATAATACAAGATAACAACTGACATACATAGAGTGCATCCATATATCGCATGCACAATACATTTATTCAGACTTA[A/G]AACTCGTAACTCGTCCAAATATTTAAGCAGCACCAGCTAAAACCTTTCGGACAGCAATAACATTCTGATTAACGGTTACGGGTCCAAT
62193 G C GTTGGCCTACTGGAAATTAATAACGCAGCTCTATGTAGTTGGACGTTTAGGTTTCCAACT[G/C]TCAATATAAATATTCTTATCCCTTCAGGCCAGCCGCCGCCTCCTCCTTAAGCAGTTCAAGTGAAAACTAGGGCGGTTTTTGGTTTTACACTGTTTCCTAG
62193 G T GTTGGCCTACTGGAAATTAATAACGCAGCTCTATGTAGTTGGACGTTTAGGTTTCCAACTGTCAATATAAATATTCTTATCCCTTCAGGCCAGCCGCC[G/T]CCTCCTCCTTAAGCAGTTCAAGTGAAAACTAGGGCGGTTTTTGGTTTTACACTGTTTCCTAGCAATCATGGCTAATAGAACACTATCACAG
62207 C T TTCGATCTCTCTGTCTGCCTGGAGGTTCTATAGCTGGAATAGGAGATGGGGTCCGCAATGATGTTCTACTTTGTGGCACCATGGGAGCTGGACGATCTGT[C/T]ATAGACGGCCTCCTGGTTGAAGCAGAGCGGACTGCTGGTACATGCTCTACAAAGTTTCGACCTAACGAAGGG
62231 T C TGTTGGCCTACTGGCTTTTTCTGCTGTGCAGTGAGCATTCGTCTTTGCCATGGTGGGGTCCTCCCACC[T/C]ACTTCATATACCTAATCCGCGCATTCCTCCACCAACCGAGCAACCCTTTCTCCTTCATAAACATCACATCCTCATGGCTCTTCCCGGATTCCCTGACCGT
62243 G A GCTTCCAAAATATTGCTCCTCCTATGTGTTGTTTTAGCCACCGTTCTCCTCGTCTCATCTGAAGTCGTCAAGCAGCAAGAAAAAACTCAGGAAGAGACTG[G/A]CGTGGGTGAGAAGAAGTATGGAGGGTACCCAGGTGGTGGCGGAGGATACCCAGGGCACGGTGGTGGTGGTGGCGGCTACCC
62251 C T GGTTATGGTGGTAGTGGTGGTGGATACACTGGAGGTGGTGGCTATGGTGGTGGAGAATATGGTGCTGCCGGAAGTGGTGGAGGATCCAC[C/T]GATGGAGGTGGTGGCTATGCTGGCAATAATTATGGTGGTGCAAGTAGTGGTGGCGGTAGCTATGCGGGGAGTTACGGTAATGCTACTGCTGGC
62363 G T CATCGTGAAAAACACTTGTCAAAAGGATTCTAAACAATAAAGTAGACTAGTCTCAGACATCCAAGGAAGGAAGAATGAACAGCATAAGCATACGCTCTCA[G/T]GCGGCCGCAAGCCTTTCCTTTTGTCATCACCGACCAGCACCCTAGTGGAGATCCAGATCCAGATCTGTATCCAGTAGGCCAACA
62429 G A AGCTCTCCATGAGGATCTTATCTTGATTCATCAGCCCAAGAGCAGCAATGGACACACCATCTTCATCCTTGGTCAAATACTTAACGACAGGAGCAGCTCC[G/A]TACTTTCTAACGACTTTGCCATCTTCACCAGTCTCCAACTTACAGGTCAAAACACTGTAACTGGCAAGCAACCTCATT
62491 C T TCATTCAGAAGGAAGATAACCGCCTCCACGGTGATGTTCCAGTGGCCATGGACATCCCAGTAATCGATCTCAG[C/T]CGCGTATCTCTAAACGACAAAGACGAGCTGGAGAAGCTAAGGCATGCTGTTCAATCTTGGGGTCTGTTTCTGGTCATTAATCATGGAATAGAACCTTATT
62607 C G GTCCTGGCATTTTCATTCAAGATAGATCGATCGCACATAAAGCGCTCATTGAGCACGGTGCCACCTTTTCTGATCGGCCATCCCCGTCTCCGGCCTCGAG[C/G]TTGTTAAACAGCAATCGGCATAATATTACCACCTCTTCCTACGGTCCTCTATGGCGCCTT
62689 G T GACCTCAAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGG[G/T]TTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTA
62689 A T GACCTCAAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGA[A/T]GCCATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAA
62689 C G GACCTCAAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGC[C/G]ATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGG
62689 C T TCAAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGA[C/T]AATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAAT
62689 A G CAAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGAC[A/G]ATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAATA
62689 A G AAAATGCGCGGAGCGGTTATAGGTTTGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGACA[A/G]TCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAATAA
62689 A G TGGGAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGC[A/G]ACGGCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAATAATCCAGTAGGCCAACAGT
62689 G A GAAAACGGAAGGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGCAAC[G/A]GCGGCCATTTCTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAATAATCCAGTAGGCCAACAGT
62689 T C GGAAGAAGGAACGGACTGGGTTTTGGAAGCCATTTTAGCAGCCACGGAACGGGTCGTAGACAATCGGAAGGCAGATCTAGCAGCGGCAACGGCGGCCATT[T/C]CTAACGGTTTTATCTTTTACTTTCGAATGGGCGGTGGCGGAATAATCCAGTAGGCCAACAGT
62719 C T TTCGGTGGTTAAAATTCGTACTCTTGATCGTGATTACTTTTGGCTATTTTATGGTTTCGTTGTTGCTGAGGAAGCATTCGCCATGTATTTATTCTGTATT[C/T]GAACTTCGGATTTAAAAAAGTTCAAGTTAACAGTTTATCGTGTGAATGGATTTCTGTTGATGCAAAATCATCAAATTGTTTTGTT
62813 A C CAAACCAACCCGTTCTCTTTTTTTCACTGCTTTCTTCCTCCTCCGGTATGGAATCCAAGCACCCATAAACCTTCGTGCTCCTAGCACA[A/C]ATTTGCAGAGTCTGTGTCAAAATCAAAGGCACGCCTCCATAACACCCAGCCACATAAACCTCCACGGTCGGATTCAAACAACTCCCTTTCACCAGACCAG
62911 T C ACAGGGTTAAGTATTGGCTTTCTGTGGGTGCACAACCATCGGATCCAGTTCAGCGTATTCTATTCAGGGCAGGGGTCCTTCCACCTCCACCAATGTTGGC[T/C]ATGGCCCAAAAAGGCGGGCCCCGTGACAGAAGGCCCATTCATCCCATGAGCGGTCGCTACTTAACAAAGCCTGAAAGCACCAAAGA
62935 A C AACAAATCCAACCCCCTGAAACCTTCAGCACTCCTCTTCCCATTACCGTTTACCCAGCTCTGATGATCTAAACTCCCTTCCCCTTC[A/C]GTAATGTCAACGCCGAACAATCTAAAAACCTTAACAGTACTAGTCCCACTAACTCCAACCCTCTTCCTGCTATCAATATACAACTTCTTCTCACCATCAT
62935 A G AACCTTCAGCACTCCTCTTCCCATTACCGTTTACCCAGCTCTGATGATCTAAACTCCCTTCCCCTTCAGTAATGTCAACGCCGAACAATCTAAAAACCTT[A/G]ACAGTACTAGTCCCACTAACTCCAACCCTCTTCCTGCTATCAATATACAACTTCTTCTCACCATCATCCTCATCCGCACACTCCTCGAA
62941 G T TGCAAGTCGTTGCTTGCGTAACCACCCACCAAGCCGCTCTGGCCAATAGCTGTCGAAGCTGCTTTTCTGAGCCGATTCAAGCTTGGGTCA[G/T]GGTCATACTTGAGTAATTACAGCTTAGATTTGAAGCTGACGACGATAAGGATTCATGAAGATACATGAAGACGCGCTCGCTTTGGCTCTTTCTTCCAT
62949 A T TCAAGTCCCTTGTTGAAAAGAGTGGCAGAATCAATAGTAACTTTCTTTCCCAAAGTCCAG[A/T]TAGGATGCTTTAATGCATCGGCAACTTTCACTTCTTTCAGCTTTTCAACTGGCCATTCCCTGAAAGCACCACCAGATGCTGTCAAAATGATACGTCTAAG
62949 T C TCAAGTCCCTTGTTGAAAAGAGTGGCAGAATCAATAGTAACTTTCTTTCCCAAAGTCCAGATAGGATGCTT[T/C]AATGCATCGGCAACTTTCACTTCTTTCAGCTTTTCAACTGGCCATTCCCTGAAAGCACCACCAGATGCTGTCAAAATGATACGTCTAAGTGCTCCCTCTG
62949 T A AAAGAGTGGCAGAATCAATAGTAACTTTCTTTCCCAAAGTCCAGATAGGATGCTTTAATGCATCGGCAACTTTCACTTCTTTCAGCTTTTCAACTGGCCA[T/A]TCCCTGAAAGCACCACCAGATGCTGTCAAAATGATACGTCTAAGTGCTCCCTCTGGCAAGCCTTGAATACACTGAAATATGGCAGAATG
62991 C CA TCCTCCCAAAAGGCCATCCTCACCGACTTCATCACTTCCTTCTCTCCCTCCAAAAACGACGGTGACCGGAAACTGCCCACCGTTTCCTCCTGGTTCAAAA[C/CA]CCCGAAAAATACTTCACGGAGTCCAAAACACGAATGCCCAAACTGGCCCTTGGCAAGCAAATCCACGACGAGTCCAACTCTTTAGGA
62991 C A CCTCCCAAAAGGCCATCCTCACCGACTTCATCACTTCCTTCTCTCCCTCCAAAAACGACGGTGACCGGAAACTGCCCACCGTTTCCTCCTGGTTCAAAAC[C/A]CCGAAAAATACTTCACGGAGTCCAAAACACGAATGCCCAAACTGGCCCTTGGCAAGCAAATCCACGACGAGTCCAACTCTTTAGGAAA
62991 C CA CCTCCCAAAAGGCCATCCTCACCGACTTCATCACTTCCTTCTCTCCCTCCAAAAACGACGGTGACCGGAAACTGCCCACCGTTTCCTCCTGGTTCAAAAC[C/CA]CCGAAAAATACTTCACGGAGTCCAAAACACGAATGCCCAAACTGGCCCTTGGCAAGCAAATCCACGACGAGTCCAACTCTTTAGGAA
63055 C T GCTGGTGGAGGTGCTGGTGCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCG[C/T]AAACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCATCGGCGAGTGCTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCAT
63055 A G GCTGGTGGAGGTGCTGGTGCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCA[A/G]ACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCATCGGCGAGTGCTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCA
63055 C G GCTGGTGGAGGTGCTGGTGCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTG[C/G]TCTCGAAACTTCATCGGCGAGTGCTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATC
63055 A G CTGGTGGAGGTGCTGGTGCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTGCTCTCG[A/G]AACTTCATCGGCGAGTGCTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATCG
63055 T C GGTGCTGGTGCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCA[T/C]CGGCGAGTGCTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATCGAACTCCCC
63055 G T GCAGTAGGAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCATCGGCGAGT[G/T]CTTCCTAAATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATCGAACTCCCCATTCCATACA
63055 A G GAGGCGCAACCTGAGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCATCGGCGAGTGCTTCCT[A/G]AATTTTCTGAATCGTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATCGAACTCCCCATTCCATACACCC
63055 C G AGGAATCGGATACGCACAAGTATCTTTCCGCAAACAACCCTCGAACATAATGTCCTGCTCTCGAAACTTCATCGGCGAGTGCTTCCTAAATTTTCTGAAT[C/G]GTCTGCCACCGCCGGTACTCCAAAATTCATCAGGACCGTCTAGATAATCGAACTCCCCATTCCATACACCC
63071 G A TGTTCATGCTAATATCAACACCTATAATAGTTCCATGAACAACAGTGCCATTCTTGAGCTC[G/A]ATTGAGACCGTCTCATTGTTCAGTCTCATCAAAAACCTTACGAGCTTCATAGTCAACAGTAATTAGATAATAAATCGAGGGAAGAGAAAGAGAAACGTAT
63071 T C TGTTCATGCTAATATCAACACCTATAATAGTTCCATGAACAACAGTGCCATTCTTGAGCTCGAT[T/C]GAGACCGTCTCATTGTTCAGTCTCATCAAAAACCTTACGAGCTTCATAGTCAACAGTAATTAGATAATAAATCGAGGGAAGAGAAAGAGAAACGTATCCC
63071 C T TGTTCATGCTAATATCAACACCTATAATAGTTCCATGAACAACAGTGCCATTCTTGAGCTCGATTGAGACCGTCTCATTGTTCAGT[C/T]TCATCAAAAACCTTACGAGCTTCATAGTCAACAGTAATTAGATAATAAATCGAGGGAAGAGAAAGAGAAACGTATCCCTATTAGCTAGGGTTCCAAAAAA
63083 C T GAAGTACAAAATAATGCGTTTAGCAGCGCACTAATTTGTTAACGGAAGCAGCCAACCGACGCTGCGCTTGGAGACTGAAACTGATTTAATAACCGGACTT[C/T]CATTTCCCAGGAGAATCAATCTTCTGAAAATTTTCAATCATCTATTTCTATGGGAAGTTCCGGCGGATCTAGCGTCGTCGTTCCTCGG
63111 G C TGTGCGCACGCACTATTTCTTGGATTGGACCACAAAATCAACAGCAGAATAGTATTCCGAGATCAGACGATACATGTA[G/C]GATGGGTTATGCCCTCCTGTATCAGTTATAATAAGGCTGACGAGCGTTGGTGGAATATAATCAAATGCAGGATTCACAACATTAAGAAGAGGAGCACCAC
63143 G T AAGTTCACCTCCTCCCAAAAGGCTATCCTCACCGATTTCATCATTTCCTTGTCTCCCTCTAAAAC[G/T]GGAGGTCATCTGAAACAACCCACCGTTTCCTCCTGGTTCAGAGCAACCGAAAAATACTTCACGGACTCCAATACACGAATGCCCAAGCTGACCCTAGGCA
63143 T A ATCCTCACCGATTTCATCATTTCCTTGTCTCCCTCTAAAACGGGAGGTCATCTGAAACAACCCACCGTTTCCTCCTGGTTCAGAGCAACCGAAAAATACT[T/A]CACGGACTCCAATACACGAATGCCCAAGCTGACCCTAGGCAAACAGGTCCACGACGTGTCCTACTCTTTAGGAAAGTCCCTCACG
63169 G C GAGCATATTTGTTTTTCTTCCGGTTTCCTTTGTTCCATTTTCTTCAAAATAATCGTGAGGAAATCTTCATTGGTTTCATTTTCC[G/C]TGGCGTGTAGTCCTTGAAGTGCTCTGTTTTGACTAGCATGTGTATTTATAAGCTACTTGCAGCATTGTATGCATGCTATTTTACTTGATAATTTGAAATT
63191 C T TCTCATAGACCTCAGCCATCATTGCCAATTGTACTGATTGTTGCGGTTACCACCAATATTAGGCCCACGGCTCGTGCCACCATAAGG[C/T]CCACCTGGTGGGTAATTCTGGGCTCCACCCCTTGGCCCACCAGTTCCTGCATAAGGAGGTCCGCGCACTTGAGGTGGGTAGGGCCCACTACCATACCCGC
63191 G T ACCTCAGCCATCATTGCCAATTGTACTGATTGTTGCGGTTACCACCAATATTAGGCCCACGGCTCGTGCCACCATAAGGCCCACCTGGTGGGTAATTCTG[G/T]GCTCCACCCCTTGGCCCACCAGTTCCTGCATAAGGAGGTCCGCGCACTTGAGGTGGGTAGGGCCCACTACCATACCCGCTTCCTTGC
63191 T C GATTGTTGCGGTTACCACCAATATTAGGCCCACGGCTCGTGCCACCATAAGGCCCACCTGGTGGGTAATTCTGGGCTCCACCCCTTGGCCCACCAGTTCC[T/C]GCATAAGGAGGTCCGCGCACTTGAGGTGGGTAGGGCCCACTACCATACCCGCTTCCTTGCCCACGACTCGGATGA
63191 G C CACCAATATTAGGCCCACGGCTCGTGCCACCATAAGGCCCACCTGGTGGGTAATTCTGGGCTCCACCCCTTGGCCCACCAGTTCCTGCATAAGGAGGTCC[G/C]CGCACTTGAGGTGGGTAGGGCCCACTACCATACCCGCTTCCTTGCCCACGACTCGGATGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
63243 T C GAAGGTTTCTCAAACCCATAAGCGTAAATTCCTCTCAGTAGATTTTCCTGAAGACCCATCGAATCGAAGCTATCATAAAC[T/C]TCATCATAGGATGTAAAGAAATCCTGCCCATCTGCTGTAAGCAGGTCATTCATTTTTGAATCAAATTTTTTAGCATCAAATTGAGAGCCTTCTTCTGCCA
63253 T C TAATTCGCGAGAGGTTGAAGCCTCGGACGACGAATCGAAACTCGGCTGTGGATCTGACCGGGACAACGATGTCCC[T/C]TGTTCCTCTCGCAGTGCGTTGAATCGTCCCAGTCAGATGGACTACCCAGACCGAACCGAATATTTCACATCTGCTGCTGCAGCGCCTGTTGCTTTTCCAC
63269 A T AAAAAGGGAGATCGTTGTCCGGGGCCCTCCTCCAAGCAACCCCGCGGTCAGATCCATGGTCTA[A/T]ATTCGATTCGGTGTTCAGGGCTACAGATCCACGGCAGAGATTCGATTCGTTGTTCAAGGCTTCAACCTCGCGCATCGCGTTTGTATTGAAGGATCTAGTC
63319 C T AGAAAAAGGCAAATGACCCAATTGCAAACCAACATCCAAATAAGGAGAAATCTATTCTAAGCATAGTCTTGAGCAACTGG[C/T]TCATAAGAATTTCCAATAAAGATATCTCCATACACAAGACCAGCCAATGCACCACCAATAAGTGGACCAACCCAGTAAATCCAGTTTCCAGAGAAGTCGC
63319 A G AAATAAGGAGAAATCTATTCTAAGCATAGTCTTGAGCAACTGGCTCATAAGAATTTCCAATAAAGATATCTCCATACACAAGACCAGCCAATGCACCACC[A/G]ATAAGTGGACCAACCCAGTAAATCCAGTTTCCAGAGAAGTCGCCAGCAGCAACAGCAGGCCCAAAAGACCGGGC
63327 A G ACCTCCGCTTCTTTTACTTCTTCTTCTACTGCAGCAGCAGGAGCAGGAGCAGGAACAGACGCAGGCGCTTCCTCTACAGCCGGTGTAGCCGTC[A/G]CAGCAGGTTCTTCTACTGCTGCAGCCGCCGGTGGTGTTGATATCTCTTCTATTGTAGCCGGTGCCTCTACCTCTGCTGCTGGTGCCTCCACCTCT
63327 A G AGGAGCAGGAACAGACGCAGGCGCTTCCTCTACAGCCGGTGTAGCCGTCACAGCAGGTTCTTCTACTGCTGCAGCCGCCGGTGGTGTTGATATCTCTTCT[A/G]TTGTAGCCGGTGCCTCTACCTCTGCTGCTGGTGCCTCCACCTCTGCTTCTTTTGCTGCTTCTGTAAC
63399 T A CTGGAGAAATAGCAAAGAAAGCCAGCCTTGAAAAAATAACATGTCCCCCCAAAGAAAATGCATGACAGCCGCCATATAGATATTTTGCTGGTTTATATTT[T/A]GCTTATAAATAAAGCAGCATTTTCATTACTTTCTCTTCATCTTACTGCACCACCATAAACAAGCAATACGATCATGGCCATCTCAGTGA
63407 G A CGAGCTTCTTCCTCACTTCCTACAACTTTAGCAAGAAGTTTAATATAATGATCAATAATTTGATCCCTAGTCCAGTTTGGATC[G/A]GGATTCTCCACGATACACAGCCAGTGCTCAAAATCGCAACCCTCAAGCAAGATTGTCTCCTTCGGTGGCCGATTGCTCCAGTTAGGAGAAGGATCATTCA
63407 G T CGAGCTTCTTCCTCACTTCCTACAACTTTAGCAAGAAGTTTAATATAATGATCAATAATTTGATCCCTAGTCCAGTTTGGATCGGGATTCTCCAC[G/T]ATACACAGCCAGTGCTCAAAATCGCAACCCTCAAGCAAGATTGTCTCCTTCGGTGGCCGATTGCTCCAGTTAGGAGAAGGATCATTCAACGAAG
63407 A T AGAAGTTTAATATAATGATCAATAATTTGATCCCTAGTCCAGTTTGGATCGGGATTCTCCACGATACACAGCCAGTGCTCAAAATCGCAACCCTCAAGCA[A/T]GATTGTCTCCTTCGGTGGCCGATTGCTCCAGTTAGGAGAAGGATCATTCAACGAAGAAGTTGTAGGGCGGCTTGAAAAG
63463 G A GCATGAGTGTCCTGTGTGCTCCCAATACTTCGTGCTTGAGGTTGTTGGAGATGGAGGCGATCCAGATGGGCATTCTGATGATGAAGAACACCATTACTAA[G/A]CGATCATTCTAAAAATAAGTTTGTGGCGAATTGTACGGTTCTATTTATATTTTGTAGCTTTGGAGAGCTTTGGTAACTTTTTGAATTT
63463 G A ATGAGTGTCCTGTGTGCTCCCAATACTTCGTGCTTGAGGTTGTTGGAGATGGAGGCGATCCAGATGGGCATTCTGATGATGAAGAACACCATTACTAAGC[G/A]ATCATTCTAAAAATAAGTTTGTGGCGAATTGTACGGTTCTATTTATATTTTGTAGCTTTGGAGAGCTTTGGTAACTTTTTGAATTTCT
63463 A G CGTGCTTGAGGTTGTTGGAGATGGAGGCGATCCAGATGGGCATTCTGATGATGAAGAACACCATTACTAAGCGATCATTCTAAAAATAAGTTTGTGGCGA[A/G]TTGTACGGTTCTATTTATATTTTGTAGCTTTGGAGAGCTTTGGTAACTTTTTGAATTTCTCTTATTCTTGTCTGAT
63463 C T TGAGGTTGTTGGAGATGGAGGCGATCCAGATGGGCATTCTGATGATGAAGAACACCATTACTAAGCGATCATTCTAAAAATAAGTTTGTGGCGAATTGTA[C/T]GGTTCTATTTATATTTTGTAGCTTTGGAGAGCTTTGGTAACTTTTTGAATTTCTCTTATTCTTGTCTGAT
63543 C T TAGGGAGGCCACAGTATCCTAGCTTTTCTTCAAAACCAACCAATTTACGAGTCTTTACTTTCTCGGAACTAAAAACAGCAACAAAGAATTTTGGTAGGTC[C/T]GTGATGATTGGAGTTGGTGGCTTTGGTTCTGTATATAGAGGCACAATAACAAGTTCTGAAGAACCAAATA
63591 T C TTCTGTTTTCCATGGTATCCTCTACACACGTTGCATGTTCCCCACCACCTCCAATTACTCCATCTCCT[T/C]CTACCGCTAAGTCATGCCCACGCGACACATTGAAGTTGGGTGTATGTGCGAATGCTTTGAACTTGCTAAGGCTTAAGCTTGGCGAACCACCAAAGAAGCC
63635 G T AGCAGACAGTGGAGTATGGCAAGCGCAAGCATGACTTCCTTTGCTGCTTCAGCCTTTGTCTTCCCTTCCAACCCATCCACTCTTACAAA[G/T]AACACTTCCAAGTTCAGCTCTTTCTCTCCATCGAAACCATGGAATAATAATTCAAAGAAGCTGACCGTGATCAGAGCGGAAACCAAAGATGCTCCGGCA
63635 C T GTATGGCAAGCGCAAGCATGACTTCCTTTGCTGCTTCAGCCTTTGTCTTCCCTTCCAACCCATCCACTCTTACAAAGAACACTTCCAAGTTCAGCTCTTT[C/T]TCTCCATCGAAACCATGGAATAATAATTCAAAGAAGCTGACCGTGATCAGAGCGGAAACCAAAGATGCTCCGGCAGCTACAGAAGAAG
63681 C T TTTTTATCTTCATTGTCATTTGGCTTGGGAAAAGGAGTCGCATCCACAAATTTACCATGCAAACTTCCAGCCTTCG[C/T]GGCAATCGATTCTAGAAGCATTCCTATAGTCATTCTGGAAGGAAATGCATGAGGATTGATGATGAGATCAGGTCTCATTCCAGTAACAGCAGAAAATGGC
63681 G A TTTTTATCTTCATTGTCATTTGGCTTGGGAAAAGGAGTCGCATCCACAAATTTACCATGCAAACTTCCAGCCTTCGC[G/A]GCAATCGATTCTAGAAGCATTCCTATAGTCATTCTGGAAGGAAATGCATGAGGATTGATGATGAGATCAGGTCTCATTCCAGTAACAGCAGAAAATGGCA
63681 C T TTTTTATCTTCATTGTCATTTGGCTTGGGAAAAGGAGTCGCATCCACAAATTTACCATGCAAACTTCCAGCCTTCGCGGCAAT[C/T]GATTCTAGAAGCATTCCTATAGTCATTCTGGAAGGAAATGCATGAGGATTGATGATGAGATCAGGTCTCATTCCAGTAACAGCAGAAAATGGCATGTCAA
63681 A G TTTATCTTCATTGTCATTTGGCTTGGGAAAAGGAGTCGCATCCACAAATTTACCATGCAAACTTCCAGCCTTCGCGGCAATCGATTCTAGAAGCATTCCT[A/G]TAGTCATTCTGGAAGGAAATGCATGAGGATTGATGATGAGATCAGGTCTCATTCCAGTAACAGCAGAAAATGGCATGTCAATGTCAG
63681 G T AAATTTACCATGCAAACTTCCAGCCTTCGCGGCAATCGATTCTAGAAGCATTCCTATAGTCATTCTGGAAGGAAATGCATGAGGATTGATGATGAGATCA[G/T]GTCTCATTCCAGTAACAGCAGAAAATGGCATGTCAATGTCAGGCCATAACTGAGAGCAGACACCCTT
63685 T C GTAGCAAAGCCGGCCTACAATTTCCAGTCGGTAGGATCGCTCGATTTTTAAAGGCTGGGAAATACGCCGAGAGGGTTGGTGCCGGTGCTCCGGTCTACCT[T/C]GCCGCTGTTCTCGAATACCTCGCCGCTGAGGTTTTGGAGCTTGCTGGAAATGCGGCAAGAGACAACAAGAA
63687 G A AGCTTGGTTTTGACTGGAGGTGGGCCACCTGCATGGGTGTCGGAGAATGGAGGAGGGACCATTGGGCCACGGGAGAGTGGGGC[G/A]TGCATTGGGTTTGCAACATTGTTTATTTGACTGACTGCATTATATCCTCCTGGAACATAGTGTAGGAAATGGCATCCATCCCCAAATGGGCAACCAGCAG
63687 T A AGCTTGGTTTTGACTGGAGGTGGGCCACCTGCATGGGTGTCGGAGAATGGAGGAGGGACCATTGGGCCACGGGAGAGTGGGGCGTGCATTGGGTT[T/A]GCAACATTGTTTATTTGACTGACTGCATTATATCCTCCTGGAACATAGTGTAGGAAATGGCATCCATCCCCAAATGGGCAACCAGCAGT
63687 A G AGCTTGGTTTTGACTGGAGGTGGGCCACCTGCATGGGTGTCGGAGAATGGAGGAGGGACCATTGGGCCACGGGAGAGTGGGGCGTGCATTGGGTTTGCA[A/G]CATTGTTTATTTGACTGACTGCATTATATCCTCCTGGAACATAGTGTAGGAAATGGCATCCATCCCCAAATGGGCAACCAGCAGT
63691 C T ACATCACAAACCTGGTGACGTTACCTGAATCGTCCTGTATGCCGTCTGCTAGTATTTGCATCCCGTACAGCTCTGCTGCTCGGGCAGATGCAATGGCTGC[C/T]GTGTCCCTTAGTCCGTTTGAAGCTATGTACTCGGCTGCGGCTGCTGTGTCGTCAAATGCCTCTCTTGCGATGTTTGATAACCCGAGCT
63691 T C GTATGCCGTCTGCTAGTATTTGCATCCCGTACAGCTCTGCTGCTCGGGCAGATGCAATGGCTGCCGTGTCCCTTAGTCCGTTTGAAGCTATGTACTCGGC[T/C]GCGGCTGCTGTGTCGTCAAATGCCTCTCTTGCGATGTTTGATAACCCGAGCTTACTGGTTAAGGT
63691 G T TGCCGTCTGCTAGTATTTGCATCCCGTACAGCTCTGCTGCTCGGGCAGATGCAATGGCTGCCGTGTCCCTTAGTCCGTTTGAAGCTATGTACTCGGCTGC[G/T]GCTGCTGTGTCGTCAAATGCCTCTCTTGCGATGTTTGATAACCCGAGCTTACTGGTTAAGGT
63721 A G TCGAGAACACTGCAATACTCAGTATTCGGGTTCCGAAAGCTAAATGACGACGAGATGGAC[A/G]CGGCGAGAGAACAGAGTTGCTGTCGCGGTTGTTGTCGAGGTTGCCGGAGCTTGAGACGAAGGCTGTCGGACTCGGAGCGGACTGTCGGAGCTTGAAGAGA
63721 A G TCGAGAACACTGCAATACTCAGTATTCGGGTTCCGAAAGCTAAATGACGACGAGATGGACACGGCGAGAGAAC[A/G]GAGTTGCTGTCGCGGTTGTTGTCGAGGTTGCCGGAGCTTGAGACGAAGGCTGTCGGACTCGGAGCGGACTGTCGGAGCTTGAAGAGAGGACGCGAGAGTT
63721 C A TCGAGAACACTGCAATACTCAGTATTCGGGTTCCGAAAGCTAAATGACGACGAGATGGACACGGCGAGAGAACAGAGTTG[C/A]TGTCGCGGTTGTTGTCGAGGTTGCCGGAGCTTGAGACGAAGGCTGTCGGACTCGGAGCGGACTGTCGGAGCTTGAAGAGAGGACGCGAGAGTTTGGAATG
63721 C T AACACTGCAATACTCAGTATTCGGGTTCCGAAAGCTAAATGACGACGAGATGGACACGGCGAGAGAACAGAGTTGCTGTCGCGGTTGTTGTCGAGGTTGC[C/T]GGAGCTTGAGACGAAGGCTGTCGGACTCGGAGCGGACTGTCGGAGCTTGAAGAGAGGACGCGAGAGTTTGGAATGAGAGGAG
63721 G C TACTCAGTATTCGGGTTCCGAAAGCTAAATGACGACGAGATGGACACGGCGAGAGAACAGAGTTGCTGTCGCGGTTGTTGTCGAGGTTGCCGGAGCTTGA[G/C]ACGAAGGCTGTCGGACTCGGAGCGGACTGTCGGAGCTTGAAGAGAGGACGCGAGAGTTTGGAATGAGAGGAGAGAGGAAAG
63721 C T CGAAAGCTAAATGACGACGAGATGGACACGGCGAGAGAACAGAGTTGCTGTCGCGGTTGTTGTCGAGGTTGCCGGAGCTTGAGACGAAGGCTGTCGGACT[C/T]GGAGCGGACTGTCGGAGCTTGAAGAGAGGACGCGAGAGTTTGGAATGAGAGGAGAGAGGAAAGGGAGAGGGCGTAAGCAA
63749 T C ACAGCGCATACTGCAACGATATCTGAGTGGGATTATCCTTGTAACTGAAATAAGGGTACACGTTCGCCAGAAGCGGTGACCCTGTATTCACCAGAAACTT[T/C]ACTATCCCCTGCAGGTACTGCGAAGCGTCCGCCGTGAACGCCGTCTTGGACGGTGGGTACGCAGGCCCAA
63789 T C CACTGTTGGCCTACTGGAGTTAATAAACTAAACTTCCTAAATCAGAAAAACAATCATGTCTAGAACTCTCCTGATTTTCCCAAT[T/C]CTCTTCCTAATCCAACTAACCCAAATCCAATCATCAACGTTCAGAATCACAAACAACTGCCCTTACACAGTCTGGCCAGGCCTCCTCTCCGGCGCCGGCA
63789 A T CACTGTTGGCCTACTGGAGTTAATAAACTAAACTTCCTAAATCAGAAAAACAATCATGTCTAGAACTCTCCTGATTTTCCCAATTCTCTTCCTAATCCA[A/T]CTAACCCAAATCCAATCATCAACGTTCAGAATCACAAACAACTGCCCTTACACAGTCTGGCCAGGCCTCCTCTCCGGCGCCGGCACAGCCC
63789 A G TCATGTCTAGAACTCTCCTGATTTTCCCAATTCTCTTCCTAATCCAACTAACCCAAATCCAATCATCAACGTTCAGAATCACAAACAACTGCCCTTACAC[A/G]GTCTGGCCAGGCCTCCTCTCCGGCGCCGGCACAGCCCCGCTCTCCACTACCGGCTTCACTCT
63823 C T TGTTTCTTTCACAAAACAGTGAAATGGAAATGACTCCATAGACATTGGTATGAACAGCTAAAGAACA[C/T]CAAGTCTATACACATCTAAATGTATTTGTATACAAAATTATCAAACAGTTCATCCAAATTTTTAATGCTGCATGTCTTGTCGCATTCTAGAACAGTAAAC
63823 G A TGTTTCTTTCACAAAACAGTGAAATGGAAATGACTCCATAGACATTGGTATGAACAGCTAAAGAACACCAA[G/A]TCTATACACATCTAAATGTATTTGTATACAAAATTATCAAACAGTTCATCCAAATTTTTAATGCTGCATGTCTTGTCGCATTCTAGAACAGTAAACCGAA
63823 T C TTGGTATGAACAGCTAAAGAACACCAAGTCTATACACATCTAAATGTATTTGTATACAAAATTATCAAACAGTTCATCCAAATTTTTAATGCTGCATGTC[T/C]TGTCGCATTCTAGAACAGTAAACCGAACTGTTTCCCACATGCTTTGGTTTTATGTCTGTATACTTTTTGTC
63833 AT A TGCAGCAGCTTCGCCTCGTATTCCTCTTCCTCTTCTCGAGAAAGAGGGGAAGACTTGAGGGATACTGGATCGGATCTTATCGGAAACTTGATAGACTTGG[AT/A]TTTTTTGTTGGATTTGGAGATGCCGGATGATTTCTGCTGTCGGTAGAAGTTCTGGATCCCTCTGGAAGCCATTTCTTATTTTTTAGT
63839 G A GCAGCCAGAGAAATGGAAGTCGTCCATCGCATTTTTGCAAGAGTAGTGGTGCTGTTGCACGCCACATCCTTCATCAATTGGAAGCCATGAATATTGTTGA[G/A]AAGGACACCAAGGGAGGAAGGAGAATGACTTCACAAGGCCGTCGGGATTTAGATCAAGTCGCTGGACGAGTTGGTGTCACTGTTT
63839 G A ATGGAAGTCGTCCATCGCATTTTTGCAAGAGTAGTGGTGCTGTTGCACGCCACATCCTTCATCAATTGGAAGCCATGAATATTGTTGAGAAGGACACCAA[G/A]GGAGGAAGGAGAATGACTTCACAAGGCCGTCGGGATTTAGATCAAGTCGCTGGACGAGTTGGTGTCACTGTTTGAGTTCTTTTGCA
63861 A G AGTTCCATATTAATGTTCATGGCGGCAAGCTCTGTGGCCAAATACTTGAAAACATGCGGCATGGCCACAGTTTCCATTCCTCTTTGACTCTTACAAGC[A/G]TGACAAGTATAACCTTTATGGGGTTTATCCTGCTGCCTGAAGCCTCTTATGTCCTGCACACCTTTCCTAGGCTGTTGCACTAGTGTTGCAG
63885 C T TTGACGACGCAGATCGACTAGGTTTTGCCGGCACGGGATTCGAGGTCACCACTTTCGCAATGAGAGTATGTCCGGTCGTACCCGGTTTCAGCTGATCGAC[C/T]TTGACGAATACTGGTTTCCTTTTCGCTGGTGCGGTTCCTGTTTGCTGATTCGACATGGCTGCTTAATAAACCCTAGCTTTCACGTTT
63885 C A TTGCCGGCACGGGATTCGAGGTCACCACTTTCGCAATGAGAGTATGTCCGGTCGTACCCGGTTTCAGCTGATCGACCTTGACGAATACTGGTTTCCTTTT[C/A]GCTGGTGCGGTTCCTGTTTGCTGATTCGACATGGCTGCTTAATAAACCCTAGCTTTCACGTTT
63913 T C GGCTGCTGCGCCGGCGTCAAGAAGCTGGCCGCGTCAGCCACGACCACCCCTGACCGCCGTACTGCGTGCGGGTGCCTCAAGTCC[T/C]TCTCCGCCAAGATCCAGGGCTTGGACACTGGCAAAGCCTCTGGCCTTCCTGGCGTCTGCGGGGTCAGCGTTCCTTACCCCATCAGCCCCTCCACCGACTG
63913 T C GCGTCAAGAAGCTGGCCGCGTCAGCCACGACCACCCCTGACCGCCGTACTGCGTGCGGGTGCCTCAAGTCCTTCTCCGCCAAGATCCAGGGCTTGGACAC[T/C]GGCAAAGCCTCTGGCCTTCCTGGCGTCTGCGGGGTCAGCGTTCCTTACCCCATCAGCCCCTCCACCGACTGCTCCAGGGTGTCTTA
63965 A G TTCGACTGCAACCCCGACTTCATTCGCGCCTTTGCTAACACCGGGATTTCCCTTGCCATCACGGCAGCCAATGGCGACGTGGTTGGGCTTTCCGAC[A/G]TCGGATTTGCGCGGGATTGGGTGAACAGGAACGTTGCTCCGTTCGTTCCGGCGACGAATATAACGATGGTGTTTGCGGGGAACGAGGTG
63989 A T CTTGAAGGCGTCGATTTCACCTCATCAATGTGAAAACTTTCTGAAGTATCCGAGCCACTGTTCTCGACACTATGCCCTTTGCTCGACCAAAGCTTGCTTA[A/T]CAGTTTCTTCGATACGGCACCTTTCTTCTTATCGTTTGACAAAGTTACAGACTTGATGGA
64067 T C GATATAATAGTTGGTTGGATAAAGTACCCTTTTTCAAGATGCTTAGGACGATTTCCACCATACAATATAGT[T/C]GCACCTTCACTCTTTGCGTTGGTAATAAAACTTTGTATCTTCTCATATTGTCCTCTGCTGACAACAGGACCCAGCCTGCAGCCTTCTTCTAAAGGATCTG
64067 A G ATAAAGTACCCTTTTTCAAGATGCTTAGGACGATTTCCACCATACAATATAGTTGCACCTTCACTCTTTGCGTTGGTAATAAAACTTTGTATCTTCTCAT[A/G]TTGTCCTCTGCTGACAACAGGACCCAGCCTGCAGCCTTCTTCTAAAGGATCTGAAACTTTAATAGATTTGGCCCATTCAACAAGTCTATCT
64067 C T TAGGACGATTTCCACCATACAATATAGTTGCACCTTCACTCTTTGCGTTGGTAATAAAACTTTGTATCTTCTCATATTGTCCTCTGCTGACAACAGGACC[C/T]AGCCTGCAGCCTTCTTCTAAAGGATCTGAAACTTTAATAGATTTGGCCCATTCAACAAGTCTATCTAAAAATTT
64075 T C CGACGATTGTCCAGTTGCATTCGTCCCACGAAATAATTGATGCATCAGCTCTAAGTTTTCTATTGGTCGTTTCTTATATTTCAAGACACTCGTTCCAAAT[T/C]CCTTAACACGATCTTCCCACCATTCATCGCTTCCAGAGACCGTTCCTTTGTATGCATTCCAATCCGCGCCAGTCTTGTTTATCAGTGCATCC
64087 A C GCTGACGTTGAGGAATATTTGGCGTCCCCTGCGAAGGAATCAGAGGCAAAAGATGCACCAGCT[A/C]AAGTATTATCAGCTCCCGGATTAAGTTACTCAGACATTCCCAATGCTCAGATTCGAAAAGTCACAGCTTCACGTTTACTTCTCTCTAAACAAACCATCCC
64087 G A GCTGACGTTGAGGAATATTTGGCGTCCCCTGCGAAGGAATCAGAGGCAAAAGATGCACCAGCTAAAGTATTATCAGCTCCC[G/A]GATTAAGTTACTCAGACATTCCCAATGCTCAGATTCGAAAAGTCACAGCTTCACGTTTACTTCTCTCTAAACAAACCATCCCCCATTATTATCTGACGGT
64087 G T TGAGGAATATTTGGCGTCCCCTGCGAAGGAATCAGAGGCAAAAGATGCACCAGCTAAAGTATTATCAGCTCCCGGATTAAGTTACTCAGACATTCCCAAT[G/T]CTCAGATTCGAAAAGTCACAGCTTCACGTTTACTTCTCTCTAAACAAACCATCCCCCATTATTATCTGACGGTTGACAGCTGTGTCGA
64087 A G AGGAATCAGAGGCAAAAGATGCACCAGCTAAAGTATTATCAGCTCCCGGATTAAGTTACTCAGACATTCCCAATGCTCAGATTCGAAAAGTCACAGCTTC[A/G]CGTTTACTTCTCTCTAAACAAACCATCCCCCATTATTATCTGACGGTTGACAGCTGTGTCGACAAACTCATGGAGCTAAGAAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
64111 C T ACCCACCGCCGCCCCAGTTCCTGTACCCACCGCCGCACCCGCCGCTTCTCCCACCGCTTCACCCGTAGCCACAC[C/T]CACCGTTTCACCAACCCTACCGCCCGCCACTTCACCTCCTTCCCCATCACCGACCGCCAGCGTGCCCTCCGCCACGACTCCTTCCGTTGGTTCCCCGCCG
64161 G A GTTTTATCGGAGGCTGGGTTTCAATTGCAAAGAGCGCGAGACTGAGTACCAAAGCAGCTGTTGGAAATTTAAGTTTTGATAAGCAATGTGCACATTGTGA[G/A]AAGGAATCAATTAACGGTTCGCTGTTAAATTTGCTTGGATATCCATGGATAGAAAAGCGAGTGAGTGAAGGAAA
64169 C A ATTTTTTCTTCCTTCGAAGAATTCCTCCTTTCTTCGTCAGATTCCAGTTACAGATCTAAATGGCAGAAGAGCAAAGGTGCCAGATCGAGAGCCACATACT[C/A]TGCGCCAACAACTGTGGCTTCTTCGGTTCACCAGCCACAAACAACCTCTGCTCCAAATGCTACCGCGACCTCCGTCTGAA
64189 G C CTGTTGGCCTACTGGAAAAGCCATCTGGAAAAGCCATTGATTTCCCAGGGAGAGAAATTTATAAGAAAAATGGCGGCTTTAACCTCATCATCCCTCTC[G/C]TCCAAATCTTTCATCTCTCCATCACCTCTCCCCTCCCAAAGTATCCCTACCGACAAGCTCGCATTTCCCAAACAACCCCTTCTCCCGTCGAT
64207 CG C TGGCATTAACTGGGCGAAGGCGACGGCCTGGAGGCGGGATGGGCGACGCGACATCGGTTCGAGGGATGGAGGGAGCGGAGGTTTGAGCGTCG[CG/C]GTAGGGGAGGGAGTTCGACGATCAGAGGAGGAGGTGACGAGGTGGAAGGAGGTGGTGGCGAAGCGTCGGCGGTGGCGGCGCCGAT
64215 G A CAACATAACCAATCCATCCTCAACTTATTAAACCTTAAACTCCGTATTCAGTGTACTGCTTCATCAGTTCACCGCACAA[G/A]GCCATAGGAGTATCCTTCACAAACCCCAAAGCATTGGCGTACCTAACGTCAGAGGCGATGCCATTGTTGCGGGTGAGGAAGACTCTTGCCCTCTCCCTGC
64215 C T CATAACCAATCCATCCTCAACTTATTAAACCTTAAACTCCGTATTCAGTGTACTGCTTCATCAGTTCACCGCACAAGGCCATAGGAGTATCCTTCACAAA[C/T]CCCAAAGCATTGGCGTACCTAACGTCAGAGGCGATGCCATTGTTGCGGGTGAGGAAGACTCTTGCCCTCTCCCTGCCATCGAGCAGCT
64219 A G AACACAAACACATCTCCCTTGTTAAGTACCTTAGTGAACAATTTGTTATCAGGGTTTGATGTAACAAATCCAACGTACA[A/G]CTTCCCTTCCAGAACTGTTAAGATCTCGGTGGCTCGTGGATGGGTGTGAGGTGCATTGAGCCCGTACGGTGCATAGTCTATGCGCACTAAGGAGACACCC
64261 G A ATTTGCCTAATCCCTTTTTCATCCAGCTTCTCCCCGAAACACATGAGTACAAGCAAACAAAACATAGCAAATTGAAAGCTACCTTTCAC[G/A]ACAACACTGCAATCTTCTGAATTTTTAGACTTTTCAGAAAGGTCCTTGATCAGAACATCAAGCACCCAATCGCGGCCTTCTCCGTAAATCTTTACTCGCG
64261 T C CCTAATCCCTTTTTCATCCAGCTTCTCCCCGAAACACATGAGTACAAGCAAACAAAACATAGCAAATTGAAAGCTACCTTTCACGACAACACTGCAATCT[T/C]CTGAATTTTTAGACTTTTCAGAAAGGTCCTTGATCAGAACATCAAGCACCCAATCGCGGCCTTCTCCGTAAATCTTTACTCGCGATGAGT
64355 G GT TGCATGGCCATGATTTTGTTAAGCGTGGCTTGATCAGTCTGTACGTTTTGTGTGTTGTTTAGCTGCAACTGCTCTTGTTCTG[G/GT]AGGCTTTTGGGATGGTAGTCGAGGATAGCTCTTCAAACTGTCGATGGGGCCAGTTCTGTTCTCACGGCTGAAATCGATCAGATCTTTCATACCATTCACG
64367 G T TGCATCAAAGGTAGGAGGAGTCAACTGGTAGGAACAAAGCTTACCTTGTAAGGATGTCAAATGCTTTCCATCCCCATATTTGTCA[G/T]TTCTAAACTTAGCTGGTGATTCTATAACATTGATTTTCTCAGTGCTTAGATCAAACGCAAATATTTCTATGACTTCACCCTCGCATATAGCACCAGTATT
64381 T A CTTCGAACAACACTGACTGCCCCATATGGAAGAACGACGTAAACTCCCTCTGTTACGATTGCGAGTCGTGTAAAGCTGGTGTTCTTGCAAATCTGAAAAA[T/A]GATTGGAAAAAGGTTGCTATTGTGAACATAGTCTTCCTTGTCTTTCTGGTTATTGTCTACTCTGTTGGGTGTTGCGCATTCCGGAATA
64381 C G ACGACGTAAACTCCCTCTGTTACGATTGCGAGTCGTGTAAAGCTGGTGTTCTTGCAAATCTGAAAAATGATTGGAAAAAGGTTGCTATTGTGAACATAGT[C/G]TTCCTTGTCTTTCTGGTTATTGTCTACTCTGTTGGGTGTTGCGCATTCCGGAATAACAGGGAGGAGAATGCTCGCCCACAGTGGAA
64381 T C TAAACTCCCTCTGTTACGATTGCGAGTCGTGTAAAGCTGGTGTTCTTGCAAATCTGAAAAATGATTGGAAAAAGGTTGCTATTGTGAACATAGTCTTCCT[T/C]GTCTTTCTGGTTATTGTCTACTCTGTTGGGTGTTGCGCATTCCGGAATAACAGGGAGGAGAATGCTCGCCCACAGTGGAA
64381 T C ACGATTGCGAGTCGTGTAAAGCTGGTGTTCTTGCAAATCTGAAAAATGATTGGAAAAAGGTTGCTATTGTGAACATAGTCTTCCTTGTCTTTCTGGTTAT[T/C]GTCTACTCTGTTGGGTGTTGCGCATTCCGGAATAACAGGGAGGAGAATGCTCGCCCACAGTGGAA
64419 C T GATCCAAATAATTGTTTAAGAATATCCGGATTCACAGAGTTCCCTAAGTAAATTAAACAATCCTCACCATTCTCTAAGAGATA[C/T]ACCCCTTCTTCACTTATATGCTCACTGGAAAGAGGAATTGTTTCAGCAATTACAGAAGCACCATCTTCCTTAGATGCAATGTCATGTACCGATATCATCC
64419 C T GATCCAAATAATTGTTTAAGAATATCCGGATTCACAGAGTTCCCTAAGTAAATTAAACAATCCTCACCATTCTCTAAGAGATACA[C/T]CCCTTCTTCACTTATATGCTCACTGGAAAGAGGAATTGTTTCAGCAATTACAGAAGCACCATCTTCCTTAGATGCAATGTCATGTACCGATATCATCCTG
64443 C G GTGTGGCTTCAATTGAAAAGAATCGCCCAGGATGCATATGATCCAATAACCGGAATTTTTTGTGTGTCT[C/G]GGTGTGGTGCTTCTGTAGTTATTTTACAGAGTTGTAAATGTATTGAAATTTTTGTTGTTTATTTGGGATTAATAACGGAAGATTGGGAGGTGCTCCAAGC
64443 G C GTGTGGCTTCAATTGAAAAGAATCGCCCAGGATGCATATGATCCAATAACCGGAATTTTTTGTGTGTCTCG[G/C]TGTGGTGCTTCTGTAGTTATTTTACAGAGTTGTAAATGTATTGAAATTTTTGTTGTTTATTTGGGATTAATAACGGAAGATTGGGAGGTGCTCCAAGCAT
64443 A G GATGCATATGATCCAATAACCGGAATTTTTTGTGTGTCTCGGTGTGGTGCTTCTGTAGTTATTTTACAGAGTTGTAAATGTATTGAAATTTTTGTTGTTT[A/G]TTTGGGATTAATAACGGAAGATTGGGAGGTGCTCCAAGCATCTGCATTGTAATTCTTTTGCTAAGAGGAATTATTCAGTACTTGCAAGC
64453 C G CTTCCAACGCGAGGCATGCTGCTGATCTTGGTATGACTGTCCACCTTAAAGAAAGCGCCCGACATTA[C/G]GCCTTCGCTATCCACTCTCGGCACCGCCTTCATCTTATGCATCGGCCTCTCAAAGCTCTTCAGCCCTCCTTCACTGTGGAACATGCAACCATTCGGAAAA
64453 A G CTTCCAACGCGAGGCATGCTGCTGATCTTGGTATGACTGTCCACCTTAAAGAAAGCGCCCGACATTACGCCTTCGCT[A/G]TCCACTCTCGGCACCGCCTTCATCTTATGCATCGGCCTCTCAAAGCTCTTCAGCCCTCCTTCACTGTGGAACATGCAACCATTCGGAAAAGGAGCGAACG
64453 T C CTTCCAACGCGAGGCATGCTGCTGATCTTGGTATGACTGTCCACCTTAAAGAAAGCGCCCGACATTACGCCTTCGCTATCCAC[T/C]CTCGGCACCGCCTTCATCTTATGCATCGGCCTCTCAAAGCTCTTCAGCCCTCCTTCACTGTGGAACATGCAACCATTCGGAAAAGGAGCGAACGACCTCC
64453 G A TAAAGAAAGCGCCCGACATTACGCCTTCGCTATCCACTCTCGGCACCGCCTTCATCTTATGCATCGGCCTCTCAAAGCTCTTCAGCCCTCCTTCACTGTG[G/A]AACATGCAACCATTCGGAAAAGGAGCGAACGACCTCCCACAGCCGCTCTTCATCACGTTCTGATCATCACAAAT
64453 A G CCGACATTACGCCTTCGCTATCCACTCTCGGCACCGCCTTCATCTTATGCATCGGCCTCTCAAAGCTCTTCAGCCCTCCTTCACTGTGGAACATGCAACC[A/G]TTCGGAAAAGGAGCGAACGACCTCCCACAGCCGCTCTTCATCACGTTCTGATCATCACAAAT
64465 A G CACGAGTGCCCAGTATTCTTGCACGCTCATATTTTGTCATATACTTCGATGTTTTACGTTCTCGGTAAACAGATTCCTGATCCTTCTCTTCACCTTCTCC[A/G]ATGATATCATCTGGAACTTCTTCGTTGTTATTTTCTATTTCTTCCTCAGCTCCATCCTCTATTTCAGGCTCTGGTGGTTCATCTTCATATCCCA
64499 T C GTCTTCTCTCAAATATTCTCATCTCCATTTGCTGTTTCACATAATCCTTCTAAATCTCAATGGC[T/C]AAGATCAAGGTTGGAATCAACGGATTCGGAAGAATCGGACGATTGGTTGCTCGAGTTATACTACAGAGCGAAGATGTTGAGCTTGTTGCTGTTAACGATC
64501 T C TTTTTGATTAATTAGAGCATTTTATATAACTGTGTATCTGTGTGTTTTGTGAGGTGCCGCTCTGCTTTACGCCCACAATACGGCAAGCTTCTTTTCGTCC[T/C]GTCACATGCTTCTAAATTGAGCGAAATCGGCTTTCGCCTTTGTGTCCCGTTTCCATGTGTGCTTCATTATAACTGCGTTAAAATAGGCTTC
64501 C T TGTGAGGTGCCGCTCTGCTTTACGCCCACAATACGGCAAGCTTCTTTTCGTCCTGTCACATGCTTCTAAATTGAGCGAAATCGGCTTTCGCCTTTGTGTC[C/T]CGTTTCCATGTGTGCTTCATTATAACTGCGTTAAAATAGGCTTCCGACATCTCGCCTCTCAGCAACAG
64531 T C ACTGATACATGAAGGAAATCTTGATGCTCTGTGTGAGCTTGCTGATATTCTAAAAATTGAAGTCCTAGA[T/C]GAACAGCTTAGCAGATATAGTGACTCACTTGCAGGATTAAGGCCCACCCTACAAAGAATATTAGCAGACATTCATGAGAGATTGACATTTTGTGCCCGAA
64531 C T TTGCTGATATTCTAAAAATTGAAGTCCTAGATGAACAGCTTAGCAGATATAGTGACTCACTTGCAGGATTAAGGCCCACCCTACAAAGAATATTAGCAGA[C/T]ATTCATGAGAGATTGACATTTTGTGCCCGAACACACATTCGTGATCAGATTGCAAATTATCGCCCTACAGAAGATGATCTTGA
64687 GT G TATATCGGAATAGGCAGAATTTTCCAGTTTTATGTTACTTCATAATTACATAAGCACTCATTTGTGCCGTGGTTTGTGCACAGCACAACAGTAAGCAAAT[GT/G]TTACATGGAGAAAACGGTACAGGCTAGAAAAGTAGCAAAAACAGCAATAAACTCACATAGGCAAATGAGACAAATTAGTGCAGATT
64687 G A CCAGTTTTATGTTACTTCATAATTACATAAGCACTCATTTGTGCCGTGGTTTGTGCACAGCACAACAGTAAGCAAATGTTACATGGAGAAAACGGTACAG[G/A]CTAGAAAAGTAGCAAAAACAGCAATAAACTCACATAGGCAAATGAGACAAATTAGTGCAGATTCATTTGTCAATTTGACCTAGTT
64687 C T ACTTCATAATTACATAAGCACTCATTTGTGCCGTGGTTTGTGCACAGCACAACAGTAAGCAAATGTTACATGGAGAAAACGGTACAGGCTAGAAAAGTAG[C/T]AAAAACAGCAATAAACTCACATAGGCAAATGAGACAAATTAGTGCAGATTCATTTGTCAATTTGACCTAGTT
64703 G A CACCAGAGCCTGAAATTGAGGAGGGAGCAGAGGAAGACATAGATAATAACAATGATGATGTTCCAGAAGATATAATCGGAGAAGGGGAAGACAAAGAGCA[G/A]GAAGAAGTTGAGAAGAGAACACGCAAAACTTCAAAGTATATGACAAAGTACGAACGTGCTAGAATACTAGGCACACGTGCTTT
64703 A G AAGACATAGATAATAACAATGATGATGTTCCAGAAGATATAATCGGAGAAGGGGAAGACAAAGAGCAGGAAGAAGTTGAGAAGAGAACACGCAAAACTTC[A/G]AAGTATATGACAAAGTACGAACGTGCTAGAATACTAGGCACACGTGCTTTGCAAATTAGCATGAA
64719 G A GAAATCCTGTAAAACACATCAGCAGGCAATACAGTGCTCCACTAGTGCCACATGAAGCAGAACCTCTGTCAACAATCTCTGCAACACGGCCGAACGTGAC[G/A]CATGGGCACCAGCAAGTCATGCAGCAGTTGCCAACGTTATCGGTGCATCCGCAGAGGCCAGTCGACCATTTTACCGGTGACTGGG
64727 A G ACAGCGGGGGAGGCGGCGGCTTCTAGGACAGAGGAGCAGCAAAGAAAACAACTTCGACGTTGATAGAAGAAGGATGTAAGGCACAATTCGCGGGTGGAAG[A/G]GAAAACGACACGACGGAGACCAGTGGAGCTTCCGCGATGTGAGTAAAAACGGCTATCGTTTCTTCGA
64795 G A GGGCACAAAATCAATCGACCATTCCAAATCAATCAACGCAACAAAGGAAGGGTCTACGGCACGAAATCAGATAAGGCGCTATTAGAATTGGCTTCCA[G/A]TTTCTGAAATTTGGAACGCATATTTCATGGCATGGCAACTTGGTGCTCATATCAGCCAAATCTGTCTACGTAACGGTGCCGAATATTCTC
64803 T C CCAGTAAAAGATACCGGTGAGAATGGTAATATTGCCTCCAATGGCAAGACCTAGAGTTACTGCAGGGTTCAAGTGACCACC[T/C]GAGATGTTTGCGGCCATTGAAACACCGACAAATAAAGCAAGTGCATGGGCAATTGCAATTGCTACTAGTCCAGCAGGGTCCAGTGCAGCATCAGCAGTCA
64803 A G AAAAGATACCGGTGAGAATGGTAATATTGCCTCCAATGGCAAGACCTAGAGTTACTGCAGGGTTCAAGTGACCACCTGAGATGTTTGCGGCCATTGAAAC[A/G]CCGACAAATAAAGCAAGTGCATGGGCAATTGCAATTGCTACTAGTCCAGCAGGGTCCAGTGCAGCATCAGCAGTCAACTTGGCAA
64809 C CA ATCACATCATCGATATTATATACCCCAATTATTTCACAAGATCCAAATTAAGAATTCCAAATCCAGTACCAGGCCAATGCTTCTCCTTGGCCTTCATCAG[C/CA]AAAACCCTACCCCAAGCCACCCACCCTTCCCAACTCACCCGCTTATCCCAGCCGCTTCCCCACTCCAAAATCAATCTCAGCCCTCTATCC
64809 A G CACATCATCGATATTATATACCCCAATTATTTCACAAGATCCAAATTAAGAATTCCAAATCCAGTACCAGGCCAATGCTTCTCCTTGGCCTTCATCAGCA[A/G]AACCCTACCCCAAGCCACCCACCCTTCCCAACTCACCCGCTTATCCCAGCCGCTTCCCCACTCCAAAATCAATCTCAGCCCTCTATCCACC
64815 C T TCCATGCTGAGGCTGTAAAGAAGAAACGCCGTGCTACAAAGAAGCCCTATGCAAGGTCAATTGTTGGTGCTTCGTTGGAAGTAATTCAAAAGAAAAGAAG[C/T]GAGAAGCCTGAAGTACGTGATGCTGCCCGTGAAGCAGCTTTACGTGAAATCAAGGAAAGAATCAAGAAAACGAAGGATGAAAAA
64899 T C AAGAAAACGTCGTGTGCCAGGTGGTATTGCGGAAAGATGGCATCCTTGTGGTCAGCTACGTCGGCAGCGATGCCGATTATCCCGTCTGGTGGAGTAGCAA[T/C]GATCGACTTGATAGTGGAAACTATGCCCTGGTGCTTCACGAGGACGGAAACCTCGTCATTTACGGAACTGATATTTGGTCCACCG
64919 G T CCATGTATCAGTTTTATCATCGGAACCAGGCGGCGGTGCAGTGCTCCGCAGCTCAGAGTTGGAGGGAGTAAAATCGACGGGAGATGGGGACGATGGATGA[G/T]AAGACAAGGGAGAAGGGGATGATGACGTGCATAGGATTCGGTGGCGACATGTGAAAGCGGTAAGTAAACGGCGTGTTGGCG
64959 T G TCTGCACCATACCATGGGCTGCCAGATGATGATACGGGCTTTTTGACGCTCTTCCTCATGGTGAACTTGCCGTTGCCCATCAGCTCCGAACTGGA[T/G]GTTGGAGCCAGTTTGACTGCATTTCCGGCTAGGGATGGAGAAGACAGTGCCATTCTGGATGCCATTCCTGCTTTAATATATTGATATGAATTA
64983 T C ATATGATGTCAATGGGAGCAAACTATGCTCGACTGAAAGTGCAGCAAGATTACTACAAGGCTAAACTCCGTGCTA[T/C]GAAGGAGAAAGAGAGCAGGGCCTCGTCCAAGATCAAGGTGCATCCACTTGAAATAAAATCGGTTAATTCCAGTTCCAGTCCTGCTCCTTGTATGCAAGGG
64983 ATTCCAG A CAGCAAGATTACTACAAGGCTAAACTCCGTGCTATGAAGGAGAAAGAGAGCAGGGCCTCGTCCAAGATCAAGGTGCATCCACTTGAAATAAAATCGGTTA[ATTCCAG/A]TTCCAGTTCCAGTCCTGCTCCTTGTATGCAAGGGCGGAGCTAGCCCCGGTCGGGACTAGGTTGCAGCCCAGTATCGAAA
64985 G A TGATTGATAGCATGAGAGCACATGCCTCTAAAATCACATAACATGATTCCTTTGACAATCAAGTCTAATAAGCAAAACATCACACACCCACCACAACCAC[G/A]GATTAAGCACAACAACCTAACAAACATCCAATGCAAAACACAAAATACGACACATATCAACAACAGACATGACACCCAGCTCTCAGTA
65009 T G GCTACGAGTGGTTGCAACTGCATGAAATGCGCGTTCGGGAACTTGGTCTTATCTTCTCACTAACACAGATTAATCCAAAGATTAGTGCAATTAGGCAAAA[T/G]GGAGTGGTGAGGTTTGTGAACAAGTTACTGCTGGGGAAATTCCTAGCCGGACTATTATAAACGATCCTCTTCGTGCCGTCTTGGTAA
65009 A T AACTTGGTCTTATCTTCTCACTAACACAGATTAATCCAAAGATTAGTGCAATTAGGCAAAATGGAGTGGTGAGGTTTGTGAACAAGTTACTGCTGGGGAA[A/T]TTCCTAGCCGGACTATTATAAACGATCCTCTTCGTGCCGTCTTGGTAACAACCGCCGTGAGGCAAACTGTGTATGTTATCACCAACG
65009 C T TTATCTTCTCACTAACACAGATTAATCCAAAGATTAGTGCAATTAGGCAAAATGGAGTGGTGAGGTTTGTGAACAAGTTACTGCTGGGGAAATTCCTAGC[C/T]GGACTATTATAAACGATCCTCTTCGTGCCGTCTTGGTAACAACCGCCGTGAGGCAAACTGTGTATGTTATCACCAACG
65079 T C TCTTCACCGACTACATGCGCGGGGCAATGCGCATCTCTGCCCTGAGCGAGGCCCGTGTCATCTACGTCATGACCCATGACTCCATCGGGTTGGGCGAGGA[T/C]GGCCCCACCCATCAGCCCATCGAGCACCTCGTCAGCTTCCGCGCCATGCCCAACATCCTCATGTTCCGACCCGCAGACGGCAACGA
65079 C T TGAGCGAGGCCCGTGTCATCTACGTCATGACCCATGACTCCATCGGGTTGGGCGAGGATGGCCCCACCCATCAGCCCATCGAGCACCTCGTCAGCTTCCG[C/T]GCCATGCCCAACATCCTCATGTTCCGACCCGCAGACGGCAACGAGACCGCTGGCGCTTACCGGGTCGCCGTCCTCAAGCC
65155 C G AAATCATATGACCCAATGCCAATTACCACAACCTCCTATCCAAACACTCTGGCCGGTAACCGTATCCATCCTGCTGGTC[C/G]ACCGCAGGATAAAAACAAGCTGAGGGAACTGACGCTGAGGATTGCGCTGCCCCATGACCAGTCATCCGATTGTCCACATAGTAACTGCTCTCTGCATGTA
65155 A C TATCCAAACACTCTGGCCGGTAACCGTATCCATCCTGCTGGTCCACCGCAGGATAAAAACAAGCTGAGGGAACTGACGCTGAGGATTGCGCTGCCCCATG[A/C]CCAGTCATCCGATTGTCCACATAGTAACTGCTCTCTGCATGTATCCTGGGATAACAACCACCAGAATCCGACCTTGGTGGTGGTGG
65183 A G TGTTGGCCTACTGGATCATCATTTTCCAAACTCAGATAAAACATGAAGTGTACTCTTATACT[A/G]TCTGTCATGCTATCCCTCTTCATCTTCTCCATTGCTTGCCCCACTTGCTCGACTCCTAAAAGTCCACCACCACCACCACCGCCAAAGGTTATAACACCAT
65183 G A TGTTGGCCTACTGGATCATCATTTTCCAAACTCAGATAAAACATGAAGTGTACTCTTATACTATCTGTCAT[G/A]CTATCCCTCTTCATCTTCTCCATTGCTTGCCCCACTTGCTCGACTCCTAAAAGTCCACCACCACCACCACCGCCAAAGGTTATAACACCATGCCCTCCGC
65183 T A CTACTGGATCATCATTTTCCAAACTCAGATAAAACATGAAGTGTACTCTTATACTATCTGTCATGCTATCCCTCTTCATCTTCTCCATTGCTTGCCCCAC[T/A]TGCTCGACTCCTAAAAGTCCACCACCACCACCACCGCCAAAGGTTATAACACCATGCCCTCCGCCACCAAAGTCCACCCCACCTCCTACAC
65183 T C TGGATCATCATTTTCCAAACTCAGATAAAACATGAAGTGTACTCTTATACTATCTGTCATGCTATCCCTCTTCATCTTCTCCATTGCTTGCCCCACTTGC[T/C]CGACTCCTAAAAGTCCACCACCACCACCACCGCCAAAGGTTATAACACCATGCCCTCCGCCACCAAAGTCCACCCCACCTCCTACACTACC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
65191 A T TTTTCTCTCTCTTGGATTCTGCTTGGGAGAAGAGGTGATGACTTGGAGCTTGAAGACTTTTTGTTTCTATTGGCATCTTTTCTTTTCTTTTTAGACATCA[A/T]ACTTATTTCTTTTCTGCAAACTTGTTGTAATAATCTTAGTTTTCTGTGACTGTGGAATTTCTGTGATTGATGACATTATATTTTTCCGCTGCT
65191 T G GTGATGACTTGGAGCTTGAAGACTTTTTGTTTCTATTGGCATCTTTTCTTTTCTTTTTAGACATCAAACTTATTTCTTTTCTGCAAACTTGTTGTAATAA[T/G]CTTAGTTTTCTGTGACTGTGGAATTTCTGTGATTGATGACATTATATTTTTCCGCTGCTATAATGTTATTACTCTATGAATCTCCTTTGCTA
65191 GTT G GACTTGGAGCTTGAAGACTTTTTGTTTCTATTGGCATCTTTTCTTTTCTTTTTAGACATCAAACTTATTTCTTTTCTGCAAACTTGTTGTAATAATCTTA[GTT/G]TTTTCTGTGACTGTGGAATTTCTGTGATTGATGACATTATATTTTTCCGCTGCTATAATGTTATTACTCTATGAATCTCCTTTGCTA
65191 A T TTTTTGTTTCTATTGGCATCTTTTCTTTTCTTTTTAGACATCAAACTTATTTCTTTTCTGCAAACTTGTTGTAATAATCTTAGTTTTCTGTGACTGTGGA[A/T]TTTCTGTGATTGATGACATTATATTTTTCCGCTGCTATAATGTTATTACTCTATGAATCTCCTTTGCTA
65191 T C TTTTGTTTCTATTGGCATCTTTTCTTTTCTTTTTAGACATCAAACTTATTTCTTTTCTGCAAACTTGTTGTAATAATCTTAGTTTTCTGTGACTGTGGAA[T/C]TTCTGTGATTGATGACATTATATTTTTCCGCTGCTATAATGTTATTACTCTATGAATCTCCTTTGCTA
65221 C G TGGGCCCGGCGTGGCTGCGACCGCGGCTACTTTGCGGCGATGGTGGCGGCGCTACAGGGCACGGGGGAGGCGGAGATTGGTACCAAATCGAAGAGCTCG[C/G]GAAGAGCTTCGAAACGGTATATGGTACGTTGAATTTCGTTGAGAAACGAGTGAGATAAGTGAGTTTGAAAATTGGGGCTGCTA
65221 G C TGGGCCCGGCGTGGCTGCGACCGCGGCTACTTTGCGGCGATGGTGGCGGCGCTACAGGGCACGGGGGAGGCGGAGATTGGTACCAAATCGAAGAGCTCGC[G/C]AAGAGCTTCGAAACGGTATATGGTACGTTGAATTTCGTTGAGAAACGAGTGAGATAAGTGAGTTTGAAAATTGGGGCTGCTA
65221 A G GGGCCCGGCGTGGCTGCGACCGCGGCTACTTTGCGGCGATGGTGGCGGCGCTACAGGGCACGGGGGAGGCGGAGATTGGTACCAAATCGAAGAGCTCGCG[A/G]AGAGCTTCGAAACGGTATATGGTACGTTGAATTTCGTTGAGAAACGAGTGAGATAAGTGAGTTTGAAAATTGGGGCTGCTAT
65225 A G AAAAATGGTCTTCAGTAGAGAATTAATTGCTGTGCAGTTGATTGTGGTTCTCTTGAGTTCAACTTGCTGCAGCAGCAAAAACGTACTCAGTGATGAAGAC[A/G]GGCATATGCTTATAGTCACTCATGCCCCCATCCCTGCCCCAATGCCCATCAAGGCCCCCCCTCTATCACCACCCATTAAGACGCCACC
65241 A G AAACATAATAACCTCTTTCTCATACTATTTTCACCATGGCCAATACATATACAATCTCTATGAGCTTTCTCGTTGCGCTT[A/G]TCATGTTAAGCAGCTCTTGCTCTGATGCTGCACGCCGTTTACTTGACACTTCACCATTGCCTAAAATTCCAACCTTGCCCAAGCCTGAACTTCCACCTCT
65241 G C AAACATAATAACCTCTTTCTCATACTATTTTCACCATGGCCAATACATATACAATCTCTATGAGCTTTCTCGTTGCGCTTATCAT[G/C]TTAAGCAGCTCTTGCTCTGATGCTGCACGCCGTTTACTTGACACTTCACCATTGCCTAAAATTCCAACCTTGCCCAAGCCTGAACTTCCACCTCTACCTC
65241 C T AAACATAATAACCTCTTTCTCATACTATTTTCACCATGGCCAATACATATACAATCTCTATGAGCTTTCTCGTTGCGCTTATCATGTTAAGCAGCTCTTG[C/T]TCTGATGCTGCACGCCGTTTACTTGACACTTCACCATTGCCTAAAATTCCAACCTTGCCCAAGCCTGAACTTCCACCTCTACCTCAGATCCC
65241 G A CTATGAGCTTTCTCGTTGCGCTTATCATGTTAAGCAGCTCTTGCTCTGATGCTGCACGCCGTTTACTTGACACTTCACCATTGCCTAAAATTCCAACCTT[G/A]CCCAAGCCTGAACTTCCACCTCTACCTCAGATCCCAACGCTACCAAAACCTGAATTACCATCCATACCCCA
65241 C G TGAGCTTTCTCGTTGCGCTTATCATGTTAAGCAGCTCTTGCTCTGATGCTGCACGCCGTTTACTTGACACTTCACCATTGCCTAAAATTCCAACCTTGCC[C/G]AAGCCTGAACTTCCACCTCTACCTCAGATCCCAACGCTACCAAAACCTGAATTACCATCCATACCCCA
65285 AT A GATCCATCACTCAGATAGCAATCAGCCTCAACTGTGGGGTTACCACGACTGTCGAATATTTGTCTCGCTTTGATGTACTTGATAGTGACTGCTGCCATTA[AT/A]TTTTCGTTTTGGATCGGTAACAAATCTATCACTAAAGCAAGTAGGAATAATGGAATTTAGGCAAATATCAAATATATCATGTGACCCA
65327 A G ATACCTTTTTGGAGGAGAATAAGCTGTTGATTGGTTGAGGTGTCGGACTCGGGTCAACCGCCTTTATGTTTCATCTCTGCCA[A/G]ATGTTTTCTGTTAATGTTCTTCTGAAGATTGTATTACAATAATCTATGTACACAACTTGGTATTTGTGTATTTTTGTGTCCCTGGATGTCATGATCAGTT
65371 A C AGTTTCTCTCTTCTTTATAACATCTCTTGTGTGCTAAGAAGTGTGTAAAGAAGAGAGGCACTA[A/C]ATATCCATACACAGCACCAACTACGACCTCAAAAACATGGGTGAATACATGCCAACTTTGATGATGGTTTTGGTTCAAGTAGGCTTCGCTGGCTTGAACA
65371 A T AGTTTCTCTCTTCTTTATAACATCTCTTGTGTGCTAAGAAGTGTGTAAAGAAGAGAGGCACTAAATATCCATACAC[A/T]GCACCAACTACGACCTCAAAAACATGGGTGAATACATGCCAACTTTGATGATGGTTTTGGTTCAAGTAGGCTTCGCTGGCTTGAACATTTTGTCGAAACT
65415 A G CAAGGTATGGGACCACCTTCCGATAGTGTATCTCTAGAGATGAATACACTGGGTTCAACAAGAACGTCTTGCAACCCGGCCCAC[A/G]CATGACCGACCACTCATTTCGCTTGAGTGTATCGAATGTATATCACCAACGGTTGGGTGCGACCCACCGTTTTCGGAAAAGGGACAGCATCGAAAATAGA
65455 T C TTGTTCTCCATCTGGGTGAGGCAAACTGAGCTCAATGGCTAATGGCTTCAAGGTACTATCTTCGTTTAAGAA[T/C]AGAACGGTTCTTGTTGCATAAACCTTATTCTTGGTAGTATTGATTCTATTCAAGTATGGGATCAATGCGTCATGGTGATCTAAAATGAAAAGTCTTTTCT
65455 A G TTGTTCTCCATCTGGGTGAGGCAAACTGAGCTCAATGGCTAATGGCTTCAAGGTACTATCTTCGTTTAAGAATAGAACGGTTCTTGTTGCATAAACCTT[A/G]TTCTTGGTAGTATTGATTCTATTCAAGTATGGGATCAATGCGTCATGGTGATCTAAAATGAAAAGTCTTTTCTGCTCCAGGGCCTGTTGA
65465 G C TGGCGATTGGGATTGATAGGGAGTCGGCTGGGACGTGCGCTACGGTTTCTGGATTTGATTTTTTGGTAGGTTTGCATCAAGATTGGTGCTTTGCTGAGGA[G/C]GCGATGGCAATTGAATCGGTTGGTATAGTCGAGGGGGACGAAGCTGCATTACAATGGGCACTAAATCTTGTTTACAAACATAAAA
65507 T C GCTTGTCTGCTTCAGCGTGGAACTTCTCTTGGTTTGCAATGAATATCTTCTCTCTTTCGCGATTGTGGACTTTGTTTGTTTCACAGTTGAGCTTCCGCTT[T/C]TCGTAGAATGCACGTTTGAATTCCTCAGCTTCCAGAATGATTTGATTTCTCAACTCCTTT
65537 G C CTCGTCATGCATTAATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAAT[G/C]CGGCTGATTAAGCTTTCCGATCATGTCAAATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGAT
65537 T C CTCGTCATGCATTAATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGAT[T/C]AAGCTTTCCGATCATGTCAAATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCT
65537 C T GTCATGCATTAATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGATTAAGCTTT[C/T]CGATCATGTCAAATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCTTATG
65537 A C ATGCATTAATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGATTAAGCTTTCCG[A/C]TCATGTCAAATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCTTATGCA
65537 CAT C GCATTAATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGATTAAGCTTTCCGAT[CAT/C]ATGTCAAATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCTTATGCA
65537 A T ATCGAAAGTTGAATTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGATTAAGCTTTCCGATCATGTC[A/T]AATCTTGCTACGCTGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCTTATGCACTGTGTGC
65537 C T TTTCTCATAAATGGACTTTAAGCTAATAGAGCAGCTTCTGCTCCATCAGACAGGGTAATGCGGCTGATTAAGCTTTCCGATCATGTCAAATCTTGCTACG[C/T]TGTCCATCGTGGTGCTCCTGAACCCTCTACCTCTGGCATTATCTCTGACAGTTGCCGATCCTTATGCACTGTGTGCACATCTGTCTTTGC
65573 G A TTTTTTTTTTTTTAAAATCATCAAGCCATCCATTAAAATTGCACCGACACATTAAGTACAGCATTTAGGCAACATATACAATGTAAATCTCAAAA[G/A]CACGGTAGAAAGGTTTGGTACTTAATACAACACCACATTTAGTTCACACTGAAATTCACAGACCATATACCAAAATAGACAAGAGCACAAAACA
65587 G C AGCCGTCGACCAGGCTGACGCCGTAGGAGGTGAGGTCCTGGTTGGGGCCGCCGTGGTGGAGGGAGATCTGGGCGAGGGTGGCTGGTGGGGCTCCGCCGAG[G/C]CCGGCGCACTGGAGGCGGTGGCCGCAGTCGCCGGTTTGGCAGGATAAGGAGGTTCCGGAGGAGGAGCAGCCGGTGCGGG
65627 C T CGTACACAGCGCTGGAGTTGGAGTTACGGACACAAGTTTTGACGAGGATGAAACAGATGGCA[C/T]TAGTTCCTGGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCT
65627 C A CGTACACAGCGCTGGAGTTGGAGTTACGGACACAAGTTTTGACGAGGATGAAACAGATGGCACTAGTTC[C/A]TGGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGA
65627 A G CGTACACAGCGCTGGAGTTGGAGTTACGGACACAAGTTTTGACGAGGATGAAACAGATGGCACTAGTTCCTGGAGGCGCATTATCA[A/G]TATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGAATATGGGTTCAGCAGC
65627 T A ACAGCGCTGGAGTTGGAGTTACGGACACAAGTTTTGACGAGGATGAAACAGATGGCACTAGTTCCTGGAGGCGCATTATCAATATCAACTTCACCGCTCT[T/A]GTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGAATATGGGTTCAGCAGCCGGTC
65627 A T TTGGAGTTACGGACACAAGTTTTGACGAGGATGAAACAGATGGCACTAGTTCCTGGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCAC[A/T]CGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGAATATGGGTTCAGCAGCCGGTCTCTACCCAGTGCC
65627 A T ACACAAGTTTTGACGAGGATGAAACAGATGGCACTAGTTCCTGGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGAT[A/T]CAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGAATATGGGTTCAGCAGCCGGTCTCTACCCAGTGCCTGCTGATCCTAT
65627 G A CAGATGGCACTAGTTCCTGGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAA[G/A]CCAGGGGCTGTGATGAATATGGGTTCAGCAGCCGGTCTCTACCCAGTGCCTGCTGATCCTATTTACTCAGCAAGTAAG
65627 T C GGAGGCGCATTATCAATATCAACTTCACCGCTCTTGTTGACTGCACACGTATTGCGATACAAACAATGAGAAAATTGAAGAAGCCAGGGGCTGTGATGAA[T/C]ATGGGTTCAGCAGCCGGTCTCTACCCAGTGCCTGCTGATCCTATTTACTCAGCAAGTAAG
65657 T C CTGTTGGCCTACTGGATAAGTTATAAGTTCAGCATTATTCAACAACAACGTATACAAATATTATGGCATCAACAAAAAGACAGCGTTT[T/C]GATTCAGAGGAATATCACTCTGAGAGCGAAGAGGCCGAGTACTTAGCCTTCTGCCTCATGATGCTATCACGAGACAACAACGATCGGACGTACAGGTGT
65683 G A CAATACTCCCGGTGGTACCAAAGCCATCAAATGAATTCGCAGCTGTTATGAAAGCATCATAAGTGTAAAATCCACGAGCAGGGCAACTATAATCGTCACG[G/A]TGGTGAAGCATCTGGTTAAACTGGTAAGCAGAAATGATGGAGGCTACTCCAGATGGTGGGCCTGGGCGTCGCCCACCACCGCACT
65683 T C ACTCCCGGTGGTACCAAAGCCATCAAATGAATTCGCAGCTGTTATGAAAGCATCATAAGTGTAAAATCCACGAGCAGGGCAACTATAATCGTCACGGTGG[T/C]GAAGCATCTGGTTAAACTGGTAAGCAGAAATGATGGAGGCTACTCCAGATGGTGGGCCTGGGCGTCGCCCACCACCGCACTGGCT
65689 A G GGTAGTGGCTTATGGTGGCTGGAGTGCTTGTCGAGCCAACGTCAGCTCAATTACGCCTCCGGTGGTCTGAATCGCAGCACCAGCCTCCACTCCGCTGCTG[A/G]ATGGTTCGCCGTTGAAAGATTTTGAAGTAGCAATTTGAGATGGTGACCGGTGATGATTTAGATAAGATAATGTACGGGCAATTTTG
65707 G A CTGTAGATAGATTTTTTTGTAACTGTGATTGGTACATTGTGCTTTTTTGCATATTCAATGGC[G/A]TCTTCTCTTCCAGTTATATCCCATTCTCTCCATGGGGCAACAACATTAAGCTCCGGGTTCAAAGCATAGAATGCCAACTCAAATCGAACCTGATCATTTC
65707 C A TTGTGCTTTTTTGCATATTCAATGGCGTCTTCTCTTCCAGTTATATCCCATTCTCTCCATGGGGCAACAACATTAAGCTCCGGGTTCAAAGCATAGAATG[C/A]CAACTCAAATCGAACCTGATCATTTCCTTTCCCTGTGCATCCATGTGCTACTGCATCTGCACCTACTTCTTTGGCAACATCAACCATTGCC
65707 A T CATATTCAATGGCGTCTTCTCTTCCAGTTATATCCCATTCTCTCCATGGGGCAACAACATTAAGCTCCGGGTTCAAAGCATAGAATGCCAACTCAAATCG[A/T]ACCTGATCATTTCCTTTCCCTGTGCATCCATGTGCTACTGCATCTGCACCTACTTCTTTGGCAACATCAACCATTGCCTTGGC
65719 T G TATTCAACCATGGATTCAAGTGACGTGGCGCAAAATTTGGTTTCTCCATCTGCCGCAGTCTTTTCACATTCTTGAA[T/G]AGTTTTTTGCATGGCTTTCGCTTTCTCGGACTTGGGATTCACGGAGAGTTTGGAGAATATAGTTTGGAGATTGGTTGAGGAGAACGGGATCGATGTCGCT
65719 C G TATTCAACCATGGATTCAAGTGACGTGGCGCAAAATTTGGTTTCTCCATCTGCCGCAGTCTTTTCACATTCTTGAATAGTTTTTTGCATGGCTTT[C/G]GCTTTCTCGGACTTGGGATTCACGGAGAGTTTGGAGAATATAGTTTGGAGATTGGTTGAGGAGAACGGGATCGATGTCGCTGCATGTCCAGAG
65741 C A TGAAGTCTAAGAAAATATCCCATCCCACACCCCGTTCTCTATCTATAAATTTTATCTGTCGGCATGAAGGCCGACGCGTTCTAAGATGCAACATCGCTAC[C/A]ATCGAGCGTCACCGAATCTAGGGTTAGGGTTTCTGTTTCCCTTTTGAGTAAGAAATAGTGCTTTTCTTATCATTGTAAGATGGAGACGA
65825 C T GATTGCATAACGTTTCCATTAGGCACAATCTGATCTTATGTCATATCTGCAAGAAAGAGACTGAATCAAGCCTTCCATCATGAACCAGGTCATCT[C/T]CAAAACACTTGACGAAGTCTGCAATGCAGCTTTCATCCTCTACAACACGATAAAAGAGGAGTAAAAAAGCAATTTGGCTCTTTGAGTTAATAA
65927 A AAGT CTGTTGGCCTACTGGACTTATAAGTACCCCTTCACCAAAGCTCTATTTTCACATCAGAGAACAAATACTTAAACCAATCAAGTGTAATTACCA[A/AAGT]TCAAACACGTAAAATTTCCCAAATGGCCAAAATTCCAGTCGTTGATTTTTCGAACTTAGATGGAGAGAATAGGACTGAAGCTCTGAAAGAGA
65927 A T CTGTTGGCCTACTGGACTTATAAGTACCCCTTCACCAAAGCTCTATTTTCACATCAGAGAACAAATACTTAAACCAATCAAGTGTAATTACCAATCA[A/T]ACACGTAAAATTTCCCAAATGGCCAAAATTCCAGTCGTTGATTTTTCGAACTTAGATGGAGAGAATAGGACTGAAGCTCTGAAAGAGATAG
65927 A T GGCCTACTGGACTTATAAGTACCCCTTCACCAAAGCTCTATTTTCACATCAGAGAACAAATACTTAAACCAATCAAGTGTAATTACCAATCAAACACGTA[A/T]AATTTCCCAAATGGCCAAAATTCCAGTCGTTGATTTTTCGAACTTAGATGGAGAGAATAGGACTGAAGCTCTGAAAGAGATAGCAAAT
65927 A C GACTTATAAGTACCCCTTCACCAAAGCTCTATTTTCACATCAGAGAACAAATACTTAAACCAATCAAGTGTAATTACCAATCAAACACGTAAAATTTCCC[A/C]AATGGCCAAAATTCCAGTCGTTGATTTTTCGAACTTAGATGGAGAGAATAGGACTGAAGCTCTGAAAGAGATAGCAAATGGATGTGAG
65959 C T TCACTGTTGGCCTACTGGATTAACCGCACCGAGTTTTGGCGAAGCGGATGCTCGTTTATTAGGGTT[C/T]TGGCTTTGTTTGAAAGATCTTTCCAATTTCAGAAGTGCCATGGATATTGGGCTTGCACCAAAAATTCCAGAGCATCAGTTACCAACAATTGCAGAGCATC
65959 T C AAGCGGATGCTCGTTTATTAGGGTTCTGGCTTTGTTTGAAAGATCTTTCCAATTTCAGAAGTGCCATGGATATTGGGCTTGCACCAAAAATTCCAGAGCA[T/C]CAGTTACCAACAATTGCAGAGCATCAGTTAAATGCCATTAAAATTGAGTGTCCACCAGAGACTCAAAAAAATCAGTCAATGTGGCAG
66005 A G CGACATCATAAGGAATGGGAGTGACAGTTTCCAGGGTAGCTGCTTCAACCATGAAACCAGGCTTAGGACCAGCAGGCTGCCTCTTTGTGCTGATAACCTC[A/G]CCACGAGCCTTAGCTTCCGCCTTCAATTTGTCATTCTTTATCTTCCTCAACCTGAAATCCTCGGAGCACCTTGATGGCTGCACATGCT
66005 C T GAGTGACAGTTTCCAGGGTAGCTGCTTCAACCATGAAACCAGGCTTAGGACCAGCAGGCTGCCTCTTTGTGCTGATAACCTCACCACGAGCCTTAGCTTC[C/T]GCCTTCAATTTGTCATTCTTTATCTTCCTCAACCTGAAATCCTCGGAGCACCTTGATGGCTGCACATGCTCTATTCGTACATGAATCCT
66017 C T ATTCCATACAAAAACATCCTTACAACAAAATATATCCAGCTACCATACCCGAGTAACTCATGAAGATGACGATGGCGAAGGATCTACATAATCAGATTCA[C/T]CATTTCTCTGAAGCGTTGTCATTACTTGTTTCATTTGTGCTTAAAAGTTTTCTTTATCTGCGTTTTGTTGTTGTGCAAGCCTTGTCTGCTC
66017 G A ATCCTTACAACAAAATATATCCAGCTACCATACCCGAGTAACTCATGAAGATGACGATGGCGAAGGATCTACATAATCAGATTCACCATTTCTCTGAAGC[G/A]TTGTCATTACTTGTTTCATTTGTGCTTAAAAGTTTTCTTTATCTGCGTTTTGTTGTTGTGCAAGCCTTGTCTGCTCTTCCTCAAGTTTTTG
66017 G T AAGATGACGATGGCGAAGGATCTACATAATCAGATTCACCATTTCTCTGAAGCGTTGTCATTACTTGTTTCATTTGTGCTTAAAAGTTTTCTTTATCTGC[G/T]TTTTGTTGTTGTGCAAGCCTTGTCTGCTCTTCCTCAAGTTTTTGGCAATTAGCTCGCTCACGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
66035 C T ATGTTTTCGCAGTTTTCAGGTAAACTGGAGACAGAAGGGAAAGGGACGAGGGAGATTTGGATTGGGTGGAGGTAGGCGGAAAGCT[C/T]GTTAGCTCGATTTAATGGTGAATGGAAGCTGGAGAGGTTGCCTTTGGTGGTGAGCACGGTGACCTTTGCTCCATGAGAAGCGAAGAGTTTGGATAAGT
66057 T C CATGTCGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTT[T/C]GCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCC
66057 C T CATGTCGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCA[C/T]GGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCC
66057 G A CATGTCGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAA[G/A]GTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCC
66057 C T CATGTCGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTG[C/T]TTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATT
66057 T C CATGTCGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCT[T/C]ACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATT
66057 A G CGTCATCTTCCCATTCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACC[A/G]AAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTT
66057 C T TCCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTC[C/T]CGCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTTCCCTTCTGTTTCCGG
66057 C A CCTCGCTCAAGGCCACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCC[C/A]GCTTCCATTCTCCATTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTTCCCTTCTGTTTCCGG
66057 A T ACATCATCCCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCC[A/T]TTAACTCGAGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTTCCCTTCTGTTTCCGGCTTACCTGAAAACTG
66057 G A CCCGCCATGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTC[G/A]AGCTAACGAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTTCCCTTCTGTTTCCGGCTTACCTGAAAACTGCGAAAAC
66057 C T TGGACCTATCGAAACTCTTTGCTTCTCACGGAGCAAAGGTCACCGTGCTTACCACCAAAGGCAACCTCTCCCGCTTCCATTCTCCATTAACTCGAGCTAA[C/T]GAGCTCTCTTCCTTCCTCCATCCCATCCAACTCTCCCTCATTCCCTTCCCTTCTGTTTCCGGCTTACCTGAAAACTGCGAAAACAT
66087 A G CTGTTGGCCTACTGGAACTAAAACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCA[A/G]TTCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATG
66087 T C CTGTTGGCCTACTGGAACTAAAACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCAA[T/C]TCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGG
66087 C T CTGTTGGCCTACTGGAACTAAAACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCAT[C/T]TGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGC
66087 T C CTGTTGGCCTACTGGAACTAAAACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCATC[T/C]GATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGCA
66087 A G CTGTTGGCCTACTGGAACTAAAACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCATCTG[A/G]TCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGCA
66087 C A ACGACTTTTGTGATCTCTGTCAAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGG[C/A]CAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGCAACCCGAATTTATGTCGCCGTTC
66087 G A CTGTCAAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTT[G/A]ACCAGTACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGCAACCCGAATTTATGTCGCCGTTCAAATCGAAGACCACGG
66087 G A AAAGCCAGCATGTTCACCGTTATCAATTCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCA[G/A]TACGCCGACCCGCAACCCGCTAATGGCCTCTTTTAGCTTTGCGCAACCCGAATTTATGTCGCCGTTCAAATCGAAGACCACGGTCTTG
66087 A T TCAATTCCTTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCT[A/T]ATGGCCTCTTTTAGCTTTGCGCAACCCGAATTTATGTCGCCGTTCAAATCGAAGACCACGGTCTTGAGTTC
66087 C G TTGTAAAGATCCATCTGATCATCCCCGAAATACAGCGAGTTCGGGTGGGCCAGACCCGCGTTGTTGACCAGTACGCCGACCCGCAACCCGCTAATGGCCT[C/G]TTTTAGCTTTGCGCAACCCGAATTTATGTCGCCGTTCAAATCGAAGACCACGGTCTTGAGTTC
66101 C T CAGCATGCTGCAGCCTTCCAGTAAGAGTTGGAGAAAGGGTTATGTTTGTAAGCTCTTGATATGACAGCTTAGCTTACAAGAAGAAAAGGTTATTTAGTCC[C/T]ACACTGCCAAGTACATAAGAAGTGCTGCATACAAATATGAGCTTTTCACGTGAACAAATGCCGAGCTCAATAGCGTGGGCTTGTAAC
66101 A G GGAGAAAGGGTTATGTTTGTAAGCTCTTGATATGACAGCTTAGCTTACAAGAAGAAAAGGTTATTTAGTCCCACACTGCCAAGTACATAAGAAGTGCTGC[A/G]TACAAATATGAGCTTTTCACGTGAACAAATGCCGAGCTCAATAGCGTGGGCTTGTAACCAAGTGGGGCACTAAGGTGATGG
66113 G A ACGCACTGAAAGATTTATCTCTTTCGAATGAAAGTAACAACGAGAATACGCATGAAGAGTTTGAAGACGGGGAAATCGAATCCGAAGCAGAAAACAACCA[G/A]TCAGTTGATGAAGCTCAGGCGACGCATCCATTAGAGCACGCATGGACTTTCTGGTATGATAAT
66181 T C CCTGGTTCAAAACAGCCTTACCGTTCTCATACTCCTGCACAACCTGCACCCTCTCGTTGATCTGCTTCGCCAGCTCCGCCTGACTCATCTTCTTCGCCAA[T/C]CTCGCCTTCTGGATCTCGGCCCTCACCTCCGTCGGCACACGGTTCAGCGTCCCAGGTTCCGTCTGCTCGTCGAGCTTTCTCGCGTT
66181 G C TACCGTTCTCATACTCCTGCACAACCTGCACCCTCTCGTTGATCTGCTTCGCCAGCTCCGCCTGACTCATCTTCTTCGCCAATCTCGCCTTCTGGATCTC[G/C]GCCCTCACCTCCGTCGGCACACGGTTCAGCGTCCCAGGTTCCGTCTGCTCGTCGAGCTTTCTCGCGTT
66199 A G CAAGGCAATGCAGATACTGTATATTAGACACAAAAACATTACTACAGAAACAAGTTTCTATTGAAATCTAAAACGCTACCAGTCAAGCAAGAGGAAAGAC[A/G]CACAAAATTAATGCTGCATCTTATGCACATGTAATTCCAAAGTCGCATTTAAGCCGCTTTCTTAGGGGACTTGGGCACAGACTTCTTC
66201 C T GGTGATTTTAGGATTGCAGAAGTCTGCAATGTGATACTGGGCAGCATACTTGTATTTTGGCCCTTCCATAGCAGTAATCGGAGG[C/T]TCATTCAGAAACGCCCAGTTGCTTCTTGTCCACCAGCAATTTCTCAACTCCGGCCGTTCCATCTTCGGCGTGCTTTCTTTTCTTTGATCAGTTGCAGGCA
66285 T A AGGATGGAGAAGGTGAAGATAAAGAGCATACGAGGGCAGGCGAAAGTTGCAGGAACAATA[T/A]TAACAGTACTAGGAGCACTGCTAATGATCGTATACAAAGGCCCAGTAGTTGAATTTATTTGGTCTAAAGGAAAGAGCCACCAGGAGGAAGCTGCTAATAC
66285 A T GAGGGCAGGCGAAAGTTGCAGGAACAATATTAACAGTACTAGGAGCACTGCTAATGATCGTATACAAAGGCCCAGTAGTTGAATTTATTTGGTCTAAAGG[A/T]AAGAGCCACCAGGAGGAAGCTGCTAATACCAATCACAGCCATTTTCTTGTTGGTACTTTCATGATCATCGTAAGTTGCATCAGTTG
66285 A G AAAGTTGCAGGAACAATATTAACAGTACTAGGAGCACTGCTAATGATCGTATACAAAGGCCCAGTAGTTGAATTTATTTGGTCTAAAGGAAAGAGCCACC[A/G]GGAGGAAGCTGCTAATACCAATCACAGCCATTTTCTTGTTGGTACTTTCATGATCATCGTAAGTTGCATCAGTTGGGCTCTCTTCTTC
66285 A T GCAGGAACAATATTAACAGTACTAGGAGCACTGCTAATGATCGTATACAAAGGCCCAGTAGTTGAATTTATTTGGTCTAAAGGAAAGAGCCACCAGGAGG[A/T]AGCTGCTAATACCAATCACAGCCATTTTCTTGTTGGTACTTTCATGATCATCGTAAGTTGCATCAGTTGGGCTCTCTTCTTCATTGTT
66307 A G CAACGCTGAAAATTTTGAATCCACGATGGTGGTAACTTGCGGTTTTACTCATAATTATGGATTGTTTTGTATCCATTTTGAATCCTGATTTCAAATTATG[A/G]CTTTGAGATGCTTTTACTGACCGTATTCAAAAGTTTAGACAGTCGCCTTTTTACATTGCAATTTAAAATTTTAAAATGCAGTTGAGCAAAC
66307 G A CGATGGTGGTAACTTGCGGTTTTACTCATAATTATGGATTGTTTTGTATCCATTTTGAATCCTGATTTCAAATTATGACTTTGAGATGCTTTTACTGACC[G/A]TATTCAAAAGTTTAGACAGTCGCCTTTTTACATTGCAATTTAAAATTTTAAAATGCAGTTGAGCAAACTGCCTGTGAAAA
66321 C T TATCCTTCATAAATTGGAACAGTATGACTAACACCATCACCAGAATCAAGCACAATACCAGTTGTTCGGCCACTTGCATACAGGGAAAGCACAGC[C/T]TGAATTGCCACATACATAGCAGGCACGTTAAAAGTCTCAAACATAATCTGGGTCATCTTTTCTCTGTTTGCCTTGGGATTGAGTGGAGCTTCA
66361 C G TCACTCCTCAAACCAACTGAACTTCACATTCCACATCCAAAGCGAAGTACATAAATAATCAAAACTCAA[C/G]AAAGGAAACAAACAAACAAAAGAAAATGTGCAACTCCACCACGAAGCCAACCGTTGCAGCCACCACCCCCTCATCCTCACCTCCGACCAAACCACTCAAA
66361 CA C TCACTCCTCAAACCAACTGAACTTCACATTCCACATCCAAAGCGAAGTACATAAATAATCAAAACTCAACAAAGGAAACAAACAAA[CA/C]AAAAGAAAATGTGCAACTCCACCACGAAGCCAACCGTTGCAGCCACCACCCCCTCATCCTCACCTCCGACCAAACCACTCAAAAAGACCCTCCAAAGATC
66361 G A ACTGAACTTCACATTCCACATCCAAAGCGAAGTACATAAATAATCAAAACTCAACAAAGGAAACAAACAAACAAAAGAAAATGTGCAACTCCACCACGAA[G/A]CCAACCGTTGCAGCCACCACCCCCTCATCCTCACCTCCGACCAAACCACTCAAAAAGACCCTCCAAAGATCGCTAACGGCACCCCTCA
66361 T A GAAGTACATAAATAATCAAAACTCAACAAAGGAAACAAACAAACAAAAGAAAATGTGCAACTCCACCACGAAGCCAACCGTTGCAGCCACCACCCCCTCA[T/A]CCTCACCTCCGACCAAACCACTCAAAAAGACCCTCCAAAGATCGCTAACGGCACCCCTCACTTCGACACCCACGCCCAAACTCGAAC
66373 T C AAACCCGGAAGGCAGTACGAGAACGTGGACGAGTAAACGTCCTTGGTCTGGGACAGAAAGGAAAGCGGGCCCCGGCCGAGCCCGAGCAGCCC[T/C]TGTGGAAGCACTGAGCTGCCTGCGGCGGTAACAACGGATCCAAACGTGAAGCTTTTGACGACCTCGGAGGACAAAGAGATGGAGTCCTGA
66435 T C CCAAAGTCTGCTTCGAGCTCCTGATCAAGCCCGTACTCGGCATGGTCACAGATGAGGAAGCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGA[T/C]GTTTATGAAGCCCGACTTTCCAAAAGCAAATACCTCGCCGGAGACGAGTTCACCCTCGCGGACTGCAACCACATGGCCTGGCTCAA
66435 T C TCTGCTTCGAGCTCCTGATCAAGCCCGTACTCGGCATGGTCACAGATGAGGAAGCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGATGTTTA[T/C]GAAGCCCGACTTTCCAAAAGCAAATACCTCGCCGGAGACGAGTTCACCCTCGCGGACTGCAACCACATGGCCTGGCTCAACGTGCT
66435 G A GAGCTCCTGATCAAGCCCGTACTCGGCATGGTCACAGATGAGGAAGCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGATGTTTATGAAGCCC[G/A]ACTTTCCAAAAGCAAATACCTCGCCGGAGACGAGTTCACCCTCGCGGACTGCAACCACATGGCCTGGCTCAACGTGCTCATGATG
66435 A G AGCTCCTGATCAAGCCCGTACTCGGCATGGTCACAGATGAGGAAGCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGATGTTTATGAAGCCCG[A/G]CTTTCCAAAAGCAAATACCTCGCCGGAGACGAGTTCACCCTCGCGGACTGCAACCACATGGCCTGGCTCAACGTGCTCATGATGA
66435 A G CCGTACTCGGCATGGTCACAGATGAGGAAGCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGATGTTTATGAAGCCCGACTTTCCAAAAGCAA[A/G]TACCTCGCCGGAGACGAGTTCACCCTCGCGGACTGCAACCACATGGCCTGGCTCAACGTGCTCATGATGACTAAGAAGGCCTGTT
66435 C T GCAGCAGAGAAACACGCTACTGACTGCCTCAAGATCCTGGATGTTTATGAAGCCCGACTTTCCAAAAGCAAATACCTCGCCGGAGACGAGTTCACCCTCG[C/T]GGACTGCAACCACATGGCCTGGCTCAACGTGCTCATGATGACTAAGAAGGCCTGTTTGGTCAGTGACAGGCCCCAC
66601 T TC CCGCCTCTCTTCCCCCTTCTCCTCCACCTCGAACCCTTCCTCCTCTCTCTTCTTCTCCAGTACACGACGCGCCGACCCCCTGACCAACCACCGCACCCCC[T/TC]CCTTGCCCGTCGCCGCTCGCCTCCCTCCCCGCCGACTGCCCCTCCTCACGACGCGACGCCTGAACCCCCCCCGTCCTTCGAAACGCAACG
66601 G GC TCTCTTCCCCCTTCTCCTCCACCTCGAACCCTTCCTCCTCTCTCTTCTTCTCCAGTACACGACGCGCCGACCCCCTGACCAACCACCGCACCCCCTCCTT[G/GC]CCCGTCGCCGCTCGCCTCCCTCCCCGCCGACTGCCCCTCCTCACGACGCGACGCCTGAACCCCCCCCGTCCTTCGAAACGCAACGACGA
66601 T TC CCTCGAACCCTTCCTCCTCTCTCTTCTTCTCCAGTACACGACGCGCCGACCCCCTGACCAACCACCGCACCCCCTCCTTGCCCGTCGCCGCTCGCCTCCC[T/TC]CCCCGCCGACTGCCCCTCCTCACGACGCGACGCCTGAACCCCCCCCGTCCTTCGAAACGCAACGACGAACGGTGACAAAAA
66629 T C AGCCCTGCTATCAGAAATAATTCTGACACAGGAAGGGGAGCCTCCAGCAGTGATCCACAGAGC[T/C]GTAACCACCTGAGAAAGAGAAAGCATGAAGAAAAATTAAGTCTTTTACACATATTTGGAGATTACCACTACAAAAGTATGCTTAATAATCAAGTTTATCA
66659 T A GGATGGCACAGGATGAGCTACTTTATCGGCCACGATTTCATGTCTGTTGAACTCGACAGACATATTAGATTGCTACACAAAGCGGTCGGCAATGC[T/A]ATGGTTGATGGTAAATATCTTGTGTTTGGTAACGGAGTGACTCAACTTCTCAACGGAGTTATTATATCACTGTCACCAAATGTTACAGCTGAC
66659 G A GGATGGCACAGGATGAGCTACTTTATCGGCCACGATTTCATGTCTGTTGAACTCGACAGACATATTAGATTGCTACACAAAGCGGTCGGCAATGCTAT[G/A]GTTGATGGTAAATATCTTGTGTTTGGTAACGGAGTGACTCAACTTCTCAACGGAGTTATTATATCACTGTCACCAAATGTTACAGCTGAC
66659 C T GCCACGATTTCATGTCTGTTGAACTCGACAGACATATTAGATTGCTACACAAAGCGGTCGGCAATGCTATGGTTGATGGTAAATATCTTGTGTTTGGTAA[C/T]GGAGTGACTCAACTTCTCAACGGAGTTATTATATCACTGTCACCAAATGTTACAGCTGACCCAACTGCTCATATAAAGAAAGTTGTTG
66661 G A GGGAACACCTAACTCAAGCTAGCACTATTATCTACTTCTTCTCCTCCCATTCAGTTATCCTATCGCCATCTCTCTCTCTCTAATGGATCCAATTCCTTCA[G/A]CAATCGAACCCGAATACGAAGATTCTACTTCATCCAAAGATTCCTCAGCAGAAGAAGATTCCATTGCCGTCGTCCCATCATCATTCTCCTCC
66683 C A CTTTTCTCTTTCTTAAATTTTCTATTGCTAGGTCGCCATGGCAGCAATTTCGGCTTCCTTTTCCCCTAATTTATCTCT[C/A]CTCTCCTTTGCCAGCTCTTCTCCTAATAAAACCAACTCTTCACTCTCATTCTCTCCTCTCAATTCTAAACACTTCCCTTCTCGCGCTTCGTTTAGCTTGT
66699 A G ACGGGGTACGGCTTCTGGCGTGTCCCCATGTTTTGAAGGCAGGTTAGGGTTTTGAAGGCGCGCGACATAGGGGACTGCCGGAACTTGCTAATCCGATTTC[A/G]GCTTCGGGTAGACGAGCTTGAGGTGGGCGCGACTCCGATTTAGGGTTGGAGGCCTTGCACGATTTGGATTGGAGGAAGATGAG
66711 A G GGGGGTGACTGATGACGCGGGTGAGGTACTCTTTGCGGACGCCAGGGAGGGCGAGGAGGCAGTGGTGGACGGGGAGCTGGACCTCGCCGACGATGTGGAG[A/G]CGGTGGCGGAGGAGCAGGTCGTAGTTGCGGTGGATGGAGCCGCCGAGGGAGTTCTCGACGGGGAGGACGGCGCGGTCG
66711 G T CGCCAGGGAGGGCGAGGAGGCAGTGGTGGACGGGGAGCTGGACCTCGCCGACGATGTGGAGACGGTGGCGGAGGAGCAGGTCGTAGTTGCGGTGGATGGA[G/T]CCGCCGAGGGAGTTCTCGACGGGGAGGACGGCGCGGTCGGCGATCCAGAGCTCGACGGCCTGGAAGGCGACCTCGAACT
66711 G T GGAGGGCGAGGAGGCAGTGGTGGACGGGGAGCTGGACCTCGCCGACGATGTGGAGACGGTGGCGGAGGAGCAGGTCGTAGTTGCGGTGGATGGAGCCGCC[G/T]AGGGAGTTCTCGACGGGGAGGACGGCGCGGTCGGCGATCCAGAGCTCGACGGCCTGGAAGGCGACCTCGAACTG
66719 A G AAAAACAACAAGCTTTTCAAAGAGGACTCACCTACTGGTGGTGCTGCTATTTCTGCTAGGCTACTCCATAACCAATGATGCTGCTCGCATTCTTCTAGAA[A/G]CACCAATTATCCCAAAACCAGAGCTTCCGTCGCTACCTGAAATTCCGACACTTCCAAAGCCCGAACTACCAAAACTGCCCCCACTACCC
66731 G A TTTCTTGCTGCTGCCAAACTTTTTTTAGCTGCAGGGAAGAAGGTCAAAGTTCCCACGTTCCTCGTCCCTGCTACGCAGAAGGT[G/A]TGGATGGACATATATGCCCTTCCAGTTCCAGGGTCTGGGGGGAAAACTTGCTCTCAAATATTTGAAGAAGCGGGTTGTGACACTCCCGCTAGCCCAAGTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
66731 T C TTTCTTGCTGCTGCCAAACTTTTTTTAGCTGCAGGGAAGAAGGTCAAAGTTCCCACGTTCCTCGTCCCTGCTACGCAGAAGGTGTGGATGGACATATA[T/C]GCCCTTCCAGTTCCAGGGTCTGGGGGGAAAACTTGCTCTCAAATATTTGAAGAAGCGGGTTGTGACACTCCCGCTAGCCCAAGTTGTGG
66731 C T CTACGCAGAAGGTGTGGATGGACATATATGCCCTTCCAGTTCCAGGGTCTGGGGGGAAAACTTGCTCTCAAATATTTGAAGAAGCGGGTTGTGACACTCC[C/T]GCTAGCCCAAGTTGTGGAGCTTGTTTGGGAGGCCCACTTGACACTTATGCTCGAATGAATGAACCTCTGGT
66743 A G CACCAAAAGATCGGTGGCATACTGCAAAGATACCATTAGAACGATATCTACCGACGTGGAGAGGAAATGTGATTGATGCAAAGTTAGAGATGAATCCAGC[A/G]AGGATACTGGGAATGTCAATATCTGTTAATGCTGATGGTGGAGTTGTTCCAGGTTCTAAATCCGGACCAGGGGATTTTACACTTA
66789 G A TGGGTTGGTTGAATGGGAATCTGATTCCCAAGTCTTTGCTGTTCTTGAATACTCTTATTGGAACATCATCTACAAAGAAGACAATTTGATACATGTTCCA[G/A]AGAACAGAGTAGGCATGGTAGGCTTTAGTTGGATCAAACCAAAGATAAATTCTTTGCTCTCTGTTGCCTTTACCACCAGT
66851 C T ACACTGAAAATATACAAGCATGTTCAAATTAAACCAAGATGATTTATCTATTTAAGGGTGCATGTTTCGACCATCTCCCAGGATTTCAATGTTTTATCTT[C/T]AGGATCAGTTTTGAAGAGACTGATGGAAGACACTTGGAAAGTGAGACCAACGAGCTCTTTATTCAATTCTTCGACTTGCTTTCGAGCTC
66853 C G GCCTACGGCTTGCAGACAATGTGAACATTCTGGAGTATCTGTTTGCAGTCATAGGAGGAGGTGC[C/G]CGGTCCTCTGAAGCAGGGGCAAATGAATCATCAAACATGTTTGCTCTTGGAATCTCACAGTCAGATAGTCTCGGAGCTCCCGACTTGGTCACCCGAACCA
66853 T G ACGGCTTGCAGACAATGTGAACATTCTGGAGTATCTGTTTGCAGTCATAGGAGGAGGTGCCCGGTCCTCTGAAGCAGGGGCAAATGAATCATCAAACATG[T/G]TTGCTCTTGGAATCTCACAGTCAGATAGTCTCGGAGCTCCCGACTTGGTCACCCGAACCAGAGCTTGAGGACTCAAAATGATAGG
66881 C A ACAAGGAAAAAGCTAATCTCACTCGCCATTAATCAAACACGTAATCGATGGGGCAAGCAGG[C/A]AGTGGTCTCGGAAAACAACCGCCGTCCGATCGGAAATCGGACCCTTCAAAGAGCGAGAAGAAATTTCAACCGCCGGCGCCGCCATCTCGAGTCGGCCGGA
66881 C T ACAAGGAAAAAGCTAATCTCACTCGCCATTAATCAAACACGTAATCGATGGGGCAAGCAGGCAGTGGTCT[C/T]GGAAAACAACCGCCGTCCGATCGGAAATCGGACCCTTCAAAGAGCGAGAAGAAATTTCAACCGCCGGCGCCGCCATCTCGAGTCGGCCGGAAACAACGCA
66881 A G ACAAGGAAAAAGCTAATCTCACTCGCCATTAATCAAACACGTAATCGATGGGGCAAGCAGGCAGTGGTCTCGGAAAACAACCGCCGTCCGATCGGAA[A/G]TCGGACCCTTCAAAGAGCGAGAAGAAATTTCAACCGCCGGCGCCGCCATCTCGAGTCGGCCGGAAACAACGCAAACAGAAAGGACCA
66881 T C AAAAAGCTAATCTCACTCGCCATTAATCAAACACGTAATCGATGGGGCAAGCAGGCAGTGGTCTCGGAAAACAACCGCCGTCCGATCGGAAATCGGACCC[T/C]TCAAAGAGCGAGAAGAAATTTCAACCGCCGGCGCCGCCATCTCGAGTCGGCCGGAAACAACGCAAACAGAAAGGACCAGAGGCA
66881 A C GGCAAGCAGGCAGTGGTCTCGGAAAACAACCGCCGTCCGATCGGAAATCGGACCCTTCAAAGAGCGAGAAGAAATTTCAACCGCCGGCGCCGCCATCTCG[A/C]GTCGGCCGGAAACAACGCAAACAGAAAGGACCAGAGGCAGCCGCAAGGCTTCCGGTGGTGACGCCAGTAACAAAGTGCAGAC
66891 T G TTGATTAGAGGGGAATTCGGGTCGGATGTGGATACCGGGTTGGTTTCGGATCCGTTGACGCCGTTGAT[T/G]GATGGGTTGAGGGATTTCATCCAGCCAAGCATGTGGTCGAAGGAGCGGTTTTCCATTACGAGGACGACCACCGTTTTTATTGGGCTGTCGGACGTGGAGA
66891 A G TTGATTAGAGGGGAATTCGGGTCGGATGTGGATACCGGGTTGGTTTCGGATCCGTTGACGCCGTTGATTGATGGGTTGAGGGATTTCATCCAGCC[A/G]AGCATGTGGTCGAAGGAGCGGTTTTCCATTACGAGGACGACCACCGTTTTTATTGGGCTGTCGGACGTGGAGAAAGGAGATCCGATAAG
66891 G C ATACCGGGTTGGTTTCGGATCCGTTGACGCCGTTGATTGATGGGTTGAGGGATTTCATCCAGCCAAGCATGTGGTCGAAGGAGCGGTTTTCCATTACGAG[G/C]ACGACCACCGTTTTTATTGGGCTGTCGGACGTGGAGAAAGGAGATCCGATAAGTAGTAGGAAGAGGATGATTGTGATGGAGTTG
66963 T G TCAGCAAACAGAAGCATAGTTGAAGGATCATCAGAGCAAAGTGCGTATGAAGAAACTAGCAGAGGACATAAAATTCATTTCATCACCAGTTTCAACTTAG[T/G]TATCAATGGGATGCATCATATCTTAGATTACTGAGAGCAATTAAGTCTTGCCCTTGCTTTAAGAAAAGAAGGAAAAACCGTAGAAA
66963 G GA AGAAACTAGCAGAGGACATAAAATTCATTTCATCACCAGTTTCAACTTAGTTATCAATGGGATGCATCATATCTTAGATTACTGAGAGCAATTAAGTCTT[G/GA]CCCTTGCTTTAAGAAAAGAAGGAAAAACCGTAGAAACTAAAACGAATAAACATTAAATTACTGGAGACTCCTTCTGATGGCAGG
66981 C A TTATTTCCCTAGTTGCCACATCTTTTCAGCTCCTCAAACGCGATTTCAGCTCGTCTCCGCAATCAGTCCCCCCAAGTCGCGAATCCTCCAAATCGCGATT[C/A]TCAGTCTTTGCAACTTTTCAGCTCCGCAGTCGGTCCACAGTGAAAATATAATCACCACGAAGCTCTAAAATCAAGTAGCAATCTCAGAAT
66985 A G AGCCCTTGATCATACAAAAAACCTTTGAATACGTGACCGCCGATTTTAACCATTGCTTGATATGCATACTCGTCTTCACCGTC[A/G]TCCTCAATCGATGTAACTCTCACACATTTGAATAATGCTGGTGCTCGGATCTGTCCTGGTAACGTCTCCCTAAATCTTGCTCCTTGATGGCTGGAACTAG
67015 G T CAGAGTATATCGAAATATAATACACAGCGGAAGATAAATTTACATAAATGTAAAACAGTGCACAGCGGAAATATAAACTACACAGCGGAAGACTGTAAAT[G/T]TCTGGACACAGCTTAAAGCTTCAATCCAGAATCCTGCTCAAAACATCTGCAAAATAAAACTACTCGACAATAGCTATCCACTC
67053 C A CCCTATCTTTCCCCATGCCTTCCAAAACTTTTCTCTCTCCTCCCAAAACCCATCGGTCTCTTATCTCTCTTTCTCCTCTTCCCAAACTACCCTTCTCCGT[C/A]TCCGCCACACCTTCGTCCTCTTCGTCCACCGCTACCAAATCATCAAATTGGGCCCCGTCGAGCTGGACTTTCAAAA
67097 CG C ACTGTTGGCCTACTGGGAGCTTCCTTTTTCTCCAGTCCTATCATTCCTCTTTATTTCAAACCCTAATTTCCTCGTATACGCGTCAAAATCAATTC[CG/C]GGAAAAAATGTCGAGCGCACTGGACATGTCTCTCGATGACCTAATCAAGAATAACAAAAAGCCTAACTTCGCCCGATCCAACGCTCGATCCGCC
67097 GA G ACTGTTGGCCTACTGGGAGCTTCCTTTTTCTCCAGTCCTATCATTCCTCTTTATTTCAAACCCTAATTTCCTCGTATACGCGTCAAAATCAATTCCG[GA/G]AAAAAATGTCGAGCGCACTGGACATGTCTCTCGATGACCTAATCAAGAATAACAAAAAGCCTAACTTCGCCCGATCCAACGCTCGATCCGCC
67123 A T TTGCTGTGGTTTCTTGCCTCCTAGAATGGTTTGCCAAATGCGGATCCAATCCTGCTCTATGAGTGAACGGATTTGATTAGATCTTACGAGATGCAGGTGA[A/T]CTTTCTTTGTTGGTTAGTTGCTTTGGTTTATCTTGTCTATGGTTCGACTGTTAGTCGGAGCACTTAGTTCAGCTGCTTGGATTTCGTTTT
67127 G A GATCAAAAACAGATTTCGGACTATCCCCAAATCAGGAAAACCTAATTTCTCAAATCGAACTCAAAATGCCAGCCACAGCAGGTCGAGTTCGCATGCCCGC[G/A]AACAATCGGGTCCACAGCAGCGCAGCTCTCCAAACCCACGGAATCTGGCAAAGCGCTATCGGTTACGACCCCTACGCTCCAACTGC
67135 CG C TGGTGCCCATACATACCTGCAACAGCTGCGACGCCACCGGCAAGTAAACCTCCCATGCCTCCTGATCCATGGCCGGCCTGATGACGTTGAGGATAAGCAA[CG/C]GGGGGGAGGACATCCATAGGGAGGGCAGCCGTAAGAATTCCCATTATTTGATGGAGGAGGATAACCGTAAGGAGGCATCTGGG
67199 T C AATATGAGTTCGTCGGAGGTGGAAGCTGAGCTGGCAGAGGAAGAGGCGGATAAGGTATGCTTAGGGTTCGAAGAAATTAGTTTTTTGTCGAGGGGTTTAG[T/C]GAAAGAATTAACATTCGAAGTCGATTTGGATGTGATTTGAGGACCGATGAGGGGCTTGTGGAGATTGAGAAGAAGAGTGGAGG
67199 C T TATGCTTAGGGTTCGAAGAAATTAGTTTTTTGTCGAGGGGTTTAGTGAAAGAATTAACATTCGAAGTCGATTTGGATGTGATTTGAGGACCGATGAGGGG[C/T]TTGTGGAGATTGAGAAGAAGAGTGGAGGAGAATGTTGCTGCCATTTTTTTTAATCTTCGCGGGTTAT
67221 C T CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTT[C/T]AGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACG
67221 G A CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTT[G/A]TGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATG
67221 A G CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAG[A/G]AAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCT
67221 G C CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAG[G/C]TTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTG
67221 T C CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGG[T/C]TGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGG
67221 C T CTCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTC[C/T]TTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGG
67221 T G TCAGCCATGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCC[T/G]TTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGG
67221 C T TGGCTTGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTG[C/T]TTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAG
67221 C T TGATAGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAA[C/T]GATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGC
67221 G A AGTCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGAT[G/A]AAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGG
67221 A G TCAACAGCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGA[A/G]AATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGT
67221 G A GCTTCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGT[G/A]AATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTAT
67221 T C TCTATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAA[T/C]ACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTA
67221 A G ATGAGCTCGAATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATAC[A/G]TTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTATG
67221 G A AATCTGATTACATTGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAG[G/A]GGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTATGTCTGTTTCGG
67221 T G TGACCACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCT[T/G]CCATAGACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTATGTCTGTTTCGGAAGTGTGAGTTT
67221 A G ACTTCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCAT[A/G]GACGAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTATGTCTGTTTCGGAAGTGTGAGTTTCTTCA
67221 C T TCAGAAACGTTGTGGGAAGAAAAGGTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGA[C/T]GAAGCTTCATGTTTGAGCTGGCTGGGGAAGAAGAGTGCGGGGTCGGTATTGTATGTCTGTTTCGGAAGTGTGAGTTTCTTCACTAC
67221 G T GTTGGCATGTCGGTCCTTTGCTGCTTAACGATGAAAATGTGAATACATTCGATAGGGGAAGTAAATCTTCCATAGACGAAGCTTCATGTTTGAGCTGGCT[G/T]GGGAAGAAGAGTGCGGGGTCGGTATTGTATGTCTGTTTCGGAAGTGTGAGTTTCTTCACTAC
67303 T C ATCTCATTCAACAACGGAGCAGCCTTGGCCTCAGCAACGAAGACGCCATGCTTCGGGTACCACAGAAGGCTCTTCAGCTGCATGGA[T/C]GAGTTACACTGTACCTTCGTAGGCAGCCTTGACAACCTGAGCTCGCTGATAAGGCAGTATGGACTGTGCAGCAAATCGACCGACGAGGCCATGCTGGTG
67303 C T ATCTCATTCAACAACGGAGCAGCCTTGGCCTCAGCAACGAAGACGCCATGCTTCGGGTACCACAGAAGGCTCTTCAGCTGCATGGATGAGTTACA[C/T]TGTACCTTCGTAGGCAGCCTTGACAACCTGAGCTCGCTGATAAGGCAGTATGGACTGTGCAGCAAATCGACCGACGAGGCCATGCTGGTG
67303 C T CATTCAACAACGGAGCAGCCTTGGCCTCAGCAACGAAGACGCCATGCTTCGGGTACCACAGAAGGCTCTTCAGCTGCATGGATGAGTTACACTGTACCTT[C/T]GTAGGCAGCCTTGACAACCTGAGCTCGCTGATAAGGCAGTATGGACTGTGCAGCAAATCGACCGACGAGGCCATGCTGGTGATAG
67303 T C GAGCAGCCTTGGCCTCAGCAACGAAGACGCCATGCTTCGGGTACCACAGAAGGCTCTTCAGCTGCATGGATGAGTTACACTGTACCTTCGTAGGCAGCCT[T/C]GACAACCTGAGCTCGCTGATAAGGCAGTATGGACTGTGCAGCAAATCGACCGACGAGGCCATGCTGGTGATAGAGGCCTACAGG
67303 C T GCTGCATGGATGAGTTACACTGTACCTTCGTAGGCAGCCTTGACAACCTGAGCTCGCTGATAAGGCAGTATGGACTGTGCAGCAAATCGACCGACGAGGC[C/T]ATGCTGGTGATAGAGGCCTACAGGACCTTGAGGGACAGAGGGCCCTACCCTGCCGACCAGGTCCTTAAAGG
67438 T C AGGACAACGACTCTCTACTCTCCTTCTTTACCTGCTCTTTCTTCCTTAAAATTGAAGAATCATATCAAAAAGAAGAAAAATATAAGTGCAGAGGTACACT[T/C]AGATCTCACTGCATTGATCCATGGCATCGAAACTAGTACTCGCCATCGTTTTCGTGGTAGATCTCATCGCTTTTGGTCTCGCAGTTGCTG
67452 T C AGAACCCTAAATCATCTCGACCGCGCCTCCCCAAACTTCAACAGCGCCGCCGCATCGTCGCGCCGCCTCCCTTCCTTTTCTAATCGCGCCGCCGCCCATC[T/C]GCCTCTTCTACTCTCGCTGTATCGCCCTCGATTCGTTCAAATCAAGAATCAATTAATGGTTCGCTGCTAAATTTGCTCGGTTATCCATGG
67536 G A AACGGAAACAACGGATCATAATGCCTATCACCAACGTTCATCGGCAACTGATCCACAGTCCTGAACCAAGTTCTCGG[G/A]AGTTTTCCACTGAATCCATAATCCCCAAATGAACATCCGTTACTCCCTTTCCCTTCCGTTCCAGGCAGCCATGCCGCCACCAGAGCGTCCATCTTCGGAA
67536 T TA ACAACGGATCATAATGCCTATCACCAACGTTCATCGGCAACTGATCCACAGTCCTGAACCAAGTTCTCGGGAGTTTTCCACTGAATCCATAATCCCCAAA[T/TA]GAACATCCGTTACTCCCTTTCCCTTCCGTTCCAGGCAGCCATGCCGCCACCAGAGCGTCCATCTTCGGAACATATTTCTCGATCACCAA
67536 TC T TGCCTATCACCAACGTTCATCGGCAACTGATCCACAGTCCTGAACCAAGTTCTCGGGAGTTTTCCACTGAATCCATAATCCCCAAATGAACATCCGTTAC[TC/T]CCCTTTCCCTTCCGTTCCAGGCAGCCATGCCGCCACCAGAGCGTCCATCTTCGGAACATATTTCTCGATCACCAATGGCCTTCCAGATA
67566 A G AAGAGATGGAGGTGTACCCGGTATGGCTTTGCCCGCACCGCCTATTCAAGTACCCAATGAAGACGATGATAAACCCGGAACCCGGATTCGAGAGAAACTT[A/G]ACCCAAGGAGACACGGAGTTTGCGCAAATGTACAGTGATATAGGAGTGTACAATGCGCCAGGGCCTGTATTGAGAGGGGAAGTG
67566 G C ACCCGGTATGGCTTTGCCCGCACCGCCTATTCAAGTACCCAATGAAGACGATGATAAACCCGGAACCCGGATTCGAGAGAAACTTAACCCAAGGAGACAC[G/C]GAGTTTGCGCAAATGTACAGTGATATAGGAGTGTACAATGCGCCAGGGCCTGTATTGAGAGGGGAAGTGTTTGATGGGACGGAA
67572 A G TGGTCAATCCAGATGTTGCTGGCAGTGGTTCCTTGGACGGCAATGGCATCACCGGCATCAGCGAG[A/G]ACCTTGGAAACCTTAAGGTTGCGGATAATTACGTTCTTCTTCTCCAGAATGCGGAGTCCGACACCGGAGAGGGTAGCACCGGCAAGACCGAGGATGGACT
67572 C G AGATGTTGCTGGCAGTGGTTCCTTGGACGGCAATGGCATCACCGGCATCAGCGAGAACCTTGGAAACCTTAAGGTTGCGGATAATTACGTTCTTCTTCTC[C/G]AGAATGCGGAGTCCGACACCGGAGAGGGTAGCACCGGCAAGACCGAGGATGGACTTGTTGCTGCCAACCTTGACAGCTTCATTTC
67572 A G TGCGGATAATTACGTTCTTCTTCTCCAGAATGCGGAGTCCGACACCGGAGAGGGTAGCACCGGCAAGACCGAGGATGGACTTGTTGCTGCCAACCTTGAC[A/G]GCTTCATTTCCGGAGATGGTACCGGAGACCCAAACAATGCGAGCAGTGTCATCAGCAAGGGCAGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
67594 C A TAATCTTTGATTAGTAGGCGGAGCTTGTGCGGGCTTGACTCGTCCCTGACTGCTACCCCTCTTTTGAGGAGATCTGT[C/A]GGCAGAGCTTCTTCCATGAAATTCCAGTCATTGTAATACTTTGCAGACATTTCTATGGCATATTTGTTTGGGAACACTATAGTTTCAAGAATTCCACCAC
67604 A G CATACAAACACAAATTTTCTTTCTCGGGATCACAAAGCTGATGGAACTTCTCGACTTCAGTTGTGAGTGCTTTGATCAATCCAGCGCGCCTGCCGCGGAA[A/G]TCTCTAAATACCTCTTCCGCCGTTCTAGGGTTGTACGATCCGGGAATACCGTCCATGACTCGTCTTTCTTAATTTATGTCGAAGGGGTA
67638 G A AACTCCACGAGATTTCATGCCAACTAGACGGTTCTCGACCATGTCCATCCTTCCAATTCCGTGTTTGCCTCCGACTTGGTTGAGTTCGGTTAGGAGAGAC[G/A]CGGGTGAGAGACTTTGTCCGTTTAGCGAGACTGGTAGGCCTTTCACAAACTCGATTTCAATGTATTCAGGTTTATCTGGAGCATCCTC
67638 T C CATGCCAACTAGACGGTTCTCGACCATGTCCATCCTTCCAATTCCGTGTTTGCCTCCGACTTGGTTGAGTTCGGTTAGGAGAGACGCGGGTGAGAGACTT[T/C]GTCCGTTTAGCGAGACTGGTAGGCCTTTCACAAACTCGATTTCAATGTATTCAGGTTTATCTGGAGCATCCTCTGGATCAACAGACAT
67638 G A CCATGTCCATCCTTCCAATTCCGTGTTTGCCTCCGACTTGGTTGAGTTCGGTTAGGAGAGACGCGGGTGAGAGACTTTGTCCGTTTAGCGAGACTGGTAG[G/A]CCTTTCACAAACTCGATTTCAATGTATTCAGGTTTATCTGGAGCATCCTCTGGATCAACAGACATCATATACATGTCTTTCTTTGGCTC
67640 T C TATCTAACAATTCATCCCAGCATGCTGAACCTGACTCCGATAATGCCTACGCAAGCTTCCAGGGACTTCTTGCCCTTGCTCGCATCACTGGCTCAAACGC[T/C]GACGACACCCGCGGTGCGTGTAAGAAGTGCGGTCGTGTTGGACACTTGACCTATCAGTGCCGAAATTTTCTTAGCATTAAAGAAGGG
67640 G C AGCATGCTGAACCTGACTCCGATAATGCCTACGCAAGCTTCCAGGGACTTCTTGCCCTTGCTCGCATCACTGGCTCAAACGCTGACGACACCCGCGGTGC[G/C]TGTAAGAAGTGCGGTCGTGTTGGACACTTGACCTATCAGTGCCGAAATTTTCTTAGCATTAAAGAAGGGGAGGAGTTGGACAACGA
67678 G C TTTACTTAGAATTGGAGTCAATTTTCGAATTATCGGATATTTGATTACCATGTCCCAAGATGGGGTTCTACCCAACGCTAGAGCGATCCAGAAACAACCT[G/C]TCCATCATATCTTATATTATCAGGAAATCCAGGTAAATTGTCAGCAAAAATTTCAACGGATCCTTTTTTCT
67690 T C AAGGTCGATCTCTACATCTTGGATGTCCACTACGTATGAAAGCTTTCCAGCAAGAGGAAGAAAATCGAGTAGAGCAGAAGAAAGAGATGACTTGAGTTGT[T/C]GTATGACTGTGGAGAATGGAAGCTGAACTGTTTCGAAGGGGGAGTAAATTAGAACTTTCTGAACGGGTTTAAATGGAATCCAGCA
67744 C T GGAAAACTTCAACAGTGCCAACTGTGTGATTGAAAAGTTACCAATACAACTATGTCAAGATAATAAGCCTAAAG[C/T]CATAAGGATCCTGCAAACAATATGATTACTAAGCAATGTATATTTAAAACTCAAATGCATCCCAGCTAAGAAGCAGAACTGAGGTAAACCCAGAAATGCA
67766 T C GATGACTTTTAGCTTCCAAGGGTCTGCCTCTTGAAATGTGGAGCACTCTTCGTTGGGTAAAAGAGAA[T/C]GAACACTGACAACATGGTACGCCTTTGCTTCTGAAACAATACAATCAACTAACATACAAGAATAAATTGTTGAGAATAGTATTAAAAGTAGGATGATATT
67838 T A GTGGCCTTTTTTTTTTTTTCGCAACACAAAAATCATAAAAGGTAGGACAACGATGAAAAACCAATAACGTTTTGA[T/A]GAAACAAGTCAATATCTGTTCTTGATTCCACAAACCAAAATATAAGAAACATAAAGAAGATCCTAGAATAGTAAATTTTAATACTGCATCATGGTATTGA
67864 C T TGCAACTTTTCTGCGGTCAGCTTTTTTGTAGAGGAGAAGGAGCTGGTTGCAGGAGAACGT[C/T]GTGAGAGGGGAGTCAAGGCCTTTTATTTTTCTGAAGATTTCCTCTGCTTTCTTTATGTTCCCAGTAGCAGCACAATTAGCTAAAATAGTTCTGTAAATGG
67864 G A TGCAACTTTTCTGCGGTCAGCTTTTTTGTAGAGGAGAAGGAGCTGGTTGCAGGAGAACGTCGTGAGAGG[G/A]GAGTCAAGGCCTTTTATTTTTCTGAAGATTTCCTCTGCTTTCTTTATGTTCCCAGTAGCAGCACAATTAGCTAAAATAGTTCTGTAAATGGGTTCGGTCC
67864 C T CAAGGCCTTTTATTTTTCTGAAGATTTCCTCTGCTTTCTTTATGTTCCCAGTAGCAGCACAATTAGCTAAAATAGTTCTGTAAATGGGTTCGGTCCTGAA[C/T]GTTTCGGGAATGTTGTTTATGTACTGTTCAGCCTTTTGGATGCCTTGTACTTTTGTAATTAAATCAAGATAGGAAACAT
67864 T A AGGCCTTTTATTTTTCTGAAGATTTCCTCTGCTTTCTTTATGTTCCCAGTAGCAGCACAATTAGCTAAAATAGTTCTGTAAATGGGTTCGGTCCTGAACG[T/A]TTCGGGAATGTTGTTTATGTACTGTTCAGCCTTTTGGATGCCTTGTACTTTTGTAATTAAATCAAGATAGGAAACAT
67864 G C CTTTTATTTTTCTGAAGATTTCCTCTGCTTTCTTTATGTTCCCAGTAGCAGCACAATTAGCTAAAATAGTTCTGTAAATGGGTTCGGTCCTGAACGTTTC[G/C]GGAATGTTGTTTATGTACTGTTCAGCCTTTTGGATGCCTTGTACTTTTGTAATTAAATCAAGATAGGAAACAT
67872 T C AATTCAGTGGTCAAGGCCAATGACATGGGCCCGCTGGTGTTGGCGGCCCGGAAAGCGGTCCGGAAGGCCTCGAAAGGGCTGGCCCGCGTTCTGCC[T/C]GAGATGGAGCAGGAAGTGGGAGAATCGACGGCGGAGGTTAGGAGAGAGAAGGTGGTCGATCGGGTTGCGTTGGTGGATGAAGAGG
67872 A G TCAAGGCCAATGACATGGGCCCGCTGGTGTTGGCGGCCCGGAAAGCGGTCCGGAAGGCCTCGAAAGGGCTGGCCCGCGTTCTGCCTGAGATGGAGCAGGA[A/G]GTGGGAGAATCGACGGCGGAGGTTAGGAGAGAGAAGGTGGTCGATCGGGTTGCGTTGGTGGATGAAGAGGACGAGACTTT
67872 A G GGTGTTGGCGGCCCGGAAAGCGGTCCGGAAGGCCTCGAAAGGGCTGGCCCGCGTTCTGCCTGAGATGGAGCAGGAAGTGGGAGAATCGACGGCGGAGGTT[A/G]GGAGAGAGAAGGTGGTCGATCGGGTTGCGTTGGTGGATGAAGAGGACGAGACTTTGGTTGAGTTCAGGAATAGGATGAGT
67882 G A TTGATCCAATATTTGGTTTTCTAAGCCCGATATTAATTCCAAGCAGTGGGATGTGCAATCCCAAGCCCGCCTCAGATGCCGAACCCGTACTTGAGTCCGT[G/A]CCGGAACCCGAACCTAAGATCGGTCCACCAGGGATTCCAGGAAATGTCTGGGGTTCGTGCCTCGGTTCCTGCTCCGC
67892 G C GATCAGCACCTTCTAAAGCTTGAGCAAGGTTCTCCTCAGAGGCAAATCCAGCAACCTCAGCAGGAGTATTGATATGGCTGACGTCAGCAGC[G/C]ACGCCAGGAGTCCCAGCGATATCGTAAAGCGCAAGCTTGGTAACTAGAGGATTCAGCTTCATCAGAAGCGACAAGGGTTGTCCGATACCTCCGG
67892 C A CAGCACCTTCTAAAGCTTGAGCAAGGTTCTCCTCAGAGGCAAATCCAGCAACCTCAGCAGGAGTATTGATATGGCTGACGTCAGCAGCGACGCCAGGAGT[C/A]CCAGCGATATCGTAAAGCGCAAGCTTGGTAACTAGAGGATTCAGCTTCATCAGAAGCGACAAGGGTTGTCCGATACCTCCGGCGG
67892 T C TGATATGGCTGACGTCAGCAGCGACGCCAGGAGTCCCAGCGATATCGTAAAGCGCAAGCTTGGTAACTAGAGGATTCAGCTTCATCAGAAGCGACAAGGG[T/C]TGTCCGATACCTCCGGCGGCGCCGAGAATCGCAACCTTCCTTTCAGGAACGGCGGCAGAGTTGTAGGATCTGCGAAGGAGAGCA
67894 T C TCCACTCCTGTCAACAGATGACGAATCCCTATGATTATTTGCAAATAATCGAGTATGATGGCGTTTTTGGACAACCACAAATGTTACA[T/C]GGGGCAGATAGTCATTCTCAATAGAAACACAGGCCTTTCGAATCGCATCAAGTTCAAATAGAAGTACTTGATAAAACTGCCCTTCGCTCACACCATCTCT
67894 A T TCCACTCCTGTCAACAGATGACGAATCCCTATGATTATTTGCAAATAATCGAGTATGATGGCGTTTTTGGACAACCACAAATGTTACATGGGGC[A/T]GATAGTCATTCTCAATAGAAACACAGGCCTTTCGAATCGCATCAAGTTCAAATAGAAGTACTTGATAAAACTGCCCTTCGCTCACACCATCTCTG
67894 A C CACTCCTGTCAACAGATGACGAATCCCTATGATTATTTGCAAATAATCGAGTATGATGGCGTTTTTGGACAACCACAAATGTTACATGGGGCAGATAGTC[A/C]TTCTCAATAGAAACACAGGCCTTTCGAATCGCATCAAGTTCAAATAGAAGTACTTGATAAAACTGCCCTTCGCTCACACCATCTCTGTA
67894 A G AGATGACGAATCCCTATGATTATTTGCAAATAATCGAGTATGATGGCGTTTTTGGACAACCACAAATGTTACATGGGGCAGATAGTCATTCTCAATAGAA[A/G]CACAGGCCTTTCGAATCGCATCAAGTTCAAATAGAAGTACTTGATAAAACTGCCCTTCGCTCACACCATCTCTGTAAAATATTATACG
67924 CA C TGGACACAACACTAAGTTCACCAAACAACACAATTAAAGTACAAAGTTTTAAAGATACACTACTCTAGCATTACATCTAGAGGC[CA/C]AAAATTGTGAAAAAACAAACTTAGGAATTAAGGAAGACAAGGTAACAGCCAGGCATGCAAGCTACTTTAAAAGCACACTAAGTAGGGCAAATAGCTGCTA
67964 G A GGATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTT[G/A]GTTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCA
67964 T C GGATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGT[T/C]GAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCAT
67964 T A GGATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAA[T/A]TTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCAT
67964 T A GGATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAAT[T/A]TTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCAT
67964 C T GGATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTA[C/T]AGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCAT
67964 A G ATGGAGGATTCGTGGTTCCAGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTACAG[A/G]CTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCATTT
67964 T A AGACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAA[T/A]CCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCATTTGGGAATGCATCGAGCTACT
67964 C T ACGCCAACGCCTTCGGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAATC[C/T]GTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCATTTGGGAATGCATCGAGCTACTCAA
67964 G A GGCCAAACATTCAGAGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGA[G/A]GAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCATTTGGGAATGCATCGAGCTACTCAACGAGTTCGTCGAC
67964 A C AGATTACGACGCCGATTCAGAGAGAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAG[A/C]ATTATGGAAAGCTGAACAGAATAGAAATGAGCATTTGGGAATGCATCGAGCTACTCAACGAGTTCGTCGACGAAAGCGATCCGGA
67964 T C AGAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAA[T/C]AGAAATGAGCATTTGGGAATGCATCGAGCTACTCAACGAGTTCGTCGACGAAAGCGATCCGGATCTGGACGAACCCCAGAT
67964 A G GAAAGGACTTGGTTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAAT[A/G]GAAATGAGCATTTGGGAATGCATCGAGCTACTCAACGAGTTCGTCGACGAAAGCGATCCGGATCTGGACGAACCCCAGAT
67964 T A TTGAAGAATTTTACAGACTCAATCACATTCATCAATCCGTCAATTTCGTGAGGAAAATGAGGGAGAATTATGGAAAGCTGAACAGAATAGAAATGAGCAT[T/A]TGGGAATGCATCGAGCTACTCAACGAGTTCGTCGACGAAAGCGATCCGGATCTGGACGAACCCCAGAT
67990 C A AATTTTTGACTTTAATTCAATTGTCACTAGGACTTACACGATGAGAATAATTAGCAGCAGAGGTATTGAACTTACTTCTATTTCCCCAATCCTTGCTTGT[C/A]CTCTGCTCTCCATACCCACGAATATGCCCATTATTCATCGGCACCATCCCATACATAGGCACTGGCATCATTCCTGGCATAGCATAAGGC
68080 T C CAGGCACAATCTTTCCAAACAAACGTGGCTGAAAAAGGTAGGGCTCTTCACCAGGGAGATTAATAACAACTCTTAACGTTTGTTCACCAAAATCTACAGA[T/C]ACGTTCTCAACAGGAATACCCTTAGCAAAAATGGTCAGTACCACTTCTGTAGGAGAATTATAGTAGTCATGCCT
68168 C A TAGCAATAGGGTTTCTTTTCCCCAAACACAACTTATATGAGGAATAGAGGAGGTGGTGGCGGAGATAGA[C/A]GGATTTCTGCCACATGGATTTTGCTTCTTTGTGTCTCTAGTTTTTGCCTTGGATTGTTCTTCACCAATAGATTTTGGACAGGTCAAGAGTCCAATGCTCA
68188 A C CACTTCTTCGAAGTACAGCTTCAAAGCCCTCACGTTCCATGACCCCAACGTCATTCACAGCTTTGCTACGCTCTCGCTCAGGGATGGTCGCTGGGTCGCG[A/C]GTGGGCAAATTTTGTACGTTACTGACCTCTTCTTCTGTGTTAGCCATAATATCCCAGTAGGCCAACAGTGAA
68206 G A TTTTTTTATGATTAGCCTTCCAGCAATAGTTAAATCTCGATCGAACCAAGTATGCCATAAACCACCACCATATGTTTGCAC[G/A]CCTACTTCGAGATACCCTCCTTTCGTTACCTTTGAAGCAGGCTTCACTTTGAGACAAGGACTATCTGTATGTGCTCCCACTATATGAAATCCATTTCCGG
68216 C G CCACCCACCACTGGCCGACGCACCCCAGTCCACCGTCGACCAAAGCAGGCCGCCACCCACCTGAAAGACCTCGTTTCGCCGCTCTCCAGCCCCGATAGCA[C/G]CACCCTCCGACCATCCACGAGCTCGGCCCCCTCTCCGCTGCCCTCGCCCTCACACTAGAACCCTCGCGCGAAACCCTAGGCTGGAGA
68234 A G ACTCGTTCCACATTGGACTTGAATATTTCATACCGTAGAGCTTTCTCTGTTGCATCCTTGTATGCT[A/G]TCCCGTGCTTTGCCATCCATTGTTCGTGTCTATCAGCCATTGAGAGTTGGTTAAGGTTTCTTGATGCTTGGATGCTTGCTACTGTTATGAACAGGGTCAG
68234 C T CGTAGAGCTTTCTCTGTTGCATCCTTGTATGCTATCCCGTGCTTTGCCATCCATTGTTCGTGTCTATCAGCCATTGAGAGTTGGTTAAGGTTTCTTGATG[C/T]TTGGATGCTTGCTACTGTTATGAACAGGGTCAGGAATAAGATATATAATGCTACTTTTGGTAATGCCATGGTAGTTAGTTATAGATGCTT
68234 T C GCTATCCCGTGCTTTGCCATCCATTGTTCGTGTCTATCAGCCATTGAGAGTTGGTTAAGGTTTCTTGATGCTTGGATGCTTGCTACTGTTATGAACAGGG[T/C]CAGGAATAAGATATATAATGCTACTTTTGGTAATGCCATGGTAGTTAGTTATAGATGCTTAACTAATTTGTATTTTGGCAATTCTTATTT
68234 T C CCATCCATTGTTCGTGTCTATCAGCCATTGAGAGTTGGTTAAGGTTTCTTGATGCTTGGATGCTTGCTACTGTTATGAACAGGGTCAGGAATAAGATATA[T/C]AATGCTACTTTTGGTAATGCCATGGTAGTTAGTTATAGATGCTTAACTAATTTGTATTTTGGCAATTCTTATTTGTGT
68272 G A AAAAACGGCAGCTTAAGATTGGATGATTGGGTGCTATGCAGACTGTACAACAAGAAGAACAACTGGGACGTGACACAGAATCTGAAAGAGCAATCTTC[G/A]TCCTTTGGAGAGACGGTAGACATGGATTCGGTCGACGACGATTTCAAGTCGGACATAGACAACGATTCATTTCAGGAGTTTGAGGA
68300 TG T GAGGACCAGGATGACCAGGCCGAGTTCCGATTGGTTGGACCGGTTTGGGTTGAGGACCAGGAAGATGAGGCCGACTTCCAATCGGTTGGACCTGTTTAGG[TG/T]GGGGGCCGTGGGGGGTGCTGGCGCAGGCAAGTAATACCACATGACGGATCAAATCCTTGCGTCCTCTCAGTGCATGAACTCA
68336 GT G ATGGTGGAACTTCAATCGGGTTTTTCGATGTGTTGAGGTTGTTATAGTGGCTGTGACAAGTCTAGAGTTATGTTTCTATAGTGAACTTCTTTAGTTGTGT[GT/G]TTTTTGTTGTCTTATTCTTTTTGTGTTGTGTATGAAACAAACTGCTATTATATATGGTTGGTATTGTAATTGTAGGAATGCTATATGAT
68336 CT C GGGTTTTTCGATGTGTTGAGGTTGTTATAGTGGCTGTGACAAGTCTAGAGTTATGTTTCTATAGTGAACTTCTTTAGTTGTGTGTTTTTGTTGTCTTATT[CT/C]TTTTTGTGTTGTGTATGAAACAAACTGCTATTATATATGGTTGGTATTGTAATTGTAGGAATGCTATATGATGTGTTCCTGGTTTGATGA
68420 G A AAAATTAGCAACTTAAACTCAATATCTGAGAAGCATGATTCATGGATGTCTCGTTACGGGCGAGTCTATGCCAACA[G/A]GGAAGAAAAGGAGTATCGTCTTACAGTATTCAAAAAGAACATGGAGTTAATAGAATCATTTAACGCGGGTGATAATCACAAATTCAAACTAGGTGCAAAC
68420 T C GAGAAGCATGATTCATGGATGTCTCGTTACGGGCGAGTCTATGCCAACAGGGAAGAAAAGGAGTATCGTCTTACAGTATTCAAAAAGAACATGGAGTTAA[T/C]AGAATCATTTAACGCGGGTGATAATCACAAATTCAAACTAGGTGCAAACCAGTTTGCAGATCATACCAAGGATGAATATGTTGAAC
68420 A G AGCATGATTCATGGATGTCTCGTTACGGGCGAGTCTATGCCAACAGGGAAGAAAAGGAGTATCGTCTTACAGTATTCAAAAAGAACATGGAGTTAATAGA[A/G]TCATTTAACGCGGGTGATAATCACAAATTCAAACTAGGTGCAAACCAGTTTGCAGATCATACCAAGGATGAATATGTTGAACTCTG
68420 A T TATCGTCTTACAGTATTCAAAAAGAACATGGAGTTAATAGAATCATTTAACGCGGGTGATAATCACAAATTCAAACTAGGTGCAAACCAGTTTGCAGATC[A/T]TACCAAGGATGAATATGTTGAACTCTGCAGCGGTTATCATCCTCACTTGATGACGTTTGTGGAAACCAA
68458 G T TGGGGTGGGCGTATGTTGGGAACCGATTGCTAAGCGCAACTGTAGAGTATGAAGAAACTGGTTGGTATGATGGACAAATATGGGTGAAGACGCCAGAAGT[G/T]TTGGCACGTGATCGACTGTTAGGTTCATTTACTGTTAAACCCGTGCTAAACAGAGTGAAGAATACATTAATTGGTCTGGCTGTAA
68458 A T TTGGGAACCGATTGCTAAGCGCAACTGTAGAGTATGAAGAAACTGGTTGGTATGATGGACAAATATGGGTGAAGACGCCAGAAGTGTTGGCACGTGATCG[A/T]CTGTTAGGTTCATTTACTGTTAAACCCGTGCTAAACAGAGTGAAGAATACATTAATTGGTCTGGCTGTAACTTTGGGCTTATGTGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
68470 G A GGATCTTCATCAGCCCAGCTCAGCGTCAACTATTACTCATCGTCATGCTCAAATGTACTGTCCACTATAAAACCAGTAGTCCAATCTGCC[G/A]TTTCTAGCGAGAAAAGGATGGGTGCTTCTCTCCTTCGCCTCTTCTTCCATGACTGCTTTGTTAATGGATGCGATGGATCATTGCTTCTTGATGACACTAA
68470 G A GATCTTCATCAGCCCAGCTCAGCGTCAACTATTACTCATCGTCATGCTCAAATGTACTGTCCACTATAAAACCAGTAGTCCAATCTGCCGTTTCTAGCGA[G/A]AAAAGGATGGGTGCTTCTCTCCTTCGCCTCTTCTTCCATGACTGCTTTGTTAATGGATGCGATGGATCATTGCTTCTTGATGACACTAAG
68470 A C CTTCATCAGCCCAGCTCAGCGTCAACTATTACTCATCGTCATGCTCAAATGTACTGTCCACTATAAAACCAGTAGTCCAATCTGCCGTTTCTAGCGAGAA[A/C]AGGATGGGTGCTTCTCTCCTTCGCCTCTTCTTCCATGACTGCTTTGTTAATGGATGCGATGGATCATTGCTTCTTGATGACACTAAGAAT
68470 A C GTTTCTAGCGAGAAAAGGATGGGTGCTTCTCTCCTTCGCCTCTTCTTCCATGACTGCTTTGTTAATGGATGCGATGGATCATTGCTTCTTGATGACACTA[A/C]GAATTTCACTGGTGAAAAGAGTGCAAACCCAAACAAGAACTCTGTAAGAGGATTTGATGTCATCGACAAA
68470 T C AGAAAAGGATGGGTGCTTCTCTCCTTCGCCTCTTCTTCCATGACTGCTTTGTTAATGGATGCGATGGATCATTGCTTCTTGATGACACTAAGAATTTCAC[T/C]GGTGAAAAGAGTGCAAACCCAAACAAGAACTCTGTAAGAGGATTTGATGTCATCGACAAA
68474 A C CGCATTGTATACCAAAACCTAAAGTAGTTTAGAAATAAAAATTTATTCAGCAAACCACAATCAGTTTTCAATCTTGTAAATCGACCAATTACAACAGCAT[A/C]AGATTTTGCCACTCTCTTATTGCCACTGTTCCAAAGGAAACTAAATTAAGATGAAATGGGTGGGGTGAAGGCTTAGAGGACAGTGGTA
68474 T C TTCAATCTTGTAAATCGACCAATTACAACAGCATAAGATTTTGCCACTCTCTTATTGCCACTGTTCCAAAGGAAACTAAATTAAGATGAAATGGGTGGGG[T/C]GAAGGCTTAGAGGACAGTGGTAGCACCCGAGGATCCCTGGCGGCATTCATTCAGCATGTTCAGGTAAAACTGGCACTTGCTGATGT
68480 A G TAACTGAACCACACCTCTTCTCCAATGCCCAACCTTACCAAGTGACGCTGTGAGCCTCTGCCACTGTCGAGAAGAGCCCATCACTGCTCCTCCA[A/G]GCCTGTAGCTTGCAAACCCCGCGCAGCAGATCTGGACAATTCACCAATCTCGAAGCTTGTATCAGCCAGAGCCATCGCGGATTGAAGCCATCA
68480 A G TGCCACTGTCGAGAAGAGCCCATCACTGCTCCTCCAAGCCTGTAGCTTGCAAACCCCGCGCAGCAGATCTGGACAATTCACCAATCTCGAAGCTTGTATC[A/G]GCCAGAGCCATCGCGGATTGAAGCCATCACTGGCGCTACAGTCTCCGGCACGTTGTCGCCTCTGGGAAGACATGGAAAACAGATAC
68490 G A ATTTTCATGAAGTGGATCCTCCACGACTGGAGCGACGAGCATTGTGAGAAATTATTGAAGAACTGCTATAAAGCACTGCCAGA[G/A]AATGGGAAGGTGATTCTCATGGAATGCATTCTTCCGGAGTATCCGGATGCCAATTGTGCAACACAAGGTGTGATCCATGTTGACCTGGTCATGCTAGCTC
68490 T C ATTTTCATGAAGTGGATCCTCCACGACTGGAGCGACGAGCATTGTGAGAAATTATTGAAGAACTGCTATAAAGCACTGCCAGAGAA[T/C]GGGAAGGTGATTCTCATGGAATGCATTCTTCCGGAGTATCCGGATGCCAATTGTGCAACACAAGGTGTGATCCATGTTGACCTGGTCATGCTAGCTCATA
68490 A G TGAGAAATTATTGAAGAACTGCTATAAAGCACTGCCAGAGAATGGGAAGGTGATTCTCATGGAATGCATTCTTCCGGAGTATCCGGATGCCAATTGTGCA[A/G]CACAAGGTGTGATCCATGTTGACCTGGTCATGCTAGCTCATAATCCAGGAGGAAAAGAAAGGACCGCAGAAGAGTTTGACGCTTT
68490 G A AAGCACTGCCAGAGAATGGGAAGGTGATTCTCATGGAATGCATTCTTCCGGAGTATCCGGATGCCAATTGTGCAACACAAGGTGTGATCCATGTTGACCT[G/A]GTCATGCTAGCTCATAATCCAGGAGGAAAAGAAAGGACCGCAGAAGAGTTTGACGCTTTGGCAAAGAAGGCTGGATTCAAAGGT
68490 G A AGCACTGCCAGAGAATGGGAAGGTGATTCTCATGGAATGCATTCTTCCGGAGTATCCGGATGCCAATTGTGCAACACAAGGTGTGATCCATGTTGACCTG[G/A]TCATGCTAGCTCATAATCCAGGAGGAAAAGAAAGGACCGCAGAAGAGTTTGACGCTTTGGCAAAGAAGGCTGGATTCAAAGGTT
68538 A T AAGGTGATTATCATGGAATGCATTCTTCCAAAGTATCCAGAAGCCAACTGCACATCACAAGGTGTGATCCATCTTGACCTTATCATGTTGACTCATTGTC[A/T]AGGAGGAAAAGAAAGGACTGCACAAGAGTTTGAGGCTTTGGAAAAGGAGGCTGGATTCAAAGGTTCCAAG
68566 T C TTGTTGAACAGCGCCGTGCTCAGGGCTGCCGTGTTTGTTCCGTACTCTTGGCCCATCATGTT[T/C]CCATACCCACACGCTCCCCCCATTGTGCCCGAAGCGTCACCCCCGCCGTAGAACGTGGCGTGTCCGCCTTCCCATTGAGCGAGCGCTGCCTTTACCATGA
68566 AC A TGTTGAACAGCGCCGTGCTCAGGGCTGCCGTGTTTGTTCCGTACTCTTGGCCCATCATGTTTCCATACCCACACGCTCCCCCCATTGTGCCCGAAGCGTC[AC/A]CCCCCGCCGTAGAACGTGGCGTGTCCGCCTTCCCATTGAGCGAGCGCTGCCTTTACCATGAGGCAGAGTAGGAAGAGAAACATGG
68588 C T AGATGGAAAACCGCGATTGATTTGAGAAGGAAACAGAAGGATGTGTTGATGCCTCTGATTAATGCAAGGAGAGAGCACAAATTGAAGCGGAAGGAAAC[C/T]GAAGAAAGATTTGTTTACTCTTATTTAGATTCTCTTCTTGATATGAAATTACCGGATGAAGGGGGTAGAAGTTTAACTGAAGATGAG
68588 G T TGTTGATGCCTCTGATTAATGCAAGGAGAGAGCACAAATTGAAGCGGAAGGAAACCGAAGAAAGATTTGTTTACTCTTATTTAGATTCTCTTCTTGATAT[G/T]AAATTACCGGATGAAGGGGGTAGAAGTTTAACTGAAGATGAGATGGTAAGCCTTTGTTCTGAGTTTTTGACCGCTGGGACTGATACA
68588 AG A TTAATGCAAGGAGAGAGCACAAATTGAAGCGGAAGGAAACCGAAGAAAGATTTGTTTACTCTTATTTAGATTCTCTTCTTGATATGAAATTACCGGATGA[AG/A]GGGGGTAGAAGTTTAACTGAAGATGAGATGGTAAGCCTTTGTTCTGAGTTTTTGACCGCTGGGACTGATACAACTGCAACTGGTT
68588 A G AGGAAACCGAAGAAAGATTTGTTTACTCTTATTTAGATTCTCTTCTTGATATGAAATTACCGGATGAAGGGGGTAGAAGTTTAACTGAAGATGAGATGGT[A/G]AGCCTTTGTTCTGAGTTTTTGACCGCTGGGACTGATACAACTGCAACTGGTTTACAGTGGATCATGGCAG
68588 G C GAAGAAAGATTTGTTTACTCTTATTTAGATTCTCTTCTTGATATGAAATTACCGGATGAAGGGGGTAGAAGTTTAACTGAAGATGAGATGGTAAGCCTTT[G/C]TTCTGAGTTTTTGACCGCTGGGACTGATACAACTGCAACTGGTTTACAGTGGATCATGGCAG
68604 C T CAAACCCACTCCGCTCCCTCTGCTTCCTCCATTTCTTCACGCTCTCAATCTCTTCCTTCTTCCTCTTTGCCCT[C/T]TCTTTGCTCTTCTGCGCCTGCACCTCCTTCGCTATCTTCTTCGCCTCTCTCGCCTTCTTCCTTTCCTCCGACTCTTCAATCTTCTTCTTCTGGGTCAGAA
68622 C T CACCCGATTCCCTTCGCGTCCCGATAAGCTTCCAGCTGAAAAGAATCAAGAGCCTAGGGTTTCCTTTCAATCATTCAATCCAAATGCAGTCAAACGTACA[C/T]GGTTCTCCGTCAGCCTTGCACCAGGAAAGTTCCACATCACCAAGGCCATTAAAATTTCGCATCAAACGGCTAGATGATACTCATAATG
68624 T C AGTTTGTGAAGGAGAAGGGCCTCAAAGCGGGCGGGGTTGTGGTTTTTGGCAGATTAACGGGTTTGGAGAAGCATTTTTACGTAGGATGTCGATATGATAC[T/C]GACAATTTGAATCAAAGTCACCGTGAAGTTGAACCTGCCGCGCCAGTAGTGGTTAGGGGTGATGTGTTTAGGCTGTTTGGGGTG
68624 A G TTGGCAGATTAACGGGTTTGGAGAAGCATTTTTACGTAGGATGTCGATATGATACTGACAATTTGAATCAAAGTCACCGTGAAGTTGAACCTGCCGCGCC[A/G]GTAGTGGTTAGGGGTGATGTGTTTAGGCTGTTTGGGGTGAATTATTCATTGGAAGTTTCCAGGAAGGAGATCCAC
68630 G T CTGTTGGCCTACTGGAAAAAGGCTTTTCAGTTGCTTCTGCGCCTTGCGATTAGGGTTTTAGTTCTTGCTCG[G/T]AGTGCTCAGTGTCCCGCTGCCGCTTATTCCACACCAGAAATGGCCGCCATTGCAGCTGGTAGATCTGTCTTCCGATCATCCGCGACGCGTTCCTTGGCTG
68630 G A CTGTTGGCCTACTGGAAAAAGGCTTTTCAGTTGCTTCTGCGCCTTGCGATTAGGGTTTTAGTTCTTGCTCGGAGTGCTCAGT[G/A]TCCCGCTGCCGCTTATTCCACACCAGAAATGGCCGCCATTGCAGCTGGTAGATCTGTCTTCCGATCATCCGCGACGCGTTCCTTGGCTGCTAAAATGGCA
68646 T C GTAACATATGCATTAAGGCGAAGCACCTTTTATACCCATGCCAAAATTTTCAAACGTCTATGTAACAGCCCGCACCTCCGTTCACGCAAGATATTGTCCC[T/C]AACTTAGCCACCGTATAGGTGTGGGGTTTTGTTCCTCAAAAGGCCTCGGCGTTAGTAAGAGATGAGATCTACTATATAAGCGCTGCGG
68646 G T TAAGGCGAAGCACCTTTTATACCCATGCCAAAATTTTCAAACGTCTATGTAACAGCCCGCACCTCCGTTCACGCAAGATATTGTCCCTAACTTAGCCACC[G/T]TATAGGTGTGGGGTTTTGTTCCTCAAAAGGCCTCGGCGTTAGTAAGAGATGAGATCTACTATATAAGCGCTGCGGTCCACACAGGAGC
68660 A T TGGCCTACTGGATTTTCATTTTCCCCGAAGAAATTAAAAGCGGCAAATCATGAAATAATCGATAATGAATTAAAAGCCGCATTTTTTTCCACCCATCATA[A/T]GAAGCCCTCGTCGTTAGAAATCGAAACCCTCGCACATCAGAATCCGAGCTCCTCCTTGTCAGTTGCCGCCACCACCTTGTAAAAGCCAG
68660 C T GGATTTTCATTTTCCCCGAAGAAATTAAAAGCGGCAAATCATGAAATAATCGATAATGAATTAAAAGCCGCATTTTTTTCCACCCATCATAAGAAGCCCT[C/T]GTCGTTAGAAATCGAAACCCTCGCACATCAGAATCCGAGCTCCTCCTTGTCAGTTGCCGCCACCACCTTGTAAAAGCCAGCGTCCATTG
68668 G A GGCAAACTTAATCCCATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAAC[G/A]TAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTT
68668 A G GGCAAACTTAATCCCATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTA[A/G]AATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCA
68668 C T GGCAAACTTAATCCCATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTAAAATCCTGGCTTCATATCTCCATC[C/T]AATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATGTGC
68668 A G CCCATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCAT[A/G]CAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATGTGCATAAACCATTCC
68668 C A CCATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATA[C/A]AGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATGTGCATAAACCATTCCC
68668 G A ATGCGCTCACATTCTTTCAGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACA[G/A]TTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATGTGCATAAACCATTCCCTC
68668 C A AGACAAATTCCCAAATCTTTCACAAAATGCTTAACGTAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACC[C/A]TGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATGTGCATAAACCATTCCCTCCACTAATCCAACCATGGT
68668 C G AATGCTTAACGTAAAATCCTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTC[C/G]ATCCATTTTTCCACATCTAAACCTGCTTTATGTGCATAAACCATTCCCTCCACTAATCCAACCATGGTTGAAGCAATTGCAATTTGATTGCC
68668 T C CTGGCTTCATATCTCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATC[T/C]AAACCTGCTTTATGTGCATAAACCATTCCCTCCACTAATCCAACCATGGTTGAAGCAATTGCAATTTGATTGCCTAGTTTCGCATA
68668 T C TCCATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTA[T/C]GTGCATAAACCATTCCCTCCACTAATCCAACCATGGTTGAAGCAATTGCAATTTGATTGCCTAGTTTCGCATA
68668 T C CATCCAATATCCTCTTCCCATACAGTTCCAAGCTTTTTGACCCTGCAGCTCCACTCGCTATTGCTTCCATCCATTTTTCCACATCTAAACCTGCTTTATG[T/C]GCATAAACCATTCCCTCCACTAATCCAACCATGGTTGAAGCAATTGCAATTTGATTGCCTAGTTTCGCATA
68708 G A CCACCGGCTGATCCTCAACAGTAACCGACGGCAGAACGGGAGCCTCACCCCAACCAACAGATCCGTCCATCAGCTCAACCCGAACCGCAACGTTACCAAC[G/A]ACTTCAAGTCTGGACGAGGCGATCGTAAACGGCGCTATCAACGGAACGTTCAACGGTTGGCCCTCCGCTTTGCTAACTGTGACAGA
68726 C G TTTGGTTGAGACTTCTTGTTTGACGCCTTTGTGGACTCCTCATCAGAACTTTCTTCAGAGTCGCTTTCTTCATCACTGCTGCTATCCTTCTTAGTA[C/G]CCTTGGAAGCAGCAGAAGACTTCTTTACTGGCTCTTCGTCACTCTCATCACTGCTGCTATCTTCTGAGCTTTCCACAGGTTTGGTCTTGGCAGCA
68730 G A CATGGTGGAGTGTTGCCTAACATAAATCCAGTGCTTTTGCCCAAGAAGATCGCTGCTAAGGAGGAGGGTGCAGTTAAGTCACCAAAGAAGAAG[G/A]CTGCAGGGAAGACCCCAAAGAAAGCTGCTGCTGCTGCAAAATGATTGTATGGGGTTAGTCATGGATTTACGTGTTTATGTAATTTACTATCA
68730 A C CATGGTGGAGTGTTGCCTAACATAAATCCAGTGCTTTTGCCCAAGAAGATCGCTGCTAAGGAGGAGGGTGCAGTTAAGTCACCAAAGAAGAAGGCTGC[A/C]GGGAAGACCCCAAAGAAAGCTGCTGCTGCTGCAAAATGATTGTATGGGGTTAGTCATGGATTTACGTGTTTATGTAATTTACTATCA
68730 A G CTAACATAAATCCAGTGCTTTTGCCCAAGAAGATCGCTGCTAAGGAGGAGGGTGCAGTTAAGTCACCAAAGAAGAAGGCTGCAGGGAAGACCCCAAAGAA[A/G]GCTGCTGCTGCTGCAAAATGATTGTATGGGGTTAGTCATGGATTTACGTGTTTATGTAATTTACTATCATCGTATATGCTGACTTT
68746 C G TTTCTCAATATTTTCACCTTAGCGCCCCTCTTAGGACCAATAGGCGGTGGCTTGGGCGCAGCCTTGGGCGCTTC[C/G]GCAGCATCAGCCTGCGCGGTTGTAGCAGGAGGGGAAGCTGAAGCAGGGGTGTCCTCCGCTCTGACCACCAACCTTCTCCCTAAACCCGAATTCCTGCTGT
68746 G A TTTCTCAATATTTTCACCTTAGCGCCCCTCTTAGGACCAATAGGCGGTGGCTTGGGCGCAGCCTTGGGCGCTTCCGCAGCATCAGCCTGCGC[G/A]GTTGTAGCAGGAGGGGAAGCTGAAGCAGGGGTGTCCTCCGCTCTGACCACCAACCTTCTCCCTAAACCCGAATTCCTGCTGTTTAAAAACACAAG
68790 G A GCTTATAGTTGTAATAGGATATGGGTTTTTATGTTTTGTCTGTTGATTTGTTCTCACTTATGATGGGCAAGGGCGCGCAATGTTTTGTGATGAATAATGT[G/A]GTTGTCATGAACTTGTGGTTTTGCTCAGTGCTTACTGTATTTGGAGAGCTTGTAATCCTTATGTTTATGAAACTTAAAATCGCAGTTTGG
68792 A G AGACCCGGAAAAAAGGAAATACCCAGGCGGGGCGTTCGACCCTTTAGGCTACTCTAAAGACCCTGAAAAACTGAAGGAGTTGAAGGTCAAGGAGATCAAA[A/G]ATGGTCGCCTTGCTTTGCTAGCATTCGTCGGGTTCTGCGTTCAGCAGTCCGCTTATCCAGGCACTGGGCCTTTGGAAAACCTCGC
68792 A G AGTTGAAGGTCAAGGAGATCAAAAATGGTCGCCTTGCTTTGCTAGCATTCGTCGGGTTCTGCGTTCAGCAGTCCGCTTATCCAGGCACTGGGCCTTTGGA[A/G]AACCTCGCAGCCCATTTGGCTGACCCGTGGCACAACACCATTGGTGACATTGTCATCCCAAGATCTGTATCTCCAT
68816 T C GCAAAAAATCAATACCGATTCAAGAGTTCTTGAAACCAGCTGAAGGAGAAAGAAGCTACGGGCGTGGTCGTGGCAGAGGAGGCAGAGGCGATCGAGGTGG[T/C]AGAGGAGGTGTCAGTTTCAATGCTAATAATGCTCCACCACCTGCAATTGGCGACGATGGTCAGTTCCCTACACTTGGTGGAAAA
68816 AGAG A CAAAAAATCAATACCGATTCAAGAGTTCTTGAAACCAGCTGAAGGAGAAAGAAGCTACGGGCGTGGTCGTGGCAGAGGAGGCAGAGGCGATCGAGGTGGT[AGAG/A]GAGGAGGTGTCAGTTTCAATGCTAATAATGCTCCACCACCTGCAATTGGCGACGATGGTCAGTTCCCTACACTTGGTGGA
68836 G C AGTACAAATTACATGGTCAATAACATAGGCTAGTGCTGTGAACAGCAACCTTGAACAGACAAGACAGAAGCCACCTATCAAGCCGCAGAAAAGTCTTGAA[G/C]CACACAACCGAAAGAACAGCAATAGGACAGAGCCCATCCCCCTACTTCCACTTGCAACGCCAAGTACATTATTCAAACCATCAGAA
68836 A C GGCTAGTGCTGTGAACAGCAACCTTGAACAGACAAGACAGAAGCCACCTATCAAGCCGCAGAAAAGTCTTGAAGCACACAACCGAAAGAACAGCAATAGG[A/C]CAGAGCCCATCCCCCTACTTCCACTTGCAACGCCAAGTACATTATTCAAACCATCAGAAAAAA
68850 A C GGTGGTGGAGCTTGATGGGCTTGTGTAGGGGGGTTTCTCATAGGAGTAGGGCGAGGTGCACGAGCTGATGAACGACCTCCAGCGCTTCGGCGAGCCATAG[A/C]TAATGCTTAATTGAAAGATTTGGAGTAAACCCTAGATTCAGGAATCAGGAACTCCAGTAGGCCAACAGTGA
68850 G A TGGAGCTTGATGGGCTTGTGTAGGGGGGTTTCTCATAGGAGTAGGGCGAGGTGCACGAGCTGATGAACGACCTCCAGCGCTTCGGCGAGCCATAGATAAT[G/A]CTTAATTGAAAGATTTGGAGTAAACCCTAGATTCAGGAATCAGGAACTCCAGTAGGCCAACAGTGA
68908 T C ACGACTTTTTTCCAAGCATCTACCTGTTTTTGAGTATATATTCCTGGGCAATGTGGAAACCCTCCAGCAGAAGGCGAAA[T/C]CAAAGTCCCTTCAGTAATCAAAAACCCTCCATTCGTCGCTCGCTGACCATAATACTCCACGTGCGCGTCGAGTGGTATCCCATTCAACGCCCTGCATCTC
68908 C A TTTTTGAGTATATATTCCTGGGCAATGTGGAAACCCTCCAGCAGAAGGCGAAATCAAAGTCCCTTCAGTAATCAAAAACCCTCCATTCGTCGCTCGCTGA[C/A]CATAATACTCCACGTGCGCGTCGAGTGGTATCCCATTCAACGCCCTGCATCTCGTCATGGGCGCCAAAACTACTCGGTGGGAGAGGC
68958 A G TTGGTGACATCTTTATGTTCATCACTTGGAGCATCGTCATAACTCCCAGATCCAATATCCAC[A/G]TTCGATGCTTGAGCTCTGATGCTCTTACTATTCAAAGATTTTAGCCTTGATAAATGTCTGTATTGCAAATTAAACCGATTCTTTGCCAGTCTAGTGTAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
68958 C T TTGGTGACATCTTTATGTTCATCACTTGGAGCATCGTCATAACTCCCAGATCCAATATCCACATTCGATGCTTGAGCTCTGATG[C/T]TCTTACTATTCAAAGATTTTAGCCTTGATAAATGTCTGTATTGCAAATTAAACCGATTCTTTGCCAGTCTAGTGTAAAATGATGGAGGCGATCCTGAAAT
68958 T G ATCGTCATAACTCCCAGATCCAATATCCACATTCGATGCTTGAGCTCTGATGCTCTTACTATTCAAAGATTTTAGCCTTGATAAATGTCTGTATTGCAAA[T/G]TAAACCGATTCTTTGCCAGTCTAGTGTAAAATGATGGAGGCGATCCTGAAATTGCAAGAGATGGCAATCTCTCGCACGAAAGAAGTCCG
68958 A C CTTGAGCTCTGATGCTCTTACTATTCAAAGATTTTAGCCTTGATAAATGTCTGTATTGCAAATTAAACCGATTCTTTGCCAGTCTAGTGTAAAATGATGG[A/C]GGCGATCCTGAAATTGCAAGAGATGGCAATCTCTCGCACGAAAGAAGTCCGCAAGCTTGCATCTTCTTCCCCTACAATTATCGCAACAA
68960 C G CTAAAGGCAGCAGCCATATTTTCGTTTTTTGGCTATTGCGGGCCCCACGAAGAGAGTTAG[C/G]TCGAGCGACTTCAGGCAGAGGTAGAGGGGAACCATACGGTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTAT
68960 G T CTAAAGGCAGCAGCCATATTTTCGTTTTTTGGCTATTGCGGGCCCCACGAAGAGAGTTAGCTC[G/T]AGCGACTTCAGGCAGAGGTAGAGGGGAACCATACGGTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTATTGG
68960 C T TCAGGCAGAGGTAGAGGGGAACCATACGGTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTATTGGAGGGGTG[C/T]TGAAAACAGGACAGTCGCAAAGATGAGTAATTTCCCGTCAATCCGTGCATTTTCAGGCGAGGTGACAAACAGAGAAGTTGTTCG
68960 A T GCAGAGGTAGAGGGGAACCATACGGTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTATTGGAGGGGTGCTGA[A/T]AACAGGACAGTCGCAAAGATGAGTAATTTCCCGTCAATCCGTGCATTTTCAGGCGAGGTGACAAACAGAGAAGTTGTTCGGGAG
68960 A G CAGAGGTAGAGGGGAACCATACGGTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTATTGGAGGGGTGCTGAA[A/G]ACAGGACAGTCGCAAAGATGAGTAATTTCCCGTCAATCCGTGCATTTTCAGGCGAGGTGACAAACAGAGAAGTTGTTCGGGAG
68960 T C GTTCTTTTGGCGGTGGTGGCATGGTCTCAGGTGGTCGGAGTTGGCCGGAATGTCAATTTTATTGGAGGGGTGCTGAAAACAGGACAGTCGCAAAGATGAG[T/C]AATTTCCCGTCAATCCGTGCATTTTCAGGCGAGGTGACAAACAGAGAAGTTGTTCGGGAGGTCGAG
68984 A G CGGGCATGTAGGTGGTGGACTGGGCCGGGTTGTAAGTGCTGGTGGACTGCGGGCAGCCCGTGCAGGTGGAGGTGGGGATCCACGAGGCGTCGCTGCTGGT[A/G]TCGATGGCGACCAGCATTGGCTGAGGCGGCGTGCCAATGCTTGCTTTGACGACGTAAGTTGGAGTTTGTAGTATTTTGGTGC
68994 T C AAAAATCACGCTCAAGCCTCAGCTACAGAGCCAACATCACCATTGGAAATTCCAATTGTACCCCTGCCACATCCAATGTT[T/C]TTCTCACACTTTTTGATCTCGTCAAACTCCCTTGAATCCAATGTCTCTGACAAAATTCCAACCTCAAAATCAATCTCTCCCTTATCAAGCCTGGCCTCTA
68994 T C AGCCAACATCACCATTGGAAATTCCAATTGTACCCCTGCCACATCCAATGTTTTTCTCACACTTTTTGATCTCGTCAAACTCCCTTGAATCCAATGTCTC[T/C]GACAAAATTCCAACCTCAAAATCAATCTCTCCCTTATCAAGCCTGGCCTCTATTCCAGTAACAGACACCCAAACGAAGAATTTTTTCGCTTT
68994 C A TGATCTCGTCAAACTCCCTTGAATCCAATGTCTCTGACAAAATTCCAACCTCAAAATCAATCTCTCCCTTATCAAGCCTGGCCTCTATTCCAGTAACAGA[C/A]ACCCAAACGAAGAATTTTTTCGCTTTAATTCCAGTAATGTCCTTGATTTTTCCGTAAGAGACTTTTCCAGT
69000 C T TTTTTGCCGATCTTAAATTAAAGTGAAGAAATGGCCGATGCTTATTTGGGTTATCGTCCGCGTTTCCAGCAAACTGCTGCCGCGGCTCCCAATTCTGGGG[C/T]GGCGATTCCTCCGTTGAAACGTCGTCATCTTGATTATGGTGCTGCACCCGTCGGGTCAGGGCAGCGTGTTATATACCCTGGCGAGGA
69000 A T CGGCGATTCCTCCGTTGAAACGTCGTCATCTTGATTATGGTGCTGCACCCGTCGGGTCAGGGCAGCGTGTTATATACCCTGGCGAGGAGGCTATAACATC[A/T]ATGAGTTCAATTGCTGACACTGAGGCCATCAATGCATCTTATGATCAATATTTACGAAATGG
69078 T G AACAGTCGGTGGTGGGGCTGATGGGGTAAGAAACGCTGACCCCGCAGACGCCCGGAAGGCCAGAGGCTTTGCTCGTGTCCAAGCCCTGGATCTTGGCCGA[T/G]AGGGACTTGAGGCACCCGCAGGCAGTACGGCGGTCAGGAGTGGTCGTGGCTGACGCAGCCAGCTTCTTGACGCCCGTGCAGC
69110 G C GGTGTTTCAGGCGTGAAATGTGCTGTGAAAACACCAAATCCTGAGTTGGCGCCTCTCTTCTTCGAATCGATTGAGGCCCTTCTTAATTGATAAGTCCCCT[G/C]CTATTATTTTCGTGTTTTCTGTAAATTTGGTTTTGATTGTGATTTTCTGTTGTGTTCGTTAT
69132 A G TGAAGTAAATTCATCTTTGTCAAACCCAAGGAACTCTCCAGAGCTCCCAAAAAGCAAGTTATTTGCAAATATATTTTTAAGAGGGATTCCAAGTTGCTCT[A/G]CAACAGGATTGATCATTTGACGAAATCCTCCTGAAATAAGATAAACATCTTTATTCCTTGCTTTTAGCTTGCTTACTAAATCAGAAATTC
69132 T A CAAGGAACTCTCCAGAGCTCCCAAAAAGCAAGTTATTTGCAAATATATTTTTAAGAGGGATTCCAAGTTGCTCTACAACAGGATTGATCATTTGACGAAA[T/A]CCTCCTGAAATAAGATAAACATCTTTATTCCTTGCTTTTAGCTTGCTTACTAAATCAGAAATTCCAGGAGACATCCTTGGAGGCCTCTT
69132 T C AAGCAAGTTATTTGCAAATATATTTTTAAGAGGGATTCCAAGTTGCTCTACAACAGGATTGATCATTTGACGAAATCCTCCTGAAATAAGATAAACATCT[T/C]TATTCCTTGCTTTTAGCTTGCTTACTAAATCAGAAATTCCAGGAGACATCCTTGGAGGCCTCTTTTCTAGAAAGTCGTGAAGCTGGGAA
69132 T A TATTTGCAAATATATTTTTAAGAGGGATTCCAAGTTGCTCTACAACAGGATTGATCATTTGACGAAATCCTCCTGAAATAAGATAAACATCTTTATTCCT[T/A]GCTTTTAGCTTGCTTACTAAATCAGAAATTCCAGGAGACATCCTTGGAGGCCTCTTTTCTAGAAAGTCGTGAAGCTGGGAAAG
69152 A G TTTTTTTTTTGTTCAGCAGAAACATGCCTGTAATAACCATCATCATTAAAAATTGAACAAAATTTCAGTGTTC[A/G]AAATTCTGCCACAAAAAAGAAATCATAAATAGATAAACGTGTCAAGATATAAAATATTTATCGTCTCCAATTTAAGAAAACACACTTCCACTTTGGCAGA
69152 T C TTTTTTTTTTGTTCAGCAGAAACATGCCTGTAATAACCATCATCATTAAAAATTGAACAAAATTTCAGTGTTCAAAA[T/C]TCTGCCACAAAAAAGAAATCATAAATAGATAAACGTGTCAAGATATAAAATATTTATCGTCTCCAATTTAAGAAAACACACTTCCACTTTGGCAGATGTC
69152 A G TTTTTTTTTTGTTCAGCAGAAACATGCCTGTAATAACCATCATCATTAAAAATTGAACAAAATTTCAGTGTTCAAAATTCTGCCACAAAAA[A/G]GAAATCATAAATAGATAAACGTGTCAAGATATAAAATATTTATCGTCTCCAATTTAAGAAAACACACTTCCACTTTGGCAGATGTCACCTTGGCACCGA
69152 T A TAATAACCATCATCATTAAAAATTGAACAAAATTTCAGTGTTCAAAATTCTGCCACAAAAAAGAAATCATAAATAGATAAACGTGTCAAGATATAAAATA[T/A]TTATCGTCTCCAATTTAAGAAAACACACTTCCACTTTGGCAGATGTCACCTTGGCACCGAGAGACCGCTCTCTTGAAAATTAGCAAAGA
69152 T C ATTAAAAATTGAACAAAATTTCAGTGTTCAAAATTCTGCCACAAAAAAGAAATCATAAATAGATAAACGTGTCAAGATATAAAATATTTATCGTCTCCAA[T/C]TTAAGAAAACACACTTCCACTTTGGCAGATGTCACCTTGGCACCGAGAGACCGCTCTCTTGAAAATTAGCAAAGAGATCCAAAAAAAT
69152 T A TTAAAAATTGAACAAAATTTCAGTGTTCAAAATTCTGCCACAAAAAAGAAATCATAAATAGATAAACGTGTCAAGATATAAAATATTTATCGTCTCCAAT[T/A]TAAGAAAACACACTTCCACTTTGGCAGATGTCACCTTGGCACCGAGAGACCGCTCTCTTGAAAATTAGCAAAGAGATCCAAAAAAATTC
69168 A T AGTTTTGTGGTCCTGTTGTTATGAGATTTGATGAGGAGCTTGGTTATTTTCCTTGGTTTTCGGGTCAAGGATCTTTCTATGCTACAGCGTTTTCTCAGTC[A/T]ATGTTTACTGGCTTGGATTTGTTTTCACCGTTTGTAGGTTATGCATGAGGTGCCGAAGGCACTAAATTTAGCCTTCAATCTATGTGTGTG
69172 G C GAAATTGGCCTGGTATCAAAATGTGTAACATGTTATACTACCAAGCATTCTAGTCTAGTCTAGATATATATTTATGAACAAGAGCCAGAAGATCGGGGCA[G/C]AACTGCGGCTGTTTCTCCCAAGGCCCTAATCACCACCAACTTGCCTTTTCCACGAGTCCTCTACAATCAGCTCATCTACTCCCCAGTCC
69172 C T AATGTGTAACATGTTATACTACCAAGCATTCTAGTCTAGTCTAGATATATATTTATGAACAAGAGCCAGAAGATCGGGGCAGAACTGCGGCTGTTTCTCC[C/T]AAGGCCCTAATCACCACCAACTTGCCTTTTCCACGAGTCCTCTACAATCAGCTCATCTACTCCCCAGTCCTCATAACTTCCATCAGGCAG
69178 T C GCGCTGCAGCCAACCATTCACGTGCATCTGTTCTCGTAACATCGCCTCCTTTCTTCCTCCGCGTCAATCTTTGTCTTATTAGTTGTGGAAGAGATGGATT[T/C]GAGGATTGGGAGAATTAGGGCATCGAGGGTTTCGCAAGAAAGAAAGTCGGTTCGGGAGTAAAAGCCAGTAGGCCAACAG
69230 T C CCTCTCCTGCACATCTCCCAGCCAACATCCCTACCAGCACCATCCTCGTCAACTCATCACTGTCTCTACGTCGCCTCTTCTGCTTGACAGATTTAGTTAA[T/C]TGTTGGCTTGAAGTTGAAATCACTCATGGCGGACGATGCACCAATTGAGCTTCCTGAGATTACTCCCTTTGAT
69244 C A CGGCGGCAGCTATGGTGGTGGTGGTGGCAGCTATGGAGGCGGTGGTGGTGATAACTATGGCAGTGGTGGTGGTGGTTGGTAACTGTATTTTACATTGGAA[C/A]TAAATGTGAATTTTTGAAGTTTCATAGTTACCACCTGCTTCTTCTCCTAATACCATGACAGTACAATGTTTCTTGTTGTTTCCCAGT
69250 T C AACCCACAAGGGTCCTACCACTACGGTCAGATCAACCTGACCAGGACCATAAGGCTGCAAAA[T/C]TCTGCTGGGTTCATTGATGGAAAGCAACGGTATGCAGTGAATGGAGTCTCCTTTGTAGCACCTGATACGCCAATGAAGTTGGCTGATTTTTATAAGATTC
69276 G A AGTGTTTTTCACGGTAATTTTGATATTTGATTTGGGTTAGTTTGCGTTCAGTTTTTCAGTGGGTGTCCTCTTTTGATGTTTGATTTTGATAGTTGTTTTT[G/A]ATGGTAATCCTTTCTACTTTCCCAGAGTAGCCATAAGTTTCAGTGGGCGTCCTCTTTTGCTCTGTTGCCAATACACTTGTGCCATTCAGTAC
69282 G GA TTTAAACAACGGAGGTAGAGGCAGATCGATGGAGACGGTGATAAATGGCAGTGGAAGGATGGCGTAAGCGGTGAAGAACGAAAGAGGTGGTGATGGAATT[G/GA]AAAGGCGGAGGCAGAAGAGAAGCAAGGGCTGAGGCGGCGGCAGAAAGGGGCGACAACCCTAGAAAAAAGGAAAAAAAG
69282 G A ATAAATGGCAGTGGAAGGATGGCGTAAGCGGTGAAGAACGAAAGAGGTGGTGATGGAATTGAAAGGCGGAGGCAGAAGAGAAGCAAGGGCTGAGGCGGCG[G/A]CAGAAAGGGGCGACAACCCTAGAAAAAAGGAAAAAAAGGACCGTGAGAACAATCCAGTAGGCCAACAG
69288 A G AGAGTCCGGTCCCATAATCCTCTTCGTGCATGGCTTTCCCCAACTATGGTACTCTTGGCGCCACCAGATTCGCTCCCTCTCCAACTTAGGCTTCCGGTGC[A/G]TCGCACCCGACTTGCGCGGCTACGGCGATACCGATGCACCAACTGACGTCACAGCTTACTCCATAATGCATTTGGTCGGCGATCTCGT
69292 A T CATATGCAGCTATAACACCAACTGATATCATGACATATAACCGGGCTTTAGCATTCAACAAGATGGCCCCAAATCAAGCGGCCCAAATGCAGGATGCCCT[A/T]AAGCAAGCTGCTGCCATGGGCCATGCCAGTCAGGGTATGTACGATGGCGCCTACCAGAATCCCCCTGCTGCACCTCACCCTTACATG
69312 A G GAAGAGGTGTGGTTCAGTTATGATGCAGGAGGAGATGCAGTTTCGACCGCCGGTGATGGAAGAAATTGGT[A/G]GACTGGGCTCAAGCGGCGAGCCGAGCTGGTTGCGAAAGGATGATGGCTTTGGGCTAGTGGCGGTTGCGATGGGAAAAAGGAGCTTGATTTGGTGGAGGAA
69312 G A GAAGAGGTGTGGTTCAGTTATGATGCAGGAGGAGATGCAGTTTCGACCGCCGGTGATGGAAGAAATTGGTAGACTGGGCTCAAGCG[G/A]CGAGCCGAGCTGGTTGCGAAAGGATGATGGCTTTGGGCTAGTGGCGGTTGCGATGGGAAAAAGGAGCTTGATTTGGTGGAGGAATTTCTATAGGAA
69312 G A GAAGAGGTGTGGTTCAGTTATGATGCAGGAGGAGATGCAGTTTCGACCGCCGGTGATGGAAGAAATTGGTAGACTGGGCTCAAGCGGCGAGCC[G/A]AGCTGGTTGCGAAAGGATGATGGCTTTGGGCTAGTGGCGGTTGCGATGGGAAAAAGGAGCTTGATTTGGTGGAGGAATTTCTATAGGAA
69312 T C GTTCAGTTATGATGCAGGAGGAGATGCAGTTTCGACCGCCGGTGATGGAAGAAATTGGTAGACTGGGCTCAAGCGGCGAGCCGAGCTGGTTGCGAAAGGA[T/C]GATGGCTTTGGGCTAGTGGCGGTTGCGATGGGAAAAAGGAGCTTGATTTGGTGGAGGAATTTCTATAGGAAGCGATTTAGGG
69312 A G AGGAGGAGATGCAGTTTCGACCGCCGGTGATGGAAGAAATTGGTAGACTGGGCTCAAGCGGCGAGCCGAGCTGGTTGCGAAAGGATGATGGCTTTGGGCT[A/G]GTGGCGGTTGCGATGGGAAAAAGGAGCTTGATTTGGTGGAGGAATTTCTATAGGAAGCGATTTAGGGGAGAAACAATTTATT
69312 T C TTTCGACCGCCGGTGATGGAAGAAATTGGTAGACTGGGCTCAAGCGGCGAGCCGAGCTGGTTGCGAAAGGATGATGGCTTTGGGCTAGTGGCGGTTGCGA[T/C]GGGAAAAAGGAGCTTGATTTGGTGGAGGAATTTCTATAGGAAGCGATTTAGGGGAGAAACAATTTATTTGATTATGGGTAAAC
69312 T C ATGGAAGAAATTGGTAGACTGGGCTCAAGCGGCGAGCCGAGCTGGTTGCGAAAGGATGATGGCTTTGGGCTAGTGGCGGTTGCGATGGGAAAAAGGAGCT[T/C]GATTTGGTGGAGGAATTTCTATAGGAAGCGATTTAGGGGAGAAACAATTTATTTGATTATGGGTAAACTAAATTTGGGGAGGA
69348 A G CGACCGCCGCATCTAAGCATGGAAACAAGAGGCTCGATTGCGCCGGAGAAGACCCGACGGTTATCCGATGA[A/G]GTCCTCGTGAGCCGTCGGATTTCTTTCGCTGCTTCCAACCTAGAATCCCGACTACCCGATCGAACTCGGTTCAGTATGTCGTGAACCGCCGCCGATTCCA
69352 G A GTCTCGCGAGTTTTAGATGATGATAAGATACTTACTGCGAAGAAGGCGGAGAGAGCGATAGAGGGGTACGTGAGGGAGAG[G/A]AAGTGGCGTGTTAGTGGTTTGATAGCTGGGGCGTATTTATCGGGTTGGGTTCAGCAAGGCGGAGGAGAAGGTGTTGTGAGTGGTTGGTTCGCGAAGTGGT
69352 A G CGAAGAAGGCGGAGAGAGCGATAGAGGGGTACGTGAGGGAGAGGAAGTGGCGTGTTAGTGGTTTGATAGCTGGGGCGTATTTATCGGGTTGGGTTCAGCA[A/G]GGCGGAGGAGAAGGTGTTGTGAGTGGTTGGTTCGCGAAGTGGTTCAGGGACAATCTGTTTTTCAGGTTTGTTCAACCAAGGC
69376 GA G GCAGAAGCCGCCTCTCAGGTTGGTAGCAAAATAGAGTCACCCCTTTGTTTAAGGAAGCATAGAAGACCGAAGAGCAAGCATTCAGAGAATCAAAAACCCC[GA/G]AAAATTAAAACGGAAGAGGAACCTAAATGCTGATGGTGATGCTCAAATTTCGAGGCATTTAACCCCTATAATTCATTTCCAAGAG
69380 C T GGACCCGGTGAAAAATCTACGCCAGAAGGTAAGGTAACACTCCCCGATAATAACAAAGCTCTCAGCCGTCCAC[C/T]AGCATGCTGTCCTGGCTATATCTAGCTGCTCCATCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAA
69380 A C GGACCCGGTGAAAAATCTACGCCAGAAGGTAAGGTAACACTCCCCGATAATAACAAAGCTCTCAGCCGTCCACCAGC[A/C]TGCTGTCCTGGCTATATCTAGCTGCTCCATCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGT
69380 T C GGACCCGGTGAAAAATCTACGCCAGAAGGTAAGGTAACACTCCCCGATAATAACAAAGCTCTCAGCCGTCCACCAGCATGCTG[T/C]CCTGGCTATATCTAGCTGCTCCATCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGTCTCCAG
69380 A G GGTGAAAAATCTACGCCAGAAGGTAAGGTAACACTCCCCGATAATAACAAAGCTCTCAGCCGTCCACCAGCATGCTGTCCTGGCTATATCTAGCTGCTCC[A/G]TCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGTCTCCAGCACCTCTCAC
69380 C A CCTGGCTATATCTAGCTGCTCCATCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGTCTCCAG[C/A]ACCTCTCACCAAGATACCAATAAGAACCTCGCGCCACGGGACAAGATATAAGTGGAAATCTCTGTCCGGCAAGCATCCTAGCAATC
69380 C T GCTCCATCGGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGTCTCCAGCACCTCTCACCAAGATA[C/T]CAATAAGAACCTCGCGCCACGGGACAAGATATAAGTGGAAATCTCTGTCCGGCAAGCATCCTAGCAATC
69380 A C GGGTAAATCATACACCGATAAGTATGTGGGTGTGGATCATCCGGAATAGCATCGAAGTCATACAACTGTCTCCAGCACCTCTCACCAAGATACCAATAAG[A/C]ACCTCGCGCCACGGGACAAGATATAAGTGGAAATCTCTGTCCGGCAAGCATCCTAGCAATC
69412 A G AGACCTCTAACGACCTTCTCCGCAAAGTCAACCTCACAGGCAATGGCCGCTTCACCATGCGTCGCACCGTCAAAAGCGCTCCGCAAAGCATCTGGTATGG[A/G]CCGGACCGTCCCAAATACCTAGGGCCGTTCTCAGAGCAAACCCCATCCTATTTGACCGGCGAATTCCCTGGTGACTACGGGTGG
69436 G A GAATCATCTGAAGATCACTGCTGCCGTCGGACTGGAGCCCAGCTCTCATATCCGCCTCCATACCATCTGCCACGTGTCGCAACACTTGTAGAGGAGTATC[G/A]CATTTCATCTTCAGCTCCTTCATTATCACGCAGGCCTCCACTGATCCCGCCACTGTACATCTCACAGCACCATCATTCCTGTCTCTCCTC
69436 C T CGGACTGGAGCCCAGCTCTCATATCCGCCTCCATACCATCTGCCACGTGTCGCAACACTTGTAGAGGAGTATCGCATTTCATCTTCAGCTCCTTCATTAT[C/T]ACGCAGGCCTCCACTGATCCCGCCACTGTACATCTCACAGCACCATCATTCCTGTCTCTCCTCCAACTCCTCCTCACTGTTGGATGCCTG
69436 C A GACTGGAGCCCAGCTCTCATATCCGCCTCCATACCATCTGCCACGTGTCGCAACACTTGTAGAGGAGTATCGCATTTCATCTTCAGCTCCTTCATTATCA[C/A]GCAGGCCTCCACTGATCCCGCCACTGTACATCTCACAGCACCATCATTCCTGTCTCTCCTCCAACTCCTCCTCACTGTTGGATGCCTGAC
69436 G C GGAGCCCAGCTCTCATATCCGCCTCCATACCATCTGCCACGTGTCGCAACACTTGTAGAGGAGTATCGCATTTCATCTTCAGCTCCTTCATTATCACGCA[G/C]GCCTCCACTGATCCCGCCACTGTACATCTCACAGCACCATCATTCCTGTCTCTCCTCCAACTCCTCCTCACTGTTGGATGCCTGACACCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
69436 A C CTGCCACGTGTCGCAACACTTGTAGAGGAGTATCGCATTTCATCTTCAGCTCCTTCATTATCACGCAGGCCTCCACTGATCCCGCCACTGTACATCTCAC[A/C]GCACCATCATTCCTGTCTCTCCTCCAACTCCTCCTCACTGTTGGATGCCTGACACCACCTACTGATCTGATGGCA
69436 A G GTCGCAACACTTGTAGAGGAGTATCGCATTTCATCTTCAGCTCCTTCATTATCACGCAGGCCTCCACTGATCCCGCCACTGTACATCTCACAGCACCATC[A/G]TTCCTGTCTCTCCTCCAACTCCTCCTCACTGTTGGATGCCTGACACCACCTACTGATCTGATGGCA
69462 G A CCGGAGTGGACGCGGCGTCGATTTCGATGAGCGAGGAGGACCTTTTGAACGCCAAGGACGAGACCTACAGTGTCACGTTGAACGCCAAGGGGACTTATAA[G/A]TTCTATTGTTCGCCACATGCTGGTGCTGGTATGTCCGGCGTGGTTACAGTTAGCTAGACGTGTGTAGTATGTCGGGTGGAGTTT
69462 T G CGATGAGCGAGGAGGACCTTTTGAACGCCAAGGACGAGACCTACAGTGTCACGTTGAACGCCAAGGGGACTTATAAGTTCTATTGTTCGCCACATGCTGG[T/G]GCTGGTATGTCCGGCGTGGTTACAGTTAGCTAGACGTGTGTAGTATGTCGGGTGGAGTTTGTTTTGTAA
69482 G A CAACTTCTCTTCCCTCTCCCTCTTCCCTCCTCTCTTCACCGGCCTTCCCACGTTCTTTCTTCCACCACTTTCCTTTTCTTTCTTCCCTGCTTCTGCTTTC[G/A]GGTTCACTACCGGATTCGGTTTTCCTCCAACCGTTTTCGCTCTACTTTGGCTCGTTCTCGAGCCTCTCGGTTTCACACTTTTTTTACCCGTATGTT
69486 T C AACACAATTTCCACAAACACCCTGTAATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGC[T/C]GCCTGTCGGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACG
69486 C T AACACAATTTCCACAAACACCCTGTAATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGT[C/T]GGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGA
69486 C T AACACAATTTCCACAAACACCCTGTAATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGTCGGTTTATCCGATATGCT[C/T]CCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGACTGCATACCTTTGTTTTC
69486 T C AACACAATTTCCACAAACACCCTGTAATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGTCGGTTTATCCGATATGCTCCCAAG[T/C]TTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGACTGCATACCTTTGTTTTC
69486 G A CCCTGTAATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGTCGGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATA[G/A]AAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGACTGCATACCTTTGTTTTCCATTAACAGGCCCGGCGG
69486 G A AATCCGCCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGTCGGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTC[G/A]GCAAGTTTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGACTGCATACCTTTGTTTTCCATTAACAGGCCCGGCGGAATTTG
69486 T C CCGCCATCACCGATGTGTCCAAGTATATACCGCTGCCTGTCGGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAG[T/C]TTCATTGGAGTGTCAGGAGCAACAAACGAGACGCTGTTGACTGCATACCTTTGTTTTCCATTAACAGGCCCGGCGGAATTTGCCAGTA
69486 C G TACCGCTGCCTGTCGGTTTATCCGATATGCTCCCAAGTTTGTAAACTCCAGGAATCTTATAGAAGTCGGCAAGTTTCATTGGAGTGTCAGGAGCAACAAA[C/G]GAGACGCTGTTGACTGCATACCTTTGTTTTCCATTAACAGGCCCGGCGGAATTTGCCAGTATTATGGTTCTGGTGAGATTGATCATAC
69502 A G ATCAAAGATTATCCATACGCGGTAGATGGACTTGAAATTTGGTCAGCAATCGAGACATGGGTCAAAGAATACTGTGC[A/G]ATTTATTACCCAACTGATGCCACCGTCCAAGCTGACCCCGAACTCCAAGCATTTTGGAAAGAAGTACGAGAAGTTGGCCATGGAGACTTAAAAGATAGGA
69502 C T CATACGCGGTAGATGGACTTGAAATTTGGTCAGCAATCGAGACATGGGTCAAAGAATACTGTGCAATTTATTACCCAACTGATGCCACCGTCCAAGCTGA[C/T]CCCGAACTCCAAGCATTTTGGAAAGAAGTACGAGAAGTTGGCCATGGAGACTTAAAAGATAGGACATGGTGGCCAAAAATGCAGA
69502 C T ACGCGGTAGATGGACTTGAAATTTGGTCAGCAATCGAGACATGGGTCAAAGAATACTGTGCAATTTATTACCCAACTGATGCCACCGTCCAAGCTGACCC[C/T]GAACTCCAAGCATTTTGGAAAGAAGTACGAGAAGTTGGCCATGGAGACTTAAAAGATAGGACATGGTGGCCAAAAATGCAGACAG
69502 A G CAGCAATCGAGACATGGGTCAAAGAATACTGTGCAATTTATTACCCAACTGATGCCACCGTCCAAGCTGACCCCGAACTCCAAGCATTTTGGAAAGAAGT[A/G]CGAGAAGTTGGCCATGGAGACTTAAAAGATAGGACATGGTGGCCAAAAATGCAGACAGTTGAAGACTTGACGCAGTCATGCACAA
69502 C T CATGGGTCAAAGAATACTGTGCAATTTATTACCCAACTGATGCCACCGTCCAAGCTGACCCCGAACTCCAAGCATTTTGGAAAGAAGTACGAGAAGTTGG[C/T]CATGGAGACTTAAAAGATAGGACATGGTGGCCAAAAATGCAGACAGTTGAAGACTTGACGCAGTCATGCACAATCATAATTTGGAT
69502 A G CCGTCCAAGCTGACCCCGAACTCCAAGCATTTTGGAAAGAAGTACGAGAAGTTGGCCATGGAGACTTAAAAGATAGGACATGGTGGCCAAAAATGCAGAC[A/G]GTTGAAGACTTGACGCAGTCATGCACAATCATAATTTGGATAGCCTCTGCTCTCCACGCTGCTGTCAATTT
69558 G C GGGGTGGTTTTGGTCTTCCTGAAGAGATCATCCAAAGTGAGAATTGGTGGCTCTGGCTCCTTGGGAA[G/C]AGGCGGAGGTGGAGGAAGCATTTCTTTTGCAGTTGCTGGTGGTGGTCCAGGTGGTGGTGGTGGGAGCTTGGGTCCGGAGGTTGTGATGGTGGGCTTACGA
69570 C G ATGGAACCCTAGAAAATGCAAAGGCTACATACTCACCATCACCACCGTCACCACCGTCGTCATCAAAACTGAAACAGTACATACTTATATCGACGTACAC[C/G]GCGTTCATCCTCTCCGGCCAAACAGTGGCCACTCTCCTAGGCAGATTCTACTACAACAAAGGCGGCACCAGCGTGTGGCTGCCCACG
69632 A G AGTAGTGAGGCGAAGCGCCTGACTGTCACTTCAAATGGCCAGAAGACTAGAAGAGGGAGTATC[A/G]TGAGAGAGGGAGGGAAAAAGATTTCACCGAAGAGAGGACAGCAACGTTGAGAGCATAACACTTCACCTGTGTTGCTAACTTTCTGATGAAACAAAGATGA
69632 C A AGTAGTGAGGCGAAGCGCCTGACTGTCACTTCAAATGGCCAGAAGACTAGAAGAGGGAGTATCATGAGAGAGGGAGGGAAAAAGATTTCA[C/A]CGAAGAGAGGACAGCAACGTTGAGAGCATAACACTTCACCTGTGTTGCTAACTTTCTGATGAAACAAAGATGAACCAGCAGGCCCAGTAACTCA
69632 T C TAGAAGAGGGAGTATCATGAGAGAGGGAGGGAAAAAGATTTCACCGAAGAGAGGACAGCAACGTTGAGAGCATAACACTTCACCTGTGTTGCTAACTTTC[T/C]GATGAAACAAAGATGAACCAGCAGGCCCAGTAACTCACAACAATACCCAGTTCAAAACCAAATAATTTCATGAAGAAATTGCCAA
69644 G GACCTATC GATAGTTATATTCAGTACTTCACCAGCAGGGAACTTATATAGCATTGTCATACTCGTACATAGTCTTTCTGCGTATGATGAAGCATGCAAGCTCTTGATA[G/GACCTATC]ACCTAACACATGTTTGTTGGAGCAATCTACACACGGACACACTAGCCCCCAACATTATTGAAAATAACAGCATATATAATTA
69644 G A TATATAGCATTGTCATACTCGTACATAGTCTTTCTGCGTATGATGAAGCATGCAAGCTCTTGATAGACCTAACACATGTTTGTTGGAGCAATCTACACAC[G/A]GACACACTAGCCCCCAACATTATTGAAAATAACAGCATATATAATTAAGCTGAACTAAATCTGAGAACTCTATTTGTTCAGACGTCCCC
69644 T C TTTCTGCGTATGATGAAGCATGCAAGCTCTTGATAGACCTAACACATGTTTGTTGGAGCAATCTACACACGGACACACTAGCCCCCAACATTATTGAAAA[T/C]AACAGCATATATAATTAAGCTGAACTAAATCTGAGAACTCTATTTGTTCAGACGTCCCCACACAATATGATCCTGTGGTAGGAA
69662 C G CAATCCAACTTCCCAAATCCGTCCACATGCTGCGCTTCCACCATCTCCATCATCGACAGCCTGAAATCGAAGTACGGATCCGTGCTCTCCGTTGCCATCG[C/G]CACCGCATCCTCCAGCGTCGGCGCGATCGACGCCGTGCCCCTCCTCGCTTCCTTTATAAGCGATCCTTTTTTCGCTTCCGGTACGAGAG
69662 C T ACCATCTCCATCATCGACAGCCTGAAATCGAAGTACGGATCCGTGCTCTCCGTTGCCATCGCCACCGCATCCTCCAGCGTCGGCGCGATCGACGCCGTGC[C/T]CCTCCTCGCTTCCTTTATAAGCGATCCTTTTTTCGCTTCCGGTACGAGAGACCTCTTTGACGCTTTGACATTCAATGGCAGATTCGCGT
69662 C T CCATCATCGACAGCCTGAAATCGAAGTACGGATCCGTGCTCTCCGTTGCCATCGCCACCGCATCCTCCAGCGTCGGCGCGATCGACGCCGTGCCCCTCCT[C/T]GCTTCCTTTATAAGCGATCCTTTTTTCGCTTCCGGTACGAGAGACCTCTTTGACGCTTTGACATTCAATGGCAGATTCGCGTACCGAG
69662 A G CAGCCTGAAATCGAAGTACGGATCCGTGCTCTCCGTTGCCATCGCCACCGCATCCTCCAGCGTCGGCGCGATCGACGCCGTGCCCCTCCTCGCTTCCTTT[A/G]TAAGCGATCCTTTTTTCGCTTCCGGTACGAGAGACCTCTTTGACGCTTTGACATTCAATGGCAGATTCGCGTACCGAGGCGGGGGTT
69662 G A CGTTGCCATCGCCACCGCATCCTCCAGCGTCGGCGCGATCGACGCCGTGCCCCTCCTCGCTTCCTTTATAAGCGATCCTTTTTTCGCTTCCGGTACGAGA[G/A]ACCTCTTTGACGCTTTGACATTCAATGGCAGATTCGCGTACCGAGGCGGGGGTTTGAGACTGTAGCTTTC
69682 A G ATGGAGTGGTGGAGAAGATGGGCGCATTTGTTGCTGGTCATCCGACGATGATGAGTCATCTCAGCCAAATCGGTCTTGGATTACTAGTACACTGGTTGAA[A/G]AAGTTTCTCATAATCGTATTAAAAATCGTCACCATCCATATTAATTCAAATTGCTAGGCAGTTTTCATTCGTATTTGATTGAGTCGAT
69704 G C CTCCTCCTCCTCTTAAGCTCGCCTCCTCCGCTTCGAAAGGGAAAACCCCCAAATCCCATCGGAACTCGAGCGCCGCACCCATCCAGCTTCCCCCCCCCCG[G/C]CTGACCTCCACCGTGCCGCCACCAACCAGCAGACGCCCCCCTTCCGAACGTGGCTACGGACGACGAAGCTGAC
69758 T C TAGCACGCAAAGATATACATGTATATAAAACCAAGCAGCGATTGATATATAAATAGATACACATAAACTCTTTCTG[T/C]TGTGCCCTCACGAACTCAAACAGCTGCTTGAATCACAACACTTAAAGGAGTAGAACTTATTATATGGCAAAGATACACTGCAATTTCTTATTCTGGAATA
69802 A T TGGTTAAGGGAATGGAGAAATCTGATGTGGAGTCTGGAGCTGATTCTGATGTTTCTGAAGCACTTGCTATGCAGGTTCGTCGTTTGGCCATGGAAGTTCG[A/T]CAACTTGCTTCTGGACGATCAATTACAGTCCTCAATGGTTCTGGTCAATCGGGGAACATGTCTGCTCTTATACTACCAGCTGCGGCT
69802 C T AAGCACTTGCTATGCAGGTTCGTCGTTTGGCCATGGAAGTTCGACAACTTGCTTCTGGACGATCAATTACAGTCCTCAATGGTTCTGGTCAATCGGGGAA[C/T]ATGTCTGCTCTTATACTACCAGCTGCGGCTATTGGAGCAGCAGGGTATGGATACATGTGGTGGAAGGGC
69802 A T AGCACTTGCTATGCAGGTTCGTCGTTTGGCCATGGAAGTTCGACAACTTGCTTCTGGACGATCAATTACAGTCCTCAATGGTTCTGGTCAATCGGGGAAC[A/T]TGTCTGCTCTTATACTACCAGCTGCGGCTATTGGAGCAGCAGGGTATGGATACATGTGGTGGAAGGGC
69810 G T CTGAGAAGAATAAGGCCATGTTCCTCTGTATTATGAGGCCATCATGGCTGTCCCTTACTTTGCGGTGGCTGTCCCTGATGCTTCTAGGGGTGCCCTCCCA[G/T]GTTAGCTTCCTTCCATTGCCACCGACCTCCAGGCTGTAGCAGTAGTTCCTGGCATCATTCTCGTCTCCCATGAAACGTAGGAATGCCA
69866 C T TTTCATTCTGGCCCAGTCTTGTTACTGGAATGCCCGTCCATCTACTTACAACCTCTGCAATTTG[C/T]TCAGGGCCGACTGTCTCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGAT
69866 G A TTTCATTCTGGCCCAGTCTTGTTACTGGAATGCCCGTCCATCTACTTACAACCTCTGCAATTTGCTCAGGGCC[G/A]ACTGTCTCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTC
69866 T G TTTCATTCTGGCCCAGTCTTGTTACTGGAATGCCCGTCCATCTACTTACAACCTCTGCAATTTGCTCAGGGCCGAC[T/G]GTCTCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAG
69866 C T TTTCATTCTGGCCCAGTCTTGTTACTGGAATGCCCGTCCATCTACTTACAACCTCTGCAATTTGCTCAGGGCCGACTGT[C/T]TCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAGCTA
69866 T G CATTCTGGCCCAGTCTTGTTACTGGAATGCCCGTCCATCTACTTACAACCTCTGCAATTTGCTCAGGGCCGACTGTCTCTGTTAACATCAAGTTTTCTCC[T/G]GTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAGCTAAATCCATTCTTCTC
69866 G A GAATGCCCGTCCATCTACTTACAACCTCTGCAATTTGCTCAGGGCCGACTGTCTCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAAT[G/A]GCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAGCTAAATCCATTCTTCTCTCCGCTTCTTGCAGAGTGAACATC
69866 G A CAGGGCCGACTGTCTCTGTTAACATCAAGTTTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATC[G/A]GCAGCTCGAGCTAAATCCATTCTTCTCTCCGCTTCTTGCAGAGTGAACATCAAATCCTCACGCCTCTGCTTCAATTTCCGTATCTCATCA
69866 C T TTTCTCCTGTCTCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAGCTAAATCCATTCTTCTCTC[C/T]GCTTCTTGCAGAGTGAACATCAAATCCTCACGCCTCTGCTTCAATTTCCGTATCTCATCAATTCTTTCCTTTTCCATTC
69866 G A TCACCTTCAAGCTTTGCAATGGCTGCATCAATCTCTTGGAGGGCACCGTATTTGAGATCGGCAGCTCGAGCTAAATCCATTCTTCTCTCCGCTTCTTGCA[G/A]AGTGAACATCAAATCCTCACGCCTCTGCTTCAATTTCCGTATCTCATCAATTCTTTCCTTTTCCATTC
69900 G T TTTTGTTTCTAAGTCCACTAATAACGTTTCAAGCAATGCTTGTTTTTATGATTGCATTTTTGTGT[G/T]TTGCAATGGCTGGATTTCTACACTTCACGCTCAGTTACAAAAGACCTTCACTTTCAGGATCTTGATTTATATTCATTCAAGATTGAAGCATTCATGTAAA
69906 A G ATTAATGGCGACAAAGAAGAGTGTTGGGTCACTCACAGCTGCTGATTTGAAAGGAAAAAAGGTCTTCGTACGCGTCGATCTTAACGTGCCTCTCGATGAT[A/G]ATCTTAAGATTACCGATGATACCAGAATCAGAGCTGCCGTTCCCACCATTAAGTACTTGATGGAGCATGGTGCCAGAATTATCCTCG
69960 C T ATGGCTTCCACTTCCACCACTGCTACCTCGCAGCCTTTTGCGAATTGGACGGACGACCGGGAGTCCGCTTTCATAGATGT[C/T]TGCGTTGAGTTCATAGCGGAGCGCAATACAAGCGTCAGTGGGTTCTACGCAACAGTCGCAACAACAATGAACAACCGTTTTAATCTGGAGTTCACAGAAA
69960 G A ATGGCTTCCACTTCCACCACTGCTACCTCGCAGCCTTTTGCGAATTGGACGGACGACCGGGAGTCCGCTTTCATAGATGTCTGCGTTGAGTTCATAGCG[G/A]AGCGCAATACAAGCGTCAGTGGGTTCTACGCAACAGTCGCAACAACAATGAACAACCGTTTTAATCTGGAGTTCACAGAAAACCAGA
69960 C T TGGACGGACGACCGGGAGTCCGCTTTCATAGATGTCTGCGTTGAGTTCATAGCGGAGCGCAATACAAGCGTCAGTGGGTTCTACGCAACAGTCGCAACAA[C/T]AATGAACAACCGTTTTAATCTGGAGTTCACAGAAAACCAGATTAAAAACAAATGGGACAACATGAAGCGAGCTTTTCGTGATTGTG
69986 C G ATCGCCTATAGATTCGTGTAGATCGTCGGTGGTGTCAACTTCGTTCAAGTCAGCGGTCGATTCCGATATGGTTTGGGGGAGATTTCTGCCTTCGGATTAT[C/G]AGGAAATTCTTAGTCGGACGGGTGAGCCTATAGAGTGGTCGTCCAAGCGTGACCTTTATTTTAAGCTCTGCGATCCGATCTTAATTG
69986 G A CGTTCAAGTCAGCGGTCGATTCCGATATGGTTTGGGGGAGATTTCTGCCTTCGGATTATCAGGAAATTCTTAGTCGGACGGGTGAGCCTATAGAGTGGTC[G/A]TCCAAGCGTGACCTTTATTTTAAGCTCTGCGATCCGATCTTAATTGATGGCGGTAAAATGAGCTTCCA
70006 A G TATTACAGCAATCTCAATATTATAAAATATCAAAATTACAGAGGGACTCTAGACAAAGAGGAGAT[A/G]GGGCAGTGAATCTCATTGGATTACAAGGTTATTTATCAACTCCAAGAGGAAGAAAAGCTAAAAAGACACAATACCACACTCAAGACGGTCATACATAACC
70006 G GA TATTATAAAATATCAAAATTACAGAGGGACTCTAGACAAAGAGGAGATAGGGCAGTGAATCTCATTGGATTACAAGGTTATTTATCAACTCCAAGAGGAA[G/GA]AAAAGCTAAAAAGACACAATACCACACTCAAGACGGTCATACATAACCTTCAAGCTCGGTCATGCATAATCTTCAAGCTCATAATA
70016 C T TGGCCTACTGGATTCGTAAATACATTTTTTCGATTGTTGATTATACACCATAATAGTTGCAATTGTATACAAAGATGCCGTATTGCAGCCTGAGTAGCAC[C/T]GGAGCTAAGCTCTTCTACAGAACGTACGGCAACGGTACCACCAAAGTGCTCATGATCATCGGATTGGCTGCGACGCATGAGGCGTGG
70016 C T TTGTTGATTATACACCATAATAGTTGCAATTGTATACAAAGATGCCGTATTGCAGCCTGAGTAGCACCGGAGCTAAGCTCTTCTACAGAACGTACGGCAA[C/T]GGTACCACCAAAGTGCTCATGATCATCGGATTGGCTGCGACGCATGAGGCGTGGGGTCCACAGATTAAGGGGTTGACCGACACCGG
70018 T TA TCATTTCAAACAGGATTTACCAGCAATCACACAAATACATATCTTTATATTACAATCCTGAAATTATGATTCAAGATTCGGGAACATCCCTTATTAAGCA[T/TA]AAAAATAGACGCATACACGATTATTTATGGTGAACAAAAGCAAAATCAAACAAACGCACAAGTCTTGGTTACATAAACTTAGGCAGTA
70038 A G CTCGCAGGGTTCAATAATGGACCGAGAATATTAAATACAGTCTTTATTTTCAACTGCTTCCTGACAG[A/G]ACTGACAATTTTAGTAGCTGGATGGTATAGCGGGGCCAACATGAAACCTATGCCTGCTTCCTCAACACATCTTTGTATACCCTCAGGGCCTAGATCAATG
70038 C A GCAGGGTTCAATAATGGACCGAGAATATTAAATACAGTCTTTATTTTCAACTGCTTCCTGACAGAACTGACAATTTTAGTAGCTGGATGGTATAGCGGGG[C/A]CAACATGAAACCTATGCCTGCTTCCTCAACACATCTTTGTATACCCTCAGGGCCTAGATCAATGCTGACACCCAGAGCTTCAAGAACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
70038 A G TGACAGAACTGACAATTTTAGTAGCTGGATGGTATAGCGGGGCCAACATGAAACCTATGCCTGCTTCCTCAACACATCTTTGTATACCCTCAGGGCCTAG[A/G]TCAATGCTGACACCCAGAGCTTCAAGAACATCTGCACTACCACATGCAGAAGAACTTGAGCGACTCCCTTGTTTTGCTACTCTAGCAC
70038 T C ACATGAAACCTATGCCTGCTTCCTCAACACATCTTTGTATACCCTCAGGGCCTAGATCAATGCTGACACCCAGAGCTTCAAGAACATCTGCACTACCACA[T/C]GCAGAAGAACTTGAGCGACTCCCTTGTTTTGCTACTCTAGCACCAGCTGCTGCAGCAAGGATAGCAGCGGC
70084 G A ACTTGTTCCTCCTGCTTCCACCTCTAAAATAACAAGAATTGCTAAAATCACGTATAAAGTTAGGGTTAGAGCGATGGCGTCAGCAGCAGGAGAGGCGGCA[G/A]TCGTACCGGCGGTGATAGTAGGCGGAGGGCGAGTGGGAAGAGCACTCGAAAGTATGGGAGATGGAAGAGATGTTCTAGTTGGG
70092 TA T TACTCCCTCCGGTTCACTTTATTTGACGTTCTATGAGGTTTGTCATTATCCAAAATATATGACGTTCTGCCTTTACTATCTTTCTCAAAGCAACTTTAAT[TA/T]AAAAAGAGTTTACTCTTTCAATGCAGCAAGGTCCATCTGGCAGGAAGGAATAGGTGAAATACTCCATCATGCGTTGAATACTCCAT
70094 C T AAAAAGGAAATGGCTCGTTCCTTTGCGATCACCTGCACACTCGTTGCACTTGCAGTGGTACTGACCATGGCACCCATCG[C/T]GGAGAGCGCGATCACCCGCTGTGGTACGGTGATGTCGTCCGTGTCCAAATGCATCCCATACACTATGGGGAAGGGGCCGATCACCGCTGCCTGCTGCGCG
70094 G T AAAAAGGAAATGGCTCGTTCCTTTGCGATCACCTGCACACTCGTTGCACTTGCAGTGGTACTGACCATGGCACCCATCGCGGAGAGCGCGATCACCC[G/T]CTGTGGTACGGTGATGTCGTCCGTGTCCAAATGCATCCCATACACTATGGGGAAGGGGCCGATCACCGCTGCCTGCTGCGCGGGCGTG
70094 T C TTCCTTTGCGATCACCTGCACACTCGTTGCACTTGCAGTGGTACTGACCATGGCACCCATCGCGGAGAGCGCGATCACCCGCTGTGGTACGGTGATGTCG[T/C]CCGTGTCCAAATGCATCCCATACACTATGGGGAAGGGGCCGATCACCGCTGCCTGCTGCGCGGGCGTGAAGACCCTGAGAGCCAT
70094 G A TGATGTCGTCCGTGTCCAAATGCATCCCATACACTATGGGGAAGGGGCCGATCACCGCTGCCTGCTGCGCGGGCGTGAAGACCCTGAGAGCCATGGCCAC[G/A]ACCCCGGCCGATTGCCAGATGGCCTGTGGCTGCCTGAAGACGTTGATCAGCAGCATTAAGGGTATCAA
70116 A G TGCTGGAACAGTGAGATGTCGCTGCCAAAACACTGCTATGTTGGGTGAGAGGAAAAATGTGAATCTGCCTGGTGTTGTGGTTGATTT[A/G]CCTACGCTCACTGAGAAGGACAAGGAAGATATTCTGCAATGGGGCGTTCCTAACAACATCGATATCATTGCACTTTCGTTTGTCAGGAAAGGTTCAGAT
70116 T C GCTGCCAAAACACTGCTATGTTGGGTGAGAGGAAAAATGTGAATCTGCCTGGTGTTGTGGTTGATTTACCTACGCTCACTGAGAAGGACAAGGAAGATAT[T/C]CTGCAATGGGGCGTTCCTAACAACATCGATATCATTGCACTTTCGTTTGTCAGGAAAGGTTCAGATTTGGTTAACGTCAGGCAGGT
70116 C G GTGTTGTGGTTGATTTACCTACGCTCACTGAGAAGGACAAGGAAGATATTCTGCAATGGGGCGTTCCTAACAACATCGATATCATTGCACTTTCGTTTGT[C/G]AGGAAAGGTTCAGATTTGGTTAACGTCAGGCAGGTTTTGGGACCTTTTGCGAAACGCATCAAATTGATGTCGAAGGTGGAGAACCA
70116 T C CGCTCACTGAGAAGGACAAGGAAGATATTCTGCAATGGGGCGTTCCTAACAACATCGATATCATTGCACTTTCGTTTGTCAGGAAAGGTTCAGATTTGGT[T/C]AACGTCAGGCAGGTTTTGGGACCTTTTGCGAAACGCATCAAATTGATGTCGAAGGTGGAGAACCAAGAAGGGGTGATAAACTTTGA
70118 G A TTTTTTACCATCCTAATCATCATCTTCATTAACGATCCTCTTCCAGAACCAATGGTTAGCCCAAAGGAGATGCATCTCCTCGATCGGCACCTGCTTC[G/A]TCTCAGGCAGAAGAAAGTAAACAAACAACGACATCACCAAAATCAACGATGCAAAAAGCACGAAAACCCCCCATTTTAAGTGGCATAAAGA
70142 G A TGGTTGCACCCAGTGCGTAGAAGTGTCTTCTGGCATCGATGATGGTAGACCTTTCTACAGTTGCGACGACATGAGCTTCCAAAACTGCCAACGCAGGTGC[G/A]GCACATTGGTTAATTGATTCACAATGCACCGCTTGAATCGCCCGTTGTATTTGATTTTCGTTGTGTGTATGTGTATGTCCAAAACTGC
70142 A G GCACCCAGTGCGTAGAAGTGTCTTCTGGCATCGATGATGGTAGACCTTTCTACAGTTGCGACGACATGAGCTTCCAAAACTGCCAACGCAGGTGCGGCAC[A/G]TTGGTTAATTGATTCACAATGCACCGCTTGAATCGCCCGTTGTATTTGATTTTCGTTGTGTGTATGTGTATGTCCAAAACTGCTATCT
70178 G A TGTTCAGGCCTGAAATGCTTCGTCCCATGGGTTTCCCGGAGGATGTTTCTGTCATTGCCTGGGGGCTTTCTTTAGAAAGGCCGACAATGATCTTATATGG[G/A]ATTGACAATATTCGTGATCTGTTTGGACCCAAGGTGGATTTAAATGTTGTAAAAAACAGCAGCATCTGCCGCTTAGGTTGGTCGTAG
70178 G A CAATGATCTTATATGGGATTGACAATATTCGTGATCTGTTTGGACCCAAGGTGGATTTAAATGTTGTAAAAAACAGCAGCATCTGCCGCTTAGGTTGGTC[G/A]TAGTCATCTCCACTGGAAAGACATTTTACTGCTTAAGATTCGATTGCGGTGGCATTTTACTGCTTTGAGTCTCAGAGTTTGGCCGATA
70180 T A ATTCAAAACTAGGGCAACCCCGCACATCTTGGCACCAAAAAAGACGCAAAACTCCTGCCCGCCGTTAGCAGCG[T/A]CAAATCAAACTTGGGCCGCGACAACTTCAGACTAGGCGACGACCGCTGAGTGAAACTCCGGTCGGACATCGACGGCGACCGGTCACGGTGAGCAGGTGCC
70180 T C CTTGGGCCGCGACAACTTCAGACTAGGCGACGACCGCTGAGTGAAACTCCGGTCGGACATCGACGGCGACCGGTCACGGTGAGCAGGTGCCTGGTGTGGC[T/C]ACGTCATAGGCAGACAGAAGTGCAGGCGGTTTGAGGACAGCGATTGTTACGATTGATCATCTTATTTGTGGACTGCGGGCTGTG
70206 C T GAAAGTACTTTATATCGAAGACGGTTTCGGGGTCCGAGGTGGGCACGATGGCCCTACCCGGAACTGTTGCTGGACAGTAGGGACGGTACTCGAGAGCATT[C/T]GGCACGGCGTTCTTGTACTCGGGATGCGAGCACGGTCCCGTGATTTCCCATGGCTTTTTTATGTATTTTCTTAGGTTTTGGATCAC
70232 C CA GTGTCTTTACCAAACAAATCAGCACTTGAAATGGATGATGATCCTGAATACTTCTGCAGTGTAATCTGGGCTTCCTGGTCTCCAGGTTTGACCTGATCAC[C/CA]AAAAACTGGGCCGATGAAATTGATTTTGCATTTGAAAACTTCTGTCTGGCTTCGTTAGTTTCCTGAATCTGCGCTTTCGATGGTGTGG
70240 G C ATGGTTTTGTGGCGGAGCTGAATAAGAAGATGAAGGATGGGTATAATGATGCCTTTTTCAGCGAGTTGCTTGGTAACAGCGTTGATGAACTTTGGGCCGA[G/C]TACAAGGCAAAGTATGGTGGATGAGTAGTTGATGCGATTGTATTACCATGTGTACTAGTGACTGCTACAATTACCTATAAT
70242 A T GCTCAGGCAAGCGAAAATCAAAGAACTCAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTC[A/T]ATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGG
70242 T C TCAGGCAAGCGAAAATCAAAGAACTCAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAA[T/C]TATTGACACTCCTGGCTGTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGG
70242 T G GAAAATCAAAGAACTCAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACAC[T/G]CCTGGCTGTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATG
70242 T C AAAGAACTCAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGC[T/C]GTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCT
70242 C A ACTCAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAG[C/A]GTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCCTATG
70242 C T CAATCAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAGCGT[C/T]GAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCCTATGATG
70242 C T CAATCATATGTCCATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAGCGTCGAG[C/T]CCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCCTATGATGATAG
70242 G A CATCGAACAAAATAACAAAAAGCCCTTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAGCGTCGAGCCCCATAGTCAT[G/A]ACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCCTATGATGATAGCACCACCAGCA
70242 A T TTCAATCCTGTTTTAACTGCACCTACTCATGAAATTATTGACACTCCTGGCTGTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTC[A/T]AGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCCTATGATGATAGCACCACCAGCAAATGTCCCTTTTCAATTTTTTCCAATG
70242 T A CTCCTGGCTGTAGCGTCGAGCCCCATAGTCATGACCCAGAAGCTTGTTTTTCTACTCAAGGCTACCCGGGCCTTCCTTGGGCTTACTCATGGGCCCCTCC[T/A]ATGATGATAGCACCACCAGCAAATGTCCCTTTTCAATTTTTTCCAATGTTTCCAGTGTTTCCTGATAT
70250 G A TCGCAATTCAGGGCTCTCCATCATCGCCGGATACAGCGGTCGCGCGCCGCCGGTTTCCACATCGACGGCGCCGCCTTTTGCCGGAGGTCGGAAGTACATT[G/A]CTGGAAAGTATCGAGAGTTTTTCGGTGATTCTTCTGTTGACGTTGATCTTAATCCAGTAGGCCAACA
70256 A G AGGAAGTTCCAAACATCGTTTCCTTCAACATTAGCCAATGGGTTCCACTTAACCAAGCTGCC[A/G]ACCCCACCTTCAAGCCCTTCAAACACAGGATCGACTTGAACCACAGGGATATGTGCCCTAGTTCCAGGGGACTGGTCCTTGCGTTGGCCAGTGATCCAGG
70256 G A TAGCCAATGGGTTCCACTTAACCAAGCTGCCAACCCCACCTTCAAGCCCTTCAAACACAGGATCGACTTGAACCACAGGGATATGTGCCCTAGTTCCAGG[G/A]GACTGGTCCTTGCGTTGGCCAGTGATCCAGGCCTTGAGACCTTTAAGAGCCCTACGTAAAGGACGGACCTTTCTGACACGGCAGCA
70256 A T CTTCAAACACAGGATCGACTTGAACCACAGGGATATGTGCCCTAGTTCCAGGGGACTGGTCCTTGCGTTGGCCAGTGATCCAGGCCTTGAGACCTTTAAG[A/T]GCCCTACGTAAAGGACGGACCTTTCTGACACGGCAGCACTCTTGATGCCCGTCTTCGTAGAATGAGAAGAGTCCTTTGTTTCTGACA
70260 C T CAGCAGTACACAATAGTGCCATCAGGAGTTAAGAAACTATCTGGGTCTAATTTTGTGGCATGTCATGCTAGAAAATA[C/T]CCATACGTGGTGTTTTACTGCCACACAACCGAAGGAATAACGGCATATGAGGCAAAGCTGTTAGGGGAGGACGGAACAACAGCTGAGGCCGTGGCTGTTT
70298 T C AATTATGGGATAGCAATTTGATCATGTACATGCAACATTTTTGTTCGTTGAGCAAATTTCACGACACAATA[T/C]ATGTATACTTATTGAGGCATAAATTGGTGGAACATGTTCAGTGTTTATCCTCCAAATCTTGGTGCTCATGTTATCAGTAATTTGATTGCCTTTTAGCATT
70298 A G AATTATGGGATAGCAATTTGATCATGTACATGCAACATTTTTGTTCGTTGAGCAAATTTCACGACACAATATATGT[A/G]TACTTATTGAGGCATAAATTGGTGGAACATGTTCAGTGTTTATCCTCCAAATCTTGGTGCTCATGTTATCAGTAATTTGATTGCCTTTTAGCATTTGAGG
70298 A G AATTATGGGATAGCAATTTGATCATGTACATGCAACATTTTTGTTCGTTGAGCAAATTTCACGACACAATATATGTAT[A/G]CTTATTGAGGCATAAATTGGTGGAACATGTTCAGTGTTTATCCTCCAAATCTTGGTGCTCATGTTATCAGTAATTTGATTGCCTTTTAGCATTTGAGGAG
70298 G A GTTTATCCTCCAAATCTTGGTGCTCATGTTATCAGTAATTTGATTGCCTTTTAGCATTTGAGGAGGTGCATTGCAGTGTATTTTTTGTATATCATCCATC[G/A]TGATTATTCTTTTGTCCTAGAGCATCCGATGGTTGATAGAATATTTATCCGAACATCCAGTTCTTA
70328 T C TGCCAATACCACCTGCTGTACTCACTGGGAGACGTGAAAAAGTTATCATTGAGAAGGAAAACAATTTCAAACAGCCTGGAGAGAGATACCGTTCCTTTGA[T/C]CCTGCCAGGCAAGAAAGATTCATCGGTAGATGGGTCGAGGCACTATCAGACAATAGGGTTACTCATGAGATCCGCCGCGTATGGA
70328 G A TGGGAGACGTGAAAAAGTTATCATTGAGAAGGAAAACAATTTCAAACAGCCTGGAGAGAGATACCGTTCCTTTGATCCTGCCAGGCAAGAAAGATTCATC[G/A]GTAGATGGGTCGAGGCACTATCAGACAATAGGGTTACTCATGAGATCCGCCGCGTATGGATATCATATTGGTCTCAGGCTGACAA
70342 A G AATTCATCCATCACCTTCTCCACCGCCTTCACTCTTCCTTTCGCCACCAACATCCTCACCAT[A/G]ACCACCAATTTCACGTACAGCTTTCCTCTTTCCACTGCTTTTCTCACCACTTTTCCCTTCTCTTCCTCTTTCACCCTTCCATCCCCCAACACCATATTGA
70342 G A CACCACTTTTCCCTTCTCTTCCTCTTTCACCCTTCCATCCCCCAACACCATATTGACTATCCTCTTCACCATCATCGCCTCTCTCGCAATCGCCATCAGC[G/A]TACCCCCGTGCTTGGCGACGTCGGAACAAGCAGCGTCGAGCAAGGCTGCTGCGTAACCAGTAGAGGCTTTCCTT
70358 C A AAGGCACCCAAGAAGACCACTGCTGCAAAGAAGGCTCCTGCAGCTCATCCACAGTACAGCGATATGGTTATCGAGGCGATCAGTGCTTTAAAAGAA[C/A]GGACCGGATCCAGCCAGAAGGCCGTTGAAAAGTATGTGAAGGAAAAGCACAACATCGAGCCCTCTACTTCGAGGAAGTACATTTTAGCT
70358 T C AGGCTCCTGCAGCTCATCCACAGTACAGCGATATGGTTATCGAGGCGATCAGTGCTTTAAAAGAACGGACCGGATCCAGCCAGAAGGCCGTTGAAAAGTA[T/C]GTGAAGGAAAAGCACAACATCGAGCCCTCTACTTCGAGGAAGTACATTTTAGCTCAGTTGAAAAAGCTTGCTGCTGCCGGTAAGC
70384 C G AAGACAACAAAGAACAAATCTGCAAACTGCAGATCCTCAAGTACACATAGTGTAATGTCGAATCTATGTTTCAAAAGTTCAAAGCCATGCACACAAGCTG[C/G]AATAGTAATTCTGCTCGTCACATTCTTTGCAGCCAACGTATATAACTACGTCGATTACAGTTTAACCTCGAGACTGACGTGGACCAAA
70410 T C CACATGGGCCGTCGTCCACCTGAGCAGCAATCTTCATAAGAATATCTTGAATATTATTGTACGCTTCTAAACTACCACCAGGCATCAAACTGGGTCCATA[T/C]CTAGCTCCGTCTTCCCCACCAGAAACACCCATCCCCAAATATAACAAACCCTTGGCCTGCGCCTCTCTAATCCTCCTCTCCGTATTCTCA
70410 G A CGTCGTCCACCTGAGCAGCAATCTTCATAAGAATATCTTGAATATTATTGTACGCTTCTAAACTACCACCAGGCATCAAACTGGGTCCATATCTAGCTCC[G/A]TCTTCCCCACCAGAAACACCCATCCCCAAATATAACAAACCCTTGGCCTGCGCCTCTCTAATCCTCCTCTCCGTATTCTCATACCATTCGT
70444 C T CGTGATGCTGTTACTTACACCGAACACGCAAGGAGGAAGACCGTTACTGCTATGGATGTTGT[C/T]TATGCTTTGAAGAGGCAGGGAAGGACACTGTACGGATTTGGAGGTTAGATGTTTTGATGCTGGTGTTTATGTGTCGCGTTAATCAGGGCAGTTAGCAGCT
70444 AT A GGCAGGGAAGGACACTGTACGGATTTGGAGGTTAGATGTTTTGATGCTGGTGTTTATGTGTCGCGTTAATCAGGGCAGTTAGCAGCTGTCAAGAAGCGTT[AT/A]TTAGGTTTACAATCTCTTTTCCATGTTTTACTTTCGTATGGTGGAGTGTTTGTGAGTATTGGGTAAAATGGATGTAATGATAGTGT
70444 GT G TGGAGGTTAGATGTTTTGATGCTGGTGTTTATGTGTCGCGTTAATCAGGGCAGTTAGCAGCTGTCAAGAAGCGTTATTAGGTTTACAATCTCTTTTCCAT[GT/G]TTTTACTTTCGTATGGTGGAGTGTTTGTGAGTATTGGGTAAAATGGATGTAATGATAGTGTCAGTAATGAATTTTATATTA
70496 C T AGCCCGGGAAGGAAAAGAGAAACCGAAAGAAAAGTGTCAGGTGAAGCAAAACCGAGCAGCGGCTAAGAGCAGGCCAGACGCAGGTCAGCCGATCAGAATA[C/T]ACCCCAATGGAAACGATTAGATCGAGGAGCAGAAGCCTGGAAGGTGGGAGATTGGCAGAAGAAGCGGTGGCAGATCCCAA
70506 T C AGTAATGTTGGTTCCAGTTCCAATAATTTAGGGTTTGGTTCCACGGGACCTCAGATGATTACAGGGATGAACGCTCCGATGAGTTTTACTTCCATGCTTG[T/C]AGATCAAACTCCAGGGTTGCGTTTAGGGCTTTCGCAGGGTGGTCAAATCGGAGGCATGAATCCATGTCAAATGAATGAGTTTCTTCA
70506 T G GATGAACGCTCCGATGAGTTTTACTTCCATGCTTGTAGATCAAACTCCAGGGTTGCGTTTAGGGCTTTCGCAGGGTGGTCAAATCGGAGGCATGAATCCA[T/G]GTCAAATGAATGAGTTTCTTCACCAGAGGCCAAATGGTCAGGCTGGGTTTAACAGCCATGGGTGTATCAGCGGTGAAGGAGCAAG
70506 C T CTTGTAGATCAAACTCCAGGGTTGCGTTTAGGGCTTTCGCAGGGTGGTCAAATCGGAGGCATGAATCCATGTCAAATGAATGAGTTTCTTCACCAGAGGC[C/T]AAATGGTCAGGCTGGGTTTAACAGCCATGGGTGTATCAGCGGTGAAGGAGCAAGTACAATCGGCGTCGGTGGAGGGCG
70510 G A CCTTAACAGCAACAGGCGGGTTGGCATGCCTACACTCCATTCCCTCGATCTTCCTCTCATGATAACTTACCTTACTCTCCGCAAACTTCAACCCATGCGC[G/A]GTACTCACCACAATTGTCCGATCATTCGCCCCGATCACCCCGCTCCTCCTCAACTTGTCCAGCGCAGCCAGCGC
70642 T TC AGGGGAAAGAAGACGGAGCAGCCGCCGAAGTTCATCGCGCCTCCACGGGGAGATCCGCCGCCCACCTCCACCGTCGCCGCCTATGGCGAGGCCCACCCTC[T/TC]CCCCCCCTGTTTCCCGTTCTGCTCGAGAAAATCCACCCCACCTGTCGACTTCTCAGCCTGGCGCGCACCACCTGCCCTCGACGAA
70652 A G GGTTCCTTTCCTCAACGGTGAGCTCCTCGCCTCCGGAAGCGGCAGCGGTGACCTTTTCCATGAACTCGACCATCTCCTCGTATCGCTCGGCCTGCTCGGC[A/G]AGTTTCGCCATGTAAACGTATTCTTCACGCGTGTTCGCCATTAAAGGTGAATAAGTTTTAAAGATTAGAAAAGGTTTCGAGAGAGGA
70652 T C TCCTTTCCTCAACGGTGAGCTCCTCGCCTCCGGAAGCGGCAGCGGTGACCTTTTCCATGAACTCGACCATCTCCTCGTATCGCTCGGCCTGCTCGGCAAG[T/C]TTCGCCATGTAAACGTATTCTTCACGCGTGTTCGCCATTAAAGGTGAATAAGTTTTAAAGATTAGAAAAGGTTTCGAGAGAGGAAGA
70660 G A TAAACCAAATTCCATTAACATTAAAACCCATTCACACAGAGCATACCACAGAGGCCATAAACTAAACACCAAAGTAGAAATCCCAGATTAAAACATAGCA[G/A]AGAAATCTAAACCCTTTCTCCCCTGATCCTCCTGGCAAGCTGGATGTCCTTAGGCATGATGGTAACCCTCTTAGCATGAATAGCACAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
70688 G A TTTGACGGACTCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGC[G/A]GTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTT
70688 A G TTTGACGGACTCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGC[A/G]ATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGAT
70688 T C TTTGACGGACTCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAA[T/C]TTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGAT
70688 G T TTTGACGGACTCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGG[G/T]GATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGAT
70688 T C CGGACTCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGT[T/C]AGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGT
70688 G A TCGAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGC[G/A]CGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGG
70688 G A GAGGCGCTGCGCGGCGATAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGCGC[G/A]GTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGGTG
70688 C T TAGGAGCGGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTG[C/T]GGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGGTGTTCGATGGAAGGAGGCT
70688 G A GGGGTGACCAGGCCTTGATGGTAGCAGGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCC[G/A]ATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGGTGTTCGATGGAAGGAGGCTGGAGCGA
70688 T A GGTTAACTCGCGGTGGTTGGCAATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGG[T/A]ACTCACGGTTTCAAGCAGATATGGTGATGGTGTTCGATGGAAGGAGGCTGGAGCGATGGATTTCGGTGGATCCATTAATTACT
70688 T G CAATTTCGTAGGGGGATTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGA[T/G]ATGGTGATGGTGTTCGATGGAAGGAGGCTGGAGCGATGGATTTCGGTGGATCCATTAATTACTTGTGAGGAGGGGTAATCAGT
70688 G A TTCCAGTTAGGCGCGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGGTGTTC[G/A]ATGGAAGGAGGCTGGAGCGATGGATTTCGGTGGATCCATTAATTACTTGTGAGGAGGGGTAATCAGTTGGCATAAATTTCAAA
70688 T C CGGTGATGGAGGCGGCTGCGGATCCGATTGGCGATGGCGGCGAATGATGGGTACTCACGGTTTCAAGCAGATATGGTGATGGTGTTCGATGGAAGGAGGC[T/C]GGAGCGATGGATTTCGGTGGATCCATTAATTACTTGTGAGGAGGGGTAATCAGTTGGCATAAATTTCAAAATTT
70694 T C TAACGGTACCGTCTTGGACTCTTGATTTTGAGGGATCACGCTCAGTTTGTTGCCGCGTGTTCACAGTTTGAAGAGGGTAGGTGAGCAGCTGAGCTATGAT[T/C]CCACCGCCGGCGCCAGACAACCCATTGATGAGGGCATCGGACATAATTCTCTTCCTCTATTTCAATGACTAAGCGGAGAAATTGGG
70694 G A AGGGATCACGCTCAGTTTGTTGCCGCGTGTTCACAGTTTGAAGAGGGTAGGTGAGCAGCTGAGCTATGATTCCACCGCCGGCGCCAGACAACCCATTGAT[G/A]AGGGCATCGGACATAATTCTCTTCCTCTATTTCAATGACTAAGCGGAGAAATTGGGTTGATTGGGATTTGTGAGTGGCTGCTTATT
70728 A G TTTCTTCTGTGTTACAACACACACGGAATCCTTCCCTCTGACACCAATGGATGTGATTCCAGATGCCTTTACAGCTTTGAATGCATATTCTACTTGAAAC[A/G]ACCGGCCTTCCGGTGAAAAGATAGTGATGTGTCTGTCGTAGCCGGCGCCGCTACCTCTGCTCATTTTGATTGAGATTTACCGTTGGTGT
70774 A G GGGCAGCTAAGGGTTTCTTCTTTAGTAAGAGTGTGGAGATTGCTGGCTTTGCTCAGAACCAGCAGTTCGGTTTAGGGGCTAACACTTTGACTTCTGGCCA[A/G]AAGGCTTTGTTGATCTATGGAAGCTTGCTCTTGTTTTTTGCTTTGTTTTTGTCCGGTTATTTCTTGCAATGATATGCGTACTTCCTCCT
70774 T C CTGGCTTTGCTCAGAACCAGCAGTTCGGTTTAGGGGCTAACACTTTGACTTCTGGCCAAAAGGCTTTGTTGATCTATGGAAGCTTGCTCTTGTTTTTTGC[T/C]TTGTTTTTGTCCGGTTATTTCTTGCAATGATATGCGTACTTCCTCCTATGACAAAAAAAAGGCCACAT
70776 A G AGATAGATCATAAAATTTCTTGAATCTCATCGAGGGCATAATTGTTGGTAGATACACCAGCATAATTCACTGCGCTGAACCTCACAACCACTGGATACTG[A/G]GTTTTTGGATCCTGATCAACAGTCACGACCGATCCGGTTCCATTGTACCAGTATGATTCTCTTCTCAGGATCTTCACCTTTGCTCCTCTC
70776 C G TCTCATCGAGGGCATAATTGTTGGTAGATACACCAGCATAATTCACTGCGCTGAACCTCACAACCACTGGATACTGAGTTTTTGGATCCTGATCAACAGT[C/G]ACGACCGATCCGGTTCCATTGTACCAGTATGATTCTCTTCTCAGGATCTTCACCTTTGCTCCTCTCTTGGGGCCGA
70776 C T CGAGGGCATAATTGTTGGTAGATACACCAGCATAATTCACTGCGCTGAACCTCACAACCACTGGATACTGAGTTTTTGGATCCTGATCAACAGTCACGAC[C/T]GATCCGGTTCCATTGTACCAGTATGATTCTCTTCTCAGGATCTTCACCTTTGCTCCTCTCTTGGGGCCGA
70778 T C CGGTTTTATTATTAATTATTGAATAGTGTCAAAGCAGTGTGTTTTTCAGTGAAATGTTTCTTGGAACAAATTTCATGTTTGAGTAATTCGACAGTTCACC[T/C]ATGTAATATTTATCAACTTGAATTTGGTTACCCAGAGCTTATTTCATGGCTTTGGGTTTGTTGTACTAGTATTTCTGTATTTAAAGCGTAT
70778 T C AATTATTGAATAGTGTCAAAGCAGTGTGTTTTTCAGTGAAATGTTTCTTGGAACAAATTTCATGTTTGAGTAATTCGACAGTTCACCTATGTAATATTTA[T/C]CAACTTGAATTTGGTTACCCAGAGCTTATTTCATGGCTTTGGGTTTGTTGTACTAGTATTTCTGTATTTAAAGCGTATTTGGTTATTAAAT
70800 C T ACACACAAACTCATGGATCTACAATCAATGGCTTGCTAGTGTTGCGTGGTAAGCAAATTTCAAGGAGTGGGAGAAGGGTGAGCTGAAACCTCGGGGCGTG[C/T]AGGTAGCTGAGGCAAAGGAGGTAGTTCAAACTTGGGAAGGGTCGGAATCTCAGGAAGAGGTGGAAACTCCACCTTTGGTAAAG
70810 C CG TTTGACTGATACTTCTTGAGGAGGAAAGATTATTCCGTACGTTTGTAGGGGTGGCTTGCATACGAGATACGATTTATAAGTAGTGTTTGGAGACAGCTCA[C/CG]TAGAGTTGATGCTGCATTCCAGCTTCAGCCAGTAGACGGCCAGTAGCTCTGTCACTTTTGTAAACCTCGATTTAGGGTGAGAAACC
70870 T C AAAAAAAAAGTGGGGAGGCGAAAACCCACTGTTCTTTTTCATCCTCATCTCCAGACTCTCCTCCATGCCTCGTTTTACCCG[T/C]CGTATCCTTTATCCGGCCTCCGTCGCCGTCAACTCCACGGCCTGCGTCTTCCCCCGTTGCATCTACCCACCCGTGGACTTCCCTTCTCCGCCTATCCCAT
70872 G T AGAGCCTTTAAAAGGTGGGATAGCGGAACTTGGACCACTGCAACCCGACCCGACCCGAACTCGGTTACAGTCAGG[G/T]GGGTGTGGTTGCAGTTGTGCAGGCTGTGTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGAC
70872 T C AGAGCCTTTAAAAGGTGGGATAGCGGAACTTGGACCACTGCAACCCGACCCGACCCGAACTCGGTTACAGTCAGGGGGG[T/C]GTGGTTGCAGTTGTGCAGGCTGTGTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGACCCAC
70872 T C AGAGCCTTTAAAAGGTGGGATAGCGGAACTTGGACCACTGCAACCCGACCCGACCCGAACTCGGTTACAGTCAGGGGGGTGTGGTTGCAG[T/C]TGTGCAGGCTGTGTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGACCCACATCAT
70872 A T AGAGCCTTTAAAAGGTGGGATAGCGGAACTTGGACCACTGCAACCCGACCCGACCCGAACTCGGTTACAGTCAGGGGGGTGTGGTTGCAGTTGTGC[A/T]GGCTGTGTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGACCCACATCATA
70872 C G GGGGTGTGGTTGCAGTTGTGCAGGCTGTGTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGA[C/G]CCACATCATAAATCATGGTTAGATCGGCATGATACATTCCGAATGATCTCTCAGAGGTCGGCCCTGGCTTCAGATCCTCGTCGTAC
70872 C T GTTGGAGGAGTACTATTACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGACCCACATCATAAATCATGGTTAGATCGG[C/T]ATGATACATTCCGAATGATCTCTCAGAGGTCGGCCCTGGCTTCAGATCCTCGTCGTACAATGCAAAAATATATGTATCTACGGA
70872 T C TACTTGTAGCAATTTGAGGTGGAGGACTAATCGGACTTGAGACGGATTTTGTAAGACCCACATCATAAATCATGGTTAGATCGGCATGATACATTCCGAA[T/C]GATCTCTCAGAGGTCGGCCCTGGCTTCAGATCCTCGTCGTACAATGCAAAAATATATGTATCTACGGA
70912 G GA TCATATAAAATAGACATCCAAGCAAAATCACAGCATATGATTCTCTGAGCAGCGCACTCCAAAGAACAGATCAAGTCGCACACTCTAAATTCAATACAAC[G/GA]AAACAATACAGCATTCAAAATTCCAGACAAGAGAGAAAAATTCTAAAACTTTCAGATAAATACCAAATAGTTCAAGCGGTAAGCAC
70924 A G CTTCAATGCTGTCTGTTTCGCAAACTGGTTATGGTTGGCTGGCTGAAGGACAAGCAGATACTAGATGATGCCAAGTCAAAGAGGAAATGTACCTTGAATT[A/G]GTAGTTTTGCTTGCAGTGATGACCCATGAAGTTTTGATGTGGATTGGATCAACTATTTCGCAAAATTTGATGTTTGTACTACGGTCA
70930 G C TCACAGCAGCAAATGACTTCTTTACCCCAGTCGAGGGGGCCTTTAAGCCATCGGGATGGAC[G/C]AAGGCAAGCGCCACATTCTACGGAGGAAGCGATGCCTCCGGCACAATGGGTGGAGCGTGCGGGTATGGAAACCTGTACTCGACGGGGTACGGGACGAGAA
70930 C T GGGGGCCTTTAAGCCATCGGGATGGACGAAGGCAAGCGCCACATTCTACGGAGGAAGCGATGCCTCCGGCACAATGGGTGGAGCGTGCGGGTATGGAAAC[C/T]TGTACTCGACGGGGTACGGGACGAGAACGGCAGCGCTGAGCACGGCGTTGTTCAACGATGGAGCGGCGTGCGGGCAGTGCT
70930 A G CCTCCGGCACAATGGGTGGAGCGTGCGGGTATGGAAACCTGTACTCGACGGGGTACGGGACGAGAACGGCAGCGCTGAGCACGGCGTTGTTCAACGATGG[A/G]GCGGCGTGCGGGCAGTGCTACAAGATAATGTGCGACTACAAGACGGATCCGAAGTGGTGCATCAAGGGCACGTCCATCCGGA
70930 C T CAATGGGTGGAGCGTGCGGGTATGGAAACCTGTACTCGACGGGGTACGGGACGAGAACGGCAGCGCTGAGCACGGCGTTGTTCAACGATGGAGCGGCGTG[C/T]GGGCAGTGCTACAAGATAATGTGCGACTACAAGACGGATCCGAAGTGGTGCATCAAGGGCACGTCCATCCGGATCACCGCTA
70932 G A AGCTAAACGGGGTGATCACCCACCTGGATGGCGTGATGTGCCTGCCCATGATCCAGTTGTGAAAGATGCAGCAGACCATGCAGTGAAGACCATCCAACAG[G/A]GGTCGAATTCCCTTACTGCTTATGAACTGCTTGAAGTTCTTCATGCCAAGGCTGAGGTGATAGGCGATCTTGCCAA
70954 A G AGCAGCAACAGAGAGCGGTCTTCTTTTGGTGGATTCTTTCCAAGCGAGAGAAGGCAAGTCGAAATAGACGGCGCTGGCAAAGCAAAGGGAGAGAAGTCT[A/G]CCTCTACTGATTATGATGTGCTTCCTGGTGAAGTTGTGGATGTGTGAGCTAATAGAGTTATTTATCCTTGGTAATTATGATAGTATT
70954 A G AAGGCAAGTCGAAATAGACGGCGCTGGCAAAGCAAAGGGAGAGAAGTCTACCTCTACTGATTATGATGTGCTTCCTGGTGAAGTTGTGGATGTGTGAGCT[A/G]ATAGAGTTATTTATCCTTGGTAATTATGATAGTATTTTACCGCAACCATGGATTTGTAGTAAATTTCCTTTATGTTGGAGAGGATTC
70958 T A ACCTTTCATGCTTCCATTTGCTCCCGTCAAACCACACCAGTAACAATGACGAAATCTCTAAATCTCGACCTCAACTAGCTTCTCATATCAAACCAAGTAC[T/A]AACTTTTTTCATCTCGATCCATTCGCTCGATTCTACTCTTCTTCATCGTCATCGGACGAGGTGGGATTCATCAGTGACGTGGCAGA
70990 C T ACATTCATCTCAGCAGCAGCAAATCTTTGGTAGTCATCCTTGCTCGCTCCTTTCACTTGCCACTCTGC[C/T]GTCCATTCTCCTACGAAGATAGGGGGGCCATTAGAAACTGTTGCAGCAGCTAGTTCTACAGAGCGTCGTCTATTGACAAAGTTGATATTTTGTTGGACGG
70990 T C ATCTTTGGTAGTCATCCTTGCTCGCTCCTTTCACTTGCCACTCTGCCGTCCATTCTCCTACGAAGATAGGGGGGCCATTAGAAACTGTTGCAGCAGCTAG[T/C]TCTACAGAGCGTCGTCTATTGACAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTA
70990 T C CATCCTTGCTCGCTCCTTTCACTTGCCACTCTGCCGTCCATTCTCCTACGAAGATAGGGGGGCCATTAGAAACTGTTGCAGCAGCTAGTTCTACAGAGCG[T/C]CGTCTATTGACAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTATATCGACCACAG
70990 A G CGCTCCTTTCACTTGCCACTCTGCCGTCCATTCTCCTACGAAGATAGGGGGGCCATTAGAAACTGTTGCAGCAGCTAGTTCTACAGAGCGTCGTCTATTG[A/G]CAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTATATCGACCACAGTACCGCTGA
70990 A G GTTCTACAGAGCGTCGTCTATTGACAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTATATCGACCAC[A/G]GTACCGCTGAACCCGCTTGCGAAGCGAAGCAATTCTCGGGTGTTTGCTCCAAGCCGATTTGACATGAT
70990 T A TCTACAGAGCGTCGTCTATTGACAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTATATCGACCACAG[T/A]ACCGCTGAACCCGCTTGCGAAGCGAAGCAATTCTCGGGTGTTTGCTCCAAGCCGATTTGACATGAT
70990 G C CAGAGCGTCGTCTATTGACAAAGTTGATATTTTGTTGGACGGTCAGGTTGTTGAATATGCTAGAGAAAAGACTGTAAAAATGTATATCGACCACAGTACC[G/C]CTGAACCCGCTTGCGAAGCGAAGCAATTCTCGGGTGTTTGCTCCAAGCCGATTTGACATGAT
71002 G T CTTGTGGAGGATACCCACTTTGTGGAGGGTAACCACTTTGCGGAGGGTAACCTCCTTGCGCTGGTGGGTAGCCTTGTGGTGGGTATGCCCCATGTTGCCC[G/T]GGCGGGTATCCAGAATGACCGGAAAGCCCATGTGCCATGTTAGAAAGAAATCCTTTGTCCTGATACTCTTCTCCTTGTTTGTCCTTT
71072 T G AAAAAAAACACCGCAAATAGCATAAAAATAATTAGATGGCGGCATACTCTATTGTAACTCCAAATCTTATATC[T/G]TCTAATCCAAAATCCCTAAATTTAACGTTTTACTCAAAATCTGTCTTAAACAACCTCTCCTTTTGCGTTTCGAACGCATCGTTTAGGTCTTTGAGCTTGA
71086 T C GACTATTGCATGGTCTTCCCTTGAATATTGTGATAAAAACTCTCTCTCGAAAAAGATATTTACACC[T/C]TCAGCTAGTAATAACCAGCAAAAACCATCATACCCCTCTTCAAAAGGAAAGGTGGACTGGGACAAGCTCGAGGCCCTAGTTAAAAAAGAGGAAAAAGAAG
71130 G C CGCCTCTCTCCTATTCATCCCCCCATCTCCATCGTTTCCTCCTCCGCCACCACCGCCTCCACCGCTTC[G/C]TCCTCCATTATCACTCCCTCCATTGCCGATCGATCGTGCAATAACCGATCGTTTGCCGTTCATATAAGAATTGGTGCATGCGATTTTAGGGTTTAGGGAT
71172 A C TTCCACAAGAAAGCTTCTAGATCCATCGCCACATAAATCCAAACTTTCCAACCTTGCGATCCATGGTGAGACTGAACAAGAGATAAACTTTGGGTTAGTA[A/C]TGATGAAACAGTTCTGGATCTCTCAGCCATGCAATTTTAGAAAATAAACGACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATC
71172 G A CGCCACATAAATCCAAACTTTCCAACCTTGCGATCCATGGTGAGACTGAACAAGAGATAAACTTTGGGTTAGTAATGATGAAACAGTTCTGGATCTCTCA[G/A]CCATGCAATTTTAGAAAATAAACGACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATCGTATTGCTCCTTTGAGGTTTGTCAAC
71172 C T AACCTTGCGATCCATGGTGAGACTGAACAAGAGATAAACTTTGGGTTAGTAATGATGAAACAGTTCTGGATCTCTCAGCCATGCAATTTTAGAAAATAAA[C/T]GACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATCGTATTGCTCCTTTGAGGTTTGTCAACCGGCTGAGGTTGAAGTTTGCAG
71172 C T AATGATGAAACAGTTCTGGATCTCTCAGCCATGCAATTTTAGAAAATAAACGACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATCGTATTGCTC[C/T]TTTGAGGTTTGTCAACCGGCTGAGGTTGAAGTTTGCAGTGGCTGTAATTGGTCAATATTGCATAAACTTCATTTGGCCTAAACCACC
71172 T G TGATGAAACAGTTCTGGATCTCTCAGCCATGCAATTTTAGAAAATAAACGACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATCGTATTGCTCCT[T/G]TGAGGTTTGTCAACCGGCTGAGGTTGAAGTTTGCAGTGGCTGTAATTGGTCAATATTGCATAAACTTCATTTGGCCTAAACCACC
71172 G A TCTCAGCCATGCAATTTTAGAAAATAAACGACCTGCATTTCTTGCACATGCCAAAATGTTCCATGTATCGTATTGCTCCTTTGAGGTTTGTCAACCGGCT[G/A]AGGTTGAAGTTTGCAGTGGCTGTAATTGGTCAATATTGCATAAACTTCATTTGGCCTAAACCACC
71192 G C TGTGGGTGATCCGGCCTGATTTGGTGGATGGAGATGTCATGGTTAAGTTGAAGCAGGATACGAAGGAGGAATTGGGATGCATAGTGGAGTGGGCAC[G/C]GCAGAAGGAGGTGTTGGGGCATGGGTCGGTGGGCTGTTTCTTGACGCATAGCGGGTGGAACTCGACGCTGGAGAGCATAGCGGCA
71192 A G TAGTGGAGTGGGCACGGCAGAAGGAGGTGTTGGGGCATGGGTCGGTGGGCTGTTTCTTGACGCATAGCGGGTGGAACTCGACGCTGGAGAGCATAGCGGC[A/G]GGGGTGCCGATGGTGTGCTGGCCGTATTTGGGGGACCAAATGATAAATAGTAGGTTCGTGGAGGAGGTGTGGGGGATTGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
71222 A AATT ATATCAGTAAATATTATACCACAATTACAGTCTCCAACCTGAAACATAAATTAACAATCCCAAAATACAGACAGCAGACACTAAGAT[A/AATT]ACCTAACTTCTTCCATGCATACATACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGA
71222 TG T TTACAGTCTCCAACCTGAAACATAAATTAACAATCCCAAAATACAGACAGCAGACACTAAGATAACCTAACTTCTTCCATGCATACATACATATAGATTA[TG/T]GATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCATTAGAGAAGGAAAC
71222 T C AACAATCCCAAAATACAGACAGCAGACACTAAGATAACCTAACTTCTTCCATGCATACATACATATAGATTATGATAATATATTAGCTGTAGGGACTCAT[T/C]CCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCATTAGAGAAGGAAACATAGTAAAACTCGGAAAGAATGGCAGTG
71222 G C TAAGATAACCTAACTTCTTCCATGCATACATACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGC[G/C]ATTGGAATCGTAAGCATTAGAGAAGGAAACATAGTAAAACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAA
71222 A G AAGATAACCTAACTTCTTCCATGCATACATACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCG[A/G]TTGGAATCGTAAGCATTAGAGAAGGAAACATAGTAAAACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAAA
71222 T C TTCCATGCATACATACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCA[T/C]TAGAGAAGGAAACATAGTAAAACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAAACACTCCCTTCCTCAGTG
71222 C T TACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCATTAGAGAAGGAAA[C/T]ATAGTAAAACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAAACACTCCCTTCCTCAGTGTTTGGCA
71222 A G ACATATAGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCATTAGAGAAGGAAAC[A/G]TAGTAAAACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAAACACTCCCTTCCTCAGTGTTTGGCA
71222 A G AGATTATGATAATATATTAGCTGTAGGGACTCATTCCAATATTAGACTTTCCATACTGCGGGCGATTGGAATCGTAAGCATTAGAGAAGGAAACATAGTA[A/G]AACTCGGAAAGAATGGCAGTGAACAAGGCAAAGGAAGCACCAGCAGCAAACACTCCCTTCCTCAGTGTTTGGCA
71232 CT C GAGGAAATATTAGTGAAAATAAAATAAAATAAAAGGATGAGTTAATTTATCTCTATGATATGCAGGCCTTTATCTTTGGTTGAGATTTTAGTTACTGTT[CT/C]TTTTTTACTCTGCTAATAAGGTTTCCACTTGTTAATATTCTGTCAGATATTTGGAGCCATTATGAGCTACCCTTTTTTGTTTATCACTTGTA
71244 G T ACTCCTGCTAGAAGAGCAAAAAACACAAAGAATCCTGTTGCATTGTTTCCCATTGGAAAGTATATCGGAGAGTATTCTGCTGGTACCTTGATGTCAGAAT[G/T]TATGACGTATCCCCGCCCAACAGCAAAATCAACTGCCCAACCAGCTATTGAGGCCAGTATGACATACATGCAGAAGTTGAGAATTAG
71244 C T GAGCAAAAAACACAAAGAATCCTGTTGCATTGTTTCCCATTGGAAAGTATATCGGAGAGTATTCTGCTGGTACCTTGATGTCAGAATGTATGACGTATCC[C/T]CGCCCAACAGCAAAATCAACTGCCCAACCAGCTATTGAGGCCAGTATGACATACATGCAGAAGTTGAGAATTAGGAACAAGGAAGC
71304 G A TAGGAGGAAGAGGAGGTCCTAGACCAATGCAACATAACATGGTTGGAATGCAACAGAGAATGGCAGCTGCAAACATGGCCCTTAACATGAACATGGCGTC[G/A]CAGGCAGCAGGGGGTATGCCTGGTGCTCTTAATCCTGGAGCCATGCCTATGCAAAGGGGTAATATTGCTCAGGCCCAGCAACAA
71304 G A ACCAATGCAACATAACATGGTTGGAATGCAACAGAGAATGGCAGCTGCAAACATGGCCCTTAACATGAACATGGCGTCGCAGGCAGCAGGGGGTATGCCT[G/A]GTGCTCTTAATCCTGGAGCCATGCCTATGCAAAGGGGTAATATTGCTCAGGCCCAGCAACAACAGCAGCAGTTGAGGAGAAAGG
71352 T C TGTCTTTGATCCAGTGCTGTTTAAGATCCCTTGGATTAGCAGGAGCAAGCAATACTTCACCGTT[T/C]TTAACAGTAAGGGAGTAACTCTCATTAGCTTTACTGAATATCCTCATTGTTTGTTCCGTTGTTTGTGACTCATCATCTGAAGCATAAGCAGTACTATAAA
71352 A G AGTAACTCTCATTAGCTTTACTGAATATCCTCATTGTTTGTTCCGTTGTTTGTGACTCATCATCTGAAGCATAAGCAGTACTATAAAATTTAGATGGAGC[A/G]GGTGCATCAAGTTGAAGCTCTCCATCGTAATTGTAGTAAGGTTGGTTGCTACTAATCAAACTCATGCTTGCTTATCGACTTGAGTATACT
71364 T G ATCAAGTCAGGAAAAGGGAGTTATTGCTTTCCTCGTAGACTCCACGTTAGAGTCGGTCTCCGTTCGTATGTAGTAACCACAGTTGAAAATCTCGCAGAGC[T/G]AGAAGATGCCTGAATGGCAACAACACAAGAAACGAAAGGCTTTACCGAAGCGAGTCAGGTCGAAGAGCTTTGAGGAGAAGAGGC
71384 T C ATGGTAGCTTCTGCGGATCAAATACCAAGGATTACGCAATGGTAAACCTAAAGTCTGTACTATTTGCGTTTGCCCTTAACAACATGATGCGAATGATAGC[T/C]GGTAAGCTGTATGGAGCTGGAACCAGCCCTGAATCCCACAAATTTCAAGAATCCGTGGAACAGTATTTTGCAAATGTTGGGGCATCT
71408 A G GAAGCCAAGCATTCATTTGCAAAACATGGAGTCAAAGTTAGTAACGTTGAAATTGATCTTCCAGCCATGTTGGCACAAAA[A/G]GACAAAGCTGTGTCTGGTCCTTACTCGTGGTATTGAAGGGTTGTTTAAAAAGAATAAGGTCACTTATGTAAAAGGCTATGGGAAGTTCATTTCTCCATCA
71408 TC T GAAGCCAAGCATTCATTTGCAAAACATGGAGTCAAAGTTAGTAACGTTGAAATTGATCTTCCAGCCATGTTGGCACAAAAAGACAAAGCTGTGTCTGG[TC/T]CCTTACTCGTGGTATTGAAGGGTTGTTTAAAAAGAATAAGGTCACTTATGTAAAAGGCTATGGGAAGTTCATTTCTCCATCAGAAATT
71408 T C TCCAGCCATGTTGGCACAAAAAGACAAAGCTGTGTCTGGTCCTTACTCGTGGTATTGAAGGGTTGTTTAAAAAGAATAAGGTCACTTATGTAAAAGGCTA[T/C]GGGAAGTTCATTTCTCCATCAGAAATTTCCGTTGACACACTTGAAGGTGGTAATACAGTAGTCAAAGGAAAGAATGTCATTATTGCT
71414 C T TCCACCAGCAACTCTCCCGCATATCCCGGGTACGCCCCCTTCCCGTACACTCCCGTGCACGCCGATGACGCCTCCAA[C/T]GGTGCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGTAACCGTGCCGGCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCA
71414 T A TCCACCAGCAACTCTCCCGCATATCCCGGGTACGCCCCCTTCCCGTACACTCCCGTGCACGCCGATGACGCCTCCAACGG[T/A]GCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGTAACCGTGCCGGCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCACGT
71414 G A CATATCCCGGGTACGCCCCCTTCCCGTACACTCCCGTGCACGCCGATGACGCCTCCAACGGTGCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGG[G/A]TTGGTAACCGTGCCGGCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCACGTCTCCGTTGGGCGCAATCAACGGTGCC
71414 A G CCGGGTACGCCCCCTTCCCGTACACTCCCGTGCACGCCGATGACGCCTCCAACGGTGCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGT[A/G]ACCGTGCCGGCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCACGTCTCCGTTGGGCGCAATCAACGGTGCCTCCTGC
71414 G A CCCCCTTCCCGTACACTCCCGTGCACGCCGATGACGCCTCCAACGGTGCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGTAACCGTGCC[G/A]GCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCACGTCTCCGTTGGGCGCAATCAACGGTGCCTCCTGCGGGCCGTAA
71414 C G CACTCCCGTGCACGCCGATGACGCCTCCAACGGTGCCTCCTTCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGTAACCGTGCCGGCCAACATGCTC[C/G]CCAGGTTTATCACCATCCCGTCCACTCCCACGTCTCCGTTGGGCGCAATCAACGGTGCCTCCTGCGGGCCGTAAATGGGCTGGTGG
71414 G C TCGGGCCCTGAAAGAACCCGTTTCCAAATGGGTTGGTAACCGTGCCGGCCAACATGCTCCCCAGGTTTATCACCATCCCGTCCACTCCCACGTCTCCGTT[G/C]GGCGCAATCAACGGTGCCTCCTGCGGGCCGTAAATGGGCTGGTGGAAAGGCCACGCGCACTGGCCCGGACACTGCGTCTCAGAGT
71442 T C AACCAAAATTAATTAATTATAGTAGTGTCTATTAAAATAAAAAGACATGTACATTCGTCAAAAGACATGTCTATGTCAAAAGTCATGTCCATTCAT[T/C]AAGAGTCATATCCGTTCATCAAGTGTCATGTCCGTTCAGTGAAGTGTCATGTTTGTTCGGTGAAAAGTCATGTTTATTTAATGTTGTGTCTATT
71442 G C GTCATATCCGTTCATCAAGTGTCATGTCCGTTCAGTGAAGTGTCATGTTTGTTCGGTGAAAAGTCATGTTTATTTAATGTTGTGTCTATTGAAATGGTTT[G/C]TAAACCACTATATATATGTGGTCATTTTAGTGAATGAAGTAAGGGAAAAAGCAAGAAATAAAATAGTTCTTCCGCCTACAAAAAAAAAA
71492 T C ACTGCATCTTCTGATGCTACTTGAAGGTTGTCGCTGCTAAGTATTGCTTCTATTGCTGCAAGAGGAAGGCTCATCACTTCATCTTGAAAC[T/C]TGGTTATGTCGCGATATTTATTGGCAAGAAAGAGTCTAGCTGCATCGGTCAATGGCTGTACCGCAGAAGCCATTGAGACGCTACAGGGGAGATCCAA
71500 A C GCATCTCCTTCTTCCTCCAATCAGTGGTCCTGTTCTGCCTGCACTTTCTCAAACCCTAATTCCAACACTCTCTGCGCTATTTGTGGCTGCAGGAACAGAT[A/C]TTCCGATACTTCTTCTTCTTTGCATGTTGATTTCGTGGATTTGGAACCCGATGAGTTATCGGATCCTAAGATTGGTTCCACCTTCCTTCCAC
71522 C T ACATGGCATGCTGCCTCATGTACAGAGGAGATGTTGTACCCAAAGACGTGAACGCTGCTGTTGCTACTATAAAGACGAAGAGGACGATCCAGTTTGTGGA[C/T]TGGTGTCCTACGGGGTTCAAGTGCGGTATTAACTACCAGCCTCCAACTGTGGTGCCTGGGGGCGATTTGGCGAAGGTGCAGAGG
71522 T C CATGCTGCCTCATGTACAGAGGAGATGTTGTACCCAAAGACGTGAACGCTGCTGTTGCTACTATAAAGACGAAGAGGACGATCCAGTTTGTGGACTGGTG[T/C]CCTACGGGGTTCAAGTGCGGTATTAACTACCAGCCTCCAACTGTGGTGCCTGGGGGCGATTTGGCGAAGGTGCAGAGGGCTGTTT
71544 A G AAAGCTGAGCAGCATGTTTCTCGATTGCCTTGGCTGCTTCATGGAGGCCACGCACTAGCCCATCGTGAGCCAAAGACTTCTTAAGCACCATTTGTAATGC[A/G]GTCATAGTATCCATGGGTTCTCCAAGAACTGGAGCTGGTGTTTCAATTGCCACCTCATCTGCCATTATTAATAGGTTCTGGAAGGAA
71560 C T TCATTACAATTCCAAACGAGATGTTTTATTATTACACTTCATATTAACCATACAACGTCACCCGATCGATAGGCCAA[C/T]ACACACAATACAACGGTACATTCATACCCTCCTGTAGTGAGAGATCTGAGCATTTTCAATCCCCAGCTTAAAATTGCTGTTCCTACGCGACTTGAAGTAA
71560 T C TCATTACAATTCCAAACGAGATGTTTTATTATTACACTTCATATTAACCATACAACGTCACCCGATCGATAGGCCAACACACACAA[T/C]ACAACGGTACATTCATACCCTCCTGTAGTGAGAGATCTGAGCATTTTCAATCCCCAGCTTAAAATTGCTGTTCCTACGCGACTTGAAGTAACGCCCAAAC
71560 G A ATGTTTTATTATTACACTTCATATTAACCATACAACGTCACCCGATCGATAGGCCAACACACACAATACAACGGTACATTCATACCCTCCTGTAGTGAGA[G/A]ATCTGAGCATTTTCAATCCCCAGCTTAAAATTGCTGTTCCTACGCGACTTGAAGTAACGCCCAAACACAAATCCATTGTACTTCGGTGGA
71560 C T CCCTCCTGTAGTGAGAGATCTGAGCATTTTCAATCCCCAGCTTAAAATTGCTGTTCCTACGCGACTTGAAGTAACGCCCAAACACAAATCCATTGTACTT[C/T]GGTGGATCATCTTCGCTGACCAACTCATCCAGTGGCTTTATCTCCGTGTAATGCGCCGGGTACAGAAAGAACGGTATCGAATACCTCG
71570 G GA GTCACAATAAGCATTCATCAACTTCTTTAGCTGAGTGCTTCGCTTGATTCTGAAGAACACCTCATTCCCATCCTGACCCTTGACCTTGAGATTGATGTGT[G/GA]CCCCCCCATCTGCTGGCTTCTTATCCTCATCGTTTCCAGGTGCAGACATCCTCTAATTTGTAGTCCTAATCGAAATAATTTGTATCCGAA
71600 A C GTTGGCCTACTGGATCATATCGCTCTATCGTTCCTCAGATCTCTTTTAAATTCCTCAAATCAAAATCCCTAATTTCGTTCTCCATGGC[A/C]CGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCG
71600 C A GTTGGCCTACTGGATCATATCGCTCTATCGTTCCTCAGATCTCTTTTAAATTCCTCAAATCAAAATCCCTAATTTCGTTCTCCATGGCACGTAC[C/A]AAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCG
71600 A C GGCCTACTGGATCATATCGCTCTATCGTTCCTCAGATCTCTTTTAAATTCCTCAAATCAAAATCCCTAATTTCGTTCTCCATGGCACGTACCAAGCAAAC[A/C]GCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCA
71600 A G GATCATATCGCTCTATCGTTCCTCAGATCTCTTTTAAATTCCTCAAATCAAAATCCCTAATTTCGTTCTCCATGGCACGTACCAAGCAAACAGCTCGCAA[A/G]TCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACCCC
71600 T C ATCGCTCTATCGTTCCTCAGATCTCTTTTAAATTCCTCAAATCAAAATCCCTAATTTCGTTCTCCATGGCACGTACCAAGCAAACAGCTCGCAAATCAAC[T/C]GGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACCCCACCGAT
71600 T A AATCAAAATCCCTAATTTCGTTCTCCATGGCACGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGC[T/A]GCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAA
71600 A T CAAAATCCCTAATTTCGTTCTCCATGGCACGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGC[A/T]CGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATA
71600 G A CGTTCTCCATGGCACGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCC[G/A]GCAACCGGTGGCGTCAAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCG
71600 A C TCTCCATGGCACGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGC[A/C]ACCGGTGGCGTCAAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGC
71600 T C TGGCACGTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGG[T/C]GGCGTCAAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGCTTTTGA
71600 C T GTACCAAGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGT[C/T]AAGAAACCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGCTTTTGATAAGAA
71600 A G AGCAAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAA[A/G]CCCCACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGCTTTTGATAAGAAAGCTTC
71600 C G AAACAGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACC[C/G]CACCGATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGCTTTTGATAAGAAAGCTTCCGT
71600 C A AGCTCGCAAATCAACTGGAGGCAAAGCTCCAAGAAAGCAACTTGCTACCAAAGCTGCACGCAAGTCTGCTCCGGCAACCGGTGGCGTCAAGAAACCCCAC[C/A]GATTCAGGCCAGGGACCGTCGCATTGCGTGAAATTCGTAAATATCAGAAAAGCACCGAGCTTTTGATAAGAAAGCTTCCGTTTCA
71602 A G CATCGAACAAAAATCATCAACGTTTTGCTCGTCAAAAGCCTCATCTCCCTGTGCCCTCGAGTTCAAGCTCGAGTTCGTCTCCCAGTTTGCGTCTGTAGCT[A/G]CGCTCGCACCATCTTCAGTAAAGCATCGAACCAAAAAGTCATCGAAACCCACACAATCATCATACCAGCTGCGGAATT
71624 T C TTAGATCATCAGAGCTGGGTAAATGGTAACGGGAAGAGGAGTGCTGACGGTTTCAGGGGGTTGGATTTGTTTTTAG[T/C]AAGCAATTCGTTGGGGTTTCGTAGTTTTCCTTTTTTGTATTCGGGTGTTTTTCCTTTTTTGGGTTTCGTTTGTACTTGGCTAATTTGCTTTTGTTGAAAC
71624 GT G GCTGGGTAAATGGTAACGGGAAGAGGAGTGCTGACGGTTTCAGGGGGTTGGATTTGTTTTTAGTAAGCAATTCGTTGGGGTTTCGTAGTTTTCCTTTTTT[GT/G]TATTCGGGTGTTTTTCCTTTTTTGGGTTTCGTTTGTACTTGGCTAATTTGCTTTTGTTGAAACACATAGAGGAGCTCAGCTAACTGTA
71624 G A AAATGGTAACGGGAAGAGGAGTGCTGACGGTTTCAGGGGGTTGGATTTGTTTTTAGTAAGCAATTCGTTGGGGTTTCGTAGTTTTCCTTTTTTGTATTCG[G/A]GTGTTTTTCCTTTTTTGGGTTTCGTTTGTACTTGGCTAATTTGCTTTTGTTGAAACACATAGAGGAGCTCAGCTAACTGTAATTATCGT
71624 G GT TGGTAACGGGAAGAGGAGTGCTGACGGTTTCAGGGGGTTGGATTTGTTTTTAGTAAGCAATTCGTTGGGGTTTCGTAGTTTTCCTTTTTTGTATTCGGGT[G/GT]TTTTTCCTTTTTTGGGTTTCGTTTGTACTTGGCTAATTTGCTTTTGTTGAAACACATAGAGGAGCTCAGCTAACTGTAATTATCGTGT
71624 A G GCAATTCGTTGGGGTTTCGTAGTTTTCCTTTTTTGTATTCGGGTGTTTTTCCTTTTTTGGGTTTCGTTTGTACTTGGCTAATTTGCTTTTGTTGAAACAC[A/G]TAGAGGAGCTCAGCTAACTGTAATTATCGTGTTTGTTTATGATGGAACTGTTAACACGTGATCCATTGGTTTGTTATTATAATGGAAGAAA
71630 T G ATTAACAGATTACAAAGCTTAACCTAAACAACAAACATCATCATATAATAAAACAAATAAAGCACCCTCACAAAGTACAAACAAGTAGATATAAAAATAG[T/G]AAATACAACATGTTATAATTAATTAAGGATTGACGACCGGAACCTTTGGAATGGCCGGAATGCCAGGCACCGTCGGGATTATTTCTG
71630 C T ATAAAGCACCCTCACAAAGTACAAACAAGTAGATATAAAAATAGTAAATACAACATGTTATAATTAATTAAGGATTGACGACCGGAACCTTTGGAATGGC[C/T]GGAATGCCAGGCACCGTCGGGATTATTTCTGGCACGGGAAGTTTGGGCAAAGGCAGTGCGGGTACAGGAAGGGTAGGAACAGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
71644 G C GACGACGGCGCAGGGTGCTTGTGAGCATGTTGAGGAAGGGGCTGGCTGGCAATGGAGGTT[G/C]GACTTCGTTGGTTTGTTGTAGAGGCTCGCATTCTTCAACGAAGGTGTCATTGCAGTTGGGGCATGTCACTTCGAATTCAATGATTGGATTTATTTGCTGG
71644 C G GACGACGGCGCAGGGTGCTTGTGAGCATGTTGAGGAAGGGGCTGGCTGGCAATGGAGGTTGGACTT[C/G]GTTGGTTTGTTGTAGAGGCTCGCATTCTTCAACGAAGGTGTCATTGCAGTTGGGGCATGTCACTTCGAATTCAATGATTGGATTTATTTGCTGGTTGCAT
71644 T C GCTTGTGAGCATGTTGAGGAAGGGGCTGGCTGGCAATGGAGGTTGGACTTCGTTGGTTTGTTGTAGAGGCTCGCATTCTTCAACGAAGGTGTCATTGCAG[T/C]TGGGGCATGTCACTTCGAATTCAATGATTGGATTTATTTGCTGGTTGCATTTGTGGCACCAGTATCTGGAGTTTGTAGACGCGTCC
71652 T A GCGCAGGGCCACCTCAGATGAAAACAAGGCCTTTTGCCAGTTCCATAGCTTTTTCATGACCAAAAAACTTC[T/A]CCACAATGGCAAGTGCAAATTCCATACTGGTTCCCGGCCCTCTGCTTGTGATCACATTTCCATCCACTACTACTCTGTTTTCACATTCACTTTGATCTGA
71652 C G CCAGTTCCATAGCTTTTTCATGACCAAAAAACTTCTCCACAATGGCAAGTGCAAATTCCATACTGGTTCCCGGCCCTCTGCTTGTGATCACATTTCCATC[C/G]ACTACTACTCTGTTTTCACATTCACTTTGATCTGAAAGTTTGTTGCACAATGCTGGGTATGCTGTTGCCTTCTTTCCTCTGAGTAAGCCAT
71668 C T AAAATCAAATCCCTACATTTTACACAAAAGGATTTCAAAAAAGTTTTCTTTCTTCCTTGTCATCATACAGCAAACTTGCTTATGCTTCAGTCTTCAATTT[C/T]CAAAGCCAGATCAAGACGTGTCTTTGTTATTCCCCACTGGACAATTGAACACCGACCTCCTCCTCCTTTTCTCATTAGCCTCACCGGTTGCT
71674 G C AACTCGAATGGGAGTGATGGAGATACTTCTCGAAGAAGATCGGAGAGAGAACGCAAGGCGACGGACAGATGAAAGGCAAGGAGAAG[G/C]CAAGTGTTGCGATCTGTTCACCGCCATTTTCGATGAGGTTGAAACTATCGAAGCGGCTATCGCCATTGAAGTGGAGTAAGATAATCGCTCAGCCATT
71674 A G GAAAGGCAAGGAGAAGGCAAGTGTTGCGATCTGTTCACCGCCATTTTCGATGAGGTTGAAACTATCGAAGCGGCTATCGCCATTGAAGTGGAGTAAGATA[A/G]TCGCTCAGCCATTGGAGATGGAGAAAGAGCAGTGTTGTGCTTCGTTTTTGTTTCTTCCAAATTATAGTTTTAGGTAGGTCAAAAGA
71694 G A AAAATACCACTTCCAGTTATCTCCCTCAGCTTATATCCTGAACAAGGTTTAGCAGCGCTTTT[G/A]AGCACATTTTCAGCTTCTTCCTCGCTCATCTGTCCCCCAAACATCACCGGACTTATTCCACTCGCTGGTTTGTTGCTTCGCCTTGGCACAGAAGCAGAAT
71694 C T AAGGTTTAGCAGCGCTTTTGAGCACATTTTCAGCTTCTTCCTCGCTCATCTGTCCCCCAAACATCACCGGACTTATTCCACTCGCTGGTTTGTTGCTTCG[C/T]CTTGGCACAGAAGCAGAATCTGCCGCGGCGGAGGAAGGAGGAACCTCGGACCACGTCAGAAGGTCGGCGGTAGAGGTATGTGGCTT
71696 A G GGGGGCCACGGGCCACCATGTCACGTAGGCTCGGCGGCACCTGTTGGTTCGCACCTTCCAGGATTTTGACCAGATCTGCTGCGTGCTTCCAGTCTTGGTC[A/G]GATATGAATGTGTATGCTATTCCCGTCGCTCCTGCCCTGCCTGTTCTCCCTATTCGGTGCACGTAGTCTTCTACCCCATTTGGAAAAT
71702 C T AAAAATAATTCGTAGCTCCTCCTTCACATTCTCTCTCTGCAACTTTCTCATCCAGCTCGTCTCTC[C/T]ACGATTTGAGAGATCAACGATCGATCGACCGACCGACTTCAACCTATGTTGATGACGCGATTGCAACGCGTCAAATCTTCTAGCTGCGACGGTGAAATGG
71710 A G AGCGCCCCACCTACACCAACCTCAACCGCCTTGTCTCTCAAGTCATCTCCTCCTTAACTGCTTCTTTACGGTTTGATGGAGCGTTGAACGTGGATGTCAC[A/G]GAGTTCCAAACCAACTTAGTCCCATACCCCAGGATCCACTTCATGCTGTCTTCGTATGCTCCAGTCATATCTGCCGAGAAGGCCTACCA
71710 C T TACGGTTTGATGGAGCGTTGAACGTGGATGTCACAGAGTTCCAAACCAACTTAGTCCCATACCCCAGGATCCACTTCATGCTGTCTTCGTATGCTCCAGT[C/T]ATATCTGCCGAGAAGGCCTACCATGAACAGCTCTCAGTCGCTGAAATCACAAACTCGGCCTTTGAACCAGCGTCCATGATGGCGAAG
71754 A C TTTTTTCAACCCGATTGCTCTTCCACACTTAGTCGCTATAACTACCCTGTCTTTTCCAGTAGCCTTCCAGTATCCACA[A/C]TCGGTAGAGCGATTAGTACGATTGCCATTTGCATACTTTGCTTCTCGTAGTGCAAAGAAGTATCTCTCTTGTTCACATCCACCTGGGAGATCCCAAGGAT
71756 G A CGTAGCCATAATACGTGATGTCGTTTCCGTGGTCTACTTGCTCCTTCTCTATATTCTTTACAACATCTTTTAAAAGTATAAGAGCTCGTTGCTGCGCGTC[G/A]TGAGAACTCCCCTCGCTGTTCAATGCCATGTAATGATGTGCTACTGCGTGTTGTAACTTGTGATCTCTCACAAACGCCCACCCCAACCGA
71784 A G TTCTTGCAAGAAGAAAGTTTTTGGAAAAATTTGGATGCGGATTTGCATCACTGGAGTAGGGCATTGCGTCCTGTACAGTGGTATCCAGGGCATATTGCTA[A/G]AACAGAGAAAGAACTGAAAAATCAGCTTAAGTTGATGGATGTTGTTATAGAAGTTCGTGATGCTAGGATTCCCTTGGCTACAGGCC
71792 T C CTGTTGGCCTACTGGGGAACACAATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAAT[T/C]TCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAAC
71792 C A CTGTTGGCCTACTGGGGAACACAATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAA[C/A]GACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGG
71792 GA G CTGTTGGCCTACTGGGGAACACAATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAAC[GA/G]ACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCG
71792 A G TTGGCCTACTGGGGAACACAATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAG[A/G]AAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAA
71792 GAC G ACTGGGGAACACAATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCC[GAC/G]ACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAA
71792 GA G ATCCAGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAA[GA/G]ACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGAC
71792 TC T AGCCTTTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACC[TC/T]CGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAG
71792 GC G TTCCCAAATTGTCCTAGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCC[GC/G]CCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCT
71792 AC A AGTCGATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGA[AC/A]CGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAA
71792 G GA ATCCCTAATTTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAG[G/GA]AAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGT
71792 CA C TTCAAAACCCTAAATTTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAA[CA/C]AAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCG
71792 C A TTCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAA[C/A]TACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGA
71792 T C TCGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAAC[T/C]ACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGAA
71792 A T CGTCATGGCCCCCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACT[A/T]CCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGAAG
71792 AC A CCAACGACTGAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTA[AC/A]CGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGAAGAGGAAGACG
71792 AC A GAAAGAAAACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCG[AC/A]CGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGAAGAGGAAGACGAAGTCTGTT
71792 AC A ACCCGACCTGAGAAGAAGACCTCGCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCG[AC/A]CGAAGAAGCTTCCTGCCAAACGAAATCGTCTGCATCCGCCGACAAGAAGAAGAAGAGGAAGACGAAGTCTGTTGAGACTTAC
71792 A G GCCGCCAGAGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACG[A/G]AATCGTCTGCATCCGCCGACAAGAAGAAGAAGAGGAAGACGAAGTCTGTTGAGACTTACAAGATCTACAT
71792 T C AGAAGCCCGAACGAGGAAAGAAAACAAACCGCTGAGAAACTACCAGCCGGTAACGAAGCCGACGAGCCGACGAAGAAGCTTCCTGCCAAACGAAATCGTC[T/C]GCATCCGCCGACAAGAAGAAGAAGAGGAAGACGAAGTCTGTTGAGACTTACAAGATCTACAT
71796 C T GGTTTAGGAAGAGTGAGTATAAGAAGTTTGATGATGTGATTGTGAGTGCGGATGAGATAGCGGGTGTTGTAGGGAGGGTGACGGGGGGTGGAGAGAAGTA[C/T]GAGGAGATGAAGAGGAAGGCGAAGGATTACGGGGAGAAGGCGAAGAAGGCGGTGGAGGAAGGTGGGAGTAGTTATAACG
71796 T C TTGATGATGTGATTGTGAGTGCGGATGAGATAGCGGGTGTTGTAGGGAGGGTGACGGGGGGTGGAGAGAAGTACGAGGAGATGAAGAGGAAGGCGAAGGA[T/C]TACGGGGAGAAGGCGAAGAAGGCGGTGGAGGAAGGTGGGAGTAGTTATAACGATGTTGTGGCTTTGATTGAAGAATTGA
71826 A AC AAGCCTCTTCCCCTCGAATTTCTCAGACACTATCTCCACCTCAAAGCTGGCACCGCATCCTCCAGATGTATCCACGACTTGGAGATA[A/AC]GAAGGTGCTAAGGATGAAGTAAGGGCGGATTCGACGATTTCCTTAGTAATGCCCATCTCCTTTTGTCGACCGGGAAGTGGAAGTAGGAGGATTATTATA
71864 A G CCATTAGCTCAACTCAAAAATCAATCCATTTAATTATGAAGCTGATTAAGAATGTTACTTCCATATTCTCCAAAAAATCGAAGAAGAAATCCATCTCCAA[A/G]CACGATCCACCCTCTTTCGGGTCATCGACGAGCAGCACTGCAACTTCGTCATCGTCTCCGCGAACAGTGTTGAACCACAAAATCACGAA
71864 T C AAAAATCAATCCATTTAATTATGAAGCTGATTAAGAATGTTACTTCCATATTCTCCAAAAAATCGAAGAAGAAATCCATCTCCAAACACGATCCACCCTC[T/C]TTCGGGTCATCGACGAGCAGCACTGCAACTTCGTCATCGTCTCCGCGAACAGTGTTGAACCACAAAATCACGAAGGAAGAGCTCGAGG
71872 TA T GGAGGGGGATCATTACAGCAGGAAAAGCAAAACGGTTAAATTCTCAGCAAGTTCGCAGCGGCGAAAGATTTAGGCAACTAAAAGAAGAAGAAGGCCGAAA[TA/T]AAAACGAACAGAGCACTTGCAACGGATGAGGTTGAAGTTGAGGTTTTGGCTTCTGATTCCGATGACAATTCAGATGGAGAATC
71876 G A ACCTCCACCACCTTCTTCGGCACGAACCTGAACCTCTCCTTCTCCGTCTGCTCCTCCACC[G/A]CGTCAGCCCCCGTCAGCGCTCTCATCATGTGCTCGCACCCCGGCGGGCCGTGGAACCACCACTCCAGGTCCGGCGCCAGCAGCTCCGCCACCGTCTCCGT
71876 T C GTCAGCGCTCTCATCATGTGCTCGCACCCCGGCGGGCCGTGGAACCACCACTCCAGGTCCGGCGCCAGCAGCTCCGCCACCGTCTCCGTCTCGTTGTTTA[T/C]CAGCCTTGCGTACAACGACTCCACGATGTGGGTCTTGTTTCTTTCCACCTTCCCCTTCGTTACGGCCATCTATTCTTTCTTCTTGAGCG
71884 A G TTTGTTTGCAATATGTATGGTTGGCCGGTTCTGTTACCCAAGAACTCGAAGTCTATTTCATCATGTTCTGAGTTTTGAGAAGATA[A/G]ATAAAATGCAGTAACAGTTCCAGCAGAGTCACCAGGAACCATCTTTATTTGCATACTGAAATGCCCAAACAAATAAGATCCCTTCGACTGAAACCCAGTT
71884 T C TTTGTTTGCAATATGTATGGTTGGCCGGTTCTGTTACCCAAGAACTCGAAGTCTATTTCATCATGTTCTGAGTTTTGAGAAGATAAATAAAA[T/C]GCAGTAACAGTTCCAGCAGAGTCACCAGGAACCATCTTTATTTGCATACTGAAATGCCCAAACAAATAAGATCCCTTCGACTGAAACCCAGTTCCTG
71884 C T TTTGAGAAGATAAATAAAATGCAGTAACAGTTCCAGCAGAGTCACCAGGAACCATCTTTATTTGCATACTGAAATGCCCAAACAAATAAGATCCCTTCGA[C/T]TGAAACCCAGTTCCTGTATATTTATCCAACTTGAGCTGAATCTCATTACCGCCATTAATGTACTGAATATGATCTAAAGCCCAAGTAGG
71884 C T CAGAGTCACCAGGAACCATCTTTATTTGCATACTGAAATGCCCAAACAAATAAGATCCCTTCGACTGAAACCCAGTTCCTGTATATTTATCCAACTTGAG[C/T]TGAATCTCATTACCGCCATTAATGTACTGAATATGATCTAAAGCCCAAGTAGGTACATAGTTCCTTTGGAAGGGCACATCAATTGGTTT
71884 G A CCATCTTTATTTGCATACTGAAATGCCCAAACAAATAAGATCCCTTCGACTGAAACCCAGTTCCTGTATATTTATCCAACTTGAGCTGAATCTCATTACC[G/A]CCATTAATGTACTGAATATGATCTAAAGCCCAAGTAGGTACATAGTTCCTTTGGAAGGGCACATCAATTGGTTTTC
71886 A G AAAACGTACGGTGTTAATAGAGAGGTCAACCGGTGTAGATATGGAGGCGGAGAGCGACGATGAGAATAGTGTAGAGAGCG[A/G]AGAAGATGAGGGTGTGAACAGCGACCGCCTTGCCGTTGGTCTTCATGTTGCCGCATCCGACGTGGCCGTGGGTGCCCGGGAGCTCGAAGAGGAGTCCGGG
71892 C T TCTAAGTTGGAGGCCGGAATCAATAACGACGGGAGGTCCTTGACCCGTAATTGGGGCATATCCGG[C/T]AGAATGATCGGACTCAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGGCT
71892 C A TCTAAGTTGGAGGCCGGAATCAATAACGACGGGAGGTCCTTGACCCGTAATTGGGGCATATCCGGCAGAATGAT[C/A]GGACTCAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGGCTGTATCCAAT
71892 T C GGAGGTCCTTGACCCGTAATTGGGGCATATCCGGCAGAATGATCGGACTCAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAA[T/C]GTATGGTAGTAGATGAGGAAGACATTTGCGGGCTGTATCCAATACTGGGCAGATGAGATGCCACGGGCACGGGCCATTGGAGCCA
71892 A G GCATATCCGGCAGAATGATCGGACTCAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGAC[A/G]TTTGCGGGCTGTATCCAATACTGGGCAGATGAGATGCCACGGGCACGGGCCATTGGAGCCATCCAGGGAAGCATGAACGTGTACA
71892 C T GCAGAATGATCGGACTCAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGG[C/T]TGTATCCAATACTGGGCAGATGAGATGCCACGGGCACGGGCCATTGGAGCCATCCAGGGAAGCATGAACGTGTACAATACACAGT
71892 G A CAGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGGCTGTATCCAATACTGG[G/A]CAGATGAGATGCCACGGGCACGGGCCATTGGAGCCATCCAGGGAAGCATGAACGTGTACAATACACAGTCCACGGGCCTGCCGGT
71892 C T AGTCGGTCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGGCTGTATCCAATACTGGG[C/T]AGATGAGATGCCACGGGCACGGGCCATTGGAGCCATCCAGGGAAGCATGAACGTGTACAATACACAGTCCACGGGCCTGCCGGTG
71892 A G TCTTTGACTTTCTCTTGAATAGTTCTCTGAAAACCGCGAATGAATGTATGGTAGTAGATGAGGAAGACATTTGCGGGCTGTATCCAATACTGGGCAGATG[A/G]GATGCCACGGGCACGGGCCATTGGAGCCATCCAGGGAAGCATGAACGTGTACAATACACAGTCCACGGGCCTGCCGGTGGACTCG
71904 T A TTCGGGTTGAACATTGGACCTGAAGATTAACATGGTGATCATCTTCCCTGATGTCTTCATCATTATAATCATTCTTGAGTAC[T/A]CCAACTTTAACTTATGATAAGCATCATGAAGTGGCTAACAGGCAATTTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCAA
71904 C T GGTTGAACATTGGACCTGAAGATTAACATGGTGATCATCTTCCCTGATGTCTTCATCATTATAATCATTCTTGAGTACTCCAACTTTAACTTATGATAAG[C/T]ATCATGAAGTGGCTAACAGGCAATTTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCAAGTCAGCCCAAA
71904 T G TGGACCTGAAGATTAACATGGTGATCATCTTCCCTGATGTCTTCATCATTATAATCATTCTTGAGTACTCCAACTTTAACTTATGATAAGCATCATGAAG[T/G]GGCTAACAGGCAATTTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCAAGTCAGCCCAAATCTCTTCCAA
71904 T A CCTGAAGATTAACATGGTGATCATCTTCCCTGATGTCTTCATCATTATAATCATTCTTGAGTACTCCAACTTTAACTTATGATAAGCATCATGAAGTGGC[T/A]AACAGGCAATTTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCAAGTCAGCCCAAATCTCTTCCAACCTGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
71904 A T TCCAACTTTAACTTATGATAAGCATCATGAAGTGGCTAACAGGCAATTTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCA[A/T]GTCAGCCCAAATCTCTTCCAACCTGCCGATTCCAGCTCCTGCTCAAGTGGGAGCCTTGAACACTAGGACAACCCAACCAGTTCAGCTG
71904 G A TTTCTTCGAAAGTAAGGTAACAAAATCATGTCCAAATGACTTGAACTGCAGCAAGTCAGCCCAAATCTCTTCCAACCTGCCGATTCCAGCTCCTGCTCAA[G/A]TGGGAGCCTTGAACACTAGGACAACCCAACCAGTTCAGCTGGTCCTGCTCGGGTTGAACATTGAATCTCAT
71910 G A AAAAAGGGCATTGAAGGAGCTACCAAATTCTTGCTCTCAAAGCTAAAGGATCTACAATTCTTTGTTGGTGAGAGCATGCATGATGATGCCACTTTAGT[G/A]TTCGCATACTACAAAGAAGGATCTGCTGACCCAACCTTTTTGTATTTCGCTCATGCACTCAAGGAGGTCAAATGCTAAGCAGCACCAAA
71950 G A TGCAGAGCAACTTCCATGGTCTCGTCATCGATATTCGCAAAGCAAACCCTGAACCAACCTGCTTCCTTACAATG[G/A]AAAGAGCTCCCAGGCGAAACATTGAGCTTCACCTCGTTGATGATCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCA
71950 T C TCCATGGTCTCGTCATCGATATTCGCAAAGCAAACCCTGAACCAACCTGCTTCCTTACAATGGAAAGAGCTCCCAGGCGAAACATTGAGCTTCACCTCGT[T/C]GATGATCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCAAATTCATCCAGCAAAACAGACCCGCATT
71950 C T CCTTACAATGGAAAGAGCTCCCAGGCGAAACATTGAGCTTCACCTCGTTGATGATCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAG[C/T]AAAGTACTCAAATTCATCCAGCAAAACAGACCCGCATTGCTTTCCAAACACTTGATTCCAACTTGCTCCAATCCTGAAGTGAAAACCTTA
71950 C T AAACATTGAGCTTCACCTCGTTGATGATCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCAAATTCATCCAGCAAAA[C/T]AGACCCGCATTGCTTTCCAAACACTTGATTCCAACTTGCTCCAATCCTGAAGTGAAAACCTTATGCCTTTTTGAAAGCCGATCCACACTCT
71950 C G TGAGCTTCACCTCGTTGATGATCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCAAATTCATCCAGCAAAACAGACC[C/G]GCATTGCTTTCCAAACACTTGATTCCAACTTGCTCCAATCCTGAAGTGAAAACCTTATGCCTTTTTGAAAGCCGATCCACACTCTCCTTTAA
71950 G A TCACCTTCCACAGTCTAATCTCCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCAAATTCATCCAGCAAAACAGACCCGCATTGCTTTCCAAACACTT[G/A]ATTCCAACTTGCTCCAATCCTGAAGTGAAAACCTTATGCCTTTTTGAAAGCCGATCCACACTCTCCTTTAAAAAATTCGTTGT
71950 T C CCTCTTCCTCGCTCCCTTCCTTCAGCAAAGTACTCAAATTCATCCAGCAAAACAGACCCGCATTGCTTTCCAAACACTTGATTCCAACTTGCTCCAATCC[T/C]GAAGTGAAAACCTTATGCCTTTTTGAAAGCCGATCCACACTCTCCTTTAAAAAATTCGTTGT
71952 T C TTGTGCAAATATATAATCAAAAGCAACTCGCACACATTAAATATTCAAAACAGTTGAACAAAATGCCTACAA[T/C]GCTTAATCATCCATGCTTCAAAGCAACATTTCCAGAGGCAGAACGGTATATTACAGTCGGATCCAAAGGTGTTAAATATAACATGCTGCTCTATCCATGC
71952 G A ACAAAATGCCTACAATGCTTAATCATCCATGCTTCAAAGCAACATTTCCAGAGGCAGAACGGTATATTACAGTCGGATCCAAAGGTGTTAAATATAACAT[G/A]CTGCTCTATCCATGCTGAAACACATTGGTTTATTCTGCTTTAGGAGCAGATTCGTCTTGAGGCTTCATTGCTGGAAAGAGGAGAACTT
71952 T A CTACAATGCTTAATCATCCATGCTTCAAAGCAACATTTCCAGAGGCAGAACGGTATATTACAGTCGGATCCAAAGGTGTTAAATATAACATGCTGCTCTA[T/A]CCATGCTGAAACACATTGGTTTATTCTGCTTTAGGAGCAGATTCGTCTTGAGGCTTCATTGCTGGAAAGAGGAGAACTTCCTTAATATT
71972 CATCT C CATGACAAAAGACTAAGAAAAAACAATATGATCTTCAAATGGCAACTGAAATATGAGGGAAAACGGCACACCCCAAAGCAACAAATATATTCATG[CATCT/C]ATCTATCTGCACATTAAGAATTGAGATGAGTAGCTTCATTCATCCTCATGCTTGGGTGCCTCCTTAACATCATCGACTCCATCATCCTG
71972 A T ATGATCTTCAAATGGCAACTGAAATATGAGGGAAAACGGCACACCCCAAAGCAACAAATATATTCATGCATCTATCTGCACATTAAGAATTGAGATGAGT[A/T]GCTTCATTCATCCTCATGCTTGGGTGCCTCCTTAACATCATCGACTCCATCATCCTGCATATCAGATGTCCATAGGGTGAGGTTGTCC
71972 T C ATCTGCACATTAAGAATTGAGATGAGTAGCTTCATTCATCCTCATGCTTGGGTGCCTCCTTAACATCATCGACTCCATCATCCTGCATATCAGATGTCCA[T/C]AGGGTGAGGTTGTCCCTCAGCAATTGCATGATGAGCGTACTATCCTTGTAAGACTCCTCCCCTAGCGTATCTAACTCAGCAATTGCTTCA
72008 T C CATTTTGCCTTGTTCTCCCCTTCTTTACCCCCAGGGACGATTTCGATGTTTCTCTTAGGCCATTCTTTCAGATGCATGTGAAGCATATCCACATCCATTA[T/C]GCCAATGACTGTCACCAAGTCCTTGGTGGAATCCACATCTACACTGTACACACCTATTATGAGAGCAGGGCAAAACCTCAGGAAGACAG
72012 A T AAAACCACAGACTTGAAGAAATCATGAAGCAACGCCTCACAACCATGCATACATATAGCCAATAAATACAGTAAATCCAAAGGTACGGTACGGTGGAGGC[A/T]CGAAATTAGCATTTGGGGAAGGGAACGCGACAGTAAGTAGCCATCTTCTTTGCATTAGGGGAGTTGAAGTACCCACTAAGGGCCG
72012 T C AATACAGTAAATCCAAAGGTACGGTACGGTGGAGGCACGAAATTAGCATTTGGGGAAGGGAACGCGACAGTAAGTAGCCATCTTCTTTGCATTAGGGGAG[T/C]TGAAGTACCCACTAAGGGCCGGATTGGCAGCATACTGGCAGAAGCATGGTTGCTGCTGCTTCAGGTTCGAGCAGCAAGATGGTG
72012 C T AAATCCAAAGGTACGGTACGGTGGAGGCACGAAATTAGCATTTGGGGAAGGGAACGCGACAGTAAGTAGCCATCTTCTTTGCATTAGGGGAGTTGAAGTA[C/T]CCACTAAGGGCCGGATTGGCAGCATACTGGCAGAAGCATGGTTGCTGCTGCTTCAGGTTCGAGCAGCAAGATGGTGGCGGTGG
72012 C T GTGGAGGCACGAAATTAGCATTTGGGGAAGGGAACGCGACAGTAAGTAGCCATCTTCTTTGCATTAGGGGAGTTGAAGTACCCACTAAGGGCCGGATTGG[C/T]AGCATACTGGCAGAAGCATGGTTGCTGCTGCTTCAGGTTCGAGCAGCAAGATGGTGGCGGTGGCGATCCATTGTT
72070 C T GAACCACCAACAAGCACTATGTCATCCACCTGGCTCTTGTCCATCTTTGCATCCCTTAAGCATTTCTCAACCGG[C/T]TCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTA
72070 A G GAACCACCAACAAGCACTATGTCATCCACCTGGCTCTTGTCCATCTTTGCATCCCTTAAGCATTTCTCAACCGGCTCCATGCATTTCCT[A/G]AACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAG
72070 A G GCACTATGTCATCCACCTGGCTCTTGTCCATCTTTGCATCCCTTAAGCATTTCTCAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTC[A/G]AATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGT
72070 T C CTATGTCATCCACCTGGCTCTTGTCCATCTTTGCATCCCTTAAGCATTTCTCAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAA[T/C]CTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTC
72070 C T TGTCATCCACCTGGCTCTTGTCCATCTTTGCATCCCTTAAGCATTTCTCAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAATCT[C/T]GCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTC
72070 G A CCATCTTTGCATCCCTTAAGCATTTCTCAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTA[G/A]AAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCT
72070 G A TTAAGCATTTCTCAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTC[G/A]TACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCTTCTCAAAGC
72070 A G CAACCGGCTCCATGCATTTCCTAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATC[A/G]ATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCTTCTCAAAGCTCTTGGGTTTCC
72070 A G TCCTAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTG[A/G]GCAGTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCTTCTCAAAGCTCTTGGGTTTCCACTAATGTCCTTTTTGTG
72070 A G TAAACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGC[A/G]GTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCTTCTCAAAGCTCTTGGGTTTCCACTAATGTCCTTTTTGTGCTT
72070 T G ACAAGTCCATGTTCAGCTCCTCAAATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGT[T/G]GAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCTTCTCAAAGCTCTTGGGTTTCCACTAATGTCCTTTTTGTGCTTCCTT
72070 T A AATCTCGCTCGAGTGATGGTGGAGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTCGCCC[T/A]CTCACAAGCGGTTCTTAACCTTCTCAAAGCTCTTGGGTTTCCACTAATGTCCTTTTTGTGCTTCCTTTTGAACTCTTGCACGAAATGGT
72070 T C AGTAGAAGTCAATCCCTTCGTACAAGGAATCAATCTCTATGGTTGTCTGAGCAGTTGAAGACAGTGTCCTCTTCGCCCTCTCACAAGCGGTTCTTAACCT[T/C]CTCAAAGCTCTTGGGTTTCCACTAATGTCCTTTTTGTGCTTCCTTTTGAACTCTTGCACGAAATGGT
72078 AT A CGTTTATGAGAAATCCTAATTAGTGATGTTGTATTGTCATGTATCATTTAGCTCTTTAGGGATTTTGAGCGTGATTATGTTTCCTTTATGAGTGGTTACT[AT/A]TTTTTGTTTGGAAATGTAAGGTTTGTAGTTTGCTGAAGAGTTGACACTTGATTCTATTTATGCTTCATGAAAGACAAAAAAAAAAAGGC
72080 CA C CAAACCACGTCCAAACCATGCACTGCTATGTGCCCTGTGAACCGAATATAGATATCCCAAGTATAATTCAAGTACTTAACAGTGGTTACCAAGCAATAAG[CA/C]AAACATAAGATCTCAATTAAAGCTGAGTTTTTGCTACAAACACCATGGAATCAAAATGAAGGCACATTAAATATCCATAGGGGCAG
72080 A C AACCGAATATAGATATCCCAAGTATAATTCAAGTACTTAACAGTGGTTACCAAGCAATAAGCAAACATAAGATCTCAATTAAAGCTGAGTTTTTGCTACA[A/C]ACACCATGGAATCAAAATGAAGGCACATTAAATATCCATAGGGGCAGCCTCACCCTCCTGTGCTCCACCTTGTCCTTCATCGGCTGGC
72128 A G GATGCATCAAGCACAGGTTCAGATTCAACTGCAAATTTTGAAGAGGATCCTTCCTCGCTTGTGATTGGTGGTGAATCTTGATTTGTAATTTT[A/G]GTTGAACCTGAATCGGCGGCAGGTGTTTCAGGTGTGTCTTTGTGGTTGAACTTCACTACGATGCATGTGATATTGTCGTCGCTGCCACGAGAGAA
72128 C T GATGCATCAAGCACAGGTTCAGATTCAACTGCAAATTTTGAAGAGGATCCTTCCTCGCTTGTGATTGGTGGTGAATCTTGATTTGTAATTTTAGTTGAA[C/T]CTGAATCGGCGGCAGGTGTTTCAGGTGTGTCTTTGTGGTTGAACTTCACTACGATGCATGTGATATTGTCGTCGCTGCCACGAGAGAAG
72128 A G ATTCAACTGCAAATTTTGAAGAGGATCCTTCCTCGCTTGTGATTGGTGGTGAATCTTGATTTGTAATTTTAGTTGAACCTGAATCGGCGGCAGGTGTTTC[A/G]GGTGTGTCTTTGTGGTTGAACTTCACTACGATGCATGTGATATTGTCGTCGCTGCCACGAGAGAAGGCGGTTTCCGTTAGCAATCGTG
72180 T C GCAAGTTTTTTACAATGCCCACACCATGGAGCGTAAAACTCGACGAGAGCGCCGCGATCTTGACCGACCTCCTTCTCGAAGTTCTCTTCCGTTAGTACAA[T/C]GACGTCATCACCGTCTGCAAGCGAAGTTCCGAAGAGGAGTGCTACACTTAGCGTTTGTGCAACAAACAGCAAAAAGAAGATCTTAGA
72194 A G TGAAGACGAAGTAAAGAACGCCGGCAGCAACGGCGAGGGAGAGAACGAGGAGGAGGAGGAGGGAGACGGACCAGAGGAAGCAGCGGCAGCAGCAGGAGCC[A/G]CGTTTGCGGGAGGCGCGGCGGCTGTAGGTCTCGAACAAGTGCGCGTTCTGAGGAGGTGGGACTCTGTAGATTTGGTCCT
72212 C T ACGCCATGGGCTGCTGAGGCTGACAAAGAAGCGGGCTCACCCCGTACATCTCCATACCGAACATATTGAACATCAAATTCAACCCCTGACTAGGGCCCGC[C/T]TCCGCCCCACAACCCGAAGGCCCCGACACCACATTGGCGTAGCAGTTGCTTAGGTCCGGGCT
72230 T C TTTTTTTTTTTTTTAAGCAAATTAACTTTCCTCTAATTTAAGAACATACCCTACACCGATATATTAATCAAGCTTCAAACTCACAATCT[T/C]TGTGTCATTAAAAACAAACTCAACAATCTAATAAGCACAAATTTAAACTCTGATGGTGCACATAAAGCTATAATAGAAAAAGATAGTAATATGATTCTTA
72230 G A ATGGTGCACATAAAGCTATAATAGAAAAAGATAGTAATATGATTCTTATTTAAGCTAATCGGGCTTAACCACGCTTGAACTTGACACTTCAAAACCACCA[G/A]TCATGAATAGACTGCAAATGCTGAAGACGTATTAAAGCTTATTTGGCAGGAGCAACAGTCGAA
72230 T C TGGTGCACATAAAGCTATAATAGAAAAAGATAGTAATATGATTCTTATTTAAGCTAATCGGGCTTAACCACGCTTGAACTTGACACTTCAAAACCACCAG[T/C]CATGAATAGACTGCAAATGCTGAAGACGTATTAAAGCTTATTTGGCAGGAGCAACAGTCGAA
72296 G A TTATAAGCTATGGCTTCATCTAAACTTCTCTTCACTTCCATTCTATTCCTCGCCATAGCTCTTCATCTCGTTCAGTCTCATCGCCTTCTTCAATCTCAAC[G/A]GGTTGTTTTGACAGGGATGAATAAAGATGAAACAGAGGCAAAAGGGGCAGCATATGTGACAAGTACCAATTGTGGAGGATTATGTGCAG
72296 T C TCTAAACTTCTCTTCACTTCCATTCTATTCCTCGCCATAGCTCTTCATCTCGTTCAGTCTCATCGCCTTCTTCAATCTCAACGGGTTGTTTTGACAGGGA[T/C]GAATAAAGATGAAACAGAGGCAAAAGGGGCAGCATATGTGACAAGTACCAATTGTGGAGGATTATGTGCAGTGAGGTGCAGCAAATCA
72296 T C CATAGCTCTTCATCTCGTTCAGTCTCATCGCCTTCTTCAATCTCAACGGGTTGTTTTGACAGGGATGAATAAAGATGAAACAGAGGCAAAAGGGGCAGCA[T/C]ATGTGACAAGTACCAATTGTGGAGGATTATGTGCAGTGAGGTGCAGCAAATCATCAAGGCCGAACCTGTGCAAGAGGGCGTGTGG
72304 C G TTCTGGTCAATTTGGTTTCCGATGATGTCCGGCACGACGAGTGTGGCATGTAAGTATCTTGCTACTACTGCTGCGGTTATGATTTGAGAAAGATGGTGCT[C/G]GGGACCGATTGTTAAGGAAAACGTTATGTAGGCGTTTGATTGATTTTGCATTGGAGGAGGATGAGAACTCCAACAAGGTTTTGGTG
72348 G A TCTGCCCCGTTGTTTTGTCTTCAGCCGAGACGTTGAGGATGCCATTGGCGTCAATGTCAAAGCACACAGTGATTTGAGGAACTCCTCGGGGTGCAGGTGG[G/A]ATTCCAGAAAGCTCGAACTTCCCAAGCAAGTTATTGTCCTTGGTTCTCGTTCTCTCACCTTCGTACACTTGGATCAAAACCCC
72366 G A TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCT[G/A]CAGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGC
72366 A T TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGC[A/T]GAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTT
72366 C A TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGCAGAAACAC[C/A]CTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCT
72366 G A TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGCAGAAACACCCTTGCA[G/A]GTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGG
72366 G A TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGCAGAAACACCCTTGCAG[G/A]TCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGA
72366 A C TGGACTTTTGAGATGGCAAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGCAGAAACACCCTTGCAGGTCTTGGTGTT[A/C]ACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTT
72366 T C AAGTTGCAACGGTTAGTGCTTTCTTTGGATTTGAAGTGCACTTCGCTGCAGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTT[T/C]TTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATT
72366 A G CTTTGGATTTGAAGTGCACTTCGCTGCAGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAAC[A/G]TCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATTGCAACTTTGGAAATATATGTAG
72366 A T AGTGCACTTCGCTGCAGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAG[A/T]CTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATTGCAACTTTGGAAATATATGTAGACCTCAGGTGTA
72366 G A TGCAGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTG[G/A]CTTGTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATTGCAACTTTGGAAATATATGTAGACCTCAGGTGTAACTTCCTGGAG
72366 T A AGAAACACCCTTGCAGGTCTTGGTGTTAACGAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCT[T/A]GTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATTGCAACTTTGGAAATATATGTAGACCTCAGGTGTAACTTCCTGGAGGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
72366 T A GAAGTGTTTGTGGAAGAATTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTTGTATACG[T/A]CCCACCAATTGCAACTTTGGAAATATATGTAGACCTCAGGTGTAACTTCCTGGAGGAGAACTATGTCAGGAGAGTGCTGCTCAATGAG
72366 T C TTTTTTCACAGGCAGTTTGCTCAACATCATACAGAAGACTTGTTTGGTGGCTTGTTTCTCTTTAACGGAGCATTTGTATACGTCCCACCAATTGCAACTT[T/C]GGAAATATATGTAGACCTCAGGTGTAACTTCCTGGAGGAGAACTATGTCAGGAGAGTGCTGCTCAATGAGATGGTTGACAGCATTCAT
72370 T C GATGGCCAATCAAGTGGGAGTCTGCTACGGAACAGTGGGAAACAACCTGCCAAGCCCACCGGATGCGGTCAGCCTAATAAAATCGACCAACGTCATAAA[T/C]GCAGTCCGTCTGTACTACCCGGACTCGAACATCCTGAACGCCCTCAGCAACACCAACATCAACGTCATCCTCGACCTCCCAAACTCC
72372 T A TGTTGGCCTACTGGAAATCACAACAAAACATACATCAAATACTATATCCCATAGTTTGATATATAGGTAGCTATGG[T/A]AACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAG
72372 T A TGTTGGCCTACTGGAAATCACAACAAAACATACATCAAATACTATATCCCATAGTTTGATATATAGGTAGCTATGGTAACATACAA[T/A]GCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAA
72372 T C ACTATATCCCATAGTTTGATATATAGGTAGCTATGGTAACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAG[T/C]ACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTA
72372 A G CTATATCCCATAGTTTGATATATAGGTAGCTATGGTAACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGT[A/G]CTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAG
72372 A C TAGTTTGATATATAGGTAGCTATGGTAACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAAC[A/C]GACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAGAGCATTTCTG
72372 A C GTTTGATATATAGGTAGCTATGGTAACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAG[A/C]CAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAGAGCATTTCTGG
72372 C A AGGTAGCTATGGTAACATACAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGA[C/A]TGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAGAGCATTTCTGGATGGACCTACT
72372 T A CAATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCT[T/A]TAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAA
72372 T G AATGCCGGCAACAAAATGCCTTTGCTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTT[T/G]AAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCGGACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAAA
72372 T C CTGCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTA[T/C]CGACTGCTCCGGACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAAATGTGAGTGCAACAACTGCTATGAA
72372 G A GCTAACACTGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATC[G/A]ACTGCTCCGGACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAAATGTGAGTGCAACAACTGCTATGAAG
72372 C T TGCTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTC[C/T]GGACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAAATGTGAGTGCAACAACTGCTATGAAGGTCCAACC
72372 G A CTTTGCATTTTCTTAACCAGTACTGCTCAACAGACAGACCTAGACTGGAGCTTAAAGGCAGCTTTAAGGGCAGAAAATGTTGCTCGTATCGACTGCTCCG[G/A]ACATGGTAGAGCATTTCTGGATGGACCTACTTTGTCTGATGGTTCTCCAAAATGTGAGTGCAACAACTGCTATGAAGGTCCAACCTG
72384 A G GAAGGCCGGGTTGGCGCTCCGTGAATGGAAAGCCTTCTTCAACAAGGAATTGCTCTACTGCCATGGATAGCCTAGGAGAAACATGCATACTACTTCTACC[A/G]TGGGACCCACCGCCGCCCAATGAAATCATGACACGTGGGCGAAGGCCCGTGGCAAGGGCCG
72420 TA T TACAAATTAATTAAATGGCATTACAAATGCAAGAAACAACCACAATCAACAAGCAGCTTAAACGAAATGCAAGCAGAACAGTAACAAAATTACAGCAAAT[TA/T]AAACAAAAGCCGAAAGGTGATGGCCATCAAAATATGATGATGAATCAGGCACACTTGAAGCCAGAAGGAACTTTTTTGCCACAAA
72420 G A ACAAGCAGCTTAAACGAAATGCAAGCAGAACAGTAACAAAATTACAGCAAATTAAACAAAAGCCGAAAGGTGATGGCCATCAAAATATGATGATGAATCA[G/A]GCACACTTGAAGCCAGAAGGAACTTTTTTGCCACAAAAGTTGACAAGCAAGCTAAGATCAACAGGAACATTCAGACTAATACCCA
72442 CA C TGGCCTTTTTTTTTTTGAACAAACATAGTGCTTCATTTTACAAAAACTACAAATGTACAATGATCCATTCATACATAAACCAAACAAC[CA/C]AAAAAATAACAGCTTTATCCCAGATGAATATGCACAGATAAAAAGAGTGGAGTGTGGAAACAGCACCATGTATACAGAAGTCCGTATATTGACAGCAGA
72448 A G CAGCTTTGTCGCACAAATCTTGAGCATAAGCAGTACAAACACGCTCTTCTATCGACTCGGTAAGCTTTCG[A/G]GCAGTTTGATTAATTTCTCCGTCTTCCATGCATTTTCTTCCTAGCTTTTTATAGCCATGTGAACATGCTAATTCACCATTTGAGCAGTAGCCATTCTCAG
72482 T C AGCTAGGATCATAACCATTGCTGGAAGTAGCTAAAATATAGTAAGCAACAATGTGACCGATGGAGCCCCAAGCGAGCACGTCGACGAGGTTGAAGCCGAC[T/C]GGGTCGTTGGACTTCAGCAGGCCAGCGTACTCCTTGGCCCGTTTATCCCCCGCCTCGAAATGCGTCTTCCCGTTCTGCTCCGGCAC
72498 AAG A AAAGTGTAGATAAGAAAGACTTGGAAGTTAATGGTGGTGACATAGCAAAGTTTATACATCTTGAAAATGATCTTTTACTGGAGGTTTTAGGCCTGATAAA[AAG/A]AGAAAAGCTAGTACCATGCAATTAGCTCCACATCATAAAGTAAAAATGGAAGAACTGAGGAAATCTTCTAATCGAATATGGTTTG
72542 A G GCATTCACTCCAAGGCTTTCCAAGATTGTATCAACAATTATGGGAGCGACATCAGCAAGTGCCAGTTTTACTTGAACATGCTGAACGAGTGCCGTCAAGG[A/G]TCTGGTGCCACCACCGTTCTTTAAAGTTGCTTTCTGCGACTACATATCTCATGGTTATGCGGAACCA
72550 C T CCAAAACGCCCCCGCAAAACTCCCAAAGTCGTCGAGGAACAGAAACAAGACGTGGGGAGTCGATCCGAATC[C/T]GACGAGCCGGTACGAGAAGATTCACTGAGCCCCGGCCATATAAATCAGTTTAGCGATGAAGAGGGGCAAAACGGAAATCCGCTTATAGGTGGGGTCCATA
72550 T C ATATAAATCAGTTTAGCGATGAAGAGGGGCAAAACGGAAATCCGCTTATAGGTGGGGTCCATATGTGGCTGAATAAGCTGGGTTTGGGGAGGTATGCAAA[T/C]GTGTTCGAGATACATGAGGTTGATGACGAGGTCTTGCCTCTTTTGACTTTGGATGATTTGAAAGATATGGGGATCAATGCAGTTG
72582 T A GCTTAGTGTTCACCCCACCCTTTCCAATGATAGCACCCGATAACGAAGAGTCCACACTTATCTTTGCAGTAGCCGACGCACCAAAACTGGCTGGGGCTGG[T/A]GGGCCTCCCATTCTAGGCCCAAACTCAGACGGATTGGTCTGAAAGCCTGATCTGGCACCAAAGCCGG
72588 G A AAGTGCAGCAGCTGCTTCAGGACTTCTTCAATGGGAAGGAACTGTGCAAGAGCATCAACCCTGATGAGGCAGTTGCTTACGGTGCAGCGGTGCAGGCTGC[G/A]ATATTGAGTGGTGAAGGGAATGAGAAAGTGCAGGACTTGCTGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAG
72588 G A TCTTCAATGGGAAGGAACTGTGCAAGAGCATCAACCCTGATGAGGCAGTTGCTTACGGTGCAGCGGTGCAGGCTGCGATATTGAGTGGTGAAGGGAATGA[G/A]AAAGTGCAGGACTTGCTGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAGGTGGTGTTATGACTGTGCTGATTC
72588 A G TCAATGGGAAGGAACTGTGCAAGAGCATCAACCCTGATGAGGCAGTTGCTTACGGTGCAGCGGTGCAGGCTGCGATATTGAGTGGTGAAGGGAATGAGAA[A/G]GTGCAGGACTTGCTGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAGGTGGTGTTATGACTGTGCTGATTCCAA
72588 C T ACTGTGCAAGAGCATCAACCCTGATGAGGCAGTTGCTTACGGTGCAGCGGTGCAGGCTGCGATATTGAGTGGTGAAGGGAATGAGAAAGTGCAGGACTTG[C/T]TGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAGGTGGTGTTATGACTGTGCTGATTCCAAGGAACACCACGAT
72588 T C AGGCTGCGATATTGAGTGGTGAAGGGAATGAGAAAGTGCAGGACTTGCTGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAGGTGGTGT[T/C]ATGACTGTGCTGATTCCAAGGAACACCACGATTCCTACGAAGAAGGAGCAAGTGTTCTCCACTTACGCGGATAACCAGCCTGGAG
72588 A G GTGAAGGGAATGAGAAAGTGCAGGACTTGCTGCTTCTTGATGTGACTCCTTTGTCTCTTGGTTTGGAGACCGCAGGTGGTGTTATGACTGTGCTGATTCC[A/G]AGGAACACCACGATTCCTACGAAGAAGGAGCAAGTGTTCTCCACTTACGCGGATAACCAGCCTGGAGTTCT
72598 AC A GCTCCTGCTCCTGCTCCTGCTCCGGCTCCTTGACCAACTACGGCTTCTGCTTCTGCTTCTACTCCTGCTTCGACTATCATCACTGCTGT[AC/A]CCCCCACGTGCGAACTCTATCCCTATCCGGGCTACGGCTATAGCTCCTATCCCTCCTCCTGTCCATGGACCTTCTCGGAGGCCCATCAAACCGTCCACCA
72598 T C TGCTCCTGCTCCTGCTCCGGCTCCTTGACCAACTACGGCTTCTGCTTCTGCTTCTACTCCTGCTTCGACTATCATCACTGCTGTACCCCCACGTGCGAAC[T/C]CTATCCCTATCCGGGCTACGGCTATAGCTCCTATCCCTCCTCCTGTCCATGGACCTTCTCGGAGGCCCATCAAACCGTCCACCAGGTGGG
72620 A T AATTCATCGGCCTTTTGGAATTATATTGCCCAGGCTTACTTCTCGGGTTTCTTTGCTTGTTTATATTAGCT[A/T]CTTTTGATGAATTTTCTGAACTTTTTATGGGCTCAGCATGAACATCATCGTCGCGTTGTTCATTACTGGTTTCACTTGAGGTGCTCCGTTTTGTAATATT
72620 G A CATCATCGTCGCGTTGTTCATTACTGGTTTCACTTGAGGTGCTCCGTTTTGTAATATTTGCTGGCAGAAACATTCCAGGGAGAATTGCTAGATTTTTCTT[G/A]GGCTCATTTAGACCGCTGTTTTCTTGCTGTTTTCTTAATATGGACTCAAAATTCTCTCTCCTCTTGTTCTCGAAGACGGATTGAAGTAAAT
72620 T C AGGTGCTCCGTTTTGTAATATTTGCTGGCAGAAACATTCCAGGGAGAATTGCTAGATTTTTCTTGGGCTCATTTAGACCGCTGTTTTCTTGCTGTTTTCT[T/C]AATATGGACTCAAAATTCTCTCTCCTCTTGTTCTCGAAGACGGATTGAAGTAAATCCTTC
72640 C A TCCTTGAGCTAGGCGGTCAGCAAGGTCCTGGCCATGGCGGTGGATTTCTTCCCATGCTTCGAAGGAACGCTCCACGGACATCAGAGCGTGTGATGCAGTA[C/A]AGATCGAGCTTTTATGATACTAAAGTTTTTCTTAATCTGTGAAATCTGGGAAAATCCAGGAGCGGTGTGTTTA
72698 C G AAAAACACAGGTTTTGGAAGCCAAATAGTAGTATAAAACAACATTGACTTTCTCAAAAATTATTCCAAAAACACTG[C/G]CTGTGGCGATGAAAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGC
72698 C A AAAAACACAGGTTTTGGAAGCCAAATAGTAGTATAAAACAACATTGACTTTCTCAAAAATTATTCCAAAAACACTGCCTGTGG[C/A]GATGAAAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAAC
72698 G A AAAAACACAGGTTTTGGAAGCCAAATAGTAGTATAAAACAACATTGACTTTCTCAAAAATTATTCCAAAAACACTGCCTGTGGC[G/A]ATGAAAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACT
72698 A T AAAAACACAGGTTTTGGAAGCCAAATAGTAGTATAAAACAACATTGACTTTCTCAAAAATTATTCCAAAAACACTGCCTGTGGCG[A/T]TGAAAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTT
72698 G A TGGAAGCCAAATAGTAGTATAAAACAACATTGACTTTCTCAAAAATTATTCCAAAAACACTGCCTGTGGCGATGAAAACCTAAGAACCAGACGACTTGAC[G/A]ATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTTCTTATCTGTCTCTTGC
72698 A G AAACACTGCCTGTGGCGATGAAAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACG[A/G]GGCCATGCCTGAAACTTCTTATCTGTCTCTTGCCACCATTCCTTCTCACTTACAGTCTTTGGAGTTGTGCCACCAAAGATCTTTCCAT
72698 A G AAACCTAAGAACCAGACGACTTGACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTTCTT[A/G]TCTGTCTCTTGCCACCATTCCTTCTCACTTACAGTCTTTGGAGTTGTGCCACCAAAGATCTTTCCATCCGAAATAGTTAAATCACAAA
72698 T C ACGATGAAGTTTTGGCGACTAATGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTTCTTATCTGTCTCTTGCCACCATTCCT[T/C]CTCACTTACAGTCTTTGGAGTTGTGCCACCAAAGATCTTTCCATCCGAAATAGTTAAATCACAAATATATGCGATTGCAAAGGATCCA
72698 T C TGGGATTCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTTCTTATCTGTCTCTTGCCACCATTCCTTCTCACTTACAGTCTTTGGAGT[T/C]GTGCCACCAAAGATCTTTCCATCCGAAATAGTTAAATCACAAATATATGCGATTGCAAAGGATCCAACAACAGCACC
72698 A G TCATGACAACGGGCGGCCCTGCAACACGAGGCCATGCCTGAAACTTCTTATCTGTCTCTTGCCACCATTCCTTCTCACTTACAGTCTTTGGAGTTGTGCC[A/G]CCAAAGATCTTTCCATCCGAAATAGTTAAATCACAAATATATGCGATTGCAAAGGATCCAACAACAGCACC
72710 T G CTTAAAATTGGGGTGGAGGTTGGTGTGAAGGAGTACTCGTTTGAGCCTGAACAGAGGACAGTGATTGAA[T/G]CAGGAAGTGTAGAGGCTGCAGTGAAGAAGCTGATGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAA
72710 A G CTTAAAATTGGGGTGGAGGTTGGTGTGAAGGAGTACTCGTTTGAGCCTGAACAGAGGACAGTGATTGAATC[A/G]GGAAGTGTAGAGGCTGCAGTGAAGAAGCTGATGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAAGG
72710 G A CTTAAAATTGGGGTGGAGGTTGGTGTGAAGGAGTACTCGTTTGAGCCTGAACAGAGGACAGTGATTGAATCAGGAAGT[G/A]TAGAGGCTGCAGTGAAGAAGCTGATGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGA
72710 A T CTTAAAATTGGGGTGGAGGTTGGTGTGAAGGAGTACTCGTTTGAGCCTGAACAGAGGACAGTGATTGAATCAGGAAGTGTAGAGGCTGC[A/T]GTGAAGAAGCTGATGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGAGG
72710 C T GGGTGGAGGTTGGTGTGAAGGAGTACTCGTTTGAGCCTGAACAGAGGACAGTGATTGAATCAGGAAGTGTAGAGGCTGCAGTGAAGAAGCTGATGGGTGC[C/T]GATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGAGGAAGGTGGGT
72710 A T CCTGAACAGAGGACAGTGATTGAATCAGGAAGTGTAGAGGCTGCAGTGAAGAAGCTGATGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAA[A/T]GGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGAGGAAGGTGGGTCGTCTTATGAGTCGATGAGGGGTTTGATTCGAGAG
72710 G A TGGGTGCCGATGAAGAAGCGGAAGAGAGGAGGAGGCGAGCAAAGGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGAGGAAGGTGGGTCGTCTTATGAGTC[G/A]ATGAGGGGTTTGATTCGAGAGTTGGAGGGTATTCGCGACAGAAGAAAAAATGGATGAAGGTCTTCGATTGGTGCATTTTTG
72710 C T CAAAGGAGCTGGCAGCCATGGCGAGGAAGGCGGTGGAGGAAGGTGGGTCGTCTTATGAGTCGATGAGGGGTTTGATTCGAGAGTTGGAGGGTATTCGCGA[C/T]AGAAGAAAAAATGGATGAAGGTCTTCGATTGGTGCATTTTTGTTTTCGGATTAAGAATATTTGTGTTTT
72716 T A GTTTCTTATATCATAATTCATTCATAAAACAGAAAGAAAATATGGGAGAGAAGGGCGCCGAGTTCAGTTCAAAAGACTATCAAGACCCACCGCCTGCACC[T/A]TTTATAGACATAGAGGAGTTGACAAAGTGGTCGCTTTACAGAGCAGTGATCGCCGAGTTTGTAGCAACTTTGTTGTTTCTTTACATA
72716 A G GTTCAAAAGACTATCAAGACCCACCGCCTGCACCTTTTATAGACATAGAGGAGTTGACAAAGTGGTCGCTTTACAGAGCAGTGATCGCCGAGTTTGTAGC[A/G]ACTTTGTTGTTTCTTTACATAACTGTAGCAACTGTTATCGGGTACAAACATCAGAGCGATACGACGTTGCTTGGCAACACCGATGGC
72722 G A ATCCAAGACCTGTGACACTTCATATCGCCATCTTTCTATAAAAGCATCTTTACTCTTCACAATTTTACTCTTATTTTCTTCAAAACCAATCGCCATGGCA[G/A]CTAAATGCGGAGGCATTCATGAAAAGGAAGGAACTGAGAACAGTGTCGAGATCGAAGAACTCGCTCGATTCGCTGTTGATGAGCACAA
72722 CA C TCGCCATGGCAGCTAAATGCGGAGGCATTCATGAAAAGGAAGGAACTGAGAACAGTGTCGAGATCGAAGAACTCGCTCGATTCGCTGTTGATGAGCACAA[CA/C]AAAAAAGAGAATGCACTACTGGAGTTTGCTCGTGTGGTAAAGGCGAAACAACAAGTGGTGGCTGGCACTATGCATCACTTGAC
72732 A G TCCAGATCTACTTTCCCATGTCCATGGCCTCCAAAATGCCGGCTTTTCTCCTCCTTTCCATCCTTCTCCTGCTCATCGACACCACTCCCAGAATAGCTGG[A/G]GTTCCTGCTTCCCCTCCAGTGACTCAGCCCGGCCACCACGCGCCTGCTCCGGCGCCGGCGCCGATAATGATAAAGAACATAACGGAATG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
72756 T C GCCAAAACCTAGATCTCTCTAACCCCAAATCCCGAAGAAAAAAACCGATCCAGAAAATAGATTTGAGTACATAAACATGCGAGTGATAGGGCAAGAGTAG[T/C]GTAAGTTATTCGACAACAACAAGAAAAGCTATGGAACGAAAGGAGAGATACAGTGGTTAGTGGAAGGTAGAGAAACGAAAGAAG
72756 A T AGAAAAAAACCGATCCAGAAAATAGATTTGAGTACATAAACATGCGAGTGATAGGGCAAGAGTAGTGTAAGTTATTCGACAACAACAAGAAAAGCTATGG[A/T]ACGAAAGGAGAGATACAGTGGTTAGTGGAAGGTAGAGAAACGAAAGAAGAAAGGGAAGATTAGGGAAGGCGATGAGAGGAC
72756 C A AGAAAATAGATTTGAGTACATAAACATGCGAGTGATAGGGCAAGAGTAGTGTAAGTTATTCGACAACAACAAGAAAAGCTATGGAACGAAAGGAGAGATA[C/A]AGTGGTTAGTGGAAGGTAGAGAAACGAAAGAAGAAAGGGAAGATTAGGGAAGGCGATGAGAGGACGATATTTAGTCCCCATT
72756 G GA GCAAGAGTAGTGTAAGTTATTCGACAACAACAAGAAAAGCTATGGAACGAAAGGAGAGATACAGTGGTTAGTGGAAGGTAGAGAAACGAAAGAAGAAAGG[G/GA]AAGATTAGGGAAGGCGATGAGAGGACGATATTTAGTCCCCATTGATGTGAGATGCCCTTATGGCAAAATTTTATCTTTTGAA
72782 G A CGTAGCCCTAACGTGTTCGACAACAAGTACTACGTGGATCTTTTGAACAGGCAGACGTTGTTCACTTCGGATCAGAGCCTGTACTCCGACTCCAGGACTA[G/A]GTCCATTGTGACTAGCTATGCAGTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGT
72782 A G ACAAGTACTACGTGGATCTTTTGAACAGGCAGACGTTGTTCACTTCGGATCAGAGCCTGTACTCCGACTCCAGGACTAGGTCCATTGTGACTAGCTATGC[A/G]GTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAG
72782 CT C TGGATCTTTTGAACAGGCAGACGTTGTTCACTTCGGATCAGAGCCTGTACTCCGACTCCAGGACTAGGTCCATTGTGACTAGCTATGCAGTCAACCAGTC[CT/C]TTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAA
72782 A G AACAGGCAGACGTTGTTCACTTCGGATCAGAGCCTGTACTCCGACTCCAGGACTAGGTCCATTGTGACTAGCTATGCAGTCAACCAGTCCTTGTTTTTCA[A/G]CCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAACTGCTCGGCCC
72782 T C ACGTTGTTCACTTCGGATCAGAGCCTGTACTCCGACTCCAGGACTAGGTCCATTGTGACTAGCTATGCAGTCAACCAGTCCTTGTTTTTCAACCAGTTTG[T/C]GGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAACTGCTCGGCCCGTAATTCGG
72782 T TG TACTCCGACTCCAGGACTAGGTCCATTGTGACTAGCTATGCAGTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAAT[T/TG]GGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAACTGCTCGGCCCGTAATTCGGGTTCAAGTGGTTTTATTGGATCCGTTG
72782 C T GGACTAGGTCCATTGTGACTAGCTATGCAGTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTAC[C/T]GGTCAGAACGGAGAGATTAGAAGGAACTGCTCGGCCCGTAATTCGGGTTCAAGTGGTTTTATTGGATCCGTTGTGGAAGAGTTGGA
72782 A G GCTATGCAGTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAG[A/G]AGGAACTGCTCGGCCCGTAATTCGGGTTCAAGTGGTTTTATTGGATCCGTTGTGGAAGAGTTGGAAGAAAGCATTTTG
72782 C T CAGTCAACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAA[C/T]TGCTCGGCCCGTAATTCGGGTTCAAGTGGTTTTATTGGATCCGTTGTGGAAGAGTTGGAAGAAAGCATTTTG
72782 G T ACCAGTCCTTGTTTTTCAACCAGTTTGTGGCTTCCATGATAAAGATGGGGCAATTGGGGGTCATTACCGGTCAGAACGGAGAGATTAGAAGGAACTGCTC[G/T]GCCCGTAATTCGGGTTCAAGTGGTTTTATTGGATCCGTTGTGGAAGAGTTGGAAGAAAGCATTTTG
72802 A G CTTATGTACATGGCGCCAATGGCGATGGCTGTGCTAGTACCGCTGAGTTTCTACATAGAAGGGAACGTGTTCGCAAAAATGATCGA[A/G]AAGGGAAGCCGAGATCCAAGACTGTTTCTGTATTTGTTCGGGAACGCGACGGTGGCGTACTTGGTTAATCTGACGAACTTTCTAGTGACAAAGCATACCA
72802 T C TGTTTCTGTATTTGTTCGGGAACGCGACGGTGGCGTACTTGGTTAATCTGACGAACTTTCTAGTGACAAAGCATACCAGCGCGTTGACTTTACAGGTGCT[T/C]GGGAATGCTAAGGCTGCTGTGGCGGCTGTGGTGTCAGTATTAATTTTCAGGAATCCGGTGAATGTGATGGGGATTTTAGGGTTTGG
72818 T A AATGTGAAACATGCAACTCCGGCCACAGAGCCGCCGAGCTCCTCCTGTGCGACGCCTGCGATACTGGTCATCACCTCTTTTGCCTTCGGCCCATCTTACC[T/A]CGTGTACCCAAAGGATACTGGTTCTGTCCGTCTTGCTCTATTCTCAAAAAACCCTGACAAAAAAATCAAAGCCGGAAATCAA
72820 C T ACGTTTCTTCATACTCTCATTCTTCATACCCAAACCCTAACCCTAGCTATCCGGCGGCGGAGCCGCACCCTCCCGAGACCTTCAAACCATCTCATTATTA[C/T]GCGAACCCCAACAGCTATCTTGCTAGCGATAATCCCTTTGCGCCGCATGGGGGTTATGCGGCGGCGGGACC
72824 G A AACTAACACACTTCATCAGCAGCTAATACTACAGCATCAGATTAACTCGACAGTAATACAAGTAAATTCTGAGAAGATACTACATATAAAGTCATTTCCA[G/A]GGCATGTTATGCGTGTTAGGCACTGGTTGCAGTCCGCTGTTATTGCCCGTGTTGTCCGTGCTATGGTTCATCGGGCTTTCACCATCACC
72824 G A ACTAACACACTTCATCAGCAGCTAATACTACAGCATCAGATTAACTCGACAGTAATACAAGTAAATTCTGAGAAGATACTACATATAAAGTCATTTCCAG[G/A]GCATGTTATGCGTGTTAGGCACTGGTTGCAGTCCGCTGTTATTGCCCGTGTTGTCCGTGCTATGGTTCATCGGGCTTTCACCATCACCG
72824 G T TACTACAGCATCAGATTAACTCGACAGTAATACAAGTAAATTCTGAGAAGATACTACATATAAAGTCATTTCCAGGGCATGTTATGCGTGTTAGGCACTG[G/T]TTGCAGTCCGCTGTTATTGCCCGTGTTGTCCGTGCTATGGTTCATCGGGCTTTCACCATCACCGCCTCCGCCGCCGCCTGAGGAGGAC
72828 C T CTCCTTTATCCATCAATTTCAGTACAGCGTTTGCCAATGTTTCACTTCTCACTGCCACTTCATCTTCAAGCAGACAAAAATAAGGCTTCTCCACTCCAAC[C/T]GCTACTCCTGTCTCGATCACCTCTACAATTAGCTTCTCATTGAAGAATTGATCCGCAAAATGCGGCCATGTCAACATCGG
72832 T G CTCTGGGTATATTCAGAGACTACAGGAGCAGCAACAGATGCAGCAGCAAGATTGCTTGTTCCCACAGGTCCCAAAGACGCCAACTGGCAAGATGCTGGTC[T/G]ATTTCCGATCTTCTTTTGAGGTTCCTTCAACGCATTCTGTGCGCCTTTTCGAGTCTTGAACAGGATGAAAGCATAACCTTTGGACTTT
72840 C G GATCGTCTCAACAGCTGCTTCCAAGGTCTATTATACAGTCTATCCTTGCAGCTTTATAATAGTAGCAATGGTACTGGCGTACTGCA[C/G]TGATACTACAATGAAATGGCAAGAAAACATTGAAATAGAGGACCTGAAACTATCATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGA
72840 A G GATCGTCTCAACAGCTGCTTCCAAGGTCTATTATACAGTCTATCCTTGCAGCTTTATAATAGTAGCAATGGTACTGGCGTACTGCACTG[A/G]TACTACAATGAAATGGCAAGAAAACATTGAAATAGAGGACCTGAAACTATCATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAG
72840 G A TTTATAATAGTAGCAATGGTACTGGCGTACTGCACTGATACTACAATGAAATGGCAAGAAAACATTGAAATAGAGGACCTGAAACTATCATAGCTGAAGT[G/A]TTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAAACATGAAACCTGTGCCTCCAAATTCAATAATTATCAACTGGGTTAATGG
72840 A T CTACAATGAAATGGCAAGAAAACATTGAAATAGAGGACCTGAAACTATCATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAA[A/T]CATGAAACCTGTGCCTCCAAATTCAATAATTATCAACTGGGTTAATGGTTTCTCTTTTGACGACTGTCAAATTTCTAATATTGTTATTG
72840 C T TACAATGAAATGGCAAGAAAACATTGAAATAGAGGACCTGAAACTATCATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAAA[C/T]ATGAAACCTGTGCCTCCAAATTCAATAATTATCAACTGGGTTAATGGTTTCTCTTTTGACGACTGTCAAATTTCTAATATTGTTATTGT
72840 A G GAAATAGAGGACCTGAAACTATCATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAAACATGAAACCTGTGCCTCCAAATTCA[A/G]TAATTATCAACTGGGTTAATGGTTTCTCTTTTGACGACTGTCAAATTTCTAATATTGTTATTGTATTCCTGTTACCAAAAATGGTTTAAG
72840 T C ATAGCTGAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAAACATGAAACCTGTGCCTCCAAATTCAATAATTATCAACTGGGTTAATGG[T/C]TTCTCTTTTGACGACTGTCAAATTTCTAATATTGTTATTGTATTCCTGTTACCAAAAATGGTTTAAGCAATA
72840 T G GAAGTGTTACATCTGGATTTACATCTTTCAGCTTCCAGGAAGAAAACATGAAACCTGTGCCTCCAAATTCAATAATTATCAACTGGGTTAATGGTTTCTC[T/G]TTTGACGACTGTCAAATTTCTAATATTGTTATTGTATTCCTGTTACCAAAAATGGTTTAAGCAATA
72848 A G GGCCTCTTCTGTGAAGTTGTAGGTTCTGATCTCTTTGAAACCCCTTGTTGCAGATCTCGCAAACGAATCGGTTCGTTGCCATCAGCGTTGTTGGCGATAG[A/G]GCAATCACTTCAGCATCAGGATCTGGCATTCCGGGGAGGTTTCTCTTCTTTTTGATGGTCGGAGGAGGAGGAGGAGGAGGCTGGGT
72858 A C TCGAAGAGCGTCAGCAACAGAGCTTTGAAATCTCAGATCTGCTTTGAAGTTTTGGGCAATTTCACAAACCAATCTCTGAAACGGAGGCTTCCCTATCAAC[A/C]GCTCGGCGCGTCTCTAATACTTGCGGATCTCGCGAAAGGCGACGGTTCCTGACCTGAATCGCTGAGGTTTCTCCACGCCCCCAGGTG
72888 G A CGTGAAGCGGGGGCTGAAAGAGGGTTGCAGTTGCGGTTGCGAGCAGGAGCGGAGACTGGAAGAGAATTGCGGCTGC[G/A]AGCAGGTTGAGTTTGGAAGAAATTGAATCCCGAGAACGATATGTACCGATGTTGAAAAAATGAAGCGATTTTGGAAGAGCGTGAGAATTTTGAGAGTGAG
72890 T C TGGATGCTTTGCAAGGTTATAAATTTGATGAACACGACCGTGATTCTGAAAGATTGAGGATCCAGTTCTCTCATTCTCCTGGACCAAAAAGCGGCTCTGG[T/C]GGTGGCCCTCGCGGAAGACGTTATTAGATATTTCGGTCGAGAGTTCCGTAGGTGACTGAATATTAGGAGAGTACATTGTGAGAGGC
72890 A T TGAACACGACCGTGATTCTGAAAGATTGAGGATCCAGTTCTCTCATTCTCCTGGACCAAAAAGCGGCTCTGGTGGTGGCCCTCGCGGAAGACGTTATTAG[A/T]TATTTCGGTCGAGAGTTCCGTAGGTGACTGAATATTAGGAGAGTACATTGTGAGAGGCAGGGGCGATGTTCCTTATCTTTTATTTCG
72894 T G CCAAAGCGACCCCAACAAAGCTTAACAATAAGCAATACATTTCTTCTTACAATCCATGGTGCAGCCGCCGCCGCC[T/G]CCTCCGCCGCCGTAGTTCTTCCCCTTTCGGCTATACGAACTGAAACACTTGGCAGGACACGTCAGCTTCTTCCCGTAACACGGGCCTCTCACGCTGCACA
72894 G A CCAAAGCGACCCCAACAAAGCTTAACAATAAGCAATACATTTCTTCTTACAATCCATGGTGCAGCCGCCGCCGCCTCCTCCGCCGCC[G/A]TAGTTCTTCCCCTTTCGGCTATACGAACTGAAACACTTGGCAGGACACGTCAGCTTCTTCCCGTAACACGGGCCTCTCACGCTGCACACCGTCGTGGGCC
72894 C T TGGTGCAGCCGCCGCCGCCTCCTCCGCCGCCGTAGTTCTTCCCCTTTCGGCTATACGAACTGAAACACTTGGCAGGACACGTCAGCTTCTTCCCGTAACA[C/T]GGGCCTCTCACGCTGCACACCGTCGTGGGCCTTATGGTCCCGCTGCGGCCATACCCGCCTCCTGGTCCGCCGTAGCCCGATCCGTATC
72894 T G AACACTTGGCAGGACACGTCAGCTTCTTCCCGTAACACGGGCCTCTCACGCTGCACACCGTCGTGGGCCTTATGGTCCCGCTGCGGCCATACCCGCCTCC[T/G]GGTCCGCCGTAGCCCGATCCGTATCCACCGCCGAAGCCCGGTATGGTATAGCCGGTTCCCGGTATGGTGAACCCGGGCTGGCTGTT
72898 T A CTTCTCCAAAATTGTAGATTTCATGAGACATTTTGAAGAAGAGTTCAGGCTGAAGACTTTTAGCTGCTTGCACTTCATCTTGATTTGATGCTCCTGAAGC[T/A]TCTTCACACGAAGTTGATGCTGCAAAATTGCAGAATCCATCTTCCCAAACAAGTATCCAGTTTCTTCTGTTCCCTCTAGTCCTGTCATACA
72904 G A TCTGGAAAATCCTCTTCCCAGTTTTTGTTCAGGAACACGTCTGCAGTGATGGCAGCCTCTAACATGACAAGCATAAAAACAAGCACCATATAACAAGACA[G/A]GCAAGGACCATTAGCGGTTTCTGCAGCAATATGACCAGAGCAAGTTACGAAGCACAAACATACTCCTAAGCCAAGGAAAGTGTACA
72904 A G ACACGTCTGCAGTGATGGCAGCCTCTAACATGACAAGCATAAAAACAAGCACCATATAACAAGACAGGCAAGGACCATTAGCGGTTTCTGCAGCAATATG[A/G]CCAGAGCAAGTTACGAAGCACAAACATACTCCTAAGCCAAGGAAAGTGTACATAAACCATGGCGGAATAGAATCGTCCCAAAAAC
72908 G A CACTCTGGATCCCATTCAAACCCGTCCAGAAAGTTCTAATTTACTCCTCCTTCGAAGCAGTTCGGCTTCCATTCTCCACGATCATTCAACAACTCAAGTC[G/A]TCTCTTTCTTCCGCTCTACTCGATTTCCTTCCTCTTTCTGGAAAGCTTGCATACGTAGCAGACATCCAGGATGTAGAAATCGATCTTTCAG
72918 G A TTTTTTTTAGCTGAGTTTGTTCTTTTAACACCATCAACAACAGCTTTTTGGGAAGGCAACTCAGC[G/A]ATGAAAAGCACATTCTGAGCCCAGCCTGCGTACTTTCCAAATTTGGACACAAAGGCATCTGACACTTGACTATGGAGTTTCGACGTTAGGCTTTTTCCAG
72918 G A TTTTTTTTAGCTGAGTTTGTTCTTTTAACACCATCAACAACAGCTTTTTGGGAAGGCAACTCAGCGATGAAAAGCACATTCTGAGCCCAGCCTGC[G/A]TACTTTCCAAATTTGGACACAAAGGCATCTGACACTTGACTATGGAGTTTCGACGTTAGGCTTTTTCCAGCTAACTCTGGCAATAAATATCGGG
72918 G A CGTACTTTCCAAATTTGGACACAAAGGCATCTGACACTTGACTATGGAGTTTCGACGTTAGGCTTTTTCCAGCTAACTCTGGCAATAAATATCGGGTTGC[G/A]ATCTTCCACACATGCGTATCCACAGGAATGGAATTGTGTTTATCAAGAGAGAAGAGAGCCATGCAAGCGGCAACTTTTGGACCTACT
72918 C A GGCTTTTTCCAGCTAACTCTGGCAATAAATATCGGGTTGCGATCTTCCACACATGCGTATCCACAGGAATGGAATTGTGTTTATCAAGAGAGAAGAGAGC[C/A]ATGCAAGCGGCAACTTTTGGACCTACTCCAGGCAAAGTACACAACGAATCTATTACATCA
72948 T C AACGGACGAAGTGGATATTCTTCCATCACCAATTTCACGGATTCACTGATAATATTCATCAACCTATCATCATCCACACCACAATCCCGGATCTCTTGAA[T/C]TGGTACGTCACCAACATCGGTTAATATGCGAGAGTCTTTTAAATCCTTGCCCTCTTCTGTAGCAGAATTTGTACTACCACACCATATAGC
72962 T C ACCGGGACCAGCGTGTATATGCTGGAAGAGAAGCACCTGTTCTAAGAAAGTTGTTCATAGTCCGAGATAGA[T/C]CTAAGCTCGGAAGCGTCGGATTGGGCGGAGGTAAGACTGTTTTGAGAGTGAGCAACGAAATCGAGAACCATGTCTTAGGAAAAGCGCTGGTGAGCTCGTG
72962 A G ACCGGGACCAGCGTGTATATGCTGGAAGAGAAGCACCTGTTCTAAGAAAGTTGTTCATAGTCCGAGATAGATCT[A/G]AGCTCGGAAGCGTCGGATTGGGCGGAGGTAAGACTGTTTTGAGAGTGAGCAACGAAATCGAGAACCATGTCTTAGGAAAAGCGCTGGTGAGCTCGTGAAT
72976 G A CAAAGCGAGCACCTGGAGGAACCAGATCACCACCAGGAAAGTCAAGCCCTGGTCTACCTCCAGTAGGAAAGAATCTAGGATCATTAGGTCCTACAAGCAT[G/A]CTTCCACCTACTCCCGGTCCCCTATTTGGTAGAACACCGGCACAAGGTCCTGGATAAAGGTCACTACTTCCAGTCGAAGGAATAGG
72990 A G AGTCCATGGCGAGATCAAAGCTGTCATCTTTTCTGTCACTGAACTCAAGGCACCTGTCTCAGACTTGCCACTGCAGTTAACTGAGGTTTTGAAGTCCGCC[A/G]TGGTGGATTTGTCTTCTGATACCTTTATATATGGAGAGAGCCACTTAGCTTTCATGTACTCTAGTTTTCTCCATGGAGGGAAGTGGAG
73008 G A ACCGCGACCTCCGTCTGAAGCAGGATCGGGAGGAATCGGCGAAGCTTGCAGTGGAGAAATCGTTCAACAGTAACGCCTCGTCCTCGTTCTCTTCTCCTGC[G/A]CTTAAATCGGACGACCTTCCTGTGGTGGTGACTACACCGCTTGAGGCGGCGACTGGACCGCAGGTGCCAGCACAGCAGAGCAGCG
73008 T C AACAGTAACGCCTCGTCCTCGTTCTCTTCTCCTGCGCTTAAATCGGACGACCTTCCTGTGGTGGTGACTACACCGCTTGAGGCGGCGACTGGACCGCAGG[T/C]GCCAGCACAGCAGAGCAGCGGTAGGTGCGGCGGATGCAAGAGGAAGGTGGGGATTACCGGATTCAAGTGCAGGTGCGGTCTCGT
73008 G A TCCTCGTTCTCTTCTCCTGCGCTTAAATCGGACGACCTTCCTGTGGTGGTGACTACACCGCTTGAGGCGGCGACTGGACCGCAGGTGCCAGCACAGCAGA[G/A]CAGCGGTAGGTGCGGCGGATGCAAGAGGAAGGTGGGGATTACCGGATTCAAGTGCAGGTGCGGTCTCGTGTTTTGTGGGACCCA
73012 C T TGGATCAGTCTAGAGTCACCCTTGCCGTTTACCGTGAGATGACTCTTTCGCATACTCAGATG[C/T]TGCATCAGCAGTACCGTAGTCATACAGAGATGTTGGAGTCTCAGATCGATGAGTTATCAGAGATGCTTAGGGCTCAGAGGCCGTTTGCACAAGCTGGTCC
73012 G T GCTTAGGGCTCAGAGGCCGTTTGCACAAGCTGGTCCGAGTTGGTCTTCGACTAGAGATTTTGATGAGGCAACTAATCTTGACGATTTGCCGACCCATTAT[G/T]CCGATCAGGACGACGATGCGGACGATGCCGATGATGCTGATGTTGATGATGACGGTGCTGATGATAAGGATGATGTAGACGACGA
73012 C A GCTGGTCCGAGTTGGTCTTCGACTAGAGATTTTGATGAGGCAACTAATCTTGACGATTTGCCGACCCATTATGCCGATCAGGACGACGATGCGGACGATG[C/A]CGATGATGCTGATGTTGATGATGACGGTGCTGATGATAAGGATGATGTAGACGACGACGTC
73022 T C GACTAAATTTTGAAGCGTGAACAATGCATGGGCCGCACACATCCTTTTCTCTTCCCTCGAGCTTCGAGTTTCGATTTTCCATTTCTTCCG[T/C]TGTACTTTAGGTCATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATC
73022 G A GACTAAATTTTGAAGCGTGAACAATGCATGGGCCGCACACATCCTTTTCTCTTCCCTCGAGCTTCGAGTTTCGATTTTCCATTTCTTCCGTT[G/A]TACTTTAGGTCATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATC
73022 C T GACTAAATTTTGAAGCGTGAACAATGCATGGGCCGCACACATCCTTTTCTCTTCCCTCGAGCTTCGAGTTTCGATTTTCCATTTCTTCCGTTGTA[C/T]TTTAGGTCATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
73022 C T TAAATTTTGAAGCGTGAACAATGCATGGGCCGCACACATCCTTTTCTCTTCCCTCGAGCTTCGAGTTTCGATTTTCCATTTCTTCCGTTGTACTTTAGGT[C/T]ATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATCGTT
73022 G A ATGGGCCGCACACATCCTTTTCTCTTCCCTCGAGCTTCGAGTTTCGATTTTCCATTTCTTCCGTTGTACTTTAGGTCATGGATGTTTCTGCGGATTTTCT[G/A]GAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATCGTTCGTGCTTGCGCCGTCTCTCGATCC
73022 A G TTCTTCCGTTGTACTTTAGGTCATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCT[A/G]TTGATATCGTTCGTGCTTGCGCCGTCTCTCGATCCTGGAGGCGATTTGTTATATTTAATGGCTTTTGCAAGAAGCTGTGTTTAAGGATA
73022 C T TTGTACTTTAGGTCATGGATGTTTCTGCGGATTTTCTGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATAT[C/T]GTTCGTGCTTGCGCCGTCTCTCGATCCTGGAGGCGATTTGTTATATTTAATGGCTTTTGCAAGAAGCTGTGTTTAAGGATATGTGCGGA
73022 A G TGGAATGGTTGGGACCGGACACATCCACAATCGTGTTCATGCTTCTAGACGATCCTATTGATATCGTTCGTGCTTGCGCCGTCTCTCGATCCTGGAGGCG[A/G]TTTGTTATATTTAATGGCTTTTGCAAGAAGCTGTGTTTAAGGATATGTGCGGATGTATCATCATTTACACGGGTTGTTGACGCAAGCG
73056 T C GTGGTGATCAAGCGACCAATGCACTCTGAGAAGGTATCGCCATCTGCACTGAAATGCTCGTAATCGATGTCTATGCCATCTAAATTGTACTGCTTTATGA[T/C]CGTGGTCAAGGATGAGACTGCATTAGACACCCAGGAGTCAATGGAAGAAGGGTTGAAGAAGACCTTGCCATTGCCTATGCTATCCC
73056 C T TGGTGATCAAGCGACCAATGCACTCTGAGAAGGTATCGCCATCTGCACTGAAATGCTCGTAATCGATGTCTATGCCATCTAAATTGTACTGCTTTATGAT[C/T]GTGGTCAAGGATGAGACTGCATTAGACACCCAGGAGTCAATGGAAGAAGGGTTGAAGAAGACCTTGCCATTGCCTATGCTATCCCCA
73056 A G AAGCGACCAATGCACTCTGAGAAGGTATCGCCATCTGCACTGAAATGCTCGTAATCGATGTCTATGCCATCTAAATTGTACTGCTTTATGATCGTGGTCA[A/G]GGATGAGACTGCATTAGACACCCAGGAGTCAATGGAAGAAGGGTTGAAGAAGACCTTGCCATTGCCTATGCTATCCCCACCTATACT
73056 T C GACCAATGCACTCTGAGAAGGTATCGCCATCTGCACTGAAATGCTCGTAATCGATGTCTATGCCATCTAAATTGTACTGCTTTATGATCGTGGTCAAGGA[T/C]GAGACTGCATTAGACACCCAGGAGTCAATGGAAGAAGGGTTGAAGAAGACCTTGCCATTGCCTATGCTATCCCCACCTATACTGAGA
73098 C T ACTTTCCTCCTCAGCTTATTCCAACCTTCTCCGGGAGTCGTTGGAGTTTTAGGCGTTCCGGGAACGGTAGCAGGCGAAGAGGGCTCGGATCCAGATCCGC[C/T]GAAATGGGAGAGGGAACGGGGAACCTGAACACCACCGGCGGCAGCGATCGATCTTCTGAGCTTGCTAAGGCCGGATGGACGGGG
73108 T A TTCCGTAAATGTCCTTTTTTTTTTCAGTTGTATTTTTTTATGTTTACGGTAAACTTTGTTGTCTGTTACTCAAAAATAAGAAAATCTGTGGCAAGC[T/A]CTACAATTTTTGACCTGTCAGCAGAATAAAAATACTTGAATGATATTATAGATGTTACACTTCTCAAGATGTTACAGTTGTGAATGAGGAAATAC
73108 A C TTACTCAAAAATAAGAAAATCTGTGGCAAGCTCTACAATTTTTGACCTGTCAGCAGAATAAAAATACTTGAATGATATTATAGATGTTACACTTCTCAAG[A/C]TGTTACAGTTGTGAATGAGGAAATACAGATGGCAACAAGATGCATCGAATCTGAAGAAATTTTTTGTATCCCCACAACACAGTCCAAC
73108 T A AAGAAAATCTGTGGCAAGCTCTACAATTTTTGACCTGTCAGCAGAATAAAAATACTTGAATGATATTATAGATGTTACACTTCTCAAGATGTTACAGTTG[T/A]GAATGAGGAAATACAGATGGCAACAAGATGCATCGAATCTGAAGAAATTTTTTGTATCCCCACAACACAGTCCAACACATTTGTCTGG
73146 A C TTTTTCCTTATTCGCATCTTCCTTCGTCGTCCATTTCCATTTCCGCTCCAACCCCTCCTCCTCCTCCTCCTCCGCCCCTTCCCCTTC[A/C]CTCTGCCGCCGCCTCCACCACCTCCTCCGTCTCAACTCCCTCTGGCCCGTCCGCCTCCTCCTCGTGCTCTTCGCCTCCCTCCTTTCCTTCTCCGAGCTCC
73146 A T TTATTCGCATCTTCCTTCGTCGTCCATTTCCATTTCCGCTCCAACCCCTCCTCCTCCTCCTCCTCCGCCCCTTCCCCTTCACTCTGCCGCCGCCTCCACC[A/T]CCTCCTCCGTCTCAACTCCCTCTGGCCCGTCCGCCTCCTCCTCGTGCTCTTCGCCTCCCTCCTTTCCTTCTCCGAGCTCCTACGCCTTCCTCACC
73146 A G TCTGCCGCCGCCTCCACCACCTCCTCCGTCTCAACTCCCTCTGGCCCGTCCGCCTCCTCCTCGTGCTCTTCGCCTCCCTCCTTTCCTTCTCCGAGCTCCT[A/G]CGCCTTCCTCACCGGAAACCACTCCTCTGCCAGATCTACTCCATCTCCTCCCAATCCTTCGCCGAACCCGCCTTCTTCGCCACCCTCCTCTTC
73160 A G CACGAATTACACTCTAACATCAAACCAACTAATCTTCTCAATTTCTGACCAGAAACAGCAGAATTGAAAGAGGGAGAAAGAGGATGAACAAGAGTCCGAC[A/G]AAACTGAAAACCCTCCCTCGCCCGCTATTCTCCTGCGGTATTTTCCGAAACTGCACCCAGTCCGTACTCAGCCCCACAGCCCCTAGT
73190 G A AGTACAATACATCAGTTCAACTGAAACATATATAGGTACCAAGCACATACAATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATA[G/A]TCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTC
73190 G A CAACTGAAACATATATAGGTACCAAGCACATACAATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCG[G/A]CATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGG
73190 G A GAAACATATATAGGTACCAAGCACATACAATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATC[G/A]ATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGA
73190 C T CAATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAG[C/T]AAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAG
73190 A G AATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGC[A/G]AATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAG
73190 A C ATATACCAGTACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGCA[A/C]ATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAGAT
73190 C T ACTAACAATCTATATATAAATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCA[C/T]TGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAGATTCCCCTGCTG
73190 C T AATAAGGTCAACCTAAATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGG[C/T]GGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAGATTCCCCTGCTGCACCATACTCCGACCTCA
73190 G A AATATAGTCTAGCTATGCTTCCGGCATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCC[G/A]GTCAAGCTGGGCCGAGTCCAACCCCCATCAGTCCTCAAAGCAGATTCCCCTGCTGCACCATACTCCGACCTCACATGCCTGACCACCT
73190 A T CGGCATCGATAGATCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCA[A/T]CCCCCATCAGTCCTCAAAGCAGATTCCCCTGCTGCACCATACTCCGACCTCACATGCCTGACCACCTCACCACCACCAC
73190 C T TCATGATGCTAGTACAAACAGCAAATCTCTTCACTGTAGTGGCTGATCAGGCGGCAGTTTCCAGCCGGTCAAGCTGGGCCGAGTCCAACCCCCATCAGTC[C/T]TCAAAGCAGATTCCCCTGCTGCACCATACTCCGACCTCACATGCCTGACCACCTCACCACCACCAC
73192 T C AAACTGCTTTTCTTATCCTTTTGTGCTGGTTTAGCAAGTGATACCTTCACATTTATCTTTAGTCCATCAGCAGTTAACTCGTCTGCACTAAAGGATTCAA[T/C]GCATGAAAGTGCCGCGTCTCGGGTTTTATAATTAACAAAGACAAAATCCTTTTTCTTTGCAGGATCTATATTGCGAGCAAGAACAATTCG
73192 A G CTGCTTTTCTTATCCTTTTGTGCTGGTTTAGCAAGTGATACCTTCACATTTATCTTTAGTCCATCAGCAGTTAACTCGTCTGCACTAAAGGATTCAATGC[A/G]TGAAAGTGCCGCGTCTCGGGTTTTATAATTAACAAAGACAAAATCCTTTTTCTTTGCAGGATCTATATTGCGAGCAAGAACAATTCGCTC
73206 T C CAGGCACAATTGGAAAACGTCTTGCAAGCATCAACGTAGAGAACGTTGAAGAAAACCGCCGTGCCCTACGTGAACTTCTTTTCTGCACACC[T/C]GGTGCCCTCCAGTACCTAAGTGGCTGCATCCTCTTCGAAGAAACCCTATACCAAAAGACAGCCGATGGAAAGCCATTTGTTGATGTCCTAAAGGAA
73206 C T AAAAGACAGCCGATGGAAAGCCATTTGTTGATGTCCTAAAGGAAGGTGGTGTCCTACCAGGAATCAAGGTCGACAAGGGAACCATCGAGCTTGCTGGAAC[C/T]AATGGTGAGACCACCACCCAAGGTCACGACGACCTTGGCAAGAGGTGTGCCAAGTACTACGAGGCTGGTGCCCG
73232 G A CAACAGAATCAAATACCGTCAACCGAGACCCCGGCATCACTGCTCAACAGTGACCTACTCTACAACATCTTACGGCGCCTCGACGGCGCGACCTTAGCAA[G/A]AGCGGCATGCGCGTGCGCCGACTTCCGCTCCATCTCAAAAGAAGAAGCCCTATGGGAAGACGTCTGTGGATCCCTGTGGCCCTCCA
73266 C T ATTTTTAAATTGCAGCAAAAAATATAATGCCAGCGCAAATTAGCGTTCACAATATACATAGTGATATACAAGTTAACTCCATCCAGCATTCCTTCATGTC[C/T]GACACTTGATGGAAGCAGTTCTGGATAAGGTATTCTTGACATCTAATGATTTAGTGTCAGCCGGGAGAGCCTCTGTTTGGATGTTATCT
73266 C G TAGCGTTCACAATATACATAGTGATATACAAGTTAACTCCATCCAGCATTCCTTCATGTCCGACACTTGATGGAAGCAGTTCTGGATAAGGTATTCTTGA[C/G]ATCTAATGATTTAGTGTCAGCCGGGAGAGCCTCTGTTTGGATGTTATCTGCACTTCCAGATTCAATTGATGCCATAAATTGCTTTAATC
73266 G T ATATACAAGTTAACTCCATCCAGCATTCCTTCATGTCCGACACTTGATGGAAGCAGTTCTGGATAAGGTATTCTTGACATCTAATGATTTAGTGTCAGCC[G/T]GGAGAGCCTCTGTTTGGATGTTATCTGCACTTCCAGATTCAATTGATGCCATAAATTGCTTTAATCCCTCATTACATCCCAAGTAATGAT
73266 A G TACAAGTTAACTCCATCCAGCATTCCTTCATGTCCGACACTTGATGGAAGCAGTTCTGGATAAGGTATTCTTGACATCTAATGATTTAGTGTCAGCCGGG[A/G]GAGCCTCTGTTTGGATGTTATCTGCACTTCCAGATTCAATTGATGCCATAAATTGCTTTAATCCCTCATTACATCCCAAGTAATGATGCT
73266 A G TCCGACACTTGATGGAAGCAGTTCTGGATAAGGTATTCTTGACATCTAATGATTTAGTGTCAGCCGGGAGAGCCTCTGTTTGGATGTTATCTGCACTTCC[A/G]GATTCAATTGATGCCATAAATTGCTTTAATCCCTCATTACATCCCAAGTAATGATGCTTTGTTATCTTGGGAGCATCCTTCAAGAACCC
73266 T C TTGATGGAAGCAGTTCTGGATAAGGTATTCTTGACATCTAATGATTTAGTGTCAGCCGGGAGAGCCTCTGTTTGGATGTTATCTGCACTTCCAGATTCAA[T/C]TGATGCCATAAATTGCTTTAATCCCTCATTACATCCCAAGTAATGATGCTTTGTTATCTTGGGAGCATCCTTCAAGAACCCATTCACCTT
73266 A G TCTTGACATCTAATGATTTAGTGTCAGCCGGGAGAGCCTCTGTTTGGATGTTATCTGCACTTCCAGATTCAATTGATGCCATAAATTGCTTTAATCCCTC[A/G]TTACATCCCAAGTAATGATGCTTTGTTATCTTGGGAGCATCCTTCAAGAACCCATTCACCTTCTTGTCTTTGTCTGACACAAA
73268 A G CAATTTCCCTCACAAGCCTTTGGAATGGAAGTTTCCTGATCAGAAGCTCAGTACTCTTCTGATACTTGCGAATTTCACGAAGAGCAACAGTTCCAGGCCT[A/G]TAACGATGAGGCTTCTTCACTCCACCAGTAGTTGGTGCTGACTTGCGAGCAGCCTTTGTAGCCAGCTGCTTCCTGGGAGCCTTCCCAC
73278 T C TCAAATTACCAGTAAAAAAGTTCACTGAAATGGAGACAGTCGTCCTCCTCTTCACCGTCATCGGCCTACTTTCACTTGTGAAATTCGCCTTCTCCTTCTT[T/C]TACTATTTCTACGCCTTCTTTCTAAGGCCAGCAAAACCCCTGAAAACCCACTACGGCCCATGGGCCGTAGTCACCGGCCCCACAGACGGC
73306 C T TCGTGACAGTAGATCAGAATCCGAAGACTCGGTACCCGGTAACCGTAAGATTCAGCAGTGTCAATTATGCTGGGATATCTACAAACAACTATGCACTGGA[C/T]GAGATAAAAGAAATATAAAGATGAAAATGCACTGAGCCGTCCAGTAATTTCAAAGTTGTACTATACCCTATTGTTTGCGCCTACTCT
73306 C A GTAACCGTAAGATTCAGCAGTGTCAATTATGCTGGGATATCTACAAACAACTATGCACTGGACGAGATAAAAGAAATATAAAGATGAAAATGCACTGAGC[C/A]GTCCAGTAATTTCAAAGTTGTACTATACCCTATTGTTTGCGCCTACTCTTGTATCTATTATTCTATTTGCCTTGTATTCGTTTACCCAAG
73306 C T TCAGCAGTGTCAATTATGCTGGGATATCTACAAACAACTATGCACTGGACGAGATAAAAGAAATATAAAGATGAAAATGCACTGAGCCGTCCAGTAATTT[C/T]AAAGTTGTACTATACCCTATTGTTTGCGCCTACTCTTGTATCTATTATTCTATTTGCCTTGTATTCGTTTACCCAAGTTTCACTTGATAG
73310 C T GGAAAAAGAGAAGAAAAGAAAAAGATGAAGAGCCTGTTACTTCAAACCTGGAGACGCCCTGGCACGCTCAACCAC[C/T]GCCGATCAGCGGTTATGTACTATACAAAGGGTGTAGGAGACACCGTGCATGAGATGGGAGACAAGGCAAGATCAACAGCCGAAGAGTTTGCACGTAGAGC
73310 G A GGAAAAAGAGAAGAAAAGAAAAAGATGAAGAGCCTGTTACTTCAAACCTGGAGACGCCCTGGCACGCTCAACCACCGCCGATCAGC[G/A]GTTATGTACTATACAAAGGGTGTAGGAGACACCGTGCATGAGATGGGAGACAAGGCAAGATCAACAGCCGAAGAGTTTGCACGTAGAGCAAGAGAA
73310 G A GGAAAAAGAGAAGAAAAGAAAAAGATGAAGAGCCTGTTACTTCAAACCTGGAGACGCCCTGGCACGCTCAACCACCGCCGATCAGCG[G/A]TTATGTACTATACAAAGGGTGTAGGAGACACCGTGCATGAGATGGGAGACAAGGCAAGATCAACAGCCGAAGAGTTTGCACGTAGAGCAAGAGAA
73310 G A AGATGAAGAGCCTGTTACTTCAAACCTGGAGACGCCCTGGCACGCTCAACCACCGCCGATCAGCGGTTATGTACTATACAAAGGGTGTAGGAGACACCGT[G/A]CATGAGATGGGAGACAAGGCAAGATCAACAGCCGAAGAGTTTGCACGTAGAGCAAGAGAAAAGAAAGAATCAATAAAAGAGAA
73310 A G GACGCCCTGGCACGCTCAACCACCGCCGATCAGCGGTTATGTACTATACAAAGGGTGTAGGAGACACCGTGCATGAGATGGGAGACAAGGCAAGATCAAC[A/G]GCCGAAGAGTTTGCACGTAGAGCAAGAGAAAAGAAAGAATCAATAAAAGAGAAGGCGGAGGAAGCAGTGGATACAGTGAAAG
73310 T C CGCTCAACCACCGCCGATCAGCGGTTATGTACTATACAAAGGGTGTAGGAGACACCGTGCATGAGATGGGAGACAAGGCAAGATCAACAGCCGAAGAGTT[T/C]GCACGTAGAGCAAGAGAAAAGAAAGAATCAATAAAAGAGAAGGCGGAGGAAGCAGTGGATACAGTGAAAGGCGCAGCTGTGA
73320 G A AACAGTCTTCCTCCTCCTCCTCCCCATCTTCTTCTGCCTATCCAACGCAGCCCAGTTCAATGTGGTGAACAAATGTCCCTACACAGTGTGGGCTGCAGCC[G/A]TCCCTGGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCC
73320 T C TCTTCCTCCTCCTCCTCCCCATCTTCTTCTGCCTATCCAACGCAGCCCAGTTCAATGTGGTGAACAAATGTCCCTACACAGTGTGGGCTGCAGCCGTCCC[T/C]GGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCCCGTAC
73320 A G TCTGCCTATCCAACGCAGCCCAGTTCAATGTGGTGAACAAATGTCCCTACACAGTGTGGGCTGCAGCCGTCCCTGGAGGCGGCAAGCAGCTCAACTCAGG[A/G]GACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCCCGTACGGGCTGCACCTTTGATGCATCCGGA
73320 C G GTCCCTACACAGTGTGGGCTGCAGCCGTCCCTGGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGG[C/G]CGCGTCTGGGCCCGTACGGGCTGCACCTTTGATGCATCCGGACATGGCAGATGTCAGACCGGCGACTGTGGGGGAGTCCTCGC
73320 T A GGGCTGCAGCCGTCCCTGGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCCCG[T/A]ACGGGCTGCACCTTTGATGCATCCGGACATGGCAGATGTCAGACCGGCGACTGTGGGGGAGTCCTCGCCTGCACGGGGTATG
73320 C A GTCCCTGGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCCCGTACGGGCTGCA[C/A]CTTTGATGCATCCGGACATGGCAGATGTCAGACCGGCGACTGTGGGGGAGTCCTCGCCTGCACGGGGTATGG
73320 T C CTGGAGGCGGCAAGCAGCTCAACTCAGGAGACTCATGGACCGTGACAGCCAACCCAGGCACCACAGGGGGCCGCGTCTGGGCCCGTACGGGCTGCACCTT[T/C]GATGCATCCGGACATGGCAGATGTCAGACCGGCGACTGTGGGGGAGTCCTCGCCTGCACGGGGTATGG
73344 G A CCTACCCAAAACCCCCTCCACATCCCTCGACAGCCCGAAAAACTCGAACTGCACTTCCAGATGAGCGAA[G/A]CAGTCATCCTCCGGCCTCCCATACCCATGCACCCTATCGTCCTCCTCCGTCACCGGAACCACATTCACCATTATCCTCGCGGTCTCCTCCACAAACACCA
73344 C T TACCCAAAACCCCCTCCACATCCCTCGACAGCCCGAAAAACTCGAACTGCACTTCCAGATGAGCGAAGCAGTCATCCTCCGGCCTCCCATACCCATGCAC[C/T]CTATCGTCCTCCTCCGTCACCGGAACCACATTCACCATTATCCTCGCGGTCTCCTCCACAAACACCACGACCGAGTTTCTAACCCCCGT
73348 T C GTTGGCCTACTGGATTTTCAACCTTCTCCGCTAAAAAATCCAATATATCCTATCATCAATT[T/C]TTACCTACACGCCTTCGCTTAACATCCAATCAATGGCATACGGAAGAAACGAGCCATCGGTGCTCGACAACTTCACCCTCTCCCCACTCCCATACCCAGT
73348 C A TTACCTACACGCCTTCGCTTAACATCCAATCAATGGCATACGGAAGAAACGAGCCATCGGTGCTCGACAACTTCACCCTCTCCCCACTCCCATACCCAGT[C/A]CTACTCATCCTCCTCATCCTCCTCCTCCTCGTCGGCATCCCGTGGTCCTTCTCCTACGAGGAGTTCATCGAAAGCACCGAAGAGCAGAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
73348 A C CCTACACGCCTTCGCTTAACATCCAATCAATGGCATACGGAAGAAACGAGCCATCGGTGCTCGACAACTTCACCCTCTCCCCACTCCCATACCCAGTCCT[A/C]CTCATCCTCCTCATCCTCCTCCTCCTCGTCGGCATCCCGTGGTCCTTCTCCTACGAGGAGTTCATCGAAAGCACCGAAGAGCAGATGAA
73348 A G TCACCCTCTCCCCACTCCCATACCCAGTCCTACTCATCCTCCTCATCCTCCTCCTCCTCGTCGGCATCCCGTGGTCCTTCTCCTACGAGGAGTTCATCGA[A/G]AGCACCGAAGAGCAGATGAACTGGCTCCTCCTCGCAACTCCCATACTCCTCCTCCTGCTCATCAAATGGACGTCTTCCATCGAGAG
73356 AT A CCATCTTGCCATTTGTATTGTCACAACTTAAATCGACATGCCTTGCCTTGCTTTCTGTTCTTTTCTTCTGCCTTGCCATGCCTACAAGCTGGTCCACATC[AT/A]TTTTTTATACCTACTGGTCTTTGGATTCGTCAGGATTATCACGTACACACCGATTACTTGATGCTGGGATTAACCTAGACATCTCAGTACT
73356 T C TATTGTCACAACTTAAATCGACATGCCTTGCCTTGCTTTCTGTTCTTTTCTTCTGCCTTGCCATGCCTACAAGCTGGTCCACATCATTTTTTATACCTAC[T/C]GGTCTTTGGATTCGTCAGGATTATCACGTACACACCGATTACTTGATGCTGGGATTAACCTAGACATCTCAGTACTTTAAGCTCTTATATTG
73358 C CA AGCCAGTGTTATTGTTCGCTTTGTCTTTCTGATGGTCCCTTTCATGATCGTTGCAAAACGCTTCAAACCCCCGTCGCTATGTTTTTCACAGTATCAGAAG[C/CA]TCATCTGCTTGACTTGGACAACCTGTAAGCTCTCCTTGGTGGTATGTGCAAGGTAACGATAGTTCACAAATGCAGAAAGCTTTCTCGG
73358 T C AGTGTTATTGTTCGCTTTGTCTTTCTGATGGTCCCTTTCATGATCGTTGCAAAACGCTTCAAACCCCCGTCGCTATGTTTTTCACAGTATCAGAAGCTCA[T/C]CTGCTTGACTTGGACAACCTGTAAGCTCTCCTTGGTGGTATGTGCAAGGTAACGATAGTTCACAAATGCAGAAAGCTTTCTCGGCTCAG
73360 T C CTGGTCGCCAGATCTAGCCGTGTGCTTTCTTTCCTGTACAACATTTTTCTACACTTGCTATGGGTGATGCTCCTGGGCCCTAGCAGAGCCT[T/C]TCTGGTTGGTGTTGACTGCAACCATGGCCGAACTTCCGAATAGCAGTTCCTAGCCGACTCATGAGTTACGGTCTACGAATAGAACGTTTTACGTTGCT
73360 C T CTTTCTTTCCTGTACAACATTTTTCTACACTTGCTATGGGTGATGCTCCTGGGCCCTAGCAGAGCCTTTCTGGTTGGTGTTGACTGCAACCATGGCCGAA[C/T]TTCCGAATAGCAGTTCCTAGCCGACTCATGAGTTACGGTCTACGAATAGAACGTTTTACGTTGCTGGTAAGTTCACTTGGCGGTTGTCT
73378 A T CCAGCACCCGCCTTTTTTCAGTGTCCTGCAAGCTGGAACCGCCGTTGTCCAGACGAACGACAAAC[A/T]CTTCCAAAAATGGTGGTAAATTAATAAAAAAGAGAATATTAAATGGAAAAGATTCGTGTTTGGTAATTCCGCCGCCAAATGGAGAAAAACCGATTGCACT
73378 TA T CCAGCACCCGCCTTTTTTCAGTGTCCTGCAAGCTGGAACCGCCGTTGTCCAGACGAACGACAAACACTTCCAAAAATGGTGGTAAATTAA[TA/T]AAAAAAGAGAATATTAAATGGAAAAGATTCGTGTTTGGTAATTCCGCCGCCAAATGGAGAAAAACCGATTGCACTTATTAAGTTTATTGGCGGCGC
73378 GA G CAGACGAACGACAAACACTTCCAAAAATGGTGGTAAATTAATAAAAAAGAGAATATTAAATGGAAAAGATTCGTGTTTGGTAATTCCGCCGCCAAATGGA[GA/G]AAAAACCGATTGCACTTATTAAGTTTATTGGCGGCGCTTTTGTTGGTGCGGTTCCTGAAGCCACTTACAGTCACTTAATGGAGCTC
73378 A C TGGTGGTAAATTAATAAAAAAGAGAATATTAAATGGAAAAGATTCGTGTTTGGTAATTCCGCCGCCAAATGGAGAAAAACCGATTGCACTTATTAAGTTT[A/C]TTGGCGGCGCTTTTGTTGGTGCGGTTCCTGAAGCCACTTACAGTCACTTAATGGAGCTCCTAGCCAGAGAAGGGTTTTTAATAATCT
73392 C T AAGAGTATTTAAGGGCTTATCAGGCCCCCTTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTG[C/T]TAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGA
73392 A G AAGAGTATTTAAGGGCTTATCAGGCCCCCTTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTAC[A/G]GGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTA
73392 C T AAGGGCTTATCAGGCCCCCTTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGA[C/T]ATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGC
73392 A G AGGGCTTATCAGGCCCCCTTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGAC[A/G]TGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGCA
73392 A G CCCTTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAG[A/G]GCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGCAGCTGCATATTATTTTT
73392 T A TTCCATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGC[T/A]CCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGCAGCTGCATATTATTTTTCTG
73392 T C CATCTGATGTGGCAGCTGAGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCC[T/C]TTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGCAGCTGCATATTATTTTTCTGGCA
73392 C T AGCTTAATGGTGTGCTAAGCAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGC[C/T]GAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAGAGCAGCTGCATATTATTTTTCTGGCAAATGATATTCTTTTTGAAA
73392 G A CAATCTTACAGGCACTAAAGAGTCAATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGG[G/A]TATTTGCTATAGATGATTCTGAAGAGCAGCTGCATATTATTTTTCTGGCAAATGATATTCTTTTTGAAAGCTTGCAACGAAGAGCGA
73392 A G ATCAGGGGAGCTAAGACATGGTTTATGCAAAGAGCTCCTTTTGCTCCAGCACTTGCCGAAGCACTTCGAGAAAGGGTATTTGCTATAGATGATTCTGAAG[A/G]GCAGCTGCATATTATTTTTCTGGCAAATGATATTCTTTTTGAAAGCTTGCAACGAAGAGCGAATCTTCAAGAGCTTGACAATGAAGC
73396 T C GCAGGGTCTGGTAGGATGGTGTGCAGTAGTTGTGGCGGATCGGGTCGGGCTAAACCCTTGCGCGCTCGAATTTC[T/C]CTTAAGTCTACATGAGATGTGCATAAAGGAACTTGAATGTATATTTGAGAATTTAATTAGTTGGGTAATTTTGGGGTTATGAATATCAGAGCCATGTCAT
73396 G C TGAGAATTTAATTAGTTGGGTAATTTTGGGGTTATGAATATCAGAGCCATGTCATATCTGGATGTTTACAAAATATGATTCTTCAGTATGTGATGACGTG[G/C]ATGTGTTTAGGCGGAGCTTGTCCAGTATCTAGCTTGTAATGAACATTTAGCTTATAACTGGAGATTGTAAGCATTAAAAAGTCAAAAA
73398 T C AAATTATTATTTTAGCACCACTCTAGACTTATGTACAAAATATGATCATCACTTTACAAAGGTAGATAGCAAATAGGTAGGCAAGAAATATTCTAGGAAA[T/C]CAATACATGTTTCTTACACCAATCTCTAACTGGAGCAATCGAAATGCCTTACCAATTACAGAAATTAGAGATCCAAACAATTATACAAA
73398 C G TTTACAAAGGTAGATAGCAAATAGGTAGGCAAGAAATATTCTAGGAAATCAATACATGTTTCTTACACCAATCTCTAACTGGAGCAATCGAAATGCCTTA[C/G]CAATTACAGAAATTAGAGATCCAAACAATTATACAAATCAATCTTGTAACACAAATAATACCTAGAAATAGATCAACGTGGATTAAAG
73398 A G CTAGGAAATCAATACATGTTTCTTACACCAATCTCTAACTGGAGCAATCGAAATGCCTTACCAATTACAGAAATTAGAGATCCAAACAATTATACAAATC[A/G]ATCTTGTAACACAAATAATACCTAGAAATAGATCAACGTGGATTAAAGGGGTTAGAGCCGGTAGAGAAGGATGAAGTCACTGGATAA
73416 C T TTCGGCCGATCCAGTTTGTTTCTACACAAAATCACGTCTAGAATCTCCTGTATGTTCGTGCACATTG[C/T]CCGGCCCTCATCGTCATTCTGTCTCTCTCTAAGCTTCTCAGCCTCCTCCCATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGA
73416 A G TTCGGCCGATCCAGTTTGTTTCTACACAAAATCACGTCTAGAATCTCCTGTATGTTCGTGCACATTGCCCGGCCCTC[A/G]TCGTCATTCTGTCTCTCTCTAAGCTTCTCAGCCTCCTCCCATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTG
73416 T G TTCGGCCGATCCAGTTTGTTTCTACACAAAATCACGTCTAGAATCTCCTGTATGTTCGTGCACATTGCCCGGCCCTCATCGTCA[T/G]TCTGTCTCTCTCTAAGCTTCTCAGCCTCCTCCCATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGC
73416 C T ACACAAAATCACGTCTAGAATCTCCTGTATGTTCGTGCACATTGCCCGGCCCTCATCGTCATTCTGTCTCTCTCTAAGCTTCTCAGCCTCCTCCCATGCA[C/T]GGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGATTCTGGGAGTAAGGACATAG
73416 T C TCTCTAAGCTTCTCAGCCTCCTCCCATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGA[T/C]TCTGGGAGTAAGGACATAGCGTCATGTTACGTTCCAAAACCACCTCATGTACTTAGCCACGGATATGGGGGATCCCTCTCGAACTCAA
73416 A G CCTCCTCCCATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGATTCTGGGAGTAAGGAC[A/G]TAGCGTCATGTTACGTTCCAAAACCACCTCATGTACTTAGCCACGGATATGGGGGATCCCTCTCGAACTCAATATTGTTATCGCGGG
73416 A G CATGCACGGTTAATACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGATTCTGGGAGTAAGGACATAGCGTC[A/G]TGTTACGTTCCAAAACCACCTCATGTACTTAGCCACGGATATGGGGGATCCCTCTCGAACTCAATATTGTTATCGCGGGCATCCCAC
73416 A G TACCAGCAACCACGTTCCTCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGATTCTGGGAGTAAGGACATAGCGTCATGTTACGTTCCA[A/G]AACCACCTCATGTACTTAGCCACGGATATGGGGGATCCCTCTCGAACTCAATATTGTTATCGCGGGCATCCCACATAGCACGATACA
73416 A C TCTCCAGTGGTGCTCTAGGAACGTACGGTGCTACCGCAGTATCGATTCTGGGAGTAAGGACATAGCGTCATGTTACGTTCCAAAACCACCTCATGTACTT[A/C]GCCACGGATATGGGGGATCCCTCTCGAACTCAATATTGTTATCGCGGGCATCCCACATAGCACGATACATCTG
73450 G A GACAGAAGGATCGCAGCGCTGAAACTCGTCACCACGAAAGCGAAGAACAAGGCAGCGGGGACAAGAACCGGGCTGAAAAGCAGAATCAGCGGCCCGGTCA[G/A]GACCAGCAGCGTCGCGGTTGCGAACATGGACAGGCCCATCAGCCCGAAAAGCGGGCCCGCCGTGATCACCGTCGCGATTACA
73450 G A AGGATCGCAGCGCTGAAACTCGTCACCACGAAAGCGAAGAACAAGGCAGCGGGGACAAGAACCGGGCTGAAAAGCAGAATCAGCGGCCCGGTCAGGACCA[G/A]CAGCGTCGCGGTTGCGAACATGGACAGGCCCATCAGCCCGAAAAGCGGGCCCGCCGTGATCACCGTCGCGATTACAGCAAAC
73454 C T TGAAGCTCATAGCTGCCACCTTCGTTCCTCTCATCGTCTCCATCTTCCTCGTCGTCCACTTTTTCCGTCCTTCAGACCCAGAGTTCAACCTCACAGATGC[C/T]ACAGTTCATGCATTCAACTTCTCGATGCAGCACAGTCTCCTTTCTTCCCAGATGCAAGTCACTCTTTCCTCACGAAACCCTAATGATCATTT
73458 G A TCCTGTAAGCGACAGGAACAATCCCAGCCTTGTATTCAGCGATCTTCAAAAACACAGGCATCGCTAAATCGAAATGCTCGCGGGGAGGATTACACCACCC[G/A]CCATTATCGGAGGCCTGAGCGAAATTAGGCGGGCAGAAGTTGGTGGCGGTTACGATAATAGATGGACTTCCGCTGTGGCACCAAC
73458 G C CAGGAACAATCCCAGCCTTGTATTCAGCGATCTTCAAAAACACAGGCATCGCTAAATCGAAATGCTCGCGGGGAGGATTACACCACCCGCCATTATCGGA[G/C]GCCTGAGCGAAATTAGGCGGGCAGAAGTTGGTGGCGGTTACGATAATAGATGGACTTCCGCTGTGGCACCAACGCTGGTCGTTGG
73466 C T AATCTCAGAATAATTCTTCAGAATCAATGGCGAGCTCAACTTTGATGACGTCATCACCTTCAACAACGCTGCCCTCACCATTCTCTTTTCCTAAAACCTC[C/T]GCTAAACCCCAAACTCTAACTTTTACTAAAATGCCCTCTTCAAATTCAAAAATCACGACTAAGGCATCATATTCGAATCCGTTCTTGATTCC
73466 CT C GAATCAATGGCGAGCTCAACTTTGATGACGTCATCACCTTCAACAACGCTGCCCTCACCATTCTCTTTTCCTAAAACCTCCGCTAAACCCCAAACTCTAA[CT/C]TTTTACTAAAATGCCCTCTTCAAATTCAAAAATCACGACTAAGGCATCATATTCGAATCCGTTCTTGATTCCAAAAGCAGAAAATTTAAA
73466 TA T TGGCGAGCTCAACTTTGATGACGTCATCACCTTCAACAACGCTGCCCTCACCATTCTCTTTTCCTAAAACCTCCGCTAAACCCCAAACTCTAACTTTTAC[TA/T]AAAATGCCCTCTTCAAATTCAAAAATCACGACTAAGGCATCATATTCGAATCCGTTCTTGATTCCAAAAGCAGAAAATTTAAAATCGGGG
73476 C T TTGGTAGATATAAGCTCTCCATTCAGCATGAACAAACAACATACGATATACTAGTTAAACAGCTTGGGAAGGAGGATCCACGTACGGTTGATTCAGAAAA[C/T]TGGATAAAGATATTTAAAACGCGTGAAGAGCAGGCCAATGCACAAAAGCAGAAAGGTCAGGTGGCTAATTCTACCCAAAAGGCTA
73508 A G CCAACAGCAAATGAAACTACCGACGCTCAGAACTGGAAGAAATCATCTAGTCTTCCTCAGGAGCAGATTTGGAAGAGCCAGCCTTCTTTGGAAGCAATAA[A/G]TTGTGAATGTTGGGCATCACCCCTCCATTAGCAATGGTAACGGTACCTAAAAGCTTGGATAGCTCTTCATCATTCCTCACTGCCAAC
73510 C T TTCTTGGTTACTCTCTAAAATCATTAGCGGATTCATTCATTCCTCTCCTAAAAACAATATT[C/T]GATCTGACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAAC
73510 C T TTCTTGGTTACTCTCTAAAATCATTAGCGGATTCATTCATTCCTCTCCTAAAAACAATATTCGAT[C/T]TGACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGC
73510 G C TTCTTGGTTACTCTCTAAAATCATTAGCGGATTCATTCATTCCTCTCCTAAAAACAATATTCGATCT[G/C]ACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCA
73510 T G TTCTTGGTTACTCTCTAAAATCATTAGCGGATTCATTCATTCCTCTCCTAAAAACAATATTCGATCTGACACCAAACGAGTATGACTCGTACGAAGA[T/G]GTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCA
73510 G A CGGATTCATTCATTCCTCTCCTAAAAACAATATTCGATCTGACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACC[G/A]ATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAG
73510 A T TCCTAAAAACAATATTCGATCTGACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACT[A/T]CTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGAT
73510 C A AATATTCGATCTGACACCAAACGAGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCA[C/A]TCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTT
73510 A C AGTATGACTCGTACGAAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCC[A/C]ATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTG
73510 T A AAGATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGC[T/A]ATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGG
73510 T C ATGTGCATCGTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTAT[T/C]AGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGGAAT
73510 A G GTCTCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCA[A/G]AATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGGAATTTGCGCGAG
73510 T C TCTTCAGAGGTGGATTACCGATTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAA[T/C]GGGCAAAGCTTTCTTAAGTACCCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGGAATTTGCGCGAGAGA
73510 C T TTCCCAGTGTTCCACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTA[C/T]CCGATTCCTCAGCTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGGAATTTGCGCGAGAGATGCTGGCAGGTGTGAATCCAC
73510 G A CACTACTGGATTCACTCAAACAAGCCATTCCTTTTCCAATGATCAAGGCAGCTATTAGCACTCAAAATGGGCAAAGCTTTCTTAAGTACCCGATTCCTCA[G/A]CTTATTCAAGATGATAAGTATGCCTGGAGAAGCGATGAGGAATTTGCGCGAGAGATGCTGGCAGGTGTGAATCCACATATC
73530 C T TTTGAATCTAGGGTTTTAAGTGAGGAACAATGTCGACACAGTCAACGGTAACGGAGAAAAGGAAGCCAGTCTTTGTGAAGGTCGATCAACTGAAGCCCGG[C/T]ACCAATGGCCATACGCTGACGGCAAAAGTCGTCAACTCCGAATCGGTGGTTCAAAAAGGACGCTCTACTTCTACGCCCCTTCGCA
73572 G C ACTGTTGGCCTACTGGATATCACCACAACTTAGAAGCACTAAATAAAACATCATGTACATCACTCTG[G/C]TAGTAGCTCTACTATCGGCACTTGTGGTAGGAACAATCAGTGGAGCAGGAAGTAGTAGTATATCAGCTGGTGAAGTTTACTGGAACAATGTCTTGCCCAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
73572 C G TGGATATCACCACAACTTAGAAGCACTAAATAAAACATCATGTACATCACTCTGGTAGTAGCTCTACTATCGGCACTTGTGGTAGGAACAATCAGTGGAG[C/G]AGGAAGTAGTAGTATATCAGCTGGTGAAGTTTACTGGAACAATGTCTTGCCCAAAACTACCATGCCCAAGGCCATTAAAGATCTTTT
73572 T A TAAAACATCATGTACATCACTCTGGTAGTAGCTCTACTATCGGCACTTGTGGTAGGAACAATCAGTGGAGCAGGAAGTAGTAGTATATCAGCTGGTGAAG[T/A]TTACTGGAACAATGTCTTGCCCAAAACTACCATGCCCAAGGCCATTAAAGATCTTTTACCAGCTGATAACGTGCTGTCGATGACCAG
73572 A T AGCTCTACTATCGGCACTTGTGGTAGGAACAATCAGTGGAGCAGGAAGTAGTAGTATATCAGCTGGTGAAGTTTACTGGAACAATGTCTTGCCCAAAACT[A/T]CCATGCCCAAGGCCATTAAAGATCTTTTACCAGCTGATAACGTGCTGTCGATGACCAGTTACGAGACTCACCGGAACAAAGGGTCA
73574 C A GTCCGTTAATAACTTACATCTGAAGGTTACATATTCTTCCAACCAAGAAAAGCAAAAATAAAGTAAGCACTAAGAAAAAACTAATGATAACAGCAGCACT[C/A]ATATTATCTTAATCCTTTGTCTGTCATCAAAATTACATTTTGTTATCAATTCTTACATGGAAGCCATCAGGGTAACATACCCGACTTTAT
73574 G A CAGCACTCATATTATCTTAATCCTTTGTCTGTCATCAAAATTACATTTTGTTATCAATTCTTACATGGAAGCCATCAGGGTAACATACCCGACTTTATGA[G/A]TCTCAGATATGATATTCTGTTGTTGGGATGCTGTCTTACATACAATAACACCCAGGCCATTGCATTCACCAAGTCAAAAGAGATTTTATTT
73574 T G CCTTTGTCTGTCATCAAAATTACATTTTGTTATCAATTCTTACATGGAAGCCATCAGGGTAACATACCCGACTTTATGAGTCTCAGATATGATATTCTGT[T/G]GTTGGGATGCTGTCTTACATACAATAACACCCAGGCCATTGCATTCACCAAGTCAAAAGAGATTTTATTTAACCTTAGCTAGTAAAAA
73582 CA C TAAGATTTCTGAAATCGGGCACGTGCACCACGTCCACCAAACTTCTTGGGCTCGCATCGCCTTGGATCTGCAACAAGCAACGTCCGATCGTACGCAA[CA/C]AAGAATGTCCTTGATTTCCTTCTTTTGCTGCTCGTCAACGAATTTCTGGTAGTAAGCGACGAGAGCCTTGGCGATGCTCTGCCTGATTGC
73582 CT C GGGCACGTGCACCACGTCCACCAAACTTCTTGGGCTCGCATCGCCTTGGATCTGCAACAAGCAACGTCCGATCGTACGCAACAAGAATGTCCTTGATTTC[CT/C]TTCTTTTGCTGCTCGTCAACGAATTTCTGGTAGTAAGCGACGAGAGCCTTGGCGATGCTCTGCCTGATTGCGTAGATCTGACTGGTG
73606 T C GATCACCATCTCCCCGTCACAGAGGAGCATCTCCCCGTCGCAGAGGAGCATCTCCCCGTCGTAGAGAAGCATCTCCTCGTTCCACATCAG[T/C]ATCTCCTCGTCTCAGAGGAGCGTCTTCTCCAGATCATAGGATGGCGTCTCCTCCAAAGAAGGTACAATCCAGGTCACCATCCCGTGGTCCTAGGTCT
73606 A G ACCATCTCCCCGTCACAGAGGAGCATCTCCCCGTCGCAGAGGAGCATCTCCCCGTCGTAGAGAAGCATCTCCTCGTTCCACATCAGTATCTCCTCGTCTC[A/G]GAGGAGCGTCTTCTCCAGATCATAGGATGGCGTCTCCTCCAAAGAAGGTACAATCCAGGTCACCATCCCGTGGTCCTAGGTCTCCAT
73606 G A ATCTCCCCGTCACAGAGGAGCATCTCCCCGTCGCAGAGGAGCATCTCCCCGTCGTAGAGAAGCATCTCCTCGTTCCACATCAGTATCTCCTCGTCTCAGA[G/A]GAGCGTCTTCTCCAGATCATAGGATGGCGTCTCCTCCAAAGAAGGTACAATCCAGGTCACCATCCCGTGGTCCTAGGTCTCCATCACC
73616 T C AGCAGAAGTTAGATTTATTTTTCTTCAACGAGATGTCGGCTTTACTGAAATTCATCAAACCAGGATTGCGTCCACAATCCACAGACGTCTTCGCCGCTGC[T/C]AGTTGGGGCGTTGCTGGCGTCACTACCGCCCTTTGGCTTGTTCAGCCTTTTGATTGGTTGAAGAAGCAGTTTGTTGAGAAGCCTCAAC
73618 C T TGTGGCCTTTTTTTTTTGAAATCCAAAATTTTCAATAGATTAAATGCTCTAAAACATGAACAGATACATAATTAACA[C/T]GAAGTACATCAATCAGACTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAG
73618 A C TTTTTTTTTTGAAATCCAAAATTTTCAATAGATTAAATGCTCTAAAACATGAACAGATACATAATTAACACGAAGTACATCAATCAGACTAATAACTATT[A/C]AACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAGCAGCAAGACATGGCGAGA
73618 T C TTAAATGCTCTAAAACATGAACAGATACATAATTAACACGAAGTACATCAATCAGACTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAA[T/C]GGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAGCAGCAAGACATGGCGAGAAAAAGTGCAGCTAAAGTAGAAGAAAAGAG
73618 T TA ACACGAAGTACATCAATCAGACTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGG[T/TA]AAGCAGCAAGACATGGCGAGAAAAAGTGCAGCTAAAGTAGAAGAAAAGAGGCAAGCAGGAGGAGAGGTAGAAGCATGGTGTT
73618 C A GAAGTACATCAATCAGACTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAG[C/A]AGCAAGACATGGCGAGAAAAAGTGCAGCTAAAGTAGAAGAAAAGAGGCAAGCAGGAGGAGAGGTAGAAGCATGGTGTTGCAGT
73618 G A AGACTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAGCAGCAAGACATGGC[G/A]AGAAAAAGTGCAGCTAAAGTAGAAGAAAAGAGGCAAGCAGGAGGAGAGGTAGAAGCATGGTGTTGCAGTAGCATAAATCCGAA
73618 A T CTAATAACTATTAAACAATCTCATCAACGAAAAAGAAAAGAAAATGGAAACAACCACATGATCTAGGGCCAATTTGCGGTAAGCAGCAAGACATGGCGAG[A/T]AAAAGTGCAGCTAAAGTAGAAGAAAAGAGGCAAGCAGGAGGAGAGGTAGAAGCATGGTGTTGCAGTAGCATAAATCCGAAGAA
73620 T G GCAACTGGTCCACGATCGCGAAGTCCATCCCAGGCAGATCCGGCAAGTCCTGCCGCCTCCGCTGGTGCAACCAGCTGTCGCCGCAGGTGGAGCACCGCGC[T/G]TTCACGGAGGAGGAAGATCGGAACATCATCTACCTGCATGAGAAGTACGGCAACAGATGGGCCACCATCGCTCGTATGCT
73652 G A AATCAGGGAAATCAACCAAGAACTGGATATACAATTTCCCCCTCATGAATGGCCTCTGATACATCGGCATTCCTTCGTCATTGATCGCCTT[G/A]AATTGATCTGGCTTAACCACCTCTCCAGGATTAGACTTGATAAGGAGTTGCCTCCCATCCAAGTGAGTTAACACAAACTGGAAACCGCAAAGGGCCT
73652 C G TGAATGGCCTCTGATACATCGGCATTCCTTCGTCATTGATCGCCTTGAATTGATCTGGCTTAACCACCTCTCCAGGATTAGACTTGATAAGGAGTTGCCT[C/G]CCATCCAAGTGAGTTAACACAAACTGGAAACCGCAAAGGGCCTCAGTGAGAGAAAGGGTATGTTTATAAAATAAATCATCCCCTTTCC
73652 T C ACATCGGCATTCCTTCGTCATTGATCGCCTTGAATTGATCTGGCTTAACCACCTCTCCAGGATTAGACTTGATAAGGAGTTGCCTCCCATCCAAGTGAGT[T/C]AACACAAACTGGAAACCGCAAAGGGCCTCAGTGAGAGAAAGGGTATGTTTATAAAATAAATCATCCCCTTTCCTTTGGAATTTGGGAT
73652 C T ACTTGATAAGGAGTTGCCTCCCATCCAAGTGAGTTAACACAAACTGGAAACCGCAAAGGGCCTCAGTGAGAGAAAGGGTATGTTTATAAAATAAATCATC[C/T]CCTTTCCTTTGGAATTTGGGATGTTCTTTCTGCTGTAGTACAAACACAATATCCCCTGTAACTGTATCTGGCGCTTCATCAGCTTCGC
73678 C T CGACAGCAGCCTCCTCTTGGTCGAGCTTGGAGCGAGCAAGGTCCGGTCGAACTTCTACCTGGTCGGTGCTGGAGACTCGAGCTGGTCGGTCACGGAGTCT[C/T]CATGCTGGTCGGTTTTAGGAGGAGCTCCAAGGCTGGTCGATTCCAAGGAGAAAAGGCAGAGACTCCAAAGAAGAAGGAACGAG
73688 T C AACCTAGCATCGCTAGACATGCCTTCTTCATACATTTGGAGAAAGTCCTTCATTTTAATGGAAGCGTCCCACATGT[T/C]CATTCCATTTGCCAATTCATGCGCTGTAGAGGGGTCTTCTACCAAGAACCATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGG
73688 T C ATTTGGAGAAAGTCCTTCATTTTAATGGAAGCGTCCCACATGTTCATTCCATTTGCCAATTCATGCGCTGTAGAGGGGTCTTCTACCAAGAACCATTTAC[T/C]GAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGGGTTACCATGGGAGAAAGATCGGTAGTCTTTCCAGCTATAAGGAT
73688 G T CATTCCATTTGCCAATTCATGCGCTGTAGAGGGGTCTTCTACCAAGAACCATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGG[G/T]TTACCATGGGAGAAAGATCGGTAGTCTTTCCAGCTATAAGGATTTTAGAATATTTCGTAAGGGAGTATAGTTCTTCTTCATCGTGGG
73688 T A TTTGCCAATTCATGCGCTGTAGAGGGGTCTTCTACCAAGAACCATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGGGTTACCA[T/A]GGGAGAAAGATCGGTAGTCTTTCCAGCTATAAGGATTTTAGAATATTTCGTAAGGGAGTATAGTTCTTCTTCATCGTGGGATAAGAA
73688 A T CCAATTCATGCGCTGTAGAGGGGTCTTCTACCAAGAACCATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGGGTTACCATGGG[A/T]GAAAGATCGGTAGTCTTTCCAGCTATAAGGATTTTAGAATATTTCGTAAGGGAGTATAGTTCTTCTTCATCGTGGGATAAGAATTTG
73688 C T TCTTCTACCAAGAACCATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGGGTTACCATGGGAGAAAGATCGGTAGTCTTTCCAG[C/T]TATAAGGATTTTAGAATATTTCGTAAGGGAGTATAGTTCTTCTTCATCGTGGGATAAGAATTTGGAGTGTACTAGAAGGCGGAGCA
73688 A G ATTTACTGAGGGAATGCCATGGACCTAGGGAATCTTGGCTGAGCATTAGGGTTACCATGGGAGAAAGATCGGTAGTCTTTCCAGCTATAAGGATTTTAGA[A/G]TATTTCGTAAGGGAGTATAGTTCTTCTTCATCGTGGGATAAGAATTTGGAGTGTACTAGAAGGCGGAGCAGACGATGAAGATGAG
73700 G A TGTTTTCCATTTTTAGCAAATTTTCCATTCCATGTCGGGTTAGATCCACTATGGACCCACTTTTGAACAGATCCGCTATTGTTTCGGTCGCCGGAGTTGG[G/A]AGTCCATTTGTGCTGTCTTTTGAGTCGGAGTTGGCAATGTTGCCTTTGTGTAGGCCGCATTCTTTGGCCTTTGCGTCCTCCCACCACCAT
73722 T G TGTTGGCCTACTGGCAACACAATGGCCGTCCTCGGCGCTTCCGAGCCGCCTTCTTCCGGCGCGTTCCGCGCCGAGCTCCTCCCTCCG[T/G]TTAAAGGCATACTCGACTTCCTGCAGAGAACGGGCTCGCAGTTCATGATAAACCCGTACCCGTACTTCGCTTACAGGGACGATCCACGACCCGAAACGTT
73722 G A CTTCTTCCGGCGCGTTCCGCGCCGAGCTCCTCCCTCCGTTTAAAGGCATACTCGACTTCCTGCAGAGAACGGGCTCGCAGTTCATGATAAACCCGTACCC[G/A]TACTTCGCTTACAGGGACGATCCACGACCCGAAACGTTGTCGTTTTGCCTGTTTGAGGCGAACCCTGGAAGATTCGACGGGAACACT
73722 C A CGTACCCGTACTTCGCTTACAGGGACGATCCACGACCCGAAACGTTGTCGTTTTGCCTGTTTGAGGCGAACCCTGGAAGATTCGACGGGAACACTAGAAT[C/A]AACTATATGAACATGTGGGACGCGCAGTTGGATGCAATAAAATCGGCATTGATGCGGGCCGGGTTTCCGGATTTAGGCTTCAT
73722 T C CGTACTTCGCTTACAGGGACGATCCACGACCCGAAACGTTGTCGTTTTGCCTGTTTGAGGCGAACCCTGGAAGATTCGACGGGAACACTAGAATCAACTA[T/C]ATGAACATGTGGGACGCGCAGTTGGATGCAATAAAATCGGCATTGATGCGGGCCGGGTTTCCGGATTTAGGCTTCAT
73730 A G TATATTAAAGACAGACTAGTCTGAATAAATATCACTCTTCATAACTTCTCTAAATTTTGTTGAAGGCCACAATATCGCAGCTCTGGATGTACTCATTACA[A/G]GGCTCTGCCGTGAGTTTCTCTTCAACCAGATCATCAACAGAAACAAGATCATCAACAATTGTCATCAT
73750 T C CTGATAATATATGTTATCGAACTTACCTGGCGTCATTATATCGTTGAATACTGCCATGGTGGAATCCTTCAAGTAGTTCCCACAAGCACTCTGCAACCCT[T/C]GGGCGAACCTCGGATTCATGCTCGGATCGAACGAGTTCCACCCCTTTCCTCCGTAGTTGAAGATCCGATCCGCAAACTCCTTGCAGTGA
73768 C T GTCCAGGAAGTATGTCCATGATTTTATCAATAAACCCCTTCTTTTCTCCCTCTTTCCCAGGCTCCACCTTCACATAATTCGCGTTGTCTCCTTCTACAGG[C/T]GCCGCTGCCAAAGGGTTGGCCGCACGTACCGGGGCAGTTTCGTCTTCGTCAACATGCGCCGGAGCCACAGGTGCTGCTGCCACAGGGT
73768 A G AATAAACCCCTTCTTTTCTCCCTCTTTCCCAGGCTCCACCTTCACATAATTCGCGTTGTCTCCTTCTACAGGCGCCGCTGCCAAAGGGTTGGCCGCACGT[A/G]CCGGGGCAGTTTCGTCTTCGTCAACATGCGCCGGAGCCACAGGTGCTGCTGCCACAGGGTCGGGCGCAACGGCAGTTTCCTTCTTTTC
73772 AC A AAAACTACTTTTTAATCCCAAAAATGACCTCTTTGCCCTTATTCATATAACCCCCTCCCCTGCATACCTAATTACACTAAC[AC/A]CCCCCACTGCATTTTTTTCATCCCCAAAAGAGGCCCTCGCAAACTTAATCCACATAGGAACTGCTACTGCTACTCATCATTCATGAATAAATAAAAGCTA
73772 TC T CTTTGCCCTTATTCATATAACCCCCTCCCCTGCATACCTAATTACACTAACACCCCCACTGCATTTTTTTCATCCCCAAAAGAGGCCCTCGCAAACTTAA[TC/T]CCACATAGGAACTGCTACTGCTACTCATCATTCATGAATAAATAAAAGCTAAACGATTACACGGCCTCGGCCACCCTCCACGCCGACGTG
73772 TA T AATTACACTAACACCCCCACTGCATTTTTTTCATCCCCAAAAGAGGCCCTCGCAAACTTAATCCACATAGGAACTGCTACTGCTACTCATCATTCATGAA[TA/T]AAATAAAAGCTAAACGATTACACGGCCTCGGCCACCCTCCACGCCGACGTGGCAATCAACGGCCTCGAGTGCCACCCCAGAGTAAGG
73772 C G GAGGCCCTCGCAAACTTAATCCACATAGGAACTGCTACTGCTACTCATCATTCATGAATAAATAAAAGCTAAACGATTACACGGCCTCGGCCACCCTCCA[C/G]GCCGACGTGGCAATCAACGGCCTCGAGTGCCACCCCAGAGTAAGGCACCCGTCCTTCTCGTCCACCACGTAGCCTTCGCCGCCGGCG
73776 T G ACTTGTTAACTCTGCAACTGGTCGGAAATCCGATATTTTGATTGATGTGCCCAGTGGTGCTAGAACTGATGCTGCACAAGCTGTTAAGAAAATGAAGATT[T/G]CTGCTGCTGATGAAGATGAAGAAATGGTTGATGATCAATAAGTTTATCTTTCAAGTTTTCCAGTCCTGGAATCTGCCAAGAAGTTAAA
73776 T C TCCGATATTTTGATTGATGTGCCCAGTGGTGCTAGAACTGATGCTGCACAAGCTGTTAAGAAAATGAAGATTTCTGCTGCTGATGAAGATGAAGAAATGG[T/C]TGATGATCAATAAGTTTATCTTTCAAGTTTTCCAGTCCTGGAATCTGCCAAGAAGTTAAAAATAAATAAATGAAGTAGAAGTGTTTTT
73782 T C ACATCAGCACATGCAGTAAGTTTCAGTATATCTATTGGGCATTGTGCAGGTTTAATGGGCGCAGGTGATGCGGGTGTGGGGGTAGATGGAGGTGTTGGCT[T/C]TGGCTTGGGATGTGGATGAGGCTTTGGTTCATTAGGTGGAGGAGGGCATGGAGTTTCCTTTGGTGGCGGTCGTGGTGAGCTTAT
73784 C T CTCCACACAACGATAAATGGCTTCAATTACTAGAACAACTCTGGTTACACTCTTTGTTTG[C/T]GCAACTGTTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTC
73784 G A CTCCACACAACGATAAATGGCTTCAATTACTAGAACAACTCTGGTTACACTCTTTGTTTGCGCAACT[G/A]TTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCC
73784 T C CTCCACACAACGATAAATGGCTTCAATTACTAGAACAACTCTGGTTACACTCTTTGTTTGCGCAACTGTTGCCTTCATAGTTGTGGA[T/C]GCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCAT
73784 G A ACAACGATAAATGGCTTCAATTACTAGAACAACTCTGGTTACACTCTTTGTTTGCGCAACTGTTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAA[G/A]CAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGT
73784 C G GAACAACTCTGGTTACACTCTTTGTTTGCGCAACTGTTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGG[C/G]TATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTT
73784 T C CAACTCTGGTTACACTCTTTGTTTGCGCAACTGTTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTA[T/C]CCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTTGCAC
73784 C T CAACTGTTGCCTTCATAGTTGTGGATGCTCAACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCA[C/T]TGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTTGCACCTGTGACAAGCCCGGCGGAGTGTGC
73784 T C AACCAGGGCCAAAAGCAGTAAGATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAG[T/C]GTCGATTGCGAACTCTGCCGCCCCATTTGCACCTGTGACAAGCCCGGCGGAGTGTGCCAAGACCCGCGCTTCGTTGGTGGAGATGG
73784 C T GATGCAAGGACAAAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCG[C/T]CCCATTTGCACCTGTGACAAGCCCGGCGGAGTGTGCCAAGACCCGCGCTTCGTTGGTGGAGATGGCATCACTTTCTACTTCCACGGC
73784 C T AAAAGGGCTATCCTCTTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTTGCAC[C/T]TGTGACAAGCCCGGCGGAGTGTGCCAAGACCCGCGCTTCGTTGGTGGAGATGGCATCACTTTCTACTTCCACGGCAAAAAGGACAGA
73784 C T TTTGCGGAGACTACCTCTTTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTTGCACCTGTGACAAGCCCGG[C/T]GGAGTGTGCCAAGACCCGCGCTTCGTTGGTGGAGATGGCATCACTTTCTACTTCCACGGCAAAAAGGACAGAGACTTCTGCCTTCT
73784 G A TTCACTGCCCTGCTACTTGTCCTACCTCATGCAGTGTCGATTGCGAACTCTGCCGCCCCATTTGCACCTGTGACAAGCCCGGCGGAGTGTGCCAAGACCC[G/A]CGCTTCGTTGGTGGAGATGGCATCACTTTCTACTTCCACGGCAAAAAGGACAGAGACTTCTGCCTTCT
73786 A G GAACCGTAGCTGTTGATGAGCAACATTGCATCTTGGGTCAAAAAGGCTGGATCATTCTTACAACTATATGGTCTTGCCTCTGCGTGGACTCG[A/G]AGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAATGACAATGCTCAAGACAAAAAAGATGAACCTGTCAA
73786 T C TAGCTGTTGATGAGCAACATTGCATCTTGGGTCAAAAAGGCTGGATCATTCTTACAACTATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATG[T/C]ACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAATGACAATGCTCAAGACAAAAAAGATGAACCTGTCAACTATACT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
73786 A G CTTGGGTCAAAAAGGCTGGATCATTCTTACAACTATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGT[A/G]CTTTTCGGGCAGAAGAGAATGACAATGCTCAAGACAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATG
73786 G A CAAAAAGGCTGGATCATTCTTACAACTATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTC[G/A]GGCAGAAGAGAATGACAATGCTCAAGACAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGG
73786 T C TCATTCTTACAACTATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAA[T/C]GACAATGCTCAAGACAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGGCGTCGTAGGCGAT
73786 C G AACTATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAATGACAATGCT[C/G]AAGACAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGGCGTCGTAGGCGATTTGAAGAGA
73786 A G ATATGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAATGACAATGCTCAAG[A/G]CAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGGCGTCGTAGGCGATTTGAAGAGAGCG
73786 A C TGGTCTTGCCTCTGCGTGGACTCGAAGCATGGGATATGTACCTGTCCTGGTACTGCAATGGGTACTTTTCGGGCAGAAGAGAATGACAATGCTCAAGACA[A/C]AAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGGCGTCGTAGGCGATTTGAAGAGAGCGAAG
73786 T C GGTACTTTTCGGGCAGAAGAGAATGACAATGCTCAAGACAAAAAAGATGAACCTGTCAACTATACTTGTTACCCAACAGCAACTTACAATGAGGATGGCG[T/C]CGTAGGCGATTTGAAGAGAGCGAAGGTAAGACAACCCAGACAAATCTGCAGTACAAACGAGGAAGCAACTACCTGGGATGAAGA
73806 T C ATTGTATAAGCATATTGTAATACAATATTGTATACGCATATTGTATACGCAGTACATCCGCACCTTCCTTGAAACACATATTGTATACGCAGTACACTAG[T/C]CTCCAAGCTAAATTGTAAAATCATTCATAATTGCCGCTCATTTACTCACGCTGCAGCTCTTTGCACATTGAACAGGTGCTGTATCCATCCT
73806 T C ATACGCATATTGTATACGCAGTACATCCGCACCTTCCTTGAAACACATATTGTATACGCAGTACACTAGTCTCCAAGCTAAATTGTAAAATCATTCATAA[T/C]TGCCGCTCATTTACTCACGCTGCAGCTCTTTGCACATTGAACAGGTGCTGTATCCATCCTTCAAGAGTTCATCAATGGGTTTCTTTCCATG
73806 T G CCTTCCTTGAAACACATATTGTATACGCAGTACACTAGTCTCCAAGCTAAATTGTAAAATCATTCATAATTGCCGCTCATTTACTCACGCTGCAGCTCTT[T/G]GCACATTGAACAGGTGCTGTATCCATCCTTCAAGAGTTCATCAATGGGTTTCTTTCCATGGTTATTTAGCTTATCAACTCC
73810 C T AAAGAACATCACATTGACTAGCTTAGTAAAAAAAGTACCCAATTAATTTCCTTCTGCATAAGTAGTTTCAAGAATAGCAGCCTCGGCTTCCTGCACCTCC[C/T]TCTCGGTCTTCTTCCCCTTCTTATTCTTATAATACACACTCATAAACGTCCCAACCGCCCCGTACTTCCTCCTACATGCTCATACAG
73818 C CG GGGAGGTAATGGAGGATATACTGAGGTTTTGTAAAGAGAAGATGCCCGGGTATTGGGTGCCCAAGAGCGTTGTGTTTGGGCCGTTGCCCAAGACGGCGAC[C/CG]GGGAAAATTCAGAAGCATTTGTTGAGGGCTAGGGCTAAGGAATTGGGCCCTGTTAAGAAGAGTAGGCTGTGATTTATGATAT
73848 A AC TTCTTCGGTTTCGCATCCCTATGCACAACGCCCGTCTAATGACAATACTTCAAAACACCGACCTACTCCTTCACAATCTTTGCCGCCTTCAGCTCTGAAA[A/AC]CATGACCACTTCCTTCATTCAAACCAAGCAGTCTCCCACCTTACTTCCTTCGATTGGAAACTGGAAAAGCTGAAGCCCATTGGATTGAA
73848 AT A CCTATGCACAACGCCCGTCTAATGACAATACTTCAAAACACCGACCTACTCCTTCACAATCTTTGCCGCCTTCAGCTCTGAAAACATGACCACTTCCTTC[AT/A]TTCAAACCAAGCAGTCTCCCACCTTACTTCCTTCGATTGGAAACTGGAAAAGCTGAAGCCCATTGGATTGAACATTCCCGTTCGCTTCA
73848 G A CCGTCTAATGACAATACTTCAAAACACCGACCTACTCCTTCACAATCTTTGCCGCCTTCAGCTCTGAAAACATGACCACTTCCTTCATTCAAACCAAGCA[G/A]TCTCCCACCTTACTTCCTTCGATTGGAAACTGGAAAAGCTGAAGCCCATTGGATTGAACATTCCCGTTCGCTTCAGGGAGCTTCTGCTGC
73850 G A ACCCCCTTCTCCGACAGCTTAACTCCATCCGCGCCTCCATCGCCGCCCTCCAATCGTCCTCCTCTTCCTCCTCTAAGTCGTCCACCACTGCTCCACCTGA[G/A]CTCCTCCTCTACGCGAAGCTCTCCCCCATCGCATCCGCCTGCTCTGACCATCCCCACCTCCTCCATTCCTACATGAACTACACCCCCTTCTC
73860 AT A AAGATGCTTTCCATCTCTTGGGGATCTGCTATCAGCTGCCATTACTCTATAAAATGGTTTGTTCTTGCATCCAAACCTCGATAATCGTATTCTTACTACC[AT/A]TTTTTTTCTTCACTGCCTTTGGAAAACACTGAAGAGGATGGGAGCCAAGACGGTGACAGAAGCGGCAGAATCGGCTGATGACGGAGG
73864 C T TGGCCTTTTTTTTTTTGGTAAATTTAACAACTATGTAACAGGCAGTGAACCAACAAACACAACGGCAAGAGT[C/T]ATAAATAATACAATAAAATTACTGGCTCCATAAACAAGAGAGTGACAGTTAACCAAGTCAATAACAAACATAAAAGACGCCCTACAAAATATTCCAGACA
73888 G A TTATTGGTGAAGGTGAAGAGAAGGACCAGGAATCAATTGAGCGAGCTCGCAAAACAACCAAGTATATGACAAAATACGAGCGTGCAAGAATATTGGGCAC[G/A]CGGGCTTTACAAATTAGCATGAATGCACCTGTGATGGTTGAGCTTGAAGGAGAGACTGATCCACTTGAGATTGCAATGAA
73892 A T GCAAATGAAGTAGACGAAACCATAAAAGCAATTAAAGTGGTATGAATCCACAGATAAGTTAAGGGTAGACATGAGTTCAGAAAGATCATTGAAAACATCA[A/T]CCCTCGCATGTTCAATAGAATCCAATGATTTTGATAAGATTTTAAGCAAGTCCCTTGAGCAAGCATGGTTTTCATTAGAGATAATAT
73892 A G TTCAATAGAATCCAATGATTTTGATAAGATTTTAAGCAAGTCCCTTGAGCAAGCATGGTTTTCATTAGAGATAATATCACAGTATTTTGAGTAGATCTCG[A/G]AAATATTGAAGGCCGCGGAAGCCATGCTTGCACAAGTACGATCAAGAGTTTCAAACTGGATTCCCGATTGAATGAAATTGAAACCCTA
73936 C T ATTGTGAAAAGGGGATACAACCCCAAAAATAACATAAAATGTTTTCACCACCAATACAGTTAAATAGATGAAGCTAATCACTATCAAAATGACCCATGAA[C/T]TGTAAAGGTACGCAGATCTATTATTCAGCCCAAACTCCTTAACTTTATCTTTGAGATGTATACAACTTCTGCTAAACCAACTTGTAAAT
73962 A G GATCAGCACCTTCTAAAGCTTGAACAAGGTTCTCCTCAGATGCAAATCCAGCAACCTCAGCATGGGTATTGATATGGCT[A/G]ACGTCAGCCGCCACGCCAGGAGTACCAGCAATATCATAAAGAGCTAGCTTGGTAACAAGAGGGTTAAGCTTCATCAGAAGTGACAAAGGCTGCCCAATCC
73982 C T TGCTCGGTGCCTTGGGCTGCGTCTTCCCGGAACTCCTGGCCCGTAACGGGGTCAAGTTCGGGGAAGCTGTGTGGTTCAAGGCAGGATCCCAGATCTTCAG[C/T]GAGGGAGGGCTGGACTATTTGGGAAACCCGAGCCTGGTGCACGCTCAGAGCATTCTGGCGATATGGGCGACCCAGGTGGTGCTG
73982 G T CCCGTAACGGGGTCAAGTTCGGGGAAGCTGTGTGGTTCAAGGCAGGATCCCAGATCTTCAGCGAGGGAGGGCTGGACTATTTGGGAAACCCGAGCCTGGT[G/T]CACGCTCAGAGCATTCTGGCGATATGGGCGACCCAGGTGGTGCTGATGGGAGCGGTGGAAGGGTACAGGGTAGCAGGTGGG
73982 C T GTAACGGGGTCAAGTTCGGGGAAGCTGTGTGGTTCAAGGCAGGATCCCAGATCTTCAGCGAGGGAGGGCTGGACTATTTGGGAAACCCGAGCCTGGTGCA[C/T]GCTCAGAGCATTCTGGCGATATGGGCGACCCAGGTGGTGCTGATGGGAGCGGTGGAAGGGTACAGGGTAGCAGGTGGGCCT
73982 C T GTTCGGGGAAGCTGTGTGGTTCAAGGCAGGATCCCAGATCTTCAGCGAGGGAGGGCTGGACTATTTGGGAAACCCGAGCCTGGTGCACGCTCAGAGCATT[C/T]TGGCGATATGGGCGACCCAGGTGGTGCTGATGGGAGCGGTGGAAGGGTACAGGGTAGCAGGTGGGCCTCTAGGGGAGGTGG
73982 C T GCATTCTGGCGATATGGGCGACCCAGGTGGTGCTGATGGGAGCGGTGGAAGGGTACAGGGTAGCAGGTGGGCCTCTAGGGGAGGTGGTGGACCCGCTGTA[C/T]CCTGGTGGGAGCTTCGACCCGTTAGGGCTGGCGGATGACCCGGAGGCGTTTGCGGAGCTGAAG
74006 C T TGCACTCGATCGATTATGGATTGATCGATACCATGATTAAGTAGTTGGAAGAATCCGAAAGTTTCGGATGCGGATCTGA[C/T]CTGGGCGGCCAGCTGGCTGCGGTCGGAGTGGAGGTCGACGGTTGGGATTTGGATGTTTGGGTTGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGT
74006 G A CTCGATCGATTATGGATTGATCGATACCATGATTAAGTAGTTGGAAGAATCCGAAAGTTTCGGATGCGGATCTGACCTGGGCGGCCAGCTGGCTGCGGTC[G/A]GAGTGGAGGTCGACGGTTGGGATTTGGATGTTTGGGTTGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGTAGTTTGGC
74006 G A ATTATGGATTGATCGATACCATGATTAAGTAGTTGGAAGAATCCGAAAGTTTCGGATGCGGATCTGACCTGGGCGGCCAGCTGGCTGCGGTCGGAGTGGA[G/A]GTCGACGGTTGGGATTTGGATGTTTGGGTTGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGTAGTTTGGCAACATGGT
74006 G A TGGATTGATCGATACCATGATTAAGTAGTTGGAAGAATCCGAAAGTTTCGGATGCGGATCTGACCTGGGCGGCCAGCTGGCTGCGGTCGGAGTGGAGGTC[G/A]ACGGTTGGGATTTGGATGTTTGGGTTGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGTAGTTTGGCAACATGGTCGTC
74006 G A GTCGGAGTGGAGGTCGACGGTTGGGATTTGGATGTTTGGGTTGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGTAGTTTGGCAACATGGTCGTCG[G/A]CCAGACCTTTGACGCCGGTTTTGGTGGAGTCGAAAGCGTCCAATTCGGCGATGCGTCGGGAGTTTGGCATGGTATGCGGACT
74006 C T TGGGGTTGTTGGTGAAGCTGTGGTGGAAGAAGGAGGGTAGTTTGGCAACATGGTCGTCGGCCAGACCTTTGACGCCGGTTTTGGTGGAGTCGAAAGCGTC[C/T]AATTCGGCGATGCGTCGGGAGTTTGGCATGGTATGCGGACTGTAGGGTTTCTGATAAGCCGGGGTTTGTTTGTCCAGTAGGCCA
74006 G C AAGAAGGAGGGTAGTTTGGCAACATGGTCGTCGGCCAGACCTTTGACGCCGGTTTTGGTGGAGTCGAAAGCGTCCAATTCGGCGATGCGTCGGGAGTTTG[G/C]CATGGTATGCGGACTGTAGGGTTTCTGATAAGCCGGGGTTTGTTTGTCCAGTAGGCCAACAG
74012 T C GCAAAGAGATGCACATACAGGATACTTCATGCATGGAACTTGCAAGTCCTAGAACTAGGATCAGAAGTAGTGAGAAGGCCACTCTGTTTAAAATCGCAGT[T/C]GTGGCGACCAGAAGCTTGATAGTAAGCATTCATGGCAAAAGACGCATGGCTTTGAAGGGTATTGGGAAAGAAGCAGGATCCCCC
74012 C T ATGCACATACAGGATACTTCATGCATGGAACTTGCAAGTCCTAGAACTAGGATCAGAAGTAGTGAGAAGGCCACTCTGTTTAAAATCGCAGTTGTGGCGA[C/T]CAGAAGCTTGATAGTAAGCATTCATGGCAAAAGACGCATGGCTTTGAAGGGTATTGGGAAAGAAGCAGGATCCCCCGCTCTGTAT
74084 A G CGCTCTTCACGAAGAAGAACGCCAGAAACAACGGCGGCAGTTGCGGTGGCGCTGTTTCCGGCGAGGAGTCGACGTGCTCGTCTGCGTCGTCGTTCACGAG[A/G]TCGTGTCTGGCGAAGAATCCGTCGGACCATAAGAGGTCCGTTAGGTTCGAGCTGCCAGCCAACGACGTCAAAATGACATGGCGC
74092 G C CGTCCCTCACCGCCACGTACAGCGGGTTCACCAGCCTCGTGAACATCGTGCCCGAATCCAGCACCGTGCCCGAGCCCGTGGCAGCGTCGAACCCGTTCCC[G/C]ACCGCTATCCACCTCCTCCCCACCCGGATCCGGACCAGGTTCACGTAGTACAGCGACGACCGCCGCGGGTTCGACAGCAGCGGCG
74108 A G TGTTTCGAACTTCGCCTCCAGTTATCTTCATCCGCCACTGCTTTCTACAGTTCCTGACCCTGTGCGGATCCTGATCTTCAGACCACCCTGCTATATCCAC[A/G]TCAAATTCTAGAACCCTAAATATGTCCAAGACTAGAAGACAAGAAAAATCTAAAAGCTCTAAACGTAAACTTGAGAAGAGGCTTCAATT
74108 A G CTGCTATATCCACATCAAATTCTAGAACCCTAAATATGTCCAAGACTAGAAGACAAGAAAAATCTAAAAGCTCTAAACGTAAACTTGAGAAGAGGCTTCA[A/G]TTTCAAGCTAAAGTTAAAGATGCTACTACCAGTTTATCTGCTACAAAAACCATTGAAAAGAAAAAAA
74150 T C GACTGAAACATTGATAGAACTTATGCTCATGATTATTCATGCACTCATTATTTACATATACACATGATTCACAATGCAAACAAACTTCCTCGGAGT[T/C]GCAACTCACAACTAGAGATTATAAGACAGTTCACCCGGGAAGTCTCAGTTCAACGGCACAGGAATCTGAATGTAGGAACAAGATACTTTCAA
74158 A G TAACTATTGACATTTTCATATAAACTTAAACTTTACCTTGGCAATCCTTCCAATTCAAGTTTACCTAATGACATTTTCATATAAAATCACCTGAACTACA[A/G]ATACTTCACAACACTTTAAAGTTTATAACTTTAGCAGAATGCAGTTCATCTGAAGTTGTCTGTACCTGATTTCGATTTTCACCTTAATTCGAT
74158 G A TTGGCAATCCTTCCAATTCAAGTTTACCTAATGACATTTTCATATAAAATCACCTGAACTACAAATACTTCACAACACTTTAAAGTTTATAACTTTAGCA[G/A]AATGCAGTTCATCTGAAGTTGTCTGTACCTGATTTCGATTTTCACCTTAATTCGATGACTTCTTCATATTTATTCAAATCTTCCCTCTCTTTTT
74194 A G ATATCCAAATGGCCTTCCACTCATACATCTTGCCATTATTGTTGCTTCTACTCTTTCCACTCAATATATCTTGTCAAAACATGAACCCAGGCACAACTTT[A/G]TCTCCATCCACTAACTCCTCAGCTGTACTCTCCCCTTCAGGTGACTTCGCCTTCGGATTCCGAGCGCTTGATACCGATCCTACCCGCTTCCT
74194 T G TCTCCCCTTCAGGTGACTTCGCCTTCGGATTCCGAGCGCTTGATACCGATCCTACCCGCTTCCTACTCGCTGTCTACTACAACAAAATCAAGGCCAAAAC[T/G]GTAATCTGGACCGCCAACGAAGGCACCTCTGTGTCGAACAATTCAAAGGCTTTGATGACTTCAGACGGCC
74210 C T GCTTCTTCTCAGCAAAATCCAGCCTTTGCTATACCAAACCCTACTTGTTGGCTCTCGCTACGGGCCAAATTGGTCGCAAAATCCGTTGGCACTGTCTGGA[C/T]CCATTTGGAAAAACTGGTTCCGTCTTCCGTGGCCAAAGAGAAGGGGTTATCAGCCAAAATCCGATTGTAGAGAACGAAATCATGAATT
74210 T G TTGGCTCTCGCTACGGGCCAAATTGGTCGCAAAATCCGTTGGCACTGTCTGGACCCATTTGGAAAAACTGGTTCCGTCTTCCGTGGCCAAAGAGAAGGGG[T/G]TATCAGCCAAAATCCGATTGTAGAGAACGAAATCATGAATTTCTCCAATTCAACAAATATTAAATCAGCCAAAAACAAACAAATCTC
74232 C T ATTATTTGGACAAAAACTAGTACATGTTCTAATCAAATAACACACCATAATCTATTACAATTACAAGGATATAAGTAATCAAAAATAGTAAACGGATATA[C/T]GTGCATGTACTTAGACGACCTAACACTACCGAACTATGTTTCCTCGAACGTGCTCATAAATCCACCTAAAAAGCCAGCTCCATTGCAAT
74232 T C ACTATGTTTCCTCGAACGTGCTCATAAATCCACCTAAAAAGCCAGCTCCATTGCAATTTCCACACAGAATTTCACGTTTTCCCCTGCATAACCAGCAGCT[T/C]GCCCCGGCTTTAAACTGCCCATTGAAATGGTCTTTAGTATTCACTCCATTTCCTTCACAC
74238 A G GAGGAATCCAGAGGCTTCTTGTATATGAGTATATGCATTATAGAAGTGTGATGGATCATCTGTCAGCGAAATCTATTGTACCTCTTCCATGGAATATGCG[A/G]TTAAAAATTGCTCTTGATGCTGCTCGTGGATTGACTTACCTACACGAAGAGATGGAATTTCAGATTATATTTAGAGATTTCAAAACAT
74244 CA C AGTCGAGAAGGCAAAACCGAGTTAGGAATTAGCGGTTTCAAAATTGGTGATAGGAAAAGAAAAGAAAACAGAAAAAGAGACAAGAAAACAAAAGCGGAAA[CA/C]AAAAAGCGAAACACAGCGGATGAGGAGAATAGATAATGGAGGACGATCATGGTGATAGAGGGAAGAGGAGATCTGGAAGA
74266 C T ACTGTTGGCCTACTGGACTCTGATATCTTCCATCAAATTTTGTCATCGATTTATTCTTCGTGCAATAGTCCATCTCTTCAAC[C/T]TTAGCCCTAATCTATTAACATGGGAGGCGGCAATGCACAGAAAGCGAAGATGGCTCGCGAAAGAAACCTGGAGAAGCAAAAGAACGCCTCGAAAGGAAGC
74266 A T CCATCAAATTTTGTCATCGATTTATTCTTCGTGCAATAGTCCATCTCTTCAACCTTAGCCCTAATCTATTAACATGGGAGGCGGCAATGCACAGAAAGCG[A/T]AGATGGCTCGCGAAAGAAACCTGGAGAAGCAAAAGAACGCCTCGAAAGGAAGCCAGCTTGAAGCAAATAAGAAGGCCATGTCAATT
74272 C G TGGCGCTCGCCGCAGGCACCAAATTGCTGTCAAGCAACTTCAAAATCCCATCGCAAATCGAAGTCAACTCCGACTCGATCTTCGATCTGTAGTTTCTGAT[C/G]GCCGCTACGTGGTCCTCGTTGCCGCGGGACTCCTCCTTCTGCTCGATCGAAGACACGATCCTCCACGACGCACGTCGAGCACCGATC
74272 T C TCGCCGCAGGCACCAAATTGCTGTCAAGCAACTTCAAAATCCCATCGCAAATCGAAGTCAACTCCGACTCGATCTTCGATCTGTAGTTTCTGATCGCCGC[T/C]ACGTGGTCCTCGTTGCCGCGGGACTCCTCCTTCTGCTCGATCGAAGACACGATCCTCCACGACGCACGTCGAGCACCGATCACGTTTT
74284 G A TGCAGCAGCTCCGTGATCAAGGGTTGTGCCTCAATTGCAACAGCATAGACACCATTAGTCATCGCTGTTTGGTTA[G/A]GAGAATCATTGTGGTGCTGCCAGATGAAGACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTG
74284 G C TGCAGCAGCTCCGTGATCAAGGGTTGTGCCTCAATTGCAACAGCATAGACACCATTAGTCATCGCTGTTTGGTTAGGAGAATCATT[G/C]TGGTGCTGCCAGATGAAGACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCC
74284 A C TGCAGCAGCTCCGTGATCAAGGGTTGTGCCTCAATTGCAACAGCATAGACACCATTAGTCATCGCTGTTTGGTTAGGAGAATCATTGTGGTGCTGCC[A/C]GATGAAGACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTA
74284 G T GCAGCTCCGTGATCAAGGGTTGTGCCTCAATTGCAACAGCATAGACACCATTAGTCATCGCTGTTTGGTTAGGAGAATCATTGTGGTGCTGCCAGATGAA[G/T]ACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACC
74284 A G CGTGATCAAGGGTTGTGCCTCAATTGCAACAGCATAGACACCATTAGTCATCGCTGTTTGGTTAGGAGAATCATTGTGGTGCTGCCAGATGAAGACCCAT[A/G]TACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCT
74284 C A TCATCGCTGTTTGGTTAGGAGAATCATTGTGGTGCTGCCAGATGAAGACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACA[C/A]TGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCTTTACCTTGTCCACCGTCACTTTATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
74284 C T GTGGTGCTGCCAGATGAAGACCCATATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCC[C/T]TACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCTTTACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGT
74284 C T TATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTG[C/T]CGCTACTAGGCCTTTACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTAC
74284 C T ATACCGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGC[C/T]GCTACTAGGCCTTTACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTACT
74284 A G CGAGCACCAACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCT[A/G]CTAGGCCTTTACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTACTCAAG
74284 T A ACCCATGGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCT[T/A]TACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTACTCAAGAGCTGCAGT
74284 T C GGAGACAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCTTTACCT[T/C]GTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTACTCAAGAGCTGCAGTTTTTAA
74284 A G CAACTGCTGTACTGAACTCCACACTGGCTTCTCTTCCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCTTTACCTTGTCC[A/G]CCGTCACTTTATCCTACTTTTGGGCCTATGAAACATAATGTTCATTATCAATCAGATGTGTACTACTCAAGAGCTGCAGTTTTTAAAGCAT
74284 A T CCCTTGCTTAAGCTCCCTACACCTCCACCTACCCTTGCTGCCGCTACTAGGCCTTTACCTTGTCCACCGTCACTTTATCCTACTTTTGGGCCTATGAAAC[A/T]TAATGTTCATTATCAATCAGATGTGTACTACTCAAGAGCTGCAGTTTTTAAAGCATTGTGTGCC
74298 A C CCGGAGCTCCGACAAGGCCTGTACCGACCGTCGGGTCGCTCTTGTCGAACGACCCCACGTTTCTAGGGTTGTTGTAGTGGTCAACCACTCGTTCGTGGTA[A/C]CATCTTGATTGAGTTATCGTCACCTCCCGTGAAATAACGGAGCGGTTACCTGTTGCAGCTGGTGCTAGAAATCGCCTCGCTACCTGT
74300 C T CATCTTCACTATTAAATTTCATTTTTAGATCTCCAGCTCAATCTCCATTCATCCGCCTTTTCCATGTCTGCCTCATCCAGTTCCTCCTACTGGTG[C/T]TACCGTTGCGCCCAATTTGTCCGCGCCGTCGACCAACCAAATTCCCCCACTTGCCCTAACTGCAGTTCTGGCTTCCTTGAGCAGATCCACTCCCCTC
74300 A C ATTTGTCCGCGCCGTCGACCAACCAAATTCCCCCACTTGCCCTAACTGCAGTTCTGGCTTCCTTGAGCAGATCCACTCCCCTCCGCCTCCCTCCGTCGAC[A/C]TCCGGCGCTCCCACCTCCGCCAGCGCCACCGTTCTTCGACCACCGCAAATCAATCTCCCTTCAACCCTGTCATCCTTCTCCGCAATAACC
74300 G A TCCGCGCCGTCGACCAACCAAATTCCCCCACTTGCCCTAACTGCAGTTCTGGCTTCCTTGAGCAGATCCACTCCCCTCCGCCTCCCTCCGTCGACATCCG[G/A]CGCTCCCACCTCCGCCAGCGCCACCGTTCTTCGACCACCGCAAATCAATCTCCCTTCAACCCTGTCATCCTTCTCCGCAATAACCCCTCC
74304 A G AAGCTAGGATTTTGGGTTCAGACGAAGATGGTATATATAATTAACAGAAAGAACATCATTTCGAGCTCTTTTCTTCTATCCCCATAACTAAGATTTCGAT[A/G]TACTCCACATAACTAGTGAGCCCAGTGTGGTTTGGCCATAGTCCTTACAAGAGCTTTAATACTTAGAGGGCTGTTCTTGCTCACGCTGC
74304 A G TTAACAGAAAGAACATCATTTCGAGCTCTTTTCTTCTATCCCCATAACTAAGATTTCGATATACTCCACATAACTAGTGAGCCCAGTGTGGTTTGGCCAT[A/G]GTCCTTACAAGAGCTTTAATACTTAGAGGGCTGTTCTTGCTCACGCTGCAAGTACCGGCATAAACATTGCAGACGGGATACTCATGAGG
74306 C T CACAACAACCAAAGCTATTTGTTGGCATGATCTTGATCCTGATCTTTGCGGAAGCTCTTGCTCTGTATGGCCTCATTGTCGGAATCATCTTGTCTTCTCG[C/T]GCTGGACAATCCCGTGCTGATTAATTTCGCATCATTGCTTTGTTTTTCGGATGTTTCTGTATACTGTATTTTGTTGCAGGGCTTGTTACAG
74312 T C AAGCAGGAAGAAGTAAGGGAAGGAGGAACGGGAGACGAGGAGGGTTCCATCTAAGTCTGCGGCGACGGAGGAGGAGGAGGAGAGGGAGGAGATGGAACAG[T/C]TGGATATTGGTGGGAAGCTTGTTTTTGGTTTTTTGCCCATGTTTTTTTAATTTTTGGGTAGGAAAGTTGGATTTTTAGGTTAA
74346 G A CATGTTTTAATACATCAGTTTGCATTCTTACATCAATCGATCAGAAATCAAAGCCAGCATCATCGAATCCGGCGTCATATCCAGCATCATAGCTACCCGC[G/A]TCCGACACCATATCACCGATTATCATACCTCCTAAGGCACCTCCAAGCAAACCCGCACCCAAACCCAAACCTGCTCCGCCAAACTTGTTC
74346 T A CATATCCAGCATCATAGCTACCCGCGTCCGACACCATATCACCGATTATCATACCTCCTAAGGCACCTCCAAGCAAACCCGCACCCAAACCCAAACCTGC[T/A]CCGCCAAACTTGTTCTTCCTACCCTGTTGTTGCTGTTGAGGAGGGTAATACCCTCCTTGCTGGGGTGGTGGATACCCATATCCGGCTTG
74346 G A ATCCAGCATCATAGCTACCCGCGTCCGACACCATATCACCGATTATCATACCTCCTAAGGCACCTCCAAGCAAACCCGCACCCAAACCCAAACCTGCTCC[G/A]CCAAACTTGTTCTTCCTACCCTGTTGTTGCTGTTGAGGAGGGTAATACCCTCCTTGCTGGGGTGGTGGATACCCATATCCGGCTTGTTG
74364 G A CTAGAAAGCAGCTATCATGAAAAGGACAAATCAACGGAGTACGAATGCCGAACGTCAGATGTGACCGTGCCCA[G/A]GATGGCCGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTC
74364 C G CTAGAAAGCAGCTATCATGAAAAGGACAAATCAACGGAGTACGAATGCCGAACGTCAGATGTGACCGTGCCCAGGATGG[C/G]CGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCA
74364 C T CTAGAAAGCAGCTATCATGAAAAGGACAAATCAACGGAGTACGAATGCCGAACGTCAGATGTGACCGTGCCCAGGATGGCCGACTATATAGAAA[C/T]GGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCT
74364 G A CGGAGTACGAATGCCGAACGTCAGATGTGACCGTGCCCAGGATGGCCGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACAC[G/A]GTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACA
74364 A C AATGCCGAACGTCAGATGTGACCGTGCCCAGGATGGCCGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAAT[A/C]TCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTT
74364 T C ATGCCGAACGTCAGATGTGACCGTGCCCAGGATGGCCGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATA[T/C]CGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTG
74364 C T GAACGTCAGATGTGACCGTGCCCAGGATGGCCGACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTC[C/T]GATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTT
74364 G A ACTATATAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAA[G/A]CTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCA
74364 C T TAGAAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTG[C/T]TCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTG
74364 C A AAACGGATGAGTGCGTAAAGGCTTGTGGAGTGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTC[C/A]CCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGC
74364 C T TGCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACAT[C/T]GTCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGC
74364 G A GCAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATC[G/A]TCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGCA
74364 T A CAACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCG[T/A]CGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGCAT
74364 C T AACGTAACACGGTCGGAATATCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGT[C/T]GATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGCATG
74364 C T TCGTCCGATTCTCTTCTTGAGCCGGAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTTCAACCTTG[C/T]TGCAGGAGAAGGGGTATTTCTACCAGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGCATGGTTGAACTCAGTAGTTCTGG
74364 C T GAGTTCACCGCAAAGCTGTGCTCCCCGCACTGTCATCAGCACTGCCCTAACATCGTCGATTTGTTCTTCAACCTTGCTGCAGGAGAAGGGGTATTTCTAC[C/T]AGAGCTGTGCCAAGCAATGAAATCGAACACACGTCGGAGCATGGTTGAACTCAGTAGTTCTGGCGCT
74370 CT C CTGCTGCACTGTGCAAGTTGTGCGGCTCCATGTGAAGTCGGATGGGTACGTGCTAACCTTTTCTCTGCTCCAACATATTATGTAATTTAATTGTATTTTT[CT/C]TTTTCTTTTTAAAGAATGTTATGTAATTGTGTCAAATAACTCCCCGTGTGGAGTGATGGTGAATGATCCACCTTAAAAACCATAGTAGA
74370 G GT AAGTTGTGCGGCTCCATGTGAAGTCGGATGGGTACGTGCTAACCTTTTCTCTGCTCCAACATATTATGTAATTTAATTGTATTTTTCTTTTCTTTTTAAA[G/GT]AATGTTATGTAATTGTGTCAAATAACTCCCCGTGTGGAGTGATGGTGAATGATCCACCTTAAAAACCATAGTAGATAGCCATTCAGTCT
74370 T TA ATATTATGTAATTTAATTGTATTTTTCTTTTCTTTTTAAAGAATGTTATGTAATTGTGTCAAATAACTCCCCGTGTGGAGTGATGGTGAATGATCCACCT[T/TA]AAAAACCATAGTAGATAGCCATTCAGTCTCTCTTTTGAAGTAATGTATTTATTATTTGGTATAATAGAAAGTGTTTACGGTCATTTTTAAA
74374 T A CTTTGCTTCAGTACAGCACTGTCTAAGGGCCTCGCTTTTTACCAAAGCACCACATACATCCTCCTTTCTGATCAACTGGAATCATTCCTCCACCCTTCGA[T/A]GTATCGATCGCCTCCAATAATGCAACCACTTCATCCATTTCTGGTCTTTTGTCAGGACTCGCATCCCAACATTTCTTCATTACATTTGCTAG
74408 C G GCGTGTGGCTGTGCGAGGTCTGCGAGCAGGCGCCGGCGGCCGTCACGTGCAAGGCCGACGCGGCGACGCTGTGCGTGACGTGCGACGCGGACATCCACGC[C/G]GCGAACCCGCTGGCCAGGAGGCACGAGCGGGTGCCGGTGGTGCCGGTTGGGAATCCGACGGTGCAGGTTAAGGAGGATCT
74416 T C GGAGCAAACTCATTCTTCCTTTTTAATTCTATGGCCACCGCAGTCAAACCCTTTTCCCCAAAAT[T/C]GAAATAAATCGCCACCTTCCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGATCTAATTGCTCCTCCTTCAAG
74416 G A GGAGCAAACTCATTCTTCCTTTTTAATTCTATGGCCACCGCAGTCAAACCCTTTTCCCCAAAATT[G/A]AAATAAATCGCCACCTTCCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGATCTAATTGCTCCTCCTTCAAGT
74416 A T GGAGCAAACTCATTCTTCCTTTTTAATTCTATGGCCACCGCAGTCAAACCCTTTTCCCCAAAATTGAAATAAATCGCC[A/T]CCTTCCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGATCTAATTGCTCCTCCTTCAAGTAATTCAACTCAAA
74416 T C CAAACCCTTTTCCCCAAAATTGAAATAAATCGCCACCTTCCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGA[T/C]CTAATTGCTCCTCCTTCAAGTAATTCAACTCAAAACCGGGTCTTGTTCAGCTTTGTCGCAAATCAAAGTTGTGAGCCTGCTAGTTCGACG
74416 G C TCCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGATCTAATTGCTCCTCCTTCAAGTAATTCAACTCAAAACC[G/C]GGTCTTGTTCAGCTTTGTCGCAAATCAAAGTTGTGAGCCTGCTAGTTCGACGCCGTCCGTTTTATGAAGCACGCACCGCCTCCGAAGCC
74416 G T CCTCCTCCTGCATATGAACAACCTTGCTCCGCCTTCTGCCCTAAATCATGGCCACCGGAGATCTAATTGCTCCTCCTTCAAGTAATTCAACTCAAAACCG[G/T]GTCTTGTTCAGCTTTGTCGCAAATCAAAGTTGTGAGCCTGCTAGTTCGACGCCGTCCGTTTTATGAAGCACGCACCGCCTCCGAAGCCT
74416 C T CTCCTCCTTCAAGTAATTCAACTCAAAACCGGGTCTTGTTCAGCTTTGTCGCAAATCAAAGTTGTGAGCCTGCTAGTTCGACGCCGTCCGTTTTATGAAG[C/T]ACGCACCGCCTCCGAAGCCTCGGATGAAGCCAGTCCGTTACATCGAAGCCAATCCGTTACGTATGCTTTTTCTTCTACCATAG
74422 A G CTGGATCGAGTCAGAATCAAATAAATCCCCATTTTCTCGTCGATTTTTAAACCCTAATTTTTAATCGCAAATGGCCCTAGTTCCTCGCGTCTTCGGACCA[A/G]CAAGCAGCGTTTTCGACCCGTTCTCCGTCGATGTGTTCGATCCGTTCTCCCTCGATCTGTTCGACCCATTCCAATCCCTAACGACTCCGTT
74422 T C CAGAATCAAATAAATCCCCATTTTCTCGTCGATTTTTAAACCCTAATTTTTAATCGCAAATGGCCCTAGTTCCTCGCGTCTTCGGACCAACAAGCAGCGT[T/C]TTCGACCCGTTCTCCGTCGATGTGTTCGATCCGTTCTCCCTCGATCTGTTCGACCCATTCCAATCCCTAACGACTCCGTTCCAATCTCTAG
74422 G A TTTTAAACCCTAATTTTTAATCGCAAATGGCCCTAGTTCCTCGCGTCTTCGGACCAACAAGCAGCGTTTTCGACCCGTTCTCCGTCGATGTGTTCGATCC[G/A]TTCTCCCTCGATCTGTTCGACCCATTCCAATCCCTAACGACTCCGTTCCAATCTCTAGCAATTCGCCCTGCTTTCAGCAACGAGGTTGCAG
74422 C A TCGATCCGTTCTCCCTCGATCTGTTCGACCCATTCCAATCCCTAACGACTCCGTTCCAATCTCTAGCAATTCGCCCTGCTTTCAGCAACGAGGTTGCAGC[C/A]CTGGCAAACACTCGCATCGACTGGAGGGAGACTCCAGAGGCACACGTGTTTAAAGCGGACTTGCCAGGTCTGAAGAAGGAAGAAGTG
74436 G A TTGCGGAGATATTGGGCGATTAAAGGTGCAGGGCGCACGCTGGACGTGCGACCCTTTGACGTCGTCGGCAACATCTCCTGTCTACTTAATTTCTTGACTC[G/A]GTAGGATCAAAACTGTATTTAATTCGATTCAATTTTGATTATTTTGTTCACTTGTATACTCTTTTTTAAGATCTGAGATAATTTTACTTT
74456 CAA C ATATCAAAAGAGATACATTTCAATTTCAACAAATAACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGA[CAA/C]AAAAAACTACAGTGTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCT
74456 A T ATATCAAAAGAGATACATTTCAATTTCAACAAATAACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGACAAAAAACT[A/T]CAGTGTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTA
74456 T C ATATCAAAAGAGATACATTTCAATTTCAACAAATAACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGACAAAAAACTACAG[T/C]GTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTA
74456 C T AGATACATTTCAATTTCAACAAATAACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGACAAAAAACTACAGTGTCTCCTAATTACAT[C/T]AAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCC
74456 A G ACAAATAACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGACAAAAAACTACAGTGTCTCCTAATTACATCAAACTCAAAATATCATG[A/G]CTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAAT
74456 C G ACAATGCAGTTACTGTGGAGAAAATTTCAGTTGAGACAATGGCAGACAAAAAACTACAGTGTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGC[C/G]TTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTC
74456 A G AATTTCAGTTGAGACAATGGCAGACAAAAAACTACAGTGTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACAT[A/G]TTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCGTTGCCAGCTTCAGCAAGCCAC
74456 C A AGACAATGGCAGACAAAAAACTACAGTGTCTCCTAATTACATCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACA[C/A]CATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCGTTGCCAGCTTCAGCAAGCCACCCGTATCTAGT
74456 A G TCAAACTCAAAATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGT[A/G]CGCCTCAATTGTCGTCGTTGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCG
74456 T A AATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAAT[T/A]GTCGTCGTTGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
74456 G A ATATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATT[G/A]TCGTCGTTGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGC
74456 T C TATCATGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTG[T/C]CGTCGTTGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCA
74456 G A TGACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTC[G/A]TTGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCATAGGC
74456 T C GACTAAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCG[T/C]TGCCAGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCATAGGC
74456 C T AAGCCTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCGTTGC[C/T]AGCTTCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCATAGGCATTAA
74456 T C CTTCATATCCACTGATATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCGTTGCCAGC[T/C]TCAGCAAGCCACCCGTATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCATAGGCATTAAGGAC
74456 G A TATACATATTATTTCACACCATAAAACTTCCTATAATATTAGCTTGAATCCACTTCGGTACGCCTCAATTGTCGTCGTTGCCAGCTTCAGCAAGCCACCC[G/A]TATCTAGTTCGCGCAACAGACAGCATAGATGTCATTAGCGCCGCTGCCGTCACACTATGCATAGGCATTAAGGACTCCACACAAAA
74458 A G AATTCATGCGTGGAAGGAGAGTTTTTGAAATCAATCCCGAGCACAAAATTATTAAAGACCTAA[A/G]TGAAGCATGTAGAACAAACCCGGAAAACCCAGAAGCTTTGAAGGCAATAGACCTTCTGTACGACACTGCTCTAATGTCTAGTGGCTACACTCCTGATAAT
74474 T C TTATCGAGATCTCGCTCCAGGTCCATGTCGCGCTCCAGGTCCAGATCCCGCTCTCTGTCTAGATCTCCATCGGTTTCTCCACG[T/C]CGAAGAAGCTATAGTCCTCTTCCAAAAAAGAGGAGCCCTTCTCTGTCTTATTCTGATCGATCCCGTTAAGGGCATTGGAGAAGTTGTCAATGGGGGATAT
74474 A G CTCTGTCTAGATCTCCATCGGTTTCTCCACGTCGAAGAAGCTATAGTCCTCTTCCAAAAAAGAGGAGCCCTTCTCTGTCTTATTCTGATCGATCCCGTTA[A/G]GGGCATTGGAGAAGTTGTCAATGGGGGATATATTATTGCTACATCATGCAGGGTTATATTATTTGCTATATCATTTGTTTGAACCTTTGG
74484 C A CGATGGATGGACTTTACATAGCTCCTGCTTTTATGGACAAGCTTGTTGTTCACATAGCCAAGAACTTCATGGACTTGCCTAATATTAAGGTTCCACTAAT[C/A]TTGGGAGTTTGGGGAGGCAAGGGTCAAGGAAAGTCTTTCCAGTGTGAACTTGTATTTCGCAAGTTGGGAATAAACCCGATAATGATG
74484 A C GCAAGGGTCAAGGAAAGTCTTTCCAGTGTGAACTTGTATTTCGCAAGTTGGGAATAAACCCGATAATGATGAGTGCTGGAGAACTAGAGAGTGGAAATGC[A/C]GGAGAACCTGCAAAACTGATCAGGCAAAGATACAGAGAAGCAGCTGATATAATAGCAAAAGGGAAAATGTGTTG
74486 A G CATACATGCAGCAGGGAGGCGACAAATGCAATGGCCACGATCGGAAGAGGCGGCGATTGCGGTTCTCCTGGAAGTGGCTGTGG[A/G]GATCCGGAGATCCAGAAGTGCGAACGTAGCGTCTCGTCTTGATTTGCGTGGAGAACACCTGATTATAGCGTTTCAGTGGTGGTTGCGCTGACTTGGAGGG
74496 GT G TATGCCGACTGTTTCCGGCCGAAGATTCTTTTGGATTGTTCTGTTCTATTTGAAGATAAGGTGATGCTTATATCCTAATTGTTATTGTTGTTATCCTTAC[GT/G]TTTTTTTTTGTCCCATTGTTATCTTTTACGTACCTTTTATCAGTTGTCGAAACACCGACTGCATGTACAATAACTTTCGAAAGAAGCTATA
74526 A G GGACGGCGCCATTAACCTTAACGTCGACGTAATCACCGACTCTGTAGGTCCTCAGGTACGTCGTCAAATTAATATAACCCTTCTTCCTGAACGGACGAGC[A/G]AATAAGTCACGAGTTCGTGACCGTAGTCCATGGCCGGCCGGCATATTTTCTACTTATGAGATTTGGGGAAATCTACTATCCAGTAGG
74536 G A AAGCGGAACCCAGTGAGCGGATTCACAAATTCCATGGCTTTTGAAATGAAATTTGATTTAATAAGATACTAAATGTGATGGTTTAAGAAGGGAGACTTGA[G/A]GGGTAAGTTGCTCTGCTTGGGCCCGTGGGCACTTTTAGTGTGCTTCCTCACGCTCAGTCGCTGCCTTGTGCCCTTGCAGGAGGAGA
74546 C T CCCTAGGGCTTCTGTACACCGGACTATCGAGGACCAGCGAAGGGAAATTGAGCACCGAAGGGGAAATCGGTTCCTCCCGACCGGTGCCGAAAGAAGGGAT[C/T]AAGGGGCTGATGAGCTTGAGGTTCTTCATGCTGTTCCGGCGCTCGTACAGCTTGTTGTTCTTCGTGGGCTTGGAGACGGGCGGG
74546 G T GGCTTCTGTACACCGGACTATCGAGGACCAGCGAAGGGAAATTGAGCACCGAAGGGGAAATCGGTTCCTCCCGACCGGTGCCGAAAGAAGGGATCAAGGG[G/T]CTGATGAGCTTGAGGTTCTTCATGCTGTTCCGGCGCTCGTACAGCTTGTTGTTCTTCGTGGGCTTGGAGACGGGCGGGATCGG
74552 A C AGAAGAGGAAGAATCGCGCGAGACGAAGAGGAGACGAACGAGCTGTCAACTGGAAATCGAGAACTTGACGGAGAATAAAGTGGCTGGATCTGGACCAGAA[A/C]TTGAAATCGGCGCTGCAAACTTGTCCTTCTCGTTTGACACGGGAATCGCTTCTCCAATTGAGAAGACGCCTAAATTTGGGTCCT
74580 T G TCCTGCCTTTAAATCCAATCTGACCAAAAGTGAGGCAGATAAAAAGGCCAAGGTGCCATGTAACAAGCCACAACCAAAACTGAGAACCTAAAGCCGGTCC[T/G]GTTGGCCAGTGAGCAAGTTCTGTTCCAATGCTGTCGAGAAACAGACCCGTTAAGCTCTTACCATCTATTGCTGGAATGCTAGAAGG
74580 T C ACCAAAACTGAGAACCTAAAGCCGGTCCTGTTGGCCAGTGAGCAAGTTCTGTTCCAATGCTGTCGAGAAACAGACCCGTTAAGCTCTTACCATCTATTGC[T/C]GGAATGCTAGAAGGAACAAGCCATCCTACCAATCCAAACCCGATTACGTTTAGATCTCTACGTAGCCAGTCCCTCTCAAAGCATGTAA
74580 T A GTTCTGTTCCAATGCTGTCGAGAAACAGACCCGTTAAGCTCTTACCATCTATTGCTGGAATGCTAGAAGGAACAAGCCATCCTACCAATCCAAACCCGAT[T/A]ACGTTTAGATCTCTACGTAGCCAGTCCCTCTCAAAGCATGTAAATTTCCCTCCTGAAGCTGATTTAATCTGTAGTGGGTTTCTCGCAGC
74606 G C ATAGAAATGTAAAGAGAGATACCTACCAGCCTATGGATAGAAGAGGCCTGAACCGTAACAATGGTAACCAGCCTCCAGTGGAGAAGTGGAAGCATGACCT[G/C]TTTGAGGATGCAAATACGAGCACCAATTCGAGGAGCGAGGAGGAAGAGATTGCCAAAATCGAAGCTCTTTTGGCCTTGTAAACA
74620 T C CTAATGGTCCTTGCCTGTCTTGTGTATCCTCTAAAGAACATAACTGCTTTATTTCCATATTTTGCAAAAAATTGCATAGACTA[T/C]TGATATCTTTTTGGATTGTCTATACTTTATACAGTGTGTTTTGTTCTTTGAATCTAGGTCGCCATAAAAATAACCTACCAATCAGCTTGAACTATTGATC
74626 A T GCAGTCGTGCTCGAAGTGGAAAATAAGTTCAAGGTAACGGCTAACGCTGTGCCCATCACAGCCGAAGAATCTAGGGTTCATAATTATGGAATTACGGAAG[A/T]AGATTGCTTTGCACATTTAGAGTTAGGGTTCAAGTTCTATTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTG
74626 T A CTCGAAGTGGAAAATAAGTTCAAGGTAACGGCTAACGCTGTGCCCATCACAGCCGAAGAATCTAGGGTTCATAATTATGGAATTACGGAAGAAGATTGCT[T/A]TGCACATTTAGAGTTAGGGTTCAAGTTCTATTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATG
74626 T C TAAGTTCAAGGTAACGGCTAACGCTGTGCCCATCACAGCCGAAGAATCTAGGGTTCATAATTATGGAATTACGGAAGAAGATTGCTTTGCACATTTAGAG[T/C]TAGGGTTCAAGTTCTATTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGAC
74626 G A CACATTTAGAGTTAGGGTTCAAGTTCTATTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGACAT[G/A]TCGTCCAATATGCCATCGATGGGAGGTGAACCTAGGTTTTCATCATCTGAATTGTTCGCACCGGATTGTGCTGTGTCAAGGTTTGG
74626 C T TTCAAGTTCTATTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGACATGTCGTCCAATATGCCAT[C/T]GATGGGAGGTGAACCTAGGTTTTCATCATCTGAATTGTTCGCACCGGATTGTGCTGTGTCAAGGTTTGGACGTGCTACTGGTCTTGC
74626 G C TTCGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGACATGTCGTCCAATATGCCATCGATGGGAGGT[G/C]AACCTAGGTTTTCATCATCTGAATTGTTCGCACCGGATTGTGCTGTGTCAAGGTTTGGACGTGCTACTGGTCTTGCCATGATGTCT
74626 A G CGCTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGACATGTCGTCCAATATGCCATCGATGGGAGGTGA[A/G]CCTAGGTTTTCATCATCTGAATTGTTCGCACCGGATTGTGCTGTGTCAAGGTTTGGACGTGCTACTGGTCTTGCCATGATGTCTGA
74626 C G CTAACGGAAGATGTGCATGGTGTCTTGGGCCAGACGTATCGTGATGGGCATGTGAGCAACGTTGACATGTCGTCCAATATGCCATCGATGGGAGGTGAAC[C/G]TAGGTTTTCATCATCTGAATTGTTCGCACCGGATTGTGCTGTGTCAAGGTTTGGACGTGCTACTGGTCTTGCCATGATGTCTGAAT
74664 T TTAA TTCGAGAATAGACGCTATTGTGCTGTCGTGCTATGGATTTATGTGCAAGGAAAGATATTCGATAACAAATAGGTATTTAGTGGTTTGCCAATGTAAAACT[T/TTAA]TCGACATTATTATAGTGCATAAACATCAGGTCTAAGGAGTCAGTGGTCTCAGACATGGATGTTGATATGATCATGTATTGCTGTA
74678 CTGA C TTTTTTTATAACGTTCGACAAGTAATTTTTACTTCTGGTGAGACATAAAATCCATGAACAACCTCAAATTCTTCCAGGATGAACCATC[CTGA/C]TGATCATCCATGGCCTTCCTAGCTTTATCACCATACTCTTTTGCCCTTCTCCTCCTCTCCTCCCCTTCTTCTCCTTTATCCATCAATTGCACTACAGCCT
74678 C G TTTTATAACGTTCGACAAGTAATTTTTACTTCTGGTGAGACATAAAATCCATGAACAACCTCAAATTCTTCCAGGATGAACCATCCTGATCATCCATGGC[C/G]TTCCTAGCTTTATCACCATACTCTTTTGCCCTTCTCCTCCTCTCCTCCCCTTCTTCTCCTTTATCCATCAATTGCACTACAGCCTTCGACACC
74678 G C ATCATCCATGGCCTTCCTAGCTTTATCACCATACTCTTTTGCCCTTCTCCTCCTCTCCTCCCCTTCTTCTCCTTTATCCATCAATTGCACTACAGCCTTC[G/C]ACACCGCTTCACTTCTCACCGCTACTTCATCTTCAAGCAGATAAAAATAAGGCTTCTCAACTCCAACCGGTATTCCTATCGCAATAACTTCAAC
74678 C G CCATGGCCTTCCTAGCTTTATCACCATACTCTTTTGCCCTTCTCCTCCTCTCCTCCCCTTCTTCTCCTTTATCCATCAATTGCACTACAGCCTTCGACAC[C/G]GCTTCACTTCTCACCGCTACTTCATCTTCAAGCAGATAAAAATAAGGCTTCTCAACTCCAACCGGTATTCCTATCGCAATAACTTCAACGATC
74680 T C CAACATGAGACAATAAAGGCAAATATTTATTCCATGGAGCTTTCGTTGTTAATACCAGGTACAACAAAGTGTAATGGATTGGAGCAAATTCTCCATCCTT[T/C]CCGTCAGCTTTTCAAATTTGTTCCCATTGACCACCTTGAATTGCTGAGCCTGCAATCTTTCTTCCTTCATGAACATGGTTTCATGTTGAT
74756 G A TGATCTGCTGTACCATCCGCCGGAAATTCGCCGGGTCGGCGTTTATGTAAGTAGTCGGCATCTTTTTGGACACGCGCGACTTTCGCTTCTTCACTCTTCC[G/A]TTCGCTACACGGTTGCTTTGCGTAGCGGGTCCGGGTGTGGAGACGGCTGATTGGGTTTGGACCGGCGATCCGGTGGCGGAGGAGTC
74756 T C ACACGCGCGACTTTCGCTTCTTCACTCTTCCGTTCGCTACACGGTTGCTTTGCGTAGCGGGTCCGGGTGTGGAGACGGCTGATTGGGTTTGGACCGGCGA[T/C]CCGGTGGCGGAGGAGTCCGATAAGGAGGTGACTAGTGCGGTGGTTAGAGCTTGGTTTTCGTGGAGGAAGGGGTCGGACATGGTG
74756 T C TCACTCTTCCGTTCGCTACACGGTTGCTTTGCGTAGCGGGTCCGGGTGTGGAGACGGCTGATTGGGTTTGGACCGGCGATCCGGTGGCGGAGGAGTCCGA[T/C]AAGGAGGTGACTAGTGCGGTGGTTAGAGCTTGGTTTTCGTGGAGGAAGGGGTCGGACATGGTGAATAAATCGGGGCGAATTGA
74810 G A AAAGACCAGCGCTTTCTTGATCGCAAGGGTCTTGGGTGTCCCGACGGGTTTATCCGCACCCGTCGCTTTCCA[G/A]TAACCCGACCCGGCAGCCCGGTTCGGCCTCGACCCGTTCGGATACTTCCGGTCTCTAGGCGAGAAGAAGTACCACTCTTTCTCCCCGTACGCAGCAAGGC
74810 A G AAAGACCAGCGCTTTCTTGATCGCAAGGGTCTTGGGTGTCCCGACGGGTTTATCCGCACCCGTCGCTTTCCAGTAACCCGACCCGGC[A/G]GCCCGGTTCGGCCTCGACCCGTTCGGATACTTCCGGTCTCTAGGCGAGAAGAAGTACCACTCTTTCTCCCCGTACGCAGCAAGGCCGGGGAGCTGCCAG
74814 T A AACTGCATATGAAGTAGAAACATTCATTCAAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACAC[T/A]CATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGG
74814 T A AACTGCATATGAAGTAGAAACATTCATTCAAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAA[T/A]CAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGG
74814 A C ATGAAGTAGAAACATTCATTCAAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAA[A/C]ACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTT
74814 C T TCATTCAAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTG[C/T]ATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGG
74814 A G TCAAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATA[A/G]TAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTG
74814 A G AAACAAAAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAAT[A/G]ACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGG
74814 T C AAATATAAATCACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGAT[T/C]AGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGAT
74814 A G ACGCACTCAAATGCTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAAT[A/G]TTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAG
74814 A G CTGGCAACTACAAGGCCCAAAAAATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATT[A/G]TATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTAT
74814 A G AATAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTG[A/G]TAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCG
74814 A T TAGAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGAT[A/T]GGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGC
74814 G C GAAACACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAG[G/C]TGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCA
74814 A C CACTCATACAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGG[A/C]GTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCG
74814 G GATC CAATCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTT[G/GATC]AATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACT
74814 T C TCAATAAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAA[T/C]AGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACTTAGGAA
74814 G A AAAAACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGA[G/A]TAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACTTAGGAAGCTCG
74814 T C ACACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAG[T/C]GGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACTTAGGAAGCTCGGGCA
74814 G T CACAAAAAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGT[G/T]GTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACTTAGGAAGCTCGGGCAA
74814 G A AAGACTGCATAATAACGATTAGGATTCAATATTCAATGAAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGG[G/A]AATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCAATTCTGGCATTGGCGGCAGCTCGAACTTAGGAAGCTCGGGCAACGGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
74814 ATTCTGGCAT A AAATTATATAGTTCTCATGGGCTTTTGATAGGTGGAGTGTTTTGAATAGGAGTAGTGGTTGGGAATGATGGCAACTTAGGGATTCCGGGTATGCTTGGCA[ATTCTGGCAT/A]TTCTGGCATTGGCGGCAGCTCGAACTTAGGAAGCTCGGGCAACGGAGGCAGGGTTGGGATCACGGGCAAGGATGG
74850 A T GGTGCGGCGATGTGACCGCGGATAGGCTGAAGTGGGGTGAAGGATTTTTGAAGAGGAGGATGGATAAGCATGAGAAGGCTAGTGAAATCAGCAAGGATGC[A/T]CTCAAGCGAATGAAAAGGGTGAAAGGTCTTACAAGAATGTCCGAGAATGTTGTTACTGGAATCCTATCTGGTGTGGTCAGAG
74852 T C ATCGACATGACCTTCTATCTCGAATAAAATCACAATCGTTGTCCCCAAAACCCTAAATGCACCGCTTTCCATTCTATTCAGTAAAATCCC[T/C]TCGCAAATTGAGACCACTGAATCGACCGGCGCTCCTCCCTTCACAACCTGGCACCGTGATTCTTGCAAATCGATCGTTGCTCCCCTGGTCAAGTCAAATC
74852 A C CCCTTCGCAAATTGAGACCACTGAATCGACCGGCGCTCCTCCCTTCACAACCTGGCACCGTGATTCTTGCAAATCGATCGTTGCTCCCCTGGTCAAGTCA[A/C]ATCCACCTACTCAAAAATTTCCAATGAAGCCACCTCCGTTTCTTTTTGCTTGGATGCTTCTTCGTCGGAATGAAGTTGGTCCACCATTTA
74852 A G CAAATCGATCGTTGCTCCCCTGGTCAAGTCAAATCCACCTACTCAAAAATTTCCAATGAAGCCACCTCCGTTTCTTTTTGCTTGGATGCTTCTTCGTCGG[A/G]ATGAAGTTGGTCCACCATTTATAGCCACCATAAAAGAACGCATCGAAGCCACTGCCTGCCTTTTCCTCTGCCATTCAAGGTTCTCA
74854 T C TCCTCTATTTCAATCCCCAAACACAATTCTCTGCCCATTTCTGTAATTTCGCCCCTCACCGCCGC[T/C]TTCTGCCCTCAGCTCACTCCTCCCTCCGCTTCTTGACCACATTTCCCGAACTGCCCCTCCAACCCCAGCAGATCAACACCGTCCAAACCACCATCCTCTA
74854 G A TCCTCTATTTCAATCCCCAAACACAATTCTCTGCCCATTTCTGTAATTTCGCCCCTCACCGCCGCTTTCT[G/A]CCCTCAGCTCACTCCTCCCTCCGCTTCTTGACCACATTTCCCGAACTGCCCCTCCAACCCCAGCAGATCAACACCGTCCAAACCACCATCCTCTACCTCG
74908 C A AAGTGATGGACCATGTTGAAAAAGCTCCGTCCACGCCTGAATCTCCGCCATGGAAACTCTACGACAATCCACATTACACAAATCGCAACA[C/A]CACAGTCAACAAATCTACTCAAAACCATCGTCCTTACGCTTGCCTCTTCAGCTCCAGATCTTCCTACAAAACCCACACCATCTCTTCCTTCTCCAACCCA
74946 C T GTGAATTTCAAGATGTATACTCTTTCAGAAGTTTGAGTCACCTTCTCAAATAAAGCTTCATCAGGAAAAATAATTTGATCAAGCTCAACAATGTTTTGTG[C/T]GCGATCAATCCACTGAAAATGGATCAAACCTTCCTCCCCCGCCCTATGCGAATAAGACCTTTGCGGGTATCTGGGACTACTCGCTTGCC
74946 A G GTGCGCGATCAATCCACTGAAAATGGATCAAACCTTCCTCCCCCGCCCTATGCGAATAAGACCTTTGCGGGTATCTGGGACTACTCGCTTGCCCTGGAGA[A/G]ACATCTTCCCAGCACGAAATTCCAACATGATCTCCTGCAACGGAGCGGCATCGACAGCTGACGAACTCATTTAAATCGCTTTCTCCCG
74946 T A GACCTTTGCGGGTATCTGGGACTACTCGCTTGCCCTGGAGAAACATCTTCCCAGCACGAAATTCCAACATGATCTCCTGCAACGGAGCGGCATCGACAGC[T/A]GACGAACTCATTTAAATCGCTTTCTCCCGGAATTGAAAAATGAATAAATGAGATATTCAAAAGC
75032 G A AATCGATACCAAACATCATATCGAAATTAGAGGAGATTGCAAAAGTTGGGAGTTTTACCTTTAGGAAGAAGGATTGTAGGGTTAGTTTAGAAGGGACGAG[G/A]GAAGGAGTGAAGGGCCCGCTTACCATTGGTGCTGAGATATTCGAGCTTACGCCTTGCTTGGTTGTTGTTGAGCTTAAGAAGAAAG
75050 G A GTCACAATTTGTTAAATAGCATTCTACAGAGTAGATAACATTTCATTTACATACTAACAATTAATAACCAAATACTAAAACCAAGTACATAGGGTACACA[G/A]CATAGTACCAAGCAGCATGAAAAGTGTAGCAGTAATATCAAGAAGTGGGCTATAGCAACTGTACCCAAAAAAGCGAACTGACATAAA
75050 C T ATTTCATTTACATACTAACAATTAATAACCAAATACTAAAACCAAGTACATAGGGTACACAGCATAGTACCAAGCAGCATGAAAAGTGTAGCAGTAATAT[C/T]AAGAAGTGGGCTATAGCAACTGTACCCAAAAAAGCGAACTGACATAAAGCAAGGCAGAGACCATACTCCAGCATGTGTTGTCTATAG
75050 T C CTAACAATTAATAACCAAATACTAAAACCAAGTACATAGGGTACACAGCATAGTACCAAGCAGCATGAAAAGTGTAGCAGTAATATCAAGAAGTGGGCTA[T/C]AGCAACTGTACCCAAAAAAGCGAACTGACATAAAGCAAGGCAGAGACCATACTCCAGCATGTGTTGTCTATAGCTCCACACCCAAA
75050 A C ATACTAAAACCAAGTACATAGGGTACACAGCATAGTACCAAGCAGCATGAAAAGTGTAGCAGTAATATCAAGAAGTGGGCTATAGCAACTGTACCCAAAA[A/C]AGCGAACTGACATAAAGCAAGGCAGAGACCATACTCCAGCATGTGTTGTCTATAGCTCCACACCCAAAAGCATGTAGCTACGGAC
75064 CT C TAAATCGGCTGGTGAAACGGCCAAGCGCACTGGCCCGGGCACTGCGTTACGGAGTTGCCAATCCACATGTACGCGAATTTAGA[CT/C]TTTTTGTGCTTACCGGCGAAACCAGATCCGTGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGG
75064 T C TAAATCGGCTGGTGAAACGGCCAAGCGCACTGGCCCGGGCACTGCGTTACGGAGTTGCCAATCCACATGTACGCGAATTTAGACTTTTTGTGC[T/C]TACCGGCGAAACCAGATCCGTGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGC
75064 G T AGTTGCCAATCCACATGTACGCGAATTTAGACTTTTTGTGCTTACCGGCGAAACCAGATCCGTGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGT[G/T]ACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGTTAG
75064 C T GCGAATTTAGACTTTTTGTGCTTACCGGCGAAACCAGATCCGTGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGA[C/T]GGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGTTAGGGACTTGCCTAAGGAGTGA
75064 T G TACCGGCGAAACCAGATCCGTGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATG[T/G]GAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGG
75064 A C TGCGTGCCGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGG[A/C]TGCGAGAGAGACGGAGGTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGGCCGAGAGAGAGTTTGGTGG
75064 A G CGCACCTGCTCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAG[A/G]GAGACGGAGGTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGGCCGAGAGAGAGTTTGGTGGGGCCGGA
75064 G A TCATGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGA[G/A]GTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGGCCGAGAGAGAGTTTGGTGGGGCCGGATTTGTAGCG
75064 T G TGCAGAAGCCTTCAACGGTGACGTCGGCGGAAGTGAAGACGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGT[T/G]AGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGGCCGAGAGAGAGTTTGGTGGGGCCGGATTTGTAGCGGTA
75064 G A CGGCGGTGATGGCGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGAT[G/A]GGGCCGAGAGAGAGTTTGGTGGGGCCGGATTTGTAGCGGTAGGTGGTGGCGAACCAGCTGGAGACGGAGGTGT
75064 G T CGTTGCGATGTGAGCCGCGGGAGGCGAGGGATGCGAGAGAGACGGAGGTTAGGGACTTGCCTAAGGAGTGATTGTCGTCGACGAGGATGGGGCCGAGAGA[G/T]AGTTTGGTGGGGCCGGATTTGTAGCGGTAGGTGGTGGCGAACCAGCTGGAGACGGAGGTGT
75078 T C ACTGTTGGCCTACTGGCTTTTGAGGGCATAAAATATTGGAAACGAAATATAATGGCGATCGCGAAAATGGAAGA[T/C]CCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTG
75078 C T CTGTTGGCCTACTGGCTTTTGAGGGCATAAAATATTGGAAACGAAATATAATGGCGATCGCGAAAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGC[C/T]GGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCC
75078 T A TTTGAGGGCATAAAATATTGGAAACGAAATATAATGGCGATCGCGAAAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGG[T/A]TCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGAT
75078 C T GGCATAAAATATTGGAAACGAAATATAATGGCGATCGCGAAAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAA[C/T]AGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCC
75078 T A GAAACGAAATATAATGGCGATCGCGAAAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAA[T/A]GCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCA
75078 G A GCGATCGCGAAAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCA[G/A]TTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTT
75078 G T AAATGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCC[G/T]GACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTC
75078 C T TGGAAGATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGA[C/T]CGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGA
75078 T C ATCCCTACTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTG[T/C]GTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGATGCGGA
75078 G A CTCTAGCATAGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAAT[G/A]CCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGATGCGGAAAAAGC
75078 A G AGACGAAGAAGCCGGAGATATTCCCGAGGTTCAAACAGCCATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCC[A/G]TTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGATGCGGAAAAAGCAACCACTAC
75078 C T ATCCTCGAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCA[C/T]GATCTTCTCCCTTCCGCAAACTTCTGATGCGGAAAAAGCAACCACTACAGAAGACTCCACGAATCTGGGGAAGAAGAGGAGTTTTGAT
75078 T G GAATGCGCCCCATTTCTCAGTTCATCTCCGGACCGCTGTGTCAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCT[T/G]CTCCCTTCCGCAAACTTCTGATGCGGAAAAAGCAACCACTACAGAAGACTCCACGAATCTGGGGAAGAAGAGGAGTTTTGATGATACG
75078 A G CAATGCCGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGATGCGGAAAAAGCAACCACT[A/G]CAGAAGACTCCACGAATCTGGGGAAGAAGAGGAGTTTTGATGATACGATGGAATCACTCAGCATTTTCG
75078 G A CGATCCCATTATGCCAACTCCGATGTCTCCTGCTGACGAACCCATCACGATCTTCTCCCTTCCGCAAACTTCTGATGCGGAAAAAGCAACCACTACAGAA[G/A]ACTCCACGAATCTGGGGAAGAAGAGGAGTTTTGATGATACGATGGAATCACTCAGCATTTTCG
75112 C A TGGTATTTCATGACTCGAGGATCTAAGCAGCAGTCTCATGAAGATTACATGGAGAAAGCTGAGAGAGCACGACGTGCAAGGCTATCCTCTTCTGGACAAT[C/A]ACAGGCACCACCTCCTAATTAGTTACGCCTGCATTTTGTTAAACTTTCATGCTCTGTTGTTATAATAAGCTAGACAGTTTTAACTATTT
75130 C A CATCTCAAGCTCGGGTTCATCCACGCCTTCTCCATCTCCACGCCAGCAATCGCAAAAGTGGTACTTCAGACCCAGGACCTGGCCTTCTCCAACCGCCCCA[C/A]CACCATCGCCATCACTTACCTCACCTACGATCGGGCCGACTTGGTCTTTACCAACTACGGCCCGTTCTGGCGCCAGATGCGCAAACTC
75138 AT A GAAACTTGGAATACGAGACTCGCCATTCGGAGCTAGAGCGATTGTTCTCAAGATATGGCAAGATTGAACGCATCGATCTGAAATCTGGGTTTGCTTTTAT[AT/A]TTTTTTGAAGATGAGCGTGATGCTGATGATGCCATCCATGATCTCCATGGTACACCTTTTGGTAATAGCAGGCGTCGTCTTACAGTG
75144 G A GCTCGTGGATGGGTGTGAGGTGCGTTCAGCCCATATGGTGCATAGTCTATACGCACTAACGAGAC[G/A]CCTAACGTGTTCAGCCCTGGAATTTGCATCACGTTCACTGCAGTCACGTTTGACCCCACTTGATTTACCGTGTTTCCTGGCTTGTCCAGTCCCGAGAAGA
75144 T C GCTCGTGGATGGGTGTGAGGTGCGTTCAGCCCATATGGTGCATAGTCTATACGCACTAACGAGACGCC[T/C]AACGTGTTCAGCCCTGGAATTTGCATCACGTTCACTGCAGTCACGTTTGACCCCACTTGATTTACCGTGTTTCCTGGCTTGTCCAGTCCCGAGAAGAAGA
75144 G C GCTCGTGGATGGGTGTGAGGTGCGTTCAGCCCATATGGTGCATAGTCTATACGCACTAACGAGACGCCTAACGTGTTCAGCCCTG[G/C]AATTTGCATCACGTTCACTGCAGTCACGTTTGACCCCACTTGATTTACCGTGTTTCCTGGCTTGTCCAGTCCCGAGAAGAAGAAATCTTCTGCTTTAGCT
75144 C A CTCGTGGATGGGTGTGAGGTGCGTTCAGCCCATATGGTGCATAGTCTATACGCACTAACGAGACGCCTAACGTGTTCAGCCCTGGAATTTGCATCACGTT[C/A]ACTGCAGTCACGTTTGACCCCACTTGATTTACCGTGTTTCCTGGCTTGTCCAGTCCCGAGAAGAAGAAATCTTCTGCTTTAGCTTGCA
75150 C T GATTGCTCCGCTGGCCCTAAAAACGACAGTCTTTACAATTGGGTGTCCACAATTATCGGTCCTCGAGGATCACCATA[C/T]GAAGGCGGCATATTTTTCCTTGACATTACTTTCCCCAGTGACTATCCTTTCAAGCCTCCTAAGGTGGTATTCAGAACTCGTATATACCACTGTAATGTTG
75188 C T ACCGCTGATCAAATCACAACCGAAAACGGGCACGGTTTTTCGAGTTATTTCGACCACTGGATAGAGCAGCAGCAGCATGACCTTCAGAGACTCCTTGCTG[C/T]CACTTCCACCTACTCTCCTTCTTCACCTGCTGAAGAACATCAACCGGAGAATCATCAGATTCAGTCTCTTATACATGGAGTCATATCAA
75214 C T TAAGGATTTTAAAGGAAGGAGGACTGCAATGATTAATGCCCTTACTAGCGATGTGGAGGATTTCTACCAGCAGTGCGACCCAGAAAAAGAAAATCTATGC[C/T]TATATGGGTTTCCAAACGAGCGTTGGGAGGTGACCCTTCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCTGCGTTAGGAATT
75250 A T TTTTGAAGTGATCAATAGAAAGTATCCCATGGCCACAGCTATTCCATCTTGGATAATTCCCCGAAGCCCCTCGTC[A/T]TCTCTTGCATTAAACGGCTTCCCCATTTCCCTTAATCCTAATAATCAGATAGCACAACTCACAGATAAGATCGCTTTCTCCTCTTCTTCGCACAGTTACG
75250 C T TTTTGAAGTGATCAATAGAAAGTATCCCATGGCCACAGCTATTCCATCTTGGATAATTCCCCGAAGCCCCTCGTCATCTCTTGCATTAAACGGCTTC[C/T]CCATTTCCCTTAATCCTAATAATCAGATAGCACAACTCACAGATAAGATCGCTTTCTCCTCTTCTTCGCACAGTTACGGCAATGGAGTCAAAA
75250 C T CTCTTGCATTAAACGGCTTCCCCATTTCCCTTAATCCTAATAATCAGATAGCACAACTCACAGATAAGATCGCTTTCTCCTCTTCTTCGCACAGTTACGG[C/T]AATGGAGTCAAAACTTTCGATAAACAAAGCGATTTAAATGTTTGCATGGCGGCGGCGGCTTCTCCGCCTTCTTCCCCTTTACCAGCAGCG
75252 AT A TTTCAGATGCTTTAAATAAGGCTTCTAAAGCCGCTGCTGATCTTGCACGCCATGGTAGTAATCATTGAAAATGTTATAGTGAGACATCTTCAAGTAAATA[AT/A]TGTCTTGTTTTTCTGTTTGAGAACGATATAAAAGTCTATAGAACAGGTGTCTGTTCCAGTTAAATTGGATACCAGGTCATGAGATGTG
75252 A G CGCTGCTGATCTTGCACGCCATGGTAGTAATCATTGAAAATGTTATAGTGAGACATCTTCAAGTAAATAATGTCTTGTTTTTCTGTTTGAGAACGATATA[A/G]AAGTCTATAGAACAGGTGTCTGTTCCAGTTAAATTGGATACCAGGTCATGAGATGTGTATTGGCATCGACATATTGCATAACTTTGTGC
75304 C A GCAATTTTTTGATCAGCAGCAACCACCATATATGCAACAATATTCAGATATGCAGCAGTTTT[C/A]AAGACCGCCTATGCCTTATCAGCCACCCCACAACTTCGAAGAATGTCAACAGCATGAAGGTATCACTTGTTTGCTTGTTTCACTTGTGCAAGAAATGTAT
75304 C A GCAATTTTTTGATCAGCAGCAACCACCATATATGCAACAATATTCAGATATGCAGCAGTTTTCAAGACCGCCTATGCCTTATCAGCCACCCCACAACTT[C/A]GAAGAATGTCAACAGCATGAAGGTATCACTTGTTTGCTTGTTTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTG
75304 T C CCATATATGCAACAATATTCAGATATGCAGCAGTTTTCAAGACCGCCTATGCCTTATCAGCCACCCCACAACTTCGAAGAATGTCAACAGCATGAAGGTA[T/C]CACTTGTTTGCTTGTTTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAA
75304 T C TATTCAGATATGCAGCAGTTTTCAAGACCGCCTATGCCTTATCAGCCACCCCACAACTTCGAAGAATGTCAACAGCATGAAGGTATCACTTGTTTGCTTG[T/C]TTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTA
75304 A T CAGTTTTCAAGACCGCCTATGCCTTATCAGCCACCCCACAACTTCGAAGAATGTCAACAGCATGAAGGTATCACTTGTTTGCTTGTTTCACTTGTGCAAG[A/T]AATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTAGTGAACAGGTTAATT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
75304 T A CCTATGCCTTATCAGCCACCCCACAACTTCGAAGAATGTCAACAGCATGAAGGTATCACTTGTTTGCTTGTTTCACTTGTGCAAGAAATGTATGTACATA[T/A]CAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTAGTGAACAGGTTAATTATCTTTTTGTTAATG
75304 A G ATGAAGGTATCACTTGTTTGCTTGTTTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAA[A/G]TTGTGTACTTTGTAGTGAACAGGTTAATTATCTTTTTGTTAATGTAATATTGCATATGTTGTCTTCACCTTCTTGTTAAAATAATGTGTAT
75304 G T TGTTTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTAGTGAACA[G/T]GTTAATTATCTTTTTGTTAATGTAATATTGCATATGTTGTCTTCACCTTCTTGTTAAAATAATGTGTATACAATATGCTGCTGAATCTACGA
75304 T TG TTCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTAGTGAACAGGT[T/TG]AATTATCTTTTTGTTAATGTAATATTGCATATGTTGTCTTCACCTTCTTGTTAAAATAATGTGTATACAATATGCTGCTGAATCTACGAG
75304 A G TCACTTGTGCAAGAAATGTATGTACATATCAGTTAGTGGACTTATTTGCTTTGTTTATTGGTTGCTGAAAGTAAATTGTGTACTTTGTAGTGAACAGGTT[A/G]ATTATCTTTTTGTTAATGTAATATTGCATATGTTGTCTTCACCTTCTTGTTAAAATAATGTGTATACAATATGCTGCTGAATCTACGAGTT
75328 C T AACAAGAGTCGGCAGGACGTAGAAAACCCTAATTTTCTCTCAATTTCAATCCGAGGTAAAAACAGTAAATAAATGGCTGGCGCTTA[C/T]TGGATGTACTCAGATCCCCGTAACCAGCCAAGCATACAAGCTACTGCTCCTTCTGCGGCGGCGTTGGTTGCGGCGGCTGCAATGCCAACGGCATTACCGG
75370 A G TTATTATGGCGCAGAATTGTTTCACTCCAAATGGGCCTCCCAAATTTGATACAGTAAACGTGCCACCCTCATAGTCTTCTGGTTTTAAACTATTATCTTT[A/G]GCTTTTTGGGCCAAATGCTTCACCTCTTCTGAAATCATGGACAATCCTTTCTTATCCGCATTCCTAATGACAGGAACAAATAATCCATTAT
75370 T C TCATAGTCTTCTGGTTTTAAACTATTATCTTTAGCTTTTTGGGCCAAATGCTTCACCTCTTCTGAAATCATGGACAATCCTTTCTTATCCGCATTCCTAA[T/C]GACAGGAACAAATAATCCATTATCAGTTTGAACAGCAACATTAATGTTCACATCATGGTACTGTCGAATGAAATCATTCATCCATGAACTG
75370 A G TTTAAACTATTATCTTTAGCTTTTTGGGCCAAATGCTTCACCTCTTCTGAAATCATGGACAATCCTTTCTTATCCGCATTCCTAATGACAGGAACAAATA[A/G]TCCATTATCAGTTTGAACAGCAACATTAATGTTCACATCATGGTACTGTCGAATGAAATCATTCATCCATGAACTGTTACATGCTGGAACT
75392 A G CACACACTCACAAACTACCACCGGAGACCTAAACTTAACCATGATGGGCCGGGTTCGGCACCTCGAAACCCGGGTTCGGAACAAACAGATCATCATTTCC[A/G]GGCAAGTACTGGCCATTAGAAGCGGCCGGAATGCTGTGATCCAACCCATGCACCGAAGGCTTTTCATGGCTTCCTAGACCGTACCT
75392 T G CAGGCAAGTACTGGCCATTAGAAGCGGCCGGAATGCTGTGATCCAACCCATGCACCGAAGGCTTTTCATGGCTTCCTAGACCGTACCTCCCGACTCCCGG[T/G]ATCAGGACCGTCCCTTCATGGGCGCACTCCTTTTCGAGTTTCCCTCCCATCGCCGCACGTGAAATCAGTATCAGAACAAAGACGCAT
75392 A G GACCGTACCTCCCGACTCCCGGTATCAGGACCGTCCCTTCATGGGCGCACTCCTTTTCGAGTTTCCCTCCCATCGCCGCACGTGAAATCAGTATCAGAAC[A/G]AAGACGCATAGCACTGATTTAAAGTGATCCATTATTTTGTGTGAATGATCCAGTAGGCCAACA
75436 C T TATCGTCCGCTTTGATCAACCCATCCAACACATTGCTGTTACCTCTTCTAGAATGCTTCTTCTCGCTTCCAAAAGACGAAAGCGCCCTGGTCTTCTTCTT[C/T]GATGACCTCCTGTAATGAGATGCAGCAATCTTCCTGGCCCGAGGTTTCTCTTCCTGGCCCGAATAAAGTGGGTCTCCATCATCATCCATG
75474 A G TAATCTGATAGAAAGCGGACATCGACGTTTAGACTAAACAAAGGCACATATACTATAATTGTAAAGCAAATGACTGATAAAACCACAAAGTCCACGCAAC[A/G]TTACCACCCACAGATAGATAGGATACAAGAAAAAGAAGAAGCATATAAGCATATAAGAAGATTAAAGCAAGACACAAACAAGACC
75474 C T AAACCACAAAGTCCACGCAACATTACCACCCACAGATAGATAGGATACAAGAAAAAGAAGAAGCATATAAGCATATAAGAAGATTAAAGCAAGACACAAA[C/T]AAGACCAAATTGACAAGCTGCTCGGCTCACTGAATGCCAACAAAGGGATGATAGGTCAGTGAAATCAAGCTCCACCGCGAAGACG
75476 A G ATAATTTAACAGTAACAGTGTTATACCAAGGCGGTCAAACCGACCTTCATGCCATTGACGTAGCTCGGTTATACTCGTCAAATTGGATGTACATGTCAAG[A/G]GACCATGGTGCGGTCTGGTCCACGACGCGTGCGCCGCCCGGCCCACTTCAGTTTAGGTTTGTGGTCACGGCTGGGTTTGATGGTAA
75476 C A AGGCGGTCAAACCGACCTTCATGCCATTGACGTAGCTCGGTTATACTCGTCAAATTGGATGTACATGTCAAGAGACCATGGTGCGGTCTGGTCCACGACG[C/A]GTGCGCCGCCCGGCCCACTTCAGTTTAGGTTTGTGGTCACGGCTGGGTTTGATGGTAAGTGGGTGTGGGCCAACAGAGAGGTGCT
75476 G T AAACCGACCTTCATGCCATTGACGTAGCTCGGTTATACTCGTCAAATTGGATGTACATGTCAAGAGACCATGGTGCGGTCTGGTCCACGACGCGTGCGCC[G/T]CCCGGCCCACTTCAGTTTAGGTTTGTGGTCACGGCTGGGTTTGATGGTAAGTGGGTGTGGGCCAACAGAGAGGTGCTGCCATCGG
75476 A G GGTCCACGACGCGTGCGCCGCCCGGCCCACTTCAGTTTAGGTTTGTGGTCACGGCTGGGTTTGATGGTAAGTGGGTGTGGGCCAACAGAGAGGTGCTGCC[A/G]TCGGATTGGACGGTTGGAATGATGTATGATACGGGTGTGAAGATCACTGATGTCAAAGAAGAAGGCTGTGGCACTTGC
75476 T G GCGCCGCCCGGCCCACTTCAGTTTAGGTTTGTGGTCACGGCTGGGTTTGATGGTAAGTGGGTGTGGGCCAACAGAGAGGTGCTGCCATCGGATTGGACGG[T/G]TGGAATGATGTATGATACGGGTGTGAAGATCACTGATGTCAAAGAAGAAGGCTGTGGCACTTGC
75484 G T CCGGGGTGATGAGCTTCACGTTGTAGGTCGCCATGGCCGTCACCTTCCCTCTGCCGAGGTTGAAGTTGAAGGTAGTGGCAAGGGAGCGGGAGAGGGTGGC[G/T]GAGCGCTGGATGAAGGGGGTTCTTAGGGTCGAGGGAGCGGATAGCGACGCCATTTTCGTGGGATTTGTTTGCTTCTGCGTGTG
75488 G A AGATATGGATAGTCACAACACGAAACAGCAACGCCCTCCTCCGCCTTTAGGATATCCAACTGGGAAGGCACC[G/A]AAGAAGAAGCCATGCTGCCCACGTACGAAGAAGAAGGATGATAAGGGATTCATTGAAGGATGCCTTGCCGCGCTGTGCTGCTGCTGGATATGTGAAGAAT
75490 G A CTTCTAATGTCACCTTGTGCATAGAATTAATGTTATCGTCGGAAACATAATCGAGCGTATCTTTCCTCTGTCTGTGAGACCATAAAGCAGCGACTGACGC[G/A]TGGCAACCCTGGGTGACTATGCTGCCAAGTGGCCAGTTGTCGATCAGATCGCGACGGAGCACCACGTACTGTACAATCACGTCCTGA
75494 C T GGATCCTGCATGACTGGAGCGACGAACACTGTGCAAAACTATTGAAGAACTGCTATAAAGCTCTACCAGACAATGGAAAGGTAATCCTTATGGAGAGCAT[C/T]CTACCACTTTATCCAGAGCCAACTTCGGTTGCACAAGGGGTGATACATGTTGACCTTATCATGTTGGCTCACAACCCTGGAGGTAA
75524 G A ATGAAGGACTTATCCTAGGTATGAAAACTGCACATGAGTTAGGCTATCAGAACGTTCATATATCTGGGGATTCTTCTCTTGTCTGCAACCAGTCCAATGG[G/A]AATTGGCGCGTTAATAACCCTAACTTGAGAGAACTCCACCAGGAGGCTCAGGGCCTGCGTAATCAATTTGCGTCATCCAGAATAGAT
75524 A G GGTATGAAAACTGCACATGAGTTAGGCTATCAGAACGTTCATATATCTGGGGATTCTTCTCTTGTCTGCAACCAGTCCAATGGGAATTGGCGCGTTAATA[A/G]CCCTAACTTGAGAGAACTCCACCAGGAGGCTCAGGGCCTGCGTAATCAATTTGCGTCATCCAGAATAGATTATGCTCCAAGGGAATA
75536 T C TTTATCAAGGGGACCAGAGACAGTTGCAATCATATCTACATGAGGATCTTCTAAAGGCTTTAGCATAATCCTTGTGCTGAACTGCCTTGACTGCTCGAGA[T/C]AATCTTCAAAAAGGCAACGCAATGCTAGTTTTCCAAATAACAAATCATAAGCTGGAACCAGCATCCTGGTACGAGCAGCAAGCGGAG
75536 C T GAGGATCTTCTAAAGGCTTTAGCATAATCCTTGTGCTGAACTGCCTTGACTGCTCGAGATAATCTTCAAAAAGGCAACGCAATGCTAGTTTTCCAAATAA[C/T]AAATCATAAGCTGGAACCAGCATCCTGGTACGAGCAGCAAGCGGAGGAAAATCGAAGATAGGTGGGACCAGCACCATCGGAGGCG
75560 T C CTCCTCGTCTACGAATACATCCCTAACGGAACTCTTGCAGATCACCTCCATGGGCCTCTCGCATCAAAACCTGGGCTT[T/C]CGTGGCCCACCCGCATGTCCATAATCATCCAAATGGCTGAAGCCCTATCCTACCTCCACTCCACGGAACCCCCAATCATCCACCGTGACATCAAAACCAA
75560 T C GAATACATCCCTAACGGAACTCTTGCAGATCACCTCCATGGGCCTCTCGCATCAAAACCTGGGCTTTCGTGGCCCACCCGCATGTCCATAATCATCCAAA[T/C]GGCTGAAGCCCTATCCTACCTCCACTCCACGGAACCCCCAATCATCCACCGTGACATCAAAACCAACAACATCCTCCTGGATGACAACT
75560 T C ACATCCCTAACGGAACTCTTGCAGATCACCTCCATGGGCCTCTCGCATCAAAACCTGGGCTTTCGTGGCCCACCCGCATGTCCATAATCATCCAAATGGC[T/C]GAAGCCCTATCCTACCTCCACTCCACGGAACCCCCAATCATCCACCGTGACATCAAAACCAACAACATCCTCCTGGATGACAACTTCCA
75560 C T ACCGTGACATCAAAACCAACAACATCCTCCTGGATGACAACTTCCAAGTAAAAGTAGCGGACTTTGGAATATCCCGACTCTTCCCTGCCAATGCCACCCA[C/T]GTATCCACAGGGCCTCAAGGCACGTTTGGATATCTTGACCCTGAGTATTACCTTCGGTTTCAGCTGACGGACAAGAGCGACGTGTAC
75590 G A AGGACGAACTACTTTTCCCCAAATACACCTGTAGTGTGTTCCATTCCTCTTAACCTTCGCCTTGTAAATATACGCTAATCTCTTCCCAAGGTAATAAGCT[G/A]CGTCTTCTTTTGTGTTCACTCCTTCGATCTGCATCAATGAAGTATTCTCATACTGATTCGATTTCGATCTCTTGTATCCCAAAATAGTTCCT
75604 CA C TGCAGTACATTACAGTCACTCAACCACTACACAAACAGTTCCAAGCTGACCACACGCCTTGCAAGTTAACCTCGCGCACTGGCGTGCACGCAGTTCTGCA[CA/C]AACAAAAACACATCGTCTACTTTATCTTCTTCTTGGGACGGATGTTGCTTGTGCGGCCACACTTCTTCTTACGACAGTTGGTAGCTCT
75604 CA C AGTACATTACAGTCACTCAACCACTACACAAACAGTTCCAAGCTGACCACACGCCTTGCAAGTTAACCTCGCGCACTGGCGTGCACGCAGTTCTGCACAA[CA/C]AAAAACACATCGTCTACTTTATCTTCTTCTTGGGACGGATGTTGCTTGTGCGGCCACACTTCTTCTTACGACAGTTGGTAGCTCTCGG
75632 A C ACAACCATGGGAGGATCATGTGCTAGCTAGTTGGCTTGTCCACTTGAAGTTTTGACGAAGCTA[A/C]TGCAAACTCTATCAACCAGGGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAAT
75632 C G ACAACCATGGGAGGATCATGTGCTAGCTAGTTGGCTTGTCCACTTGAAGTTTTGACGAAGCTAATGCAAACTCTATCAA[C/G]CAGGGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACT
75632 G T ACAACCATGGGAGGATCATGTGCTAGCTAGTTGGCTTGTCCACTTGAAGTTTTGACGAAGCTAATGCAAACTCTATCAACCA[G/T]GGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGA
75632 T C ACAACCATGGGAGGATCATGTGCTAGCTAGTTGGCTTGTCCACTTGAAGTTTTGACGAAGCTAATGCAAACTCTATCAACCAGGGCCGCTGACGATGTT[T/C]ATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGAAATT
75632 G A ACCATGGGAGGATCATGTGCTAGCTAGTTGGCTTGTCCACTTGAAGTTTTGACGAAGCTAATGCAAACTCTATCAACCAGGGCCGCTGACGATGTTTATT[G/A]ACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGAAATTTTG
75632 A G GTCCACTTGAAGTTTTGACGAAGCTAATGCAAACTCTATCAACCAGGGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGAC[A/G]TTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGAAATTTTGAGATCCGTGTTACGGGATGTGATTTCAGATGAAG
75632 A T TGACGAAGCTAATGCAAACTCTATCAACCAGGGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGAC[A/T]CCGATCCAAATGCGGTGAAGAACAACTGGAAATTTTGAGATCCGTGTTACGGGATGTGATTTCAGATGAAGTATCGAACTGAGGG
75632 A G CTAATGCAAACTCTATCAACCAGGGCCGCTGACGATGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCC[A/G]AATGCGGTGAAGAACAACTGGAAATTTTGAGATCCGTGTTACGGGATGTGATTTCAGATGAAGTATCGAACTGAGGGCAGTATCG
75632 C G TGTTTATTGACGGCGGTGTAAAACGGAATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGAAATTTTGAGATC[C/G]GTGTTACGGGATGTGATTTCAGATGAAGTATCGAACTGAGGGCAGTATCGAACTGAGGGCTCCTGGACGGATCGATTGAATGAGA
75632
AAGTATCGAACTGAGGGC A AATCCACCGTTGGGACATTGCTGCCTTGGACACCGATCCAAATGCGGTGAAGAACAACTGGAAATTTTGAGATCCGTGTTACGGGATGTGATTTCAGATG[AAGTATCGAACTGAGGGC/A]AGTATCGAACTGAGGGCAGTATCGAACTGAGGGCTCCTGGACGGATCGATTGAATGAGAATGGCGGC
75632 G A GAGATCCGTGTTACGGGATGTGATTTCAGATGAAGTATCGAACTGAGGGCAGTATCGAACTGAGGGCTCCTGGACGGATCGATTGAATGAGAATGGCGGC[G/A]GATCGATTGAAGATGGAGAAAACGTGGGTTCGCAACCTAGGTTTAAGAAGTGGAAAGTGAGGAA
75640 G C ATGCAACGCAAACCCAAACCCAAACCTCGTCCGAATCAAATAAAAAGCTCAAAACTTTCTCGATCTACAGATGGAACCCTAATTCTCCCGAATCCAAGCC[G/C]ACTCTCCACAACTACACGATCGACCTCAATGAATGTGGGCCCATGGTGCTGGACGCGTTGATCAAGATAAAAAACGAGGTGGACCCC
75640 A T TGCAACGCAAACCCAAACCCAAACCTCGTCCGAATCAAATAAAAAGCTCAAAACTTTCTCGATCTACAGATGGAACCCTAATTCTCCCGAATCCAAGCCG[A/T]CTCTCCACAACTACACGATCGACCTCAATGAATGTGGGCCCATGGTGCTGGACGCGTTGATCAAGATAAAAAACGAGGTGGACCCCA
75640 T C CCGAATCAAATAAAAAGCTCAAAACTTTCTCGATCTACAGATGGAACCCTAATTCTCCCGAATCCAAGCCGACTCTCCACAACTACACGATCGACCTCAA[T/C]GAATGTGGGCCCATGGTGCTGGACGCGTTGATCAAGATAAAAAACGAGGTGGACCCCACTTTGACGTTCCG
75644 T A GTGGCCTTTTTTTTTTGCATAAACATACATCAAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAG[T/A]TTCAAATGATAATATTATCAAACTATGCACATAAAACATTGACAATTATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCA
75644 A T TTTTTTTGCATAAACATACATCAAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAA[A/T]CATTGACAATTATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCG
75644 T C TTTGCATAAACATACATCAAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAAACAT[T/C]GACAATTATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCGAAC
75644 A G ATAAACATACATCAAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAAACATTGACA[A/G]TTATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCGAACTTCAA
75644 T C AAACATACATCAAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAAACATTGACAAT[T/C]ATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCGAACTTCAACA
75644 T C AAACCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAAACATTGACAATTATTCACTTTC[T/C]CTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCGAACTTCAACACCAGCATCCTTG
75644 T C CCACTAAAAGATGAACTTACAAACGAAGAAAAGAATAAGTTTCAAATGATAATATTATCAAACTATGCACATAAAACATTGACAATTATTCACTTTCTCT[T/C]AAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGCGCTTTGCTGTCGAACTTCAACACCAGCATCCTTGCCG
75644 G A TTATCAAACTATGCACATAAAACATTGACAATTATTCACTTTCTCTTAAAATTGACACGGTGACCTCCCGCCTACTCACGCTCCCATTCGGGTCACCAGC[G/A]CTTTGCTGTCGAACTTCAACACCAGCATCCTTGCCGGTAGCCTCCCCGGTAACAGCAGGCGTAGCCAAAAACGTAGGATTATCGTCACC
75644 A G TTTGCTGTCGAACTTCAACACCAGCATCCTTGCCGGTAGCCTCCCCGGTAACAGCAGGCGTAGCCAAAAACGTAGGATTATCGTCACCCGCCATAATCAC[A/G]GCCACACTTCCGGCGAAGCAAGGCGTCGTTCCAACACAAGCATCGTCAGCTAGCTTCTGGTCG
75658 C T GAGAGGGATGCAAAAGCTCTACAAGAAAAGCTGGCAAAGAAAGCTGCGCAAGCTGCAAACAGCGGAGGTGCAGGAACTAATCCAAGCACTAAAAAATAAC[C/T]GTTATCCGGGTACTGTGTTTATTTATGGACATGCTTTATGCTAGAAATCAGTTTTTCTAGTCAAGGTGGAATATGTGTGACTATTA
75660 A T AAAAACAGCTGGTTACGAGTGCAGTTTAAATTGGAGCTTTGACCATTTTGTCTTTTACAG[A/T]AGCTGGAAAATGAAACTGGGGATGGCCCTGAAGCAAGATGGGCATCACACGCAGACATAGATATAGGGGATAAAGCCATTGCCTACAACAATGAGCTGAC
75660 A G TAGGGGATAAAGCCATTGCCTACAACAATGAGCTGACCTCCAAACACCTCTAGTGATATTGTACTCGACATCGTTCTTTCATCGCAAAACTGAAGTATGT[A/G]AGGAGAACTTTTGCCGTTAAATCAAGGCAGAGCGCCGTTTTCGTTGAGCAGCGGCCATTTTTAAACAAGGTAGAAGGGTTTTGGTGG
75672 G A GTCGTTTTCACCATCATTTTCAATCAGGGGTTTGGGTACCACCTCGGGTTCAGATTGAGGTTCAGGTTTGGGTTGAGATTCGGGTATCGATTTTTTTACA[G/A]GTTGAGGCTGAGAAGAGGGAGTGGAGGTTTGAGAGAGCTTACGTTTTCCGGCCATGAGAAATGAAGGATTGAGAAAGATGAGAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
75682 T A CACTGGCAGCAGCTTCATCTCCTCTTGGTGTGATCGGTGGAGCACTGGCTGGTCATGGTCTTGCGACTGTGCTTGC[T/A]GTAATTGGTGGCTCTTTGCTGGGAAGCTTTTTTTCTGAAAAAGTTATTGCTTACGTAGGCGGAGTCCTCTTTTTAGTCTTTGCTGTAGTGACATTAGTCG
75714 G A AAGCAGCAGCAAGCTCAGCAACAGCAGCAGTGGAATTCTTCCTTTTCCACCCTCCATCCACAGTACCGTTCATAACAATCACCCCGCCACCGTTGTACGT[G/A]CCCGTGGACCAAACGTCCGATCCATAAATGACGACGTTCCTATCCTTCTGCAGCACCAGCACATAATGCCCTTTCCCTTTGTTGCTGTT
75714 C T TCAGCAACAGCAGCAGTGGAATTCTTCCTTTTCCACCCTCCATCCACAGTACCGTTCATAACAATCACCCCGCCACCGTTGTACGTGCCCGTGGACCAAA[C/T]GTCCGATCCATAAATGACGACGTTCCTATCCTTCTGCAGCACCAGCACATAATGCCCTTTCCCTTTGTTGCTGTTGCTAGCCCAAACGAC
75718 A C GTGTTCCGTATGTATCCGATTATGTAGCCGTTGTATGTACATATTCTAAATCATATTGTATTTTGTGCTGCTGAAATTGTAAGATGTATCTTGGTCATTA[A/C]GTCTGAATGATCTTGTGTGCGAGTCATTCAGAATTTGTAGCATGCTATATTCTGGTGTTT
75724 T C TACTGACCGGCCTTCGACTAAGGTTCACGCTGCTCCAGGTGGTGGTTCTTCCCTTGGCTATTTGTTTGGTAGTGGTGGCAAATGAGAGTGGTCATCTATT[T/C]ATAATGCAGTTGCAAAACAAACGGCAGTATATTGTTTAAGCAGTTAAGTACACAACACTGTACGTGTTTGCACAAAATGTTTCGACTG
75736 T C CGCCGCAGCCTCCGGCATGCCCTCCTCCTCCCTCCGGAGGCGGCGGCGGTGACTGGCCTCCTCAGTCGCCGTCTGTTCCCTATTCCCCTTCCCTGCCGTA[T/C]GTCACACCTGGCGTTCTATATCCTGTCGACCCTGCCTACCGTCCATCTCATGCTAGCAAGAATTTGATACATGTCTGGCCTTTGCTGTT
75736 T C GTCGCCGTCTGTTCCCTATTCCCCTTCCCTGCCGTATGTCACACCTGGCGTTCTATATCCTGTCGACCCTGCCTACCGTCCATCTCATGCTAGCAAGAAT[T/C]TGATACATGTCTGGCCTTTGCTGTTCATCGTGTTAGGGTTGTTTTTGTGAATTGGTCGGTTGTTGATTAACTAGTGGATGAATATGTCTTT
75736 C T CTATTCCCCTTCCCTGCCGTATGTCACACCTGGCGTTCTATATCCTGTCGACCCTGCCTACCGTCCATCTCATGCTAGCAAGAATTTGATACATGTCTGG[C/T]CTTTGCTGTTCATCGTGTTAGGGTTGTTTTTGTGAATTGGTCGGTTGTTGATTAACTAGTGGATGAATATGTCTTTGTTCTGTGATTTGAT
75750 T C GAACTAGCATCAGTGACGTGCTTGGAACTTGCTGACATATGCAAGGAAGTGAATCTACCTGCTGGTGTTTTGAA[T/C]GTAGTAACAGGACTTGGGACTGAAGCTGGTGCTCCTTTAGCATCTCATCCTAAAGTAGACAAGATTGCTTTTACGGGGAGCACGGAAACAGGAAGAAGGA
75750 C T TACCTGCTGGTGTTTTGAATGTAGTAACAGGACTTGGGACTGAAGCTGGTGCTCCTTTAGCATCTCATCCTAAAGTAGACAAGATTGCTTTTACGGGGAG[C/T]ACGGAAACAGGAAGAAGGATTATGACTGCTGCTGCTCAACGTGTTAAGCCTGTTTCTTTGGAGCTTGGTGGGAAAAGTCCTATAATC
75750 G T GAAGCTGGTGCTCCTTTAGCATCTCATCCTAAAGTAGACAAGATTGCTTTTACGGGGAGCACGGAAACAGGAAGAAGGATTATGACTGCTGCTGCTCAAC[G/T]TGTTAAGCCTGTTTCTTTGGAGCTTGGTGGGAAAAGTCCTATAATCATATTTGAAGATGTGGATATTGAGAAAGCTGTGGAGTGGA
75750 A G AACGTGTTAAGCCTGTTTCTTTGGAGCTTGGTGGGAAAAGTCCTATAATCATATTTGAAGATGTGGATATTGAGAAAGCTGTGGAGTGGACTCTCTTTGG[A/G]TGCTTCTGGACTAATGGGCAAATATGCAGTGCCACTTCTCGTCTAATTTTACATGAAAGTAT
75772 G A TAGCGAGACGCAAAGGATTTGCTGTCCTAGCAAGATTCGATGCTGTAAGATGCTCCTCTGTTCATCGCGCTTTCTCGTCTGCAGCGGACGAGAATGACGT[G/A]GTTGTGATTGGTGGAGGCCCTGGAGGTTATGTGGCGGCCATAAAGGCTGCGCAGCTCGGTCTGAAAACGACTTGCATTGAAAAAC
75784 G A TAGCGTTCATCCCATACCCGGGCCGCGGCCACATAAACGCGATGCTGAACCTCGCCCGCATCCTCTCCTCCGGTTACAAAAAGAAAGACGTGAAATCATT[G/A]ATAATATCTGTGATAGTGACGGAGGAATGGGAAAGCCTGCTTTCGTCGGAACCGCTTCCGTTCAACGTCCGACTGGTATCCATACCA
75784 A G AAAAGAAAGACGTGAAATCATTGATAATATCTGTGATAGTGACGGAGGAATGGGAAAGCCTGCTTTCGTCGGAACCGCTTCCGTTCAACGTCCGACTGGT[A/G]TCCATACCAAACGTGATTCCTTCGGAAAACGGACGCGCTTCGGATTTTGTCGGTTTTTTGGACGCCGTTTATGAGGAAATGGGACC
75784 T G TGATAATATCTGTGATAGTGACGGAGGAATGGGAAAGCCTGCTTTCGTCGGAACCGCTTCCGTTCAACGTCCGACTGGTATCCATACCAAACGTGATTCC[T/G]TCGGAAAACGGACGCGCTTCGGATTTTGTCGGTTTTTTGGACGCCGTTTATGAGGAAATGGGACCCGTAGTGGAGGAG
75796 A T TGGTGTAACGATGCCCATCCTGATTCTGTGCTTCCTGCCATCAGAAGGAGTCTACATAACCTGAAAATGGATTACTTGGATCT[A/T]TACCTCGTGCATATGCCATTTAGTTCAAAACCTGGATCACACCCATTTCCAATAGATAAAGATGACATCGTACCACTGAACATGAAATCGGTTTGGCAAG
75796 T C TGGTGTAACGATGCCCATCCTGATTCTGTGCTTCCTGCCATCAGAAGGAGTCTACATAACCTGAAAATGGATTACTTGGATCTATACCTCGTGCA[T/C]ATGCCATTTAGTTCAAAACCTGGATCACACCCATTTCCAATAGATAAAGATGACATCGTACCACTGAACATGAAATCGGTTTGGCAAGCGATG
75796 C T CCTGAAAATGGATTACTTGGATCTATACCTCGTGCATATGCCATTTAGTTCAAAACCTGGATCACACCCATTTCCAATAGATAAAGATGACATCGTACCA[C/T]TGAACATGAAATCGGTTTGGCAAGCGATGGAGGAGTGCCAAATGCTTGGACTTGCTAGAGCAATTGGCGTTAGTAATTTCCGAGAAC
75796 G C ACCTCGTGCATATGCCATTTAGTTCAAAACCTGGATCACACCCATTTCCAATAGATAAAGATGACATCGTACCACTGAACATGAAATCGGTTTGGCAAGC[G/C]ATGGAGGAGTGCCAAATGCTTGGACTTGCTAGAGCAATTGGCGTTAGTAATTTCCGAGAACATAAATTAGCTGAGCTACTCACTACA
75796 A G GGAGTGCCAAATGCTTGGACTTGCTAGAGCAATTGGCGTTAGTAATTTCCGAGAACATAAATTAGCTGAGCTACTCACTACAGCTAAAATACCTCCAAAA[A/G]TCAACCAGGTGGAAATGAATGTAGCTTGGCAACAGATAAATTTAAGGAAGTACTGCATGGAGAA
75824 G GC GGCTTGCACCATCACCGGATTCTCTTCGACAAATACCATCCCGGCTACTTTGGAAAGGTCGGTATGCGCTACTTCCATAAACTAAAGAACAAGTTCTATT[G/GC]CCCACCGTCAACGTGGACAAGCTCTGGTCCCTTATACCAGATTCCGTTAAGGAGAAGGCTAATGGATCCCAATCCGCTCCGATGATC
75830 T C TATAGTGTATGGTGCATCCAAATGGTTCCAACCTCTTTGCAATTCTTAACCCGATAGACCCCAAGCCCACTATGCCTACCCGCCTGCTGCCTAGCTTGGA[T/C]CCAAGTCGAAAATCGCCGCCAGAAATCCACTTCTTAGCCCGAACAAATCGATCAGCGGCGGAAACACCCCTCAAGACGTCGATCAGCA
75834 C T GAGGGGGTGCCCGGGTCCGTGGCCGCGGACAGCACGCCGAGCTCTTCGGCCTTGGACAGCAGGCCCAGTCTCTCCACAGTGGACAG[C/T]GACAGCCCGAACTTCTCCGCCGCGGACAGAAGCCCGGCCTTTTCAGCCTTGGTCAGAAGGCGCAGCTTTTCCACGTTCGACAGCAGTTTCACTGGACG
75858 G A AGATCAACAAACAGGTTGGCAACAGAATCATAAGGAAGAGGATTCATGTTCGAATAGAGCACGTGCAACCATCAAGATGCAGCGAAGATTTCCGCCTTAG[G/A]AAGATAAAGAACGACAAGTTGAAGGCAGAAGCAAAGGCACGTGGTGAAGTTATCAGCACAAAGAGACAGCCTGAAGGACCCAA
75858 T C GGAAGATAAAGAACGACAAGTTGAAGGCAGAAGCAAAGGCACGTGGTGAAGTTATCAGCACAAAGAGACAGCCTGAAGGACCCAAGCCTGGTTTCATGGT[T/C]GACGGTGCGATGCTTGAGACGGTCACTCCTATTCCATATGATGTTGTCAATGATCTCAAAGGCGGTTATTAGTGCATTGCTTGAT
75896 C G ATGATGTCCAAGAAAGCGGCTGTCACATGCACCGTCGTGGCGGCGGCGGCGGTCACGTGCTCCGTGGCTACGCTGGTTGTGCGGCAGCGAAGGAAGAGCT[C/G]TAGTAGGTGGTCACGAGTCGAGGCGATCATTAAAGAGCTCGAGGACAAGTGTGCTACCCCGATTGAGCGGTTGAGACTTGTGG
75896 A C CACCGTCGTGGCGGCGGCGGCGGTCACGTGCTCCGTGGCTACGCTGGTTGTGCGGCAGCGAAGGAAGAGCTCTAGTAGGTGGTCACGAGTCGAGGCGATC[A/C]TTAAAGAGCTCGAGGACAAGTGTGCTACCCCGATTGAGCGGTTGAGACTTGTGGCGGACGCTATGACAGTCGAGATGCAAGC
75902 A T ACAAACTGAACAATCTTTTTTGATCAAAATATTAACGCAAGAAAATATAGAAAATAGAGATAAAGTTGCAATGAAAGATGGCATAATTATACAGCAAAGT[A/T]AAGAATTTGTTAGCCTGCCTTCACATCACCAACGTATTAAATACAAAGGTATCTTTAACATATACCGCCGCATTAGGCTTAGTTCAGC
75902 A G CAAACTGAACAATCTTTTTTGATCAAAATATTAACGCAAGAAAATATAGAAAATAGAGATAAAGTTGCAATGAAAGATGGCATAATTATACAGCAAAGTA[A/G]AGAATTTGTTAGCCTGCCTTCACATCACCAACGTATTAAATACAAAGGTATCTTTAACATATACCGCCGCATTAGGCTTAGTTCAGCT
75902 C T ATCAAAATATTAACGCAAGAAAATATAGAAAATAGAGATAAAGTTGCAATGAAAGATGGCATAATTATACAGCAAAGTAAAGAATTTGTTAGCCTGCCTT[C/T]ACATCACCAACGTATTAAATACAAAGGTATCTTTAACATATACCGCCGCATTAGGCTTAGTTCAGCTTGAGATTTTAGCATAAGCCAG
75902 G A ACGCAAGAAAATATAGAAAATAGAGATAAAGTTGCAATGAAAGATGGCATAATTATACAGCAAAGTAAAGAATTTGTTAGCCTGCCTTCACATCACCAAC[G/A]TATTAAATACAAAGGTATCTTTAACATATACCGCCGCATTAGGCTTAGTTCAGCTTGAGATTTTAGCATAAGCCAGTTTCCAAGTATG
75910 C T AAAGCACGGTGGAAATCATTGAATACTTTTCTTTCTTTTTAAATCCAACCAGCAAGTTCCGATACATGGTAAACTTTAACTCATGGGAACGATA[C/T]TAGACAAGTGGTATTTCGCCACAGTCGCTAATGAAAACCTTCTGCTTAGGACGATCACCTCTATCTGTTGGCTGAGATTCAATCAACCTAACCAC
75924 G T TGGCATACAAGTGTCGTCTAAACAACTCGACGTCTCTGCCCATTGGATCGTGTTCACGAACAACCCAGACTATGAGATGGCCGCGCTTTCTTGCAACAGA[G/T]ACCGCTCGAATGACGTTAGGGATGATAGAGTGGGAGTTGGGTAATTGAAATGGACTTGTTGGTGCAATGAAATCATTCTGCATGTC
75926 T C CAAATTAAATTAGGTGTTGCCATGGCGATATTGTCGCGTGTCAGATCTGGTGGGTTTCCTCTTTATCAGAGGCTGCTCAAAGCCAATTCAAACCCTAGCT[T/C]GGCTAATGTCGAGGGTTTGAGGAGCTTCTCCATCCAAGCCAAATCGGCTGAGACAAAGGTTAAGGGAGTGCCGAAGAACTTCTACTC
75926 C T CAAACCCTAGCTTGGCTAATGTCGAGGGTTTGAGGAGCTTCTCCATCCAAGCCAAATCGGCTGAGACAAAGGTTAAGGGAGTGCCGAAGAACTTCTACTC[C/T]ATACCACGAGCGCTGAGCACCCAGGCGGCAACAACATCGCCGACTCCTCAGGCTCCACCACCGCCTCCACCTCCTGA
75930 G A GGCCAACTGGCTCCAATTCTTTATATTGGCAACTTGTGGCAATTTTCTCCAGACCCAAAATTTCAGCTTTCTCCCTTAGTGGTATGAACTCAAAATACCC[G/A]ATATTCGGTAAAACAGCAAAAGTCACCAACTCTGGAGGCAGTTCAGGATCGATATTTACTCCAATCCAGCCCTCTGATGATCCATAATC
75930 G A GACCCAAAATTTCAGCTTTCTCCCTTAGTGGTATGAACTCAAAATACCCGATATTCGGTAAAACAGCAAAAGTCACCAACTCTGGAGGCAGTTCAGGATC[G/A]ATATTTACTCCAATCCAGCCCTCTGATGATCCATAATCTGCACTCATCAATGGCATGTTTCCAGCATAATGCCTCAGTTTTTTAAG
75930 A G CCAAAATTTCAGCTTTCTCCCTTAGTGGTATGAACTCAAAATACCCGATATTCGGTAAAACAGCAAAAGTCACCAACTCTGGAGGCAGTTCAGGATCGAT[A/G]TTTACTCCAATCCAGCCCTCTGATGATCCATAATCTGCACTCATCAATGGCATGTTTCCAGCATAATGCCTCAGTTTTTTAAG
75934 T C AAAAAAAAGAATATTACTCACAAAAGATTAACTATCCTGGATTTGTTCACCAGCTGAACACAACAGATAAG[T/C]GTTGTTGATACAGTGATGTTGTACGTTAACCCTTGGACAACATTTTTCGCAAATCTCTACACATAAAAAACATAAAATTACAAGACTTGGTTTGATTTCT
75934 T C CACAAAAGATTAACTATCCTGGATTTGTTCACCAGCTGAACACAACAGATAAGTGTTGTTGATACAGTGATGTTGTACGTTAACCCTTGGACAACATTTT[T/C]CGCAAATCTCTACACATAAAAAACATAAAATTACAAGACTTGGTTTGATTTCTAGATCACCTTCCTTTCTCCTCCAAATGCCCATATCTTA
75946 G A ACGTAACCACCGTTTACCCTAATTACCTGCCCATTAATCCACTCCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCA[G/A]CCGGCCCATCGGATTGTCCGCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGC
75946 T A TACCCTAATTACCTGCCCATTAATCCACTCCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGA[T/A]TGTCCGCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACAC
75946 G A CCCTAATTACCTGCCCATTAATCCACTCCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATT[G/A]TCCGCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTT
75946 C T CTAATTACCTGCCCATTAATCCACTCCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATTGT[C/T]CGCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTAT
75946 C T TAATTACCTGCCCATTAATCCACTCCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATTGTC[C/T]GCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATC
75946 T C CCGCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATTGTCCGCTTCCAAAGCCCTAACCAGCTC[T/C]TTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCC
75946 T C GCCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATTGTCCGCTTCCAAAGCCCTAACCAGCTCTT[T/C]TGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCCAG
75946 T C CCTCATCACTAACCAAAAAACCCACCGTCGCAGCCACATCCTTGGGCTCACCCAGCCGGCCCATCGGATTGTCCGCTTCCAAAGCCCTAACCAGCTCTTT[T/C]GTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCCAGC
75946 C T TCGGATTGTCCGCTTCCAAAGCCCTAACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTAT[C/T]CCACTCCCCTTCAACTCTTTTGCCAGCACCTTAGTCATTACTTCAATTGCAGCTTTGCTGGCTGAATAGATAGCGTAGCCCGGCCTTATTG
75946 G A ACCAGCTCTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCCA[G/A]CACCTTAGTCATTACTTCAATTGCAGCTTTGCTGGCTGAATAGATAGCGTAGCCCGGCCTTATTGCTCCAACGGAGGAGGATGACATAG
75946 A T CTTTTGTCTTCCCTCTATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCCAGCACCTT[A/T]GTCATTACTTCAATTGCAGCTTTGCTGGCTGAATAGATAGCGTAGCCCGGCCTTATTGCTCCAACGGAGGAGGATGACATAGTCACGATC
75946 T C TATAAAACAGCTCCGTCTTCACCGGACCAGGCGCTACAGCGTTCACACTTATCCCACTCCCCTTCAACTCTTTTGCCAGCACCTTAGTCATTACTTCAAT[T/C]GCAGCTTTGCTGGCTGAATAGATAGCGTAGCCCGGCCTTATTGCTCCAACGGAGGAGGATGACATAGTCACGATCCGACCGCC
75948 T A TGCTTAAACGCATTCGACCCCAAGTGCACCGGTTCAAACCCGGCCCGGCCCAACCTCTTCTTCCACTGACCCAGCTTCTCGTGCCTCTCCTCCCTCTCCA[T/A]ACCTTCGCACGCCACCACGTTGCATATCTCCTTCCCCAGGTAGATCTCGGCCATAATCCGATTCTCCCCTCCATCGGAGCCGCATCCTCC
75948 A G TCTCGGCCATAATCCGATTCTCCCCTCCATCGGAGCCGCATCCTCCTTCCAACGAATCGAACATCGTCGAATAGTAATGCAACGCCTCCTTGAATCGTGC[A/G]GAAAACGAATCCGAATTGTGATCCGCTTCCTGCTCCACTACCGTCACGATTTTGGGATTCATCGCCTTCACCGTGCTTAGCACTTTCTC
75960 A G TTTTTTTTTTTTTTAGAGCAGAACTCATTGATTAAGCATTAGAGTAGTCGATAAAAAGAAGACAA[A/G]CATACTCAATTCAATAATATTAATACATGCAGCAACATAACCATCATATTGAATACACATAGAAAGTGAACATAGAAAGGGACAGACAGAAAGGGAAAAC
75960 A AAGC TACTCAATTCAATAATATTAATACATGCAGCAACATAACCATCATATTGAATACACATAGAAAGTGAACATAGAAAGGGACAGACAGAAAGGGAAAACAC[A/AAGC]GGAGAAAGAGAAGACACACAAAGTCACTATAGTAGTGAAAATACCACTACTGATACGGTGACACACCCCATACATGCATGCAT
75960 G C CATGCAGCAACATAACCATCATATTGAATACACATAGAAAGTGAACATAGAAAGGGACAGACAGAAAGGGAAAACACAGGAGAAAGAGAAGACACACAAA[G/C]TCACTATAGTAGTGAAAATACCACTACTGATACGGTGACACACCCCATACATGCATGCATATACATATACTACCAACTAATCAGC
75962 AC A TCATAAGCGTTGCTCTCCTTCCTCATCGCGAAAGAAGCTGACTTTTTAAACTTGTTCAACTCCTCCCCTTCCATTCCCCAATCCAATTTTCCGTTAGGCG[AC/A]CCCCCACTGCGTACTCACTTTCTTTGTAGGAGAAAAGCTTGCTCCTCTGTCAATGAAACTCTGACTTCTTTGCGCAAAGCTTGCCGCCGC
75970 GT G ATCTTGGGTTTTAAGACGACTTCTCTTCTTTTAGTTTTTAATTACATCTTATGATAAAATTTTAGAACATGAAGTTTGGTATAACCTTTTTTTTGTTCAT[GT/G]TTTTTCGCATGGATTTGATGTCTTTTACCGTGTTGGTTTATTTTCTGTGCAATTGGTGTTTTGATTTGAGCTATTTGATTGTAGTTGTGCTG
75978 CA C TAACTTAATTCACGCAATGCACTCATTTAAAAGGTAATGCTGATAATGCAGTTACAATACTAACACAGGACATATTTATTCTATCTAA[CA/C]AAAAGAAGTGACAGGTATTCTTCTCCATCTTCCCAGGCTGACTTGCTCAAGCCTTCACATGCTACATGAATCCATCATCTATGACAAACGACCTAATAAA
76004 A C GTCTCAAAATTTTAAACTTGTTCCTGCAATATGACTTCACAGCTCATATTTCTCCTGCTGCTCTC[A/C]ATCTATATTCCAACATCCAAATCATTTGAAGATTTCAAGCTTTATGGACTGGGTGATCTGGACAACGGAAAGATACTGATAAAGGGAGGAACAGTCGTGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
76040 T C CGTGACATCGTACAAATCCGAGAGCGACCGAAACCGGTGATTCTTCCTTCCGCTGCTGTGTTCGTCGTCCTCTTCTTCGTCGATCGATTTCAGCAGCCTG[T/C]TGTTGTTGTTGTTGCTTTCGCAGCAGTTGTTTACGGATCTCGGGGTGCAGGAGTTGGTCGATTCCTGATCGTTGGCCGACTCGGCGCT
76082 A G ACTGGCATTCCTGTAAACCTTGCTTGTCTTAAACTAACACAGAACACAAACATGCCGATTACATAACAGCTGTAAAATTACCAAGAAGCCCTTTGTTGCA[A/G]ATGCTTCAAACTCTGCTCCATGCTAACCTGCACCATCTCCGCGAGTATCTTCTTCGCCTTCCCCATTCTGTCCTCTCCATCGATTTTCGAT
76084 G A CAGTAATGCCAGCAGGAGCTTCATTGCTCTTAGTTTCAGAAACAGATAATTTGTCAAGCAATTCAGATGCAGAAACTGCTTCTTTGTTATCTTTCTCCTC[G/A]GCTTTACCCATCGATTCTGCAACACTTTCTATTGTTTCCATGAATCTCTTGTTGTTTTCAACAGAACCAAAGCGAATACAAAACATCTCTT
76084 C T GAACCAAAGCGAATACAAAACATCTCTTCCTTCACCTCTCCATCTGAATAATCAGGTGCATGCCAAACACAGGACTTTTCATTCCCAGCATGCTCTTGCA[C/T]TTTAATTTCCGGAAATACATAGTGATTGGCACATATCTTCAGAGTTTTTGCCTGCCTCATAAC
76088 G C GAACTTAATCAGCTTCTTCTGTTGCCAAACTGGATTCAACTCCACCTGATTAACAGCAGGAGGAATTACAGCAGTTTGTAAAAGCTGTTCCAGTTTCTTA[G/C]ATGAGAAATTGCTCACACCGATGGATTTAGCAAGCCCTAACTTGCTGCATTTCTCCATTTCTTTCCACACTGATTCCATATCCAGTGCAC
76108 G A AAATGGAGCCTCCTCCGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTAC[G/A]TGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGT
76108 C T AAATGGAGCCTCCTCCGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAG[C/T]GAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCG
76108 T C AAATGGAGCCTCCTCCGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGT[T/C]GAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAG
76108 G A AAATGGAGCCTCCTCCGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCG[G/A]TTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAG
76108 C T AGCCTCCTCCGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGG[C/T]TTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGG
76108 A G CGACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACG[A/G]TTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGA
76108 T G GACGATTATCCACCATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGA[T/G]TTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAG
76108 C A ATGCACCTTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGA[C/A]GAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTT
76108 A G TTCTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGC[A/G]GTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATT
76108 T C CTCGGCACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAG[T/C]GAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTG
76108 T C CACACGTGCGATGGCTACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAG[T/C]TGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGG
76108 A T TACGTGGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTG[A/T]TGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTG
76108 C T GGGAGCAAGCGAGGCGTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTG[C/T]ACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTT
76108 A T GTACGGAGGTTGAGCGGTTGGTGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATAT[A/T]TTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATG
76108 C T TGCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAG[C/T]AAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATAATGGCTGCGGCCGGGA
76108 A C GCGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGC[A/C]AGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATAATGGCTGCGGCCGGGAT
76108 A C CGGGCTTTGTACGATTTTGGGAAGGAGACGAAGGCAGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCA[A/C]GAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATAATGGCTGCGGCCGGGATT
76108 G A AGTGAAGTTGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCG[G/A]TTGAGTTTAAGGAGATGATTTATGAGATAATGGCTGCGGCCGGGATTGATATTGGGGATTTTGTGCCGGGAGTGGGTTGGATG
76108 T C TGTCGGAGTTGGTGATGTGCACGTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTT[T/C]AAGGAGATGATTTATGAGATAATGGCTGCGGCCGGGATTGATATTGGGGATTTTGTGCCGGGAGTGGGTTGGATGGATTTGCA
76108 A G GTTGGCGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATA[A/G]TGGCTGCGGCCGGGATTGATATTGGGGATTTTGTGCCGGGAGTGGGTTGGATGGATTTGCAGGGGGTTGAGAGGAAGATGAA
76108 T G CGAATATATTAGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATAATGGC[T/G]GCGGCCGGGATTGATATTGGGGATTTTGTGCCGGGAGTGGGTTGGATGGATTTGCAGGGGGTTGAGAGGAAGATGAAGGGG
76108 A T AGGGTTGGCGACTATGAGCAAGAGGGTGTTTGGGGATTTGGAAGGAGGAGAGTCGGTTGAGTTTAAGGAGATGATTTATGAGATAATGGCTGCGGCCGGG[A/T]TTGATATTGGGGATTTTGTGCCGGGAGTGGGTTGGATGGATTTGCAGGGGGTTGAGAGGAAGATGAAGGGGATACATA
76116 T C ACAAACCCCAGTCCAAATCCGAACCCAAACCCTCCGTCGCCGTCGATCAGGAGAAGCACACTTCTGAGTACCCGTCGGTGGATGCGGCAGTGAGAGATCA[T/C]CAGGCGACGGTGATGCCGGAAGAATCAAATCCTTATGTTGCTCCAGCTCCCGCCAGTCAATCTTCTAAGTATACAATCGAGACAGT
76116 C G AGAAGCACACTTCTGAGTACCCGTCGGTGGATGCGGCAGTGAGAGATCATCAGGCGACGGTGATGCCGGAAGAATCAAATCCTTATGTTGCTCCAGCTCC[C/G]GCCAGTCAATCTTCTAAGTATACAATCGAGACAGTAAAAGATGTGCTTGGGAGGTGGGGAAAGAGATGGGTGAAGC
76140 AT A TCCATGTATCAAGGAAGCTTGTACGCTCCATTTTCCCATCCTCGGAGAAGAAAACATGCAGTGAAATCTTAGCATTGAAATACATTACTGGTTGCTGATT[AT/A]TTTTTTACTGCAACTTGCAAAAGCGTGCTAGGGGGGCCTTGTGAGATATTCTGATAAGGAAGCATTGGTAGAAGAGTCCTGGTTGA
76146 C T ACATAAGTTCCATGTCTAAAGAGGATCTTGGGTCGGCAAAGGAAGAAAGACAGTTAGTTGAATCGCTTTGGAACGCGTGCTTTGATGAGCCGTCATCTCT[C/T]AGAGAGAAAGGATTGGTGGTTCTTCCTGGAGAAGAAGAGACAGAGGCTGCTCCTGATGTTGCTAGCAAGTTTTTTGAACCTCCATT
76146 A G TGGTGGTTCTTCCTGGAGAAGAAGAGACAGAGGCTGCTCCTGATGTTGCTAGCAAGTTTTTTGAACCTCCATTGCGTGCTTGGTCTGCTAGACCTGATAC[A/G]AGCTTGGAGGAGAAGCCGGAAAAGAAGCAGCAACCTCCACTGTTACTTGGACCCAGTAATCCCACTTAGTCTAGACAGATATGCAT
76146 G A GAGAAGAAGAGACAGAGGCTGCTCCTGATGTTGCTAGCAAGTTTTTTGAACCTCCATTGCGTGCTTGGTCTGCTAGACCTGATACAAGCTTGGAGGAGAA[G/A]CCGGAAAAGAAGCAGCAACCTCCACTGTTACTTGGACCCAGTAATCCCACTTAGTCTAGACAGATATGCATCATTACATAGTAAGC
76148 T C GGACTTATTTAAATCTTCCTTCTGAGATTGTACCTGCTACTTTGAAGAAGTCTGCCAAGCCTCCAGGTAGACCATTTGGGTCTGGCCCACCTGGTGATCG[T/C]CCAAGGGGCCCACGATTTGAAGGAGACAGGCCCAGATTTGGAGACAGGGAGGGATACAGAGGTGGTCCTCCTCGTGCCGGTCCAG
76158 C T CAAGAGTCGGTGGAAGATGTTCCCTGTGGTAACACGGTTGCTATGGTTGGTTTGGATCAGTTTATCACCAAGAATGCAACTTTAACAAACGAGAAAGAAG[C/T]AGATGCACACCCAATTCGTGCCATGAAATTTTCTGTGTCCCCTGTTGTCCGTGTCGCTGTTCAGTGCAAAGTTGCGTCTGACCTGCC
76158 T C ACACGGTTGCTATGGTTGGTTTGGATCAGTTTATCACCAAGAATGCAACTTTAACAAACGAGAAAGAAGCAGATGCACACCCAATTCGTGCCATGAAATT[T/C]TCTGTGTCCCCTGTTGTCCGTGTCGCTGTTCAGTGCAAAGTTGCGTCTGACCTGCCTAAGTTGGTTGAAGGTCTAAAACGTCTTGCAA
76158 C T ATCAGTTTATCACCAAGAATGCAACTTTAACAAACGAGAAAGAAGCAGATGCACACCCAATTCGTGCCATGAAATTTTCTGTGTCCCCTGTTGTCCGTGT[C/T]GCTGTTCAGTGCAAAGTTGCGTCTGACCTGCCTAAGTTGGTTGAAGGTCTAAAACGTCTTGCAAAATCAGATCCTATGGTTGTGTGCA
76158 G A TCACCAAGAATGCAACTTTAACAAACGAGAAAGAAGCAGATGCACACCCAATTCGTGCCATGAAATTTTCTGTGTCCCCTGTTGTCCGTGTCGCTGTTCA[G/A]TGCAAAGTTGCGTCTGACCTGCCTAAGTTGGTTGAAGGTCTAAAACGTCTTGCAAAATCAGATCCTATGGTTGTGTGCACAATTGAAG
76158 T C ACGAGAAAGAAGCAGATGCACACCCAATTCGTGCCATGAAATTTTCTGTGTCCCCTGTTGTCCGTGTCGCTGTTCAGTGCAAAGTTGCGTCTGACCTGCC[T/C]AAGTTGGTTGAAGGTCTAAAACGTCTTGCAAAATCAGATCCTATGGTTGTGTGCACAATTGAAGAGAGCGGGGAGCACATTGTTGCA
76158 C T CTGTTGTCCGTGTCGCTGTTCAGTGCAAAGTTGCGTCTGACCTGCCTAAGTTGGTTGAAGGTCTAAAACGTCTTGCAAAATCAGATCCTATGGTTGTGTG[C/T]ACAATTGAAGAGAGCGGGGAGCACATTGTTGCAGGAGCAGGCGAGCTCCATTTGGAAATCTGTCTGAAGGATCTGCAAGAGGATTT
76158 G A AGTTGCGTCTGACCTGCCTAAGTTGGTTGAAGGTCTAAAACGTCTTGCAAAATCAGATCCTATGGTTGTGTGCACAATTGAAGAGAGCGGGGAGCACATT[G/A]TTGCAGGAGCAGGCGAGCTCCATTTGGAAATCTGTCTGAAGGATCTGCAAGAGGATTTCAT
76160 C T GGCTACACTGACTCTAGTTTAATTATATGTTTCGGGGAAATGTTGATCGACTTCGTTCCGAC[C/T]ACGTCCGGCGTCTCCCTAGCCGAAGCCCCTGGCTTCGTGAAAGCCCCCGGTGGCGCACCTGCCAACGTGGCGATCGCTGTGAGCAGACTTGGAGGCAGGT
76160 T C TGTTGATCGACTTCGTTCCGACCACGTCCGGCGTCTCCCTAGCCGAAGCCCCTGGCTTCGTGAAAGCCCCCGGTGGCGCACCTGCCAACGTGGCGATCGC[T/C]GTGAGCAGACTTGGAGGCAGGTCGGCCTTCGTCGGAAAGTTGGGAGATGACGAGTTTGGAAGGATGCTTGCGAATATTTTGAGG
76160 C T TCTCCCTAGCCGAAGCCCCTGGCTTCGTGAAAGCCCCCGGTGGCGCACCTGCCAACGTGGCGATCGCTGTGAGCAGACTTGGAGGCAGGTCGGCCTTCGT[C/T]GGAAAGTTGGGAGATGACGAGTTTGGAAGGATGCTTGCGAATATTTTGAGGGATAATGGGGTCGTCGACGGCGGGATTTGCTTT
76172 C T ATTACAACATCCAAAAGGAGTCAACCCTTCATCTTGTCCTGAGGCTAAGAGGTGGAACAATGATCAAAGTGAAGACACTCACTGGAAAAGAAATTGAAAT[C/T]GATATCGAACCCACTGATACTATTGACAGGATTAAAGAGCGTGTCGAGGAGAAAGAGGGGATTCCACCTGTGCAGCAGAGGCTGA
76228 G A GGTAGGCCACCAGAGGGAGGTGGTGGTGGGCCCAACTTTATGGGCTTTGCAGTTGCTGCAAGGGCAGCGTCCTTCGTGTCGAATGC[G/A]CTGCCTAGCATCAGTCCAGCAGTTGCAGCAAGGCCGAGTGCTGCTGCTCTACGGCTCGAAGATAACTGGTCCTGATGATTTGGTTGGACGATAACTTG
76228 T A GGTAGGCCACCAGAGGGAGGTGGTGGTGGGCCCAACTTTATGGGCTTTGCAGTTGCTGCAAGGGCAGCGTCCTTCGTGTCGAATGCGC[T/A]GCCTAGCATCAGTCCAGCAGTTGCAGCAAGGCCGAGTGCTGCTGCTCTACGGCTCGAAGATAACTGGTCCTGATGATTTGGTTGGACGATAACTTG
76228 T A GTGGGCCCAACTTTATGGGCTTTGCAGTTGCTGCAAGGGCAGCGTCCTTCGTGTCGAATGCGCTGCCTAGCATCAGTCCAGCAGTTGCAGCAAGGCCGAG[T/A]GCTGCTGCTCTACGGCTCGAAGATAACTGGTCCTGATGATTTGGTTGGACGATAACTTGATCAGCAGCATCAGTTTTGATTTGTGC
76228 C T CAAGGGCAGCGTCCTTCGTGTCGAATGCGCTGCCTAGCATCAGTCCAGCAGTTGCAGCAAGGCCGAGTGCTGCTGCTCTACGGCTCGAAGATAACTGGTC[C/T]TGATGATTTGGTTGGACGATAACTTGATCAGCAGCATCAGTTTTGATTTGTGCCTTTGTTATGAAGCGAGGTGATGGCAGTGCGTT
76270 C T CAAAAATCCATCACATGCAAGTTTGTAATTGCTATCATCATGCGTCTTAGGCACAACCCTCTCATCGACCCAAAACACATGCCATTTTGTCCAATCAACA[C/T]CATTAACATACGGGTTTTCTAGCAATTTCCTGAGGCAAGCTATGAGGTACCCACCGGATAAAACGACAGTAAAAGCGCCTCTCTCTTCT
76270 C T ACATGCCATTTTGTCCAATCAACACCATTAACATACGGGTTTTCTAGCAATTTCCTGAGGCAAGCTATGAGGTACCCACCGGATAAAACGACAGTAAAAG[C/T]GCCTCTCTCTTCTGTGTACTTCTTCGACAGATCTGCAACGTAAGCGGCTAATCCGGCTGCCACGTCATCATCGTTGGGGTAGATAAGC
76270 G T CATGCCATTTTGTCCAATCAACACCATTAACATACGGGTTTTCTAGCAATTTCCTGAGGCAAGCTATGAGGTACCCACCGGATAAAACGACAGTAAAAGC[G/T]CCTCTCTCTTCTGTGTACTTCTTCGACAGATCTGCAACGTAAGCGGCTAATCCGGCTGCCACGTCATCATCGTTGGGGTAGATAAGCA
76272 C T AATGCTAGGAGTGCACCAGATGTGATGGTGCAAGCTTTCAGAACAGAACTCCTTGTTGCAATTCTCCTTTTAATATCACTGGTGGCATCAGCATAGTTTT[C/T]AGTAGTATTGCCGACTGTTTCTTCGGACGCTAAGGAAAGTTGTTCATCTCCTTTTAAATTTCTTTGTTTGGAATCCTTGAATGTTGTTGT
76272 T C AACAGAACTCCTTGTTGCAATTCTCCTTTTAATATCACTGGTGGCATCAGCATAGTTTTCAGTAGTATTGCCGACTGTTTCTTCGGACGCTAAGGAAAGT[T/C]GTTCATCTCCTTTTAAATTTCTTTGTTTGGAATCCTTGAATGTTGTTGTTCCATCCCTTGATCTTTTTTCACTCTTTCTTGTCGCAAGACTTT
76286 T C AATCATTTATAAGTTTTGAGGCTGCATATTTTTGTGTTTGCTAATATTCAGAAGTTGCTATATCTGAGCCGATCTGAATGTTAAAGCTTTTATTTTCCAC[T/C]TTTTCAGTCATGATATCACGGATTTGAATTGTTTCATTTATGGCTCAATTTATGTCGTTAGGTCATTTTATGTTTTATTTCGTTTGTGAATTG
76286 T C GGATTTGAATTGTTTCATTTATGGCTCAATTTATGTCGTTAGGTCATTTTATGTTTTATTTCGTTTGTGAATTGCATTTTTTCTGTTGATGCATTGTGTT[T/C]CAACTCTTTTAGTCCTCATAAGCAGTTCCAATTTGTACCTTGAAATAATGATGTTCATTTGCGAATACAAGGCGGCTTTTTTT
76286 T G TGTTTCATTTATGGCTCAATTTATGTCGTTAGGTCATTTTATGTTTTATTTCGTTTGTGAATTGCATTTTTTCTGTTGATGCATTGTGTTTCAACTCTTT[T/G]AGTCCTCATAAGCAGTTCCAATTTGTACCTTGAAATAATGATGTTCATTTGCGAATACAAGGCGGCTTTTTTT
76286 A T TTATGGCTCAATTTATGTCGTTAGGTCATTTTATGTTTTATTTCGTTTGTGAATTGCATTTTTTCTGTTGATGCATTGTGTTTCAACTCTTTTAGTCCTC[A/T]TAAGCAGTTCCAATTTGTACCTTGAAATAATGATGTTCATTTGCGAATACAAGGCGGCTTTTTTT
76292 A G AAAGTTTCACTGATCTTCCTCTGTGTCACTCCGAAAACTTCAAACTCCAAAAACCCTACCCCTTCCTCCGCTTTCTGATGTCCAATCCACACCTCATCCA[A/G]CGCCTGCAAACCCGCATCGCAGCGCAGAACCAGGACCTCCAAACTTTACTCCTCGACAATCAAACTCTGGCCGCCAGCCATGTGGCCCTC
76292 G T AGTTTCACTGATCTTCCTCTGTGTCACTCCGAAAACTTCAAACTCCAAAAACCCTACCCCTTCCTCCGCTTTCTGATGTCCAATCCACACCTCATCCAAC[G/T]CCTGCAAACCCGCATCGCAGCGCAGAACCAGGACCTCCAAACTTTACTCCTCGACAATCAAACTCTGGCCGCCAGCCATGTGGCCCTCAA
76304 T C ACTCTAAGCCAATCTTTTCATGTCTTTTCTTTATTACATCAATATATTTAGATGGTAATGCATGTGGCTTGAGGAGGAGATCTTGCAGGGTAGCATGAAT[T/C]GTACTACAGTCACCACTGCAAAACCAGTTTCCTTCAGGCAATTCCTTCAAGTTACACATCTTATTGTCCCTTAAGCACCCAACA
76354 G A AAAGGAATGCATTGCAAATTTGGCCATGATAGGAATTATCAGACTGACTCGAAACCAATTTGCTTCTATTACCAGAGAGGAAACTGTACTTATGGTAGTC[G/A]GTGTAGGTATGAACATGTGAAAAATTCTCATCAGCAAATATCTACACCATCAAATTTTCAAACCCATTTAGCATCAAGTTCTTCCCAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
76360 C T CAACAAATGCAACTCCTGCAGCAGGTCAGATTCAGTCGGGCGAACCAAGCGTGAAGCTTACACTTGCAGGGCTGCCAAGAAGAGAAGGAGCAGTGGCATG[C/T]CCGTTCTACATGAAGACAGGCATGTGCAAGTTTGCAGTGGCATGCAGATATGATCACCCGCCACCCGGTGAGGCTGTCGCCAAA
76362 A T CTGTTGGCCTACTGGCAAAAACTTTTCAGTCATGGTCAATAGATAAAAATCGCGCCTCCACCCTTAATTGAGGATTAG[A/T]AATGTTGGTCCCTTCCTACCCTTTTTCTGCAAAAATCCATCAGTTATTTCAACAAGTTTTCTACATCAAGGGGTGCGTCTCCTTAAGTACTACATTCTGG
76362 T C TCCACCCTTAATTGAGGATTAGAAATGTTGGTCCCTTCCTACCCTTTTTCTGCAAAAATCCATCAGTTATTTCAACAAGTTTTCTACATCAAGGGGTGCG[T/C]CTCCTTAAGTACTACATTCTGGTCGGTTGCGATGGGATTTAGAGCCCCGTGGTCGCTGGAAAGGGAGCTCGAACAGGTGGCAGTTCAT
76362 T C CTTAATTGAGGATTAGAAATGTTGGTCCCTTCCTACCCTTTTTCTGCAAAAATCCATCAGTTATTTCAACAAGTTTTCTACATCAAGGGGTGCGTCTCCT[T/C]AAGTACTACATTCTGGTCGGTTGCGATGGGATTTAGAGCCCCGTGGTCGCTGGAAAGGGAGCTCGAACAGGTGGCAGTTCATGACGAT
76362 C T TTCTGCAAAAATCCATCAGTTATTTCAACAAGTTTTCTACATCAAGGGGTGCGTCTCCTTAAGTACTACATTCTGGTCGGTTGCGATGGGATTTAGAGCC[C/T]CGTGGTCGCTGGAAAGGGAGCTCGAACAGGTGGCAGTTCATGACGATTGGGCAGACTAGGACTGTCAATAGTCTTGGCAAACGAAG
76390 C T CGGGCTTTGCGGATGAGGATGTACGAACGGCTCAGCAAGGAAAGCTGTGTTCCTGATAAAAA[C/T]GAGCTTATCGGGCCCGACGTGGGATGGGTTTCCGATCTGCTCATGTAAATACCGACCTACTACGTACGTCTACTACGGAGTATATGGGAGGAAGAGGCGA
76390 A T CGGGCTTTGCGGATGAGGATGTACGAACGGCTCAGCAAGGAAAGCTGTGTTCCTGATAAAAACGAGCTT[A/T]TCGGGCCCGACGTGGGATGGGTTTCCGATCTGCTCATGTAAATACCGACCTACTACGTACGTCTACTACGGAGTATATGGGAGGAAGAGGCGATGACATT
76390 T C CGGGCTTTGCGGATGAGGATGTACGAACGGCTCAGCAAGGAAAGCTGTGTTCCTGATAAAAACGAGCTTA[T/C]CGGGCCCGACGTGGGATGGGTTTCCGATCTGCTCATGTAAATACCGACCTACTACGTACGTCTACTACGGAGTATATGGGAGGAAGAGGCGATGACATTT
76400 T G CTATTTGTCGTTCTTTATTCCCTCTCCTTGCCTTCGTTTTCCTCATCAAATTCTCAATCATGAAGGTCGGACCCTTCCTCTTACTCGCCCT[T/G]CTCACTCTTCTGCAATCCTCCTTCTCAAAATCACAGTCCTTCCTCGGCGTAAACTACGGCCAAGTCGCCGACAATCTACCGCCGCCCGACGCCACCGCAA
76424 A T CTCCTCTTTTCACTCCCATACCTGAATTGGACAAAGAAGAAGAGGAAGAAGATGAGATCACTGAAACCAAACTGGGCGAACTTCCAGAACAGGAAATAAA[A/T]TCTGAATCCAGAAACCAAGGCCTTACCCCGTCCCACACAAATTCCCCTTCCCGGGTCAAACCCAACAAAAACAATCAAATTTCAGTA
76436 C T GCCATACCAACCCTCAATCATCATAAGTGCGGCATTCATCGGTTTCCGGGTTGTCCTTGCAATACTCCTCTAAGGGATCCGACTTATCGGCCTTCACACG[C/T]GCATCCTTCGCAGTTGCACTCAACTCCTCGACCTCGTCCCAAGCAGCCGCGCACTCTCCTTTCGCGTTCTCATCAGCGCATGTCTCCTTC
76436 T C CGACCTCGTCCCAAGCAGCCGCGCACTCTCCTTTCGCGTTCTCATCAGCGCATGTCTCCTTCGCCTTCTCTATGCTGTCCGATAGCTTATCCGATATATC[T/C]GAAGGCGTGGGCGAGCTCCTAACGGGTTCCAAACGGGTTTGCTTGAAATTAAGCTTGGTTGTCCGGGTAGAAACAAAGCCCATTTGCA
76436 G A ACTCTCCTTTCGCGTTCTCATCAGCGCATGTCTCCTTCGCCTTCTCTATGCTGTCCGATAGCTTATCCGATATATCTGAAGGCGTGGGCGAGCTCCTAAC[G/A]GGTTCCAAACGGGTTTGCTTGAAATTAAGCTTGGTTGTCCGGGTAGAAACAAAGCCCATTTGCATGGGCTGTTTAACATTGGTTGGAT
76440 C T TTGCTTTCTATGTGAGGCACTTCTGACATATATATACCAACAGATGGCAGGAACAATATAATGTTACAGAAACATTAAAACAAAAATGAA[C/T]GCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAG
76440 C T TTGCTTTCTATGTGAGGCACTTCTGACATATATATACCAACAGATGGCAGGAACAATATAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAG[C/T]GAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAG
76440 T C TCTATGTGAGGCACTTCTGACATATATATACCAACAGATGGCAGGAACAATATAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACA[T/C]CCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAGTTAAGC
76440 G A AACAGATGGCAGGAACAATATAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTG[G/A]CTTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTTTACTGAAATAAATCA
76440 C A ACAGATGGCAGGAACAATATAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGG[C/A]TTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTTTACTGAAATAAATCAA
76440 T C TAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAA[T/C]AATCATCCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTTTACTGAAATAAATCAAATTATTTTGCATGTAGTTTGC
76440 T TAATCATCCCTAATGTTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAA[T/TAATCATCCC]AATCATCCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTTTACTGAAATAAATCAAATTATTTTGCAT
76440 T TCCCAATCACTACAGAAACATTAAAACAAAAATGAACGCAACAGCGAACACATCCTTTATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAATAATCA[T/TCCCAATCAC]CCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTTTACTGAAATAAATCAAATTATTTTGCATGTAGTT
76440 T G ATAATTGGTAATGGAAGATAAACCTGGCTTATGTGTAGAACATTAATAATCATCCAATCAGACGCTCTAAACTAGAGTTAAGCTTCATTTTTGCTCCCTT[T/G]ACTGAAATAAATCAAATTATTTTGCATGTAGTTTGCTGTAATGATCGGCAGCATTGGACAGTGATGTTATTGTGATAGGATAACCCGGA
76452 G A TTGCTTCTGTTCCTTTGTACATTTCTATTACATCAGGTTCTATCGGTAAATTTTCATGCTCACTGGGTGGGAAGACAAAGTGGCCAGATAAGAACAAGGC[G/A]TTTGCTGGTTCTTGATTGTTTTCATCATCATCATCGATACTTTTCGGATCATGTTCTTTTGTGCCAGACGTAGCATCAAATGTTGACCCT
76452 C T CTTTTGTGCCAGACGTAGCATCAAATGTTGACCCTGTGAGAGACACAACTTCCCAATCAGCCCCACGAGACTGTGTCACCTCTCCCTCTTTCCTTTCATC[C/T]AACATAAGTTGTCCATCTCCCTCCTTCCTCTCATCTTCCATATGTTGACCCTCTACCTCTGTCTTTCCATCCGCCATTATCATAAAAAAAA
76466 ATGCAATACATCAGATGTGATCAACTCT
A TGCCAGGGATAGCTGTAGTAAAGGGTATATAGCTCTAAATGTATCACACTTATTTCGAACATCATGGATCGACTGTCGAATTTGTGGAATCTTCTTTTCC[A/ATGCAATACATCAGATGTGATCAACTCT]TGCAATACATCAGATGTGATCAACTCTTGCAATACATCATGGTGTCTATTTCTAGAAGCAAC
76518 G GA AAGTAAAATGAAAATCAAGCCTTGCGACGTGCAACACGAGCCACGAAACCAGTCCTGATAGGTGCAACCGATCGTGAAGAACCACACTTTTCACAGCGTA[G/GA]AAAAATAACCGGCTTTCTTTAGTGAGTAAAGTATCCGAGCTTTTGCACCCATTGCATATGACATATTCATTGGCATATTTTTGAAG
76524 C T CTTTAAACTTGATTGCTCGTCTGCCGGTTGTTGCCTCTTATGTCTATAGGAGGATCTATAAGAACGGCCAAGTTGTACCCGCTGACAATTCTCTAGATTA[C/T]GGTGCAAATTTCTCCCACATGCTTGGATTTGACAGTCCCAAGATGCTTGAGTTGATGAGACTTTATGTTACTATTCACACTGATCATGAA
76524 T C GATTGCTCGTCTGCCGGTTGTTGCCTCTTATGTCTATAGGAGGATCTATAAGAACGGCCAAGTTGTACCCGCTGACAATTCTCTAGATTACGGTGCAAAT[T/C]TCTCCCACATGCTTGGATTTGACAGTCCCAAGATGCTTGAGTTGATGAGACTTTATGTTACTATTCACACTGATCATGAAGGGGGAAA
76530 C T TTTACTTTATCACTTTCACGAACATCCCCTCAAAACCCTAAAAATTTCAGTTCACTTCACAAACTCCGGGACCCCTAATATATCGGCATTCACTCCAGCA[C/T]CCCGTGAGGCGACAATCTTCGATTCAATACACCGGTAAATCGTTTCACTCCAGCATCCTCAAGTCGACCATCGTCAATTCAGTATATTGCA
76536 A T TTTTTTTTTTTTTTTTGTAACACATACAAGCAATTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGA[A/T]TCACAATGCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGAT
76536 T G TTTTTTTTTTTTTTTTGTAACACATACAAGCAATTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAA[T/G]GCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGAT
76536 T C TTTTTTTTTTGTAACACATACAAGCAATTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAATGCTGATGAT[T/C]CAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTC
76536 A G TTTTTTTTGTAACACATACAAGCAATTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAATGCTGATGATTC[A/G]GCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAG
76536 C T TTTTGTAACACATACAAGCAATTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAATGCTGATGATTCAGCT[C/T]ATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAA
76536 CA C TTCAATTGCTACAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAATGCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTA[CA/C]AAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAAATATATAAGTAAATATCAGT
76536 TGTA T CAGAACTACAGCAAATCAAACCAAAAGGAGAACCAAACCAAATGAATCACAATGCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCA[TGTA/T]GTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAAATATATAAGTAAATATCAGTACTTCTCGG
76536 T C CAAACCAAATGAATCACAATGCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATA[T/C]AAAATCAAGGATAACTCAGAAAATATATAAGTAAATATCAGTACTTCTCGGCCAACCGAGCTGTAACAGCTCTAAGCTTAGAATAAAC
76536 AG A ATGCTGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTC[AG/A]GAAAATATATAAGTAAATATCAGTACTTCTCGGCCAACCGAGCTGTAACAGCTCTAAGCTTAGAATAAACCTTTCCAGCAGGGGAC
76536 A G TGATGATTCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAA[A/G]ATATATAAGTAAATATCAGTACTTCTCGGCCAACCGAGCTGTAACAGCTCTAAGCTTAGAATAAACCTTTCCAGCAGGGGACCCCAA
76536 A T TCAGCTCATGTTCCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAAATATAT[A/T]AGTAAATATCAGTACTTCTCGGCCAACCGAGCTGTAACAGCTCTAAGCTTAGAATAAACCTTTCCAGCAGGGGACCCCAAAATGAGA
76536 G A CCAGTTTCAACAGTACAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAAATATATAAGTAAATATCA[G/A]TACTTCTCGGCCAACCGAGCTGTAACAGCTCTAAGCTTAGAATAAACCTTTCCAGCAGGGGACCCCAAAATGAGACTACAAAGAGAG
76536 C T CAAAAATAGCATGTAGTAGGTAGGTAACCATAACATAACCGATATAAAATCAAGGATAACTCAGAAAATATATAAGTAAATATCAGTACTTCTCGGCCAA[C/T]CGAGCTGTAACAGCTCTAAGCTTAGAATAAACCTTTCCAGCAGGGGACCCCAAAATGAGACTACAAAGAGAGTCCCTAGCAACTTTG
76564 T C CTGTTGGCCTACTGGAAGGCAAAGGAATAACATGACCAAAGACGTTGAGGCACCGTATGCACCAAAAGACTACACCGACCCACCACC[T/C]GCACCGCTGATCGACAGACACGAGCTGACGACATGGTCCCTGTACCGAGCCGTGATAGCCGAGTTCGTCGCCACCCTCCTCTTCCTCTACGTCACGGTC
76564 A C GGCCTACTGGAAGGCAAAGGAATAACATGACCAAAGACGTTGAGGCACCGTATGCACCAAAAGACTACACCGACCCACCACCTGCACCGCTGATCGACAG[A/C]CACGAGCTGACGACATGGTCCCTGTACCGAGCCGTGATAGCCGAGTTCGTCGCCACCCTCCTCTTCCTCTACGTCACGGTCGCCAC
76592 A T ATCTGGCTTCTGGGCGAACTATATGCAAGCTTCATCTCACAGAAGGAGGACTACATGCTGATATTAATGGAGATGGTGTTCTTGACCATGTTCAGGCTGT[A/T]GGAGCACATGGAGCTGAGCAAACTGTAGTGAGTGGCTCAATGGAAGTATTAAAACCATGTCATGCAGTGGCAACTTCAGGCGTACC
76628 A G TTGATTCCGGCCTCCAACTTAGACGAGATGACAAATGGGTTTTTGGCGTTGTTCAAGGAAGCGTTCCTTAC[A/G]CTGCAGGCGGAAAAGGAAATTATGGAGACAAAGCCAAAAGTGTTGGTAAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCG
76628 A T TTGATTCCGGCCTCCAACTTAGACGAGATGACAAATGGGTTTTTGGCGTTGTTCAAGGAAGCGTTCCTTACACTGCAGGCGGAAA[A/T]GGAAATTATGGAGACAAAGCCAAAAGTGTTGGTAAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCGAATTGATCGCTGTC
76628 A T TTGATTCCGGCCTCCAACTTAGACGAGATGACAAATGGGTTTTTGGCGTTGTTCAAGGAAGCGTTCCTTACACTGCAGGCGGAAAAGGA[A/T]ATTATGGAGACAAAGCCAAAAGTGTTGGTAAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCGAATTGATCGCTGTC
76628 G A TTGATTCCGGCCTCCAACTTAGACGAGATGACAAATGGGTTTTTGGCGTTGTTCAAGGAAGCGTTCCTTACACTGCAGGCGGAAAAGGAAATTATGGA[G/A]ACAAAGCCAAAAGTGTTGGTAAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCGAATTGATCGCTGTC
76628 C T AAATTATGGAGACAAAGCCAAAAGTGTTGGTAAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCGAATTGATCGCTGTCGG[C/T]CCGGCATTAGAATCGGGTGCGACGGCTAAGTCAAACATAATGGATATCAAGCCGGACGAAGGGTACGTCGAGTGGCTGGATTCG
76628 T A AAACACATTTGAAGAACTTGAGTCGGCTGCGCTTGCGAGCGTGGAAGACATCGAATTGATCGCTGTCGGCCCGGCATTAGAATCGGGTGCGACGGCTAAG[T/A]CAAACATAATGGATATCAAGCCGGACGAAGGGTACGTCGAGTGGCTGGATTCGAAGCCGGAGAGATCGGTCGTGTATGTGTCA
76668 A G TTTCAGACTCAACTGGGCTGCTGCTGGTGAAAAGCGTGGCGATGATGGTCCTGAGTATACTGTATTTGTTGGTGACTTGGCGCCGGATGTCACTGATTAT[A/G]TATTACAAGAGACTTTTAAAAGCCATTATCCTTCGGTTAGAGGAGCTAAGATAGTTACTGATAGAATCACAGGGCGTTCCAAGGGC
76684 C CA GTATCATTGTCATTATGACTATTTTGTTGACTGTAAACTTGAAGTTGATGACCTGTCCTCGTATCGAACAGCCTACAGGTACCATCATCGGAGCCAGTTC[C/CA]AAATCTTTGCCCATCTGGAAAGAACTTTACAGTGTTAACAGCCCCTTCATGTCCATAATACGTGCGTACAGCTCGACTAGCTATACGT
76684 T TA GTCATTATGACTATTTTGTTGACTGTAAACTTGAAGTTGATGACCTGTCCTCGTATCGAACAGCCTACAGGTACCATCATCGGAGCCAGTTCCAAATCTT[T/TA]GCCCATCTGGAAAGAACTTTACAGTGTTAACAGCCCCTTCATGTCCATAATACGTGCGTACAGCTCGACTAGCTATACGTGCGTCCCA
76686 CT C ACAGGGATCAAAATAGTCTCTCTGACTTCCTTTCTGGAGGAGGTCATCTCTTCCCTGACAACAGTAATTACATCTGGGACAGGGGGCAGAGACCACCATC[CT/C]TTTCCAGCAGTGATCCAGAGAACTACCAAGGTGATTACAGGCAATCTGACTTCCTATCTGGAGAAAGCTACCTCAGCCCTGCTATC
76686 G A CAGTAATTACATCTGGGACAGGGGGCAGAGACCACCATCCTTTCCAGCAGTGATCCAGAGAACTACCAAGGTGATTACAGGCAATCTGACTTCCTATCTG[G/A]AGAAAGCTACCTCAGCCCTGCTATCAGAAATAATTCCTGACACAGGAAGAGGAGCCTCCAGCAGTGATCCAGAGAGCTGTAACCAC
76718 A G TGTTGGCCTACTGGAAAAAGTATTTATGCGGGAGTAGCAAAACTCTTACGGGTTTAGTAGCATC[A/G]ACTCTTTTTAGAAACCCTAAATCTGAAGATTCCCGTAAATTTTCCCTTCTCCTGAAATTCTATGCCGGACGTTCAATCGCTGGTCACCGAGTTTGTCCTC
76718 G A TGTTGGCCTACTGGAAAAAGTATTTATGCGGGAGTAGCAAAACTCTTACGGGTTTAGTAGCATCAACTCTTTTTAGAAACCCTAAATCTGAA[G/A]ATTCCCGTAAATTTTCCCTTCTCCTGAAATTCTATGCCGGACGTTCAATCGCTGGTCACCGAGTTTGTCCTCAAACTCAAGAGACGTAAAATAGAAG
76718 A AG GAAATTCTATGCCGGACGTTCAATCGCTGGTCACCGAGTTTGTCCTCAAACTCAAGAGACGTAAAATAGAAGGGTCGCACGCAAGCGCAAGGCAGACAGC[A/AG]GAGCTACTACGGTCGGTGATTTCGCAGCAGAGGTTGCCGTACACTAATCAAGCTGCGATTTTGATCGATGCTATACAAGCTGTC
76718 T C GGTCGCACGCAAGCGCAAGGCAGACAGCAGAGCTACTACGGTCGGTGATTTCGCAGCAGAGGTTGCCGTACACTAATCAAGCTGCGATTTTGATCGATGC[T/C]ATACAAGCTGTCGGTGAACAGCTTGTTGCTGCTAACCCTGTTGAGCTTGCCGTTGGTAACATAGTGAGGCGTGTTTTACA
76720 C G AAGGTAAAACATGGCTTGCGAGTAATGGCGGATAGAAGAATGGATTAGTGAGGTTTGAGGGGGATTTGGGGGAAGAAGATTTTATTGATGAAACTAGTTG[C/G]TGAAGTGTGCGGAGTTGGGAAAATAAATGTGCTTATTTAATACTCCATTTGGGTTCCAGTAGGCCAACAG
76720 G C GGTAAAACATGGCTTGCGAGTAATGGCGGATAGAAGAATGGATTAGTGAGGTTTGAGGGGGATTTGGGGGAAGAAGATTTTATTGATGAAACTAGTTGCT[G/C]AAGTGTGCGGAGTTGGGAAAATAAATGTGCTTATTTAATACTCCATTTGGGTTCCAGTAGGCCAACAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
76728 C A ACATAGCTAACCAAAAAATATATGAATTGGCTTCGCCCTTGTTAAAACAAGCTCCCTTCTCATGTTACATACCAACAGGATTTGGTGCTACATGGACTGT[C/A]TGAAACAAGTATCATTAATCACTGTCGACATCCGAAACAGATCATGTGGAACAAAATGGTGGGCTCGACCACTGGAGCGCCTAGAAA
76776 A G GATTGACATCCACTTGGTCCATCGTTGATGACAACTCTGTAGCCATCTTCTAGGCCTTCTTGTTTAGCCACGACTTTAGCTATGTATA[A/G]AAGGTAGCCAAGGATTTCAATGTGTTTCTCTTCTGCCTTTGCCAACCTTGTCAACCCATCTCTGACTTTGGGTATAATTACGATATGTGTTGGGGCTTGA
76812 A T TCACTGTTGGCCTACTGGATCACCAGAGCACTTCTTCAAGGTTACAACCGCAATAATGGCCTCCATTGCTGCTGCAGCTGCTCC[A/T]ACTTCCCTTGGCGTCTCCGAATTATTTGGAAACTCATTGAGTGCAGCCAGGTCAGCCCAGCCAGCTGCTTCTAACGTAGGAAGCACTTCCAAAATCGTCG
76812 G A GGTTACAACCGCAATAATGGCCTCCATTGCTGCTGCAGCTGCTCCAACTTCCCTTGGCGTCTCCGAATTATTTGGAAACTCATTGAGTGCAGCCAGGTCA[G/A]CCCAGCCAGCTGCTTCTAACGTAGGAAGCACTTCCAAAATCGTCGCTCTTTTTGGAAAGAAACCTGCGGCTCCCAAGGCAAAGCCCG
76812 C A AATCGTCGCTCTTTTTGGAAAGAAACCTGCGGCTCCCAAGGCAAAGCCCGTCGCTGTTTCTCCTGCTTCAGACGAGCTCGCCAAGTGGTATGGTCCTGAT[C/A]GGAGAATCTTCTTGCCTGATGGCCTTCTTGATCGATCCGAGGTTCCCGAATATCTTAACGGAGAGGTCCCCGGAGACTATGGTTACG
76818 T C TGGAAAGGGTGCTGCTCAGGAAGGAGAGCGCGGTGACGGCGATCGCGGTGTCGGAGGAAGGGGACGTGGCGTACTG[T/C]GGGTCGTCGGACGGGGAGGTGAATTTCTGGGAGATGAAGGGAAGGAGGCTGGTGTACGGCGGGGTGCTGGTGGGGCATAAGAAGGCGGTGCTGTGCGTGG
76818 A G GGAAGGAGAGCGCGGTGACGGCGATCGCGGTGTCGGAGGAAGGGGACGTGGCGTACTGTGGGTCGTCGGACGGGGAGGTGAATTTCTGGGAGATGAAGGG[A/G]AGGAGGCTGGTGTACGGCGGGGTGCTGGTGGGGCATAAGAAGGCGGTGCTGTGCGTGGTGAGCGTGGGGAGGCTGGTG
76818 T C AGGAAGGGGACGTGGCGTACTGTGGGTCGTCGGACGGGGAGGTGAATTTCTGGGAGATGAAGGGAAGGAGGCTGGTGTACGGCGGGGTGCTGGTGGGGCA[T/C]AAGAAGGCGGTGCTGTGCGTGGTGAGCGTGGGGAGGCTGGTGATAAGCGGATCGGCTGATCGGACGATCAGGATATGGA
76842 ATG A TCACTGGCACACCTTCACATTTGTGCTGATATTATTTGAAGTGTAATATGATAGTATTTTCATTGGAAATGTGTAACTGACATGTCAGTAACATATTTAT[ATG/A]TGTGTGAGTAGTGGTTGTAACATAAAATTATCATGTGGTACATATGTGGATTCTTTTATGTATCGTTTTGATGGAATGTATGAAAATA
76846 T C GGCACCGGATCATCAACGCTCCTCGAATCCAGAAACGTCACAACAAATTCATCCGACGAA[T/C]CGGCCGATAGAAGAGGCGGAGTAGGACACATCGCGTTTGAAAATCAAATTTTACCTGTCAACTAGTTTCCGATTGCTAAATCAGTATCAAAATCAAAATT
76848 A G ACAACAACAACAACAACAACAATATTAATTAAACCCCCCCACTTCGCCTAGTCGTTATTCAACAATACTGATTTATGCTTCAGTAAAATGGG[A/G]CGATCAATTATGTTAGAATAACCATGAAGCCTTTAAGTAGACGTAGTAATGCACCAGGGCTCCCATATGAATAACGACTTCCTCGATTCACTGCACC
76848 T C AATTAAACCCCCCCACTTCGCCTAGTCGTTATTCAACAATACTGATTTATGCTTCAGTAAAATGGGACGATCAATTATGTTAGAATAACCATGAAGCCTT[T/C]AAGTAGACGTAGTAATGCACCAGGGCTCCCATATGAATAACGACTTCCTCGATTCACTGCACCTCTTAATGTCATGCAAAAGCTCTTCTT
76848 G A CACCAGGGCTCCCATATGAATAACGACTTCCTCGATTCACTGCACCTCTTAATGTCATGCAAAAGCTCTTCTTTGTTCTTCTTTTTTGATGTGAACAATA[G/A]TTTGTTATCAGTCAAAGAATTTTCACCCTCTGCAAAGACATTTGTACTTACAGACGATGCGGCAACTGCAGCTGCAGCTGCGGTGGTCGT
76848 T A GCAAAAGCTCTTCTTTGTTCTTCTTTTTTGATGTGAACAATAGTTTGTTATCAGTCAAAGAATTTTCACCCTCTGCAAAGACATTTGTACTTACAGACGA[T/A]GCGGCAACTGCAGCTGCAGCTGCGGTGGTCGTTGTTGCAGATTGTCGTTTCATCTGCATCGTGCCTAAAA
76862 T A CACACAGAAGTTTGGCAATTTGAGCAAAGGCAAAAGCAAGAAGTTCACTATAGTTTACAGTACCCCTAAGCACACCTTCATCCATAATATATACATAAAC[T/A]AGGAACCATCACAGATACAACTTTATACATATGCCAAATTTATCAGCGGAGGAACAATTAGCGAAGCACAGCAAAGCAAACAACGCT
76862 C T GCACACCTTCATCCATAATATATACATAAACTAGGAACCATCACAGATACAACTTTATACATATGCCAAATTTATCAGCGGAGGAACAATTAGCGAAGCA[C/T]AGCAAAGCAAACAACGCTCAGACTCATCAGTTGAATTATGCTGCCTCTGCAAATCCAACCTGAAAGTTGCCGTAATCGAACACGGTGT
76862 C G ATATACATAAACTAGGAACCATCACAGATACAACTTTATACATATGCCAAATTTATCAGCGGAGGAACAATTAGCGAAGCACAGCAAAGCAAACAACGCT[C/G]AGACTCATCAGTTGAATTATGCTGCCTCTGCAAATCCAACCTGAAAGTTGCCGTAATCGAACACGGTGTGATATACGCCCATGAAAA
76872 A C CATCCTCTAGCAGTCTGCACGCAAGCTTTAACAATGGCGTCGACACTCTCGATTCAATCCCTTTTCATCTTGCAAACCTTTACGAAATTTCCAACCCACC[A/C]CGCATCGTCATCCTATACCACGCACTTTCTCCCCCTTCGTTTCAGCAAGAAAGTTGCCCCTCCGCTTTCGTTGTCTAACAGTCGCCGTGAA
76872 A G CTCTAGCAGTCTGCACGCAAGCTTTAACAATGGCGTCGACACTCTCGATTCAATCCCTTTTCATCTTGCAAACCTTTACGAAATTTCCAACCCACCACGC[A/G]TCGTCATCCTATACCACGCACTTTCTCCCCCTTCGTTTCAGCAAGAAAGTTGCCCCTCCGCTTTCGTTGTCTAACAGTCGCCGTGAAAAG
76872 C T TTGCAAACCTTTACGAAATTTCCAACCCACCACGCATCGTCATCCTATACCACGCACTTTCTCCCCCTTCGTTTCAGCAAGAAAGTTGCCCCTCCGCTTT[C/T]GTTGTCTAACAGTCGCCGTGAAAAGTCCACCGTTGTAAAAGCTTCTGGGGCCAAAGAGCAGAAGTTAGTCCACGAAGGTTTGATTACCG
76884 A G CTCTCTGCAGCCCTCTGTCTCTCTTTTTCGAGTGACCGGCTTAATTGTGTTTGCTCTGTTCGTAGACAAGCAATCTGGGTTTCTAA[A/G]ACTGTTATGCGAGACTGACTCTGAGACAGGCGGTCACTCATGACTCGTTCCTTCTCTTCAGCAGCAGCTGCTTTGGCTTCAGCTTCCTGGAGTCGAGAGT
76892 A G CTACAAACCGATCCAGGTTACCATACAAACTAAGAGCCATACCAAGGAACACATACACCAATGTCAGTGCACACTTGGGACCAAAAGTTATTAAAATGCA[A/G]AATGTGGCCACAGAAAATATTACTTATCTAGGCCTCTTTGATGTCACACTACTCGATTTGGTACATGCATGAAAAGAACATATTTAAA
76892 T G TACCAAGGAACACATACACCAATGTCAGTGCACACTTGGGACCAAAAGTTATTAAAATGCAAAATGTGGCCACAGAAAATATTACTTATCTAGGCCTCTT[T/G]GATGTCACACTACTCGATTTGGTACATGCATGAAAAGAACATATTTAAACAACCATGTCCCGTCCACATAGCAAAACACAAGTACAGA
76892 G A ACAGAAAATATTACTTATCTAGGCCTCTTTGATGTCACACTACTCGATTTGGTACATGCATGAAAAGAACATATTTAAACAACCATGTCCCGTCCACATA[G/A]CAAAACACAAGTACAGACTAACATCACAACAGCTAACAGGAGTCTTCTGCAATGCAAAAATAAACAAAAGGAGAATCTTCCAGGGGAG
76892 T G GATTTGGTACATGCATGAAAAGAACATATTTAAACAACCATGTCCCGTCCACATAGCAAAACACAAGTACAGACTAACATCACAACAGCTAACAGGAGTC[T/G]TCTGCAATGCAAAAATAAACAAAAGGAGAATCTTCCAGGGGAGAAAGCTAGAATATTCCAGTAAGTAGGTTTGCAGCAGTGCTTAT
76914 A G TCTCTTCCAAATCACTTGCAAGTTTCCTCCTTTTCACTCCATAGAGCTCGTCCCTTTTTCGCTTCTCGATTCCCGCCCTTACTTTTGCGTCGTACACGCT[A/G]CGCTTCGATTCATCCATCAAAACATCGAAGGAAGACTTCAGAAGTTGGAAATCCGCCGTAGCGTTGGGGTCATCGGGACGCTTGTCGGGG
76914 A C AGAGCTCGTCCCTTTTTCGCTTCTCGATTCCCGCCCTTACTTTTGCGTCGTACACGCTACGCTTCGATTCATCCATCAAAACATCGAAGGAAGACTTCAG[A/C]AGTTGGAAATCCGCCGTAGCGTTGGGGTCATCGGGACGCTTGTCGGGGTGACGGAGTCGGGATTGGGCCCGGTAGGCATTTTTTATA
76914 A G CCCTTTTTCGCTTCTCGATTCCCGCCCTTACTTTTGCGTCGTACACGCTACGCTTCGATTCATCCATCAAAACATCGAAGGAAGACTTCAGAAGTTGGAA[A/G]TCCGCCGTAGCGTTGGGGTCATCGGGACGCTTGTCGGGGTGACGGAGTCGGGATTGGGCCCGGTAGGCATTTTTTATATCTTCTGAG
76914 G A TCTCGATTCCCGCCCTTACTTTTGCGTCGTACACGCTACGCTTCGATTCATCCATCAAAACATCGAAGGAAGACTTCAGAAGTTGGAAATCCGCCGTAGC[G/A]TTGGGGTCATCGGGACGCTTGTCGGGGTGACGGAGTCGGGATTGGGCCCGGTAGGCATTTTTTATATCTTCTGAGCTTACTTGAAGG
76914 T C CGTTGGGGTCATCGGGACGCTTGTCGGGGTGACGGAGTCGGGATTGGGCCCGGTAGGCATTTTTTATATCTTCTGAGCTTACTTGAAGGGATTCGGGCCC[T/C]GAAGGCAAGCCGAGATTAGAGTAATGGTCAATTGATTCCATGGGTTCGGGCGGCGCCATAGGTTTGGATTTCGAATTTAGGGTTT
76914 A G TGGGGTCATCGGGACGCTTGTCGGGGTGACGGAGTCGGGATTGGGCCCGGTAGGCATTTTTTATATCTTCTGAGCTTACTTGAAGGGATTCGGGCCCTGA[A/G]GGCAAGCCGAGATTAGAGTAATGGTCAATTGATTCCATGGGTTCGGGCGGCGCCATAGGTTTGGATTTCGAATTTAGGGTTTTGT
76920 A G AGCGGTTGCAGCTAAATCTGACTGGCTTATCTTCAATTTTGAAGATCTGACGGCTTCTTTGCAGTAGTGATTCTTCTATTGTCGTTCTTACAACATTCAT[A/G]CCAATGCTTTTGATTGTTTCTGTATATTTGTGTGCCTGCAAGCGAGACACATTCTTGTCAGCATGTGATGCTAATAATTTGTGAACGAAG
76920 A T ATTGTCGTTCTTACAACATTCATACCAATGCTTTTGATTGTTTCTGTATATTTGTGTGCCTGCAAGCGAGACACATTCTTGTCAGCATGTGATGCTAATA[A/T]TTTGTGAACGAAGCGTGCTATTCTGAGACAAATTGTGTTGTATTAATTGAACTTAAAATTACGTTTGGATCTACCACATTACAATCAATAT
76920 A G GTGCCTGCAAGCGAGACACATTCTTGTCAGCATGTGATGCTAATAATTTGTGAACGAAGCGTGCTATTCTGAGACAAATTGTGTTGTATTAATTGAACTT[A/G]AAATTACGTTTGGATCTACCACATTACAATCAATATAGATTAAGTTGGTATTAAAAAAAAGGCCACATGT
76930 G A CGCATCTATCCCGTGCTCCGCACATACCACTTCCCAGAATTTCGCGCCAATTTGGTTCCCGCATTGGCCCCCTTGAATGTGTAGAATCTCTCTCATTGCA[G/A]CGGTTTACTTAGTTATAATTTTGGTATTTTGTTCGTTTATTTTGGAGATTGGAATCAGAAAGAGCCAGTAGGCCAACAG
76936 C G CGTCAACTGCTGTGGATCCAAATACCCAAATTTCGTTCACTGGTCCGCTTTCTGTTGCTGGCCAATCGTACGCGCAAAACACTCAAGAACAAGAAGCTTA[C/G]TACGCTTACTTAGCTGCGTATGCTGCTAATCAGGTGAATCAGCAGCTGTATGCTGCGAGTTCTACTTATGGAGCTGTTCGACCTGGTG
76938 A T TCTTGATTCAGAAAATTTTCCATGCTTGAAAAGTCGTAGCAAAGACTTCCTTCACATTGCTTTCTTATATCATAGTAATTAATATTTCCAGCAAGTCTTA[A/T]AATGGAATTGAAAATACTGGTACAGACCACATATGAAGCCAAGCACGATAGTGATCCAGATGTACCACAAAGCTTAATACCAAATTCACA
76938 G A GATTCAGAAAATTTTCCATGCTTGAAAAGTCGTAGCAAAGACTTCCTTCACATTGCTTTCTTATATCATAGTAATTAATATTTCCAGCAAGTCTTAAAAT[G/A]GAATTGAAAATACTGGTACAGACCACATATGAAGCCAAGCACGATAGTGATCCAGATGTACCACAAAGCTTAATACCAAATTCACATGC
76938 G C CCATGCTTGAAAAGTCGTAGCAAAGACTTCCTTCACATTGCTTTCTTATATCATAGTAATTAATATTTCCAGCAAGTCTTAAAATGGAATTGAAAATACT[G/C]GTACAGACCACATATGAAGCCAAGCACGATAGTGATCCAGATGTACCACAAAGCTTAATACCAAATTCACATGCTGGTAAATATTTGTT
76946 T C TGTTGTACATGATTGCGCAGTGTCTAGGTGCGATATGCGGTGTAGGATTCGTGAAGGCTTTCCAAAGTGCATATTACGTCAGATACGGAGGTGGAGCGAA[T/C]GGACTGAACAGTGGGTACACGAAAGGAACCGGACTGGCTGCTGAAATAATTGGCACATTCGTGCTGGTGTACACTGTTTTTGCTG
76946 G A TGGCTGCTGAAATAATTGGCACATTCGTGCTGGTGTACACTGTTTTTGCTGCCACTGACCCCAAACGAAATGCCCGTGACTCTCATGTTCCGGTTTTGGC[G/A]CCACTGCCAATTGGCTTTGCGGTTTTTATGGTTCATTTGGCGACTATTCCGATCACCGGTACCGGGATCAACCCGGCTAGGAGCTTTG
76958 T C CTCATCGAGCATGGTGCTACCTTCTCCGATCGATTACCCCCTCCTCCCGCTTCCAGATTCTTAAGCAG[T/C]AATCAGCATAATATTTCTTCCGCTGGTTACGGTCCCTTGTGGCGGCTTTTCCGCAGGAACCTCATGTCGGAAATTCTTCATACATCGCGGGTAAAGATTT
76958 C A CTCATCGAGCATGGTGCTACCTTCTCCGATCGATTACCCCCTCCTCCCGCTTCCAGATTCTTAAGCAGTAATCAGCATAATATTTCTTC[C/A]GCTGGTTACGGTCCCTTGTGGCGGCTTTTCCGCAGGAACCTCATGTCGGAAATTCTTCATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGG
76958 C T TCGAGCATGGTGCTACCTTCTCCGATCGATTACCCCCTCCTCCCGCTTCCAGATTCTTAAGCAGTAATCAGCATAATATTTCTTCCGCTGGTTACGGTCC[C/T]TTGTGGCGGCTTTTCCGCAGGAACCTCATGTCGGAAATTCTTCATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACT
76958 C T TCTCCGATCGATTACCCCCTCCTCCCGCTTCCAGATTCTTAAGCAGTAATCAGCATAATATTTCTTCCGCTGGTTACGGTCCCTTGTGGCGGCTTTTCCG[C/T]AGGAACCTCATGTCGGAAATTCTTCATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGA
76958 G C CCCCTCCTCCCGCTTCCAGATTCTTAAGCAGTAATCAGCATAATATTTCTTCCGCTGGTTACGGTCCCTTGTGGCGGCTTTTCCGCAGGAACCTCATGTC[G/C]GAAATTCTTCATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTC
76958 C T TTCATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGG[C/T]GGTGTTGTCGTTAAAGAAAGCATTCAATTTGCTATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGG
76958 G C CATACATCGCGGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCG[G/C]TGTTGTCGTTAAAGAAAGCATTCAATTTGCTATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGGGA
76958 T G GGGTAAAGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCGGTGTTGTCGT[T/G]AAAGAAAGCATTCAATTTGCTATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGGGATTAGGCAAAT
76958 A T AGATTTATGGAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCGGTGTTGTCGTTAAAGA[A/T]AGCATTCAATTTGCTATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGGGATTAGGCAAATTGAGAA
76958 A G GAGAAGGTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCGGTGTTGTCGTTAAAGAAAGCATTCA[A/G]TTTGCTATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGGGATTAGGCAAATTGAGAAGGCACAAA
76958 T A GTCGCGATTGGGTACTTGATGTTCTGATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCGGTGTTGTCGTTAAAGAAAGCATTCAATTTGC[T/A]ATGTTTTGTTTGTTGGTACTCATGTGTTTTGGGGAGAAGCTCGATGAAAAGGGGATTAGGCAAATTGAGAAGGCACAAAGAGACAT
76958 T G GATTAAGGACCTTTCTGAAAAGTCGAAGAATTCAGAAGATGGCGGTGTTGTCGTTAAAGAAAGCATTCAATTTGCTATGTTTTGTTTGTTGGTACTCATG[T/G]GTTTTGGGGAGAAGCTCGATGAAAAGGGGATTAGGCAAATTGAGAAGGCACAAAGAGACATTCTGTTATAT
76984 C T TGGTTCCTGCTTAATACGAATATTGTCCATGTTATTAGTTGAGCAGTTGTTCCCTGCCCACCAAGAAAGAAATTCTGGCACTCTGCTATAATGTCATCTA[C/T]GCTCAATGCTGTTCCTTTTTGATTCTTGGATGACTCAATTAGTAAATCCAGTAGATCATCTTCA
76992 C T TGTTGGCCTACTGGAAAATGTATCTCGTGGCCAACCTAAACTAGCAGCCGCCTCAACCAAAAC[C/T]GACGGTCAGAAATACGTTGGTTCCTCCCTCAAATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCG
76992 G A TGTTGGCCTACTGGAAAATGTATCTCGTGGCCAACCTAAACTAGCAGCCGCCTCAACCAAAACCGACG[G/A]TCAGAAATACGTTGGTTCCTCCCTCAAATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTG
76992 T A TCAACCAAAACCGACGGTCAGAAATACGTTGGTTCCTCCCTCAAATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTC[T/A]CTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCTAAGCACTGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAG
76992 A G CCTCAAATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCT[A/G]AGCACTGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGG
76992 C T AATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCTAAGCA[C/T]TGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAG
76992 T C ATTCTCCATGTTCTTTCCTCTAATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCTAAGCAC[T/C]GAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAGG
76992 A G ATCTATGAAACTCCCCTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCTAAGCACTGAGGCGGTCGAAATTCGAACG[A/G]AAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAGGGCGGATGATGATGGGTTGAA
76992 C G CTACGAAGATGATCAGCTCTCTGAGAGCTCGAAGTGGACCCGTCATGATCAGGTTCTAAGCACTGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGT[C/G]GAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAGGGCGGATGATGATGGGTTGAAGGCGCTCGTGCCTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
76992 A G TCGAAGTGGACCCGTCATGATCAGGTTCTAAGCACTGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGC[A/G]TCGGGTCTGAAGGGGTTCAGGGCGGATGATGATGGGTTGAAGGCGCTCGTGCCTGTGGTGGAGGATCGCCCTCCGATCGTCTA
76992 G A TGAGGCGGTCGAAATTCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAGGGCGGATGATGATG[G/A]GTTGAAGGCGCTCGTGCCTGTGGTGGAGGATCGCCCTCCGATCGTCTAAGAGGGAAGCGGTTGGGGATTGTCTAAGGG
76992 T C TCGAACGAAAGGAAGCTGTTGTCGAGGAGTTTTTCTAGGCTAAGGGCAGCATCGGGTCTGAAGGGGTTCAGGGCGGATGATGATGGGTTGAAGGCGCTCG[T/C]GCCTGTGGTGGAGGATCGCCCTCCGATCGTCTAAGAGGGAAGCGGTTGGGGATTGTCTAAGGG
76996 A C GATGCAGATGTACAGAAATGGGTTGGTACAGCGGTCATCCTTCTGGTTGCTTACCTATTCCATTTCTTGTCTGAAGTTCCTCCACAGACCCTTGGCATAC[A/C]ACGATCCTCTTTGGAGTCGCCATCGCTTATTGGCAGACAATGTTGAATATATCTTGATGAGCAAACTTGTCCAACTTCTTGCTTCCCCG
77000 C T CCCCCTCTTCACTCCAAACCCAATCGGAAAACAGCCCAAACCGTTTGACTCCATCTTAATCCAGCGCCTCAACTCGCTGATCAAATC[C/T]CAGCCGTCCAACTCCATCGCCTTCCTCGTCGCGGCCGTCCAGCTTCTGTCGTCGACCATATCCACTTTCTCGGCTTTCCTATCCGACCCCAACCTCTCCA
77000 G A CGGAAAACAGCCCAAACCGTTTGACTCCATCTTAATCCAGCGCCTCAACTCGCTGATCAAATCCCAGCCGTCCAACTCCATCGCCTTCCTCGTCGCGGCC[G/A]TCCAGCTTCTGTCGTCGACCATATCCACTTTCTCGGCTTTCCTATCCGACCCCAACCTCTCCAGATCCGAACATGATACCAAATCCCTTC
77000 C G TCCCAGCCGTCCAACTCCATCGCCTTCCTCGTCGCGGCCGTCCAGCTTCTGTCGTCGACCATATCCACTTTCTCGGCTTTCCTATCCGACCCCAACCTCT[C/G]CAGATCCGAACATGATACCAAATCCCTTCAATCGCATCTGAACTTCTCCCTTTCTCTTCTTGACAAAATCAACTCCCTTTCCTGCGCCATCG
77000 T C GATCCGAACATGATACCAAATCCCTTCAATCGCATCTGAACTTCTCCCTTTCTCTTCTTGACAAAATCAACTCCCTTTCCTGCGCCATCGACCAGATCTC[T/C]CGCCGACGCTTGCACGCCAGTCTCGCCGTTCACCTCCTCGCTGGAGAAAAGCTCACGGTACAGATCTCGAGCAAAGCTCGTGCCTC
77034 A G AGTACTTCTGGCATAGGTACATGCACATGAACAAGTTCTTGTACAAGCACATACACTCCTGGCATCACAGGCTGGTAGTCCCATACTCATTTGGAGCGCA[A/G]TACAACCACCCTATAGAAGGCTTTCTCCTCGACACCATTGGTGGTGCACTCGCCTTTCTGCTCTCTGGAATGACTCCTAGAACTTCCAT
77044 G A ATTTCCTCCCATCAGATCCTGAAGCAACGAATTTCTTCCCCAGCAAGAAATCAAGCAAGAAAGCTTTATATGAAGAAAAGATGACAACTGTGAGTAAGAG[G/A]TCTTCTCAGACTCGGTCATTTCCTCCTCCCCTGTCATCGATCTTGCAACATGATGGCCAACACATGCAGATGAGGACCCAACGCCGTG
77046 C T GAGGCAGAGGCGTAGAGCGAGCATGCACTGAATTGGGCTCGAGGCTGTGCAGCACAGTAATTTGCTTGAGCAATACAAATATGTTGA[C/T]AGCAAGGCTTTGGAGTAACCTACATCAAATCAATACTGGCTGCATCGCCATTTCTTTCATTGTTTCATGGTCGTTGTTCATACAAATCGAAAAAGGAGA
77086 G A ACAATCCTTCATTGAAAACTTCTCGCAAGAGAAGAACCATAACAGTCTACTTCGTGCTAGAAGGAAGCAACAACGATAAGCCTACAGGCGGCGATATCCT[G/A]AACTTTAACGACATTGAAGAAACCGCAAAGCAAGAGCAGACGCTGCGTTCACAAAAGAAAGCATTAGA
77086 T A CTTCATTGAAAACTTCTCGCAAGAGAAGAACCATAACAGTCTACTTCGTGCTAGAAGGAAGCAACAACGATAAGCCTACAGGCGGCGATATCCTGAACTT[T/A]AACGACATTGAAGAAACCGCAAAGCAAGAGCAGACGCTGCGTTCACAAAAGAAAGCATTAGA
77092 T C CTGCGAAATCCGAACCCGAAACGACGGTGACGCAGGCGCATCCACGTCAACAGAGAGGTACGTTTGGAGCTCCACAGGAGGGGTACGTTACGGTTTTAGG[T/C]GCGGATGGGAATCTGTACCATGTGTTTCCAGCAGCGTCCGGACCGCAGGGGGTTTTCGGTAATATGCAGAGCGCGGTGGCGCC
77092 G T CGAAATCCGAACCCGAAACGACGGTGACGCAGGCGCATCCACGTCAACAGAGAGGTACGTTTGGAGCTCCACAGGAGGGGTACGTTACGGTTTTAGGTGC[G/T]GATGGGAATCTGTACCATGTGTTTCCAGCAGCGTCCGGACCGCAGGGGGTTTTCGGTAATATGCAGAGCGCGGTGGCGCCGCA
77092 C A GCGTCCGGACCGCAGGGGGTTTTCGGTAATATGCAGAGCGCGGTGGCGCCGCAGGTGTACGGTAACTATTATGCGCCGAAGATGGAGCAGGTTAGCAGGG[C/A]TGTTTACTTCGCGGGGGCAGCTGGCAATCACCAGCCAGTTTCCAGCAACGTGGCGTTTTGTGCGGAAGGCAGTGGGGCTTTTA
77096 A T ATACACCACGAGCGTGCATAAACGGGTTCAAGGAGTCCACTGCTTCTATCACACTTTCGTTTATGATCTCGGAGTATGAATGACCCTTCTTTCGCAGGAC[A/T]TCAATCTGAGCCATCATTAAAGCTACAAAAACTCCAGCCGTGAAGGGATGCAGAGGTCCCAAATCACCGTTAGGCCTCACTGAACGG
77124 T C TCCCATTCAACATATCGAGCGAAGAAATGTACGATATTTTCGGGAAATACGGGGCGATTAGGCAGATACGTATCGGAACCAACAAGGATACCCGAGGCAC[T/C]GCTTTTGTCGTTTACGAAGACATATATGATGCGAAGACAGCTGTGGATCATTTGAGTGGGTTTAATGTTGCGAATCGGTATTTGAT
77164 CT C TCCGGTTTTGTGGTGTAAAAGGGTTGAAACAGACTGTTACTTGCTAGAACTTGTACTGCTTCACTGGTATGTTGTCTTCATATTGCAAATAAAATGGCGC[CT/C]TTTTTTGGCTTAAGCCATACCCCAGTAGTCTGTACGATTGCTTTCTTCCAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCT
77164 C T GGTTGAAACAGACTGTTACTTGCTAGAACTTGTACTGCTTCACTGGTATGTTGTCTTCATATTGCAAATAAAATGGCGCCTTTTTTGGCTTAAGCCATAC[C/T]CCAGTAGTCTGTACGATTGCTTTCTTCCAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAAT
77164 C T ACTTGTACTGCTTCACTGGTATGTTGTCTTCATATTGCAAATAAAATGGCGCCTTTTTTGGCTTAAGCCATACCCCAGTAGTCTGTACGATTGCTTTCTT[C/T]CAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTCTGTGCTTTGC
77164 T C TTCATATTGCAAATAAAATGGCGCCTTTTTTGGCTTAAGCCATACCCCAGTAGTCTGTACGATTGCTTTCTTCCAAACATCCAGGATATGAGAAATGCTT[T/C]TCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTCTGTGCTTTGCACACGGTAGTATGTAGTATTGAATGAT
77164 T C CTGTACGATTGCTTTCTTCCAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTC[T/C]GTGCTTTGCACACGGTAGTATGTAGTATTGAATGATGTAATTATTGTTTCGCTGGAAGAAGATATGCCACTGTTTGTATAGTTTAATGTG
77164 C T CTTTCTTCCAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTCTGTGCTTTGCA[C/T]ACGGTAGTATGTAGTATTGAATGATGTAATTATTGTTTCGCTGGAAGAAGATATGCCACTGTTTGTATAGTTTAATGTGAAGTTGGATG
77164 A G TTTCTTCCAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTCTGTGCTTTGCAC[A/G]CGGTAGTATGTAGTATTGAATGATGTAATTATTGTTTCGCTGGAAGAAGATATGCCACTGTTTGTATAGTTTAATGTGAAGTTGGATGG
77164 T C CAAACATCCAGGATATGAGAAATGCTTTTCTAAACTTCCCTGTTGACATTCAGTAATAGAAATCCTTACTAGTGAGTGGTCTGTGCTTTGCACACGGTAG[T/C]ATGTAGTATTGAATGATGTAATTATTGTTTCGCTGGAAGAAGATATGCCACTGTTTGTATAGTTTAATGTGAAGTTGGATGGAAAGAT
77192 T A TATTAACAGTAGCTGCGCTGGGGATGCATGCTAAGGACGACGTAATTGTAATTTCATCCACGAGCATCGAGAGAGAATCAGAAGCAACATGTTGAACTTG[T/A]ACTAATTCAGGTTACGCAAGAGATGCAAACCCTAAATCAGCATAAGGAAGATTCGTTACCCTTGAAACTGGAACAAGCAGGTCAGA
77194 A G TCCTAATGATATCATTGAAGAAACAATCGGGGATTTCGACAAGTTAGCAGCAGATTTGGAAAACGCTTCTCCTCTTGAAATCATGGATCGTGCTCTTGCA[A/G]AGTTTGGAGATGACATCGCAATTGCATTCAGCGGGGCTGAGGATGTGGCCCTAATAGAATACGCACGCCTAACAGGCCGCCCCTTC
77194 G A AGTTAGCAGCAGATTTGGAAAACGCTTCTCCTCTTGAAATCATGGATCGTGCTCTTGCAAAGTTTGGAGATGACATCGCAATTGCATTCAGCGGGGCTGA[G/A]GATGTGGCCCTAATAGAATACGCACGCCTAACAGGCCGCCCCTTCAGAGTCTTCAGTCTAGACACAGGCAGACTAAACCCCGAAAC
77212 C T AAAGATCTCTAAAATTTCGGGATCATGTCTTCCTCATTCGACACATTCAGCAACGACGGCGACTATTTAGTGGTTGG[C/T]GGCGGTAACGGAGCTGGAGACTTTTTCTCTTCCTCCGTTGGCGACGAAACAAGCATCCCAATCACACCTCCGACTCCGGAAACGTATGGATATGGCTCCG
77212 C G TTGGCGGCGGTAACGGAGCTGGAGACTTTTTCTCTTCCTCCGTTGGCGACGAAACAAGCATCCCAATCACACCTCCGACTCCGGAAACGTATGGATATGG[C/G]TCCGATCCGCTTCAGGATTTCATAATTCCTGAATCAAACGGAACTTATGATGGCGTTGTAGATCATAATAATAACGGTCCGATTTTA
77214 A G TACTGGACAACATTCATTACACTTAATTTGAATACAATGGCTCTTCTTTTCAAGTTGCTTACAGTTCTCACTCTTTCTCTTGTCCCACTTTGCTTTGGTG[A/G]GTACCATGGAAGCCCTAGTCCTACTACAACTGGCCCTCTTTTTCCTCAATACTACTCCCACTCCTGCCCTCAAGCACAAAAAATAGTGCAAA
77214 C T GACAACATTCATTACACTTAATTTGAATACAATGGCTCTTCTTTTCAAGTTGCTTACAGTTCTCACTCTTTCTCTTGTCCCACTTTGCTTTGGTGAGTAC[C/T]ATGGAAGCCCTAGTCCTACTACAACTGGCCCTCTTTTTCCTCAATACTACTCCCACTCCTGCCCTCAAGCACAAAAAATAGTGCAAAGTGTA
77214 T G CTCTTTCTCTTGTCCCACTTTGCTTTGGTGAGTACCATGGAAGCCCTAGTCCTACTACAACTGGCCCTCTTTTTCCTCAATACTACTCCCACTCCTGCCC[T/G]CAAGCACAAAAAATAGTGCAAAGTGTAGTTGCAAAGGCAGTTGAAAAGGAGACTAGGATGGCTGCTTCCCTGCTGAGGCTGCATTTTCA
77214 A G TTGTCCCACTTTGCTTTGGTGAGTACCATGGAAGCCCTAGTCCTACTACAACTGGCCCTCTTTTTCCTCAATACTACTCCCACTCCTGCCCTCAAGCACA[A/G]AAAATAGTGCAAAGTGTAGTTGCAAAGGCAGTTGAAAAGGAGACTAGGATGGCTGCTTCCCTGCTGAGGCTGCATTTTCATGATTGTTT
77232 T C GGTGATGGAGGTACCTTCCATGGAATTAATGAAAACAACACAATTATCAGTAGTCAAGGACTCTTTAGCATACATATGCCACCTTACTACAATTCCATAA[T/C]CAAGGGTGTGTCTACGATTATGGTTTCATATTCGAGTTGGAATGGAGTAAAAATGCATGCTAACCGT
77240 T TC CAGCAGACATTTCCTTCTCGACTTTAGCCTGCATCTCACGAAGTGCACTCGCTTCTTCTTCAATGTCTTTTAGCCTCTTTTTCATCTCCTCCAGATTCTC[T/TC]TAGACGACTGGGGATCTTGGCCATCGTTGTAAGCACTGGCCATGTCTTCGTTGTCGGCTTCCATCTCTCCATCCTCGTCGGGGATCTCTG
77240 C T CATGTCTTCGTTGTCGGCTTCCATCTCTCCATCCTCGTCGGGGATCTCTGCTCCATAAACTTCGTGCTCTTGCTCGTGATCCATAGATATCTTAACCTTA[C/T]AATTTATTTTCTACTAACTTGTACTGAATGATATCAGAACAAATGGGTCTTTGATGTCAGCCAGTAGGCCAACAGT
77258 T C AAAGCTAGGCGGCATGGTGTACGATGGCTATCTAAATGGAGAGCTGTCAGTTGCAAGAGCCCTGGGCGACTGGCATCTGAAGGGCCCAAAGGGGTCTATC[T/C]ACCCTTTAAGCTCTGAACCTGAAATTCAAGAAACAACGTTAACGGAAGAGGATGAGTTCTTAATCATGGGCTGTGATGGCTTATG
77288 G A ATGATGCAAGTGATGCTCGTCCAGGAGAAGCAGCTTTCATTTGGCTAGGAGATGATGCAGTATTAGTTGGCGAAGAACCAGCAACAGGCCAAGACGAGCC[G/A]CTTCCACGATTACCCCGATTTGACTGTGACTTCGTTGAAGCATTTGGCACTGGAATTTGTAGTTGCGGAGCAGATGGGTTCGAAG
77288 C T CTTTCATTTGGCTAGGAGATGATGCAGTATTAGTTGGCGAAGAACCAGCAACAGGCCAAGACGAGCCGCTTCCACGATTACCCCGATTTGACTGTGACTT[C/T]GTTGAAGCATTTGGCACTGGAATTTGTAGTTGCGGAGCAGATGGGTTCGAAGAGCTTTTTTT
77310 C T GGATTATGGTGACTCTCAGAGGGTGCAATGTGCACAGCAGTGAGAACGTTGTTGTACCCGTTCAAAGTCGCTACAATTGTTTTACCTGGGTATACCGTAC[C/T]GTGCTTTCTTCTCCAGTTTTACGCTGCAATTTTGAGGTGCAATTGAAGCGGTCATGATTTATTCATGATGCAGTTATAATTTCCATATT
77310 C T GTACCCGTTCAAAGTCGCTACAATTGTTTTACCTGGGTATACCGTACCGTGCTTTCTTCTCCAGTTTTACGCTGCAATTTTGAGGTGCAATTGAAGCGGT[C/T]ATGATTTATTCATGATGCAGTTATAATTTCCATATTTTTATGTAAACAACATTAATGTAAGATGTATTGACTCTATTCCTGCGGTTAAACT
77314 CCGTCTTTAGCAGGTGCAGGAG
C AAAATCAAAGTAGAGCAAAACAGCGACTTAGGCACTAACTGGAACGTCTTTAGCAGGAGCGGGTGCTTCTGGCTTCTTCACTGCAGCAGCAGTCGCTTGG[C/CCGTCTTTAGCAGGTGCAGGAG]CGTCTTTAGCAGGTGCAGGAGCGTCTTTAGCAGGTGCAGGAGTGTCTTTAGCAGGCGGCGGCT
77316 A G GTGGATCATGGCAGAGCTTGTGAGAAACCAACATGTGCAGAAGAAGCTGGTCGAGGAGATCGAGAGGGCGGTTGGGCATGAAGGGCGAGTGAAGGAAGA[A/G]GAACTGAGCAAAATACCTTACTTGAAAGCTGTTGTTTTGGAGGGACTGAGAAGGCGTCCGCCTGCTCATATCGCGTTGCCGCA
77316 G A AGAAGAAGCTGGTCGAGGAGATCGAGAGGGCGGTTGGGCATGAAGGGCGAGTGAAGGAAGAAGAACTGAGCAAAATACCTTACTTGAAAGCTGTTGTTTT[G/A]GAGGGACTGAGAAGGCGTCCGCCTGCTCATATCGCGTTGCCGCATTCGGTGAGTCAAGAAATCAAAATCGAAGGGTATGTCAT
77316 C T GCTGGTCGAGGAGATCGAGAGGGCGGTTGGGCATGAAGGGCGAGTGAAGGAAGAAGAACTGAGCAAAATACCTTACTTGAAAGCTGTTGTTTTGGAGGGA[C/T]TGAGAAGGCGTCCGCCTGCTCATATCGCGTTGCCGCATTCGGTGAGTCAAGAAATCAAAATCGAAGGGTATGTCATACCGAAG
77334 G A GGGAAGGACGGGTTTGCCGCAGACGTCGGGATAAACTCGAAAGCTGTTGGGTTCCAGCTCCAAGCA[G/A]CCGCGTACGGCGATGGCGTTGCAGCGGCCGAAGACGAGCCTGGCACGGGCCGCGTCCGTGATCCCGGACTTGTTGATTATGTACGAGTCGGAGAACAGAC
77334 A G CGTGGAGGCGGAATCGGATGTTGGAAGGGAACGGGATCCACGGCGGAGGGACTGTGAGCTGCTCTGGAGTGCTGTATACTGGAGCAGCCGAATCGAGAGG[A/G]CCGAAGTTAAGCAAGAAGGTGACGGTGAAGACGCTGAAGTAGATTGTGGGTACGTTTGCTTCGGCGGCTATGTCGGGGAGC
77334 T A TTGGAAGGGAACGGGATCCACGGCGGAGGGACTGTGAGCTGCTCTGGAGTGCTGTATACTGGAGCAGCCGAATCGAGAGGACCGAAGTTAAGCAAGAAGG[T/A]GACGGTGAAGACGCTGAAGTAGATTGTGGGTACGTTTGCTTCGGCGGCTATGTCGGGGAGCCAGTGCTGGACGAAGTCTTGG
77384
ATACCATCCACACTGCAATT A ATTTGTGCGCAAAATAAGATCAAGACCATATTATTTGGAGAAGAAGCAGAGAAGGAAACATTTATTGAGAAGCGGTACACTGATGACATGGAACTTGAGA[ATACCATCCACACTGCAATT/A]TACCATCCACACTGCAATTTTGATCTTAAAGAAGGGTTTGAAGGCCAAATTTCATCAAAGAATGTTGA
77384 A AC GACCATATTATTTGGAGAAGAAGCAGAGAAGGAAACATTTATTGAGAAGCGGTACACTGATGACATGGAACTTGAGAATACCATCCACACTGCAATTTTG[A/AC]TCTTAAAGAAGGGTTTGAAGGCCAAATTTCATCAAAGAATGTTGAAACTGGAAATGTCAGTGCAAAATTCAAGGTACTGACCCAG
77384 G A,T TTGAGAAGCGGTACACTGATGACATGGAACTTGAGAATACCATCCACACTGCAATTTTGATCTTAAAGAAGGGTTTGAAGGCCAAATTTCATCAAAGAAT[G/A,T]TTGAAACTGGAAATGTCAGTGCAAAATTCAAGGTACTGACCCAGCAGATATTGATGATTATCTGGCTGAAGTAGAGTAGATGACA
77390 T C CGCAAGAAATCCCTGGGTTCTGCTATTGATGACATCGATCTCATGTAGATTCACACAATGCACAACCTCCTTCCT[T/C]TTCTGCAACTCTCCCTCGGGACATCTAACAAACTTCGTCTGTGGACCCATAGCATCATAATCTCTGGAACGTCCAATTGATCTTCCAAGCTTTGTCACCT
77390 A G TGCTATTGATGACATCGATCTCATGTAGATTCACACAATGCACAACCTCCTTCCTTTTCTGCAACTCTCCCTCGGGACATCTAACAAACTTCGTCTGTGG[A/G]CCCATAGCATCATAATCTCTGGAACGTCCAATTGATCTTCCAAGCTTTGTCACCTTTCCAGACGCCTTGTCTAATGCGATAACATCCCCAC
77390 A T GTAGATTCACACAATGCACAACCTCCTTCCTTTTCTGCAACTCTCCCTCGGGACATCTAACAAACTTCGTCTGTGGACCCATAGCATCATAATCTCTGGA[A/T]CGTCCAATTGATCTTCCAAGCTTTGTCACCTTTCCAGACGCCTTGTCTAATGCGATAACATCCCCACTCTGTACCTTCTCCTTGTTCAATGA
77390 C T ACTCTCCCTCGGGACATCTAACAAACTTCGTCTGTGGACCCATAGCATCATAATCTCTGGAACGTCCAATTGATCTTCCAAGCTTTGTCACCTTTCCAGA[C/T]GCCTTGTCTAATGCGATAACATCCCCACTCTGTACCTTCTCCTTGTTCAATGACTCGATCATCTTGCCTCCCAGCTCGTACACTGTTTCCAT
77390 C T CCATAGCATCATAATCTCTGGAACGTCCAATTGATCTTCCAAGCTTTGTCACCTTTCCAGACGCCTTGTCTAATGCGATAACATCCCCACTCTGTACCTT[C/T]TCCTTGTTCAATGACTCGATCATCTTGCCTCCCAGCTCGTACACTGTTTCCATGTCTGTGGTCTTCATTGTCAGTTTCCCTGTTTTTGAAGC
77390 C T CTCTGGAACGTCCAATTGATCTTCCAAGCTTTGTCACCTTTCCAGACGCCTTGTCTAATGCGATAACATCCCCACTCTGTACCTTCTCCTTGTTCAATGA[C/T]TCGATCATCTTGCCTCCCAGCTCGTACACTGTTTCCATGTCTGTGGTCTTCATTGTCAGTTTCCCTGTTTTTGAAGCTGATTTGGAGTCTCC
77422 A G ACACCAAATGCAACTCGCTCGACGAAATCAACCCGTTCCCGTTCATATCGTACGTATCGAACGCATCCTTCAAATCCGCATCGACGCCTTCGTCCAACTT[A/G]CTATTGTGAAAGTCGAAGAATTCCTTCCGGTCCACGTACCCGTCTTTGTTGGAATCCATCTCGTCGATCATCACTTCCACCTCTCGATCG
77422 G A CCGGTCCACGTACCCGTCTTTGTTGGAATCCATCTCGTCGATCATCACTTCCACCTCTCGATCGGTGACGGCGGAGTTGAGAGCGCGTACCGTCTTGCTG[G/A]GCTCTTGGGGCAGATCTTGCCGTCGCCGTTTTCGTCGATTTTGTTGAACACTTTCTCCATTTCTCTTGCCATTTCTAGTTTTGTGTTTTT
77422 C CT TCCACGTACCCGTCTTTGTTGGAATCCATCTCGTCGATCATCACTTCCACCTCTCGATCGGTGACGGCGGAGTTGAGAGCGCGTACCGTCTTGCTGGGCT[C/CT]TTGGGGCAGATCTTGCCGTCGCCGTTTTCGTCGATTTTGTTGAACACTTTCTCCATTTCTCTTGCCATTTCTAGTTTTGTGTTTTTGAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
77432 C G TCATAGCCTGTTCCGCTTCCCCTGCTCATAATCTTAAATTATAAAATCTTCGACGGGATTTTGATCAGATTTGAAGCTAAAACGGAGAAATGGTGGTTAA[C/G]AGCAGACGTATCGTCCGGCTTTTTTAATCAGTCGAAATCAACGGTACAACCCTAATCAAATCAATGTCCAAGCCCACTTCGAAATCAAG
77436 A G AGATTTCCCTTCCTGTTTCAGGGAAAACGCAGTCCAGATAGCAGCAGCAAGCTCCCCATCCACCTCCACCGTCAGACCATCCCAAAACCTCATAACCTGC[A/G]TCTACAAGGTGAAACTCCACCGCCGTTCATACACGATCACCATCACATGGATCAAGAACCTGATGGGCCCGCTCCTCTCGGTCGAAAT
77436 T C TCCTGTTTCAGGGAAAACGCAGTCCAGATAGCAGCAGCAAGCTCCCCATCCACCTCCACCGTCAGACCATCCCAAAACCTCATAACCTGCATCTACAAGG[T/C]GAAACTCCACCGCCGTTCATACACGATCACCATCACATGGATCAAGAACCTGATGGGCCCGCTCCTCTCGGTCGAAATCCAACAAGA
77436 C T GACCATCCCAAAACCTCATAACCTGCATCTACAAGGTGAAACTCCACCGCCGTTCATACACGATCACCATCACATGGATCAAGAACCTGATGGGCCCGCT[C/T]CTCTCGGTCGAAATCCAACAAGAGCCCACGTCCCAACCCATCTGCACCCTGACCATCAAACCCTGGAACCTCTTCTCCAAATGCAAAG
77436 C T TACAAGGTGAAACTCCACCGCCGTTCATACACGATCACCATCACATGGATCAAGAACCTGATGGGCCCGCTCCTCTCGGTCGAAATCCAACAAGAGCCCA[C/T]GTCCCAACCCATCTGCACCCTGACCATCAAACCCTGGAACCTCTTCTCCAAATGCAAAGGCTCCAAAACCTTCAACCACTCGACCAAG
77436 A G ACTCCACCGCCGTTCATACACGATCACCATCACATGGATCAAGAACCTGATGGGCCCGCTCCTCTCGGTCGAAATCCAACAAGAGCCCACGTCCCAACCC[A/G]TCTGCACCCTGACCATCAAACCCTGGAACCTCTTCTCCAAATGCAAAGGCTCCAAAACCTTCAACCACTCGACCAAGATCGACGTCAT
77454 A G TCGGACTCAGCCTTTCCGCATCAGAAAACGGCCAATCCAGATTCTTAATGGCTTCAAAGCCATAAGCCGATCC[A/G]CTGCCTTCTTCGCATTGCTGCAGAACATAATTTGGCTTGCAGCCCTTATATTTCCTGCTTTGATCTATGAAAGTGTAGTGAGGGGGGCATTGACAGTTTG
77454 G A TCGGACTCAGCCTTTCCGCATCAGAAAACGGCCAATCCAGATTCTTAATGGCTTCAAAGCCATAAGCCGATCCACTGCCTTCTTC[G/A]CATTGCTGCAGAACATAATTTGGCTTGCAGCCCTTATATTTCCTGCTTTGATCTATGAAAGTGTAGTGAGGGGGGCATTGACAGTTTGTCAACCCACTTT
77454 C T CTTCTTCGCATTGCTGCAGAACATAATTTGGCTTGCAGCCCTTATATTTCCTGCTTTGATCTATGAAAGTGTAGTGAGGGGGGCATTGACAGTTTGTCAA[C/T]CCACTTTCGTACTGTGTGCAGTAGCTATTGAAGCCACATATCCCACTACCAAGGTTGAAATTTAGGCCGCATAAGTCTTGAACAAGGTT
77458 G A TGGACACGGCTTCCGCGCACTGGAGAAGAAGCCCTAGCAGGCCAAGTCCTTGGGCTTCGGGCCCATGGGATGGCCCTTCTTCCGGAATGGAAGCAGAAGA[G/A]GACGCACTAGCACTGTCTTGCTTCTTCCTTTTGTTGGGTCTCATGATGTGTGCATCGGATTGGGGAGGTGGTAGGCTGTGTAGCA
77466 T G TGCTGGTGATGGGATTGTTATGCAGAAGCTTTTGGGCCAGTTGAATCAATTAAAATGCTGGTTTGAGGAGCAGACCATTTGGCATTTTTACTCAGCTTCT[T/G]TACTGGTTATTTACGAGAAAGGGAAGACGGTCAGAGTGAAGATGGTTGATTTTGCGCATGTTACTGATGGAAACGGAGTTATTGAT
77466 T C AAGGGAAGACGGTCAGAGTGAAGATGGTTGATTTTGCGCATGTTACTGATGGAAACGGAGTTATTGATCACAACTTTTTGGGAGGGCTTTGTTCTTTAAT[T/C]AACTTTGTTAAGGAGGTGGTTGAAGAGTTTTATAAAGTGTCAGGCAAGAAGAAAGAACCTGAATTGGAAAACGGAAATATCCCGG
77466 G A GGCTTTGTTCTTTAATTAACTTTGTTAAGGAGGTGGTTGAAGAGTTTTATAAAGTGTCAGGCAAGAAGAAAGAACCTGAATTGGAAAACGGAAATATCCC[G/A]GAGTGATGTCGTGGTATGTTGAATGTTTTATAGTTTATAAATACATATGACGAAATGCAGACCTT
77472 T A CCTACAACTACAACTATGGGCCAGCAGGAAGAGCTATAGGTGAAGACTTATTAGCCGATCCTGATTTAGTCGCATGGGACCCAATCGTGTCATTTAAAAC[T/A]GCAATATGGTACTGGATGACGCCTCAGTTCCTGCAGAAACCATCTTGCCATGATGTGATCACCGGACATTGGTTTCCTCTTCCAACAG
77472 G A TAAAACTGCAATATGGTACTGGATGACGCCTCAGTTCCTGCAGAAACCATCTTGCCATGATGTGATCACCGGACATTGGTTTCCTCTTCCAACAGACATA[G/A]TCGCTGGGCGATATTCAGGCTATGGCACCATTACCAACATTATAAATGGTGGCTCCGAGTGCGGGCGCGGTGAAGATGACAGGGTT
77472 G C CAATATGGTACTGGATGACGCCTCAGTTCCTGCAGAAACCATCTTGCCATGATGTGATCACCGGACATTGGTTTCCTCTTCCAACAGACATAGTCGCTGG[G/C]CGATATTCAGGCTATGGCACCATTACCAACATTATAAATGGTGGCTCCGAGTGCGGGCGCGGTGAAGATGACAGGGTTAATGATAG
77474 T A GGTTCGGGAACACGTCGAGCAGCTCGCTGTGGTACGAGCTGAATTACATCGAGGCGAAAGGGGGGATGAAGAAGGGGGATAGGGT[T/A]TGGCAAATTGGATTCGGAAGCGGGTTCAAGTGCAATAGTGCGGTTTGGACGTGTATGAGGAGCCTGAAGGCGCCGGCTGAAGGGCCGTGGGCCGAT
77494 G A CTATTCCCTTCCTCACGACTTTAATCTTGGATAGTTTGTTAGGGGCGCCGCCGGTAACTTTAGCAACGCGAAGCAAAGCCAGTTCAGATTTCAACTCGTT[G/A]AGTTGGGTCAGAAGATCGGCCTTTGACTTGGTGCGTAACTCGTGGACCTTGATTCTGGCCATTGCAGAAGCTGAACGATGAAAGATT
77494 G A CTTTAATCTTGGATAGTTTGTTAGGGGCGCCGCCGGTAACTTTAGCAACGCGAAGCAAAGCCAGTTCAGATTTCAACTCGTTGAGTTGGGTCAGAAGATC[G/A]GCCTTTGACTTGGTGCGTAACTCGTGGACCTTGATTCTGGCCATTGCAGAAGCTGAACGATGAAAGATTAGAAATGGCTAACTCCA
77506 G A AGGATTAGGTTGTTTGTTGCGAAAATGAATGGAGCTAGAATGACGAAGCAGGCGGTTAAGAGGAAGA[G/A]CTGGAAGGAGACGAGTTTGAGGTTGAGTTTGTCGAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCAT
77506 T C AGGATTAGGTTGTTTGTTGCGAAAATGAATGGAGCTAGAATGACGAAGCAGGCGGTTAAGAGGAAGAGCTGGAAGGAGACGAG[T/C]TTGAGGTTGAGTTTGTCGAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCAT
77506 G A GGATTAGGTTGTTTGTTGCGAAAATGAATGGAGCTAGAATGACGAAGCAGGCGGTTAAGAGGAAGAGCTGGAAGGAGACGAGTTTGAGGTTGAGTTTGTC[G/A]AAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTT
77506 A G TTGTTTGTTGCGAAAATGAATGGAGCTAGAATGACGAAGCAGGCGGTTAAGAGGAAGAGCTGGAAGGAGACGAGTTTGAGGTTGAGTTTGTCGAAGAAGT[A/G]CAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGATGC
77506 G A GCGGTTAAGAGGAAGAGCTGGAAGGAGACGAGTTTGAGGTTGAGTTTGTCGAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAA[G/A]ATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGC
77506 T C GTTGAGTTTGTCGAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTAC[T/C]GATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGG
77506 T A GAGTTTGTCGAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGA[T/A]GCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTT
77506 G A GAAGAAGTACAAGGACATGAGCATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGATGCCAGTGC[G/A]TTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATC
77506 C T CATCACGTCGCCTGGGATTATGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGATGCCAGTGCGTTATTTTTTCTTGATTATCA[C/T]GCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAGAGATGGC
77506 C T TGTCGCCAAGATCTCCGATGGTTCATGCTACTACTTAACCATTTTACTGATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAA[C/T]CAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAGAGATGGCTCGTATGACGTTCATTGTAAA
77506 GT G GATGGTTCATGCTACTACTTAACCATTTTACTGATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATT[GT/G]TTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAGAGATGGCTCGTATGACGTTCATTGTAAATGTAATCAATGTGG
77506 T G CTACTACTTAACCATTTTACTGATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTT[T/G]TTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAGAGATGGCTCGTATGACGTTCATTGTAAATGTAATCAATGTGGCAAGTGATATAT
77506 C T CTGATGCCAGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGC[C/T]AGATCTGCAGTGTTGTAAGAGATGGCTCGTATGACGTTCATTGTAAATGTAATCAATGTGGCAAGTGATATATAAAGATCTAGTTGCTAATG
77506 C T AGTGCGTTATTTTTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTG[C/T]AGTGTTGTAAGAGATGGCTCGTATGACGTTCATTGTAAATGTAATCAATGTGGCAAGTGATATATAAAGATCTAGTTGCTAATGTG
77506 A G TTTCTTGATTATCACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAG[A/G]GATGGCTCGTATGACGTTCATTGTAAATGTAATCAATGTGGCAAGTGATATATAAAGATCTAGTTGCTAATGTG
77506 G T ACGCTTTTTTCTTTTTGGCAACCAAAAGGATTCTATTGTTTTTTTCTTTTTTCTTGTTGGTTTTTGCCAGATCTGCAGTGTTGTAAGAGATGGCTCGTAT[G/T]ACGTTCATTGTAAATGTAATCAATGTGGCAAGTGATATATAAAGATCTAGTTGCTAATGTG
77528 A G TACCATCCCGGTTATTTCGGTAAAGTCGGCATGCGGTACTTTCACAAACTCCGCAACAAATTCTACTGCCC[A/G]ACTGTAAACATCGATAAGCTCTGGTCGCTCGTTCCTGAATCCGTGAAGGAAAAGGCCGGATCTGGCGGAGAAGCGCCGTTGATTGATGTCGGTCAGTTTG
77528 G A TACCATCCCGGTTATTTCGGTAAAGTCGGCATGCGGTACTTTCACAAACTCCGCAACAAATTCTACTGCCCAACTGTAAACATCGATAAGCTCTGGTC[G/A]CTCGTTCCTGAATCCGTGAAGGAAAAGGCCGGATCTGGCGGAGAAGCGCCGTTGATTGATGTCGGTCAGTTTGGATATTTCAAGGTGTT
77528 T G ATCCCGGTTATTTCGGTAAAGTCGGCATGCGGTACTTTCACAAACTCCGCAACAAATTCTACTGCCCAACTGTAAACATCGATAAGCTCTGGTCGCTCGT[T/G]CCTGAATCCGTGAAGGAAAAGGCCGGATCTGGCGGAGAAGCGCCGTTGATTGATGTCGGTCAGTTTGGATATTTCAAGGTGTTGGG
77528 A T TTCACAAACTCCGCAACAAATTCTACTGCCCAACTGTAAACATCGATAAGCTCTGGTCGCTCGTTCCTGAATCCGTGAAGGAAAAGGCCGGATCTGGCGG[A/T]GAAGCGCCGTTGATTGATGTCGGTCAGTTTGGATATTTCAAGGTGTTGGGAAAAGGACAGCTTCCCGAAGGGAAGAGTGTGGTGA
77528 T C CGAAGGGAAGAGTGTGGTGATCAAGACGAAGTTGGTCAGTAAGAATGCCGAGAAGAAGATTAAAGCTAACGGAGGTGCTGTTTTGCTCACTGCTTGATTT[T/C]AGTTTTGCTTAATGTCGGGTGAACAACTTGCTGTTGCTTTGTTTCATGTTGTTGATTATGTGCTATTTCTGGTTTT
77542 A G GCGCAGGCTTCCTGCTCCACCAAATAAAAGCATAATCTCTTCAATCACAAACTCTCCGATCGTCTACAAGTCTAAAGCCGCCGCATGCAGCGCTGCCACT[A/G]TCGCGAAAAAGCTAGCTTGGAGCACAGGCCGTGCAGCTTGGATCGCAGGAACCACTTTCTTGATACTCGCGGTGCCGCTGATCATAG
77560 C T ATAATAGGGCGACCTTAGGTAGGCATATATCTCCGTCACCACTTCAAGATTATTGGCAGTT[C/T]GAAGGTATTGAATGATACATGTATATTTGACGCTAATCATCTAATATATATGGATATGATGTGACTATTGGAGCGAAATTTTCCATATGTTTTTCATGTA
77578 C T CCCAGAACACAAGGAAACACCAGTTTCCATCTGTTGAAACATCTCCTCTAGTAATGCAGAGGCCAAATTCGAGGATAATCCTGCAAAGATCACAACCAAG[C/T]CCGGAATTATCGGGGCAATTCACGGTGACGACACTAGCCTCGCCCTTCCGTTTGGCGACCTGTATCTCGACGACGTCGTCGTTCGCC
77588 G A CTCCTCCTCTTCCTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACC[G/A]CCACCACCACGGGCCCCACCACCACCGCCACTACCCACCAGCGGACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCG
77588 A G CTCCTCCTCTTCCTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACCGCCACCACCACGGGCCCCACCACCACCGCC[A/G]CTACCCACCAGCGGACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCC
77588 A G CTCCTCCTCTTCCTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACCGCCACCACCACGGGCCCCACCACCACCGCCACT[A/G]CCCACCAGCGGACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCC
77588 C T CTCTTCCTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACCGCCACCACCACGGGCCCCACCACCACCGCCACTACCCAC[C/T]AGCGGACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTT
77588 G C TCCTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACCGCCACCACCACGGGCCCCACCACCACCGCCACTACCCACCAGC[G/C]GACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCAC
77588 A T CTCCTCCTCCTTCTCTCTCCTCTTCTCATGAACCCTAGGCCAAACACCCACCACCGCCACCACCACGGGCCCCACCACCACCGCCACTACCCACCAGCGG[A/T]CTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCA
77588 C A CACCGCCACTACCCACCAGCGGACTCCCCACGCCACCTCAGGCCCCACGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATC[C/A]CCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCC
77588 T A CGCCCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGT[T/A]TTTCGTCAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTAT
77588 T C CCCCCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTT[T/C]CGTCAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATG
77588 T A CCTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCG[T/A]CAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAA
77588 C G CTTTGCCTCCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGT[C/G]AATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAG
77588 C G CCCCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACT[C/G]CTAAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTT
77588 T C CCCAATTCCGACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCC[T/C]AAACCGTGTACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTG
77588 T C GACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTG[T/C]ACTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTGGAGTTCGG
77588 A G ACCGTGGGCCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTGT[A/G]CTTTTAGCCAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTGGAGTTCGGA
77588 C T CCCCACATGGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTGTACTTTTAG[C/T]CAAAGTCCCTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTGGAGTTCGGAGCTGCCCGG
77588 C T GGCCAATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTC[C/T]CTCAAGACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTGGAGTTCGGAGCTGCCCGGAAAACGC
77588 A T ATATCCCCCTTTTCACCAAAAATCCCGTTTTTGCATAAAAGTCCCTGACCGTTTTTCGTCAATAACTCCTAAACCGTGTACTTTTAGCCAAAGTCCCTCA[A/T]GACCAAAGTCGTAGAGCACGAAATTCTCTTCGATTTGGCTATATGGAAGTCGTGTTTTGGAGTTCGGAGCTGCCCGGAAAACGCGTTTA
77602 AC A AAAAAAAAAACAAATCGATGAAGGCCGCTCGACCCCAGGCGATCGCCACCGCGCCCCACCTCCGCTCGACCGTCAGCCTCCTCGATC[AC/A]CCCCCTCCCTCCGTCGCTCGCGACCAACCTCCCGCCCCCACGCGAGAATCGAGACGCTTCCCTCTGGAACCCGCGTCGGCCCTGCCTTCCATCGCAAGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
77602 TC T ATGAAGGCCGCTCGACCCCAGGCGATCGCCACCGCGCCCCACCTCCGCTCGACCGTCAGCCTCCTCGATCACCCCCTCCCTCCGTCGCTCGCGACCAACC[TC/T]CCCGCCCCCACGCGAGAATCGAGACGCTTCCCTCTGGAACCCGCGTCGGCCCTGCCTTCCATCGCAAGTCCACCACCTCCGTCGCG
77602 A AC CTCGACCCCAGGCGATCGCCACCGCGCCCCACCTCCGCTCGACCGTCAGCCTCCTCGATCACCCCCTCCCTCCGTCGCTCGCGACCAACCTCCCGCCCCC[A/AC]CGCGAGAATCGAGACGCTTCCCTCTGGAACCCGCGTCGGCCCTGCCTTCCATCGCAAGTCCACCACCTCCGTCGCGAGCTCCGCCTG
77626 C T TCGCCTCCGGCGCCGCCGCCGCAAAGCCCCGAGGCCTCGATTCGAAAGTGCTCAGCTCGATCCCAGTGGTCGTCTACGAAGCTGACGTGGCGTCGGACGA[C/T]GAGGCGGTGGAATGCGCGGTGTGCCTGTGCGAGATCGAGGACGGAGAGAAGGTGAGGGTTCTTCCGAGATGCGAGCACTGCTT
77638 C T AGATTGATTAGGCAAAGTTTTTCAAAGGAATCCCCTGAAACTGAATATATCAAATAAGGAATCAAGATGTCTCAGCAGCAGCCCGGGTCCGTCCTTCGTC[C/T]TCCGCATGCAGCGACGCCATTCGTCCAATTTCACGGGCCATCATAACTGTATTGCCCGCAATCGACAATTCCAACAAATCCCG
77640 G A ATAAGCAATTTCAAATTACATAAAAACTTCAAGCAACATCAAATGACAGCAATAAATCTACCCTCAACAACCACAAATCTTTAAAACTTGGAGGCAGCCC[G/A]TACAATGTTAATAAACAGGGAAAAATACAACTGCATTGCCAACAATTTCTGAAATTCATCAAACTCCTCCTCACGAACATCTTCCAGTA
77640 G T TAAAAACTTCAAGCAACATCAAATGACAGCAATAAATCTACCCTCAACAACCACAAATCTTTAAAACTTGGAGGCAGCCCGTACAATGTTAATAAACAGG[G/T]AAAAATACAACTGCATTGCCAACAATTTCTGAAATTCATCAAACTCCTCCTCACGAACATCTTCCAGTAGCCAGTACTCTAATAACCTC
77650 T C GTTAGGGAATAATTTTTTAGCTTGCTCAAGAGCGCGAGCATGCCCAAAATGAAATAAATCATAAATTCCATCTGCATAAACACGAACAGGCTTTTCTTCT[T/C]GTTTACCTTCTAACTTATTGATTCCATCAGTTTCTTCTCTCCCCTCATTATCAGTGGATAGAAAAGATAGAGGCTCATACCATGTAGTCG
77650 C G TCTTCTCTCCCCTCATTATCAGTGGATAGAAAAGATAGAGGCTCATACCATGTAGTCGGTGTCGAAGGGGCTTCGACGAACTCTTCGTCGTCGTCCATTT[C/G]TCCGCCAACAATAGACGACTGGATAAGTGGCAAACCCTTCATTGTTATTGTTCGAAGTCGATCAGCCAATCGCCTCGAACATAGAGAA
77662 T C TGGAGTAGAAATCGGTGTGATTGAAACTGGAGCCTCTGGGAGTTGGATTCCTCGAGCTCTGCAGGGAGTAGATTTCCGCATTTGTTAAATTGGACGGACG[T/C]GGAGTCGTGCTGGAGAATCCGTGGGAGCGTCTCGAGTAAATGTCCGATCGGGACGCGTTCGACCTTCGTACCGTGACGTGGATT
77662 A G AGTAGAAATCGGTGTGATTGAAACTGGAGCCTCTGGGAGTTGGATTCCTCGAGCTCTGCAGGGAGTAGATTTCCGCATTTGTTAAATTGGACGGACGTGG[A/G]GTCGTGCTGGAGAATCCGTGGGAGCGTCTCGAGTAAATGTCCGATCGGGACGCGTTCGACCTTCGTACCGTGACGTGGATTTTAC
77662 G A CATTTGTTAAATTGGACGGACGTGGAGTCGTGCTGGAGAATCCGTGGGAGCGTCTCGAGTAAATGTCCGATCGGGACGCGTTCGACCTTCGTACCGTGAC[G/A]TGGATTTTACCGTCTTCCTTGATTTCGGCTTCGGTTTCGACCATGTCGCGCCCGCCGTCGAGTGACATGACGTCGGAGTCGACGTT
77686 G C TGTCTGTTAAGCGTGTTATCCAGGAAGAATGCTACAAATCCCGCTACAAAAGGCTCCGACGAAAATATAACATTCACAATATCGTTGAACCAACGTGCAC[G/C]GGTATGAACAGGACCGTATCCAGCAACCGCGGTGTATTCGTTGAAATATTGTGGGACTGATAAACCCATGAAAAATGAAAATCCCA
77704 T A CAAGAAGAAGAGCTTTCTTCTTTATCTGAAAACAGAAATACTCGGTGCTTAAGCATCCGATAAAGCCAAATATAAAAAATAAGCATGATCTCCAGATTGG[T/A]GTGAACATAATCCTACTAATACAAGCAAATGCCATCAGCAAAGAGACTCTTTAACAAGGTACAACAACCATCCAAGAAAACCGTACA
77732 C G GCATGGAAATCCCAGTCGAAAAGATCTTCCTGGCTCAAAAGATGATGATCTACAAATGCAACCTTGCTGGCAAGCCTGTCGTGACCGCCACCCAAATGCT[C/G]GAGTCCATGATCAAGTCCCCCCGCCCCACCCGTGCTGAAGCCACCGACGTGGCCAACGCCGTCCTCGACGGCACCGACTGCGTCAT
77732 C T GCAAGCCTGTCGTGACCGCCACCCAAATGCTCGAGTCCATGATCAAGTCCCCCCGCCCCACCCGTGCTGAAGCCACCGACGTGGCCAACGCCGTCCTCGA[C/T]GGCACCGACTGCGTCATGCTCTCCGGCGAGTCCGCTGCTGGCGCCTACCCCGAAATCGCCGTGAAAGTAATGTCCAAAATCTGCAT
77732 C T CCCAAATGCTCGAGTCCATGATCAAGTCCCCCCGCCCCACCCGTGCTGAAGCCACCGACGTGGCCAACGCCGTCCTCGACGGCACCGACTGCGTCATGCT[C/T]TCCGGCGAGTCCGCTGCTGGCGCCTACCCCGAAATCGCCGTGAAAGTAATGTCCAAAATCTGCATTGAGGCCGAGTCCTCCCTCGA
77732 T C TGATCAAGTCCCCCCGCCCCACCCGTGCTGAAGCCACCGACGTGGCCAACGCCGTCCTCGACGGCACCGACTGCGTCATGCTCTCCGGCGAGTCCGCTGC[T/C]GGCGCCTACCCCGAAATCGCCGTGAAAGTAATGTCCAAAATCTGCATTGAGGCCGAGTCCTCCCTCGACTACAACACCATCTTCAAG
77732 G A TCGACGGCACCGACTGCGTCATGCTCTCCGGCGAGTCCGCTGCTGGCGCCTACCCCGAAATCGCCGTGAAAGTAATGTCCAAAATCTGCATTGAGGCCGA[G/A]TCCTCCCTCGACTACAACACCATCTTCAAGGAGATGGTCCGCTCCGCCCCTCTCCCCATGTCCCCCCTCGAGTCCCTCGCCTCCACCG
77742 A G TGGACTAGAAGGGCAGCTAAAGATCCGTGCCCGTGCTTTATCATAATCCTCTAATCTTTCTTCAACGCTTCTCATCAGATTTCTACTAGCTGCATTTTCT[A/G]AAGAATCATCCATGGACATTTGGCTGGTTCTCGAACGAATAACAAATTTAACATGGTTAGATTTCGCAGTTTCCGTTTCCTTTTGTTTTAT
77766 C T TAATCAGATCTAAGATAGCATTTAAATTCTCTGATTTGATACTGAAAGGCGGATCTAAAACATCTGAAGTAGATGCAGCTATCAGAAC[C/T]GAGGATGTGAAAAATGATCTGATTTCTGAAGACTTTGTTCTCTCCAAAGATGGTGTAGATGATAATGATATTCCTGCAGAAAATGTGACAGAGGCTGCG
77766 A G GATGATAATGATATTCCTGCAGAAAATGTGACAGAGGCTGCGACTAAAGGGCCTTCATCAAGCAAGCATCAGCAAAAGAAGAAGAAGAAGAGGCAGGGTA[A/G]GAAAAACAATAGACGTTGAAGGAAGAAAATTTCATTTTGCTATTTTGTAATATGTACAGTAAACCCTTACAGCTAGGATGGTGGT
77770 A G TCCATGGAAGTTCACAGGAGAAACAGTGATAGTACTATTTGCATCAAAGAGCATTGTTCCTTTGATG[A/G]CTGTATCATTTCTCCGGATCTTGTATTCCATCTTTCCAGTAGTTGGGTCTAAGATTACCCATCGCTCATTCCACTTCTTTAACGTTTCGGATCTTTTAAG
77770 CT C CAAAGAGCATTGTTCCTTTGATGACTGTATCATTTCTCCGGATCTTGTATTCCATCTTTCCAGTAGTTGGGTCTAAGATTACCCATCGCTCATTCCACTT[CT/C]TTTAACGTTTCGGATCTTTTAAGAAGCGGACCCTGAAGAACAGTCCGACCTGAACCAGATAATAGCTGTCGCTTGATCTTCTCCAAGCT
77776 T A GCAGCAACTAAGATGGACAGGCGGCCAAGAAGCAAGCTCGAAGGTGACAAAGATGATGCAATAGCAGCGATTACCGGTGGCGCGTGGCGTTGCTGCTGTG[T/A]GGCTCCGATGAGAACGACCTGAAATGTTTCGACTTCGACCGGAGGAGGATTTCGTTTTAGGGAAAGGCGACTTAGGGCTTTCG
77806 A T TTTTCTAGTCTGCATCCATCTCCTCTAATGCTAATTTTGCGGCAGTCTTCGCTTCTTCAAGGATATCATCTGGGACCTTTTCATGTAGACGTTTAGATTC[A/T]TCACATACCCAGCTTAATTCCAACTCAAAATCTTTATCCTTTGCCTCATCGTGAACACTGTATATAATCTTTGCAACTTCTATAACACCTTGC
77828 A G GCAGTAAATAAGTTCGGGTTCAGGAAGAGAGATCATCTGCATCCCTGTACCACCTTTGATGGGTTCTAAGCTCCCAACGTTTGCTGTTTTCTTTTCGAAC[A/G]GCACATGAGGGTTCGATCTTTTACGTTGGGAAATTATTTGGAATTTTGAAGATTTTATTTGGATTTAGAAGGCAAAACCGAGCTCGTA
77872 T C CAGCTATTCAAAGTGTGCTTTCAACTGAAAAAGACATTTCTACAAGTCCAAATGTTCAAGGGTTACGTGGGAAATTAAACAAAGTGGT[T/C]TTAGCGTACAGTGGTGGTCTTGATACATCGGTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAA
77872 G C CAGCTATTCAAAGTGTGCTTTCAACTGAAAAAGACATTTCTACAAGTCCAAATGTTCAAGGGTTACGTGGGAAATTAAACAAAGTGGTTTTAGC[G/C]TACAGTGGTGGTCTTGATACATCGGTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAA
77872 G A TTTCAACTGAAAAAGACATTTCTACAAGTCCAAATGTTCAAGGGTTACGTGGGAAATTAAACAAAGTGGTTTTAGCGTACAGTGGTGGTCTTGATACATC[G/A]GTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGA
77872 T C AAAAAGACATTTCTACAAGTCCAAATGTTCAAGGGTTACGTGGGAAATTAAACAAAGTGGTTTTAGCGTACAGTGGTGGTCTTGATACATCGGTCATTGT[T/C]CCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTAT
77872 G A CAAGTCCAAATGTTCAAGGGTTACGTGGGAAATTAAACAAAGTGGTTTTAGCGTACAGTGGTGGTCTTGATACATCGGTCATTGTTCCATGGCTAAGGGA[G/A]AATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTATGAATAAAGCAATAG
77872 G A AATTAAACAAAGTGGTTTTAGCGTACAGTGGTGGTCTTGATACATCGGTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTAC[G/A]GCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTATGAATAAAGCAATAGCTAGTGGTGCTTGTGACCTTGTTGTAAAGG
77872 T C ACATCGGTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTA[T/C]GAATAAAGCAATAGCTAGTGGTGCTTGTGACCTTGTTGTAAAGGATTTAAAAGAAGAGTTTGTGAAAGATTTTATATTTCCTTGTTT
77872 G A CATCGGTCATTGTTCCATGGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTAT[G/A]AATAAAGCAATAGCTAGTGGTGCTTGTGACCTTGTTGTAAAGGATTTAAAAGAAGAGTTTGTGAAAGATTTTATATTTCCTTGTTTG
77872 T C GGCTAAGGGAGAATTATGGGTGCGAAGTAGTGTGCTTTACGGCTGATGTTGGTCAAGGTGACATGGAATTGGATGGGCTTATGAATAAAGCAATAGCTAG[T/C]GGTGCTTGTGACCTTGTTGTAAAGGATTTAAAAGAAGAGTTTGTGAAAGATTTTATATTTCCTTGTTTGCGTGCCGGAGCAATTTA
77872 T C AAGGTGACATGGAATTGGATGGGCTTATGAATAAAGCAATAGCTAGTGGTGCTTGTGACCTTGTTGTAAAGGATTTAAAAGAAGAGTTTGTGAAAGATTT[T/C]ATATTTCCTTGTTTGCGTGCCGGAGCAATTTATGAACGAAAATATTTGCTTGGGACATCAATGGCTCGTCCCTGCATTGCCAAGGCA
77882 C T GATAACCATCAGGGTTATTTGGTGAAGTCACAATCTCAATGAAATCTTGTGGATTAGTTGTATTTACATAGTCCAATGCATTTCCCTTCCATCGGTATCC[C/T]GTGTGGTTAAAAAAAGTGGTTTGGCTCTTGAACACAGGGTAGTAAGGAGCAGCAGCAACAACATTCATCACCGTAGCATTTGGGTTTG
77882 T C GTGAAGTCACAATCTCAATGAAATCTTGTGGATTAGTTGTATTTACATAGTCCAATGCATTTCCCTTCCATCGGTATCCCGTGTGGTTAAAAAAAGTGGT[T/C]TGGCTCTTGAACACAGGGTAGTAAGGAGCAGCAGCAACAACATTCATCACCGTAGCATTTGGGTTTGCATTAAGATCTGGCGACAAAG
77882 G A TGAAATCTTGTGGATTAGTTGTATTTACATAGTCCAATGCATTTCCCTTCCATCGGTATCCCGTGTGGTTAAAAAAAGTGGTTTGGCTCTTGAACACAGG[G/A]TAGTAAGGAGCAGCAGCAACAACATTCATCACCGTAGCATTTGGGTTTGCATTAAGATCTGGCGACAAAGAGATAATGACTCCATTTA
77882 C T CATCGGTATCCCGTGTGGTTAAAAAAAGTGGTTTGGCTCTTGAACACAGGGTAGTAAGGAGCAGCAGCAACAACATTCATCACCGTAGCATTTGGGTTTG[C/T]ATTAAGATCTGGCGACAAAGAGATAATGACTCCATTTAGAAGTTGAGTTATTCCGTTTCCAAACACGATTTTGTGTTCATCTGTGAC
77900 G A GTTGGCCTACTGGATCTCAAAATGCCTTCCTCCCTTTTTCTTTTTTCTTTTCCCTTTAAATAAAACATTTGGTACTGGCCGGCTGGAATAC[G/A]GAAGATCCGAGACATGGACGGCAGAAAACAGGCGAAACGACTAGGCGGCATGGCGGAAGCTCTCTCCATCGCTTCTGATCTTGGATTTCCCATTCAA
77912 T C CATGCTCGGCGCACACCACTTCCCAGAACTTAGCTCCGATCTGGTTACCGCATTGGCCACCTTGTATGTGCAGAATTTCTCTCATGTTTCGGGAGTAATT[T/C]GATTACCGTTCAATTGATTCAGAAATTTAGGGTTTAAAGACTCGGGTTAAAATGATTTCCAGTAGGCCAACAGT
77932 A G TTGATATTTGAGGTGACAAATGAATACCTGTGGCACTTGGATTTTGGTTCGGGTTCGACGCACAATGACCCATTCGAAATCTAACAGCCTTTGCGGA[A/G]TATATTGGACTTCCATATTGGAAGTATGCTTCAAAAGGCTGTATTTTTATTGCAGCAACAACACACAATCTGGAGCATAACCTATAAAGCA
77932 C T TTCGACGCACAATGACCCATTCGAAATCTAACAGCCTTTGCGGAATATATTGGACTTCCATATTGGAAGTATGCTTCAAAAGGCTGTATTTTTATTGCAG[C/T]AACAACACACAATCTGGAGCATAACCTATAAAGCAAAGTCTCGGGAGTTCCAGGATCACATTCACCTCGACTAGACCAATAAGAAGGT
77932 C T TTTTATTGCAGCAACAACACACAATCTGGAGCATAACCTATAAAGCAAAGTCTCGGGAGTTCCAGGATCACATTCACCTCGACTAGACCAATAAGAAGGT[C/T]GCATATTCACCCGGTCAACCTCTATCAACGTATTTTCGATGCTCTCCTTGGGATAATTGTCAGTGCTTGAAGCACGAATTGCCTCATTG
77932 C A AAGTCTCGGGAGTTCCAGGATCACATTCACCTCGACTAGACCAATAAGAAGGTCGCATATTCACCCGGTCAACCTCTATCAACGTATTTTCGATGCTCTC[C/A]TTGGGATAATTGTCAGTGCTTGAAGCACGAATTGCCTCATTGATGCACTCCCCATATCCAGTAGGCTTAACAAGCCAGTGACATAGAT
77932 T C GTCTCGGGAGTTCCAGGATCACATTCACCTCGACTAGACCAATAAGAAGGTCGCATATTCACCCGGTCAACCTCTATCAACGTATTTTCGATGCTCTCCT[T/C]GGGATAATTGTCAGTGCTTGAAGCACGAATTGCCTCATTGATGCACTCCCCATATCCAGTAGGCTTAACAAGCCAGTGACATAGATAG
77932 A G CTCGACTAGACCAATAAGAAGGTCGCATATTCACCCGGTCAACCTCTATCAACGTATTTTCGATGCTCTCCTTGGGATAATTGTCAGTGCTTGAAGCACG[A/G]ATTGCCTCATTGATGCACTCCCCATATCCAGTAGGCTTAACAAGCCAGTGACATAGATAGGAATATGCCT
77946 A G GTAAGGAGAAAAGGAAGTGATCAGTCATCATCGCCAAAGGCGGAATACATACATGCAGTGACAAAACAAGAGTATCAGTCTACATCGCCGAAGGCGGAAT[A/G]CATATACATATAGTCAGAAATACGGAAAGTAAATCAGTCTGCATCGCCAGTGGCGGAATCATAAACATAAATACGGGAATGGCG
77946 T C GGCGGAATACATATACATATAGTCAGAAATACGGAAAGTAAATCAGTCTGCATCGCCAGTGGCGGAATCATAAACATAAATACGGGAATGGCGGAAAATA[T/C]CTAAGTCATCACTATGAAGTCAGCCTCGCCATGAGCCAAAAGTGCATGCTGTGCAGCAGTGCAGGACCAAAAATCACCTGTCACC
77960 TC T GAGCTTCTTTCTCCTTTTTCTCTCCATCTTCTTCTCCATCTTTATCCTCCTTCACTTGTTCAACAAATTCAAAGACCGGAAACTCCCTCCTGGGCCACCC[TC/T]CCTACCCAATTATCGGAAACCTCATCTGGCTAAGACGGTCCATCCTCGACCTCGAGCCCGTCCTCCACGAGCTTGTCCAAAAGTATGGACC
77970 G C CCCCTGCACCGAAAAGGTACACCAAGCATTTACCACCACGCATACAGAAGAGGAGGCACATGCGGTATTCCAATTAGGGCAGTGTTTTATCCTAAAAGTT[G/C]GATGTTTGGGGTTAAAATGAATTTTAATTTAGAAGCTGTAGAAGTAATATAGGCGTAATAGGGCTGCAATGGGTCAATCAGTATAT
77970 A T ACCACGCATACAGAAGAGGAGGCACATGCGGTATTCCAATTAGGGCAGTGTTTTATCCTAAAAGTTGGATGTTTGGGGTTAAAATGAATTTTAATTTAGA[A/T]GCTGTAGAAGTAATATAGGCGTAATAGGGCTGCAATGGGTCAATCAGTATATTAGGGTTACATATGTTTTACATATGTTTTTGCTGT
77970 A T CCAATTAGGGCAGTGTTTTATCCTAAAAGTTGGATGTTTGGGGTTAAAATGAATTTTAATTTAGAAGCTGTAGAAGTAATATAGGCGTAATAGGGCTGCA[A/T]TGGGTCAATCAGTATATTAGGGTTACATATGTTTTACATATGTTTTTGCTGTGCTGTAGTTTGTGGTCAATGGTCAGTTATATATGCA
77974 A G GGGACTCGAACCTGCGCGCTCCACATTACTAACCGGGTAGTGGTAACAGATAACTAAAAGCATTCATTATGCT[A/G]GGGACATAGGCTTAAACCGATGAATGCAAGAGGTCCAGCATTTTCAATACGAATTATTCTGGAGCAGCGCTAATTAGATATACCTCTACAATCTGTTATC
77974 C T GGGACTCGAACCTGCGCGCTCCACATTACTAACCGGGTAGTGGTAACAGATAACTAAAAGCATTCATTATGCTAGGGACATAGG[C/T]TTAAACCGATGAATGCAAGAGGTCCAGCATTTTCAATACGAATTATTCTGGAGCAGCGCTAATTAGATATACCTCTACAATCTGTTATCGTAATTCTGTG
77974 T TG GCTCCACATTACTAACCGGGTAGTGGTAACAGATAACTAAAAGCATTCATTATGCTAGGGACATAGGCTTAAACCGATGAATGCAAGAGGTCCAGCATTT[T/TG]CAATACGAATTATTCTGGAGCAGCGCTAATTAGATATACCTCTACAATCTGTTATCGTAATTCTGTGTCACCTTACACATTCAGTTAT
77974 A G AATGCAAGAGGTCCAGCATTTTCAATACGAATTATTCTGGAGCAGCGCTAATTAGATATACCTCTACAATCTGTTATCGTAATTCTGTGTCACCTTACAC[A/G]TTCAGTTATCTGGATGAGTTTTCATCGATTTTATGTTGTTTTTGCCAACTCAACACATATATGCATGTCATCTTCAACCTTTGTCTTACAG
77978 T A GTACTAGAAGGTCAGGAAAACAGTACTCCAGCTATGAAAACCTGCTCCATAAGGCGATGCAGAACTTCATAGGAGGGGTGACAGAGGCAGGCATATGTTC[T/A]AGCATTAAGATCTAGAATGATAATTACGTTGAAGCACCACTGATCAAATCTGAAGAGTCAAAGGCTCGGATTCCAGAAATACACT
77992 GT G AAATACAGACATGGTTTTATGTTAAAACATCCGTTCACCAGCCAAAATCATACTCAATTCACACTGCACTTCATCTCTGTGGACTGCATATCACATTTTG[GT/G]TCTCGAACAGTACACATAGTATATACAATATTTTACCTATCGTGATTTCTCCGAAAATAACATTTCATTTCAGCAAGTGTATCACCCAAT
77992 GT G TGTTAAAACATCCGTTCACCAGCCAAAATCATACTCAATTCACACTGCACTTCATCTCTGTGGACTGCATATCACATTTTGGTCTCGAACAGTACACATA[GT/G]TATATACAATATTTTACCTATCGTGATTTCTCCGAAAATAACATTTCATTTCAGCAAGTGTATCACCCAATCAGGAAACATGCTTAATGC
78010 G C TGGAACGTTGAATCCATCCACCAAACTGAGGTCGTAAGTGTCTTTTCCATTGTTCCCCATGAG[G/C]TTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
78010 T G TGGAACGTTGAATCCATCCACCAAACTGAGGTCGTAAGTGTCTTTTCCATTGTTCCCCATGAGG[T/G]TGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGA
78010 A C TGGAACGTTGAATCCATCCACCAAACTGAGGTCGTAAGTGTCTTTTCCATTGTTCCCCATGAGGTTGATCTCCATGAGCGT[A/C]GCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGG
78010 T G TGGAACGTTGAATCCATCCACCAAACTGAGGTCGTAAGTGTCTTTTCCATTGTTCCCCATGAGGTTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCT[T/G]GTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGG
78010 G C GGAACGTTGAATCCATCCACCAAACTGAGGTCGTAAGTGTCTTTTCCATTGTTCCCCATGAGGTTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTT[G/C]TCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGC
78010 T C CTTTTCCATTGTTCCCCATGAGGTTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGA[T/C]GAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTT
78010 G A ATTGTTCCCCATGAGGTTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCAC[G/A]TGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGA
78010 A G TGAGGTTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCC[A/G]GATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCCGG
78010 A G TTGATCTCCATGAGCGTAGCTGGAGGTGCTCCTCCTTGTCCGTTGCATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATG[A/G]GTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCCGGGTGGG
78010 A T ATGCTACCTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCC[A/T]GCTGGACCGGCTATGGTTACTGGAGCAGATCCGGGTGGGAGAGCGAACCCGGTATTTGATAGCTGTGGAGAGCCTGCATTGTTCA
78010 C G CTGGCCCGACCCGCAGTCGGCGGATGAGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGA[C/G]CGGCTATGGTTACTGGAGCAGATCCGGGTGGGAGAGCGAACCCGGTATTTGATAGCTGTGGAGAGCCTGCATTGTTCAGCGTTG
78010 G A AGCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCC[G/A]GGTGGGAGAGCGAACCCGGTATTTGATAGCTGTGGAGAGCCTGCATTGTTCAGCGTTGCTGGCCATACTGGGTATGCGCACTTGT
78010 G C GCACGTGAACTTTCCAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCCG[G/C]GTGGGAGAGCGAACCCGGTATTTGATAGCTGTGGAGAGCCTGCATTGTTCAGCGTTGCTGGCCATACTGGGTATGCGCACTTGTT
78010 C T CAGATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCCGGGTGGGAGAGCGAA[C/T]CCGGTATTTGATAGCTGTGGAGAGCCTGCATTGTTCAGCGTTGCTGGCCATACTGGGTATGCGCACTTGTTATTGAGGGAGAAGG
78010 G A ATGAGTCCGTGCTGCATCCGGTTCTGGCCCAGAATCGCCCACTCCACCCAGCTGGACCGGCTATGGTTACTGGAGCAGATCCGGGTGGGAGAGCGAACCC[G/A]GTATTTGATAGCTGTGGAGAGCCTGCATTGTTCAGCGTTGCTGGCCATACTGGGTATGCGCACTTGTTATTGAGGGAGAAGGTG
78048 A G ACTGATGAATGGGAGGATACATAGAATTAATGCAGACAGGACATTCTAGAAGTTCATGAATGCTACTGGCCGGAGGAACAACGATACCGCCGCCTGTGCT[A/G]GTGCCTGAGGTACCGTTTCCAACGCTTCCGCCGTTAGATTTCATGGAGAATGGATTCTGGTCTTCATCGATAACATCGGTTGTGGT
78048 C G ATGAATGGGAGGATACATAGAATTAATGCAGACAGGACATTCTAGAAGTTCATGAATGCTACTGGCCGGAGGAACAACGATACCGCCGCCTGTGCTAGTG[C/G]CTGAGGTACCGTTTCCAACGCTTCCGCCGTTAGATTTCATGGAGAATGGATTCTGGTCTTCATCGATAACATCGGTTGTGGTTACG
78048 G C TGCAGACAGGACATTCTAGAAGTTCATGAATGCTACTGGCCGGAGGAACAACGATACCGCCGCCTGTGCTAGTGCCTGAGGTACCGTTTCCAACGCTTCC[G/C]CCGTTAGATTTCATGGAGAATGGATTCTGGTCTTCATCGATAACATCGGTTGTGGTTACGCACTCGATATTTTCTAAATCCAAATGG
78058 C A GCGGAAAGCCAAAAAGAGGCCCTTCTACAGATCCGTGGTAAGTAATCGAAGACGAAGAAGTCAAGAGTCAAGACTGAAGAAGAACAGCAGCGCCTGCCGC[C/A]TGCACCCTGCTGCGGCTTCTCTGCGATTTGGATTTTGCGATCGTTTGGAGTTGAACGCCGGAAACTGGAGTACCTCGCGATTTG
78058 A G AGAGTCAAGACTGAAGAAGAACAGCAGCGCCTGCCGCCTGCACCCTGCTGCGGCTTCTCTGCGATTTGGATTTTGCGATCGTTTGGAGTTGAACGCCGGA[A/G]ACTGGAGTACCTCGCGATTTGGATCTTCCGATTTTTTTTATTTTTTTTTCTCGGCAGCAGAATCGGTGATATGATGCCCTGGTGCCC
78062 T A AAGCAACTCGATTTCCTTCCTTTCACCTGCAGCGGATGCCACAAGGTATTTTGCCTGGAGCATAGAACGT[T/A]CAGATCCCACGACTGTCCTAGATCGGAGCACGGAAGCAGAGTGGTGGTCGTATGCGACATCTGTTCCGGCACGATCGACAAAGAAAGCGCGTATGTGGAA
78062 G C GCAACTCGATTTCCTTCCTTTCACCTGCAGCGGATGCCACAAGGTATTTTGCCTGGAGCATAGAACGTTCAGATCCCACGACTGTCCTAGATCGGAGCAC[G/C]GAAGCAGAGTGGTGGTCGTATGCGACATCTGTTCCGGCACGATCGACAAAGAAAGCGCGTATGTGGAAGACGAGGTCACTTTGGA
78062 G A TCCTTCCTTTCACCTGCAGCGGATGCCACAAGGTATTTTGCCTGGAGCATAGAACGTTCAGATCCCACGACTGTCCTAGATCGGAGCACGGAAGCAGAGT[G/A]GTGGTCGTATGCGACATCTGTTCCGGCACGATCGACAAAGAAAGCGCGTATGTGGAAGACGAGGTCACTTTGGAGGCGCATAGGA
78062 G A CCACAAGGTATTTTGCCTGGAGCATAGAACGTTCAGATCCCACGACTGTCCTAGATCGGAGCACGGAAGCAGAGTGGTGGTCGTATGCGACATCTGTTCC[G/A]GCACGATCGACAAAGAAAGCGCGTATGTGGAAGACGAGGTCACTTTGGAGGCGCATAGGAAGTCCGGAGAGTGCGATCCGGCG
78062 A T TCCCACGACTGTCCTAGATCGGAGCACGGAAGCAGAGTGGTGGTCGTATGCGACATCTGTTCCGGCACGATCGACAAAGAAAGCGCGTATGTGGAAGACG[A/T]GGTCACTTTGGAGGCGCATAGGAAGTCCGGAGAGTGCGATCCGGCGAAGAAGAAGCAGAGGAAGAAGTGCCCGGTCCACCGG
78062 G C CTTTGGAGGCGCATAGGAAGTCCGGAGAGTGCGATCCGGCGAAGAAGAAGCAGAGGAAGAAGTGCCCGGTCCACCGGTGCAAGGAAGTGCTGACGTTCTC[G/C]AACACGAGCACCTGCAAGAGCTGCAGGGTGCAGGTTTGCTTGAAGCACAGGTTTGCTTCTGATCATGACTGCAAGCGCGGCG
78090 T C TTTGGTTTGAGCAAGAAGCCCGAAGATTTTGCCAAGTACCAAGGGTATGAGTTGATTCACGCAAGATGGGCAATGCTTGGTGCTGC[T/C]GGCTTCATCATCCCTGAAGCCTTCAACAAATATGGTGCTAACTGCGGGCCAGAAGCTGTTTGGTTCAAGACTGGTGCTCTTCTTCTGGATGGAAACACAT
78098 T C GCGCAACGACGGCATCCCCTTTCCTACACAAACCTTTCTCAACCCCGGACCTAAGTGCCGCCTCCAAAATCTCCTCCGTCGACTCTGCATCTGTCGCCTT[T/C]GCAGACCCCTCCGCTAGGAGCGGTATCAACCCCCTATACATTAAGCTGTGCCTCGCTGGCGATTCATCGCTCACCATCCAATCGAAAGA
78098 C T CATCCCCTTTCCTACACAAACCTTTCTCAACCCCGGACCTAAGTGCCGCCTCCAAAATCTCCTCCGTCGACTCTGCATCTGTCGCCTTTGCAGACCCCTC[C/T]GCTAGGAGCGGTATCAACCCCCTATACATTAAGCTGTGCCTCGCTGGCGATTCATCGCTCACCATCCAATCGAAAGAGTCCGTCGTCAGA
78100 T C TGTCGACCCCCTTGCTGACCACAACCATCGAACCCACGTGGTCGTCGCTCCCCAAAACTCTAGCACCTCCCTTTAACAGCCACGATCTCTCACTTCTTCG[T/C]GCTAGACTAGTACATCGCCCTCGCCTTGCTCCTTATTTCTACTGTACACCGAAGCCGCTTGGCGCCGTGACTGCCGTGACATCGGAGTG
78108 AG A ATAACATTTCCTCCCTTCTCCTTACTCTTCCTACTTGCTTTCTTTGCCTTCCTACTATGTGAATGCTTCCTCTTCATCGCCAATAC[AG/A]GGCGAACCTCCATCGCCACCACAACCTAATTCATCTAAAGAAGTCCTCACATACTCAACGTCAAAATTGAGCATTGCATCCTGCCCTCTCGTAGCCAGAG
78112 A T TCATAGAAGCCGCAAAGCATCTCAAATCGAAGCCACCAGTATTGAAGTTCGCTGATTACAACTGTTTCTTTTGTTCTTCGCTGTTGCCGACTCGAGCATT[A/T]CAGATTTAAAGATTACAGCTTAGGATCCGAAGATTGGCGAAACGGGGGGTTTCGAAGACGCACACTCTGATGATTTCAAATAGTAAAG
78134 T A TTTTCCATATTGAAGTCTTCTCCTTTTCATCTATCTTCTCCTCGAAAACTTCACTTTTCTTCAGATACCAGGGCGCTT[T/A]CACTCCCTTCCCTGCTAATCCGTAGCCCAACTTATACTTCATATCCTCTGCAGTCATCACGACCTTCTCTTTCTCCTTTTCCTTTTCATCCCTCTTCCTC
78134 T C CATCTATCTTCTCCTCGAAAACTTCACTTTTCTTCAGATACCAGGGCGCTTTCACTCCCTTCCCTGCTAATCCGTAGCCCAACTTATACTTCATATCCTC[T/C]GCAGTCATCACGACCTTCTCTTTCTCCTTTTCCTTTTCATCCCTCTTCCTCTTCTTGCCCTTGCTACTATCGCCATCATCACAAGCAAACAAGT
78134 C T TTCCCTGCTAATCCGTAGCCCAACTTATACTTCATATCCTCTGCAGTCATCACGACCTTCTCTTTCTCCTTTTCCTTTTCATCCCTCTTCCTCTTCTTGC[C/T]CTTGCTACTATCGCCATCATCACAAGCAAACAAGTTTATATGATTCGAACTGAGATCAATAGAGGAACCTGGGTTAGGGTTTGAATTAGTCT
78142 G C AAGGACGTTTGTCCTCACGAGTTTGTGAAAGCGTATTCCGCTCATCTTAAGCGATCTGGGAAGATGGAGCTTCCCCAGTGGACTGACATTGTGAAGACAG[G/C]AAAGTTCAAGGAACTTGCTCCTTATGATCCTGATTGGTATTACATTAGAGCTGCTTCCATGGCAAGGAAGATCTACTTGAGGCAAG
78142 TAG T,TG CAGGAAAGTTCAAGGAACTTGCTCCTTATGATCCTGATTGGTATTACATTAGAGCTGCTTCCATGGCAAGGAAGATCTACTTGAGGCAAGGAATCGGGGT[TAG/T,TG]AGGTGGCTTTCAAAAGATCTACGGTGGCAGCCAGAGTAATGGAAGTCGTCCATCACATTTCTGCAAGAGCAGTGGTGCGGT
78142 C T TCCTGATTGGTATTACATTAGAGCTGCTTCCATGGCAAGGAAGATCTACTTGAGGCAAGGAATCGGGGTTAGGTGGCTTTCAAAAGATCTACGGTGGCAG[C/T]CAGAGTAATGGAAGTCGTCCATCACATTTCTGCAAGAGCAGTGGTGCGGTCGCTCGCAGCATTCTTCACCAGTT
78164 G A GTAATATGTCCACGTTCCAGTTGCAGTCGTAGTCCCTAAAGCACAGCCATGGCTTATTCCCTAGGTAATGGATCACGTACAGTTCAGGCGGGTCTGCCCC[G/A]AACAGCCTTACCTTCTTTGCCTTTATTTGGTCGTCGTCTCCAACCCAGAAGTTCTTCAGGAAGTTCATGTGTTTGGGGATTCTGTGCCA
78168 A G TCATTCACTATCGCTGTCATAATTCTGACAAAGAGAAAGAAGTCCTTTTTCAGCTTCGATTCCATCTGTAGTAACAGTTGGTTTGCTATTTTC[A/G]GTATCGGATTCGACGCAAAGCCTCTTTACGGGTTGAATATTCGACTTTCTCTTCACAACGAATATGGGCTTCATTCTAGATGGTCCACTCCTGCTCC
78168 G A TCATTCACTATCGCTGTCATAATTCTGACAAAGAGAAAGAAGTCCTTTTTCAGCTTCGATTCCATCTGTAGTAACAGTTGGTTTGCTATTTTCAGTATC[G/A]GATTCGACGCAAAGCCTCTTTACGGGTTGAATATTCGACTTTCTCTTCACAACGAATATGGGCTTCATTCTAGATGGTCCACTCCTGCTCCC
78168 T A TAGTAACAGTTGGTTTGCTATTTTCAGTATCGGATTCGACGCAAAGCCTCTTTACGGGTTGAATATTCGACTTTCTCTTCACAACGAATATGGGCTTCAT[T/A]CTAGATGGTCCACTCCTGCTCCCTTCAGTGTTCTTAGAGCTATTAAAGATGCTTGTTTTACTCAAAGTGTCCGTGGGTTTCTCCACTATG
78168 G A AGTTGGTTTGCTATTTTCAGTATCGGATTCGACGCAAAGCCTCTTTACGGGTTGAATATTCGACTTTCTCTTCACAACGAATATGGGCTTCATTCTAGAT[G/A]GTCCACTCCTGCTCCCTTCAGTGTTCTTAGAGCTATTAAAGATGCTTGTTTTACTCAAAGTGTCCGTGGGTTTCTCCACTATGCTTGGGA
78168 T C GACTTTCTCTTCACAACGAATATGGGCTTCATTCTAGATGGTCCACTCCTGCTCCCTTCAGTGTTCTTAGAGCTATTAAAGATGCTTGTTTTACTCAAAG[T/C]GTCCGTGGGTTTCTCCACTATGCTTGGGACGACTCCACCTTTCCCCTTCTCGTTGAAATCATCTTCATCCTCATCCTCATCCTCGATTCTTC
78168 C T GGTCCACTCCTGCTCCCTTCAGTGTTCTTAGAGCTATTAAAGATGCTTGTTTTACTCAAAGTGTCCGTGGGTTTCTCCACTATGCTTGGGACGACTCCAC[C/T]TTTCCCCTTCTCGTTGAAATCATCTTCATCCTCATCCTCATCCTCGATTCTTCTGATGTACTCTTTATGACCTATTGATTTGATAACTTCTTC
78182 T C CAGTGAAGAGGAAGCTTATCCTGTAGAACCTCGTAGTGATATCCCTAGCGATATGGATTCGGATGATGAAAAAAGGCGATA[T/C]GATGAGCAATTGTTAGAAATGATTGATCGAGCCTATGAACAGTACATAAGTAAACAGAGAAGTGTCACAAATCAGCGCAAGCGCGTGAAGCAAGCTCGTT
78182 T G CAGTGAAGAGGAAGCTTATCCTGTAGAACCTCGTAGTGATATCCCTAGCGATATGGATTCGGATGATGAAAAAAGGCGATATGATGAGCAATTG[T/G]TAGAAATGATTGATCGAGCCTATGAACAGTACATAAGTAAACAGAGAAGTGTCACAAATCAGCGCAAGCGCGTGAAGCAAGCTCGTTCTAA
78182 T A CAGTGAAGAGGAAGCTTATCCTGTAGAACCTCGTAGTGATATCCCTAGCGATATGGATTCGGATGATGAAAAAAGGCGATATGATGAGCAATTGT[T/A]AGAAATGATTGATCGAGCCTATGAACAGTACATAAGTAAACAGAGAAGTGTCACAAATCAGCGCAAGCGCGTGAAGCAAGCTCGTTCTAA
78182 T C AAGAGGAAGCTTATCCTGTAGAACCTCGTAGTGATATCCCTAGCGATATGGATTCGGATGATGAAAAAAGGCGATATGATGAGCAATTGTTAGAAATGAT[T/C]GATCGAGCCTATGAACAGTACATAAGTAAACAGAGAAGTGTCACAAATCAGCGCAAGCGCGTGAAGCAAGCTCGTTCTAATGGCC
78210 T G TTAAGACGGTTTAGCTTAGCGGATTCGGGTTCGGATGAGAATCCGTAGCTGGAAGAATCGGATGAGCTGGAGTAGGTTTGCCTGGGCTCCCGGCCTC[T/G]GTCGTTCTTCTTAACGGGTAGCGGTGGAATCCACCTGTGCTCGGGCAGGGGTTTCGATTTCAAATGAGGTGGGGGATCAGGTGCTCC
78210 C A CGTAGCTGGAAGAATCGGATGAGCTGGAGTAGGTTTGCCTGGGCTCCCGGCCTCTGTCGTTCTTCTTAACGGGTAGCGGTGGAATCCACCTGTGCTCGGG[C/A]AGGGGTTTCGATTTCAAATGAGGTGGGGGATCAGGTGCTCCGCGGTCGGCTTTACTGATCCTGATCTCGTCATCGATAGACTGGT
78210 G T AGTAGGTTTGCCTGGGCTCCCGGCCTCTGTCGTTCTTCTTAACGGGTAGCGGTGGAATCCACCTGTGCTCGGGCAGGGGTTTCGATTTCAAATGAGGTGG[G/T]GGATCAGGTGCTCCGCGGTCGGCTTTACTGATCCTGATCTCGTCATCGATAGACTGGTAGATGGAGTCGAGTAGGGAGGAGGAG
78210 C T GGGCTCCCGGCCTCTGTCGTTCTTCTTAACGGGTAGCGGTGGAATCCACCTGTGCTCGGGCAGGGGTTTCGATTTCAAATGAGGTGGGGGATCAGGTGCT[C/T]CGCGGTCGGCTTTACTGATCCTGATCTCGTCATCGATAGACTGGTAGATGGAGTCGAGTAGGGAGGAGGAGAACGAGGGGTAGT
78210 C T CCTCTGTCGTTCTTCTTAACGGGTAGCGGTGGAATCCACCTGTGCTCGGGCAGGGGTTTCGATTTCAAATGAGGTGGGGGATCAGGTGCTCCGCGGTCGG[C/T]TTTACTGATCCTGATCTCGTCATCGATAGACTGGTAGATGGAGTCGAGTAGGGAGGAGGAGAACGAGGGGTAGTCGCACATGCG
78210 A G GTGGAATCCACCTGTGCTCGGGCAGGGGTTTCGATTTCAAATGAGGTGGGGGATCAGGTGCTCCGCGGTCGGCTTTACTGATCCTGATCTCGTCATCGAT[A/G]GACTGGTAGATGGAGTCGAGTAGGGAGGAGGAGAACGAGGGGTAGTCGCACATGCGGCGAGTGGAGGGTTTCTGTATCCGTTC
78212 T C GGTGGAGGACGGGGTTATAACGCAGTTCAGAGAGTACTTCAATACCTGCGTCACTGTTAGAGAGCTCGGAGGCGAGCTTTGGCGCAGCAGTGAGGTTAAT[T/C]TGGGTAGCCATTTGCCTGGGATGGTCCTTGCAATCTGAGGTCCATAAGTTATGAAAAATTGTTAATACGGAAGACTCAATAGTCA
78212 T C ACTGTTAGAGAGCTCGGAGGCGAGCTTTGGCGCAGCAGTGAGGTTAATTTGGGTAGCCATTTGCCTGGGATGGTCCTTGCAATCTGAGGTCCATAAGTTA[T/C]GAAAAATTGTTAATACGGAAGACTCAATAGTCAATATACTTTGTCTTTTTTGCATTGATATGATGAATAATACGTTTCATTGCTGCCA
78212 A G AGAGAGCTCGGAGGCGAGCTTTGGCGCAGCAGTGAGGTTAATTTGGGTAGCCATTTGCCTGGGATGGTCCTTGCAATCTGAGGTCCATAAGTTATGAAAA[A/G]TTGTTAATACGGAAGACTCAATAGTCAATATACTTTGTCTTTTTTGCATTGATATGATGAATAATACGTTTCATTGCTGCCACTTGC
78212 A G TTGGCGCAGCAGTGAGGTTAATTTGGGTAGCCATTTGCCTGGGATGGTCCTTGCAATCTGAGGTCCATAAGTTATGAAAAATTGTTAATACGGAAGACTC[A/G]ATAGTCAATATACTTTGTCTTTTTTGCATTGATATGATGAATAATACGTTTCATTGCTGCCACTTGCTATGTGTATGCGTAAGTGATG
78212 A G GGGATGGTCCTTGCAATCTGAGGTCCATAAGTTATGAAAAATTGTTAATACGGAAGACTCAATAGTCAATATACTTTGTCTTTTTTGCATTGATATGATG[A/G]ATAATACGTTTCATTGCTGCCACTTGCTATGTGTATGCGTAAGTGATGTGGACGTAGACTGCAAAAGTTGAATAATATAAGCTTTCGA
78242 A G CCCCGCCGTTGGTCCTGGCACCGTCCGTGGAGCCGGCGATGGATATGTGGGTCCTGGAGGAGAGGCGGCTGTACTTTCGGAAGAGGCT[A/G]AACAGAGGGCACCTAGGTTTAAGAATACCCACACTTCTTGCTGTTATTTGTCCCAATTTGCTTATAATATCATCTGTTTTGCTTTGGGATCCCGTTTGG
78242 C G CCCCGCCGTTGGTCCTGGCACCGTCCGTGGAGCCGGCGATGGATATGTGGGTCCTGGAGGAGAGGCGGCTGTACTTTCGGAAGAGGCTAAACAGAGGGCA[C/G]CTAGGTTTAAGAATACCCACACTTCTTGCTGTTATTTGTCCCAATTTGCTTATAATATCATCTGTTTTGCTTTGGGATCCCGTTTGG
78242 T G CCGTGGAGCCGGCGATGGATATGTGGGTCCTGGAGGAGAGGCGGCTGTACTTTCGGAAGAGGCTAAACAGAGGGCACCTAGGTTTAAGAATACCCACACT[T/G]CTTGCTGTTATTTGTCCCAATTTGCTTATAATATCATCTGTTTTGCTTTGGGATCCCGTTTGGAAATGATTATCTGCTTCTTCTTCTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
78242 C T CACCTAGGTTTAAGAATACCCACACTTCTTGCTGTTATTTGTCCCAATTTGCTTATAATATCATCTGTTTTGCTTTGGGATCCCGTTTGGAAATGATTAT[C/T]TGCTTCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCAC
78242 T C ACTTCTTGCTGTTATTTGTCCCAATTTGCTTATAATATCATCTGTTTTGCTTTGGGATCCCGTTTGGAAATGATTATCTGCTTCTTCTTCTTTTAAGTTT[T/C]TTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAATTCGCCAGGTACGTGCAG
78242 C T TTTTGCTTTGGGATCCCGTTTGGAAATGATTATCTGCTTCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAG[C/T]ATGCTTATATTCTGGGAGTGTTCACAAAATTCGCCAGGTACGTGCAGTCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAA
78242 T G GGAAATGATTATCTGCTTCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTG[T/G]TCACAAAATTCGCCAGGTACGTGCAGTCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGC
78242 T C ATCTGCTTCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAAT[T/C]CGCCAGGTACGTGCAGTCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGCAGTGCAAAACT
78242 A C CTTCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAATTCGCC[A/C]GGTACGTGCAGTCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGCAGTGCAAAACTTTGAA
78242 G A TCTTCTTCTTTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAATTCGCCAG[G/A]TACGTGCAGTCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGCAGTGCAAAACTTTGAATT
78242 G A TTTAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAATTCGCCAGGTACGTGCA[G/A]TCTTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGCAGTGCAAAACTTTGAATT
78242 C T TAAGTTTTTTGAATTTACAAGTGCAATAATTGCAAGATCTGATGAGAACAGCATGCTTATATTCTGGGAGTGTTCACAAAATTCGCCAGGTACGTGCAGT[C/T]TTTTCAGAATCGCGCAAAATGCAGTCTTATTATAAGCTCAAATTACTCTGTTCGGATCGGCAGTGCAAAACTTTGAATT
78250 T C ACGTCTCCTGCTTGATCGACACCTGAAATTTCTTCCCGTGGGACCTCGCCGTCTTCGTGCTTTTGCCGTTGAACGCTTCGCCCTTGTGTATGGCCTTCAG[T/C]TTCTGCTTCAGCAGCTCGATCTGCTCTTCTATTAGGTTGCATTTCTTGTACAGGTCGATTAGAAGGTTGTCCAGCGACTCTTGCGCTTGC
78250 T G TCTTCCCGTGGGACCTCGCCGTCTTCGTGCTTTTGCCGTTGAACGCTTCGCCCTTGTGTATGGCCTTCAGTTTCTGCTTCAGCAGCTCGATCTGCTCTTC[T/G]ATTAGGTTGCATTTCTTGTACAGGTCGATTAGAAGGTTGTCCAGCGACTCTTGCGCTTGCTTCGAGCATAGGTGCCGGAACGATTTTAT
78250 C T CTATTAGGTTGCATTTCTTGTACAGGTCGATTAGAAGGTTGTCCAGCGACTCTTGCGCTTGCTTCGAGCATAGGTGCCGGAACGATTTTATTGCTTCGAT[C/T]GCTTCTTCCGATCTGTTTTGCTGTTTCAGTACCACCGACATGTCCTTCAGGGCGCTGTCTACTCTGTCCTTGGAGTTTATCGCTTTACAG
78280 A T AATTTATACCATCTTTTCCATCCAACCCCCTCAGTTCTTGTGCTCAGTCCTGAGTTCTCGCATTTTAAATGGCCACCGCTGTCCCAACTGTAGGAGC[A/T]GTTAACCGAGTTTTGTTGAAACAGGGGACAAGCCTGGGAGCTTCAGTACCAAGCTCTGCATTCTATGGAAGCAGCTTAAAGAAGTCTAACCT
78280 C T CAGTTCTTGTGCTCAGTCCTGAGTTCTCGCATTTTAAATGGCCACCGCTGTCCCAACTGTAGGAGCAGTTAACCGAGTTTTGTTGAAACAGGGGACAAGC[C/T]TGGGAGCTTCAGTACCAAGCTCTGCATTCTATGGAAGCAGCTTAAAGAAGTCTAACCTCAACACAAACCATGGCAGAATCTTAACAG
78280 A G ATGGCAGAATCTTAACAGGAAGCTTCAAAGTCATGGCTGCAGATCTGGACGAGACAAAGCAAACCAAAGCAGACAGATGGGCAGGCCTGGGTACAGACAT[A/G]TCCGATGATCAGCAAGATATCACCAGAGGAAAGGGTTTGGTTGATTCCCTCTTCCAAGCTCCAAGTGGCGATGGAACCCACATT
78304 G A TCTTGTCAAAGTCTTTTGATGTACCCACAATCTTGCAGCCAAGAGAGCAGAAGCGAAAGGAATCGAGGAGGCTGCGTTCGCAGAC[G/A]TGACAAGTATTGGTAACTCCTTTGCCTGGCCTTTGCTGAGGACGTTCGTTGAGGAAGACTATTCGTGCACTGTTGATGATGTAGGTTTGAACTCCACTAA
78306 C T CTTTAACCAACATCACCCTTTCTCTGCTTACCAATTTGTAATCGTTGCTTAATATGTTCCTTCCGAAATCGGAGCTGCCTACCGACATGCGCGCCACTGA[C/T]TCCGCTACCTCGTTCGCCCTAATCACGCTCGGCCCTAGCTCTGGCACATCACACCCTCCAATCGAGCAAAGCTCGATGTCCTTGACTGTT
78318 A T TGTTTCATACCAAGGACAGAATTATCCGATAAAGAAGGATCTGCAATGTGAGACAGACAAATTAACACACGTCTACACATTTATACTTAGGCCTGATGCC[A/T]CATACAGTTTGCTAGTCGATAACCGGGAAAGAGAATCTGGAAGCTTGTACACTGATTGGGACATTCTTCCACCACGAAAAATCAAAG
78324 C T CCAAATGCTTAGGAAGCACATAGACCTTCTTCTCATACTTCCCGCTCGCCTTCTCATTCCAGAGCTCCAGCTGCGCAATCACCTGATTCGTGAACGAGCA[C/T]GACATGACAAAGCTAGGGTGCCCAGTAGCACATCCGAGGTTCATCAGCCTCCCCTCAGCGAGGATGATGACACCGGACTTGGTGTCG
78324 G A CAGCGAGGATGATGACACCGGACTTGGTGTCGGGGAACACCCATCTATCGGTCTGGGGCTTGATGGTGATCCTCTTGACACCAGGGAAGGTCTCGAGGCC[G/A]TTCATGTCAATCTCGTTGTCGAAGTGGCCGATGTTGCAGACGATGGCGTTGTTCTTCATCTTCCT
78328 T C TCCTTATTTGCTGCAGATGCCTCTAACTGGGATCTCGTATACATGTCCTGGGTTGATTTTGATCTGGATACATGTCCACTTCCATTTCCACATCTGAAAT[T/C]CCCTACTGATTGATTCCGTCTTAGATCAGGTGGAGACGACTGGACGTCCTCATCCCAGTTAGCCCAATCTCCATTATTCCTCGAGGAATT
78340 T C CGATGACGTAGGTTTTAGGGTTTGCAGCAGCTTCGATTTGGGATGAGCGCTTCCGTAGCAACGAGCGGCTTTGATCTGAAAAGGCAACAACTTGCGGAAG[T/C]GGCGGAGCAACGACTTCGATACCCGATTTGATTCAATCGAAGGACCATTCACTCGATTTCAGGGGCTAGGGTTCCGGAGTAAATT
78340 C T AAGTGGCGGAGCAACGACTTCGATACCCGATTTGATTCAATCGAAGGACCATTCACTCGATTTCAGGGGCTAGGGTTCCGGAGTAAATTAGAGGGATGGT[C/T]TCCGATGGCAGCGGCAATAGATTTGGGAAGGACGGGTTTCCGGATTTGGGGGATGAAATGATTTATCTGCTGAGGAAGGAAAAG
78342 T C CGGCGAAAACATCCAAGCCGTCCATGTTATCCATGATCTGAAAGTAGGTATCATCCATGGACGAACTTTGATGGTCGGGAGAAGGATGAAGAACCCGGCT[T/C]GATTCTTTGTACTCTCTTTGTTCTTTCTGATGCTTGGCCTTGAGCCATCTAAGCTCCTGCCTAATCTCATTCTCGGACTCATCGGATA
78342 C T GAGAAGGATGAAGAACCCGGCTTGATTCTTTGTACTCTCTTTGTTCTTTCTGATGCTTGGCCTTGAGCCATCTAAGCTCCTGCCTAATCTCATTCTCGGA[C/T]TCATCGGATAGGTTCATCCAGTAATATTCAGGTACATCGAAGCTGATATTGAGGTCTCCCATGGACTTGCCCATTCGGGCACGGCGCGC
78342 A G TCTGATGCTTGGCCTTGAGCCATCTAAGCTCCTGCCTAATCTCATTCTCGGACTCATCGGATAGGTTCATCCAGTAATATTCAGGTACATCGAAGCTGAT[A/G]TTGAGGTCTCCCATGGACTTGCCCATTCGGGCACGGCGCGCATTGTTGATCTGCTTTAGTTTGTCGTCGTTTTCGAAGTCTTC
78404 G A CCTTATCACACAAATGGGTGGGGCCGCATGCGTACTTCGAAAGTATGGAGATCATGAGAAACAGGGAAGGTCAGCAAGCGGAGGCTGCACCATC[G/A]TCCTCCATTCGCAGTGCATGTAATTTGGACAATGCAGATAAAGCCGTCCCTCCAGGGATGAGAAGTACGCGAAGCAGTAGGAATGATGAT
78442 C T GATTAATCCCGGTCCCAGTAATCGGAATCGTAGCCAAGTGCACCATAAACACGGCGAAACCAATCGGCAGCGGCGCCAGCACAGGCACATGCGAATCCCG[C/T]GCATTCCGCTTCGGGTCAGTAGCGGAAAACACCGTATAAACCAAAACAAACGTCCCGACAACCTCCGCGGCAAGCCCGGTCAAGG
78442 A G ATCGTAGCCAAGTGCACCATAAACACGGCGAAACCAATCGGCAGCGGCGCCAGCACAGGCACATGCGAATCCCGCGCATTCCGCTTCGGGTCAGTAGCGG[A/G]AAACACCGTATAAACCAAAACAAACGTCCCGACAACCTCCGCGGCAAGCCCGGTCAAGGTAGAGTACCCATCGTTCAGCCCGTTA
78450 T C CCATCTCCACCCTCCATTCCGTCGCCTCCCTCTCCACCTCCAGATCCCGCGTCGCTTCCATCGTCGCCGCTGATTTACGATCTAAAGCTGCAGAGTACCG[T/C]GCTCAGGCCGCCAGGGTTAAGGAGATTCTAGATGCGATCGGGTTGGGGTTCGATAAACTGTCGCCTAATGCCGTTGACTGTGTTAAGG
78462 A T GTGTTGGTGCCGTTAACAGGGTGCTCACAAAGATGGAAGGAGTGGAGTCATACAATGTGGACATCGAACAGCAAAAAGTGACGGTGAAAGGTAATGTGAC[A/T]CCTGAAGCGGTTTTTCAGACAGTCTCGAAAACCGGAAGAAAACTGCCTTCTGGGAAGATGCTGCAGTAGCTCCTGCTGTAGAAG
78462 G GA GAAGGAGTGGAGTCATACAATGTGGACATCGAACAGCAAAAAGTGACGGTGAAAGGTAATGTGACACCTGAAGCGGTTTTTCAGACAGTCTCGAAAACCG[G/GA]AAGAAAACTGCCTTCTGGGAAGATGCTGCAGTAGCTCCTGCTGTAGAAGAAGCATCGCCTGCTGCAGAAGCTCCTGCTGTAGA
78482 G A CTCCTCGGTATTTAAATACTTATCCCGCGATACCTTAGGGCCATGAATGAGGAGAGCAAGATCCTTGGTCATTTTTCCTGATTCCACGGTTCCTACGCAG[G/A]CAGCTTCGAGCTTCTGAGTGAAATCTAGGAGTCTACCATTCTTGTCTAGCTTTGCCCTGTGAGCAAGCCCACGTGACCAGGCAAAAAT
78486 G GT TGGCCTTTTTTTTTTTAATGGCCGCGATTATAAGCAAGTTTATGGAAAGAACGTAATAATTTTAAGAGGATGACATACAGTGCAATGCTACTAGCATTTT[G/GT]ATCAAATTATTTGAAGCACCTCGGTTCAAAATAAATTAAAAACCAAATACTGGAATTAGACAGCTTATAGCTCATCATCTGGATTTAA
78486 T C AAAAACCAAATACTGGAATTAGACAGCTTATAGCTCATCATCTGGATTTAAGCTCGAGTTTTCAATGTTGGGAACTACAGTTCCAAAATAGACCTTTTTA[T/C]GCTGAGGAATTAGACCGATTGCAAAACTTTCTTCTTTTGATAACTCAAAGTCGAATATTTCAAAGTTTGTCTTCAGCCTTTCCTTGTTGA
78508 C T GGGGATATTGTGTTTGTACTACAACAAAAGGAACATCCCAAATATAAGAGGAAAGGAGATGATCTGTTTTACGAGCA[C/T]TCACTGTCACTCGTTGAGGCTCTTTGTGGCTTCCAGTTTGTTTTGACCCATTTGGATGGCAGGCAACTCCTTATTAAATCTGAACCTGGAGAGGTCATTA
78516 C T GCCGCATGACCTCTAGAACTGCTTCCCAAGACGGCCCTACAGCAGCAACAGCCCTTAATCCAAAGGCAGGAGAAACACTGCTAAGAAGGCGTGACTTGGA[C/T]ATGATTTTCATGGATTTAGTGGCCGGTAACACTCAGCTTAAACAGCAAGCAGCCGGAAGGTTCCGTGAACTGACCGGACTGGACG
78542 A G GTACTTCACAGATTAACAGCAAATCAACTGGAAGCGTAAGCAAGGAATCACTTACAAAGTGAATATTTCCATACAATAATTGATAGCAATAGTAATAGTA[A/G]TTGTATGTGAGCCTAAGAGGTAATGAATCTATCGGTAAATAAATTTAGGAGATGACCATGATCAATTTATTCTTTAGTTTTAGGCAAA
78542 G T AAGGCCTAGATTGCTAATATGCACTAAATGACTTGAAATATCTTTGTGATAGGATTTTTGCCTTTTTATAATTACTGTTTTTACCTTCTTCTAGCACTGT[G/T]TCAATTAACATGTGTTGAACGTGCCACTCATATTCTGTATAAATTACAGGGTCTGTGAAAGGAAGTATC
78548 A G TCAGCCTGATGGGACGATGGCTTATAACGTGGGGCTTAATCAAGCCATGAGTCAGTCAAGTGTTTCTGCTTCTTCCCTTATTTTCTCTGCTGCTAATGAG[A/G]GAAACAATGCAGCAAAGCTTAGAAACATATTCTACAGGATTTTCTTAGTTTTCTTGCTTTT
78576 A T CACAACGAACTGGAAATATGATAAGCAACCTGTAGAGATCTCACTTGTTTCACTTAACACACATAAACAAGCGAAATAACTATTATTCTCAGACACTTTG[A/T]AGTAGAGATGATAACCAAATAGACATAGCAACACTAGGGATAAAATAGCTATGTGGAGAGGTGTTCTTAGTGCTTGACGTCAGGCAA
78586 A G GTTGGCCTACTGGATTAAAAAAAGTTCTTATTCCCACTAACCTTCTGATGCCAACATGGCCGCCGCCTCTTCTTCCTTCTCCGTGCTCC[A/G]TCTGTCATCTGTCCCTTCTTCCGGAGACCACCACCACAAACTTCGCCTTCCCATTCTACCCGCCCTTTTTCCAAAAATTCCTTCACTCCCCCTTCACCTC
78586 A G AAAAGTTCTTATTCCCACTAACCTTCTGATGCCAACATGGCCGCCGCCTCTTCTTCCTTCTCCGTGCTCCATCTGTCATCTGTCCCTTCTTCCGGAGACC[A/G]CCACCACAAACTTCGCCTTCCCATTCTACCCGCCCTTTTTCCAAAAATTCCTTCACTCCCCCTTCACCTCCGCTCCCAAAGCCCCAACCTCTC
78586 G A TTCACTCCCCCTTCACCTCCGCTCCCAAAGCCCCAACCTCTCCGAACCCATCCTCTCCGATTCTGGCTCTGACGTCCACAGTAACAGCGGATCTGGATCC[G/A]GCTCCAACAATGGAAAAGGAGGCGGCGGAAATGGTGGCGATAAGGGAGATCCCTCTGGCGACAACTCTGACAGTGGCTCTCCAGTA
78592 G A ATCTTCACCAACCCCATCACCACCACCACCACCAGTCTAGGCATGATTGATCTGGGATTAAATAGCTCTGCACCCTAACTGATACGATCATTGTTCTTAG[G/A]GTTTTATTTTGTTTTTCTTTGTTATTATCTTGATTAATGGCAGGTGCTGAAGTTTCGGTATGTGTGGATACTAGGTGATGTTTAGCTTCCA
78610 T C TGTCTCTTTCAGCTTGTAGTTTGAATACAATGTCTACTTGCAGCACTGTCTCGAGAAATATTTTATTGGGTGCAAAGCGTCTTGATATTTCCACTCGAAT[T/C]AGTAATCCGATTATTAATAATGCTATTGTATCAAACTATGGATACCTGAAGAATGCTTATAGTGGAAGAGTATGTGCAAGGTTAAACAG
78610 G A TCTCGAGAAATATTTTATTGGGTGCAAAGCGTCTTGATATTTCCACTCGAATTAGTAATCCGATTATTAATAATGCTATTGTATCAAACTATGGATACCT[G/A]AAGAATGCTTATAGTGGAAGAGTATGTGCAAGGTTAAACAGTCGAAAGCCATGGGGTTCTAATATGCTGTACAAGTTTTTCTGGTCAA
78620 TG T TGTCAAAGAAGAAGATACTGGTAGATGGGTTGAAGGAAGTTGGCTTTGCGGTGTACCCTTCTAGTGGGTCGTTTTTCGTAGTGGTGGATCATACTCCGTT[TG/T]GGGTTTGGCAATGATGTCGAGTTTTGTCAGTATTTGGTGAAGGAAGTTGGTGTTGTTGCCATTCCTATGAGCGGATTTTACCT
78702 T G GGTCAGACGTCAAACCATCAAAAAGGTTTCTCATACTGGAAGTGACAACGGGATCGCTTACAGAGAAAGGGAGGAGGAGAACGGCGTCGATCGTGCCGAT[T/G]CTGGAGAACGTGAAGCCGCTCGAAATGGAAAGCATGGATCCGTACTTCGATTTCAAGAGGTCAATGATGGAGATGGTGGAAGC
78702 A T CGGCGTCGATCGTGCCGATTCTGGAGAACGTGAAGCCGCTCGAAATGGAAAGCATGGATCCGTACTTCGATTTCAAGAGGTCAATGATGGAGATGGTGGA[A/T]GCGCGGCATGTGGATGGATTTGGGATGTTGGATTGGGATTTTTTGGAGCAGATGCTGATTTATTTGTTGGAGCTGAACGATAAG
78708 T C TTCCCAAATCACCGTATTACCAATTTACCAGGGCCTCAGTTGTTTTGTTTTTGTTTTTGCCTTGGGCCACCAATCCTTCAGGGCTGGCCTTGGCTACGAC[T/C]ACAGAGCCGGTGAAAAGAACCACGCGATTCTCAGTGTTAAATCACGAACCTCCAACGAAATAGTTGCTACTGTCCATCTAGGCGGAGC
78718 A C GTTTGCAGGCTCAACAATTTCGGATTTTGTTTTCCTCGACTGCTTCAATCTCGCACAAATGTAGACCAACAGAAACCCTAGTTACTTCAGCGATCAAAAA[A/C]CCTCCATTTGTTACTTCTGCATGAGGCAGCGATGAGTTTCTGTCTGATCTGAATCTTGTTCTTGGCAGCAGTATGATTAAGTTACTTTAA
78720 G A AAGAACGTGGAGAGCGCGAAGAAGGCATTGGAGGAACCGCATAAGAATTTTGATGGGTGTATTTTGCATTGTTC[G/A]AAGGCAGTGGATGGGCCAAAGGGGAACAAGCCAGGTGCTTTTGGTGGAGGGCATATGATGACGCCTACAGCAGGACAGATGGCTCCTCCCGTAGGGCAGG
78720 A G TTGATGGGTGTATTTTGCATTGTTCGAAGGCAGTGGATGGGCCAAAGGGGAACAAGCCAGGTGCTTTTGGTGGAGGGCATATGATGACGCCTACAGCAGG[A/G]CAGATGGCTCCTCCCGTAGGGCAGGTTCCTACCGCACAAGGGTTGAATCCAGTGCTTGGACAGGCACTGACTGCCCTTTTAGCA
78720 C T TGGTGGAGGGCATATGATGACGCCTACAGCAGGACAGATGGCTCCTCCCGTAGGGCAGGTTCCTACCGCACAAGGGTTGAATCCAGTGCTTGGACAGGCA[C/T]TGACTGCCCTTTTAGCAACCCAAGGGGTTGGAGGCTTGACAAATATTTTGGCATCAGCCAATCAGGGAATGACACCCGGAATGC
78720 C T CGCCTACAGCAGGACAGATGGCTCCTCCCGTAGGGCAGGTTCCTACCGCACAAGGGTTGAATCCAGTGCTTGGACAGGCACTGACTGCCCTTTTAGCAAC[C/T]CAAGGGGTTGGAGGCTTGACAAATATTTTGGCATCAGCCAATCAGGGAATGACACCCGGAATGCAGGGCGGTTATGGAAGTGGT
78720 C T CCCTTTTAGCAACCCAAGGGGTTGGAGGCTTGACAAATATTTTGGCATCAGCCAATCAGGGAATGACACCCGGAATGCAGGGCGGTTATGGAAGTGGTCG[C/T]CCGTGGCAGGGAGGGGCACAAGGTGGGTATCAAGGAGGCGTGGGTCGCGGGCAGCAAGGGTATGGTGGTGGACCGTC
78742 T C CAAAGGATTCTCGATCTTCCAGCCATGGCGTACGTTGAAAACGGTGCTATCAAAGGAAAGCGATCAATATGGAGGCTTAGTACCAT[T/C]GTCCATTTCATCAAGTCCATTATCAACTTCATTTCAGTTTTTGTTCTTACCATGTTCTCGATGGATAAGACAAACGAGTACAAGAAAAGGTCCGGCTCCT
78742 A T CAAAGGATTCTCGATCTTCCAGCCATGGCGTACGTTGAAAACGGTGCTATCAAAGGAAAGCGATCAATATGGAGGCTTAGTACCATTGTCCATTTC[A/T]TCAAGTCCATTATCAACTTCATTTCAGTTTTTGTTCTTACCATGTTCTCGATGGATAAGACAAACGAGTACAAGAAAAGGTCCGGCTCCTCG
78742 A C GTACAAGAAAAGGTCCGGCTCCTCGAAAAAGTGGGATGGTGGGCCAAGTGGTGGGGGACCAGGTGGCCCATCTGGTGGAGGTGGTGGCCCACGAGGGCCT[A/C]GGTTTATGTCTGACATCCGCTCTAATGACCATAGTTCACTTCCTGCATGTGGATCCTGCTGTGGTTAATACTACTATGACGACCA
78746 G T AATAACCGTTAACTGTAAGATTCTTATTTCTCTATGGAGTTTGAAAATGTCTGTTCATGGGGCTAGGCTGAAACTGTGAAAAATAATGCCTTCCCCTTGT[G/T]ACTGTTAACTGTAAAATTCCTATTTCTCTATGGAGTTTGTTACTACAAAAAAAAAAGGCCACA
78762 G A TTACATATTTTCTGGGACTGAAGTATTCATCTCCAACAATTGCTTGTGCCTTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAG[G/A]ATGGAAACGGTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATAGCTGGAACAGTGCTAGGAATAGGAGGGTCGATGCTGATGAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
78762 G T TTCTGGGACTGAAGTATTCATCTCCAACAATTGCTTGTGCCTTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAGGATGGAAAC[G/T]GTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATAGCTGGAACAGTGCTAGGAATAGGAGGGTCGATGCTGATGACGTTCTACAA
78762 G A TGCCTTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAGGATGGAAACGGTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATA[G/A]CTGGAACAGTGCTAGGAATAGGAGGGTCGATGCTGATGACGTTCTACAAGGGGTCGTTGGTGCGCATATGGCCGTCACACATCCA
78762 C T GCCTTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAGGATGGAAACGGTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATAG[C/T]TGGAACAGTGCTAGGAATAGGAGGGTCGATGCTGATGACGTTCTACAAGGGGTCGTTGGTGCGCATATGGCCGTCACACATCCAC
78762 T G CCTTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAGGATGGAAACGGTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATAGC[T/G]GGAACAGTGCTAGGAATAGGAGGGTCGATGCTGATGACGTTCTACAAGGGGTCGTTGGTGCGCATATGGCCGTCACACATCCACT
78762 G GGAA TTGAACAACTTGTTGCCTGCTATCACATTCATTATGGCTGTCCCCTTTAGGATGGAAACGGTGGGAGTGAAAACGGCATCAGGGACAGCAAAGATAGCTG[G/GGAA]AACAGTGCTAGGAATAGGAGGGTCGATGCTGATGACGTTCTACAAGGGGTCGTTGGTGCGCATATGGCCGTCACACATCCA
78766 T C CAGTTCCGGCATGCCCTTGTCCCTGAATGGGCTGACCATACTCATCGGTCTTCTGATGCCCAGGCAGCTTCTCCTTTATCTTCTGCTTCAGCCCCTTCTT[T/C]CTCCTCCCTCCCATTCCATCATCCTCCGAAGAGCTGGAACTGGAGCTGCCGGAGCGATGCAGGATGCCACCACCCTTCTGCTGGTGCTG
78860 T C GGGGCGTGTGTTAAATCAGGTATTCCCACCTTCGCCCTGGTGAGAGAGCTTGCACCTCAGGA[T/C]CCTGCCAAGGCCAAACTTGTACAAGATTTTTCCAGCTCTGGAGTTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGC
78860 T A GGGGCGTGTGTTAAATCAGGTATTCCCACCTTCGCCCTGGTGAGAGAGCTTGCACCTCAGGATCCTGCCAAGGCCAAACTTGTACAAGA[T/A]TTTTCCAGCTCTGGAGTTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGCAAGTTGATGTTGTGATATCAACTGT
78860 T C CCAAACTTGTACAAGATTTTTCCAGCTCTGGAGTTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGCAAGTTGATGT[T/C]GTGATATCAACTGTTGGAAACATGCAGCTGGCCGATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATT
78860 A G ACAAGATTTTTCCAGCTCTGGAGTTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGCAAGTTGATGTTGTGATATCA[A/G]CTGTTGGAAACATGCAGCTGGCCGATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCG
78860 A G TCCAGCTCTGGAGTTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGCAAGTTGATGTTGTGATATCAACTGTTGGAA[A/G]CATGCAGCTGGCCGATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCGAGTTCGGAC
78860 C T TTACTCTTCTCAAGGGAGACTTGTACGATCATGAAAGCTTGGTAAACGCAGTGAAGCAAGTTGATGTTGTGATATCAACTGTTGGAAACATGCAGCTGGC[C/T]GATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCGAGTTCGGACTTGACGTGGATCG
78860 T C AAGTTGATGTTGTGATATCAACTGTTGGAAACATGCAGCTGGCCGATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCT[T/C]CCATCCGAGTTCGGACTTGACGTGGATCGAGCACATACGGTTGAACCGGCAACCTCGGCCTTTGCCACCAAAGCTCAAATAAGAAG
78860 C T ATGTTGTGATATCAACTGTTGGAAACATGCAGCTGGCCGATCAAACTAAGATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATC[C/T]GAGTTCGGACTTGACGTGGATCGAGCACATACGGTTGAACCGGCAACCTCGGCCTTTGCCACCAAAGCTCAAATAAGAAGAGAGAT
78860 C T ATCATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCGAGTTCGGACTTGACGTGGATCGAGCACATACGGTTGAACCGGCAACCT[C/T]GGCCTTTGCCACCAAAGCTCAAATAAGAAGAGAGATAGAGAAAGAAGGAATCCCTTATACGATTGTGTCTGCCAACTACTTTGC
78860 G A CATTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCGAGTTCGGACTTGACGTGGATCGAGCACATACGGTTGAACCGGCAACCTCG[G/A]CCTTTGCCACCAAAGCTCAAATAAGAAGAGAGATAGAGAAAGAAGGAATCCCTTATACGATTGTGTCTGCCAACTACTTTGC
78860 C A TTGCAGCAATCAAAGAAGCTGGAAACGTCAAGAGATTCCTTCCATCCGAGTTCGGACTTGACGTGGATCGAGCACATACGGTTGAACCGGCAACCTCGGC[C/A]TTTGCCACCAAAGCTCAAATAAGAAGAGAGATAGAGAAAGAAGGAATCCCTTATACGATTGTGTCTGCCAACTACTTTGC
78878 C A GAAGACCTAGCGACTACAATCCTTCTCTTGCTGCAGCACTTGGTCCGAGCCAACCAAATCCAAATCTCAATCTAGCTGCAGTTGGACTGACTCCTGGTTC[C/A]GCTGGAGGTCTCGAAGGCCCTGATCGTATATTTGTAGGAGGACTGCCGTATTATTTCACTGAATCTCAAGTAAGGGAGCTGCTTGAA
78884CCTTTCAAAAATGCAAAT C GCGAGACTAACATGCATTTTATTAGGTCCGATGAGTCAAGAAGAGGGAATATGACCTTTAGGGTTTCGCCGTATGGCCAGTCCATGTTCAATGTTGATAT[CCTTTCAAAAATGCAAAT/C]CTTTCAAAAATGCAAATCTTGCTTTGGGATCATCATCGACTTAATCTTCGATTTGCAGTTTGAATGACTCTC
78888 T C CGGTAATCCATAGGGCAAGCAATTTGAGAGAAGTTCAAGGATATGCCAATTAGATGTAAGTTTATCCATATAAGGCAATGATGCCTTCAATTCCTTCAGT[T/C]TTTGTAAATTTGATAAATCACGAATTGAAGGGAAACAAGCTATAAGTTCTGACTGTAATTTGTGAAGATCAGCCTTTTTCAGCAAATC
78888 T C TGCCAATTAGATGTAAGTTTATCCATATAAGGCAATGATGCCTTCAATTCCTTCAGTTTTTGTAAATTTGATAAATCACGAATTGAAGGGAAACAAGCTA[T/C]AAGTTCTGACTGTAATTTGTGAAGATCAGCCTTTTTCAGCAAATCTTGCAAAGAGTGCAAATCTACAACTTTTGGAACTTGAGTTGCTG
78888 G A GTTTTTGTAAATTTGATAAATCACGAATTGAAGGGAAACAAGCTATAAGTTCTGACTGTAATTTGTGAAGATCAGCCTTTTTCAGCAAATCTTGCAAAGA[G/A]TGCAAATCTACAACTTTTGGAACTTGAGTTGCTGTGTATATGGTAAGAGCAAGAAAAATGAAGAAACCAATCAAGTGCGTCCAGACA
78892 A G CGATCATCCCGATCTTTAAGCCCACCCAAAGCCCAAATTGCAGTATCAATTCACAGTATATGTCTGAC[A/G]TAGCTGACGACCTTGACCTTCTCCCAATCCTAACCAAATCAACACATCTCCAAAACCCCAAATTAGATTTACCAGCACTGATCGGTCTCCCATGTTCTAC
78892 G A CGATCATCCCGATCTTTAAGCCCACCCAAAGCCCAAATTGCAGTATCAATTCACAGTATATGTCTGACATAGCT[G/A]ACGACCTTGACCTTCTCCCAATCCTAACCAAATCAACACATCTCCAAAACCCCAAATTAGATTTACCAGCACTGATCGGTCTCCCATGTTCTACGACGAG
78892 T C CCTTCTCCCAATCCTAACCAAATCAACACATCTCCAAAACCCCAAATTAGATTTACCAGCACTGATCGGTCTCCCATGTTCTACGACGAGCACCATAACT[T/C]GCAGATCTAGATCGCACATAGCTCAAACGCCCAAACGAATTTCCCCGATCGTAATCGGCTCGCTTATCCGGATCAGAAAGCGTGGAATA
78892 C T TCTCCCATGTTCTACGACGAGCACCATAACTTGCAGATCTAGATCGCACATAGCTCAAACGCCCAAACGAATTTCCCCGATCGTAATCGGCTCGCTTATC[C/T]GGATCAGAAAGCGTGGAATACGCGTCGTGTATTCTCATAAACTCATCCGCTGAAGCATCGGGTTGTTTGCAGACATCGGGATGGCAG
78892 A C ATGTTCTACGACGAGCACCATAACTTGCAGATCTAGATCGCACATAGCTCAAACGCCCAAACGAATTTCCCCGATCGTAATCGGCTCGCTTATCCGGATC[A/C]GAAAGCGTGGAATACGCGTCGTGTATTCTCATAAACTCATCCGCTGAAGCATCGGGTTGTTTGCAGACATCGGGATGGCAGGAGAG
78904 C T TTGACAGTTGGGCTTGAGCATCGACGATGTCTTGTTTGTCTCGCATGACTTGAACACCGGTTTGTACCTCTCTTAAGATATTCTCAAGCTGCCTCAGCTT[C/T]CCATCAGTGCTTCCACTATTATTCCCAACAGTAGTTTTTAGCTCATCAACAGAAGTTTCAAGGTGACGTGTTACACCCTCCAGCTGTATC
78904 A G TATTATTCCCAACAGTAGTTTTTAGCTCATCAACAGAAGTTTCAAGGTGACGTGTTACACCCTCCAGCTGTATCAACCGTGAACTTAAACCTTCCAATGT[A/G]CGCAGAAGACTGTCGACGTATTTTTTCACGGTTCGGTCAACTTCATTAACTGTAGCTACATCATAAGCATCCCTTTCCATCTCATGGCTC
78908 A G GAAAAATGGCGTACTTATAGCAAGCGATAACTAGAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGC[A/G]CCGGCCTTTCCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGG
78908 A G AGCAAGCGATAACTAGAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGAT[A/G]GAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCAC
78908 G C AGCGATAACTAGAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAA[G/C]ACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACC
78908 A C GCGATAACTAGAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAAG[A/C]CTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCG
78908 G C TAACTAGAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAAGACTT[G/C]AGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGT
78908 T G GAACTACCCAATATTTTTGATAGCAAATTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAAGACTTGAGGGA[T/G]CCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGT
78908 T A TTCCCTATCAAAGAGTTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTA[T/A]GGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCA
78908 A G TTCTGAAAACTCATTACAAAGTGGCACCGGCCTTTCCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAA[A/G]GTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTT
78908 G A ACAAAGTGGCACCGGCCTTTCCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGC[G/A]GTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGAAACGA
78908 A G AAGTGGCACCGGCCTTTCCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGT[A/G]TTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGAAACGAAGA
78908 G A CCGACGATAGAAGACTTGAGGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGA[G/A]GTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGAAACGAAGACGTTGTTCTCGACGAGG
78908 A G GGGATCCGTTGGCAATGGTGGAGTAGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAAC[A/G]GCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGAAACGAAGACGTTGTTCTCGACGAGGAGCTGAGCACCAACACGGG
78908 G T AGGAGTATGGGACGGAGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGAT[G/T]GGCTTGCCGACGGAAACGAAGACGTTGTTCTCGACGAGGAGCTGAGCACCAACACGGGTGTTGATTCCGTCATTGCAGCTCTC
78908 A G AGGTCAAAGTACCAGCGGGGGCGGTATTGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGA[A/G]ACGAAGACGTTGTTCTCGACGAGGAGCTGAGCACCAACACGGGTGTTGATTCCGTCATTGCAGCTCTCGAAGTAGTTGTTAACG
78908 C T TGGCTCCACCACCGAGGTCGTTGTTGCGGGCAACAGCGTATCCGTTATCAGCGAAGATGGGCTTGCCGACGGAAACGAAGACGTTGTTCTCGACGAGGAG[C/T]TGAGCACCAACACGGGTGTTGATTCCGTCATTGCAGCTCTCGAAGTAGTTGTTAACGACGTGACCGGTACCGAAGCGGAAGGAT
78912 G GA GACAGAAGGAAGAGGCAGTGACCCATTCCTTGCTTGCGTCGGGTAGAAGGGAAAGAATCAAATTTGATTTGGGAAATTTGATTGTTATCGGCTTTTAAAG[G/GA]AAAAAAGGAACAACAGACGAAGTTCATTAAAGTGAAGAGGGTTGATTCAATTTTTTGGGAAAAAGGAACAAAATTTGGGGTTTC
78926 A G CACCTCCCTCACGGCGCTGACCTCCACCAAAACCGCCACCGCCTCCGCCGCCTCCTCCACGAGACTGAGCTTCGTTCACGGTGATATTCCTACCATCAAG[A/G]TCCTGACCATTCATCCCTTCGATAGCATCACGCATCGACTGCTCGGAGCTGAAGGTAACGAATCCGAAACCCCTGGATCTTCCAGTCT
78926 C T CTCCGCCGCCTCCTCCACGAGACTGAGCTTCGTTCACGGTGATATTCCTACCATCAAGATCCTGACCATTCATCCCTTCGATAGCATCACGCATCGACTG[C/T]TCGGAGCTGAAGGTAACGAATCCGAAACCCCTGGATCTTCCAGTCTCGCGATCGTTGATGATCTTGGAATCAACGACTTCTCCAAACTG
78994 T C GCTTGAAAGTTCAATGGCGAAAAGATCCACTCCTTGACTCTGCCATCGACTCCGACAAGCGCTACCACCTCATCTCCCGCGTCGTGCGCGAAGTGCTCAA[T/C]GAACCTGGCCACGTCATTCCCTTACGCTATCTCGAGAACCGCCGGGCCAGGCTCAAGCTCTACGTTAAGGCGAAAACCTTTATCTCCC
78996 A C TGCACTCCGTAAAGGAGATCCCACCCATCAGCTTCCTTGCACCTTCCGAGTTTTCACACCCCATCGATTTGCATGCATGTCAGACTCCTTGGTCCGTGTT[A/C]CAAGACGGGTCGAATGGGGAGCCCGCTAGACGGTGCTATGAGCGCACAAGAGCGCCACAAAGGACGCGCCATTGAGGCGTGCACTG
79004 T TAGA GCTAGGATCCACCGTAGGACCTTAATTGCATGAATCATTTATGCAATCCAATACCCATACAGCTTTTGCCCTTTCTTGTA[T/TAGA]AGAAGTACCCCTCAGCCTATCGCGGTAGAAGAAGAGGGATGATGGACGCCAAACTGTCGATGATGCATCGTAGTTAACCATCTCCGATGGGCAGAGAAGA
79010 T C TCTACTTTTTACATGGATCAACAAGGGGTTTTTGCCGACAGGATAGATGGGCATTGACATTTTAACTATGTCCCTCCACGTCTTGCGCACGCATGCCAAC[T/C]TCTTCTGATCCTCGTGTTGCAGCTTCGGTAATATCAATTCTATCACATCAGTAGGTAGGTCTGACCATGAGAATT
79014 A G TTTGAAAATTCAAATACACTCGATTTATTACAGCAGTAAAACAATTCTGTTACAGGCTACAACAAGCCCCACTCACATAAACAAAATTAC[A/G]CTTGAGATAAATCACCAGCTTCCAAAAAATCGAAAGAAACATAAACCACATCCAGAGGAAATTTTGAATAGAAGGTCCAAGCTTGTTATTTTGACCTTT
79014 T A ACATAAACAAAATTACACTTGAGATAAATCACCAGCTTCCAAAAAATCGAAAGAAACATAAACCACATCCAGAGGAAATTTTGAATAGAAGGTCCAAGCT[T/A]GTTATTTTGACCTTTTTAACAAATATAGTAAAAATTTCCTTTGAAAAAGGTACGTACTTGAGTTTAATTGACAACATCAACAACCAACT
79014 G A AAATTACACTTGAGATAAATCACCAGCTTCCAAAAAATCGAAAGAAACATAAACCACATCCAGAGGAAATTTTGAATAGAAGGTCCAAGCTTGTTATTTT[G/A]ACCTTTTTAACAAATATAGTAAAAATTTCCTTTGAAAAAGGTACGTACTTGAGTTTAATTGACAACATCAACAACCAACTTTCTTGATTT
79016 G A CACCAACACCAAAAATGGAAAGAAGCAGTGTAATCCTGCTCGTGGCCGCTATCATAGCGATATTCAGCA[G/A]CACGGCCCAAGCCCAAAACAGCCCGCAGGACTACGTAAACGCACACAACGATGCCCGTGCAGCGGTAGGTGTGGGGCCCGTATCCTGGGACACTAGACTG
79016 C T CACCAACACCAAAAATGGAAAGAAGCAGTGTAATCCTGCTCGTGGCCGCTATCATAGCGATATTCAGCAG[C/T]ACGGCCCAAGCCCAAAACAGCCCGCAGGACTACGTAAACGCACACAACGATGCCCGTGCAGCGGTAGGTGTGGGGCCCGTATCCTGGGACACTAGACTGG
79016 A G CACCAACACCAAAAATGGAAAGAAGCAGTGTAATCCTGCTCGTGGCCGCTATCATAGCGATATTCAGCAGC[A/G]CGGCCCAAGCCCAAAACAGCCCGCAGGACTACGTAAACGCACACAACGATGCCCGTGCAGCGGTAGGTGTGGGGCCCGTATCCTGGGACACTAGACTGGC
79024 T TTCCTTGATGA GATAGATACCGCTGAAAATAGTTAAACGGTTGCGAGTGACGATGAAGCCAATCGATGTTATGGATTGACGAAATCAAGTCACGATGTAGCGAAATCATGT[T/TTCCTTGATGA]TCGAGAGATTCATGAATAGGTTAGAGCTTCGGAAATGAGATGGGATTAAAGCCGGATTCAAGAACGAGATTCGGA
79038 T C AATCCAAGCTCTTGGCTGAACCTGACTCTCGGCCTAAACAGTGATGTTCAGTCTCTCACAAGCTCTTCTAGCTC[T/C]CAGTCCGGACCGACCACTCACAAAGTTTTCTCGTGCAACTTCTGCATGAGGAAGTTCTTCAGCTCGCAGGCGCTGGGAGGCCATCAAAATGCACATAAAC
79082 G A CATAAACCAGAAAACCGAATAAGTCCCGTAGACTTCCTTGACACAGAGCTTCAAGTCCCAGTGATCAATCTTGAAGGAATCGAAAACCCAA[G/A]CATACGCAAAAAGGTGATACAAGAAGTGTACAATGCTTCGAATAAATGGGGCTTTTTTCAGGTAACAAACCATGGGATACCGTCGAGGGTACTTG
79094 T G CAATGCAGTTTTGCACACGGTGAGAGCGAGTTGCGCAAATCTAATGTTTAGAGTGTGCTTGACTGGTTTTGTTGCAGTTTAGTATCTTTTTTCCTTGTTT[T/G]GGGTATTGCATTTCTAATAGTACTTAAGCTATGAAGTTTAGAGTGCAGACTCTGCTTTGATTCTGCATTTTGTTGTTGTAGCGTTTTATT
79094 T C CTTGACTGGTTTTGTTGCAGTTTAGTATCTTTTTTCCTTGTTTTGGGTATTGCATTTCTAATAGTACTTAAGCTATGAAGTTTAGAGTGCAGACTCTGCT[T/C]TGATTCTGCATTTTGTTGTTGTAGCGTTTTATTTGATGGATTCTAATGGTGACTCCTTGAATGAATGGCTTGTTGTGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
79096 C T TATATTTTGCTTTCGACTGCGTGGTCGGCATATCGAGAATGTTTATTAATTTCCAGATCTGAACCTTTACATGCCCAAATTCTCGATTTCTCTTATCGTC[C/T]CACAATTTTCTACCTCCTTACCTTCTTCAGTAGCCCTTCAATCGTTACGCGGTGGCCTACTGGCAACTATAGGCCTCGCTCGTTATTCAACA
79142 G A TGCAAGCGCGGGTTCCTCTCGAATAGCGTCCACACTTGTTGTGATGACATGAAGTGTAGCGTGTCAGATATGACGGCGCAGGATGTGTCAACCACCGGGC[G/A]CGAGTGTGGGTTCGTTAACCCGAATCTAAGTACATCTTTAGGTTCGTGGCAATAGTTTCTAAATACATCTGTGTTGGGGCCTCTTT
79146 G C GCCAAGCCCAAAACCGCCCGCAGGACTACATAAACGCCCACAACAAGGCCCGAAAAGAAGTGGGGGTGGGACCCGTAACATGGGACAGCAGAGTTGCCGA[G/C]TACGCGCGTAACTACACCAGAAAGCGGGCCAAGGACTGCCGGCTGATCCACTCGGGTGGACCGTATGGGGAGAACCTATTCA
79146 G A CAAAACCGCCCGCAGGACTACATAAACGCCCACAACAAGGCCCGAAAAGAAGTGGGGGTGGGACCCGTAACATGGGACAGCAGAGTTGCCGAGTACGCGC[G/A]TAACTACACCAGAAAGCGGGCCAAGGACTGCCGGCTGATCCACTCGGGTGGACCGTATGGGGAGAACCTATTCACTGGGCGA
79146 C T CCCACAACAAGGCCCGAAAAGAAGTGGGGGTGGGACCCGTAACATGGGACAGCAGAGTTGCCGAGTACGCGCGTAACTACACCAGAAAGCGGGCCAAGGA[C/T]TGCCGGCTGATCCACTCGGGTGGACCGTATGGGGAGAACCTATTCACTGGGCGAGGCAAGGCCTGGTCCGGCCTGGATGCTG
79146 A G GGACAGCAGAGTTGCCGAGTACGCGCGTAACTACACCAGAAAGCGGGCCAAGGACTGCCGGCTGATCCACTCGGGTGGACCGTATGGGGAGAACCTATTC[A/G]CTGGGCGAGGCAAGGCCTGGTCCGGCCTGGATGCTGTTGCCTCGTGGGTGTCCGAGGAGCAGTATTATGACTACGAAAGCAA
79154 A C CACTGTTGGCCTACTGGCTTGTCGGGAAAAAAATAAAAATAAAAAATGGCGGCTGTAATCAACACCCATTCCTCTTCTTCAATTAT[A/C]TCTCCTTCCACTAACAGAAGCCCAACTAAGCCACTACCTACCTACCACTTAGCTTTCAGTTACGTACCCAGAACCATAACCCGACATGTCCGATCCAACG
79192 GT G AGTTTCGAGTTCGGCCCTTCGCCTGATTCTTCCCGGATTGGCCGGAAATTGATCATCTATGTTCTGAGCTCGCCGGAAATTTCTGTTTTGCTCCAATTCA[GT/G]TTTTTCTCGATTTCGGTGCCCTTCCATCGACTTTCAGACAAAACTTTCTGAAGCAAAGTTGTAGATCTTTGTCTCCTCTACAATTTCTTC
79192 A C ATCATCTATGTTCTGAGCTCGCCGGAAATTTCTGTTTTGCTCCAATTCAGTTTTTCTCGATTTCGGTGCCCTTCCATCGACTTTCAGACAAAACTTTCTG[A/C]AGCAAAGTTGTAGATCTTTGTCTCCTCTACAATTTCTTCCATTGCGCCATCCTCCAATTCTTCACGGTTTGGCCAGAAAACACCAAAATCTG
79192 T C AACTTTCTGAAGCAAAGTTGTAGATCTTTGTCTCCTCTACAATTTCTTCCATTGCGCCATCCTCCAATTCTTCACGGTTTGGCCAGAAAACACCAAAATC[T/C]GAAACTGAATTTTTGCAATCAAACTCAGATCCCGGCGAATCCGTGCGACGATAGGTCTTGAAT
79196 T C TTTGTTTCCATTGCAGCTCAACTCATGCACGCACTCGGCTTCACTTCCAGAAGCAAGTGACCAAACACGGACTGAGTCCTCACTAACTGAAGCCACTAAT[T/C]CACCAGTAGGATCCCAACAAACTGAATCAACATGTTTTGTGTGCCCCTGTAGTGAATGGCGACAAGCTTGTGTTTCCACATCGAGTAT
79216 AT A TTTTTTTACAGTTTTGGATGGTCTGACAGCAGGTTTTGCTTTCTTTTTTGCCTTGACTGGTGGTTTCTCCGATTGCCTTTT[AT/A]TTCTTTTTAGGAGCCTGCTCTCCATTTTCATTATCTGCGTCACCTTGAGGAGCTGAAGTTTTAGGTGCCTTGACACCTTCCTCATCAGAATCAAACGAGA
79216 C T CCTTGACTGGTGGTTTCTCCGATTGCCTTTTATTCTTTTTAGGAGCCTGCTCTCCATTTTCATTATCTGCGTCACCTTGAGGAGCTGAAGTTTTAGGTGC[C/T]TTGACACCTTCCTCATCAGAATCAAACGAGAATCCATCAAGAGTACCTTCAACCATAGTTTCAGCTTCATAAACATTTGACAATGGTTCCA
79216 C T TTTTATTCTTTTTAGGAGCCTGCTCTCCATTTTCATTATCTGCGTCACCTTGAGGAGCTGAAGTTTTAGGTGCCTTGACACCTTCCTCATCAGAATCAAA[C/T]GAGAATCCATCAAGAGTACCTTCAACCATAGTTTCAGCTTCATAAACATTTGACAATGGTTCCAGCTGAATGAAGTCAGTCATAACTGCC
79216 C T CCATTTTCATTATCTGCGTCACCTTGAGGAGCTGAAGTTTTAGGTGCCTTGACACCTTCCTCATCAGAATCAAACGAGAATCCATCAAGAGTACCTTCAA[C/T]CATAGTTTCAGCTTCATAAACATTTGACAATGGTTCCAGCTGAATGAAGTCAGTCATAACTGCCTCTATCTTTGCTTCTGACTGTCCTAC
79216 A G AAACATTTGACAATGGTTCCAGCTGAATGAAGTCAGTCATAACTGCCTCTATCTTTGCTTCTGACTGTCCTACACTAACAATGCAAAATGTCCGTGACGG[A/G]GCTATTGTCGACTTGTATATTGTTCCTTTCATATCTAGGAGCATTTCATTACTACCGGAAGGGTCTTCTGACATTACTATGCGACCA
79234 A G GCTACGGTCTCGTGATTTACGGCCAGTGATGTACAGCATGGAAGATACCAAGACGCTAAATATAAAAGTAGTTGATAAAAGTTCAGGTCCTTTGTCTGCG[A/G]CCACCGTAGGAGAGATCAAATTTTTATAAACCCCAAAACCCAATGTAGCCATCAACACAAGAAGAGATAGTAAACCATTGC
79236 C T ATAAATCTCAAAATCTGAAATTTTAACTTTCCCAGTTCTTGATGGCGGCAGTCACCCGCGTCCTTCGCTCCGCTGCTCGATCTCCGGCTAAGTTGACCTT[C/T]TCCTCTCTCTCGAATGAACCTTGGGCCCCGGCTAGCTTGAAATCGGCGGCATCTCCGTTGGCGGATAGGAAGAAAGAGGTGGATAGAA
79248 T A TGCTAGATCTACTTTCAAATTCTCAGGATCAACAAGCGAACTCTCCATTTCTTAATAGAGCAGCTGCCATGAAAATGAATCGAACTGAAGACGAAGACAA[T/A]GAAGCATCCAAATCTCTTCGTCCTTCGAAACTTCAGAAGAAATCAAGCGCTGTTCTTCCGCATTCACGTCAGTTAGCTATAAACTTAAA
79248 C A TACTTTCAAATTCTCAGGATCAACAAGCGAACTCTCCATTTCTTAATAGAGCAGCTGCCATGAAAATGAATCGAACTGAAGACGAAGACAATGAAGCATC[C/A]AAATCTCTTCGTCCTTCGAAACTTCAGAAGAAATCAAGCGCTGTTCTTCCGCATTCACGTCAGTTAGCTATAAACTTAAACTGTCCTCC
79258 T C ACCAATTCAAAAATTAAGTATTGTACCAACTTTTTTCCATCAACAATAAACATAGTTGCTGCACGGGTGAATTGTTCTGTCCCCATCCCCCGTGTGCCCA[T/C]GCAATCATAGCCCCGTGATTTCCAACTTTTGCATTTAAATCCCTCAATTGTTATAGGACTTAATTGCAAAAAGTGAAAATCAGAGAAACC
79258 A G CCAACTTTTTTCCATCAACAATAAACATAGTTGCTGCACGGGTGAATTGTTCTGTCCCCATCCCCCGTGTGCCCATGCAATCATAGCCCCGTGATTTCCA[A/G]CTTTTGCATTTAAATCCCTCAATTGTTATAGGACTTAATTGCAAAAAGTGAAAATCAGAGAAACCTAGGTCGTTGGGCACACGGAGACG
79264 T C TTCTTGTTAGCATTTGATGGGAGTTGCCATGCATTTTTTATCGAATTTAAACCAAAAACGTAAGAAGTGCCAC[T/C]GCTGCATATTCTCCAATAGGTAATGTTGTTTGAAACTGAGAAGGAACAGAGTGAAATATCCGTCCAATTACAACAGATAATACAGTCATCAGCGAGAGGG
79278 G A CAGCCATACAATCACATTCAATTGAAAGTGATGATTTCAATAACAATAAAGTCTGAAGAATAAATTAATCACCCTTCTTTCTAAAGGAGCAGCCCTCCGT[G/A]AGACGGGCACGGCCTCCAGTAGGCTGGCAAAGCACTGTCTGGCAGTTACCACACACAACCACCGTCTGCGAATGGCTGAACACAGTT
79278 C T CACCCTTCTTTCTAAAGGAGCAGCCCTCCGTGAGACGGGCACGGCCTCCAGTAGGCTGGCAAAGCACTGTCTGGCAGTTACCACACACAACCACCGTCTG[C/T]GAATGGCTGAACACAGTTGTTATGTTGAAGCAACCCTGGCACTTGACATCCATGAAAAACGAGTTGGGAGACTGCACTAGTCTCTT
79278 C T AAAGCACTGTCTGGCAGTTACCACACACAACCACCGTCTGCGAATGGCTGAACACAGTTGTTATGTTGAAGCAACCCTGGCACTTGACATCCATGAAAAA[C/T]GAGTTGGGAGACTGCACTAGTCTCTTCAATTTGTGCCTCCTTTTCTCAAGTTCAGCAGGTGGGTTCAAGAGGTCAATATCGTTGGGA
79280 C G TGCTTCTAGACTTGTACCGAAGCTTAGTGTGGAAGTGAATTTCAGTGGCGATCAAGGAATGGAATCTGATAGAACTGCATGTCACAGTTCTCATGGGCAG[C/G]AAATGACAAAGCCTTTCACGCAGAATATGCCAAGATCAAGTTTGACAACTTCTGGAGCAGCAACTACTCGTCCTTCAGCATCGAGT
79280 A C ATCAAGTTTGACAACTTCTGGAGCAGCAACTACTCGTCCTTCAGCATCGAGTTCCAAAGATACACGCCGTACGGCTAGCTCTACTTGAGTATATTATATG[A/C]TGATATTTATTTCATTGATCGTAAAAGGGTTGCGGGTACCGATCTATAGTAGAAGTTTGGAGCATCACTCCCTCAATTTAATTATTTCA
79286 A G CTATACACCCATCACTTGCGCAAAGACCAGTTTGTAGGCTTGATCCAAAGGACCTACCAGGCTACCATTCACTTCCACAAGGCATTACCTGGAGACCCTT[A/G]CATCACCAATTTGACATAGTTAGGATGGCGAGCACGAACCTGATAAGAGAGGAGGGATTAAAGGCCAAGCACAACAGGGATTTGAG
79286 A C TTACATCACCAATTTGACATAGTTAGGATGGCGAGCACGAACCTGATAAGAGAGGAGGGATTAAAGGCCAAGCACAACAGGGATTTGAGCCTTAGCTTCC[A/C]TTGTGCTGCTGAAGGCCATACATTGAACCAGAATAGCTCTCTATCTAGTCATGCATAGCAAACTAATTATTACATGGAAAAGTAAG
79286 A AT GAGGAGGGATTAAAGGCCAAGCACAACAGGGATTTGAGCCTTAGCTTCCATTGTGCTGCTGAAGGCCATACATTGAACCAGAATAGCTCTCTATCTAGTC[A/AT]TGCATAGCAAACTAATTATTACATGGAAAAGTAAGCAGGCAATAATGTTCGACATCAAATGAGCACAGCCCATCGGACAGCGAGA
79288 G C TCTCGCTCCAAAGGACAGACTCATCAAGGTATTCAGGGTTATAAGGGACAAGCCTAACCGGGTGATGAGGTCCAAGGGAGTGCTTGATAGCCTGACCAGT[G/C]ACTTTGTTGATGAGGGCGAAGCTTGGAAATCCTTCTTCGTCCTTCACCTCTGTACTGTGCCTTATGTCCTTTATCCAGTGCTGAAAC
79288 T C AGGACAGACTCATCAAGGTATTCAGGGTTATAAGGGACAAGCCTAACCGGGTGATGAGGTCCAAGGGAGTGCTTGATAGCCTGACCAGTGACTTTGTTGA[T/C]GAGGGCGAAGCTTGGAAATCCTTCTTCGTCCTTCACCTCTGTACTGTGCCTTATGTCCTTTATCCAGTGCTGAAACTCATCCCTCGG
79288 T G GGAGCCAAGACAACGTCCCCGTTTCTAACAGTTAGCGAGTAATTCTCTTCAGCTTTTGTGTATATTCTCACCGTGTGCTGCTGCGGCTGCGGTTGGTGGC[T/G]GCTCTGCTGTTGTTCATGATGATGTCGATGACCGAATAGACTCATTTCTCTAAAGTTTTATTACAATTTTTGATCGATCTGAGTTAAAT
79290 T C CTCGGGAAGTGAAGATGTGCAAATGTATGATCAAGTAAAAGGATTCTCTTCAAGTCAACGTCTTACATGAGAGATGGATGTTGATTTGCTACAAGAGAAA[T/C]GGTTGATCAATTAAGTAGTTGGGCAGTAGACTTTAGTATGAAGTTATGGTACCTGATTAAAAAACATTGCCAGTTTTTAAGATCTTT
79290 TA T CGTCTTACATGAGAGATGGATGTTGATTTGCTACAAGAGAAATGGTTGATCAATTAAGTAGTTGGGCAGTAGACTTTAGTATGAAGTTATGGTACCTGAT[TA/T]AAAAAACATTGCCAGTTTTTAAGATCTTTTAGATAAGAAAGGTTAGATTTGTCATTTTATTGTCATTTACTTTGATTTATTTGAGTTG
79304 G A AATGGCATCGAAGGCTGTTGCATCTCCGGTTGCTGCCATGACTTGTGTGCCTCAGTTCAGTGGCCTCAAAGCTCAGCCAATGACCATGGTTAAAGT[G/A]CCATCGATGAAGAGGAAGGGAAACGGTGCACTCAGTGCTCGATGCGGAGATTTCATCGGCTCCTCTACCAACATTATAATGGTGACAACA
79318 T C TTGCATCACTATTCGGCGTTGTTCGATGCGTTAGGAGATGGTTTACATGAAGATAGTTTGGAGAGGCACACGGTGGAGCGACAAGTGTTTGGAG[T/C]GGAGATACGAAATATCGTGGCGGTTGGAGGACCGAAAAGGACCGGAGAAGTGAAGGTCGAGAAATGGGGAGAGGAGATGAGAAAAGTG
79318 C G ATAGTTTGGAGAGGCACACGGTGGAGCGACAAGTGTTTGGAGTGGAGATACGAAATATCGTGGCGGTTGGAGGACCGAAAAGGACCGGAGAAGTGAAGGT[C/G]GAGAAATGGGGAGAGGAGATGAGAAAAGTGGGGTTGGAGAGAGTGAGTTTGGAAGGGAGTCCGGCTACGCAAGCGAATTT
79318 A G TGGAGGACCGAAAAGGACCGGAGAAGTGAAGGTCGAGAAATGGGGAGAGGAGATGAGAAAAGTGGGGTTGGAGAGAGTGAGTTTGGAAGGGAGTCCGGCT[A/G]CGCAAGCGAATTTGTTGCTAGGTATGTTTCCGTGGAAAGGTTATACCTTGGTTGAAGAAAATGGATGTTTGAAGTTGGGAT
79318 T C GGGGAGAGGAGATGAGAAAAGTGGGGTTGGAGAGAGTGAGTTTGGAAGGGAGTCCGGCTACGCAAGCGAATTTGTTGCTAGGTATGTTTCCGTGGAAAGG[T/C]TATACCTTGGTTGAAGAAAATGGATGTTTGAAGTTGGGATGGAAGGATTTGCCGTTGCTGACCGCATCTGCATGGCAATTCGA
79332 T C GGACCAACTGGACGAATGCAGGCCGTCTGTGAGCGGGACGAACCCGACCGACCCGTCGGTAGAATGCTGCGCTGCACTGAGAGGAGCAGATCTGGAGTGC[T/C]TGTGTTCGTATCGCCACTCCTTGCTGCTGCCTTCGCTTGGAATAGACCCCGACCTCGCCTTGCGTTTGCCTCTGAAATGTGGGCT
79332 T C CTTCGCTTGGAATAGACCCCGACCTCGCCTTGCGTTTGCCTCTGAAATGTGGGCTTGCGACGCCTCAAGATTGCTTTTGAACGTTGTTCTTTCACCCTTG[T/C]TATGTTTTTAAATTTCAGTTTTATGGTTTATGTTATTGTTTGCATGGTCTGTAGGTTTTGAGACTCTTTGGTCTGGATGTAGATTTGTACG
79362 G A TTTTTTTTTTTTGAAGACCGTAACGAGGGCTTTATTAACACATATAACACATATAAACTGTAAACAAAGATGAAACAGCTCAAAC[G/A]GAAAATCAAACAACAGCACCAGCACCGGCGCCGGCACCGGTCATCATAGCCTTAAACTCATCGAAATCAACGCAGCCATCGCCGTCGCGATCGACGGACC
79362 A G TTTTTTGAAGACCGTAACGAGGGCTTTATTAACACATATAACACATATAAACTGTAAACAAAGATGAAACAGCTCAAACGGAAAATCAAACAACAGCACC[A/G]GCACCGGCGCCGGCACCGGTCATCATAGCCTTAAACTCATCGAAATCAACGCAGCCATCGCCGTCGCGATCGACGGACCGGATCAT
79362 G A GACCGTAACGAGGGCTTTATTAACACATATAACACATATAAACTGTAAACAAAGATGAAACAGCTCAAACGGAAAATCAAACAACAGCACCAGCACCGGC[G/A]CCGGCACCGGTCATCATAGCCTTAAACTCATCGAAATCAACGCAGCCATCGCCGTCGCGATCGACGGACCGGATCATCTTCTCGCA
79362 T G CGTCGCGATCGACGGACCGGATCATCTTCTCGCAGTCCTCCAAGCTGCACTTCTCGCCCAACCTGTGCAGCACGCGGTGCAGCTCCTGGGCCGTGATGGC[T/G]CCGGTCCCGCTCACGTCGTAGGCGTCGAAGGCGTCCTTCAGCTCCACGTCGCCGACGTTCCTGTTGAAGGCGGAGAACTCGTTGAG
79398 C T AGCTTGTAAAGGAAAAGATGTCTGAGAAACTCACAAATCCCCTTGAGATTATTTGGAAGTCTTTCAGTGTTGTTTTCTTTGCCGAATGGGGTGATCGTTC[C/T]ATGCTAGCTACCATTGCCTTGGGTGCTGCACAGTCGCCATGGGGCTAGCTACTGGAGCAATTACAGGGCATTTGGGTGCAACTATTA
79398 C CG AGATTATTTGGAAGTCTTTCAGTGTTGTTTTCTTTGCCGAATGGGGTGATCGTTCCATGCTAGCTACCATTGCCTTGGGTGCTGCACAGTCGCCATGGGG[C/CG]TAGCTACTGGAGCAATTACAGGGCATTTGGGTGCAACTATTATTGCAGTTTTAGGTGGTGCATTGCTGGCCAAATACATTTCTGAG
79434 TA T AGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTT[TA/T]AAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATG
79436 A G GATTGAGAGCTTTACGAATCTTGAACACGGCCCATGCTGTTCCAATGGCATGTCCTGCTGCCCCAAGCCCTTCATGCGTAACCTCTGCTGCCTGATCCCC[A/G]TACTTGTGAGATACAAGGCCGGTTGTAACAGTAGATGATGTATGCAGGACGTTTTTCCCAGCCATTTCAGCAGCATCACAAATTTTCG
79446 T TA CGGCGTACGTTCTCAAATATAAACACAACACAGATACCTACCTACAGAGTCCATACATGCATACCAACCATACCTCTACATTCCTAGCTAACATATATAT[T/TA]AAAAGGCATATAACTAAAACGACAGGCAAGTTGATAGATGTACAACGCTCATTTTGAGCCTTCAGTGCCGCCGCCATGGTGCAGGCC
79452 C T GCCCACGTGGCCTCATCCGCGCCATCCACAACTCCTCCTTCCTCCACAGCTCAGTCGGCCCCAGCCGCACCGACTGGCAGTCCACCTGCTCCATTCTATC[C/T]TCCTCCCAAAACACCAACGACGACAGCAACCTCTTCGTCAACGGCAACAAACCCGCCTCTCCCATCTCTCCAACCCTCGATCTGGTCCC
79452 T C TCCCCGTCCCCAACTCCAATCTCACAACCAACCTCCCGAAACCCCTTTCCATCACCGACCTCTCCCCGGCGCCGATGCACGGATCCACCCTCCGCGTCGC[T/C]TACCAAGGCGTCCCGGGCGCCTATTCCGAAGCCGCCGCCGGCCGAGCTTACCCCAAGTGTGAAGCCATCCCCTGCGACCAGTTCGAG
79452 T C CAACCAACCTCCCGAAACCCCTTTCCATCACCGACCTCTCCCCGGCGCCGATGCACGGATCCACCCTCCGCGTCGCTTACCAAGGCGTCCCGGGCGCCTA[T/C]TCCGAAGCCGCCGCCGGCCGAGCTTACCCCAAGTGTGAAGCCATCCCCTGCGACCAGTTCGAGGTCGCCTTCCAGGC
79452 C T AACCCCTTTCCATCACCGACCTCTCCCCGGCGCCGATGCACGGATCCACCCTCCGCGTCGCTTACCAAGGCGTCCCGGGCGCCTATTCCGAAGCCGCCGC[C/T]GGCCGAGCTTACCCCAAGTGTGAAGCCATCCCCTGCGACCAGTTCGAGGTCGCCTTCCAGGC
79484 G A CAGCGTGGACTGATGGGATGACCGCGGGGTCACGGGCACGAGCTGGTAGAGCTCTCGAATCTGGACTAGCAGGAGGGCGGAAAATTCGAAGTGGGGATGG[G/A]AGAAAATAAGGGGACAACTGCTATGTCCATTTTTGTTTTGATGAAGGAGTAGCCTGTTGTGATGGGGTAGAACGAATACTTTC
79530 A G GATTGTAAGTCCTAGTGGCAGTGGAGGGATCTCTAAAAGGCATCTTCGTTTAATTTCTGTTTTCTTTGTAGTTGTTCTGTAGCTTGGTGGTGCTATGTCT[A/G]GCTTTGCTTTCAGTTTATCATATTGGAGATCTAGCTGTTGTTTATTTTAGTTTTTGCCTATCTGATGTTTATTTGGGAGTTTTTGGAAGAT
79548 T C AAGTATGCTGAAGATCAAGATGCATTTTTCAAGGATTACGCTGAAGCACATGCCAAACTTAGCAATCTAGGTGCTAAGTT[T/C]GATCCTCCAGAGGGTATCCCCATTGATGCAGCACCTGAAAAGTTTGTTGCAGCCAAGTATTCTTCTGGCAAGAGAGAATTATCAGAGTCCATGAAGCAGA
79548 G A TGAAGATCAAGATGCATTTTTCAAGGATTACGCTGAAGCACATGCCAAACTTAGCAATCTAGGTGCTAAGTTTGATCCTCCAGAGGGTATCCCCATTGAT[G/A]CAGCACCTGAAAAGTTTGTTGCAGCCAAGTATTCTTCTGGCAAGAGAGAATTATCAGAGTCCATGAAGCAGAAAATTAGGGCAGAG
79548 C A ATTCAAACTATTTTCTAAATATTATCATATTTGTTGGTGTATTAGCTCTTTTATCGTCATTAGTGGTAAACTAAGTAATTTTGTCGTTTGTTTATGTTTT[C/A]TCCACTCTGATTTGGGAGACAACGTAATGTACTCTCCAAGTAATGCAAAGAATTAATGTTTTGGTTTAAAAAAAAAAAAA
79568 T A AGCGAGCACATGCAATGGATCTGTGGGAGAATGCCAAGGTGAGGAGGCGGAGTTCCTCATGGACTCGGAGGTCCATAGGAGAATCCTACAAGGGAAGACG[T/A]CAATAACGTATCATGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
79568 A C AATGGATCTGTGGGAGAATGCCAAGGTGAGGAGGCGGAGTTCCTCATGGACTCGGAGGTCCATAGGAGAATCCTACAAGGGAAGACGTCAATAACGTATC[A/C]TGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCAAGAAGTTCAAATAT
79568 T A GAGAATGCCAAGGTGAGGAGGCGGAGTTCCTCATGGACTCGGAGGTCCATAGGAGAATCCTACAAGGGAAGACGTCAATAACGTATCATGCCATAGACAA[T/A]TCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCAAGAAGTTCAAATATACCAAGCAGCGG
79568 A T GAGAATCCTACAAGGGAAGACGTCAATAACGTATCATGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGC[A/T]TTGCAAGAAGTTCAAATATACCAAGCAGCGGTTGCAACACTTATTACCGTTGTAAAAATAAGCTATGAATGTTGACTTTGTTCTTTT
79568 T A ACGTCAATAACGTATCATGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCAAGAAGTTCAAATA[T/A]ACCAAGCAGCGGTTGCAACACTTATTACCGTTGTAAAAATAAGCTATGAATGTTGACTTTGTTCTTTTTCTTTTTTGTGATCGATTGT
79568 G T ATAACGTATCATGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCAAGAAGTTCAAATATACCAA[G/T]CAGCGGTTGCAACACTTATTACCGTTGTAAAAATAAGCTATGAATGTTGACTTTGTTCTTTTTCTTTTTTGTGATCGATTGTCTGCT
79568 G A GTATCATGCCATAGACAATTCGGGTCCCGTGTGCAACCCCGGAAGAGGCAAACCTTACGGCGGCAACTGCATTGCAAGAAGTTCAAATATACCAAGCAGC[G/A]GTTGCAACACTTATTACCGTTGTAAAAATAAGCTATGAATGTTGACTTTGTTCTTTTTCTTTTTTGTGATCGATTGTCTGCT
79598 T G TTTTTTTTGATCAAAGAAAAAGAGTTGAATAACACATGTATGTCAAAAATTAAACAATTTTTGCTCTTATCACAACTATATAAACACACATAATAAAAAA[T/G]TGAAGCATTTTGAAGCTCCACTCCCATAGTAGAAAGACATGATGATTAATGATTACTTAAACAGCTATTTTAGCGGCCTCCAGTATCTTA
79612 G A CAAGAAGGCTTCATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGT[G/A]TATACCGAAACAAGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTT
79612 T C CAAGAAGGCTTCATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGTGTA[T/C]ACCGAAACAAGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGC
79612 A G CAAGAAGGCTTCATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGTGTATACCGAA[A/G]CAAGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTT
79612 A C CAAGAAGGCTTCATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGTGTATACCGAAACAAGTC[A/C]GCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCAT
79612 G A CAAGAAGGCTTCATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGTGTATACCGAAACAAGTCAGCTTGAGTTGG[G/A]GTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCAT
79612 C G CATCAATATATCGAATTCTTCCATATACATTATGAGATATAAAGAGAGCACTGCTAATGTGTATACCGAAACAAGTCAGCTTGAGTTGGGGTAACAGGCA[C/G]AAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCT
79612 T C AATGTGTATACCGAAACAAGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTC[T/C]AATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGG
79612 C T ACCGAAACAAGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGC[C/T]TCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTA
79612 T A AGTCAGCTTGAGTTGGGGTAACAGGCACAAGAAAGTTCCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAA[T/A]GCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTG
79612 G A CCCAAATGGTGAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTT[G/A]TATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAG
79612 A G GAATCAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTG[A/G]CATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTT
79612 A C CAAAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACAT[A/C]ACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTC
79612 C A AAGCTTCTAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAA[C/A]TGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTC
79612 C A TAAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGAT[C/A]AGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAG
79612 A G AAAGTTTCCAAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATC[A/G]GATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGG
79612 G A AAGCCAACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTG[G/A]GCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTA
79612 T C AACCTTCTAATTTTGCCTCTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAA[T/C]GGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTATCTTTT
79612 G A CTGTTAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTC[G/A]TTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTATCTTTTTCTTCTCCATGGTAGAA
79612 C T TAATGCATAATTCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTA[C/T]GGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTATCTTTTTCTTCTCCATGGTAGAACTATC
79612 A G TCTTGGCCTGTTGAATTTGCATATCTTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGA[A/G]CCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTATCTTTTTCTTCTCCATGGTAGAACTATCCACACAAACT
79612 A G TTTTGTATCAACTGACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCA[A/G]TCTTTCTTCTCTTGGGAGGAGGGATTATCTTTTTCTTCTCCATGGTAGAACTATCCACACAAACTCTTGGTCTGCGAGTAGGCAAGGGG
79612 G A ACATAACTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTT[G/A]GGAGGAGGGATTATCTTTTTCTTCTCCATGGTAGAACTATCCACACAAACTCTTGGTCTGCGAGTAGGCAAGGGGCAGCGAT
79612 A T CTGGGATCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGG[A/T]GGGATTATCTTTTTCTTCTCCATGGTAGAACTATCCACACAAACTCTTGGTCTGCGAGTAGGCAAGGGGCAGCGAT
79612 T C TCAGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGAT[T/C]ATCTTTTTCTTCTCCATGGTAGAACTATCCACACAAACTCTTGGTCTGCGAGTAGGCAAGGGGCAGCGAT
79612 T C AGATTGCTGGGCAATGGTAACTTGCTCTGTTCGTTACGGGCAAGTGAACCTAAATTCCCTCCTTCAGATTCAATCTTTCTTCTCTTGGGAGGAGGGATTA[T/C]CTTTTTCTTCTCCATGGTAGAACTATCCACACAAACTCTTGGTCTGCGAGTAGGCAAGGGGCAGCGAT
79620 A G GCTTTGGCTAATTACATTTCTCCTCTTAACATCCCTTGTAGTAAACCTATATTTCTACTATGACAACAGTTTCACTTTGAGCAACCCTTTCCTCAAACTG[A/G]CTTGGACTACCAAGGCAGCAACCGAGGCTGAGCGGGTGGCTGCTATATACTGTTCTTATCATGGTAGAGCTTATTTGGATGGGGTGCCT
79620 G A CTTGTAGTAAACCTATATTTCTACTATGACAACAGTTTCACTTTGAGCAACCCTTTCCTCAAACTGACTTGGACTACCAAGGCAGCAACCGAGGCTGAGC[G/A]GGTGGCTGCTATATACTGTTCTTATCATGGTAGAGCTTATTTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAAT
79620 T C CTTTGAGCAACCCTTTCCTCAAACTGACTTGGACTACCAAGGCAGCAACCGAGGCTGAGCGGGTGGCTGCTATATACTGTTCTTATCATGGTAGAGCTTA[T/C]TTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCCTCCAAC
79620 G A CTTTCCTCAAACTGACTTGGACTACCAAGGCAGCAACCGAGGCTGAGCGGGTGGCTGCTATATACTGTTCTTATCATGGTAGAGCTTATTTGGATGGGGT[G/A]CCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCCTCCAACTGCACTGCTGAT
79620 T C CAGCAACCGAGGCTGAGCGGGTGGCTGCTATATACTGTTCTTATCATGGTAGAGCTTATTTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTG[T/C]CATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCCTCCAACTGCACTGCTGATGCCACTACTGGTGATGCAATGTTTCTAGAG
79620 T C TTATCATGGTAGAGCTTATTTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCC[T/C]CCAACTGCACTGCTGATGCCACTACTGGTGATGCAATGTTTCTAGAGAACTACTGGCTCCGTCACAGAGTTAACACCGCAATGCTGG
79620 C T ATGGTAGAGCTTATTTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCCTCCAA[C/T]TGCACTGCTGATGCCACTACTGGTGATGCAATGTTTCTAGAGAACTACTGGCTCCGTCACAGAGTTAACACCGCAATGCTGGAATCA
79620 T C GAGCTTATTTGGATGGGGTGCCTGTTAATGGTGCCCCAATGTGTGAGTGTCATAATTGTTACAGCGGTCCTACATGCTCAGTGTTGGCCTCCAACTGCAC[T/C]GCTGATGCCACTACTGGTGATGCAATGTTTCTAGAGAACTACTGGCTCCGTCACAGAGTTAACACCGCAATGCTGGAATCAGGATGG
79632 T C ATTCGAATGGTTGTTGATACATGTTCTCCCACTGACATAAGGGAAGAAACAGATCCAGAGTACTACTCCAGGTATGTTCCTCTTTGTCGGGTTAATCTTC[T/C]GTTGACAACTGAAAATTCAGCCTTCTTTGGAAGCCCCTTGTCTTCTTTGATCTTGTCCCATGAGACCGAAAGTACAAAACCACGCCACG
79638 G T AAATAGAGCAGGAGATTGAGCGAGCTAGACAGCAGGGGTTGCGCATAGGTGGACAGTCAGGAGATTCTAGTTTTAATGTATCGGGAGCTATTAATTCAGG[G/T]GTTGCTGTTTTTGAGATGGAATATGGTCACTGGATTGAAATCCATATCACTCAAATGAGCGAGTTAAGATCTGCATTGCAAGCTC
79648 C T CCACTCACATACTATTTTCCAAATCTCAGAACAACTTCGTGTTTCATCTCAAATGCATGTTCCCATGGTCCTGATGATCCATCGAAGGTTCGATCTAGCG[C/T]GAAAACATGAACCACTTCTGGTTGCTGCTCATTCACACTACCACGCCCACCTCATGTCGAGATTGGTCACAGTTGGCGAAGCTTGGTTCT
79652 C G TTTCCGCTCGAGGGTGCCCGCATCGCCTCCTCAAGGCACCGAATCGTGTCAGAGAAAGCAAAAGCGAGGGGTTCCTGGTTCAAATTAGAATAGTTGCT[C/G]ATGATATTTCCGTCCAGAAGCTGTTCTGTAAGACGACGGATTACATGGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTA
79652 A G TTTCCGCTCGAGGGTGCCCGCATCGCCTCCTCAAGGCACCGAATCGTGTCAGAGAAAGCAAAAGCGAGGGGTTCCTGGTTCAAATTAGAATAGTTGCTC[A/G]TGATATTTCCGTCCAGAAGCTGTTCTGTAAGACGACGGATTACATGGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTA
79652 T C TCGCCTCCTCAAGGCACCGAATCGTGTCAGAGAAAGCAAAAGCGAGGGGTTCCTGGTTCAAATTAGAATAGTTGCTCATGATATTTCCGTCCAGAAGCTG[T/C]TCTGTAAGACGACGGATTACATGGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTAGAATAGGCGAGAGAGTGCGCG
79652 T G TGATATTTCCGTCCAGAAGCTGTTCTGTAAGACGACGGATTACATGGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTAGAATAGGCGAGAGAG[T/G]GCGCGAGAAGACGGGGCTGTGACTGCAGGATACACATGAGGAGATACGGTATATCTGTTAGAGGGGATGAAGTGGACGAGA
79652 A C CGACGGATTACATGGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTAGAATAGGCGAGAGAGTGCGCGAGAAGACGGGGCTGTGACTGCAGGAT[A/C]CACATGAGGAGATACGGTATATCTGTTAGAGGGGATGAAGTGGACGAGAATAGAGAAGAGGAGGAGGAAGAGGCGGCGG
79652 T C GGTACTTGCGGGACGAGGCAGGAACGGAAGAGACGGCGTAGAATAGGCGAGAGAGTGCGCGAGAAGACGGGGCTGTGACTGCAGGATACACATGAGGAGA[T/C]ACGGTATATCTGTTAGAGGGGATGAAGTGGACGAGAATAGAGAAGAGGAGGAGGAAGAGGCGGCGGAGGAGATGAAGG
79652 T C GGGACGAGGCAGGAACGGAAGAGACGGCGTAGAATAGGCGAGAGAGTGCGCGAGAAGACGGGGCTGTGACTGCAGGATACACATGAGGAGATACGGTATA[T/C]CTGTTAGAGGGGATGAAGTGGACGAGAATAGAGAAGAGGAGGAGGAAGAGGCGGCGGAGGAGATGAAGGAGAAAAAGT
79652 A G TGACTGCAGGATACACATGAGGAGATACGGTATATCTGTTAGAGGGGATGAAGTGGACGAGAATAGAGAAGAGGAGGAGGAAGAGGCGGCGGAGGAGATG[A/G]AGGAGAAAAAGTAAGATGGAATCCAGGCTAGAGGAAGAAGACGATGCAGCAGGAAAGAAGGATGAGAAGAGCGAGTTTC
79674 CT C TTGAAAAGTACAGTCCTCCCAAAAATTAATAGCAAGAGTGATTCATGGTAAAGCATCGGTCTCTGGAATGATGTAACCGATGAATACAACAACCGGGTTG[CT/C]TGAGTACCAAGTTCGCGAAAGGGATATGCCGAGTCTCGTACATCTTGCAATGAAACTCGACTTTTGTCACTGCATGAGGGGAGAG
79674 T C ACCGATGAATACAACAACCGGGTTGCTGAGTACCAAGTTCGCGAAAGGGATATGCCGAGTCTCGTACATCTTGCAATGAAACTCGACTTTTGTCACTGCA[T/C]GAGGGGAGAGGAGCAGGAAAGAAATGAAAGCACAAGGGATACTCTGATGAAAGAGAATGAGACACCAGCGAAAGAGAACGAGA
79674 A T CCAAGTTCGCGAAAGGGATATGCCGAGTCTCGTACATCTTGCAATGAAACTCGACTTTTGTCACTGCATGAGGGGAGAGGAGCAGGAAAGAAATGAAAGC[A/T]CAAGGGATACTCTGATGAAAGAGAATGAGACACCAGCGAAAGAGAACGAGACACTAGCAAA
79676 C T TGTAGTGAGCTCTGTTACTGCGGCCGAAAGACACTTCTACACACTCGTTGCAACCAGGACGGCATGTACTCATCAAGTCTCTGCATTTGCATCTCGCTAC[C/T]GCTGTGTCTCCCAAGTCGCATTGCCCGCAGTTGTTGCAGCAGGCGCCGCTTGCATCGTCTTCGTCGTGAGCTTTCTGCTGAAGAAGAC
79684 C T GAGGACGCCCTTTCGGCAGCACGAGCGCGAGCTTGGCTGCCGCCGCTGCTACAGGCGTCGATTCGTCCACCGCCGCCTCCCTTCTTGG[C/T]CCTTCTCTTCACCTCCCTGCTTTCTCCGAACAGACCAACAAAAGGATAGTCCTTGCTCTACAAAGTGGACAAAAGAGTGACTTGACATGGGCTCTGAAC
79684 T C GAGGACGCCCTTTCGGCAGCACGAGCGCGAGCTTGGCTGCCGCCGCTGCTACAGGCGTCGATTCGTCCACCGCCGCCTCCCTTCTTGGCCCTTCTCT[T/C]CACCTCCCTGCTTTCTCCGAACAGACCAACAAAAGGATAGTCCTTGCTCTACAAAGTGGACAAAAGAGTGACTTGACATGGGCTCTGAAC
79684 C T GCAGCACGAGCGCGAGCTTGGCTGCCGCCGCTGCTACAGGCGTCGATTCGTCCACCGCCGCCTCCCTTCTTGGCCCTTCTCTTCACCTCCCTGCTTTCTC[C/T]GAACAGACCAACAAAAGGATAGTCCTTGCTCTACAAAGTGGACAAAAGAGTGACTTGACATGGGCTCTGAACACTCTAACCGTACTTT
79684 G A TTGCTCTACAAAGTGGACAAAAGAGTGACTTGACATGGGCTCTGAACACTCTAACCGTACTTTCTTTTAAAGAGAAGGATGATACACGAAAAGAAGCCAC[G/A]CCTCTTGCTAAGATACCAGGGCTTCTAGATGCTCTTCTTCAAGTTGTCGATGAGTGGCGTGACATTACTTCGTCTTGGGACTCCACTA
79684 C T TGACTTGACATGGGCTCTGAACACTCTAACCGTACTTTCTTTTAAAGAGAAGGATGATACACGAAAAGAAGCCACGCCTCTTGCTAAGATACCAGGGCTT[C/T]TAGATGCTCTTCTTCAAGTTGTCGATGAGTGGCGTGACATTACTTCGTCTTGGGACTCCACTAAACCTTCAAGAATAAGATTGTTAGG
79684 G T AGAAGGATGATACACGAAAAGAAGCCACGCCTCTTGCTAAGATACCAGGGCTTCTAGATGCTCTTCTTCAAGTTGTCGATGAGTGGCGTGACATTACTTC[G/T]TCTTGGGACTCCACTAAACCTTCAAGAATAAGATTGTTAGGGGCTGCTCAGGTTACGGGTTTTGGAAATAAATACCAGTCTGATAAT
79696 A G AATGTGGAATTCACCTATTTTCAACTTTTCCCAATTACCATTCACTTGATTAGATGCCTCCTCTTCAATGGTATTGAAGTAACCAAAACGAGGCGCGCCA[A/G]CTACGAACTGCGAAGTCACCCGACGTGTATCATACAATCGTACTTCGCATTCAGAGACTACATTAGTTCCGACTTTTACTGATGCCTCGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
79720 A G TTAAACTCATCTCTTCAACCCAAACCGAATCATTCATTCGATTTCCCCAGTAAATGGACAATCAAAACCAAATATACAGGCCCTTGGCAGGTCCAACATC[A/G]AACCTAACCCGCTACGGGTCCGCGCCCACTTCCTTACTCAACAGCCTCGTTGACTCCATCAACGGGTCCGGACCCTCCGAACCCGCTGC
79720 T C ACGGGTCCGGACCCTCCGAACCCGCTGCCACCTCCCCCTTACACATGTCGCGATTCTTCAACGGAGGCAGCAGCAACGACAATCATATGAGTTATTCGGA[T/C]GGCTTCTCGACTTCAAGTACCAGTGCCACTAATCAAGTGGGCCCTGCCTATCGGGTCGGTGAAGACAGCAAGAAAGCCCACGGCGA
79720 G T CGACAATCATATGAGTTATTCGGATGGCTTCTCGACTTCAAGTACCAGTGCCACTAATCAAGTGGGCCCTGCCTATCGGGTCGGTGAAGACAGCAAGAAA[G/T]CCCACGGCGACGGATGCGGAGGAGGAGGCGGCGGCGGCGGGGGGTTGCTTAGACATAGCAGC
79768 G A GTCTGCGGATCAGCTCCAACCTGACCCGGTTCACCAACTGTGGGCCAACCTGTTTCGCCCACAACGATCTCTAC[G/A]TCACCAAATCCCAGCTTCTTCATTGCAGTGTGAACCGCATCCATCTGGGCATCAAAGAGGTTGAAATAGGTGATTTTGGTTACAGGGTCATGGACTCCAT
79768 A G TGGGCCAACCTGTTTCGCCCACAACGATCTCTACGTCACCAAATCCCAGCTTCTTCATTGCAGTGTGAACCGCATCCATCTGGGCATCAAAGAGGTTGAA[A/G]TAGGTGATTTTGGTTACAGGGTCATGGACTCCATGGTTGGGCCTGAAGGTGGCATAGTTCAGCCTGGCGGGGTTGTATCCGTACCC
79788 A G CCCCGACTGCCGGCCTGTTCTTCTTCTTAATCAGGACGAAAGAAAAATGGCAGCGATTTGATTTGGCAATGGAGGAAGATGAAGGATTTGGAAAGGAGGG[A/G]GTGTAAGAAGGCGGCGATTCTTTTAATATCTGTTAATATTCTTGTGTCATATACACTTTCAAATTAGTCATTTGAGGTAAGCTATTT
79796 T C CTTTCTCATGTTTTCTTCCTACTTTCAACCCTAAACTACCTCTAAATTTCCTTCTTACTCGACCATTAATTCCTACTCTTCTCACCTGTTACTGTCTTCA[T/C]CTTCTCCCATCTGCCAGTATTTTATGCTTCGGAGCTGCCAGTCGGTAACTGAGCCATGATCAAATCGGAACTGCCAATCACCAAAACACTTCG
79796 C T TTCGGAGCTGCCAGTCGGTAACTGAGCCATGATCAAATCGGAACTGCCAATCACCAAAACACTTCGGAATCAGCGGATCTGGCACTCCTCCACACGTCTG[C/T]TAGCGGACGAGCCCTTATTCCGCCTCCACGACTAGATCGTACGTTAAATCGTTTTATATTTCCTTTCTTGCTACAAATCGCGTTTTTGC
79796 C A CATGATCAAATCGGAACTGCCAATCACCAAAACACTTCGGAATCAGCGGATCTGGCACTCCTCCACACGTCTGCTAGCGGACGAGCCCTTATTCCGCCTC[C/A]ACGACTAGATCGTACGTTAAATCGTTTTATATTTCCTTTCTTGCTACAAATCGCGTTTTTGCTGTTGTATGTTCAAAATTTGGCACTCCT
79796 G A CACTCCTCCACACGTCTGCTAGCGGACGAGCCCTTATTCCGCCTCCACGACTAGATCGTACGTTAAATCGTTTTATATTTCCTTTCTTGCTACAAATCGC[G/A]TTTTTGCTGTTGTATGTTCAAAATTTGGCACTCCTCTTCAGCTATGGCCGTGGAAGAACCCTTC
79800 G C AGCGGATGACGTCGGCGATGGAGGTCGAGTGGAGGAGGTCGCTGGATCTGGTGAGGTATTTGTTGGGAACGGCGAGGATGGTGAGGGAAGAGCGGGACGA[G/C]AGCTCGGTGGCTACGAGGGTGGAGAGAAGGCCGTTGAAGATGGAGAAGTCGGGGTTGTCGGAGAGGATGGAGGAGACA
79800 C CG ATGGTGAGGGAAGAGCGGGACGAGAGCTCGGTGGCTACGAGGGTGGAGAGAAGGCCGTTGAAGATGGAGAAGTCGGGGTTGTCGGAGAGGATGGAGGAGA[C/CG]ATTGACGGAATTTGTATGCGTTAGGGGCAGCAGCAGGAGAAGAAGGAAGATATTGTTGAGATTTGGAGAGTGCAGCGC
79832 G A AATTCCCGAGTTTTTCCTTAAGCAGAGCATTGTGAGAAAAAAGCTGTTCGTAGTCGGCCCTTATTCG[G/A]TTTAACTCCGCCTTGAGAGAAGCATTTTCATCTTTCAAAACCTCAACTTTCTGAGCCAGTTCTTCACATTCAGCCTGCTTGCGTAGCCTGGATCGACGAG
79832 CT C ATTTTCATCTTTCAAAACCTCAACTTTCTGAGCCAGTTCTTCACATTCAGCCTGCTTGCGTAGCCTGGATCGACGAGCAGATTCCCTATTCGATTGCTTT[CT/C]TTTTTTGCCTCTTAAGCTCTCTTTCATCCAGCATCCATGGTTCAGAGGGGCCGCCAGAGGCCATAGTTCCAACTGCAGCAACGGGCGCT
79892 C T GGACCCGATTTGCTGTCTGACAGGTGATTGCATACAACACGAGTGGTGCATACTGGAGGACCAAAGCTGCTGTTCAGATGCAGGGTCATTGCTGAGGAAC[C/T]GAAGTCCAACACAATGAATATTAGAGCAGTTTAATTCAACTGGAATAACAACACACAGATTCCTCTGAACTTGATGCATGGCGCAG
79894 A G ACAAAGAGAAGTAACATCATGATCTTCATAACAATATGGACACGAAAACTCAGCTTTGCAGTCCTCTTCAACCTCGAAATCTTCAATCCCGAACCGATCT[A/G]AACGTGAGCTCTGATTATGCTGGATCGCGAAGTGCCTTTTAGCTGCTGCCAATCGAGAGATCCATTCAGAATCCATTCTAGGTACTGT
79908 T C TATCTAGATTTATCCATTCATTTACGCACATATCTACAAGCAAATAGATACATGGATAAATGTAGGAATACAATAACATAAACACATAGAGCTCCATCTT[T/C]TACCCAAGATCAGGAACAGTGAAATATTCCTCTTCGTCGGAGACTGCAGTCCTTGGCCTTTTGTTGTACTGCATGCTTTTGCTGTTGTAA
79908 A G ACGCAGCATTGTTTGTTTGTGGGCTTGGCATTTCTGGAACTTCAGCTGCTTGCATTGTTGTCTTGGGACCTAACTGTTCTTGAAAAAGACCCATGTCTGT[A/G]AACCAGTCTAGCTCCCCAAATCCAGCTTGAGGCCCTTTACTCAACTTGTCGTTAGATTCATAATCAGAAAGCTGGAGGAATT
79936 A T CAAGACTTCGAAATCTTAACTGTGAATGGCAAGGAAGAATAAATTTATGAAGAAACATTTGGTTTATTCAT[A/T]TTACTGCAAAGAATTGCCTCTATTTGAATCCGGGGATGGTGCTGCTATTCTTTTAATTTGCTTGAGTTGAACTGAGATCTGGCAATGGTGATGTCCTTTC
79936 G C TATTCATATTACTGCAAAGAATTGCCTCTATTTGAATCCGGGGATGGTGCTGCTATTCTTTTAATTTGCTTGAGTTGAACTGAGATCTGGCAATGGTGAT[G/C]TCCTTTCTATCTGCAGCTTGTGGCGTCCAGTGCAAAGAATGACTTGTTGTGATGTCAATTAGTAATAAGAGAAGCTTGTTTGATCGAAT
79936 T A GTGATGTCCTTTCTATCTGCAGCTTGTGGCGTCCAGTGCAAAGAATGACTTGTTGTGATGTCAATTAGTAATAAGAGAAGCTTGTTTGATCGAATGACGA[T/A]TATGTTAGGAAAATTGTCCAATGAAGCTTTTCTCCGTTCGTTGTTGCATCTGATAATTGTTTCCTCTTTTATGTTCTTTTATTTATATAGG
79942 C T TGACATCCACCATCCAATCCTAAGAAAACCATGGCGCTTCCTTTAAAATTTACACCGAACCCCTCAAAGCAATTCCAGTTTATCCTCTTTCCTCGAAGCC[C/T]CAAACCAACCAGGCTTCCTTTTGACCGCCGTAGCTTCTCCCTCTCTATCAAGGCCACCACGCTTACCGCTGACACGTCCTCCTCTACTGCC
79942 C T TTTATCCTCTTTCCTCGAAGCCCCAAACCAACCAGGCTTCCTTTTGACCGCCGTAGCTTCTCCCTCTCTATCAAGGCCACCACGCTTACCGCTGACACGT[C/T]CTCCTCTACTGCCTTTAAATCACCGAATGTTCTTCTAGAGGTCAAGAATCTGAAGGCTGTGATTGCCGAATCCAGGCAGGAGATCTTACG
79942 A G CCAAACCAACCAGGCTTCCTTTTGACCGCCGTAGCTTCTCCCTCTCTATCAAGGCCACCACGCTTACCGCTGACACGTCCTCCTCTACTGCCTTTAAATC[A/G]CCGAATGTTCTTCTAGAGGTCAAGAATCTGAAGGCTGTGATTGCCGAATCCAGGCAGGAGATCTTACGAGGAGTTAATCTCACTATTCA
79948 A G ATTTGGTTGAGATGTATGTTTTCCGCCATTCTTATACATTTGAAAGTATCGCCTAGATCATGGCTCTCGCTCCATAGGATCGACTTGTCGAAGATTTTCG[A/G]GTTAAACGGAACCATACGAACCGGTTTTCCAGGTCCCGAAGGATGCTGCATGGCTTGGCCGGTCCCTTTGTTGATGAGAGCAAAACTT
79964 C T CTGGTTTTATAAAGTCAATACCCCATCTGCTACCTTCTCATCTTTTGCTGAAGCAGAAGATAAACCAGCTGCTTCATCTACGCCCTCCGAAGAAATACAA[C/T]CAAATGGAGGTCACATGCCTGAAATGGCAAAAGCACTTCATATATCGTCTAGAACAGCTACTGCCATTTGCTTATGCATTGCATTTGCA
79964 T C TTCATCTACGCCCTCCGAAGAAATACAACCAAATGGAGGTCACATGCCTGAAATGGCAAAAGCACTTCATATATCGTCTAGAACAGCTACTGCCATTTGC[T/C]TATGCATTGCATTTGCAACACTAACATTTCCGTTAGCAATGAAGTCACTAGGACAAGGAGTAAGCTTGAAAATCAAAGCCTTGTCTTA
79964 T C CTACTGCCATTTGCTTATGCATTGCATTTGCAACACTAACATTTCCGTTAGCAATGAAGTCACTAGGACAAGGAGTAAGCTTGAAAATCAAAGCCTTGTC[T/C]TATTTGACATTACTATCAGGGTTTTATATGGCTTGGAATATAGGTGCTAATGATGTAGCTAATGCAATGGGGACATCTGTTGGTTCTGG
79984 A G TAAATCATCCTGAAAACAAACCTTTATTACAAGAAACCCCCAGCACAACCTTCAAAGAAAGAAACTAAGGCAAAGCAACAAATATTGCAAGGAATGCACT[A/G]TATAAATAATAAATCTTAACTGTGAGGCACCTTCTTAAACATAGGAGGATACTTTGGGTAATGTTTCTTGAAGAAAGGGGGACATGG
79984 G A AAATATTGCAAGGAATGCACTATATAAATAATAAATCTTAACTGTGAGGCACCTTCTTAAACATAGGAGGATACTTTGGGTAATGTTTCTTGAAGAAAGG[G/A]GGACATGGCTTCTTCTTTATGATCGGTGGAAACTTAGGAAGAGGAGGCAATTGTGGTTTGTGAAATGGAGGCAAGTGCGGAAGTG
79984 A G TAGGAGGATACTTTGGGTAATGTTTCTTGAAGAAAGGGGGACATGGCTTCTTCTTTATGATCGGTGGAAACTTAGGAAGAGGAGGCAATTGTGGTTTGTG[A/G]AATGGAGGCAAGTGCGGAAGTGGGGGGCATGGTTTCTTGTATATAGGCCCGGGGGGTGGTAAAGGTTTCACGTAAGG
79996 T C TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCA[T/C]CCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTC
79996 A G TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCT[A/G]TGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCA
79996 C T TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCAC[C/T]TGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGG
79996 A G TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTC[A/G]TTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGT
79996 T C TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTC[T/C]TGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACA
79996 T C TCCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTG[T/C]TCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGT
79996 T C CCATCTTTGCATTCTCAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCT[T/C]CTCTCCCCGCTTATTTGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCG
79996 T C CAGGCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTAT[T/C]TGTAGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCC
79996 T C GCAGCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTG[T/C]AGTACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTC
79996 T A GCCTAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAG[T/A]ACGTTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAG
79996 G C TAAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTAC[G/C]TTGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCG
79996 T C AAACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACG[T/C]TGCCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCGA
79996 G T ACCTCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTT[G/T]CCTTCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCGATG
79996 T C TCCTCACAAACTTGCCGCTGCTTCTCTCCATCCTATGCCACCTGTCATTCTTCTCCTCTTGTTCCTTGCTTCTCTCCCCGCTTATTTGTAGTACGTTGCC[T/C]TCCTCCACCTCCACCTTCACCTCTTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCGATGCGC
79996 A G TTCCTTCTTCACTCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCGATGCGCGTGTTTGCCAGCGTGGAGGCTTCGGTGAGC[A/G]CGCCACCGACATCGGATCGGATTTGGCTTGGGAAGGGAAAGCCCTGGAACGGGTCCCACGCGTCGAGGGAGAATGGATCGAACG
79996 T A TCCCGGCATGTCAGCCTTGAACACGTGCGCTTGAGGCGTCTCCTTCCAGTCGATGCGCGTGTTTGCCAGCGTGGAGGCTTCGGTGAGCACGCCACCGACA[T/A]CGGATCGGATTTGGCTTGGGAAGGGAAAGCCCTGGAACGGGTCCCACGCGTCGAGGGAGAATGGATCGAACGAGTTGTTTTTCT
80010 T A CAATATGCTTTGAATGATTCAATCCCCAAGTCTATGTTCCATTTTAGATTCAGAACCAACATGACAAACCATTATAAGCCTAATATCCAAAGTGGCATCA[T/A]ATAATTTCATTTAATACAATGAGCCTAGTATAGCAAGTTCTTCCAATATAAACCCATTATAAGGCATGCTTCTAACTTCTAAGCAGTTAGA
80010 A G TCCCCAAGTCTATGTTCCATTTTAGATTCAGAACCAACATGACAAACCATTATAAGCCTAATATCCAAAGTGGCATCATATAATTTCATTTAATACAATG[A/G]GCCTAGTATAGCAAGTTCTTCCAATATAAACCCATTATAAGGCATGCTTCTAACTTCTAAGCAGTTAGAAACTACCACCAGGATTAGTAT
80010 T C CCTAGTATAGCAAGTTCTTCCAATATAAACCCATTATAAGGCATGCTTCTAACTTCTAAGCAGTTAGAAACTACCACCAGGATTAGTATTGTATAATCTT[T/C]AACGGCGGTAGATAACTGTCTCTAGATCATGCAGCTTTATCAAAGTTCATCCCAAGCCTTATCCCTGCTTTCCAAATTCCGTGTTTTTCGG
80010 A C ATGCTTCTAACTTCTAAGCAGTTAGAAACTACCACCAGGATTAGTATTGTATAATCTTTAACGGCGGTAGATAACTGTCTCTAGATCATGCAGCTTTATC[A/C]AAGTTCATCCCAAGCCTTATCCCTGCTTTCCAAATTCCGTGTTTTTCGGTCTCAATTAGCTGAATGCAGTTCCCGATTTTGTTGATATCAG
80014 T C CAAATAAACAGAACTGCTCATATACGCAAATAAACAGCAGTGCTCAGGCTGGAGTAGAAATATTGGCAAACTCTCCCACTGTCCAAATAAAGATCTGAGG[T/C]CCTAAAAAAATGGTGACACCACCTTCAGCACTAGAAGAACACTCACGGAGCAAGCTTAGTTATGAGTAACGCTATAGCATATTGAG
80024 A G AAAAAAGCCGAAGATGCTCCCGTCATTAGTGGTAGTCTCACCACTCATCGTCTTCCTTACC[A/G]TCCTCAGCCTACAGCTCGCAGTATCTTCTGTAGAACCCAGCTGCTCCAACATTGTCCCTTTCAGAACCCGTCCCGAAACCATATCCATAACCGACTTCGG
80024 T C GGCGTTCGTGGAAGCCATTTACAGAATCGAGCACCTCCATCGTGACGGCGGCACCACTCTGTATGTTCCGAAAGGCGTTTGGCTCACCGCCCCTTTCAAT[T/C]TGACTAGTCATATGACTCTCTTTCTTGAACAAGGCGCTGTCATTAGAGCTGTTCAGGATACGGAGAACTGGCCATTAGTGGAGGCAC
80040 T C GTTGGCCTACTGGATTTTTTGCTCTCCAGCTTCAAAAACCCTAAACCCAAACTAATTTAGTTGATTCTGAATTATACTGTTT[T/C]CTGTAAAGTTATCGTATGGCGGCGAGGGCAGTTCTCTTTCGAATTGCAAAGAACAGTTTTGCTAAACGAATAATTTTCGAATCCAAACGGAAAGAACAGC
80040 T C CATTCTGTTCTTTGAATCACTTCAATTCGATGTGTTCTTCCAAGTCACTTACCCCGAATGCTGCATTCCAAAGATTTGGTTATTCTTCAAATGCAACTTC[T/C]GAGAACAAGGAGAAGGAACCTCCATCTGAGAACAATGAGAAGGAAGCTGAGGAACCCGCAAACCAAGATACTAACGAGGCTAAAAAAA
80056 A C CCAAACACACATGTCAAATACTCATCACGCTAATCAAACCACTTACTATAGTTTCTTATCAAACAAACCAATGGCACAAGATATACGCATATATTCTTCA[A/C]ACAACGCTGCACCTTGTATGACAGGCAGTGGCATTCATGCTCATGCACGTGTAACGTGGAGGCAATATCTGATATGCTGCTGCTTCCAC
80056 G A AGTTTCTTATCAAACAAACCAATGGCACAAGATATACGCATATATTCTTCAAACAACGCTGCACCTTGTATGACAGGCAGTGGCATTCATGCTCATGCAC[G/A]TGTAACGTGGAGGCAATATCTGATATGCTGCTGCTTCCACACAATTTTCGCAACCATCCCCACACTTGGGAACGATATCCAGGCATTC
80056 T C ACAAGATATACGCATATATTCTTCAAACAACGCTGCACCTTGTATGACAGGCAGTGGCATTCATGCTCATGCACGTGTAACGTGGAGGCAATATCTGATA[T/C]GCTGCTGCTTCCACACAATTTTCGCAACCATCCCCACACTTGGGAACGATATCCAGGCATTCGCATTTTGCTGTATCTGTACCCGCTTC
80056 C T TTTCGCAACCATCCCCACACTTGGGAACGATATCCAGGCATTCGCATTTTGCTGTATCTGTACCCGCTTCTGTGCACGACCCACAGTTATCACAGCATAA[C/T]ACCTCTACGTCTACGTCTATGTCTTCGTCTCCTGTGTCGTCATTTTTATGTGTTGACTGAAGAAGATTGCTCTGAAAGTGTGCAACCAAG
80088 T TA GGAGGTCGCGGTGGACGAGGTGGTCGGGGGCCTCGTGGAGGAGAAGAAGGAGACAAAGAATGGGTTCCTGTTACAAAACTTGGTCGCCTTGTTAAGGATT[T/TA]AAAGATCAAGACTATTGAGGAGATCTACCTATTCTCACTTTCCCATCAAGGAGTGTGAAATTATCGACTACTTCTTGGGCCTCA
80088 CT C AGGAGAAGAAGGAGACAAAGAATGGGTTCCTGTTACAAAACTTGGTCGCCTTGTTAAGGATTTAAAGATCAAGACTATTGAGGAGATCTACCTATTCTCA[CT/C]TTTCCCATCAAGGAGTGTGAAATTATCGACTACTTCTTGGGCCTCAACACTAAAAGATGAGGTCCTCAAGATCATGCCAGTGCAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
80088 C CG TCCTGTTACAAAACTTGGTCGCCTTGTTAAGGATTTAAAGATCAAGACTATTGAGGAGATCTACCTATTCTCACTTTCCCATCAAGGAGTGTGAAATTAT[C/CG]GACTACTTCTTGGGCCTCAACACTAAAAGATGAGGTCCTCAAGATCATGCCAGTGCAAAAACAGACCCGTGCTGGACAACGAACTCG
80088 GC G TTGGTCGCCTTGTTAAGGATTTAAAGATCAAGACTATTGAGGAGATCTACCTATTCTCACTTTCCCATCAAGGAGTGTGAAATTATCGACTACTTCTTGG[GC/G]CCTCAACACTAAAAGATGAGGTCCTCAAGATCATGCCAGTGCAAAAACAGACCCGTGCTGGACAACGAACTCGCTTCAAGGCATTCG
80102 T G CATCTCCGTCGATGTCACCGGCGCACCACCGATCATCCTCGGGATCAGGCTTCGCCTTAACCAATATTAAGAGGACTCAGAATTTGGCGGCGAAGGCAGC[T/G]AACGCGAGATTAGCGCAGGTGATGGCATCGCAGCAGAGTGCAGATGAAAATGACGACGAGGATGACGACGACATGGAAGAGGT
80102 A C GCAGAGTGCAGATGAAAATGACGACGAGGATGACGACGACATGGAAGAGGTGAGCGTGCCAATGGGTGCGGGGAGGTTTGGTGTTGGTGCTAGAGGTAGT[A/C]TCGGGATTAGCAGTAATAGCAGTAACGGGTCTTCTTTGCTTGGTAGGCCTGCTAGGTCTCCTTCCCC
80102 C T AGAGTGCAGATGAAAATGACGACGAGGATGACGACGACATGGAAGAGGTGAGCGTGCCAATGGGTGCGGGGAGGTTTGGTGTTGGTGCTAGAGGTAGTAT[C/T]GGGATTAGCAGTAATAGCAGTAACGGGTCTTCTTTGCTTGGTAGGCCTGCTAGGTCTCCTTCCCC
80112 G GA TGCCCCTTGTCTCCTGTATCCACCAAGTCCATGCTGTCTCACACAGTTTCGTCCGAGGCTGAGTACATAATACAGCAGTTTCTAGCTACCACAGGGTGTG[G/GA]AAAAATGGAGGGAGAAGGAAAGAAGAAGAAGAAGAGCATGTATGCATCGGGCAGGGTGAAAGTTGTAATTGTGCAAGACGATAA
80122 GA G TTACATCGATATGATTCTCAAAGCATTGCATTACATCAAGAAATTACATCCAACTACAAATATATCACTTGCATCATTTCATTAACCTCGGACAGAATCA[GA/G]AAAAGAAAATCTTCAAACTAAGCTGCAGGAGCAGGCAAAGCAGCAGCACCATTCTCAACTTCATTCTTGACCCTATCTCTCTCCTCCAA
80142 C T GATGTCAAATCAACCACTGTAGCACCCTCCTGACCACTTCCAAAGGATAAGTCTTCACTTTTGTTCATGTTCTCGAGATGAGGAAAATGGTGGCGAATTG[C/T]ATAGTCTGCCAAAAGCTGGACAATTTTTAGATCTTCTTTGCCTCTAATAGCATGAAGCTGATATGAACCAAACCGAAGAAATGATGGA
80146 T C AATTCTACCAGTTCTCTTTTGAAGCCAACGAATTTATAGAAATCCCTGAATTGTCAAAATCACCATTG[T/C]TATCATCATTGGTAGACAATCCACATATTTTTATCAGGTCTTCTCATGGTTGGTTGTTTTTGCTTGATCTGCATACTAAATCTGTTTTATTAATTAACCC
80146 C A AATTCTACCAGTTCTCTTTTGAAGCCAACGAATTTATAGAAATCCCTGAATTGTCAAAATCACCATTGTTATCATCATTGGTAGACAATC[C/A]ACATATTTTTATCAGGTCTTCTCATGGTTGGTTGTTTTTGCTTGATCTGCATACTAAATCTGTTTTATTAATTAACCCCCTCACCGATTCCGTTATCTGT
80152 T G AGCGCTCTAAGAAAGGGGCGAAGTGGGAATTACGGGAGAAGGAGTTCGACCTTATCCATATCCTGCTGAGGATTTGGGGGTATTTCCGTAATTTGGAGTC[T/G]GATTCGAGGATCACGGTCAGACCCGCCATTAGCGATGTGTTTTTCTTCTCTGTTAAGCTTAAAATCCAGTAGGCCAACAG
80154 A G AGCTAATGTGGTAAGCAAGCCCCACGTTATTCTTCGATATCACCACAACCTGTAAGCAGTCACTCTCAATGCACCTTAGAGCA[A/G]TCGGTGGAAGGACTGATGGCATAAGGAATGCTAACGCCGCACTTGGAAGGAACTCCAGCGACAGCGCCATAGTTGATACCCTTAATGCTGCTGGTCAACC
80154 T G CAAGCCCCACGTTATTCTTCGATATCACCACAACCTGTAAGCAGTCACTCTCAATGCACCTTAGAGCAATCGGTGGAAGGACTGATGGCATAAGGAATGC[T/G]AACGCCGCACTTGGAAGGAACTCCAGCGACAGCGCCATAGTTGATACCCTTAATGCTGCTGGTCAACCTCTTCAGGCAGCCACAGG
80160 C G TGCTTGGGCTTCTGTCTGAAGGACTGGGAGTGGAATACGAAAAATTAGAAAAGATGACGATCT[C/G]TGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTG
80160 G A TGCTTGGGCTTCTGTCTGAAGGACTGGGAGTGGAATACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTT[G/A]ATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATC
80160 C T TGCTTGGGCTTCTGTCTGAAGGACTGGGAGTGGAATACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTTGATGG[C/T]CTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTT
80160 A G TGCTTGGGCTTCTGTCTGAAGGACTGGGAGTGGAATACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCC[A/G]TGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAG
80160 A G AAGGACTGGGAGTGGAATACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAA[A/G]ACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATG
80160 T G ATACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCC[T/G]TGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGG
80160 T C TACGAAAAATTAGAAAAGATGACGATCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCT[T/C]GCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGA
80160 G T CGATCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGT[G/T]ACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAA
80160 C T TCTCTGAAGGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGAC[C/T]GTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCT
80160 C T GGGAGGTTGATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTG[C/T]TCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGG
80160 A G ATGGCCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATC[A/G]AGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTA
80160 T C CCTGTCATTATTATCCATGGTGCCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGT[T/C]GGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCA
80160 A G CCCTGAGCCGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATG[A/G]AAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGA
80160 C T CGGAGAAAACAGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCC[C/T]ACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCA
80160 T C AGTTGGTACAGCCTTGCATACAGATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAG[T/C]GGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTAC
80160 T A ATCCAGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACC[T/A]CTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCA
80160 G A AGGTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTC[G/A]ACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGC
80160 C T GTGCAGTGACCGTGCTTGCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGA[C/T]GGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAA
80160 A T GCTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCA[A/T]TGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGG
80160 T C CTCAAGATCAAGTTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAA[T/C]GTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTA
80160 A G TTGGAGGGCTACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTT[A/G]TTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTG
80160 T A TACAGGTAAAGATGAAAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGAT[T/A]ATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTT
80160 G A AAGGTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGA[G/A]TACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAG
80160 C T GTCCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTA[C/T]AAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGG
80160 A G CCCACTGGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACA[A/G]AAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCG
80160 C T GGGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTG[C/T]GGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAG
80160 G T GGGAGTGGGGATGGGTAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGC[G/T]GAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGA
80160 C T TAGATGTTAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCAT[C/T]GCAAACACCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGATTTCTTTGGACCTCTTC
80160 A T TAAACCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAAC[A/T]CCCGTGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGATTTCTTTGGACCTCTTCCTGA
80160 G A CCTCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCC[G/A]TGAGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGATTTCTTTGGACCTCTTCCTGA
80160 G A TCTCGACGGTGCCTTTGTAATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGT[G/A]AGGAGGGTAGAGTTTCACTTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGATTTCTTTGGACCTCTTCCTGA
80160 C A AATCAATGTTGGTGATTTATTGCAGATTATTTCCAATGATGAGTACAAAAGTGCGGAACATCGAGTCATCGCAAACACCCGTGAGGAGGGTAGAGTTTCA[C/A]TTGCAACTTTCTTCAACCCCACGAAAAGAGGCGAGTCAGATTTCTTTGGACCTCTTCCTGA
80170 G C GGTGGTAAAAGCGACAAGGGCTTCTTTGGGGAATCTACTTTGGGTGCTTCTTTTATGGCATTGGCTGTTGCTGTAATTCTAGTTATTTTGCTGAAGAGGG[G/C]TTAGATGATTTACCAAAAAACTACTCGTCGACTATGCTACTGGCTTTGCTTATCAAGTGCATTTTCATGTTGGTGTGAGTTTATGTACA
80194 C T AATTCATGGCTCCCATGAAAATTCCCAAATTGAGAAGATCGGTCCGCCCGTGACCTTCCGCCACCGCACCCTCAACGCCCCTTCCACC[C/T]TCCTCGGCGCAACTGCCGTGACTCCTCCCTCCATCGCCCTCCAATTTAAGTCCACCGTGAAGACTACAAACCGCAGCCACCCCATCCGCTGTTTCCGTTT
80194 G A TGGCTCCCATGAAAATTCCCAAATTGAGAAGATCGGTCCGCCCGTGACCTTCCGCCACCGCACCCTCAACGCCCCTTCCACCCTCCTCGGCGCAACTGCC[G/A]TGACTCCTCCCTCCATCGCCCTCCAATTTAAGTCCACCGTGAAGACTACAAACCGCAGCCACCCCATCCGCTGTTTCCGTTTGAACTGC
80194 A G TTGAACTGCCGCTGTCACCAAATGGAGCCTGCTCCGCTTCCGTCCCTTTGAGCGCCACCTTGAATTTTGGTCCGGTCCTTGCTTGTTTGCTCCATCTCAC[A/G]TTCCTTCCAGCGCTGCAACAACTGCTGCTCCAGTCGAATCACCACCGTTCGATCCACCAGCGGTGTCGCCAAACCATTCCAGCGCCCCC
80194 A C AATGGAGCCTGCTCCGCTTCCGTCCCTTTGAGCGCCACCTTGAATTTTGGTCCGGTCCTTGCTTGTTTGCTCCATCTCACATTCCTTCCAGCGCTGCAAC[A/C]ACTGCTGCTCCAGTCGAATCACCACCGTTCGATCCACCAGCGGTGTCGCCAAACCATTCCAGCGCCCCCGGGCCCAATGTCATGTCCAT
80194 G A GGTCCGGTCCTTGCTTGTTTGCTCCATCTCACATTCCTTCCAGCGCTGCAACAACTGCTGCTCCAGTCGAATCACCACCGTTCGATCCACCAGCGGTGTC[G/A]CCAAACCATTCCAGCGCCCCCGGGCCCAATGTCATGTCCATCTCCATTTGCGCTTCAGCCTAGTCCCG
80210 C T AGGACCGGAGGCGGAGTCGGAGCTCATAGGACGTGCTCAGGGCATGTACGCCTGCGCTGC[C/T]TTGCAGGAGCTTGGCTTCTTACAGGCCATGAACCTTTACTTCACTGCAGGGAAGTATAATGGGAGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGA
80210 C G AGGACCGGAGGCGGAGTCGGAGCTCATAGGACGTGCTCAGGGCATGTACGCCTGCGCTGCCTTG[C/G]AGGAGCTTGGCTTCTTACAGGCCATGAACCTTTACTTCACTGCAGGGAAGTATAATGGGAGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCC
80210 T C AGGACCGGAGGCGGAGTCGGAGCTCATAGGACGTGCTCAGGGCATGTACGCCTGCGCTGCCTTGCAGGAGCT[T/C]GGCTTCTTACAGGCCATGAACCTTTACTTCACTGCAGGGAAGTATAATGGGAGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCCGACGAGGG
80210 G A TCATAGGACGTGCTCAGGGCATGTACGCCTGCGCTGCCTTGCAGGAGCTTGGCTTCTTACAGGCCATGAACCTTTACTTCACTGCAGGGAAGTATAATGG[G/A]AGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCCGACGAGGGAGATGGCGGTGATAGGAGGAAGCGGACTGTTCAG
80210 G A AGCTTGGCTTCTTACAGGCCATGAACCTTTACTTCACTGCAGGGAAGTATAATGGGAGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCCGAC[G/A]AGGGAGATGGCGGTGATAGGAGGAAGCGGACTGTTCAGATTTGCAAGGGGCTTTGCTTTGGCCAGGACTCACTGGATTGATTTT
80210 G A GCAGGGAAGTATAATGGGAGCGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCCGACGAGGGAGATGGCGGTGATAGGAGGAAGCGGACTGTTCA[G/A]ATTTGCAAGGGGCTTTGCTTTGGCCAGGACTCACTGGATTGATTTTGGAACTGGGGATGCTGTTGTACATTACAACGTTACCG
80210 T C CGTGCTAACGGTAATGGGGCGCAACGCTCCGATGAATCCGACGAGGGAGATGGCGGTGATAGGAGGAAGCGGACTGTTCAGATTTGCAAGGGGCTTTGCT[T/C]TGGCCAGGACTCACTGGATTGATTTTGGAACTGGGGATGCTGTTGTACATTACAACGTTACCGTTCTCCACTACTGAAAGTCTAA
80210 C T AATGGGGCGCAACGCTCCGATGAATCCGACGAGGGAGATGGCGGTGATAGGAGGAAGCGGACTGTTCAGATTTGCAAGGGGCTTTGCTTTGGCCAGGACT[C/T]ACTGGATTGATTTTGGAACTGGGGATGCTGTTGTACATTACAACGTTACCGTTCTCCACTACTGAAAGTCTAAAATAATGCTTGC
80212 G A TAGGACTAATCCAAGCTCTCTCGTCTACGAACCAAAATCATAAAGCCCCCAAATTCCTTTTGTCCCTCACTCAAATCCCTAAATCATGAGGATATCCAAT[G/A]ATGAAAACAAGGATCCAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCA
80212 C G CTCTCTCGTCTACGAACCAAAATCATAAAGCCCCCAAATTCCTTTTGTCCCTCACTCAAATCCCTAAATCATGAGGATATCCAATGATGAAAACAAGGAT[C/G]CAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGG
80212 C T CGAACCAAAATCATAAAGCCCCCAAATTCCTTTTGTCCCTCACTCAAATCCCTAAATCATGAGGATATCCAATGATGAAAACAAGGATCCAATTCCGACT[C/T]CAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
80212 T C ATCCCTAAATCATGAGGATATCCAATGATGAAAACAAGGATCCAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGA[T/C]GTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCACACATAAAATTGAACAAGAATCCGGCAAAGAAGATCTGCTTCCGTG
80212 A G TCCAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCC[A/G]CACATAAAATTGAACAAGAATCCGGCAAAGAAGATCTGCTTCCGTGCAGACCCGATAAATTTGTATTTTTTCCCAATCTGAAATTTAT
80212 C G CCAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCA[C/G]ACATAAAATTGAACAAGAATCCGGCAAAGAAGATCTGCTTCCGTGCAGACCCGATAAATTTGTATTTTTTCCCAATCTGAAATTTATT
80212 A G CAATTCCGACTCCAAAAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCAC[A/G]CATAAAATTGAACAAGAATCCGGCAAAGAAGATCTGCTTCCGTGCAGACCCGATAAATTTGTATTTTTTCCCAATCTGAAATTTATTC
80212 A T AAAGCCGAAAAAGCAGCAGACTCCGCCCGAAACCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCACACATAAAATTGAACA[A/T]GAATCCGGCAAAGAAGATCTGCTTCCGTGCAGACCCGATAAATTTGTATTTTTTCCCAATCTGAAATTTATTCCTGAATCCGAAGAAG
80212 G A CCGCTCTCGGATGTCACAAACATTCAAACTACTTCACCCGGAGCTGAAGCCACACATAAAATTGAACAAGAATCCGGCAAAGAAGATCTGCTTCCGTGCA[G/A]ACCCGATAAATTTGTATTTTTTCCCAATCTGAAATTTATTCCTGAATCCGAAGAAGTTGCTTC
80228 T C GGGGACGAAGTTGCTGCGGAATCAGTGGTCGATTCAAAGGATTTGCAGCAACAAAGCAAGGCACTAGATAAGCTTACTGATCGTGTAGAAGATCGACAGC[T/C]GGATTCAACCCGTGTTCAATCGGCCATGGCGTCTCTAGCTTCGTCTAAAGAAGCTGACCTCAATGCAATGAGATTGAGGGAAAAG
80228 A G GAATCAGTGGTCGATTCAAAGGATTTGCAGCAACAAAGCAAGGCACTAGATAAGCTTACTGATCGTGTAGAAGATCGACAGCTGGATTCAACCCGTGTTC[A/G]ATCGGCCATGGCGTCTCTAGCTTCGTCTAAAGAAGCTGACCTCAATGCAATGAGATTGAGGGAAAAGGAATTGGCTGCAGTGAAA
80228 T C TAGATAAGCTTACTGATCGTGTAGAAGATCGACAGCTGGATTCAACCCGTGTTCAATCGGCCATGGCGTCTCTAGCTTCGTCTAAAGAAGCTGACCTCAA[T/C]GCAATGAGATTGAGGGAAAAGGAATTGGCTGCAGTGAAAATCAATTCCGCAGATGTTGATATAATTGCAAACGAGCTTGAGTTGGA
80240 T C CCTCGTTTCCAAATTCTTCAAAGCGATCAACGAGCCCAATCCATCCACGGACCCTGCCAAAGGAGGCCATTCCGACAGTGTCGACTATGGCGATAA[T/C]GACGACGATGTGTATGAGAGGGAGAAGGCTGCCAGGAAAGGTGGAGCCTGCATTCCTCCTCCGGCAAGCCTGCAGAAGCAGGATCAGG
80240 C A CCTCGTTTCCAAATTCTTCAAAGCGATCAACGAGCCCAATCCATCCACGGACCCTGCCAAAGGAGGCCATTCCGACAGTGTCGACTATGGCGATAATGA[C/A]GACGATGTGTATGAGAGGGAGAAGGCTGCCAGGAAAGGTGGAGCCTGCATTCCTCCTCCGGCAAGCCTGCAGAAGCAGGATCAGG
80240 G C GCAGTGTTGAACGTAAAAGCGGGTCTGGAAGACTTGGGCTTGGTGCTGCCGCCGACCCGAATGAGATTAGTCAGTACGATGATGTCTACAGCTCCTATCG[G/C]AAGAATCGCAGTACCAATTACCATTCGTCCATGAGCGCAAGAGCAACCACTAGGTGATCACAGATTTTGTACTTTGAAAAAGTGAT
80240 C G AACGTAAAAGCGGGTCTGGAAGACTTGGGCTTGGTGCTGCCGCCGACCCGAATGAGATTAGTCAGTACGATGATGTCTACAGCTCCTATCGGAAGAATCG[C/G]AGTACCAATTACCATTCGTCCATGAGCGCAAGAGCAACCACTAGGTGATCACAGATTTTGTACTTTGAAAAAGTGATTTGTATTGT
80290 A C AGGGTTAGGGTTGGCTGCCGCTTCTGAGCTCTACAATGGTTAAGTTTCTGAAACCAAACAAAGCTGT[A/C]ATCCTACTGCAAGGCCGATTCGCCGGCCGTAAAGCGGTCATTGTTAGGAACTTTGACGATGGCACCCGCGACCGTGCTTACGGTCACTGCCTGGTCGCCG
80290 C T TCCGTAAGGATTCGGCGAAAAAGACTGCGAAGAAATCCAGAGTTAAGGCTTTCGTGAAGGTTGTGAACTACAGTCATATAATGCCTACTCGGTACACACT[C/T]GATGTCGATTTGAAGGATGTTGTTACCCTTGAAGCGCTACAGTCGAAGGATAAGAAAGTTGAAGTTAGCAAAGAGGTGAAGAAGA
80290 T C TCGTGAAGGTTGTGAACTACAGTCATATAATGCCTACTCGGTACACACTCGATGTCGATTTGAAGGATGTTGTTACCCTTGAAGCGCTACAGTCGAAGGA[T/C]AAGAAAGTTGAAGTTAGCAAAGAGGTGAAGAAGAGGTTCGAGGAGAGATTCAAAACCGGAAAGAACAGGTGGTTTTTTA
80316 T C GTTGAGCCAGAGGTTGCAAAGGTGGAGGAGGTCGATCATGGACTTGATGAGAGTGACAGTGAGAGCAAACCAGCCGTCGATGAAGAGGCACATCATGGTG[T/C]TGCTGATGGAGAGGGTGTAGAGGAAGAGGGGGTCGACTATGAGGCCTGCTGCACACGTTACTAAGTATGCTCTCTTCCATTCT
80342 C T ATTTTATATAACGTGTATAAGTCACACGATTTACACGTTTAAGAATAAATGAAACAATTACTTATATTCTGTATACATGCACAAATTGATATATACACAG[C/T]CATATGTGTGTTGGAAACTTGGAATAAACGCATATTCTATAAGCTGGAAATGGAATTATCCTGCAACGGCTCCCTTTATTGCACCAAACA
80342 G A TAACGTGTATAAGTCACACGATTTACACGTTTAAGAATAAATGAAACAATTACTTATATTCTGTATACATGCACAAATTGATATATACACAGCCATATGT[G/A]TGTTGGAAACTTGGAATAAACGCATATTCTATAAGCTGGAAATGGAATTATCCTGCAACGGCTCCCTTTATTGCACCAAACAGAGCTAA
80342 C T ATAAATGAAACAATTACTTATATTCTGTATACATGCACAAATTGATATATACACAGCCATATGTGTGTTGGAAACTTGGAATAAACGCATATTCTATAAG[C/T]TGGAAATGGAATTATCCTGCAACGGCTCCCTTTATTGCACCAAACAGAGCTAAAATGGAAGCAATAATAGCCGCAATAGTGCAAGCAA
80362 G C ACATTTCGTTTTCCATGCAAAACAAAGGAAAACTCGTGTTCCCCGACCGTTCCGTCCGAGACATCATGCAGCCGACAACTGTAGCAGAGCTGATGCTGGA[G/C]CACCCACAGTATTTCGTGATCGAGTTCGAGCAGAGCTCGGCTTACAAGCCAATTCCACTTCACGCCGACCATGCGCTACGATCCAGC
80362 A G TAGCAGAGCTGATGCTGGAGCACCCACAGTATTTCGTGATCGAGTTCGAGCAGAGCTCGGCTTACAAGCCAATTCCACTTCACGCCGACCATGCGCTACG[A/G]TCCAGCAGGCTCTACTTAATGGTTCCGATGAGTCAGTACAGAGCGAACGGGTTTTCGGTTAGCGAAGCAAATCGCATGGTGTTGG
80362 C T AGCTGATGCTGGAGCACCCACAGTATTTCGTGATCGAGTTCGAGCAGAGCTCGGCTTACAAGCCAATTCCACTTCACGCCGACCATGCGCTACGATCCAG[C/T]AGGCTCTACTTAATGGTTCCGATGAGTCAGTACAGAGCGAACGGGTTTTCGGTTAGCGAAGCAAATCGCATGGTGTTGGGAGCTCG
80362 A T AATTCCACTTCACGCCGACCATGCGCTACGATCCAGCAGGCTCTACTTAATGGTTCCGATGAGTCAGTACAGAGCGAACGGGTTTTCGGTTAGCGAAGCA[A/T]ATCGCATGGTGTTGGGAGCTCGAAAGGCGAAGGCTTTTTCGCTGTTTGGAGCTTGCGCGGCGGGAGAAGGGAAGGAGGAGGCCG
80362 G A TGAGTCAGTACAGAGCGAACGGGTTTTCGGTTAGCGAAGCAAATCGCATGGTGTTGGGAGCTCGAAAGGCGAAGGCTTTTTCGCTGTTTGGAGCTTGCGC[G/A]GCGGGAGAAGGGAAGGAGGAGGCCGAGGAAGCGGTGAAGAAATGCGGAGAGGGAGAAGGGATGATAATGGA
80388 T C TGCATGTATCTGTGCATGAAGTATTGCCATGTGTCCATTATGATCATTGCTATCAAGAATTGTTTTGCGTACAATAGCATGGATG[T/C]GGGCTGTGGGGATGTGGTTTCGGTGCTTCCAGCAACCGCAAACAACAAAAGGGAGACAGCAGCCTGAATTGATTGCTGAAACAGGACTCCTTTGACTACA
80390 G A GAGAGACGGAGGCAGTAGTTCTGGCAATTGGGCCAGGTACGCGACCCGATGCAGAAGCCTCCGCCGTGGAAGTAGAAGAGGATCGGGAGTTTGGAGGAGT[G/A]GGATCGAGGTTTGTAGAGACGGAGGGAGAGGTCGTGGGTGGGATCGAACTGGACGTCCTTCCAGTCGACGGTGCCGTCGTC
80390 G A GGAAGTAGAAGAGGATCGGGAGTTTGGAGGAGTGGGATCGAGGTTTGTAGAGACGGAGGGAGAGGTCGTGGGTGGGATCGAACTGGACGTCCTTCCAGTC[G/A]ACGGTGCCGTCGTCGTGGATGGGGACGGGGAAGCTAGGGTTTGGGGACCGGACGATGGACCCGTCGCTGTAGACTCTTAG
80406 C T AAATTTCCCACATATCCTTTGATTTTCTCCTCTAGAACAAAAATCTCAGGTAGGACAGACGGTTGGGCCAGCAAAGGCAGTGCGTATTGTAGCCCACTAA[C/T]ACAAACAGCTGGTCGCCTCGGAGATGAAGGAAGTCGAAGGTATTACAAACGTCGAAAGCAGCAGAGCACGAAAAGGCGAAATCAA
80406 G A CACATATCCTTTGATTTTCTCCTCTAGAACAAAAATCTCAGGTAGGACAGACGGTTGGGCCAGCAAAGGCAGTGCGTATTGTAGCCCACTAACACAAACA[G/A]CTGGTCGCCTCGGAGATGAAGGAAGTCGAAGGTATTACAAACGTCGAAAGCAGCAGAGCACGAAAAGGCGAAATCAACTCGTAAG
80406 G A TTTCTCCTCTAGAACAAAAATCTCAGGTAGGACAGACGGTTGGGCCAGCAAAGGCAGTGCGTATTGTAGCCCACTAACACAAACAGCTGGTCGCCTCGGA[G/A]ATGAAGGAAGTCGAAGGTATTACAAACGTCGAAAGCAGCAGAGCACGAAAAGGCGAAATCAACTCGTAAGAAGACGCGAATAGT
80406 C T TAGGACAGACGGTTGGGCCAGCAAAGGCAGTGCGTATTGTAGCCCACTAACACAAACAGCTGGTCGCCTCGGAGATGAAGGAAGTCGAAGGTATTACAAA[C/T]GTCGAAAGCAGCAGAGCACGAAAAGGCGAAATCAACTCGTAAGAAGACGCGAATAGTGTCGAGTGGAGAAATGGGATGGCTG
80406 C A AGCAAAGGCAGTGCGTATTGTAGCCCACTAACACAAACAGCTGGTCGCCTCGGAGATGAAGGAAGTCGAAGGTATTACAAACGTCGAAAGCAGCAGAGCA[C/A]GAAAAGGCGAAATCAACTCGTAAGAAGACGCGAATAGTGTCGAGTGGAGAAATGGGATGGCTGAGGCGAAGAGATTTGGCTG
80412 C T CGCTTCACAAACTCGAGCAAAAGGCCAAAGAGTTCTTCGCTCTTCCTTTACATGAAAAAAGACGCGCCAGAAGAGACAAAGACAACTTCATGGGTTACCA[C/T]GACTCTGAACACACAAAAAACGTCAGGGATTGGAAGGAAGTTTTCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAA
80412 T G TCACAAACTCGAGCAAAAGGCCAAAGAGTTCTTCGCTCTTCCTTTACATGAAAAAAGACGCGCCAGAAGAGACAAAGACAACTTCATGGGTTACCACGAC[T/G]CTGAACACACAAAAAACGTCAGGGATTGGAAGGAAGTTTTCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTC
80412 T C ACAAACTCGAGCAAAAGGCCAAAGAGTTCTTCGCTCTTCCTTTACATGAAAAAAGACGCGCCAGAAGAGACAAAGACAACTTCATGGGTTACCACGACTC[T/C]GAACACACAAAAAACGTCAGGGATTGGAAGGAAGTTTTCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTCATC
80412 T C AGTTCTTCGCTCTTCCTTTACATGAAAAAAGACGCGCCAGAAGAGACAAAGACAACTTCATGGGTTACCACGACTCTGAACACACAAAAAACGTCAGGGA[T/C]TGGAAGGAAGTTTTCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTCATCCATAATCGCTGGCCGGAGTTCCCC
80412 G A TGAAAAAAGACGCGCCAGAAGAGACAAAGACAACTTCATGGGTTACCACGACTCTGAACACACAAAAAACGTCAGGGATTGGAAGGAAGTTTTCGATTTT[G/A]CAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTCATCCATAATCGCTGGCCGGAGTTCCCCCTTGATATGAGGGACGTGTGC
80412 T C ACAAAAAACGTCAGGGATTGGAAGGAAGTTTTCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTCATCCATAATCGCTGGCCGGAGT[T/C]CCCCCTTGATATGAGGGACGTGTGCATGGAGTACAAGAATGCTCTTGAAGTGCTAGCATTCAAGATAATAGAGCTTATCTCACTGTC
80412 G A TCGATTTTGCAGCCAGGGAGCCTATGCTTCTCTCTGACTCCAAACTCATCCATAATCGCTGGCCGGAGTTCCCCCTTGATATGAGGGACGTGTGCATGGA[G/A]TACAAGAATGCTCTTGAAGTGCTAGCATTCAAGATAATAGAGCTTATCTCACTGTCTTTGAAACTACCTGCTAA
80414 C G AAAGTGTTTCATGCCTCTCGGGATCAATTTGTAGGGCTTCTTCTAATTTAGATTTAGCAACTTCACAGTATTCAACGGACTCAGCAGGAGACTGAAAACC[C/G]GCGAGTTCAAGGAGAGCTCCACCCCACTTCGTCAAATTTTCAGCGTCGAGAGGGTTCTGGGCGTAAGCGAGCTCGGCAGTCTTTCGC
80414 G T TCAACGGACTCAGCAGGAGACTGAAAACCCGCGAGTTCAAGGAGAGCTCCACCCCACTTCGTCAAATTTTCAGCGTCGAGAGGGTTCTGGGCGTAAGCGA[G/T]CTCGGCAGTCTTTCGCGCGTGCTCCATCATGAGAAGGCGATCCAAATCGCTCTGTGAACTTTCCATTTGTTCCTTTCAACTACACTA
80426 T C GTGGCGCATTGAGTTAAGGGCTCGAATTTGGTGTCTTTTAGGGTTTGATAGATGAGGGAGTTTCTGGTGATTATGAGTTTGGA[T/C]GATTTGGGGAGGGACGCACGGAGGTTTTGGAGGTGGGTTGTTGAGAGGCCGTTGCAGTATATTCCGGCGATCAGGTGGCAATTGCTCAGCTGGCGGCGGA
80426 T C ATATTCCGGCGATCAGGTGGCAATTGCTCAGCTGGCGGCGGAGAGTTTGCTTCTTTGTGAGGGAGATGATAGGGCGGATTGACATTGAATTGCGATCAGG[T/C]GCAAGGGTGAACCTTTCTACCGTTCTACGTTAAGCACGGCTGCAGGCATCAAGCAAGAAAAACAATAAATCGCACAATTAGAAAT
80430 C G GTTCACATCAATAACAGAAATACATAATCATCAGTCGACATGCAAACCCATATAGAAGGTCATACAAACAGAAGGCTATAAAGTGGGAATGGGAT[C/G]AGATGCAAATTCACAAATTTCACTTGGTCAGTCCACCGAAGAAGTTCTTAACACCTCCAACGACGCCTTCATCCTTCTTCTCAGGAGTACCCT
80476 T C TCAGCCCTATGTTGTTGACCATTCTTATGCACCGGAAGCCTTCTCCCGTGTCCTTGCTCTCGGCCCACAGCACTGACTCGTCCAGATAGTCCGGGTTGTA[T/C]GGGACCAAACGCACCGGATGGGTTGCACCCACTGCATGCTTTATGGCCTCACCTGTGGCTTTGTTCACTAGCGCGAAGCTTGGCTGTT
80476 A G ATGTTGTTGACCATTCTTATGCACCGGAAGCCTTCTCCCGTGTCCTTGCTCTCGGCCCACAGCACTGACTCGTCCAGATAGTCCGGGTTGTATGGGACCA[A/G]ACGCACCGGATGGGTTGCACCCACTGCATGCTTTATGGCCTCACCTGTGGCTTTGTTCACTAGCGCGAAGCTTGGCTGTTGCTCAGCA
80476 A G CCTTGCTCTCGGCCCACAGCACTGACTCGTCCAGATAGTCCGGGTTGTATGGGACCAAACGCACCGGATGGGTTGCACCCACTGCATGCTTTATGGCCTC[A/G]CCTGTGGCTTTGTTCACTAGCGCGAAGCTTGGCTGTTGCTCAGCATCCTTCACCCTTGTGCTGTACTTCATGTCTTTTATCCAGTGCTG
80476 A T GGTTGTATGGGACCAAACGCACCGGATGGGTTGCACCCACTGCATGCTTTATGGCCTCACCTGTGGCTTTGTTCACTAGCGCGAAGCTTGGCTGTTGCTC[A/T]GCATCCTTCACCCTTGTGCTGTACTTCATGTCTTTTATCCAGTGCTGATGCTCATCTGCAGGATTTGCAGGGGCCAGAACCACCTTTC
80476 C T CCTTCACCCTTGTGCTGTACTTCATGTCTTTTATCCAGTGCTGATGCTCATCTGCAGGATTTGCAGGGGCCAGAACCACCTTTCCATTCCTAACGGAAAG[C/T]GAGTAGCTCTCATCCGCCATAGTATAAACCCTAAACGGGCGCTGAAGTGGCAAGCCAGCAGGTGCAGGCCCAGGCCTATTCACGTGA
80476 G A CCCTTGTGCTGTACTTCATGTCTTTTATCCAGTGCTGATGCTCATCTGCAGGATTTGCAGGGGCCAGAACCACCTTTCCATTCCTAACGGAAAGCGAGTA[G/A]CTCTCATCCGCCATAGTATAAACCCTAAACGGGCGCTGAAGTGGCAAGCCAGCAGGTGCAGGCCCAGGCCTATTCACGTGAGTCGCC
80480 G A TTCTCTCCCGGAAACAGTTTGTGATTGACGTGACACATCCAGGCAAGGCCAATGTATCAAAAGCTGAGTTGAAGGAGAAACTTGCTAGCATGTATTCTGT[G/A]AAGGATCCAAATGCGATCTTTGTATTCAAGTTCAGAACTGATTTTGGAGGTGGGAAGAGTACCGGGTTCGGGTTGATTTATGATTC
80488 TG T TTGAATTGTTGTACGATACAGCTTTGATATCAAGTGGTTTCACGCCCGATAGCCCATCTGAACTGGGAAACAAGATATACGAGATGATGGCAATTGCCCT[TG/T]GGGGGTAGATGGGGAAGATCAGAATCGGATAGTGTAGAAGAAAAGGGCGAAGAACAAAGCGTGGAAGCAGAAGAATCATCAGA
80504 C CT TCTCCGCCTGCGGATTCTGTGCTGCTTTCAGCAAAAAGGGCGCTGCCAAGAAGAAGGGTAATAACAAGCCACGAAGAAGATAATCTTTTCCTTCCTCTTC[C/CT]TTTTTTCTTTTTACTGTGTGCTGTGATCATCTAAAAGATTTCGTTGCCCTATTTTCTATTTGATTATTGGTACATATCAGATTTCCCATA
80518 A G TTCCATCCATTGCTTCAACATCGTAACAAATTTTCTGATTAGGATGACTAGTTTGATATATCAACAAGACGGAGAAGAATGAAAAGAGCGGGGTCAATTT[A/G]CAAAAGGGTGCTCTAGAAGCTGCGACGCAGTGGGTCTTTTTGCCGGATTTGACTGCACGCATTGGACAATGAAGTCACGTGCATCTT
80540 G A CTGGAAGAAAATAATTATTTTTTAAATAAATAAAATCACACTGTTAGCAAGAACAGATAATGGGTAACTTGTTGTGCTGTGTGCAAGTCGATCAATCTAC[G/A]GTAGCTGTTAAAGAACAGTTTGGAAAGTTCGACGAGATTCTTGATCCAGGATGCCATTGCATGCCTTGGTTTCTTGGCAAAAGAGTTG
80540 A C AAGAACAGATAATGGGTAACTTGTTGTGCTGTGTGCAAGTCGATCAATCTACGGTAGCTGTTAAAGAACAGTTTGGAAAGTTCGACGAGATTCTTGATCC[A/C]GGATGCCATTGCATGCCTTGGTTTCTTGGCAAAAGAGTTGCTGGTTATCTTTCCCTTCGCGTGCAACAACTAGATGTCAAATGCGAG
80540 T C GAAAGTTCGACGAGATTCTTGATCCAGGATGCCATTGCATGCCTTGGTTTCTTGGCAAAAGAGTTGCTGGTTATCTTTCCCTTCGCGTGCAACAACTAGA[T/C]GTCAAATGCGAGACTAAAACTAAGGACAATGTTTTTGTTAATGTTGTTGCATCCATTCAGTATCGTGCTCTGGCCAGCAAGGCAAGCG
80550 A G CGAACATCGATATAGAAGGAATTATGAAGTCGCTGCCGAGCGATGGCAGAGTTCCCAAAACCAAAATTGTATGCACTCTGGGCCCTGCATCTAGATCCGT[A/G]CCGATGATCGAAAAGCTTCTCAGAGCTGGGATGAACGTTGCCAGATTCAATTTCTCACATGGATCGCACGAGTATCATCAGGAAAC
80550 G A CGCTGCCGAGCGATGGCAGAGTTCCCAAAACCAAAATTGTATGCACTCTGGGCCCTGCATCTAGATCCGTACCGATGATCGAAAAGCTTCTCAGAGCTGG[G/A]ATGAACGTTGCCAGATTCAATTTCTCACATGGATCGCACGAGTATCATCAGGAAACTCTCGATAATCTGAGAATCGCCATGCAGAA
80550 T C GCGATGGCAGAGTTCCCAAAACCAAAATTGTATGCACTCTGGGCCCTGCATCTAGATCCGTACCGATGATCGAAAAGCTTCTCAGAGCTGGGATGAACGT[T/C]GCCAGATTCAATTTCTCACATGGATCGCACGAGTATCATCAGGAAACTCTCGATAATCTGAGAATCGCCATGCAGAACACTCAAATC
80550 T C TTGCCAGATTCAATTTCTCACATGGATCGCACGAGTATCATCAGGAAACTCTCGATAATCTGAGAATCGCCATGCAGAACACTCAAATCCTTTGCGCTGT[T/C]ATGCTTGATACTAAGGGTCCTGAGATTCGCACGGGCTTCTTGAAAGATGGGAAACCTGTCCAACTAAAAGAGGGTCAAGAAATAACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
80594 T C AAAACTCTCTCCAAAAACCATCTCAGGCAAATGAGCTGTTTTTAGCTTCTTTTCCCATTCTTCAGTAGCAAGAGAGGTAAGAATAGGACGATTGGAAGAT[T/C]CGATCTGCCATCCTTTGATAGTCAATCCAAACCGTCCATCTGGCAGTAATACGGCGCCGGATTCTTTCAAATCGGTCTCTTTTCCTACT
80596 C T GTTGATATTAGCATGAACACGCACTTGAAGACAGTAAAGCTTACCTTGAAAGGGAAAAACCCAGTAACACTTGATCAC[C/T]TAAGTGTTAGAGGGAACAATATAAGATACTATATTCTACCTGACAGCTTGAATCTCGAGACTCTGCTTGTTGAAGAGACACCTAGGATTAAGCCTAAGAA
80596 C T TACCTGACAGCTTGAATCTCGAGACTCTGCTTGTTGAAGAGACACCTAGGATTAAGCCTAAGAAGGCTACTGCTGGGAAAACTGTGGGTCGTGGAAGAGG[C/T]AGAGGAAGAGGTCGTGGTCGTGGCCGAGGCCGCTAATATGTCGTCTGTATTCTGTGCACTTGTTTTTGTAATGATGAATCGTGCT
80596 G A ACCTAGGATTAAGCCTAAGAAGGCTACTGCTGGGAAAACTGTGGGTCGTGGAAGAGGCAGAGGAAGAGGTCGTGGTCGTGGCCGAGGCCGCTAATATGTC[G/A]TCTGTATTCTGTGCACTTGTTTTTGTAATGATGAATCGTGCTTAAAGAGAGTATTGTTACCTAAGGCTATGTATAAGCCTATGTA
80624 T C CTAACGGCGAAAGCAACGGCAAGTTAAAAATCCCACCTCCGTCCAAAAACGCCGTCCAACTCGACGGCGTCAGCGGACACTCCAGCTCCATCTCCGTCTC[T/C]TCTCTCACCCTCTCCTTCTTAACCACGACCTCCCTCTCCTCCACCGCAGTCTCCTCCCTCCCTCTCTTCCCCAACTCCGTCGCCCCTCCTG
80640 GA G CGAATCATCACAGACAGAAAAACCGAATAGTTTACGATCATTTTATTTCAAGTTTGACAACACTATTGATGTTGGCATTGACGGTTGCTAGTGTAAAAAA[GA/G]AAAGAAAACATTCATCCCCCATACCGACTCTTGAGAGATTCAGGAGGCTCCTCTTCCATGATGCCAGAACCAGTTGAACCCAAATAT
80642 T C GTATACGAGATCCAATTCAATCCTTTCTTCGAGCAGGTAGCCTAACCCATCGCCGTACAG[T/C]CACCGTCTTCCGGCTCTGGATCCGCATTCAGATCCAACCCCAATCCTCTAATTCCAGTCGCCTCACTTCCCGTAATCTCGCCGCTGACGCCTCCGCCTCC
80642 A T GGTAGCCTAACCCATCGCCGTACAGTCACCGTCTTCCGGCTCTGGATCCGCATTCAGATCCAACCCCAATCCTCTAATTCCAGTCGCCTCACTTCCCGTA[A/T]TCTCGCCGCTGACGCCTCCGCCTCCTTTAACCCCGCCGTCGAAATCCTCCCTCACGAAAGCCGGCTCCCATAGCGACTTCTGTGCCTCCT
80642 C G CGTACAGTCACCGTCTTCCGGCTCTGGATCCGCATTCAGATCCAACCCCAATCCTCTAATTCCAGTCGCCTCACTTCCCGTAATCTCGCCGCTGACGCCT[C/G]CGCCTCCTTTAACCCCGCCGTCGAAATCCTCCCTCACGAAAGCCGGCTCCCATAGCGACTTCTGTGCCTCCTCCTCCGTCTTCTTCACGG
80642 A C CGTCTTCCGGCTCTGGATCCGCATTCAGATCCAACCCCAATCCTCTAATTCCAGTCGCCTCACTTCCCGTAATCTCGCCGCTGACGCCTCCGCCTCCTTT[A/C]ACCCCGCCGTCGAAATCCTCCCTCACGAAAGCCGGCTCCCATAGCGACTTCTGTGCCTCCTCCTCCGTCTTCTTCACGGCGTCGATTGCT
80642 A C TCTAATTCCAGTCGCCTCACTTCCCGTAATCTCGCCGCTGACGCCTCCGCCTCCTTTAACCCCGCCGTCGAAATCCTCCCTCACGAAAGCCGGCTCCCAT[A/C]GCGACTTCTGTGCCTCCTCCTCCGTCTTCTTCACGGCGTCGATTGCTGCGACGCCATTGATGTATTGTGAAATTTCGCTCATTCGCCTCA
80642 GCCT G CGCCTCACTTCCCGTAATCTCGCCGCTGACGCCTCCGCCTCCTTTAACCCCGCCGTCGAAATCCTCCCTCACGAAAGCCGGCTCCCATAGCGACTTCTGT[GCCT/G]CCTCCTCCTCCGTCTTCTTCACGGCGTCGATTGCTGCGACGCCATTGATGTATTGTGAAATTTCGCTCATTCGCCTCACGATCCTGT
80642 C G CCATAGCGACTTCTGTGCCTCCTCCTCCGTCTTCTTCACGGCGTCGATTGCTGCGACGCCATTGATGTATTGTGAAATTTCGCTCATTCGCCTCACGATC[C/G]TGTAGAACTCTTCCACTTCGGCATCGGTGATGGAGTAGGAAGCGGCGACGTTGTGGTGATTGAGTTTCTGATGCTTTTGGCGATTGGT
80654 A G TAGGGTTAGGGTATCTAGGGTCTGGCGGAGGTCGATGGAGGATGGAGGTGATGTGATGGTCGAATGGAACGTTAGCATCAGCCTCTTTTCTGATTGTCTT[A/G]AAGCTTATTTTGATTCCGATAATTCTAATCTTGTTGCCACTGATACCATGAAGAACACCGTGTATGCAAAAGCAAAAGAATGCTCT
80654 T C TCTGGCGGAGGTCGATGGAGGATGGAGGTGATGTGATGGTCGAATGGAACGTTAGCATCAGCCTCTTTTCTGATTGTCTTAAAGCTTATTTTGATTCCGA[T/C]AATTCTAATCTTGTTGCCACTGATACCATGAAGAACACCGTGTATGCAAAAGCAAAAGAATGCTCTGAAGTTTTGCCAGTGGAAAAT
80656 A G TGGCATTCACTAGACGGCCCACCTTCTGTGGTTGGAATTTGACTTTCTTTGGCATCTACAAGAAACCTCAACTTGTTTTTGAACGGATGTGCATAGCTAA[A/G]GAAACAAACAATTTGCACAACTGCATCGATAATTATGCCATTGAGATAAGTTTCGCCTATATTAAGGGTGAACTGGCCGTTTGCCACA
80668 G A ATCCGACGGCAGAGGTGGACTTGGAGGAGCTGTTGCCGGAAGGGTTCATGGAGAGGACGAAGGAGGTGGGGATGGTGGTGAAGGCATGGGCACCGCAAGC[G/A]CAGGTGCTGAAGCATGAGGCGGTGGGTGGGTTTGTGAGTCATGTCGGGTGGAACTCCACCTTGGAGGCAGTGTGTGCAGG
80672 T C TTTCTCGAGCTTAGAAAAGCTTCAGACATCAAAGATGCTAAACCAATACACTCAAAGCAATAATCAGCCCCTCCGTTTGTCATCTCTATTATAACCTCAC[T/C]GACTGATTTTTCACCAATTTCTTTTGGGTTCACAAAATCTGTTAGCCCAAACTTTTTCCCCAATTCAAACTTGTCTGGATTAAGATCAACA
80696 C T ATCTCCCTTCTTAAATTTTTAATACCCGTAGCCAATTCGATTTTCCCAAAACCAGTCCTCCACCCTCGCCGTTCAGCCGCGCCTCGCACCACGGTCGCTA[C/T]TCATGCGCCATGCCCCTTTCCCGAACTTCGAGCTTCTGCCCTGAAGAAGTCGAGAAGCTGTAGCCTTCCTTCTTAAATAAAAAAGGCGGT
80718 T C CGCGGTCTCCGCCCGCGCCATCGCTCGAATGGACGAGCTGGAAGGCACGCGGTTGGGGCATTACGAGAGG[T/C]TGCCGCTGAAAATCGTGAAGAACGATGACGGAACCGTGGTCGATGGAGAGGCGTATTTTGCTCATCGGAGTTATGCGGATGAAATGTGGAAGGTCAACGC
80718 A G CGCGGTCTCCGCCCGCGCCATCGCTCGAATGGACGAGCTGGAAGGCACGCGGTTGGGGCATTACGAGAGGTTGCCGCTGAAAATCGTGAAG[A/G]ACGATGACGGAACCGTGGTCGATGGAGAGGCGTATTTTGCTCATCGGAGTTATGCGGATGAAATGTGGAAGGTCAACGCGGAGAAAGGAGG
80718 G T GCCATCGCTCGAATGGACGAGCTGGAAGGCACGCGGTTGGGGCATTACGAGAGGTTGCCGCTGAAAATCGTGAAGAACGATGACGGAACCGTGGTCGATG[G/T]AGAGGCGTATTTTGCTCATCGGAGTTATGCGGATGAAATGTGGAAGGTCAACGCGGAGAAAGGAGGAGGGTTTTTTGGAGTT
80718 A T CCATCGCTCGAATGGACGAGCTGGAAGGCACGCGGTTGGGGCATTACGAGAGGTTGCCGCTGAAAATCGTGAAGAACGATGACGGAACCGTGGTCGATGG[A/T]GAGGCGTATTTTGCTCATCGGAGTTATGCGGATGAAATGTGGAAGGTCAACGCGGAGAAAGGAGGAGGGTTTTTTGGAGTTT
80718 A T AAAGGATATGTGAGGAGAGTTGATCGCCCAAAAGGTGTGCCTTTTCTTCATCATATTAGGGTTTTCGTTGGTGCCGAAAGTTGAAAATTTCAAAATTATA[A/T]ACAGTATGTTGATTGAATTTTGCAGATCTGTGCTTAATATTGAAATTTGAAACTTGTTTTAACGATTGGTCATGCATACGTGCAGTGG
80718 T C TGAGGAGAGTTGATCGCCCAAAAGGTGTGCCTTTTCTTCATCATATTAGGGTTTTCGTTGGTGCCGAAAGTTGAAAATTTCAAAATTATAAACAGTATGT[T/C]GATTGAATTTTGCAGATCTGTGCTTAATATTGAAATTTGAAACTTGTTTTAACGATTGGTCATGCATACGTGCAGTGGTGTATATTTAT
80724 G A CGTCGTTCGCGTTCATCGATTTACCGTCGAAACATCGTTGGCAGACGGACATGGTAGGACCGAGCCTGGCGCCCTCGGCCTTCCAGGGAGTCAGACCCTG[G/A]CAGCTCCGGCAAAGGAGAGTTCGGCGGTGCCGCGCTACTAGGAAGTTGGCACTGTGCACTTTGGCGTCGCAGTTGAAGCAGAGA
80724 A T TCATCGATTTACCGTCGAAACATCGTTGGCAGACGGACATGGTAGGACCGAGCCTGGCGCCCTCGGCCTTCCAGGGAGTCAGACCCTGGCAGCTCCGGCA[A/T]AGGAGAGTTCGGCGGTGCCGCGCTACTAGGAAGTTGGCACTGTGCACTTTGGCGTCGCAGTTGAAGCAGAGACGCGCCTCGTCC
80724 T C TACCGTCGAAACATCGTTGGCAGACGGACATGGTAGGACCGAGCCTGGCGCCCTCGGCCTTCCAGGGAGTCAGACCCTGGCAGCTCCGGCAAAGGAGAGT[T/C]CGGCGGTGCCGCGCTACTAGGAAGTTGGCACTGTGCACTTTGGCGTCGCAGTTGAAGCAGAGACGCGCCTCGTCCGATTCGCA
80724 T G GTTGGCAGACGGACATGGTAGGACCGAGCCTGGCGCCCTCGGCCTTCCAGGGAGTCAGACCCTGGCAGCTCCGGCAAAGGAGAGTTCGGCGGTGCCGCGC[T/G]ACTAGGAAGTTGGCACTGTGCACTTTGGCGTCGCAGTTGAAGCAGAGACGCGCCTCGTCCGATTCGCAGTACATGCGAGCTGT
80724 T C GGCAGACGGACATGGTAGGACCGAGCCTGGCGCCCTCGGCCTTCCAGGGAGTCAGACCCTGGCAGCTCCGGCAAAGGAGAGTTCGGCGGTGCCGCGCTAC[T/C]AGGAAGTTGGCACTGTGCACTTTGGCGTCGCAGTTGAAGCAGAGACGCGCCTCGTCCGATTCGCAGTACATGCGAGCTGTTCC
80746 G A ACTGTTGGCCTACTGGCTAAAATTTCACAATCACAATCTGCACTCCAGTGAGCCCGAATA[G/A]AAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTC
80746 T C ACTGTTGGCCTACTGGCTAAAATTTCACAATCACAATCTGCACTCCAGTGAGCCCGAATAGAAGTTAATGGCTTCACT[T/C]AAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGA
80746 C G ACTGGCTAAAATTTCACAATCACAATCTGCACTCCAGTGAGCCCGAATAGAAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGG[C/G]GTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCG
80746 C T GCTAAAATTTCACAATCACAATCTGCACTCCAGTGAGCCCGAATAGAAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTC[C/T]GCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGA
80746 C A TTTCACAATCACAATCTGCACTCCAGTGAGCCCGAATAGAAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGAC[C/A]GTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATC
80746 G A TTCACAATCACAATCTGCACTCCAGTGAGCCCGAATAGAAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACC[G/A]TTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCA
80746 G T AATAGAAGTTAATGGCTTCACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATC[G/T]GTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTG
80746 C T ACTTAAGATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATG[C/T]CGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGA
80746 C A GATCGCCGCTCCATCAACCCACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATC[C/A]GTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGAATCAA
80746 T C ACTTCACCGGCGTCCGCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGA[T/C]GAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGAATCAAACGCTACATGCGGCAAAAGG
80746 C A GCCGACCGTTTGATCGAACTGGAGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAAC[C/A]GCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGAATCAAACGCTACATGCGGCAAAAGGCTGGATTCAATTGGC
80746 G A AGCTTCAGGCCGACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCT[G/A]GGCGTGGAATTCTTGCAATTGATGAATCAAACGCTACATGCGGCAAAAGGCTGGATTCAATTGGCTTGGAAAACACAGAAACTAATC
80746 C A ACAATCGGTTCGGCGTGTTTCCATGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATT[C/A]TTGCAATTGATGAATCAAACGCTACATGCGGCAAAAGGCTGGATTCAATTGGCTTGGAAAACACAGAAACTAATCGTCAAGCTTATA
80746 T C TGCCGATCCGTGCTGGATCTTACACCGATGAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGAATCAAACGC[T/C]ACATGCGGCAAAAGGCTGGATTCAATTGGCTTGGAAAACACAGAAACTAATCGTCAAGCTTATAGACAGCTGTTGTTGACTACCCCT
80746 G A GAGCTCATCAAAACCGCTAAAACCATTGCTTCCCCTGGGCGTGGAATTCTTGCAATTGATGAATCAAACGCTACATGCGGCAAAAGGCTGGATTCAATTG[G/A]CTTGGAAAACACAGAAACTAATCGTCAAGCTTATAGACAGCTGTTGTTGACTACCCCTGGCTTGGGTGAATACATCTCAGGTGCCAT
80756 A G TGCAATCCATACGTCCATCACTCTGAGCAGCACCAGGTGTACAAAAAACGATGCGAAGACCCGTGGTAGATCCAATCCCCGATGGTGATTGCTCCAATAG[A/G]TCGTGAACGCGATTTAGGGATTTTGAGAGTCGTATACGGAGAAACGAAACATGGAGGGAAATTGGAAATAGACCTAGGGTTATGC
80788 A G TACATTTATATGAATACTTCTCCTTTGCATGGCTGCTGCTGTACAAAACAGCACGTAGAACGGCAGACACGGTCGGGATATATAGACTCTTGTTCTTCGC[A/G]AGCAGCCATGTCAGCCCCATCAACTGGCAGTCTCTGTTGAACATTTTCGTTGCTCTTCCTCCCTTCTTGCTCCATTCTTTTCCCTCTCCCT
80790 C G ACTGTTGGCCTACTGGACAATTACTTCTTCAAACTGAAGCTGTTTCTTGCTTCTGCGCTATGGACCTAATGGGAGACCTTCAACCCCGAAACG[C/G]TATTATATTCGGTGCGGTGACCGCATCGCTAGGCATAGCGGTCCGCTCCATCTCACATATACAACATCCGTTGAATGTGGTTTCGCCCATTAGTG
80796 C T CATTAAAACTCAAACCAAAACCACAGCGATGGTCTCTCTTCCCGAACCCGACACCTCCAACACCACCAAGAAATCTCCGCCACCTTTTTCCACAAAAACG[C/T]TCCTTCAACTGGAGCCGAACCTGCTGCTTACACGCAAGCACGTTTCCAGTCATGTACTCCACACTTCACGCCACATACACATCTTCATTT
80808 G C CACGGTCTTGCAATATTCACACAGTTTCTTCACTGATGAACGCACCTTCATGACTCGACTGCAGGCAACGACGGAAAAACAAGAATGAAGTATTTCGAGG[G/C]TTGGTACCAGGTTGGGAGGAAGACAATTCGTGGGAGACGGAGAAAAAGGGTGGCGGGCCTGCGGCTTATGTATATTGAATTT
80820 T G GATTACTCAGGGTGGCCTTTTGATTACTAGCTGGGTTCTGTGCTTTGTTGATATTCTGTTTGGTTGGATAAAACTGTATGATGGAGGCTTTTGGATTGAG[T/G]AATGGTGAAGCTTTTAATAAGGTGTCTTTTTTTCTCTTAAAGTTTGGGTGAGGAAACTCTTTTAGTTGCTGGATGTTGTTGGACCGATT
80830 C T GGTAGAAATGGCAGTCCCTTTGTTGACGAAGAAGATCATTAAGAAGAGAGTGAAGAAGTTCAAGAGGCATCACAG[C/T]GATCGATACAAATGCCTCAAGCAAAGTTGGCGTAGGCCGAAGGGTATTGACTCTCGTGTTAGAAGAAAGTTCAAGGGAGTTACGTTGATGCCGAACATCG
80830 C T CTGACAAGAAAACTCGCCACTACCTACCAAATGGTTTCAAGAAATTTGTGGTTCACAATGTGGCCGAGCTCGAATTGCTTATGATGCACAACAGGACTTA[C/T]TGTGCTGAAATTGCACACAATGTGTCCACAAGGAAGAGGAAGGACATTGTTGAGCGTGCAGCTCAGCTCGACATTGCTGTAACAAA
80832 T C TTTTCGATGGCGATCTGAAATCCATAAAACGCGCGTGCTTCAGAAACTTGAATTTCCTTCATAAA[T/C]CTGACGGCGAGGTTCTCTAATACGATGCCGTCGGAAGCAGCGAAGAAGGCGAGCACGTGAGTGATGAAGTGTCTTTCGCCGTCGTCTAAGGCAGCCCAGT
80832 G A TTTTCGATGGCGATCTGAAATCCATAAAACGCGCGTGCTTCAGAAACTTGAATTTCCTTCATAAATCTGACGGCGAGGTTCTCTAATACGATGCC[G/A]TCGGAAGCAGCGAAGAAGGCGAGCACGTGAGTGATGAAGTGTCTTTCGCCGTCGTCTAAGGCAGCCCAGTGTTTTAAATCCTGAGAAAGAT
80832 A C AAAACGCGCGTGCTTCAGAAACTTGAATTTCCTTCATAAATCTGACGGCGAGGTTCTCTAATACGATGCCGTCGGAAGCAGCGAAGAAGGCGAGCACGTG[A/C]GTGATGAAGTGTCTTTCGCCGTCGTCTAAGGCAGCCCAGTGTTTTAAATCCTGAGAAAGATCGACTTCTTCAGCGGTCCAGAAGGA
80832 T C TGACGGCGAGGTTCTCTAATACGATGCCGTCGGAAGCAGCGAAGAAGGCGAGCACGTGAGTGATGAAGTGTCTTTCGCCGTCGTCTAAGGCAGCCCAGTG[T/C]TTTAAATCCTGAGAAAGATCGACTTCTTCAGCGGTCCAGAAGGAAGCCTCTGCTTTCTTATACATTTCCCAGATCGATGGGTAATT
80836 G A TTCTTTTTACCAGTGCTACTGCAAATAGCAATCGTACCTTTGCCTTCGACCTGAACTTTTTTGTCATCACCAAGTCGAACCTC[G/A]GATTTCTGTGAGATGTCTAGATTCTCAAACAACAATCGAGAATTTGACATATGGTTGGAGCATCCACTATCAATGAACCAGACATTATGATCAGTTGTGT
80842 GC G TACTCCAAAGGCAAACCAGTACAGACCAACCGCCGGACCGACGAAAACAGTGGGAAGATGGCTGAAGGACAGGAGGGAAAAGAAGAAAGAAGAGACCCGG[GC/G]CCCACAATGCCCAGGTGCATGCAGCTGTGACGGTGGCTGGTGTTGCTGCTGCAGTGGCAGCGATTGCTGCAGCCACGGCTG
80844 A G AAGAGGTCTGCTTACCCGACCTCGCTCTTCTGTTCAAACCGTGCCCCTCGCTGAAGTCTTAATCAATAACAAAAACAGTACAGAAACTGTAGATGCAAAC[A/G]GATCGAAAGATGCAAAAACACCGGTTGGATTGGGAGCTGGATTAGCATCTCTGGACTCCAAGAAGCAGAAACATAAACTAACCAAA
80854 G A TTTCAAATCAAATTGATTTTATCTGAGTTGCAATTAACATGTCTAAAGGTGAAGGTCCTGCGATTGGAATTGATTTGGGGACAACCTACTCGTGTGTCGG[G/A]GTATGGCAGCACGATCGCGTCGAGATCATAGCCAATGATCAAGGAAATCGTACCACGCCGTCCTATGTGGCGTTCACTGATTCCGAA
80854 T C GTGAAGGTCCTGCGATTGGAATTGATTTGGGGACAACCTACTCGTGTGTCGGGGTATGGCAGCACGATCGCGTCGAGATCATAGCCAATGATCAAGGAAA[T/C]CGTACCACGCCGTCCTATGTGGCGTTCACTGATTCCGAAAGGTTGATCGGCGATGCTGCTAAGAACCAGGTCGCCATGAATCCCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
80860 CA C AGGCGGAACGCAATGGCACTCCTCACAACATAAATTACAGTACTTCAGACACCCGTCCCTCACACTCGCCTTCGAGCACCTCACGTTGCATTTGCTGCTG[CA/C]AAAAAACTGAGCCGGCGAAGGCAGCATGGATGTAGGCAAACACAAGAAGAAGGAAGAAGAAAGTAGAAAGCTGCTTCTTCATCCT
80872 A C AAACTTCTTTATGAAGTTCAACAACAAAACACTTCCAACTTACACATACCCATACACAAGAAACTGAAC[A/C]ACATTCCAAAGCAAAACACTACTTACAAAAGAACCCCACGTTTATTTAATATTATGAACTTGGGATTGTCTGGCTAGACGGCCTCGACAGTGTGAGTCGG
80872 A T CAGTGTGAGTCGGGGAGTTGGAGACAGGTGGCAGCTGAGCAGAGGAACTGTTCTGAGAATTCACTCTGTGCAGGCGACACTTGAAGGATCCAGCATGAGT[A/T]GCTGGTGCGCACACACACTTACGTGATGGGCCTTCCTGAATGCAAGAGTTATTAGTTGAGGAATTTGACGAGTGTGTTCGCCTC
80886 C G GAGAGCACGAGTGAATACAACTTGCAATTTCTGTTCTTCTTTTTTGATTTACAATCCTTAAACCATTCTATTTCGAATCGTTCACCGATAGTCGAAATTT[C/G]AACACGACCAAAATTTCGACAATGGCGTTTCTATTTACATTCAGAGAGGGACAATCTAAATCCATTCAAAACCTTATTTCTCTCATTCATT
80886 A G CGATAGTCGAAATTTCAACACGACCAAAATTTCGACAATGGCGTTTCTATTTACATTCAGAGAGGGACAATCTAAATCCATTCAAAACCTTATTTCTCTC[A/G]TTCATTGCAATTCTAAACAGCCCATTCATCTCATTCCTCAGACCATCCAAACCCTCAATCAAACTCCCCACCGCTGCTTCCGCCTTCGCCA
80890 A T AGCGACAACAACAAAGTTCAATTCCAGCATATAAAAAATACCGAACGAGCAAATTTACAAAGACAACCCCCACAAGTTAAATCTTATCCAGCTTCGCCGC[A/T]ACCACCACCGGGTTCGCCCGCGCCAGCTCCTCCTTCCCCTTCCCTTTGTAATCAAAGTCGCAGTTGTGCTTCTCCGGGTATCTGTGGG
80890 TC T AAATACCGAACGAGCAAATTTACAAAGACAACCCCCACAAGTTAAATCTTATCCAGCTTCGCCGCAACCACCACCGGGTTCGCCCGCGCCAGCTCCTCCT[TC/T]CCCCTTCCCTTTGTAATCAAAGTCGCAGTTGTGCTTCTCCGGGTATCTGTGGGTCCCACAGAACGTTATACCGCATCTGCATTTGAAC
80890 G C CGTTGCTCGGACGAGCCGTCTCCGGCGGCGGGACCACCGCATCCGGTACCGACACGGTCACGACCGCGGGAGAGGAAGACGAGGTGAGGTTTGTGTTTAG[G/C]GATTTTTCGACAGCAAGCTTGGCGGATTCGGCCTGGTCTTGCTTCAGACGGAGGTCGCGGTA
80892 C T TGTTCTTCCCCTTCTTGGGACCAGGTCACTTATTCCCGATGATCGACATGGCCTGCATCTTCGCCTCCCACAACGTACGCTCCACCGTCGTCGCCACCCC[C/T]TCCGACGCCTCCAAAATCCCCCTTTCAAAATCCAAATTCATCTCCATCGTCACCGTCCCCTTCCCTTCTCCGTCCATCACCAACCTCCCTCC
80892 A G CATGGCCTGCATCTTCGCCTCCCACAACGTACGCTCCACCGTCGTCGCCACCCCCTCCGACGCCTCCAAAATCCCCCTTTCAAAATCCAAATTCATCTCC[A/G]TCGTCACCGTCCCCTTCCCTTCTCCGTCCATCACCAACCTCCCTCCCGGCCACGAAAACATCGCAACCATCCGTTCTTCCATGTTCGACCA
80892 A C CCAAAATCCCCCTTTCAAAATCCAAATTCATCTCCATCGTCACCGTCCCCTTCCCTTCTCCGTCCATCACCAACCTCCCTCCCGGCCACGAAAACATCGC[A/C]ACCATCCGTTCTTCCATGTTCGACCACTTCATTTCTGCCCTCTCCCTCTTCCAGTCCCCCTTAGAAAAGCTCATCCACGACCTCAAACCCGA
80892 A T TTCATCTCCATCGTCACCGTCCCCTTCCCTTCTCCGTCCATCACCAACCTCCCTCCCGGCCACGAAAACATCGCAACCATCCGTTCTTCCATGTTCGACC[A/T]CTTCATTTCTGCCCTCTCCCTCTTCCAGTCCCCCTTAGAAAAGCTCATCCACGACCTCAAACCCGACTGCCTCATCTCCGATTCCCTCTTCCC
80892 T C TCGTCACCGTCCCCTTCCCTTCTCCGTCCATCACCAACCTCCCTCCCGGCCACGAAAACATCGCAACCATCCGTTCTTCCATGTTCGACCACTTCATTTC[T/C]GCCCTCTCCCTCTTCCAGTCCCCCTTAGAAAAGCTCATCCACGACCTCAAACCCGACTGCCTCATCTCCGATTCCCTCTTCCCCTGGACTGC
80912 A C GTCCGTGGGACTTGATCATCGGCACGACGCATAGAGGGACGGTGGCGGTTGCAGGGGACGC[A/C]TTCCATCCCATGACGCCTGACCTTGCGCAGGGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATG
80912 C G GTCCGTGGGACTTGATCATCGGCACGACGCATAGAGGGACGGTGGCGGTTGCAGGGGACGCATTCCATCCCATGACGCCTGACCTTG[C/G]GCAGGGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAA
80912 G A GGGACTTGATCATCGGCACGACGCATAGAGGGACGGTGGCGGTTGCAGGGGACGCATTCCATCCCATGACGCCTGACCTTGCGCAGGGCGGCGGGTCAGC[G/A]CTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAAGGCAGA
80912 G A TGATCATCGGCACGACGCATAGAGGGACGGTGGCGGTTGCAGGGGACGCATTCCATCCCATGACGCCTGACCTTGCGCAGGGCGGCGGGTCAGCGCTCGA[G/A]GATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAAGGCAGAGAGAGC
80912 C A TAGAGGGACGGTGGCGGTTGCAGGGGACGCATTCCATCCCATGACGCCTGACCTTGCGCAGGGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCC[C/A]AGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAAGGCAGAGAGAGCTATCGAGGGGTATGTGAAT
80912 G A CCATGACGCCTGACCTTGCGCAGGGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGAT[G/A]CTTACTACAAAGAAGGCAGAGAGAGCTATCGAGGGGTATGTGAATGAGAGGAAGTGGCGTGTAGCTGGTTTGATAGTTGGTGC
80912 A G CTGACCTTGCGCAGGGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTAC[A/G]AAGAAGGCAGAGAGAGCTATCGAGGGGTATGTGAATGAGAGGAAGTGGCGTGTAGCTGGTTTGATAGTTGGTGCTTATTTGTCG
80912 G A GGCGGCGGGTCAGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAAGGCAGAGA[G/A]AGCTATCGAGGGGTATGTGAATGAGAGGAAGTGGCGTGTAGCTGGTTTGATAGTTGGTGCTTATTTGTCGGGCTGGGTTCAGC
80912 G T AGCGCTCGAGGATGCTGTCGTGCTTGCCCAGAACGTCGCGCGTGTTTTGAATGATGATGGTAAGATGCTTACTACAAAGAAGGCAGAGAGAGCTATCGAG[G/T]GGTATGTGAATGAGAGGAAGTGGCGTGTAGCTGGTTTGATAGTTGGTGCTTATTTGTCGGGCTGGGTTCAGCAGGGTGGAGGA
80912 A G CGAGGGGTATGTGAATGAGAGGAAGTGGCGTGTAGCTGGTTTGATAGTTGGTGCTTATTTGTCGGGCTGGGTTCAGCAGGGTGGAGGATCCGGAGTAGTG[A/G]GCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATAGATTTATTCAGCCAATTGTCGCTGCGGGTCAATACGATTGCG
80912 G A ATAGTTGGTGCTTATTTGTCGGGCTGGGTTCAGCAGGGTGGAGGATCCGGAGTAGTGAGCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATA[G/A]ATTTATTCAGCCAATTGTCGCTGCGGGTCAATACGATTGCGGAAGCCTTGAATGAATATTTCTGATGTCATTATGAATTTTCTTAAG
80912 T C TCGGGCTGGGTTCAGCAGGGTGGAGGATCCGGAGTAGTGAGCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATAGATTTATTCAGCCAATTG[T/C]CGCTGCGGGTCAATACGATTGCGGAAGCCTTGAATGAATATTTCTGATGTCATTATGAATTTTCTTAAGTTATTT
80912 G T GTTCAGCAGGGTGGAGGATCCGGAGTAGTGAGCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATAGATTTATTCAGCCAATTGTCGCTGCGG[G/T]TCAATACGATTGCGGAAGCCTTGAATGAATATTTCTGATGTCATTATGAATTTTCTTAAGTTATTT
80912 A G CAGCAGGGTGGAGGATCCGGAGTAGTGAGCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATAGATTTATTCAGCCAATTGTCGCTGCGGGTC[A/G]ATACGATTGCGGAAGCCTTGAATGAATATTTCTGATGTCATTATGAATTTTCTTAAGTTATTT
80912 A T AGCAGGGTGGAGGATCCGGAGTAGTGAGCGGTTGGTTTGTGAAGTGGTTCAGAGACCATGTGTTTTATAGATTTATTCAGCCAATTGTCGCTGCGGGTCA[A/T]TACGATTGCGGAAGCCTTGAATGAATATTTCTGATGTCATTATGAATTTTCTTAAGTTATTT
80922 T C AGGAAGAAGAGAAGGCAGCTGGGCTTTCTGATGGCCTTTCAGGCTTCCATAAAACCGTGTT[T/C]GACCTTCTCTACAAGGTCGCTGATATTCCATTACTTGCATCCCAGAAGAGCAAGATAATTGATTTGATAGAAAAGGGAGAGACACAGCCCAACCTAACCT
80922 G A ATAAAACCGTGTTTGACCTTCTCTACAAGGTCGCTGATATTCCATTACTTGCATCCCAGAAGAGCAAGATAATTGATTTGATAGAAAAGGGAGAGACACA[G/A]CCCAACCTAACCTTAGGTATTCTTGTATCGATTGCAGTCGTCATCCTTACTGTTCTCTTTGGACTTCTTTTTGGTGGGAAGAAGGCTGT
80922 C T CGTGTTTGACCTTCTCTACAAGGTCGCTGATATTCCATTACTTGCATCCCAGAAGAGCAAGATAATTGATTTGATAGAAAAGGGAGAGACACAGCCCAAC[C/T]TAACCTTAGGTATTCTTGTATCGATTGCAGTCGTCATCCTTACTGTTCTCTTTGGACTTCTTTTTGGTGGGAAGAAGGCTGTGGTGGC
80922 G A GAGCAAGATAATTGATTTGATAGAAAAGGGAGAGACACAGCCCAACCTAACCTTAGGTATTCTTGTATCGATTGCAGTCGTCATCCTTACTGTTCTCTTT[G/A]GACTTCTTTTTGGTGGGAAGAAGGCTGTGGTGGCACCAAAGCCTACACCAGTAGCAAAGACAGAGGCTTCTCCAAGTGAGGCGGAG
80922 G A TCCTTACTGTTCTCTTTGGACTTCTTTTTGGTGGGAAGAAGGCTGTGGTGGCACCAAAGCCTACACCAGTAGCAAAGACAGAGGCTTCTCCAAGTGAGGC[G/A]GAGGCTGAGCCAGCAGGAAGCAGCGGGGAGAAAGAGGACAGTGAGAAAGAGGATGCGGCAGGTCCTCGCCCAAGGAGGTCAA
80922 G C AGAAGGCTGTGGTGGCACCAAAGCCTACACCAGTAGCAAAGACAGAGGCTTCTCCAAGTGAGGCGGAGGCTGAGCCAGCAGGAAGCAGCGGGGAGAAAGA[G/C]GACAGTGAGAAAGAGGATGCGGCAGGTCCTCGCCCAAGGAGGTCAAGAAGAGAGACATAAGGACGAGCTGTCTACAATTTG
80926 G A GAAAGAAGCCAGGGAAAGCAGGTAATCGACTTTGGCGTAATGTTGGCCTTGGATTCAAAACCCCAAGAGAAGCAATTGAAGGAACTTACATCGATAAGAA[G/A]TGCCCTTTCACTGGTCATGTCTCCATTAGAGGTCGTATTATTGCAGGAACATGCCACAGTGCAAAGATGAACAGAACCATCATTG
80926 T A ATGTTGGCCTTGGATTCAAAACCCCAAGAGAAGCAATTGAAGGAACTTACATCGATAAGAAGTGCCCTTTCACTGGTCATGTCTCCATTAGAGGTCGTAT[T/A]ATTGCAGGAACATGCCACAGTGCAAAGATGAACAGAACCATCATTGTCAGAAGAAACTATCTTCATTATGTGAAAAAATATCAGAGG
80928 C CA CTGTTGGCCTACTGGAAATCTAATTTATCAACATAAATTCGTTACTTATTCCTCTCTTCTTCGTCCTCCTCTTCCCAGATCCAT[C/CA]AAACCCTAACCCTAGCCATGGGCGGCGGCGGTCCTTCCGACACCCTCGTCCGCAAGATCCTCCATTCCTACTGCTATGTGGCCATCTGGATCTTCCTGTC
80928 G A GCTATGTGGCCATCTGGATCTTCCTGTCCTTCGCCGTCATCGTCTACAACAAGTACATACTCGATCCCAAAATGTACAATTGGCCTTTTCCCATCTCTCT[G/A]ACCATGATCCACATGTCCTTCTGTTCCTTTCTCGCCTTCCTCATCATCCGCGTCCTCCGTCTCGTTGAGCCCCCTTCCTCGCCTCCCATGAC
80950 G A AGAGAGAGACCGGACTCTTCATCCTCTTCAAGGGAGGAAGCATAGACAAAGTAAAGGGCCCAAATGAGTCCGAACACTCCAAGCA[G/A]GATCCACCCAAGCAGGTTGCTGCTGAGCCCGAGGCTCAGCCCGGTTCCTTCGGTGCTCATCCTTTCATCGACCAGAGCAAGTGCAGGGCCTGACATGCTC
80950 G A CTGCTGAGCCCGAGGCTCAGCCCGGTTCCTTCGGTGCTCATCCTTTCATCGACCAGAGCAAGTGCAGGGCCTGACATGCTCATCATGCTAGCTACCCCCA[G/A]AAGCGATGCTCCAGCTACGCCTTTTGCATTTTCCGACGAACACCTCACCCCTCCTCCTTGCTTCTTTGTCATTTGTGGCAAACCAAGAG
80950 C T CGCCTTTTGCATTTTCCGACGAACACCTCACCCCTCCTCCTTGCTTCTTTGTCATTTGTGGCAAACCAAGAGCAGGTGAAGTTGAGATCTTGCAACTCCT[C/T]CTACTGAGGAGAGCAACTGTGACTGTAGAAGCAGAGATGGTGGCCATTACTGCAGCTGGAAAGTAGACAAAGAAGTAATATTGCAAT
80956 T A ACGTCCGTCGACCTGCGCGCCTCTATCTTCCCCTCCGCCACGTCGGCCTCCCCCACCTGCGCGCCCCGGTAGTACAGCTGGGCCTTCCCGGGCCGGTGCG[T/A]GAACGAGGCGTAGTTGGGGTTCCGCACTCTGATCACCAGATCCAGCGTGACGTTGATCTGGAGGTTGAGCGGGTTGGTGATGTCA
80956 A T TCCCGGGCCGGTGCGTGAACGAGGCGTAGTTGGGGTTCCGCACTCTGATCACCAGATCCAGCGTGACGTTGATCTGGAGGTTGAGCGGGTTGGTGATGTC[A/T]ATACGGGGCGAGATGCCGGTGACGTTGGCGGAGATCAGCGTGGTGGTCGGATCTCTGGGCCGGAACACGGTGACGGCCAGGA
80956 G T GGTTCCGCACTCTGATCACCAGATCCAGCGTGACGTTGATCTGGAGGTTGAGCGGGTTGGTGATGTCAATACGGGGCGAGATGCCGGTGACGTTGGCGGA[G/T]ATCAGCGTGGTGGTCGGATCTCTGGGCCGGAACACGGTGACGGCCAGGATTACGGCGGTGAGGACCAAGGCGAGGACGACGA
80956 G C TGATCACCAGATCCAGCGTGACGTTGATCTGGAGGTTGAGCGGGTTGGTGATGTCAATACGGGGCGAGATGCCGGTGACGTTGGCGGAGATCAGCGTGGT[G/C]GTCGGATCTCTGGGCCGGAACACGGTGACGGCCAGGATTACGGCGGTGAGGACCAAGGCGAGGACGACGACGGAGCAGATG
80956 G T GTGACGTTGATCTGGAGGTTGAGCGGGTTGGTGATGTCAATACGGGGCGAGATGCCGGTGACGTTGGCGGAGATCAGCGTGGTGGTCGGATCTCTGGGCC[G/T]GAACACGGTGACGGCCAGGATTACGGCGGTGAGGACCAAGGCGAGGACGACGACGGAGCAGATGACGCAGGGGAAGAGGC
80956 C T GGTTGAGCGGGTTGGTGATGTCAATACGGGGCGAGATGCCGGTGACGTTGGCGGAGATCAGCGTGGTGGTCGGATCTCTGGGCCGGAACACGGTGACGGC[C/T]AGGATTACGGCGGTGAGGACCAAGGCGAGGACGACGACGGAGCAGATGACGCAGGGGAAGAGGCATCTGCGTCGCCTGCG
80958 G T TTCAGGCTAGGTCCTTCGTTCAACACTTTTATATCTTGCAGTTGTCTCTGCCTTTGGGTTGAAGACATGGCAACAGGTTTAGAGTCATGTATATATTGTC[G/T]TCGGTTGAAATTGCCAAATGTACAAACATCAGTTTCTCCAGATCAAGCTGATGTCAGCTGTAGTGCGTTAATGCGATGATACCAAGTGC
80968 AC A CATACCTGCTCCGCACATACAATTTGCTTCTTCACCTCACCCTCCTCCCTAACACACTTCAAATGGACCTCGTACCCACACCCGAGACACTGATAAGCCC[AC/A]CCCCGAACCCTGCTCGTTGCACTCGCAACATATATACGCCCCGCCACCCGAGTTCTCCGAAACCAAGTTAAGCATGTGCCTATGTCCC
80980 G A ACGCTGCTAGGCGCAGTGGCGCTGAGATCGAAACAGTACGAAAAGCTGCTGCTGGTACGAACAAAGCTGCTTCTAGCAGTACGTCTTTGAACACAAGGAA[G/A]CTTGCAGAGGAAACAGAGAACCTGACCCATGAGAGAGTTCCAAGTGAACTGAAGAAGAACATCATACAAGCTCGAACAGATAAA
81020 G A GTTGCGAGCTGAAATTTCTAAGCCTGGAACACTTAGGATGATTGTCGCGACGTTGGACGGTGGAGAACTCCATGACTGTTGTGAACGGTGCAGCAGCGAG[G/A]CGCAGGCGATCGGAAGCGCTGCGCGGCAAAGAGATCGCCGGTGGTTGGTCTGAGCGATGCGCATGACTGGACGGCGGCGGCT
81020 C T CTGTTGTGAACGGTGCAGCAGCGAGGCGCAGGCGATCGGAAGCGCTGCGCGGCAAAGAGATCGCCGGTGGTTGGTCTGAGCGATGCGCATGACTGGACGG[C/T]GGCGGCTTCAATGTGGACATGGCTTCGGCGAAGGCGAGGCGACGAGATCGGGTTAATCGAAGAAGGGGTTCTCGGTTTACA
81020 T C GCGAGGCGCAGGCGATCGGAAGCGCTGCGCGGCAAAGAGATCGCCGGTGGTTGGTCTGAGCGATGCGCATGACTGGACGGCGGCGGCTTCAATGTGGACA[T/C]GGCTTCGGCGAAGGCGAGGCGACGAGATCGGGTTAATCGAAGAAGGGGTTCTCGGTTTACAACGGATTTGGGCAAAATGAG
81020 A G ATGCGCATGACTGGACGGCGGCGGCTTCAATGTGGACATGGCTTCGGCGAAGGCGAGGCGACGAGATCGGGTTAATCGAAGAAGGGGTTCTCGGTTTACA[A/G]CGGATTTGGGCAAAATGAGGAGCCGATTCAATTTTGGAGCGGAGCAAGGGCTACAACATTGGTGGTTAGCAAGGAGGTGAAG
81020 G A CTGGACGGCGGCGGCTTCAATGTGGACATGGCTTCGGCGAAGGCGAGGCGACGAGATCGGGTTAATCGAAGAAGGGGTTCTCGGTTTACAACGGATTTGG[G/A]CAAAATGAGGAGCCGATTCAATTTTGGAGCGGAGCAAGGGCTACAACATTGGTGGTTAGCAAGGAGGTGAAGCGATGGATTT
81028 GTT G,GT GGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTGGGCCATCGCCCTGATAGACG[GTT/G,GT]TTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCG
81032 A G ATGGCTAATCACATCCTGATGTTCCCCTTCTACGCACAAGGTCACTTGCCAGTGATGCTGCAGCTAGCCGAACTCCTGTCCAAGTCCAACCACAACATCC[A/G]CATCACCTTTATCAACAACAACTTCTACAACTTCACAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGT
81032 T C ACATCCTGATGTTCCCCTTCTACGCACAAGGTCACTTGCCAGTGATGCTGCAGCTAGCCGAACTCCTGTCCAAGTCCAACCACAACATCCACATCACCTT[T/C]ATCAACAACAACTTCTACAACTTCACAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTT
81032 C A GCCAGTGATGCTGCAGCTAGCCGAACTCCTGTCCAAGTCCAACCACAACATCCACATCACCTTTATCAACAACAACTTCTACAACTTCACAGTACACACC[C/A]CACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGAGGAACTTCCCAAATCTTTCCATG
81032 G A ACAACAACTTCTACAACTTCACAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGA[G/A]GAACTTCCCAAATCTTTCCATGAACTGATCTGCCAGGAAGAATTGAGAAGAGCGAGTTGCAAGGATGAGTACAGGAGAGTGTTGGGA
81032 A C TACAACTTCACAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGAGGAACTTCCCA[A/C]ATCTTTCCATGAACTGATCTGCCAGGAAGAATTGAGAAGAGCGAGTTGCAAGGATGAGTACAGGAGAGTGTTGGGACCTTTAGATGG
81032 T A ACTTCACAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGAGGAACTTCCCAAATC[T/A]TTCCATGAACTGATCTGCCAGGAAGAATTGAGAAGAGCGAGTTGCAAGGATGAGTACAGGAGAGTGTTGGGACCTTTAGATGGATGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
81032 T C CAGTACACACCCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGAGGAACTTCCCAAATCTTTCCA[T/C]GAACTGATCTGCCAGGAAGAATTGAGAAGAGCGAGTTGCAAGGATGAGTACAGGAGAGTGTTGGGACCTTTAGATGGATGGCCAAGA
81032 T G CCCACACAGTCTTGAGTACTACTCGGGGCTACCCAATTTCAGGTTTCTTTCCCTTAACACCTCTCATGAGGAACTTCCCAAATCTTTCCATGAACTGATC[T/G]GCCAGGAAGAATTGAGAAGAGCGAGTTGCAAGGATGAGTACAGGAGAGTGTTGGGACCTTTAGATGGATGGCCAAGAGTAACTTGTG
81042 G A AACCCACCAACCTTCATCCAAGCAGACACCTCTTCCTTCAAGAAGGTAGTCCAACTCCTAACGGGTTC[G/A]CCCGAAACCATCTCCACCCACCAACCCAAACCCGTACCCGGACCCAAAAAGCACTCCTTCAAGCTCTACGAACGTCGGAACACCCTCAGAAAGTTCAACC
81042 C T AACCCACCAACCTTCATCCAAGCAGACACCTCTTCCTTCAAGAAGGTAGTCCAACTCCTAACGGGTTCGCCCGAAACCATCTCCACCCACCAACC[C/T]AAACCCGTACCCGGACCCAAAAAGCACTCCTTCAAGCTCTACGAACGTCGGAACACCCTCAGAAAGTTCAACCTCGTCAACCCACTTACAAGC
81042 C T ACTCCTAACGGGTTCGCCCGAAACCATCTCCACCCACCAACCCAAACCCGTACCCGGACCCAAAAAGCACTCCTTCAAGCTCTACGAACGTCGGAACACC[C/T]TCAGAAAGTTCAACCTCGTCAACCCACTTACAAGCGCAGGCACCTTCCACTCTTCAGAAGCGCTTTCTCCCAGCACACTCGATTTTCCT
81042 C A CCAAACCCGTACCCGGACCCAAAAAGCACTCCTTCAAGCTCTACGAACGTCGGAACACCCTCAGAAAGTTCAACCTCGTCAACCCACTTACAAGCGCAGG[C/A]ACCTTCCACTCTTCAGAAGCGCTTTCTCCCAGCACACTCGATTTTCCTTCTCTGTTGCTCAGCCCCGACACCACTTTGTGCCATGACAT
81042 A T AGCTCTACGAACGTCGGAACACCCTCAGAAAGTTCAACCTCGTCAACCCACTTACAAGCGCAGGCACCTTCCACTCTTCAGAAGCGCTTTCTCCCAGCAC[A/T]CTCGATTTTCCTTCTCTGTTGCTCAGCCCCGACACCACTTTGTGCCATGACATCAATTTGGTGGCAGAGGAGAAAGCCATAGCTCAAA
81056 A AT TATTTTTTTACTAACGAAACGTTACTTACTAATTTAATTTTACTTAAACCAAAACGAAAACGAAAACCAACTAAAACTAAAACTTACTTACTAAATTTAA[A/AT]TTTTACTTAAACCCAAAAAACCCAAAACGACGACCGAACCGAACCAACTAAACTAAACGTTTTAAGGGTTTTACGGACTAACGTACCGA
81064 G A AGCCAGCAGTGACCTCATAATCAACCGACGACGTAATGTTCGTATGCGGCAGAAACGCAGCGGCATGCTGCAAGTCGAGCATCTCACCGGCCAGCTTGTC[G/A]GCGTTCGCGTCGAGAAGGGCAAGATCGTCGGCGATGTTTTGGGTCAAAATCGTCTGCGCGATGGCCATGCCGACGTTGCCGACG
81064 G A GCATCTCACCGGCCAGCTTGTCGGCGTTCGCGTCGAGAAGGGCAAGATCGTCGGCGATGTTTTGGGTCAAAATCGTCTGCGCGATGGCCATGCCGACGTT[G/A]CCGACGCCAATGACCGATATCTTGGTGCGGTGGTTAGTCGGGACGATCGGATCGGATTGGTCTTTGATTGGGGTGAAGAAAAAG
81068 A G TGTGGTAGAAGGCAACATTTTGGTTCTAAGTCTAGGCTTTTCCCATCCAGTTAGAATGGAAATACCAGAAGGGCTCAAAGTTAAAGTCGAAGAAAATACG[A/G]GAATCACAGTTAGTGGATATGATAAATGCTCAATTGGAGAGTTTTCAGCTGCCATTAGGAAGTGGAGGCCTCCTGAACCTTACAAG
81068 A G GAATCACAGTTAGTGGATATGATAAATGCTCAATTGGAGAGTTTTCAGCTGCCATTAGGAAGTGGAGGCCTCCTGAACCTTACAAGGGAAAAGGAGTTCG[A/G]TACGTCGATGAAATTGTGAGGAGAAAAGAAGGCAAAGCTGGGAAGAAGAAGTAGAACTCCCCCCTTTTGGTTTTGTAATATTGCC
81104 A G ACGATTTCGCGGTTGATTTCTGGGCGTTGGGGATTCTGACGTACGAGATGGCGTACGGGAAGACTCCGTTCAAGGGGAGAGATCGGAAGGAGACGTTCAG[A/G]AATGTGATTATGAAGGAAGTGGAGTTCGTCGGTCGGTCGGGATCGGATCTGACGGATCTGATCGGACGGCTGCTGGAGAAGG
81104 T A AAGACTCCGTTCAAGGGGAGAGATCGGAAGGAGACGTTCAGAAATGTGATTATGAAGGAAGTGGAGTTCGTCGGTCGGTCGGGATCGGATCTGACGGATC[T/A]GATCGGACGGCTGCTGGAGAAGGATCCGGAGCGGAGATTGGGATGCAATGGAGGCGTGGAGGAGGTGAAGGAGCACGTGT
81108 G A GCACTCTTGTGGCTTAAGATGTATTCCTCAAGTTTTGCAACCTCGAGTAGTATTTTATGCAGAACTAGCTTTTGAAGCTTATGTTTTGATCATTGTATTG[G/A]TGTCTTGAGTAATTGGGTTGACTGTTTTGTTGTTTGTGGATCTGAATTTTTTTAAGGTTTCTTCCATTAATATGTATGTTTACATTTTG
81112 G C GTATGGATCATTTATCGACGCACTAGGCTTTTAGTGGTCATTCAGCTTGGTTTTTTGGCTCGGGACTGGATCTGTTTTCTCTAGCTTTGTGGTTGTGCTG[G/C]TGTTTTTCATCGTGGTGTCGCGTCTTGCTATATCTTGCTTACTGGCCATATTGTTTTTGGGTTGTATGTTTAGT
81158 C G CTGAAGCTTTTTTCCTAATATAAACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCAC[C/G]ACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCAC
81158 A G TGAAGCTTTTTTCCTAATATAAACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACC[A/G]CAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACG
81158 T C TCCTAATATAAACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACT[T/C]AAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAA
81158 G A ATATAAACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAAT[G/A]TGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAG
81158 G A ATAAACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGT[G/A]AGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGAC
81158 C T AACTCATAGAAAAGGAGAGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAG[C/T]ACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCAT
81158 A G AGCTTCAAAATTTCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATA[A/G]TACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCC
81158 G C TCAGATCTAAATTGCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAA[G/C]GTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTA
81158 C G GCGGTTTCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTT[C/G]ATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGA
81158 A G TCCGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAG[A/G]AGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGA
81158 G A CGAATTACAAATTTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAA[G/A]CACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATG
81158 C T TTTTCTTTTAAGTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCA[C/T]TCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAA
81158 G A GTCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAA[G/A]GGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGAC
81158 G A TCACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAG[G/A]GAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACG
81158 A C ACCACAACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGG[A/C]AACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGAC
81158 A G ACATAACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACAC[A/G]GACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTT
81158 C G AACTTAAATGTGAGCACTGCAATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGAC[C/G]ATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGG
81158 A C ATAACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCC[A/C]AGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGGTGAAACACTTCGAGAAAGAG
81158 G T AACAAATAATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAA[G/T]CTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGGTGAAACACTTCGAGAAAGAGAT
81158 T C ATACAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTT[T/C]AATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGGTGAAACACTTCGAGAAAGAGATCGTTTCTTA
81158 T C CAGAAGAAAGGTACTTCAACTTCATCAGAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAA[T/C]TCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGGTGAAACACTTCGAGAAAGAGATCGTTTCTTATCA
81158 A G GAAGCACAAAGCCCACTCCACGACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACG[A/G]GAATCAGCACGACGACGAGGTTTTGGTGAAACACTTCGAGAAAGAGATCGTTTCTTATCAGGGCTTTGGTTGCTAGAAGGCTTCCT
81158 T C ACAAGGGAAACACAGACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGT[T/C]TTGGTGAAACACTTCGAGAAAGAGATCGTTTCTTATCAGGGCTTTGGTTGCTAGAAGGCTTCCTTCGAGGAGACAAGCTCCTTCGAG
81158 C G ACCATTCCTAAGCAGTTTCATCCAAGCTTTCTTTAATTCCTAATCTGAGAGAGATGGACTACGAGAATCAGCACGACGACGAGGTTTTGGTGAAACACTT[C/G]GAGAAAGAGATCGTTTCTTATCAGGGCTTTGGTTGCTAGAAGGCTTCCTTCGAGGAGACAAGCTCCTTCGAGGAGACAAGCTCCTT
81160 G A GAGGTGGATATGGCTAGACAATAGTAACATGATGAGGCTGAGCAAGCAGGTGAGTCCTACACAAGGGACAGACAGCATTCCCCAATAACCAAGCGTCGGC[G/A]CAGCTTCTATGAAAAGCGTGCCTGCACTCCGGCATGACCCTAGCCACCTGCCCCTCCTCTATCTCCTCCAAGCAAACCGCGCACTC
81160 C T GAGTCCTACACAAGGGACAGACAGCATTCCCCAATAACCAAGCGTCGGCGCAGCTTCTATGAAAAGCGTGCCTGCACTCCGGCATGACCCTAGCCACCTG[C/T]CCCTCCTCTATCTCCTCCAAGCAAACCGCGCACTCCACGCCTCTCACCGCTCCCCCTTCCTCCACTCCCGGAATCTCCTCAAGCTCCG
81160 C T TCCCCAATAACCAAGCGTCGGCGCAGCTTCTATGAAAAGCGTGCCTGCACTCCGGCATGACCCTAGCCACCTGCCCCTCCTCTATCTCCTCCAAGCAAAC[C/T]GCGCACTCCACGCCTCTCACCGCTCCCCCTTCCTCCACTCCCGGAATCTCCTCAAGCTCCGACCTCGTCAACCCTTTCGTTCCCGATTTA
81160 G A CCAATAACCAAGCGTCGGCGCAGCTTCTATGAAAAGCGTGCCTGCACTCCGGCATGACCCTAGCCACCTGCCCCTCCTCTATCTCCTCCAAGCAAACCGC[G/A]CACTCCACGCCTCTCACCGCTCCCCCTTCCTCCACTCCCGGAATCTCCTCAAGCTCCGACCTCGTCAACCCTTTCGTTCCCGATTTACGA
81160 GTTA G CGCCTCTCACCGCTCCCCCTTCCTCCACTCCCGGAATCTCCTCAAGCTCCGACCTCGTCAACCCTTTCGTTCCCGATTTACGATCGCCGCGATCATCGTT[GTTA/G]TTATTATTATTAGCGAGCGGTGGCTGGCCCAGGGAAGCGTACCAAAGAATGCATATGTAGATCAGGAATATGACGCTTATTCCTGC
81160 T C CACCGCTCCCCCTTCCTCCACTCCCGGAATCTCCTCAAGCTCCGACCTCGTCAACCCTTTCGTTCCCGATTTACGATCGCCGCGATCATCGTTGTTATTA[T/C]TATTAGCGAGCGGTGGCTGGCCCAGGGAAGCGTACCAAAGAATGCATATGTAGATCAGGAATATGACGCTTATTCCTGCGCATAGCAG
81172 TG T TCGAAGGTACCCTTGATGACGGAGGCGGTGGCCAATGCGGAGTAGCCAGCAGAGGCGGGGAGAGTGGTGGTAAGACCAGTAGGAGCGGGTCCAGCGGTTG[TG/T]GGGGGTGGTAGTAGTACCGGGCTTGGTGGTGGTGGTGGAAGTCTTGGTGGTGGTAGTCTTGGTGGTGGTAGTTCCGCCGC
81184 G A CTTTTGAAGTAGTCCTTAAATGCAAAGTTCAAGGCCTGAGTAGGAAAATATCGGATGACATTTGCGGTGTTCCCTCTCCACAAAGAAGC[G/A]AACCCTTCTTCTCTAATCGTTCTCTTAAAACAGTCACCAATTCCCTTGTATGGCTCAGACAAACGGCCTGACTTAATCATTTCATCTTGATTCTGTATCA
81184 C T TTTGAAGTAGTCCTTAAATGCAAAGTTCAAGGCCTGAGTAGGAAAATATCGGATGACATTTGCGGTGTTCCCTCTCCACAAAGAAGCGAACCCTTCTTCT[C/T]TAATCGTTCTCTTAAAACAGTCACCAATTCCCTTGTATGGCTCAGACAAACGGCCTGACTTAATCATTTCATCTTGATTCTGTATCAAAA
81184 C T AAGAAGCGAACCCTTCTTCTCTAATCGTTCTCTTAAAACAGTCACCAATTCCCTTGTATGGCTCAGACAAACGGCCTGACTTAATCATTTCATCTTGATT[C/T]TGTATCAAAAGCTTCACTCGCTCAATTGGAGCAGCCGCAGTTTTAGAAACTGCAGCGGAGACCCCACCCATCAGAAAATCAACCACAAA
81184 A T CAGCGGAGACCCCACCCATCAGAAAATCAACCACAAAATTCTTCTCAGCTGGTGCTTGCGCAAACACTGGAGATGCACTAGAAATCATAGATAAAACAGA[A/T]CCTTGGGACAGTGGCAATTGTAGCCCACCATTTACATAGCTTGTGTTCGAGAATCGGTTGTAAATGGGAGATCTATATGCAGTTTGT
81184 G T AGACCCCACCCATCAGAAAATCAACCACAAAATTCTTCTCAGCTGGTGCTTGCGCAAACACTGGAGATGCACTAGAAATCATAGATAAAACAGAACCTTG[G/T]GACAGTGGCAATTGTAGCCCACCATTTACATAGCTTGTGTTCGAGAATCGGTTGTAAATGGGAGATCTATATGCAGTTTGTCGAGTA
81184 T C TCAGAAAATCAACCACAAAATTCTTCTCAGCTGGTGCTTGCGCAAACACTGGAGATGCACTAGAAATCATAGATAAAACAGAACCTTGGGACAGTGGCAA[T/C]TGTAGCCCACCATTTACATAGCTTGTGTTCGAGAATCGGTTGTAAATGGGAGATCTATATGCAGTTTGTCGAGTAAAATCATGGGG
81184 A G CAACCACAAAATTCTTCTCAGCTGGTGCTTGCGCAAACACTGGAGATGCACTAGAAATCATAGATAAAACAGAACCTTGGGACAGTGGCAATTGTAGCCC[A/G]CCATTTACATAGCTTGTGTTCGAGAATCGGTTGTAAATGGGAGATCTATATGCAGTTTGTCGAGTAAAATCATGGGG
81186 G A TCCAAAGAAGAATCGTAAAGACCGATTTAAACAAGATAACGCATAAAGGCAGACAAGATAACATGTTCCATACACAGATAAAAACACGCACATTGCATAC[G/A]TCACAGTGATCACACAAACGGACAACACATCTATTTTTATATGTAGATAGACATAAGCTAAAATGGAAGAGCAAATCAAGGGAGTG
81186 C T GATTTAAACAAGATAACGCATAAAGGCAGACAAGATAACATGTTCCATACACAGATAAAAACACGCACATTGCATACGTCACAGTGATCACACAAACGGA[C/T]AACACATCTATTTTTATATGTAGATAGACATAAGCTAAAATGGAAGAGCAAATCAAGGGAGTGGTGCAGGCTTCTGTACATCTTCTG
81186 G C TATTTTTATATGTAGATAGACATAAGCTAAAATGGAAGAGCAAATCAAGGGAGTGGTGCAGGCTTCTGTACATCTTCTGAAGGACGAAACCAAACAGTCT[G/C]GTTCAACACCGTAGAAGTAGACGCATCCGAGGACTGATGAGCTTGAACATGATCAGCACTTGCACCAGCACCAAATGAGGAATCCG
81186 C A ATATGTAGATAGACATAAGCTAAAATGGAAGAGCAAATCAAGGGAGTGGTGCAGGCTTCTGTACATCTTCTGAAGGACGAAACCAAACAGTCTGGTTCAA[C/A]ACCGTAGAAGTAGACGCATCCGAGGACTGATGAGCTTGAACATGATCAGCACTTGCACCAGCACCAAATGAGGAATCCGCAGGC
81186 T C TCAAGGGAGTGGTGCAGGCTTCTGTACATCTTCTGAAGGACGAAACCAAACAGTCTGGTTCAACACCGTAGAAGTAGACGCATCCGAGGACTGATGAGCT[T/C]GAACATGATCAGCACTTGCACCAGCACCAAATGAGGAATCCGCAGGCCCGAAAACACCGGTCTGAGGATGTGGGCACCAGTATT
81186 A G GGACGAAACCAAACAGTCTGGTTCAACACCGTAGAAGTAGACGCATCCGAGGACTGATGAGCTTGAACATGATCAGCACTTGCACCAGCACCAAATGAGG[A/G]ATCCGCAGGCCCGAAAACACCGGTCTGAGGATGTGGGCACCAGTATTTATTGGAGTCCGACTCGATCGCATTATCTGGAACCACA
81186 T C GACTGATGAGCTTGAACATGATCAGCACTTGCACCAGCACCAAATGAGGAATCCGCAGGCCCGAAAACACCGGTCTGAGGATGTGGGCACCAGTATTTAT[T/C]GGAGTCCGACTCGATCGCATTATCTGGAACCACAACCGGAGGCACCTCATCTTCAATGTTCTTATCATAAGA
81190 A C CCGCCTCTGACGATCAACTCCGTCCTATCCACTTTCGCGCCGCCTTGGTCCATTACTCCGGCCATCCGTACAGTTCCTCCGCCCTCCGACCTGCTCTCCG[A/C]CAAAAGCCACACCCAAGCCGGCTCCCCTCCGCTTGAAACACCGAGCGAGTCCACCTGAGCCACGTTGCTGGCTCAACAAGCTTCTGCCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
81190 T C AAAAGCCACACCCAAGCCGGCTCCCCTCCGCTTGAAACACCGAGCGAGTCCACCTGAGCCACGTTGCTGGCTCAACAAGCTTCTGCCACACCGGATTGGT[T/C]GTCTCCTACGATAGCAGTTCACATAGGGAAGACACCCACCTCAGTTGCTCAAGTTCTCGACCCGCACGGGAAAGAATAATTTACAAT
81212 A C CAGCAAAAGTAGGAACCGCCGGAGGAGCACCCCTGGCCGTTTCATCAACCTTCTCAACGCCAGGTAAATCAGCCATCCCAATGCTCGCAAGCATCTCCAG[A/C]GTCTCTTTATCAACCTCGATAAGGTCAACCTTGATCTCAGACTCATCCGGCACGAAATCCATCCTCCTCTCTCTTTCCTCCTCTTGAAG
81212 G A CCGGAGGAGCACCCCTGGCCGTTTCATCAACCTTCTCAACGCCAGGTAAATCAGCCATCCCAATGCTCGCAAGCATCTCCAGAGTCTCTTTATCAACCTC[G/A]ATAAGGTCAACCTTGATCTCAGACTCATCCGGCACGAAATCCATCCTCCTCTCTCTTTCCTCCTCTTGAAGCTTCAACGATATCCCTCGC
81212 A G CAACCTTCTCAACGCCAGGTAAATCAGCCATCCCAATGCTCGCAAGCATCTCCAGAGTCTCTTTATCAACCTCGATAAGGTCAACCTTGATCTCAGACTC[A/G]TCCGGCACGAAATCCATCCTCCTCTCTCTTTCCTCCTCTTGAAGCTTCAACGATATCCCTCGCACCGGTCCTTTCTGGATCCTGCGCATC
81212 G A CCTTGATCTCAGACTCATCCGGCACGAAATCCATCCTCCTCTCTCTTTCCTCCTCTTGAAGCTTCAACGATATCCCTCGCACCGGTCCTTTCTGGATCCT[G/A]CGCATCAGATGGGTCGAGAAGCCAGCGATCTTGTTGCGGAGTCGCTTAGACGGAATGATGGCCACTTCCTCCAAAATCTTCTTGTTTGTG
81214 C G TAGTTAATTTTCTTAGAAGCCTGAACTCAATTGAGCGTGCAACACTGCTCTTTACATGTATAAAATATTCCTGACGACAGCAAACTAAATATCAAAAACA[C/G]AAGCAGCTTTCATTTCAGATGATAAGCAAACAGAAGAGACGAAAGCAGTAGATAAAGGAAACAAAAACGCAAGTACACAACAATCAG
81214 GA G TATAAAATATTCCTGACGACAGCAAACTAAATATCAAAAACACAAGCAGCTTTCATTTCAGATGATAAGCAAACAGAAGAGACGAAAGCAGTAGATAAAG[GA/G]AAACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAGACCCCTGTTTATTTAAGGAAGCACGCTAACTA
81214 A AC CATTTCAGATGATAAGCAAACAGAAGAGACGAAAGCAGTAGATAAAGGAAACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAG[A/AC]CCCCTGTTTATTTAAGGAAGCACGCTAACTACACCAGCTAGTAGAACTATAGGACATGAGCAGAGACAAAGGGGCACCCATTA
81214 T C AAGCAAACAGAAGAGACGAAAGCAGTAGATAAAGGAAACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAGACCCCTGTTTATT[T/C]AAGGAAGCACGCTAACTACACCAGCTAGTAGAACTATAGGACATGAGCAGAGACAAAGGGGCACCCATTATTAGCAAGTGCATG
81214 G A GTAGATAAAGGAAACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAGACCCCTGTTTATTTAAGGAAGCACGCTAACTACACCA[G/A]CTAGTAGAACTATAGGACATGAGCAGAGACAAAGGGGCACCCATTATTAGCAAGTGCATGGATTACACATGCAGTTGGCTCCACA
81214 A T AGGAAACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAGACCCCTGTTTATTTAAGGAAGCACGCTAACTACACCAGCTAGTAG[A/T]ACTATAGGACATGAGCAGAGACAAAGGGGCACCCATTATTAGCAAGTGCATGGATTACACATGCAGTTGGCTCCACACATACACT
81214 T C ACAAAAACGCAAGTACACAACAATCAGAAGGAGAGGTCTAAACACACAAGACCCCTGTTTATTTAAGGAAGCACGCTAACTACACCAGCTAGTAGAACTA[T/C]AGGACATGAGCAGAGACAAAGGGGCACCCATTATTAGCAAGTGCATGGATTACACATGCAGTTGGCTCCACACATACACTCTCCGT
81214 T C TAGAACTATAGGACATGAGCAGAGACAAAGGGGCACCCATTATTAGCAAGTGCATGGATTACACATGCAGTTGGCTCCACACATACACTCTCCGTTCTCT[T/C]TTCCTTCGTGTCCTCCCCCTTGATCAAACTGCCCTTTGAGAGGAGCTACGCCAAGGATGGC
81224 T C CTTGTATATAAATGCTCCGCAACATGAGATTGTTGATAAAACTATTACAATGCAAGAGATCACTCCAAAAATAGCCCATCCTCTTACACCATCATCTTCT[T/C]GCCCTTGCTTATATGCACATGACTTTGTCAGTGTGAACTCAACTGGATCATAATTCTCAATCGGGATTGAAATGTTGACCGTATATGGGA
81224 T A CTTACACCATCATCTTCTTGCCCTTGCTTATATGCACATGACTTTGTCAGTGTGAACTCAACTGGATCATAATTCTCAATCGGGATTGAAATGTTGACCG[T/A]ATATGGGATGTTCCTAGCCTTTTCACATCTCCAGTTTATTATCAAGACCGAAGGAGACAAGGTAGTAGGGGGGATTCCACTAGCTCCTG
81266 A G CTAGGGCGGAGATAGCAGCGGCGCTGAACAAGATGAAGAAGGAGACGTCGGTGGAGCTGGAGGCAAAGATGGCGGAGGGAAGGAAGAAGGTGGAGGCTGA[A/G]CTGGCGGAGGCGCTTGAGAGCTTGGAGAAGCAGAAAGTGGAGACCATTAAGGCGCTGGATGATCAGATTAGTCAGCTCA
81266 G C TGGAGGCAAAGATGGCGGAGGGAAGGAAGAAGGTGGAGGCTGAACTGGCGGAGGCGCTTGAGAGCTTGGAGAAGCAGAAAGTGGAGACCATTAAGGCGCT[G/C]GATGATCAGATTAGTCAGCTCAGCAACGACATTGTCAAGAAGGTCTTGCCCAGTGGCCGCGCTCCGTAATAGGTGATCGTTA
81270 T C CCAGCACCTCCACCAGTACCCCCACCAAGCCCGCCTACACCGCCTACACCACCAACACCACCAAGTCCACCTACTAAAGGCACCCCAGCCACACCACCAA[T/C]GCCGCCCATGCCAGCAGCCCCACCTACAACAGGAATGCCTCCTATAGAGGCACCCCCTATTCCAGCATATCCTCCCACTCCACTAAAA
81276 T C AACAACCAAGTTCAATGTTCATTGCTGACAGAATAAGTAAAAGTTTATCACATAAAAAGATGAGTCCAATATTATA[T/C]AACCAGTATAGAAATATCCAAAAGTACAATAAGGCTACTCTAGGAATCTTCAACAGAGCACAAGAGCCGCTAAAAAAACATAGCCCTGAACAGCAAATGC
81276 G C CTCTAGGAATCTTCAACAGAGCACAAGAGCCGCTAAAAAAACATAGCCCTGAACAGCAAATGCAACCAATATATGTGCAGCAGTCCTCCAACTCTTTAGC[G/C]CCAGCCATTCAAAGCTGATCAAGGCATTTACCGTTGATATATTCAATCACTTGAGCAACTGCTTGGTCTAATGCAGCGGTTACTGCAA
81276 C A ATTCAATCACTTGAGCAACTGCTTGGTCTAATGCAGCGGTTACTGCAACCAGATTCTGCAAAAATTCCTCTGCTGTTGGCTTTTCACCATCCACGATATC[C/A]GTCACTGCTTTTACGTATATTGATGGCACCGAAAACATGTCCGCAACATATGCCACTGCAGCCCCCTCCATATCTTTAATTGAGG
81280 T C ATCTTTATCTTATCAAACGTGAAAGTAACATAAGTCAAAGGTTGACTAAACATCCCCCATCGTCAGGTGAAGCTTCTTGATCAGATTTAGCACATGCCAT[T/C]GTGGAGCAAGACAATGCACTATAGTTGAGGCAATGTTGTGATTTATCATTGAGAAGGAAGTTAATAACGATACAAGTGTCGAATCACC
81288 T C ATAACTTGCAACAATGAATTATATTACATTTGAGAAGTATATATCCTACACCTCATATTTACATATATTACCAAAGCCCATGTACTCATGATTTCCAATC[T/C]TGTTAACTATGTTTGAAATGCCCACTCCACCTAGAGAAATCGCACTGATAAAAATCGTAAAAGCTAAAATAAAGATGATGATTGATGCTC
81288 G A TCGCACTGATAAAAATCGTAAAAGCTAAAATAAAGATGATGATTGATGCTCTTCCCAGCACGATGATAATCTTCCTCACTACATGTTGGCCTACAAATGC[G/A]GAAATAGTCGCCACGACAACGAAATATATAGCGTATGGAACCGGAAAACGACGAAGAAGGTAGTATTCAACCACGGACATGGATGC
81288 C T TTGATGCTCTTCCCAGCACGATGATAATCTTCCTCACTACATGTTGGCCTACAAATGCGGAAATAGTCGCCACGACAACGAAATATATAGCGTATGGAAC[C/T]GGAAAACGACGAAGAAGGTAGTATTCAACCACGGACATGGATGCTGAGAATGTCATGGCAAAGGTGGCAGTAGCACTTGACACCTG
81314 C T TTTTTTTTTTTTTTACCAGTAAAGCTTAAATTAATCTAAGTCTGAATACTATTTCCTGTTTTAATTCTTCCATGAAA[C/T]TAATATTAAATTTCATCATGCCGTATTCTTACCTCAAACAAGTACTACAGGAACAAAATTGACAAAACAGACTGGATGGTATAATTTGCTAATCCTCTTC
81314 G A CTGTTTTAATTCTTCCATGAAACTAATATTAAATTTCATCATGCCGTATTCTTACCTCAAACAAGTACTACAGGAACAAAATTGACAAAACAGACTGGAT[G/A]GTATAATTTGCTAATCCTCTTCCTCTTCCGCAGAAGGCATATCAGTACCTTCTTCGCACCTTCCACTTCCAGCTTCTTTCCCAGGAGCACT
81326 G A TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAG[G/A]AGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCA
81326 A G TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGG[A/G]GGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCAT
81326 G A TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAG[G/A]GGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCA
81326 G A TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGG[G/A]GAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCAC
81326 C G TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAA[C/G]AAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATAT
81326 T C TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCT[T/C]CACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCT
81326 C T TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCA[C/T]ATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTC
81326 A T TGTTGGCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCAC[A/T]TAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTC
81326 A G GCCTACTGGATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCC[A/G]TGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACT
81326 C T ATCTCAATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGC[C/T]TTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACG
81326 T C ATTTCAAATATCAATAAACAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGG[T/C]CATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCAC
81326 C G CAACAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCT[C/G]GACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTC
81326 C G CAGTAGACAGAAGAAAACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGA[C/G]CTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCC
81326 T G ACAGACAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTC[T/G]CCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCT
81326 G A CAATGGAGGAGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCA[G/A]AGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATAC
81326 T C AGGGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCA[T/C]CACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCC
81326 A G GGGAACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATC[A/G]CATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTC
81326 A C ACAAGAAGCTTCACATAGTAGTATTCCCATGGCTAGCCTTCGGTCATATGATCCCATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACAT[A/C]TACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACAC
81326 G C ATTCCTCGACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAAC[G/C]ACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCAC
81326 A T ACCTCTCCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATC[A/T]GACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAG
81326 T C CCAAGGCACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCT[T/C]ATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGA
81326 A G CACTCTCCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACA[A/G]TTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCT
81326 C A CCCAGAGAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCAT[C/A]CCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAAT
81326 A C GAGGCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCT[A/C]CACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCT
81326 C G GCCATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACA[C/G]CTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGA
81326 C T ATCACATATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCT[C/T]CCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGG
81326 C G TATACTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAA[C/G]GTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCA
81326 T A CTTCATCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTC[T/A]CAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTT
81326 C T TCTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGG[C/T]TTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTT
81326 T C CTCCACTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGC[T/C]TACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTC
81326 C T CTCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACC[C/T]TCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGA
81326 T C TCCCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCC[T/C]CCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGAC
81326 C A CCAGAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTC[C/A]GACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCT
81326 C T GAAACGTCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGA[C/T]GCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCT
81326 G A TCCACAGACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGA[G/A]TCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCTCAGAGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
81326 T C ACTCCGTCCCAAAGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACG[T/C]TGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCTCAGAGACCTCAAC
81326 C G AGTCCCCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCA[C/G]AATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCTCAGAGACCTCAACCCCAAACCGGAC
81326 C A CCAACGACTTATCAGACCTTATACAATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATC[C/A]AAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCTCAGAGACCTCAACCCCAAACCGGACTACAT
81326 C T ATTCATCCCTCTACACCTCCCTAACGTCTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCC[C/T]TAGACGGCCTCCAGCTTCCCTTCTCAGACCTCCTCAGAGACCTCAACCCCAAACCGGACTACATCATCCAAGACTTCGTCCAGCACTGG
81326 G A CTCAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCA[G/A]ACCTCCTCAGAGACCTCAACCCCAAACCGGACTACATCATCCAAGACTTCGTCCAGCACTGG
81326 C T CAGGCTTACCCTCCGACGCAGAGTCGACGTTGGACGTCCCACAATCCAAGGTCGACTACCTCAAAATAGCCCTAGACGGCCTCCAGCTTCCCTTCTCAGA[C/T]CTCCTCAGAGACCTCAACCCCAAACCGGACTACATCATCCAAGACTTCGTCCAGCACTGG
81334 T C TTTTTTTTTTTTTTGAACAAATTCTAGAAAATATCAATTATATTTCAAAATGCTGCTGCCGGAGTTCACGACTACAAAACCCA[T/C]CAACAAATAGATCACGGATAGCAAGCGAAAGGCGACACTGACACAAAATACTGCACCTTTCACAGTTGGGAACAAAGCAACACTACATACATAATCAACT
81334 CA C AAAATATCAATTATATTTCAAAATGCTGCTGCCGGAGTTCACGACTACAAAACCCATCAACAAATAGATCACGGATAGCAAGCGAAAGGCGACACTGACA[CA/C]AAAATACTGCACCTTTCACAGTTGGGAACAAAGCAACACTACATACATAATCAACTCGGAACATTAGTCAACCTTTTATTATTAGGA
81340 G T ACAAGATCAAGGACATGTCTCAGGCCGACTTCGGCCGCCTCGAGCTCGAGCTAGCCGAGGTTGAAATGCCCGGCCTCATGGCATGCCGAACCGAATTCGG[G/T]CCTTCCCTACCCTTTAAAGGTGCCAGAATAACGGGATCTCTGCACATGACCATCCAAACCGCAGTCCTCATCGAAACCCTAACGGC
81344 T C TCCTTTCAACAACCATGTTGCATTGTCCTGGAGTCATGGGCTCGTCATATATACCAAAGATCAAAGCCTGGGTCGTCTTCTTTATGGTGATCCCCCCTGA[T/C]CCCTTCTTTCCACGGATAACAGCTCCAGGTTCTCCTTGGATGACCATGTACTTCGTACCACCAAGAAACAAACCAGTAGGTGCAAGGGA
81346 G A CTGGCCCAAAAACTCGACGATCTCAACATCAACGTTTACGTCGGCGTCGGCGCCGCCCAAACCGACGACGCAGCTAAGAACGCGCTCGAAAACCCGTACC[G/A]AGCACGGGATCCTGAGAACCCCTCTTTGCTCGTACCCGTACTCCTGGGCCGATCTTCTCAGCAGCTCGGAAAAAACCGGGTGGTTG
81346 A G TGGCCCAAAAACTCGACGATCTCAACATCAACGTTTACGTCGGCGTCGGCGCCGCCCAAACCGACGACGCAGCTAAGAACGCGCTCGAAAACCCGTACCG[A/G]GCACGGGATCCTGAGAACCCCTCTTTGCTCGTACCCGTACTCCTGGGCCGATCTTCTCAGCAGCTCGGAAAAAACCGGGTGGTTG
81346 G A CGGCGCCGCCCAAACCGACGACGCAGCTAAGAACGCGCTCGAAAACCCGTACCGAGCACGGGATCCTGAGAACCCCTCTTTGCTCGTACCCGTACTCCTG[G/A]GCCGATCTTCTCAGCAGCTCGGAAAAAACCGGGTGGTTGAGCAACTCCGCCCTGATCACGAACCGCTCCTTCTCCTCGCCCACGTA
81346 A G CTCCTGGGCCGATCTTCTCAGCAGCTCGGAAAAAACCGGGTGGTTGAGCAACTCCGCCCTGATCACGAACCGCTCCTTCTCCTCGCCCACGTAGACCGGC[A/G]CGTGCCCTTCTAGAACGTTCCCGTTGCCGCAGTCGGCGCTTCTCAATTGCTCGTATCGTACGGACGAGCTGTCCGCTACCTTCGACA
81368 C T TGCAGGCGAACAGCTCGCTCGAGGATTCCTGTCAGATTGAATCTGGGTCGTTGATCGACGGCTCCGTGAATAATTCGTGTGGCACTTTTGTCGGTGTTTA[C/T]GATGGACACGGTGGTCCAGAGACTTCCCGGTATATTACAGATAATCTGTTCAATAATTTAAAAAAGTTTGCTTCGGAACAAAAAGGA
81368 CA C TGGCACTTTTGTCGGTGTTTACGATGGACACGGTGGTCCAGAGACTTCCCGGTATATTACAGATAATCTGTTCAATAATTTAAAAAAGTTTGCTTCGGAA[CA/C]AAAAAGGAATTTCAGCAGATGTAATAAGAAGGGCATATACTGCCACAGAAGAAGATTTTCTTTCTCTAGTTAGAAAACAATGGAAA
81376 T C ATTACTATGCCAATGACACCAAATTGTACAACGGGGATAGCTTTGCTCAGAATTTGCTTTGGAAGGGGTGGAGGGTAATTTGACAAAATCACATCAATCC[T/C]AGGAAAAGAAGCTTCTAGCATCTTCTTCATTGTAATAGCATTTCCTTTGTAAGAGCATGAAGTGCAAAATTTGATTTCCACAATAGTG
81376 A G GTGGAGGGTAATTTGACAAAATCACATCAATCCTAGGAAAAGAAGCTTCTAGCATCTTCTTCATTGTAATAGCATTTCCTTTGTAAGAGCATGAAGTGCA[A/G]AATTTGATTTCCACAATAGTGCCATAGGCATGTCCTCGGACTTGGGTATTCTGAGCGGCTGAAAA
81384 T C CCATTCTGCAATCACCTTCTTCGCTGGGTACACCAGGAGTGACTGGAGCAGTGATGTGGGATAGTGGAATAGTTCTTGCTAAATTTTTGGAGCATTCATG[T/C]GATTCCGGTTCGATTGAGCTTCATGGGAAGAAAGTTGTTGAATTAGGCTCAGGTTGTGGGTTAGTTGGATTCATAGC
81392 T C AATCCAAACCCTAATACCTTAGATCTGATTTTATGATTCCTACCTAACGATTCGATGTCGACTAAATCCCGGCCCTGCCCAGCTCTGCTCCATCATGTGG[T/C]GGCCCTTATTCCATTTTCTATCTTAACGTGCTGTCAACTCGCGACTCTTTCCACATTATGCTGCATGCTACTAGATCTAGACCACCAAAGG
81398 G A AGAAAGCTATGGGGACAAACGACGTGAGGGTGGACGTGAAGCTGAACAAGCACGTATGGAGCAGGGGAATAAGAGGGGTGCCAAGGCGTGTCAGGGTTAG[G/A]ATTGCACGTAAAAGGAACGAGGAAGAAGATGCAAAGGAAGAGCTCTACTCATTGGTCACCGTGGCTGAAGTACCTCCCGAA
81398 G A TCAGGGTTAGGATTGCACGTAAAAGGAACGAGGAAGAAGATGCAAAGGAAGAGCTCTACTCATTGGTCACCGTGGCTGAAGTACCTCCCGAAGGGCTCAA[G/A]GGCTTAGGCACCAAGGTCATTGATGAGGCTGATTAATTATGTTTCTCTTGTCTTTCTTTTTTGTTT
81426 A G TTGCAGGAATTTGGCCAATCTTCTTCAAAGTGTCCTTGGCAGGCGCATCATCTACACCAATAGCCATAACGGCCTGTTTCCTTGGAGCAGTCCTACCAAC[A/G]CTCATGAAGCTAACATTCACGTTTTGCTCTCCCAAAATGCTTCCAACCGTACCTATCATGCCAGGCTGATCGACTTGCCTGCACAGAAT
81426 C T CATCTACACCAATAGCCATAACGGCCTGTTTCCTTGGAGCAGTCCTACCAACACTCATGAAGCTAACATTCACGTTTTGCTCTCCCAAAATGCTTCCAAC[C/T]GTACCTATCATGCCAGGCTGATCGACTTGCCTGCACAGAATCAAACTCCCTTCCATGCTAACATCCACTTCAAATGACCCAATCTTCGTC
81440 G A CAAGCGCTATAGCGAGCATCTACACATTGATAGCACTTGTTCTCTTTGTGATGATAAATAAATGGAAGAAGAGGGGCAATTTGGTAGCGTTAGTGATATC[G/A]ATGGCCGATGTGGTGATCCTTATTGTGCTGTTTACTGGAAACGCTGCAGCTGCTGCGATAGGGATGGTGGGAGAGAAGGGAATAG
81440 G T GCATCTACACATTGATAGCACTTGTTCTCTTTGTGATGATAAATAAATGGAAGAAGAGGGGCAATTTGGTAGCGTTAGTGATATCGATGGCCGATGTGGT[G/T]ATCCTTATTGTGCTGTTTACTGGAAACGCTGCAGCTGCTGCGATAGGGATGGTGGGAGAGAAGGGAATAGATGAAGTGCACTGGC
81444 T C ACTTTACTCTGTACTACATCAGAATTATGTACAAGAATTGAAGCTGAGACTCCACGAGCTCTGCCACATGCTTTAGTTGTATGGCTAGAAACATTTTTAC[T/C]ATCAGGAACCTGAGTTCCTATTTGCGAGGATTCTGAAGCAGAAGATCCAGACTGTGGTAAAGGAGAATATTGGTGTTGTAATTGTATG
81484 A G GTCTTCTAGAGTGTGGATTTTCGAGTTAAGATCGGTGTTTGGATTTGGGTTGTCATAGCGTAGAGCTGCTACCCCTTGGTTTCTTACAGTCCGATCAATC[A/G]GTGGTGGTTACACGTTTTGCTGTAGCTTACGTGAAGAAATGTGAGTTTGGGTTTGTGGAGCCGTGCGAGTGAGGAGGTGCGGATGT
81484 G T TCTTCTAGAGTGTGGATTTTCGAGTTAAGATCGGTGTTTGGATTTGGGTTGTCATAGCGTAGAGCTGCTACCCCTTGGTTTCTTACAGTCCGATCAATCA[G/T]TGGTGGTTACACGTTTTGCTGTAGCTTACGTGAAGAAATGTGAGTTTGGGTTTGTGGAGCCGTGCGAGTGAGGAGGTGCGGATGTC
81484 C T TCGAGTTAAGATCGGTGTTTGGATTTGGGTTGTCATAGCGTAGAGCTGCTACCCCTTGGTTTCTTACAGTCCGATCAATCAGTGGTGGTTACACGTTTTG[C/T]TGTAGCTTACGTGAAGAAATGTGAGTTTGGGTTTGTGGAGCCGTGCGAGTGAGGAGGTGCGGATGTCAATGCTCAGTTTGGTGGTG
81484 G GT GTCATAGCGTAGAGCTGCTACCCCTTGGTTTCTTACAGTCCGATCAATCAGTGGTGGTTACACGTTTTGCTGTAGCTTACGTGAAGAAATGTGAGTTTGG[G/GT]TTTGTGGAGCCGTGCGAGTGAGGAGGTGCGGATGTCAATGCTCAGTTTGGTGGTGAGATCAGAATGATGAATGGTGATTTGTGG
81484 T G GTGGAGCCGTGCGAGTGAGGAGGTGCGGATGTCAATGCTCAGTTTGGTGGTGAGATCAGAATGATGAATGGTGATTTGTGGTGAATGATGGAAGTGTCGA[T/G]ATGGGGTCAGTTGATGGTGGTTGCCTGTTGCTACATTTTGACAGGGAGGAAAGGCAGTGAATTGGCTTAGGGTGATGCCATAG
81484 G A GATGTCAATGCTCAGTTTGGTGGTGAGATCAGAATGATGAATGGTGATTTGTGGTGAATGATGGAAGTGTCGATATGGGGTCAGTTGATGGTGGTTGCCT[G/A]TTGCTACATTTTGACAGGGAGGAAAGGCAGTGAATTGGCTTAGGGTGATGCCATAGATGGACTATACAAGTCAGATAATACAAG
81484 A G AATGCTCAGTTTGGTGGTGAGATCAGAATGATGAATGGTGATTTGTGGTGAATGATGGAAGTGTCGATATGGGGTCAGTTGATGGTGGTTGCCTGTTGCT[A/G]CATTTTGACAGGGAGGAAAGGCAGTGAATTGGCTTAGGGTGATGCCATAGATGGACTATACAAGTCAGATAATACAAGAGAGAA
81490 A G GTCACGTAAGGCGGGCTTATTCTGTTGATTCCATGGGAAATAACACTCCTCCTGATAGCCCTCGGCGGTCTAGATCTCCCCTCATGTTTGCTCCTCAGAT[A/G]CCTGTAGCTCCGTTGCAAAGAGCTACCGATGTACCTCCAGTTTTCAACCAGTCATGGATGAATGAAAATCATGAAATGTTTGATGAGC
81490 T A TGATAGCCCTCGGCGGTCTAGATCTCCCCTCATGTTTGCTCCTCAGATACCTGTAGCTCCGTTGCAAAGAGCTACCGATGTACCTCCAGTTTTCAACCAG[T/A]CATGGATGAATGAAAATCATGAAATGTTTGATGAGCATGTTGAGAAGGGCATCCCAACATTGATTAC
81496 C G CAGTCATAGTTGATGATTCGAAGCCTACTACTTCAATACAGCTCCGCTTGGCTGATGGGTCGCGTACTGTCGGGCGCTTCAACACAGATCACACTGTAGG[C/G]GACATCAGGTCCTACATCAATAATCACTTGGCCAGCAGTGGAAAAGCTGTTGCTGCCAATTATACTTTGCAGACGGTCGGCTTTCCA
81502 T C CCCAGCTTCGCAAATCTTCGAATCATAAGCTGTAATCTTTAGATCTGAAATGCTCAGCTC[T/C]TAATACGCGACTCAGACGATGGGCTGGGCCATTTGAGTTCTTCAGAAAATAGCGACGAGGGCGACTGCTTTGAGTACAAACGAAACAACGGACTTCGGTC
81502 C T TCTCGAGCGATGATGATAACAATTTAGCGAAGTGAAAAGGGATTGATCTGTAGGTGTTTGCGAGGGAGTTATGGGGTCTCGATAGTCTCGGTCAGTGGCA[C/T]TAGAGTTTAGATTTTTGGGGAAAATGATTTGATTTGGGGATAAAGTTTTCTGGCTGAAGCCCTAAAAATGGAAAGGGGAATGACT
81518 C T ACAAACAGACATACGAGAGTAACAAGGAAAGTCTTACAAACAAACAAGAGTCCTTCAGATGCAACACGTTTATTTACTTCTTAAACATAAACATCAATTC[C/T]CATCCTGGTTACTCGAATGCCCATTGATTCTCCCTTCGGACTTCTTCCTCTTCTTCAGGTGTGAAATCATTCTTTATGTTGAACGTTTTCC
81518 C G CAAACAGACATACGAGAGTAACAAGGAAAGTCTTACAAACAAACAAGAGTCCTTCAGATGCAACACGTTTATTTACTTCTTAAACATAAACATCAATTCC[C/G]ATCCTGGTTACTCGAATGCCCATTGATTCTCCCTTCGGACTTCTTCCTCTTCTTCAGGTGTGAAATCATTCTTTATGTTGAACGTTTTCCT
81534 A G CTCAAACAAGTTACACTTTCAAAGGCATCGTTTTATTATGTATTTTTACAGCAGTTTGATGCCTTCCCGCTATTTTAAAAAGGGAACCACAATCTTCCCT[A/G]TAATATATCAATGTATTATCACTATTTCTTCTTCATTCGTTTTTCTTGTGTGAAGCTCGAGATTGAGTACCATTCAGTGCAGCATGGTAAAC
81534 A G ATCTTCCCTATAATATATCAATGTATTATCACTATTTCTTCTTCATTCGTTTTTCTTGTGTGAAGCTCGAGATTGAGTACCATTCAGTGCAGCATGGTAA[A/G]CTCTCTTCTCCGGCAGCCCAATATCCGCCATTGTTAGGTTCCCCTTAGCTGCCATGAACTTTCTAACATTGCTGGCATAAAGCTTGGGATC
81536 TA T CTAGCTGTTTCAAAAACTATATTCAGTGTTATTCTGTCTCATATTGCAGCTATATATTTTATTGTTTTGAATTTCTTTAAGGGGAAACTGACCGGAGTCA[TA/T]AAAACCCCGTAGTGCACCTAGCCCGGTCCACGAGCACCACATAAATGATAGATCTTGGCGTATGTACATGGGAACTCTATTGCGAAGT
81570 T C TTTGACCATGAGTCAGTTAGGGCTCACACCATAGATATTTTCCCAGGTGTTGTGAAAGTGGTGGTCAGGGATGATGATAATTACAACGTGGATGATGAAA[T/C]GGAGTTGGATAGGTGGAGGTTCAGGCTTCCTACCGGGACTAGGCCTAGACTTGCGAGGGCAGAGTTGGTTAACGAGGAGTTGGT
81572 T C CAAGACAGATAATTTGAGCACACAATATCCTAGGCAACACTAGTGCATTACATCTCTTCTATAACAGCCTTCTTCAAATTCAATCCCTTACCTTTGGATT[T/C]ACCAAGTTTTGCACCGGCTTGATTCACATCTAAAACCGAAGCTCTCTCGATCTCCAGCATATTGACCAAAGACGCCCAAATATCTTCTACC
81590 C T CCCAAAGGTTGGAACACGCCTTAATTCTTTCTCTTATCGTGGAAATGGCGACGTCTTCAGGCTCGGACCAAGCGGAAATGACTATTGATTCAGCACCTGC[C/T]TCTCTTCCGCCAAAACCTCAATTCAAAGCTTTGACGGCGCACGAGATGTCAGATGGGAAAGTTCAGTTTCGCAGAGTGAATGTCCCG
81590 T A CTTCAGGCTCGGACCAAGCGGAAATGACTATTGATTCAGCACCTGCCTCTCTTCCGCCAAAACCTCAATTCAAAGCTTTGACGGCGCACGAGATGTCAGA[T/A]GGGAAAGTTCAGTTTCGCAGAGTGAATGTCCCGCGACACAGACTCTCACCGTTGAAGAAGAACTGGATGGAGATTTATACTCCTATC
81608 T C GTTGGCCTACTGGATTTTCCTCTGCTTATTTCCAAATTCAACATCATTTAAAAAATATACAACGTTACATTCAGAGATAGACGTACGTATTCTTTCGA[T/C]TAACATATATAAAAGGGGATTTAATAAGGTTTCGAAGGGTGGTTTTCTATTTAATTTGCACCTAAATGGCGGAAGAAAAAAAGGGCGAGGA
81608 T G AGGAAGAATCATCAGAAACAATGGCGGTTCTCGATTTCGACATGCTTTGCGCAACAGTCGCCCTTCAGACCCAGGGCTTTGCGGAAACCGAGAAGAGCGG[T/G]GATGGATTCGGAAGAAGTAACGATGAATTTGGAGGGGTTCAAAGGATGTGGGAAGGCGGTGTTTTTGATTGCTTTGATGATACG
81608 T A AAGAATCATCAGAAACAATGGCGGTTCTCGATTTCGACATGCTTTGCGCAACAGTCGCCCTTCAGACCCAGGGCTTTGCGGAAACCGAGAAGAGCGGTGA[T/A]GGATTCGGAAGAAGTAACGATGAATTTGGAGGGGTTCAAAGGATGTGGGAAGGCGGTGTTTTTGATTGCTTTGATGATACGAGA
81618 T TA ATTCAAAATCAGCAGTTAAATTCCAAATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACA[T/TA]AACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGAC
81618 G GA ATTCAAAATCAGCAGTTAAATTCCAAATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACATAACTC[G/GA]AAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCA
81618 A C ATTCAAAATCAGCAGTTAAATTCCAAATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACATAACTCG[A/C]AAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCAT
81618 G A ATTCAAAATCAGCAGTTAAATTCCAAATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACATAACTCGAAAAA[G/A]AAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCAT
81618 A C AATCAGCAGTTAAATTCCAAATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAAC[A/C]CAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTG
81618 C T ATATACAGGGATCCACCACAATCCGGATCAAATTCCAACCCCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAAT[C/T]TTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGC
81618 T C CGGATCAAATTCCAACCCCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACC[T/C]GGTAATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGA
81618 T A ATCAAATTCCAACCCCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGG[T/A]AATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCG
81618 C A TTCCAACCCCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAA[C/A]GATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCGAAGTAG
81618 C A CCACACAAAATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAA[C/A]GCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCGAAGTAGATAATTG
81618 A G AATCACATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTG[A/G]ATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCGAAGTAGATAATTGTATGGACG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
81618 G C CATAACTCGAAAAAGAAAAAGGCAAACACAGTAACAAAACCTAGAATCTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCG[G/C]ACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCGAAGTAGATAATTGTATGGACGAGGAT
81618 A G CTTCACTCTCAAACAAACCAACCTGGTAATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGAT[A/G]GTCAAGAGAGCGAAGTAGATAATTGTATGGACGAGGATCGACAACCCGCTGGTCTGCATGCTACCGAACGCTATGAACCTTCCGT
81618 T A GGTAATAACGATAGAACGCAAGTGAATCGGACAATCATCCAGTGTAAATGTGAACGCCAACCGCGATGAGCAAGATAGTCAAGAGAGCGAAGTAGATAAT[T/A]GTATGGACGAGGATCGACAACCCGCTGGTCTGCATGCTACCGAACGCTATGAACCTTCCGTTGCCGGGCAGCTGAAAGAGCAGC
81628 G T CTGGATGGGAATTGAGATTGGGATTGGAACGACAACGTGATGCAAGTCGAAGCCTCAGTTTAATTTTAATTTAGGATATGGTAGTGGGATTTGGGAGATA[G/T]GGTTTTTGAGAGCGACGTTGATTAAGGGAAAATGAATTTTGACGATGAATGATTTTCGAAG
81636 A C TCTATCACTCCAGACATTACTTCCCAAATCATCGGATGTTCCTCAAGCCATAAAATCATTATTTGTTATGGATGGTGTGGTTAGTTACCAAGGGCATTGT[A/C]GGCCTCTTGCTTCTTTTCAAGTTACTAAGCTTGGGGACGGTGCCATATTCATAGGCTGCAGCATCAACCATGCTGTAACAGACGGTACC
81636 C T TTCCTCAAGCCATAAAATCATTATTTGTTATGGATGGTGTGGTTAGTTACCAAGGGCATTGTAGGCCTCTTGCTTCTTTTCAAGTTACTAAGCTTGGGGA[C/T]GGTGCCATATTCATAGGCTGCAGCATCAACCATGCTGTAACAGACGGTACCTCTTTCTGGAACTTCTTCAATTCATGGGCAGAAATTTG
81636 A G TGTTATGGATGGTGTGGTTAGTTACCAAGGGCATTGTAGGCCTCTTGCTTCTTTTCAAGTTACTAAGCTTGGGGACGGTGCCATATTCATAGGCTGCAGC[A/G]TCAACCATGCTGTAACAGACGGTACCTCTTTCTGGAACTTCTTCAATTCATGGGCAGAAATTTGTAAAAGCACAGTTCAGTTGCCAAA
81636 T C AGGGCATTGTAGGCCTCTTGCTTCTTTTCAAGTTACTAAGCTTGGGGACGGTGCCATATTCATAGGCTGCAGCATCAACCATGCTGTAACAGACGGTACC[T/C]CTTTCTGGAACTTCTTCAATTCATGGGCAGAAATTTGTAAAAGCACAGTTCAGTTGCCAAAACCATCGCGACTGCCAAATCACGAACG
81636 G A GCAGCATCAACCATGCTGTAACAGACGGTACCTCTTTCTGGAACTTCTTCAATTCATGGGCAGAAATTTGTAAAAGCACAGTTCAGTTGCCAAAACCATC[G/A]CGACTGCCAAATCACGAACGGTGTGGTTTGTTTAGCAATTCGAAAGCTGTACTTAGATTTCCAGACAAAAATGGTCCTGAACTGACTT
81636 A G ACCATGCTGTAACAGACGGTACCTCTTTCTGGAACTTCTTCAATTCATGGGCAGAAATTTGTAAAAGCACAGTTCAGTTGCCAAAACCATCGCGACTGCC[A/G]AATCACGAACGGTGTGGTTTGTTTAGCAATTCGAAAGCTGTACTTAGATTTCCAGACAAAAATGGTCCTGAACTGACTTTCAACCCGA
81636 A G TGCCAAATCACGAACGGTGTGGTTTGTTTAGCAATTCGAAAGCTGTACTTAGATTTCCAGACAAAAATGGTCCTGAACTGACTTTCAACCCGAAAGCACC[A/G]TTGAGAGAAAGACTATTCCACTTCAGTCGAGAAGCTATACTCGAACTTAAAAAAAGAGCAAACTTCATGTCC
81648 T C TCTGAAAATGCTTTTCGAACTGCTTCCCTCTTCAATTTGAGGGCTGCTGTGACTAGGCCAGATTCTGGAGTCCATGCTTCGCTCATCAGTTTGATTTTTG[T/C]TGGTATTTCAAATTTCTCCAGTTTTGAATCTTTTCCAGCCTTCATTAAGGACTCCTGAACTTCTTTCAAGACTTCTTGCTTACTACATAAAT
81670 C T CACCGCAAGCCGCTGCATGTTGCCTGAACCGCCTCCGTCGAGACCTCGCCTCCTCCTCGATTGAAACCCAACATCGCACCGTCCCCTTCGAGCCTCAGAC[C/T]AGAACCCGTGCCAGTGGAGCCTGTTCCGCCTCTTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAG
81670 C T AGCCGCTGCATGTTGCCTGAACCGCCTCCGTCGAGACCTCGCCTCCTCCTCGATTGAAACCCAACATCGCACCGTCCCCTTCGAGCCTCAGACCAGAACC[C/T]GTGCCAGTGGAGCCTGTTCCGCCTCTTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGC
81670 A G CCAGTGGAGCCTGTTCCGCCTCTTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTC[A/G]ATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGC
81670 A G TGTTCCGCCTCTTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCT[A/G]TGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGT
81670 C T CTCTTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTA[C/T]TCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGTTTGGGTTC
81670 T C TTTCTCTTTCAGCGAACCACCACCAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTACTC[T/C]GACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGTTTGGGTTCATC
81670 T C CAGGCTTGAAAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCT[T/C]GAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGC
81670 G A AAGGCCGCATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGC[G/A]CGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGCTGTTTTAAG
81670 C T CATCTTTTTAACCAAAGCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAG[C/T]CGCTTGCTCCATGACTGCCAATCGAAGCCGCAGCCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGCTGTTTTAAGGTCTCTTT
81670 T C GCCCTAGCCTCGTTCAGATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGAC[T/C]GCCAATCGAAGCCGCAGCCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGCTGTTTTAAGGTCTCTTTTGATTT
81670 C T AGATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCG[C/T]AGCCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGCTGTTTTAAGGTCTCTTTTGATTT
81670 G A ATCGTCAATCCACCTCTATGACTTACTCTGACCTTCGAAATTTCAGCACCTTGAGACCGCGCGGAAGCCGCTTGCTCCATGACTGCCAATCGAAGCCGCA[G/A]CCACGTTTGGGTTCATCGAAACTGTTGCTCCTTTCCCTGCTGTTTTAAGGTCTCTTTTGATTT
81684 G A AAGGACACAGAGGTGTATCATTATCCAAAGATCTAATAGCAATTGCGGGCGATGCCCTAAAATCCAATATAACGACGATGGGACCCTTAGTGCTTCCGGC[G/A]TCAGAACAAATCTTGTTCTTACTCAGCCTGATTGGGCGCAAACTAATAAACCCTAAATGGAAGCCTTATGTTCCGGACTTCAAACAA
81698 C A GTGGCCTTTTTTTTTTATTGAACAAATTTACGTAAATACATAAATAAAAAACCGAAAACGTAGTGTATACATGATCATGCATCATACACATTAAAAACT[C/A]AAAACAAACATACAAATATTTGAAGTTCAAACAGAGAAATATATAGCTTTAAAAAGAGCTGGTGGTGGTAGATGCATAGGCTTTTGGCG
81698 A C GTGGCCTTTTTTTTTTATTGAACAAATTTACGTAAATACATAAATAAAAAACCGAAAACGTAGTGTATACATGATCATGCATCATACACATTAAAAACTC[A/C]AAACAAACATACAAATATTTGAAGTTCAAACAGAGAAATATATAGCTTTAAAAAGAGCTGGTGGTGGTAGATGCATAGGCTTTTGGCG
81702 T C GATCTGCCCAAGGACCCACTGGTTTAGGTAAATATCTAATGCGTTCCCCTACGGGAGAGGTTATTTTTGGAGGAGAAACTATGCGTTTTTGGGATCTCCG[T/C]GCTCCCTGGTTAGAACCTCTACGGGGTCCCAATGGTTTGGACTTGAGTAGGCTGAAAAAAGATATACAACCTTGGCAAGAACGACG
81704 G A TTTCCAGAAGATGGAGGAAATGGGAAGATTGCAGGTTTTGACTCTCGGTTTGCAGACTGCCAAGTGTTTGAATGTTTTGTTCGTGAGGATGCGTGTTGGC[G/A]TTCTTTGCTGCGTGGTTGGAATTGCTGGAGGGAGTTTGTTTACGTTGTGGTTGAAATGAGGTACCTTTACCAATGGTTAGTTGGAA
81704 T C AGAAGATGGAGGAAATGGGAAGATTGCAGGTTTTGACTCTCGGTTTGCAGACTGCCAAGTGTTTGAATGTTTTGTTCGTGAGGATGCGTGTTGGCGTTCT[T/C]TGCTGCGTGGTTGGAATTGCTGGAGGGAGTTTGTTTACGTTGTGGTTGAAATGAGGTACCTTTACCAATGGTTAGTTGGAATAATT
81760 G C TTTGCAAAAATGTATGCTTCCAAATTTGGAGTCGATGAATCGAAAATGATGGAGAGACTTTGGGGTGAGAACTTTTTTGACCCGGCGACCAAAAAATGGA[G/C]TAGCAAGCATACTGGTGCATCTACTTGTAAGCGTGGATTCGTCCAATTCTGCTATGAACCAATAAAGCAGATCATCAATACTTGTAT
81760 T C ACCCGGCGACCAAAAAATGGAGTAGCAAGCATACTGGTGCATCTACTTGTAAGCGTGGATTCGTCCAATTCTGCTATGAACCAATAAAGCAGATCATCAA[T/C]ACTTGTATGAACGATCAGAAGGATAAGTTGTGGCCCATGCTTAAGAAACTTAATGTTACAATGAAGTCAGATGAAAAAGATTTGATG
81760 C A AGATCATCAATACTTGTATGAACGATCAGAAGGATAAGTTGTGGCCCATGCTTAAGAAACTTAATGTTACAATGAAGTCAGATGAAAAAGATTTGATGGG[C/A]AAAGCTCTGATGAAGAGAGTGATGCAAACGTGGCTCCCTGCTAGCACTGCTCTTCTAGAGATGATGATATTTCATCTCCCTTCGCCG
81760 A G TGAACGATCAGAAGGATAAGTTGTGGCCCATGCTTAAGAAACTTAATGTTACAATGAAGTCAGATGAAAAAGATTTGATGGGCAAAGCTCTGATGAAGAG[A/G]GTGATGCAAACGTGGCTCCCTGCTAGCACTGCTCTTCTAGAGATGATGATATTTCATCTCCCTTCGCCGTTTACAGCACAGAGATA
81760 T C TTAAGAAACTTAATGTTACAATGAAGTCAGATGAAAAAGATTTGATGGGCAAAGCTCTGATGAAGAGAGTGATGCAAACGTGGCTCCCTGCTAGCACTGC[T/C]CTTCTAGAGATGATGATATTTCATCTCCCTTCGCCGTTTACAGCACAGAGATACCGTGTTGAGAATCTGTATGAAGGGCCTTTGGAT
81760 G T AAAAAGATTTGATGGGCAAAGCTCTGATGAAGAGAGTGATGCAAACGTGGCTCCCTGCTAGCACTGCTCTTCTAGAGATGATGATATTTCATCTCCCTTC[G/T]CCGTTTACAGCACAGAGATACCGTGTTGAGAATCTGTATGAAGGGCCTTTGGATGATATTTACGCAAA
81764 CA C CAGGCACCACGGGTATGAGTAAAGGCGTGATTATAACACATGGGAACTTCATATCTTCTAGTTTGATGCTTACAGCAGATCAAGATGAGAACGGTGAACC[CA/C]AAAAATACTATACTGTGTTTCTTGCCTATGTTTCATGTGTTTGGTCTTTCTGTTGTGTGTTATGCACAGTTGAGGAGAGGGAACAC
81764 G A AATACTATACTGTGTTTCTTGCCTATGTTTCATGTGTTTGGTCTTTCTGTTGTGTGTTATGCACAGTTGAGGAGAGGGAACACGGTGGTGGTTATGGAGA[G/A]TTTTGATATGGGTGTTATGTTGAGATCGATTGAGAAGTATAGGGTTAGCCATTTGTTTGTAGTGCCACCTGTCATGATTGGGTTTGCT
81764 G T TTCATGTGTTTGGTCTTTCTGTTGTGTGTTATGCACAGTTGAGGAGAGGGAACACGGTGGTGGTTATGGAGAGTTTTGATATGGGTGTTATGTTGAGATC[G/T]ATTGAGAAGTATAGGGTTAGCCATTTGTTTGTAGTGCCACCTGTCATGATTGGGTTTGCTAAGCAAGGGAATGTGCTCAAGAAGTA
81764 A G TGAGGAGAGGGAACACGGTGGTGGTTATGGAGAGTTTTGATATGGGTGTTATGTTGAGATCGATTGAGAAGTATAGGGTTAGCCATTTGTTTGTAGTGCC[A/G]CCTGTCATGATTGGGTTTGCTAAGCAAGGGAATGTGCTCAAGAAGTATGATTTGAGCTCTTTGAAGTGGATTTGTTCTGGGGCAG
81778 C A CCAATCCTTTATGCTCGTTTTGAACAAAATTCTCTTCACTGAATCCATGGTGGCGCTTTCTTAGGGGTTCCATATCCTAAACTCCTGTGCGGCTTACAAC[C/A]GAGATCCCAGGGCGAAAATTCCTCCTGATCGTCGGGAAGAGGATGGACTTACAGAAGTGCGTTCCAAGAAGGACAGAAGGGCCCCTC
81778 G A TGAATCCATGGTGGCGCTTTCTTAGGGGTTCCATATCCTAAACTCCTGTGCGGCTTACAACCGAGATCCCAGGGCGAAAATTCCTCCTGATCGTCGGGAA[G/A]AGGATGGACTTACAGAAGTGCGTTCCAAGAAGGACAGAAGGGCCCCTCTATACAGGTTCCCAGATACACGAATTATAGGAATGGTG
81778 A T CTTTCTTAGGGGTTCCATATCCTAAACTCCTGTGCGGCTTACAACCGAGATCCCAGGGCGAAAATTCCTCCTGATCGTCGGGAAGAGGATGGACTTACAG[A/T]AGTGCGTTCCAAGAAGGACAGAAGGGCCCCTCTATACAGGTTCCCAGATACACGAATTATAGGAATGGTGGCGGTTTCTCTTCAGA
81778 C T TGGACTTACAGAAGTGCGTTCCAAGAAGGACAGAAGGGCCCCTCTATACAGGTTCCCAGATACACGAATTATAGGAATGGTGGCGGTTTCTCTTCAGATC[C/T]GAGGGATGGACGAGTTAATGGTCGGTCCGGTTGCTGAGGGTCACGGGGACAACTCAAAGTCAGTTGATTATTCTCAGGAAATCAA
81778 A G AGGTTCCCAGATACACGAATTATAGGAATGGTGGCGGTTTCTCTTCAGATCCGAGGGATGGACGAGTTAATGGTCGGTCCGGTTGCTGAGGGTCACGGGG[A/G]CAACTCAAAGTCAGTTGATTATTCTCAGGAAATCAAGCAGCAGACTGATACAGAAAGAAATCGCGGCGAAATTGACCAGTAGGC
81782 T C AGCAGTTCCCACGTTACCAGCAGCAGCATTGCGTGCATCCATTGTCAGTGAGGCTAAGGCATCCCCAGCCGCATACCATGAATTTCCACATGCCTGACAC[T/C]CCAGCTGATATCGGTTGCCATGGCCACCAGAAATGATATCTTTAACAGCTACTTTCTTTTCTGTACATCTTAGACAACTAGTATCCGTC
81836 C G CCCTGCTCCGACCACAGCTGTTTACAAGCTCGACATACATTGTGAAGGCTGCGCCTTGAAAATCAAGAAGGCAGTAAAGAATTTTGAAGGAGTGGATGCG[C/G]TTTCGACCGACATAGCGAACAACAAGCTAACAGTGATAGGCAAAGCGGATCCGTGGAAGATCCGAGAACGGCTGGAATCCAAAA
81836 GA G GGAGTGGATGCGCTTTCGACCGACATAGCGAACAACAAGCTAACAGTGATAGGCAAAGCGGATCCGTGGAAGATCCGAGAACGGCTGGAATCCAAAACCC[GA/G]AAAGAAAGTGGATCTTATTTCGCCCGCAAATGCACCCAAGAAGGAATCAGCTGCCAAAGATTCTGAAGCTAAAAAAGAACAAG
81842 T TA AAAAAATCTATTTCCATGTCCACCGCAAAGTTAAAACATCATCTCCCTTCATTGTCTGTCGCCCCGTCGCCACCGCGCAATTGCAGCGCGTCGTTACCAG[T/TA]GAAAACCGCGCCTCACCAGTCTCCTCACTGGCCTAAAGCCAACGTGGACCCTGTACCCTCCACCATCAGTCTACCCGCACCGCCTTCC
81854 T A CCGAATTAGATTAGATCATGAAAACCATGGCAACGGCGGAAGCAAGGACGAATAATCCACTTGAAAGAGATCCAGCGGCGGAGGTAGGGGCTTCAGCCGG[T/A]GGGGTATCGACTGAAGGCGTCATGGCAGGGGACTGACCTGGTGGCGAGGCAGTCGAAGATGGCGGTAAGACTACGGGAGCT
81854 T G AGATTAGATCATGAAAACCATGGCAACGGCGGAAGCAAGGACGAATAATCCACTTGAAAGAGATCCAGCGGCGGAGGTAGGGGCTTCAGCCGGTGGGGTA[T/G]CGACTGAAGGCGTCATGGCAGGGGACTGACCTGGTGGCGAGGCAGTCGAAGATGGCGGTAAGACTACGGGAGCTGTGGCGG
81854 A G CCACTTGAAAGAGATCCAGCGGCGGAGGTAGGGGCTTCAGCCGGTGGGGTATCGACTGAAGGCGTCATGGCAGGGGACTGACCTGGTGGCGAGGCAGTCG[A/G]AGATGGCGGTAAGACTACGGGAGCTGTGGCGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGG
81854 A G AGATCCAGCGGCGGAGGTAGGGGCTTCAGCCGGTGGGGTATCGACTGAAGGCGTCATGGCAGGGGACTGACCTGGTGGCGAGGCAGTCGAAGATGGCGGT[A/G]AGACTACGGGAGCTGTGGCGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGC
81854 T A AGGTAGGGGCTTCAGCCGGTGGGGTATCGACTGAAGGCGTCATGGCAGGGGACTGACCTGGTGGCGAGGCAGTCGAAGATGGCGGTAAGACTACGGGAGC[T/A]GTGGCGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGG
81854 T TC ACTGACCTGGTGGCGAGGCAGTCGAAGATGGCGGTAAGACTACGGGAGCTGTGGCGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTAC[T/TC]TTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCACTGCAAATAAGAAGAAGA
81854 C CG GAGGCAGTCGAAGATGGCGGTAAGACTACGGGAGCTGTGGCGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAG[C/CG]GGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCACTGCAAATAAGAAGAAGAAGAAGAAGACGAGG
81854 C T CGGGTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAA[C/T]GAAGTCACTGCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAA
81854 A T GTGCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGA[A/T]GTCACTGCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATT
81854 T C GCAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAG[T/C]CACTGCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTG
81854 C T CAGGAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGT[C/T]ACTGCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTGG
81854 T C GAACGGCAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCAC[T/C]GCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTGGAGA
81854 TAAGAAG T CAGCAGATCTGGGAGAAGGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCACTGCAAA[TAAGAAG/T]AAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTGGAGA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
81854 A G GGAGCCGGTGCTACTTTGGGTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCACTGCAAATAAGAAGAAGAAGAAGA[A/G]GACGAGGCAGATGTTTTGGGAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTGGAGAAATATATGACTGAAGAGATAACGT
81854 G A GTGAAGGAGCGGGGGCCATTTTCGGTGCAGCAGAAGGAGACTGAGCAAACGAAGTCACTGCAAATAAGAAGAAGAAGAAGAAGACGAGGCAGATGTTTTG[G/A]GAGTAAGCCATTGATTGATTCTTTTGTGAAAATTTGGAGAAATATATGACTGAAGAGATAACGTAGGGTTTGGGCTTGAATCC
81864 T C TGTTGGCCTACTGGAAATAAAAACCCCTAAATTTCCCTATAATCTCAATCTGCGAATCTTCTTTGTCAAGTAGGAACGATCATCTTAGA[T/C]ACATGGAAAACGGTAAAGGCAGTCGCGGTAAGCTCACCCGCCAGCTGAGCAAGAGGCTCCAGATGCAGGCGCCGTCGTCGATCCAGGTGGATTCCACC
81864 T A AAAACGGTAAAGGCAGTCGCGGTAAGCTCACCCGCCAGCTGAGCAAGAGGCTCCAGATGCAGGCGCCGTCGTCGATCCAGGTGGATTCCACCGCCGCAGC[T/A]TCCTCCATGGCGGACTGGAAGGCGGCGATCCCGCTGCTGTCGCCGCTGGATATCGTGTCCCTACCCAATCACAGGAGGGACACG
81874 T A AGAGACATGGAAAAGGATCGTAGTGATCCTGACTACAATCGCAGCTATGACAGGTATTCGAGGGGATCTGTTCCTT[T/A]CCCTGACTTCCACTTAGGAGCGTGCGATGTTCTTCAGCCTTCATTCATGCAATATGATCCTGGTTTTCATCAGTTGAATAATTTTTCAAGGGCTCAGACC
81874 G A AGACATGGAAAAGGATCGTAGTGATCCTGACTACAATCGCAGCTATGACAGGTATTCGAGGGGATCTGTTCCTTTCCCTGACTTCCACTTAGGAGCGTGC[G/A]ATGTTCTTCAGCCTTCATTCATGCAATATGATCCTGGTTTTCATCAGTTGAATAATTTTTCAAGGGCTCAGACCTCTCCCTTAAACTAC
81878 C G TTCTGAAATGATCTATTGAAATCTGTTTATTTTGGATTGGACCTCACCAACAATATTAAATGATACGTATAGTAGAAATGAATAAGATTGTTTACATTCA[C/G]TCGCATATATATCACAGAAAGGGCAACCTATGAGAAAGGCGAGAAACACTATCACGCAGTATATGATAGAATTTGTTATTCATCCGTGC
81878 G A ATCACGCAGTATATGATAGAATTTGTTATTCATCCGTGCACATCACAAAATAGAAGTTTCATCAGAAGGATAAAATGAGTTGATAGCTGCTGCATACGTA[G/A]CCAACAAGACCAATTACGCTACGTTACTGCTTCTGTTTTGGCTTCTTCACTATCATGACGCTGCAATGAGCGTGATGAGCACAGTAAT
81878 C G GCAGTATATGATAGAATTTGTTATTCATCCGTGCACATCACAAAATAGAAGTTTCATCAGAAGGATAAAATGAGTTGATAGCTGCTGCATACGTAGCCAA[C/G]AAGACCAATTACGCTACGTTACTGCTTCTGTTTTGGCTTCTTCACTATCATGACGCTGCAATGAGCGTGATGAGCACAGTAATCGCTC
81878 C G ATTCATCCGTGCACATCACAAAATAGAAGTTTCATCAGAAGGATAAAATGAGTTGATAGCTGCTGCATACGTAGCCAACAAGACCAATTACGCTACGTTA[C/G]TGCTTCTGTTTTGGCTTCTTCACTATCATGACGCTGCAATGAGCGTGATGAGCACAGTAATCGCTCACGCTTCCCAAAACAGT
81880 A G ATCGTGACAGAGCCAACTGAGCCATCAGGAACCGCAGCTGCATCATTTGAACGGGATTCAGCGCATAAAGCCAGAGCATGGACAGGCGATAAACAACATC[A/G]TTAGAAAAAGCAGGACTAGGACTGCCAGAGTGAGAAGAGAGCGGACACACAGGAACAGTAACGGCCGTACCACCGGAAGCAA
81898 CAGA C TTGTGTTTCCTTGATTTTTTTTTTATCTAGTGCCTAAATCGGGCTGCAAATCTTCATCGTGCAAATCCACAATTTGCCAATCTGTAG[CAGA/C]AGAAGGTCTACCGTACGTGGAGTCTATCATAGAGATTGATGACCTCTTCCTAGCAACTACCCCCTATTCAAGTGCACGAAGAATGAAGAAGAAACCCAA
81898 CTACCG C TTGTGTTTCCTTGATTTTTTTTTTATCTAGTGCCTAAATCGGGCTGCAAATCTTCATCGTGCAAATCCACAATTTGCCAATCTGTAGCAGAAGGT[CTACCG/C]TACCGTACGTGGAGTCTATCATAGAGATTGATGACCTCTTCCTAGCAACTACCCCCTATTCAAGTGCACGAAGAATGAAGAAGAAACCC
81898 A G TCAAGTGCACGAAGAATGAAGAAGAAACCCAATCTCGAATCAAACGTTCAAGGACCGAGCGGACCATCAAGGGAGAGGAAGGCAGAAGAGCCGCAGGGAG[A/G]ACGATGGTGGGAAATGATCGGAAATAACGTGGAAACACTTGATTTTACAAATTGCGCAGAGGGTTTACAGAGGAGGAGGTG
81904 G T GAAGGATGGCGATGAGCACGGTGGACGCCATGTTGGCCACATGGCATTTAGGGGAGGCGGAGAAGGAGGAGGAGCAGAGCAGGACGGAGGAGGCGATGGT[G/T]GTGATGTGGAGGAGGATGGTGAAGAAGCCCACCAGCGAAGGGATCAGGCGGAGCGAGAGAGTTAGGAAGATGCAGCTT
81904 CG C GAGGCGATGGTGGTGATGTGGAGGAGGATGGTGAAGAAGCCCACCAGCGAAGGGATCAGGCGGAGCGAGAGAGTTAGGAAGATGCAGCTTGTGGCGGCAC[CG/C]GGATCAGTACGTAGTTTGCGAGGAGGAAAAACTTGTGAGTGCGGGTTTGGTTTGAGCTTATTGATGTTATTCCCATTTTTG
81906 G A AAGCGCCACATAACGTGTTTTCATGTTCCCCTTCATCTTCTTCCTCTCCTTCTTCTTCACTGTCTTCGTCCTCTTTTGGCGGGGAGATGTTTGAGGTTTT[G/A]ATCTCTGACTGTCTTGATTGCTTTGGTTTACTGCTTCTGCTACTATTGGTAGGTGTTTTTCTTTTGCTTGCCTCTTGGCAGTTCCAGAAACAA
81910 T A TTTTTTTTTTGTTCTCAAATGATATCATATGAAAAGAAAAATACACTAACAGCCCCTTTCACAGCAAAT[T/A]CTTGTCTGCCACGATAAAATTCCAAAAATTTGAACTTCTTTCAACCAAAACATGCACTAGAAATCAATAAACACAGAAAAATAAAATGGAATACAAATAT
81910 A G CATATGAAAAGAAAAATACACTAACAGCCCCTTTCACAGCAAATTCTTGTCTGCCACGATAAAATTCCAAAAATTTGAACTTCTTTCAACCAAAACATGC[A/G]CTAGAAATCAATAAACACAGAAAAATAAAATGGAATACAAATATACATATCAAGTTCAAACTTCAATTTCAGAAGTCGGTGTACTTTCC
81910 GA G CTAACAGCCCCTTTCACAGCAAATTCTTGTCTGCCACGATAAAATTCCAAAAATTTGAACTTCTTTCAACCAAAACATGCACTAGAAATCAATAAACACA[GA/G]AAAAATAAAATGGAATACAAATATACATATCAAGTTCAAACTTCAATTTCAGAAGTCGGTGTACTTTCCGAATCAACCCGTCTAATCTC
81910 A G TACTCGGCCTCTTGTTCGGATCCCTAGAAGAACAAGCCAACCCCAGTTGCAACATATGCACCATATCCTCCTCGATATTCTCACCCTTCATTAACTCAAC[A/G]TCAAACACCTCAGCAGTCCATTCCTCTCTGACGACCGAGTGCACCCACCTCGGCAAATCGGACACGTCGTCGTACCCATGCCCTTGAAC
81916 G A CTTCGAGATCCCCTAGAGACCTCTCTATCTACCGGAGGTGATGGAGATTTGTGGCACGGACTGCTCAGATTTGGAGCTCGAACGCGGGGCATTGGGAGCC[G/A]CTTCCACGGTAGCGCAGAGGTTCGAATTGGCTGGCGTTGGGCGAGCGGCAAGGTGGTGCTGCTGCGGTTCTGATGGTGGTGGC
81918 C T TTGGCCTACTGGAAAAAAATGAAAATTAAACAAAATCCCTCCAGATTTCGGTTAAATCCCGCCTCCACTTGGTTCCGATCCACTCAATAGAAGAAAACG[C/T]GCCTCTCTCCGGTTCCGTCTCTTCGCTTTCGATCTAGACATCAGTCTCCGACCCCGACGTCATCGACTCCTGCAGAAACCTTATTTCAGA
81918 G A GGAAAAAAATGAAAATTAAACAAAATCCCTCCAGATTTCGGTTAAATCCCGCCTCCACTTGGTTCCGATCCACTCAATAGAAGAAAACGCGCCTCTCTCC[G/A]GTTCCGTCTCTTCGCTTTCGATCTAGACATCAGTCTCCGACCCCGACGTCATCGACTCCTGCAGAAACCTTATTTCAGATCTGGGTGAT
CTGAATTGAAGTGTACCGCTTAAAGGTCGATATATTGGAAGCTGAAAGGTCTGATAGGTCAAAAATTTGAA
81918 G AAAACGCGCCTCTCTCCGGTTCCGTCTCTTCGCTTTCGATCTAGACATCAGTCTCCGACCCCGACGTCATCGACTCCTGCAGAAACCTTATTTCAGATCT[G/GGTTCAAGCTGAATTGAAGTGTACCGCTTAAAGGTCGATATATTGGAAGCTGAAAGGTCTGATAGGTCAAAAATTTGAA]GGTGATGCAA
81918 T C CTTTCGATCTAGACATCAGTCTCCGACCCCGACGTCATCGACTCCTGCAGAAACCTTATTTCAGATCTGGGTGATGCAATGGAGCCTATGAAGTGCATCT[T/C]CGTGATTTTGCTAAAAGATTTCCTTCGATGAATTTTCTGCATTCAATATCACACGCTGGACAAATTATAAAGCCTCTGCCTCAGCTTTAA
81918 T A TCGATCTAGACATCAGTCTCCGACCCCGACGTCATCGACTCCTGCAGAAACCTTATTTCAGATCTGGGTGATGCAATGGAGCCTATGAAGTGCATCTTCG[T/A]GATTTTGCTAAAAGATTTCCTTCGATGAATTTTCTGCATTCAATATCACACGCTGGACAAATTATAAAGCCTCTGCCTCAGCTTTAAAC
81918 G A TTTCAGATCTGGGTGATGCAATGGAGCCTATGAAGTGCATCTTCGTGATTTTGCTAAAAGATTTCCTTCGATGAATTTTCTGCATTCAATATCACACGCT[G/A]GACAAATTATAAAGCCTCTGCCTCAGCTTTAAACATTTCATGTGCATCACCATCTACGTGAGCAATCAAATCCACTTGAGAGTTTCTAGC
81918 C T AAGATTTCCTTCGATGAATTTTCTGCATTCAATATCACACGCTGGACAAATTATAAAGCCTCTGCCTCAGCTTTAAACATTTCATGTGCATCACCATCTA[C/T]GTGAGCAATCAAATCCACTTGAGAGTTTCTAGCATCAATCTCCGTTGTTTTATACATCCCTCCTTGAAGTTGCACGTCCCTTTTGCTTGATT
81918 C T CAATATCACACGCTGGACAAATTATAAAGCCTCTGCCTCAGCTTTAAACATTTCATGTGCATCACCATCTACGTGAGCAATCAAATCCACTTGAGAGTTT[C/T]TAGCATCAATCTCCGTTGTTTTATACATCCCTCCTTGAAGTTGCACGTCCCTTTTGCTTGATTTCGCAAGATGACGAAGTTG
81918 G A GACAAATTATAAAGCCTCTGCCTCAGCTTTAAACATTTCATGTGCATCACCATCTACGTGAGCAATCAAATCCACTTGAGAGTTTCTAGCATCAATCTCC[G/A]TTGTTTTATACATCCCTCCTTGAAGTTGCACGTCCCTTTTGCTTGATTTCGCAAGATGACGAAGTTG
81920 C CTAT AAAATCTTTTATTGACCAAACAGGGCATTAGTTACAAATGCTTGATTATCAGTTGAAAGCTGCTCCATGAACAACTCCTTATTGAATACTTGCGTCCGAG[C/CTAT]TCGAAATGCTCAGATCATAAAACTAACTAAACTAGACTTCATCATCCCACAAGTCTTGAAGTGACCTGAACGGGCTAGTCTCAGCG
81920 T C AGCTGCTCCATGAACAACTCCTTATTGAATACTTGCGTCCGAGCTCGAAATGCTCAGATCATAAAACTAACTAAACTAGACTTCATCATCCCACAAGTCT[T/C]GAAGTGACCTGAACGGGCTAGTCTCAGCGATTATGAACTCGCCGCTACACCCCCTCCATTGTGGAATTTTGCTTATCTCCTGCAGCTCT
81920 A G TGCTCCATGAACAACTCCTTATTGAATACTTGCGTCCGAGCTCGAAATGCTCAGATCATAAAACTAACTAAACTAGACTTCATCATCCCACAAGTCTTGA[A/G]GTGACCTGAACGGGCTAGTCTCAGCGATTATGAACTCGCCGCTACACCCCCTCCATTGTGGAATTTTGCTTATCTCCTGCAGCTCTTCTT
81920 G C TCATCATCCCACAAGTCTTGAAGTGACCTGAACGGGCTAGTCTCAGCGATTATGAACTCGCCGCTACACCCCCTCCATTGTGGAATTTTGCTTATCTCCT[G/C]CAGCTCTTCTTTGCTCAATTCCCAGTCAAATATGCTCGCATTCTCCACCATTCTGCCTTTGTTAAAGCTTTTGCAAACGAACCCTGCTCCT
81922 G GC ACGGTGGTCCTTTGCTTCTTCGATAGAGCTCTTGTGCCACTGCTGATCCTTTTTATTGAGCTCCTCACGTCATGTAGCTTTGTATTATCCTGTGCTAGTT[G/GC]ACTATGATGCTGTATTTTTTTGGGTTTCAGTGATGTTGCTATGTTGAGAACTTAGCAATTGCGTTATGCAACGGAGTTCCCATCGTGTG
81922 AT A CTTCTTCGATAGAGCTCTTGTGCCACTGCTGATCCTTTTTATTGAGCTCCTCACGTCATGTAGCTTTGTATTATCCTGTGCTAGTTGACTATGATGCTGT[AT/A]TTTTTTTGGGTTTCAGTGATGTTGCTATGTTGAGAACTTAGCAATTGCGTTATGCAACGGAGTTCCCATCGTGTGGTGCTTCCGGTGAT
81922 C T TGTAGCTTTGTATTATCCTGTGCTAGTTGACTATGATGCTGTATTTTTTTGGGTTTCAGTGATGTTGCTATGTTGAGAACTTAGCAATTGCGTTATGCAA[C/T]GGAGTTCCCATCGTGTGGTGCTTCCGGTGATGCTTTGTTTGCTCTTCTGTGTGCATCTTGTCTTCTAACAAGCAAGGATAAATCATCTAA
81922 G A GCTGTATTTTTTTGGGTTTCAGTGATGTTGCTATGTTGAGAACTTAGCAATTGCGTTATGCAACGGAGTTCCCATCGTGTGGTGCTTCCGGTGATGCTTT[G/A]TTTGCTCTTCTGTGTGCATCTTGTCTTCTAACAAGCAAGGATAAATCATCTAAAGTGATGTTCCTATGTCAAATATTCTCCCTGGCATGT
81954 G C TAGGGGTCACGATTTTGTCAAAAAGATGCTCTTTTTCTATGGTTTGGGAAGAAGATGATGGTGGAGTTTGATTGGGTTGAACTGGAGATGAAGAAGAAGG[G/C]GCAGTTATTGGGTTAATGGTTTGTGAAAAGTCCATGAAATGAGCTACGAAGAATAATGGGTTTTGTTCTAAGTGTTGAACATGAA
81956 T C CTCTAGAATCTTCTCCTTCAGGAGGCCTGGCATGCACGGTCGCTGCCCTAGCCGAACGCCAACACTTGAACGACGATGCATCGTCCAACAATTTCGAAGA[T/C]GATCACGCTTCCAATGTGGCTGATGTAGGGACCAGCTATGCTAGCTCAGCAGGCATGATCACGCCCGATGCCTTGGGGCCCACCCT
81956 T C TTAGTTACATTGGTGGGCCTGGCAACCTTGTTCCAGAGACTTACGAAGAGCAAGTGATGCTCGCTATGGCTGTTTCTTTAGCGGATGCTCGTGGTAGGAC[T/C]ACTAGTCAACAAGGCGTCACTTGGATGTAGTCGTGTTTTTCTTATGTTCCTTTTTCTTTT
81958 A G AACCAGGACCCCTGTTTTGACGCTGAAATTCCCGCTGCTGAGAGCCTGGAACAAAGTTATATGAACCAGGGGCTGCATTATCAGGACTAGGTGAATAACC[A/G]TACAGGCTGGGCCTAATAGTCTCAGTGCGTGGTGCCAGACCATACGGGTCTGGCCTAACACTCTCAGTGCCCAACGCAAGACCAT
81972 AC A CGATCTCGTCCCTACCTCACTACTAATCCTTGCTTTCTCCAGCGTGATTGGAGCTCTGAACCAAGATTTCAATCGTTATTCTCTACCATTTCTCCTATAC[AC/A]CCCCCACTTCCTAAGACCCTCACTTCCACAGTCCTAATTTTGTCGTGCTCGCTCCTCTATCACTCTCATCCTGGGTCGTGGTGTCCCTCCA
81982 AT A CACTGTTGGCCTACTGGACAACGATGAAAACCAAACATTTTCTCCTCACCAATTGAAACTACGGACCAAAACCTCTCTCTGTCATGCAAGGCCTTTTTAT[AT/A]TTTTTTTGAACCAACGCTTGTGTCATTACAGGAGAAACCCAAGCTCTTGAACCCATTTATATTTACGAACGGCGTCAACAGGAAGATC
81982 G A CTCTCTGTCATGCAAGGCCTTTTTATATTTTTTTGAACCAACGCTTGTGTCATTACAGGAGAAACCCAAGCTCTTGAACCCATTTATATTTACGAACGGC[G/A]TCAACAGGAAGATCGAAGCTAGGGAAGCGGGCCGTACTGCATCGGAGGAGGCGTAGCATGTCGAAAACAGTAGAGTTATGCAGGCG
81982 T A GATCGAAGCTAGGGAAGCGGGCCGTACTGCATCGGAGGAGGCGTAGCATGTCGAAAACAGTAGAGTTATGCAGGCGGTCGGAGGTGGGAGCTCATGCAGG[T/A]GATCGGTTTCAGGGTGGCAACGGCATGGGGAGTTTAGTTCTTCGGTTCTGTCGGCATGGGAGAGGGACATGAGCAGTTGGA
81982 C T CGGTCGGAGGTGGGAGCTCATGCAGGTGATCGGTTTCAGGGTGGCAACGGCATGGGGAGTTTAGTTCTTCGGTTCTGTCGGCATGGGAGAGGGACATGAG[C/T]AGTTGGACTGTTAAAAATAAGTAAAATAAAATATAAGACTAGGAAGCTCGAAGACCCAAGGAGAGGGTAGCTGAATCAAAGAA
81992 A G TTGCTGCATATTTGCTTGCTGTATTGGGCGGAAACACCTCCCCAACGGTTGCTAATATCAAGGATATCTTGGGATCAGTTGGTGCTGATGCGGACGAAGA[A/G]AGGATTGAGTTCCTTTTATCAGAGGTAAAAGGAAAAGACATAACCGAGTTGATTGCTTCTGGAAGGGAAAAGTTGGCATCGGTTCC
81992 C T AAAGGATTGAGTTCCTTTTATCAGAGGTAAAAGGAAAAGACATAACCGAGTTGATTGCTTCTGGAAGGGAAAAGTTGGCATCGGTTCCTTCAGGCGGTGG[C/T]GGTGGTGCCATTGCTGTCTCTGCACCTGCTGCTGGTGGCGCTGCTGCACCTGCAGCAGCAGCTGAGGCCAAGAAGGAAGAGAAG
81992 A G GCGGTGGCGGTGGTGCCATTGCTGTCTCTGCACCTGCTGCTGGTGGCGCTGCTGCACCTGCAGCAGCAGCTGAGGCCAAGAAGGAAGAGAAGGTTGAAGA[A/G]AAGGAAGAATCTGATGATGATATGGGATTCAGTCTTTTCGATTAAGCGTCGTTTTTGGGGCATTGTTATTGTTTCTTTGTAGTAT
81992 T C GTGCCATTGCTGTCTCTGCACCTGCTGCTGGTGGCGCTGCTGCACCTGCAGCAGCAGCTGAGGCCAAGAAGGAAGAGAAGGTTGAAGAAAAGGAAGAATC[T/C]GATGATGATATGGGATTCAGTCTTTTCGATTAAGCGTCGTTTTTGGGGCATTGTTATTGTTTCTTTGTAGTATGCAAAATCAGCTA
81992 G A GCAGCAGCAGCTGAGGCCAAGAAGGAAGAGAAGGTTGAAGAAAAGGAAGAATCTGATGATGATATGGGATTCAGTCTTTTCGATTAAGCGTCGTTTTTGG[G/A]GCATTGTTATTGTTTCTTTGTAGTATGCAAAATCAGCTAGTTTTGTCTTCTGAACTGTTT
82002 C T ATTTTTGCCACAGCTCACAATGTCTAGTTTATACTTGTCCATGATACTAAGAAGCTGTTTCCTCACATCTTGCGCCCTCCTGAG[C/T]GAACGTGATTGCACAAAGTTCTCAAAACACCATGGTCCAGAGAAATTCTTTGCTTTCCAAGCTTCATAAACTGCAAGTAGTGTGAGATGGTCGCCTTCAG
82002 T C ATTTTTGCCACAGCTCACAATGTCTAGTTTATACTTGTCCATGATACTAAGAAGCTGTTTCCTCACATCTTGCGCCCTCCTGAGCGAACGTGA[T/C]TGCACAAAGTTCTCAAAACACCATGGTCCAGAGAAATTCTTTGCTTTCCAAGCTTCATAAACTGCAAGTAGTGTGAGATGGTCGCCTTCAGGCTGA
82002 G A CCCTCCTGAGCGAACGTGATTGCACAAAGTTCTCAAAACACCATGGTCCAGAGAAATTCTTTGCTTTCCAAGCTTCATAAACTGCAAGTAGTGTGAGATG[G/A]TCGCCTTCAGGCTGAAAAAACTTGGCTCTTTTCTGATCTGCCTGAGCTTGTTTCTCCCTCGGTCTGTAAAATGTGTTTCGAGTTTGTAT
82002 G A TCCTGAGCGAACGTGATTGCACAAAGTTCTCAAAACACCATGGTCCAGAGAAATTCTTTGCTTTCCAAGCTTCATAAACTGCAAGTAGTGTGAGATGGTC[G/A]CCTTCAGGCTGAAAAAACTTGGCTCTTTTCTGATCTGCCTGAGCTTGTTTCTCCCTCGGTCTGTAAAATGTGTTTCGAGTTTGTATCAT
82002 A G AAGCTTCATAAACTGCAAGTAGTGTGAGATGGTCGCCTTCAGGCTGAAAAAACTTGGCTCTTTTCTGATCTGCCTGAGCTTGTTTCTCCCTCGGTCTGTA[A/G]AATGTGTTTCGAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTTTGATAAT
82002 G A TTCATAAACTGCAAGTAGTGTGAGATGGTCGCCTTCAGGCTGAAAAAACTTGGCTCTTTTCTGATCTGCCTGAGCTTGTTTCTCCCTCGGTCTGTAAAAT[G/A]TGTTTCGAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTTTGATAATGGGG
82002 C T AACTGCAAGTAGTGTGAGATGGTCGCCTTCAGGCTGAAAAAACTTGGCTCTTTTCTGATCTGCCTGAGCTTGTTTCTCCCTCGGTCTGTAAAATGTGTTT[C/T]GAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTTTGATAATGGGGGATCA
82002 T C TCTCCCTCGGTCTGTAAAATGTGTTTCGAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTT[T/C]GATAATGGGGGATCAAGTGGAAATTCTGCCATTTTTCTCCCTAATTTGGTTAATAATCCTTCTTCATCTAGTGCTCCTAAACTATACAACTG
82002 T C TCGGTCTGTAAAATGTGTTTCGAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTTTGATAA[T/C]GGGGGATCAAGTGGAAATTCTGCCATTTTTCTCCCTAATTTGGTTAATAATCCTTCTTCATCTAGTGCTCCTAAACTATACAACTGCTCCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
82002 A G TGTAAAATGTGTTTCGAGTTTGTATCATGGCAATTATTGTCAATATTTCATCACTGCAACCAAGATCCACACTTGCTAACAACATTTTTGATAATGGGGG[A/G]TCAAGTGGAAATTCTGCCATTTTTCTCCCTAATTTGGTTAATAATCCTTCTTCATCTAGTGCTCCTAAACTATACAACTGCTCCATAGCTG
82050 G A TCGAGCGTTTCTTTTGATATATTTTCCGAAGATTCAATCCTTTGCTTTGATTGACTTGTACGAGAAGATAGAGCATATAGGCATCGAAACATGCACGAGC[G/A]AGATGTTTATGATCCATCAGATGATGTAAAACTGTCCGAGCACAATAATGACACATCAGCTAGCGACTTCCGTGGTGGGAAAGATAT
82050 C T AAGATAGAGCATATAGGCATCGAAACATGCACGAGCGAGATGTTTATGATCCATCAGATGATGTAAAACTGTCCGAGCACAATAATGACACATCAGCTAG[C/T]GACTTCCGTGGTGGGAAAGATATGCAAGGTTTCCCATGGGGGAAGTTGAATTACAGTAGAAACACATATCGTGAAATGAGGCTGA
82104 C T TAGGAGTAGCTTCAATGGGAGTAATGAGACCGGAGCTTGTAATGAAATCGATCGTGCCTGTTGTTATGGCTGGAGTTCTTGGAATTTATGGATTAATTAT[C/T]GCTGTTATTATTAGTACGGGAATTAATCCTAAGGCTAAGCCATACTACTTGTTTGATGGCTACGCTCATCTTTCTTCTGGATTGGCCTG
82104 T A CATACTACTTGTTTGATGGCTACGCTCATCTTTCTTCTGGATTGGCCTGTGGTCTTGCAGGTTTGTCTGCTGGTATGGCAATCGGGATTGTAGGCGATGC[T/A]GGTGTTAGGGCTAATGCACAACAGCCTAAGCTCTTTGTTGGGATGATACTGATTCTCATCTTTGCTGAAGCACT
82110 T C GTTGGCCTACTGGAAATAAATCAGTTTGTTCTCGTTGATTTTTGAAGCCGCCTCTATTAATGGGCAGCTGGGGGCTTGTCTCCCTTTCT[T/C]TCTCTACATCTTCTATCTTTATCGCTCCCTCTGCCTTTCTTGTAAATCTCCAATTCCCCTTTGATCCATTCCCTCCTTTCCTCCTTCCTCTCCTCCCAGC
82112 C T GAGAAAAAGAGCATTGGATTTTTCATTCTGCTACTTCTCGCAATAACTTTCGTCAGCGTGCAGTCTAAGGAAAAGAAGTC[C/T]AAGGAAAAGAAATGCACCAAGGGTTGGGAATGCAAAAACAGCGTGTATTGCTGTAACCAAACGATTTCAGATCTGTTTCAGGTGTATCAGTTCGAGGATT
82112 G A GCGTGCAGTCTAAGGAAAAGAAGTCCAAGGAAAAGAAATGCACCAAGGGTTGGGAATGCAAAAACAGCGTGTATTGCTGTAACCAAACGATTTCAGATCT[G/A]TTTCAGGTGTATCAGTTCGAGGATTTGTTCGCCAAAAGGAACTCGCCTGTGGCCCACGCGGTAGGGTTTTGGGACTACCAGTCGT
82112 A T CCGGTGGCAAGACTATGCAGATGAAGGAAGTTGCCGCTTTTCTTGGCCATGTTGGTGCTAAGACTTCATGTGGTTATGGTGTTGCAACTGGAGGTCCACT[A/T]GCATGGGGTCTATGTTATAACCATGAAATGAGTCCGAGCCAGTCCTATTGTGCTGAGCACATTGATTA
82118 A G GATTAGCAGCACATATGAAGCTTGCTCTCGACGCTACTGATCAACTTCTGGCACCCTCCGCACTCAACACGACTGGGGCTACTTCAATGTTATCTACACT[A/G]GGATGTTAACTAGTTGCGGCAAGCGCTGGTTGTCATGTGATGCTTCGTCACTGTCAAGGTGATTTGAACTGGCGTGGGAAGCTTGGA
82118 A G ACTGATCAACTTCTGGCACCCTCCGCACTCAACACGACTGGGGCTACTTCAATGTTATCTACACTAGGATGTTAACTAGTTGCGGCAAGCGCTGGTTGTC[A/G]TGTGATGCTTCGTCACTGTCAAGGTGATTTGAACTGGCGTGGGAAGCTTGGACCTCTGCCCACGACAATGGTTCATGTCCTACCTGC
82118 G A GCTACTTCAATGTTATCTACACTAGGATGTTAACTAGTTGCGGCAAGCGCTGGTTGTCATGTGATGCTTCGTCACTGTCAAGGTGATTTGAACTGGCGTG[G/A]GAAGCTTGGACCTCTGCCCACGACAATGGTTCATGTCCTACCTGCCACAGGCATGCTTTTGGGAGGGGCTCAAGTTGTTCTCACGTG
82162 C CA GCTTTGGATGTTCAAGGCCGTTGTTATACATGGGGCCGAAATGAGAAGGGGCAATTGGGACATGGAGATCTTCTTCAGCGCAATATCCCAACGGTTGTGT[C/CA]AAAATTATCAAAATATAAAGTAGTCAGAGCAGGTTCTGGGAGGAGCCACACAGTGGTAGTAACTGAAGATGGAAAATCTTT
82170 G C AGAAAAAGAAAAAAGAAAAAGCTGAATCCAATCCCGATCCGCGACAACACCAAAACGCCTCCAGCAAACTATTGCGCCGCACAGCCCTAGAGCCAATCAC[G/C]TTCTCTAATTCAGTACCTACTAGCTCTGCAGCTTTAGCGCTCGTTGTCCTGATCCATACTTGCTGCCCTTTGCTCGCAGATTGTGAAT
82170 A G CTCCAGCAAACTATTGCGCCGCACAGCCCTAGAGCCAATCACGTTCTCTAATTCAGTACCTACTAGCTCTGCAGCTTTAGCGCTCGTTGTCCTGATCCAT[A/G]CTTGCTGCCCTTTGCTCGCAGATTGTGAATTTGTGAGATATCAATTGTATCATTTGGACAGTATTAGTAATGGACTCAAACAATCCCCAT
82170 A G TACTAGCTCTGCAGCTTTAGCGCTCGTTGTCCTGATCCATACTTGCTGCCCTTTGCTCGCAGATTGTGAATTTGTGAGATATCAATTGTATCATTTGGAC[A/G]GTATTAGTAATGGACTCAAACAATCCCCATACAGAAGATCAGCGGCAGACAAAGATTGAAGCTGAAGAGGAAAAGCCAGTTGATTTTG
82170 G C GAGATATCAATTGTATCATTTGGACAGTATTAGTAATGGACTCAAACAATCCCCATACAGAAGATCAGCGGCAGACAAAGATTGAAGCTGAAGAGGAAAA[G/C]CCAGTTGATTTTGATCCCAGTCGAATGGTTGGCATAATCAAAAGAAAGGCATTGATAAAAGACCTTGCTGCTGCCTACCATGCTGA
82208 T C AAGAAAGAAAGGAAATGAAATTACATGTCATTTTGTTTCACATTTCTAACCCTGTTCTTCCTCTTCCCTCTTCTAACCACCCTCCTTCCCTTCTCAATAT[T/C]AAACTTGGTATGCCCTGACTTCGAAAACCTCTCCTTCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCAT
82208 G A AAGGAAATGAAATTACATGTCATTTTGTTTCACATTTCTAACCCTGTTCTTCCTCTTCCCTCTTCTAACCACCCTCCTTCCCTTCTCAATATTAAACTTG[G/A]TATGCCCTGACTTCGAAAACCTCTCCTTCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCATAGCAAAAC
82208 T C TTTCACATTTCTAACCCTGTTCTTCCTCTTCCCTCTTCTAACCACCCTCCTTCCCTTCTCAATATTAAACTTGGTATGCCCTGACTTCGAAAACCTCTCC[T/C]TCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATT
82208 C T CATTTCTAACCCTGTTCTTCCTCTTCCCTCTTCTAACCACCCTCCTTCCCTTCTCAATATTAAACTTGGTATGCCCTGACTTCGAAAACCTCTCCTTCAG[C/T]GATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTC
82208 A G CTTCCCTTCTCAATATTAAACTTGGTATGCCCTGACTTCGAAAACCTCTCCTTCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCA[A/G]CACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAAA
82208 C T TTCCCTTCTCAATATTAAACTTGGTATGCCCTGACTTCGAAAACCTCTCCTTCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAA[C/T]ACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAAAG
82208 A G TCTCAATATTAAACTTGGTATGCCCTGACTTCGAAAACCTCTCCTTCAGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATC[A/G]TAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAAAGCCTCCA
82208 G T AGCGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCA[G/T]TTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAAAGCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTC
82208 T C CGATTCATCCACCACACAATCCGGCATCGACTCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGT[T/C]CCCTTTTCTCCGGAGTCATAACTGCATACTCCAAAGCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTA
82208 C T GGCATCGACTCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAA[C/T]TGCATACTCCAAAGCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTAATGGGCTAGTCCTACACCCTTT
82208 C T TCTGGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACT[C/T]CAAAGCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTAATGGGCTAGTCCTACACCCTTTTAG
82208 A T GGGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCA[A/T]AGCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTAATGGGCTAGTCCTACACCCTTTTAG
82208 A G GGTATCTCAACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAA[A/G]GCCTCCACCTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTAATGGGCTAGTCCTACACCCTTTTAG
82208 C G AACACATCATAGCAAAACGAATAAGTCATGTACTTGCTTCTATATTTCTTCATCAGTTCCCTTTTCTCCGGAGTCATAACTGCATACTCCAAAGCCTCCA[C/G]CTCGGCCTTCGCGTCTTCGCATTGTTGTGCCGACGGGTACAATTCTAATGGGCTAGTCCTACACCCTTTTAG
82212 C G TCAGCAAAGCTATGGATCCAAAGCCGGATCTGCAACATCGAGCAAGGCAGTTGATTGAGTTGTCCCGGCCTATTGAACTGATGAGGGAACTTGAATC[C/G]GAGTAGGAATTGTCTGAACTTCCATTTTCATTATTTGCATGAGTGATGGAGTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTT
82212 A G TGCAACATCGAGCAAGGCAGTTGATTGAGTTGTCCCGGCCTATTGAACTGATGAGGGAACTTGAATCCGAGTAGGAATTGTCTGAACTTCCATTTTCATT[A/G]TTTGCATGAGTGATGGAGTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATTAGAGTCTA
82212 A G CTGAACTTCCATTTTCATTATTTGCATGAGTGATGGAGTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATT[A/G]GAGTCTAGCGAGTGAGAGTGTTTTGGCTTATTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGA
82212 A G TGATGGAGTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTT[A/G]TTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATAT
82212 T G GATGGAGTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTTA[T/G]TGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATT
82212 C A GTCGCTGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTTATTGCAT[C/A]TTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATTAAGCAA
82212 G A TGGGGTTAGCCTTTTTTCTTGTTTTCTCTAAATTTTGATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTTATTGCATCTTTC[G/A]TGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATTAAGCAAGACTG
82212 G A TGATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTTATTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACC[G/A]GTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATTAAGCAAGACTGATTTTTCAACATAAAGCTTTCAGCCAAAGTTAGT
82212 T C ATCGAGCCCATTTTGGAGATTAGAGTCTAGCGAGTGAGAGTGTTTTGGCTTATTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGG[T/C]GAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATTAAGCAAGACTGATTTTTCAACATAAAGCTTTCAGCCAAAGTTAGTTTC
82212 A G GCGAGTGAGAGTGTTTTGGCTTATTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAA[A/G]GCTCTTGATATTAAGCAAGACTGATTTTTCAACATAAAGCTTTCAGCCAAAGTTAGTTTCCCGATCTTATAGATAACAAACTCTCTATG
82212 C T TATTGCATCTTTCGTGCTGGTTATATAGGTTATATGTCATGTAAAACCGGTGAGGTTCTTGATTGTGCAAGCTAAGCAAAGCTCTTGATATTAAGCAAGA[C/T]TGATTTTTCAACATAAAGCTTTCAGCCAAAGTTAGTTTCCCGATCTTATAGATAACAAACTCTCTATGACTTCTTCAGTTATTGGTTAAA
82232 A G AAGAAAAAATATCCTCCTTTATGTTCATTGAAAAACTATTTCATCTTACAATCAACTATCTGCAGAGAACAAAAGAATTAACAATCGTATTTCTGTACAT[A/G]ATCAGTGTGAATCTAAAAGTTCTAAAGCCTAAACTAAGCAGGTATAAACAACAAAGGCTACTTTGCATCCAAATTTTAGTCTACTTTATC
82232 A G TTATGTTCATTGAAAAACTATTTCATCTTACAATCAACTATCTGCAGAGAACAAAAGAATTAACAATCGTATTTCTGTACATAATCAGTGTGAATCTAAA[A/G]GTTCTAAAGCCTAAACTAAGCAGGTATAAACAACAAAGGCTACTTTGCATCCAAATTTTAGTCTACTTTATCAATATTATTCCGTGACCA
82232 A C TAACAATCGTATTTCTGTACATAATCAGTGTGAATCTAAAAGTTCTAAAGCCTAAACTAAGCAGGTATAAACAACAAAGGCTACTTTGCATCCAAATTTT[A/C]GTCTACTTTATCAATATTATTCCGTGACCACCTACTAAATCCAAGCTCCTGAATAACAGGTAGATTCAAATCAAACCCAGCAACCTCCTT
82232 G A AACAATCGTATTTCTGTACATAATCAGTGTGAATCTAAAAGTTCTAAAGCCTAAACTAAGCAGGTATAAACAACAAAGGCTACTTTGCATCCAAATTTTA[G/A]TCTACTTTATCAATATTATTCCGTGACCACCTACTAAATCCAAGCTCCTGAATAACAGGTAGATTCAAATCAAACCCAGCAACCTCCTTT
82232 A G ATCGTATTTCTGTACATAATCAGTGTGAATCTAAAAGTTCTAAAGCCTAAACTAAGCAGGTATAAACAACAAAGGCTACTTTGCATCCAAATTTTAGTCT[A/G]CTTTATCAATATTATTCCGTGACCACCTACTAAATCCAAGCTCCTGAATAACAGGTAGATTCAAATCAAACCCAGCAACCTCCTTTATAC
82232 A G AATCCAAGCTCCTGAATAACAGGTAGATTCAAATCAAACCCAGCAACCTCCTTTATACAAGTTTTGGGTTTTCTAAACCCGGATCCAATAATGCCTTCAT[A/G]GTGACGTCGCTTATGCCCGCCCAAGGCCTGGCCCGTCCCGAACGTTTTAGAGCAGATAGAACATTTATGCACTCTTCCTGTTGATGGTA
82232 C G CCCAGCAACCTCCTTTATACAAGTTTTGGGTTTTCTAAACCCGGATCCAATAATGCCTTCATAGTGACGTCGCTTATGCCCGCCCAAGGCCTGGCCCGTC[C/G]CGAACGTTTTAGAGCAGATAGAACATTTATGCACTCTTCCTGTTGATGGTACCATAGCAGGTGCATGACCATGAGGAAGATGGTCGTG
82232 T A ACCTCCTTTATACAAGTTTTGGGTTTTCTAAACCCGGATCCAATAATGCCTTCATAGTGACGTCGCTTATGCCCGCCCAAGGCCTGGCCCGTCCCGAACG[T/A]TTTAGAGCAGATAGAACATTTATGCACTCTTCCTGTTGATGGTACCATAGCAGGTGCATGACCATGAGGAAGATGGTCGTGCTCTGGA
82290 A T TCTACACACTGATATACTTTGTTTTTGGCTCGATCAAACTTCCTCAGTATCGACGTGTGTACATTCGACCTAGACAGGTAGTTGACGTTGTCCAAGGAGG[A/T]GATAGGGGAGCGTGGAGTTGGCGTACGATCCTGAGGTGCTAGGCACATGCATGTGCGAAATCTGGTGGGATTAAAGCTGTCGACGC
82290 G A GCTGTCGACGCGGTTTGGTTTAGGGGTGAGACGCGGTGAACTTGGTGAGGAAGTTGAAGTGAACGAGTTGAGGGATTTAACGGTGAAGGATTTTGCTGTC[G/A]ACTTTGAATGTGGAAGCTTGGGTCACGGACACGCCTACTGGGAGTGATGGTTTTAGTCTTGGATGTGTTATGCGTGAAGGGAG
82296 A G CCTTCGCGATCTTTTCCCATCAACAAACATCCCTGCTGTTGCCGCAAAATTTCAATGCCTAATCATGAAATTTCAAAACTTCCCTCTTTATTGCTACACA[A/G]CAAACGTTCTAACCTAATATCTATATCAAGGAAAGCACTGATACTGGCAAGGGCTGTTGCCGATAGCAGCGGCGACCAATTCACTGCTTC
82296 C G ACTTCCCTCTTTATTGCTACACAACAAACGTTCTAACCTAATATCTATATCAAGGAAAGCACTGATACTGGCAAGGGCTGTTGCCGATAGCAGCGGCGAC[C/G]AATTCACTGCTTCCCCTGATAATGATGTTCATGACGATTTCGCAGATAGCACCTCCTTTTTCTGGGCTTTTTCGCGGTCGTTTAATGAT
82296 C G TTGCTACACAACAAACGTTCTAACCTAATATCTATATCAAGGAAAGCACTGATACTGGCAAGGGCTGTTGCCGATAGCAGCGGCGACCAATTCACTGCTT[C/G]CCCTGATAATGATGTTCATGACGATTTCGCAGATAGCACCTCCTTTTTCTGGGCTTTTTCGCGGTCGTTTAATGATGTTTTACAACTTG
82296 T C AACGTTCTAACCTAATATCTATATCAAGGAAAGCACTGATACTGGCAAGGGCTGTTGCCGATAGCAGCGGCGACCAATTCACTGCTTCCCCTGATAATGA[T/C]GTTCATGACGATTTCGCAGATAGCACCTCCTTTTTCTGGGCTTTTTCGCGGTCGTTTAATGATGTTTTACAACTTGGGGCTTTGTTTGC
82298 T C ACTAGGGTTTTTGTGATTTTGGAAAAATTTGGATTTTGATTTTGGGGAAAGTGGGTAAGCTTCGATTGACTCAAGAACTAAAGGGAAGAGGAGTTAGTGA[T/C]TCTTCGGTGGCCATTAACAATTGAAAAGGAAGAACAAAATTTTTTGCTCCAGTAGGCCAAC
82310 A G AATGGGTGAACTGAAGGAGTTGAATGTAAAGCGAAAATGGTTCGAATTTGGGAGAAGTGGCTGAACCAGCAACAGCGAAGTTTGCACCATTTCTGAAACC[A/G]GTACCAAGAGAATCCAGATAAGGGTTTACATAGCTCATGTTCAGGCTTTCACAGAGAAAATCAAGAATGAGCCTGCCATCAGAAA
82310 G T ATGGGTGAACTGAAGGAGTTGAATGTAAAGCGAAAATGGTTCGAATTTGGGAGAAGTGGCTGAACCAGCAACAGCGAAGTTTGCACCATTTCTGAAACCA[G/T]TACCAAGAGAATCCAGATAAGGGTTTACATAGCTCATGTTCAGGCTTTCACAGAGAAAATCAAGAATGAGCCTGCCATCAGAAAA
82310 C T TTTGGGAGAAGTGGCTGAACCAGCAACAGCGAAGTTTGCACCATTTCTGAAACCAGTACCAAGAGAATCCAGATAAGGGTTTACATAGCTCATGTTCAGG[C/T]TTTCACAGAGAAAATCAAGAATGAGCCTGCCATCAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAGAGG
82310 A G AAGGGTTTACATAGCTCATGTTCAGGCTTTCACAGAGAAAATCAAGAATGAGCCTGCCATCAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCC[A/G]TTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACC
82310 A G CATAGCTCATGTTCAGGCTTTCACAGAGAAAATCAAGAATGAGCCTGCCATCAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAG[A/G]GGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACCATCTTCACCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
82310 A C GAAAATCAAGAATGAGCCTGCCATCAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGT[A/C]AGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACCATCTTCACCGCTGCATTCACATACTATGAACTGGCCG
82310 C T AATCAAGAATGAGCCTGCCATCAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAG[C/T]CCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACCATCTTCACCGCTGCATTCACATACTATGAACTGGCCGTTG
82310 G A CAGAAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGA[G/A]TCGCCGAAGATGAATATAACACCATCTTCACCGCTGCATTCACATACTATGAACTGGCCGTTGTACTGAACGATCAGTACAATC
82310 G A AAAACCTGCCGGTAGCACGACCAAAGAAGGCGCGTCCATTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTC[G/A]CCGAAGATGAATATAACACCATCTTCACCGCTGCATTCACATACTATGAACTGGCCGTTGTACTGAACGATCAGTACAATCAAT
82310 A G ACGACCAAAGAAGGCGCGTCCATTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATA[A/G]CACCATCTTCACCGCTGCATTCACATACTATGAACTGGCCGTTGTACTGAACGATCAGTACAATCAATGGAATCACTGCAGTGG
82310 C T TTGGGCAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACCATCTTCACCGCTGCATT[C/T]ACATACTATGAACTGGCCGTTGTACTGAACGATCAGTACAATCAATGGAATCACTGCAGTGGCAATCAATTTCATTTCTTTT
82310 A T CAGAGGAATGGGGTAGCCAAGCCCGGCGGTAAGCCCACCGGTGTCGGAGTTGGAGTCGCCGAAGATGAATATAACACCATCTTCACCGCTGCATTCACAT[A/T]CTATGAACTGGCCGTTGTACTGAACGATCAGTACAATCAATGGAATCACTGCAGTGGCAATCAATTTCATTTCTTTT
82324 C A TTTTTTTTGAACTAAACAAAACAGATGGCTGATTAACAGAGCTTTTTGCACTGCACTGGTATATGAAGAAAAAAATCCGT[C/A]ATCAGTTCTTACATTTTATTCAAAAGCTGCAAATCTCAAACGCTGTAAAATTCAGCAACAAAGCTAAATTTAAAAACACAAAAGGCACGAACAAAGAGAC
82324 A C TCCCCATCCCAAAGCTCTTCTTCACTCTTGTATACTCCATCGGGCTTAATGAAAAAGTGCCCTCTTAGAAGCCTTGCCTGTTCAACTTGAGAAAACTTAG[A/C]AAGAAGGTGGTCAGGAATGGACCAATCAAAGATATCAAGATTGGCCTTGATCCTTTCTACGTTCGTGCTTTTAGGAAGCACGCTGTGTC
82352 G T TGGAATCCCCAGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTG[G/T]GTCATACGGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTT
82352 C T TGGAATCCCCAGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATA[C/T]GGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAG
82352 C T TGGAATCCCCAGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATACGG[C/T]CGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCG
82352 C T TGGAATCCCCAGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATACGGCCGTGTTCT[C/T]CTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGG
82352 T C TGGAATCCCCAGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATACGGCCGTGTTCTCCTAGGGTTAATCG[T/C]AGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGG
82352 G A AGTTTTGCAAATCTTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATACGGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCT[G/A]TTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGGGGACAAGGTT
82352 A G TTTGAATCCTAAGCTGAAATTTTTAAATCTGCACTGCTTGGGTCATACGGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTC[A/G]GCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGGGGACAAGGTTGAGCAGTCAACC
82352 C T TAAATCTGCACTGCTTGGGTCATACGGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGA[C/T]AGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGGGGACAAGGTTGAGCAGTCAACCGGTGGAAGCAGTCACTGGCGGT
82352 G A AATCTGCACTGCTTGGGTCATACGGCCGTGTTCTCCTAGGGTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACA[G/A]CGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGGGGACAAGGTTGAGCAGTCAACCGGTGGAAGCAGTCACTGGCGGTGC
82352 G A GTTAATCGTAGATGTCGCGGCTGTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAG[G/A]GGACAAGGTTGAGCAGTCAACCGGTGGAAGCAGTCACTGGCGGTGCGACTATGATGGTCTGGAAATCATCGCAGGAAGGGAAATC
82352 C T GTTTCCATTCTTCAGCGGTGTTCGTTCATAAATTGACAGCGACGTCTTTACTTTGATAAAGGCGATGGCTTGGAGGAGGGGACAAGGTTGAGCAGTCAAC[C/T]GGTGGAAGCAGTCACTGGCGGTGCGACTATGATGGTCTGGAAATCATCGCAGGAAGGGAAATCGATAACATGGAGGAAGGCGTG
82352 G A ATGGCTTGGAGGAGGGGACAAGGTTGAGCAGTCAACCGGTGGAAGCAGTCACTGGCGGTGCGACTATGATGGTCTGGAAATCATCGCAGGAAGGGAAATC[G/A]ATAACATGGAGGAAGGCGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCTAATCAACAGAAGGAAGAGGAAGC
82352 G A GACAAGGTTGAGCAGTCAACCGGTGGAAGCAGTCACTGGCGGTGCGACTATGATGGTCTGGAAATCATCGCAGGAAGGGAAATCGATAACATGGAGGAAG[G/A]CGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCTAATCAACAGAAGGAAGAGGAAGCAACCGATTTAAGGAAGA
82352 A G CGACTATGATGGTCTGGAAATCATCGCAGGAAGGGAAATCGATAACATGGAGGAAGGCGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCT[A/G]ATCAACAGAAGGAAGAGGAAGCAACCGATTTAAGGAAGAATAAATTTTTGGAGGAAAACGATTTGCGGAGGCGGCCATTAAAAT
82352 G A TCTGGAAATCATCGCAGGAAGGGAAATCGATAACATGGAGGAAGGCGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCTAATCAACAGAAG[G/A]AAGAGGAAGCAACCGATTTAAGGAAGAATAAATTTTTGGAGGAAAACGATTTGCGGAGGCGGCCATTAAAATGAATTGGAAAAA
82352 G T GGAAATCATCGCAGGAAGGGAAATCGATAACATGGAGGAAGGCGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCTAATCAACAGAAGGAA[G/T]AGGAAGCAACCGATTTAAGGAAGAATAAATTTTTGGAGGAAAACGATTTGCGGAGGCGGCCATTAAAATGAATTGGAAAAAGA
82352 T C GGAGGAAGGCGTGACTTTTGTTTGTGAACCAGGTGGGTGATTTCGAGTTTCTAATCAACAGAAGGAAGAGGAAGCAACCGATTTAAGGAAGAATAAATTT[T/C]TGGAGGAAAACGATTTGCGGAGGCGGCCATTAAAATGAATTGGAAAAAGAATGGATTTTCTCCCAGTAGGCCAACA
82356 A T GTAGGCGGCACAAAAGTGCCAGGAGTAAACGGAAACGATTTGAAGTTGGATCCAGTTTCAGGGAGAGGAGGAGTGATAGTGGATTCGGGCACGTCCGT[A/T]ACCAGGCTAGCCCGACCGGCTTACGCGGCGCTTAGGGACGCGTTCAAGGCCGGTGCAGCCGGTTTGAAATTTTCGCCAGGTGGG
82356 G A TGATAGTGGATTCGGGCACGTCCGTAACCAGGCTAGCCCGACCGGCTTACGCGGCGCTTAGGGACGCGTTCAAGGCCGGTGCAGCCGGTTTGAAATTTTC[G/A]CCAGGTGGGTTTTCGTTGTTCGACACATGTTATGATTTGGCGGGGAAGACGGAGGTGAAGGTGCCGACTCTGGTGATGCATTTC
82360 T C CTGTCACAAATCAAATCTTCAAAATGAAAAAAAATCCTATGGTTTCATGTAGCAGACAGACAATACATATAGCTTTATAACTTAACCTATAGGGACAGTA[T/C]GGTTGTGTATATCTGAGCATGATTTGCACATGGAAAATCTAACACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGT
82360 T C AAAATGAAAAAAAATCCTATGGTTTCATGTAGCAGACAGACAATACATATAGCTTTATAACTTAACCTATAGGGACAGTATGGTTGTGTATATCTGAGCA[T/C]GATTTGCACATGGAAAATCTAACACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGT
82360 G A AAATGAAAAAAAATCCTATGGTTTCATGTAGCAGACAGACAATACATATAGCTTTATAACTTAACCTATAGGGACAGTATGGTTGTGTATATCTGAGCAT[G/A]ATTTGCACATGGAAAATCTAACACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTT
82360 T C TATAACTTAACCTATAGGGACAGTATGGTTGTGTATATCTGAGCATGATTTGCACATGGAAAATCTAACACAATCTGTACCATTCCCTGTTGAAACACCA[T/C]GCAGAAATCAATGTCTTCATCACCCACAATTCGTTCGTATAACACAGCTGCAAATGAAAAGGGACAATCACCTAGGATCTAAGCACAG
82360 C T ATCTGAGCATGATTTGCACATGGAAAATCTAACACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTT[C/T]GTATAACACAGCTGCAAATGAAAAGGGACAATCACCTAGGATCTAAGCACAGAAAAAGCCTAAACCTATGATATAACCAACCGATTGA
82360 C T TAACACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTTCGTATAACACAGCTGCAAATGAAAAGGGA[C/T]AATCACCTAGGATCTAAGCACAGAAAAAGCCTAAACCTATGATATAACCAACCGATTGAGACATTGATCTAATCTAAAAATTCTACCAC
82360 C G ACAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTTCGTATAACACAGCTGCAAATGAAAAGGGACAAT[C/G]ACCTAGGATCTAAGCACAGAAAAAGCCTAAACCTATGATATAACCAACCGATTGAGACATTGATCTAATCTAAAAATTCTACCACTATA
82360 A G CAATCTGTACCATTCCCTGTTGAAACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTTCGTATAACACAGCTGCAAATGAAAAGGGACAATC[A/G]CCTAGGATCTAAGCACAGAAAAAGCCTAAACCTATGATATAACCAACCGATTGAGACATTGATCTAATCTAAAAATTCTACCACTATA
82360 G T ACACCATGCAGAAATCAATGTCTTCATCACCCACAATTCGTTCGTATAACACAGCTGCAAATGAAAAGGGACAATCACCTAGGATCTAAGCACAGAAAAA[G/T]CCTAAACCTATGATATAACCAACCGATTGAGACATTGATCTAATCTAAAAATTCTACCACTATA
82380 C T TTCTTCTTCAAATGGGCCTTAAAGCCCATAATATCCCCATCCCACTTGGTAACGGCCTGATTCTCGCAGACCCAAATCTCCTTGGCAACCTGA[C/T]TAATCAACCTAAAATCATGACTAACCAAAACCAGTCCTCCATCCCACTCGTTAAGTGCATCTGCCAAAGAATCGATTGTTTCAATGTCCAAGTGGTT
82408 T A TCTTCCGAACCAGTGCAAATTGTCTTACCATCAGGAGTAAAGTTTCCACAAGTAACGCTGC[T/A]ACCATGACCATAAAATGTATGGAGTATTTCGCCTTTTTCAGCATTCCACATCCACACCGTGCCATCTTTCAATCCTGCCAAGATTACTGGGCCTCTAGGA
82408 T A TCTTCCGAACCAGTGCAAATTGTCTTACCATCAGGAGTAAAGTTTCCACAAGTAACGCTGCTACCATGACCATAAAATG[T/A]ATGGAGTATTTCGCCTTTTTCAGCATTCCACATCCACACCGTGCCATCTTTCAATCCTGCCAAGATTACTGGGCCTCTAGGATGCCATTTAAGCCACTCA
82408 T C AAGTAACGCTGCTACCATGACCATAAAATGTATGGAGTATTTCGCCTTTTTCAGCATTCCACATCCACACCGTGCCATCTTTCAATCCTGCCAAGATTAC[T/C]GGGCCTCTAGGATGCCATTTAAGCCACTCAATATCTTCTCCTGAGCCCTCTAATGAACATACTACGCTTCCTGATGATGTGTCCCATATTT
82408 C T TTTCAGCATTCCACATCCACACCGTGCCATCTTTCAATCCTGCCAAGATTACTGGGCCTCTAGGATGCCATTTAAGCCACTCAATATCTTCTCCTGAGCC[C/T]TCTAATGAACATACTACGCTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATCTAAACCACCCGATGCAAATAGTTTCCCATCAGCAC
82408 G A ACACCGTGCCATCTTTCAATCCTGCCAAGATTACTGGGCCTCTAGGATGCCATTTAAGCCACTCAATATCTTCTCCTGAGCCCTCTAATGAACATACTAC[G/A]CTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATCTAAACCACCCGATGCAAATAGTTTCCCATCAGCACTAAAAGCTAAACTGTTA
82408 T C CTCTAGGATGCCATTTAAGCCACTCAATATCTTCTCCTGAGCCCTCTAATGAACATACTACGCTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATC[T/C]AAACCACCCGATGCAAATAGTTTCCCATCAGCACTAAAAGCTAAACTGTTAACGGTGTCTTTGTGACCTCGAAGCTCAATCAATGGCTCC
82408 C A GCCATTTAAGCCACTCAATATCTTCTCCTGAGCCCTCTAATGAACATACTACGCTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATCTAAACCACC[C/A]GATGCAAATAGTTTCCCATCAGCACTAAAAGCTAAACTGTTAACGGTGTCTTTGTGACCTCGAAGCTCAATCAATGGCTCCTGAGCACCA
82408 A G TATCTTCTCCTGAGCCCTCTAATGAACATACTACGCTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATCTAAACCACCCGATGCAAATAGTTTCCC[A/G]TCAGCACTAAAAGCTAAACTGTTAACGGTGTCTTTGTGACCTCGAAGCTCAATCAATGGCTCCTGAGCACCAATTCTCCAGCAATATCCT
82408 C T CATACTACGCTTCCTGATGATGTGTCCCATATTTGGATCAGTCCATCTAAACCACCCGATGCAAATAGTTTCCCATCAGCACTAAAAGCTAAACTGTTAA[C/T]GGTGTCTTTGTGACCTCGAAGCTCAATCAATGGCTCCTGAGCACCAATTCTCCAGCAATATCCTTTATCATCTGAACTTCCCGTAGCCAC
82408 T G CATATTTGGATCAGTCCATCTAAACCACCCGATGCAAATAGTTTCCCATCAGCACTAAAAGCTAAACTGTTAACGGTGTCTTTGTGACCTCGAAGCTCAA[T/G]CAATGGCTCCTGAGCACCAATTCTCCAGCAATATCCTTTATCATCTGAACTTCCCGTAGCCACTACAAATTCATCTAATGGACTACATGC
82438 C A CGGCCCTTGGTTTGATCCAGCCATCTCGAGACTGCTTCACTCCCTTGTGTTCAACTCGGTCCCAAAAGAGAACGATGGACAGCGTAGCAGTAGCACGCAC[C/A]ACTCGAGGCCGACGCAATCGCCTCCTCCTCAGTCTGAAGTCGCTGCTGCCTCCTACCCGTTTTCTGTTCTTTGCGAGTGCAAAGATCT
82438 C T ATCTCGAGACTGCTTCACTCCCTTGTGTTCAACTCGGTCCCAAAAGAGAACGATGGACAGCGTAGCAGTAGCACGCACCACTCGAGGCCGACGCAATCGC[C/T]TCCTCCTCAGTCTGAAGTCGCTGCTGCCTCCTACCCGTTTTCTGTTCTTTGCGAGTGCAAAGATCTTGAGCGTTACAGATTTAGAGAT
82442 A G CTCCACCTGCTGGCATTGTAGCCAACTTCTTACGTCCTGCATCCATAAGTTCCTCAATGTTCTTTCCCTTCAATTCATCCACGACTTTCTTGAGGCTCGC[A/G]GCATCGACATCAACTCCTACGCTGCTCAGAATTTTTTTTACGTCGGCCTCTGAAGGGCTGGCGTTACCCCCGAGTGCTGCCAATAGGTAT
82454 G A ACATATAAGCTGTTTCCAGGATTTTCTACATCACTAGAATCTTGAGATCTTGTTGGACTCCTTGATCTTGAAAACGATCTGGAACAAGAACTCGCACGAC[G/A]AGGTGTAGATGATCGTGAAACATATCCTGACCTTCCTGAGCGTGCCATTCTGAATCTTTGATCAGATTCAAAGGATCTCCCTTCGGTTT
82466 T C TGATGACTAAGAGCGTACCTTCTTTTGAAGGGCTCAGAAGTGCACCTTCGATTTTCAGAATTTCTCCGTTAATTGGTGCCTTAGGTGCTGAAATTAATAG[T/C]AGAAAGTTCAAGAGTGTTGTTATACAAGCTGCCAATGTTGTTTCGCCTAAGTATACATCCCTTAAGCCAATGGGAGACCGAGTGCTTG
82472 T TA AAGCCCATGAATATTGCCGAAATTTGGATTTCATTATCCCCTTACCAGGAAGTTCCATTACATTTAATTTGTATAAATTCAAACAAGAATTACAATATGA[T/TA]AAAAAAATGACTATACCAGGAATAAATCTGATTACTGCATAATCGGAATCTTTTTCTTTGAAAACCCGGAAATAAAATCTCAGTAAAAG
82496 G A AAGCAGGGCTTCTATCCCTCACCCTTTCCCTACTGTAAGAAGTTGGTCCAGTGTACCGATCATAAACAGGGCTGTGAGCTCGACCGTAATCAGGACTAGG[G/A]CGGGATCTCCGATACACTGGACTGATCGATCGTTCACGACGAGGACTGTCCCGACGTCTACCACCATATCCTCTTCCGCTGATGTCA
82512 T A GCACTGGGAGGATGAGGTATCTTCGTCATGTGTCTCGCAGGTTCAAGAGTGGTTTCAGAGAAGGCACCCAAGCTGCTCCTAGGAAGAAGGCTGCTGCTGC[T/A]GCAACATCTTAATTTTGAGTGACTATGAACCATTTGCATGGAGGGACATCACTTGTAGCATTTATTTATCCGAATGTCATGCTGAG
82518 AT A ATCTTGATTGGACCCAATTTAGTTCTGTTTTTAATCGAGATGTTATTCAATTAGTTCCCAAAGCACTTTTTGCCTTTTCGCTGCATCCTTTATTTCTCCA[AT/A]TTTTTTAAGATTATTTATCATGGCTGTAAGAATTACTTTTTCCATGTCCGCTTCAATGACCCAAAACCTAGCCGCCAGTCTACGGCACGGC
82518 A G CGAGATGTTATTCAATTAGTTCCCAAAGCACTTTTTGCCTTTTCGCTGCATCCTTTATTTCTCCAATTTTTTAAGATTATTTATCATGGCTGTAAGAATT[A/G]CTTTTTCCATGTCCGCTTCAATGACCCAAAACCTAGCCGCCAGTCTACGGCACGGCGGCCCTGGTCGCCGTGCCACCAGAACCCTAGTTTC
82518 A G ATTATTTATCATGGCTGTAAGAATTACTTTTTCCATGTCCGCTTCAATGACCCAAAACCTAGCCGCCAGTCTACGGCACGGCGGCCCTGGTCGCCGTGCC[A/G]CCAGAACCCTAGTTTCTGACCGTAGGGTGCTGGATCGGTTGATGTTTTCATCTCTATCCTGTAACAGTAGATCTGGTACGGATGGAGA
82518 C G TATTTATCATGGCTGTAAGAATTACTTTTTCCATGTCCGCTTCAATGACCCAAAACCTAGCCGCCAGTCTACGGCACGGCGGCCCTGGTCGCCGTGCCAC[C/G]AGAACCCTAGTTTCTGACCGTAGGGTGCTGGATCGGTTGATGTTTTCATCTCTATCCTGTAACAGTAGATCTGGTACGGATGGAGATT
82518 C T TTCCATGTCCGCTTCAATGACCCAAAACCTAGCCGCCAGTCTACGGCACGGCGGCCCTGGTCGCCGTGCCACCAGAACCCTAGTTTCTGACCGTAGGGTG[C/T]TGGATCGGTTGATGTTTTCATCTCTATCCTGTAACAGTAGATCTGGTACGGATGGAGATTGCATGATGCGATATAAGTCGAGTGCGT
82518 G C ACCAGAACCCTAGTTTCTGACCGTAGGGTGCTGGATCGGTTGATGTTTTCATCTCTATCCTGTAACAGTAGATCTGGTACGGATGGAGATTGCATGATGC[G/C]ATATAAGTCGAGTGCGTGTTTGAATAGTTTGAGGAATGATGCAAAGACTGTTTTTGCTGCGGTTACTGTTCCGTTTTTGAAAAGTTCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
82518 C T TCTGACCGTAGGGTGCTGGATCGGTTGATGTTTTCATCTCTATCCTGTAACAGTAGATCTGGTACGGATGGAGATTGCATGATGCGATATAAGTCGAGTG[C/T]GTGTTTGAATAGTTTGAGGAATGATGCAAAGACTGTTTTTGCTGCGGTTACTGTTCCGTTTTTGAAAAGTTCAAGGTTGGCGGAGCC
82518 T C TACGGATGGAGATTGCATGATGCGATATAAGTCGAGTGCGTGTTTGAATAGTTTGAGGAATGATGCAAAGACTGTTTTTGCTGCGGTTACTGTTCCGTTT[T/C]TGAAAAGTTCAAGGTTGGCGGAGCCAAAAGAGATCCCTACGATGTCCATGTATCCAACTTT
82522 T C GGTGGCAGAACTCGGACGTGGTGATGAGCGAGGTGTTTTGGAGAAGCAAGTGTGGCTGCGGTGGTTTGGAGAACCAACTCAATGGCGGCAACGATGGGCT[T/C]GTCATGTGCGGTGGACGTTTGTGTCCACGGAGGAGCCGAACTATGTGAAGGCGGCGCTGCTGATTTTGGTGAGAGAGGAAAA
82522 T C GATTTTGGTGAGAGAGGAAAATCGATTTGGGGAAACGATTAAACTTTGATTTTGATGGCCATTAAAATCTAACAAGGGAAATAAGATTGGGATTCGGCCA[T/C]TTCAAATTTGAAAAGGAAGATTGATTGCTGCTAAATGAAACTGAGGAAAGAAGTGATTTTTTTCCAGTAGGCCAA
82540 T C CATTACTTGCGTTATCTGAGCTTCGAGGAAGCGCCTTAGTAGCTATAGTAGCTTGACTATCGGAATTTGGTCTCCGGTTTGGCTGAACTACCATTCTTTG[T/C]AAAGAAGCATCTGAATGAGAGGGCAGTGGCGGAGTCTGTTTTGCCGTTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTC
82540 C T GCGTTATCTGAGCTTCGAGGAAGCGCCTTAGTAGCTATAGTAGCTTGACTATCGGAATTTGGTCTCCGGTTTGGCTGAACTACCATTCTTTGTAAAGAAG[C/T]ATCTGAATGAGAGGGCAGTGGCGGAGTCTGTTTTGCCGTTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAA
82540 G A TTCGAGGAAGCGCCTTAGTAGCTATAGTAGCTTGACTATCGGAATTTGGTCTCCGGTTTGGCTGAACTACCATTCTTTGTAAAGAAGCATCTGAATGAGA[G/A]GGCAGTGGCGGAGTCTGTTTTGCCGTTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCC
82540 C T GACTATCGGAATTTGGTCTCCGGTTTGGCTGAACTACCATTCTTTGTAAAGAAGCATCTGAATGAGAGGGCAGTGGCGGAGTCTGTTTTGCCGTTTGAGA[C/T]GGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTT
82540 C T GAAGCATCTGAATGAGAGGGCAGTGGCGGAGTCTGTTTTGCCGTTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGG[C/T]TCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGGGATCGACAGCTAAATTCTGATGCATA
82540 A G GTGGCGGAGTCTGTTTTGCCGTTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCC[A/G]GGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGGGATCGACAGCTAAATTCTGATGCATAAGCATGGCAGGTCCTCCGATTAG
82540 C T TTTGAGACGGCTGTTGAGAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTTCTTATC[C/T]CCGCCAACTTGAGAGGGATCGACAGCTAAATTCTGATGCATAAGCATGGCAGGTCCTCCGATTAGACCCTTCATTTGTTGTTTTTGC
82540 G T GAATACATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGG[G/T]ATCGACAGCTAAATTCTGATGCATAAGCATGGCAGGTCCTCCGATTAGACCCTTCATTTGTTGTTTTTGCAGATGCGGATTTCTTGG
82540 A G CATTTTGTGTGGCATATTCGAAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGGGATCG[A/G]CAGCTAAATTCTGATGCATAAGCATGGCAGGTCCTCCGATTAGACCCTTCATTTGTTGTTTTTGCAGATGCGGATTTCTTGGCTGGT
82540 A G AAGTCAAGGCTGAGGCTCCAGAAAAGAAGACCGAGCCAGGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGGGATCGACAGCTAAATTCTGATGCAT[A/G]AGCATGGCAGGTCCTCCGATTAGACCCTTCATTTGTTGTTTTTGCAGATGCGGATTTCTTGGCTGGTGCACTTGCAGATGGGGCCT
82540 C T AGACCGAGCCAGGTTGCGACATTTTCTTATCCCCGCCAACTTGAGAGGGATCGACAGCTAAATTCTGATGCATAAGCATGGCAGGTCCTCCGATTAGACC[C/T]TTCATTTGTTGTTTTTGCAGATGCGGATTTCTTGGCTGGTGCACTTGCAGATGGGGCCTTAACTTATTAGGATGAGAGGTCACCTGA
82558 A G CCATTTACTCCTTTTTGTTCTTCAACAGTTGCTTTATACTCCTTAGTTCGGTCCAAAACGCCTATCTCTGCTGGAATGCTTGTTAGATGAGTGTAAAACA[A/G]CTTCTATAACAACTTTTGTTTTGGCACATCTGAACAGTAGATGGACCTATAATATACTGCTTATTCTCCTCGAGTGACTTTTTATAATAAGT
82558 T A GAGTGACTTTTTATAATAAGTAGATCCATGCTTTTATACAAATTGAGTTGCTTCGCGTGCTTTTAATTTTAACAAATTTAGCTTTGATGACATCTTGCTC[T/A]CGGCCTGACTTATCGGTTAGAGCGAATGATGCCAGTTACTGTCATGGCTTCCCCAATCATCGTTGAACACTTCACGCCAATCAACGCCGG
82558 G A GTGACTTTTTATAATAAGTAGATCCATGCTTTTATACAAATTGAGTTGCTTCGCGTGCTTTTAATTTTAACAAATTTAGCTTTGATGACATCTTGCTCTC[G/A]GCCTGACTTATCGGTTAGAGCGAATGATGCCAGTTACTGTCATGGCTTCCCCAATCATCGTTGAACACTTCACGCCAATCAACGCCGGCA
82562 T C GATTCATGTAGTTATCAAACATAATCACCATGCATACTCTTTTACAACGTTTTACACCTCAAAAAAAGGCATGAATTATTTGTTACAATAAAGCACAATA[T/C]GAGTCACAAACCAACCAAGAAACAACAGGAATCAAAGTCCACTGATTCAAAAGTTCAGACTTAGTAATCATTCTTGCCAAAGTTTTTGCA
82562 T C CTGATTCAAAAGTTCAGACTTAGTAATCATTCTTGCCAAAGTTTTTGCACCAGAGCTGAGAAGGGATGGGACGTACAGGCATATGTGGGCGTTGCTCAAG[T/C]TCCGCAGATTTCATGGCGATAGGAATGCAAACGAGGAAGACACCAAACATAGCTATGGCAGTGTTACGTTTCCAGTGGACTGGCTT
82562 A G TGCACCAGAGCTGAGAAGGGATGGGACGTACAGGCATATGTGGGCGTTGCTCAAGTTCCGCAGATTTCATGGCGATAGGAATGCAAACGAGGAAGACACC[A/G]AACATAGCTATGGCAGTGTTACGTTTCCAGTGGACTGGCTTGCAGTAGGGCCCACCTGTCATGCTCCATACTTTCGCTCTAAAAT
82584 A G AGAAGCAGAGCTTTCGTCATCTATAAAGGGTGCGAAAATATTGCATCCATGGCCAGAATGGACGGAACTGTTGCAGCTCCTATACAAAAGCGGATTCTTA[A/G]ACGTCGATGCTTTGGGTAACCATAGAAATTACAATTCGATTCGCAGTGGCTGCCTCGATTTTGCTAGGAGTCATGCTCATCTCATCA
82604 C T TACAATTGGGCTAACGTAAAAAATAAGGGAGATAACAACCTACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAA[C/T]AATTGTGAAATTTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCC
82604 A G TACAATTGGGCTAACGTAAAAAATAAGGGAGATAACAACCTACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAACA[A/G]TTGTGAAATTTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCT
82604 T C TACAATTGGGCTAACGTAAAAAATAAGGGAGATAACAACCTACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAACAATTGTGAAA[T/C]TTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTG
82604 G C CAATTGGGCTAACGTAAAAAATAAGGGAGATAACAACCTACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAACAATTGTGAAATTTTGGTAAAGTCAA[G/C]ATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGA
82604 T C AACCTACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAACAATTGTGAAATTTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGT[T/C]GACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCC
82604 CA C ACTGCTAGAAGGTTAGCCGATTTCCGGAGGTAGAACAATTGTGAAATTTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACT[CA/C]AAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCG
82604 T G GAGGTAGAACAATTGTGAAATTTTGGTAAAGTCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGG[T/G]GCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAA
82604 G T TCAAGATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCA[G/T]ATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATT
82604 A G ATCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCC[A/G]AAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAG
82604 A G TCAAACGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCA[A/G]AAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGT
82604 G A CGGATCCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAAC[G/A]AGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGT
82604 A G CCAAAAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCT[A/G]AAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGAT
82604 C T AAAGCTTAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAG[C/T]TTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAG
82604 A G TAAAACTTGAGTTGACTCAAAAAAAGATTGCAGTGGCAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCC[A/G]GCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCT
82604 T C CAATTGGTGCTGAATCCCTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGG[T/C]AGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCA
82604 C T CTCTTTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGA[C/T]GGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACG
82604 G A TTACTTGAAATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGC[G/A]ATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGG
82604 T C ATCAACCAGATCCAAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAG[T/C]AAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATT
82604 A G AAAAACGAGCTAAAGCTTTCCAGCGACCGAAGAAGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCT[A/G]GAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATTAGGCAAGTGGCC
82604 A G AGTCCTGGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACAC[A/G]AGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATTAGGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAG
82604 T G GGTCAATGGCAACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCT[T/G]GGTCAACCGGTGACGACGACGAGGAGTTTGATTAGGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCG
82604 T TGAC ACGCCGGTAGTAACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGG[T/TGAC]GACGACGACGAGGAGTTTGATTAGGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATT
82604 G C ACTCGCTGATGACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGA[G/C]GAGTTTGATTAGGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATTTATTATCTTTTTACTA
82604 T C GACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGAT[T/C]AGGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATTTATTATCTTTTTACTAAGGAAAAT
82604 A G ACGGCGATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATT[A/G]GGCAAGTGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATTTATTATCTTTTTACTAAGGAAAAT
82604 G A ATTAAAAGTAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATTAGGCAA[G/A]TGGCCATGAAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATTTATTATCTTTTTACTAAGGAAAAT
82604 G T TAAGGTCAGATCTAGAGCTCTCTGGCAATTGACAAATCTCTGACACAAGCCTTGGTCAACCGGTGACGACGACGAGGAGTTTGATTAGGCAAGTGGCCAT[G/T]AAATTTGATTGCAAAATTTTTTTCCTCAACAGATCTCGTCTGCCATTTATTATCTTTTTACTAAGGAAAAT
82628 T C TAGTTTCTTGCATATTCCCCACATCTGATGACGCACAGCCGTCCATCCAATCATTGACCCTTTTCAGCTGGGACAGCATCCCAGCCACCGAATCCCTGTC[T/C]GATGGCAGACATTCTCCTGCATCCAGAAACCTCTCCACAAATACCAAGAACCAAACTTTGGACTCTTCCTTCATTAGCCTTGCCAATTCA
82634 C A TGCTGTTCATTCCCAGAAAACTAAAACTGCAATGAATTTGAAAAAGAAAAAAAAACCCTTGCTTGGGGCACCGCGGTTCCTGCTAGGGGCTACCAGAGCC[C/A]GCCGCCCCAATGTCGATCGGCCGGCGATTAACCCTACCTTTCCTGCATTTTCAAGTTCCACGGAGCCAATCCATTTTTGTTGATTGCT
82636 G A TCTGAGTTATGGCCGGAAAAGGAGGAAAAGGGCTTCTCGCTGCCAAAACTACCGCCGCCAACAAGGATAAGAAAGCTCCAACCTCTCGATCTTCTCGAGC[G/A]GGTCTTCAGTTTCCAGTCGGACGTATTCACCGTCAATTGAAGACAAGAATCTCCGCTCATGGTCGTGTCGGGGCCACCGCCGCTGT
82656 T C GTCAATCCAGGTATGCTGCTGAGTCCACTGCAGAGCAGGTTGGTCGAACCTGCAGGAAGATGGGGCTGAAATCTGTCGTTATTAAAGTGAAAGGCGCTGT[T/C]TATTTCCGAAAGAAAAGGAAAGTTATCATGAGCTGGAGAGATGGGTTTAGAGGCGAAGGACTTGGGGCCAGGACTAGGATTTTG
82656 C A CAGGTATGCTGCTGAGTCCACTGCAGAGCAGGTTGGTCGAACCTGCAGGAAGATGGGGCTGAAATCTGTCGTTATTAAAGTGAAAGGCGCTGTTTATTTC[C/A]GAAAGAAAAGGAAAGTTATCATGAGCTGGAGAGATGGGTTTAGAGGCGAAGGACTTGGGGCCAGGACTAGGATTTTGTCTGTGC
82656 G T TGAAATCTGTCGTTATTAAAGTGAAAGGCGCTGTTTATTTCCGAAAGAAAAGGAAAGTTATCATGAGCTGGAGAGATGGGTTTAGAGGCGAAGGACTTGG[G/T]GCCAGGACTAGGATTTTGTCTGTGCAGGATGAGACGCAGCTTGCTCACAACGGTTGCCGATTGCCTAAAAAACGACGTATTTAAA
82656 GA G GATGGGTTTAGAGGCGAAGGACTTGGGGCCAGGACTAGGATTTTGTCTGTGCAGGATGAGACGCAGCTTGCTCACAACGGTTGCCGATTGCCTAAAAAAC[GA/G]ACGTATTTAAAATGGGTTTCTTTTACTTGTTGATGAGTGTTTTTGTTATGCTTCGATAATTGTGTTGAACTATGCGCCTCGCTCTT
82656 T A AGGACTTGGGGCCAGGACTAGGATTTTGTCTGTGCAGGATGAGACGCAGCTTGCTCACAACGGTTGCCGATTGCCTAAAAAACGACGTATTTAAAATGGG[T/A]TTCTTTTACTTGTTGATGAGTGTTTTTGTTATGCTTCGATAATTGTGTTGAACTATGCGCCTCGCTCTTGCTGTTGTAATGTGCTCTT
82656 CT C GGCCAGGACTAGGATTTTGTCTGTGCAGGATGAGACGCAGCTTGCTCACAACGGTTGCCGATTGCCTAAAAAACGACGTATTTAAAATGGGTTTCTTTTA[CT/C]TTGTTGATGAGTGTTTTTGTTATGCTTCGATAATTGTGTTGAACTATGCGCCTCGCTCTTGCTGTTGTAATGTGCTCTTGCTGTTGCA
82672 T A TTCCTCAGTTGCCACGTCCTACCGTATAGCGGAATGCCCATCACGAGCTTTTCTGGAGGAAATCCAGCTTCGATCCAGGATTC[T/A]ATTCCACGACTCGTGGAAATAACGGTCTGGTTCGAAGGGTACAGCGCTGCAGGTGCGTTCGTTTCAGTCACATTCCAGCTTCCGTAGTAGTCAAAGCACA
82680 G GT AACAGAGCCAGACTGAGGGGTGGAGGACAGCCAGAGAAGAAGACAGCGTTGAGCACTATCTCCTACCCGATCGATACTAGCATCGTAACCAGCCTGCGGA[G/GT]AGAAAGCAGTTTAAGGTGTAGCTAACTATTACGGGTTAGGCAGAAGGACAGCAGCTGAAAAAGGCTCGTAATGGAATCAAGG
82684 GA G ATGTGATGAATGCAGCTCAAATTATGAAGGAGAAATCTGCAAACAAACCTGTTGAATGCCTTGTTCGGTTCTGAGATGAGTAGGTAATCAAGTTGTGTTT[GA/G]AAAAAACAGTTACACATTCACCTCCTTCCCAAATCCGCAAATATTCGCAATATGACTCAATTTTTCGGTTGTGAATAATTTCCAGCA
82726 C T GCGCAAGACAAAGGTGGCGTTTTATATCTCTTCTGATATCCTTTGGAAGGTTCTGAAGCAGACTCTCCTCATCAACTCCTCTTGTTTCTTGCCATCTATA[C/T]TGTTCATACCGTCGTATTCTGCTTTTTATGTCATCTGGAAGCAAGCGATGAGACATCCATTGCTCTGCATCTCTCCTTTTCACCCTCATTTC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
82726 T C TATCTCTTCTGATATCCTTTGGAAGGTTCTGAAGCAGACTCTCCTCATCAACTCCTCTTGTTTCTTGCCATCTATACTGTTCATACCGTCGTATTCTGCT[T/C]TTTATGTCATCTGGAAGCAAGCGATGAGACATCCATTGCTCTGCATCTCTCCTTTTCACCCTCATTTCTTCTATCCTCACTGTTGTAGATTGC
82742 AC A ACTGTTGGCCTACTGGTTAACTTCAACAACCTTCAAGTTCCTCAAACCACAACCCCTCTTCACTTAACCTTACAATGTCTGGCAAGGGTGGAAA[AC/A]CTCCGGAAAGACTGGTGGCAAGGCCTCTTCTGATGCCAAGGGTGCTTCTCGCTCTGCCAAGGCTGGTCTCCAATTCCCAGTCGGTCGTATTCA
82744 A G AATTCATGCCCAAATTATCTGATTTTGGACTGGCAAGAGAGGGGCCTGTGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGG[A/G]ACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAG
82744 C A ATTTTGGACTGGCAAGAGAGGGGCCTGTGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAAC[C/A]GGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGA
82744 C T GGCCTGTGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAG[C/T]GATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAA
82744 T C CTGTGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGA[T/C]GTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAAAAA
82744 G A TGTGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGAT[G/A]TGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAAAAAC
82744 G A TGGATGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGATGT[G/A]TGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAAAAACTCG
82744 G A TGGGCGTAGCCATGTATCAACAGCGGTTGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGATGTGTGG[G/A]GCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAAAAACTCGTGAA
82744 G C TGTGGGAACTCATGGATACGCTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTC[G/C]TTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAACGAGCAAAAACTCGTGAATTGGGTGAGGCAGTTTCCAGTAGACAG
82744 C T CTGCACCAGAATACATAGAAACCGGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCT[C/T]GACAGAAACCGGCCCACTAACGAGCAAAAACTCGTGAATTGGGTGAGGCAGTTTCCAGTAGACAGCAAAAAATTTAACATGATAA
82744 G A ACATAGAAACCGGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCG[G/A]CCCACTAACGAGCAAAAACTCGTGAATTGGGTGAGGCAGTTTCCAGTAGACAGCAAAAAATTTAACATGATAATGGATCCTAGAC
82744 C T CCGGGCACCTTACAACCAAAAGCGATGTGTGGGGCTTTGGAGTAGTCCTATACGAACTCGTTACAGGGCGGCGTTCCCTCGACAGAAACCGGCCCACTAA[C/T]GAGCAAAAACTCGTGAATTGGGTGAGGCAGTTTCCAGTAGACAGCAAAAAATTTAACATGATAATGGATCCTAGACTGCAAAACA
82744 T A AAAACAAATACTCGTCAAAAGCGGCTCGAGAAATTGCAAAACTAGCAGAGAGATGTTTATTGAAGCAAGCCAAGGAAAGACCAAAGATGAGCGAGGTGGT[T/A]GAAACACTGAGGTCGATCATTAATACTAATGATCTGTAAAGGTGTGGGATGGTGTTTGAATTGT
82744 A T ACAAATACTCGTCAAAAGCGGCTCGAGAAATTGCAAAACTAGCAGAGAGATGTTTATTGAAGCAAGCCAAGGAAAGACCAAAGATGAGCGAGGTGGTTGA[A/T]ACACTGAGGTCGATCATTAATACTAATGATCTGTAAAGGTGTGGGATGGTGTTTGAATTGT
82752 A G AAAATTACAACGCAGTGGGGGTTTAGTTGAACTTTAGACACAGTTACCCAAAGCTTGACCACTAATTTGAGCATCCACCTTCGATGTAAGGATTGCCGTC[A/G]TAACCTTTCTCACAACTGCATGTATAACCTGATCCATTCTCAGAGTCCTTGCAAGTGCTATTACGACTAACACACGCATAGTCCCCTGT
82752 C T CACCTTCGATGTAAGGATTGCCGTCATAACCTTTCTCACAACTGCATGTATAACCTGATCCATTCTCAGAGTCCTTGCAAGTGCTATTACGACTAACACA[C/T]GCATAGTCCCCTGTCTTGTTCAATTTTGCTTCTTTGCAGTTTTCATTTCCTACGACCCAATCTAGCATCAAAGGAGCCTTTTCAAACCGTT
82752 G C ACATTCTGTATCAGATTTACTAAAGGTATAGAAGTCGTTTTCTGCAAGAAATCCATAGTTGCAAGGACTGTAGCCCTGAATATCTTTATTTAGAAATCCA[G/C]GATCGAAATTTATTTCGTAATACGAGAGTCCCGTTGGTATAGTCAATTGGCAACATCCTATTCCCGAACACGTTGAATT
82754 A C ACAAATTCAAATTCAGGTAAGGGTTTCAAGCTTCTTTTCTTCCATGAGGCAAATCTTCAGCTTCTTCCTCCATGCGAAATCCGAAAGTTTTCTCCTCTTC[A/C]ATGCGAGATCCGCCTTTAATTACCTCCACTTTGTCACGTAATTTTTTCCTCAAAGCCGCAAACATTCCCATGACCACAGAACCGCCTAATT
82754 C T TCTTCCATGAGGCAAATCTTCAGCTTCTTCCTCCATGCGAAATCCGAAAGTTTTCTCCTCTTCAATGCGAGATCCGCCTTTAATTACCTCCACTTTGTCA[C/T]GTAATTTTTTCCTCAAAGCCGCAAACATTCCCATGACCACAGAACCGCCTAATTTCCTATCGCTTTATGCCCTGCTTTTGGCTGAAAGCTGC
82754 G A TGCGAAATCCGAAAGTTTTCTCCTCTTCAATGCGAGATCCGCCTTTAATTACCTCCACTTTGTCACGTAATTTTTTCCTCAAAGCCGCAAACATTCCCAT[G/A]ACCACAGAACCGCCTAATTTCCTATCGCTTTATGCCCTGCTTTTGGCTGAAAGCTGCAACCAATTCAATTCAACCTAACAATATCAATTCC
82754 T C ATGCGAGATCCGCCTTTAATTACCTCCACTTTGTCACGTAATTTTTTCCTCAAAGCCGCAAACATTCCCATGACCACAGAACCGCCTAATTTCCTATCGC[T/C]TTATGCCCTGCTTTTGGCTGAAAGCTGCAACCAATTCAATTCAACCTAACAATATCAATTCCTAATTTTATGCCACTTGAAAAACTGGGAG
82754 G A GCTTTATGCCCTGCTTTTGGCTGAAAGCTGCAACCAATTCAATTCAACCTAACAATATCAATTCCTAATTTTATGCCACTTGAAAAACTGGGAGCAGATA[G/A]CAGCAGCCTTCAATCCGCCGTCGCTTCAGAATTTAGGTAGAAGGAGAAAAGCATGATTGCGAATTTGATTACTGACTTCGGTTCTGGT
82754 G A CTGAAAGCTGCAACCAATTCAATTCAACCTAACAATATCAATTCCTAATTTTATGCCACTTGAAAAACTGGGAGCAGATAGCAGCAGCCTTCAATCCGCC[G/A]TCGCTTCAGAATTTAGGTAGAAGGAGAAAAGCATGATTGCGAATTTGATTACTGACTTCGGTTCTGGTAAATCAATTTTTCACTCTAAC
82780 G A CTGATTATATAACGCCTGAAATGAACATATCTTGTTTTAGTAAGGAGATCGATGTATGCCCTAACTCGCCGGAGAAATCTGTTAGAACTAAGGCTAAGAG[G/A]CACAGAATTGATAGCAAATGCAACAACGATGAGTCCCCTGAGCTGTTGACTGATCTGCATGTTGATACATTGGCTTCGGAGGAACTT
82800 C T AACAAATCAACCACACAGAATCACTCAAATTACATATACTTCCCACCAAGGGGTCTAGTCCCATATGCAGTATTACCGGCAGCCGTAGTCGAAGGAACGG[C/T]ATGCGTGAAGGGTACATGTGGCGCAGTTGCCTTATGAGCAGCAGTCTCCGCCCTATGCTCCGCCTTCTCCGTATGCAGTTCCGCCTT
82800 T A ATCACTCAAATTACATATACTTCCCACCAAGGGGTCTAGTCCCATATGCAGTATTACCGGCAGCCGTAGTCGAAGGAACGGCATGCGTGAAGGGTACATG[T/A]GGCGCAGTTGCCTTATGAGCAGCAGTCTCCGCCCTATGCTCCGCCTTCTCCGTATGCAGTTCCGCCTTCGCCTGCGCTTCTTTTGCCT
82820 T C GGGGAATCACTAAGCCTAAGCTTGTGTCTCCGGCGCTCGAAGCGGTCGTTGGTGTCAAAGAGATTCCAAGGACTCAAGCACTTAAAGTTATTTGGGCGTA[T/C]ATTAAGGAGCATAATCTTCAGGATCCAAATAACAAGAAGATTGTTGTGTGCGATGAGAAACTGAAGGCTGTATTTGCTGGCAAAG
82820 G T TTGGTGTCAAAGAGATTCCAAGGACTCAAGCACTTAAAGTTATTTGGGCGTATATTAAGGAGCATAATCTTCAGGATCCAAATAACAAGAAGATTGTTGT[G/T]TGCGATGAGAAACTGAAGGCTGTATTTGCTGGCAAAGAGAGGGTTGGATTCCTTGAAATTTCTGGCTTGTTGAATCCGCACTTTGCA
82820 A G AGAAGATTGTTGTGTGCGATGAGAAACTGAAGGCTGTATTTGCTGGCAAAGAGAGGGTTGGATTCCTTGAAATTTCTGGCTTGTTGAATCCGCACTTTGC[A/G]AAGTGATTATGTGACTTTGCCTTCTGCAAAGAGTGAACTTGAACATTGCCTCCTGTTATTTAGTTGTAGGCAGAAACTTTATTTAGG
82820 C G AGAGAGGGTTGGATTCCTTGAAATTTCTGGCTTGTTGAATCCGCACTTTGCAAAGTGATTATGTGACTTTGCCTTCTGCAAAGAGTGAACTTGAACATTG[C/G]CTCCTGTTATTTAGTTGTAGGCAGAAACTTTATTTAGGTTTTTCTGTTTTTTTTTAAGGTTGCCATT
82822 AT A ATTTCTGGGGAGTCAGATTGACGATTTTGTTGCTGATGCAATTATTAGTCAGCTACTGCTCCTTGATGCGCAGGATCATACGAAGGACATAAGGCTTTTT[AT/A]TTAATTCTCCTGGTGGTTCACTCAGTGCTACAATGGCTATATTCGACGTAATGCAATTAGTAAGAGCAGACGTGTCGACAATAGGCA
82822 A G AGCTACTGCTCCTTGATGCGCAGGATCATACGAAGGACATAAGGCTTTTTATTAATTCTCCTGGTGGTTCACTCAGTGCTACAATGGCTATATTCGACGT[A/G]ATGCAATTAGTAAGAGCAGACGTGTCGACAATAGGCATGGGAATCACAGCCTCGACATCTTCCATAATACTAGGAGGCGGCACAAAA
82822 A G GCTACTGCTCCTTGATGCGCAGGATCATACGAAGGACATAAGGCTTTTTATTAATTCTCCTGGTGGTTCACTCAGTGCTACAATGGCTATATTCGACGTA[A/G]TGCAATTAGTAAGAGCAGACGTGTCGACAATAGGCATGGGAATCACAGCCTCGACATCTTCCATAATACTAGGAGGCGGCACAAAAG
82822 C T CAATGGCTATATTCGACGTAATGCAATTAGTAAGAGCAGACGTGTCGACAATAGGCATGGGAATCACAGCCTCGACATCTTCCATAATACTAGGAGGCGG[C/T]ACAAAAGGCAAAAGACTAGCAATGCCCAACACAAGAATAATGCTTCATCAACCTCTAGGCGGCGCAAGCGGTCAGGCAATAGACG
82826 G T GTACTGCTCGGGTCTTGAAGGGAAAGGCGGGGGCTTTGATTTGGAAGAGACGCTGGCGAGTTGCTAGAGGCGAAGGCAGCGACTTGCATGTTGTTGAAGC[G/T]ATGGCAAATGGGTGCTTGGATCTGATGTGGATGGCAGCTCGAATCCCAACGCGGTGGTGGAGGTGGAGCACTCTAGCTGCTG
82826 C T GCTCGGGTCTTGAAGGGAAAGGCGGGGGCTTTGATTTGGAAGAGACGCTGGCGAGTTGCTAGAGGCGAAGGCAGCGACTTGCATGTTGTTGAAGCGATGG[C/T]AAATGGGTGCTTGGATCTGATGTGGATGGCAGCTCGAATCCCAACGCGGTGGTGGAGGTGGAGCACTCTAGCTGCTGGTGGG
82836 A G AGTGGGCAAAAGATAAATTACTAGATGAAGAAAATCTAATCAAAGTGGTGATGGATAAGAGGTTAGAAGGACAGTATAATCCGGAAGCTGCAATTCAAGC[A/G]GCTCAGCTCACCGTGCGTTGCTTTGCCCGTGCTCCCAGGAAAAGACCTTCCATGGACCAAGTA
82868 T C GTTGGCCTACTGGATAATTTCCAAATTACTCCAGCCCTTTTTGACTAAAACCGATAAATTAAACCACAAACCTGTGAATTTCGTGC[T/C]ATTTCGTAATTCTGATCGGCAGTGATCTGATCGCTGCCGCTGTGAATCAGGCAATTGATGGGATCTTGCGTCTCTCGGCCGGAAGGGTGCGCCGGAGTGA
82868 AT A GTTGGCCTACTGGATAATTTCCAAATTACTCCAGCCCTTTTTGACTAAAACCGATAAATTAAACCACAAACCTGTGAATTTCGTGCT[AT/A]TTTCGTAATTCTGATCGGCAGTGATCTGATCGCTGCCGCTGTGAATCAGGCAATTGATGGGATCTTGCGTCTCTCGGCCGGAAGGGTGCGCCGGAGTGAG
82868 A G TACTGGATAATTTCCAAATTACTCCAGCCCTTTTTGACTAAAACCGATAAATTAAACCACAAACCTGTGAATTTCGTGCTATTTCGTAATTCTGATCGGC[A/G]GTGATCTGATCGCTGCCGCTGTGAATCAGGCAATTGATGGGATCTTGCGTCTCTCGGCCGGAAGGGTGCGCCGGAGTGAGGCGACGA
82880 G A TAGCCACAGCCAAAGCCCTAGCAGAAACAGGAAAATGGAACGTTATAATGGCATGCCGGGACTTTCTAAAGGCAGAAAAAGTGGCAAAGGCAGCAGGCAT[G/A]CCCAAAGAGAACTACAAAATAATGCACCTCGACCTAGCTTCTCTGGACAGTGTGCGCCAGTTTGTCGATAACTTAAAGAGAACCG
82892 T A GAAGATAGGATTCACTGTAAACGTAGTACATAGATGAAATATAACATACTGAAATACAAGAGAATACGACACTCTAATACAATACAGGTAGCTGTGCCG[T/A]TGAAAGTTCAGTATCTCTTTCAATTGATGATGTTGCAGTTGACTGTAGGGCTAACAGGAATATTGAGCCTAAGCTTGCACAAAGGAG
82892 G A CTGTAGGGCTAACAGGAATATTGAGCCTAAGCTTGCACAAAGGAGGAAGATGCTTGGCCCGTGCAGGCACCACCCCAAAAGAAGGGCCAGTGGTCTTTAG[G/A]CACTGACATAAATCACGTCTGCTCTTCACGGTTGCAGCCATCTTGTTCAGAGCCTGTGCGCTCGAGCAGCACTCGGAGCTGGGAT
82892 G A TTGCAGCCATCTTGTTCAGAGCCTGTGCGCTCGAGCAGCACTCGGAGCTGGGATTGTCACCACCGGCTCCAAGTAAGAAGGGTCCGCATGGGATAAGTGC[G/A]TTCACTGCGTCCGAGCATGACATTGCCTCTGTATGGTTTGCCATCAGCAATGCAGCTACCAGTGTTAATAGCAGGTATGTTAACTT
82914 T C CATTCGTCATCGTATCAAGTGGAATGGAGCCACTCATCCGCGCGATTTTAGCCAACCTTGTTGGAGATGAGGACGCAAGCATGATCGATATTATCGCTAA[T/C]GACGTAGAACATGATAACAAAGGAAGGTGGCATATTAAGTACAGGCATCCGGACAGTGGATACGGCCATGACAAGTCCCAAGCAA
82914 A G TGGAATGGAGCCACTCATCCGCGCGATTTTAGCCAACCTTGTTGGAGATGAGGACGCAAGCATGATCGATATTATCGCTAATGACGTAGAACATGATAAC[A/G]AAGGAAGGTGGCATATTAAGTACAGGCATCCGGACAGTGGATACGGCCATGACAAGTCCCAAGCAATCCTCCCATACCGAAGCCT
82914 C T ATCGATATTATCGCTAATGACGTAGAACATGATAACAAAGGAAGGTGGCATATTAAGTACAGGCATCCGGACAGTGGATACGGCCATGACAAGTCCCAAG[C/T]AATCCTCCCATACCGAAGCCTGCCTCACGCACCAACATTATTTTTCTTCGGTGATGGTGTATCAGACTTGTCAGCTGCACGACATGC
82942 G A ACAGAAATCAGCCATCCCTTCTACGGCTACACAAAACCAACTAAACTCTAGCAAGCCGTCTGACTTCCGTCCCGAGTCCCCGCCTCATTCATACTAACCT[G/A]TGCCGGACAGTCAAGCACAATCGAAAACTTCCCAACCGGCGCAGGAGGCAATGAATGACGTAGGCGGTTCTCAACTAGTGGTATCCA
82946 G A TTCAGCTCACCATCGAGCTCGTCCTTCCACCCGTCTAAGTCGTTCGACTTGGAACCATCGCCGTGAACCCGGCCGAGCTCCGAAAGTAGAGTTTCGAGTA[G/A]CGAGTTCGAGGTGACGAGACGTCGATTTAAATCAGAAACTTGAGCTAGAGCGTGGGTGAGCTCGGTTTGGGTGGAGTTCAGGCTA
82946 G A CGAGCTCGTCCTTCCACCCGTCTAAGTCGTTCGACTTGGAACCATCGCCGTGAACCCGGCCGAGCTCCGAAAGTAGAGTTTCGAGTAGCGAGTTCGAGGT[G/A]ACGAGACGTCGATTTAAATCAGAAACTTGAGCTAGAGCGTGGGTGAGCTCGGTTTGGGTGGAGTTCAGGCTAGTGGTGTACTGCA
82956 A G CCTTAGTTCTTGATATGCAGCGTAATACTGTGGATATCTGCCTCCTGCTCCTCCAAACGCATCTTGCCATGTGTCAATGAGAACCAATATTTTTTCTCTT[A/G]CATTTAGGTCTGGCTTTTTCTTTACTACTTTAACCATATCATGCAAGATATCACGTTCGACGATTTGCAAGTGGACAATCTCTCCACAATT
82956 A G ACGTTCGACGATTTGCAAGTGGACAATCTCTCCACAATTTTTGCTTAACGTCTCTAGAACAAAGAGAGCAAGGAGCTGTATTTTGGGATCTTTACTTCCT[A/G]TCCGCTTCTTCAGAACCTTGAGGGCCTCCTTTGCTTGACTAGGATCACTGTTAATAATATCGCATAGCTCGATATTTATAGCCCAATCG
82958 T C TTTTTTTTTTTTTTACCATCAATACTATTTCACTCAGATTCCATCAATACATTTACAAATTCAACTATTCTTTACAGTTCTTGATTAGAAGAGCATCAAC[T/C]AAGTACAAACACAAACTAGCAGCATACAACGACAGCGAATCAATGCAAATCAGCTTTGTTTCCATACTGATGCCCGTAAATGACATTGAAA
82958 A C TTCACTCAGATTCCATCAATACATTTACAAATTCAACTATTCTTTACAGTTCTTGATTAGAAGAGCATCAACTAAGTACAAACACAAACTAGCAGCATAC[A/C]ACGACAGCGAATCAATGCAAATCAGCTTTGTTTCCATACTGATGCCCGTAAATGACATTGAAAGGATAGTAGTTTACACACCAAAGTAA
82958 T C AATTCAACTATTCTTTACAGTTCTTGATTAGAAGAGCATCAACTAAGTACAAACACAAACTAGCAGCATACAACGACAGCGAATCAATGCAAATCAGCTT[T/C]GTTTCCATACTGATGCCCGTAAATGACATTGAAAGGATAGTAGTTTACACACCAAAGTAAATAACCACTGGACATAGATGCCTATATA
82958 T C TATTCTTTACAGTTCTTGATTAGAAGAGCATCAACTAAGTACAAACACAAACTAGCAGCATACAACGACAGCGAATCAATGCAAATCAGCTTTGTTTCCA[T/C]ACTGATGCCCGTAAATGACATTGAAAGGATAGTAGTTTACACACCAAAGTAAATAACCACTGGACATAGATGCCTATATATAAAAGTA
82958 A G ATCAACTAAGTACAAACACAAACTAGCAGCATACAACGACAGCGAATCAATGCAAATCAGCTTTGTTTCCATACTGATGCCCGTAAATGACATTGAAAGG[A/G]TAGTAGTTTACACACCAAAGTAAATAACCACTGGACATAGATGCCTATATATAAAAGTACACACTGCTTTGTACGAAGCACGGTAGT
82958 GA G AGCGAATCAATGCAAATCAGCTTTGTTTCCATACTGATGCCCGTAAATGACATTGAAAGGATAGTAGTTTACACACCAAAGTAAATAACCACTGGACATA[GA/G]ATGCCTATATATAAAAGTACACACTGCTTTGTACGAAGCACGGTAGTGCCTATGCCTGCAAAACATTATTTATCACGGGAAAACCTC
82958 A G CTGATGCCCGTAAATGACATTGAAAGGATAGTAGTTTACACACCAAAGTAAATAACCACTGGACATAGATGCCTATATATAAAAGTACACACTGCTTTGT[A/G]CGAAGCACGGTAGTGCCTATGCCTGCAAAACATTATTTATCACGGGAAAACCTCTTCTTTGCATATTGGACAAGCCTTGTTGCTCTTC
82958 A AGTGCAACAGTAGTTTACACACCAAAGTAAATAACCACTGGACATAGATGCCTATATATAAAAGTACACACTGCTTTGTACGAAGCACGGTAGTGCCTATGCCTGCAA[A/AGTGCAAC]ACATTATTTATCACGGGAAAACCTCTTCTTTGCATATTGGACAAGCCTTGTTGCTCTTCAGCCATTTGGAAATGCAGATAG
82958 T C TTTGTACGAAGCACGGTAGTGCCTATGCCTGCAAAACATTATTTATCACGGGAAAACCTCTTCTTTGCATATTGGACAAGCCTTGTTGCTCTTCAGCCAT[T/C]TGGAAATGCAGATAGAGTGGTACTGGTGTTGACACGGCAAATCGATTAGTTTGTCCCGATGTTCGTAAGCAGCTAGGCAAATCACACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
82960 CTA C AGAGGGCGCCTGAGCAGCCATTTAAGCATCTAACAACAAGATACAATTATGAAGTATAATTTAGGTGGAGAAGAAGAGGAGAGGACTTAATATGACCTAG[CTA/C]TATATATGTAAGAGTTACAGATATAAGTAGGAAAGAAGAAAGAATGAGAAACAACAACTACTTATAAGTTATAAAATAGGTGT
82992 T C ACTTGTGTGCCATACATGCCAAACGCGTTACAGTTATGCAAAAGGACATTCAGCTGGCGAGGAGGATCGGTGGCTCACGACATTTTTCGTGATTCGATAT[T/C]GGCATTAGTTACTAATTAACTTGTGTTTTGCTTCTACCTAATTCTTTAACTAGCTGAAACTCTCACTGTTTGTTTACATATTATTCTGGT
82992 A ACT AGGAGGATCGGTGGCTCACGACATTTTTCGTGATTCGATATTGGCATTAGTTACTAATTAACTTGTGTTTTGCTTCTACCTAATTCTTTAACTAGCTGAA[A/ACT]CTCTCACTGTTTGTTTACATATTATTCTGGTGTATTCACGTCTAATCAGCATTTTAAGCAATGTTATTAGCTTTATTGTTTGTTTTATACT
83006 C G AGTTCCAGGAGCTTCCGCTTTCTACTCCAGTCGCACCCTCTTCTCCCCCGCTTCGCATCGCCCTCGTTTCGCTCCATTTCAGTTTCGCAGGATATCTATG[C/G]CCGTTGCATCGGTTTCATCGTCCAAAACTGATAAAGACATTCCTGTTTATAAACCCACTCCTGCAAATCGATCGTTACGAACTCCTCATAG
83022 G A TATACCACCACAAAGGGCTCCAAATCCAGTAGCAAGAACTACACCATGCGGACTCTTGGAATATTTAAATGAGATTCCACCCAAATGAGCTGCTCCAAGC[G/A]CAGCCCCAACCATGGCGAACTTCCTCGACTCACGTATTGCTTTTAACTGAGGGCCGTATATCGGATCTGAAGCAATGAACTCCTCCA
83022 GT G ACGTATTGCTTTTAACTGAGGGCCGTATATCGGATCTGAAGCAATGAACTCCTCCACGTCAGCATCGGTCCACTTCGGGAGGGGCTTTTTCCAGCCGAGG[GT/G]TTTTTTTGTAATAATCTAGGAAGGAGAGGTTAGATTTCCAGTGATCTTTCACGTCTTCGAAGTGCCTCTTAACAAAACTTAGAATTT
83026 C G AGCTGTCAACAAATAACATCCAAGACAGGGTTTTAACACAGATTATTAAAGCCTAAATATGATCAAAGATGCAAGTTAATAC[C/G]ACAAAGTAAGGGAAGTTATAATCACATGTGTTGCTCGATTTTCTTGGGCAACTCATCCTTGCGAGCGCCAACGATTTTGTCGACTATGGTGCCATCCTTC
83026 C T ACATGTGTTGCTCGATTTTCTTGGGCAACTCATCCTTGCGAGCGCCAACGATTTTGTCGACTATGGTGCCATCCTTCATGAATATAAATGTAGGCATTGC[C/T]TCTATCGCCCAGTCCTGTGCCACTGTCTTCAGCTCGTCAACGTCAACCTTTAGAAACATAACATTAGTGAACTTTCTAGCAAGCTCGGA
83072 G T TCTCCGGCTTAACCCTGACCGGCACGGTCATTGCCCTAACCGTCACGTTTCCGCTCTTCGTAATCTTCAGCCCTGTTCTCGTCCCTGCTGCCATCCTGCT[G/T]GGCTTGGCCCTTACAGGGTTTCTGGGCTCTGGGGCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCA
83072 T C CGGCTTAACCCTGACCGGCACGGTCATTGCCCTAACCGTCACGTTTCCGCTCTTCGTAATCTTCAGCCCTGTTCTCGTCCCTGCTGCCATCCTGCTGGGC[T/C]TGGCCCTTACAGGGTTTCTGGGCTCTGGGGCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCACGA
83072 C A TAACCCTGACCGGCACGGTCATTGCCCTAACCGTCACGTTTCCGCTCTTCGTAATCTTCAGCCCTGTTCTCGTCCCTGCTGCCATCCTGCTGGGCTTGGC[C/A]CTTACAGGGTTTCTGGGCTCTGGGGCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCACGATATTCT
83072 T C CCCTGACCGGCACGGTCATTGCCCTAACCGTCACGTTTCCGCTCTTCGTAATCTTCAGCCCTGTTCTCGTCCCTGCTGCCATCCTGCTGGGCTTGGCCCT[T/C]ACAGGGTTTCTGGGCTCTGGGGCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCACGATATTCTCTG
83072 G A CCCTAACCGTCACGTTTCCGCTCTTCGTAATCTTCAGCCCTGTTCTCGTCCCTGCTGCCATCCTGCTGGGCTTGGCCCTTACAGGGTTTCTGGGCTCTGG[G/A]GCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCACGATATTCTCTGCGGAGAATTTGGAGAGGATC
83072 C T GTCCCTGCTGCCATCCTGCTGGGCTTGGCCCTTACAGGGTTTCTGGGCTCTGGGGCCATGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGA[C/T]GCTCGGCACGATATTCTCTGCGGAGAATTTGGAGAGGATCAAAAGGAAGATGGCTGAGGCAGCTGGGCAGGTCGAACAGCAGAC
83072 G A TGGGCCTCACCGGCGTCACGGCCTTTTCATGGGTGTTGAGGACGCTCGGCACGATATTCTCTGCGGAGAATTTGGAGAGGATCAAAAGGAAGATGGCTGA[G/A]GCAGCTGGGCAGGTCGAACAGCAGACCAAGGATGTTGGGCAGGGGATTCGATCCAGGGCTCATGACTTTTCTAGAACTTAAATT
83110 G A ATGTTAAAATGATGCCTTCTACTGCACACTCACTATTTATTGAACGCATTGCACAAAATACAACAGGGAATGTTTCTGATTGCAATACGAAAATACTTCT[G/A]CATTAATTTGCTATAACTCCCTACCAAACAATGGCCTCAAGGCTTAGCAGTTTAAGCGCTTTAACAGGCAATGTGTTTACCATAGATTCA
83110 A G AAAATGATGCCTTCTACTGCACACTCACTATTTATTGAACGCATTGCACAAAATACAACAGGGAATGTTTCTGATTGCAATACGAAAATACTTCTGCATT[A/G]ATTTGCTATAACTCCCTACCAAACAATGGCCTCAAGGCTTAGCAGTTTAAGCGCTTTAACAGGCAATGTGTTTACCATAGATTCACCTCG
83110 A T AAATACTTCTGCATTAATTTGCTATAACTCCCTACCAAACAATGGCCTCAAGGCTTAGCAGTTTAAGCGCTTTAACAGGCAATGTGTTTACCATAGATTC[A/T]CCTCGACCTAAACTGCATAAAATGAGTTAACTTTCCATGCAGGAAAATTTATGTTACCAGTAAGCTG
83120 C G ATCCTATTTACTCAGCAAGTAAGGGTGGTGTTGTTTTGTTCACTAGATCATGCGCTTTATTAGC[C/G]CGTCACGGCATCCGAATCAATGCCCTTTGCCCTGAGTTTGTGAATACCGACTCCGTAGGCGAGAAATATCTTCCTCATGTGAATATGGTTGGAGGCTTTT
83120 C G ATCCTATTTACTCAGCAAGTAAGGGTGGTGTTGTTTTGTTCACTAGATCATGCGCTTTATTAGCCCGT[C/G]ACGGCATCCGAATCAATGCCCTTTGCCCTGAGTTTGTGAATACCGACTCCGTAGGCGAGAAATATCTTCCTCATGTGAATATGGTTGGAGGCTTTTTGCC
83120 C A ATCCTATTTACTCAGCAAGTAAGGGTGGTGTTGTTTTGTTCACTAGATCATGCGCTTTATTAGCCCGTCA[C/A]GGCATCCGAATCAATGCCCTTTGCCCTGAGTTTGTGAATACCGACTCCGTAGGCGAGAAATATCTTCCTCATGTGAATATGGTTGGAGGCTTTTTGCCTA
83120 G A GGTGGTGTTGTTTTGTTCACTAGATCATGCGCTTTATTAGCCCGTCACGGCATCCGAATCAATGCCCTTTGCCCTGAGTTTGTGAATACCGACTCCGTAG[G/A]CGAGAAATATCTTCCTCATGTGAATATGGTTGGAGGCTTTTTGCCTATGGAGACTATTGTACAGGGAGCATTGGAGCTTATAACAGAT
83120 C CA AACGAAGGCTGGTGCATGTCTATGGATCACCAACCGTAGAGGCATGGAATACTGGCCATCTCCGGAAGAGGAGGAGAAGATACTTGGAGATTTAAAACCC[C/CA]AAAATGAGAATTTACTGTTCCTACAAGATGGTGTTAATTTAGTCTGTTGTTTTGAATTTTATAAGTTATGCTACTTTTCCTGTAATA
83120 A G GCATGGAATACTGGCCATCTCCGGAAGAGGAGGAGAAGATACTTGGAGATTTAAAACCCCAAAATGAGAATTTACTGTTCCTACAAGATGGTGTTAATTT[A/G]GTCTGTTGTTTTGAATTTTATAAGTTATGCTACTTTTCCTGTAATAAGCTGAGGACTTTACTGTTCTCACAAATAAAATGAGTGTTTG
83122 T C TGGAAAAGTTCAAGCAACTTCAACAAGAGCAACAAGAAAAGAAAACTAGTGAATCTAAACCAGCCACCTCATCAGGTGTAAAGCCTGTTATAATTGCCAA[T/C]AAGAGACCTTTTGAGGTAAAAGCTAACAACAAAAACACAAATAGTACCCTGTCTTCTGGTGGGAAATTAGCTTTTAGCTTGAAGTCA
83130 A C AACTAAATGAGGTCAATGGAGACACCGTGTTCATGACTGGAAACTTCACAGAGTTTAAAGTTGATAATCAAGTCAGCGAGTCATGGAATGAACAAAATGC[A/C]ATGACGAATACCGCAGATTTTCTGGCGAATTTTGAGGCTTCAGCTGCAGCAAATTCATCTGCTAATTCTGATCTCCAACTGGCTATT
83130 A G AGCAGCAGCAGCGTCAGCAGACGCAACAACCCCAACAACATTCAGCAGCAAGTGGTCACTCCAGGCTTGTTACAGGTCCCCAGGTTTCAAGGACCTCCCA[A/G]CATGCTTCACAAAAGAATGAGACAAAGAAAGAGAAGTGCAGCATAATGTAGAAACTGTTGAGAACCTTTAAGATGTTT
83136 T C AAGAAAGAATACCGTTGTTAACTCCACACAAGGTCGGAAGATTTGAACTCTCTCACAGAGTGGTACTGGCGCCATTGACAAGATCGAGATCTTATGGATT[T/C]GTTCCTCAGCCACATGCCATTAAATACTACTCTCAAAGAGCTACCAAAGGCGGTCTAATGCTCACGGAAGGAACTGGGCCGTCGGA
83136 G A CGAGATCTTATGGATTTGTTCCTCAGCCACATGCCATTAAATACTACTCTCAAAGAGCTACCAAAGGCGGTCTAATGCTCACGGAAGGAACTGGGCCGTC[G/A]GAGACTTCAATAGGGTATCCAAATACGCCTGGAATATGGACAAAGGAGCAAGTGGAAGCATGGAAGCCGATTGTGAAAGCGGTTC
83136 A C CTACTCTCAAAGAGCTACCAAAGGCGGTCTAATGCTCACGGAAGGAACTGGGCCGTCGGAGACTTCAATAGGGTATCCAAATACGCCTGGAATATGGACA[A/C]AGGAGCAAGTGGAAGCATGGAAGCCGATTGTGAAAGCGGTTCACGACAAGGGGGCCATCTTCCTTTGTCAACTCTGGCACGTAG
83144 AG A AGGTGAGTGGAGTCAGGCTATGGACGGGATCGGAATCTAGGGACAGAATGTCGACAGAGGATAAAGTGGCGACGGCGATAGTGCGGGAGAAAGGGGAGGG[AG/A]GGGGGGAGGAAGCGGACGGATTGGATTGGTTTTGATTGAGGAAGGCTGTAAAAATTGGAGGTTGACATTGCTTAATGTT
83230 G A ATTGTGTTCGAGAACAAGGAGAATATTGTTCAGTCTTGGCATATTGATGGTTACTCCTTCTGGGTTGTAGGAATGGATGGAGGAACATGGAGTGCAGCAA[G/A]TAGAAACAACTACAATCTGATTGATGCAGTGAGTCGTTGCACGACTCAGGTGTATCCTAACTCGTGGACGGCGATATACATATCAC
83230 C G ATCTTGGGCAGCAGTTCTATCTGAGAGTATATTCGCCTGTGGAGTCGATCAGGGATGAGTATCCGATACCTATCAATGCTTTACGTTGTGGCAGAGCTTC[C/G]GGCAGAAGGACTAGGCCATTTTGAAATTGCCTGGTAGCAGAGTGCTTCAGGGACATCAACTTGATGTAACCATTAATGCTTGCTTGA
83250 C T AGTATTTGCTAAAATCTGGGGGTCTTGAACGTGAGAGCGAGTACCCATATACTGGAACTGACCGTGGCACTTGTAAATTTGATAAGTCTAAGATTGCTGC[C/T]GCAGTATCTAACTACAGCGTCGTCTCTATTGATGAAGATCAAATTGCTGCTAATCTTGTCAAGCATGGGCCTCTTGCAATCGGTATCA
83250 A G TGCTAAAATCTGGGGGTCTTGAACGTGAGAGCGAGTACCCATATACTGGAACTGACCGTGGCACTTGTAAATTTGATAAGTCTAAGATTGCTGCCGCAGT[A/G]TCTAACTACAGCGTCGTCTCTATTGATGAAGATCAAATTGCTGCTAATCTTGTCAAGCATGGGCCTCTTGCAATCGGTATCAATGCG
83252 C CA GGAATGTGCCATCTGAAATCACGATTGCAACAATGTCTCTTTCTTCCAACATTCTTTCTTCTTCGTATTTCGCTCTCACTGAATCTAAGGTTTCTAACCC[C/CA]AATTAAAGTTGCTTGTTTCTTCTAAAGTCCCAACAGTTACTTCCCATCCTCTCTTGGATGTATCCATTAGAGCTGATTGGAGCGAGGCAT
83266 T C ACAAGACATATAGAAAGAGAGCGATAGCAATGGCAGCAGCAGCTCTGTCCACCAGCTTAACCTTCTCAAACCCACCCAAAACACCTT[T/C]AAGTTCAACCCATCACAACAAACGCGGCCTTTCCTTCAACCTAAAGCTAACGGGTCGAACACTTAGCATCAACGGACCCGTTAGGAGCACGCCAAGCGAA
83266 A G ACAAGACATATAGAAAGAGAGCGATAGCAATGGCAGCAGCAGCTCTGTCCACCAGCTTAACCTTCTCAAACCCACCCAAAACACCTTTAAGTTCAACCC[A/G]TCACAACAAACGCGGCCTTTCCTTCAACCTAAAGCTAACGGGTCGAACACTTAGCATCAACGGACCCGTTAGGAGCACGCCAAGCGA
83266 T A CCAGCTTAACCTTCTCAAACCCACCCAAAACACCTTTAAGTTCAACCCATCACAACAAACGCGGCCTTTCCTTCAACCTAAAGCTAACGGGTCGAACACT[T/A]AGCATCAACGGACCCGTTAGGAGCACGCCAAGCGAAATCGCGACCAGAGTGGAAGAGAGCATAGAGAAGGCAAAGGAGACATGCTC
83266 G A ACGTAGACAGCGGCGAATGCGCCGCTGCATGGGACGAGGTAGAAGAGTTGAGTGCTGCTGCGAGCCATGCCAAACTGAAGGCAAAAGGCAACGAGGATCC[G/A]TTAGAGGCTTACTGCAAGGATAATCCCGAAACGAATGAATGCAGGATTTATGAAGATTGAGTTCGTATTCCTTTTGCTTTTGCA
83292 T C ACATCCGCCACCGGCACACCCCACTCCGCCTCGCCATCGCCCTCATCGCTTCCGTACACGAAACTCAAATTGGATCTCATCCTCTTCAGCGAAAGCCCCT[T/C]CGCTTTATTACGGCCCTTCTTCGTTCCATCGGTTTTCCGACAAGCTCTCTTGCAGATTCCGAGCGGTAGCCTTACCGCGATGCTAAGGA
83292 T C CCGAGCGGTAGCCTTACCGCGATGCTAAGGAACAGGTCTATAAGGCCGCAGGGGCACAAGCAGCAGATGGCCGCGCAGCCGGCCGCGGCGCTTCCGGCGA[T/C]CTCGCTGGTCGAGGGTTGGGCGCGAGTTCGCGATCCGGTTGATGGCGTCATCGGTGAGGATTTCGAGATCGGCTTCGTTGATT
83292 T A GAGCGGTAGCCTTACCGCGATGCTAAGGAACAGGTCTATAAGGCCGCAGGGGCACAAGCAGCAGATGGCCGCGCAGCCGGCCGCGGCGCTTCCGGCGATC[T/A]CGCTGGTCGAGGGTTGGGCGCGAGTTCGCGATCCGGTTGATGGCGTCATCGGTGAGGATTTCGAGATCGGCTTCGTTGATTAT
83338 A T TTTAGTAAATTTCATCAAAAAAATACCAGTAGCAAAAATATGGCAGCAATGGCGAAGAGCTTGCTCTCTCTCATCTTTGTCCTCCTCCTC[A/T]TCTTCTTCTCCGCCACTGAGGCGAGGACGTGTTTATCGCAGAGCCACAACTTCAAAGGGCCGTGCTTCAGACGCAGCAACTGCGCCAACGTCTGCCGT
83338 C T TTAGTAAATTTCATCAAAAAAATACCAGTAGCAAAAATATGGCAGCAATGGCGAAGAGCTTGCTCTCTCTCATCTTTGTCCTCCTCCTCATCTTCTTCTC[C/T]GCCACTGAGGCGAGGACGTGTTTATCGCAGAGCCACAACTTCAAAGGGCCGTGCTTCAGACGCAGCAACTGCGCCAACGTCTGCCGTA
83338 C T AAAGGGCCGTGCTTCAGACGCAGCAACTGCGCCAACGTCTGCCGTACCGAGGGATTTCCTGGCGGCGAGTGCAGAGGATTTCGCCGTAGATGCTTCTGCG[C/T]CAAGAAGTGTTAATGTTTCATTTCTTGACACTGCTGCTTCAGTTGATTGTTATTGCTACTATTATCAGTATCCTCCTTGCTACTGAGT
83338 T C CAACTGCGCCAACGTCTGCCGTACCGAGGGATTTCCTGGCGGCGAGTGCAGAGGATTTCGCCGTAGATGCTTCTGCGCCAAGAAGTGTTAATGTTTCATT[T/C]CTTGACACTGCTGCTTCAGTTGATTGTTATTGCTACTATTATCAGTATCCTCCTTGCTACTGAGTTTAGTGTGCTTGATTATGTGTGGA
83338 C T AACTGCGCCAACGTCTGCCGTACCGAGGGATTTCCTGGCGGCGAGTGCAGAGGATTTCGCCGTAGATGCTTCTGCGCCAAGAAGTGTTAATGTTTCATTT[C/T]TTGACACTGCTGCTTCAGTTGATTGTTATTGCTACTATTATCAGTATCCTCCTTGCTACTGAGTTTAGTGTGCTTGATTATGTGTGGAT
83338 T C CAACGTCTGCCGTACCGAGGGATTTCCTGGCGGCGAGTGCAGAGGATTTCGCCGTAGATGCTTCTGCGCCAAGAAGTGTTAATGTTTCATTTCTTGACAC[T/C]GCTGCTTCAGTTGATTGTTATTGCTACTATTATCAGTATCCTCCTTGCTACTGAGTTTAGTGTGCTTGATTATGTGTGGATGTGTTCCC
83370 TA T TTAAGGTCGAATCCAAATCTCTCTCTCTCTCCCCACAAAATTAGTTCTTCTCCTTAAAATCAGAAAATTTCTCAAAACCCTCTTTAATGGCCACCGAAAG[TA/T]AAAAATCCAATCTTTTCACCCAAATCTCGCATTCATGACCACCGTGCCTCAGATTTGACTGGCCATCGAGCCTCTCTGTTGTTCCGAATC
83370 A G CTCTCTCCCCACAAAATTAGTTCTTCTCCTTAAAATCAGAAAATTTCTCAAAACCCTCTTTAATGGCCACCGAAAGTAAAAATCCAATCTTTTCACCCAA[A/G]TCTCGCATTCATGACCACCGTGCCTCAGATTTGACTGGCCATCGAGCCTCTCTGTTGTTCCGAATCATTGAAAACGCCAACACGTCGCGA
83370 G C TCCGCTTTGTCGCCATTGCTCTTTTGAAGCGAAGCCACAACAGAAAATCGCTCCAATACTGCGGCAGTAGACCCGAGTGTTACAGATTTAGAGATTACAG[G/C]TCAGGATTCAAAGATTGGCAAAGCTGGGTATTTGGAAGACGCGCACTCTGATGTTTACAAAACA
83370 C T CGCTTTGTCGCCATTGCTCTTTTGAAGCGAAGCCACAACAGAAAATCGCTCCAATACTGCGGCAGTAGACCCGAGTGTTACAGATTTAGAGATTACAGGT[C/T]AGGATTCAAAGATTGGCAAAGCTGGGTATTTGGAAGACGCGCACTCTGATGTTTACAAAACA
83376 G A GTCTGACCACAAAACGTCCATTCTTGTCAGGGTATACAAAAGCAAAAGAAAGCTTAGCATCTCTTCTTCTAGCAGCCGGCGCAACTTCTTTCACAAGGTC[G/A]GTAAGCTCTCTAAGTGTGGCATCCTTCCATGTATATATCTGGACCTCGTCTTTAGGCTCTTTCCCTCTCACGGCAAAGTCCTGATTTAA
83376 T A CAAAAGCAAAAGAAAGCTTAGCATCTCTTCTTCTAGCAGCCGGCGCAACTTCTTTCACAAGGTCGGTAAGCTCTCTAAGTGTGGCATCCTTCCATGTATA[T/A]ATCTGGACCTCGTCTTTAGGCTCTTTCCCTCTCACGGCAAAGTCCTGATTTAAGTGATGACCGCCAGTCTTAGTGAAAACACGAAGCAG
83376 A G CTTCTTTCACAAGGTCGGTAAGCTCTCTAAGTGTGGCATCCTTCCATGTATATATCTGGACCTCGTCTTTAGGCTCTTTCCCTCTCACGGCAAAGTCCTG[A/G]TTTAAGTGATGACCGCCAGTCTTAGTGAAAACACGAAGCAGCAGGGGACATGTCTTCTCGCGATCTACGGGCAGAGCACGAGTACGG
83382 C T TGTTTCTTCATGCATGACTTTGTTTGGGTTCGTTTGGGTTACAAATTGATGAAGTTTGAGGTAGAAAATTGAACACAGTGAAACGTTTTGGTATCGGATG[C/T]TCAGGATATCATAGTGGTATTTATATGAGAACGAGATTGGAGATAAGGCCGATGTCGAGTCAGTAGGTCTGCGGCTACGTATTCCCC
83382 A G TTCATGCATGACTTTGTTTGGGTTCGTTTGGGTTACAAATTGATGAAGTTTGAGGTAGAAAATTGAACACAGTGAAACGTTTTGGTATCGGATGCTCAGG[A/G]TATCATAGTGGTATTTATATGAGAACGAGATTGGAGATAAGGCCGATGTCGAGTCAGTAGGTCTGCGGCTACGTATTCCCCGTTCAT
83382 G C TGTACAGTGATGGTTGAGGCTTCAGACATGAATTGTCTTTTCAACAGGTGTGCTATTGCTTGGTAGAGTAGATTAGGCATACAGTTTTGAGAGTAGTCTC[G/C]TTGCAAAGTGTTGTTATTCATCAACAATAGTGATGTTGAAAATCTGCAGAAGCAACATGTGCTGGATTGATGTATGGGGAGTCTACG
83386 G T TTCCATCGACAGTGTCACGCTGAGGGTTGAACTCGACCACATCGGCACCTACGACATCGCCTTGTAAGTTGTGCAAGATGTTTAGAACATCACGAAAGGA[G/T]AGACCTCCAGGCTCGATATGCGACACACCTGGAGCGAATGCAGGATCGAGGCAGTCTACATCTACTGATATGTACACTCCTTTCGC
83386 T A CTCCAGGCTCGATATGCGACACACCTGGAGCGAATGCAGGATCGAGGCAGTCTACATCTACTGATATGTACACTCCTTTCGCTCCCTCTCCTAGTTTCAG[T/A]TTCTCTAAATTGTGACGATCTCCTGAAAATGTACGCATTTCATATTGCTCCACGCCAAATCTCTTCCCCTGTTCTCGTCCTTCGTCAGTA
83388 A G CTCTATGATCGACATAAGCCACGACTTCCTTGGACACACCCGTCGACTGTAGTTTGCTTTCGAACGTTTCGAACAGATTCCTGGCCACACTGAAGCACGA[A/G]ATAAGATCATGGACGTTCATCTTGGAGCTCTCGCTGAGCTCGTGATTTTCTCAGTTGAACATTTCCGATATGGATGATCGGATCGAGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
83390 C CTAATCAG AACGAACGTCAGTTTTGGGTTCAATGTTGAAAAGGAGGAACAGTTTAAGGATTTTGATCCTGCAGATTTTATGCTCGATAGTTTGGTGCCTTGCCTATAG[C/CTAATCAG]TAATCAGTAAGACAAGTAATTCGTGAGTAAATTTTGGTATTAAATTAAATTAAATAGTGGCATAGTTTTGGCAGAGAGTTT
83390 T G GTATTAAATTAAATTAAATAGTGGCATAGTTTTGGCAGAGAGTTTACTAGTGTTTCCCGGATATTACGCGTTTTAAATTATATTTGATGAGAGAAATTTT[T/G]GTCAATGTGCGTGAAAGTGTTTGCTTGATATAAACGTTTGTAATTGTGTAAAGCTTGGAGAAAATGTATTCAATAGCGATTTTATAAAA
83402 C T TCCGCCGCCACCGTATGTACCGCAGCCGCAGTATGCACAACCCCCGCCTCCTCAGCAGCAGCAGAGTAGCGGCTGCATGGAAGGATGCCTGGCTGCTTTG[C/T]GCTGTTGCTGCATCTTGGAAGCTTGCTGTGATTGAAGAAGAGAAAAGAAGTGGATGCATTTCAGTTTTTTTTAAAGCCTTCAACTG
83412 C T TCTCGGTCTCAGCTAAAGCGAACGATACGTCTATACAGGACGAACTCCAGAAGTACGGCCTACCACGCGGCCTGATCCCAGACGCAATCGAGTCACACTC[C/T]CTCGCACCGGACGGCAGCTTCAAAATCGGGCTCCGATCCACGTGCTACGTCCACTTCTCCCGACTCGTCTACTACGACAAGACGATT
83412 C T AGTACGGCCTACCACGCGGCCTGATCCCAGACGCAATCGAGTCACACTCCCTCGCACCGGACGGCAGCTTCAAAATCGGGCTCCGATCCACGTGCTACGT[C/T]CACTTCTCCCGACTCGTCTACTACGACAAGACGATTACCGGTAAAGTATCCTACGGCAAGATCACCGATCTGACCGGGATCCAAGC
83412 A C CACGCGGCCTGATCCCAGACGCAATCGAGTCACACTCCCTCGCACCGGACGGCAGCTTCAAAATCGGGCTCCGATCCACGTGCTACGTCCACTTCTCCCG[A/C]CTCGTCTACTACGACAAGACGATTACCGGTAAAGTATCCTACGGCAAGATCACCGATCTGACCGGGATCCAAGCCAAGAAGCTGTT
83414 A G ATGGACACAATTCAAAAGGGATCAGACCATGTTCCTTTCAAAAGGATTGAGCCATTCTCTTCTTGAACAAGTTACGGACAAAAGAAAGGTTGGCGGATGA[A/G]AACAAGTAAGGCGGTTCGAGGCAAAGACTGTTCGATGCATTTACTGTGTTGTCGCGGATTGAGGTTGGTCACGGTGCCATGGAGT
83436 C CGTAG CGCCACGCAAACACAATCCAATTCAGGCATGAAGTGCTCCTCTTTAGGGATGTTACTCCGTTGTTGAAGCCAACAGGGAAAATATAGATCAACGAGCATA[C/CGTAG]CTAGGCCCAGGTTCAGTAGAAATGAAGGCACCACACTGAAATCAGCAATGGAGACTATCTTTTACGGAGAATGGTCTACTTC
83452 G T TCCCCTCTCACCCCCTATACAAACCATGTCCCTTTTCGCCCGCGCTCCTTTGAACCCCAGAAACAAGGATGAGGTGCTAGGATCCAAGGCGAAGAACCAT[G/T]CTGGATCATCGAATGTAGTAAAGAAAACGCCGTCTCCAGCGTCGACCTCAAGTGACGAAGCCATAACGGTATCGCCTGTTAGGTCCT
83452 T C GGTGCTAGGATCCAAGGCGAAGAACCATGCTGGATCATCGAATGTAGTAAAGAAAACGCCGTCTCCAGCGTCGACCTCAAGTGACGAAGCCATAACGGTA[T/C]CGCCTGTTAGGTCCTTGTCAGAGGAGAAGGGAAGCGTTCTGTCGGGATTCATTGCTCGGTCTCCGCCAAAAGAGAAGGATAGTG
83466 T G AAATGAGGAAAAACACATCCCGACATATAGCTAAGGCACAATAACACCAGACATATCTTCATTTTCGTAAGAAAGAACAGAACTAGAAAGACGTGGAAAA[T/G]TGTTTAAATTCCATCCTGAATGGACATATTCATTCATACTGTTCGACAATGAAGTTGCTGCCTTAGGAAATCCACTACCAAACACCG
83466 T C GTGTAAATGAAAACGAGCGATCAACGATTTCGGTTGACAGAAAAATCCGAGATTTGATCGTACATAACACGAGGAAGAAGATGTTCCACTTTCCTGAAGA[T/C]CGGAAGACTGCGTTTTGAGGGAGGATTTCCCTTTGCGGGATCTAAAGGATCCAATTGTCTGAAATGCCAGAGGAAGAACTAGGGT
83486 A G TGCATCATCTCGACTGCGCAGCAGGCGAGACCAAAAGTCATGGGCCAGATCGAGCCTCTCCTGGCCCAGTTCATCAGATCGTCTACCTTGGATATCACGA[A/G]TTCCGCAGCTTTCGACAATCCAGCTGGAGAAGACGTCGCAGGAGGCGGAGCTCTCGAGTA
83532 CT C CTCTTGGACTAGAATACAACATGCACACTGTTATTGGCATAACCGTCCAAAGAAGAAGCACTGGACACTTTCACAACAGACGAAGGATTGGTTTTTTTAA[CT/C]TTTTCCAGTTTATATTTAATGCAACTTCTGCATTCGTGGATTAGTACATATTATGACAATTAGATGCATTCGTCGGTTCGTACGTCGA
83548 CGAAGAA C CAAGAGAACAAAACCTGCCCTTGTTCGATAATCCGAATCGAAGAAACTGATTACAAATATTCGCCGAATATTTGGCTGTCGAAGTAAGAGCGAGATTGGT[CGAAGAA/C]GAAGAAGAAGAAGAAGAAGAGACGGGTTTAGAAGAGAGAAGAGAACGCGGGAGAATAGAGGCGACAGTCGGCATGC
83556 A G TGTTGGTGAGAATAAGATATCATCCACCAGTTGAGAAAAGTAGCAATTAACAAATAGCAGTGGGTGTATAGGAGCAAAAAATGATGGTTTGTTTGGAGAA[A/G]TGTTAACGGATTGAAGCTGGGTACAGAGCACAGCAGTCCGTTGTCCATCCACCGCTGAGAGAAAGGAGTTTTCGCTGCTCTGTGA
83564 A AG CCAAAGACAAGTGAGAACTTCCGTGCCCTGTGCACTGGTGAGAAAGGATTTGGATTCAAGGGAAGCAAGTTCCACCGCATCATTCCAGGGTTTATGTGTC[A/AG]GGGGGCGACTTTACGAGGGGGAGTGGAACCGGTGGCAAGTCTATCTACGGTGAGAAGTTTGCTGATGAGAACTTCACCTTGAA
83564 A G GTGCCCTGTGCACTGGTGAGAAAGGATTTGGATTCAAGGGAAGCAAGTTCCACCGCATCATTCCAGGGTTTATGTGTCAGGGGGCGACTTTACGAGGGGG[A/G]GTGGAACCGGTGGCAAGTCTATCTACGGTGAGAAGTTTGCTGATGAGAACTTCACCTTGAAGCGCACTGGACCCGGTATTCTAT
83564 AG A GTGCCCTGTGCACTGGTGAGAAAGGATTTGGATTCAAGGGAAGCAAGTTCCACCGCATCATTCCAGGGTTTATGTGTCAGGGGGCGACTTTACGAGGGGG[AG/A]GTGGAACCGGTGGCAAGTCTATCTACGGTGAGAAGTTTGCTGATGAGAACTTCACCTTGAAGCGCACTGGACCCGGTATTCTA
83564 G A AGGGTTTATGTGTCAGGGGGCGACTTTACGAGGGGGAGTGGAACCGGTGGCAAGTCTATCTACGGTGAGAAGTTTGCTGATGAGAACTTCACCTTGAAGC[G/A]CACTGGACCCGGTATTCTATCTATGGCCAATGCTGGTAAGAACACCAATGGATCTCAATTCTTTCTGTGCACTGCTCAGACCGCTT
83582 T G AAAAAAGCTCCAAATTACAGAGCTTCCTAACCTTAACATAGTGGGGGCCGTAGTCAGCCCAAACCAGGTCCATCCCATCCCTACTGAACC[T/G]TGCCGTGGCTCTGTTCCGGGGCCTGTCGCTGAGAAAGTGGTCATTTGTTTTGAGCACCTCCTTGGCCATGTCTGGGCTAGACACCACCACGTTCAAG
83582 G A CCTTAACATAGTGGGGGCCGTAGTCAGCCCAAACCAGGTCCATCCCATCCCTACTGAACCTTGCCGTGGCTCTGTTCCGGGGCCTGTCGCTGAGAAAGTG[G/A]TCATTTGTTTTGAGCACCTCCTTGGCCATGTCTGGGCTAGACACCACCACGTTCAAGGTGGTGCCAAACCAGACTGACATGATAGG
83582 T C TTGTTTTGAGCACCTCCTTGGCCATGTCTGGGCTAGACACCACCACGTTCAAGGTGGTGCCAAACCAGACTGACATGATAGGGCCGTACTTCTGGGACCA[T/C]TCAGCAAAGCACCTGAACATGAGCGGTTTGACTTGGTAGAGGTTGCCTACTATTGGGTAGGGAGTTGGGCCGGGCGGTAGTTTTG
83582 G A CGTTCAAGGTGGTGCCAAACCAGACTGACATGATAGGGCCGTACTTCTGGGACCATTCAGCAAAGCACCTGAACATGAGCGGTTTGACTTGGTAGAGGTT[G/A]CCTACTATTGGGTAGGGAGTTGGGCCGGGCGGTAGTTTTGGTGACCGCAGTTTTCTGAGGAGGAGGAGGACTAGGAGGAGAGA
83582 C T TGATAGGGCCGTACTTCTGGGACCATTCAGCAAAGCACCTGAACATGAGCGGTTTGACTTGGTAGAGGTTGCCTACTATTGGGTAGGGAGTTGGGCCGGG[C/T]GGTAGTTTTGGTGACCGCAGTTTTCTGAGGAGGAGGAGGACTAGGAGGAGAGAGATGAAAAGCGTGATGATGGTTACTAGTGA
83582 T C GGCCGTACTTCTGGGACCATTCAGCAAAGCACCTGAACATGAGCGGTTTGACTTGGTAGAGGTTGCCTACTATTGGGTAGGGAGTTGGGCCGGGCGGTAG[T/C]TTTGGTGACCGCAGTTTTCTGAGGAGGAGGAGGACTAGGAGGAGAGAGATGAAAAGCGTGATGATGGTTACTAGTGAAGGGA
83582 G A GACCATTCAGCAAAGCACCTGAACATGAGCGGTTTGACTTGGTAGAGGTTGCCTACTATTGGGTAGGGAGTTGGGCCGGGCGGTAGTTTTGGTGACCGCA[G/A]TTTTCTGAGGAGGAGGAGGACTAGGAGGAGAGAGATGAAAAGCGTGATGATGGTTACTAGTGAAGGGAGGAGTTCCATTGATG
83616 G A TAGCTTTCCATCCTTTTACAAGTAAACACCTTTCATAGGTCTCATCCAAGATGATTGCACCAGTCACTGGAACGCGAAACTTGTATGAAGTGAAGTCCTT[G/A]TATATGTCATCAATATGAGCTTTGTACGGTTTCAATGCAGCACAGCTATTGAACATGAGAGAAGTAAATTCCCTAAATGAAAGAGATTT
83618 G GA AAATGATGATGGATTCGCAAGGCTTCCTGTCAAAAGAGCAGCAAACCGAGATCATGCATCACTGCAAGAAATCGAACCTAATATGGGTTGGGCTTCACAA[G/GA]CTGAGCCCTATACAGCCCAACCAAGTGGAAATGATGCTAGGGTACCCTGAAAATCACACAGAGGTCTTGAACTTGGCTGCAGCC
83652 C T ATTGAAGGCCTATGTTATGAGCATGGCTTCCTGCTACTAGGATTTTCTTCGCCTTCTTTGTAAGAGGGAGCAGAGGTACATTATGTTTTCCATTTTTCAA[C/T]AGCACAAGTGATTTCCTCACTGCTTCTCGGGCTAGTTCTCTATGTTCCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGG
83652 T C CTACTAGGATTTTCTTCGCCTTCTTTGTAAGAGGGAGCAGAGGTACATTATGTTTTCCATTTTTCAACAGCACAAGTGATTTCCTCACTGCTTCTCGGGC[T/C]AGTTCTCTATGTTCCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCA
83652 C T TAAGAGGGAGCAGAGGTACATTATGTTTTCCATTTTTCAACAGCACAAGTGATTTCCTCACTGCTTCTCGGGCTAGTTCTCTATGTTCCTTCTTCCCCAA[C/T]TGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTC
83652 C G GCACAAGTGATTTCCTCACTGCTTCTCGGGCTAGTTCTCTATGTTCCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAG[C/G]CCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGAT
83652 A G ATTTCCTCACTGCTTCTCGGGCTAGTTCTCTATGTTCCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGT[A/G]AACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAA
83652 T C CTCTATGTTCCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGAC[T/C]GCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATA
83652 G A CCTTCTTCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATT[G/A]ATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCA
83652 G A TCCCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCT[G/A]CCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCC
83652 C T CCCAACTGATTAGCCAAACTATAGTCAGACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGC[C/T]CATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCCAG
83652 A G GACATGGGGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCA[A/G]TAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATG
83652 C T GGTTTTCAAAAAGCCCCATTGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTT[C/T]AGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTT
83652 T C TGTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGT[T/C]CGTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTG
83652 C T GTAAACTTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTT[C/T]GTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTGA
83652 G C TTAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGT[G/C]GGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTGATTCTGT
83652 G A TAACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTG[G/A]GTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTGATTCTGTC
83652 G C AACCCGCAATATTCTTCTGACTGCATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGG[G/C]TTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTGATTCTGTCA
83652 T G CATCATTGATTCTGCCCATGGGGATGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAAT[T/G]CCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTTTATACCCGGAGGGTACGTGATTCTGTCAATACCTTCCCAGTCTGATATCAC
83652 C T TGACCTTTTTCTTGATCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAAC[C/T]GAGTATGTGTAGTTTATACCCGGAGGGTACGTGATTCTGTCAATACCTTCCCAGTCTGATATCACAAAGCCCCTGAATTT
83652 T C TCAATAGTTTCAGATCATTGAGAAATGGTTCGTAGTGGGTTGGGATCATAATCATATCAATTCCAGCATTAACTCCAGCTTGAACCGAGTATGTGTAGTT[T/C]ATACCCGGAGGGTACGTGATTCTGTCAATACCTTCCCAGTCTGATATCACAAAGCCCCTGAATTT
83654 CTAAGATTAGGGTTCAGATGTAAAATCGA
C AAAATGACCAGACTCGCCACCACACTATAGTCCAGAAGTGTCGGGAGAGTATGAGTGGGTTACAGAGTCTATAGCAATATGGACTAGATAATAGGAGGAG[C/CTAAGATTAGGGTTCAGATGTAAAATCGA]TAAGATTAGGGTTCAGATGTAAAATCGAAATTAGGGTTCAACAAACTGCCACGCAGA
83696 C T ACAATTAAGCATGTAGTAAAATTAAATAAAAATCACAAAATTCTCAGAACAAAAAACATATAAGCTAAATAGGTTCTCTCCTTAAAAACAAACAATTCAA[C/T]GAAACAAGTTGACAAAATACATGAAATACTGAAAAATTAAGAAGCAGCAGCTGCCTTGCCCTTCTTCTTTTGGAGCTTCTTCATGTAGA
83696 A G TAAAAATCACAAAATTCTCAGAACAAAAAACATATAAGCTAAATAGGTTCTCTCCTTAAAAACAAACAATTCAACGAAACAAGTTGACAAAATACATGAA[A/G]TACTGAAAAATTAAGAAGCAGCAGCTGCCTTGCCCTTCTTCTTTTGGAGCTTCTTCATGTAGAACTCAAGCTCTTTCCCTTCCAAAATA
83696 TA T AATTCTCAGAACAAAAAACATATAAGCTAAATAGGTTCTCTCCTTAAAAACAAACAATTCAACGAAACAAGTTGACAAAATACATGAAATACTGAAAAAT[TA/T]AAGAAGCAGCAGCTGCCTTGCCCTTCTTCTTTTGGAGCTTCTTCATGTAGAACTCAAGCTCTTTCCCTTCCAAAATATACCCATCAGCT
83696 A G ACAAAATACATGAAATACTGAAAAATTAAGAAGCAGCAGCTGCCTTGCCCTTCTTCTTTTGGAGCTTCTTCATGTAGAACTCAAGCTCTTTCCCTTCCAA[A/G]ATATACCCATCAGCTCTGCCGCATTGGCCAGGGCGAGAAGAGATGCATGCCAAAAGTCTACCGCTACCAAATTGCTCCTCAATATGAG
83696 G A AAAATTAAGAAGCAGCAGCTGCCTTGCCCTTCTTCTTTTGGAGCTTCTTCATGTAGAACTCAAGCTCTTTCCCTTCCAAAATATACCCATCAGCTCTGCC[G/A]CATTGGCCAGGGCGAGAAGAGATGCATGCCAAAAGTCTACCGCTACCAAATTGCTCCTCAATATGAGAATCAAGTGTGCGCTCCTTTTG
83696 T A CCTTCTTCTTTTGGAGCTTCTTCATGTAGAACTCAAGCTCTTTCCCTTCCAAAATATACCCATCAGCTCTGCCGCATTGGCCAGGGCGAGAAGAGATGCA[T/A]GCCAAAAGTCTACCGCTACCAAATTGCTCCTCAATATGAGAATCAAGTGTGCGCTCCTTTTGACGCTTCTCAAGCTTCCTTTTTACATGG
83696 C T TATACCCATCAGCTCTGCCGCATTGGCCAGGGCGAGAAGAGATGCATGCCAAAAGTCTACCGCTACCAAATTGCTCCTCAATATGAGAATCAAGTGTGCG[C/T]TCCTTTTGACGCTTCTCAAGCTTCCTTTTTACATGGTCACTTTTCTTCACTTCTGCCACTGGTTCACTCTCCTCAGTTGCAGTTGCTTCC
83706 AG A GGCACTGGTAGCTATCGGGGTAGGTGGTCGTTGTGTTAACACAGCACCAGGAAGGAGATGTAAAGGGGTTACTCACAGTGGTGACAGTGGTGATAGATCG[AG/A]GGCGGGTTCAGGTGATCTGACGTCGGTTGCGAGGAAATCATGGAGAAGTGGACACGGTGTACTGGTCAGTGGGTGGTGCAG
83706 T C GGTTACTCACAGTGGTGACAGTGGTGATAGATCGAGGCGGGTTCAGGTGATCTGACGTCGGTTGCGAGGAAATCATGGAGAAGTGGACACGGTGTACTGG[T/C]CAGTGGGTGGTGCAGTCAAGTGAAGGCCGATGGTTGGTGATAGATCGACGGGAAGTAAGGCGGGTCGACGGATGTATGGTTG
83706 TG T ACAGTGGTGACAGTGGTGATAGATCGAGGCGGGTTCAGGTGATCTGACGTCGGTTGCGAGGAAATCATGGAGAAGTGGACACGGTGTACTGGTCAGTGGG[TG/T]GGTGCAGTCAAGTGAAGGCCGATGGTTGGTGATAGATCGACGGGAAGTAAGGCGGGTCGACGGATGTATGGTTGCATGTA
83720 G A AAAAAAACTTGGCAACCCCTCTCTACCTCCATATGCTATGGCTATGGTGCTACCACCCTTCAATCCAACTGCTGCAGTGCCGCTTTGCCTTGATTTTAAG[G/A]TCATGCGCCGTTGTTGCCCTCGTCTGCTAAGCGATACTCTGCCAGTTTGCCCGATTCTTAATTGAAGAAGGAGGATCTGTTGTCGTCGA
83724 T G AAGTGTTGAAAGCAGTTGCTGCTGAAGCCGGTTGGATTGTTGAAGAAGATGGTACCACTTACCGTAGGGGATGCAAGCGGCCGCCTGCAGAAGAAAACGC[T/G]AGCAACAACGCCGTTATGGGCGGGCCATCGACAAACATAAGCCCAATGTCCTCCGCATATCCGAGTCCGGTGCCTTCGTACCAT
83724 C T CAGTTGCTGCTGAAGCCGGTTGGATTGTTGAAGAAGATGGTACCACTTACCGTAGGGGATGCAAGCGGCCGCCTGCAGAAGAAAACGCTAGCAACAACGC[C/T]GTTATGGGCGGGCCATCGACAAACATAAGCCCAATGTCCTCCGCATATCCGAGTCCGGTGCCTTCGTACCATGCGAGCCCGTCCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
83724 G A GCAAGCGGCCGCCTGCAGAAGAAAACGCTAGCAACAACGCCGTTATGGGCGGGCCATCGACAAACATAAGCCCAATGTCCTCCGCATATCCGAGTCCGGT[G/A]CCTTCGTACCATGCGAGCCCGTCCTCTTCTTCCTTTCCAAGCCCGACCCGCCATGAGAACCCAAACCCGAACCCTAATATCCCTCCG
83724 G C GGCCGCCTGCAGAAGAAAACGCTAGCAACAACGCCGTTATGGGCGGGCCATCGACAAACATAAGCCCAATGTCCTCCGCATATCCGAGTCCGGTGCCTTC[G/C]TACCATGCGAGCCCGTCCTCTTCTTCCTTTCCAAGCCCGACCCGCCATGAGAACCCAAACCCGAACCCTAATATCCCTCCGTCTTAC
83738 A G GCAGTGTTGAGAAAATACATCTTTATCCCCAATGACTTCACAAACCGGTCGAATTTAATCTTGTTAAGAACATCTTGTTCATTTAACCCTGGAAATTTCA[A/G]TCTCGACTCTAACCAATATTTGTAAAACTTGATTGTTCGATAGTTTGACTTCACGTAGATGAATCCTCCATTTGGTCTGTTGTTCTTATCT
83750 G A GTGCTAAAAATTTCCCCATGTCTTCTTCTTCAATAACAATCATTTCAATTCCAGTCAGCTTCTAGGAACGCCAGAATGGGCAAAAAGCAGCTAGATCCTA[G/A]TGCGACGGACAATCACCGGTTGCATTTCACCCTCATTTTTCTGCTTTTCATCTCTTGCTTTTTTGCCTATAAAACATTCTCAAATTTCATCC
83750 T C ATCCAAAACTCTTCCGAAATAGAATCAAACGTCGACAACTTTCAGAATAAACTACTTGGATCTTCAAATTTAGGGGAGTGCTGTAGAGGAATCGAGAATA[T/C]GGAGCTTTGGGGGTCAGCTGTGAAATGGGGCACGGACCATAAGTCCAATAATTCAAAAGATTGTTGTAATGCTTGTAAGAGTATGT
83750 C T AATAAACTACTTGGATCTTCAAATTTAGGGGAGTGCTGTAGAGGAATCGAGAATATGGAGCTTTGGGGGTCAGCTGTGAAATGGGGCACGGACCATAAGT[C/T]CAATAATTCAAAAGATTGTTGTAATGCTTGTAAGAGTATGTGCAGTGGTGAGGGTGGGCCTTGCCTTTGCGATTCTTGGGTTTTTT
83766 G A CTAAGCTGTAATCTTTAAATCTGAAATGCTCGAGTCTGACCCGAGCGTTCCATGCGAAATCATAGGGCGCGCGCGATATGCTGCAGTTGCAAGCGAC[G/A]GTCAAGACAGCAGAGTGATTCGCAGTCGCGTTGGTCCATCAAAGGTGACGGCTTTGACCCAAAATGAGGACGGCGGTGCTTCAGGTGA
83766 G T GTAGAGATGGATTCAAAGGACAGCAGGCTCGACTTTAAGGTGGAGTTAGGGTTTCGATCAGTAACTTCGATGCTGGTGGCTATGATTTTGATTTGGGAAT[G/T]ATGAAGGAGGAGCTGCCGATTAAATAGGAGGCGGAGCAGTCATCTTTCCGATTTGGGGGAGAAACTGATTACGATTTTTGGGGA
83766 T C GGGAATGATGAAGGAGGAGCTGCCGATTAAATAGGAGGCGGAGCAGTCATCTTTCCGATTTGGGGGAGAAACTGATTACGATTTTTGGGGAAGGAGCATT[T/C]AAGGCTTCGGCCATTTTTAATGAAGAGGAAATAACTCAATTTTGCAGCTAAATAAATTAGGGAAAAGATGAGATTTT
83784 A G CTCCTATGGGACAAGGACATATTATGGGCATGAATCAAATGCAGTCAGGACCTCAAACTACTAACATACC[A/G]CAAAATATTGGTGCATTTCAGAATGCCATGTCTAACATTCAGGGAGGAGTGCAAAATTTCATGTTCAATCGGCCACCACAAATGGGCCAAATGCCACAAA
83784 G A GCCAAATGCCACAAATTCCAGGATTGAATAATTTTCAGCCTGGAATGATGGGTGGGGGAAATTTGGGGCTTCCACCACCACCTCAGCCACCATTACCACC[G/A]GGTCCAGCACCGAAGTAAGTTGAAGTTTTGATGCAAAGATGAGCAGAGACTTAAATGTTTTAGAGAACTTGCAAACAAAGCACTAT
83804 T G GTTGTTCATGAGTCCAGCGATTGGGTTAAAATCTGTTAGGTCGAATGGGTCCAAGCTGAATCAAACTTAAGTACTTACTATTTCCTTCCAGCATTTTGAT[T/G]TGAAGCTGGACAATGGATCCCCAACTTTTTGATTTGCTGTCATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCA
83804 G A TGAGTCCAGCGATTGGGTTAAAATCTGTTAGGTCGAATGGGTCCAAGCTGAATCAAACTTAAGTACTTACTATTTCCTTCCAGCATTTTGATTTGAAGCT[G/A]GACAATGGATCCCCAACTTTTTGATTTGCTGTCATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAG
83804 T C GCTGAATCAAACTTAAGTACTTACTATTTCCTTCCAGCATTTTGATTTGAAGCTGGACAATGGATCCCCAACTTTTTGATTTGCTGTCATTCCAATGGAA[T/C]TTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTCGGCCTCAAAGGTAT
83804 T G TTTGATTTGCTGTCATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGA[T/G]CTCGGCCTCAAAGGTATTGGTGTGTACACACATCCAAACAGTAGCTGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTAC
83804 G A ATTTGCTGTCATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTC[G/A]GCCTCAAAGGTATTGGTGTGTACACACATCCAAACAGTAGCTGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTACCAAT
83804 A C GTCATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTCGGCCTCA[A/C]AGGTATTGGTGTGTACACACATCCAAACAGTAGCTGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTACCAATTTATGTC
83804 G C ATTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTCGGCCTCAAAG[G/C]TATTGGTGTGTACACACATCCAAACAGTAGCTGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTACCAATTTATGTCCCA
83804 T A TTCCAATGGAATTTGTTTGACTTCTTGTTGGTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTCGGCCTCAAAGG[T/A]ATTGGTGTGTACACACATCCAAACAGTAGCTGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTACCAATTTATGTCCCAC
83804 C T GTTCACTCAGAAACTTCATTATCAAGTAAGTCTGTTTTTCTGCATCTGTTAGGGATCTCGGCCTCAAAGGTATTGGTGTGTACACACATCCAAACAGTAG[C/T]TGAAGCATAAGTAACTAACAGCGCTGCAGAATCTGAGGATGTACCAATTTATGTCCCACCGTCATTGGAAGAGTAGAAGAAAATGCTT
83808 A G CAGGAGCTTTTGATTTTGTTTTCAATTTGAATGCTGTTGCTGGTTTTACGATAGCTTTCCGAGGTAGCAAACTTCGAGCTTTCGCTTGACCTCTAATGGT[A/G]CTGATTTCTGTTTTTGAATCTTCTTCTTGCTTTTGAGGAACTGCATTGGCAATTTGAAGTCTCAGTTTATCCCAAGAAAAGTTGCCCTCTG
83832 G A TCTACGACACTGGGCTGCCTTAAACGACGGCGAAAAGCACTTCATCACTCACGTGCTTGCCTTCTTCGCCGCCTCCGATGGCATCGTTCTGGAAAACCTA[G/A]CCGTTAGATTCATGAAGGAGGTTCAAGTTGCCGAAGCCCGCGCCTTTTACGGATTTCAGATCGCCATCGAAAA
83886 A G AGTGGTACATGATAAGAAAAATGAAAAGTATAGCTTAGAATGGAATGCAAAGATTGGAAAGTTGCTAATGGATGGCCGGTATGGTGGGCGCACAATACTT[A/G]GCAATATGCCAAAGAGATTCCAGGTGGAAACCGAAGATATGAAAATGGAGGTCAAGGAAGAAC
83892 C T GAAAAAGGAGAGATCAATGGGGAGTGGTGAAAGCAAAGAAGGAGCCGGGGAAGCATCGACGG[C/T]GGAGGAAACTTCTCTTTCAAAGACAGCAGTCAAAGCTTTGGGCGCTGCTACTGCCGTAGCTGCAGGTGCTGCTCTTCTGTACCATGCTTCTGGGTCGAGT
83892 G C GAAAAAGGAGAGATCAATGGGGAGTGGTGAAAGCAAAGAAGGAGCCGGGGAAGCATCGACGGCGGAG[G/C]AAACTTCTCTTTCAAAGACAGCAGTCAAAGCTTTGGGCGCTGCTACTGCCGTAGCTGCAGGTGCTGCTCTTCTGTACCATGCTTCTGGGTCGAGTGCGCC
83914 A G GGCTAAGTTTACTGCTTTCTTGATAAAATCGATACACAAGCTCAGGCGAGGTATGTAATATGTGATAAAATTGCTGAACAAACGCATTTCCAACCACTTG[A/G]GCTGGAGGCTGAGATCCGGGAGCAGCTGACTGATCTGAGGCCATTGACAGGACCCTGATGGGAGTAGATCGTGGAGAGATTCTTA
83920 A T CCGCCCCACCCACCACCTGCTGCGCGCCTCTCAAGGACGCTATAGAGAACGATCTTCCCTGCCTTTGCTCCATTTTCAACGACGCTGCAATTCTTAAGGC[A/T]TTTAAGATCGACCTCAACGCTGCTCTCCTGCTTCCTGTGCACTGCGGCATGCCGTCTTTATCCTCTACTAATGCCTGTGCTAAATATGCT
83920 C T GCTGCGCGCCTCTCAAGGACGCTATAGAGAACGATCTTCCCTGCCTTTGCTCCATTTTCAACGACGCTGCAATTCTTAAGGCATTTAAGATCGACCTCAA[C/T]GCTGCTCTCCTGCTTCCTGTGCACTGCGGCATGCCGTCTTTATCCTCTACTAATGCCTGTGCTAAATATGCTGCTGGTGCTCCTGGTGCT
83920 A G GCCTTTGCTCCATTTTCAACGACGCTGCAATTCTTAAGGCATTTAAGATCGACCTCAACGCTGCTCTCCTGCTTCCTGTGCACTGCGGCATGCCGTCTTT[A/G]TCCTCTACTAATGCCTGTGCTAAATATGCTGCTGGTGCTCCTGGTGCTTCCACCATCCCTCCTCCAGCTACTCCTGGAGGTAACTCGAAT
83920 C T CCTCTACTAATGCCTGTGCTAAATATGCTGCTGGTGCTCCTGGTGCTTCCACCATCCCTCCTCCAGCTACTCCTGGAGGTAACTCGAATAATGCGGCAAA[C/T]AGCAGAAGCTGGATTGGGTTATCAAGTTTACTGGCCGTGCTGATAATCTGCTGCTCCATCATGGTGTAAAGAGGATGAGTTCAAAGTA
83920 T C CCTGGTGCTTCCACCATCCCTCCTCCAGCTACTCCTGGAGGTAACTCGAATAATGCGGCAAACAGCAGAAGCTGGATTGGGTTATCAAGTTTACTGGCCG[T/C]GCTGATAATCTGCTGCTCCATCATGGTGTAAAGAGGATGAGTTCAAAGTAGCCTTATGCTTGTTTTTCGATTGTCATGTGCC
83920 A T TTCCACCATCCCTCCTCCAGCTACTCCTGGAGGTAACTCGAATAATGCGGCAAACAGCAGAAGCTGGATTGGGTTATCAAGTTTACTGGCCGTGCTGATA[A/T]TCTGCTGCTCCATCATGGTGTAAAGAGGATGAGTTCAAAGTAGCCTTATGCTTGTTTTTCGATTGTCATGTGCC
83932 TA T ATTATTAACGAAACATCATTAACAAGTCACTAGTCGAAAATAAATTACTTCAGAAGCTACATAATACCAAGATTAACACTACAACCAACGTTACAAAACC[TA/T]AAAACCAAAAGCGACTAATGACAGAAGATAACCTTAAGCTCCCTAGGACTGGAGCAGTCATGAGTCAAGCTAGGGCTATCGTGCGC
83938 G A GCCAATTCACTACTGCTAGTCAAAGAAAATCCATCTTGATACATTCATTTTCTTTCCTAGAAAAAACATCTGAAAGCAGAGACTTAC[G/A]TCAAGCCTGCGGCCTCGACTGAACTACGAAGACATCCTCGCCGACCACACAGCCTTCAACATCCTGCGGACCCCCAAACTGCTGCTCGAGAAAAAGCCCG
83938 G A AATCCATCTTGATACATTCATTTTCTTTCCTAGAAAAAACATCTGAAAGCAGAGACTTACGTCAAGCCTGCGGCCTCGACTGAACTACGAAGACATCCTC[G/A]CCGACCACACAGCCTTCAACATCCTGCGGACCCCCAAACTGCTGCTCGAGAAAAAGCCCGACAGCACAAAGCCTCTGGCCCAACCGC
83938 A G CATTTTCTTTCCTAGAAAAAACATCTGAAAGCAGAGACTTACGTCAAGCCTGCGGCCTCGACTGAACTACGAAGACATCCTCGCCGACCACACAGCCTTC[A/G]ACATCCTGCGGACCCCCAAACTGCTGCTCGAGAAAAAGCCCGACAGCACAAAGCCTCTGGCCCAACCGCTTCCTCCAACCCGACTCC
83938 G A GTCAAGCCTGCGGCCTCGACTGAACTACGAAGACATCCTCGCCGACCACACAGCCTTCAACATCCTGCGGACCCCCAAACTGCTGCTCGAGAAAAAGCCC[G/A]ACAGCACAAAGCCTCTGGCCCAACCGCTTCCTCCAACCCGACTCCTTCGTCGGCTCCTTCTTGCTATAATCGACAGTCAACCCAACG
83938 A G CCTGCGGCCTCGACTGAACTACGAAGACATCCTCGCCGACCACACAGCCTTCAACATCCTGCGGACCCCCAAACTGCTGCTCGAGAAAAAGCCCGACAGC[A/G]CAAAGCCTCTGGCCCAACCGCTTCCTCCAACCCGACTCCTTCGTCGGCTCCTTCTTGCTATAATCGACAGTCAACCCAACGACCTTCC
83948 C A TCGAACTGGACTCCAAACCCTTCATCCTCTTAGAAACTCGGCCCGGTTCGTCCAACCTCTTATTGCACCTCCTGAACCGGATACGACTTCTGTCACCTGC[C/A]GCTTTTCCAGCATGCCTTATATCGCTCGTTTTCAAAGGCTGCACTATGCCCCCATCGAGGGTAACTCGATCAATCGACACGCCACGCAG
83986 C A CAGCTCTTCATGGATGGATAGATGTTGCTAAATGCTTGATAGAGTTTGGGGCTGATATTAATGCTCAGGATCGCTGGAAAAACACACCGCTGGCTGATGC[C/A]GAAGGAGCTAAAAAACACGGCATGATTGAGCTTTTGAAGTCCTATGGAGGCTTGTCTTTTGGTCAAAACGGGAGTCATTTTGAGCC
83992 C T TCAGGACAAGTGAAAGTACTAGGTAACTCAAGGGCAAAAGGTAATCAAATAGGTAGCAGCACCAGCGCAAGTGAAAGTACTAGAGTTATCATCATGGGCG[C/T]AACTGTAGGCTTGAGGGCAAGCAGTCTTAAACATCTGGGAATACTTAGAAGGCTTGCACGCAGCGGTAGGTTCAAACGCATTTC
83992 C T TTAAACATCTGGGAATACTTAGAAGGCTTGCACGCAGCGGTAGGTTCAAACGCATTTCTGCAACAGTATTCATCAGTGTTGAACGCAAGGCAGGCGCTCT[C/T]GCAACCGACCACTGCTCCACCGCGATCCTTCGCCTGCAGTTCCTGTGGGCATTGGCGGTTCACGTCAGCTGCACACGAGCTGGTGA
84014 C G ACCCCGCCACCGAAAGGGCTTGAGAATCCAAAAAACTCCGCAAATATATCATCTGCACTTCTCGGATTGAATCTAAACAC[C/G]GTAGGTCCATCTCCACCGCTTGAGAAGAACGATCCGCCACCTGGCATATCCGCTCCTGGTGGCGGAACCTGGCCTTTCAACCCTTCTTCTCCGTACTGGT
84014 T C GTCCATCTCCACCGCTTGAGAAGAACGATCCGCCACCTGGCATATCCGCTCCTGGTGGCGGAACCTGGCCTTTCAACCCTTCTTCTCCGTACTGGTCGTA[T/C]ACCGCTCGTTTTTGCGGATCGCTTAAAACATCGTATGCTTCGGAAATTTGCTTGAATTTAGCCTCTGCCTCTTTCTTGTTGTTGGGATTT
84016 T TA CCATCACTACACGAAGCGGTGAGTCTTCGGCCGCCTTCCAGCCTCGGACTCTGGCACGACCGGTCTGCAATGCCATTCTTGCTGAGACTCAGGTTGCCAT[T/TA]ACGTTGCTCACACAGTACCCCAGGCTAAGACGACTGCCATACGTCCTACCATTCTTGGCCCTACAGCTACAGCGAAGCCACCACCC
84024 AC A CAAGCAGCGGATCGGAACAAACCATGGATGGCTAGTGATGAGGAAGCATCCGCCATTGCAGACAACATGCTAGAGCTACGAATCCTCCAACTTGTAGGAA[AC/A]CCCCCTAACCGACAAAGGTCTCATTCGAATCCTCAACAAGTGCAAACATCTTGAAAGCACTGACATTCGTTGTTGCTTCCATGTCA
84024 A G GCATCCGCCATTGCAGACAACATGCTAGAGCTACGAATCCTCCAACTTGTAGGAAACCCCCTAACCGACAAAGGTCTCATTCGAATCCTCAACAAGTGCA[A/G]ACATCTTGAAAGCACTGACATTCGTTGTTGCTTCCATGTCAATGTTAATGCTGAAGCTGGGTTACTCACAAACCCTTCTTAGAGCACT
84024 C A CCCCTAACCGACAAAGGTCTCATTCGAATCCTCAACAAGTGCAAACATCTTGAAAGCACTGACATTCGTTGTTGCTTCCATGTCAATGTTAATGCTGAAG[C/A]TGGGTTACTCACAAACCCTTCTTAGAGCACTTTTTTCTGGTTCTCGGGTTGAACATTGAATCTCA
84034 T TA ATATGCTGCCGTTGCTGTTAATGTTCGGGTGGAATACTTTGGTTCGGAAAGACACCTTAGGTGGCTTAAATGGATAATCTGGAGGAAAGTGGATAGTAAC[T/TA]AAAACACACCACCTGCGAAGGGGCTATCTGCAGGTCCCATGATTGTTGCTTGCCAATGGAACATATCCTCCGCAACAGGACCAGC
84034 C T GGATAATCTGGAGGAAAGTGGATAGTAACTAAAACACACCACCTGCGAAGGGGCTATCTGCAGGTCCCATGATTGTTGCTTGCCAATGGAACATATCCTC[C/T]GCAACAGGACCAGCACTGCATGACGTTGGTGGATCCTTCTGCAAATCTTTCAACTCCTTCAAAATCCTTTTCGAAGCCATAAATTAG
84048 G C CGAACAAGCGTACCCGAATTTGGCTGGGCTCCTACTCCACCTCCGTGGCTGCTGCCCGCGCCTACGATACTGCCGTCTATTTGCTGCGCGGTCAGGCCGG[G/C]CGGTTCAATTTCCCAAATGAGGTCCAGTTGGTTGATGTCAGTGAAGAGGGGATCGGTAACCTGTCTTCGGCGGAGGTTAGGAGGA
84048 A G GAATTTGGCTGGGCTCCTACTCCACCTCCGTGGCTGCTGCCCGCGCCTACGATACTGCCGTCTATTTGCTGCGCGGTCAGGCCGGGCGGTTCAATTTCCC[A/G]AATGAGGTCCAGTTGGTTGATGTCAGTGAAGAGGGGATCGGTAACCTGTCTTCGGCGGAGGTTAGGAGGAAAGCCGGCGAGGTC
84050 T TC TAGCGACCTGAAACATAGCTCGAACTCTATCTCTCCCAAACTCTTCAGCCGACTGACCCATCAACCAATACGAGTTCCACCCATTCACATATAACGGCCT[T/TC]CCCCCTCCATAAACCGAGTTCCATTTCTGCTCACAAAACTCACCTTTCCGACTCCTGAACTGAACTCCAGATCTCCAAACGACATGTATA
84056 C A TGATTTCTCCGTCCAATTCGATGGCACCTGCAGCTTCGCTCTCGAAGGGTCGTACCAGCTCCGATACAAGTCCGAGATATCGGGCCGAATCGAGAAGGAC[C/A]GGCTCCGAGATCTGAAGGGGGTAAGTGTAAAAGTATTATTTGCTTGGTTGAGTATTTCGGAGGTCGATAGGAGAGGTGATACTCT
84056 C T ACAAGTCCGAGATATCGGGCCGAATCGAGAAGGACCGGCTCCGAGATCTGAAGGGGGTAAGTGTAAAAGTATTATTTGCTTGGTTGAGTATTTCGGAGGT[C/T]GATAGGAGAGGTGATACTCTAGGGTTTTATGTCGGGATTTTGTCTGCTAGTTTTCCTGTCGATAATTTCGATTTGGTGCCCCATTG
84056 C A GGCCGAATCGAGAAGGACCGGCTCCGAGATCTGAAGGGGGTAAGTGTAAAAGTATTATTTGCTTGGTTGAGTATTTCGGAGGTCGATAGGAGAGGTGATA[C/A]TCTAGGGTTTTATGTCGGGATTTTGTCTGCTAGTTTTCCTGTCGATAATTTCGATTTGGTGCCCCATTGTGGATGCGGGTTGATTT
84072 AC A CAAATTTTCGTGAAACACATAGATGGCCACACTCAGTGCCTTCAATTCCCAAAACCATCTCTCCGAATCCAAACCCTAGTCGAAACACTAGCCCTGCCCT[AC/A]CCCCCTCCGCCTCATCACCGGAACCGAAACCCTAGAACCTATATCCTCCCTTTCTGCAGCCACCGGTGGCCTTTTCCCTACTGTTACCG
84092 CA C GATCATTCTGGGTGCCATTAATAGAGGACTCATGCAAGCAGATAATGGATGCTGCCAGGAACACAAATGCTAAGACCATGGGTCCAGTTCCTCTTCCCAC[CA/C]AAAAAAAGGGTCTACTGCGTCCTCAAATCGCCTCACGTGCACAAAGATGCACGGTTCCATTTTGAGATCAGAACCCATCAGCGCCT
84098 G A AAAACAAAGTTTGATTCAAATCAATGGCAATGGCAACCAGTGCCTCGGCTCTCTGCAAACCCA[G/A]CCTGAGGTTTGTGACTGCAAAATCAGTACAAGGATACAATAAAAATTATTTGGTAAGACAAGTGTAACTCGCACTGGAGCAGGTAAAGGAGTATCAAGTG
84098 C T AAAACAAAGTTTGATTCAAATCAATGGCAATGGCAACCAGTGCCTCGGCTCTCTGCAAACCCAG[C/T]CTGAGGTTTGTGACTGCAAAATCAGTACAAGGATACAATAAAAATTATTTGGTAAGACAAGTGTAACTCGCACTGGAGCAGGTAAAGGAGTATCAAGTGT
84098 A AT AGTTTGATTCAAATCAATGGCAATGGCAACCAGTGCCTCGGCTCTCTGCAAACCCAGCCTGAGGTTTGTGACTGCAAAATCAGTACAAGGATACAATAAA[A/AT]ATTATTTGGTAAGACAAGTGTAACTCGCACTGGAGCAGGTAAAGGAGTATCAAGTGTTTGTCAGCCTCTACCTCCTGATAGACCTC
84098 T G AAATCAATGGCAATGGCAACCAGTGCCTCGGCTCTCTGCAAACCCAGCCTGAGGTTTGTGACTGCAAAATCAGTACAAGGATACAATAAAAATTATTTGG[T/G]AAGACAAGTGTAACTCGCACTGGAGCAGGTAAAGGAGTATCAAGTGTTTGTCAGCCTCTACCTCCTGATAGACCTCTCTGGTTCCCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
84098 A G ATGGCAATGGCAACCAGTGCCTCGGCTCTCTGCAAACCCAGCCTGAGGTTTGTGACTGCAAAATCAGTACAAGGATACAATAAAAATTATTTGGTAAGAC[A/G]AGTGTAACTCGCACTGGAGCAGGTAAAGGAGTATCAAGTGTTTGTCAGCCTCTACCTCCTGATAGACCTCTCTGGTTCCCTGGCAG
84098 C A CTCTCTGGTTCCCTGGCAGCTCTCCTCCTGAATGGCTTGATGGCAGTCTGCCTGGAGATTTTGGCTTTGATCCTCTTGGATTAGGATCCGACCCGGAACT[C/A]CTCAAATGGTTCGCACAAGCAGAACTGATGCACAGCAGATGGGCCATGCTAGCCGTGGCCGGAATCCTGATCCCTGAATGCATGGAA
84098 C A TTGGCTTTGATCCTCTTGGATTAGGATCCGACCCGGAACTCCTCAAATGGTTCGCACAAGCAGAACTGATGCACAGCAGATGGGCCATGCTAGCCGTGGC[C/A]GGAATCCTGATCCCTGAATGCATGGAAAGGCTCGAATTCCTCGACTCGTTCTCATGGTACGATGCAGGTTCCCAACAGTACTTCACC
84100 G C TCGAATCGCACTACTACTTTCTAGCCTTAGTTCCGATCCTCGTCTGTTTGGTCTGCACTGCGATTTTGGTGGTGAATCCGGACTCTTCGCATCTGCGACT[G/C]GGGAGGGCGGTGGGGTTGGCGATGCACGGGACGTGGCTGATGCAGATGGCGTTTTCGTTCTTCACGACGGCTGTCACGCACGGGTG
84114 T C ATAGCTGGCTATTCAGCTGAATCATTTACCAATTTATATGAACTCAAAGCCCTAATTCGGATTATTGGAGGTTATGGATTCGATAAAATCGACCGAGCAA[T/C]ACGTGAACATGTCGCCGCTTTATTGAACTGCATTGACACATCACTTCGATCTAACGGTGATGCTTTAGAGGCTGTATTTGGGTGTACA
84134 TG T ACTACTGAGATAACTATGATTTTAAAGTTTTCCCAAGCAATCTCTCGTACGCTTCCATTTTCCTGTCTTAATGCCTGCAAAAAATACTTAAAGGCTTTAA[TG/T]GGCGATGAATTTAGGTGTGAGGACACGCTGGAGGCGACGCGAGTGGTCACGGGATTTTTGCTGTAGTTAGCGGAGGATAGAGAAGT
84142 A T TTAAACACGTCTTCAGGAGTGCGGGCGACATAAGGCTCCATCCCCCGCCAAAATAATAATTAGGGTTTCGAAAGGATTTAATCCAAATTTTGGTGAATTT[A/T]AAAGAGAGGAGAGAGTGGTTTTGGTTCAAGATTTCTTTTATAACGAGCGGAAACTAACCGTATTATTGCATAATTTGCATTT
84168 T C TTTAGGCTCAACTGGGAGTGGTAATAGTTTTTTCGTTTGTTCGAGTTCTTGTTGAGCGATCTTCTTGGCAGC[T/C]TCGGACAAGGCAAGCTTTTCTTTGAGTTTCTTGACTTCTTCTTTAGTTAGAGTAAGTTTGGTCTCTAGCTCTGACACACGGGTCCCACGTTTTTTCTCAT
84168 A T GATCAATGGAGTGACGAGTAATGCCATTTGCTTCCGAGCAAACTGTGGTTTTTAGATGGATTGGGAGCCTTGGAGAGTTCCCTTTTGGCGCTTCTGAAGA[A/T]GATCCTCTTGATCTCGGCATTGAGTTTGAATTTTAAGTGTTATGGTAGATGCTCTTTGTCTTAGATTGGGTTATGGTCAACCATAAAA
84168 C T TTGATCTCGGCATTGAGTTTGAATTTTAAGTGTTATGGTAGATGCTCTTTGTCTTAGATTGGGTTATGGTCAACCATAAAAAACCAAACTTGAAGCTTCA[C/T]AATGTGAATAAAGGAAAGGGAAAAGGCGAAAGAAGCAAGGAAGAGTTTGAAAAATCCAGTAGGCCAAC
84176 G C AAGATCAGACCCGGTGCTGCAAGGAGAAGATATACAGGGGAGTGAGGATGAGAAAGTGGGGGAAGTGGGTGGCCGAGATCAGGGAACCGAACAAGCGGTC[G/C]AGAATATGGCTGGGTTCGTACTGCAGCGCGATAGCCGCGGCCCGCGCGTACGACACGGCCGTCTTCCTCCTCAGAGGCCCC
84176 C G TCTTCCTCCTCAGAGGCCCCTCCGCCAAGCTCAACTTCCCGGACGAGGCGTCCAAATTGGACGAAGAAGACATGGGGAATGGAGCCGGATGTTACACGGC[C/G]GCGTATATAAGGAAGAAAGCGACTGAAGTTGGAGCAAGGGTAGATGCCGCCGCCGCCGCCGCCGCCG
84192 C G CAATATACTTTGTACTCACCCGGTCACTCGCCATAAATACAGTTTCACCTATACGCCATTAAACCCAACATCAATTCTTGAATAGCATCTGTGCCAAACA[C/G]AGAGCCTAACAAACAAACAAGAGCAAACAACAAAACAAAGAAAGACGGCGTTAATGAATTAGCGGGCGCAAACAAAGCTACCTCAGC
84196 T C GGTGGTTAGCTACCATCACCCTTCTGTGCGCCTCCCTTATCCTGTCCACGGCAGCATGTTCTCTAACACCAAGAATTAATGCAGCTTCTCGTCTTGTCAT[T/C]GTCTGCTCAAATCCGCCATTATAGAATCGTCTGACTCGTGGAACAACTGGTCTGGCTTTAAATGCTTGCCACGCTTGAATAGCAAATCTA
84196 G A TCACCCTTCTGTGCGCCTCCCTTATCCTGTCCACGGCAGCATGTTCTCTAACACCAAGAATTAATGCAGCTTCTCGTCTTGTCATTGTCTGCTCAAATCC[G/A]CCATTATAGAATCGTCTGACTCGTGGAACAACTGGTCTGGCTTTAAATGCTTGCCACGCTTGAATAGCAAATCTACCGGCTAATGCAGCT
84196 T G CGTCTTGTCATTGTCTGCTCAAATCCGCCATTATAGAATCGTCTGACTCGTGGAACAACTGGTCTGGCTTTAAATGCTTGCCACGCTTGAATAGCAAATC[T/G]ACCGGCTAATGCAGCTGCTGCAACTGAAAAGGTAGCTACTACAGGAGTTGTCATAACCTACAACGAAGCTCAAATCGTTATTTGCGAA
84196 C T TGGCTTTAAATGCTTGCCACGCTTGAATAGCAAATCTACCGGCTAATGCAGCTGCTGCAACTGAAAAGGTAGCTACTACAGGAGTTGTCATAACCTACAA[C/T]GAAGCTCAAATCGTTATTTGCGAACACAGCACGGCCACTCGGTTAACTTAGCTTGTGATTCCTGCTTGAAGAAAAGAATTTGGTATAA
84196 C A CCGGCTAATGCAGCTGCTGCAACTGAAAAGGTAGCTACTACAGGAGTTGTCATAACCTACAACGAAGCTCAAATCGTTATTTGCGAACACAGCACGGCCA[C/A]TCGGTTAACTTAGCTTGTGATTCCTGCTTGAAGAAAAGAATTTGGTATAATTTGGGGAAAATCGAGTATTTGTTAATTT
84196 T C CTGCAACTGAAAAGGTAGCTACTACAGGAGTTGTCATAACCTACAACGAAGCTCAAATCGTTATTTGCGAACACAGCACGGCCACTCGGTTAACTTAGCT[T/C]GTGATTCCTGCTTGAAGAAAAGAATTTGGTATAATTTGGGGAAAATCGAGTATTTGTTAATTT
84224 C T TCCTAATGCGGCTAGGTGGTACGATAGTGTTAATTCACTTCTTGCTGCCAGATTTGTTGGTCAGGCTGTTGGTGTGAAATTTGTATCTGCACCTGGTGCA[C/T]CTGCTGCTGCACCTGCTGCATCTGCTGTTGAGGAGAAAAAGGCAGATGGAGATGATGATGATTTGGATTTGTTTGGTGACGAGACAG
84228 A C TAAAGAAGAATGTTTCACAAAAGGAAATTGTAACATTAAAATACATAGGCGGATCTGTAGCTGAAAACAAAAGGCCAATGGTGCAAACGAAGA[A/C]CACAAACTAGATAAACAAGAACAACCAATAAAATTTGTGCGTTCAAGAAAAGCAAAAGGAAACCAATCGAGATTAAGATGTAGCAGCAGCTG
84228 A T TTCACAAAAGGAAATTGTAACATTAAAATACATAGGCGGATCTGTAGCTGAAAACAAAAGGCCAATGGTGCAAACGAAGAACACAAACTAGATAAACAAG[A/T]ACAACCAATAAAATTTGTGCGTTCAAGAAAAGCAAAAGGAAACCAATCGAGATTAAGATGTAGCAGCAGCTGCAGCCTTCTTCCTT
84246 G T CTGCATATTAGTTCAAGTTGATTACGATGATGAATCATGAGCGGGCAGCCAACATCGCTCTTTTAGCTCTTACGTGTGCACCGCTTGTTGTGAACGTGGA[G/T]CCCAATATAAATGTGGTTTTGACAGCCTGTTTAACTGTTTACGTTGGCTGCTATCGATCCGTGAAGGCAACACTACCGACGGAAACAA
84246 C T TGATGAATCATGAGCGGGCAGCCAACATCGCTCTTTTAGCTCTTACGTGTGCACCGCTTGTTGTGAACGTGGAGCCCAATATAAATGTGGTTTTGACAGC[C/T]TGTTTAACTGTTTACGTTGGCTGCTATCGATCCGTGAAGGCAACACTACCGACGGAAACAATGTCCAAAGAACATGCTATGCGCTTTC
84246 G A AATGTCCAAAGAACATGCTATGCGCTTTCCTTTAGTTGGCAGTGCAATGCTGTTCTCGTTATTTTTGGCTTTCAAGTTTCTTTCAAAAGATCTAGTCAAC[G/A]CTGTGCTAACGTGTTACTTTTTTGTGTTGGGGATAATTGCTTTTTCTGCGACAATTCTACCATTTATCAAGCGTTTCCTTCCAAAGAACTG
84256 A G CGGACCATGGTTCATCCACAATGATGTCGTACTGAAGGCGGAAGATGGAAGCAACAGATCTGAGGTAACTCAAGTGGGAGCATGGTTCATCCACTGCCAG[A/G]TCTGAGGAGGAGTTGCAGATCTGAGGTAAGTTGGTAGTTCAACGCCAGGTATAAGCGTGAATTGTAGGGATGGAGGAGTATGA
84264 GA G TGGTTCGATCCTACTGCAGCGTTTCATAACTATGCTATCATCTGGAATCCTGCAGAAATCATATTCTTTGTGGATGACATTCCAATAAGAAGATATCCAA[GA/G]AAAAATAGATGCCACATTTCCACTGCGTCCAATGTGGGCGTATGGGTCGATATGGGATGCATCATCCTGGGCAACGGAGAACGGGA
84270 C T TTCAGCACGGAGGTCTGTCATAGCCATATTTCTACGATGAAATTCTTCTTTTACAGCAGAAAGTTCTTGCTGAAATACCATGCGATCATCAGCCAGTCTC[C/T]GGTTATCTGCTACGAGTCTGTGAATTTCATGCTGTTGCATATCGAGTTCTTCTAAAAGGGAAGG
84280 T C TCAAATCCTGGATAGTAAGGAGTGGGAATAAGGAAAGCATCTCCAGGATCAGCCAGGCAAAA[T/C]GCAATCAGTTCTTGAGCTCCAGTAGCTCCACCACTCATCACTATTCTTTCTGGATCAAATTTTGCACTTCCACCCCTAACTTTCTCCATAAATTTTGCCA
84280 A G TCAAATCCTGGATAGTAAGGAGTGGGAATAAGGAAAGCATCTCCAGGATCAGCCAGGCAAAATGCAATCAGTTCTTGAGCTCC[A/G]GTAGCTCCACCACTCATCACTATTCTTTCTGGATCAAATTTTGCACTTCCACCCCTAACTTTCTCCATAAATTTTGCCATTGCTTGTCTGAAAGCAGGGA
84280 A G TCAAATCCTGGATAGTAAGGAGTGGGAATAAGGAAAGCATCTCCAGGATCAGCCAGGCAAAATGCAATCAGTTCTTGAGCTCCAGT[A/G]GCTCCACCACTCATCACTATTCTTTCTGGATCAAATTTTGCACTTCCACCCCTAACTTTCTCCATAAATTTTGCCATTGCTTGTCTGAAAGCAGGGAGAC
84280 A G TAGCTCCACCACTCATCACTATTCTTTCTGGATCAAATTTTGCACTTCCACCCCTAACTTTCTCCATAAATTTTGCCATTGCTTGTCTGAAAGCAGGGAG[A/G]CCATGATAGTCTTGAAAGTTAGCAATGGACTTGAACTCGGAAACACCTTCTGTAGTGCAAATGGAAGCTTCTGGATTGTTCTTAATCCAA
84280 A G TAACTTTCTCCATAAATTTTGCCATTGCTTGTCTGAAAGCAGGGAGACCATGATAGTCTTGAAAGTTAGCAATGGACTTGAACTCGGAAACACCTTCTGT[A/G]GTGCAAATGGAAGCTTCTGGATTGTTCTTAATCCAATCTTCTATCAAATCATGGCAAAGTTGGTTTTCTGCTAAACCCATTTGAATGAC
84280 A G CTTGAAAGTTAGCAATGGACTTGAACTCGGAAACACCTTCTGTAGTGCAAATGGAAGCTTCTGGATTGTTCTTAATCCAATCTTCTATCAAATCATGGCA[A/G]AGTTGGTTTTCTGCTAAACCCATTTGAATGACTCCTCCTACATTATTTGTGAGATGAAATGGGTCGTTTTCATATGCTTTCCATCCATCA
84280 T G TCTTAATCCAATCTTCTATCAAATCATGGCAAAGTTGGTTTTCTGCTAAACCCATTTGAATGACTCCTCCTACATTATTTGTGAGATGAAATGGGTCGTT[T/G]TCATATGCTTTCCATCCATCAAAGTATGATGAATTTTCTCCATGGCCATCGTTAGTTGCAATTTTGGAAAGAAGTTGATTGCTCCTGGTAG
84280 G T CTAAACCCATTTGAATGACTCCTCCTACATTATTTGTGAGATGAAATGGGTCGTTTTCATATGCTTTCCATCCATCAAAGTATGATGAATTTTCTCCATG[G/T]CCATCGTTAGTTGCAATTTTGGAAAGAAGTTGATTGCTCCTGGTAGCCATTGTTTGTTTGGTTGTGAATAATACGAA
84280 G A CCATTTGAATGACTCCTCCTACATTATTTGTGAGATGAAATGGGTCGTTTTCATATGCTTTCCATCCATCAAAGTATGATGAATTTTCTCCATGGCCATC[G/A]TTAGTTGCAATTTTGGAAAGAAGTTGATTGCTCCTGGTAGCCATTGTTTGTTTGGTTGTGAATAATACGAA
84280 A G TGACTCCTCCTACATTATTTGTGAGATGAAATGGGTCGTTTTCATATGCTTTCCATCCATCAAAGTATGATGAATTTTCTCCATGGCCATCGTTAGTTGC[A/G]ATTTTGGAAAGAAGTTGATTGCTCCTGGTAGCCATTGTTTGTTTGGTTGTGAATAATACGAA
84284 C T TGAGATTCCCATCTCCCTGTTCTTCGATAGAAAGTAACACCTCTGTATTGAGAACTCCTTGACCGTGGTCCCCTTCTGCTCTTCTTAGCCGC[C/T]ACTGCCACGGCAGCAGACTTATCAACGGTGGTAACATCACCGGCTATGGTTCTCTGTTCCGTCTGCTCATTGACTGGAAAGAATTGGAAGGTGACTG
84286 C G GCTATGTGACGGTTAGAGGCGAGAAGGCAATGCAGCTCTTGGAAAGTGGACTGAAGGTCAAGGAGTACGAATTGGTGAGAAGGAACTTCAGTGATACTGG[C/G]TGTTTTGGCTTTGGTATCCAAGAACATATCGATCTTGGGATCAAGTATGACCCATCCACTGGTATCTATGGAATGGACTTTTACG
84288 T A AAAAAAATATTCAGGGATCAGCAGCCGTAGGATTCTCACCTCTCAATCTCCTCAATCGATCCACCCAGTTTTCTTCATCAACTTCGTCGGCCCAATCGGG[T/A]GCAGATCCAATAAACCTCACTTGTCTCATTGCCTCCATGACCCGCGAAACGTTCTCTTGCGCTAATGGCGCGTTTCTTCTCATCTCATCC
84288 G C GCCGTAGGATTCTCACCTCTCAATCTCCTCAATCGATCCACCCAGTTTTCTTCATCAACTTCGTCGGCCCAATCGGGTGCAGATCCAATAAACCTCACTT[G/C]TCTCATTGCCTCCATGACCCGCGAAACGTTCTCTTGCGCTAATGGCGCGTTTCTTCTCATCTCATCCTCTCTGAATGCTTTTGCAATAGTA
84288 G A CCTCCATGACCCGCGAAACGTTCTCTTGCGCTAATGGCGCGTTTCTTCTCATCTCATCCTCTCTGAATGCTTTTGCAATAGTATCTTCTCTTTCTTCTTC[G/A]GCTAGTACCAACTCTTCTTCTTTCTCTATTCTTCCATTCAGATCTACTGGGGGTAAAGAAGGTTCCGAAGGAAGTGGGTTGTCGGATTCTG
84288 A C TCTCTGAATGCTTTTGCAATAGTATCTTCTCTTTCTTCTTCGGCTAGTACCAACTCTTCTTCTTTCTCTATTCTTCCATTCAGATCTACTGGGGGTAAAG[A/C]AGGTTCCGAAGGAAGTGGGTTGTCGGATTCTGACTCGGAGTCAGAGTTCAAGGATACAGGGCGGTACGAGGCTTCGAAATCCGAACTGT
84288 C G CCAACTCTTCTTCTTTCTCTATTCTTCCATTCAGATCTACTGGGGGTAAAGAAGGTTCCGAAGGAAGTGGGTTGTCGGATTCTGACTCGGAGTCAGAGTT[C/G]AAGGATACAGGGCGGTACGAGGCTTCGAAATCCGAACTGTCGGCTTCAGAGTCCGAGTCGGTGACAGCGTCAGGAGCACCAATACC
84288 A C TGTCGGATTCTGACTCGGAGTCAGAGTTCAAGGATACAGGGCGGTACGAGGCTTCGAAATCCGAACTGTCGGCTTCAGAGTCCGAGTCGGTGACAGCGTC[A/C]GGAGCACCAATACCCTGAATTTGATCGTCGCTGGCTTCCATTTTCTGAAGCAGCACAGTAGGAGAGGCGCTGTT
84322 C T TCACCTTTAACCAGAATTTTAGCGCTTCCAAAGTCACACAATTTCACTTGATGAGTAAGCGGATCAACCAGTATGTT[C/T]TGTGGCTTTACATCTCTATGACAAACTCCAGGAACAGCATGAATATAAGCTAGAGCTCTAAAAATCTGATATGTGTAGAGCTTCACAAATATTAGCGGCA
84326 A G AAAATAAATGATAGGAACTATTGATTTTGTTTGTTGCTGTCCTGTGTTTTGGTAGACTCGGCGGCGGCGGCAGGGGCGGGGGC[A/G]GCGGCGGCGGCAGGGGCAGCAGCATCCTGAATCCTGACATATGGATTCCTGGTCAGTGTCTCCCCCTTTAAAGCAGCTACATACCGATCATTTGTGTTTT
84326 C T AAAATAAATGATAGGAACTATTGATTTTGTTTGTTGCTGTCCTGTGTTTTGGTAGACTCGGCGGCGGCGGCAGGGGCGGGGGCAGCGG[C/T]GGCGGCAGGGGCAGCAGCATCCTGAATCCTGACATATGGATTCCTGGTCAGTGTCTCCCCCTTTAAAGCAGCTACATACCGATCATTTGTGTTTTCTT
84334 C T CGCTTGGCCTCTCGTACGCGTCGGACAATGATTTTCTACGAAAGCGGTTCCATTCCTTTCCTCCTCCACCACCAGCAAACGGAGACACCGGAGGTGTAGA[C/T]CCAGCCGGAGACGCGGGTGGTGTTCCGCTGACCGGGGACGGACATCCAGTCGGCCTCTTAATCATTATGCTCCTCGTAACCTTCGG
84334 G A ACGCGTCGGACAATGATTTTCTACGAAAGCGGTTCCATTCCTTTCCTCCTCCACCACCAGCAAACGGAGACACCGGAGGTGTAGACCCAGCCGGAGACGC[G/A]GGTGGTGTTCCGCTGACCGGGGACGGACATCCAGTCGGCCTCTTAATCATTATGCTCCTCGTAACCTTCGGTGCAACCTCCGCTAC
84334 A G CGGGTGGTGTTCCGCTGACCGGGGACGGACATCCAGTCGGCCTCTTAATCATTATGCTCCTCGTAACCTTCGGTGCAACCTCCGCTACTTGTTCCGCTTC[A/G]TCTTTGGTTGATCGGAAAGAGAAGGTCGAGTGTTTTCTGAGCTTGCTGAGGCCAGTATCGGGGCGAGGTCCGGCGAGAGTGTCGTC
84344 CA C AAAAATGATGCGTGCCGTTCAGTACGCAGGGTATGGCGGCGGCGCCGCCGCCCTCAAGCATGTGGAGATTCCCGTTCCTAAGC[CA/C]AAAAAAGACGAGGTACTATTAAAAATTGAGGCTGCATCTCTTAATCCAGTTGATTGGAAAATTCAGAAGGGAATGATAAGGCCTATTTTGCCTCCTAAAT
84348 T A TCAGCAAAGAAGGCATCCTCATCTGCAGCATATTTCTCTACAAGAGGACGGAAGACAGGATCAGTGAGAAGAGCCTTGTC[T/A]GATGGTAGCTGAAGAAGACCTTCCTTCTCACCGCTTAGAAGCTCCTTGAAGTATGAGTTGTCAAATATGAGAGGGTTTGCAGTCCAAGGACCCTCAAAGC
84348 G A CCAAAGTGTGGCCCCCAGATAAAGCAACGATATCCTTATCGCTCAGACCCATCTGTTCACCAAACACCGTTCTGAGGTGATCGCAACCTTTGGTGGCATC[G/A]GGAAGGCGACCTTCCACAGGTGGCTCGTCTTTGTCCTCTCTGCCAGGATGAAAAGGAACCTCAGGTCCTCCGGTTACCTCAACAGCA
84348 G A TGAGGTGATCGCAACCTTTGGTGGCATCGGGAAGGCGACCTTCCACAGGTGGCTCGTCTTTGTCCTCTCTGCCAGGATGAAAAGGAACCTCAGGTCCTCC[G/A]GTTACCTCAACAGCAACTACTCCAGCCAACTGATAGAAATCAGCATAAGAAAGGATGGGGAACTGCTCCTTGATAGGTTCAAGAAG
84352 GT G ACAAACTCCCGTTTTCATCTGGGGCTATTGATTCCAACCAAGATCTGACAGAACTCACTATCTAATCCTTTCATCATCAATTCTTCGTTTCTTATTTTAC[GT/G]TTGTTCACCTACTGAATCAACGCCTCAAAATTGAATTTTGATTTAGGGATTTCCATCTCGAGCAATACGCAGCCAAAGCCATGCCATCGA
84352 C A TCACTATCTAATCCTTTCATCATCAATTCTTCGTTTCTTATTTTACGTTGTTCACCTACTGAATCAACGCCTCAAAATTGAATTTTGATTTAGGGATTTC[C/A]ATCTCGAGCAATACGCAGCCAAAGCCATGCCATCGATTCCATCAATAGCCGATTCCAACTACTGGTGCTCCCGCTGCAATAGATTGGTTTC
84352 A T CTTATTTTACGTTGTTCACCTACTGAATCAACGCCTCAAAATTGAATTTTGATTTAGGGATTTCCATCTCGAGCAATACGCAGCCAAAGCCATGCCATCG[A/T]TTCCATCAATAGCCGATTCCAACTACTGGTGCTCCCGCTGCAATAGATTGGTTTCGGTCCCGCCCAATGCAATGGTCTCTTGCCCGGACT
84352 A G GCAATACGCAGCCAAAGCCATGCCATCGATTCCATCAATAGCCGATTCCAACTACTGGTGCTCCCGCTGCAATAGATTGGTTTCGGTCCCGCCCAATGCA[A/G]TGGTCTCTTGCCCGGACTGCACTGGCGGATTTGCAACCGCAACCTCCACTCCACCCCGCTTGCCTGCAGCCTTCCGCCGCGGCAATC
84352 A G GGTCCCGCCCAATGCAATGGTCTCTTGCCCGGACTGCACTGGCGGATTTGCAACCGCAACCTCCACTCCACCCCGCTTGCCTGCAGCCTTCCGCCGCGGC[A/G]ATCCACGTCATTATACCGGCGATCGTTCTCCGTTCAATCCGGTCATCGTCTTTCGTGGTG
84354 A G GACAGCTAGGGATTAAATTAATTAACCAAAAACACGAAAATGGACAGCTAAAAGCCATTAAGTAAAGGTTCTTCCTCAAAATATGATCACATTGTAATGC[A/G]TCATAAAATGACTAGTAAATCTACTTGGCTTTTCTAGCTTTTCCCCTTCCTCGGCCAGAACTTTTCTGTGCAGAAGGCTTCTGTTGAGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
84364 A G TGTAGGTTGGAGGAGTTGGTGGATCCAGACTTGGGATATAAGGACAGTCTGGAGATCAAAGAGATGATC[A/G]ATCATGTTGCTCAACTGGCGTTTAGGTGTTTGCTACCCGATGCAGAGACGAGGCCAAGTTTAAGGGAAGTTCTCGCTATTTTGAAACGTATAAATGGTGA
84364 A G TGTAGGTTGGAGGAGTTGGTGGATCCAGACTTGGGATATAAGGACAGTCTGGAGATCAAAGAGATGATCAATCATGTTGCTCA[A/G]CTGGCGTTTAGGTGTTTGCTACCCGATGCAGAGACGAGGCCAAGTTTAAGGGAAGTTCTCGCTATTTTGAAACGTATAAATGGTGAAGTCGATGCAGAGG
84364 G A TGTAGGTTGGAGGAGTTGGTGGATCCAGACTTGGGATATAAGGACAGTCTGGAGATCAAAGAGATGATCAATCATGTTGCTCAACTGGCGTTTA[G/A]GTGTTTGCTACCCGATGCAGAGACGAGGCCAAGTTTAAGGGAAGTTCTCGCTATTTTGAAACGTATAAATGGTGAAGTCGATGCAGAGGG
84364 C T GTTGGAGGAGTTGGTGGATCCAGACTTGGGATATAAGGACAGTCTGGAGATCAAAGAGATGATCAATCATGTTGCTCAACTGGCGTTTAGGTGTTTGCTA[C/T]CCGATGCAGAGACGAGGCCAAGTTTAAGGGAAGTTCTCGCTATTTTGAAACGTATAAATGGTGAAGTCGATGCAGAGGGTGTTGG
84364 A G AGTTGGTGGATCCAGACTTGGGATATAAGGACAGTCTGGAGATCAAAGAGATGATCAATCATGTTGCTCAACTGGCGTTTAGGTGTTTGCTACCCGATGC[A/G]GAGACGAGGCCAAGTTTAAGGGAAGTTCTCGCTATTTTGAAACGTATAAATGGTGAAGTCGATGCAGAGGGTGTTGGTTGTGATC
84364 A C AAGCGACTATGGTGAGATATGTGAAAAACAGGTCTGTTATTTTGTTGTAATATTCGAAATAGCCATCAAACAGCCAAACAACGTAGCAACAACATTATCA[A/C]AGTACGAGATTTTATTGATTTCAGTAAGTCTAGCACGTTTTCCCAGCATATGTATGATCGTGATTTATTTTGATGAGCTTTGTTCATAA
84366 T C CTGTTGGCCTACTGGACAAGAGGCCTTTAGTAACAAGGGATAAAAGATGAAAGGAAGCTTGCTCCA[T/C]GAGTATGAAGTCGACTTACCAGCAAATGAAATATGGCAAGTGTACGGCACCCTCGAACTCGGGCAGCTTCTGGTTGAATTGCTGCCAACCATGGTCTCTA
84366 A C CTGTTGGCCTACTGGACAAGAGGCCTTTAGTAACAAGGGATAAAAGATGAAAGGAAGCTTGCTCCATGAGTATGAAGTCG[A/C]CTTACCAGCAAATGAAATATGGCAAGTGTACGGCACCCTCGAACTCGGGCAGCTTCTGGTTGAATTGCTGCCAACCATGGTCTCTAAAATAGAAGTCGTA
84366 T G GAGGCGCCGGCACTGTCCTTCGCTTCACTCTACCTCCAGGACTCCCAGGTGTTACAACTTACAAAGAAAAATTTGTGACGGTCGATCACCAGAAACGCCT[T/G]AAGGAAATAACGGTAATAGAAGGTGGATATTTGGCCATGGGCTTTAAGTCCTACAATGTGAGCTTCCAAATACTAGAAAAGAACAG
84366 C A TCCCAGGTGTTACAACTTACAAAGAAAAATTTGTGACGGTCGATCACCAGAAACGCCTTAAGGAAATAACGGTAATAGAAGGTGGATATTTGGCCATGGG[C/A]TTTAAGTCCTACAATGTGAGCTTCCAAATACTAGAAAAGAACAGCAATGTCTCTATCATTAAATCGACAATAGATTATGAGGTTGAG
84366 A C CGGTAATAGAAGGTGGATATTTGGCCATGGGCTTTAAGTCCTACAATGTGAGCTTCCAAATACTAGAAAAGAACAGCAATGTCTCTATCATTAAATCGAC[A/C]ATAGATTATGAGGTTGAGGAAGAACACAAGGAAAATGCATCATATGCTTCCATTGCTGCTCTCGCTGCTATCAGTGAAACCATCTC
84366 G C GTGGATATTTGGCCATGGGCTTTAAGTCCTACAATGTGAGCTTCCAAATACTAGAAAAGAACAGCAATGTCTCTATCATTAAATCGACAATAGATTATGA[G/C]GTTGAGGAAGAACACAAGGAAAATGCATCATATGCTTCCATTGCTGCTCTCGCTGCTATCAGTGAAACCATCTC
84372 A G CTCGCAGTACGAATCCATAAACACATCGAGCTCAGGATCTACTCCAATCTCCAAACATTTCGTGTCCTTCGTTCCTTTTCCAACCTCCTCCAGCTTCATC[A/G]TCGTCTCCGACGTTGCACCCACCTGTATGCACTGGATATACGCGGAAACAAGTTTAGGGTACTTCGGATGCCTCGAAATATAAGATTTG
84378 A C GCCAACATGCGCAATCCGGTGCTTAGTGTATGACCCAGTTTGTGGGGTTAATGGAATCACTTATGGCTGCGGCTGCCCTGATGCTGCCTGTAACTGTGTC[A/C]GTGTCGCTCGTCGTGGTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAAA
84378 T C CCAGTTTGTGGGGTTAATGGAATCACTTATGGCTGCGGCTGCCCTGATGCTGCCTGTAACTGTGTCAGTGTCGCTCGTCGTGGTGCATGCTGAGTAACAC[T/C]CGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAAATATCGAAAGATGTCATTACTATGTGCTATCTCTGA
84378 G A TGCTGCCTGTAACTGTGTCAGTGTCGCTCGTCGTGGTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTG[G/A]AATAAAATATCGAAAGATGTCATTACTATGTGCTATCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGC
84378 A C TGTAACTGTGTCAGTGTCGCTCGTCGTGGTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAA[A/C]TATCGAAAGATGTCATTACTATGTGCTATCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGCTAGCGA
84378 A ATT GTCGCTCGTCGTGGTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAAATATCGAAAGATGTC[A/ATT]TTACTATGTGCTATCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGCTAGCGAGCCTGTATAAGGA
84378 T C TCGCTCGTCGTGGTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAAATATCGAAAGATGTCA[T/C]TACTATGTGCTATCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGCTAGCGAGCCTGTATAAGGACAC
84378 A T GTGCATGCTGAGTAACACTCGCATGCATATCCGTTTATTTACAACACAAGTACTTTAGTTTCTTGGAATAAAATATCGAAAGATGTCATTACTATGTGCT[A/T]TCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGCTAGCGAGCCTGTATAAGGACACGTGGTATGAACT
84378 G T CTTGGAATAAAATATCGAAAGATGTCATTACTATGTGCTATCTCTGATGTGTATTCACCTAGTGTTATGTGATTATCTAAATTTTATGTTTACTGCTAGC[G/T]AGCCTGTATAAGGACACGTGGTATGAACTTTATAATACTTCCCACGAAATCGAGTATCCGATTCCA
84382 CA C TTTCAACACATGAATATATATTTGATTTCAACACATGAATATATATTTTATTTCAACTCCAATCACACAATCAATTTTCACAACACATCAATCAAA[CA/C]AAACAAGCCATCCATGGTCTGTGGACGACGGGTATCAGGTGTTGCTAAGCACCGTCTGCATCCTAGTATATATTTCAACTAGAAAACAATTAA
84382 C CA CACATCAATCAAACAAACAAGCCATCCATGGTCTGTGGACGACGGGTATCAGGTGTTGCTAAGCACCGTCTGCATCCTAGTATATATTTCAACTAGAAAA[C/CA]AATTAAAAGTGAGGAGTTCTCACCTTTGGGTTCCACTCCTTCATTCTTTATCGGATGGTTTTGATTTGTTTCTCGTTCGTTCCATTGTA
84398 TA T ACGCCTATGTGCGGATGATGTTAGGGTTTGCTGACATGGGCGCAATTTCTGGCGGATTCGGGTACGCTGGGAAAGGGGTCGACGTGTTTGGGGTCGGAAA[TA/T]AGAAAAATGAAGGAGTACGATGAAAAAATGCTGGTTCAGATTTACAGGAATCTTTTGGTGCAGAGGCCGGATTTAGTCCCAGC
84424 C T AAATTGAAATGCAAAATAAGAGAATCATCGAATATAAACCCTAATAAGCAAACATAGCTAAGAAAATATTTCAAGAACACGTCCTGAGATCCACTCCACG[C/T]TTCTCGTAGCAGACTCTCTTAACGATACTTGACGAAGCCAATCTCTTTGGCATTTTCCCTGAAGCATTGCCTGCAGCACATGATCCCAT
84446 T C TCTCTTGCAAAACACCTTCGTTCAATTGGTGCTAAAATGTATGGGGCTTTCTGGTGTTCACATTGCTTAGAACAGAAGCAGATGTTTGGTCGTGAAGCTA[T/C]GCAAATAATAGACTATGTCGAGTGTTTTCCTGAAGGAGCAGGTAAAGGAAAAACAATAGCAAAAATATGCTCGGATGCTGCAATCGA
84446 T C TTGGTGCTAAAATGTATGGGGCTTTCTGGTGTTCACATTGCTTAGAACAGAAGCAGATGTTTGGTCGTGAAGCTATGCAAATAATAGACTATGTCGAGTG[T/C]TTTCCTGAAGGAGCAGGTAAAGGAAAAACAATAGCAAAAATATGCTCGGATGCTGCAATCGATGGCTTCCCAACATGGATTATAAA
84458 T C GTCTCGATAACTCCACAGCTTGCGGTTCTCATCTCTTCTTGTTTCGGAGTTTCAACCTTAAGCTTCTT[T/C]CAATGGAAACTGCCACCCTCGTCTGGTCAATATCCGGCGCCTCCATCGCTGCCATCTACTGGTTCGTCTGGATAATGGGCTCCGCCGAAACCAAAGGCAA
84458 G C GTCTCGATAACTCCACAGCTTGCGGTTCTCATCTCTTCTTGTTTCGGAGTTTCAACCTTAAGCTTCTTTCAATGGAAACTGCCACCCTC[G/C]TCTGGTCAATATCCGGCGCCTCCATCGCTGCCATCTACTGGTTCGTCTGGATAATGGGCTCCGCCGAAACCAAAGGCAAACGCGCCATGGATCTGAAAAT
84460 TC T CGCGATGGACTGCTTTGAAATCACATGCCCGCAGGGCATCAGCATGGGCGGATTCTCCTTGCTCCCCTGCTCCCTCAAAACAGGGCACACGAACACCGAG[TC/T]CGGTACTGAAACTCCCTCCCCAGCTCTATTGGAACCGGCAGCTGCTCCATCGTCTGCCACTCCTGCCTCTTATTCGCCGCCATCACC
84470 T C CATTTGGCTGGCGAGGCTACTACTACAGTAACTTCTGCTTCCACCTCCACGAAAAACACTGCCACTAATATAGCTGCTTCCAGTTCGCACAAGTTCCTTC[T/C]GATTTAAACCGTGCAAGGGCCGAGTAGCATTCTCTTCGAAGTTATAAGTTACAAGACTAGATCCACTTGACCTAGCAGTTCCCTTCTCA
84470 A G AACCGTGCAAGGGCCGAGTAGCATTCTCTTCGAAGTTATAAGTTACAAGACTAGATCCACTTGACCTAGCAGTTCCCTTCTCAATAATTATCCTTGCTCC[A/G]TCAAATGGCTTAGATGACAAAGTGCATCTCCTTGCTTGGCAAACTGAAGGAGTCGATCTTTTTGTTTGTTTGAGGAGACCTCCAATACT
84478 G T TTGGTCATCGCGCTTGGTCGAAAAACCAGTGGCGCGAAGCTACCGTGTGTCGGATTATGACTGAACGCCTCTAAGTCAGAATCCAGGCTAGAGAAGCGGC[G/T]CTTAATCTCAATGACCTTGTCCCGACCCACAGTAGGTGTGCGAAAGCATACCCATGGGCACATGCCGAAGGACTCGGCCCGCTCG
84478 G A CCGTGTGTCGGATTATGACTGAACGCCTCTAAGTCAGAATCCAGGCTAGAGAAGCGGCGCTTAATCTCAATGACCTTGTCCCGACCCACAGTAGGTGTGC[G/A]AAAGCATACCCATGGGCACATGCCGAAGGACTCGGCCCGCTCGACGTATTCGTCGTAGGGTCTTCCTTAGATTGAAATTCCGTAAG
84482 A G TCTCCCAGTACGGCGAGATTCAAGATCTGAAGGCCGTTAAGGATAAAGCTACCGGAAAGTCAAAAGGTTATGCCTTTATCACCTATAAGAATAGGAAGGG[A/G]GCTGCTAACGCCCTCAAAGAACCACAAAAGCAGATTGGTGGCAGGAAGGTTTCATGTCAGTTAGCTGCTGTTGGTCCAACCACTC
84482 A G CTGTTGGTCCAACCACTCCACAGCAGCAGCAGCCTGTGAAGCAGGAACCACCAGTGTCTGAACATACGCTGAAGAAGATTTTTGTGAGTAATGTGGGTGC[A/G]GATGTAGATCTGAAGAAGTTGGTTGAGTTCTTTGGGAAGTTTGGAGAGATTGAGGATGGGCCCTTAGGGTTGGATAAGGTAACA
84514 G T ACGTCGTGACGGAGGAGGAGGAGGAAGGAGTGGAGAGGGTTGTTCTGAACGGGGAGATGGTCGAGATAGGATTCCCTGCGGGGTTGCCGAGGTTGCATAC[G/T]GTTGTTGAAGGTACTACAAACTCTTATATGCTTGATAGGTTCCTGTCGGAGTTGATTGTGGATTGAGAGTAAAATTTAGTACC
84556 G A GCGGCCCAGTACCTGCGGCCCATTGTCCAGTTCTTGATCAATACCGGCTCTCCCCTCCTGTGTAATATTTATCC[G/A]TACTTCAGCTACCAAGGCAACCCGAGTCAGATATCGCTTCCGTACGCATTATTCACGGCGCCTGGAGCAGTGGTTCAAGACGGTTCAAACAGCTACCAGA
84556 G A TACCGGCTCTCCCCTCCTGTGTAATATTTATCCGTACTTCAGCTACCAAGGCAACCCGAGTCAGATATCGCTTCCGTACGCATTATTCACGGCGCCTGGA[G/A]CAGTGGTTCAAGACGGTTCAAACAGCTACCAGAATCTGTTTGACGCGCAATTAGACTCGGTTTACTCGGCGTTGGAAAAAATTGGAG
84556 A G CAAACAGCTACCAGAATCTGTTTGACGCGCAATTAGACTCGGTTTACTCGGCGTTGGAAAAAATTGGAGGCGGCGGCGTCAGAGTTGTGGTGTCTGAATC[A/G]GGATGGCCATCTGCAGGTGGATTCGCGGCGGACATTGGGAAAGCGCAGACCTTCAACACCAATTTGGTTAGACATCTGAATAAAG
84618 C T TGATATAGAGGATTGGCTCCTCAACGCGTGACTCCTTGGTAGAGCGGAGCTTTTCGATAACCCCTTCAAGATAGCTAATAGCAACATCTTTCTCAGAGTA[C/T]TGACGTGAAACTATCACGGCAAAGTGTGCGAGTTTCAGAAGATTGATCTTTGTCTCGAAGTCGGAAATGAAATTGTGATATAGCTGC
84618 A G AGCTAATAGCAACATCTTTCTCAGAGTACTGACGTGAAACTATCACGGCAAAGTGTGCGAGTTTCAGAAGATTGATCTTTGTCTCGAAGTCGGAAATGAA[A/G]TTGTGATATAGCTGCACAAGTGCATCTCCTGCCTGAACAACAGCAAGCGCGACGAATTGTTCTAGCTTGAGAGTCAACTGATGCCAC
84618 T C CGAGTTTCAGAAGATTGATCTTTGTCTCGAAGTCGGAAATGAAATTGTGATATAGCTGCACAAGTGCATCTCCTGCCTGAACAACAGCAAGCGCGACGAA[T/C]TGTTCTAGCTTGAGAGTCAACTGATGCCACAACTTTTTCTCGTATAGATCCGCAAGAGCATTGTACCATTCTTCCAGCTCAGGCTGAG
84624 CT C CCCGATGAGGATATCGCGGCCAGTGCGCTGTCCCTCATCCCCGCCAAGTTCGGGTCATATCCCATTGGGGGGGACAGAGCCGCAGTT[CT/C]TTTGTAGAGGAGGTTGGTTTCCTCTTTGCCGAGGAAGGATTCCTTGCCATAACGGATCATGCAGGCGTCGAGCTGGACAGCTGCGCCGGAGGAGGA
84624 T C CCTCTTTGCCGAGGAAGGATTCCTTGCCATAACGGATCATGCAGGCGTCGAGCTGGACAGCTGCGCCGGAGGAGGAGGAGCAGGTGGACGACAGATGGTT[T/C]AAGGCTGAACGGATGCATGATTGGCAGTCAGAGGTGGGGAGGTCGCCTCGGCACTGGAAGATTCCAGAGACGGAGGAAGAG
84644 G A ATCAGGAGCTGCCAGCACAATGCTCCAGTTTTACACAGACGACACTTCTGGACGCAGAATGTCTCCCAATACCGTGCTTATCATGAGCGTCGGCTTCATT[G/A]CCGTCGTTTCTCTTTTGCATGTTTTTGGCAAACTTCTTCGCTAGATGTGTTTTATAACCATTTTCATTGTCTTCTATACTTCAATAAACAG
84668 C T TGGAGCATGATGCTATGAAGTTGAGCTCTGACTCATCTTGAACTAAGGTGAAGTTGGTTTTGGCATCAGGGCCTCTGAATTTGTAGGCCGCGATGTCGTA[C/T]GAGAGAGCGGCTTCCAATTCGGTTTCAAATGTGCCGAGCCACACCCTGTGATGCTTCTGGTAGATCTGGGATCCCCAACGGCCATT
84670 C A ACAAAAATTAAAAGATAGTTTAGATGGTCTAATCAGCTTCATCGATAACCTTGGTTCCCAGTCCTTTGAGCCCTTCAGGAGGTACTTCTGCAGCTGTAAC[C/A]AGAGAGTAGAGTTCTTCTTTGGCGTCTTCTTCTTCGTTTCTTTTACGAGCGATTCTGATGCGAACACGCCTAGGAACACCTCGGATTCC
84670 GT G CTTCATCGATAACCTTGGTTCCCAGTCCTTTGAGCCCTTCAGGAGGTACTTCTGCAGCTGTAACCAGAGAGTAGAGTTCTTCTTTGGCGTCTTCTTCTTC[GT/G]TTTCTTTTACGAGCGATTCTGATGCGAACACGCCTAGGAACACCTCGGATTCCACGGCTCCAGATGTGTTTGTTCAGTTTCACATCTAC
84670 T G TCTACCCTAACATCGTTGGTTCCCATCGCCTTTTGTGCAAACTTCCTGATCTCTTTTATTGCATTCGGAGCCTTCTTCTTGAATGTGCATCCATGGAGTC[T/G]CTTGTGGAGGTTGATGGTGTATTCCCTGGTAACCACTTCCTCCTTCCTTCCTTTCGCGCCCTTTTCGACCATTGTCGCCTAACCCTAATTTG
84704 T C TTTTTTTTTTTTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGC[T/C]CGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAAT
84704 C T TTTTTTTTTTTTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATA[C/T]ATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGA
84704 C T TTTTTTTTTTTTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAAT[C/T]TTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCA
84704 A G TTTTTTTTTTTTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTT[A/G]ATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCA
84704 C A TTTTTTTTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAA[C/A]GTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTC
84704 A G TTAAATAAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGC[A/G]TTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGT
84704 C A AAAACAAAAAATATCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGA[C/A]TGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTG
84704 A C TCTGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATT[A/C]AGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAA
84704 G C TGATTTTCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAA[G/C]AACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAA
84704 T C TCTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTA[T/C]TGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACAC
84704 TG T CTTCAGATTGGGTAGGAAAGTGATTCTTAAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTAT[TG/T]GTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACAC
84704 G A AAAATACAAGCTCGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGA[G/A]AATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
84704 C T CGCAATACATGCAAAATCTTAATCAACGTTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAAT[C/T]GTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAG
84704 G A TTGCATTCGACTGAAACATCATTAAGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGT[G/A]TATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCA
84704 A T AGAACTATTGTTTAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAA[A/T]TTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAAT
84704 T C TAAAGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTG[T/C]GGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTT
84704 A G AGTTCCCTTTGTCAATCCTGAGAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGG[A/G]GATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTTACA
84704 A AG GAATAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACG[A/AG]GGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTT
84704 CATAG C TAACACAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGG[CATAG/C]ATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTT
84704 A G CAATCGTATTGACTTCCAGCTCTTGGTTTTGTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAG[A/G]TAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTTCTCAATGTA
84704 C T GTGTATAGCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAA[C/T]CTGCCATTGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTTCTCAATGTACCCTTTAAATGCCTTCAACCATTCAGCACC
84704 T C GCCTCCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCA[T/C]TGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTTCTCAATGTACCCTTTAAATGCCTTCAACCATTCAGCACCAACTGCA
84704 G C CCAAAAATAACACAAATTGACAAGTTGTGGAGATTTACAAAAGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGC[G/C]CAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTTCTCAATGTACCCTTTAAATGCCTTCAACCATTCAGCACCAACTGCACCAT
84704 A G AGAATCAACGAGGCATAGATAGAACCTTATTCATAAAGCAAAAAATAACCTGCCATTGCGCAATGGCAGCAGTTTACAGTAACATGGAGGTAGGGTTCTC[A/G]ATGTACCCTTTAAATGCCTTCAACCATTCAGCACCAACTGCACCATCAATGACGCGATGATCACAACTTAATGTGACCGACATATAT
84720 G A CATAACTTGTTTTTGGGGAAAGTGATCTGGCCTCAAATTTTCCATTGAACTCCAGCCAGCATACGTTCAACAGCTCTATAATCTCTGGAAAACTCAAATC[G/A]GAAGAAGGGGTCCATTTCCAGAAATGGGGATTCTCATTCCAAACGATATTCATTGCCCTAGGCCAAATCATGTAGCACTTTTTTCCACT
84728 G A CAGAGTTTGCCCTTCAAAGTTCTTATGTGGCTCTTCTAATGCCTTATTAGCACTCTCCGCGTTCTTATATGCAAACAAGCAAAACCCACGAGGCTTCCCT[G/A]TATTCTTATCCAAACCTAATGGCCCTTCTTCGATCTCTCCAAACTTTCCAAAAAACTCAACCAA
84730 A C GAATGAAGGCAATGACACATTGATTAGTGCATTTCTTGTTCTATTGCGAGCTAAGGGTGAAACTTATGAAGAGATTGTGGGAATGGCTAGAGCAATGATA[A/C]AACATTGTGTAAAGGTTGAGGGCTTGTCAGATACAGTAGATATAGTAGGAACAGGAGGAGACGGGGCCAATACCGTCAACATTTC
84748 A G TCGCAATTCCCAATTCGCGGATCAGGAAGCCGAATCTCCAAATCACGAAACCGAAACCACAAAATCGCCTATATAAACCACAAAAGCAACGACAACGACG[A/G]TCCACAAACAGCAACTATCCAAATCGCAGTTCGGCCCAGGCAAAAGTTGAAAGGCGCGCACGATAGTTTATTGTTCAATTTGACGC
84808 G A TTCGAATTCATGAACTACACGATAATAACAAGCAAATGCAAAGGACCTCAGTACCCAGCCAAACTCTGCTGCGATGCCCTAAA[G/A]GAGTTCGCATGCCCCTACACGGACGCCATTAATGATGGAAGCAACGACTGTGCTTCTACCATGTTCAGCTACATCAATCTCTACGGCAAGTACCCACCTG
84808 C T ATCTCTACGGCAAGTACCCACCTGGCCTTTTCTCTAGCGAGTGCAAAGAAGGGAAAGAAGGTCTTGCATGTCCCGATGAGGCTCCTACGGGAGCTCCAAG[C/T]GATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATG
84808 C G AGTGCAAAGAAGGGAAAGAAGGTCTTGCATGTCCCGATGAGGCTCCTACGGGAGCTCCAAGCGATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAAC[C/G]GTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGGGTTTGTGTTGTCTTTGTTTAGTTGGGTGATATT
84808 A T AAGGGAAAGAAGGTCTTGCATGTCCCGATGAGGCTCCTACGGGAGCTCCAAGCGATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGC[A/T]TTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGGGTTTGTGTTGTCTTTGTTTAGTTGGGTGATATTTATGGCTATG
84808 T A AAGGTCTTGCATGTCCCGATGAGGCTCCTACGGGAGCTCCAAGCGATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGCATTTGCGCT[T/A]ATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGGGTTTGTGTTGTCTTTGTTTAGTTGGGTGATATTTATGGCTATGTATTTTGTA
84808 A G TACGGGAGCTCCAAGCGATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGA[A/G]TGTGGGGGGTTTGTGTTGTCTTTGTTTAGTTGGGTGATATTTATGGCTATGTATTTTGTAAAGTATGGGGATGTTCATGAAGGATGAA
84808 GT G TCCAAGCGATAAGTCCAGTGCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGG[GT/G]TTTGTGTTGTCTTTGTTTAGTTGGGTGATATTTATGGCTATGTATTTTGTAAAGTATGGGGATGTTCATGAAGGATGAATGTATATAC
84808 A G GCTGCTCAGGATGTGCTTCTTTTAACCGTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGGGTTTGTGTTGTCTTTGTTT[A/G]GTTGGGTGATATTTATGGCTATGTATTTTGTAAAGTATGGGGATGTTCATGAAGGATGAATGTATATACATTGTGATTGATGAAGAGT
84808 G A TCTTTTAACCGTACTCGCATTTGCGCTTATTGTGGGTTTTGTTTTCAACTGAAGAATGTGGGGGGTTTGTGTTGTCTTTGTTTAGTTGGGTGATATTTAT[G/A]GCTATGTATTTTGTAAAGTATGGGGATGTTCATGAAGGATGAATGTATATACATTGTGATTGATGAAGAGTTTCCGATGGTACATTACA
GAGCATATCTTATTTTCTTTTGCCGCACACTCCCATCAAAAGTCATCAATCAAC
84822 A CAAGCTGATTACTCCTTAAAAAACAAAACTTTGTAATACTTCTTCCTCTTGAATCCACTTCAATATGCTTCATACATCATCATTACA[AGCTAGAGCATATCTTATTTTCTTTTGCCGCACACTCCCATCAAAAGTCATCAATCAAC/A]GCTAGAGCATATCTTATTTTCTTTTGCCGCACACTCCCATCAAAAGTC
84830 A T TGTTAGTTGAGGATTACGTATGATTGTGAGTTCTGTGAGCTTCTTTAAGTTGCCCAGAGTGGAAGGGATAGAGCCAGTGAGGTCGGGGTGGCCTTTTATG[A/T]AAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGAC
84830 C T TGAGGATTACGTATGATTGTGAGTTCTGTGAGCTTCTTTAAGTTGCCCAGAGTGGAAGGGATAGAGCCAGTGAGGTCGGGGTGGCCTTTTATGAAAAGCT[C/T]GGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCT
84830 G A GAGGATTACGTATGATTGTGAGTTCTGTGAGCTTCTTTAAGTTGCCCAGAGTGGAAGGGATAGAGCCAGTGAGGTCGGGGTGGCCTTTTATGAAAAGCTC[G/A]GTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTT
84830 C G AAGGGATAGAGCCAGTGAGGTCGGGGTGGCCTTTTATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGT[C/G]TCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTG
84830 G A AGCCAGTGAGGTCGGGGTGGCCTTTTATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAG[G/A]TAGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGG
84830 T A GCCAGTGAGGTCGGGGTGGCCTTTTATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGG[T/A]AGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGA
84830 T C GAGGTCGGGGTGGCCTTTTATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGG[T/C]TGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGC
84830 T C AGGTCGGGGTGGCCTTTTATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGT[T/C]GGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTG
84830 C G TATGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTA[C/G]CAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGAT
84830 A G TGAAAAGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACC[A/G]GATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCT
84830 C T AGCTCGGTGAGCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACCAGATA[C/T]ATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCA
84830 G A GCCCGCTGAGCTTGCCTATGGATGGAGATATTGTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTA[G/A]ACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAG
84830 C T GTTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGT[C/T]TGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCT
84830 T G TTCCGGAGATGTCGGTCTCTTCTAGGTAGAGGTTGGTGACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTC[T/G]GTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTG
84830 C A GACTCTGCCTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGAT[C/A]TTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATA
84830 G A CTTTACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCAT[G/A]TCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAAC
84830 T C TACCAGATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTC[T/C]AGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAG
84830 A G GATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTA[A/G]GGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGA
84830 G T ATACATCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAA[G/T]GCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGG
84830 C T TCGCAGTAGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAG[C/T]TGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGA
84830 T C AGACGTTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTC[T/C]TTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGA
84830 T C TTGCTCCAGGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTT[T/C]GCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGAGGAGC
84830 C T GGTGCAGCAGTCGGTTGAGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCAT[C/T]TGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGAGGAGCCCTGAAGA
84830 G C AGTCTGTCCAGCTGGATAAAGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGA[G/C]AGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGAGGAGCCCTGAAGAAGAATTAAATGTAACCA
84830 G A AGCTGATGGGTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGAT[G/A]TGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGAGGAGCCCTGAAGAAGAATTAAATGTAACCATGACGATTAATTTGTATATC
84830 A G GTTATTGAATGATCTTTTCATGTCTAGTAAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGAT[A/G]CTGTAAACAAGAGGAGGAGGAGGAGGAGGAGCCCTGAAGAAGAATTAAATGTAACCATGACGATTAATTTGTATATCCAGTAGGCC
84830 G A AAGGCAGCTGAGTCTTTTTTGCTGCATCTGAAATCTGTGTTTGAGAGTGTGCATGATATGGATGTGAATGATACTGTAAACAAGAGGAGGAGGAGGAGGA[G/A]GAGCCCTGAAGAAGAATTAAATGTAACCATGACGATTAATTTGTATATCCAGTAGGCCAACA
84858 C T GGTGGTACATGGACTGCAGGGCGACGATGGAGGAGACGGAGATCAGCCTGAAGTTCCTGTTCGTACTGCTCCCGGTGGTGCTGGTGCTCATGGTGAAGGA[C/T]CTGTTCAACGAGGAGGGGAGGCTGGCGGTCAGGCTGCTGCCGGACGCCGAACAGCAGGCCATTCATAGGGCTGGTGGGTCGC
84908 A T CACTAAAAATGTTGAGCACGGTTGCGGAGCAAAAACACAAAACAACAGACCATCCAAACTAAAAGACTCAACTCGAAACAGGCATAAACAGATCCAAAAA[A/T]CATCTAAACAAAACCTCAAACCACACAGTAACAAAAACGCATACCAGAAGACTCAAAAATTCATAGTAAACACAGCGAGAACTACC
84908 G A AAAAAACATCTAAACAAAACCTCAAACCACACAGTAACAAAAACGCATACCAGAAGACTCAAAAATTCATAGTAAACACAGCGAGAACTACCATGTTCCA[G/A]AACCGTGTACATCCCAACTCTCGATAGCTGATAACAGTCTCGTTTAAGAGGCGGATGTGAGTTAGAGAGGCCTAAATGGAAACATG
84908 T C AGAGGCGGATGTGAGTTAGAGAGGCCTAAATGGAAACATGGAGGTGTTGCGTCACCGTGTAACCTCCCAAGCTCAAGGATCTTCGATTCCGTATTGAGGG[T/C]GGAAGCAGAAGTTAGATGAGGTGGATCTGAGAATATGGAGGGTTTCGAGTGTAAGGCTTCAGCGTCGAACCATGCATGTCGAAA
84924 T C CCTCCTGGTATTGTTGTTTCTGAGACCGATTTATATTTACGTAGATTGTGGGGAGACCCAAATGAGGACCTGACTAGGAAGCCAAAATACTTGGTGGCAT[T/C]CGCTGTTGGATTTGATCAGTCTGCAAATATTGATGCTGCAATCAAAAAGTTTTCTGAGAATTTCACAATCTTGCTTTTTCACTATGATG
84924 G A CTTGGTGGCATTCGCTGTTGGATTTGATCAGTCTGCAAATATTGATGCTGCAATCAAAAAGTTTTCTGAGAATTTCACAATCTTGCTTTTTCACTATGAT[G/A]GTCGAACAAGTGAGTGGGAAAAATATGAGTGGTCAAAGCGTGCGATTCATGTCAGTGTAAAAAAACAACAAAATGGTGGTATGCAAA
84944 G T AGTGCCAAATTAAATTATAAAAAACAATGGAGGTTGGATTTCTGGGTCTGGGAATCATGGGAAAAGCTATGGCGATTAATCT[G/T]TTGAAAAATGGATTCAAAGTTACAGTTTGGAACAGAACCATTTCTAAGTGCGAAGAGCTTGTGGAATTAGGTGCTTCTATTGGAGAAACGCCTGCAGCAG
84950 G A GAAATAACAGTTTTCAGGCTGCAAGTGCAGTTCAAAGCCAAACAAGGCACGTGCCTTCCTATTTCAATGACTTCAAGTATGGATTTCCGTCAAATGGTTT[G/A]TCTTGTGTTTCTAATAAATGGTGGGGAAGCAGCTGTGAGAGTGATACCGACAATAGTAATCCAGAGAAGCTCACAATAAGTGATGTG
84950 G A GAGAAGCTCACAATAAGTGATGTGGAAAATAAGGGTATTGATACTATTGCAGCTCCGTCAGTTTCGTTGGTGTTGATGAGAAAAAGAGCTTTAGAATGTT[G/A]TCGCAAGTCACTGCATGGTGCGATGCATTTGAATGCTGAGTCCTACAAGTTGAGTAAGAAAAAGAGATCACTGATGTTTCAGCTGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
84956 T C CGCTTCCTTTCTTCTTTCCTTCTGCGTCCTCTTTATCACCGTCCTCGATCCCTAACCCGCTTCATTTCTCCATCACTTGCGACAGCGGCGACACGGTTCA[T/C]CCCTGTCCATTTCATGTCGAACTATCGTGGAAACTCCCCCTACACCTCTATCATATCGGGCGGTGACAATGGGTACGGCAACTACGCGCCA
84956 A G TCGATCCCTAACCCGCTTCATTTCTCCATCACTTGCGACAGCGGCGACACGGTTCATCCCTGTCCATTTCATGTCGAACTATCGTGGAAACTCCCCCTAC[A/G]CCTCTATCATATCGGGCGGTGACAATGGGTACGGCAACTACGCGCCACAGGATACAGGGCCGCTTTTTCCAGGATGCGATTACAGACA
84960 T C AGATCAAAAGCCCAGTCGTTCCTCCGGCGTAAACATCGCCATTGGCCGACCATTCTTCAGGTGTGTAGATAGGGCTGTAGCCATCAACATTTGCACCATA[T/C]TTGTCAGCATATTGGTAAACTCCCTTTCCCTTGGGTTTTCTCCCTGATGCATCAACACCATTTCTCAAGTTCATCCCACCTCCAGTTCCA
84962 A AC GCCGCCGCCGCTCACAACGTCGGAGAGAAGCCAGCCTCAGCCGACGGTGAAGTCCCTGTTGCCAAAAAGGCATCCGCTAAACCAAAAGGCAACTGCTGCT[A/AC]CAAACCCCGTGTTCCGCCGGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGAT
84962 T G CTCACAACGTCGGAGAGAAGCCAGCCTCAGCCGACGGTGAAGTCCCTGTTGCCAAAAAGGCATCCGCTAAACCAAAAGGCAACTGCTGCTACAAACCCCG[T/G]GTTCCGCCGGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATG
84962 T A ACAACGTCGGAGAGAAGCCAGCCTCAGCCGACGGTGAAGTCCCTGTTGCCAAAAAGGCATCCGCTAAACCAAAAGGCAACTGCTGCTACAAACCCCGTGT[T/A]CCGCCGGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATGCCA
84962 C T CGTCGGAGAGAAGCCAGCCTCAGCCGACGGTGAAGTCCCTGTTGCCAAAAAGGCATCCGCTAAACCAAAAGGCAACTGCTGCTACAAACCCCGTGTTCCG[C/T]CGGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATGCCATCAC
84962 T C GTGTTCCGCCGGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATGCCATCACCAAGTT[T/C]ATCGAGGACAAGCATAGCTCAAAGCTTTCATCAAATTTCAAGAAGACTGTTCTCCATCAGCTGAAAAAACTCACAGCCAGCGGTAA
84962 A C GGCACATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATGCCATCACCAAGTTTATCGAGGAC[A/C]AGCATAGCTCAAAGCTTTCATCAAATTTCAAGAAGACTGTTCTCCATCAGCTGAAAAAACTCACAGCCAGCGGTAAGCTCATCAAG
84962 T C ATCCTCCATACGCTGAAATGATCACCGAGGCAATCAGCGCATTGAAGGATAGGACGGGATCTAGCCAACATGCCATCACCAAGTTTATCGAGGACAAGCA[T/C]AGCTCAAAGCTTTCATCAAATTTCAAGAAGACTGTTCTCCATCAGCTGAAAAAACTCACAGCCAGCGGTAAGCTCATCAAGATCAAA
84962 C T GATCTAGCCAACATGCCATCACCAAGTTTATCGAGGACAAGCATAGCTCAAAGCTTTCATCAAATTTCAAGAAGACTGTTCTCCATCAGCTGAAAAAACT[C/T]ACAGCCAGCGGTAAGCTCATCAAGATCAAAGCTTCATACAAGCTTTCATCTGTCACCACAACCAAAAAAACTGCTGCAAAACCTAAAA
84962 A G TCGAGGACAAGCATAGCTCAAAGCTTTCATCAAATTTCAAGAAGACTGTTCTCCATCAGCTGAAAAAACTCACAGCCAGCGGTAAGCTCATCAAGATCAA[A/G]GCTTCATACAAGCTTTCATCTGTCACCACAACCAAAAAAACTGCTGCAAAACCTAAAACTAAGAAGTCTGCTGCTGGGGTCAAGAAA
84976 A G CCTCTGCAATTCGGTCACTGCATTCTTTAATTAATTTGGAAAATCTTGAATCTTCAGGTGCCAATTTCAGACCTGCTTCAAGAGCTGCTTTTGCGGTCTG[A/G]TACTCTTCTAATTTGATGCACGCAGTGCCTTTGCGCAAGTAAGCTTTGGACATTGAAGGATCAAGTTCAATTGCTTTATTGGCATCAGCA
84976 C A CTAATTTGATGCACGCAGTGCCTTTGCGCAAGTAAGCTTTGGACATTGAAGGATCAAGTTCAATTGCTTTATTGGCATCAGCAACAGCTTCAGTAAAAGA[C/A]TTGATCTTGATGTTAGCCTGAGCACGATCAGCAAACAGCCCTGCATTGTTTGGGTCCATGTCGATCGCCTGACTGTACAAATCGACGG
84976 G A TGATCTTGATGTTAGCCTGAGCACGATCAGCAAACAGCCCTGCATTGTTTGGGTCCATGTCGATCGCCTGACTGTACAAATCGACGGCGAGATCGAAATC[G/A]TCGTCCACGAAAGCTTCCTTTGCTTTCTTCTCAAGATCTGATGCCATTTATTGATTTGTGATGGAGGGAGAGAAAGAAGATAACGAG
84978 A G ATGTGCCATTGGAAGAGACCCTTCAACCAAAATATACTGTTGATAATCTCAAGCTCCAATGCCAACCCATCACCAAATGTAGCATCTATGCCTTGTTAGC[A/G]ATGTTGTTTGAGAGCCAGTCTAACCCCTCGTACAGACCTTCTCCAGATGTGGCACATGTGCTCTGAATATACCAGTGACGCTGACGAA
85000 G A CATCTCTTCGCTTCTTTTGAGTTTCAAATCGATTTCATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAA[G/A]TTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACT
85000 C G TTTGAGTTTCAAATCGATTTCATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTG[C/G]TGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTG
85000 G C TGAGTTTCAAATCGATTTCATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCT[G/C]GCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGC
85000 G A TCAAATCGATTTCATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGC[G/A]ACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTG
85000 G A CGATTTCATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGA[G/A]GGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGG
85000 A G CATTTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATC[A/G]ATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGG
85000 A G TTACATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAAT[A/G]CTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGA
85000 C T ATCTTCTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTC[C/T]TCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAAT
85000 G C CTTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCAC[G/C]GCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTG
85000 G A TTCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACG[G/A]CTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGG
85000 C A TCAATTTTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGG[C/A]TTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGA
85000 G C TTCCTAACTGTTTTCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCT[G/C]GGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGG
85000 T C TCAGATTCTTCCGAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAA[T/C]CTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGT
85000 A G GAACCAAGAATCCACGGAAAGTTTTCTGAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAAT[A/G]GAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGA
85000 C A GAATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGC[C/A]GACTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGA
85000 G C AATCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCC[G/C]ACTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGAG
85000 C T TCTTGCTGGCAGCGACTGAGGGATCAATACTCCTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGA[C/T]TGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGAGCC
85000 A G CTCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGG[A/G]GCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGAGCCATACGATTTTCGGAAATCTTAGACTGAGGTAG
85000 G C TCACGGCTTTCTGGGAATCGACGAATCTGACAGGAATAGAGATCGACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGGA[G/C]CGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGAGCCATACGATTTTCGGAAATCTTAGACTGAGGTAGC
85000 G A ACTTGGGTTTCTTCGCTGCCGACTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAAC[G/A]CGAGCCATACGATTTTCGGAAATCTTAGACTGAGGTAGCACTCTGATGGTTTATTGGATAACTTTTTATTTTCGTTGCAATGCGAT
85000 A G CTGCGATGGCGGGGAGAAAATATTGGAAGCGGAGCGATTAGGGTTTGAATATAGAGGGCTTTTGAAAACAGGATTAACGCGAGCCATACGATTTTCGGAA[A/G]TCTTAGACTGAGGTAGCACTCTGATGGTTTATTGGATAACTTTTTATTTTCGTTGCAATGCGATGGCCATCGAAATCGAGGGTTTG
85008 T A GCACTAAAGGTCCATTTCCTAGAAGCACCGTTTATTACTGTGTTATCAATCTTGCCGCTTATCAACTGAAAATAGATTAGATGCCCATAATTTTCTGAAT[T/A]TCTCCTCATGCTGAATTAGAATCCCATCCTCACAGCTCCTTATGTAATGGCCTTCAATTTTCCCATGTCTTCTACTTTAAACGCTTCACCTT
85008 T G CACTAAAGGTCCATTTCCTAGAAGCACCGTTTATTACTGTGTTATCAATCTTGCCGCTTATCAACTGAAAATAGATTAGATGCCCATAATTTTCTGAATT[T/G]CTCCTCATGCTGAATTAGAATCCCATCCTCACAGCTCCTTATGTAATGGCCTTCAATTTTCCCATGTCTTCTACTTTAAACGCTTCACCTTT
85008 C A ACTAAAGGTCCATTTCCTAGAAGCACCGTTTATTACTGTGTTATCAATCTTGCCGCTTATCAACTGAAAATAGATTAGATGCCCATAATTTTCTGAATTT[C/A]TCCTCATGCTGAATTAGAATCCCATCCTCACAGCTCCTTATGTAATGGCCTTCAATTTTCCCATGTCTTCTACTTTAAACGCTTCACCTTTG
85008 T A CTAAAGGTCCATTTCCTAGAAGCACCGTTTATTACTGTGTTATCAATCTTGCCGCTTATCAACTGAAAATAGATTAGATGCCCATAATTTTCTGAATTTC[T/A]CCTCATGCTGAATTAGAATCCCATCCTCACAGCTCCTTATGTAATGGCCTTCAATTTTCCCATGTCTTCTACTTTAAACGCTTCACCTTTGG
85044 G A CAGCCCTTGCCTGAGAAACAGCTTGCTTGCACAACTGATGGACGGTTTCATCATTCATAATAACCCCATCTTCCCTTACTATCCCATCATGTCCATCGGA[G/A]TTATATGGGTCCAACGCAACATCAGTGTATATCACAATGTCAGGAAATTTATCTTTCAGAAGACGAATCGTACGAGGAACAAGACCATT
85044 C T CAGTGTATATCACAATGTCAGGAAATTTATCTTTCAGAAGACGAATCGTACGAGGAACAAGACCATTATCATTGTATGCCTCGTCTCCTGTTTGTGACTT[C/T]AGTGCATCTGGGATTTTAGGGAAAAGAACAAAACTATTGACACCAACGTCCCTTGCCTTGTAAACCTCATCTATAAGTCCGTGCCTCCA
85048 TA T ACTTATGATACAACAATCATGGGTGCGGAAACGGCCATTAAGCCACAACTTATGACAAGGTACAATCCGAAACATATCAATACCATCTTGCTTTCATTAT[TA/T]ACGTAAAATATGAGTAAAACTAAAAAATTATAACTAAAAAAAAACATATCATCATTTGGCACTAGCCAATTCCTTCCTGAGTTGCTTG
85048 AAC A ATGGGTGCGGAAACGGCCATTAAGCCACAACTTATGACAAGGTACAATCCGAAACATATCAATACCATCTTGCTTTCATTATTACGTAAAATATGAGTAA[AAC/A]ACTAAAAAATTATAACTAAAAAAAAACATATCATCATTTGGCACTAGCCAATTCCTTCCTGAGTTGCTTGGCAGCCTGGACCATGTT
85050 C T AAGCTCAGATTCTCGAGTCAATTGGCGTTGACTACATCGATGAAAGCGAAGTCCTGACCCTAGCGGACGAAGACAACCATATCAACAAGCACAACTTCCG[C/T]ATCCCGTTTGTCTGCGGCTGCCGTAACCTAGGAGAAGCACTTCGTCGGATCAGAGAAGGCGCGGCTATGATAAGGACGAAAGGGG
85050 C G TAGCGGACGAAGACAACCATATCAACAAGCACAACTTCCGCATCCCGTTTGTCTGCGGCTGCCGTAACCTAGGAGAAGCACTTCGTCGGATCAGAGAAGG[C/G]GCGGCTATGATAAGGACGAAAGGGGAGGCTGGGACCGGAAACGTTGTGGAGGCAGTGAGGCATGTTAGATCTGTGATGGGGCA
85050 C A TCCGCATCCCGTTTGTCTGCGGCTGCCGTAACCTAGGAGAAGCACTTCGTCGGATCAGAGAAGGCGCGGCTATGATAAGGACGAAAGGGGAGGCTGGGAC[C/A]GGAAACGTTGTGGAGGCAGTGAGGCATGTTAGATCTGTGATGGGGCAGATTAGGGTTTTGAGGAACATGGATGATGATGAGG
85050 G A TCTGCGGCTGCCGTAACCTAGGAGAAGCACTTCGTCGGATCAGAGAAGGCGCGGCTATGATAAGGACGAAAGGGGAGGCTGGGACCGGAAACGTTGTGGA[G/A]GCAGTGAGGCATGTTAGATCTGTGATGGGGCAGATTAGGGTTTTGAGGAACATGGATGATGATGAGGTGTTTACCTT
85056 T G TAAACGTTAACGTTCCAGTGGATTCTGTGGTAGCCTCAGACATTCTGAAAGACGCCAGTAAGATCGTCGCTAAAACCCTCGGCAAGCCCGAATCGTATGT[T/G]ATGGTGATCGTCAATGGTGGAGTGCCTATAGTATTTGGTGGAAGCGAAGAGCCAGCTGCATATGGAGAGGTTATATCAATCGGTG
85056 C T ACGTTCCAGTGGATTCTGTGGTAGCCTCAGACATTCTGAAAGACGCCAGTAAGATCGTCGCTAAAACCCTCGGCAAGCCCGAATCGTATGTTATGGTGAT[C/T]GTCAATGGTGGAGTGCCTATAGTATTTGGTGGAAGCGAAGAGCCAGCTGCATATGGAGAGGTTATATCAATCGGTGGCCTCGGTC
85056 G A CCTCGGTCCTGGTGTGAATGGAAAATTAAGCTCAGCGCTTGCGGATCTTCTAGAGACTAAGCTCTCTGTCAGCGGTTCTAGGTTCTACATTAAGTTCTAT[G/A]ATGTTCAGCGGTCAAACTTTGGCTTCAATGGATCGACGTTTTGATCTGTGGGCTGCAATTATTTCCATTTCAAGTTAAGCTGCTGCAAC
85056 T A AGCGCTTGCGGATCTTCTAGAGACTAAGCTCTCTGTCAGCGGTTCTAGGTTCTACATTAAGTTCTATGATGTTCAGCGGTCAAACTTTGGCTTCAATGGA[T/A]CGACGTTTTGATCTGTGGGCTGCAATTATTTCCATTTCAAGTTAAGCTGCTGCAACAATGGGGCATCGTAGATCATTTTGATTATTAAA
85094 G A GCAACATCATCCTTCTGCTGGCTCTCCTCGCCGTGGCCATGGCAGCAGCTTCGTCTATGGCTGAGGAGCTTGGAATCAACTTGGATGCGGCGAAGCATAA[G/A]CATAAGCATTCTGGATTAGCTGAATCAGAATGTCCAGATGCATGTCAATTCAGGTGCTCAAAGACACAATACAAAAAACCATGTCTT
85094 CT C TGCGGCGAAGCATAAGCATAAGCATTCTGGATTAGCTGAATCAGAATGTCCAGATGCATGTCAATTCAGGTGCTCAAAGACACAATACAAAAAACCATGT[CT/C]TTTTTTACTGCCAAAAATGCTGCAAAACTTGCAAATGTGTGCCTCCAGGTACTTACGCCAACAAGGAAAAGTGCTCATGCTACAAT
85106 T C GTAGAGCTCATCCAGATAGGTCAGGGTTTGATGGTGCTTGGACAAAAGAACCCCTCAAATTTGACAACTCCTACTTTGTTGAGTTGTTAAAGAATGAACA[T/C]GATGGGCTTCTGAAGCTTCCTTCTGATAAGACTTTGGTGGAGGATCCTAAATTCAGACCTTATGTAGAGTTGTATGCAAAGGACGAG
85110 C T CCGCAACCACGCACGAGTTCAACCATATGATTGCCACGCTGTCCCTATTTCACCAGCGCCATCCAACTACACCACCCCGAGCGCCTCCAGATCCTCCACC[C/T]TCGGTCCAAACATCTTCACCTCCGGTCAAAGCCATCCGCATCCGGTGAAGCCCCAAAAGCCATGCCCATCTGAGTAGATCACGACCAC
85112 A G TCTTCCTTGTGTACCTTCTCCATGCAGCTTGGATGAAGCATGCAGCCCACGTTCTCCATTGCTGCGAGTAAAACCGAAATGCGTGCCTCAGTTGCTTACT[A/G]TGAAGTCTGCGAAATTGTGTTGCGACAAATTTAAGGTCATCTGCCATTAACGCAAAGGCTTCTACTTCGGTTAGCGTTTTTACGGTTCG
85114 A AC GCAAAGTCTTGTGGTGATGATCAAAGCACGGCCTTTGTGGCGTAGCTTTGTGTAACGTTGACTCGCGAGTTTCACACCCGGTATGAACCAAAAACGGGAG[A/AC]GGACGTCAGGGAGGGCATGCGTTTCTTTCTAGCTAGAAGTGGCGTCAGTGGTTTTACACGCCCTGACGAGTTTGACTTATGTGG
85114 G C GAGAGGACGTCAGGGAGGGCATGCGTTTCTTTCTAGCTAGAAGTGGCGTCAGTGGTTTTACACGCCCTGACGAGTTTGACTTATGTGGTTGTTGCTGTTG[G/C]GAGGCGCCTCGGTTATATCGGTTTCGGCCGAATGCATTCTGGTCGGCTGACGGACCAGACTTACACCCCATAGGGTGGGGAGACG
85134 C T GAACTGCATTACAGGTTCTGAACATACATAAGCAACAACAGATGAACACACAGTCGATAG[C/T]GTACATAAGTAACAAATACCCACACGCGGCTGACATTAACATTTAGCATATATATATATAAACTACATGTAACCCTTGTCTTGATCACACCAACAAATTT
85134 CAT C ATTACAGGTTCTGAACATACATAAGCAACAACAGATGAACACACAGTCGATAGCGTACATAAGTAACAAATACCCACACGCGGCTGACATTAACATTTAG[CAT/C]ATATATATATATAAACTACATGTAACCCTTGTCTTGATCACACCAACAAATTTTAAACAAACACCACATCATTTATGCAGCAACTCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
85142 A T CCGATGTGTGGATGCCAGTCATAACTGCCACTGCTGATCAGAGGCGTGAATTTGCTGGAACCAGCAATGACAAAGACGAAGATGCCCAATAATAAGTTAC[A/T]TGCAATCTTCGTGATCCTGCATATATGACATTGATCATTCACCAAAGTATTCATGTTCATTTCAGTACCAAATTGTTTTT
85150 G A GCAAGGAATTCAACGTCGTCGCCTCCATGCTGGACGCATCCGGAGTGAGATCGGAGTTCGAGCATGACGAGAAAGGCGCCGGAATCACAATGTTCGTTCC[G/A]ACCGACGACGCATTCGGCGATCTGGCCGTAACAGAACAATTTCAGTCTCTGTCGGCCGATTTAAAAGCCACCATTCTCAAATACCA
85150 C T TCGCCTCCATGCTGGACGCATCCGGAGTGAGATCGGAGTTCGAGCATGACGAGAAAGGCGCCGGAATCACAATGTTCGTTCCGACCGACGACGCATTCGG[C/T]GATCTGGCCGTAACAGAACAATTTCAGTCTCTGTCGGCCGATTTAAAAGCCACCATTCTCAAATACCACGTGCTGCATTCTTATTAT
85150 A G CCGGAGTGAGATCGGAGTTCGAGCATGACGAGAAAGGCGCCGGAATCACAATGTTCGTTCCGACCGACGACGCATTCGGCGATCTGGCCGTAACAGAACA[A/G]TTTCAGTCTCTGTCGGCCGATTTAAAAGCCACCATTCTCAAATACCACGTGCTGCATTCTTATTATCCGCTTGGTTCGCTCGAGTC
85150 G A TCGTTCCGACCGACGACGCATTCGGCGATCTGGCCGTAACAGAACAATTTCAGTCTCTGTCGGCCGATTTAAAAGCCACCATTCTCAAATACCACGTGCT[G/A]CATTCTTATTATCCGCTTGGTTCGCTCGAGTCGATCGTGAATCCGGTGCAGCCAACGATTGCGACGGAGACGGAAGGTCCAGGAAA
85150 T G CATTCGGCGATCTGGCCGTAACAGAACAATTTCAGTCTCTGTCGGCCGATTTAAAAGCCACCATTCTCAAATACCACGTGCTGCATTCTTATTATCCGCT[T/G]GGTTCGCTCGAGTCGATCGTGAATCCGGTGCAGCCAACGATTGCGACGGAGACGGAAGGTCCAGGAAAGTACACATTGAATATAACG
85150 A G TCAAATACCACGTGCTGCATTCTTATTATCCGCTTGGTTCGCTCGAGTCGATCGTGAATCCGGTGCAGCCAACGATTGCGACGGAGACGGAAGGTCCAGG[A/G]AAGTACACATTGAATATAACGAGGGTCAACGGATCTGTGGCTATCAGCACCGGAATCGTACAGGCGTTGATCACCAGAACGGTTT
85150 A G CGGTGCAGCCAACGATTGCGACGGAGACGGAAGGTCCAGGAAAGTACACATTGAATATAACGAGGGTCAACGGATCTGTGGCTATCAGCACCGGAATCGT[A/G]CAGGCGTTGATCACCAGAACGGTTTTCGACCAGAGTCCGGTTTCTGTTTTTGCGGTTTCCAGGGTTTTGTTGCCGAGGGAGGTG
85158 G A CGTCAGATGGTGCAATATTCAAAGATTTGAGGCTGTGATGAAGGTAAAAGGCTTCTTCGAAGTTGAATTTAATTCGCTGCCAAGATCATGTCGAAAAGCA[G/A]GTCTTTATCAACTTTAGCGAATTTAACAAACTCAGCATCCCAATTTTCCAGGTCATCACCGTCAGATATACCGTCGCTTGCAGACTCA
85164 G A AGTTGAATCGGATGAAAGGGAAATTTTCTATAGGCTAGTTGATGACAAGTTGGTCATCTGCGATGAAGGAGAATTTGGTGCAAGAAATGAAGCGATTCTG[G/A]CGGCGAAGGACTGGGATAGGAGGGTCATCTATACTAGTCGCTCTCCCGGTCACCGGCCTGACCTTTTTAGCTGGTTTCGTCGCTG
85164 G T TTGAATCGGATGAAAGGGAAATTTTCTATAGGCTAGTTGATGACAAGTTGGTCATCTGCGATGAAGGAGAATTTGGTGCAAGAAATGAAGCGATTCTGGC[G/T]GCGAAGGACTGGGATAGGAGGGTCATCTATACTAGTCGCTCTCCCGGTCACCGGCCTGACCTTTTTAGCTGGTTTCGTCGCTGTG
85164 G T TTTCTATAGGCTAGTTGATGACAAGTTGGTCATCTGCGATGAAGGAGAATTTGGTGCAAGAAATGAAGCGATTCTGGCGGCGAAGGACTGGGATAGGAGG[G/T]TCATCTATACTAGTCGCTCTCCCGGTCACCGGCCTGACCTTTTTAGCTGGTTTCGTCGCTGTGCTGGTATCTGATTGTGTCTTTTTG
85164 T A GACTGGGATAGGAGGGTCATCTATACTAGTCGCTCTCCCGGTCACCGGCCTGACCTTTTTAGCTGGTTTCGTCGCTGTGCTGGTATCTGATTGTGTCTTT[T/A]TGTTGTTTCATTTTGCATATGCTGTGTATTTGGTAGTTTGACCGCCTTTATGTCGACTTCGGTCTTCGGGGTCTCTCTGTGGCTAGCGG
85164 C T ACCGGCCTGACCTTTTTAGCTGGTTTCGTCGCTGTGCTGGTATCTGATTGTGTCTTTTTGTTGTTTCATTTTGCATATGCTGTGTATTTGGTAGTTTGAC[C/T]GCCTTTATGTCGACTTCGGTCTTCGGGGTCTCTCTGTGGCTAGCGGTCAGGCATTGTTGACCATCCTTTTTATAATTTATG
85164 C T CTTTTTAGCTGGTTTCGTCGCTGTGCTGGTATCTGATTGTGTCTTTTTGTTGTTTCATTTTGCATATGCTGTGTATTTGGTAGTTTGACCGCCTTTATGT[C/T]GACTTCGGTCTTCGGGGTCTCTCTGTGGCTAGCGGTCAGGCATTGTTGACCATCCTTTTTATAATTTATG
85170 C G TCATCCGACGTGGCATCAGATGAGGAACACGATGGGAGCCACGTGGCTGCGTCTAACAGAA[C/G]CATTGCATGGGATCTGATCCAACGGTTGAAAGAAGATCGTCGGATGGACGCTCAGCTTGAGCAAATAATCGTTGACTTCTTCGTTGAGACGATGTCGGTT
85170 G A ACGTGGCATCAGATGAGGAACACGATGGGAGCCACGTGGCTGCGTCTAACAGAACCATTGCATGGGATCTGATCCAACGGTTGAAAGAAGATCGTCGGAT[G/A]GACGCTCAGCTTGAGCAAATAATCGTTGACTTCTTCGTTGAGACGATGTCGGTTTCCTTAGAAACATCCAATGCAGAGATCCAAC
85184 G A GTGATGTTGAAGATGAAGAAGAGCAGGAACCTCAAGCTGTTATGATATGCTCCTCCATACGGAAAATGTGGAAAGCATACCAATCTGATATGAAAGTATT[G/A]ACGTTAAAGGTTCCATCTAGTCAGAGATTTGTACAGTTTGCGTGGGATGATGAAGGGAGGGATTCTCATAGTCGAACGAAGCCTA
85190 T C TATTAACCTCGATCTCACTAGTTACACCAAAAAGATCATTGCCGAGTATATATGGATTGGGGGAAGTGGTATGGATATCAGGAGCAAAGCAAGGACACTT[T/C]CTGGTCCAGTTAGTCATCCTAGTGAACTACCAAAATGGAACTATGATGGTTCCAGCACAGGCCAAGCTCCTGGAACGGATAGCGAA
85192 G A AATCAGGACTGAGGCTGCGACTAATGCTTCTACTTCGGTAACCATACCTATCTCTTTCTCTCTCATAGTGTCTTCCATAGCTATGCCTTTCCCTGCTTCT[G/A]CTACGGCTTCGCCCTCTATGGTATCTATCACGATAATAATCATCCCTGGACCTTGATCTAGGACTACGGCTTCTCGAACTTCTTACGACTT
85254 AT A AACAACATAGAACTCGGTAGTGGTTTAATTGGAAAGAGAAGTTGCTTTGGTTAAATGATTTCACTTTGGGGAAAGGAAACGATTTTAGGCTTCGGCCATT[AT/A]TTAGGTTTTTGGGTAAAAGGAACGGATTTTTGATTTAGGGATTTTGCTGAAGGAAAAATAGGAAAAGGCGCTGATTTGTAAAATA
85280 A G GCGTCGTTTCAAGCTTTGGGAGGGCATAGGGCCAGCCATAAGAAACCGAAGATATTGACTGGTGAGGAGGAAGAAGGGCAGAAGGAGGAAAGGGCGATGA[A/G]GAGGAAAATGCATGAGTGCTCTATTTGTGGGGTGGAGTTTAAGATAGGGCAGGCGCTTGGAGGGCACATGAGGAGACACA
85302 C T CATCCAGAAGTGAATCTAAGTAAGAGTACACATACCTTTCCTCGGTCTCCTCATTCTTGGACTTCTTATGCAATCTCCTTGCCTTAATCAAAGGAAGCAC[C/T]ACATCGGTTTGCCTTTTAAGCATCTCCACAGCAGTGTCCATTCTGCTTTTGAACACATACTTTGATATCCATGGGAAAAAAGCAAGAACA
85302 A G TGGACTTCTTATGCAATCTCCTTGCCTTAATCAAAGGAAGCACCACATCGGTTTGCCTTTTAAGCATCTCCACAGCAGTGTCCATTCTGCTTTTGAACAC[A/G]TACTTTGATATCCATGGGAAAAAAGCAAGAACATTAAGGTTACCGGAGTAGAGAAGAAGTGTTCTATGTGCGTCTTCTATTTCCCTTAT
85302 G A CAGCAGTGTCCATTCTGCTTTTGAACACATACTTTGATATCCATGGGAAAAAAGCAAGAACATTAAGGTTACCGGAGTAGAGAAGAAGTGTTCTATGTGC[G/A]TCTTCTATTTCCCTTATGGCTTTCTCATCGAGCTTCTCCCCGTAGCACATAAGAACTAGAAGGCAGAACATGGCGAACTGGAAGCTC
85302 C T GTGTTCTATGTGCGTCTTCTATTTCCCTTATGGCTTTCTCATCGAGCTTCTCCCCGTAGCACATAAGAACTAGAAGGCAGAACATGGCGAACTGGAAGCT[C/T]TGGGAAGCGACTACAGGCCCGCACTGTGACTGTACATGCAAATGGTTGATGAGAACACTAAGCACCCATGTACGTCCATTAGCGTAG
85314 T TGTA TCTTCAAGAGCAATAGCTGTCATTGTAATGCATGCAGACTATAAATATTTGATCAGGCAAGTTCAGTTTGGCGGACCTTGCAAGTCAAAGATAACATTTT[T/TGTA]GGTATTAGGCACTATTATTGCACCTTCAGATCCTGATATGTGGGATGGTTTAGATCCTCACAAATGGCTGTATTTCCACGGTGTAA
85318 AT A CAAGCGAATGCACAAGAATGTCGATGGTTCCAAAATCATTCTTAACTGTTTCAGCCACTTCCTTAACTGTCCAGTTGGAGGAACCTGCATACCTTTTGTT[AT/A]TTTTTTATATCTTCAGGAACATCCTCAGGACTGTCAAAAACAGCATCTAGTGGATACACTTTGGTGATCTCCATCAGAGAACCATCAG
85318 A G CTGTTTCAGCCACTTCCTTAACTGTCCAGTTGGAGGAACCTGCATACCTTTTGTTATTTTTTATATCTTCAGGAACATCCTCAGGACTGTCAAAAACAGC[A/G]TCTAGTGGATACACTTTGGTGATCTCCATCAGAGAACCATCAGGCAGTAAGCGTGATTCGTCAAACTTCCCACGACGTAAGCTAGTCTC
85318 A C CATCCTCAGGACTGTCAAAAACAGCATCTAGTGGATACACTTTGGTGATCTCCATCAGAGAACCATCAGGCAGTAAGCGTGATTCGTCAAACTTCCCACG[A/C]CGTAAGCTAGTCTCAAAAATATTCAATGCAGGAACCCAGGTACCAACAAGAATTTCCGCACCTGCAGCAGCGAGGGCCTTAGCAATT
85318 A G CAGCATCTAGTGGATACACTTTGGTGATCTCCATCAGAGAACCATCAGGCAGTAAGCGTGATTCGTCAAACTTCCCACGACGTAAGCTAGTCTCAAAAAT[A/G]TTCAATGCAGGAACCCAGGTACCAACAAGAATTTCCGCACCTGCAGCAGCGAGGGCCTTAGCAATTGCCCAACC
85322 GA G GTGGGGATTCTGGGAGATGTACGTGCGCGAGAACGGGCATTTGGTTGATGGTGAAGGCGAGGTTAACGAAGCGGGTAAACGGGTTATTGGGCTTAAAAAG[GA/G]AATGGATGTCGCATGCTCGGGGCGTTTTGGATAAAGATGGGGAGTTCAGATTTAGAGGGTTTCATGGAGATTACGTTGTGG
85322 CG C TGCGCGAGAACGGGCATTTGGTTGATGGTGAAGGCGAGGTTAACGAAGCGGGTAAACGGGTTATTGGGCTTAAAAAGGAATGGATGTCGCATGCTCGGGG[CG/C]GTTTTGGATAAAGATGGGGAGTTCAGATTTAGAGGGTTTCATGGAGATTACGTTGTGGAGGTTGTGAGTGCGAGCAAAAGG
85360 C T ATCCGTCAGATCGAGATGCAAAACCACGATTCAGAGGATGATGCAAGTGAGAATGATAGGGTTTTGGATGAGGTGGAGTTCGAGAGGTTCTGCGTGGAGC[C/T]GTACACGGGGATGATAGTGGAGAAGGTGATGAGGAGGAGGAAGAGGGTCGTGGCGGTGGGTGCGGGTGCGGTGGGTCTTGG
85360 T C CCGTCAGATCGAGATGCAAAACCACGATTCAGAGGATGATGCAAGTGAGAATGATAGGGTTTTGGATGAGGTGGAGTTCGAGAGGTTCTGCGTGGAGCCG[T/C]ACACGGGGATGATAGTGGAGAAGGTGATGAGGAGGAGGAAGAGGGTCGTGGCGGTGGGTGCGGGTGCGGTGGGTCTTGGT
85360 G T GATGATGCAAGTGAGAATGATAGGGTTTTGGATGAGGTGGAGTTCGAGAGGTTCTGCGTGGAGCCGTACACGGGGATGATAGTGGAGAAGGTGATGAGGA[G/T]GAGGAAGAGGGTCGTGGCGGTGGGTGCGGGTGCGGTGGGTCTTGGTGGCGTTTTGGGTGGAGCCCACGTTGTTGGGAGGG
85376 T C TGGAAGAAGAAAGAGCGAGGCAAGAAGCTGCTGCCAAAAAAGCAGCAGAGGAGGGTACTGGTGAACAGGGGAAAAAAGACGAGGGAGCTTCTACTTCTCA[T/C]GATGCCACTATGACTGAAGCCACAAGTGCACCTGATGTGCAGAAGGATGAATTGATGGATGATGAGAACGCCTTATTGCAACA
85376 C T AAGAAAGAGCGAGGCAAGAAGCTGCTGCCAAAAAAGCAGCAGAGGAGGGTACTGGTGAACAGGGGAAAAAAGACGAGGGAGCTTCTACTTCTCATGATGC[C/T]ACTATGACTGAAGCCACAAGTGCACCTGATGTGCAGAAGGATGAATTGATGGATGATGAGAACGCCTTATTGCAACAGGCTCT
85390 A G CAAGTAAACATTCCCCCATATATACACTCCAAAATAGACCAACCACACAATCTAAACAACATAATTAACAACTCGTTTCTAACAAGATGACTCTCAGACA[A/G]TCAAAACATCATGGATTGCCCAACATTGATCAGCCCACAAACCCGAGATGCCAATCAATTTCCCAGCAACTCATCAAGTAAGAGACAAA
85390 G A CCCCATATATACACTCCAAAATAGACCAACCACACAATCTAAACAACATAATTAACAACTCGTTTCTAACAAGATGACTCTCAGACAATCAAAACATCAT[G/A]GATTGCCCAACATTGATCAGCCCACAAACCCGAGATGCCAATCAATTTCCCAGCAACTCATCAAGTAAGAGACAAAGAACTAACCCAAA
85400 A G GCAGCGAAAATCGACGTTTCTGATCTCGCTGCGCATCTTCTCGATGTGACTGGATCTTATGAAGGGCAGCAGGAAATACAGCTAATGAGATTTCTGGATT[A/G]TTTTGGGAAAGCATTTGCTGCGGTCAATGCCTCACAGTTTCATTGGCAGAAGCTGTTTAAGGAATTACCTGTGGCGAAGTTAATTGA
85402 T C CAAGCAGAAAAACCCTGAATAAAAACCCTCGTATGTTACAGCAAAAACTCAAAAATAACACAACCAGCATGTACATGTAAAACATACGCGTTCAGTACAT[T/C]CATAACCTTACAAGTATTCAGTAAATCCGATGATAATTTTTGATATAAAAGGATAAATAAAGGCATAAATGACTGACAAGGAGAGAT
85402 T C TCTGAATACTCTGCTTGCCTTTCTGGAAAATATTTTATCACCGGACTTCCGGAAGCTTCGTCAATGAATATGTCAAATGCAGGGGACAGAGGCCGTCCGA[T/C]CACTTGAACGTGGCAAATGCATATGTAATACTGATTATCCATATCTTGAACTTGAACCCGGCCCAACAATTCAATCTG
85406 G C GAGTTTGCATTGTCCATGGACTCGAGCCTGGACTTGATGGTTTTGGCCTTCTTGAGGACCTGGTTGATGGTGGAGTTGATTTGCGTTCGGGTTTTGTGAA[G/C]GGACTCCGGATTGGAGAGGGATTTGGAAGCTTCATTTAAGGTTTGAAGGTTCGTTAAGAGGGATTTGATGGAGGTCATCTCTTCCT
85414 A C CGTTCAAGCAACCAGGTCCTTCAACACCAACGCAATGCGCGAGGTTGACGTCTCAGACGACGA[A/C]TCGAATCTTGATCGTCGATCTGACCGCAGGGTTGCTCGAAGGAGAGTCCGGGACAACGATCTCCCCTTCTACTCTGGAGTGTTTGATCCGTTCAATCCGA
85414 T C CGTTCAAGCAACCAGGTCCTTCAACACCAACGCAATGCGCGAGGTTGACGTCTCAGACGACGAATCGAATCT[T/C]GATCGTCGATCTGACCGCAGGGTTGCTCGAAGGAGAGTCCGGGACAACGATCTCCCCTTCTACTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCC
85414 A G TTCAAGCAACCAGGTCCTTCAACACCAACGCAATGCGCGAGGTTGACGTCTCAGACGACGAATCGAATCTTGATCGTCGATCTGACCGCAGGGTTGCTCG[A/G]AGGAGAGTCCGGGACAACGATCTCCCCTTCTACTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAAC
85414 T C ACCAGGTCCTTCAACACCAACGCAATGCGCGAGGTTGACGTCTCAGACGACGAATCGAATCTTGATCGTCGATCTGACCGCAGGGTTGCTCGAAGGAGAG[T/C]CCGGGACAACGATCTCCCCTTCTACTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAACCTAATCGA
85414 C T ACGCAATGCGCGAGGTTGACGTCTCAGACGACGAATCGAATCTTGATCGTCGATCTGACCGCAGGGTTGCTCGAAGGAGAGTCCGGGACAACGATCTCCC[C/T]TTCTACTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAACCTAATCGACAATTTCACATCTGCTGCC
85414 A T ATGCGCGAGGTTGACGTCTCAGACGACGAATCGAATCTTGATCGTCGATCTGACCGCAGGGTTGCTCGAAGGAGAGTCCGGGACAACGATCTCCCCTTCT[A/T]CTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAACCTAATCGACAATTTCACATCTGCTGCCGGATTG
85414 T A CGATCTCCCCTTCTACTCTGGAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAACCTAATCGACAATTTCACATCTGCTGCCGGA[T/A]TGCCTGCTGCCGTTTCACCAGCAAGTCGCCGTGGGTGGTATGCGAAGGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAG
85414 A G GAGTGTTTGATCCGTTCAATCCGACCCGCTCCCTCACTGACGTCCTAAACCTAATCGACAATTTCACATCTGCTGCCGGATTGCCTGCTGCCGTTTCACC[A/G]GCAAGTCGCCGTGGGTGGTATGCGAAGGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATG
85414 T G CAAGTCGCCGTGGGTGGTATGCGAAGGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGA[T/G]CAGAACACTTTGATAATCAAAGGAGAAGGAGAGAAGGAAGAAGGAGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGAT
85414 T G GTGGGTGGTATGCGAAGGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACAC[T/G]TTGATAATCAAAGGAGAAGGAGAGAAGGAAGAAGGAGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACC
85414 A C AGGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACACTTTGATAATCAAAGG[A/C]GAAGGAGAGAAGGAAGAAGGAGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACCTGATGGGTATAAGATG
85414 G A GGAGGATGAGAATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACACTTTGATAATCAAAGGA[G/A]AAGGAGAGAAGGAAGAAGGAGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACCTGATGGGTATAAGATGA
85414 G A ATGGGCTTCAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACACTTTGATAATCAAAGGAGAAGGAGAGAA[G/A]GAAGAAGGAGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACCTGATGGGTATAAGATGAATGAGATCAAG
85414 G A CAGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACACTTTGATAATCAAAGGAGAAGGAGAGAAGGAAGAAG[G/A]AGACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACCTGATGGGTATAAGATGAATGAGATCAAGGCTGAGAT
85414 A G AGCTACGAGTGGACATGCCAGGATTAGGGAAAGAGCATGTTAAGGTGAGTGCGGATCAGAACACTTTGATAATCAAAGGAGAAGGAGAGAAGGAAGAAGG[A/G]GACGAAGAGGGTGGGAGAAGGTATAGCAGCAGGATTGATTTACCTGATGGGTATAAGATGAATGAGATCAAGGCTGAGATG
85420 A T GTAAAAACAAATCCGACAGTCCTCACCTCTACTTCTCCATCCTGCTGTTTCATCCGGAAACTCCGTAAAACTTGCCCAAATCTCAACTTCTTGATTCCAT[A/T]CGTATTAAAACAATGGAGTCCGCCGCCTTATCCCGAATCGGTCTAGCTGGCCTTGCTGTGATGGGACAGAATCTGGCCCTTAACATCGCT
85420 T A ACAAATCCGACAGTCCTCACCTCTACTTCTCCATCCTGCTGTTTCATCCGGAAACTCCGTAAAACTTGCCCAAATCTCAACTTCTTGATTCCATACGTAT[T/A]AAAACAATGGAGTCCGCCGCCTTATCCCGAATCGGTCTAGCTGGCCTTGCTGTGATGGGACAGAATCTGGCCCTTAACATCGCTTCAAAC
85424 A G CTCCTTCAATGGCTCCGTCTATGAGTCCTTCGGCTTCAATGGCTCCTTCGTCTATGATGTCCCCTTCATCTTCCATGGCACCAACGCC[A/G]GATACTGCTGGAGCTATGCCAGGGTTAATGGGTTCAGAACCACCTGCACCAGCACCAGCCCCGAAAGCGGAGTCAGCAGGCTCTGCTTTGGGTGCGGCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
85424 T C GCTATGCCAGGGTTAATGGGTTCAGAACCACCTGCACCAGCACCAGCCCCGAAAGCGGAGTCAGCAGGCTCTGCTTTGGGTGCGGCGAGTGTTACAATTG[T/C]GATTGCGATTGTGGGCAGTGTTATTCTTGCTTGATGTGTACGTTCCTTTGATTCGTTTGCTTCAGAGAGTTAAAAGGTGAGATGTT
85424 G A TTCAGAGAGTTAAAAGGTGAGATGTTATCAGTATGTATATTTTTGTTGTGTTATAACTGGGTGTTTGTTTTAGCTGAATATATTGTTTATTAGGACATAT[G/A]TGATTGTAATAAAGCTTGAATTTGTTTGTCCTTCCCTCGTTGTGATGTAATGAGTTTGGCCAAATTTGGATTGAGCTGTTTGTGATGTTC
85424 T C TTTGTTGTGTTATAACTGGGTGTTTGTTTTAGCTGAATATATTGTTTATTAGGACATATGTGATTGTAATAAAGCTTGAATTTGTTTGTCCTTCCCTCGT[T/C]GTGATGTAATGAGTTTGGCCAAATTTGGATTGAGCTGTTTGTGATGTTCAGTTTTGTTCAAGTTGAATGGAATATTTTCTTGCTTTAAAAA
85448 T C ACTGTTGGCCTTCTGGAATTAAACTGACAATAGCAAACATGAACGCGGATCGACTCAAAAT[T/C]TTACAGGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCG
85448 C A ACTGTTGGCCTTCTGGAATTAAACTGACAATAGCAAACATGAACGCGGATCGACTCAAAATTTTA[C/A]AGGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCC
85448 C A ACTGTTGGCCTTCTGGAATTAAACTGACAATAGCAAACATGAACGCGGATCGACTCAAAATTTTACAGGAATTCGATTCAACACGGAC[C/A]GGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCGGTG
85448 T A TGACAATAGCAAACATGAACGCGGATCGACTCAAAATTTTACAGGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTC[T/A]ATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGAT
85448 T A ACTCAAAATTTTACAGGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCT[T/A]CTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGA
85448 T A AGGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCC[T/A]CTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCG
85448 C G GGAATTCGATTCAACACGGACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCT[C/G]TGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCG
85448 G A ACCGGCGTCAAAGGTCTCGTGGACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCG[G/A]TGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTC
85448 C T ACTCCGGCATAACTTCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCAC[C/T]GTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCG
85448 TC T TCTATTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCC[TC/T]CCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGT
85448 C T TTCCTTCATTTTTCCATCACCCTGCTTCTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCC[C/T]CACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCG
85448 C T CTAATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCG[C/T]TCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGT
85448 C G ATCTCGACCCTCTGTTATCATCTTTCACCGGTGATCAACCATCGATCCCCACCGTCGATCTATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTC[C/G]GCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGTTTC
85448 C G TATCCCTCCCCCACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGT[C/G]GACAGTGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGG
85448 T A CCACTCAGTCGCCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCT[T/A]TATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTA
85448 T C CCGTCGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGT[T/C]AGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTCTAATGT
85448 C T CGATTTGGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGA[C/T]GTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTCTAATGTCGAT
85448 A G GGTCCGCTCCGCTGCCAGAAACACCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGTTTC[A/G]ACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTCTAATGTCGATTTGTTT
85448 G A CCGGGTTCTTCTACGTCATTAACCACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAG[G/A]AAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTCTAATGTCGATTTGTTTAGAGCGGATGCTGCCAGCTGGCG
85448 G C ACGGCGTGCCGTCCGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGAT[G/C]GTGGGAGGTGTTACCTACTCTTCTAATGTCGATTTGTTTAGAGCGGATGCTGCCAGCTGGCGAGATACGATCCAAATCAATTTGG
85448 A T CGATGTTGTCGACAGTGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTT[A/T]CCTACTCTTCTAATGTCGATTTGTTTAGAGCGGATGCTGCCAGCTGGCGAGATACGATCCAAATCAATTTGGGTAGGGTTGATCC
85448 T C ACAGTGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTC[T/C]AATGTCGATTTGTTTAGAGCGGATGCTGCCAGCTGGCGAGATACGATCCAAATCAATTTGGGTAGGGTTGATCCGGCTAAGATAC
85448 G A TGCTTTATCTTCAGTTAGACGTTTCAACGAGATGGAAAGCGAGGAAAGGAAGAAGTACTACACGAGGGAGATGGTGGGAGGTGTTACCTACTCTTCTAAT[G/A]TCGATTTGTTTAGAGCGGATGCTGCCAGCTGGCGAGATACGATCCAAATCAATTTGGGTAGGGTTGATCCGGCTAAGATACC
85456 C G AAAAATGCTGCGTCTGGGTGGAGACGAGGCCGAAGCTGGACATTTTACGGGCGATGGTGACGACGTCGTCGTTGTAGGAGTAGACGAT[C/G]CCGACTCTGAAGCCTGGGAGGCCGAGGACTTTGGAAAGGCTGTAGACAACGTGGATTAGGTTTCTGTCGTATGGGATCTGGGATTGGTCGAGAAT
85456 A G AGACGATCCCGACTCTGAAGCCTGGGAGGCCGAGGACTTTGGAAAGGCTGTAGACAACGTGGATTAGGTTTCTGTCGTATGGGATCTGGGATTGGTCGAG[A/G]ATTTCGGAGATGCTGGTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGA
85456 G A TGAAGCCTGGGAGGCCGAGGACTTTGGAAAGGCTGTAGACAACGTGGATTAGGTTTCTGTCGTATGGGATCTGGGATTGGTCGAGAATTTCGGAGATGCT[G/A]GTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGA
85456 C A GAGGACTTTGGAAAGGCTGTAGACAACGTGGATTAGGTTTCTGTCGTATGGGATCTGGGATTGGTCGAGAATTTCGGAGATGCTGGTGAATTTAGGGGAG[C/A]TGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGT
85456 T C ATGGGATCTGGGATTGGTCGAGAATTTCGGAGATGCTGGTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCG[T/C]TTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGC
85456 G A CGAGAATTTCGGAGATGCTGGTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGC[G/A]AGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGA
85456 T C ATTTCGGAGATGCTGGTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGA[T/C]GGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCG
85456 C T AGATGCTGGTGAATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGT[C/T]AGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAA
85456 G A ATTTAGGGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGG[G/A]TCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGT
85456 G A GGGAGCTGAAGGTGGTGCCGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGAC[G/A]GCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGG
85456 C G CGGCGAAGATCTCGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTT[C/G]GATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTG
85456 C T CGTCGCAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGT[C/T]AGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTT
85456 T G CAGACGAGGTGGATGCGTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCA[T/G]GATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTTGTTTG
85456 G A GTTTGGATTGGGCGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTT[G/A]ATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTTGTTTGAACTGTGGCTGTGGATT
85456 A G CGAAGGCGAGGATGGAAGTCAGGGTTTCGGGGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGA[A/G]ATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTTGTTTGAACTGTGGCTGTGGATTGGTACGAGTTGT
85456 G A GGTCGACGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGC[G/A]GAGGCTGTTATTTTGAAGTTGTTTGAACTGTGGCTGTGGATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAA
85456 T C CGGCTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGC[T/C]GTTATTTTGAAGTTGTTTGAACTGTGGCTGTGGATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAATCCTGGA
85456 T G CTGTGCCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGT[T/G]ATTTTGAAGTTGTTTGAACTGTGGCTGTGGATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAATCCTGGATAG
85456 T G CCGAGTGGGTTCGATGGGTTGGTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTT[T/G]GAAGTTGTTTGAACTGTGGCTGTGGATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAATCCTGGATAGTAAGG
85456 T A GTCAGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTTGTTTGAACTGTGGC[T/A]GTGGATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAATCCTGGATAGTAAGGAGT
85456 G C AGCATGATGCCTTTCACTTTGATGTCGGAGGAAATGGCATTGTTGTAGGCGGATTCCATGGCGGAGGCTGTTATTTTGAAGTTGTTTGAACTGTGGCTGT[G/C]GATTGGTACGAGTTGTACTCCTGTTCTCCATCTGAAATCTCTATCAAATCCTGGATAGTAAGGAGT
85458 CA C GAAGCCTCAAGCAAGCAGTTCAAATCCAGCTGCATCGAACTGGAGTTAGACTCTGGACACGATAAGGGTTTCAGCTCGAGGCAGCGTCTTCTCTTCGGAA[CA/C]AATTCATCATAGAGGCTAGATCCGTTCTATCGGGTTTGAGTTTAGATGATGTTAGCAGGTCTCTTATCGGCTTTGGGTCAGGGTTT
85502 G A TTGTTATACCCCAGTATAGCAGTAGCAAGCAAAACCTTATGGATTTCGACTACTATTGTCAAAATATACATGAATATCAATGACCAATTCCGGGACTCGG[G/A]ACAGAACCCAACATTCGTTTCATGCCAGTAACCATGTGTGCACTTTGCATGCGTCCATTTCTTGTCAGCACGTCCATGCCGACTCTTGT
85502 T C AATATACATGAATATCAATGACCAATTCCGGGACTCGGGACAGAACCCAACATTCGTTTCATGCCAGTAACCATGTGTGCACTTTGCATGCGTCCATTTC[T/C]TGTCAGCACGTCCATGCCGACTCTTGTAGCCGGAGGAGGTACGCACCCTCCTCGTTGAAGTAGGCTAATAATTAGTGGCGGATTCAA
85502 A G ACCAATTCCGGGACTCGGGACAGAACCCAACATTCGTTTCATGCCAGTAACCATGTGTGCACTTTGCATGCGTCCATTTCTTGTCAGCACGTCCATGCCG[A/G]CTCTTGTAGCCGGAGGAGGTACGCACCCTCCTCGTTGAAGTAGGCTAATAATTAGTGGCGGATTCAAAGCGACATGTCTCTTGTTTCC
85526 C T GAAGGGTCTGACAGATGCACACTTAACAGGCCTCCACAATTGTATGTATGTAAAAAGCCAATTGAAGATGACTCTGGCATAAAACATCTGAATATTTGAG[C/T]TACTCATTGGATCAAGGTGAAGTGTAAAGTGAACGCTGCAGTCCTCTTATTCCTCTTTGTAAAATAACCTGTTGGAATCTTTTAATGT
85526 A G CCACAATTGTATGTATGTAAAAAGCCAATTGAAGATGACTCTGGCATAAAACATCTGAATATTTGAGCTACTCATTGGATCAAGGTGAAGTGTAAAGTGA[A/G]CGCTGCAGTCCTCTTATTCCTCTTTGTAAAATAACCTGTTGGAATCTTTTAATGTCCAACCACCTGTGCTCGGTTGATACAACAATCAA
85548 A G AAAAGTCGGTGGAAACAAGATCTTCATCAACATACCCAAGAATTCCCTTCAAGCTTCCCTCAGATTCAGCCTTGATTGCAGCTTTGATCTCATC[A/G]TAAGTAGCTTTCTTCTCAAGTCTGACAGTAAGATCAACAACTGAAACGTCCACGGTGGGAACACGGAAAGCCATTCCAGTCAATTTACCGTTCA
85548 T C AGTCGGTGGAAACAAGATCTTCATCAACATACCCAAGAATTCCCTTCAAGCTTCCCTCAGATTCAGCCTTGATTGCAGCTTTGATCTCATCATAAGTAGC[T/C]TTCTTCTCAAGTCTGACAGTAAGATCAACAACTGAAACGTCCACGGTGGGAACACGGAAAGCCATTCCAGTCAATTTACCGTTCAAAGC
85548 G A TCAAGCTTCCCTCAGATTCAGCCTTGATTGCAGCTTTGATCTCATCATAAGTAGCTTTCTTCTCAAGTCTGACAGTAAGATCAACAACTGAAACGTCCAC[G/A]GTGGGAACACGGAAAGCCATTCCAGTCAATTTACCGTTCAAAGCAGGAAGCACTTTACCAACAGCCTTGGCAGCACCAGTGCTGCTAG
85548 A G TCTTCTCAAGTCTGACAGTAAGATCAACAACTGAAACGTCCACGGTGGGAACACGGAAAGCCATTCCAGTCAATTTACCGTTCAAAGCAGGAAGCACTTT[A/G]CCAACAGCCTTGGCAGCACCAGTGCTGCTAGGAATGATGTTGAAGCTGGCAGCTCTTCCACCTCTCCAGTCCTTGCTGGAAGGTCCA
85556 G A CATCTTTATCGATTCTTCGCTTAAATTTGGCAATTATATTCTTGCACTTTCTCTGTAGGCTTTCAGACATATCCATGCTTATTGGAGAGTGGACATCACG[G/A]TTGATGGGCTTATAACTCCGCTTCTGCCTCACAGATCTATGTTCAACTCTGCTAACAGTACGTTTTGGACGACCACGTAAAGTACGCTTA
85556 GT G ACATCACGGTTGATGGGCTTATAACTCCGCTTCTGCCTCACAGATCTATGTTCAACTCTGCTAACAGTACGTTTTGGACGACCACGTAAAGTACGCTTAC[GT/G]TTTTATTTGCGGTGGTTTCTTAATTTGATCCTCAGAATCATCATTCCAATTCACAAACTCTTCATCTTCATCATCCTCCACCAACGCTTT
85556 C T GTAAAGTACGCTTACGTTTTATTTGCGGTGGTTTCTTAATTTGATCCTCAGAATCATCATTCCAATTCACAAACTCTTCATCTTCATCATCCTCCACCAA[C/T]GCTTTGTTGTTTGAATCATCGTCTTCATACTCTTCCATATCATCTGAGCTTGAATCAGATTTCCCTTCATCTTCTTCATCCGAAGATTCCACA
85558 A G CATCAGATGGTAAAGACTCAGGGTCCACAGCATAGTTGTGGTTCTGAGCACTGATCTCTACACGTCCACTGCGAAGATCAGAAACGGGATGATTCCCACC[A/G]TGATGCCCAAACTTCATTTTGAAAGTCTTTCCACCCAAAGCTTGACCAATCAATTGGTGACCCATACAAATTCCAAATACTGGAACTT
85574 T C CTGCAATTGAATCCTACCTCTCGGCCACGTGCACCGAACGTGCTAAGAGGTTGAAGGCGGATATGGGAAAAGACAGTAGCAACCTTGTGTTGAGCATGGA[T/C]GAACATGAAGAGGTTACCGATGAATTTCAGGGTATTAGGGTAAAGTGGCATGCCACAAAGAGTCAGTCCATTAGGCAGAGCTTTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
85578 T C CCTCATCTTCGTCATCACCGGACCCTAAGTTGACACGAGTCATACTACCAAAGAAGAAGCCGGAGAAATGGTCGACGGGCGTCGCCCCTGGCGAATACGG[T/C]GGGCCTCCGACGAGGACGAAGCTGAGAAAGTACTGGGGCGGGAAGGGATTTGAAGATCCCGTTACGTCTACTGACGATTTTATC
85582 T C TCCACGTTGTCCGCGCTTCCACCTCGTCCGCGCTTCTGCCTCCTCAAACCTTCCGCCTCGAAGTCAGGATTGCAAGAGAGCATCTGATGAATCCATGGAG[T/C]TAATCAAAGAAAATCTTCAAGAGAAGCTTTCCTCTTATAACGGGCCTATTGAAGCAAGAGCAGAAGCTATTGTACTTCTCAAGCAGTT
85582 C CAA GATTGCAAGAGAGCATCTGATGAATCCATGGAGTTAATCAAAGAAAATCTTCAAGAGAAGCTTTCCTCTTATAACGGGCCTATTGAAGCAAGAGCAGAAG[C/CAA]TATTGTACTTCTCAAGCAGTTGAACTTCCCAGTTGGCATTCCATCCTTCTACTTTCCAATAAGATCAAATTCTTATTTGCTTGCAAA
85582 C A AAGAGAAGCTTTCCTCTTATAACGGGCCTATTGAAGCAAGAGCAGAAGCTATTGTACTTCTCAAGCAGTTGAACTTCCCAGTTGGCATTCCATCCTTCTA[C/A]TTTCCAATAAGATCAAATTCTTATTTGCTTGCAAAATGTTATTTCTTGTTGTTTTTTGTATGCGTGCGTGCACGTGCTTTTTGTTATTGTT
85582 T G CTTCTCAAGCAGTTGAACTTCCCAGTTGGCATTCCATCCTTCTACTTTCCAATAAGATCAAATTCTTATTTGCTTGCAAAATGTTATTTCTTGTTGTTTT[T/G]TGTATGCGTGCGTGCACGTGCTTTTTGTTATTGTTGTTGTTGTTGGAGGCATTACAGTATCATATTTACTAGAAATTACCCGTAATTTTGTG
85602 C T CCCGAAGCTGTGCTTCACGGGAAGTTCCCTCCGTGTTCCTTCCCATGAATTCTATCATTTTGTTAAACAAATTGTCGTCCTTTATCAACGCCCATCCAAA[C/T]CGACTGCCGGAATGTCCAGTGAATTTAGACATGGTAAACAACATGATATCATGATCGGCTTTATACGTGATTGGTGTGTAATGCGGCCA
85602 A G GGGAAGTTCCCTCCGTGTTCCTTCCCATGAATTCTATCATTTTGTTAAACAAATTGTCGTCCTTTATCAACGCCCATCCAAACCGACTGCCGGAATGTCC[A/G]GTGAATTTAGACATGGTAAACAACATGATATCATGATCGGCTTTATACGTGATTGGTGTGTAATGCGGCCAATAGTAAACCAAGTCGTG
85602 C A TCAACGCCCATCCAAACCGACTGCCGGAATGTCCAGTGAATTTAGACATGGTAAACAACATGATATCATGATCGGCTTTATACGTGATTGGTGTGTAATG[C/A]GGCCAATAGTAAACCAAGTCGTGAATGACTCTAGCGCCTTTGATTATCCCATCACGTACAATATTGCCATCGGGATTATTCGGTGA
85602 T C GCCGGAATGTCCAGTGAATTTAGACATGGTAAACAACATGATATCATGATCGGCTTTATACGTGATTGGTGTGTAATGCGGCCAATAGTAAACCAAGTCG[T/C]GAATGACTCTAGCGCCTTTGATTATCCCATCACGTACAATATTGCCATCGGGATTATTCGGTGA
85606 A G CGGCTATCCGAATACACTCTGCGTCCCCAGCAATTGTCACTTTCCTATCGTTTGTGCCTGGCATGAAATCACCTCTATCAGATATCTTGATTCTTGCTCC[A/G]CTGGCCTGAGTAATTTCCATTATGTTTCTTCCTGCTCGGCCAACTACTGCTCCAATATGCTCATCTGCAACACCAATTGTGACCGAATGGC
85610 G C AGTTTGATCAAATCTCTAAGCATTCTCGGTTTCATAGTGCTCGCAAACATAGCAGCATTCAAAGTAGCAAACGGCGCAAATGAATGCGGAAATGTTTCAG[G/C]TGATTCAATGGCATTCAAAATGGCTCCATGCATCTCTGCATCACAAGATGCAAACGCGCGCGTTACAGGAAGTTGCTGCTCTGAGAT
85610 T C CATTGCCGATAGACCTATCGGCTATAAGTGTGGAGGTTACACCTTGCCATGATCGACTACTGTGACTAGGAACCTGCTGGGGTTGATCATCTAAATAAAC[T/C]GTTACTTTGTGTAATTCAATATGGTGCATGTACGTGTATACTGCGATGTTTGCAAGATCAATAGTAATAATATTGTGCTTTA
85616 T C AAACTCCCCTCCGGGTAAAAGTGCATTTTAGTGTGATTAGAAACAATTTCTTTGAGTTCGTTTGTGTTGATGCATGCCTGAAAATCCAGGTAAAATTATT[T/C]GACCCAAGTAGGTCTCCACTTGTACTCGACTTGTTGCAGGTAAATTCAGTCGTTATCATCAAGGATGGCTACATAACTACAGAACTTCA
85618 T A TCACAGATTTTCTTGTTTGGTAGCATAGATATTTTGGATTCATAGTTATGAAAAACCCACCTGCAGAATGGCCAATTAGATTTACCTTTAAAAATATCAA[T/A]TTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGCCAAATTC
85618 G T AGATTTTCTTGTTTGGTAGCATAGATATTTTGGATTCATAGTTATGAAAAACCCACCTGCAGAATGGCCAATTAGATTTACCTTTAAAAATATCAATTTC[G/T]ATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGCCAAATTCCACT
85618 A T TTTTCTTGTTTGGTAGCATAGATATTTTGGATTCATAGTTATGAAAAACCCACCTGCAGAATGGCCAATTAGATTTACCTTTAAAAATATCAATTTCGAT[A/T]AACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGCCAAATTCCACTAGG
85618 G GTGCA AGTTATGAAAAACCCACCTGCAGAATGGCCAATTAGATTTACCTTTAAAAATATCAATTTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATT[G/GTGCA]TAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGCCAAATTCCACTAGGCAAAAAGGAGCAAAACTTTGAGCATCTGCA
85618 A G ACCCACCTGCAGAATGGCCAATTAGATTTACCTTTAAAAATATCAATTTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAAT[A/G]ATGATACAAAAAGGATGTTCCAAAAAGCCAAATTCCACTAGGCAAAAAGGAGCAAAACTTTGAGCATCTGCAATAGTAAAGAACATA
85618 G T ATGGCCAATTAGATTTACCTTTAAAAATATCAATTTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAA[G/T]GATGTTCCAAAAAGCCAAATTCCACTAGGCAAAAAGGAGCAAAACTTTGAGCATCTGCAATAGTAAAGAACATAATACACAAAAAATG
85618 C CAA ACCTTTAAAAATATCAATTTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGC[C/CAA]AAATTCCACTAGGCAAAAAGGAGCAAAACTTTGAGCATCTGCAATAGTAAAGAACATAATACACAAAAAATGTTATACACCAGTTA
85618 C A AAAATATCAATTTCGATAAACAAAATAACCAGTAAACTAATAGGTAAGCAATTGTAATAATAATAATGATACAAAAAGGATGTTCCAAAAAGCCAAATTC[C/A]ACTAGGCAAAAAGGAGCAAAACTTTGAGCATCTGCAATAGTAAAGAACATAATACACAAAAAATGTTATACACCAGTTAGTGATCGC
85632 A G TGCCTGATCCAGCTTCAAATGCAACACCAGTATCTACCATTAATCAAGTTGCTCAGCCAAATCTCTCTACAAGCATACAGGCCCAAGCTCCACTTCAGTC[A/G]CCCCAATCAGTTGGTTTTCCAGGTGGTGTTACAGCCCAAGTGCCAGCTGTCCACCAGCCTCGTTTTCTTTGGTCGCACGCATTAATTGC
85632 T C CTCCACTTCAGTCACCCCAATCAGTTGGTTTTCCAGGTGGTGTTACAGCCCAAGTGCCAGCTGTCCACCAGCCTCGTTTTCTTTGGTCGCACGCATTAAT[T/C]GCTGCAGGTGTGCTTGCTGCCTCTGGTGCTGGAACTGCTATATTTTTCAAGAAAGTTGCTATCCCTAAGCTCAAAAGTTGGATTCGAAA
85632 T A TTTTTCAAGAAAGTTGCTATCCCTAAGCTCAAAAGTTGGATTCGAAAAGTTGTAGCTGAAGAAAAAGAATCAGAGAAGCAAGATGAACAAACTTCAGTTC[T/A]TGCTGAACAAACTACGGAAGCCGCCAAAGCTGCTGCTACTGCTGCTGCTGCTGTTGCTAAAGCAAGCCAAGAATTGTTGAGTTCAA
85632 C T AGCTCAAAAGTTGGATTCGAAAAGTTGTAGCTGAAGAAAAAGAATCAGAGAAGCAAGATGAACAAACTTCAGTTCTTGCTGAACAAACTACGGAAGCCGC[C/T]AAAGCTGCTGCTACTGCTGCTGCTGCTGTTGCTAAAGCAAGCCAAGAATTGTTGAGTTCAA
85658 A G ACCTTTTCAACCGCCTTCACGACATCCATACCGCCAATTACCTCTCCAAAAACGACGTGCTTGCCGTCAAGCCAACTGGTCACGACAGTTGTGATGAAGA[A/G]CTGGGAGCCGTTGGTGTTAGGTCCGGCATTCGCCATAGACAGAAGTCCGGGCTTGGTATGCTTTAGTTGGAAGTTCTCGTCTGCGAA
85658 A G AGAACTGGGAGCCGTTGGTGTTAGGTCCGGCATTCGCCATAGACAGAAGTCCGGGCTTGGTATGCTTTAGTTGGAAGTTCTCGTCTGCGAACTTTTCTCC[A/G]TAGATAGATTTGCCGCCGGTTCCGTTGTGCTTGGTGAAATCGCCTCCTTGAAGCATAAATTCAGGAATGACGCGGTGGAAGATCGA
85660 G A TTGTAGCTTTATGTGAGGAAGCAGTGGAGTCTCTATCTGCTATGAACCATCCTGATGGAGATTGTCCATTATGCCTATATCCTTTAGTGGCTGAAGATAA[G/A]TCCGGCCTTGCCTTGCCATTCATGAAGCTGATGTCATGCTATCATTGCTTTCATAGTGAGTGCATCATTAGGTTCTGG
85666 G C CGAAGATCACCATCGGTGAATGTTCCGATTAAATGATAGCTATCATCGACCACTAGAAGGCATCCACA[G/C]CCTTTACTTGTGAGTTCTGTGAGTTGATTCATAATCATGTCTCCTTCCTTACAAAATGGAAGCTCCTCTTGCTTCTTCATCACATCTTTCACCTTAAAAA
85666 G A CCATCTGCACTGCCGCTGATGTAACAGGCGCCATCCCAAATGGACATAGCTCTCCTTTTAATGGCAAATGCACGTTCATGTCACACACTTTCTCCAACGG[G/A]TTTCCCTCCACTGATGTCACCGATATCAACCTCGCGCCTTTAGCTTTAGCACAAGGCACCAAATTGAGCAACTCCTCCGAAGATCCAGA
85670 T C GAGTAGTAATTAGTGGATAAGGGAGAAGTACCACTGGTGTGTATGGTTAAAGATGAGAAGAGGATGACCAGGAGAAAGTAATGGAAGTTTGTGGAGGCTG[T/C]GATATTCTCCATGACGAGAATTATAGTGGGCAGTGATGAAGAAATTGGGCAGAAAAGCTGAGGAAGAAGGTAGATGTTGGAA
85674 C A TCCTGAACGGCTTGATTTTATTCAGGTATTTGTTGATGACGCTCTTTCTCTCCTCCATTGCATCCCGTTTCTTAAGCAAAGACGCGATGCGTACTTCTTC[C/A]ACTGGTTTCGGCTTAGACTTGAATTTTAGAAGGAATACATGGACTTTGGATGAAAATTGCGTTCTCGACGTGGACTCCGGTTTTGGTGCG
85674 C T TCTTAAGCAAAGACGCGATGCGTACTTCTTCCACTGGTTTCGGCTTAGACTTGAATTTTAGAAGGAATACATGGACTTTGGATGAAAATTGCGTTCTCGA[C/T]GTGGACTCCGGTTTTGGTGCGCTTTTGGCTTGATTGTTGGTATCGGATTCGGAAATTGAGGAATCGGATTCGGAAGTGAAATCGGAT
85674 C G AAGACGCGATGCGTACTTCTTCCACTGGTTTCGGCTTAGACTTGAATTTTAGAAGGAATACATGGACTTTGGATGAAAATTGCGTTCTCGACGTGGACTC[C/G]GGTTTTGGTGCGCTTTTGGCTTGATTGTTGGTATCGGATTCGGAAATTGAGGAATCGGATTCGGAAGTGAAATCGGATTTGTCCGGG
85674 T C CGATGCGTACTTCTTCCACTGGTTTCGGCTTAGACTTGAATTTTAGAAGGAATACATGGACTTTGGATGAAAATTGCGTTCTCGACGTGGACTCCGGTTT[T/C]GGTGCGCTTTTGGCTTGATTGTTGGTATCGGATTCGGAAATTGAGGAATCGGATTCGGAAGTGAAATCGGATTTGTCCGGGATGGTG
85682 G A CAAAAATGTATTTTTGCTGAAGTCGCTATCCAAATTAATGTATGCCCATCTGCATTTTCTTGGTTGTTTTTACATCGACGAGGAGAGAAGGTAACTGCTT[G/A]GCTATATACTCATTCTTAATGCACTAAAAGTCTGCATGGTACAAACAAACTAAACTAGAATGAGTGATAGGAGTACGACAAAGAGGAC
85682 C T ATTTTTGCTGAAGTCGCTATCCAAATTAATGTATGCCCATCTGCATTTTCTTGGTTGTTTTTACATCGACGAGGAGAGAAGGTAACTGCTTGGCTATATA[C/T]TCATTCTTAATGCACTAAAAGTCTGCATGGTACAAACAAACTAAACTAGAATGAGTGATAGGAGTACGACAAAGAGGACATTCAGGCT
85682 CA C GTCTGCATGGTACAAACAAACTAAACTAGAATGAGTGATAGGAGTACGACAAAGAGGACATTCAGGCTTCTCATTACACCATTCCATAATGCAGTTCCAG[CA/C]AAAAAACATGACCGCATGGAGTAGAAGTAGGGTGATGGCGAATGCTTAGGCAGAGCGTACACTTGCTTGAACCACTTGAAGTTTG
85688 C T TCTTAGTTCCAAAAATTGTGTTGGTCGGGTTAGTTACAGCTTGACGTTTAGCAGGGGTTCCCACAAGTAGTTCGCCTTTCTGATTGAAAGCAACAACTGA[C/T]GGAGTCGTCCGTGCTCCTTCAGAGTTCTCAATTACTTTAGGGTTCTTCCCTTCCATAACGGCAACACAAGAATTAGTGGTTCCTAAATC
85688 G A AGCTAAACGACCTAGTAACACTTGCCCACTTCTGTAGGAAAGGGGTTGATGAAGGTGATGCTTTCGCACTTCCAATAATGGATCCAAGAGGAGATGAGAC[G/A]GATGAAGCAACACCCCGTCGCCTAAGGGCACGAAGAAGAAGAGAAGTCGCCATCAGTCAGAGCTCTGAAACTAACAGATTACGA
85688 G C AAAGGGGTTGATGAAGGTGATGCTTTCGCACTTCCAATAATGGATCCAAGAGGAGATGAGACGGATGAAGCAACACCCCGTCGCCTAAGGGCACGAAGAA[G/C]AAGAGAAGTCGCCATCAGTCAGAGCTCTGAAACTAACAGATTACGAAGATGAAATAGGAAGAGATTAGGGCTTTGAAGGAGAG
85692 T C CAGAAGGTTCTTGCTCATCCTTCGATCTCTTGCTTTGTGTCACACTGTGGGTGGAACTCGGTGATTGAAGGGATCACGTATGGCGTTCCCTTTC[T/C]ATGTAAGCCTTATTTTAGTGATCACGTTTTTATTGAGAGGTGCATTTGCGAGGCTTGGAACGTTGGTTTAAGACTGGAGAGAGATGACAATGG
85758 GA G AGCTATCCATGTTGCTGGAAGTCTTTCAGGCAACCACCAACGTTACCTAGCCACTGGCATTCGTGTTGGTTTGAAATCAATATGCAGCAGCAAAGATTCT[GA/G]AAAAAATCCAGTATGAACCCCCTAACCAGAATTTTGCACTCCTAGGCCACAAGATTTCCCTCCCTCAAGAACAAGTATCCCCTTTCAT
85760 T A ATTGATGATAATAAAGTACCGCTTTGTCTCCAGATTCATTTCAACCATCTGTTCTTCGTCAAATCCTCATGTTCTCCTTCATCATGCATGCATTTCCTTG[T/A]AAGGCAGCAAAATTCGCCAGAGCTCTGATGATTTCTCCAATTACCAACTCTAACCAATTCTTATAAAGCAACATCTCTCATTACCACCGCTA
85760 G A ATGTTCTCCTTCATCATGCATGCATTTCCTTGTAAGGCAGCAAAATTCGCCAGAGCTCTGATGATTTCTCCAATTACCAACTCTAACCAATTCTTATAAA[G/A]CAACATCTCTCATTACCACCGCTATGACCAATTACCAACTCTAACCAATTAACAATTCTAACCAATTCATACAAAACAGCTTAGGCTCCCA
85800 T A AACGACACCATTCACGATTTCATAACGCTTGGTGTACAAAGGTTCATAAAGCTTTTGATACTTGGCTTCAAGAGCTGCTCTTTCCTCAAAAAATTTAGCC[T/A]CAAGCTCATCATGGTGGCTCTGAATCTCCCTCAAAACCTCAACGCGCTTTCTTACTTTGGGAGTCAAAGTCTCCAACACATCTGTATGCT
85800 G C CATAAAGCTTTTGATACTTGGCTTCAAGAGCTGCTCTTTCCTCAAAAAATTTAGCCTCAAGCTCATCATGGTGGCTCTGAATCTCCCTCAAAACCTCAAC[G/C]CGCTTTCTTACTTTGGGAGTCAAAGTCTCCAACACATCTGTATGCTTATCCTGCAAATTTTGTAGTTTATCCTTTAGAGCGCTGACAAGG
85812 A G GGCCGGACTATGTAAATCTAACGAATAAAAAATGCAAAAAATCTGTGGATTTTTCTCTTCTACTACTGGTTATGCTGTTAGCTACCATTGGTTCGAGTAA[A/G]CAATAGAGAAGCGGGACTGAGATCAAGTGAAGGGTTTAGCTGACGAGGCACTTGCATTCCTTGAAAAAA
85818 G T CTACTGCAAAAGGCTTAAAATTTCAGGAAAGAAATAAATCAGGCAGACATTGACATAATCTGGCGGGCAAGATTTGGATCTTGCTGTAACAGTTCTCTGA[G/T]GTTTGTCTCCACTTCTCCCATTTGTTTCTCCAGTTTTTCTTTCGATATCTGCATGGAAGCTATTGCTGCCTCGCTGTCTTTCAGCTTCTG
85818 C T CTTCTCCCATTTGTTTCTCCAGTTTTTCTTTCGATATCTGCATGGAAGCTATTGCTGCCTCGCTGTCTTTCAGCTTCTGCTCTTGTTCCTTCATCAAAAC[C/T]GACTTTGGCTCCAACGCAAACATTCTTCCTATAGATTTATATGTATTTGTATCATCGGGTAATTGCTTTAGTTCTTCAAGTGTTAAGAATGCT
85824 C T ACTGGAAGTTTGTGGGACCTGACACGAAGGTGGCGGTGGCTTTTGGGCAGTTAGCGGCCGGAAGATACGGAACAAACATGAGCTTGATGGAGGGGCTGAG[C/T]GGAAGAGGAGATGTGTATAGAACACTTCTCAGAGAAGCAACTGCAGCACTCCTCAATTCATACAACAGCATTTTATTTCCATAT
85848 C T CACTGTTGGCCTACTGGAGCAAACTTTACCAACAGATCCAATGGCGCAAGCGTTCATGTCGTGGTTCATGAATCCAAACAAAAACCCGCTGGC[C/T]CGCATCCACCGCGACACCATCGCCAGGCGGCTTAAGAATTATGGATTGAGATACGATGATTTATATGATCCGATGTATGAATTGGATATTAAAG
85876 C T ATCTCTTAAATTTCTCAGCTTCATCCCCCACCCTTTCGGTCCTTACCTCATACCAAAAGCAAGCAAATTCTCAAACCGTCTAGAAACATCTGGAATCGAC[C/T]TAGTACGTTCGAATTAACTTACATGGCTCAACCCAGCAACCAGGAAGAGATCTTAACCTGCTTCAAATCCAAAGTCCAAGCCGCCGAGC
85876 A T CTCATACCAAAAGCAAGCAAATTCTCAAACCGTCTAGAAACATCTGGAATCGACCTAGTACGTTCGAATTAACTTACATGGCTCAACCCAGCAACCAGGA[A/T]GAGATCTTAACCTGCTTCAAATCCAAAGTCCAAGCCGCCGAGCACGAATCTGAACCGGAAGTATGTAATTCTGGATCCGGGAAACTT
85876 C A TAGTACGTTCGAATTAACTTACATGGCTCAACCCAGCAACCAGGAAGAGATCTTAACCTGCTTCAAATCCAAAGTCCAAGCCGCCGAGCACGAATCTGAA[C/A]CGGAAGTATGTAATTCTGGATCCGGGAAACTTAAATCGGAACCGACCCGGATTGTAGCGGTTGGGAAGCTGGAAAAGGCGGAGGG
85882 G A CCACATCTGAGATCGTCACTTCATCAACTATCGACTTTCCAGCGCAATAGCATCTTGCTTCTCTACATGGGTCGGCTTGGGCTGCAATTGCTTTGTCCCC[G/A]GCTCCTAAACCTACCTTAGATCCTATACATGGCTGCACAAGGATAGTGGTTGAGTCGGAGAACAAGGTCGAAACGTTGAAGAAAGAG
85940 GC G ACAAGGATTTAGTTGCACAGCAGAATATGTACGCCCAATTACTACCTCTAGCGTTGCCAGCACCACCTGGTATGGGTGGTTCATTTGGAGGTCCGCCACC[GC/G]CCCCCACCGATGGGTATGGGTGGTATGCCTCCAATGCCTCCAATGGGAATGCCAGGTTATGGGATGCCTCCTATGGGATCCTATT
85942 G GC AGAATCAATAAGAAAGCTGTTTCAAATCATCTCCATCATTCTAGCGTTGTAACCGTACCTAGATCTCCTGATATTTTCCTGCCTCCTTTTGTAAACAAGC[G/GC]CCCCCAATCCAACCACAGCAGCGGCTGCAATCACCCCAAACGCAATCCCAACCTTCTTTCCACCGCTCATTCCAGATCCATCACCGCTC
85948 T C CAATGTCCTGTTTACTCAGCCGTATCTCCATTCTCCTCTTCCTACTCCTAACATTCTCCCCACTTCCCGCCTTCACCGCCGTAGTATGCAATAGCGCCGA[T/C]AAGCAAGCCCTCGATGCCATCAACGCGCACTTCGGCTTTCCCTATCACTTTGCTTCCTGGACTAACAACACTGACTGCTGCGATTGGTACG
85948 A G CCGTCTTCCAAGACACCGCTCTAAACGGTACAATCCCCGACGCAGTCGGAGACCTTCCATTCCTGCAACAACTCATGTTCCATAAACTACCAAAACTGGT[A/G]GGCTCAGTTCCTTCCTCCATAACCAAGCTCACTCGTCTATCACAACTGGACCTAAGCTCGAACTCGCTTTCAGGACCAGTCCCTTCATT
85948 T C ACACCGCTCTAAACGGTACAATCCCCGACGCAGTCGGAGACCTTCCATTCCTGCAACAACTCATGTTCCATAAACTACCAAAACTGGTAGGCTCAGTTCC[T/C]TCCTCCATAACCAAGCTCACTCGTCTATCACAACTGGACCTAAGCTCGAACTCGCTTTCAGGACCAGTCCCTTCATTTCTCTCTAGCCTA
85958 T C AGCCTCATCACTCGCAGTCGCAGCTTCTTCTTCATCTCTCCCCGACCCAACGGCCACGATGGTTTCATGCACAATGTGCTCCACCTGCTTCCCGTGCCAG[T/C]CGCCTCCCGTTCCCACCCCGCCGTCCTCGTCGCCGCCGCCGTCGCGTACTACATACCCCTCTCAGCCACCTCCAGCTTCACCCAGCTCTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
85958 G C ACCCAACGGCCACGATGGTTTCATGCACAATGTGCTCCACCTGCTTCCCGTGCCAGTCGCCTCCCGTTCCCACCCCGCCGTCCTCGTCGCCGCCGCCGTC[G/C]CGTACTACATACCCCTCTCAGCCACCTCCAGCTTCACCCAGCTCTGGTGACGACGGAGGAAGAGGAGAACCCAGCTACTTGCCACCTC
85958 T G CAATGTGCTCCACCTGCTTCCCGTGCCAGTCGCCTCCCGTTCCCACCCCGCCGTCCTCGTCGCCGCCGCCGTCGCGTACTACATACCCCTCTCAGCCACC[T/G]CCAGCTTCACCCAGCTCTGGTGACGACGGAGGAAGAGGAGAACCCAGCTACTTGCCACCTCCTTCAGCTCCGGGAGGCGACGACACC
85958 C T CGCCGTCCTCGTCGCCGCCGCCGTCGCGTACTACATACCCCTCTCAGCCACCTCCAGCTTCACCCAGCTCTGGTGACGACGGAGGAAGAGGAGAACCCAG[C/T]TACTTGCCACCTCCTTCAGCTCCGGGAGGCGACGACACCAAGTCTACTTTCCCCACGCCGCCGCCGCCAATGCCGATAATGCCCTAC
85958 C G CCACCTCCAGCTTCACCCAGCTCTGGTGACGACGGAGGAAGAGGAGAACCCAGCTACTTGCCACCTCCTTCAGCTCCGGGAGGCGACGACACCAAGTCTA[C/G]TTTCCCCACGCCGCCGCCGCCAATGCCGATAATGCCCTACTATCCCTTTTACTATCACAATCCTCCTTCCTCTGGCTTCAACTCCTCC
85958 G T CTTCACCCAGCTCTGGTGACGACGGAGGAAGAGGAGAACCCAGCTACTTGCCACCTCCTTCAGCTCCGGGAGGCGACGACACCAAGTCTACTTTCCCCAC[G/T]CCGCCGCCGCCAATGCCGATAATGCCCTACTATCCCTTTTACTATCACAATCCTCCTTCCTCTGGCTTCAACTCCTCCTTTTCTTCGTC
85988 C G TCATCGCTGATGAAGCTTCGGTCAATGACAGGGAGGTGCAGCGTCTCTTTCTCTGATGAAGTGGTGGGGTTGAAAGTTCGATCGTGAACAAAAACATACA[C/G]GAAGAAACAGTTCGGCCATAATGGTTAAAACGCAAATTGCTTATTGATTAGAGTTTTAATTAGAACTAAACTAAGGTATTAACTAA
86000 A G GAACGCTGCTTTGCCATTCAGAAACACCTTCTGGGAACCACAAAGCAATCTCCTTCCTTGCACTCTCTACTGCATCGCTTCCATGAATTATGTTCCTGCC[A/G]ACCATGATGGCATAGTCACCACGGATGGTTCCAGGTGCAGACTCAGCTGGGTTGGTTGCACCGATAATTTTACGACCAGTCAACACCA
86000 A G CAATCTCCTTCCTTGCACTCTCTACTGCATCGCTTCCATGAATTATGTTCCTGCCAACCATGATGGCATAGTCACCACGGATGGTTCCAGGTGCAGACTC[A/G]GCTGGGTTGGTTGCACCGATAATTTTACGACCAGTCAACACCACATTTTTGCCTTCCCATACCATTGCAACAACCGGACCAGACACAAT
86000 C A CTGGGTTGGTTGCACCGATAATTTTACGACCAGTCAACACCACATTTTTGCCTTCCCATACCATTGCAACAACCGGACCAGACACAATGTACTCTACAAG[C/A]CCAGCAAAGAATGGTTTCGAAGAAAGGTCTTCATAGTGCTTCTCAGCAAAAGATCTCTCCACCGTGATGAGCTTCATTGCTTTCAAATA
86000 T G CAGACACAATGTACTCTACAAGCCCAGCAAAGAATGGTTTCGAAGAAAGGTCTTCATAGTGCTTCTCAGCAAAAGATCTCTCCACCGTGATGAGCTTCAT[T/G]GCTTTCAAATAGAAACCCTTCTTCTCGAATCGGCTAATAATCTCTCCGACCAATCCTCTTTGAACACCATCGGGCTTGATCATAATAAA
86012 T C CAAATGTACACCGACATTGGTGTGTATTACACTCCCGGCCCTGTCTTCCGAGGCGAGGAATTCGATGGTGCGGAAGC[T/C]GTCCGCCGTCTCGAAGACTGGCTCATCAAGAACCATGGCTTCCAGCCCCAGTACGCTGTTTCTGAACTAAACGAGAAGAACTTTTGGAGAATGTTCGACG
86012 A G CCCAGTACGCTGTTTCTGAACTAAACGAGAAGAACTTTTGGAGAATGTTCGACGGCGGTCTGTACGAAAGCTGCCGTAACAAATACGGTGCTGTTGGAAC[A/G]TTCATGAGCGTGTATTATAAGTCGAAGAAGGGGAGGAAGACCGAGAAGGAGGTCCAGGAAGCCGAGGCTGCCATTGCTGAGCC
86012 G GT TGCTGAACAGGGTTGATGACGATGATGGTGGTAGGATGGGCCTTTTTATGGCTTGTCTTTTAGGTGTATGTATTTGGTTTATGTGCGTGTTTGAGGCTTT[G/GT]TCTGTATTTGCTATTGCTGTTGCATCGGTAGGACTAGACTCGTGTACTGTTATGTGATATGAACTGAGCATGGTAAGAACTACGATG
86012 C T CTGAACAGGGTTGATGACGATGATGGTGGTAGGATGGGCCTTTTTATGGCTTGTCTTTTAGGTGTATGTATTTGGTTTATGTGCGTGTTTGAGGCTTTGT[C/T]TGTATTTGCTATTGCTGTTGCATCGGTAGGACTAGACTCGTGTACTGTTATGTGATATGAACTGAGCATGGTAAGAACTACGATGGTT
86012 A G ACAGGGTTGATGACGATGATGGTGGTAGGATGGGCCTTTTTATGGCTTGTCTTTTAGGTGTATGTATTTGGTTTATGTGCGTGTTTGAGGCTTTGTCTGT[A/G]TTTGCTATTGCTGTTGCATCGGTAGGACTAGACTCGTGTACTGTTATGTGATATGAACTGAGCATGGTAAGAACTACGATGGTTTGTA
86014 A G AAAACTTGGATCGGTTCCCCAACTACACCGACTCAGATGGCGACAGAAGGAATTTCTCTCCTATCCATGTACAACGACGATGACGAAGAAGATGAACTGG[A/G]ACCTCAAAATCAGTCTGGGATCAATGCAGAAACAAACAATCTTCCGCACAATGCAGGTCCAGACTCGAATTTACATTCCATTCCTTC
86014 A G GATGGCGACAGAAGGAATTTCTCTCCTATCCATGTACAACGACGATGACGAAGAAGATGAACTGGAACCTCAAAATCAGTCTGGGATCAATGCAGAAACA[A/G]ACAATCTTCCGCACAATGCAGGTCCAGACTCGAATTTACATTCCATTCCTTCTGAATCTCCTCCGCAGAATTTGATATCCCCGTCGC
86014 T C CAGAAGGAATTTCTCTCCTATCCATGTACAACGACGATGACGAAGAAGATGAACTGGAACCTCAAAATCAGTCTGGGATCAATGCAGAAACAAACAATCT[T/C]CCGCACAATGCAGGTCCAGACTCGAATTTACATTCCATTCCTTCTGAATCTCCTCCGCAGAATTTGATATCCCCGTCGCCTGAGATTA
86022 G C ACTGTTGGCCTACTGGATAGCGAAGCATATCAGAATAAATTCATTGATGGCTTCTCCTTCTTTTCCTCGAATCTCTTAGAAACTTTCAGCA[G/C]TGCAAAGGAATGGCGAAAATCGACCTCTCCGGGCTCCGCCTGTTTCATCTCATCCGGCGGAAACTTCTACAGAGCATCATCTGCGGCGGAGGCTGTG
86022 A T TTGATGGCTTCTCCTTCTTTTCCTCGAATCTCTTAGAAACTTTCAGCAGTGCAAAGGAATGGCGAAAATCGACCTCTCCGGGCTCCGCCTGTTTCATCTC[A/T]TCCGGCGGAAACTTCTACAGAGCATCATCTGCGGCGGAGGCTGTGGCTCCAGCTTCTCCCGCAAGAAAACGAACCTCGATTCTCGCAA
86022 G C CTCGAATCTCTTAGAAACTTTCAGCAGTGCAAAGGAATGGCGAAAATCGACCTCTCCGGGCTCCGCCTGTTTCATCTCATCCGGCGGAAACTTCTACAGA[G/C]CATCATCTGCGGCGGAGGCTGTGGCTCCAGCTTCTCCCGCAAGAAAACGAACCTCGATTCTCGCAAAACCCTTCCGTCTTCCCTATCC
86022 C A TCGAATCTCTTAGAAACTTTCAGCAGTGCAAAGGAATGGCGAAAATCGACCTCTCCGGGCTCCGCCTGTTTCATCTCATCCGGCGGAAACTTCTACAGAG[C/A]ATCATCTGCGGCGGAGGCTGTGGCTCCAGCTTCTCCCGCAAGAAAACGAACCTCGATTCTCGCAAAACCCTTCCGTCTTCCCTATCCA
86022 G A CCGATCGGTTGTCGGAGCTTCTGAAAGCAGAGGCGTTGATCTGCGAAGTGTCGGAAAAGGCGAATGCGACCAGGAAGGAGATGTTTCTGGAAGAGGTGAA[G/A]AATGTGGTTAGAAAGCTCGAGGTAGAAGTTTCTAGAAAGGTGGCCACGAGTGAGGTGAGGAGGATGACGAAAGATGACGTG
86026 G GA TAAATAAGAGGGGAAGAGCGAGAAAAACTTGAGCAAAGGAGGAACGATTTTCTCCTTTTGATTTAGGGAGTAAACAATTTTCTCGAAGGCCATTATAATT[G/GA]AAAATTAGGGAAGATAATTTTGGGAAAAGAACGGATTTTGAAGGAATTGGAGAAAGCAGCGACTTTTGCTCCAGTAGGCCAACA
86044 T C CTAAAGCTCCGATCAGGCCCAAAACCGCATTGAAAAAGGGCAACAGCATCGCTACCAATGTCGTGACTAATACGAGCGTGGTTCTCAGTACGAGTTTGGA[T/C]AGCGTGAAGGTCAAAGTGCCGTCGCTGGAGAATGGAAGGCTGAATGTGTACGTTGTGTTGATGAACTTTGCTTCTGGCCATTTCAT
86044 G T GGCTGAATGTGTACGTTGTGTTGATGAACTTTGCTTCTGGCCATTTCATTGCTACCCTGCTTTCCACTTGGGCGAAAACTGGTTGGGCGTATACCTGATA[G/T]GCTCCGAGAAGATGAACGATGATGCAAAGGTTGGCGATGTCGACAAGCCAAAACGGTTCATAAAACCCGAACCCGGTAAGAATATT
86044 T C GGCCATTTCATTGCTACCCTGCTTTCCACTTGGGCGAAAACTGGTTGGGCGTATACCTGATAGGCTCCGAGAAGATGAACGATGATGCAAAGGTTGGCGA[T/C]GTCGACAAGCCAAAACGGTTCATAAAACCCGAACCCGGTAAGAATATTTCCAGGCGCATTGTTTCCAAATGCAGCGTATCCTGCAC
86052 T C TGAAACAACAAAAGATGAGCCACTTACAATTCTACTGGCACGACATCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAA[T/C]ACATCGTCAACTGGATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAG
86052 A G AACAACAAAAGATGAGCCACTTACAATTCTACTGGCACGACATCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAATAC[A/G]TCGTCAACTGGATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGC
86052 T A AGATGAGCCACTTACAATTCTACTGGCACGACATCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAATACATCGTCAAC[T/A]GGATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTT
86052 A G AATTCTACTGGCACGACATCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAATACATCGTCAACTGGATTCGGGCTGGT[A/G]AGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTATGGGTCTGCGTC
86052 G A TTCTACTGGCACGACATCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAATACATCGTCAACTGGATTCGGGCTGGTAA[G/A]CATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTATGGGTCTGCGTCGC
86052 G A TCGTAAGCGGGAAAAACCCAACCGTGGCTCCAATTGCCCAGGCTTCCATGACCAATACATCGTCAACTGGATTCGGGCTGGTAAGCATGATCGACGACCC[G/A]TTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTATGGGTCTGCGTCGCTTGAGACTCTGGGAC
86052 G T CCCAGGCTTCCATGACCAATACATCGTCAACTGGATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCT[G/T]GGCAGGGCCCAAGGGTTCTATGGGTCTGCGTCGCTTGAGACTCTGGGACTGATGATGGTGATGAACTTCCATTTCGTGCAAGGGAA
86052 T C CATCGTCAACTGGATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTA[T/C]GGGTCTGCGTCGCTTGAGACTCTGGGACTGATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTA
86052 G C GATTCGGGCTGGTAAGCATGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTATGGGTCTGCGTC[G/C]CTTGAGACTCTGGGACTGATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTACCGTGATAGGG
86052 G C TGATCGACGACCCGTTAACATCCGGTCCAACGATGCAGTCCAAACTCCTGGGCAGGGCCCAAGGGTTCTATGGGTCTGCGTCGCTTGAGACTCTGGGACT[G/C]ATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTACCGTGATAGGGAGGAACGAGGTGCTTAAT
86052 T C GGGCCCAAGGGTTCTATGGGTCTGCGTCGCTTGAGACTCTGGGACTGATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGAT[T/C]ACCGTGATAGGGAGGAACGAGGTGCTTAATAGCGTGAGGGAGATGCCTGTTGTGGGTGGAAGCGGGCTGTTTCGGTTTGCAAC
86052 G C GAGACTCTGGGACTGATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTACCGTGATAGGGAGGAACGAGGTGCTTAATA[G/C]CGTGAGGGAGATGCCTGTTGTGGGTGGAAGCGGGCTGTTTCGGTTTGCAACTGGGTATGTTCAGGCCAGGACTCACAGTTTTGA
86052 C T GATGATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTACCGTGATAGGGAGGAACGAGGTGCTTAATAGCGTGAGGGAGATG[C/T]CTGTTGTGGGTGGAAGCGGGCTGTTTCGGTTTGCAACTGGGTATGTTCAGGCCAGGACTCACAGTTTTGATCCTAAGAGCGGTG
86052 G A GATGGTGATGAACTTCCATTTCGTGCAAGGGAAGTACAACGGAAGCACGATTACCGTGATAGGGAGGAACGAGGTGCTTAATAGCGTGAGGGAGATGCCT[G/A]TTGTGGGTGGAAGCGGGCTGTTTCGGTTTGCAACTGGGTATGTTCAGGCCAGGACTCACAGTTTTGATCCTAAGAGCGGTGATG
86068 C T GTTCAGTCACATCATAGTCATCTAACTTTCGTGGGAAATATCCTGCGTATTTTTCATCTTCGAGCAGCCACCGCCTTCACTTGTTCCCGAATCTTCGCAA[C/T]GGCTGAGCAGACCGAGAAGGCTTTCTGAAGCAACCGACAGTCTTTCTGTACTCCAAAAAAACTGGTAAGGG
86074 A G ACTTGATCTTATCTGAGCAAATGAGCTTGCAGCCGCCACCGTCTCTCCCCATCCGTTTGATTGA[A/G]CATTGCTTGATTCGCTGCCGCCTGATTTAGGTCAGGATGTGGCGGCGTTTCGTCGTGTTTCCTTCTAACATCTGTTCGGGGTTTGAAAATCTGGCCGCTG
86074 C T ACTTGATCTTATCTGAGCAAATGAGCTTGCAGCCGCCACCGTCTCTCCCCATCCGTTTGATTGAA[C/T]ATTGCTTGATTCGCTGCCGCCTGATTTAGGTCAGGATGTGGCGGCGTTTCGTCGTGTTTCCTTCTAACATCTGTTCGGGGTTTGAAAATCTGGCCGCTGC
86074 T C ACTTGATCTTATCTGAGCAAATGAGCTTGCAGCCGCCACCGTCTCTCCCCATCCGTTTGATTGAACA[T/C]TGCTTGATTCGCTGCCGCCTGATTTAGGTCAGGATGTGGCGGCGTTTCGTCGTGTTTCCTTCTAACATCTGTTCGGGGTTTGAAAATCTGGCCGCTGCTT
86074 T G AGGATGTGGCGGCGTTTCGTCGTGTTTCCTTCTAACATCTGTTCGGGGTTTGAAAATCTGGCCGCTGCTTTGCCTCTGCGATGAAGACTGCCCGCCATTG[T/G]AGCACGTTATAATATGCTTGTGCCGTGATATAAAGGCGGGCTATCCCAAAACCACACTTATTTTATTTTCTTTTACGTTTGCAATCGCT
86074 T C CCCGCCATTGTAGCACGTTATAATATGCTTGTGCCGTGATATAAAGGCGGGCTATCCCAAAACCACACTTATTTTATTTTCTTTTACGTTTGCAATCGCT[T/C]TTAAGTTTGGAGGATGCATGTTTTTTGTGTTTGCTAATAATCAGATTTCGCTATTTGCCAGCTGATCCGAGCATTACAGCTTTTCTTTTCC
86074 C G TTATAATATGCTTGTGCCGTGATATAAAGGCGGGCTATCCCAAAACCACACTTATTTTATTTTCTTTTACGTTTGCAATCGCTTTTAAGTTTGGAGGATG[C/G]ATGTTTTTTGTGTTTGCTAATAATCAGATTTCGCTATTTGCCAGCTGATCCGAGCATTACAGCTTTTCTTTTCCCCTTCTTTCAATCATGGT
86074 C A CTTTTACGTTTGCAATCGCTTTTAAGTTTGGAGGATGCATGTTTTTTGTGTTTGCTAATAATCAGATTTCGCTATTTGCCAGCTGATCCGAGCATTACAG[C/A]TTTTCTTTTCCCCTTCTTTCAATCATGGTATCACGGATCTGAACTACGGATCTGAACCGGTTCGTTTATGGCTCAATTTATCTCCTCTGGTA
86074 A G GTTTGGAGGATGCATGTTTTTTGTGTTTGCTAATAATCAGATTTCGCTATTTGCCAGCTGATCCGAGCATTACAGCTTTTCTTTTCCCCTTCTTTCAATC[A/G]TGGTATCACGGATCTGAACTACGGATCTGAACCGGTTCGTTTATGGCTCAATTTATCTCCTCTGGTAATTTTATGTTATATTTCATTTGTGA
86074 G T GCTATTTGCCAGCTGATCCGAGCATTACAGCTTTTCTTTTCCCCTTCTTTCAATCATGGTATCACGGATCTGAACTACGGATCTGAACCGGTTCGTTTAT[G/T]GCTCAATTTATCTCCTCTGGTAATTTTATGTTATATTTCATTTGTGAGTTCCAGTTTTTTGTTGATGCAGTGTCG
86078 T C TTATTAACATTTTGCGATCCATGCCTATGTAGTTGTGGAGGTTGCCATTGCTTTCCAACACTATTATTCCCATCACCTGAAATATTACTAGTTGTCACTG[T/C]GGTATCATTTCCAACTATATTTCTCTGAGGTGAACCACAGCTGACTTGGGCATTTGTGGTCATAGACGAGGTTGTGTTAGTATCACATTTT
86078 T C ATCCATGCCTATGTAGTTGTGGAGGTTGCCATTGCTTTCCAACACTATTATTCCCATCACCTGAAATATTACTAGTTGTCACTGTGGTATCATTTCCAAC[T/C]ATATTTCTCTGAGGTGAACCACAGCTGACTTGGGCATTTGTGGTCATAGACGAGGTTGTGTTAGTATCACATTTTGCCTCTACAGATTTTG
86096 G A CATCTGCTTTGGTGTAGTACCTAACAGCAAAAGCTAAAGCCAGAATCATGATAGGGACAAGGAACTGTAAAATTTTGATGATGAATTCGGAAGTTTTATC[G/A]TGGTTGTAAGCTGGCTGCTGCGGAGGAACATAGGCTTGTTTGGCTGGAACGGATGATGCATCGATCTGTCCGATGTAGTACTTTTG
86096 A T TGATAGGGACAAGGAACTGTAAAATTTTGATGATGAATTCGGAAGTTTTATCGTGGTTGTAAGCTGGCTGCTGCGGAGGAACATAGGCTTGTTTGGCTGG[A/T]ACGGATGATGCATCGATCTGTCCGATGTAGTACTTTTGCATTGTATCTCTTGCAGAGTCGCTGTGGCCGACATCCTCGAAATCATTT
86104 G A AGAATGGCCCTACTACTGTTAATATACAGTAATGATGGTGATCAGTCATGATCAGATCTGCCTCACCATGTTTAATTGCTCATTATGGAAAAAGTTCAAT[G/A]ATACATCTATTGCCAAAAGCAGATAGTATCGTGTAGCGTTTAAACTCTGCTTGGGTGAATATTTCACTCCACTCTTCCTCGTTCCGTTCT
86104 G C TTCAATGATACATCTATTGCCAAAAGCAGATAGTATCGTGTAGCGTTTAAACTCTGCTTGGGTGAATATTTCACTCCACTCTTCCTCGTTCCGTTCTGCT[G/C]CATCAAGTGCCACCATCATCGTCATATCAAAGCGTAGATCAACCTTCCTTGAATTTTCGTTCGATTTATTCAAGC
86104 G A ACATCTATTGCCAAAAGCAGATAGTATCGTGTAGCGTTTAAACTCTGCTTGGGTGAATATTTCACTCCACTCTTCCTCGTTCCGTTCTGCTGCATCAAGT[G/A]CCACCATCATCGTCATATCAAAGCGTAGATCAACCTTCCTTGAATTTTCGTTCGATTTATTCAAGC
86132 C T GCCCCCACCTGACAAAAGCACTCGGGCCATGAGTTAGTATAAAACGACTCAGGCCTGACCCGTTTATGCGGCTCACCAAACTTGGTCCTGGCCATAACGC[C/T]CTTGACCCTTTCTTCAAACTTGGCCCCACGACCCTCTTCTCTATCCATGAAAATTGGAGCCAGGGCCTTCCTATCGGGATGGATTATG
86132 G A CCACCTGACAAAAGCACTCGGGCCATGAGTTAGTATAAAACGACTCAGGCCTGACCCGTTTATGCGGCTCACCAAACTTGGTCCTGGCCATAACGCCCTT[G/A]ACCCTTTCTTCAAACTTGGCCCCACGACCCTCTTCTCTATCCATGAAAATTGGAGCCAGGGCCTTCCTATCGGGATGGATTATGGTCC
86132 A G TGAGGTTGTTAGCGAAATTGCTGGGCCCGTCGTAGGTAGGCATGAAGATGTCAGATAAGAGGCAAACCATGTAATCAATGGCGGAGCCCGCAAGCCCTTG[A/G]GCATTTTCTTCAAGCTTTTCAGGTCCTACTGTGTTGTGGTTTTCGAGGTGAGGGAAGAGAGCTCGGAACGGTTTCATGAAGCGGT
86152 T C ACCTCCCATTTCCCAAACTACCCCTTGCCACAGCCACCGTCATCAACCGCCACGCAACCCTCTCCACTCCAGTACGCCTCCCTGCTACCGCCTTTTCCTG[T/C]TCCGCCGTCCCAGTTGAACCCGCTTTCGCAAATGCGAATATTTTCAACTTCACTGCTGGTTATAACGTTCAGATATTGGTCGACGAAGGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
86188 G A GAGGAAGAAGTCACAATCAATCATCCTAAAACACGAATTTTCTACAAACACTCATAAAATTAAACCAGAACTCATAGACAAGAATCCGCCAATCTCCACC[G/A]GACAGGGACAGAAAACTTACTGACGAAACACACCAATGAACATAGCGGCAGCAGTCCAGATGAAGGCAGTGGCAATCGGAGCGGA
86188 A T TCACAATCAATCATCCTAAAACACGAATTTTCTACAAACACTCATAAAATTAAACCAGAACTCATAGACAAGAATCCGCCAATCTCCACCGGACAGGGAC[A/T]GAAAACTTACTGACGAAACACACCAATGAACATAGCGGCAGCAGTCCAGATGAAGGCAGTGGCAATCGGAGCGGAAATCAGCGGAG
86188 G A CGGCAGCAGTCCAGATGAAGGCAGTGGCAATCGGAGCGGAAATCAGCGGAGCGGCGGAGGTGGGGCTGGGAGCAGGCTCATCGGCGCCGAATGCCACATC[G/A]GCAAAGGCGATAATTGCGATCAAACCAACAACGATAGCCTTTGATCCAAAACGGGCCATTTTTTGTTTTTGGTCTGATCTATTT
86214 G C ACTTCCAGCAAAGTCTCCTAACTTCCATAACCCTCTTCCTATCGATTCTGATCTCCAGCGATGGATCCTTGACTCCGACGACGTCGCATTCTATCGACAC[G/C]TCATGATATCTACCATCGTCTCCAAACTGAACTTTGGTTTTGTGCACACTCTTTCCGAATACGTACTCCTTTCTTGCTATGCACGCAGCGT
86226 CT C GCTGCTAGACCACACTGAATTGTTGGGTTTCTCTTCATCAGTGGAGGTAGTGGATGATGGAGGAGGTAAGTCTCCATATAACCCGCCTAACATGTTCGTT[CT/C]TTTTTTGGTGTTACGATGGATTAGGGATTGGAGGTGATCCAGAGTATGAAATTTTGCAGATAGGTTTTACTCTCCTTCGGCTTTAAT
86238 A T GTTGGCCTACTGGAAACATAAAAATAAACTAGGGCTACGGAATCAGTAATCAATCATGCCGAAAAACAAGGGAAAAGG[A/T]GGTAAGAATCGTAAGAGGGGAAAGAACGAAGCAGACGATGAGAAGCGAGAACTAGTTTTCAAAGAAGACGGGCAAGAATACGCCCAAGTCTTGAGGATGC
86238 A G GAATCGTAAGAGGGGAAAGAACGAAGCAGACGATGAGAAGCGAGAACTAGTTTTCAAAGAAGACGGGCAAGAATACGCCCAAGTCTTGAGGATGCTCGGT[A/G]ATGGACGATGCGAGGCGATGTGCATTGATGGGACGAAACGGCTCTGTCATATACGTGGAAAAATGCATAAGAAGGTGTGGAT
86238 T C AAATGCATAAGAAGGTGTGGATTGCTGCTGGAGATATAGTACTGGTGGGACTTAGAGATTACCAAGATGATAAAGCAGATGTGATCCTCAAATACATGCC[T/C]GATGAAGCCAGGCTACTCAAAGCATATGGAGAATTGCCTGAAAATACAAGGCTCAATGAAGGTATTGCTGGTGTATATGAAGAGG
86244 A G CTAGCGATTTAACGCAAAGTTCATCAATCGTTCATTTTGTTGTCTCCCTCTAGTTAGTCTGTAGACTCTGTACAGATAATATAATGGTGGCTTCTTTCGA[A/G]AACCTTTGGTCAGCCAATGGCAAACACATCAATCTACAGACTTCTGCATTTTGTGATTCCGGTATTGGTACTTGTGCATATATAGATGAA
86270 T C AAGGTTGTTTCTTCACAACTTCCAAGGGTTTGCAAAGCTTTGAACATCCTTTTAATGAAGTGAAGCCAGTTCCTAGGGTTGACAGTCAAGGACAAGTATG[T/C]GGTGCGAATTACACAGTGGATAAGCAATCGAAGAAGGATACTTCCAAAATGCCAAGAGTAGGCAGTGCTGCAGATTGGTCTTCTCA
86270 G A ATGCAAGTATTACCTGACTAGACCTGAAATTTGTATTCTTCTATCTATTGATCGCTTTGAACTATTTACGGTGCTTAAACTTATTGTGAACCTTTCCTGT[G/A]CGTTATCTTGAGCTTGGCATGTGTCTGTGTTAAATAAATAAACTTGGATAGTCCTCGGCTATGTAAGTGTGATTTTCTAGTTTAACGACTA
86270 G A ACTAGACCTGAAATTTGTATTCTTCTATCTATTGATCGCTTTGAACTATTTACGGTGCTTAAACTTATTGTGAACCTTTCCTGTGCGTTATCTTGAGCTT[G/A]GCATGTGTCTGTGTTAAATAAATAAACTTGGATAGTCCTCGGCTATGTAAGTGTGATTTTCTAGTTTAACGACTAACTAGGCAATGTGCG
86272 G A TCGCCAACCAGGACTGATAGTCGCGGGTGAACCATCCAGACACACAGCGAATCCTTTCAATTGTTTTCCTTCTCCCGAACTCGTGTTGGCTCCGTTGTGC[G/A]AGGAAATCTGCGGCTTTGAAGGGATGGAGCGGACTTCAATCAGTGGTACAGTGGCAAATATCGAACGACGGTGGCGAACGCCAATA
86280 G T AAACCAGAAAGATGTAACCTCATATTGAATAAATTGTACTAATATACAACAAACTCATTATAGAGTTATCTACTAAGAGATTTAGTACA[G/T]CTATACAACGCATAGACACATACATACATACATATATTATATGAACTGGTTTAACCGGATGCACTTCAGCAAATGAGAAGTAATCTCTAATTTTTTCGTC
86280 C T AAACCAGAAAGATGTAACCTCATATTGAATAAATTGTACTAATATACAACAAACTCATTATAGAGTTATCTACTAAGAGATTTAGTACAG[C/T]TATACAACGCATAGACACATACATACATACATATATTATATGAACTGGTTTAACCGGATGCACTTCAGCAAATGAGAAGTAATCTCTAATTTTTTCGTCC
86280 C T TATTATATGAACTGGTTTAACCGGATGCACTTCAGCAAATGAGAAGTAATCTCTAATTTTTTCGTCCATGAGTCAAAAATTGGGCTGGCTGGTTGCCCTC[C/T]TTAGCTTGGCGATCGAAGTATTCAACACCTGCTGCACCGACTAACGCGGCAAGGGTAAAAAACTGAGCATGTAACCTTGCATGAATGA
86280 G A TGAGAAGTAATCTCTAATTTTTTCGTCCATGAGTCAAAAATTGGGCTGGCTGGTTGCCCTCCTTAGCTTGGCGATCGAAGTATTCAACACCTGCTGCACC[G/A]ACTAACGCGGCAAGGGTAAAAAACTGAGCATGTAACCTTGCATGAATGATCTTGACACTAGGCTTCATATTAGGCTTGGACCAATTG
86280 C T GGGTAAAAAACTGAGCATGTAACCTTGCATGAATGATCTTGACACTAGGCTTCATATTAGGCTTGGACCAATTGTAAGCAGCTGAAGCCGCAATACCACT[C/T]AGCCAAAGACAACCAACTGTTCGGAGCTTGTGCTCGGCGACCCACGACCTGATCGAATCAATTTTGCTGTGCTGGTCTGCCATTAGT
86312 TA T AAAAACATGCGGCTGATGGTATTGGGAGAGTGGATTATGCATTGGGTGCTGCTGGGTCCCAGGTTACTATGCATTCAGAACCACATTCTTCTGGAAAAAA[TA/T]AATAAATGGTTTGATAAAAATAGCAGAGTTCATGCTAATGCAAAGAAGATGTTGGAACCAAGTTTTGGTGAACCGGGTCAGTGTT
86318 T C GTTGGCCTACTGGAAAAATTCACAGAAATTGTAGTTAAAGAGTAACTCGAAATAAGGATTATTTTTCATGGATGGTGAGCTTCTTCTAAATC[T/C]GCCCCCCTTTCCCCGCATCTCTCTCATCCTCTATTCCAAATCACTCACTCTCTACTTCTAAACCGTCTGAATTACCATTTTGCGTTTATAATATTTGCAC
86318 C G GTTGGCCTACTGGAAAAATTCACAGAAATTGTAGTTAAAGAGTAACTCGAAATAAGGATTATTTTTCATGGATGGTGAGCTTCTTCTAAATCTGCC[C/G]CCCTTTCCCCGCATCTCTCTCATCCTCTATTCCAAATCACTCACTCTCTACTTCTAAACCGTCTGAATTACCATTTTGCGTTTATAATATTTGCAC
86318 C G CGTCTGAATTACCATTTTGCGTTTATAATATTTGCACCAAAGATCTGGTTTTGAGGTATGGGTAATGGCGTTTCTGGGTTATTCGATGCTGATCACGAAA[C/G]CGGGTCCGACCAGACGAGTCTCAGAAACTTGCCCGACGACTGTGTTGCGAGAATTTTGATGGGGTTTGGGGCAATGGAGATCTGTCA
86318 G A TTGCACCAAAGATCTGGTTTTGAGGTATGGGTAATGGCGTTTCTGGGTTATTCGATGCTGATCACGAAACCGGGTCCGACCAGACGAGTCTCAGAAACTT[G/A]CCCGACGACTGTGTTGCGAGAATTTTGATGGGGTTTGGGGCAATGGAGATCTGTCAGCTAGCGAGGGTTAATCGGACTTTTCGCA
86318 C T TCAGAAACTTGCCCGACGACTGTGTTGCGAGAATTTTGATGGGGTTTGGGGCAATGGAGATCTGTCAGCTAGCGAGGGTTAATCGGACTTTTCGCAGGGC[C/T]GGGGATGCCGATTTTATATGGGATAAGCTGTTGCCTGAGAATTATGGCATGTTTATCGACAGAGTGATTGGTTGTGAGTTCAATG
86322 A G GATGATGCGGCCTAGTGTCCAATTAAGCTTTTGCCCCACATTTGGTGGAAGCAATCCTGGGATGCGAACAGAGCTTATTCAGTCCATCAAAGAGGAACTC[A/G]ACCTGATATATGGTTGTTCTTGCACCCGAAATCCTTCTGCATATGCTTGTATCTCGCTTGGTCGATCGAAGTGGAATGGGCAAGTAG
86322 A G CCGAAATCCTTCTGCATATGCTTGTATCTCGCTTGGTCGATCGAAGTGGAATGGGCAAGTAGGCAACTCTGGGGCGGTATTTAGAATGGAATGTCCTCTC[A/G]GTAACATTGGCAGGCCACATTTTTCTCTCCAGTTAAACAGTGGTTTTGAGTTTTGACCCTACCTTTGGGTCATCTTATATGTGGCACT
86322 C T ATCCTTCTGCATATGCTTGTATCTCGCTTGGTCGATCGAAGTGGAATGGGCAAGTAGGCAACTCTGGGGCGGTATTTAGAATGGAATGTCCTCTCAGTAA[C/T]ATTGGCAGGCCACATTTTTCTCTCCAGTTAAACAGTGGTTTTGAGTTTTGACCCTACCTTTGGGTCATCTTATATGTGGCACTATGTAA
86322 T A CTTCTGCATATGCTTGTATCTCGCTTGGTCGATCGAAGTGGAATGGGCAAGTAGGCAACTCTGGGGCGGTATTTAGAATGGAATGTCCTCTCAGTAACAT[T/A]GGCAGGCCACATTTTTCTCTCCAGTTAAACAGTGGTTTTGAGTTTTGACCCTACCTTTGGGTCATCTTATATGTGGCACTATGTAAAA
86362 A G AACCCTCTGACCCAGCTTCTTTCCCCGCACTTCACCGTCCACCACTACGTCCTCGATATGCCCTACTTTTCCACAGCCTCGTAAGAACTTCTTCTCTATG[A/G]ACACAGATCCTGTGGCTACGATTTTGTGCGAAATCCGATCCTCAACGACGACAATAAGGTGGTCATCTGAAAGTGAAGTCACCTCGTTG
86384 TTGCGGCTGCTGAGATTGGGGCAGA
T CCGCTGCTCCTGCCAAGATCGAGACAACAGATGCTGCCGCCTGGATTGATGAAGTCGAGATTGGAGAAGATGCTGAGATTAATGAAGCCGAGACAACAGA[T/TTGCGGCTGCTGAGATTGGGGCAGA]TGCGGCTGCTGAGATTGGGGCAGATGCGGTGCTGAGAAGAAGATAATCCACGCCAGTTG
86386 G A CGGCCCACGTTGTAAATGCTGCTCATTCTTCTCTAGAAAGCTTACTGCTTCATTCCAAGAAAATGGTATCACGCCAGCTTCTTTATTGATTTAATCCACT[G/A]TCAGTTTACACCACTGACTTCTACACATTTACCATTCCATTTTCTTTACACTTCTCACCCAAATGCATGTTCCTTCAAAAACAAACACACCC
86386 A G ATCCACTGTCAGTTTACACCACTGACTTCTACACATTTACCATTCCATTTTCTTTACACTTCTCACCCAAATGCATGTTCCTTCAAAAACAAACACACCC[A/G]TCGTTTCACCGTTTGTTTTGATCCCCCGTCCCACGTGTTTAACTCCCATTCACTTTTTTATTTTCTATTCATGAAACACTCCCAGTATTTTGTA
86386 T C TCCACTGTCAGTTTACACCACTGACTTCTACACATTTACCATTCCATTTTCTTTACACTTCTCACCCAAATGCATGTTCCTTCAAAAACAAACACACCCA[T/C]CGTTTCACCGTTTGTTTTGATCCCCCGTCCCACGTGTTTAACTCCCATTCACTTTTTTATTTTCTATTCATGAAACACTCCCAGTATTTTGTAT
86386 A C TTTCTTTACACTTCTCACCCAAATGCATGTTCCTTCAAAAACAAACACACCCATCGTTTCACCGTTTGTTTTGATCCCCCGTCCCACGTGTTTAACTCCC[A/C]TTCACTTTTTTATTTTCTATTCATGAAACACTCCCAGTATTTTGTATTTCAACAACATCACTGACCCTGTTTACGCCTACACCTTCCTCCCCTT
86386 T G CTTCTCACCCAAATGCATGTTCCTTCAAAAACAAACACACCCATCGTTTCACCGTTTGTTTTGATCCCCCGTCCCACGTGTTTAACTCCCATTCACTTTT[T/G]TATTTTCTATTCATGAAACACTCCCAGTATTTTGTATTTCAACAACATCACTGACCCTGTTTACGCCTACACCTTCCTCCCCTTCCCTTCGTAA
86386 T G ACAAACACACCCATCGTTTCACCGTTTGTTTTGATCCCCCGTCCCACGTGTTTAACTCCCATTCACTTTTTTATTTTCTATTCATGAAACACTCCCAGTA[T/G]TTTGTATTTCAACAACATCACTGACCCTGTTTACGCCTACACCTTCCTCCCCTTCCCTTCGTAAGTATGTCCCCCTCGTCACCAGATCTTGCC
86386 A C CCTACACCTTCCTCCCCTTCCCTTCGTAAGTATGTCCCCCTCGTCACCAGATCTTGCCACTCGCCCCCAGTATTTTGAAATCATCCACCTCAATGAAACC[A/C]ATACACCCTTCACTCAAAGCCAATACCGATCCTTCCCAGACAATACGCACCCAACTGTACACAATACAAA
86408 C G TCAAGCCGATCACCCCAACCGCGCATATCTGCCAGGCCAAGGCAGTGCCTACCAGCACCAGCACATAGGCCACCCTCCCCTTCTGAAACCCATGCATCTC[C/G]CCGCTCACCCTCCTCCAGTCCCCACTCCCAAACAGCCCCACCACCGAAGTCAAAGCAGCGACGATGTTGGTGTACACTTGCATTTCCA
86408 T C CCTTCTGAAACCCATGCATCTCCCCGCTCACCCTCCTCCAGTCCCCACTCCCAAACAGCCCCACCACCGAAGTCAAAGCAGCGACGATGTTGGTGTACAC[T/C]TGCATTTCCAGGACAACATAGAAGCTCTCCCTCTTGACAACTTTCTGAAACGTGCGCTGCATCAGGGACAGGATGAGGGAGTACGTG
86412 C T CGAAAATAATCAGGGAGAAGCTGAAATGGTGTTATAGAATTGAAGGAGTGAATTATTTGCAGAAGTGTAGGCATTTGGTCGATCAGTATTTGGAGTCAAC[C/T]CGTGGTGTTGGGTGGGGCAAAGATCATCGCCCTCATGAGCTTCATGGGCCAAAGAAGGAAGCAGTGGAAGAGGAGTAGTGCCA
86412 C T AGATCATCGCCCTCATGAGCTTCATGGGCCAAAGAAGGAAGCAGTGGAAGAGGAGTAGTGCCAAAGTTATCAAGGGGTAATCAGTGGTCAAGGCCAATAA[C/T]GAGTCTTCATCTCCTCATGTACTTGATTGTTTTGAATGTAATAATACTTCAGTATTCCAATAATTCTGAGAGGATACTTCGTGCTTC
86412 G A CAGTGGTCAAGGCCAATAACGAGTCTTCATCTCCTCATGTACTTGATTGTTTTGAATGTAATAATACTTCAGTATTCCAATAATTCTGAGAGGATACTTC[G/A]TGCTTCCCTTCAGTAAGGATTTTCATTGATATTTCATGACTCTTTCCCAGTCTGATCTTTATACTGTGTTGTAA
86422 AT A TTGAAGAAGAGAACTGTAGGAATGCTTCTAATTCCATACTTGCTCGCTATATTTGGGCTTTCGTCCGTATTGACCTTGTAGCATGAAACTTTGCCTGCAT[AT/A]TTCTTTTGCCAGTTCGTCAATGATCGGTGCAATCATACGACATGGGCCGCACCATGGAGCCCAAAAATCCACTACAACTGGTATGTCA
86422 A G CACCAGATTTTCCCAGTTCTCATCTGTTACGGCTGCCACACCATCCACGGCATTCTTTGCTTCACAAACAATTCGTGCTGCGCGGCCATTCATGAGTCTG[A/G]AAGTGTTGAAAGCAGAACTTGAAGACGAGGAAAGTGAATATTTAGATTTCCTTGAAATTACATTGAGCTTTTCTGTCTGGAAGAAACT
86422 C T ATTCATGAGTCTGAAAGTGTTGAAAGCAGAACTTGAAGACGAGGAAAGTGAATATTTAGATTTCCTTGAAATTACATTGAGCTTTTCTGTCTGGAAGAAA[C/T]TCAATTTGGTTGTGGCAGGAGAAGCTGCTGCATAAGAAGAAATGGTGCTTACTTGGAATAATGTTTCTAATGCCATTTAATTAGTTCA
86454 G GT TACCATTGGCTGTGGATTGATGGATGATGGAAGAAGCGCTTTTGGGTTTGGGGTCTGGAAGGTGGCTGAAGCTGTTGTTTTCTTGTGTTTGGGGCGAGAG[G/GT]TTAGCGGATCCAATCCCATTGGAGTCGGAATCTTTAATGGGTCGGATTGCATGTTTAGGTCGCTTGTTTGGGAGCGATATGCAG
86462 T TC GTGCTCATGGCTTCTGTCTGCCTCAGCTACAAGGAAGCTCCGGCTCGAACGGCTTGAGATCACCTGGTCCTAAATTGCATAGACGGGTGGACCAAACACA[T/TC]TGACCCCTGAGATTTCGTATGGGTTCCACCGAAATCAATGACCCGGATTTGTTTGGTCCATCGGTCCATGCATATCCGGTCCAGGG
86462 AC A CTCATGGCTTCTGTCTGCCTCAGCTACAAGGAAGCTCCGGCTCGAACGGCTTGAGATCACCTGGTCCTAAATTGCATAGACGGGTGGACCAAACACATTG[AC/A]CCCCTGAGATTTCGTATGGGTTCCACCGAAATCAATGACCCGGATTTGTTTGGTCCATCGGTCCATGCATATCCGGTCCAGGGGAT
86462 G A CTGCCTCAGCTACAAGGAAGCTCCGGCTCGAACGGCTTGAGATCACCTGGTCCTAAATTGCATAGACGGGTGGACCAAACACATTGACCCCTGAGATTTC[G/A]TATGGGTTCCACCGAAATCAATGACCCGGATTTGTTTGGTCCATCGGTCCATGCATATCCGGTCCAGGGGATTTGAACCCGTCTCGA
86462 T C CGTCTCGAACTGCTGTATTGGGATGGGGTTGCCTTGCGCATATTTTCTGGCCGTGCTGTCTTGCTAGAGCTCACTGTTTTGTTGCACTGTTTTCTTGATG[T/C]TTGGTCCATTTGCTGTGTACCTATGTAGATGTACTAGGTTATACTTTATTAGCATGTAATAGTATATGTAACTCACTACTTTGTAGTATGT
86462 C CTGTGTACTATGTATTGGGATGGGGTTGCCTTGCGCATATTTTCTGGCCGTGCTGTCTTGCTAGAGCTCACTGTTTTGTTGCACTGTTTTCTTGATGTTTGGTCCATTTG[C/CTGTGTACTA]TGTGTACCTATGTAGATGTACTAGGTTATACTTTATTAGCATGTAATAGTATATGTAACTCACTACTTTGTAGTATGTTATG
86462 C CT TTCTGGCCGTGCTGTCTTGCTAGAGCTCACTGTTTTGTTGCACTGTTTTCTTGATGTTTGGTCCATTTGCTGTGTACCTATGTAGATGTACTAGGTTATA[C/CT]TTTATTAGCATGTAATAGTATATGTAACTCACTACTTTGTAGTATGTTATGTAATTGATAATGCTAAGACATTGTAGTTTAGTT
86466 T C TATATACAGCAGAATTTAAAAATAGTTTGAATACAATGAAAGTATTACTGGTTTAAGTCTTCAGAGTGCGTCGTCTTTGGAATCCCCAGCTTCATCAGTC[T/C]TCATCAATCTTCAAAAATATTACTTTCAACGCCAGGGACGGAGAACTTCATGGGCCGATGCGGATTACGAGGCAGCGCCAGTCTATGA
86466 G A AGTATTACTGGTTTAAGTCTTCAGAGTGCGTCGTCTTTGGAATCCCCAGCTTCATCAGTCTTCATCAATCTTCAAAAATATTACTTTCAACGCCAGGGAC[G/A]GAGAACTTCATGGGCCGATGCGGATTACGAGGCAGCGCCAGTCTATGATGACACAAGCTGGAAGCCAAAGGCTTAAAGGTGGAGAC
86466 A T GGGCCGATGCGGATTACGAGGCAGCGCCAGTCTATGATGACACAAGCTGGAAGCCAAAGGCTTAAAGGTGGAGACTTCGATGGGCACAGCGGCGACAGTG[A/T]GCGGTGACGCGAGGTGAACTAATGGACAGTGGTGAACTGATGCTCGAGCACGAGTCCTATCAAGCCGCGGCAGCACAAGTAG
86476 C T TGTTGGCCTACTGGATAAAGGAATAAACATAGAAACATGCAACTCACAATAAAAGGGTGCATATTTTA[C/T]ATTACCTTTTGAAGATATTGGCCTCCTGACGATTGCTGACTTCTGTATTGCAGAGTAGAGGAAGAAGAATGAAATTGCTCTCCTTCCTTTTCCTAATATT
86476 C T TGGATAAAGGAATAAACATAGAAACATGCAACTCACAATAAAAGGGTGCATATTTTACATTACCTTTTGAAGATATTGGCCTCCTGACGATTGCTGACTT[C/T]TGTATTGCAGAGTAGAGGAAGAAGAATGAAATTGCTCTCCTTCCTTTTCCTAATATTGATTACAGTACTAGGAACCGAAGGAGGTAAA
86476 T A TGACTTCTGTATTGCAGAGTAGAGGAAGAAGAATGAAATTGCTCTCCTTCCTTTTCCTAATATTGATTACAGTACTAGGAACCGAAGGAGGTAAATTAAG[T/A]ACAGTACATAGAGATGACTTCCCAAAAGAATTTGTGTTCGGTTCAGGTACTTCAGCTTATCAGGTCGAAGGAGCAGCAAGTGAAGAT
86476 AT A GACATGGGAAAGGAGCTACAGGTGATGTGGCTTCTGATGGGTATCACAAGTATAAGGAAGACATCAAGCTAATGAAAGAAACTGGACTGGAAGGTTATAG[AT/A]TTTTCGATCTCTTGGTCAAGGCTGATTCCTGATGGAAGAGGGAAAATAAATCCCAAAGGCCTCAAGTTTTACAACAACTTCATTG
86490 G A TTTTTTTTTAGTCCAAAGTAGCCAAAACATGAAATATATCATATACATTGTTAATTCAATCAACATTTACACCCAAGTTTGCT[G/A]TATTTTACATGTAAAAAAGCTTTAACAATACAAAAACAGGTAAACGCTGGAACAAACAAGAACTGGCATATTTGATGCAAATTTTGCAAAGGAAAAGGTA
86490 GA G AGTTTGCTGTATTTTACATGTAAAAAAGCTTTAACAATACAAAAACAGGTAAACGCTGGAACAAACAAGAACTGGCATATTTGATGCAAATTTTGCAAAG[GA/G]AAAAGGTAAAAGCAAAGTTAAAGACAGCACTATTGGAAGTTTTGAAGCCCAATGTCCATGTAAAATATTTCTGCGGGACACTTACA
86490 A T AGGAAAAGGTAAAAGCAAAGTTAAAGACAGCACTATTGGAAGTTTTGAAGCCCAATGTCCATGTAAAATATTTCTGCGGGACACTTACATAGGACTAAGA[A/T]CACGTTGATTTCCTGGTCTTGAGCATAGCAAAACACCATTGCAAGCGTTCATGGAGGAGAGCTTTCTGCAACTCCAAACACCCGGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
86530 A G TTTTATTTTGAAGCACTAGACCAACTTTTGCGTGGAATAAATCCCAAAGGGTCGAGCTCAAGCTCTCGCCATGGCGTCTTCACG[A/G]ACTCCGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAA
86530 T C TTTTATTTTGAAGCACTAGACCAACTTTTGCGTGGAATAAATCCCAAAGGGTCGAGCTCAAGCTCTCGCCATGGCGTCTTCACGAAC[T/C]CCGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCT
86530 C T TTTTATTTTGAAGCACTAGACCAACTTTTGCGTGGAATAAATCCCAAAGGGTCGAGCTCAAGCTCTCGCCATGGCGTCTTCACGAACT[C/T]CGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCTC
86530 A T TATTTTGAAGCACTAGACCAACTTTTGCGTGGAATAAATCCCAAAGGGTCGAGCTCAAGCTCTCGCCATGGCGTCTTCACGAACTCCGCTCTCCCTCAAT[A/T]CACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCTCATCGT
86530 C G GCGTGGAATAAATCCCAAAGGGTCGAGCTCAAGCTCTCGCCATGGCGTCTTCACGAACTCCGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAA[C/G]AACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCTCATCGTCTTCTTCGTCTCCTGCTGACATTTCA
86530 C G AGCTCAAGCTCTCGCCATGGCGTCTTCACGAACTCCGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTC[C/G]TAAACGCTAACCCTAAAATGTCATTCAAAACCTCATCGTCTTCTTCGTCTCCTGCTGACATTTCATGTCCAGTCCCACTCGAGCAGCAACC
86530 A G AACTCCGCTCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAA[A/G]CCTCATCGTCTTCTTCGTCTCCTGCTGACATTTCATGTCCAGTCCCACTCGAGCAGCAACCCATCAATGAGTACCGGAGTCTAACTACATC
86530 G C TCTCCCTCAATACACTATTCCTTTTCCAAAACCCTAACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCTCATC[G/C]TCTTCTTCGTCTCCTGCTGACATTTCATGTCCAGTCCCACTCGAGCAGCAACCCATCAATGAGTACCGGAGTCTAACTACATCTGCACCTTT
86530 C T ACAACAAACTACCGTTCGTCAAATTCCTAAACGCTAACCCTAAAATGTCATTCAAAACCTCATCGTCTTCTTCGTCTCCTGCTGACATTTCATGTCCAGT[C/T]CCACTCGAGCAGCAACCCATCAATGAGTACCGGAGTCTAACTACATCTGCACCTTTCTCATGGGCAGCCGGTGACGTGGATACGTATGC
86530 G A CTACATCTGCACCTTTCTCATGGGCAGCCGGTGACGTGGATACGTATGCTTCTCGCCTCATTTCAGCAGGCGCAGCCACAGCTTTGCTTATTGGTCTTCC[G/A]GTTGCTGTCTTTGGGACTCGTGGTGCTATCGACCTTCAGGCAGATGGATTGAGGTGGTCTATTACATCAGTTTCAACTGGGATTCTTG
86530 T C CCGGTGACGTGGATACGTATGCTTCTCGCCTCATTTCAGCAGGCGCAGCCACAGCTTTGCTTATTGGTCTTCCGGTTGCTGTCTTTGGGACTCGTGGTGC[T/C]ATCGACCTTCAGGCAGATGGATTGAGGTGGTCTATTACATCAGTTTCAACTGGGATTCTTGCAGCAACTTTGGTAGCGGTTAGGATG
86530 C T GTGACGTGGATACGTATGCTTCTCGCCTCATTTCAGCAGGCGCAGCCACAGCTTTGCTTATTGGTCTTCCGGTTGCTGTCTTTGGGACTCGTGGTGCTAT[C/T]GACCTTCAGGCAGATGGATTGAGGTGGTCTATTACATCAGTTTCAACTGGGATTCTTGCAGCAACTTTGGTAGCGGTTAGGATGTATT
86530 T A TTTCAGCAGGCGCAGCCACAGCTTTGCTTATTGGTCTTCCGGTTGCTGTCTTTGGGACTCGTGGTGCTATCGACCTTCAGGCAGATGGATTGAGGTGGTC[T/A]ATTACATCAGTTTCAACTGGGATTCTTGCAGCAACTTTGGTAGCGGTTAGGATGTATTTGGGATGGGCATATGTTGGGAACCGATTG
86678 T C AGTCACCAAGTCCATCTCTTTCCTACTACCGGGTTTCTTGCTGCTTTTACCCGAATCCGATTTCAACCTCGAACCAGCATTCACGTTTCCGAACCTCTCC[T/C]TTCCATCGCTCACGCTCCTCCTCCATTCCCATATCTTCTTCCATTTCGATCTCGATCCCGATTCCACTCCGGATCCACTACCAGTAGAAGCG
86678 G A AGTCCATCTCTTTCCTACTACCGGGTTTCTTGCTGCTTTTACCCGAATCCGATTTCAACCTCGAACCAGCATTCACGTTTCCGAACCTCTCCTTTCCATC[G/A]CTCACGCTCCTCCTCCATTCCCATATCTTCTTCCATTTCGATCTCGATCCCGATTCCACTCCGGATCCACTACCAGTAGAAGCGCTCCTCTTC
86682 C T CTCTCATCTGATACGCGGCTCGATCGTACGCCCTCGCCGCCTCCTCCGCCGTCTTGAACGTGCCCAGCCACACCCGAACTCCCTCGCCTCTCTTCGAGTC[C/T]CTGATCTCCGCCGCGTACTTCCCCCATGGCCTGTACCTCACCCCTCTGTACCTCCCTGATCCGCTCCCGTTTTCCTTCCCTCCACGGCCG
86682 G A CGGCTCGATCGTACGCCCTCGCCGCCTCCTCCGCCGTCTTGAACGTGCCCAGCCACACCCGAACTCCCTCGCCTCTCTTCGAGTCCCTGATCTCCGCCGC[G/A]TACTTCCCCCATGGCCTGTACCTCACCCCTCTGTACCTCCCTGATCCGCTCCCGTTTTCCTTCCCTCCACGGCCG
86692 T G AATATTGCGTAGGATCCATATCTTCGTCATCTGCCACAGCTTGGGTTTTTGACTGGGACTGAGCGCTTGCCATCATCTCAGCCTTTTTCTTCAGCTTCTC[T/G]GCTTCTTTCTTCAACCGCTCCTCCTCTTTCTGTTTCATCTTCAATTCCTTCTTTAAAGCATTCTTGCTCATTGACGCGGAATCAGCTGGACC
86692 C T TTGACTGGGACTGAGCGCTTGCCATCATCTCAGCCTTTTTCTTCAGCTTCTCTGCTTCTTTCTTCAACCGCTCCTCCTCTTTCTGTTTCATCTTCAATTC[C/T]TTCTTTAAAGCATTCTTGCTCATTGACGCGGAATCAGCTGGACCGCCGGATGCAGGTGCGATCGAAAGACTAGATACTTGATCCGATATGA
86692 T C GGGACTGAGCGCTTGCCATCATCTCAGCCTTTTTCTTCAGCTTCTCTGCTTCTTTCTTCAACCGCTCCTCCTCTTTCTGTTTCATCTTCAATTCCTTCTT[T/C]AAAGCATTCTTGCTCATTGACGCGGAATCAGCTGGACCGCCGGATGCAGGTGCGATCGAAAGACTAGATACTTGATCCGATATGAAATTGG
86692 C G TCAACCGCTCCTCCTCTTTCTGTTTCATCTTCAATTCCTTCTTTAAAGCATTCTTGCTCATTGACGCGGAATCAGCTGGACCGCCGGATGCAGGTGCGAT[C/G]GAAAGACTAGATACTTGATCCGATATGAAATTGGAATTGGCAGCGCCGTCGGCCATTATAATTAGATTGATTTTTTTAGTGCTGCAAAT
86704 A T CATCATCTACGATTCCTCTGAGTTCATGGTTGCCTCTTGCACTGTTCATTTCTTCTACAAAGCCACTGTCGCATACAGGGCATTTCATTATCTCGATTCC[A/T]ATGATGGGGTCAACGATTTGAGAACACATGTGGCACCAGTATTCTTCAGCCATTGTGTGAAGCTTTTACTTCGCTTTCAGATCTCTGCGA
86722 CA C TTTAAATGCAATATCCTTTGCTGTTTTGGACTTCCATAAGGTGGTTCTAGTGTAAGCGTCACGTCAGGTTCAGTATTAGAGTTGTTTTTCATCATGATTA[CA/C]AAAAATAACTTGGTATTTAACCCTTGGTTCAAGTATGCTCGTACGAATCTTCCCTCGCACTTCAAGCCAGTTAAATCCTATCAGCTCTGC
86724 A G TTCGAATTCATGAACTACACGATCATAACGAGCGAGTGCAAGGGGCCTCGATACCCTGTAAAAGAATGCTGCGAGTCGCTGACCGAATTTGCATGCCC[A/G]TATGCTGAATCCATAAATGATGCGACCAACGACTGCGCCTCGATCATGTTCAGCTACATCAACCTTTACGGTAAGTACCCTCCTGGTTT
86724 T C AATTCATGAACTACACGATCATAACGAGCGAGTGCAAGGGGCCTCGATACCCTGTAAAAGAATGCTGCGAGTCGCTGACCGAATTTGCATGCCCATATGC[T/C]GAATCCATAAATGATGCGACCAACGACTGCGCCTCGATCATGTTCAGCTACATCAACCTTTACGGTAAGTACCCTCCTGGTTTGTTC
86724 T C ACACGATCATAACGAGCGAGTGCAAGGGGCCTCGATACCCTGTAAAAGAATGCTGCGAGTCGCTGACCGAATTTGCATGCCCATATGCTGAATCCATAAA[T/C]GATGCGACCAACGACTGCGCCTCGATCATGTTCAGCTACATCAACCTTTACGGTAAGTACCCTCCTGGTTTGTTCGCAAGTGAATGC
86724 G A CCATATGCTGAATCCATAAATGATGCGACCAACGACTGCGCCTCGATCATGTTCAGCTACATCAACCTTTACGGTAAGTACCCTCCTGGTTTGTTCGCAA[G/A]TGAATGCAAAGGAGATAAGAAAGGACTTGCATGTCCTGATAATTCCACCATGTTGTCTGAAAAAGATAGCGCTGAGGCTAGCTCCGG
86724 A G ATAAATGATGCGACCAACGACTGCGCCTCGATCATGTTCAGCTACATCAACCTTTACGGTAAGTACCCTCCTGGTTTGTTCGCAAGTGAATGCAAAGGAG[A/G]TAAGAAAGGACTTGCATGTCCTGATAATTCCACCATGTTGTCTGAAAAAGATAGCGCTGAGGCTAGCTCCGGCTGTGTTGGCAGTG
86724 TG T AAGGACTTGCATGTCCTGATAATTCCACCATGTTGTCTGAAAAAGATAGCGCTGAGGCTAGCTCCGGCTGTGTTGGCAGTGGGAGTTTCTTTGTTTTGGT[TG/T]GGGGGTTTGGTTATGTTTGCTCTGGATTATTTGTACTGAGACGATTCTTTTGGTGTGTTTTGTATGAAGTATTGGGGTCCCCGCTTA
86724 C CTTT AGCGCTGAGGCTAGCTCCGGCTGTGTTGGCAGTGGGAGTTTCTTTGTTTTGGTTGGGGGTTTGGTTATGTTTGCTCTGGATTATTTGTACTGAGACGATT[C/CTTT]TTTTGGTGTGTTTTGTATGAAGTATTGGGGTCCCCGCTTACACGTATTTCGTTTAATGTTTTATACGCTGTGCATTTGTATGTTTAA
86724 T C GTGGGAGTTTCTTTGTTTTGGTTGGGGGTTTGGTTATGTTTGCTCTGGATTATTTGTACTGAGACGATTCTTTTGGTGTGTTTTGTATGAAGTATTGGGG[T/C]CCCCGCTTACACGTATTTCGTTTAATGTTTTATACGCTGTGCATTTGTATGTTTAATGGTGTATGGTTATGGTTGTTAACTTGTTAATATA
86724 C G GGGAGTTTCTTTGTTTTGGTTGGGGGTTTGGTTATGTTTGCTCTGGATTATTTGTACTGAGACGATTCTTTTGGTGTGTTTTGTATGAAGTATTGGGGTC[C/G]CCGCTTACACGTATTTCGTTTAATGTTTTATACGCTGTGCATTTGTATGTTTAATGGTGTATGGTTATGGTTGTTAACTTGTTAATATAG
86724 C CGT TTGTTTTGGTTGGGGGTTTGGTTATGTTTGCTCTGGATTATTTGTACTGAGACGATTCTTTTGGTGTGTTTTGTATGAAGTATTGGGGTCCCCGCTTACA[C/CGT]GTATTTCGTTTAATGTTTTATACGCTGTGCATTTGTATGTTTAATGGTGTATGGTTATGGTTGTTAACTTGTTAATATAGTAGTTGATA
86724 G A ATTCTTTTGGTGTGTTTTGTATGAAGTATTGGGGTCCCCGCTTACACGTATTTCGTTTAATGTTTTATACGCTGTGCATTTGTATGTTTAATGGTGTATG[G/A]TTATGGTTGTTAACTTGTTAATATAGTAGTTGATACACGCATGTATTTCATTAAGTGTTTAT
86736 G A TCGGGTACAACCGCGAATCCGGGTTCGTGTGGATGCGCCAGAAGAAAGCCGTGACCCACACATTCAAAAAAATCGGAAAGCAAGTTTCCTACGCCCAGGA[G/A]GTGACTGCTTTCGTCGAGGATAAGAAGATGAAGAAGCTTACTGGGGTCAAAAGCAAAGAGCTGCTGATTTGGATCACGCTTTCC
86736 T C TTTCGTCGAGGATAAGAAGATGAAGAAGCTTACTGGGGTCAAAAGCAAAGAGCTGCTGATTTGGATCACGCTTTCCGATTTTTTCATCGATCGCAATGAT[T/C]CAGAAAAGATCATCTTCAAAACTCCGACTGGTTTGTCCAGGACTTTTCCGACTGCGGCATTTGCGACAGAGGAGTAACTTATAATGT
86748 C T GTTGGCCTACTGGATTTTCTTCTGTCTTCTCATGCAAACATTAACATGTTCCTCTCTCCCCTAAGAAAAAG[C/T]TTAAATGCATCAAAATCAACCATGGATCACGAACACAACACCAGATCCATAGACTGGAAACTCTACAACAACCCGCATTACTCGTTCTCGGCCCAAAAGC
86748 A AATCACC GTTGGCCTACTGGATTTTCTTCTGTCTTCTCATGCAAACATTAACATGTTCCTCTCTCCCCTAAGAAAAAGCTTAAATGCATCAA[A/AATCACC]ATCAACCATGGATCACGAACACAACACCAGATCCATAGACTGGAAACTCTACAACAACCCGCATTACTCGTTCTCGGCCCAAAAGCTCCTTGCCAATCC
86748 G C ATGGATCACGAACACAACACCAGATCCATAGACTGGAAACTCTACAACAACCCGCATTACTCGTTCTCGGCCCAAAAGCTCCTTGCCAATCCAAGTACTT[G/C]TTCGTCCAAAAAGTCGTCGGAACTTGAAAAGGCACTGGCAGAGATCAAGGACTTGAGAGCGGAGCTGGAGAGGGAAAAGGGAATG
86748 T C TGGTGGAAGAAAGAAGAGCGAGAGAAGGGGCCAATGAGATGTGTAGGAGTTTGAGGAAGGAGAACTTGCCTGTAAGTGGTAAAGAAGTTGGTAAGGAATG[T/C]GTCGAGAATCCACATATAAAGAGAGGGATCAGTGGAGTAGAGTTCTTCAGGGCGACGCGGGCGAAAAGGTCGGCTTTTGTG
86752 A G TCGTCGGGAAAGTCACCGTCCCAGTAATCGAACTTCTGAGAGGAGGGTGCGACGGATCCGTTAGGCACGTCAGTTACCAGGTCATCGGAAATGACGGAAA[A/G]CCGAACGGCGTTATGACGTTTTCGTACGAGATCAAGCAAAAGTTGGTAAAATTACCCGCGAGTCACGGTAACAACAACGTCTATC
86752 G T TCGGGAAAGTCACCGTCCCAGTAATCGAACTTCTGAGAGGAGGGTGCGACGGATCCGTTAGGCACGTCAGTTACCAGGTCATCGGAAATGACGGAAAACC[G/T]AACGGCGTTATGACGTTTTCGTACGAGATCAAGCAAAAGTTGGTAAAATTACCCGCGAGTCACGGTAACAACAACGTCTATCCGA
86752 T A CGGATCCGTTAGGCACGTCAGTTACCAGGTCATCGGAAATGACGGAAAACCGAACGGCGTTATGACGTTTTCGTACGAGATCAAGCAAAAGTTGGTAAAA[T/A]TACCCGCGAGTCACGGTAACAACAACGTCTATCCGATGCCAGCTAAACAGGAGCCCTATGCACCTCCATATCAGCAATT
86778 T C TCCTAAGCTGGAGTGCATCAAAACGAAACAATCATAGAGCAAATCCAAAACATGAGTTGTGCAAAGTCTTGTGATAACCAAACTGAGTTGCAAGTCCGTG[T/C]AGAAGTTGCGGTCAACTGCCGATTCAGAAGAACGGCCGGTTCAAACAACACTGTTACTGCATGAATCCGCAACGATCAACAAACTG
86790 C T CATCAATTCATCCATAGAAAATGGCTTCAGTTTCTGGTGATTTGATTTGGGAGATTGTGAAGAAGAACAATGCATTTTTGGTGAAGCAGTTTGGAAACAG[C/T]CATGCTAAGGTTCAGTTTAGCAAAGAGAAGAACAATTTGTACAACATCCACTCATACAAGTTCTCAGGTTTGGCAAACAAGAAGACC
86790 A G TTGTGAAGAAGAACAATGCATTTTTGGTGAAGCAGTTTGGAAACAGCCATGCTAAGGTTCAGTTTAGCAAAGAGAAGAACAATTTGTACAACATCCACTC[A/G]TACAAGTTCTCAGGTTTGGCAAACAAGAAGACCGTTTCCATCCAGGCAGCTGGTGATGGCCAATCCATTGAATTTGCGACCACAAA
86790 G A TTGAATTTGCGACCACAAAGAGAAGGAAGCAAAGGAAGCCTGCAAAGCTTTATCGCAAGTCAGTGATGAAAAAGGAGCTTCCTAAAATGGCAAAGGCTGT[G/A]ATTAATCAGGTGCGGGACAATAACTATAGGCCTGACCTGACCCAAGCAGCACTTGCTAGACTGAGTTATGTGACTAGAGCTCTCA
86810 A G GACGTTTCATTGAATACCCCAAATCCTCTGCTTCTGTAATAAGGCATATTAGAAAGCAAGGTTTCGTCAACATCGAACACCCAAATGTCTTTTCCGTCCA[A/G]ACCGACCTCGACCTTTGCAGCAAAATCAATAGCTTCAGTCGTAATCATATCCGAATCGGTGTAATATCTCTCGCCGTTCATGTATTTAGA
86810 G C GGTTTCGTCAACATCGAACACCCAAATGTCTTTTCCGTCCAAACCGACCTCGACCTTTGCAGCAAAATCAATAGCTTCAGTCGTAATCATATCCGAATCG[G/C]TGTAATATCTCTCGCCGTTCATGTATTTAGAAACGTAAGAAACGCATGCAGAAGGGATGGTAGTCCATGGGCCGGCGTTGTTTGTTTC
86832 A G GAATTGCACGTAAGAAAAGGGAGAATCTTCATAGACTGGCTTCCACCAATCGAAGTTTCGCGCATTTCAGATGGTGGTAAAGTAGAGACCACATAATAGA[A/G]TATTCCTCATTCAGTCAGATTATGAAGTAAGATATGCTTTGACTTCGTTCGCCACATTTACCGATC
86834 CG C CATGGGTTTCGACGAAGGGGAGCTTACTGTAAATGAAGGAAGGGCGGACATCGAAGTCTTCCTGGTTTTGTGAGTTCACTGTCTCGGATACTGAAGCATG[CG/C]GGGGGTTAGATGGAAGAAAATAATAAGGCGATGGGTTAAAATATAATGAAGTGGTTAAGAGTTGTTTAGGGTTTTGGTCACCG
86834 GT G GTTTTGTGAGTTCACTGTCTCGGATACTGAAGCATGCGGGGGTTAGATGGAAGAAAATAATAAGGCGATGGGTTAAAATATAATGAAGTGGTTAAGAGTT[GT/G]TTTAGGGTTTTGGTCACCGTGAATTTCGTGGCTTTACTGTTGCGTCATGGGCCACAGTTCACTGGGTATCGCAAGGAGTTTGGG
86836 G A CATTTCTTATAGGTTTTAGAAATGGAACCCGAAGGCGTAGAAAGAGTAGGAGAGTCACAGGATATAGTCCAACGCTCGAGGATGACGTCGGCAGGGGACA[G/A]GACGACGTCGATTATGGTCGGATCGGTCAATCCGCTGCCATTTTTCGCCACTGCGTTGTCCAACGCGGAGGAGAGACCGGGAAG
86840 A G ACAAAATAGTCACAGTTTCACATGATCGAAATTCATATGTATGGAATCAAGAAGCATCAGAATGGGTACCAACACTTGTCATTCTCAAGATTAATCGTGC[A/G]GCTCTTTGTGTTCAGTGGAGTCCTAAAGAAAACAAATTTGCAGTTGGTAGCGGTCAGAAGAGAGTTTGTATCTGTTATTACGATCAAG
86856 T C CATATCCATCATGATAAGCTTTTCAATGCCCCCTCGTCCTCGTAAAAGACGCCTGACAGCCTCTGAAGAGCCTCCCAAACATAATGTAGTAGGAAATGTT[T/C]TCTTACAATCCTCCAATCTATCCAACAAATTATCTGCAACTGAATCAACAAACTGATCTTTACCTTTCATCAACCACGCAGCCCGATCCC
86860 A G GCCGGCGAGCGTGGAGGATTTGATGAGGGAACGAGATTGTTCGGGCGGCGGATCGAAGATGGTGGTGACGGTGTGTCGGAGTTGCTTTCAGTATTTGTTG[A/G]TATCGAAAGACGATCCGAGATGCCCCAACTGCAACCGGGTCGTCTCGGTTGCGGATGAGTTGTTTAGTAGGAAGAAGTCTAAG
86864 C T GTACAGATGTTTTTTCCTTCTTATATTCAATACAATACAATGTTTCAAGAGATTCCGAACAAACAAAATTACATACATGGTCACACTAATTAAATCCAAT[C/T]TGCAGCAGTTCATCATCCAATTAAGTTAACTAGTCATAAGAAATATCATGATCATCACCAAATACATAAAATTGATGGATCGCAGCAGCA
86864 T C ACAATACAATGTTTCAAGAGATTCCGAACAAACAAAATTACATACATGGTCACACTAATTAAATCCAATCTGCAGCAGTTCATCATCCAATTAAGTTAAC[T/C]AGTCATAAGAAATATCATGATCATCACCAAATACATAAAATTGATGGATCGCAGCAGCACTCATCAATAAGGCAGCAGCAGCAAAGTG
86864 A G GTCACACTAATTAAATCCAATCTGCAGCAGTTCATCATCCAATTAAGTTAACTAGTCATAAGAAATATCATGATCATCACCAAATACATAAAATTGATGG[A/G]TCGCAGCAGCACTCATCAATAAGGCAGCAGCAGCAAAGTGCAGCAAGACATCCTTCAATAAAGCCAGTTTCTCTTCGTGGTGGCGGCG
86864 C T TTCGTGGTGGCGGCGGCGCTGCAGCATATTGATATTGGTATTGCGGTGGTGCCATCACTGGCGGCGGCCCTTGGTAATTTCCTTGTGCAGGGTATGGATA[C/T]GCATACTTTGGATCACTCATATTCTTTACAGAGTTTCAGAAACCTGAATAATTCTGCCTTTTCTATGAATTTGAAGAAGGTGTTAAAA
86864 A G GCGGCGCTGCAGCATATTGATATTGGTATTGCGGTGGTGCCATCACTGGCGGCGGCCCTTGGTAATTTCCTTGTGCAGGGTATGGATACGCATACTTTGG[A/G]TCACTCATATTCTTTACAGAGTTTCAGAAACCTGAATAATTCTGCCTTTTCTATGAATTTGAAGAAGGTGTTAAAAATAAAATAGAGA
86870 G C CATTTCTCCGACTTCACCGCTTCAACCACGAAGGTGTTGGAGCTCGCGTTCGGAAATATCACGGCTAGGGCTTGTATCCA[G/C]GTGAAATCACGGCTGCGGCCCGATGGCCTGAGTCCTATGAACCGCGCGTTGATCTGAATGCTGCTTTTCGGGTCTGAAACTAGGGCGAAGTTCTCGTCCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
86870 C T GCTCGCGTTCGGAAATATCACGGCTAGGGCTTGTATCCAGGTGAAATCACGGCTGCGGCCCGATGGCCTGAGTCCTATGAACCGCGCGTTGATCTGAATG[C/T]TGCTTTTCGGGTCTGAAACTAGGGCGAAGTTCTCGTCCTTCTTTCCATGGAAGTAGAACACTGATCCATCCCCTCCAACGAAACGTG
86870 T G AATCACGGCTGCGGCCCGATGGCCTGAGTCCTATGAACCGCGCGTTGATCTGAATGCTGCTTTTCGGGTCTGAAACTAGGGCGAAGTTCTCGTCCTTCTT[T/G]CCATGGAAGTAGAACACTGATCCATCCCCTCCAACGAAACGTGGGTCGTAGCATCCGGCGCCCAGTCCGTCGCAGTTGGGCTTCCG
86870 C T CCGATGGCCTGAGTCCTATGAACCGCGCGTTGATCTGAATGCTGCTTTTCGGGTCTGAAACTAGGGCGAAGTTCTCGTCCTTCTTTCCATGGAAGTAGAA[C/T]ACTGATCCATCCCCTCCAACGAAACGTGGGTCGTAGCATCCGGCGCCCAGTCCGTCGCAGTTGGGCTTCCGTACTCGGCATACTGCT
86910 C T GGCAAGACCTTATTTGGGTTTGGATATGACTTCCGGCAAAGCAATAGGATTCAGGAAACCATGGAGAGATTTGCTGCAAAGTTAGAGTTGGTTTTTGCTT[C/T]ATCAGGAGGAAGAAAAATCAACATTATAACTCACTCTATGGGAGGGTTATTAGTGAAATGCTTCATGTCTCTGCATAGTGATATTTT
86910 G C AAACCATGGAGAGATTTGCTGCAAAGTTAGAGTTGGTTTTTGCTTCATCAGGAGGAAGAAAAATCAACATTATAACTCACTCTATGGGAGGGTTATTAGT[G/C]AAATGCTTCATGTCTCTGCATAGTGATATTTTTGAGAAATATGTGAAAAATTGGGTTGCAATTGCTGTGCCATTTCAAGGTGCTCCTG
86910 T C ATTATAACTCACTCTATGGGAGGGTTATTAGTGAAATGCTTCATGTCTCTGCATAGTGATATTTTTGAGAAATATGTGAAAAATTGGGTTGCAATTGCTG[T/C]GCCATTTCAAGGTGCTCCTGGATATGTAACTGCAGCTTTCTTGAATGGATGCTCCTTTGTTGAGGGATGGCAGCAGAACTTTTT
86940 A G AGACTATTTCATCTAACGAGTACGATTCGTACGGCGAAGATGAATTTGGTGGGAAAGGGACGTACTTGGCGGAGAATGAGGTGTATTTCTGGTTGCATCT[A/G]GCGGCTTCTTCGCGGATGTTTTCGTCGGCGGGGCGACGTTGGTGTTTGGACGATGCAGAGGATGGGATGGTGGTGCAGGAAGTG
86940 C A TACGGCGAAGATGAATTTGGTGGGAAAGGGACGTACTTGGCGGAGAATGAGGTGTATTTCTGGTTGCATCTAGCGGCTTCTTCGCGGATGTTTTCGTCGG[C/A]GGGGCGACGTTGGTGTTTGGACGATGCAGAGGATGGGATGGTGGTGCAGGAAGTGATTTGGAAAGGTCTTGCTGGGCATTTTC
86940 G T ACGGCGAAGATGAATTTGGTGGGAAAGGGACGTACTTGGCGGAGAATGAGGTGTATTTCTGGTTGCATCTAGCGGCTTCTTCGCGGATGTTTTCGTCGGC[G/T]GGGCGACGTTGGTGTTTGGACGATGCAGAGGATGGGATGGTGGTGCAGGAAGTGATTTGGAAAGGTCTTGCTGGGCATTTTCG
86966 C G AAAATCACTCTTTCTCTTTTCTGCTCACACAAAGAAGAAAAAGCAAAAAGTATACATATCAGGAACCCTAGGAGAGAGAGAGAGACAGAGAGA[C/G]AGCCAGATAATGGATCGTAGTACTCCTGTTCGCAAGCCGCATACCTCCACAGCCGATTTGCTAACATGGTCCGATACTCCGCTCCCATCGGCG
86966 G A AGAAGAAAAAGCAAAAAGTATACATATCAGGAACCCTAGGAGAGAGAGAGAGACAGAGAGACAGCCAGATAATGGATCGTAGTACTCCTGTTCGCAAGCC[G/A]CATACCTCCACAGCCGATTTGCTAACATGGTCCGATACTCCGCTCCCATCGGCGCTGCCAGAACCTGCTTCTGCGTCCAGGCGAA
86974 T C CTGCGACGGTGGAGGATTGCTGGTCTGTGGTCGAACAGTTTTGCAGTTCATAGTGGCCACGTGGTTGCTGCGCCAGGAGGTGATGCGGTCCGATCTAATA[T/C]GGTGGCGACGAAGGTTGTCAGTGGGAATTTTCAATTTGAAGGAGCAGAGATTTTAATTGATTTGAGGAGGCGATTCAGAAGGAG
86974 A AT TGATGCGGTCCGATCTAATATGGTGGCGACGAAGGTTGTCAGTGGGAATTTTCAATTTGAAGGAGCAGAGATTTTAATTGATTTGAGGAGGCGATTCAGA[A/AT]GGAGAAAGTTGTCACTTGAATTGAAGAGGGTGAAGACCGATTGGAGGCATCGGCCATTAAAAGGGGGAAAAGGTTGAGAAAG
86994 T G AGACAATATACTGAAGAAGCTGAAAGAAAGTTGCACCATGGAAAAGCATACTAAGATGGTAGTGGTAATG[T/G]TGGCTCTTCTTCTTGCAGCAACGGCAATGTCGACCGAAGCAAGAACGCTCAAGGCCGAAGAGCCCAAGTATGAACCTCAGACATTTCCAGGCTTTCCCGG
86994 A G GAAGCTGAAAGAAAGTTGCACCATGGAAAAGCATACTAAGATGGTAGTGGTAATGTTGGCTCTTCTTCTTGCAGCAACGGCAATGTCGACCGAAGCAAGA[A/G]CGCTCAAGGCCGAAGAGCCCAAGTATGAACCTCAGACATTTCCAGGCTTTCCCGGTGGGCCTCCACTACAACCTGGAAGCTCTAT
86994 A T CATTTCCAGGCTTTCCCGGTGGGCCTCCACTACAACCTGGAAGCTCTATCCCTGGGTTTGGGCTTGGACGGCCTATGTTCGGCCTACCAGGTTCAGGGCT[A/T]CCAAGTTTTGGGTCCAACCCTCTGGTGCCTGGGATCGGAAATGGAGCGCCTGGAGTTGCTACTAAGCCGTAACAAGTTCACACTCAT
86994 T C TACAACCTGGAAGCTCTATCCCTGGGTTTGGGCTTGGACGGCCTATGTTCGGCCTACCAGGTTCAGGGCTACCAAGTTTTGGGTCCAACCCTCTGGTGCC[T/C]GGGATCGGAAATGGAGCGCCTGGAGTTGCTACTAAGCCGTAACAAGTTCACACTCATCAGTTATCCCTGCTAGCAGTTATCATTATT
86994 A G CCCTCTGGTGCCTGGGATCGGAAATGGAGCGCCTGGAGTTGCTACTAAGCCGTAACAAGTTCACACTCATCAGTTATCCCTGCTAGCAGTTATCATTATT[A/G]GTAGGAGTTTCGAGTCATCATGTTATAAAGCTCGGTCTGAGTTATATAACATGAGTTAAATAAATAAATAACCAGTTATCATCTCATG
86994 A G ACACTCATCAGTTATCCCTGCTAGCAGTTATCATTATTAGTAGGAGTTTCGAGTCATCATGTTATAAAGCTCGGTCTGAGTTATATAACATGAGTTAAAT[A/G]AATAAATAACCAGTTATCATCTCATGATTGTGATGATTGTGTGTATGTCATAGGTTGTGATTTGTATCGTATGGTTTGATTAAATTTCAT
87004 G A TTGAAAAATCAAAACCGTTGACCTGTCCATCAAGCCCAACTTTTTGGGACAAAAGGAAAGCCAAATCGCCACTCCCGCAGCACAAATCCAACACTTTATC[G/A]CCCCTCTTAGCTCTGCTCCAAGTGACGCACATCCTCTTCCAGGTTCGGTGCTGACCCAAGCTAAGCAAATCGTTCAAATTATCATAAAC
87004 T A TGTCCATCAAGCCCAACTTTTTGGGACAAAAGGAAAGCCAAATCGCCACTCCCGCAGCACAAATCCAACACTTTATCGCCCCTCTTAGCTCTGCTCCAAG[T/A]GACGCACATCCTCTTCCAGGTTCGGTGCTGACCCAAGCTAAGCAAATCGTTCAAATTATCATAAACGGGGGCGATGCGATTAAAAAGA
87004 A G TGACGCACATCCTCTTCCAGGTTCGGTGCTGACCCAAGCTAAGCAAATCGTTCAAATTATCATAAACGGGGGCGATGCGATTAAAAAGAGATTGACGGTC[A/G]ACAGCAGAGCACCATACTGCGCGGCTTCCCTCAGGAAAGCGACGTGTCCGACCGTGAGAGCGGCGGAGTGAGCGTATGCTGGGA
87008 GTT G,GT AATGGCCCGCCTGGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCATGGTGATGCG[GTT/G,GT]TTTTTGGCAGTACATCAATGGGCGTGGATAGCGGTTTGACTCACGGGGATTTCCAAGTCTCCACCCCATTGACGTCAATGGGA
87012 T C GGTTCGACGGGATGGTCGGGATGAGTGAGCTCTCAGGCGAACTCGGCTGGCCGTGTTTAGGGGAAGGAAAGACGGGCATTATGTCAGGGGAAAGAGTGGG[T/C]GGCATTGTCATGGAAGAAGTCGGAGACGGCAGCGTCGTCGGCGATGAAGATATGGTGGATATCAGTTGACATGATATCTGTT
87012 A G ATATCAGTTGACATGATATCTGTTTGATGCTTCCCAATGTTAGAAGAATGGCTAGAGAACAGAAGAAACTAGAGCTGGTAGCAGCCATTTATTTTTGAGA[A/G]GTGCTAGCTACCAAGTACAAAACGAAGTGGTGATGATGATGAGTTGATGAATCCAGTAGGCCAAC
87028 T C CGTCTTGGTTCGCCCTCTAGCATCCCTCGACCGTCGCTGCTTCACAGCGCAATACCAGGCCGCCACGTCTAACTACCAGCGATCATGACCGTTGATATTA[T/C]GGTTCTCAATCCCCTCTAGAAGTTTTCAGTTGAATGTTGGGTGAAAGGGTGGTTGGATTTCGTGAAAATTGGGAGAGAACGTGAGGA
87032 CA C TTTTCTGCTGAAGAAGCCTTTGCTTTCCTGACGAAAAGCAAAATGCTTAAAAAGCAAAAATCAGGATTTACTGGACTGTTCAC[CA/C]AAAAAGAACAGTAACAAGAAGTTCGGCGAGATCTTCAAAAATGAAGAAACGTTGAAAGAAGCAATTAAACCGTTGCTGATTCCTTGCTACGATTTGGTGA
87042 T C AATCGGTGATTTTTGTGGAAAAAAGAAAACCTAGCCCCTTACCCACTTTCATCTCCCATTTTCAGCTCCCCCAATTCGAAGACACC[T/C]AATCCACCTCCTCCAGTCCAGACCCCCTTTGCCGACCCTGTTCCGATGTTGGTGACCCCTCCGGTGACTGATACACAGATTGATGATGATGGCTTCCAAC
87056 G C TTCTGCCCCTCCTCCCACTACCAATTACCCTTCCGCTCCTTCCTCAAATTACCCTTCCACTCCTTCCTCAAATTACCCTTCCGCCCCTCCCTCAAATTAC[G/C]CTTCCGCCCCTCCTCCCTCTTCCAACTACCCTTCCGCCCCTCCTCCATCCTCAGATTATCCGTCCACCTTTCCTTCCCCCTCGAGTTACGATTTC
87056 C T CCCCTCCTCCCACTACCAATTACCCTTCCGCTCCTTCCTCAAATTACCCTTCCACTCCTTCCTCAAATTACCCTTCCGCCCCTCCCTCAAATTACGCTTC[C/T]GCCCCTCCTCCCTCTTCCAACTACCCTTCCGCCCCTCCTCCATCCTCAGATTATCCGTCCACCTTTCCTTCCCCCTCGAGTTACGATTTCGCCTC
87056 A G TCGCCTCTCCTCCATCATCTAATTACCCTTTCGCCTCTTCATCATCTAATTACCCTTCGGCACCTCCACCCTCAACTAATTATCCTTCCTCAGCTTCTGC[A/G]TCCTCTAATTACTCTTCTGCTGCACCTTCTCCTTGGCCGTTTGGCTACTCGTCTTCTTTCTCTGGCGGGCAGATCGGGTATTTTCCACCAGGC
87058 A G CTGTTGATTACTCAGGATTCCTTGCCGTTTTGTTCGGAGTCGCTGGAGCCATGTTGCGGTACAAGCTTTGCTCATGGCTGGCAATAATATTCTGTGCCCA[A/G]TCCCTTGTGAACATGAAGAACTTCGAAAATGACATGAAGCAAATCTCAATGGCAATGATGTTTGCTATAATGGGGCTAGTTACAAACT
87058 C T GCTGGCAATAATATTCTGTGCCCAATCCCTTGTGAACATGAAGAACTTCGAAAATGACATGAAGCAAATCTCAATGGCAATGATGTTTGCTATAATGGGG[C/T]TAGTTACAAACTACTTTGGAGCTGCTCGGACTCCAAAACCACAAAGTTAAAGATCCTTTCAGATCCTTTCATAAGTACTTTGAGCAGC
87058 A G CAATGGCAATGATGTTTGCTATAATGGGGCTAGTTACAAACTACTTTGGAGCTGCTCGGACTCCAAAACCACAAAGTTAAAGATCCTTTCAGATCCTTTC[A/G]TAAGTACTTTGAGCAGCCTTATTTATCGGCCAAGGCTTGTTGGACCTTTTTGTAACTCAAAATCATTATTTTTATGTACAATGCTTACCG
87058 AT A CCACAAAGTTAAAGATCCTTTCAGATCCTTTCATAAGTACTTTGAGCAGCCTTATTTATCGGCCAAGGCTTGTTGGACCTTTTTGTAACTCAAAATCATT[AT/A]TTTTTATGTACAATGCTTACCGATTGCTTTTAAGTAGAGAGTCACCGTCGTTTCTAAAATGCACCATCGTATGAGGAAATGTTTT
87072 A G GACATATCTATAAAAGTACATAAAAGACTCGTCCGTTAACAGCTGTTAAACTTTGATGTAGGCAGATGAATTGAAGTGTGTGACTTCCGGTCTGTTATCA[A/G]TCATCGTAAACACATCGGACACCAGATAACAAGAACCTTGCAAAGCATTTCCTCCATACTGGAAAAACGCGGCCTTGCACTCACATTT
87072 C G ATCTATAAAAGTACATAAAAGACTCGTCCGTTAACAGCTGTTAAACTTTGATGTAGGCAGATGAATTGAAGTGTGTGACTTCCGGTCTGTTATCAATCAT[C/G]GTAAACACATCGGACACCAGATAACAAGAACCTTGCAAAGCATTTCCTCCATACTGGAAAAACGCGGCCTTGCACTCACATTTGTTCA
87072 T A GAAGCTGTTTCGATTCACAAGTCACACCCTTCAACAAAGCGCATCCAAAGTTAGGTTGCCTCTCAACAATGGGTTTGAAGTAAGCCTTCCCACCTCCAAC[T/A]GGGCACGTGCACTGCCCGCTCGAGCAAATCGCATACCTTCCACACGCAGTCGGGTAAGCACAATCATCCGGAAGCAGGCCGATTAGT
87072 A G ATCCAAAGTTAGGTTGCCTCTCAACAATGGGTTTGAAGTAAGCCTTCCCACCTCCAACTGGGCACGTGCACTGCCCGCTCGAGCAAATCGCATACCTTCC[A/G]CACGCAGTCGGGTAAGCACAATCATCCGGAAGCAGGCCGATTAGTACATCTCCCACCAGTTTCCACCTAAACCCATCGCTCC
87072 A G TCTCAACAATGGGTTTGAAGTAAGCCTTCCCACCTCCAACTGGGCACGTGCACTGCCCGCTCGAGCAAATCGCATACCTTCCACACGCAGTCGGGTAAGC[A/G]CAATCATCCGGAAGCAGGCCGATTAGTACATCTCCCACCAGTTTCCACCTAAACCCATCGCTCC
87074 C T CCTCCCGAACCTCCAATCGGTTCCTTGCCCACTGCCTGCGCTGCAACTATCAGTCCTCCACGTTCCGCTCTGCGCTGACGTCAG[C/T]GAGATCCAGTCTTCTTCTGCGTCTCGAGTCTGGTGGCTGCCGTACCTATCTTCGTCCGCCTTCTGCTTCCAACACCTCACCGCCGATCCCCGTCTGTCTG
87104 G A ACTGTTGGCCTACTGGATTACTCACACATAAAAAACTCAAATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCT[G/A]ACCCTAACCTCCATCCTCCTCCTCGCCACCTCCACCCTCGCCCAGTCCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGC
87104 C G ACTGTTGGCCTACTGGATTACTCACACATAAAAAACTCAAATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCTGAC[C/G]CTAACCTCCATCCTCCTCCTCGCCACCTCCACCCTCGCCCAGTCCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGC
87104 T A CACATAAAAAACTCAAATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCTGACCCTAACCTCCATCCTCCTCCTCGCCACC[T/A]CCACCCTCGCCCAGTCCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGCCCGTACCCACGCCCACTGCGGCAC
87104 A G ATAAAAAACTCAAATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCTGACCCTAACCTCCATCCTCCTCCTCGCCACCTCC[A/G]CCCTCGCCCAGTCCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGCCCGTACCCACGCCCACTGCGGCACCCA
87104 C T AAAAACTCAAATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCTGACCCTAACCTCCATCCTCCTCCTCGCCACCTCCACC[C/T]TCGCCCAGTCCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGCCCGTACCCACGCCCACTGCGGCACCCACAC
87104 T TC AATTTCCCTCAAACAACATACAGCTAAAATGAAATCCCAATCAATCATCTTCCTGACCCTAACCTCCATCCTCCTCCTCGCCACCTCCACCCTCGCCCAG[T/TC]CCCCCATCCCTTCCCCCAAAGCCGCACCCGTACCCGCACCGAAACCTGCGCCCGTACCCACGCCCACTGCGGCACCCACACCCTCCGCA
87104 G C AGCTAAAATGAAATCCCAATCAATCATCTTCCTGACCCTAACCTCCATCCTCCTCCTCGCCACCTCCACCCTCGCCCAGTCCCCCATCCCTTCCCCCAAA[G/C]CCGCACCCGTACCCGCACCGAAACCTGCGCCCGTACCCACGCCCACTGCGGCACCCACACCCTCCGCAGGCGCCACCCCACCGTCCGTC
87104 A G ACCCACACCCTCCGCAGGCGCCACCCCACCGTCCGTCGCCTCCCCTCCTTCTCCTCTTCCTTCCTCCGACTCACCTTCCTCCTCCCCTCCTCCTTCCTCC[A/G]CGTCCTCTCCTCCATCCGTGACTCCTTCAGCGTCACGCCCTGCCGATAACGCCGCTTCTCGCCCTCTCGCCGGTTTCCTCCTCGCCGGCTCG
87104 A G CGTCCGTCGCCTCCCCTCCTTCTCCTCTTCCTTCCTCCGACTCACCTTCCTCCTCCCCTCCTCCTTCCTCCACGTCCTCTCCTCCATCCGTGACTCCTTC[A/G]GCGTCACGCCCTGCCGATAACGCCGCTTCTCGCCCTCTCGCCGGTTTCCTCCTCGCCGGCTCGGTCGTCTTCGCCTCTGCTGTTGTTTTCGCT
87104 A C TCGCCTCCCCTCCTTCTCCTCTTCCTTCCTCCGACTCACCTTCCTCCTCCCCTCCTCCTTCCTCCACGTCCTCTCCTCCATCCGTGACTCCTTCAGCGTC[A/C]CGCCCTGCCGATAACGCCGCTTCTCGCCCTCTCGCCGGTTTCCTCCTCGCCGGCTCGGTCGTCTTCGCCTCTGCTGTTGTTTTCGCTTTCTAA
87104 C G ACTCACCTTCCTCCTCCCCTCCTCCTTCCTCCACGTCCTCTCCTCCATCCGTGACTCCTTCAGCGTCACGCCCTGCCGATAACGCCGCTTCTCGCCCTCT[C/G]GCCGGTTTCCTCCTCGCCGGCTCGGTCGTCTTCGCCTCTGCTGTTGTTTTCGCTTTCTAATTGAGCTGGATCTCTGATTTGTCATTGCCAGC
87110 A G CAGAATATAAAATATTTTTATGACATCAAAGACCTTGGAAATTTCAAGGCCAATCCAGATTACAAAGGTGT[A/G]TGCCATGTTGCTTTAGCCCAAGAAGGGCACTGCAGACCAGGAGAGGTTTTGCTTGGAACAGATTCTCACACATGCAATGCAGGAGCATTTGGACAATTTG
87110 T C CAGAATATAAAATATTTTTATGACATCAAAGACCTTGGAAATTTCAAGGCCAATCCAGATTACAAAGGTGTATGCCATGTTGCT[T/C]TAGCCCAAGAAGGGCACTGCAGACCAGGAGAGGTTTTGCTTGGAACAGATTCTCACACATGCAATGCAGGAGCATTTGGACAATTTGCTACAGGTATTGG
87110 C T CAGAATATAAAATATTTTTATGACATCAAAGACCTTGGAAATTTCAAGGCCAATCCAGATTACAAAGGTGTATGCCATGTTGCTTTAGC[C/T]CAAGAAGGGCACTGCAGACCAGGAGAGGTTTTGCTTGGAACAGATTCTCACACATGCAATGCAGGAGCATTTGGACAATTTGCTACAGGTATTGGTAA
87110 C T ATTTCAAGGCCAATCCAGATTACAAAGGTGTATGCCATGTTGCTTTAGCCCAAGAAGGGCACTGCAGACCAGGAGAGGTTTTGCTTGGAACAGATTCTCA[C/T]ACATGCAATGCAGGAGCATTTGGACAATTTGCTACAGGTATTGGTAACACTGATGCAGGTTTCGTCATGGGCACTGGAAAACTTTTG
87110 A G ATGTTGCTTTAGCCCAAGAAGGGCACTGCAGACCAGGAGAGGTTTTGCTTGGAACAGATTCTCACACATGCAATGCAGGAGCATTTGGACAATTTGCTAC[A/G]GGTATTGGTAACACTGATGCAGGTTTCGTCATGGGCACTGGAAAACTTTTGCTGAAGGTACCCCCTACACTGAGATTTGTATTAGA
87110 C T CAATGCAGGAGCATTTGGACAATTTGCTACAGGTATTGGTAACACTGATGCAGGTTTCGTCATGGGCACTGGAAAACTTTTGCTGAAGGTACCCCCTACA[C/T]TGAGATTTGTATTAGACGGAGATATGCCTGATTATCTGCTTTCCAAGGATTTGATTTTGCAGATTATTGGTGAAATAAGTGTTGCTGG
87110 C T GACAATTTGCTACAGGTATTGGTAACACTGATGCAGGTTTCGTCATGGGCACTGGAAAACTTTTGCTGAAGGTACCCCCTACACTGAGATTTGTATTAGA[C/T]GGAGATATGCCTGATTATCTGCTTTCCAAGGATTTGATTTTGCAGATTATTGGTGAAATAAGTGTTGCTGGTGCAACATATAAAGCTA
87110 T A GTATTGGTAACACTGATGCAGGTTTCGTCATGGGCACTGGAAAACTTTTGCTGAAGGTACCCCCTACACTGAGATTTGTATTAGACGGAGATATGCCTGA[T/A]TATCTGCTTTCCAAGGATTTGATTTTGCAGATTATTGGTGAAATAAGTGTTGCTGGTGCAACATATAAAGCTATGGAATTTGTGGGTT
87110 C T TTGGTGAAATAAGTGTTGCTGGTGCAACATATAAAGCTATGGAATTTGTGGGTTCAACCATTGAGAGTTTAACAATGGAAGACCGAATGACTCTATGCAA[C/T]ATGGTTGTTGAGGCCGGAGGTAAAAATGGAGTTATCCCTGCAGATGCAACTACATTCAACTACCTTGAGGGCAAGACATCTGTGAG
87126 T A TCCCTGCTTTTAGGCCCTGCCATGGAAGACTTCCCCTTAGAAAATACATTAGAACAAACCCAAGAGATTCCAAATCATCCCTCCTGCTTTGTTCTATCCC[T/A]AGATGTGTGTTCATACTTGCATATCTTGCTGTGCCTGTCAGATTCTTATTTTCTCTATAAGGTATGTGCTGTTGAGTAGCGGTATCTCTGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
87142 G A TCACTCGCATCAACCAAAAAAAACCCTTATATCGATAGAATCAAAATTCAACGAGCAATGGGAAAAAGAACGAGAGACGCAGAAGCAGAATTGA[G/A]TCTGCCGCCGGGATTCAGATTCCATCCCACCGACGAAGAACTCGTCGTCCATTACCTCTGCAAGAAAGTGACGCTCCAGCGCCTACCCGTTC
87142 G A TGGGAAAAAGAACGAGAGACGCAGAAGCAGAATTGAGTCTGCCGCCGGGATTCAGATTCCATCCCACCGACGAAGAACTCGTCGTCCATTACCTCTGCAA[G/A]AAAGTGACGCTCCAGCGCCTACCCGTTCCGATAATCGCTGAGGTCGATCTGTACAAGTTCGATCCGTGGGAGCTTCCCGAGAAGG
87142 G A CGCCGGGATTCAGATTCCATCCCACCGACGAAGAACTCGTCGTCCATTACCTCTGCAAGAAAGTGACGCTCCAGCGCCTACCCGTTCCGATAATCGCTGA[G/A]GTCGATCTGTACAAGTTCGATCCGTGGGAGCTTCCCGAGAAGGCATTATTTGGGCAGAAGGAATGGTACTTCTTCACTCCGAGAGA
87144 A AC ATCTGAACATTCAAGCAAACCAAGGTTTGTTCACATCAGATCAGGTGCTTGGTGCTGATGGCACAACTGCAAGACAAGTGAGAGCGAATGCGGGTATCCC[A/AC]TGCTTTGGAAAAATAAATTTTCTCTGGCCATGGTTAAGATGGGTCAGATTGGGGTGCTCACTGGCACTAATGGAGAGATACGGA
87162 T C AAAATTTCCCCTTCCTTCTGTCAGTCAAAATTCAAAATTTATGGCGAACTCTGTGGACCAACGCACCCT[T/C]TTCGCGTCGACTCTCGTCATCTTGATCTCCCTTTTCTCCTTTTCAGCTGCTGACACCTCTTTCGATTACTGCAGTAGGAAAGCAGATTATCCTGTTAAGA
87166 T A CTGTTGGCCTACTGGATCAACCCCACAATTCCACATACCAGGATAGCCCAAAATTTCAAA[T/A]TTCAAAAAAACAAATCAATACAAAGAAATGGCGGACGAAGGCGGAGCACCACACGGAATCCTGCTAGCCGCAGTGGTAGCAATAGTCGTCGGAGCACCAG
87166 C A CTGTTGGCCTACTGGATCAACCCCACAATTCCACATACCAGGATAGCCCAAAATTTCAAATTTCAAAAAAACAAAT[C/A]AATACAAAGAAATGGCGGACGAAGGCGGAGCACCACACGGAATCCTGCTAGCCGCAGTGGTAGCAATAGTCGTCGGAGCACCAGTCCTCCTCAACGGCGG
87166 T C ACGGAATCCTGCTAGCCGCAGTGGTAGCAATAGTCGTCGGAGCACCAGTCCTCCTCAACGGCGGCGGCGAGGCGATAACCGACTTCATTTCCGACATGCT[T/C]AGCCCCGCCGGTCTCCTGCTTCTCCCCGTCGGCCTCATTCTGGTCATCCGCTTACTGTCCAGCGACCGCGCCAACGCGTTCTTGGAC
87166 A G TCAACGGCGGCGGCGAGGCGATAACCGACTTCATTTCCGACATGCTTAGCCCCGCCGGTCTCCTGCTTCTCCCCGTCGGCCTCATTCTGGTCATCCGCTT[A/G]CTGTCCAGCGACCGCGCCAACGCGTTCTTGGACGTGTTCTCGTTCGGCGGACCCGACTCGATTCACAAGGTCGGAGGTTCGCCTCTC
87166 T C CTTCATTTCCGACATGCTTAGCCCCGCCGGTCTCCTGCTTCTCCCCGTCGGCCTCATTCTGGTCATCCGCTTACTGTCCAGCGACCGCGCCAACGCGTTC[T/C]TGGACGTGTTCTCGTTCGGCGGACCCGACTCGATTCACAAGGTCGGAGGTTCGCCTCTCGGCGTCGCGGTGGTGCTTCTGATTCTGCT
87166 G A TCATTTCCGACATGCTTAGCCCCGCCGGTCTCCTGCTTCTCCCCGTCGGCCTCATTCTGGTCATCCGCTTACTGTCCAGCGACCGCGCCAACGCGTTCTT[G/A]GACGTGTTCTCGTTCGGCGGACCCGACTCGATTCACAAGGTCGGAGGTTCGCCTCTCGGCGTCGCGGTGGTGCTTCTGATTCTGCTGC
87212 G T AGTTCGGGCTCCTCTGCGGGTCGGATGGGCTGCCCCACTTGATAGTGAGCGGAGACCAGAGGCATTGGGGCGAGTTCATCACTCCCGGGGTTCTGTTTCT[G/T]TACATAGCCGGGTGGATAGGGTGGGTAGGGAGGAGCTATTTGATTGCCATTAAGGGGGAGAAGAAGCCTACCCAGAAGGAGAT
87214 A G AAGAGTGGGAGGAAATAATTAAAGATTTAATGAAAAGGCTACCAGCTATGAAAGAGCTCATTGATATGTATGCTGGCTCTGATAGGATAACATCGAAACA[A/G]CAGATGCAAGAACTGGATAGAGTGGCAAAAACCATACCACAGAATGTGCCTTCTTCAGTGAAGAGGTTCACGGATCGTGCTGTTC
87224 A G CAAAATTATAAATAGAACGCAGCTCCTAATTTTCTTCAATCGGCGATCTTCTTCCTATCGACTTCAGTAGAAAATGAGTTCAGAGGCACCAAGCTGGGCG[A/G]ATCAATGGGGGTCGAGTGGAGCTATTGATGACTATGATGGCAAAGCTAACAAGAACAAAGACAAAGGGAAGAAAATGGAAAATGT
87224 T C TGAAGAGTGGTACTAGTCAGGGACTTAGCTGGGTCAAGAATCAATACAAGAAAAGAACCTCCAAATGACTGTTGTTCTTCGTCGTTTTGTTTAACGAAAA[T/C]CGATCTTCTCATTATACTACATTCAGATCTTTACAGACAAAAAAAAGGGTTTCTTCTACCGATTGTGAATTATGATACTTTGGCATCTT
87224 CA C AATCAATACAAGAAAAGAACCTCCAAATGACTGTTGTTCTTCGTCGTTTTGTTTAACGAAAATCGATCTTCTCATTATACTACATTCAGATCTTTACAGA[CA/C]AAAAAAAAGGGTTTCTTCTACCGATTGTGAATTATGATACTTTGGCATCTTGCATATACATTCCTCCTGCAATGCTAAGAATAAGATATT
87224 C T CCAAATGACTGTTGTTCTTCGTCGTTTTGTTTAACGAAAATCGATCTTCTCATTATACTACATTCAGATCTTTACAGACAAAAAAAAGGGTTTCTTCTAC[C/T]GATTGTGAATTATGATACTTTGGCATCTTGCATATACATTCCTCCTGCAATGCTAAGAATAAGATATTGAATAAAAAAAAAAAAAA
87244 T A TCGGAGATAGCACAACCACCATCATCTTCTGTCCATTCATGCATTTCTGAGCATCGCCGCTGATGAAATAGTACGGTCCCGACCTCGTAAGCTGAAAGCT[T/A]CCGCCTTGCACTTTGCTGATAGGACTGCTACCGCTGCAAGAGTCGTAGTCTTCCTTCTTCACCACCAAAATCGACGCCGATTGGTCGT
87260 T C GATCCATCCATCGATCTAATGGCTGTTCCAAAGAAAAAGACTTCTAAGTACAAGAAAAGACTGAGAAACGGTCCCAAGGCTTTGAAACCTATTCCTGTCA[T/C]CGTCAAATGCAAAGCTTGCGGCAAAGTTAAGCTGCCTCACTTCTATTGCTGCAGCGGTGAAAGAGGGATTGGGAGCTCTGCCCCTAG
87264 A G CCTAGTCCCATGTTATCCATAAAATCTTTGACTCCTGTGCCGCCGCCACTTGCGCTACGAAAATCTTCTCGTGCCTTCTCGGGGTTGATCTCTAGAGCAA[A/G]GAGTGGTGAATCAAGCCCTTGTACAGGTACCAGGGTTCCTCCAGTCAAGTCCTGTGCAAAGGAGTCACTTAGAGAATGAGCAGGATC
87272 G A CTTCATTTCCACCGCATGTAAGATAGTATCTTGAGTTTATGAAAAGCATACCATGAAGCAAAAAGCGCATACATGACGAGTTGATCGACCAGCAGCTACG[G/A]CAGTTAATACTTGGGCATGCAGGATTCCGACTGTTCTCATCGGTTGTCTTCAGCTTCAGTAACAACTATACAGATTCATTATTTCATAG
87272 C T TTCATTTCCACCGCATGTAAGATAGTATCTTGAGTTTATGAAAAGCATACCATGAAGCAAAAAGCGCATACATGACGAGTTGATCGACCAGCAGCTACGG[C/T]AGTTAATACTTGGGCATGCAGGATTCCGACTGTTCTCATCGGTTGTCTTCAGCTTCAGTAACAACTATACAGATTCATTATTTCATAGC
87274 AC A CACCCAACTATACACATCCCAAAACACCTCCACCCCAACCCCATCCACCCACACCACCTCATTCCCTCTAAACTTCCACCCAATCCTCTCCACCCTCAGC[AC/A]CCCCCTCCCCGTCCACCCGTATCTCCAGCACCGGATCCTCCACGCCGACCACCTCGCACTCGATCTCCACGTCATGCATCCCGCCGCCCT
87274 G A CCACCCACACCACCTCATTCCCTCTAAACTTCCACCCAATCCTCTCCACCCTCAGCACCCCCTCCCCGTCCACCCGTATCTCCAGCACCGGATCCTCCAC[G/A]CCGACCACCTCGCACTCGATCTCCACGTCATGCATCCCGCCGCCCTCCCTAAACCTCGCCCTCGTGCAGTGCACCCTCTTCCCGAACACGT
87274 C G CTAAACTTCCACCCAATCCTCTCCACCCTCAGCACCCCCTCCCCGTCCACCCGTATCTCCAGCACCGGATCCTCCACGCCGACCACCTCGCACTCGATCT[C/G]CACGTCATGCATCCCGCCGCCCTCCCTAAACCTCGCCCTCGTGCAGTGCACCCTCTTCCCGAACACGTGCTCCTTCCTGCTCACGAACAC
87278 T C TCCATTTAGAAGAAAAGAACCTCGGAAATTAGTCAGTTTATGTATTGGTGTTCTTGGACAACATTTAGAAGATATTGTTGAAGATTTAGCGGACATTGCT[T/C]CAGAGTTCCCTCCTGATGTGAAGTTAGCTTTGCTGGCTATTGCAAGGAGAAGGCAATTATTAAATGATAACGTCCTTCTTGCACTGGC
87280 G A TCCAACCTTAGCCCAATACGACTCCTTTGGCCCCCCAGTCGATAAAGTAGTCATCTATGGCGACGGAAATACCAAAGTTGCTTTCGTGAACGAGGAAGAT[G/A]TTGGCATGTACACAATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTC
87280 A G CTTAGCCCAATACGACTCCTTTGGCCCCCCAGTCGATAAAGTAGTCATCTATGGCGACGGAAATACCAAAGTTGCTTTCGTGAACGAGGAAGATGTTGGC[A/G]TGTACACAATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATG
87280 A C TTGGCCCCCCAGTCGATAAAGTAGTCATCTATGGCGACGGAAATACCAAAGTTGCTTTCGTGAACGAGGAAGATGTTGGCATGTACACAATCAAGGCTGC[A/C]GTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGTGTCGCTGTGGGA
87280 C T GCCCCCCAGTCGATAAAGTAGTCATCTATGGCGACGGAAATACCAAAGTTGCTTTCGTGAACGAGGAAGATGTTGGCATGTACACAATCAAGGCTGCAGT[C/T]GATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGTGTCGCTGTGGGAGGA
87280 A G CAGTCGATAAAGTAGTCATCTATGGCGACGGAAATACCAAAGTTGCTTTCGTGAACGAGGAAGATGTTGGCATGTACACAATCAAGGCTGCAGTCGATCC[A/G]AGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGA
87280 A C TGCTTTCGTGAACGAGGAAGATGTTGGCATGTACACAATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAAT[A/C]TGTATACTCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGT
87280 A T TTCGTGAACGAGGAAGATGTTGGCATGTACACAATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGT[A/T]TACTCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTA
87280 G A TTGGCATGTACACAATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGT[G/A]TCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTT
87280 G A AATCAAGGCTGCAGTCGATCCAAGAACATTGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGTGTCGCTGTGGGAG[G/A]AGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAAC
87280 T A TGAACAAAATTGTGTACATACGACCTCCAAAGAATATGTATACTCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGT[T/A]TATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTC
87280 C A TATGTATACTCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTT[C/A]AAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATCATCACTGAT
87280 T C TCATAATGAGCTCGTGTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCT[T/C]CATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATCATCACTGATCCATCCTTTG
87280 T A GTCGCTGTGGGAGGAGAAGAGTGGTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAAC[T/A]TTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATCATCACTGATCCATCCTTTGCTGCGGAAGCTTCT
87280 C T GTAAAAAACTAGAGAGGGTTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTC[C/T]GGATTCGTGGAGGGAGATACGACTAACATCATCACTGATCCATCCTTTGCTGCGGAAGCTTCTGAATTGTATCCAGATCTGAAGTACA
87280 T C TTTATCTCACCAAGGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGA[T/C]ACGACTAACATCATCACTGATCCATCCTTTGCTGCGGAAGCTTCTGAATTGTATCCAGATCTGAAGTACACAACAGTCGAGGAGTATA
87280 A G GGAAGAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATC[A/G]TCACTGATCCATCCTTTGCTGCGGAAGCTTCTGAATTGTATCCAGATCTGAAGTACACAACAGTCGAGGAGTATATCAGCCGCGTTG
87280 C T GAGGTGTTACGGAAAGTTCAAGAGTCTTCATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATCATCA[C/T]TGATCCATCCTTTGCTGCGGAAGCTTCTGAATTGTATCCAGATCTGAAGTACACAACAGTCGAGGAGTATATCAGCCGCGTTGTGTGA
87280 T C CATTTCCATTCAACTTTGTGTTGGCTATTAACTATTCCGGATTCGTGGAGGGAGATACGACTAACATCATCACTGATCCATCCTTTGCTGCGGAAGCTTC[T/C]GAATTGTATCCAGATCTGAAGTACACAACAGTCGAGGAGTATATCAGCCGCGTTGTGTGA
87286 T A ATTGGTTGTACAAGCGGAACATGATGGAGAAACAGCGGGCTTTGCCTATCGAGTGGGACCCGGAAAGTGCGACTAGATCGACGATTGAGAGGTTGAATCT[T/A]TGGAACAGTGTTATGAGGGTTGATGCATTGGCTCTTGGACTTGGCATTATGTTGTTCGAGTCTTCCTGGCTTGCCGTTAGGCTGT
87310 T G TAACCGGTGCCGGATCCGCGCAAGCCCTCGTTGCCGCCTCCGGATCCGAAAAAGTCACAAATCCATAGCCCTTGGATCTTCCGGTGTTCTTATCCGTGAT[T/G]ACAACCGCTTCCAAAATATGACCGAACTGATCGAAGTACTTCATCATGGTATCCTTTTTGGTCTCCCATGGCAAACCGCCCACGAATA
87316 GT G AATTTTTAGCACTGCGTAGATAACCCATCTTGAATTTGGAGCACTACGGTAGAAGAAGGGGTTGCGGTTTGGATTGAACGGACAGGCTGACGGTGGCAAT[GT/G]TTTTTAGTCGATCTGGACGATGGAGGAGCCGTGTGCAGCGTGGAATCAACGCCGGATAGACGGAGCAATACAGCAGAAGAAG
87316 C G GTTTTTAGTCGATCTGGACGATGGAGGAGCCGTGTGCAGCGTGGAATCAACGCCGGATAGACGGAGCAATACAGCAGAAGAAGAGTCTGCGGTTTGGATT[C/G]AGTAAATAGGAAGATGGCAACAATGTTTTTAATCGATCGAGAGGATTGAGGTTTCGTGGGTAACGTGGATTTGATCCAGGGTTT
87326 A G TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAAT[A/G]TCAAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTA
87326 C T TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATAT[C/T]AAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATT
87326 C T TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAA[C/T]TGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACT
87326 A T TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAA[A/T]ATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTAT
87326 T TG TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAA[T/TG]ACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTA
87326 AC A TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACG[AC/A]CTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTA
87326 A C TTAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACT[A/C]GTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTAT
87326 G A TAAAACAACTCACATAAGAAAATGCATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACTA[G/A]TATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATG
87326 G A CATGCAGGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAG[G/A]GACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAA
87326 G A GGGTGATCTTACTTACAATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCG[G/A]TAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAA
87326 T C AATCACACAACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGT[T/C]TCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTG
87326 T G ACAGACATACATACAATTAATATCAAACTGAAAAAAATACGACTAGTATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCT[T/G]TAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCCGGC
87326 A T ATAGCTATTCGAAGTTGACAAGGGACCGGTAAGTAGCTCCAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGC[A/T]GTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCCGGCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAGAGCGCCATAT
87326 G C CAGGTTTCCAACCTTTAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCC[G/C]GCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
87326 T C TAGGGATCACATTTTTAGCTATTAACTTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCCGGCATCAAGCTTCCA[T/C]ACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCC
87326 A G TTCCTATGTGAATGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCCGGCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAG[A/G]GCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGC
87326 A G TGCTGGGCAGTTACTCTAATGGAAATGGGAGCTTTTAGTTGTCTTCCGGCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTG[A/G]TCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTG
87326 T A TGGGAGCTTTTAGTTGTCTTCCGGCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTT[T/A]AGTTCCACTCGTTCCAGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAG
87326 C A GTCTTCCGGCATCAAGCTTCCATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTC[C/A]AGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTGT
87326 T C CATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCCCGATCTG[T/C]GAACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTGTGGATACTCACATGGTACTCT
87326 G A ATACAGCACCCCATGATTCCTTCATAGAGCGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCCCGATCTGT[G/A]AACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTGTGGATACTCACATGGTACTCTT
87326 C A CGCCATATTGATCTGTATTGTAGGCTTGATTCTTTTAGTTCCACTCGTTCCAGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTG[C/A]GTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTGTGGATACTCACATGGTACTCTTGTGTATAGGATAGGTAGGACTCCAGTAC
87326 T G CCACTCGTTCCAGACTTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTG[T/G]GGATACTCACATGGTACTCTTGTGTATAGGATAGGTAGGACTCCAGTACCACGCAGTTTATCACTACGACCATGCAGAGCCATGGCTC
87326 T A TTCCATCCCGATCTGTGAACTCGATTAGGACTGCTAAGTAGTTTGCGTTTGAACCAACATCCACACGGAAGGTTATTGTCTTGTGTGGATACTCACATGG[T/A]ACTCTTGTGTATAGGATAGGTAGGACTCCAGTACCACGCAGTTTATCACTACGACCATGCAGAGCCATGGCTCCAAATGCACTGCCAC
87330 G A CAGAGTTCATAAAGACTTCTTGCAGCACCACAACGTACCCAACACTTTGCTTTGCTTCCCTCTCATCTTACTCCAACATCATCCAAAGTAACCCAAGGCA[G/A]CTAGCTTACATCGCTCTTTCGGTTGCTTTAAACGCTACTCATTCCGCTTCCGAAGCCATACACCAAATACCCTTGAGCAGAGGCCTGAAC
87330 C T CATCTTACTCCAACATCATCCAAAGTAACCCAAGGCAGCTAGCTTACATCGCTCTTTCGGTTGCTTTAAACGCTACTCATTCCGCTTCCGAAGCCATACA[C/T]CAAATACCCTTGAGCAGAGGCCTGAACCCTAGAGTAAAAGGAGCGTTAAGCGACTGCATGGAGACAGTAGGAGACTCGGTAGCCGAG
87336 G T CGTCAGAGGGCTTAGCTTGCATTAATGCATGGGGAAAGCTAGGCAAAGTAGAGAATGCAGAGAAGGTATTTGAAAGAATGGGAAGAACAAGAAATAAGCT[G/T]TCACCTAGATATTACAACGATATGATAAAACTGTACGCAGGCCATAAGCTTCTGGCTAAGGGTAAGAAAATGGCAGAGGAAATG
87336 T C CAGGCCATAAGCTTCTGGCTAAGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTA[T/C]GTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACT
87336 G T AGGCCATAAGCTTCTGGCTAAGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTAT[G/T]TGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTT
87336 C G ATAAGCTTCTGGCTAAGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGA[C/G]TGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATG
87336 A G TGGCTAAGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGA[A/G]GTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTG
87336 T A CTAAGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGT[T/A]GAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAG
87336 A G AGGGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGA[A/G]AAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAG
87336 A G GGTAAGAAAATGGCAGAGGAAATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAA[A/G]AGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAGTA
87336 A G AATGGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAG[A/G]AGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGGAGATGTTC
87336 G A GGCTGAGAAATGGAGGGTAGGCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAG[G/A]CAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGGAGATGTTCATA
87336 G A GCCCTTCAACTTGGGATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTT[G/A]AAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGGAGATGTTCATAATGCAGAAAAAATATTTCAGAA
87336 G A GATGCTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACA[G/A]CACTTATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGGAGATGTTCATAATGCAGAAAAAATATTTCAGAATATTAGGCAAAAT
87336 T C CTTTAGTAAAACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCAC[T/C]TATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGGAGATGTTCATAATGCAGAAAAAATATTTCAGAATATTAGGCAAAATGGGT
87336 G T ACTGTATGTGGACTGTGGAGAAGTTGAAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTT[G/T]TGTTGGAGCAGTATGCTAGGAGAGGAGATGTTCATAATGCAGAAAAAATATTTCAGAATATTAGGCAAAATGGGTATACAGGAAG
87336 A G AAAAAGCTGATTCATTGCTTCAGAAGGCAGTGGAGAAAAAACAGTTGAAGCCGCTATACAGCACTTATATGCTTGTGTTGGAGCAGTATGCTAGGAGAGG[A/G]GATGTTCATAATGCAGAAAAAATATTTCAGAATATTAGGCAAAATGGGTATACAGGAAGGATGGGGATGTACTGTGCTTTGCTGA
87350 T A TTCGACGAGGAGTAGTTGTCTCCGCAGCAGGATTCGGAATCGTCGTTCACGACGGCGTTCTCCGCCAGCAGCCGCTCCAGATTCGCGCTCAATGC[T/A]GCGGCGGTCGATTCATGGCTCCGCGCCAGATACTTCCACGCATTGCTCTCGAGCACTAGATTCTTCGTCCTCTCTTCCAAGGCGTAGTTTAA
87354 C T TGTTGTTGCTATGATTGTTGGTGCTAGGGGTTTTGGCTTTGCTCTTTCCATTCACTACTTCAAATATGGTAGGTAGGTCATTCATCATCCCAAAAAGACG[C/T]TTTCTGTCTGACTTGTCGAATCCAAATCTAGCTCCAAAATAAAATGCAACAGAAAGCAACCAGGCATCACTGTGCACAGCAACTAAGGA
87364 CA C AATGGTGTGGTTCTCACTCCCATTCATACATTGCGATACAATACAATACAATATAAGCATTATATGTGATTGCATTACATTAGTAGTTCTATCCAAAGTC[CA/C]AAAAAGGTAACATGATTACATTAATGCAACCGCTACATAGTTAATTCCAACTCTATAGTTTCCAACTTCGGTCTGCATTCACTGCTCCCC
87372 T A AGAATTCCGTAGTTCTCCTTCTTCTCCAAACCCTATCTTTCCCCCTTTTTCTCACAATGGGTCGCGTTCGTACCAAAACCGTTAAAAAGTCCTCTCGCCA[T/A]GTCATCGAACGCTATTACTCCCGCATGACGCTGGACTTCCACACCAACAAAAAGATCCTCGAAGAGGTAGCTATCATCCCATCGAAGCGT
87372 A G GTACCAAAACCGTTAAAAAGTCCTCTCGCCATGTCATCGAACGCTATTACTCCCGCATGACGCTGGACTTCCACACCAACAAAAAGATCCTCGAAGAGGT[A/G]GCTATCATCCCATCGAAGCGTCTCCGTAATAAAATCGCCGGATTCTCCACCCATTTGATGCGTCGGATCCAGAAAGGACCTGTTCGTG
87372 T C CCTCTCGCCATGTCATCGAACGCTATTACTCCCGCATGACGCTGGACTTCCACACCAACAAAAAGATCCTCGAAGAGGTAGCTATCATCCCATCGAAGCG[T/C]CTCCGTAATAAAATCGCCGGATTCTCCACCCATTTGATGCGTCGGATCCAGAAAGGACCTGTTCGTGGCATATCACTGAAGCTGCAAG
87372 A G AAGAGGAAGAGAGAGAAAGGAGAATGGATTTTGTGCCGGATGAAAGCGAAATTAAGGTGGATCGCATTGAGGTTGACAAGGAAACGATCGAATTGTTGGC[A/G]TGTATCGGCATGGCGGATTTGCCTGGGGTTGTGCAAGTCGATGAAGCAGCAGCGCCACAGCAAGTGGTTTTTGGCGGCGGTC
87390 T C ATGGCGACTCGTCGCGTCCTCTCTTCTCTCCTTCGTTCCTCTTCCCGCAAATCCACCTCCCGCATAATCTCTAACTCCAGATCCCCCGCTCCGCCTCTCT[T/C]CCGACCAAATCCCACCGGATTCCTCCTCTCTCGCGCTGTCGAGTACGCTACTTCAGCAGCAGCTCCGTCGACTCCTTCTAAAGCGCCGACG
87390 A G TCCGCCTCTCTTCCGACCAAATCCCACCGGATTCCTCCTCTCTCGCGCTGTCGAGTACGCTACTTCAGCAGCAGCTCCGTCGACTCCTTCTAAAGCGCCG[A/G]CGACGCCAGCAGCGAATACGAGTGGTAAGATTACTGACGAGTTCACAGGAGCTGGATCGATAGGAAAGGTGTGCCAGGTGATTGGA
87390 A C TCCGACCAAATCCCACCGGATTCCTCCTCTCTCGCGCTGTCGAGTACGCTACTTCAGCAGCAGCTCCGTCGACTCCTTCTAAAGCGCCGACGACGCCAGC[A/C]GCGAATACGAGTGGTAAGATTACTGACGAGTTCACAGGAGCTGGATCGATAGGAAAGGTGTGCCAGGTGATTGGAGCCGTTGTTG
87402 T C ACGAACATAGAAAAATTGAAGTTTATTCCAGCTCAATCCTTCTTTCTCCAGCCTAGATCACGGCATATTTCCAACTGCTCCTCCACAGAAAACCCCAAAT[T/C]AAAATTCCGTCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGT
87402 G T GAAAAATTGAAGTTTATTCCAGCTCAATCCTTCTTTCTCCAGCCTAGATCACGGCATATTTCCAACTGCTCCTCCACAGAAAACCCCAAATTAAAATTCC[G/T]TCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGT
87402 A T CTTTCTCCAGCCTAGATCACGGCATATTTCCAACTGCTCCTCCACAGAAAACCCCAAATTAAAATTCCGTCAATCATTCGACCCCCAGTTTTTTTCCCCA[A/T]TCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGTAGTATCAGTCTTGATATTACTCTTCAACGTCT
87402 A G CACGGCATATTTCCAACTGCTCCTCCACAGAAAACCCCAAATTAAAATTCCGTCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCA[A/G]AATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGTAGTATCAGTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTAC
87402 T C CTGCTCCTCCACAGAAAACCCCAAATTAAAATTCCGTCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAA[T/C]CTCGCCCTGGTAATAGTGGCCATAGTAGTATCAGTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACG
87402 G A CACAGAAAACCCCAAATTAAAATTCCGTCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCT[G/A]GTAATAGTGGCCATAGTAGTATCAGTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAA
87402 G A CGTCAATCATTCGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGTAGTATCA[G/A]TCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTGGTCGTAG
87402 A G CGACCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGTAGTATCAGTCTTGATATT[A/G]CTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTGGTCGTAGTCATCGGACTC
87402 C G CCCCCAGTTTTTTTCCCCAATCTCCCCTCAAATTCAAAATGGGCGATTTCAATCTCGCCCTGGTAATAGTGGCCATAGTAGTATCAGTCTTGATATTACT[C/G]TTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTGGTCGTAGTCATCGGACTCAGC
87402 G A GGCCATAGTAGTATCAGTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTG[G/A]TCGTAGTCATCGGACTCAGCGTCGCGGCGATTTCGATTCTCATGCTGCCTGCTGACGTGGCCAACCGACAGGCCTGCCGGCATGCGCT
87402 A C CAGTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTGGTCGTAGTCATCGG[A/C]CTCAGCGTCGCGGCGATTTCGATTCTCATGCTGCCTGCTGACGTGGCCAACCGACAGGCCTGCCGGCATGCGCTCTATAATGGCGCTT
87402 T C GTCTTGATATTACTCTTCAACGTCTATCTCTTAGTCAACTACCAGCACCCCGACGACGTCAACCAAGCCTACTTTCCGAAAGTGGTCGTAGTCATCGGAC[T/C]CAGCGTCGCGGCGATTTCGATTCTCATGCTGCCTGCTGACGTGGCCAACCGACAGGCCTGCCGGCATGCGCTCTATAATGGCGCTTGC
87402 T A CCTACTTTCCGAAAGTGGTCGTAGTCATCGGACTCAGCGTCGCGGCGATTTCGATTCTCATGCTGCCTGCTGACGTGGCCAACCGACAGGCCTGCCGGCA[T/A]GCGCTCTATAATGGCGCTTGCAATTTGACGTTACCGATGAAGACGTTGTGGCTTGTTGTTTATATCGTTGATGCGGTTTTAGTGTTTT
87402 T C ACTCAGCGTCGCGGCGATTTCGATTCTCATGCTGCCTGCTGACGTGGCCAACCGACAGGCCTGCCGGCATGCGCTCTATAATGGCGCTTGCAATTTGACG[T/C]TACCGATGAAGACGTTGTGGCTTGTTGTTTATATCGTTGATGCGGTTTTAGTGTTTTTCTTTATTCCGTTCGCTATGTTTTACTATGAA
87402 G A TGGCCAACCGACAGGCCTGCCGGCATGCGCTCTATAATGGCGCTTGCAATTTGACGTTACCGATGAAGACGTTGTGGCTTGTTGTTTATATCGTTGATGC[G/A]GTTTTAGTGTTTTTCTTTATTCCGTTCGCTATGTTTTACTATGAAGGGGACCAGGACAAGAG
87410 C T AGGGCCGATAAATGGTTCGATTTAGTCTTTGATTTGCTAAGGGGTGCTCGCAGTCCTCGTGGTGGCGGCGGTTCAGAGTTTGTCATGGCGGCTACGACGT[C/T]GGGGTTGCTGGCTTGAGATTTCAGTGGCAGTGGATTGATTTTCGGTGGCCGACTAAAATTTGATTTAGGGATGAAGTGAACCATT
87442 T C AATCTCTCCATTCTTTCACTTTCCTCTCATCCGTCGCCGCCGCGTCCGCTGCCGCAGCCACGATCTCCGCTGGAAAACCCTTCGCTTCTCGTTATATTTT[T/C]GGCAATGGCTTAATCCCAGTTGCTCATTGTGATGCTGGTGCTACATTTGATGGGACTTACATTCCTTATATTCATGATGTATCTGATGCTC
87442 T C ATCTCCGCTGGAAAACCCTTCGCTTCTCGTTATATTTTTGGCAATGGCTTAATCCCAGTTGCTCATTGTGATGCTGGTGCTACATTTGATGGGACTTACA[T/C]TCCTTATATTCATGATGTATCTGATGCTCTACTGGATCACAAGTCTATTGCATATACACCTAAACAATATGATATAGAGCTAAAACCTCTT
87442 A G CAATGGCTTAATCCCAGTTGCTCATTGTGATGCTGGTGCTACATTTGATGGGACTTACATTCCTTATATTCATGATGTATCTGATGCTCTACTGGATCAC[A/G]AGTCTATTGCATATACACCTAAACAATATGATATAGAGCTAAAACCTCTTTTCTCTGCATTTGGGCTGAAGTCTCTTGCTATTACATCCGT
87450 T C TCCGGCTGATTTTGGATCTATTCTTATCTTCTGCGCAGCCTCTCTTCCGTCCCGGCACCCGTCCGCCGCCAGGTAAAGATTACTCAAATTAAGGCATATA[T/C]TCTAGAGATGCTCTAGAGTTTTGTAAGAGCTCTTCTTTAGCACATCGCCTTGGCATCTCATAAGGAAACATGCCTAGCTATTCTTTCTCA
87460 T C TTATGCTTAAAATTAATTCACAGTGAAACCGGTGACATCAATTTTTGCTTAACTTAGGTTCCTAAGTATGGTTCATGATAAAGCAGAGCTGCAAGTCTAT[T/C]GGATTCTATAAATCCCTTAAGCGGGATCATGACTGCTCTAATTAATCACTTCCTTTACAGCTTCTGCTGCTTTAAGCTCCTCGCCTTATCT
87460 A G GAGCATTTGAAGCAAGCCTTTCCACCCCCTAATTCTAGATCCCTGTAATATGGTGTATCGGTCAATCTTTGCCATTCATTTTCGCCGGTGCGCACTTCAC[A/G]ATAGTGTATTAACTTCCCATCGGCATCGGTCTCGCTCTTTGCTGGCAATAAATAGGCCCCC
87482 C T CAGATGCTGCCCGTGCCACGAACTATTCATGCCGGCCGATTCGAACAAGGAATCGTGATGCGGAACCACGACGAACGCATCGCGCAGGCCGACGACGCTG[C/T]TCATGTCGGAGAAGCTGTAATTGACGTGCTGCTGGTGGTGGTGGCGAGCGGCGGAGGCGGATGCAGCGCCTCCTCCGCCGCCG
87482 A T AGGAATCGTGATGCGGAACCACGACGAACGCATCGCGCAGGCCGACGACGCTGCTCATGTCGGAGAAGCTGTAATTGACGTGCTGCTGGTGGTGGTGGCG[A/T]GCGGCGGAGGCGGATGCAGCGCCTCCTCCGCCGCCGGAGAAGCCTAGACACAGATCGTGATCGTCTCCTCGAGCCGCGGCGG
87482 G T CGTCTCCTCGAGCCGCGGCGGCTGATGTGGCCACCCAGTCGGCGAAGGCGCCTGTGTGGTCCGAAAATCTCCTAGTGGAAGCCAGAATAAAAGCCTAATC[G/T]ATATTTAACAAATAAAAGTTGGAAGAAAAGAAAAAAAAAGAAAAGTGGAAGAGAGAGAAAGAGGAGAGAAGATTCTGAAATTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
87492 G GA CTAAGGAGACCATTCCCAAGTGAGACGGATCCTCGAGCATCATTTTTGCTACCAGGTATCCTGCAATTGACCATGTTTGGTATTTTCTTGCTTGTTTCCC[G/GA]CAAATCTTCCTAGTTTTCCATCATAATATTCGGGCCAGCTGTCCTTTAATAAACGGGCCTCTGCAAGCTCTATCGCTCGTCTTGCTATT
87502 T TA ATCTGAAAGAGAAGGCAAATTTGAGTTCAGATTGGAGAGAGCTTGTTCAAAGGATATGGGAGAAATCTAGGTAGAGAAGAAGAAACTAAAAGGAGTTTTT[T/TA]GAGGAGAAGAGAATGGAGGAAAGATATGAAAAAGGGTTAGAAGCGGGAAGTGAAGAAGAAGACAGACCAAGTCCCCATGGC
87510 T C CCTCCGCTTTCCTCGTAGGCGGCTCTGAGGCGTCCGATGAGGGCGTCGAGGGACCCCCACGCCTGCTTCAGCGGGCACGCGCACGGCGCCGGCGGGTTAG[T/C]CTGGCCGTAGTAGGCGCAGCCCTCGACGTGCACTTTGGTCTTCCCGTACTGGTCGAGGTATTTTAAGAACTCGATCACGTGCGCG
87522 C T TTAATCTCTTTCTCAAATACTTTTCCATGGTGCAACCTTATGATACATGTTGACTGTAAAAGGACCCTGGATGCGGCTGCGCTTTCCCACGTGGCGGCAA[C/T]GTAGCAGAAGCAAGTTTTTTGATAGGTGCAGCTAAGTGCTTACTTCTCATGGCTTATTCTT
87542 T TAC CATTTCAGTTTCCATTTATAGATAAGAGTCGTACATACAATAGCATTTCACCTGTACAGATATTCATACAGCTAGATATGATATAACACCAGTTTGCACA[T/TAC]ACAATCAAAAACTACAACAACCGAAACATATGGAGTAACAAAATAAAAGGGAAAAAAACACCCAAATTTCAAATCTGTAGCAAAATC
87542 C A ATAAGAGTCGTACATACAATAGCATTTCACCTGTACAGATATTCATACAGCTAGATATGATATAACACCAGTTTGCACATACAATCAAAAACTACAACAA[C/A]CGAAACATATGGAGTAACAAAATAAAAGGGAAAAAAACACCCAAATTTCAAATCTGTAGCAAAATCTAAGAGCTTTTAGCTACATAGA
87550 A C AAAGAAAGCAGACACCAAGCATAAATGGCATCATGCATCCAACAATCGCTGCTAAACTTAGCTTTGATCTGACAGTGGTGAGACCAGAAGATCCACAGTA[A/C]ACGCAGTTGAAAGGCGCCGGAGTATCTTTAAACATGGTCTGCTGAATCGGAATCCCCTTTGGGTCGACGTCGAACAAGGCATTCGG
87550 A G TCATGCATCCAACAATCGCTGCTAAACTTAGCTTTGATCTGACAGTGGTGAGACCAGAAGATCCACAGTAAACGCAGTTGAAAGGCGCCGGAGTATCTTT[A/G]AACATGGTCTGCTGAATCGGAATCCCCTTTGGGTCGACGTCGAACAAGGCATTCGGCGGAATCATCCCAGCCTGATGAGGATTAGG
87550 A T GCGCCGGAGTATCTTTAAACATGGTCTGCTGAATCGGAATCCCCTTTGGGTCGACGTCGAACAAGGCATTCGGCGGAATCATCCCAGCCTGATGAGGATT[A/T]GGGGCCGCATAGTAGGCCTGCTGCGGGTAGGGAACTCCTAAGGCTGGTTCGTTCTTGCTGAAATCGCCGGTCTTCATCTCCATTGT
87560 T C AGATCGACTGCACTCATACTAAAGGCGGTCTCTGCGTCGACTCTGTTTTCATATGTCCTAAGAGATTCTAGATGACACTTGTATCTTGAGTTTACGTAGG[T/C]CTGCGGTATAAAAAAGGCCAAAATGGCACGTAGAAGGTTGATTTTTTAAAAGGCTTTCTACCTGCTAGTGAGTTTGGAGG
87586 C T CAAAAAAACATCGAAAGACCCACAATAATATCCGACGGTGTGTCATACTCTCCTTGGCGGTGCTGGGGATCTGCATCATCGTAGTCGTGACGCTGGCCTT[C/T]ACGGTGTGCAAAATAAGAGAGCCGACGATGCACATAAACTCCATCCAGTTCAAGATCAACCTGGACCCGACGAAGAACACGACGG
87586 C T ATCTGCATCATCGTAGTCGTGACGCTGGCCTTCACGGTGTGCAAAATAAGAGAGCCGACGATGCACATAAACTCCATCCAGTTCAAGATCAACCTGGACC[C/T]GACGAAGAACACGACGGTCATGACCGACGTATCGGTGAAGAACCCGAACGTGCTCGACTTCAGGTTTGGATCGAGCACAACGTCG
87586 A G AGTTCAAGATCAACCTGGACCCGACGAAGAACACGACGGTCATGACCGACGTATCGGTGAAGAACCCGAACGTGCTCGACTTCAGGTTTGGATCGAGCAC[A/G]ACGTCGCTGAGTTACAGGAAGCAGGAGGTGGGGGTGGCGATCGGACCTCCTGGCAGGGCGAAGGCGCGCAGGAGCACGAGG
87588 G A ATGGACCTCCACCATCTTATCCACACTTAAAAATACCTGGATTGAATGCTCCCATACCACCTGGTGCAAGCTTCGGTTATCATCCCGGTGGCTGGGGAAA[G/A]CCACCTGTTGATGAGACTGGTCGTCCATTGTACGGTGATGTTTTTGGGGTTCACCAGCAAGACCTACCTAACTATGAGGAAGAACCA
87588 A C GAGGATGAAGAAATGGGCGAAGAAGACTTGGCAGATGGAATTGAATCAGTTGATAGTCTTTCTAGCACGCCCACTGGAGTGGAAACACCTGATGTTATTG[A/C]CTTGCGTAAGCAGCAACGTAAAGAGCCGGAGAAAGCTCTTTACCAGGTTCTTGAAGAAAAGGAGGAAAAA
87592 C T AATTGACTCTGTTAGAGATGCTGGTGTTAAGTTGCTCTGATATAATCTGTTTGGAGATTTTCTATTGTGGACATGCTTCATAAACTGTTGAATATCTGAA[C/T]TATAGTGATGTTGTTATTGGCTCTGCTAAATTAGTTCTGCTGCTTATGCAACAATGGACTGTTTTGGGCTTT
87602 GT G GGTGGAAGTGATCGTAGTAGTATTCATGGATAACATTGTCGGTGGTGAGTTCCACTCCCATGCAGTAGCCGTAGAGAAGGACGAAGATCCATGTTCGATA[GT/G]TTTGGAGACAGCGTGCCATAAAACCTTGGAGAATTTATCCCTTTTAACCTCACCGGACTTCTGCAAACTTCCCAAGTTACCGTCAG
87602 A G CACTCCCATGCAGTAGCCGTAGAGAAGGACGAAGATCCATGTTCGATAGTTTGGAGACAGCGTGCCATAAAACCTTGGAGAATTTATCCCTTTTAACCTC[A/G]CCGGACTTCTGCAAACTTCCCAAGTTACCGTCAGGTAAATCTTGGCCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACAT
87602 G A ATAGTTTGGAGACAGCGTGCCATAAAACCTTGGAGAATTTATCCCTTTTAACCTCACCGGACTTCTGCAAACTTCCCAAGTTACCGTCAGGTAAATCTTG[G/A]CCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGGCACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCA
87602 G A TGGAGACAGCGTGCCATAAAACCTTGGAGAATTTATCCCTTTTAACCTCACCGGACTTCTGCAAACTTCCCAAGTTACCGTCAGGTAAATCTTGGCCCAT[G/A]ATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGGCACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCACCGGCT
87602 C A TAACCTCACCGGACTTCTGCAAACTTCCCAAGTTACCGTCAGGTAAATCTTGGCCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGG[C/A]ACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTA
87602 T G TTCTGCAAACTTCCCAAGTTACCGTCAGGTAAATCTTGGCCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGGCACGAAAAACGCGA[T/G]TCTCCACGCAGTGAATGGAGTAGCACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCAT
87602 G C GTAAATCTTGGCCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGGCACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCACC[G/C]GCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTG
87602 C T CTTGGCCCATGATGAGGACTGCTAGCCCCATTATCAGATGCATACATCCTGGCACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCACCGGCTTT[C/T]CTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTC
87602 T C TCAGATGCATACATCCTGGCACGAAAAACGCGATTCTCCACGCAGTGAATGGAGTAGCACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAG[T/C]TGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTCCGATAATTTTACTGTTAAACATGGTGCTCATCCA
87602 A C ACGCAGTGAATGGAGTAGCACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGC[A/C]GTTCCATTTGCTAGTCCGATAATTTTACTGTTAAACATGGTGCTCATCCAGTACTGACATGTTACAAAAGTGGCAAGTGAAAATCCGA
87602 T A GAGTAGCACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGC[T/A]AGTCCGATAATTTTACTGTTAAACATGGTGCTCATCCAGTACTGACATGTTACAAAAGTGGCAAGTGAAAATCCGATCATGAATCTCAC
87602 G A CACCGGCTTTCCTTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTCC[G/A]ATAATTTTACTGTTAAACATGGTGCTCATCCAGTACTGACATGTTACAAAAGTGGCAAGTGAAAATCCGATCATGAATCTCACTGCTAT
87602 G A TTATCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTCCGATAATTTTACT[G/A]TTAAACATGGTGCTCATCCAGTACTGACATGTTACAAAAGTGGCAAGTGAAAATCCGATCATGAATCTCACTGCTATGTAACCTTCTGC
87602 A G TCAGATCATACACCAATGGCATCAAAAGTTGGGTAGCACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTCCGATAATTTTACTGTT[A/G]AACATGGTGCTCATCCAGTACTGACATGTTACAAAAGTGGCAAGTGAAAATCCGATCATGAATCTCACTGCTATGTAACCTTCTGCTGA
87602 A G CACCACCTCCCATATTTCCCCAACCAGCAGCAGTTCCATTTGCTAGTCCGATAATTTTACTGTTAAACATGGTGCTCATCCAGTACTGACATGTTACAAA[A/G]GTGGCAAGTGAAAATCCGATCATGAATCTCACTGCTATGTAACCTTCTGCTGAAGATATTATGGACATGCAGAAGACTGC
87604 C T TCTTTCCTCCATAAATGGTTTGCCTGCTACGGATCCAAATTTAGAGCTTACGAGTTGCAATGGACCTTTTGGTGCCATCTTCTGCTATCCTTCTTTTGGG[C/T]CAGCTCTGCTTTCATCTGCTCGAGCTACTAGTGTTGGATCTTTCTAGTTGATGTAGTATGGTCATCTTCGTCCAATGTTTGCCGAAGTGTC
87604 C A ATGTAGTATGGTCATCTTCGTCCAATGTTTGCCGAAGTGTCTTGATGGTCTTTGGGGTTGTGCATTTCCAGTTATGTCGCCTGCTTCTTCTCAACTTCAC[C/A]TATCGTGTTGATTGTTGTTCTTCTTGGGAGATTGGCTTGAAGTATCCTGGTGGCGCTCCTTTGTCCTTGTCTTTGTTGTCCGTTTTTACTT
87604 T C TGGTCATCTTCGTCCAATGTTTGCCGAAGTGTCTTGATGGTCTTTGGGGTTGTGCATTTCCAGTTATGTCGCCTGCTTCTTCTCAACTTCACCTATCGTG[T/C]TGATTGTTGTTCTTCTTGGGAGATTGGCTTGAAGTATCCTGGTGGCGCTCCTTTGTCCTTGTCTTTGTTGTCCGTTTTTACTTGCACTGGC
87618 A G GCGAAACATCACCATGAAAGAAGCAAGCACACTCCAGCCATCAAATAAGCGATTGACCAACAGAAAAATCGTAATTAGAAAAAAAACAGAATACAAATAT[A/G]GATCCAAACCGATTACAAACTGATCAATGCAAAAGCAAAAGAAATAAGGACATATATGCAAAAGCAACCGGTGAACGCTGCTCTG
87618 T C ATTACAAACTGATCAATGCAAAAGCAAAAGAAATAAGGACATATATGCAAAAGCAACCGGTGAACGCTGCTCTGGTAAGATCTTTCCTTTTTGAACGCTG[T/C]CTGCCATACAGAAAGAAGCGAACGAAGCTTAAGCACAAAGCAATACAACTTAATTACAAACACATGGAGACAATCGAACCGATGGA
87618 TG T GCTGCTCTGGTAAGATCTTTCCTTTTTGAACGCTGTCTGCCATACAGAAAGAAGCGAACGAAGCTTAAGCACAAAGCAATACAACTTAATTACAAACACA[TG/T]GGAGACAATCGAACCGATGGATAGGCAAATGAGCTGAAGGGATCTGAGATGAAAAGGGGTGAAATCGGCATGGCTGAAAGATAG
87622 G A ATCAGGGTAAAGTAGTCCGATGATTTTAAACTGCCTTCTCAGTTCCGCTTCAACTCTCAATATCAGCTACCTTTTGCTTGGAAATCATTAAGCATTCAAC[G/A]TTAGGGCTCTTCTCTTAATTAATGGATAGAGCTGACACTTCCGGCTTTGTTAGCGGTGGTTGCTTCAAATTAAAGTTCCGTTTATATTTCC
87622 T G ACTTCCGGCTTTGTTAGCGGTGGTTGCTTCAAATTAAAGTTCCGTTTATATTTCCAGTTCATTTACACTCAATAAAAGTACCCATTATCCTGTAAATACA[T/G]TTCTCAGCTTCTTAGACTACAAACCCTGTCGCTCTTCACAACATTTCAATGAACCTCAACAATTTCAATCCCATGTTCAATAACTTCTACGA
87622 G A AATTAAAGTTCCGTTTATATTTCCAGTTCATTTACACTCAATAAAAGTACCCATTATCCTGTAAATACATTTCTCAGCTTCTTAGACTACAAACCCTGTC[G/A]CTCTTCACAACATTTCAATGAACCTCAACAATTTCAATCCCATGTTCAATAACTTCTACGACTCTTCCCAAGACGACGGGTGCAAGTTAGTT
87664 G A TTGATTTAGCAATGGGGTCTGATGAGGAAGAAAGTTATGATGACTCAGATGCTTCAGCCTTATCAGAAGATGAGCCTAATAAGGCTGTAAAGAAGGCAAA[G/A]CAACCAAGATTATTTGAAGTGAAGGACGCTCGGCATGCTGAAGCGTTCCTAAACAACATATCGCTAGCAGAGGAGGACGCTCTTC
87664 G A CAGATGCTTCAGCCTTATCAGAAGATGAGCCTAATAAGGCTGTAAAGAAGGCAAAGCAACCAAGATTATTTGAAGTGAAGGACGCTCGGCATGCTGAAGC[G/A]TTCCTAAACAACATATCGCTAGCAGAGGAGGACGCTCTTCCTATAGGCGAAAGGGTGGCTAAGCAGGAACAGAAGCAGCCGAAG
87664 C T GACGCTCGGCATGCTGAAGCGTTCCTAAACAACATATCGCTAGCAGAGGAGGACGCTCTTCCTATAGGCGAAAGGGTGGCTAAGCAGGAACAGAAGCAGC[C/T]GAAGTGGGGGCCTGATGTGAAATACGGGCCTGGTGGGTCTAGAGAAATATCATTTGTCCCTAGAAGCTCGAGGAAACATAGTG
87664 T G TCGGCATGCTGAAGCGTTCCTAAACAACATATCGCTAGCAGAGGAGGACGCTCTTCCTATAGGCGAAAGGGTGGCTAAGCAGGAACAGAAGCAGCCGAAG[T/G]GGGGGCCTGATGTGAAATACGGGCCTGGTGGGTCTAGAGAAATATCATTTGTCCCTAGAAGCTCGAGGAAACATAGTGGTGGT
87670 G A ATGAACTTATGTTCAGTCAATGAATGTCCTGATCCAAACCCAAGCAGGTGGAGGCGCCGGGCATCCCATCAGGGTGCGTGGTCCGGTTGTTCCTCCGACC[G/A]GCTCCGACGGGCACGGTGCGCAAGGTGCCTCCGGCAGTCCAGTACCGGCGGCAGCTTCTACAGAAGTGCCGGGGCTGATTAACA
87670 T C ACTTGGTCTCCTTGCTCTTGCATCTCGGGCACGATATCGCTGCCGCTTTGGATGATCCTCCTCCTGCTGCTTTCTCCATGCCTGTGCTCGTCTCCTGATC[T/C]GCTTCCAACGATGTCGACGTCGACGAGGAAGACGATGTTGTATGCGATGAATTGGATTGCATGTCCTCCACCCGCTGGCTGATCGTTTT
87694 G A ATGATCTCAAGCAGCAGGAGAATGTGTTGGGCGAGTCGAGGATGATGGTTCCTGATTGCCACAAAAGACTGGAATCTTCACTCGCAGACCTAAAGGCAAC[G/A]CTTGCAGAAATAAAGGAGTCAAACCAGGAAGGTGTCGAAATAAGCGAAGCCGAAACCATGATTACTGAAGTCGAAGCACTGTTT
87694 A G AAATAAGCGAAGCCGAAACCATGATTACTGAAGTCGAAGCACTGTTTAAAACCGAGGAAGATTGGAAGGGAAATGATGCATGACTTTCAAAATGTTAAGT[A/G]CTGAACAATTTGAAATTAAAACTACTGCATTCTGGTACATTTGGGTTTTGGAATATGAGATGATCTAGGTGAAATATTCAATATGC
87694 TA T ACCATGATTACTGAAGTCGAAGCACTGTTTAAAACCGAGGAAGATTGGAAGGGAAATGATGCATGACTTTCAAAATGTTAAGTACTGAACAATTTGAAAT[TA/T]AAAACTACTGCATTCTGGTACATTTGGGTTTTGGAATATGAGATGATCTAGGTGAAATATTCAATATGCAAACTATTTATGAAAGA
87712 A G TCGACAATTGCCAAAGGAGTGCTTGAAACGCTTTCCCTTTGCAGTCTTCTTGTCCCCTCTTCCGCAGTAAACTAGCAGGGAAGGAATAGAATCGGAAGCA[A/G]TAGTCAATGGCGCGGTAGCAGTGAGTGTAGCGGAAGGGGCAGTAAGGGAGAAAGAAGCTACGGTTAGGGTTTCGGTTTTAGAAA
87712 A G CAGTCTTCTTGTCCCCTCTTCCGCAGTAAACTAGCAGGGAAGGAATAGAATCGGAAGCAATAGTCAATGGCGCGGTAGCAGTGAGTGTAGCGGAAGGGGC[A/G]GTAAGGGAGAAAGAAGCTACGGTTAGGGTTTCGGTTTTAGAAAACGAGAGACGAGAAGAATGCGAGTTTGCAAGAGAAGAAG
87712 A G TCCGCAGTAAACTAGCAGGGAAGGAATAGAATCGGAAGCAATAGTCAATGGCGCGGTAGCAGTGAGTGTAGCGGAAGGGGCAGTAAGGGAGAAAGAAGCT[A/G]CGGTTAGGGTTTCGGTTTTAGAAAACGAGAGACGAGAAGAATGCGAGTTTGCAAGAGAAGAAGATGAAAGAGAAAACGGTA
87726 T C ACGGGTGGAGGGCCCCGACCCCTATCGCGGTCGTGGTAACCACCTCCAGTTCCTGGGCCACGGAAGCCCGATGAGTAGCCGCGTCCTCCTCTGCCGCCTG[T/C]GCCGTAATCATAGTCGCGAGGGTCGTCGGTGGGCTTCGGTTGGGCCTCGTTCACGGTGATTGTTCGTCCGTTCAGGTCTTGGTTG
87734TGATTAATCATGAGTGA T TGGGTCCGCTTCAGGGAAGATGCCGACTGGAACAGGAATATAGTTAGAATGGCCAGTTGTTCCAGCTCCTGGGTATGATAAGAGTAATATTGGTTCTTCT[TGATTAATCATGAGTGA/T]GATTAATCATGAGTGACTGCAATCGCGATGAATAGGCAGGGCTAGGGCAGGCACAGGTGATCTCAGCGG
87734 C T GATGAATAGGCAGGGCTAGGGCAGGCACAGGTGATCTCAGCGGTGGCACCAAGTGGTGTTCAGTCAAGCGGAGTCAGTGGTCATGATCCAGGGCATCGAA[C/T]TGATCAAGGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGA
87734 A T AGGCAGGGCTAGGGCAGGCACAGGTGATCTCAGCGGTGGCACCAAGTGGTGTTCAGTCAAGCGGAGTCAGTGGTCATGATCCAGGGCATCGAACTGATCA[A/T]GGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGAGATGGAA
87734 G T GCAGGCACAGGTGATCTCAGCGGTGGCACCAAGTGGTGTTCAGTCAAGCGGAGTCAGTGGTCATGATCCAGGGCATCGAACTGATCAAGGCGGCGACTTT[G/T]ACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGAGATGGAAGCTTCGATCTTTAG
87734 G A GTGGCACCAAGTGGTGTTCAGTCAAGCGGAGTCAGTGGTCATGATCCAGGGCATCGAACTGATCAAGGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCC[G/A]AAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGAGATGGAAGCTTCGATCTTTAGGCCATTTTGAAGAAAGGCGATTG
87734 T C GTGGTCATGATCCAGGGCATCGAACTGATCAAGGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTC[T/C]GATAGGAGATGGAAGCTTCGATCTTTAGGCCATTTTGAAGAAAGGCGATTGGATTTTCGCGGATGTTGGCTGCCATTAAAAACTTG
87734 G T TCAAGGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGAGATGGAAGCTTCGATCTTTA[G/T]GCCATTTTGAAGAAAGGCGATTGGATTTTCGCGGATGTTGGCTGCCATTAAAAACTTGGGAAGAATTGATTTTTCTGCTGAAGCGA
87734 G T CAAGGCGGCGACTTTGACGCTGGCGGCTTTGCTTTCCGAAGCGGGGCTAGGTTTCCGACCTACTGGCGTTCTGATAGGAGATGGAAGCTTCGATCTTTAG[G/T]CCATTTTGAAGAAAGGCGATTGGATTTTCGCGGATGTTGGCTGCCATTAAAAACTTGGGAAGAATTGATTTTTCTGCTGAAGCGAT
87754 G C GAGCACACCACTACCAAAAATAAACACAGATAAATATCCTAGAAATGTTGATGCAGCAAAAACCTACCGTGTATATACCATCGTGGTCGCCGTTGTACGA[G/C]GATTTGACTCCCGTCGACGTGATGCGAGCTTACGAGAACGAAGATGAATCCGACGACGAGTTTTCTCCGTCGGACGCGACTTACTC
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
87754 C T GCGTCCGTGGGAGGAGCCATGACTGGACTGATTGCCCTTTTGCCCATCCGGGTGAGAAGGCCAGGAGGAGAGATCCACGAAAGTATCATTATTCTGGCAC[C/T]GCTTGTCCAGATTTTCGTAAAGGTAACTGCAAAAGGGGAGATGCATGCGACATGGCACATGGGGTATTCGAGTGCTGGCTGCAC
87764 C G TGTTATGGAGATTCAAGTGGAAGAAGACGTCACCAAAAGCAAGGGAGTAAATAAAATGGACGAGGATGTGAGGTGCTTCTATAAGGGGAAGGTTGATGGT[C/G]GAGTTATGGTAGGATGGTCTGACAGATGCTAAAGGGGTTGTGGTGGTGAGGAGAGTTCCAGTAGGATCTAGAAAAGTGATCG
87764 A C GGTCTGACAGATGCTAAAGGGGTTGTGGTGGTGAGGAGAGTTCCAGTAGGATCTAGAAAAGTGATCGAGACAACAGCTGGTTTGAAGGTGGCTGCTGTGA[A/C]GTCGGAGGACTCGGCATGGTTCTACTATTGTGTTGGAGGGACAAGGCTGATGGGTTGCTAATGAGGACGGCTGTAGCTGGTGT
87764 A C CTGTGAAGTCGGAGGACTCGGCATGGTTCTACTATTGTGTTGGAGGGACAAGGCTGATGGGTTGCTAATGAGGACGGCTGTAGCTGGTGTTTTGGTCATG[A/C]GTTGAGGATAGGTAAAAGGGACTGAGGAGGATCGGTTGCTCGATGCATTGCATGAGTTCACATTTGAAGCTGATGGACTTTGCA
87764 G A TTGTGTTGGAGGGACAAGGCTGATGGGTTGCTAATGAGGACGGCTGTAGCTGGTGTTTTGGTCATGAGTTGAGGATAGGTAAAAGGGACTGAGGAGGATC[G/A]GTTGCTCGATGCATTGCATGAGTTCACATTTGAAGCTGATGGACTTTGCAGGTTCAGGTTGGGGTTTATTGCTATGGCAGTGAT
87764 T A TGCATTGCATGAGTTCACATTTGAAGCTGATGGACTTTGCAGGTTCAGGTTGGGGTTTATTGCTATGGCAGTGATGACAATTGTAATTATGTCAATTGTA[T/A]TTATGTCAATTTAGAAATAACCAGAAAGAGAGCATTGCCTATAACGTTAAGACTTGACTTTCA
87774 A G GTCTTTCGTGATTCAGTTCCTCAAAATACAACAAAAATATGTTTTTCATAAGTTATATACAGTAGTTTAAGAAATCAAAAGGCTAAGAACAGCGGTAGCA[A/G]AGACAAAAAAGAAACAATTACGGAATGTACAGTTCATACTGAGGTCAGAAGGCTGATACTGGAAGATTTCCAATTGTGTCACTGTTTC
87778 T G TTCATGAACCACGGCAACAAAAAATGACCAATCTACTGTGACACTTCTATGTACGCTATGTGATCGTCGTTACCGTCGTTGGGCCGGTTCA[T/G]GTAACTCTAACGAGAAATATACTGATATCCGGCCCACAGTTCCCATCTGGGCTAATCATGTACAGCGCCTCCGTATCCTTCGACCCCACCCTCTCAAA
87778 GC G ATGACCAATCTACTGTGACACTTCTATGTACGCTATGTGATCGTCGTTACCGTCGTTGGGCCGGTTCATGTAACTCTAACGAGAAATATACTGATATCCG[GC/G]CCCACAGTTCCCATCTGGGCTAATCATGTACAGCGCCTCCGTATCCTTCGACCCCACCCTCTCAAACCTAGCCCTAATGTAAGTCAAC
87778 AC A GTCGTTGGGCCGGTTCATGTAACTCTAACGAGAAATATACTGATATCCGGCCCACAGTTCCCATCTGGGCTAATCATGTACAGCGCCTCCGTATCCTTCG[AC/A]CCCCACCCTCTCAAACCTAGCCCTAATGTAAGTCAACTGATCCGCCTCCTTCTCCTCCCCTCCCCTCGCTCCGGCAGCACCCCGCCCC
87778 G GA TCCTTCGACCCCACCCTCTCAAACCTAGCCCTAATGTAAGTCAACTGATCCGCCTCCTTCTCCTCCCCTCCCCTCGCTCCGGCAGCACCCCGCCCCCATC[G/GA]AAACCCCTCTCAGCACCTTCATCACCTCCCTCTCGTCCTCCGACCCCGATTTCCGCCTGATCGCGAACCCCGACTTCCTCCCGTTGCAGT
87778 C T CCTCCGACCCCGATTTCCGCCTGATCGCGAACCCCGACTTCCTCCCGTTGCAGTACACCGTCCACACGAACTCCTCCCAGATCTTCTTCTTCTGCGTCTT[C/T]GTCTCGCTCTCCAGCGCGATCTTGACCAGTCCCGTCGACATTTCCTTGTGGAGGGTGGACGTGAGGATGGGGAGCTCGATCAGGAAGT
87788 C T TGTTGGAGCTGTATCAAAGACAATAACGTCGTAGTTCATTGTTTGCACTAGCTTTAACATTTCTGCAAAGCTCATTGCTTCATCGATTCCAGGTATAGAA[C/T]TGCTTAAGTCAGATAAATAACCGCCGATGCCATCATTGGTGGTCAGGTCATCACTTTCAACTTTTGGGTCTATTTCCATTGCAAACAAGT
87788 C T ATAACGTCGTAGTTCATTGTTTGCACTAGCTTTAACATTTCTGCAAAGCTCATTGCTTCATCGATTCCAGGTATAGAACTGCTTAAGTCAGATAAATAAC[C/T]GCCGATGCCATCATTGGTGGTCAGGTCATCACTTTCAACTTTTGGGTCTATTTCCATTGCAAACAAGTTGGTGAAACCGTTGACTAACGT
87806 A G CTCTTCGTCTTTTACTCTCAGTGTCTCCTTCATTATTGTCAGATCATCTAACTGAGGTTC[A/G]TTGGTGTTGTTTGAAACCAAACCAAGAGCTGTTCTCATAGATATCTTCATTGCTGCTTCAATTTCTTGTGTGGCTTTCATTGCAGTTGAGTTGGCAGCAG
87822 A G CCCTCCACTGCCGCTGTCGTGTCAAGATGTTCTTCCGCCTCCTTACAGTGCTCCTCTGTCGCTGCGGCCTCAGTGCTGGATGTTGCGAAGAAGGAAAAGG[A/G]AGCGGCTGTGAAGTTGATGATAGGTAGCTTGGTGGAAGATGGGTTGTCGTACAAAGAGAATTTTGTTGTTAGATGCTATGAAGTCG
87822 GT G GGCCTCAGTGCTGGATGTTGCGAAGAAGGAAAAGGAAGCGGCTGTGAAGTTGATGATAGGTAGCTTGGTGGAAGATGGGTTGTCGTACAAAGAGAATTTT[GT/G]TTGTTAGATGCTATGAAGTCGGAATTAACAAGACTGCCACTGTTGAAACCATAGCCAATTTGCTTCAGGAAGTTGGTTGCAATC
87822 C T CGGCTGTGAAGTTGATGATAGGTAGCTTGGTGGAAGATGGGTTGTCGTACAAAGAGAATTTTGTTGTTAGATGCTATGAAGTCGGAATTAACAAGACTGC[C/T]ACTGTTGAAACCATAGCCAATTTGCTTCAGGAAGTTGGTTGCAATCATGCGCAAAGTGTTGGGTTTTCCACAGATGGGTTTGCGAC
87828 CA C GGAACTCTCGCACCCTTACAACGTTGAGCTATCAAAATTTCAGCTATAGGCGAGATCACTCCACCTTCACCATGTTCCCACAGCATCCCTTCTTCTTCTC[CA/C]AAGTAAAACTCCTGATTCTCTTTCCAAACTTCCCCATTTTCATAAACCTCCTTCTTCCAAATCGGAACTCTGGCCTTCAACTCATCAATCA
87828 A G TCAACTCATCAATCATAAATCGACACGCCTCCATCGCATCGTCTCTATGAACAGACGACGCTGCCACAAAAACGCTGGCCTCTCCGACCTCCACGACGCC[A/G]AGCCTGTGCGCCACCGCGACTTTGATCAGATTCCACTTGGATCTGGCGGAGGAGATGACGTATTCGAGCTGGCGGATGGCCATCGG
87828 C G CGGAGGAGATGACGTATTCGAGCTGGCGGATGGCCATCGGGACGTACGCTTCGTAACGGAGCTCCAGCACGCGCTTTCCGTTGAATGAATCTCGAGTCGT[C/G]CCCTCGAACGTGGCGATTGCGCCGGCGGAGGGGGAGCGGACATGGTTGGTGTATTTGGTAAGGTCGAGGGGAG
87842 A G CTGTAGACCTAGAAAAATCGCGTGCATCAGCATCATCTAGAAAGGGCAGTGCATCAAAGCGGTCGATAAAGCCAGGCGACAGCAGACTGAGCTCTGGTGA[A/G]CACAGCGACTCACACCAAGTAAGCAGAGCAAGTCGCTTACTCTCAAGTGGTGGCAGCAATAGTCGAGCCACAACAGCTGCTGCT
87842 A AC TCTCTCTCTCGGTGGCAATAAAAGAAAGTAATTCTCGCTCGACCGTTTTCCCCATCGGGGAACTACTATATATCTATTATCAAGAATACCCTTCAAAAAA[A/AC]TTTGTTTATATGAGACAGACATCATTCAAAGAAATGAAGACTAATCAAACTTGTGTGATGTTTATAATTATGTATACATGTAATTTGCT
87856 T A ACATATCAGTACCTGGAATGTACTTTAAAGCTGCATTTGAGCTCTGTATATGTCAATGCATGATGAAGAAGGGTAAATTGGGCAAAAATGCATAGAAAAA[T/A]TGTAGGGCACTGGAGGAACCAAATATTCATCATGGACGCAAGGAGACCAGCTGTCGTCTCCTCCTACACCCATGTGCTTGTGATCCA
87856 G A CAATGCATGATGAAGAAGGGTAAATTGGGCAAAAATGCATAGAAAAATTGTAGGGCACTGGAGGAACCAAATATTCATCATGGACGCAAGGAGACCAGCT[G/A]TCGTCTCCTCCTACACCCATGTGCTTGTGATCCAGGTGCACCTCGATGTTGTCTCCTTTTACCAGTTCATGATTATGAGTTGCCCTA
87866 A AG CTGCTACAGTTCACGAATAAAGCAGCGTAGTTGATATCTAGCTGCTTCATGCTGCCTTCCACCATAAAACCTTCATCCCTGACGAGATATGCTGACTCCC[A/AG]TTTTTTCTCACACTGGTTTGAGGAGTTACGCAGGAGGCTTGGCTCCAGGCCTGAACCTCGGAGGAGGAGTGCGGTCCTTCCTCGCCT
87870 T C ATTGGAACGTCTATGAATTGGTGACAGGATTTTTCGCTTTCGGGGACGAAAGTTTGAAGGCTTATAGCCATTCATGAAGAAATAAAGGCGATCGAAAGTC[T/C]GTTGACCCACTCCTAGGGTTTGACGCGTGTAGAGGGATTTGGGGATTATGAAGTCTCCCTTTTGGTTGCTGAAGGAAAGGAACGA
87872 A G TCAAGCCCCTCCTATCTATGATCTGGCTCGCTTTCACCGATTTCACCAGTGCCTCTGCCTTCACAACCGTAGAAAAAGAAGAAGAGACTGATCTGGCGGC[A/G]GAGCGTATCGTGGGTTGGTGGGGAGCAGATGGCATTGGCGATATTGTTGTCGGATGAGGGGATTGAATTTTGTTTTAGGGAATAAT
87874 T C ATCTTTATTGAGAGCTTGAAAATATACTTACAACATCAGAGTGCCACAGACAATCTGGACAGCTATAACAACCTGTCCTCAAAATAACATAGCGGAATAA[T/C]ATTTTGTCTAAATCATACGCCTGGACCTCTCCAGCTCGTCTCTGAACTTCAGAGCATCTGGTAACCTGAACCTGCAACCCGGGCTTGAT
87874 A G GGTAACCTGAACCTGCAACCCGGGCTTGATTTCATTTACCGCCTGAAACAGTTCGGTTTACAAGCTTTCAGCAGTGTTCAATTCCGTCTGTTCCAATTCC[A/G]AAATGTAGCGTTTGTCGTTACGGTACCGACATCCTTGTTTTTGTTTGATTTTGTCACGTTACTGTTCATCGTTCTTCAACATTCCTACTTG
87902 T C GTTTTGTTTGCAGCCTGCACCAAAGAAACGATGGGTTCCACGATAATAGCGAGGACGTCGGCAGTTTTCCTCC[T/C]TAAACCCCCTCAATTGGCCACCAATTACAAATCAATCTCTTTCTTCATCCCCAAATTACAAAACCCTGTCTTCCCCAAGTCACGATTTACAGCATTCGCG
87902 A G GTTTTGTTTGCAGCCTGCACCAAAGAAACGATGGGTTCCACGATAATAGCGAGGACGTCGGCAGTTTTCCTCCTTAAACCCCCTC[A/G]ATTGGCCACCAATTACAAATCAATCTCTTTCTTCATCCCCAAATTACAAAACCCTGTCTTCCCCAAGTCACGATTTACAGCATTCGCGGAAGGAGGAAAT
87902 G A GATCTTCTTTATCTCCGGTGCTATTCTCCTGTCCGCACTTAAATACTCTTTCATTGCTGCTTTGATTTTGTTCATACTCATTACACTTCTTTAGTTACAA[G/A]TATAGACATATGTATTATGGTTCATAACATTGAATGCTGTGTTTATAAACGATTGATGTTGATAAAATTTCCAGTCTGACAAACGGCATTTA
87902 A G GTGCTATTCTCCTGTCCGCACTTAAATACTCTTTCATTGCTGCTTTGATTTTGTTCATACTCATTACACTTCTTTAGTTACAAGTATAGACATATGTATT[A/G]TGGTTCATAACATTGAATGCTGTGTTTATAAACGATTGATGTTGATAAAATTTCCAGTCTGACAAACGGCATTTAAAGTCCAAAAAAAAAA
GATTTGAAATTTTTATCAATGGTCTTATTTCCTTACCATGTTGCA
87946 G CGCACTCGTAGAATTGTTCAATACGAAGCGCGCTAAGCAGAAGATGCTACTAAGCTTGTGGATGGTCTAGCCTTTAGGCGAGCATATACAGTGACATCGT[G/GATTTGAAATTTTTATCAATGGTCTTATTTCCTTACCATGTTGCA]ATTTGAAATTTTTATCAATGGTCTTATTTCCTTACTATGCTGCAAT
87958 C T CGTCTGTGAAGTTACTGACAGTAAACTAACTAACCTCAGCTGCATGATAACATGATACCCTCCCCATTAAACATGACCCAGGACCTCTATTATCATACTG[C/T]GCATAGTACAATGTATTAAGCGCAAAATTCTCAACCCGCTCCAACCACCCGACAGGATCGATAAGGCTCCCTACATCCGAGTCCATACA
87964 C T AAATGAATTGAATAATAATTCTGAGAAAAGACGAAATCTAAAAGAATAATCTAATGGCGTGGAGAGGGCAACTGGCGAAAAA[C/T]ATTAAGGAGCTCCGCCTCCTATTTTGCCAGACGTCACCAGCCAGTTCTCAAGCTCGTGAATTTGTTCAAAAAAATTACAAGGATCTGAAGACTCTCAACC
87972 C T CGAACATTGAATCTAATTATGATGTTGCCACTGTTTTACCTATGGATGGCTTCCATCTTTATCGGCACCAACTCGATGCCTTGGAGAATCCCGAAGAAGC[C/T]CATGCAAGACGTGGAGCACCTTGGACATTCAATCCGGAGCTGCTTCTTAAATGTCTTCAAGCCATAAGGAATAAGGGATCAGTGCAAG
87972 C G AAGCCCATGCAAGACGTGGAGCACCTTGGACATTCAATCCGGAGCTGCTTCTTAAATGTCTTCAAGCCATAAGGAATAAGGGATCAGTGCAAGCTCCATC[C/G]TTTGATCATGGTGTTGGCGACCCCGTTGAAAATGATATTTTTGTGAGTCTTAAGCACAGGGTGGTGATCGTTGAAGGAAATTATCTT
87974 G T GGCGTCGATAGTTCACAAACCTCTCCCCGCTTGATCTGTAGGACTTCCTTGACTCCCCGAAATCAACGTTGCACTCTGGAAGAGGAGTTGGATACCGCTC[G/T]CTATCGTAGCAATATGAATAAGTCATGTGCTTCGCACGGGTTTTCTCCATCACAGATTTTTGATCATTGGAAATTCTGATACGGTTGTA
87976 G C TGTAGCCACAGAATTCCTAAAAAGATACGAGCATAAGTCTCCGCCACCACGACCTTAACGCCCGACGCACCCAAGGCCACAGGG[G/C]CGTGCTCTCGGGACGATCCGCAGCCGAAGTTGTCACCGGCGATGATGATCGGGAAGTTCGTTTGGGTGGATCCGGGCTGGACAAAAGGGATAGGGTAGA
87980 CT C CTCTAGCAGTTAAAGTTTACTGCAGTACAACAGGAGGCCAATTCTTCTGTACCAACACCTCTATCTCCGCGTGTGCCCACCAATCAGATCTCTCCATTTT[CT/C]TTTTTTTGTATTTAAGTCTCTGGACAATTGAGGGATTTAACTGCAAAAGGAGGAAATCAGAGGGCTCTGATTGCCTGGGGACACGGA
87986 T G TGTTTATCATCCCTAGGATTAGCAGGAGCAAGCACTGCATTCCCATTCCTAACAGTAAGTGAGTAAGTCTC[T/G]GCAGCTTTGCTGAATATCCTCATTGTAGGTTCCAATGTTGGTGGTGGATTATATGCAAGTATTTGCCCATATGGAACGATCTTCCATCTCTGGTTGTTTC
87986 G A CAGGGTCTCCATGGAAGGCGTCGAAGTTCAAACGGATGTTGTTCACCATTCTTACGCAGCGGAAACCGTCTCCTAAGTCTCTGCTTTCGCTCCAAAGAAC[G/A]GACTCGTCAAGGGAATTTGGATTGTATGGGACAAGTCTTACAGGGTGATGTGGTCCAATGGAGTGCTTGATAGCCTGCCCAGTAGC
87986 T C AAGTTCAAACGGATGTTGTTCACCATTCTTACGCAGCGGAAACCGTCTCCTAAGTCTCTGCTTTCGCTCCAAAGAACGGACTCGTCAAGGGAATTTGGAT[T/C]GTATGGGACAAGTCTTACAGGGTGATGTGGTCCAATGGAGTGCTTGATAGCCTGCCCAGTAGCTTTGTTAACCAGTGCAAAACTTGG
88002 A G TACCCACCTATTCATCAGTGTATAAATGGACACACAATTTGCTCATCTTGCAAACCGCGTGTGCATAATATATGCCCTACATGCAGACATGAATTGGGCA[A/G]TATCAGATGCCTTGCCCTTGAAAAAGTAGCAGCTTCTGTTGAACTGCCTTGCAAACACCAATG
88010 A G AACAACAGATGGTTCTGTGATCGAAGAGAAAGAGACTGCACTTGTTTGGTCGTACGAAGACTCCGACCCAGACTTTGGGTCATGTCAGGCTAAGGAGTTG[A/G]TGGACCATCTTGAAAGTGTACTTGCCAATGAGCCTGTTTCAGTCAAGCCTGGCCCAAATAACGTAGAAGTCAAACCTCAGGGAGT
88014 G A CATGGGCTTTGGACAGTTGGTGCATTAGGAACAGAAGGGATAGCTGGAATTATTGGAAGCTTAGGAACATGAACTCCAGGTATGCTCGGAAATTCTGGCA[G/A]TGGCGGCAGCTCAAACTTTGGCAGCTCAGGCAATGGTGGTAGCTCCGGCTTTGGCAGTGCAGGCACAACAGGTAATGGTGGTAA
88014 A G TAGGAACATGAACTCCAGGTATGCTCGGAAATTCTGGCAGTGGCGGCAGCTCAAACTTTGGCAGCTCAGGCAATGGTGGTAGCTCCGGCTTTGGCAGTGC[A/G]GGCACAACAGGTAATGGTGGTAATTCCGGCTTTGGCAAAGCTGGCACTGCAGGTACAGGTGATTTTTCATCCTTGCTAATGGCTG
88014 G A ACTCCAGGTATGCTCGGAAATTCTGGCAGTGGCGGCAGCTCAAACTTTGGCAGCTCAGGCAATGGTGGTAGCTCCGGCTTTGGCAGTGCAGGCACAACAG[G/A]TAATGGTGGTAATTCCGGCTTTGGCAAAGCTGGCACTGCAGGTACAGGTGATTTTTCATCCTTGCTAATGGCTGGTATTTTGGGC
88014 A G CAGTGGCGGCAGCTCAAACTTTGGCAGCTCAGGCAATGGTGGTAGCTCCGGCTTTGGCAGTGCAGGCACAACAGGTAATGGTGGTAATTCCGGCTTTGGC[A/G]AAGCTGGCACTGCAGGTACAGGTGATTTTTCATCCTTGCTAATGGCTGGTATTTTGGGCAAATCTGGTAGAGGAGGAAATTCTAT
88014 G A CAGTGCAGGCACAACAGGTAATGGTGGTAATTCCGGCTTTGGCAAAGCTGGCACTGCAGGTACAGGTGATTTTTCATCCTTGCTAATGGCTGGTATTTTG[G/A]GCAAATCTGGTAGAGGAGGAAATTCTATTTTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAG
88014 A G TAATTCCGGCTTTGGCAAAGCTGGCACTGCAGGTACAGGTGATTTTTCATCCTTGCTAATGGCTGGTATTTTGGGCAAATCTGGTAGAGGAGGAAATTCT[A/G]TTTTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAGGTAAAGTTGGCAGCCCAGGTTTTGGTA
88014 T C TTTTTCATCCTTGCTAATGGCTGGTATTTTGGGCAAATCTGGTAGAGGAGGAAATTCTATTTTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGT[T/C]CTGGTTTTGGTATTTCAGGTAAAGTTGGCAGCCCAGGTTTTGGTAGTGTAGGGATCTCTGTTAAAGGCGGCAGTTCTGGTTTTGGAAG
88014 A T GGTATTTTGGGCAAATCTGGTAGAGGAGGAAATTCTATTTTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAGGTA[A/T]AGTTGGCAGCCCAGGTTTTGGTAGTGTAGGGATCTCTGTTAAAGGCGGCAGTTCTGGTTTTGGAAGCGTTGGTATTTCTGGAATTGG
88014 C T CAAATCTGGTAGAGGAGGAAATTCTATTTTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAGGTAAAGTTGGCAGC[C/T]CAGGTTTTGGTAGTGTAGGGATCTCTGTTAAAGGCGGCAGTTCTGGTTTTGGAAGCGTTGGTATTTCTGGAATTGGACTATCAATTA
88014 T G TTTGGTAATGTTGGGATTAATTCAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAGGTAAAGTTGGCAGCCCAGGTTTTGGTAGTGTAGGGATCTCTG[T/G]TAAAGGCGGCAGTTCTGGTTTTGGAAGCGTTGGTATTTCTGGAATTGGACTATCAATTAATATACGCGCTGCATGACAATAAGTGCT
88014 T C CAGGTATTTGAGGATGTTCTGGTTTTGGTATTTCAGGTAAAGTTGGCAGCCCAGGTTTTGGTAGTGTAGGGATCTCTGTTAAAGGCGGCAGTTCTGGTTT[T/C]GGAAGCGTTGGTATTTCTGGAATTGGACTATCAATTAATATACGCGCTGCATGACAATAAGTGCTGTTTAATAACATGAGCACTATG
88014 T C GAGGATGTTCTGGTTTTGGTATTTCAGGTAAAGTTGGCAGCCCAGGTTTTGGTAGTGTAGGGATCTCTGTTAAAGGCGGCAGTTCTGGTTTTGGAAGCGT[T/C]GGTATTTCTGGAATTGGACTATCAATTAATATACGCGCTGCATGACAATAAGTGCTGTTTAATAACATGAGCACTATGAAACAGCTG
88016 G A TTGCAACATGCATATGCGGTTGGTCATAGTACCGATTTGATGATCCCGAAGCCATGGCGGCACTAGGTCCCACTTCGGGCAGTTTAGACAGTAGGGCTTC[G/A]AGGCTGCTCATTGATGGCGTTATGTGCGTGGTCGACAGATGATCGTAAGCATCCATGTGTGGCGGTGGCAGCATCGATGGTGTAG
88016 T C GCAGTTTAGACAGTAGGGCTTCGAGGCTGCTCATTGATGGCGTTATGTGCGTGGTCGACAGATGATCGTAAGCATCCATGTGTGGCGGTGGCAGCATCGA[T/C]GGTGTAGGGATGTTGTACGAGTGCCAGTGCTCGGTGGGTGGCAGCGTCATTGGGATTCCTGAAGAGGATGGGTGTGGAAGGAA
88016 T C GTGGCAGCATCGATGGTGTAGGGATGTTGTACGAGTGCCAGTGCTCGGTGGGTGGCAGCGTCATTGGGATTCCTGAAGAGGATGGGTGTGGAAGGAACAC[T/C]CCTGGAATGCTTTCTAAGTATGCGAACTTCTTCCGTAGGGCTACTATGTAGCTTAAGTCTTCTACCACCTTGCTAAGAGACCCGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
88020 T G AAGGGGGGGTTGGTTTTGCTGGAGTTAGTGTTGTCGGTGGAAGCTCAGACTAAAGGGTTTGAAGTGGCAGGAGAAGGGGTAGTCATGGTGGCGGTTCCAG[T/G]TGTCAGCGACAGTCTGTGCATGGCCGTATTTGTGGAGTTTCGGTTGGTCTGGAAGCTGAGTTTGTGGTGGTAGGATATGTAAC
88026 AC A GCCCGGAAAAGGCTTGCTGCTAACTACCAGGAAGCTCAAAATGCTAAGAAGCAAAGGACAATACAAGTCATGGACATTCATGAAATTCCAAAACCAAAAA[AC/A]CGGATTCATTTCACGTAGCAAAGGCGGACAACACAACACACACCAATCGTCGCGATGGTGATTCGGATTTTTTTGATAGGAAAAA
88030 C CG GGCGCTTCAGGACGGCATGAGCGTCCCGCTCTATATTCATCTCGCCGGTAGCCAGGGTCGCCAGGACGATCAGCGAATCGGCAGCG[C/CG]TTTTATCTGGCTGGACGATGGACAGCTACGCATCCGGAAAATACAGCTGGAAGAGAGTGAAGATAACGCCAGTGTCAGCGAACAAACTCGACAGCAG
88034 T C TACTGGAGGAGACACCTTTGCATCATTCAAGGCGCTTCTCCCTAGTTTTGAGCACCATCATTATGGCTAGATCAGCTCTAGATGAGATGACAAACACTGG[T/C]GCTTTCGACCGAACTCCGTCAACATTCCGGAACTTCATTTCTAAAGATAAGGCATCACAATTTCCAGCAGAAGCAGGAAGATACCATC
88060 T C GCAATATCAAAAGTCTCCATCTCGTGCTGGCTCCTAAAACAGAAATTATTTCCTTGTTTTGCCATTCTATTCGCCGTATTTCTGTATTTCTTCTTCAACC[T/C]GCGTAATTTCTCGGTCAACTGGTTCTTGTTGAAATCTAACTCCAATTCATTCTTAATCTGGTCGTAAAATGGACCTGTATCATACTGATGCG
88060 A G CAACCTGCGTAATTTCTCGGTCAACTGGTTCTTGTTGAAATCTAACTCCAATTCATTCTTAATCTGGTCGTAAAATGGACCTGTATCATACTGATGCGAT[A/G]CGAAAGTAGTGCCACGAGACGATGTAAAATCGAGGAATCCTTTTAGGATCTTAATTTCATCTTCATCAGTCCATAGGCGCTGGAAAAGG
88062 G A TGCCCAGACAGTCCGCCACCATGTGCCTTCACAAACACATCATATGTGCTCTCATATCCTAATGTCATTAAGGGGGTCTTTAC[G/A]TACTGTAGCCATAAAGGATTTCCTTGCAAATATTCCTTTGCATCACGGTAATTAATTATGAACTTCCCAGATCCTTCTTGAAGAACAACACGAGCAATGG
88062 G A CTTGCAAATATTCCTTTGCATCACGGTAATTAATTATGAACTTCCCAGATCCTTCTTGAAGAACAACACGAGCAATGGCGCACTTCCTTCTTCCAGTTCC[G/A]ATAATGGTCTGAGCAGCAAATCCACCAGGCAGTCTCGACTTAACCAGCTTCTCCAAATTGATTTCCTCCACTTCCGATGTGCCTTCGGCG
88062 C G ACTTAACCAGCTTCTCCAAATTGATTTCCTCCACTTCCGATGTGCCTTCGGCGACAGTGGCGACGATGGTTGCAGAAGGGCATTTCTGTAATGTGATAGA[C/G]GATTTGGGAAAGCGGAGGGAAAACGAAGTTCGATTTGAGGGGATTTGGGAGGAGAAGGATAGGGAGGAGAGCGACGAGGCGAG
88062 G A ATTTCTGTAATGTGATAGACGATTTGGGAAAGCGGAGGGAAAACGAAGTTCGATTTGAGGGGATTTGGGAGGAGAAGGATAGGGAGGAGAGCGACGAGGC[G/A]AGTGAGGAGAGGGAAATTGACATTATGGATTTTCTATGAGCTGTTGTGCTACTACTCTCTTTGTTCTGGATGGAGTAGAAAGG
88062 T A ACGAAGTTCGATTTGAGGGGATTTGGGAGGAGAAGGATAGGGAGGAGAGCGACGAGGCGAGTGAGGAGAGGGAAATTGACATTATGGATTTTCTATGAGC[T/A]GTTGTGCTACTACTCTCTTTGTTCTGGATGGAGTAGAAAGGATATGAAACGGATAAAATGTCCAGTAGGCCAACA
88080 G T TTAAATTCCCTACATTCAGTTCATCTCCAGTAATAAAATTTCCCAATCGGGCCTCAATAATAATTTTGATTCAAAGTAATGGAAGTTAGCGGCAGAAGCG[G/T]TGTTTTAGGCGGCAGCGGTCCTGCGGCACGGGATTTCTGGATTGCCTTTCTGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGG
88080 C A GTAATAAAATTTCCCAATCGGGCCTCAATAATAATTTTGATTCAAAGTAATGGAAGTTAGCGGCAGAAGCGGTGTTTTAGGCGGCAGCGGTCCTGCGGCA[C/A]GGGATTTCTGGATTGCCTTTCTGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGG
88080 C T TCGGGCCTCAATAATAATTTTGATTCAAAGTAATGGAAGTTAGCGGCAGAAGCGGTGTTTTAGGCGGCAGCGGTCCTGCGGCACGGGATTTCTGGATTGC[C/T]TTTCTGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCA
88080 C T GCCTCAATAATAATTTTGATTCAAAGTAATGGAAGTTAGCGGCAGAAGCGGTGTTTTAGGCGGCAGCGGTCCTGCGGCACGGGATTTCTGGATTGCCTTT[C/T]TGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGC
88080 A G ATTTTGATTCAAAGTAATGGAAGTTAGCGGCAGAAGCGGTGTTTTAGGCGGCAGCGGTCCTGCGGCACGGGATTTCTGGATTGCCTTTCTGTTTGCAGTT[A/G]GTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAA
88080 T C TTCAAAGTAATGGAAGTTAGCGGCAGAAGCGGTGTTTTAGGCGGCAGCGGTCCTGCGGCACGGGATTTCTGGATTGCCTTTCTGTTTGCAGTTAGTTTGC[T/C]GCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTT
88080 G A CGGCACGGGATTTCTGGATTGCCTTTCTGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATT[G/A]CTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACAT
88080 C T GGATTTCTGGATTGCCTTTCTGTTTGCAGTTAGTTTGCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCAC[C/T]CCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTC
88080 T C GCTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGG[T/C]TGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGAC
88080 T A CTGCCGGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGT[T/A]GTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACA
88080 A G GGTTCGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCT[A/G]AGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACC
88080 G T CGGTATCTTTTGGACTCTATCGTCTTCAAGCCGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGA[G/T]AGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGG
88080 T C CGTTGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTT[T/C]ACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGG
88080 A G TGTCTGGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTAC[A/G]TATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGG
88080 A C GGTTTATTGCTGCACCCCAGTGCAGCCAAAAAAATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATT[A/C]TGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAA
88080 A G AATGACTCTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATC[A/G]TGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCT
88080 C A CTTGGTGTTAGGTTGTCTAAGAGAGCGAAAAGCTCAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGA[C/A]AGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTG
88080 C T CAGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTT[C/T]GATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTC
88080 G A AGAATCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTC[G/A]ATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCT
88080 G A TCAATGTGGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATG[G/A]GTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCTCCTC
88080 T G GGAAGTTTACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCC[T/G]AACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCTCCTCACATGGG
88080 A G TACATATTATGTCACAATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAG[A/G]AACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCTCCTCACATGGGAAACTCT
88080 C T AATGCAGCTTTGGGTAATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAGAAACTTACTCAATCG[C/T]TGAAGCTATTCTACCTGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCTCCTCACATGGGAAACTCTGAGAAAAGATTTTGC
88080 C A AATATCAATCATGCAGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTAC[C/A]TGTGCCAAGGTGGTTTTTATGCATATAGCATTGTCGCTCTCCTCACATGGGAAACTCTGAGAAAAGATTTTGCAGTTATGA
88080 T C AGACAGAACCATGGTTGTTAAAGACAAATGAGTACTTCGATGGGTGGCCTAACCAGAAACTTACTCAATCGCTGAAGCTATTCTACCTGTGCCAAGGTGG[T/C]TTTTATGCATATAGCATTGTCGCTCTCCTCACATGGGAAACTCTGAGAAAAGATTTTGCAGTTATGA
88100 T G TTCTTCTAATCACAACTCTTCTAGTCTTTTTGCCGTTAACGAGTTTCAAGCGCATAGATTCCTTGAGATTCACATCGGCTTTATCAGTCGCTCTAGCGGT[T/G]GTTTTTGTTGTGATCACAGCTGTAGTCGCCGTCTTCAAATGGTTTAACGGAAGCGTTTCAATGCCAAGACTGTTTCCTGAAACAACTGAT
88148 TG T TCATAGTAACAATACTATCATCATACGTAGCAATATCAAACGCTGTAACATGTTCAGATGTGTACAACGATCTATTCCCATGCCTTAGTTACTTCCAAGG[TG/T]GGGGGAGGCAAGCCTTCATCGGAATGCTGCGATGGCATCAAGGCTGTGCTGGCTGTGGCAAGTACGGCTGCTGACCGGAGGTCGA
88148 CA C AGACCGTGGCTTCAGGTGTCTCTGCTCCTAATCTGAAACTCGCCAGTGGGCTTCCTTCTGCCTGTGGTGTCTCCGTGCCCTTTATGATCAGTCCTAAAAC[CA/C]AACTGTAACAAGGTTAAATGATGGTCAAAAGAAGAGATGCCAGTGTAATGGTTTTTCCAGTTAATTTGGAGATGTTTCCTTTTGTTTA
88148 CA C CTTCAGGTGTCTCTGCTCCTAATCTGAAACTCGCCAGTGGGCTTCCTTCTGCCTGTGGTGTCTCCGTGCCCTTTATGATCAGTCCTAAAACCAACTGTAA[CA/C]AAGGTTAAATGATGGTCAAAAGAAGAGATGCCAGTGTAATGGTTTTTCCAGTTAATTTGGAGATGTTTCCTTTTGTTTAATTCGTTGCT
88148 C CT CTTTATGATCAGTCCTAAAACCAACTGTAACAAGGTTAAATGATGGTCAAAAGAAGAGATGCCAGTGTAATGGTTTTTCCAGTTAATTTGGAGATGTTTC[C/CT]TTTTGTTTAATTCGTTGCTTACTGCCATTAGTGGCATATGAATCATGAAGTCTTGTTCTACCTTAGAACCATTGTTGCAATATCAGTTG
88162 A AG TCGAATGAGCGTTTAACTGCAAAGCCAGATCCGCGTTTGAAGCTACAGTTCTCGCATGAAGATGCGGCAATCTCTGCCAAATATGAGCAGGAGGGATCCT[A/AG]TTTTTTAAATCGTTGATAGATTTCCTCAAGCTTGATGCTTTTTGATCGAGATTCAATGCATGTTGTTGCTGTTCTCGGCTAAAGGCG
88174 C T CCAGCGCAGGTGCCATAAGCTCACCCTCGCGCTGGCGACGGAGAAGCTGAAGAATGTCAGGCGCGGGCTGGGGTTGGTCGGAGACGATGATCAGGTTTGC[C/T]ATCAGGAGCCGCCGGAGAGTTATTTAGGCAAGTTCAAGAGGATTTGGGCCTTGTATTTTGCCTTTCTGGTTCTTACT
88186 T C CGGCACCGGCGAGTACTCCACCCCATGCACGGCCTGCAGAGGCGACGGTCACATTCGAAAACCCAAAACTATTACATTAAAAGTCCCGGCTGGGGTCGAC[T/C]CCGGCAGCAGACTCAGGGTCAAATCCGAAGGCAATGCTGGCAAACGAGGCGGTGGCCCTGGAGACCTTTACGTGTTCATCGATG
88204 T TC ATGGCCGTAGCCAATCCTTTTTGCCCAATTCGATTGCTTCTTCCTCCCTCTGTTGATCGAAAACCAAAACCAGCCCTAAATAAATTCGCACTTTCTTCTT[T/TC]AGGTTATCACAGCAACGCCTCTTTCCCTAAAGACGGAGTCTTGCGCCGCCTCAAGCTCTGTCTGCTTCTCCGTGGCTTGTCCGACCAGTT
88204 T G GTCTGCTTCTCCGTGGCTTGTCCGACCAGTTGAAGCTGCAGCCATCGTCGAGGCACCAACCATCTGAAAGTAAATAGTCAAAGCCCCAAAACCCTAAATC[T/G]TAAATTCCTTCAATCGAAACCCTAATTCGCTCTTTCTATAATCGAAGTGTCTCCAATATCGCCCTCAGATCCAAACGCAGCACTCAGCG
88204 A G GCCATCGTCGAGGCACCAACCATCTGAAAGTAAATAGTCAAAGCCCCAAAACCCTAAATCTTAAATTCCTTCAATCGAAACCCTAATTCGCTCTTTCTAT[A/G]ATCGAAGTGTCTCCAATATCGCCCTCAGATCCAAACGCAGCACTCAGCGGATCGAAGCTACTACCATCCCTTGCCCAAATTTCAACGCT
88216 C T ACCCTTGCCCCGGTTTCGATCCCTCTCATCCATCGATCCTTGGATCTGCTTGAATCGATTCATTCGTGATTCAGATCTTCAAGAAAGATAAAATGTTGAG[C/T]TGTTGTATGAGAGGTGAAGAGCCATGGGACCCGGATTCATATTACGCAACTCGACCCGAATGTCGTGATGATATTCCCAAGACTCATTT
88226 T C ATCATTTTTCTCTTTCTTCATGAAGAGAAAACCATCTCCTCCAGGCCCCTTAGCACTTCCTATAATCGGCCATCTATATTTGTTGAACCCCAAAAAGCCT[T/C]TCCACCACAGCCTGAACCGCATCCATGCCCGCTTCGGCCCAATCCTCTCCCTCCGTTTTGGGTCCCGTAAGCTCATCGTCGTGGGCACGTG
88296 C A CCTCCTTTCGCCACTGCCGTTCCAGGTTCAGGTAAGTCAACAAACACAACTTCTCCCAAATGATCCTGAGCATGGTCTGTAATGCCTATGGTAGCCACAG[C/A]GCCTTCATGCTTAACCCATTCATGGGAAGGACTGTACTTCAGCCCTTCCAAAACGGAAGAGAAGCATCTTGAAATGGAGAGAGCCGA
88302 G A GTCCTTTCTCAGGTTCTTCACCAAGTAACATGGCTTTCTCTTGCTTTCTTTTTACAAGAGCAGCTTGTTTCTGAGCAGCTTCTATACCAGCTCTTTCCTT[G/A]GCTGTTTCTTCTTCCTTGCACTTCCTCTCAACTTCTGCCGCTTCTCTTTCCAATCGGTCTTGTTCTTCTTTTCTTTGACGCTCTCTAGCTTGATC
88310 A G TTTTACGTCCACACATAATCTTACCATCATAATCATCTAATAAACTTCTTTTAACCCCTTTATTTGCCACGCTTCGTATATCTCCACCAATAACTTCAAT[A/G]ACTTCTTTATCAATCACGCGATTGTCTGACGCTCCTGATTTCTTCCTAATTCCACTTTCAAGCAAGCAGTTACTAACCTGATCTTCAATTTCAC
88310 A G CCTGATCTTCAATTTCACGGCATTTTTTCAGTGGCAAAAAGCGAAGCGCAGGGGTCGCACGATCAACTTTTGGGGGATCTGCCGATCTGAGACGCTCCCT[A/G]GGGAGGACAGAAAAATCATCGGACGTGAAGTCTGTGAGGAGGTCGAATGCATTGCGAGTCGCCATTGAGAAAAAAA
88324 T C CAGGAAGACCGGTAATCCTCCCCGGGTCGTCAAGGAATACTCAGCAATTTCCCGGGCCCACATGTCTACAGCGTTGTAAAACGTCTGTCTGTCATTGACA[T/C]TGTAGACAATAAGGTAGACGCTGCCTCGAGAATAGGAGAACCTTCGACGAAGATGGTATTCGTCTGGACCAAGAAATTGACATCCC
88324 A G ACGTCTGTCTGTCATTGACATTGTAGACAATAAGGTAGACGCTGCCTCGAGAATAGGAGAACCTTCGACGAAGATGGTATTCGTCTGGACCAAGAAATTG[A/G]CATCCCAGATCATTAAGCCGACATGCACACTGTTCGACAATGGTATGCCTGGTATATGGTGG
88334 T C AGATTATCATAAATAGTAGGAACAAAGAATCTTGTAAGAAAAGTTTAGATGATGCGCTTGTTATGACCAAAAAAATTGCAGCAATCTCTCCTTCTGGAAA[T/C]GAGATTACCAGAATCCCCCTTGCATTGATCATTGATGGTACCAGTTTGGTTTATATTCTTGAGTCTGAATTGGAGGAAATACTTTTCAA
88334 G A CATGCGATGTGGTGTTGTGCTGCAGGGTGGCTCCGTTGCAGAAGGCTGGAATAGTTGCGCTCATTAAACACCGAACAGATGACATGACTCTTGCCATAGG[G/A]GATGGTGCCAATGATGTTTCAATGATCCAAATGGCGGATGTCGGGATCGGCATTAGTGGACAAGAGGGAAGACAAGCTGTTATG
88348 T C AAAATGTTGTATATAAGTCCGTAGTTTTTCAGTCCGAATAGTTCAGATGCAGTAGGAACAGTTACAGCTAAACGAACGCCGTAGCAGATGCCGACTATGA[T/C]TGAACCGAGGAAGAGAGAGCCAGGCAATGCCATGGCCATTATGATGTACCCTACTGCCATTAGTATTTGCGACGCTGCGTTCCATA
88352 GGAAA G TTTTTGAATAACAAGGCCAAATCATTGAAATAGCAATTTATGTTCATCCTTCGATTATGTTCCAATCTACTCACACCACCCATTAACAGAACAAACCCAG[GGAAA/G]GAAAAAAAATAAGCACAAAATTAACACAACAAACCTGGCAATCTTTCACAATCACTACAACCATATCTTCCCCTCTTCCTGCGGTC
88352 T A ACAAGGCCAAATCATTGAAATAGCAATTTATGTTCATCCTTCGATTATGTTCCAATCTACTCACACCACCCATTAACAGAACAAACCCAGGGAAAAAAAA[T/A]AAGCACAAAATTAACACAACAAACCTGGCAATCTTTCACAATCACTACAACCATATCTTCCCCTCTTCCTGCGGTCCATCCCCAAATCCA
88352 C A GCACAAAATTAACACAACAAACCTGGCAATCTTTCACAATCACTACAACCATATCTTCCCCTCTTCCTGCGGTCCATCCCCAAATCCAACGGCTCACGTG[C/A]TACTAAAACTAGCGCATACGAAAAAAACAAGTGAACGGCAAACAAATAATTATCCCTAACAATAAATCAAGCCACCAAAATTACACCCA
88352 C T AAACAAGTGAACGGCAAACAAATAATTATCCCTAACAATAAATCAAGCCACCAAAATTACACCCACACCCAAACCCACCGCCAGACCCACCCATCCACAC[C/T]TACTTCTCGAACCCCCACTCTCATCGGCCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTCCCTCCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
88352 C T CCGCCAGACCCACCCATCCACACCTACTTCTCGAACCCCCACTCTCATCGGCCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGC[C/T]GACTTCCCTCCCTTCTTCTTCTTCCCCTTCCCCGCCTCCGGCGCATCCGCCACTACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCC
88352 C G ACCCACCCATCCACACCTACTTCTCGAACCCCCACTCTCATCGGCCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTC[C/G]CTCCCTTCTTCTTCTTCCCCTTCCCCGCCTCCGGCGCATCCGCCACTACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCCGGCTTAA
88352 C T TCGAACCCCCACTCTCATCGGCCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTCCCTCCCTTCTTCTTCTTCCCCTT[C/T]CCCGCCTCCGGCGCATCCGCCACTACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCCGGCTTAAACAGCTCCACCGGCTCCAGCAC
88352 C T TCTCATCGGCCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTCCCTCCCTTCTTCTTCTTCCCCTTCCCCGCCTCCGG[C/T]GCATCCGCCACTACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCCGGCTTAAACAGCTCCACCGGCTCCAGCACCTC
88352 C T CCGCCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTCCCTCCCTTCTTCTTCTTCCCCTTCCCCGCCTCCGGCGCATCCGC[C/T]ACTACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCCGGCTTAAACAGCTCCACCGGCTCCAGCACCTC
88352 T C CCTTCTGTTCCTTCGGCTGCTCCTCCGGCCCCGCCGGTGCCATCGCCGACTTCCCTCCCTTCTTCTTCTTCCCCTTCCCCGCCTCCGGCGCATCCGCCAC[T/C]ACATCTGGTGCCGGTGCAGGCGCCGGAACCTCCGCCGGCTTAAACAGCTCCACCGGCTCCAGCACCTC
88366 A G TCACAGTGTCGAGTATAGTACTCGTCGTATAGCTGTTTGATTGCAGTCTTATGCGCCTTGCATCATAATCAACAGGACTTTTAGACCAAAATGCAAATAT[A/G]TTTGAATCTAGTACTTCCCATCTAGTCACATTTTCAAGTGGGTAGATTCTGAGTGTCCTGCTGGTGCTTGGATCAAGCATGCGGATACC
88366 T C ATTGCAGTCTTATGCGCCTTGCATCATAATCAACAGGACTTTTAGACCAAAATGCAAATATATTTGAATCTAGTACTTCCCATCTAGTCACATTTTCAAG[T/C]GGGTAGATTCTGAGTGTCCTGCTGGTGCTTGGATCAAGCATGCGGATACCATCCAAACCAATCTGACAAAGTACATCCGTACTAGTAAC
88366 G C TGCGCCTTGCATCATAATCAACAGGACTTTTAGACCAAAATGCAAATATATTTGAATCTAGTACTTCCCATCTAGTCACATTTTCAAGTGGGTAGATTCT[G/C]AGTGTCCTGCTGGTGCTTGGATCAAGCATGCGGATACCATCCAAACCAATCTGACAAAGTACATCCGTACTAGTAACACTAGTACCTTC
88384 GC G CTCCTCCAAGCCGCCCACGCCTTCTTCAACCTCAACGTCCTGTCCACAACATGCTCCATTTTCCTCATCATCATCGCCTCCACCATCTACTTCATGTCCC[GC/G]CCCCCGACCTGTCTACCTCGTCGACTACGCCTGCTTCAAACCTCCATTCTACTACCGTGTCCCATTTGCCACCTTCATGGAGCACAGCCG
88384 C T ACTACCGTGTCCCATTTGCCACCTTCATGGAGCACAGCCGCAAAATCCCCTACTACACCGAGAAAACCACCCGGTTCCAAACCTACATCCTCGAACGCTC[C/T]GGCCTCGGCGAGGAGACCTACCTCCCTCCCAGCATTCACTGCATCCCTCCCAAAGCCACCATGCAGAAAAGCAGAGACGAAGCCGAG
88432 A C GATTTCGCTACACTCTTTAGGCCTCATCAGTGACAATCTTTCATTTCCAAGCTCATCTCGGATCTGCTCGCCTGAACATTCTCTTCCAATTATGTAAGAT[A/C]CATCTTCTAAAATATCATTCATCCCAAATACATAATCTTTTGGCACCCCAAAGTCCTTGGCTTCCATGACAACCATGCATGAGTCAACAGC
88432 A C CACTCTTTAGGCCTCATCAGTGACAATCTTTCATTTCCAAGCTCATCTCGGATCTGCTCGCCTGAACATTCTCTTCCAATTATGTAAGATACATCTTCTA[A/C]AATATCATTCATCCCAAATACATAATCTTTTGGCACCCCAAAGTCCTTGGCTTCCATGACAACCATGCATGAGTCAACAGCACCAAGGTTG
88432 T C ATGAGTCAACAGCACCAAGGTTGAATCCATTAACACTCTTCCCAAGAAGCTTAGAGCAAAAGTCCCTTATTGCAGATACGAATCTTGGGGAAGATAATAG[T/C]GAAGAACCCTTTTGATCCATCGCAGTCATGGAAATGATAACATCTTCATCACTAAAAGAACTTAATCCTCTTTGTTTACCAGTAATGTT
88432 A G CACTAAAAGAACTTAATCCTCTTTGTTTACCAGTAATGTTTGAAAAGGAAGTATCATTAGGGACCTCACCAAAGTTGTACCTTAAGCTCTTGTCAGTTGT[A/G]GAGTTTAAGACCCCTTTGGTAGAAAGTATAGATGGCATGCATCTTACTGCGTGGTAAATGGATGAAGTAGACCTAGCATTTAGTTTAA
88436 A G TTTTTTTTTTTTTTTGTTAAGTTACACGAATTTTACACTTAAGACTGAAAGTCTGAAATATAAGA[A/G]TAGAAGAAGAATCAAACTACCATTGAAGTACAACAAGTAGACCTAAGACAACAAAAATGGAAAGCTCACGAAATTACAAAGAAAGAAACACACACTGGAA
88436 C G TTTTTTTTTTTTTTTGTTAAGTTACACGAATTTTACACTTAAGACTGAAAGTCTGAAATATAAGAATAGAAGAAGAAT[C/G]AAACTACCATTGAAGTACAACAAGTAGACCTAAGACAACAAAAATGGAAAGCTCACGAAATTACAAAGAAAGAAACACACACTGGAATTAAGAAGACATC
88436 C A TTTTTTTTTTTTTTTGTTAAGTTACACGAATTTTACACTTAAGACTGAAAGTCTGAAATATAAGAATAGAAGAAGAATCAAA[C/A]TACCATTGAAGTACAACAAGTAGACCTAAGACAACAAAAATGGAAAGCTCACGAAATTACAAAGAAAGAAACACACACTGGAATTAAGAAGACATCACAT
88436 G GAATTA GAATAGAAGAAGAATCAAACTACCATTGAAGTACAACAAGTAGACCTAAGACAACAAAAATGGAAAGCTCACGAAATTACAAAGAAAGAAACACACACTG[G/GAATTA]AATTAAGAAGACATCACATGGGTACAATGGATCTAATGTAATGAAAGTGGGATGGAGCATGGAGAAAGAAATCAGCAAT
88436 T C CTACGGCGGAAGCCTTTGCATTCGCCGCCGGGAAAGCCTTCGGTCTTGCAAACGTTGGCGCAGTTGCTGCCCCTGATGCACGATCCCACGAACCTGTGGC[T/C]TTGCGACAGGCACACTCTTGCTTCTGCTACCATTATTCCTCCTCCTCTTCCACCCATTCCTGTAGCAGTGAGAAGGAAGCAGAGCAG
88436 T C ATTCGCCGCCGGGAAAGCCTTCGGTCTTGCAAACGTTGGCGCAGTTGCTGCCCCTGATGCACGATCCCACGAACCTGTGGCTTTGCGACAGGCACACTCT[T/C]GCTTCTGCTACCATTATTCCTCCTCCTCTTCCACCCATTCCTGTAGCAGTGAGAAGGAAGCAGAGCAGAATGGCTGAAACAATACTTT
88436 A G GCGACAGGCACACTCTTGCTTCTGCTACCATTATTCCTCCTCCTCTTCCACCCATTCCTGTAGCAGTGAGAAGGAAGCAGAGCAGAATGGCTGAAACAAT[A/G]CTTTTGGTAGATGCCATCCTCGTTGTGCTTCTGAAGATTTAAGTGAAGTGATTTAACTTTAAGAGATTGATCCAGTAGGCCAACA
88440 A G CGATAACTCCATACCGAAAACAGGCAATTATTAGTAACCAAATGAAAATAACCGCTAAAAT[A/G]TCCACGTACCAAATTTGCACGTATAAAACGTGCCCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAA
88440 G T CGATAACTCCATACCGAAAACAGGCAATTATTAGTAACCAAATGAAAATAACCGCTAAAATATCCACGTACCAAATTTGCACGTATAAAACGT[G/T]CCCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAACCGAATGATCATCATCTGTGTATTAGCC
88440 C G CGATAACTCCATACCGAAAACAGGCAATTATTAGTAACCAAATGAAAATAACCGCTAAAATATCCACGTACCAAATTTGCACGTATAAAACGTG[C/G]CCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAACCGAATGATCATCATCTGTGTATTAGCC
88440 G C CACGTATAAAACGTGCCCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAACCGAATGATCATCATCT[G/C]TGTATTAGCCGCAGAGCCAATAAGGGATGGAGGTTAATTTAGAACTTGAATATTGCAGCACCACTTGAAGGTTTGGAGGCAAATACA
88440 T C TAAAACGTGCCCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAACCGAATGATCATCATCTGTGTAT[T/C]AGCCGCAGAGCCAATAAGGGATGGAGGTTAATTTAGAACTTGAATATTGCAGCACCACTTGAAGGTTTGGAGGCAAATACATACAGA
88440 A G TGCCCCATTATCTACAGAAAATATAACTAAGATCCTAGAAGTATTTATTGATAAGAGTTCATAATAAAAACCGAATGATCATCATCTGTGTATTAGCCGC[A/G]GAGCCAATAAGGGATGGAGGTTAATTTAGAACTTGAATATTGCAGCACCACTTGAAGGTTTGGAGGCAAATACATACAGACCAAGAT
88440 A T TGATCACACCCTTCTCAATTCTTGACTGGTAAAATGACTCCTTTAAATTGAGAATGAACTGAGGGACAATGCTTTCTTTAACTAAAGCAACTGCACAACC[A/T]CCCCATCCGGCTCCAGTAAGTCTTGCTCCAAGTGCACCATTATCTCTACATGCTTTCACTAGCTCCTCCAACCCGGGCAGCTGCACTCAT
88440 C CT TTTCTTTAACTAAAGCAACTGCACAACCACCCCATCCGGCTCCAGTAAGTCTTGCTCCAAGTGCACCATTATCTCTACATGCTTTCACTAGCTCCTCCAA[C/CT]CCGGGCAGCTGCACTCATACAAAACACTACAGCTGTGGTGACTCTCATTCATTAAATCACCAAGTTTTTAAGCATGTCTTCATCACT
88456 T C TGGAGAGAGAAAGCACCCCCAGCCTCAACCCTTCAGAACCGCTCTCGCTCCTTCCGCCTCCGCTCCCCATCCCTCAACACCCTCCGCCTCCGGCGCGTCT[T/C]CGACATCTTCGATCAGGACTCCGACGGCCTCATCACCGTCTCCGAGCTCTCCCGTGCCCTCGACCGCCTCGGCCTCGGCGCCGATCCG
88456 GC G CCATCCCTCAACACCCTCCGCCTCCGGCGCGTCTTCGACATCTTCGATCAGGACTCCGACGGCCTCATCACCGTCTCCGAGCTCTCCCGTGCCCTCGACC[GC/G]CCTCGGCCTCGGCGCCGATCCGAAGGAGATAGCCCACACCATGTCGTCTTTTATTCGCGATGATAAAAAGGGGCTGGAGTTCGAGG
88456 A T TTTAGTGGTATTGAGGAAGTCAGCGAGGAGGAGGAGGATACGGATATGGAGGAGGCGTTTAGGGTGTTTGATGAGGATGGAGATGGGTACATCTCGGCTA[A/T]GGAGTTGCATACCGTGCTTGGGAAGCTGGGGATGGAGATGAGTATGGGGAAGGTGAAGGACATGATTTTTAGCGTTGATAGT
88456 C T AGGAAGTCAGCGAGGAGGAGGAGGATACGGATATGGAGGAGGCGTTTAGGGTGTTTGATGAGGATGGAGATGGGTACATCTCGGCTAAGGAGTTGCATAC[C/T]GTGCTTGGGAAGCTGGGGATGGAGATGAGTATGGGGAAGGTGAAGGACATGATTTTTAGCGTTGATAGTAATTGTGATGGA
88464 A G TGATTGTTCAAACGAACTAAAAAACAGGCAGAAAGACGCCGCCTTCAACCACCAACCCTTTCTTTGTATGCAAAGGTTTTTCGTCACGACCA[A/G]TAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCA
88464 A G CTTCAACCACCAACCCTTTCTTTGTATGCAAAGGTTTTTCGTCACGACCAATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTT[A/G]AATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGG
88464 A G TCAACCACCAACCCTTTCTTTGTATGCAAAGGTTTTTCGTCACGACCAATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAA[A/G]TTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTT
88464 T C TTCTTTGTATGCAAAGGTTTTTCGTCACGACCAATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAA[T/C]CCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGG
88464 C T CTTTGTATGCAAAGGTTTTTCGTCACGACCAATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATC[C/T]AAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGG
88464 A G TTTGTATGCAAAGGTTTTTCGTCACGACCAATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCC[A/G]AACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGG
88464 G A ATAAGAGAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCA[G/A]GTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTG
88464 T C GAGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGA[T/C]GTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAA
88464 G T AGAATTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGAT[G/T]TTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAA
88464 G C TTTGACTTCTTCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTC[G/C]TTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACT
88464 A C TCGCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTT[A/C]GTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAA
88464 T C GCCCTGCTGTTTAGTATCTTTAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAG[T/C]TGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACA
88464 T G TAGTTTTAAATTCTCCAATCTTAATCCAAACCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGG[T/G]TTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACATATGGTTCAAGTAAGTTCGT
88464 T C CCCACTCATTTTTTGGCAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAG[T/C]CGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACATATGGTTCAAGTAAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATA
88464 C T CAATTTATTCAGGTCGATGTTCGTTTTTGTTTAGTTGCATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGA[C/T]TGCAAAAAACACTTCATATTTAACATATGGTTCAAGTAAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTC
88464 T C CATTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACATATGGTTCAAG[T/C]AAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACC
88464 A T TTTGGTGGTTCCAGGTTTAGTGTAGTTGGTGGGGGAACATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACATATGGTTCAAGTA[A/T]GTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACCCA
88464 A G CATGAGAGTCGTTTTTCATCTTGACTGCAAAAAACACTTCATATTTAACATATGGTTCAAGTAAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATA[A/G]ACGTGTCTCAGTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACCCAGCGCCAGTAAGTGGGATCGTTTCCCCAAGAGATTGCA
88464 A G ACACTTCATATTTAACATATGGTTCAAGTAAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTCTGCAACTTCCACCTTGTT[A/G]TCGTCTTCATGAGGAACCCAGCGCCAGTAAGTGGGATCGTTTCCCCAAGAGATTGCAAGAGCTCTTGCTGGCACGGTACACACCTTAAT
88464 A G AAGTTCGTCTTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACCCAGCGCCAGT[A/G]AGTGGGATCGTTTCCCCAAGAGATTGCAAGAGCTCTTGCTGGCACGGTACACACCTTAATTCCTTGCTTCTTTAGATCATTCTGAAATAT
88464 C T TTGATCTTTCCTTGAACTTCAAGCCAATAAACGTGTCTCAGTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACCCAGCGCCAGTAAGTGGGAT[C/T]GTTTCCCCAAGAGATTGCAAGAGCTCTTGCTGGCACGGTACACACCTTAATTCCTTGCTTCTTTAGATCATTCTGAAATATGACCATTGT
88464 A G GTTCTGCAACTTCCACCTTGTTATCGTCTTCATGAGGAACCCAGCGCCAGTAAGTGGGATCGTTTCCCCAAGAGATTGCAAGAGCTCTTGCTGGCACGGT[A/G]CACACCTTAATTCCTTGCTTCTTTAGATCATTCTGAAATATGACCATTGTTAATTTTGTTGGGGATGGAGCTGATGTTTT
88468 GT G GGGGATGTGTTTAAGTCGAAAGAACATGTGTGGAGGTGGTACGGAGAGATTTCGGAGAGTGAGTCGTGGAAGAAGGTGGTTGGAATGTTTTAGAATTTTT[GT/G]TTTTATCTTATTTTCTCTTGTATCAATTAGATCCCCTTTTGTTTACATCTCCAATGGTTTATGTATGGTTTGCATTTGGCTAACCTT
88474 T G GGCCTCTGCCACGACCACGGCCTCTAAAATCATTGCGACCACTGCCTCTTAAATTACCACGCCCCCCTTGGTAGCCGTTTCCTCTGAAGCCATCATTTCC[T/G]GCTCTGAAACCGTCCGTTCCACCATCGTTTCTTCTAAAATTACCGTTCCCACCAACATTTCTTATAAAATTGTCCCCATTTACGTTTCTTCT
88474 C T TTTCTTATAAAATTGTCCCCATTTACGTTTCTTCTGTAGTTGCTGGGTCCGTTCCTGCCTCTGAAATTGTTGCTTGCTTGTCGGACAACGCCACTTCTAC[C/T]GCTGATGATGGCAACTCCATTCACCACTCGTGTCTTAGTTTTTTTTGCTTCTACAATCAGCTTGTAGTTTCCCATAGTAACTGGCGAGGCCT
88474 A G TTGTTGCTTGCTTGTCGGACAACGCCACTTCTACCGCTGATGATGGCAACTCCATTCACCACTCGTGTCTTAGTTTTTTTTGCTTCTACAATCAGCTTGT[A/G]GTTTCCCATAGTAACTGGCGAGGCCTTGATCGCAGCTTGCATGGATTCAGAGTTGACAAA
88480 T C GATTCGAATTCGAGTTCGAAGCCGAGTCAGATCAGAACCTGCTCCGAGTGCAAAACGACGAAAACCCCCGTTTGGAGAG[T/C]GGGTCCTAACGGACCGAAGTCGCTGTGCAATGCTTGTGGGATCAAGTATAGGAAAAGGAAAAGGGAAGTGAAAGTGAAGGATATAAATAGGAAAGTGATC
88484 T TA GACATGGTGCAGGCCAGAAAGAGGCCAGAAAACACACACCGTGATGGTGTCAAGAAGCTACCACACCCAAAGCAAGAAGAACCAAAACCAAAAGCTGTCG[T/TA]ATCCCACTGATCTGTCCACGACAGGAGCACCAGCAGACGAATCTCGACACAAGAACTGCAATGGAAAATCAGCGTGGTTGCCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
88500 A G AAATCCAAAACAGAAACCTTCATCAACATCCACATCCGACAACAATGAAAATATGAGTTCAATTCTTGAGGAGAAAGGTCCGATTGTCTTTGTGGAAACA[A/G]CGATCGATTTGTTGAGGAAGAAGTGCGGATTGTTCAAGGAAGATGCGGCGAAAAATAGGGTGATCCAAATTGTGAAGGAGGAGTT
88500 G GA AAACAACGATCGATTTGTTGAGGAAGAAGTGCGGATTGTTCAAGGAAGATGCGGCGAAAAATAGGGTGATCCAAATTGTGAAGGAGGAGTTGTTGAAAAA[G/GA]AGAATGAAAAAGAAGAGGCTGAGAAGAGGAGGAAAGAAAAAGGAGCAGAAGAGATGAATAAGAGAGCTAAGAAGGAAGA
88500 GA G ATTTGTTGAGGAAGAAGTGCGGATTGTTCAAGGAAGATGCGGCGAAAAATAGGGTGATCCAAATTGTGAAGGAGGAGTTGTTGAAAAAGAGAATGAAAAA[GA/G]AAGAGGCTGAGAAGAGGAGGAAAGAAAAAGGAGCAGAAGAGATGAATAAGAGAGCTAAGAAGGAAGAGGAGACATCGAA
88510 T C AAGAGGCTGAACAGCAATCTCTCAAAGAGTCGGAAAGGCTGGAAAAAGAGATAGAAGAATGTAGAGAAATGAAGAAAAAGATCAGCACGATGACTGCAGA[T/C]GAATACTTTGAAAAACATCCTGAGCTCAGAAAGAGGTTTGATGATGAAATTAGGAACGATAACTGGGGCTACTAAACTTACAGT
88510 C G AGTCGGAAAGGCTGGAAAAAGAGATAGAAGAATGTAGAGAAATGAAGAAAAAGATCAGCACGATGACTGCAGATGAATACTTTGAAAAACATCCTGAGCT[C/G]AGAAAGAGGTTTGATGATGAAATTAGGAACGATAACTGGGGCTACTAAACTTACAGTTTAGAACACTCAAATTTCCTTT
88516 T C TGGGATGAAGGTGTTTTGGACATGCAAATTGGAGAAGTTGCAAGACTCGAGTGCACCCCTGACTATGCTTATGGAGCTAGTGGATTTGCAGCATGGGGAA[T/C]TCAACCCAATTCTGTTTTGGTCTTCGAGATCGAAGTCCTCAGCGCGCAGTAGTTGCGTATGCATACGATATAACAAAAATGTCTTTA
88516 A T GAGATCGAAGTCCTCAGCGCGCAGTAGTTGCGTATGCATACGATATAACAAAAATGTCTTTAAGAATCTACAGGTGCTTTTGTTATTACAACTGAAATAA[A/T]AATGTTCCATGAATGGTGACCTTGCGCTTGATTGACATGTTTTGTATGTGGACTTGAACAAA
88524 GT G ATGTGTAAAAATGACTCAATATCAACTTAACGTATTAAAAATTGTTAAGGATATCTTATACGAATCTATTCAGCTGGCTTTTCTTAGTGTTTACATGATG[GT/G]TTTTTTTGCAAGCAACCAGTAACTGATATCACAAATTATAGCCTGGACCATGTTTAGCTTATCATTTGATTCATATTTTTCATCCCTGGG
88524 TGC T AACTGATATCACAAATTATAGCCTGGACCATGTTTAGCTTATCATTTGATTCATATTTTTCATCCCTGGGTCTACCTTCAATTGGCTTAAAACCATATAA[TGC/T]GCGTGTATTGGTCGTTTTGTGAAAAGCTGACTTTGCAATACAACAAGGATGCAGTAAAAGAAGTTAAGCATACGGTCAGAAAAACAA
88536 T C CTCCACTATCAAATGTTAGTCCTTTCCCAACAATCGCTATCTTTGTTTTCACATCACCATTTGGTGGTCGATAACACAGATGAATGAAATGAGGAGGATT[T/C]GATGAAGCAGCAGCAACACCTAAATATGAACCCATATTCAATTCCGTGCACTGCTTTTCATCTAATATTTTAGCAGTGAAAACATCACTA
88536 A C CTATCTTTGTTTTCACATCACCATTTGGTGGTCGATAACACAGATGAATGAAATGAGGAGGATTTGATGAAGCAGCAGCAACACCTAAATATGAACCCAT[A/C]TTCAATTCCGTGCACTGCTTTTCATCTAATATTTTAGCAGTGAAAACATCACTATACATTGAAGCAACTTTTGAAGCCTCTTCTGCTAG
88568 A T GTCGAACTGCGCCTTGGAAACACACAATAGAAGGTCCAGATGACATGCCAGCACATATTAAGTCATCTATGTTTGGATGTGCCCTTAGTGTTCCCATTAC[A/T]GATGGCCGGCTCAATATGGGAACTTGGCAGGGTATATGGCTATGTGAGCATCGTGACCATGCGACCCCGCGTAAAGTTGTAGTCAC
88572 G C GTACAGAAGCAAAAATTAACAAACTCCAAAAGCAAAACAAATTAATAAACTGGAGGAAATTCAAACAGTGAACCCAATCCAAATAGAGCTCCAACATGTC[G/C]AGGTGCGTTAGCTGCACCAACAAGTTTCTTCTTCATGATGAACTCCATGGCTGTTAAGGCAATAAGCAAACAGTCCGATCCCGCCTG
88572 G C GAAGCAAAAATTAACAAACTCCAAAAGCAAAACAAATTAATAAACTGGAGGAAATTCAAACAGTGAACCCAATCCAAATAGAGCTCCAACATGTCGAGGT[G/C]CGTTAGCTGCACCAACAAGTTTCTTCTTCATGATGAACTCCATGGCTGTTAAGGCAATAAGCAAACAGTCCGATCCCGCCTGATGAG
88574 CG C ATATAAATTTCTAAACGACCAAAGCCATGACCATGGCCAATACTCCAACCGCTGCCTTCACATGAAAACCTTCAGCTCCCGATGATCCAGAAGGAGGAGG[CG/C]GGGGGCGGCGATGGAGTGGTTCCTGCTGGACCATCAGCAGGAGTAGAAGGAGATGTGTTTGAACCATCAACCGTATCGATCTCG
88588 T C TGTTGGCCTACTGGAGATATTTTGTAATCTTCCCAAAAATTACGATACCATCACATATATATTAAGCGGTTAACCCCCGTTGTTGGATC[T/C]AGCCATGGACGGCGACAGATCCGGATCCGATAACACCTGTTTCTACTCTCTCCTTAACATCCGCCCTGACTCCTCCCAGTCTGACATCCGTGCCGCTTAC
88588 G A TGTTGGCCTACTGGAGATATTTTGTAATCTTCCCAAAAATTACGATACCATCACATATATATTAAGCGGTTAACCCCCGTTGTTGGATCTAGCCATG[G/A]ACGGCGACAGATCCGGATCCGATAACACCTGTTTCTACTCTCTCCTTAACATCCGCCCTGACTCCTCCCAGTCTGACATCCGTGCCGCTTACC
88588 C T GGGAATTCATGAAGGATTTTATGAGTGCTGTGGAACGGGTGAAGTCAGAGCCTGTGAAGAGCTTTGAGGAAATACAGCAGATGTTTGATGATTTAGTGAG[C/T]GGAATGGGGATGGATTTCAATGGCAACGGGTACTCGGAGCAGCAACCCGATATGGGGAAGAGGACCAGAGTCAGTTGAT
88618 G A CTGTGAAAGAAATTCTTGTCGCTGATCCCAAATCAGGTGTTGTTGTACTTGATATCGGGATGGCTCAGAAGCAACTTTCTGCTTCGATTTTTGAAAATCC[G/A]CCTGATTGTGAAGGAGGCAATTTCATACATCAAGTCGGATTTGAAGATCAACGGCGGAAGATTAACCTAAAGTAACGTGCAATATTTA
88618 C T TTCTGCTTCGATTTTTGAAAATCCGCCTGATTGTGAAGGAGGCAATTTCATACATCAAGTCGGATTTGAAGATCAACGGCGGAAGATTAACCTAAAGTAA[C/T]GTGCAATATTTAAGCATTCTTCCGGTGTGCTTTCTGTGTTTTTTCAGTGTTGATACTTCATATGAATTTTATATCTTGTAAATTGCTGTG
88620 GA G ACAATCTCTGTAACAATACTCTGGTTCCTGCTCAAAATTGCTCTATACTGACCCTATCTTCAACTTTAATCCCAGTACGTGAAATTAGTGGATCAGAAGG[GA/G]AAAAACGTAAACCCAGTGCAAAGTGACTAGTGGTGTTGTCTTCGAGGCGTTAAACGGGTTCGTAGACTGGTAGATATGAACATAGG
88622 C T GCAGGGCTCCACGTCACCGCCACATGCGGTTCCCGCAACATGGACTTTGTCAAAAGCTTGGGAGCGGACGAGGTGCTGGACTACAAAACCGAAGCCGGCG[C/T]GAGCCTCAAAAGTCCCTCTGGCAAAAAGTACGATGCGGTCGTGCACTGCACCATAGGCATTCCATGGTCGACTTTCGAGCCAAAT
88622 T A GCAAAAAGTACGATGCGGTCGTGCACTGCACCATAGGCATTCCATGGTCGACTTTCGAGCCAAATCTAAGCGACAGTGGGAAGGTGATAGATTTGACTCC[T/A]GCGAGTGCAACGTTTGCTAGATGGGTGGTTAAGAAGATGACCTTTGCTAAGAAGCAGATTGTGCCGTTGCTTGCTGTGCCGAAGA
88622 AT A GGAAGGCAAGATGAAGACGGTTGTGGACTCAACGTACGAGTTTGGTAAGGCCGAGGAGGCTTGGGCTAAAATCATGGAAGGGCATGCCACTGGAAAGATT[AT/A]TTGTTCAGATGTAAGCAGCGCCTATTCATATTTAACAATGTGTCAGTTCGTTGTTTGTTTGTTTGATGTAAATACGACTT
88642 T C AGAGCAATCCGAACCAGTGTAGCAGTTGTTACATTCACAAAGATGAATACCTTTAGTAGAAACTGTTCCATCAAGATAAGCTCTGCCGTGGCCTGAACAG[T/C]GTAGATTAGCTATCTTCTCCGCCTCTTCTGCAACTATAGCCGTCCATGTTGGCACGAACCTAAGGTAAACCTTCTTGATGAATATGGT
88642 T C TTCTGCAACTATAGCCGTCCATGTTGGCACGAACCTAAGGTAAACCTTCTTGATGAATATGGTTGCAAGGAACAATATTGCTGCTGTTAGCATCAGCAGT[T/C]TTTTATTCTTGCTGTACAGCTCCTCGGCTCGCCTCGCTGGATGCCTTGCTGATTTTCGCGGCCGTTTTGTCTTCCAGTAGGCCAACA
88642 T A TGGCACGAACCTAAGGTAAACCTTCTTGATGAATATGGTTGCAAGGAACAATATTGCTGCTGTTAGCATCAGCAGTTTTTTATTCTTGCTGTACAGCTCC[T/A]CGGCTCGCCTCGCTGGATGCCTTGCTGATTTTCGCGGCCGTTTTGTCTTCCAGTAGGCCAACA
88650 C A CACCGTCAGGGCTGTGTCTGAAGTGGAAGCGTTCTCACTTGTGGCAGATGACTTGGTGTTCGTGGCTGCGCAGTTTAGGAGGCTGCATAGCAAGAGGATC[C/A]GGCATAAGTTCAGGTTTTATTCCCAGCACTGGAGGACATGGGCCGCTTGTTTTATACAAGCGGCTTGGAGAAGGCATTGGCAGAG
88682 G T CTTGAAAGCTAGCTTCGTGTTAGTGGATTTCGAATCATGGGGTTATGTTCATTTTTCTATTCACGTGACTCTGTATAAATAGAGTGCTGCTAGTTCATTC[G/T]TTGTTGCAAGTCATTTTTGACACTTCTAAGAGTCATAAAGATGAGTTATGGAAGCAGCTCTATTGGTTCTGGTGCTAGAAGTGCTAAGG
88682 A G GGCTTCATGGTTTAGGAGACAATGGATCAAGTTGGTCTCAGCTCTTGGAAACACTTCCGCTTCAAAATATAAAATGGATTTGCCCCACTGCTCCGTCTAG[A/G]CCAGTTGCCATTTTCGGGGGATTCCCTTGCACTGCTTGGTTCGATGTTAAAGAACTTTCAGAAGAGGGCCCTGATGACGTGGAAGGA
88702 C T CCCTTTACTTGCATGGTTTTTTTGCTTGTATTTCCATCTAAAGGTAGAATCTTTCGACAGATTGCTTCAAAGATCGCCAATATTTGAATCTTGTTCATAG[C/T]CACAGATACATATTCAATCAACCAGCTTGTGTTTGCTGTAAAGATTGGATCTTTTATAACAAAAACCATGAAGGATTTCCCTTCCTGTTTCG
88738 C T CCTGAACTATGCGCCACTTTATGTATCCTGTATTGCATTAGGACTTGTGAGCGAGTACGCTTTATTTTTATTTTGACTGTTTGTGCGAAATTTAAATAAG[C/T]AGTTGCCATACTGGTAAATATAATCTGTTGAGATATTGTTCGTTCCTGGAGTTCCATGTTTCCATCTATA
88742 A C CAATGCAGGCTTGGACAGCTTCCGTCATTGATCGACCCCACTTTTTGTTCATTCGAGAGTCAGTAACCGCATATAGAAACAGATAGTCAGCACCGAACGT[A/C]GATATGTTTCCTGAATAGTGTCTGTGGATTCTTAGACTGAAAAGATGGTCAAATGGTCCTTGTGGTCCGTTCCCAATTACTATGTCTT
88742 G A AATGCAGGCTTGGACAGCTTCCGTCATTGATCGACCCCACTTTTTGTTCATTCGAGAGTCAGTAACCGCATATAGAAACAGATAGTCAGCACCGAACGTA[G/A]ATATGTTTCCTGAATAGTGTCTGTGGATTCTTAGACTGAAAAGATGGTCAAATGGTCCTTGTGGTCCGTTCCCAATTACTATGTCTTT
88742 A C GCAGGCTTGGACAGCTTCCGTCATTGATCGACCCCACTTTTTGTTCATTCGAGAGTCAGTAACCGCATATAGAAACAGATAGTCAGCACCGAACGTAGAT[A/C]TGTTTCCTGAATAGTGTCTGTGGATTCTTAGACTGAAAAGATGGTCAAATGGTCCTTGTGGTCCGTTCCCAATTACTATGTCTTTACTA
88742 T C GTCCGTTCCCAATTACTATGTCTTTACTAAAATTGAGTGCTTCTTCAACATATCTTTTAGCCACCTGCACTGCTTGAAGAATGGAAGAACCTTTCGCTAG[T/C]TCCGCAGCTATAGAAGAAGCCAAAGTACAACCTGTTCCATGTGTATTACGAGTTGTGATGCGGGACCCTCTGATCTCGTGGAATTGCTC
88742 T C GTGTATTACGAGTTGTGATGCGGGACCCTCTGATCTCGTGGAATTGCTCTCCATCAAAAAGAATATCTATTGCATCTAATGAATTTGGAAGGTCACCGCC[T/C]TTCACAAGCACATTCCTGGGACCAAAACCATGTATTGCTTTCGCTGCAGAGCACATGTCAGCTACAGTATTCATTGATGTTCCTCCGAG
88760 AT A GATGCCTTCATGGGCCCGCTCAAGAAGCACCAGACCAAGGAGACTGCTTAAAGTCTGCCTGCTGCCGTCAGCCAGTGAAGAAAACATTAGAGACTGGGTT[AT/A]TTGTTGAATTTAAAAACTTTTGGAAGAGTTAAAAACTGATCCATTTGTTGCTGGCTTGGTAATTGTGTGAAAATAAATATTGTTCA
88798 A G CTCTTGCTAACGCCGTCAATATGCTCCGTTACTTCCTTCTCCTCCTCTCCATCTCCCTCCTCCTCTCCCCCTTGGTTCACGGTGGGCAATCGGAAGATAA[A/G]GAGGACCTTTTCATCCGTCAAGTCACCGATCAAAGTCAGAACGATATAACCCTAGACGCCGAGTACCACCACTTCGCCAAGTTTATCGAG
88798 G A TTGCTAACGCCGTCAATATGCTCCGTTACTTCCTTCTCCTCCTCTCCATCTCCCTCCTCCTCTCCCCCTTGGTTCACGGTGGGCAATCGGAAGATAAAGA[G/A]GACCTTTTCATCCGTCAAGTCACCGATCAAAGTCAGAACGATATAACCCTAGACGCCGAGTACCACCACTTCGCCAAGTTTATCGAGAA
88798 T C TAACCCTAGACGCCGAGTACCACCACTTCGCCAAGTTTATCGAGAAGTTCAAGAAGTCGTATAGGAGTGTGGAAGAACATGCTCATAGGTTCGGTGTGTT[T/C]AAGGCGAACTTGAGAAGGGCGAGGAGGCACCAGGTGCTGGATCCAGGTGCGGAACATGGAGTCACGCAGTTCTCGGATCTGACA
88812 A G CCGTATCTGCAACAGCAGGAGATGCGGTAGCTTCTGCTGGAGCAGCACCTTCAATTTTAACTCCTTTCCCCTCCTCAGTCACGCCACTGATTCTAATGAG[A/G]GCATCAATGTGTTTGAACCATCTAGCAACATTGACATGGTCGGACGAAGGCAATGAATGAAACGCTGAATAAACAGCCAAGTCATCC
88818 A G TCTTCATGTCGTCGTACGACACGAGCTTCTCCTTCGCCCAGAATACGGAGCCGGTCGAGTCGGGTGGGCCTGCGCAGTATCGAACGCAACCCGGTGCCCC[A/G]TCCGTGCCGTCTATCTTTTGACACGTGGACAATGATGGAAGAAACTTGTGGAGGCTGCAGAAATCTTTCAGGTGCGACCATGCTTC
88822 T A CAAAAAAGCCATATGTCCCAAAAAATAAAAATCTCATAAACAAAACCGCATTTTAACATCTAAGCAGAGCAACAAGACCTCTTGGCACCGCCACTCTCAG[T/A]AACATCAATAGTCGTCCCTTTAAGCACAGTCGTGGCGCTACCGGCCGCCTCCTGCGCCGCGAGCGCCTTCCTATTGACAATCTGATAG
88822 A G TCTCAGTAACATCAATAGTCGTCCCTTTAAGCACAGTCGTGGCGCTACCGGCCGCCTCCTGCGCCGCGAGCGCCTTCCTATTGACAATCTGATAGATCTC[A/G]TGCAGAACGGTCTGGAAGGCATTCTCAATGTTGAGCGCCTCCAGAGCGGAAGTTTCCAGAAAAGAGAGCCCTTCCTTCTCGGCGAAG
88822 A G GAGCGGAAGTTTCCAGAAAAGAGAGCCCTTCCTTCTCGGCGAAGAGCTGAGCGTCTTCGGGGGAGACGGAGCGTAGATGGTTGAGGTCGGACTTGTTGCC[A/G]ATCATCATGATCACTATGTTGGAGTCCGCGTGATCGCGCAGCTCCCTCAGCCACCTCTGCACATTCTCGAAAGTTTGGGTCTTTG
88830 T C TGTTTGGTCAACAAAGATGGATGATTTAGGTGGTCGTGATTGTAGAAAAGCATCACGCATTTTTGAAAGTTTGGACGATCTTTCTATTGACTTAGCAGAA[T/C]ATGTCTCAGAAATCTCGGAGATCTCAGTAAAAGAAAGAGGAGTTTTTACGATTGCTATAACTGGAGGCTTACTTATCAGCTTGTTGAG
88830 G A CTTATCAGCTTGTTGAGGAAACTTTGTGAAGCTCCTTACAACAAGATTGTGGATTGGACAAAATGGTATGTTTTTTGGGCTGATGAGCGTGCAGTAGCGA[G/A]GAATCATAGAGACAGCAACTATAAGATGGCGAAGGATACGTTTATTTCCCAGCTACCAATTCTGAGCAGCCATGTGTATGCGATCA
88832 G C CCCATTGAACGAGCTCTTTTGAACCAATGTTGCGAATTGATGATCAATTGTAACGCCATAAATATCTACCAATGTCAAGACCTGGGTAGTACAGTA[G/C]GTAGATAGCGGAAGCCATTGAGGAGTTTGAAGTGAGACAAGGGTAGCTTTTCATTCTGCTGTGGAATATGAGCTCGAGTGTGAACTGGTT
88850 A G CAGTAATTCCCAAACTTCAGCCCTTAACTTACTAAAACAAGCCGATGCAAGACCTAACCCCGCAATCGCCGCGATTCTTTTTCTCGAACGCCGCCGCTTC[A/G]GCTCCATCCAACGCCTCCCACCGTCGCATCGCGATCGCCGTTGATCTCTCCGACGAATCGGCATACGCCGTGAGATGGGCCGTCCTGA
88860 T C CTCCTTTAATGGGTACTCCTTAATGCTGTCCGGATGCTCCGTTAAAGCCTGAACCAAGGCCCAGGTTGCCTGAATTTGAAGAGGGTAGTGGGAGCCAGCT[T/C]GACTTTGATGGCAGCTAGATTTGAACATGGACTCTGGATTTGTTTGAATGTCTCGTTTAAATATCCAATTAAATGTCTTGTTACCGTT
88870 T C AAATTAAGTTCAAGGCTTTTGATCTCGGAGGACACCAGATTGCCCGACGTGTCTGGAAAGATTACTATGCTAAGGTTGATGCAGTTGTGTACTTAGTTGA[T/C]GCGTTCGACAAGGAAAGATTTGCTGAGTCAAAGAAAGAGCTCGATGCACTTCTTTCTGATGAATCACTGGCGACCGTCCCATTCCTC
88870 C T TCGATATCACATATGCTGCATCTGAAGAAGAACTCCGATACCACCTCGGACTCAGCAATTTCACTACTGGAAAGGGCAAAGTCAACCTGACCGATTCCAA[C/T]GTGCGTCCTCTTGAAGTTTTCATGTGCAGCATCGTTCGGAAAATGGGCTATGGAGATGGGTTCAAATGGATGTCACAGTATATTAAG
88878 GA G CTGTTGGCCTACTGGATGATTAATTGATGCTCCCATCTCTCTTCCCTCTTTCATTTCTCTCCTCCCAACCTCAAAACTAAAGGAAAACCTCCATTAC[GA/G]AAAAAACTAAAAATCCTATAGTAACTAGTTTAAGATGAAACGAGAGCATGGAGATAGCAGCAGCGGCCCACCGCCGCCGTCGAAGAACGG
88896 G A CACAAATCTTAAGGCGAGGTGCAGTACTTCCATCCAATAGAGTGTTTTCAAGTTTTAAGTCGCGGTGACAAACTTGCATGGAGTGGCAGTAGCTAACACC[G/A]GATATAAGTTGTTGAAAAAAGAAACGAGCCTCATCTTCACTGAATTTACCAGCATTACAAATACGCTCGAAAAGCTCACCCCCGGAA
88896 G A GGCAGTAGCTAACACCGGATATAAGTTGTTGAAAAAAGAAACGAGCCTCATCTTCACTGAATTTACCAGCATTACAAATACGCTCGAAAAGCTCACCCCC[G/A]GAAGCATACTCCATAACAATTGCAAGATGTGTTGGAGTTAAAATAACCTCCTTGAATCTAATAATATTCGGATGCCTTAATGACCTGT
88900 T C ACTTCTGTCAATTCAACACTCTGTGATGGTGTCTGCCAGCTTAAGTCATCTCTTTTGGAAGGGTTATTTGTGGCAATAGTGTTGCTTATAATATTGATAT[T/C]GGGACTCTGCTGCATGATGGGAATAGACACACCTACAAGATTTGAGGCTCCTCAAGAATCATAATTTGCTCTTCAAGTAAAATGAGTTT
88908 TC T GAGGCTACTGTCTCTGTTCCTCCAAACATTACGTCCATGATAATAGCCTTGATATGATTTCTGGTAAGCCTCAACTCATCAGAATCCTTACCGGAGCCCT[TC/T]CCCCTCCCCAACAAACGCCAGCATCTCATCCACCATGTCGGCGTCCAAATCATCCACCTCCTTCCTATTCTCGACATGCTCATCTATTAT
88908 A C TTGATATGATTTCTGGTAAGCCTCAACTCATCAGAATCCTTACCGGAGCCCTTCCCCTCCCCAACAAACGCCAGCATCTCATCCACCATGTCGGCGTCCA[A/C]ATCATCCACCTCCTTCCTATTCTCGACATGCTCATCTATTATCCTATCAATAAACCCATCCAGCTCCTTCCTCACCTTCCTCATCCTTCTTCC
88908 C T CTCCCCAACAAACGCCAGCATCTCATCCACCATGTCGGCGTCCAAATCATCCACCTCCTTCCTATTCTCGACATGCTCATCTATTATCCTATCAATAAAC[C/T]CATCCAGCTCCTTCCTCACCTTCCTCATCCTTCTTCCTATCCCCTGCGGATCCAAATACCTCAAACCCGGTATGAAGTCCGCAACATTGAAT
88920 CA C ATAATGTTCCTGCCCATAATTATGGCATAATCGCCACGGATAGTACCAGGGGCAGATTCAGCTGGATTGGTCGCACCAATGATTTTACGACCTGTCAAAA[CA/C]AACATTCTTTCCTTCCCAGACCATAGCAACAACTGGGCCAGAGATGATGTACTCGACTAGTTTGCCAAAGAAGGGCTTTTCCGATAA
88920 A G CGACCTGTCAAAACAACATTCTTTCCTTCCCAGACCATAGCAACAACTGGGCCAGAGATGATGTACTCGACTAGTTTGCCAAAGAAGGGCTTTTCCGATA[A/G]ATCCTCGTAGTGCTTCTCAGCAAATGATCGTTCCACAGTTATAAGTTTCATTGCTTTCAAATAAAACCCCTTTTTCTCAAACCGGCCAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
88922 CAT C CTTCCTATTTACCAAATTTTTATTACAGTTCATGACGTTTTTATGCAAGGAACTTATGATTTAGTTTTCAGCATTTTTGTTCAGAGAGATTTTGATGCAT[CAT/C]ATAGACTCAATAGTCCTGTTCCTCCTTTCCAGCTTTTCAGTTGTATTATTTGCAATCAGTGGCTCTGTACAAGTTTAAATGTGGTTCTATT
88938 G A TTCATTGATGTTCCTCCGAGTAAAGCAGATGCTTCTTTCAAATTAGGCGTCACAATATCAGCCATCTGAAAAAGTTCTTCCTGATATCC[G/A]GATAGGGTAGAAGAAGCTGAAAGCAAATGTCCACTAGTTGACACCATGACAGGATCAACCACTAAAGCTCGTACAGGGAACTCTCTGAGGCTGTTGCA
88938 C T TCGATATGCATATCAGAAAGCACTGACCTCAATTGCTCCTTCACCAGTTCCTCAGACACCATTTCCCATTTCTGAACCCCCACAGTGTTTTGTGCAGTGA[C/T]GGCGGTTATGACGGAGGAGCAGTATGCGCCGTGAGCCCCACACGCTTTAATGTCAGCTTGTATTCCCGCTCCGCCGCCGGAATCTGAT
88942 TA T GTTTTTTTTTTTTTTCAAACATAATCGACTAAAGTACAAAACCAAAATAGTAATCAACAAGCAACCAAACCTGTGCTTACATATACGCTTGCGTAAATT[TA/T]AAGTAAAACAGTACCCGAAGCATTTAATGTCTTTGAACCAACGGCCCTGACCACGCCACGTGTCCATCATCTAATGAATCAGTATCCAAA
88942 T C AACCAACGGCCCTGACCACGCCACGTGTCCATCATCTAATGAATCAGTATCCAAATCGACATCACCACCCCACGACGACGGTCGCCTCACCGACGTAAAC[T/C]TCCTCATCCCTCCCAACCCTGGCGGATCCACCTTCTCCGGTCCCCTCCTGCTTGACGGAATATTCGTTTCTTTCACCGCCGGAATATTC
88944 T C TTGGCAGTTATGGACCAGCCACACCATTGCGGATAGAATGTTAGCCTTTGTTGGGATCCGATAAGGATCCGACGTCCCTTCAGTAAGAACAAGAATACAC[T/C]CATCGGGAAACCCGAACTTCGTGGTAAGTAAATATTTCATGCAATTCACATCATTCACAGTCCCCTTCAGCTCATAACTCCTTCCGGT
88944 T C ACTCGTGGGTAGCTATCAGGGAAACTCAGGCTGCCTTGTTCAGGTAAGGCATATGATGATGAAGGCATCTTATCTGTAATAACACTCCGTACCCACCCAG[T/C]CACGCTTCTGAATAGACTGTGGGTCTGGGTGACACCACGGCACACCGGACATCGCACTGTCCAGGATAGTCTATGAACCTGCAGGC
88944 C T TTCAGGTAAGGCATATGATGATGAAGGCATCTTATCTGTAATAACACTCCGTACCCACCCAGTCACGCTTCTGAATAGACTGTGGGTCTGGGTGACACCA[C/T]GGCACACCGGACATCGCACTGTCCAGGATAGTCTATGAACCTGCAGGCTTATGCCACAATTGCTGCATCTCAAAGTTTTGCTGCAAC
88948 GA G GGTTGCGACTTCTGCTGAAGCTTGTGTGCTTATATATAGGTATAAGCCTTGTCCTCTAAGTAATGAGACATATAGGGATGTACAGGCTAAGATGGGTCAT[GA/G]AATTGATGGAGAAAATTCACATCTGAAAGGGAAAGAGAAAGATATAGCCCTTGAAAAAGTCCATCAATACAGTGTAGGCAAGGC
88948 G GT ATATATAGGTATAAGCCTTGTCCTCTAAGTAATGAGACATATAGGGATGTACAGGCTAAGATGGGTCATGAATTGATGGAGAAAATTCACATCTGAAAGG[G/GT]AAAGAGAAAGATATAGCCCTTGAAAAAGTCCATCAATACAGTGTAGGCAAGGCATGTATTCAGTTATCATTTCAAACATAGGTCA
88970 T C CTACTGGATCAAGCAGCTCATCTACACTTCTGCTCTTTCAAATCGATCAAATCGAAATGGCTCCCCAATACAACTCCAGACTCCCAGCTGGCAGCCGTGT[T/C]GTTATCAGGAACGACCAGGCCAACACCGCGATTGAAATGCTCGAGAATACTCAGGTCGTCTGCAACAATACCACTCGAAACACCAGTC
88974 A AC CCACCCTATCTCCGCTAACCCTAAATCCCTAATTCCTTCTTCCACCAACTCGCACACACTCAAAACTTCATTGGCAGTCCGCTCTGAACTCACCACCGCC[A/AC]CCTCCCTATTCTCAACTTCTCCGGCGAAACCCTTCCCAACACCGTGACCCTAACCCTGTTCTCCGCGCCTCCATCTACCGCTCGCGCTATT
88976 G A AACAGAGACGCACGACCCCTCCATTCTGTGGACGAGCGACCCCTCTATGTAATGTACGACCCGAAAAGGTGGAGGCACCTCGTGACCGAGCAGCGCCAAG[G/A]CCGACCTGGTGGGGGCATCTCGTAACCGAGCAGGTGGTGCTTCTCTCGACCGAGCAGGCAAAAGCTGTTCGACGAAATGCTTGA
88976 T A ACGCACGACCCCTCCATTCTGTGGACGAGCGACCCCTCTATGTAATGTACGACCCGAAAAGGTGGAGGCACCTCGTGACCGAGCAGCGCCAAGGCCGACC[T/A]GGTGGGGGCATCTCGTAACCGAGCAGGTGGTGCTTCTCTCGACCGAGCAGGCAAAAGCTGTTCGACGAAATGCTTGAATGAGAT
88978 T C CGGCGTTGTACAGTGCGGTGAATATAAGAGTGGTAGACAAATCGAGATGGTTGACTAAAGAAAGTGCGAGCACGATCGGGATGTAGGTTCCCAAGTCTCC[T/C]ACCGAGCCTGACAGCTCCGACCATATCGATGTCTGGAGGCGGAACGGAGTGAAATAGGATGGTTGTTGACGGGGTTGAGTGGC
88980 A G TCAAAATCAACTACTTCTTCCCATTTCTCAGACATTATGTAATCCAACAGTACGGCATTTGCAGATGGCTCTTTCAAAGTCAGCTGGTTAGTCCCATCTG[A/G]TCCAGACTGGCGCCAATTCTTTGATGAATCCCTTGAATAGAGCTGCACCACCGGATCTCGTCCCTTCTTATTTGGAAGCTCCTCTAAATT
88994 C T GGGCGTCGGAGGAAGAAGGCTAGAAACCCCCGTTGGACCCTACCTAAGTACTAGTACTAGGCACAGGATCAGAGAAATTGGCCGGTAACCGCCAGCCGAA[C/T]TCTAGTGCAATTGGACATTATCCTGACAATACCCCAGGATGCGTCCCAATTGTCACGATCCGCAAGAGGAACTACGTAACCGGCA
88994 G A CAATTGGACATTATCCTGACAATACCCCAGGATGCGTCCCAATTGTCACGATCCGCAAGAGGAACTACGTAACCGGCAGATGCGCGAGAAATTGTATCGC[G/A]AGCGATACCAGTGACTCTCCAGGCGTCATTAGTGCCGGACCTAACACCAGGGTCTAATATGATCGAAGAATATTCTCGATCGCTTG
88994 C T ATTCTCGATCGCTTGGCAACGTGATGGTGTAGGCACGTACAGAGTGGACGATCAGTCGGGTATAACCACTTGTTCCAGCATCTGCAGTAAGAACTGCTGA[C/T]GCAAGGACTGTTTTCCACGCGTTAGCCACAGTGTCAATGTCAACATAGACAGTGCGGGTGACTTGAACGTGGGACGGCTCACCTTG
89004 T A CCAGCTCCAACATCACCTTGAATTTTCCATCTTCTAACGGCGCCTCTCCTTTCTGTACTATCTTTGGTTTTGCTTTTCCCTCCATAAACATCGCACCATT[T/A]CCTGATTGCCCTTTGGCTGCGATTATCTGTTCATATCCCTCCAATTTCATTTCGAAGAAGAAAGGTATGCAATACCAAATACAAGTAGTTAG
89028 A G GAGGCAAAATGGCTGGTCCTTTCCAGGAAGTTGCATTTAACACGCCTGTTGGTGCAACCAGTGCACCTTTCAAATCCACCCATGGCTATCATATCATCTT[A/G]TCCGAGGGCCGGAAAAATTAAGTTGATGCTTCCATTCAACACTATTTACATGTTGTGCATGCTTTCATGAAAGGGAAAAAAAC
89032 C A ATTACCAAGGCGGACAGAGATTGGAGCGTAGTGATACAACTCACCGCTCTTGCTGAACAGTACAAGTGCAAGCCTTGCAAGATGTTTGCACCTTCATTTG[C/A]GTCTGTTGCTCAGGCGTGGACGAAAACTCCCCAAAAACAACGTGATGCGCATTTCTTTGCCACTTTGGATTTTGCGGATGGCCAAGA
89036 GT G CAAGTCGACAACTGACAATCTGCTAGTCGAGATTCATGCGTAAAGGGAGCTACACAGACAATTTTTTACAGAATGTGGCACTTAATTTCATTCTAGCGGG[GT/G]TCGGGACACATCGTCCGTGGCCCTTTCGTGGTTCTTCTGGCTGGTACTGAACAACCCTAGTCGTAGAACATAATATTGTGGCTGAG
89046 T C CCTACTGGAGATTTATCCTTTTATCTCAAACCTCAGAGACGCATTCTCCTCATCTTTCCTATTCTCCTACACCCACAATGGCCACATCCTCCTTTCGCCT[T/C]CTATTCCCGCCAAAATCACCCCCACACCTGCCGTCCTGCCAAAAAGGGATCCGCATCCTCAACTGCTCCGCAAACCCAACAAACGCCTCTC
89046 AC A CCTCTCTCGAATCCGAATCTGGCACCTCCTCCCTAGACTTGGAAACACAGAAAAAGCTCTCCCTTCTTAAAGAGCAGCAAACCTCCATAACCCAAAAGGA[AC/A]CCCCCCAACTTCGAGATCGGGTGGAAAAGGACCAAACCCGTTAACCCGCCAAAACCCAAAGGGTGGCAAATCGCCGACTACATCGA
89064 T C TACCAGAGCCACCGAGTGGATTTATAGGGACGCCAGAAATATTCGACGGAGGAGTAAACGCCATTAGAAGAGCTGTCATCATTGGAAATGGATTTGCCGG[T/C]GCTGAGAACCAGAGCATTGGTTTGGTCCGCGCTCTAGGACTTGCTAATAGTCATTCAGTTTATCGAGTGATCAGACCAAGAGGAG
89070 A C ATGGATACATAACTGTCTCACTCGTGGGACGAATTGCAATTGGAATTTCCATTTCACTTTGTCCTGATTTTGTAACCCATGCAACCTCTGGGGCAAAACC[A/C]TCAATATGATCTTTCTCCTTTTGCAGAACAGTTTCAGTAACAAACAGAGGGAAGTAACAATTTTTCACCTTCAACTTCTTTATCTCAGCA
89070 A T TGCAGAACAGTTTCAGTAACAAACAGAGGGAAGTAACAATTTTTCACCTTCAACTTCTTTATCTCAGCATCAAAGAACATTTGCATAGTTTCCCAAATTG[A/T]CATTGTCCATGGCCTAAGAATATAGCAGCCCGAGATGTCGTAGTACTCGATCATCTCGCCGTTGACCACAACCTCTGAATACCATTCAC
89070 T C CACCTTCAACTTCTTTATCTCAGCATCAAAGAACATTTGCATAGTTTCCCAAATTGACATTGTCCATGGCCTAAGAATATAGCAGCCCGAGATGTCGTAG[T/C]ACTCGATCATCTCGCCGTTGACCACAACCTCTGAATACCATTCACCAAAATTCTCATCCTTCTTATATGTAAGTCCTAGACCAGTCTCCTT
89070 C T TTCCCAAATTGACATTGTCCATGGCCTAAGAATATAGCAGCCCGAGATGTCGTAGTACTCGATCATCTCGCCGTTGACCACAACCTCTGAATACCATTCA[C/T]CAAAATTCTCATCCTTCTTATATGTAAGTCCTAGACCAGTCTCCTTCTTCACTTCCTTCTTTTTTGAATTTTTCGAAGCCATGTCACTCTTT
89076 G A TGTCAAAGTCACCCCCTTGAATCATGAAATCCTGGATGACTCGATGGAATGCAGACCCCTTGTACCCAAATCCTTTTTCACCTGTACAGAGGGCTCGGAA[G/A]TTTTCTGCAGTTTGAGGCACGTCATCCCCAAAAAGTCCTATTACTATTCTACCAACTGGATTCCCCATTGGGTTTCCAATGCTTATATCA
89076 A C TAGCCTGAACTTCTGGTTCCTGCAACGCAGCTCGAATAGATGTGGCTAATCGGGTTTGGATCCGATAAGGAGGTGACTGGGCAAAAGAAGTCGACGATAG[A/C]GAACTAGAGGATAGGGAGGGGATATTGTTGGCAGATCGATGGCATTTAGAAAAGTTTGTGGCTGAGCAAGACCGACGAGATTG
89110 A G CTTGACTAAGGGAAATATTAGAACTGCAATTGATACTGGGTGTGGTGTTGCAAGTTGGGGAGCTTACCTTCTAAAAAGGGATATAGTGACAATGTCATTC[A/G]CTCCAAGAGATACACACGAGGCGCAAGTGCAATTTGCACTAGAAAGAGGTGTTCCAGCCATGATTGGAATAATGTCTTCTCAAAGG
89110 A G GGAATAATGTCTTCTCAAAGGATTCCATATCCCGCTAGAGCATTTGATATGGCTCATTGTTCTAGATGCTTGATACCTTGGGCTTCATTTGATGGGTTAT[A/G]TCTAATTGAAGTAGACAGAGTTCTAAGACCAGGAGGGTACTGGATTCTTTCAGGCCCACCAATTCACTGGAAAAAGTACCACAGAGGG
89112 C G TTCCGGCGACGGACTCGGCCTCGTCCAACTCTATGACGGCCGGGTGCGCCCCCACGGCCAGGAACAGCCGCTTGATGACGTGGCACATGCAGCATGCATG[C/G]CGCGAGAATATGACCACCGGGTTCTCCGTTATCAGCCGTTCGATCCTCTCCTCCGTCGATTCGGCTACGTCCATCGATAGGAAGG
89112 A AT CCGTTCGATCCTCTCCTCCGTCGATTCGGCTACGTCCATCGATAGGAAGGGCTGGCGTAGATCGACGGTGGACGGCTGGGGATAGAGGAGGAGGTCTTGC[A/AT]TTTTTTAGAAGATGAATGATTAATGGTTATATTGATTTCTGGAGTTGAGAAATGGGAAATGAGCCGACCAGTAGGCCAACAGTG
89168 G A TCACTGTTGGCCTACTGGGAGCACATTAAAGCAGCTGTTAATTGCCGAGCTCCTCCACTTCTTAAAACCCTAG[G/A]GAAGGCAACCCCATTCCGGTTTCCGGTATGATCCTCGCTCGCCTTCTTGCTCGCTCCCTTACTCATCACCTCAACACCCTTACTCTAGTTCCATCACACT
89168 G T TCACTGTTGGCCTACTGGGAGCACATTAAAGCAGCTGTTAATTGCCGAGCTCCTCCACTTCTTAAAACCCTAGGGAAGGCAACCCCATTCCGGTTTCCG[G/T]TATGATCCTCGCTCGCCTTCTTGCTCGCTCCCTTACTCATCACCTCAACACCCTTACTCTAGTTCCATCACACTCTCCCAAATTCTCACCTC
89168 G T CCTACTGGGAGCACATTAAAGCAGCTGTTAATTGCCGAGCTCCTCCACTTCTTAAAACCCTAGGGAAGGCAACCCCATTCCGGTTTCCGGTATGATCCTC[G/T]CTCGCCTTCTTGCTCGCTCCCTTACTCATCACCTCAACACCCTTACTCTAGTTCCATCACACTCTCCCAAATTCTCACCTCGCCCTCGCTT
89168 C A AGCACATTAAAGCAGCTGTTAATTGCCGAGCTCCTCCACTTCTTAAAACCCTAGGGAAGGCAACCCCATTCCGGTTTCCGGTATGATCCTCGCTCGCCTT[C/A]TTGCTCGCTCCCTTACTCATCACCTCAACACCCTTACTCTAGTTCCATCACACTCTCCCAAATTCTCACCTCGCCCTCGCTTCCCTCTCTTC
89168 G A TTAAAACCCTAGGGAAGGCAACCCCATTCCGGTTTCCGGTATGATCCTCGCTCGCCTTCTTGCTCGCTCCCTTACTCATCACCTCAACACCCTTACTCTA[G/A]TTCCATCACACTCTCCCAAATTCTCACCTCGCCCTCGCTTCCCTCTCTTCCAGTCTCTTCATCCCTTCTCTTCCAACGACGGCAATGATGGC
89168 C T CATCACACTCTCCCAAATTCTCACCTCGCCCTCGCTTCCCTCTCTTCCAGTCTCTTCATCCCTTCTCTTCCAACGACGGCAATGATGGCTCATGGAGCTT[C/T]CCACCGGATTCCGATAACCTATTCGGTGAAGAAGGCGGCGATCTAAGCGGCCTAACTGATGATGCCAGTATGTTCTCCGAGAAACCGAA
89170 T C GAAGCAACTGATATTCTAGGTCCAGTCTCATTTGCAAGTACTCTGTGCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGT[T/C]GATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGA
89170 A G TTCTAGGTCCAGTCTCATTTGCAAGTACTCTGTGCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGC[A/G]CCAGGAATCGGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAAT
89170 C A CAGTCTCATTTGCAAGTACTCTGTGCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGCACCAGGAAT[C/A]GGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAG
89170 G A CATTTGCAAGTACTCTGTGCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGCACCAGGAATCGGAGG[G/A]ACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGC
89170 A G TGTGCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTG[A/G]TCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGC
89170 T C GCTCGACACTCTTAAACCTATCATTTGTTATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTGATC[T/C]TGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGCGTT
89170 G T ATCAGCTGCATAAGGTCACCAATGTTGATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATAT[G/T]ATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGT
89170 G A CACCAATGTTGATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAAC[G/A]GTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGA
89170 T C ATCACGAGTGCACCAGGAATCGGAGGGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAAT[T/C]AGGATCAGTGTGCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTG
89170 A G GGACATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCC[A/G]AGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTGCACATCCCAGTTTTTCCAAATGATCG
89170 C T CATCAACCCACTGATCTTGATAACGAACCTGGAGACCCCCAATATGATCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAG[C/T]GTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCT
89170 A C TCTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAG[A/C]AATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAGTCCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCT
89170 A T CTTGTAAAAGAACGGTAATGAAATTAGGATCAGTGTGCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGA[A/T]ATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAGTCCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCTT
89170 G A GCTTGCTCGTCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTGCACATCCCAGTTTTTCCAAATGATC[G/A]CTCTTCAGTCCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCTTTTGCACTTCACTTGTGTACTCGATAATTGCATCCCTG
89170 T A TCCCAAGCGTTAGATGTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAG[T/A]CCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCTTTTGCACTTCACTTGTGTACTCGATAATTGCATCCCTGCATGAGTAG
89170 T A GTGGCTCTGGGCATGCTGGGTAGTAATGCATTGCTAAAGAAATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAGTCCCAATGCTTCAGA[T/A]AGCAATCCAAATATTCTCTTGCTTAGCTTTTGCACTTCACTTGTGTACTCGATAATTGCATCCCTGCATGAGTAGGGCAACTCTTCCGGT
89170 C T AATACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAGTCCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCTTTTGCACTTCA[C/T]TTGTGTACTCGATAATTGCATCCCTGCATGAGTAGGGCAACTCTTCCGGTTTAGGGCCATCAGGTGCCAT
89170 T C TACCATCTGCACATCCCAGTTTTTCCAAATGATCGCTCTTCAGTCCCAATGCTTCAGATAGCAATCCAAATATTCTCTTGCTTAGCTTTTGCACTTCACT[T/C]GTGTACTCGATAATTGCATCCCTGCATGAGTAGGGCAACTCTTCCGGTTTAGGGCCATCAGGTGCCAT
89174 T C ATAATCTCACTCAAATTTGAATCATCCCCACTTTGAGAGGCCAACTGTACAAGCCCATGATAAGCT[T/C]CTACTATATAAGGGTTTTTCTGCAGAATTTCCTCAAAACCCAACTTTGCAGCCTCTAAGTCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAA
89174 C G AATCATCCCCACTTTGAGAGGCCAACTGTACAAGCCCATGATAAGCTTCTACTATATAAGGGTTTTTCTGCAGAATTTCCTCAAAACCCAACTTTGCAGC[C/G]TCTAAGTCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAAGTCGTGCTCACCTGGCTCAAGCTCAATCAGCCTATTGACGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
89174 G A CCCCACTTTGAGAGGCCAACTGTACAAGCCCATGATAAGCTTCTACTATATAAGGGTTTTTCTGCAGAATTTCCTCAAAACCCAACTTTGCAGCCTCTAA[G/A]TCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAAGTCGTGCTCACCTGGCTCAAGCTCAATCAGCCTATTGACGATTCTAAT
89174 T A TATATAAGGGTTTTTCTGCAGAATTTCCTCAAAACCCAACTTTGCAGCCTCTAAGTCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAAGTCG[T/A]GCTCACCTGGCTCAAGCTCAATCAGCCTATTGACGATTCTAATTGCTTCTGGAAGTTGCTTAGACTTGACTTTCAATTCAACTAGTGAT
89174 T C AAACCCAACTTTGCAGCCTCTAAGTCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAAGTCGTGCTCACCTGGCTCAAGCTCAATCAGCCTAT[T/C]GACGATTCTAATTGCTTCTGGAAGTTGCTTAGACTTGACTTTCAATTCAACTAGTGATCGGAGTGCAGAAATGTCATCGGGATTAGCG
89174 A G CAACTTTGCAGCCTCTAAGTCTCCGCTATAGCTCAAAAGATGAGATTTCAAAAGGGGTAAGTCGTGCTCACCTGGCTCAAGCTCAATCAGCCTATTGACG[A/G]TTCTAATTGCTTCTGGAAGTTGCTTAGACTTGACTTTCAATTCAACTAGTGATCGGAGTGCAGAAATGTCATCGGGATTAGCGCGAA
89174 G T TCAAGCTCAATCAGCCTATTGACGATTCTAATTGCTTCTGGAAGTTGCTTAGACTTGACTTTCAATTCAACTAGTGATCGGAGTGCAGAAATGTCATCGG[G/T]ATTAGCGCGAAGCTGGGATTTTACAGATTCTTCATCGATGTCACTGGAAATGGATTTGGATTGGGTGGCTACTGGAGGCTCAGCAAC
89174 G A AGCCTATTGACGATTCTAATTGCTTCTGGAAGTTGCTTAGACTTGACTTTCAATTCAACTAGTGATCGGAGTGCAGAAATGTCATCGGGATTAGCGCGAA[G/A]CTGGGATTTTACAGATTCTTCATCGATGTCACTGGAAATGGATTTGGATTGGGTGGCTACTGGAGGCTCAGCAACAGCGGCGGCAG
89174 A T CGATGTCACTGGAAATGGATTTGGATTGGGTGGCTACTGGAGGCTCAGCAACAGCGGCGGCAGGATGGCGCGATAAAAATAGGGCTGCGGCGGCGATAGC[A/T]GCGACGGAAGCGGGTTTAAGGACTGTGGTTAATACGGTCTGTATAGGATTCGGGTTTCCATTAGAGCGAATTTTAGAAGCAAG
89206 C T ACTGTTGGCCTACTGGGCGTTACTTCACTCAAATTTGTCCAAATATCATTGGAGTTATCCCTACTTCGCTCAAATTTCCCTTCTT[C/T]ATCTTTTCACACAGCTCACTCAAAACTAAACAGCACTCGGAAAGACGGAAAATCAACCGCTACGATAAACAGAGAACACAAGGATGGCGAAATCAGTACT
89206 A G CTACTGGGCGTTACTTCACTCAAATTTGTCCAAATATCATTGGAGTTATCCCTACTTCGCTCAAATTTCCCTTCTTCATCTTTTCACACAGCTCACTCAA[A/G]ACTAAACAGCACTCGGAAAGACGGAAAATCAACCGCTACGATAAACAGAGAACACAAGGATGGCGAAATCAGTACTTATCATCACTGGC
89206 T C GAGTTATCCCTACTTCGCTCAAATTTCCCTTCTTCATCTTTTCACACAGCTCACTCAAAACTAAACAGCACTCGGAAAGACGGAAAATCAACCGCTACGA[T/C]AAACAGAGAACACAAGGATGGCGAAATCAGTACTTATCATCACTGGCGACTATGTGGAGGACTATGAGGCGATGGTGCCATTTCAAG
89206 C T TGCAAGCTTATGGAGTTGCTGTTGATGCAGTGTGTCCTGGCAAGAAATCGGGTGAATTTATCAGAACTGCGGTGCATCAGGGTTTGGGCCATCAGACGTA[C/T]TCAGAGTCCCGAGGCCATAATTTTACGCTAAATGCTACATTCAGCGAAATTGACCCCAACAAGTACGATGGCTTGCTTCTTCCAGGA
89206 A G AGACGTACTCAGAGTCCCGAGGCCATAATTTTACGCTAAATGCTACATTCAGCGAAATTGACCCCAACAAGTACGATGGCTTGCTTCTTCCAGGAGGTCG[A/G]GCACCAGAGTATCTTGCTATGAATGAATCAGTCATAAATATTGTACGTAAATTTCATGAAAACAAGAAACCAATTGCTTCCATCTGTC
89206 A G ACTCAGAGTCCCGAGGCCATAATTTTACGCTAAATGCTACATTCAGCGAAATTGACCCCAACAAGTACGATGGCTTGCTTCTTCCAGGAGGTCGAGCACC[A/G]GAGTATCTTGCTATGAATGAATCAGTCATAAATATTGTACGTAAATTTCATGAAAACAAGAAACCAATTGCTTCCATCTGTCATGGGC
89244 GA G TGACTTCATTGCTGCTCTGTGGAAATGGGATAATTGCAGATATATGGCAGAATTTGAGGCTAGGGACGATAGGAAAAAAGTGGCATAACTTTTGATTGAG[GA/G]AATACCAGGTTTTATGCTTGCTGGAAGGAGACTGAAAGACTGATGTTGTTGCTGCTGTTAAAATGATATTGAATGCTATCTTTCTC
89246 T A AAAAAGCCCCGAACCTTCTTAACTAAAACCCATGGCAGGCTATTATATGAGTGCCACTGCCCATCAG[T/A]TACAAGCTCCCACTGCTAGTTTCTTAATTCCATCGAAACAAGGTTGCCGGAAAATTAGTTTGAAAATCAGAGCAAAATCAATGGCGACTGAGAAGCTTGG
89246 G C GAACCTTCTTAACTAAAACCCATGGCAGGCTATTATATGAGTGCCACTGCCCATCAGTTACAAGCTCCCACTGCTAGTTTCTTAATTCCATCGAAACAAG[G/C]TTGCCGGAAAATTAGTTTGAAAATCAGAGCAAAATCAATGGCGACTGAGAAGCTTGGAATCGTAGTTGAAAGGAATCCACCTGACTC
89246 G A CTTAACTAAAACCCATGGCAGGCTATTATATGAGTGCCACTGCCCATCAGTTACAAGCTCCCACTGCTAGTTTCTTAATTCCATCGAAACAAGGTTGCCG[G/A]AAAATTAGTTTGAAAATCAGAGCAAAATCAATGGCGACTGAGAAGCTTGGAATCGTAGTTGAAAGGAATCCACCTGACTCCAAACTTG
89246 T A TGCGGCGAGGAGTACGTGGAGATTGGAGCTGGAGACTACGTGGAATTTCCAAAGGGAATGAATTGCACTTGGGATGTTTCTATAGCAGTTGATAAGCATT[T/A]TAAGTTTGAGTAATGCAACATGTATTCTGGCACTGTAACTTAACGTGAATCAGTGCAATGTACCCTTTATTTGTCTGCGACGTACG
89246 A G GGAGCTGGAGACTACGTGGAATTTCCAAAGGGAATGAATTGCACTTGGGATGTTTCTATAGCAGTTGATAAGCATTTTAAGTTTGAGTAATGCAACATGT[A/G]TTCTGGCACTGTAACTTAACGTGAATCAGTGCAATGTACCCTTTATTTGTCTGCGACGTACGTAGTGATATGTTATTATGATTAGCTC
89246 TA T GGAATTTCCAAAGGGAATGAATTGCACTTGGGATGTTTCTATAGCAGTTGATAAGCATTTTAAGTTTGAGTAATGCAACATGTATTCTGGCACTGTAACT[TA/T]AACGTGAATCAGTGCAATGTACCCTTTATTTGTCTGCGACGTACGTAGTGATATGTTATTATGATTAGCTCTTGAGAATGGGGTTCCT
89246 A G TGAATTGCACTTGGGATGTTTCTATAGCAGTTGATAAGCATTTTAAGTTTGAGTAATGCAACATGTATTCTGGCACTGTAACTTAACGTGAATCAGTGCA[A/G]TGTACCCTTTATTTGTCTGCGACGTACGTAGTGATATGTTATTATGATTAGCTCTTGAGAATGGGGTTCCTTG
89252 G T CTTCTCTCTCAGCTCTTCTCATTCTTTCATTCATTCTTCTCCGCCCTTGATTGTACCCATTTCTCCTCCTCTGATAATTCTCAGGATTTCCGGTAACATC[G/T]CGACCGGAATCCATGCTACCGTAATAATTATTATATTGATCCATTGAAGCAACAAAAAGAGGAGCGTCTGCATTCAATCTCTTAGTGGACGG
89252 G A AGCCTCCAGCTTCCGAACATCACTTTCATATTCCTTCACCGTCTCAGAAGCCACTGGAGAAGCGTCAGAGATCGTTGGAGCTGTGTCGAAGGCCTTTGAA[G/A]CTTCGTCGGAGATCGCCGGAGGTGTGATCATGTTTCCGGTGGCCGCAGACATCGATCAAGAGTTAATCTTTACTACTATCGTGTATA
89270 A G CTTGGAATGCTCGACAAGCTCCATTGCATGTTCTAATCAACAATGCTGGAATTTTTAGCATTGGAGAACCTCAACGGTTCTCGGAAGATGGTAATGAAGA[A/G]CATATGCAAGTGAATCATCTAGCCCCAGCGTTATTATCTATGCTACTTTTGCCATCTCTTTTGCGAGGATCTCCTAGCAAAAATCATCA
89286 GTCC G CAGACATACTGCTGCTTCTGTGAAAATAGTACGCTGGAGCAGGAATGGCTGGATGCTGCTGCTGTGGAGGAATAAGCATTGTCCTTCTATGATCGTAGGA[GTCC/G]TCCTTGATTCCCGTATTCCTTTCATATGGCATTACTGAACCCACTACTTTTCCTGGCTTTGCTGCGGTAGGAGGGACCCTTTGAG
89316 G C ATGCTCGAAACCTTCAGATCTGAGAAGGAGAGCAACAAGCGCGACGTGGCTCGAATCCATGGCTTGGAGCGAAAAACCTGATGATGAGCAGTCGAAGTTG[G/C]CGTCAGTCACTAGATCTTTAATCGCTTCAAGAACCTTCTTTAGAAGACTGCCTTGAACAAGCCTTAACTCCAACATTTTCTTCTGCT
89316 C T GTCACTAGATCTTTAATCGCTTCAAGAACCTTCTTTAGAAGACTGCCTTGAACAAGCCTTAACTCCAACATTTTCTTCTGCTTGGAATTAGTTTTTGGAA[C/T]CGGATGGGAGGAGATTTCTCACTCTAAATTTTCGGGAATGGAGTAAATGGAGCGACGAAGAGTGGGAAGAAAT
89318 C T CTTGTCCAACTCCTAGGCTACTGCCGAAGGAAAGGAGAGCTTCTACTAGTCTACGACTTCATGCCAAATGGTAGCCTGGACCGATTTTTGCATGACCGGA[C/T]CAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCA
89318 G A GGAGAGCTTCTACTAGTCTACGACTTCATGCCAAATGGTAGCCTGGACCGATTTTTGCATGACCGGACCAAACCAACCCTGAACTGGGACCAAAGGTTTC[G/A]CATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCA
89318 G C TAGTCTACGACTTCATGCCAAATGGTAGCCTGGACCGATTTTTGCATGACCGGACCAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGG[G/C]GTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGA
89318 T C TCTACGACTTCATGCCAAATGGTAGCCTGGACCGATTTTTGCATGACCGGACCAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGGGGT[T/C]GCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGG
89318 A G TTTTTGCATGACCGGACCAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGG[A/G]GCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTA
89318 A G ACCGGACCAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGT[A/G]GTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTA
89318 G A GGACCAAACCAACCCTGAACTGGGACCAAAGGTTTCGCATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGT[G/A]CATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATAC
89318 G A ATCATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACG[G/A]AGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGATAGAGGAGTTGATCCGCAGACAACGCACGTGGTGGG
89318 G C CATCAAAGGGGTTGCTTCTGGTTTGCTTTACATGCATGAAGACTGGGAGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGA[G/C]AGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGATAGAGGAGTTGATCCGCAGACAACGCACGTGGTGGGG
89318 T G AGCAGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGA[T/G]AGAGGAGTTGATCCGCAGACAACGCACGTGGTGGGGACGATGGGGTACATATCTCCTGAGCTTGCAATGAACGGGAAGGCTAC
89318 A G AGGTGGTAGTGCATAGAGACATCAAAGCAAGCAACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGATAG[A/G]GGAGTTGATCCGCAGACAACGCACGTGGTGGGGACGATGGGGTACATATCTCCTGAGCTTGCAATGAACGGGAAGGCTACAAC
89318 G T ACGTGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGATAGAGGAGTTGATCCGCAGACAACGCACGTGGTGGG[G/T]ACGATGGGGTACATATCTCCTGAGCTTGCAATGAACGGGAAGGCTACAACAGTGTCAGACGTGTATGCGTTTGGGGCATTCTTG
89318 G A TGTTGTTGGACGGAGAGCTAAATGGCAGACTTGGAGATTTCGGACTAGCAAGATTATACGATAGAGGAGTTGATCCGCAGACAACGCACGTGGTGGGGAC[G/A]ATGGGGTACATATCTCCTGAGCTTGCAATGAACGGGAAGGCTACAACAGTGTCAGACGTGTATGCGTTTGGGGCATTCTTGCTA
89318 T C GTGGGGACGATGGGGTACATATCTCCTGAGCTTGCAATGAACGGGAAGGCTACAACAGTGTCAGACGTGTATGCGTTTGGGGCATTCTTGCTAGAAGTGG[T/C]GTGTGGAAGGAGGCCGATAGATAGGCAGACGGGGTGCGAGGAGATGGTGCTGGTGGACTGGGTGCTGGAGAAGTGG
89320 T G CCATTGGATCGATGTGCTATTGCATTGTGATGCATAGGATTGAAGAGAAGAGTTTGAGGAACATAAGGAGGCCCTCTGGGAGTTTGTCGAGGTCATGGGG[T/G]ATGTCAGTTGTTTCTGATAATGACATGATGAATAATGAATATAAGAAGATGTATGCTCTTTAAGAGTTTGATGGCGTATGATATAG
89336 T A CAAAGCATGATAAAGCTTCCACCTTCGCCATGACCTGCAACCTTCTCAGCCAGTTCATCAAAGAAAAGGGCTCGCTCGGCGATCTCGGACGCGAATTGGC[T/A]ATCGGCGCAAGCGCTACGTACCGGCCACCAACTACGATGAACCTGCTACAAAGCGTGGATGCATCGGGGACTGCTGCTGCGAAAG
89336 A G TGGTGTTTGATAATTTTCCTGCAAATAAGGCAAATGATTTGATGATGCTCGCAGGAAAAGGATGTGATCTGAAATCGGAGAAATTTAAAGCTGCAAATTC[A/G]AATTTGGTTGCTGCACCTGCTAACGGTCCAGTTGTGCAACCAGTATCCGTCCAAACTGTGGCTTCTGATCTACCCATTGCAAGAAAA
89346 A C AGCAAGCTGTTAAATCTGATTGAGTTTTAAGTTAGGGTTTGAGCTTTGCATAATTGAGTAATGGAAGTTGAATCCAGTTCTCTTCAGTCAATCTGCTACA[A/C]GCGTGGCTCGCTTCGCTTACTCGATCAGAGGAAGCTTCCACTTGAAACTGTGTACTTGGATATTCTGAACTCTGCAGACGGATGGAAC
89346 C T CAATCTGCTACAAGCGTGGCTCGCTTCGCTTACTCGATCAGAGGAAGCTTCCACTTGAAACTGTGTACTTGGATATTCTGAACTCTGCAGACGGATGGAA[C/T]GCAATAAGAGATATGGTTGTTCGTGGTGCACCTGCAATTGCAATAGCAGCGGCTTTGTCTCTTGCAGTTGAAGTATGTAACCTTGAT
89370 C T GGAGGCGGTTGATGGAAACGAGGAACTGTACGGATCGGAGAGCGGCTGGGTTGAAGCTCGAAGTTCATGCGATCATCTCTCTGCACTGTCGTCTGATCTC[C/T]TTCAGATTCCAATTCCTACTTCCCCTTGTTTCAGATGCCACCACCCAAATGAAAACTGGCTATGTTTGAGCTGCAAAGAAGTCCTGT
89382 G GT AGTCGTTGATTTGGAAACGGGAGGATTCGGCCCATTTGTTGAGAGAATCTTCGGGAGATGCAGGAACTTTCCAGGCATGAAGGGAGCCACCAACCAGGAA[G/GT]TTTTTTGCGTTTGATGTGTATAGGAGTGTGGTCATGAATGCTGCAAGGAGAATGCATGAGTATGATGAAGAAGAAGAAGAAGC
89424 TC T TTCTCTCTTGAGGTATATGTGTGGGCCCTCGCCATTGGGTCGTTTGTAGTGCTCGGTAAGTCGCTCTGCAAAGTAAAGTGGGCTCTCTCGACCTACGTAG[TC/T]CCTTTTAGTATGCCATCAAGTTCTTTCTGAAAATCCTCATCTTTCGCCAATTTATGGAACGCCTCCTCGAGCTCAGTCAATGCATGCA
89458 A T TCTGGTCTTCTCCGCCTGTGGCAGCATGTCCGGCTAACATAACCCGGAGTTCCTCCGAGTGGTTCTTCCAGAAGTTTCTAGAAGAAGAAGCCGCCATTTC[A/T]AAACAAAATGGCAACCCTAATGTTCACAATGAGCTCGCAACCTCAACGACCGATAAGGATGCTGTGGAGATAAAGGAAACGCAGAT
89458 G A CGGTTCTGAAGCAGCAGCTTGATATGTATTGTCAGGCAGTTGCAATTGCACGGGGCTCGAGCATAAAACCTCAAGATTCTATTTCAGTCGATTCAAGATC[G/A]CCAGCTTCAAATTCATCACCGCTAGGACCTGAAGCACCTGTTATTAGTAGTGGATCAAATGGAGTTTCAGCAAATCTGCAGAATT
89458 A G TGTATTGTCAGGCAGTTGCAATTGCACGGGGCTCGAGCATAAAACCTCAAGATTCTATTTCAGTCGATTCAAGATCGCCAGCTTCAAATTCATCACCGCT[A/G]GGACCTGAAGCACCTGTTATTAGTAGTGGATCAAATGGAGTTTCAGCAAATCTGCAGAATT
89470 T A ATGCTCAGACCCCTCTCTGATGCTGTAATCGGAATACATTTAGCCTGAGAGCCGTGAACCTACAGATTGAGATAATACACATAGCATGTATCATCGTCCG[T/A]TCGTTCAATTACTTAGTAACAATGTCCATGATGGAGTAGATCAGTAGCTTTTCTTGGTTGGGCAATCGGAAGCTCTGTGCCCGGGCTT
89470 C A AGACCCCTCTCTGATGCTGTAATCGGAATACATTTAGCCTGAGAGCCGTGAACCTACAGATTGAGATAATACACATAGCATGTATCATCGTCCGTTCGTT[C/A]AATTACTTAGTAACAATGTCCATGATGGAGTAGATCAGTAGCTTTTCTTGGTTGGGCAATCGGAAGCTCTGTGCCCGGGCTTTCCGCA
89486 A G TCTCTTCTTTAATTCCTACTGATGTCTCTTGTTTCTGCTGCTCCAAGGTCTTTACTTTTTTACTTAAATCGCGGTGAAACAGATAAAGATCTTCAACTGC[A/G]GCAGAAGTACGGCTTAAGTAGGCAGCAACATCGCGTCGAGCACCAAAATCCATGGACTTGCAAAACTTGCTGATGACTTTTGCTGCTAG
89486 A T CTTCTTTAATTCCTACTGATGTCTCTTGTTTCTGCTGCTCCAAGGTCTTTACTTTTTTACTTAAATCGCGGTGAAACAGATAAAGATCTTCAACTGCAGC[A/T]GAAGTACGGCTTAAGTAGGCAGCAACATCGCGTCGAGCACCAAAATCCATGGACTTGCAAAACTTGCTGATGACTTTTGCTGCTAGTTTT
89486 G C TGCTGATGACTTTTGCTGCTAGTTTTACTGTTGCTGGTTCTCTTGAAGTCACTGTTCCAGTCACCGCTCTCATTTTCCTGTCTTTGGGGCTAGATTATTG[G/C]CTATCACAATTTAAGAGTTGGTGGCCACCAGTGCAAGAGCTCTCCAACCAAAGTCAAGCTGGAACTTTGAGCACTTAGCGTTTGATTGC
89490 T C GCAGCTTCTAGGCTAACGAGATCCTTCGAAAAATCAAGCACCTCTGGAAGTTTTTCAGCAAGAACCGGAGGTGATTGCGTCGATGGACTGAGAAAAGGCC[T/C]GCCGACCTTGTTGCTCCCCTTTACTTGAACCTGTGCTTCGTCTTCACGCTAAGAAGGAGGAGGAAAACTATGGACCAAAATGATAG
89490 A G AAAATCAAGCACCTCTGGAAGTTTTTCAGCAAGAACCGGAGGTGATTGCGTCGATGGACTGAGAAAAGGCCTGCCGACCTTGTTGCTCCCCTTTACTTGA[A/G]CCTGTGCTTCGTCTTCACGCTAAGAAGGAGGAGGAAAACTATGGACCAAAATGATAGCAATGACGACCGTTGGGAGAGATCGATA
89506 TA T TTGTTGTGTAGATGAAGAAGGTGAGATGATGAAGCCACGAAGGTGGTTGGAAACTGAGTTTGGGTTGTTAATTAAAACTGAGTTTGGGTTGTTAATATAA[TA/T]AAAAACTGAGTTTGGGTTGTTGGAGGTAGCGCCGTAAATGTGACTGTGAATGTGGATTTGTTGTAGGCTGTGTATGTCAGCTAA
89518 C T GGTAGAACTGGCGCATGGCATGCGCATAAAGGGTGTCTTGGTAGCCAACGAAGCTGCATTTGTAGAAGGCGGAGAAGTCCCCGTTGCTCCGGAGGGCTAC[C/T]GCTTGGTGTTTCGACGGTCCCGCCGAATTCTCGATTGTTAGGTCTCGAGCAATGAAGTTCGGTGCCGAGATAGCAACAGTGGCA
89518 A G AAAGGGTGTCTTGGTAGCCAACGAAGCTGCATTTGTAGAAGGCGGAGAAGTCCCCGTTGCTCCGGAGGGCTACCGCTTGGTGTTTCGACGGTCCCGCCGA[A/G]TTCTCGATTGTTAGGTCTCGAGCAATGAAGTTCGGTGCCGAGATAGCAACAGTGGCAGACCTATAAGTGGTAAATCCATCAACAA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
89518 A G CTCGAGCAATGAAGTTCGGTGCCGAGATAGCAACAGTGGCAGACCTATAAGTGGTAAATCCATCAACAACATTCCGGCTCCCCCTTATCACAGTCTTCCC[A/G]ATCCCATCGCCTTGGAACATCAAATTCGTCTTCTTCTTAGCAACATCCACATTTTCCTCGTACAACCCTGCTTTTATATGAATCACAATC
89518 G A TGAAGTTCGGTGCCGAGATAGCAACAGTGGCAGACCTATAAGTGGTAAATCCATCAACAACATTCCGGCTCCCCCTTATCACAGTCTTCCCAATCCCATC[G/A]CCTTGGAACATCAAATTCGTCTTCTTCTTAGCAACATCCACATTTTCCTCGTACAACCCTGCTTTTATATGAATCACAATCCTGCTCTTG
89518 A T CAGACCTATAAGTGGTAAATCCATCAACAACATTCCGGCTCCCCCTTATCACAGTCTTCCCAATCCCATCGCCTTGGAACATCAAATTCGTCTTCTTCTT[A/T]GCAACATCCACATTTTCCTCGTACAACCCTGCTTTTATATGAATCACAATCCTGCTCTTGCTCTTATCAGGCGTTGCATTCAGCGCTTCCGC
89518 C A AAGTGGTAAATCCATCAACAACATTCCGGCTCCCCCTTATCACAGTCTTCCCAATCCCATCGCCTTGGAACATCAAATTCGTCTTCTTCTTAGCAACATC[C/A]ACATTTTCCTCGTACAACCCTGCTTTTATATGAATCACAATCCTGCTCTTGCTCTTATCAGGCGTTGCATTCAGCGCTTCCGCTATGGTTTT
89518 C T TTATCACAGTCTTCCCAATCCCATCGCCTTGGAACATCAAATTCGTCTTCTTCTTAGCAACATCCACATTTTCCTCGTACAACCCTGCTTTTATATGAAT[C/T]ACAATCCTGCTCTTGCTCTTATCAGGCGTTGCATTCAGCGCTTCCGCTATGGTTTTGAAGTTTCCACTCCCGTCTTTGGCCACCACTATCGTG
89518 C G CTTCCCAATCCCATCGCCTTGGAACATCAAATTCGTCTTCTTCTTAGCAACATCCACATTTTCCTCGTACAACCCTGCTTTTATATGAATCACAATCCTG[C/G]TCTTGCTCTTATCAGGCGTTGCATTCAGCGCTTCCGCTATGGTTTTGAAGTTTCCACTCCCGTCTTTGGCCACCACTATCGTGGCAGCCACG
89518 G A CCTGCTCTTGCTCTTATCAGGCGTTGCATTCAGCGCTTCCGCTATGGTTTTGAAGTTTCCACTCCCGTCTTTGGCCACCACTATCGTGGCAGCCACGGCG[G/A]CACTCTCGTTTGCTAACAGCTTTTGATCGCTGCTTGAAACCCATTCTGGAAATCCGTTCTTTACTTTTCCGTATTCTTCAAATACTTCGTC
89564 G T TGGTAGATGTTCATAGCTTCTCTGCATAAATATCTGATCATAAACCAGGCCAGCAAGAGGTCCACCAATGAGAGGTCCAACCCAGTACACCCAGTGATCA[G/T]TCCAGTTTCCACTTGCCAAGGCCGGCCCAAAAGATCTAGCTGGGTTCATAGATGCACCCGAAAATGGGCCGCCTGCTAGGATATTAG
89576 TG T CGGCCAAATCTGCTAAGTCCTCCGCTACATATGCCAGTTCAAACAACGAAGGTACCAGTCATGTTAAAGCTTTGGATATCAACTTGAACCTCTTTGAAGG[TG/T]GGGGGTCCTTGTCATTTTGGGGAACTGGGTCCTATCATAAACCCCAACGCTACTGACGTCGGACCCCGTGAACCTCCACATATTCAT
89598 T C TATTCGCCGTCCCCCTTTGTTCATGCTTGTAGTCCACCAGCAAAACATTCAGCCGCGTCTTGCTCTCCATTTCGTCATCAATACAAAGATAAAATTACTG[T/C]ATTCATCTTCAGCCGTCGATTGTGCGTGTAATAGAAGAATCTCCGGTTGCAATGCCAGTGATTTGCTACATGGGTTCTACATGCTCTTGA
89610 A G AAAATCAACCGAAGAATGACTAAACAACTGGGCTTAACCACAAAAACAAATCCGATCTAATAAAGACAAACTATGACACTGAAGCACAACTCTCCAAGTT[A/G]AAACACTACATCAAACACAGTGAAACCAACACTTTCAGATGCAGACCATACCCAACAAAGTCAGACATAAACTATCCCACAAGCATA
89610 A T AGACAAACTATGACACTGAAGCACAACTCTCCAAGTTAAAACACTACATCAAACACAGTGAAACCAACACTTTCAGATGCAGACCATACCCAACAAAGTC[A/T]GACATAAACTATCCCACAAGCATAGACAACATGCTAACTCACCAGCATGTCGAAACGAAGTCTGATCCACAACCAGTTAGATCTGCCT
89610 G A CCAGCATGTCGAAACGAAGTCTGATCCACAACCAGTTAGATCTGCCTTTTGGTGAGAGCGTGAGTGCTGAAGCAAGTGGAAGAGCGGATCTGGAAGTCGC[G/A]AGAGTGGTCGAACGTAGGAGCAGCAGCTAGACAGAGCGGAAAACGAGAGGAACACCCCGGAGAGGGACAAATGATTAGTTAA
89622 A G AGAGAACACGCAGAACGCCAAATGAAGCTTATGGAAGAACAAAATGCTGCAGCTGAAGCACAAAACACTGCAGCCATCGACTGAAAATTTTCATTTTATC[A/G]ATCCTTCTTTGTGTTTTCCGTGTATTTATTTCCGTATAGATTATATTAATGACAAAAGTTTTATGTTGTTTCCAGTTTCCATAAACATG
89622 T C ACGCCAAATGAAGCTTATGGAAGAACAAAATGCTGCAGCTGAAGCACAAAACACTGCAGCCATCGACTGAAAATTTTCATTTTATCAATCCTTCTTTGTG[T/C]TTTCCGTGTATTTATTTCCGTATAGATTATATTAATGACAAAAGTTTTATGTTGTTTCCAGTTTCCATAAACATGTATGACATTATGAGC
89622 C T GGAAGAACAAAATGCTGCAGCTGAAGCACAAAACACTGCAGCCATCGACTGAAAATTTTCATTTTATCAATCCTTCTTTGTGTTTTCCGTGTATTTATTT[C/T]CGTATAGATTATATTAATGACAAAAGTTTTATGTTGTTTCCAGTTTCCATAAACATGTATGACATTATGAGCTGCAACCGTTTAAACCCTG
89622 A G CAATCCTTCTTTGTGTTTTCCGTGTATTTATTTCCGTATAGATTATATTAATGACAAAAGTTTTATGTTGTTTCCAGTTTCCATAAACATGTATGACATT[A/G]TGAGCTGCAACCGTTTAAACCCTGAGTAGGTATGGTAGACTTATTAGAATGTTTCCTGGATTGCTTTCAACTTTTC
89624 T C CTCAAAGTCCACATGAGCATAGCCCTTGAACTCTCCTGTTACTTTATCCATGCCGAACCGGACAGTGGAGATTCTGCAGTCTGAGAAAAATGATTTTAGA[T/C]CGTCTTCGGTTATGTCCCAAGACAGGTTTCCTATATAAGCTCTATTATAACCCTCTATGGCTTCTGGCGTGAATTCGGGTTTTAGAGGT
89636 G A GCTCATCAACTTCATCATCTTCCAAATTTAACTCATTTTCGAGATCATCTTTCTTTTCCAAATGTTTAGTGCCGGTAGGACCTGATTTCTTACCGTCTTC[G/A]GTGTTCGCACTTTTACCCTTATTATTCTTTTTGTCTAACATGGAGGGGTTGTTCATATACTGCATGAGTTTGCGGAGCTTGGAAGGAACAA
89636 G A AACTTCATCATCTTCCAAATTTAACTCATTTTCGAGATCATCTTTCTTTTCCAAATGTTTAGTGCCGGTAGGACCTGATTTCTTACCGTCTTCGGTGTTC[G/A]CACTTTTACCCTTATTATTCTTTTTGTCTAACATGGAGGGGTTGTTCATATACTGCATGAGTTTGCGGAGCTTGGAAGGAACAACATCAAC
89636 A G CTTCGGTGTTCGCACTTTTACCCTTATTATTCTTTTTGTCTAACATGGAGGGGTTGTTCATATACTGCATGAGTTTGCGGAGCTTGGAAGGAACAACATC[A/G]ACTTCTTTCGACTTAACAGGAGCGGGTAGTCGACTGTCGCCGCCGTGTGCCGACAGGTAATTTTTCACCCGCCGCCGCTGACCTTTTCC
89636 G A TGTCTAACATGGAGGGGTTGTTCATATACTGCATGAGTTTGCGGAGCTTGGAAGGAACAACATCAACTTCTTTCGACTTAACAGGAGCGGGTAGTCGACT[G/A]TCGCCGCCGTGTGCCGACAGGTAATTTTTCACCCGCCGCCGCTGACCTTTTCCGCCCATTGAGTTTAATTTTTGTATTTTCTGTCGTC
89644 AG A CATGAGCTTTCATCACAGCAGCACCGAGTATGGTACGTGCTTCAATAATTTGACTTTCTCAAATCAACCTACCGTGATAACTAACGGAGAAAAGAGAGGA[AG/A]GGGGGAGGGTCGGCCAACGGGGATGAAGCGGTGCATAGCAAAGACGATAGGATGGAAGTGTAGATCACGTTGCTTAAGTGGG
89644 T C ACTAACGGAGAAAAGAGAGGAAGGGGGAGGGTCGGCCAACGGGGATGAAGCGGTGCATAGCAAAGACGATAGGATGGAAGTGTAGATCACGTTGCTTAAG[T/C]GGGTGTTTGCATGGGAAGGTCAGCGTGGCCATGAGGAGTCGCCAAAACTTAAACGAGGGGGAGAATGAGAAAGGGGCTGT
89644 C T GGGGATGAAGCGGTGCATAGCAAAGACGATAGGATGGAAGTGTAGATCACGTTGCTTAAGTGGGTGTTTGCATGGGAAGGTCAGCGTGGCCATGAGGAGT[C/T]GCCAAAACTTAAACGAGGGGGAGAATGAGAAAGGGGCTGTGACGCTGGTGATGGCAGCAACTCAGTCCGACGGCAGAGGGG
89652 TA T TGTGGCCTTTTTTTTTTTGATAGCAGAATAAAACTTCTATTTATTTATCAAAGTTTTGAATACAAGATATTTATACACATGTAGCGGAA[TA/T]AAAAAAACAATTTGAACATAGAAAAAAAATCTTTACTGTTTGCAACTTCAGAGTGCGCCGTATTTGGAATCCCCAGCTTCGCCGATCTTCGAATCCTACG
89652 A G TTCTATTTATTTATCAAAGTTTTGAATACAAGATATTTATACACATGTAGCGGAATAAAAAAACAATTTGAACATAGAAAAAAAATCTTTACTGTTTGCA[A/G]CTTCAGAGTGCGCCGTATTTGGAATCCCCAGCTTCGCCGATCTTCGAATCCTACGCTGAAATCTTTAAATCTGTAATGCTCGGGTCTTGG
89652 T C CATAGAAAAAAAATCTTTACTGTTTGCAACTTCAGAGTGCGCCGTATTTGGAATCCCCAGCTTCGCCGATCTTCGAATCCTACGCTGAAATCTTTAAATC[T/C]GTAATGCTCGGGTCTTGGAACCACCAAAAAATGGAGCAGGCGGAGACGAATTAAGAGCAGAAAGAGGGCTCGATTTCAGGTCACGTC
89652 A G ATTGAAGAGATTGGAGCGAGCTCCAGTGGTGATGGAGCTAGGTCAGACGTGGAAGATTAATTGGGGAAAATATCAATTCAGGCTTCTGCTGTTATTTGAG[A/G]GTTTAGGGAACAACTGGATTTCGGTGGCCATTGAATTGAAGAAAGTAGATTTTATACAAGGGAAAAAGGGTTGATTTTTGCTCCA
89658 CG C AAAAAACAAATCGTGATTAACAGCTATCGCAAACTTGCAATTACACTACCGTCCTCAACCAAAGCACTGGTCAGCAGGCAA[CG/C]GGGCCGGGGATATACCCTCTTTCAACAAACTGCAGCCCGAAAACGACAACTATAGCGAGCAGAGTCAAATACGAAAGCCCTTCGACGGCACCAAGCAGGC
89658 T G ACTTGCAATTACACTACCGTCCTCAACCAAAGCACTGGTCAGCAGGCAACGGGCCGGGGATATACCCTCTTTCAACAAACTGCAGCCCGAAAACGACAAC[T/G]ATAGCGAGCAGAGTCAAATACGAAAGCCCTTCGACGGCACCAAGCAGGCCGTAAGGCCCATTGGGCAAGCCAGAACCGGTTTTGA
89658 A C AACCAAAGCACTGGTCAGCAGGCAACGGGCCGGGGATATACCCTCTTTCAACAAACTGCAGCCCGAAAACGACAACTATAGCGAGCAGAGTCAAATACGA[A/C]AGCCCTTCGACGGCACCAAGCAGGCCGTAAGGCCCATTGGGCAAGCCAGAACCGGTTTTGACCTTGGTGTAGGCCGACCAACCC
89658 G A AGCTGACGCCTTCAGCCGCACCTACGGACCCTCCTGGGCCGGGCGGGAGCCCACAGCCGGTGGTTTTGAGGGTGTAGAGGGAGTACCCGATTATAGGGCT[G/A]GATAGCAGGCCTCCGACGATTGCGGATATTTGTAGAGGCGACGCGGTGGTTGGCGGTGGAGGGGTGATGGTTGATTTGTTGG
89658 G A GGGCCGGGCGGGAGCCCACAGCCGGTGGTTTTGAGGGTGTAGAGGGAGTACCCGATTATAGGGCTGGATAGCAGGCCTCCGACGATTGCGGATATTTGTA[G/A]AGGCGACGCGGTGGTTGGCGGTGGAGGGGTGATGGTTGATTTGTTGGTGTTTTTGGCTTTGCACGTGACGGAGAAGGATGGC
89658 G T GGAGCCCACAGCCGGTGGTTTTGAGGGTGTAGAGGGAGTACCCGATTATAGGGCTGGATAGCAGGCCTCCGACGATTGCGGATATTTGTAGAGGCGACGC[G/T]GTGGTTGGCGGTGGAGGGGTGATGGTTGATTTGTTGGTGTTTTTGGCTTTGCACGTGACGGAGAAGGATGGCACGTGAGGCT
89672 C CA TTGAGGCACCAGCTACAACATTATGAGCAAGATGTGCGACCTGATCCTCGATTTCGTAATATTTGTACGCTTTCAAATTTGACTGTCGAGTTGGTTAAAT[C/CA]AAAAAAGCCGAAAGATATCCTCTTGTTTATTGATTGATTTGTCTTGTATTAACTCTTCCTGTATCAACTACAACCACAGAGTGAGCATT
89676 G A TTGCCAGGCAATCCCAGACGATCCTGCACATGATCGAAGACGACTGCACAGACAGCGCAATACCGATTCCCAACGTCAACGGCAGGATCCTAGCCAAAGT[G/A]ATAGAGTATTGCAAGAAACATGTCGAGTCTACTGCCGCTGCCAAGGCTTCTGAGAGTAAGAAAGCGGCTTCAGATGATGAGATCA
89694 C T CCTGCAGCACATCACAGGGAGTCGGACTCACCCCACTCACCACCCCTTCAATGTCCGTACAATTCCAGATAGGTTTCTTCGACTTAATAACTTCAACGGT[C/T]ACGTTAGACATACAAATCCCTTTAAAAGTATCTCCAGGAATCCCGGTCAAACTTCCAGCCATGGTCACATTCTCGGCCACCACATCACT
89696 G A CATAGACGTTGCCCACCATGTGATCTGCAAGATTGTCGCAGATGTTCAGGCTCTCTATGTCGCCATATTTACTAAGCTCTTCGTATATGTCCTCGTAAAA[G/A]TCTTCAAAATGTTCTTGTATGGTCTGTGGATCAATGGGTTTGCCGTTAGCATCGACTCCAGGTGTTATCATATCTGGGCGCTGGTACAT
89756 C T GACTCCACCACCAACTATGTACAGGAGCGCGAAGAGGAGGAAGGGCATTCCTCATAGAGCTCCATTTGCGAGCTTCATGATAGAGTATTACTGATGATTA[C/T]GAAGGTTATTAGTAATATTTCGCGCTGCGTATATATGTATGTGATAATTTGTGTATATCTGATGCATAGACGGAGATGATGATGATG
89756 A G CAACTATGTACAGGAGCGCGAAGAGGAGGAAGGGCATTCCTCATAGAGCTCCATTTGCGAGCTTCATGATAGAGTATTACTGATGATTACGAAGGTTATT[A/G]GTAATATTTCGCGCTGCGTATATATGTATGTGATAATTTGTGTATATCTGATGCATAGACGGAGATGATGATGATGATGATGCATA
89756 G GCC GAGCGCGAAGAGGAGGAAGGGCATTCCTCATAGAGCTCCATTTGCGAGCTTCATGATAGAGTATTACTGATGATTACGAAGGTTATTAGTAATATTTCGC[G/GCC]CTGCGTATATATGTATGTGATAATTTGTGTATATCTGATGCATAGACGGAGATGATGATGATGATGATGCATATCTCTCCAACTA
89756 C T TCTGATGCATAGACGGAGATGATGATGATGATGATGCATATCTCTCCAACTACTGCAGTCTGTGCTTCCAGAGATGAGGAGGCCGGTGCCTTTGTTGTTG[C/T]TACCTGCGTTGTATACTTTTGGTAAGTATTGTGTTAATTTAGACTAATTCCATCTTTGTAATGTGTACATAGGAAGTGAATATCATGG
89756 TA T TGCGTTGTATACTTTTGGTAAGTATTGTGTTAATTTAGACTAATTCCATCTTTGTAATGTGTACATAGGAAGTGAATATCATGGGGTATATAAAGTGAAA[TA/T]AAAGATTGCATCCAGGATGTATTATGATTTACTAATGTTTTTACTCTCTATTGAATATTTCTCTGTACCATGGCTATTAATCATTAAAAA
89760 A C TCGAGCGCTACTACTCGCGCATGACGCTCGATTTCCACACGAACAAAAAGATACTAGAAGAAGTTGCCATCATTCCGTCCAAGCGTCTCCGCAACAAGAT[A/C]GCCGGATTCTCTACGCATCTGATGCGTCGTATCCAGAAAGGGCCGGTCCGCGGAATTTCTCTCAAGCTGCAAGAGGAGGAGAGGG
89760 A G TTCCGTCCAAGCGTCTCCGCAACAAGATAGCCGGATTCTCTACGCATCTGATGCGTCGTATCCAGAAAGGGCCGGTCCGCGGAATTTCTCTCAAGCTGCA[A/G]GAGGAGGAGAGGGAGAGGAGAATGGACTTTGTTCCCGACGAGAGCGAGATTAAGGTTGATAATATCAAGATCGACAAGGAGTCG
89760 C T AGGAGTCGATGGATATGTTGGCGAGTATCGGAATGGCTGATTTGCCTGGACTCGAGCTGGTTGCTGATGTTGGAACTGTGCCTCAACAGGTTGGATTTGG[C/T]GGTGGGCGTGGTGGATTTCCTGCTGGTAGGAGGAACTGAGATTGTGTTGGTAATATCTGTTTTGTTCTTTATAAGGTTTTTCAAAT
89760 G T ATGTTGGCGAGTATCGGAATGGCTGATTTGCCTGGACTCGAGCTGGTTGCTGATGTTGGAACTGTGCCTCAACAGGTTGGATTTGGCGGTGGGCGTGGTG[G/T]ATTTCCTGCTGGTAGGAGGAACTGAGATTGTGTTGGTAATATCTGTTTTGTTCTTTATAAGGTTTTTCAAATTTGAATCATTTTTG
89780 T C TATTGCCCGTTAGATCCAAATCTGACGGTTTAGATCTTTCGTCTACATCAAAAACCGAAACCGATTCGAAACTGCTTCTTCCTGAGTCAGATCTGAATCT[T/C]CTTTTTGCTGGTCCTGCGTTTGTTAGTTCACCTCCGGCAAGTGATGTTCCGATCCCCACTTTTTGCAGGAATAACAACAAAACCATGGCA
89780 T C GAATAACAACAAAACCATGGCAGCTGGCCTGAGAAATTTGTTGAAGCTATAATCACTGCAGCGGCTAAAGAATTTCTGGATGTTTTCTTTTTTCAAACTT[T/C]GGGTGATTCTGAATATTTTTTTCAAAGGAATCACCCGGATTTTCTGAAGGTTAGATCCATGAAGAAGTTATTTACTTTTAGTTCCTTTTG
89780 AT A CATGGCAGCTGGCCTGAGAAATTTGTTGAAGCTATAATCACTGCAGCGGCTAAAGAATTTCTGGATGTTTTCTTTTTTCAAACTTTGGGTGATTCTGAAT[AT/A]TTTTTTTCAAAGGAATCACCCGGATTTTCTGAAGGTTAGATCCATGAAGAAGTTATTTACTTTTAGTTCCTTTTGTGTATTGCTAATTAA
CCTGGTCGGTCCAAGCTTCATGAGCTGATCGGTCTTGGAAGCAAGTGGTG
89800 C CCACCAGACCGTTGTCGAGGTTACCACCTCCAACTCGTATGGGCAACAGCATCACCTCTGGTCGGGCAAGAAGCTCTGATGGGGACTCCTAAACTCCATA[C/CCTGGTCGGTCCAAGCTTCATGAGCTGATCGGTCTTGGAAGCAAGTGGTG]CTGGTCGGTCCAAGCTTCATGAGCTGATCGGTCTTGG
89806 A C GTTCCAAGTCGAATCCAACATCTTTCAGAAAGCAATAATAAGTACCAAATGTTATGTTGCAAAACTTGAAGATTATTACATTGTAGAACAAACTTCCAGG[A/C]AGAGAGTTTCCTACTAGTTGTGAATTAAACATAGCATAAATAAAACACAGGAAAATAATGCTTCCGATATTGTAAAGAGGAACACTCA
89818 C G CCCTACGAGAAAGAATGGCGACATTTTCTGAAGCTCCGCCTGGAAACGAGAAAGCTGGAGAGAAGATCTTCAAAACTAAGTGCGCTCAATGTCACTCCGT[C/G]GAAAAAGGGGCTGGTCACAAACAAGGTCCTAATTTGAATGGATTGTTCGGAAGGCAGTCTGGAACAGCTGCTGGATATTCATATT
89818 C T GAACAGCTGCTGGATATTCATATTCTGCTGCGAACAAGAACAAGGCTGTGGTTTGGGAGGAAAATACATTGTACGAATACTTGCTTAATCCAAAAAAGTA[C/T]ATCCCTGGAACAAAGATGGTGTTCCCTGGTCTGAAGAAGCCACAGGACCGTGCGGATCTGATTGCCTACCTCAAAAAAGCTACAGC
89818 G A AAAATACATTGTACGAATACTTGCTTAATCCAAAAAAGTACATCCCTGGAACAAAGATGGTGTTCCCTGGTCTGAAGAAGCCACAGGACCGTGCGGATCT[G/A]ATTGCCTACCTCAAAAAAGCTACAGCTTGATTTTCTGAATCAACCTGGCAATCTGTTTGTAGCTAATGAGGCCTCTGGGTATCGCCA
89818 A G ACAAAGATGGTGTTCCCTGGTCTGAAGAAGCCACAGGACCGTGCGGATCTGATTGCCTACCTCAAAAAAGCTACAGCTTGATTTTCTGAATCAACCTGGC[A/G]ATCTGTTTGTAGCTAATGAGGCCTCTGGGTATCGCCATTATTGAAAACAAGCTTAAGTCGTTGCCTCGATAGCATTTATT
89818 G T GTGTTCCCTGGTCTGAAGAAGCCACAGGACCGTGCGGATCTGATTGCCTACCTCAAAAAAGCTACAGCTTGATTTTCTGAATCAACCTGGCAATCTGTTT[G/T]TAGCTAATGAGGCCTCTGGGTATCGCCATTATTGAAAACAAGCTTAAGTCGTTGCCTCGATAGCATTTATT
89862 T C AAGCTTTACGTGGGGCAGATTGTGTATTTCACCTTGCTTCATATGGCATGTCCGGTAAGGAAATGCTTCAAGCAGGACGTGTTGACCAGGTCAACATAAA[T/C]GGGACATGCAATATATTAGATGTATGTCACGAGGTTGGCGTCAAAAGACTCATCTATGTGAGTACATACAACGTAGTATTTGGTGG
89862 C T GTGGGGCAGATTGTGTATTTCACCTTGCTTCATATGGCATGTCCGGTAAGGAAATGCTTCAAGCAGGACGTGTTGACCAGGTCAACATAAATGGGACATG[C/T]AATATATTAGATGTATGTCACGAGGTTGGCGTCAAAAGACTCATCTATGTGAGTACATACAACGTAGTATTTGGTGGAAAGGAGAT
89888 A G TGGGGTAAGGGCATCGCTTCTGATGCGGTCAGGTTGGTACTCAAGGAAGTGTTTGATGAAATGCCTGAGTTAGAAAGGGTTGAAGCTTTGGTCGATGTGG[A/G]AAACTTTGCAAGTCAGAGGGTTCTGGAGAAGGTTGGGTTTCTGAAGGAAGGCGTTTTGAGGAAGTATGGTTTTACCAAAGGGAA
89906 T C TCCTTTAGTTTCTACATCAGTATTGAATATTTTTTGCAGCAGCTCTTTACTTCAATTTTCCTTACTCAGATGGCTCCTTTGCTGCTTCTGCTCTTTCTAT[T/C]TGCAATAGCTGGAAGTTCAGATGCTGCATGGTGTGTGTGCAAGCCTGATGCAAGCAGTGCTGATCTTCAAAAGGCATTAGACTATGCTTGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
89906 G A CCTTACTCAGATGGCTCCTTTGCTGCTTCTGCTCTTTCTATTTGCAATAGCTGGAAGTTCAGATGCTGCATGGTGTGTGTGCAAGCCTGATGCAAGCAGT[G/A]CTGATCTTCAAAAGGCATTAGACTATGCTTGTGGAGCTGGTGCCGACTGCAACCCTATTCATCAAAATGGACCTTGCTATAATCCCAA
89918 A G GGGTTTTATTAACTCCCACTACTGACCTTGGGAAGATTTTGGCCTGCATGCATGGTCTGGATATGGGTGGTGAGATAAATCTCACAGCAGGGATTCAAAT[A/G]GCACAATTGGCTTTGAAGCATCGCCAGAATAAAAATCAGCAACAAAGGATCATTGTTTTTGTAGGGAGCCCAGTGAAATATGAGAA
89918 T C TCCCACTACTGACCTTGGGAAGATTTTGGCCTGCATGCATGGTCTGGATATGGGTGGTGAGATAAATCTCACAGCAGGGATTCAAATAGCACAATTGGCT[T/C]TGAAGCATCGCCAGAATAAAAATCAGCAACAAAGGATCATTGTTTTTGTAGGGAGCCCAGTGAAATATGAGAAAAAGACATTAGAG
89918 A G CAGGGATTCAAATAGCACAATTGGCTTTGAAGCATCGCCAGAATAAAAATCAGCAACAAAGGATCATTGTTTTTGTAGGGAGCCCAGTGAAATATGAGAA[A/G]AAGACATTAGAGGCAATTGGTAGAAAGCTGAAGAAGAATAGTGTCTCGCTGGATGTCATTGATTTTGGAGAATCGGAGGATGGA
89922 G A GAGACACCCTCGTCCCAAGTGCGAGCTTTCTGTAGAGATACACCGCTGCCTTTCAACGCTACGATGTCATCGCCCACGGCAACCGAGGCGAAGGAGCGAT[G/A]ACTAAAGGCCCGTGCTGCAGCTGTAGTGATTGCAACCGACGCTCTGATTCTTCCCATCATAGCCGACATTTCCTTTCTGTTTCTTCG
89952 T A TTACAGGCAAGGGAAACAGTGCAAAACCAGAAGGTTTAACGGACATTGTAAAGGCAGGTGCCATGGGGTTGAAGTTGCATGAAGATTGGGGAAGCACACC[T/A]GCTGTGATCGATAATTGCCTTGCTGTTGCAGATGAATTTGATATTCAGGTGAATATCCACACTGATACGCTAAATGAATCTGGAT
89956 C T GTCCTGGACCGTCACCGTCCCCATTTTCTACCCGTGACCAGACGTCGGTTTCCGTTCCGATGTCCTTCGCTACTGGATCCATAATAGGAAAGAAATTCTA[C/T]AAACAGGTTACTACAAGAGAAGCTGAAGATGGCAATGGATGGAGCGTCATGTTGGATTATAGAACGTTGAAGACCCCTGCCAAGCGC
89992 C T TCGCCGCTTCCTTGTGCTGCGCCAATGGTTTCAGAGTTGTTATTTGAAGAAGGCATTGCATATGGATTAAATGGGTGTGAACCCGG[C/T]GGGAAAGAAGGATGAGCATACATTCCTCCAGGATACATGACATATGGATGAGGAGGTGTACCATAAGGAGACATGACGGGCTGAGGTCCCCACATGTAA
89992 A T GATGAGGAGGTGTACCATAAGGAGACATGACGGGCTGAGGTCCCCACATGTAAGGTTGAGCCAGGGAACCCGATGCCATGGGTGAAGGAAAGTACGCAGG[A/T]GGTGGAATTGGCGAATATGCCTGAAAGCTAGACCAATCACCATATGCTGGAGCAACTGGAGTTTGATCCTGAGCTAAAGCGG
89994 C T TTGGGTTGAAGTATTACGCGACACTGTACAATTTTGGAGCGCTTGCGACTCCGATTGGGTTGTATGTGTTGAATGTGAAGATTACAGGGCAGTGGTATGA[C/T]AGAGAAGCTGCTAGGCAGAACAATGGAGTGAGGGAGGCTACTTGTATGGGTGTGGTTTGTTTTAAAAAAGCTTTTCTTGTGATTGT
89994 T A AGTATTACGCGACACTGTACAATTTTGGAGCGCTTGCGACTCCGATTGGGTTGTATGTGTTGAATGTGAAGATTACAGGGCAGTGGTATGACAGAGAAGC[T/A]GCTAGGCAGAACAATGGAGTGAGGGAGGCTACTTGTATGGGTGTGGTTTGTTTTAAAAAAGCTTTTCTTGTGATTGTTGGAGTGA
89994 T C TTCTTGTGATTGTTGGAGTGACTGTTTTTGGTGCTCTTGTTTCGTTGATTTTGGTGTGTAGGAGTTGGGGTTTTTATAAAGGGGATATCTATAGAAGATT[T/C]AAAACGGAAGGGTGGAAGATGAAAACAAACTTGACAGTGAAGTGGCGATGGAGAAAGTAGATGAGAAGCGTGAAGAACGGAGATA
89994 G A TTTTTATAAAGGGGATATCTATAGAAGATTTAAAACGGAAGGGTGGAAGATGAAAACAAACTTGACAGTGAAGTGGCGATGGAGAAAGTAGATGAGAAGC[G/A]TGAAGAACGGAGATAAATGCAAGTCAAGCCTTCGACTTGAAAGCAAAGCTTCAATTTCAAATATGCAAATTGTGTGTTGGATTG
89994 C G AACTTGACAGTGAAGTGGCGATGGAGAAAGTAGATGAGAAGCGTGAAGAACGGAGATAAATGCAAGTCAAGCCTTCGACTTGAAAGCAAAGCTTCAATTT[C/G]AAATATGCAAATTGTGTGTTGGATTGTAATTTCGATAGTAGAAAATGCACTGCCCTAGGCACAATCGGGTCGTGAGAGAATT
90000 T TA TTGAAGATAGACATGGAAGAAGAGTTAGTGATGTTCAACCGTAGATGTTCGAGCTCTAAAACTAGAGGAGAAAACAGCAAGGGAGGCAGTCTGCATTGTG[T/TA]AAAGAGTCCTATGAGGATGAAAAGAACTATGTCGAGTGGGAGGCTTGGGTTTTCTAGGCAGGGGAGGGGCAGGAACACTTTG
90000 G GA TTGATTGATTGCAACGTTTTTGATGGTAGGAAGTCTATATGATTTGTTTTCAATGGTTTTGTTCAAGATGATGAATATACATCCTTGGTTGTTTGCAATG[G/GA]AAAAAAGAGAGAAAGAAAATGAACACTACAGCATGTGTGTCTGTTTTAGTGCAATGAAAGTCAGATGTTTTAGCAAAAAAAAAAAAA
90016 A G AACATCTCATAAGCGATCAAATGAACTTCACAAATTTAGTCCCTATTTTCCCAAAAAGCCCGCGCTTTCCTAAAATAGTCCCAAAAGCGTCGAAAGACGT[A/G]CCCTACAGCTTTAGGTACCCTCAAATGATGAAAAAGCCCCGATGGTTTTGGCGTACCCTAGCCTGCATACCCTACCTCATGCCCTT
90030 A G GACTATTACGGCAAAAGAATAGCGACATCATCTTCAGACTCCACAGTTAAAATAATCGGAGTGAGCGGGTCGACCCACACCCTCCTAGCCACTCTCACAG[A/G]CCACCAAGGCCCAGTCTAGCAAGCTGCATGGGCCCATCCCAAGTTTGGGTCCATGATCGCCACATGCAGTTATGATGGTCGAGTCA
90030 C T CAAAAGAATAGCGACATCATCTTCAGACTCCACAGTTAAAATAATCGGAGTGAGCGGGTCGACCCACACCCTCCTAGCCACTCTCACAGACCACCAAGGC[C/T]CAGTCTAGCAAGCTGCATGGGCCCATCCCAAGTTTGGGTCCATGATCGCCACATGCAGTTATGATGGTCGAGTCATCATCTGGAAAG
90030 A G ATAGCGACATCATCTTCAGACTCCACAGTTAAAATAATCGGAGTGAGCGGGTCGACCCACACCCTCCTAGCCACTCTCACAGACCACCAAGGCCCAGTCT[A/G]GCAAGCTGCATGGGCCCATCCCAAGTTTGGGTCCATGATCGCCACATGCAGTTATGATGGTCGAGTCATCATCTGGAAAGAAGGCA
90068 T A CCCCCATTCCTCTTTAAATTCCTTTCAACTCTGGTACTATACCGTCATCTTCCCTAAAATGGGCTCTTTCCTTATCCACTTACTAGGCAGTACCTTCTGG[T/A]GCTTGCTCTTCTTCGCTGGAGTCGGCAACGTCTTCTGTGCCCAGATCAATGCGAATGCCACTCAAGCCACTGCTGTGGTTAACGCCAATTT
90068 G A ATTCCTCTTTAAATTCCTTTCAACTCTGGTACTATACCGTCATCTTCCCTAAAATGGGCTCTTTCCTTATCCACTTACTAGGCAGTACCTTCTGGTGCTT[G/A]CTCTTCTTCGCTGGAGTCGGCAACGTCTTCTGTGCCCAGATCAATGCGAATGCCACTCAAGCCACTGCTGTGGTTAACGCCAATTTTCCGA
90072 T C CGTACGCTGACCACAAACGTTGCAAGTAAAAGCGACCCGCATGCGTCGCCTTGGCGATTTCGTGAACAAGGACCAAGGAAAAGTCGATATGAGCTGATTA[T/C]CGAAATCGGCTTCGGGCTCAGGCGGTCCTTGCATGCCCGACCCGGTAGTCCAACCCCTCCCTGTTGCTGCGCTTAGCACCAGTCCC
90078 C T AACAATGGGAAATAAATCGGAGTATAACATCAATACAAATTAGTATAGATAACAGGTATCTATCCATCCATATACCAAA[C/T]ACGAAATATATAATATAATGATCTTAAGCTGTTGGTTTCTCCCACTTGAGTGGTTTAACAATTTCCCAAGTGAAGTCGGGGTCATCCCTTCCAAAGTGTC
90078 G C AACAATGGGAAATAAATCGGAGTATAACATCAATACAAATTAGTATAGATAACAGGTATCTATCCATCCATATACCAAACACGAAATATATAATATAAT[G/C]ATCTTAAGCTGTTGGTTTCTCCCACTTGAGTGGTTTAACAATTTCCCAAGTGAAGTCGGGGTCATCCCTTCCAAAGTGTCCATAAGCTGC
90078 A G TAATATAATGATCTTAAGCTGTTGGTTTCTCCCACTTGAGTGGTTTAACAATTTCCCAAGTGAAGTCGGGGTCATCCCTTCCAAAGTGTCCATAAGCTGC[A/G]GTCTTCAAAAACCTGTTATTTCCACCTCTCTTCAAGTCAAGGTTGATGGTGATCATCCCGGGCCTGAAATCAAAGCTCTCCTTCACAATC
90078 G A TGAAGTCGGGGTCATCCCTTCCAAAGTGTCCATAAGCTGCAGTCTTCAAAAACCTGTTATTTCCACCTCTCTTCAAGTCAAGGTTGATGGTGATCATCCC[G/A]GGCCTGAAATCAAAGCTCTCCTTCACAATCTTCAAAATTTCCTTATCCGGTATCTTACCAGTTCCGTAACTATCCACAAACACCGACAAC
90078 A G CAAGGTTGATGGTGATCATCCCGGGCCTGAAATCAAAGCTCTCCTTCACAATCTTCAAAATTTCCTTATCCGGTATCTTACCAGTTCCGTAACTATCCAC[A/G]AACACCGACAACGGCTCAGGGACACCAATAGCGTAGGATACCTGCACAATGCAACGTCTAGCGAGTCCGTTAGCGACAATGCTCTTTG
90078 G A CAAAGCTCTCCTTCACAATCTTCAAAATTTCCTTATCCGGTATCTTACCAGTTCCGTAACTATCCACAAACACCGACAACGGCTCAGGGACACCAATAGC[G/A]TAGGATACCTGCACAATGCAACGTCTAGCGAGTCCGTTAGCGACAATGCTCTTTGCAGCCTGCCTGACAATGTAAGCGCCGCTCCTGT
90078 G A TAGCGTAGGATACCTGCACAATGCAACGTCTAGCGAGTCCGTTAGCGACAATGCTCTTTGCAGCCTGCCTGACAATGTAAGCGCCGCTCCTGTCCACCTT[G/A]GTTGGATCCTTACCCGAAAATGCACCACCTCCGTGGGCTCCCCAACCACCGTAGGTGTCGATGATGATCTTGCGACCTGTTAGACCC
90086 C T AAGGATGAATGTTTAGTGGTGTTATACCATAACTCGGCCCAAGGCAAGCAAGTCACCCATTTTCTTGGTACATCCCCTACCACTGCTCGTAAATAATTCT[C/T]GAGACATCTGTTAACCACTTCGGACTGACCATCCGTTTGCGGGTGGTACGCACTGCTCATGCGCAGTTTAGTTCCATGCAAGCGAAAT
90128 T C GGGGTTTCCTAGAGCTGGATTTGGTTTTAGGGAATTGGGTTGAAGAGAATATCAAAAATATGGATGATGCAAAGATCAAAGCTTTAGTGGATGTTCTGGA[T/C]TTGGAAAATCCAGATTTGTGGAAATGGTTAACTGATCAGGAACAACCACCAGAGGCAGTGAGCAGCAACCCAGTATTCGCAGCTG
90128 A G AAGAGAATATCAAAAATATGGATGATGCAAAGATCAAAGCTTTAGTGGATGTTCTGGATTTGGAAAATCCAGATTTGTGGAAATGGTTAACTGATCAGGA[A/G]CAACCACCAGAGGCAGTGAGCAGCAACCCAGTATTCGCAGCTGTTCGATCACGAGTTGTGGAAAATCTGACTCGGTCTGCTCCAG
90140 T C CTGTTGGCCTACTGGATTTCTAAGTCAGTCTAAAGCTGCAAACTTATTTCAAGTGGCCACATCTTATATTGATGAAGACCTACTGGGGTCTGAG[T/C]TCTCCAAAGCATTTGGAGGAACCAAGGGGCTAGACATGTTTTTCCCCTTCGGTTCATGTCTTTTGAAGGAATCTTGCAGATTCATCAGGCCCAA
90140 A T TCCAACCATTATGACACAACCATGATGATGTTGAAGTTGAATTATATCTCGGCAGGATGTCAATAACGGCCAAATTATCTACTTTTCATTACCTTGTGGA[A/T]GATAAATTTACCAGTGGCACCCAAATGCCTGCCAGATTGAGCCTTCGGTGAGCTAGCCCATAAGAATTTGTAATTATCAGCTGTACTAG
90144 G A CAAATCAAGGTCATAAACAAAACAATATTAATTCATATACAACACCAGAAGACAGGGCAGACAACTCTGCGATCATTTCTTGAGAACAATAGGAAGAACA[G/A]TAACGAGAATGATGATCAACAACAAAACAATGGCGTAACAGGTCCACTTTCTACTATTCTTCTGGCTTTTCCTTGCCTCCACGAGTTG
90144 C T TCAAGGTCATAAACAAAACAATATTAATTCATATACAACACCAGAAGACAGGGCAGACAACTCTGCGATCATTTCTTGAGAACAATAGGAAGAACAGTAA[C/T]GAGAATGATGATCAACAACAAAACAATGGCGTAACAGGTCCACTTTCTACTATTCTTCTGGCTTTTCCTTGCCTCCACGAGTTGTTCG
90144 C G CCACATGGCCTCGCCCTTGTTCTTCGATTGCTCGTTGGAGGAAGCGCTCCCCTTCTCCGGTTGAGATTAGGGTTTCCACCATCTCCTCGCTCGGTTGTTC[C/G]CCTGTTACCGTGTAGTACCTTCGTTGAATGGTTTCTTTGTACTCATTACCAATCTCCTTTCTCAAATCCTGAAAACTCTCCAT
90150 GT G TGGAGTCGACATATACACTGGGCATCGGAGTTGGCATACCGGGTGTTGGAGGCAGTTGAGACTGGGTGGATGGATTGGCTGCAATTGGAAATGCAAATTC[GT/G]TTTTCCTTTTATTAAGAACTCAAGATGAAAAACAAGTTTTTGCCTGGTCGTCAAGGATTTGGGATCTTGGTAGTTCAGCGAAGA
90154 A T CAGTACAACTTCCATCAAACAAAACAATTAACCCACAATTCGAGAAATAGAAAACAAAAGTACAAAACATGTAATAGCCAACGGTT[A/T]ACACATATTACTACCTTACTCTTATCCTCCTTTTCAGCTTCAGCAGCCCTTTTAAGTCTTTTTCCATGGTGACGCTTGTTTGTTCGTTCAAGGCGAAGCT
90154 C CT CAACTTCCATCAAACAAAACAATTAACCCACAATTCGAGAAATAGAAAACAAAAGTACAAAACATGTAATAGCCAACGGTTAACACATATTACTACCTTA[C/CT]TCTTATCCTCCTTTTCAGCTTCAGCAGCCCTTTTAAGTCTTTTTCCATGGTGACGCTTGTTTGTTCGTTCAAGGCGAAGCTTCTGATATG
90154 GT G AGAAATAGAAAACAAAAGTACAAAACATGTAATAGCCAACGGTTAACACATATTACTACCTTACTCTTATCCTCCTTTTCAGCTTCAGCAGCCCTTTTAA[GT/G]TCTTTTTCCATGGTGACGCTTGTTTGTTCGTTCAAGGCGAAGCTTCTGATATGCTCTGAATGATCTCATTTCCTCATTGATCTTCACAAG
90154 C T TTTTTCCATGGTGACGCTTGTTTGTTCGTTCAAGGCGAAGCTTCTGATATGCTCTGAATGATCTCATTTCCTCATTGATCTTCACAAGATCAACAGAAGG[C/T]TTCTCAAGAGCGACAGGCATGAACGCACCTTTGACCTGAGTTGCTGATGCAAGCTCTTCAACACTCGAATCCCCACTCTTGACTTTGCCA
90154 C T TGACGCTTGTTTGTTCGTTCAAGGCGAAGCTTCTGATATGCTCTGAATGATCTCATTTCCTCATTGATCTTCACAAGATCAACAGAAGGCTTCTCAAGAG[C/T]GACAGGCATGAACGCACCTTTGACCTGAGTTGCTGATGCAAGCTCTTCAACACTCGAATCCCCACTCTTGACTTTGCCAGGGCGTCGTG
90154 C T TTCGTTCAAGGCGAAGCTTCTGATATGCTCTGAATGATCTCATTTCCTCATTGATCTTCACAAGATCAACAGAAGGCTTCTCAAGAGCGACAGGCATGAA[C/T]GCACCTTTGACCTGAGTTGCTGATGCAAGCTCTTCAACACTCGAATCCCCACTCTTGACTTTGCCAGGGCGTCGTGGAAAAACTAGAA
90154 T C CAGGCATGAACGCACCTTTGACCTGAGTTGCTGATGCAAGCTCTTCAACACTCGAATCCCCACTCTTGACTTTGCCAGGGCGTCGTGGAAAAACTAGAAG[T/C]TTTGCCGTGTACTCCTTCAGCCTCTGCACATTAGCTTGCATTCCTTCCAAGGACCTGTTCCTCCTCCTGTGGTCCACGGCAATCCCAAC
90166 G T TGAAGTTCCCTCCGCCTCCGCCGGATGACGTAGTTCTCCGACGACGCATGCCAGCCGTTGCTGCGGCGGATCCACGGGGTCCCACAGTCGTCGGACGGGC[G/T]GTTGCGCCTGCTGAGGAGGTAGTCTGCGATTGGGAGCTGCCTTTCGCCATTATCGTTGAATTGTTTTGTCCTGGCTGAGATTATTT
90172 T C CACCATCCATGGCGGCTGCTACCACCTCTCTTCTTTCAACGCAAGCTTACTTGGAGTGCGATCTGGTAAAATCGACTCGCTCCCTCGTCTCTGAACTCTG[T/C]CGCCACTTTTACAGCCAGGGTTGGGTTTCCGGTACCGGAGGTAGCATCACCATCAAAGTACATGACGATTCCGTGCCCAGACCTAATC
90172 T C CGCCTAAGTGTACAGATTGCGCTTCATTATTCATGAAGGCATATGAGATGCGCAATGCTGGAGCAGTCATTCACAGTCATGGCATGGAATCATGCCTTGC[T/C]ACAATGATCCACCCTTCCTCCAAGGAGTTTCGAATAACTCACATGGAGATGATTAAGGGAATTAGTCGTGGG
90188 A G ACCATTTGGTCCATTTTAATTTGACATTGACAAAGATTATCAACTGCAGCACACGTCCTCGCCTTCCCTGTCTTACTGAAGTCTGATTGCAGCAGTTGCC[A/G]CCAGTGCATCATTGCCACCGTTCTAATCATTCTGGAGTCCCTGGTTCTAGAATGTCACGTCTGACTGTTTATTTTTTTACTGTGCCGGCTG
90188 G A CTGTCTTACTGAAGTCTGATTGCAGCAGTTGCCACCAGTGCATCATTGCCACCGTTCTAATCATTCTGGAGTCCCTGGTTCTAGAATGTCACGTCTGACT[G/A]TTTATTTTTTTACTGTGCCGGCTGATGGGGAGTAGTGCCCCAGACTTTAACGATGCCCAAAGTGGATGCATTCTCAGATGGCC
90188 C T TTGCAGCAGTTGCCACCAGTGCATCATTGCCACCGTTCTAATCATTCTGGAGTCCCTGGTTCTAGAATGTCACGTCTGACTGTTTATTTTTTTACTGTGC[C/T]GGCTGATGGGGAGTAGTGCCCCAGACTTTAACGATGCCCAAAGTGGATGCATTCTCAGATGGCC
90192 C A TTTGGAAGAAAAAAAATCTCTAAAACTGAATGTTCAAAAGAATCCACAGTCCTAATACATCAG[C/A]TTCAATTCAACATCTAAGGTACACAATCTCCAAAACATGCATAAATTAATCTGAGAAGGTTAAGATCTCCTTCAGCTACATTTAAAAAGAGAACAAACTT
90192 C T ATCCCGCACCTTGAAGGGCCTCATGCACGCAGACCAACATCGGTTGCCCTCTTGTCCTTCCACGATGTATGGTGATTGTTGATTCGGTACAAATCGTCCA[C/T]GATTGTCGTTGCACAAAGCTCTTTTATCCATTAACTGTAAGTTCAGTTGGAGTTTCCATCGCAGAAGAAGGTAGATCAGAACTACTCG
90192
CATCGCAGAAGAAGGTAGATCAGAACTACTCGGCAAGGGA
C TTCCACGATGTATGGTGATTGTTGATTCGGTACAAATCGTCCACGATTGTCGTTGCACAAAGCTCTTTTATCCATTAACTGTAAGTTCAGTTGGAGTTTC[C/CATCGCAGAAGAAGGTAGATCAGAACTACTCGGCAAGGGA]ATCGCAGAAGAAGGTAGATCAGAACTACTCGGCAAGGGAGAAAAGGA
90206 A G CTGCCTTTACTCCTCCGCAGCCAGCAAACAAAGAGCCGGACGCCGATCCCAACCCCAATCTCTTTGTTTCAGGTCTTAGCAAAAGAACAACAACAGAA[A/G]GGTTAAGGGATGCCTTCGCTAAATTTGGTCAAGTAATTCATGCTAAAGTAGTCACAGATGCTAGATCTGGTTACTCCAAGGGATTTGGT
90206 A C TCATGCTAAAGTAGTCACAGATGCTAGATCTGGTTACTCCAAGGGATTTGGTTTTGTGAGATATGCAACCTTGGAGGAGGCAATGAAAGGCAAAGAGGGC[A/C]TGGATGGCAAGTTTCTTGATGGATGGGTTATCTTCGCAGACTATGCCAGACCCCCAAAACCCAGACCTCCTCCTCAAGAGAATTAC
90206 T A CCTTGGAGGAGGCAATGAAAGGCAAAGAGGGCATGGATGGCAAGTTTCTTGATGGATGGGTTATCTTCGCAGACTATGCCAGACCCCCAAAACCCAGACC[T/A]CCTCCTCAAGAGAATTACCAGCCCCAACCCCAGTCTGCATACGATCCTTCACTGTATTATCGCAATCAGTAACCTTTTAAAGGTTCT
90206 A G GCAAGTTTCTTGATGGATGGGTTATCTTCGCAGACTATGCCAGACCCCCAAAACCCAGACCTCCTCCTCAAGAGAATTACCAGCCCCAACCCCAGTCTGC[A/G]TACGATCCTTCACTGTATTATCGCAATCAGTAACCTTTTAAAGGTTCTCGCTTAATAATTAAGTTATCGATTAAGGTTATAAAATTACCT
90206 C T CTATGCCAGACCCCCAAAACCCAGACCTCCTCCTCAAGAGAATTACCAGCCCCAACCCCAGTCTGCATACGATCCTTCACTGTATTATCGCAATCAGTAA[C/T]CTTTTAAAGGTTCTCGCTTAATAATTAAGTTATCGATTAAGGTTATAAAATTACCTATAATTGTGGACTATGGCGGATATGTGTGCTAGA
90206 A T AAGGTTCTCGCTTAATAATTAAGTTATCGATTAAGGTTATAAAATTACCTATAATTGTGGACTATGGCGGATATGTGTGCTAGATACAATTATCATTGGT[A/T]TTTGTGTATGACTGGAAGATTCTGAGAATCATTTGCTCAGAAGTTTTGTTATATTATGGGACATTAACTTTCTAAAAAAAAAAAAAAA
90206 G A CTCGCTTAATAATTAAGTTATCGATTAAGGTTATAAAATTACCTATAATTGTGGACTATGGCGGATATGTGTGCTAGATACAATTATCATTGGTATTTGT[G/A]TATGACTGGAAGATTCTGAGAATCATTTGCTCAGAAGTTTTGTTATATTATGGGACATTAACTTTCTAAAAAAAAAAAAAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
90212 A C ACTTCATGTGACTCTTAACAAGCTGACCAGAAGCAAGTGCCCCCATCAAAGATAGTTCACCAGCCAAAACCGAACCGGCCACAACAGTCGCTAACAACCT[A/C]GCGTTAGATCCAGGTGATTCGACGCTTGCGCCCTTCACCCCAAGCAGGTCTAAGCATGCTGACTGGGACGCCAGTTGGGTCCCACC
90212 A G TAGCGTTAGATCCAGGTGATTCGACGCTTGCGCCCTTCACCCCAAGCAGGTCTAAGCATGCTGACTGGGACGCCAGTTGGGTCCCACCGCCAACCGTACC[A/G]ACCTCAATGGAGGGCATGGTGACCGAAACATGTAGGTCTCTGCCTTCGTTCACGGCTTCCATCATGGTGATGCAGTGCGAGCTCTC
90212 G A TGACCGAAACATGTAGGTCTCTGCCTTCGTTCACGGCTTCCATCATGGTGATGCAGTGCGAGCTCTCTATGTTTTGGGCTGGGTCTTGGCCCGTTGCTAT[G/A]TATATGGCTGATACTATGTTGCTCGCGTGCGCGTTAAAGCCGCCTAAGGATCCTGCTACTGCCGATCCTGCTAGATTCTTCACTGTGT
90228 G T CACTGTTGGCCTACTGGCTTCGTCATCCCGCAACATAAAAGCACACCGTAAAAGTACTAAAGGGGCACCAGGG[G/T]TCCGACCTTTTGATTCCAACTTCGTTAATGGCGCGAGCTTTAGAGTACTTAGACACACAAAGGAAGGCGCAGCCTGACCTCGAAGACTGGTACAGTGTGC
90228 G A AAGATGGCGCTATTAAGTATCTTGAAAGTGTTATTGAAAAGGTTCAGGCTACAAAGGAGTCCGGTATTGAGGAACCAATCCTGTATGTGAAGATGCAAAT[G/A]GCTGCATTATATCTTGAAAAAGGAAGTCAAAAAGAATGTAGAAGTATATTATATGATGGAAAGACCACTCTGGACAGTATGAATGA
90252 A T TGTCATGATTCTAGAGGAGAAGAAGGAAGGTGTGTGGTTGGAGCAATAAACAATTATACAGAACAATTGTATAGCTATGGAAGTTCAATCACAGGATATA[A/T]CTTAACTGAAAGCCTTATGTTCCTTGCACATTTTGTTGGAGACGTACACCAACCTTTGCATGTAGGATTTGCGGATGATGAGGGTG
90264 C G TAAGCCCAGAGAAAGAAGCATCAGCTGCATTAACCTTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAA[C/G]TTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGAT
90264 G A TAAGCCCAGAGAAAGAAGCATCAGCTGCATTAACCTTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATC[G/A]TATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGAT
90264 A C AAGCCCAGAGAAAGAAGCATCAGCTGCATTAACCTTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGT[A/C]TGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATA
90264 G A TCAGCTGCATTAACCTTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGC[G/A]TGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACC
90264 C T TGCATTAACCTTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGAT[C/T]GAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATA
90264 G T TTTCTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGA[G/T]CCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGC
90264 A G CTGCTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCC[A/G]GAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTG
90264 G A CTACCATTTTCATCCCTTTGTTGTACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGA[G/A]ATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAAC
90264 A G ACTCTTCTATCACCGCACAGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACAT[A/G]AGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGA
90264 G A AGAACTTGAAGTAATCGTATGGCCAAAGAGAGCGTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGA[G/A]GATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAG
90264 A G GTGCGTGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCT[A/G]TTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAAC
90264 C G TGATCGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGG[C/G]TGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAACTTGAG
90264 A C CGAGAGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGA[A/C]CGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAACTTGAGATCA
90264 C T AGGGGAGCCAGAGATAGTGAAGCCCTCGGACCACATAAGCTTGGAGAAAAAAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGC[C/T]CGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAACTTGAGATCAACACC
90264 G A AAGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTG[G/A]AACTCTAAATTATGAAGCAACTTGAGATCAACACCATGGCATATGACTTGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAG
90264 A G AGAGGATATCGGGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGG[A/G]ACTCTAAATTATGAAGCAACTTGAGATCAACACCATGGCATATGACTTGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAGT
90264 A G GGGCAAGCCCGTAACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATT[A/G]TGAAGCAACTTGAGATCAACACCATGGCATATGACTTGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAGTGAGACTGCATC
90264 G T AACCCGATATGCTATTGGCTGAACGCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAACTT[G/T]AGATCAACACCATGGCATATGACTTGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAGTGAGACTGCATCGGGCGAGGAAAG
90264 T C GCCCGGCCTTGAGCTTTTGTTGAGTGGGTAAAGAGAACAGTCTTTTGGCTTGGAACTCTAAATTATGAAGCAACTTGAGATCAACACCATGGCATATGAC[T/C]TGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAGTGAGACTGCATCGGGCGAGGAAAGGTCGATAACGGGTACGGATTCGT
90264 A T TCAACACCATGGCATATGACTTGAAACACGCCCCATGATTCACAAGCTTGGCCTATGAGTGAGACTGCATCGGGCGAGGAAAGGTCGATAACGGGTACGG[A/T]TTCGTTGGACCCGCTGGCAGGGTTGGGTTGGATAGTGGGCCAAGTGTGGGAGTCAGGGACTTCTAGGGCCGATTCGAGATCGA
90264 TG T AACACGCCCCATGATTCACAAGCTTGGCCTATGAGTGAGACTGCATCGGGCGAGGAAAGGTCGATAACGGGTACGGATTCGTTGGACCCGCTGGCAGGGT[TG/T]GGGTTGGATAGTGGGCCAAGTGTGGGAGTCAGGGACTTCTAGGGCCGATTCGAGATCGAAGTGTTTAGGATGATGGATGGG
90264 T G CTGCATCGGGCGAGGAAAGGTCGATAACGGGTACGGATTCGTTGGACCCGCTGGCAGGGTTGGGTTGGATAGTGGGCCAAGTGTGGGAGTCAGGGACTTC[T/G]AGGGCCGATTCGAGATCGAAGTGTTTAGGATGATGGATGGGTTGAGGGAAGTGGGTTGGTTGTTCCATTGAAATGGAAGGCA
90264 A T TGCATCGGGCGAGGAAAGGTCGATAACGGGTACGGATTCGTTGGACCCGCTGGCAGGGTTGGGTTGGATAGTGGGCCAAGTGTGGGAGTCAGGGACTTCT[A/T]GGGCCGATTCGAGATCGAAGTGTTTAGGATGATGGATGGGTTGAGGGAAGTGGGTTGGTTGTTCCATTGAAATGGAAGGCAT
90270 T A GGTAAAGGTGGAGCCGGAGGCGGTAGAGTCGATATGGGAGGAGGCATGGGTCACCCGATGAAGTATCCAAATTCTATTTTTCAAGGGATTAACGTTGGCT[T/A]GATGGCCCCCTCTCAAACGGGCCATAACATTTATAACATGGTTGCGGCATCTGCGGCTCAAGGGCTGCTGGCTAGTGCCATGCCG
90294 C T CTCGGGTCCCAAGCCCTAAAAAGGAATCGGCTTCTAGATTTCAAAATATGGAACCAATCGGCGGCGGAAACTCC[C/T]TGCCCTCCGCTTCCTCCTCAGATGCCACTAAACGCAAAGTCTGCTACTTCTACGATCCAGAAGTCGGCAACTACTACTACGGACAAGGCCATCCGATGAA
90294 T C CTCGGGTCCCAAGCCCTAAAAAGGAATCGGCTTCTAGATTTCAAAATATGGAACCAATCGGCGGCGGAAACTCCCTGCCCTCCGCTTCCTCCTCAGA[T/C]GCCACTAAACGCAAAGTCTGCTACTTCTACGATCCAGAAGTCGGCAACTACTACTACGGACAAGGCCATCCGATGAAACCACACCGCATT
90294 T C ACTCCCTACTCTCCCACTACAACCTCCTCCCTCTCCTCCAGCTCTACAAACCCAACCCTGCTCGCGACCGCGATCTAACGAGATTTCATTCCGACGATTA[T/C]ATAAACTTTCTTCGTTCTATTACGCCGGAGACGACGCAGGATCAGATCAGAGCTTTAAAAAGGTTTAATGTGGGGGAAGATTGTCCGGT
90294 T C TTCATTCCGACGATTATATAAACTTTCTTCGTTCTATTACGCCGGAGACGACGCAGGATCAGATCAGAGCTTTAAAAAGGTTTAATGTGGGGGAAGATTG[T/C]CCGGTTTTTGATGGGTTGTATAATTTTTGTCAGACGTATGCTGGAGGAAGCGTTGGCGGGGCTGTGAAGCTGAACCATGGGTGTGA
90294 A G CGACGCAGGATCAGATCAGAGCTTTAAAAAGGTTTAATGTGGGGGAAGATTGTCCGGTTTTTGATGGGTTGTATAATTTTTGTCAGACGTATGCTGGAGG[A/G]AGCGTTGGCGGGGCTGTGAAGCTGAACCATGGGTGTGATATTGCGATCAATTGGGCTGGTGGGTTGCATCATGCTAAGAAGTGT
90296 A C ACATGTGGCCTTTTTTTTAGAAAGGAAAAAATAACATAATAAATGTCATGCTACAACGATTTTTCTTTCACGTTTCCCTGTTACCTAAC[A/C]AATCAAAATAACTAGAAACGAATAGTCGTTAACCAATCAATTGTCCGGCCTCGAGTGGAAAAAACTCACTAAGTCCGTCAAAACAAACACCATCACTGAA
90296 C T TCAATTGTCCGGCCTCGAGTGGAAAAAACTCACTAAGTCCGTCAAAACAAACACCATCACTGAACCCCGTCCCCAGAAACGCCGCCACATCATCTTCGAA[C/T]CCCCAAATTCGATCAAACCCTTCGTTCTCCACCTCCACGAGATCCCCACCGTCGGTCGCAGGCGAAGAGGGCTCCGTGTTGACAGCA
90296 A G GTCCGGCCTCGAGTGGAAAAAACTCACTAAGTCCGTCAAAACAAACACCATCACTGAACCCCGTCCCCAGAAACGCCGCCACATCATCTTCGAACCCCCA[A/G]ATTCGATCAAACCCTTCGTTCTCCACCTCCACGAGATCCCCACCGTCGGTCGCAGGCGAAGAGGGCTCCGTGTTGACAGCAGGCGG
90296 A G AAACACCATCACTGAACCCCGTCCCCAGAAACGCCGCCACATCATCTTCGAACCCCCAAATTCGATCAAACCCTTCGTTCTCCACCTCCACGAGATCCCC[A/G]CCGTCGGTCGCAGGCGAAGAGGGCTCCGTGTTGACAGCAGGCGGAATCCCTAATTCGTCATCGGAAGCTTCTAGAAGATACTCGTAA
90296 G A GCGTCGGCGTTACGATCTCCTCCTCTAGGCTTTTCATGACATCTTCGAGTTGGCCGACGCTAGGGTTGAAGTCGTCTTCGTCCAGTATCTCCAACATAAT[G/A]ACTTCGGCTTCTTTAAACCGCTTCGTATCGGACGATGCATCGTCGTCGGTGTCGTCTCGGACTCTCTTATTGCAGCAAAGGGCAGATT
90296 T C TCGGCGTTACGATCTCCTCCTCTAGGCTTTTCATGACATCTTCGAGTTGGCCGACGCTAGGGTTGAAGTCGTCTTCGTCCAGTATCTCCAACATAATGAC[T/C]TCGGCTTCTTTAAACCGCTTCGTATCGGACGATGCATCGTCGTCGGTGTCGTCTCGGACTCTCTTATTGCAGCAAAGGGCAGATTCTGC
90296 C T CCTCTAGGCTTTTCATGACATCTTCGAGTTGGCCGACGCTAGGGTTGAAGTCGTCTTCGTCCAGTATCTCCAACATAATGACTTCGGCTTCTTTAAACCG[C/T]TTCGTATCGGACGATGCATCGTCGTCGGTGTCGTCTCGGACTCTCTTATTGCAGCAAAGGGCAGATTCTGCCGCCATGACTAG
90312 C T TCATGGACTTCGCGAACTGTTCAAAGAACAGTTCATTGCTGTCGGCATACTTCTTAACCAGCTCCATGGTAACACTACTCTTAGTAAACAGTATCTCGTC[C/T]GAACTCAAAAGTCCCCTCCTTGCAACGATGTTCTTGAAGTAGAAGTTGTCGAATTTCATCGGGCTTACATAGTCCAAAACAAAGAGATT
90312 G A CGATGTTCTTGAAGTAGAAGTTGTCGAATTTCATCGGGCTTACATAGTCCAAAACAAAGAGATTTTGATCACCTCCAGACTTTGGACAGTTCTTTTTCCA[G/A]ACAGCTGCATAGTACGGGTCCAGTGTTGAATCAGGAAGCCCATTTCCAGTTTGGTTGTATAGCCGTTGTCTAAAGCTCGTGCATCGCG
90312 C G ATGTTCTTGAAGTAGAAGTTGTCGAATTTCATCGGGCTTACATAGTCCAAAACAAAGAGATTTTGATCACCTCCAGACTTTGGACAGTTCTTTTTCCAGA[C/G]AGCTGCATAGTACGGGTCCAGTGTTGAATCAGGAAGCCCATTTCCAGTTTGGTTGTATAGCCGTTGTCTAAAGCTCGTGCATCGCGCA
90312 C G GTTGAATCAGGAAGCCCATTTCCAGTTTGGTTGTATAGCCGTTGTCTAAAGCTCGTGCATCGCGCATCTCCTATAGTATGGCTACCTGAGAGGGCGACGA[C/G]GTCGGTGATATCGAGGCCTTTAAGCTTGAATTTTGTGATGATGGTAGGTAGCGTATTGTTTGGTGCTGGAATGTTGTTGTTTGATCC
90312 G A GCCCATTTCCAGTTTGGTTGTATAGCCGTTGTCTAAAGCTCGTGCATCGCGCATCTCCTATAGTATGGCTACCTGAGAGGGCGACGACGTCGGTGATATC[G/A]AGGCCTTTAAGCTTGAATTTTGTGATGATGGTAGGTAGCGTATTGTTTGGTGCTGGAATGTTGTTGTTTGATCCACTTAAGCTTGCAG
90322 G A CTTATAAATCCGATATTCAGTGATACTCAAGTGGAGCTGGACACTTCTGCAATTCCTGCCCTTGAAATTGAATGTCAGAAGCATAGTGATTGACATCACG[G/A]TGATGGGCCTCATCAGCCCTAACAACCATCACAACATCTCGAAGGGTTGCATCAGCAGGGAGGCGCCAGTAATCAATAGCAATAGCA
90322 G A TCTGCAATTCCTGCCCTTGAAATTGAATGTCAGAAGCATAGTGATTGACATCACGGTGATGGGCCTCATCAGCCCTAACAACCATCACAACATCTCGAAG[G/A]GTTGCATCAGCAGGGAGGCGCCAGTAATCAATAGCAATAGCAGGAGCAGGAACATTCTCTATTTTTCCAGCATCAAGCTCCTTAAGA
90322 C T CAGGAACATTCTCTATTTTTCCAGCATCAAGCTCCTTAAGAAACTCCGTATAAGAGTGGATCGCTTCCTCCTCGAGATACCCGGTGACTCTATGAGCAAA[C/T]TTGGGTGAAATGAGGTATCCCAGGAAGTAAGCGTTGAAGAATATCCCTTGGACCACGATGACAAGGGCGCGTTCGTACCATTTGGGT
90322 T C TTCCAGCATCAAGCTCCTTAAGAAACTCCGTATAAGAGTGGATCGCTTCCTCCTCGAGATACCCGGTGACTCTATGAGCAAACTTGGGTGAAATGAGGTA[T/C]CCCAGGAAGTAAGCGTTGAAGAATATCCCTTGGACCACGATGACAAGGGCGCGTTCGTACCATTTGGGTTTGGCCACTTCCATGAA
90322 C T CCGTATAAGAGTGGATCGCTTCCTCCTCGAGATACCCGGTGACTCTATGAGCAAACTTGGGTGAAATGAGGTATCCCAGGAAGTAAGCGTTGAAGAATAT[C/T]CCTTGGACCACGATGACAAGGGCGCGTTCGTACCATTTGGGTTTGGCCACTTCCATGAAGGTCATTAGATGCATTCTTTCGTTCTCA
90322 G A CCTCCTCGAGATACCCGGTGACTCTATGAGCAAACTTGGGTGAAATGAGGTATCCCAGGAAGTAAGCGTTGAAGAATATCCCTTGGACCACGATGACAAG[G/A]GCGCGTTCGTACCATTTGGGTTTGGCCACTTCCATGAAGGTCATTAGATGCATTCTTTCGTTCTCAGCTTCTTCTAGAAGGACACGG
90322 A G CGTTGAAGAATATCCCTTGGACCACGATGACAAGGGCGCGTTCGTACCATTTGGGTTTGGCCACTTCCATGAAGGTCATTAGATGCATTCTTTCGTTCTC[A/G]GCTTCTTCTAGAAGGACACGGATCCAGCCACCACTCTGCTCGAAGCGACGTAGCGAGCGGAGGTGAAGGAGCATTCCTCCAACCAT
90322 G A CCACTTCCATGAAGGTCATTAGATGCATTCTTTCGTTCTCAGCTTCTTCTAGAAGGACACGGATCCAGCCACCACTCTGCTCGAAGCGACGTAGCGAGCG[G/A]AGGTGAAGGAGCATTCCTCCAACCATCCCTGGTACTGCTGCCACGGTTTCAAGCATCATGGCTCGACATCCATAACGCCTCTGAAAA
90322 T C TTAGATGCATTCTTTCGTTCTCAGCTTCTTCTAGAAGGACACGGATCCAGCCACCACTCTGCTCGAAGCGACGTAGCGAGCGGAGGTGAAGGAGCATTCC[T/C]CCAACCATCCCTGGTACTGCTGCCACGGTTTCAAGCATCATGGCTCGACATCCATAACGCCTCTGAAAAA
90322 A T GATGCATTCTTTCGTTCTCAGCTTCTTCTAGAAGGACACGGATCCAGCCACCACTCTGCTCGAAGCGACGTAGCGAGCGGAGGTGAAGGAGCATTCCTCC[A/T]ACCATCCCTGGTACTGCTGCCACGGTTTCAAGCATCATGGCTCGACATCCATAACGCCTCTGAAAAA
90338 A G AAGCTCAATCCGGAACAGGGAAAACTGCAACTTTCTGCTCTGGCATTCTTCAACAACTCGATTACGGGTTGGTCGAGTGCCAATGCTTGGTCCTTGCTCC[A/G]ACAAGAGAGTTAGCTCAACAGATCGAGAAAGTTATGAGAGCTTTGGGTGATTATCTGGGTGTGAAAGTTCATGCTTGTGTCGGAGG
90338 G A CCGGAACAGGGAAAACTGCAACTTTCTGCTCTGGCATTCTTCAACAACTCGATTACGGGTTGGTCGAGTGCCAATGCTTGGTCCTTGCTCCAACAAGAGA[G/A]TTAGCTCAACAGATCGAGAAAGTTATGAGAGCTTTGGGTGATTATCTGGGTGTGAAAGTTCATGCTTGTGTCGGAGGTACGAGTGT
90370 A G CAACACTGCTGATATGCTGGATTTGGCTGTAGACTACATCAAGGATCTCCAAAAACAAGTTGAGGGTTTAACAGACAGTCGAGCTAACTGTACTTGCTCC[A/G]GCAGCAGTAAGCATCGGCAGTATATGAACCCTCAAGTGTGAATCTAGCTAGTTATCAAATGATAGTAAGAGTTGAATATCTCTGTAG
90382 A AT AAGTAGATCCATTAAAATTAGTCAGAGTAGGCCTATTTCTAACATTAAAGTTGGAGGAATGATCATTTGTAGATCCTTTAAAGTTGGACATAGGATGCTT[A/AT]TTTTTATATTTGGTGGATTGGTACGCAAATTTGAGTGATTTTTGTTGGAAGTAAGTGCACGAGGAGGAGGCATCAGAAGTCGAGCG
90388 G A ACTGTTGGCCTACTGGAACAATAACAAAAGAAAAAGAAAAGAAAATAGGCGCAAGAATCGCTGCGCTT[G/A]GTTTCGTCCGTCGATCTCCAGCGAAGGAAGGATCCCACGGAAGTACACAGGAGACGGGCAAGGAGCCCAGAAGGACATATCACCCCCCTTACGAATGGTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
90388 G C CCTACTGGAACAATAACAAAAGAAAAAGAAAAGAAAATAGGCGCAAGAATCGCTGCGCTTGGTTTCGTCCGTCGATCTCCAGCGAAGGAAGGATCCCACG[G/C]AAGTACACAGGAGACGGGCAAGGAGCCCAGAAGGACATATCACCCCCCTTACGAATGGTACGACGTGCCACACGGCACGAAATC
90388 AC A GCAAGAATCGCTGCGCTTGGTTTCGTCCGTCGATCTCCAGCGAAGGAAGGATCCCACGGAAGTACACAGGAGACGGGCAAGGAGCCCAGAAGGACATATC[AC/A]CCCCCCTTACGAATGGTACGACGTGCCACACGGCACGAAATCGCTGGCCATCGTGGTGCAGGACATCGACGCGCCGGATCCG
90388 A T GCTGCGCTTGGTTTCGTCCGTCGATCTCCAGCGAAGGAAGGATCCCACGGAAGTACACAGGAGACGGGCAAGGAGCCCAGAAGGACATATCACCCCCCTT[A/T]CGAATGGTACGACGTGCCACACGGCACGAAATCGCTGGCCATCGTGGTGCAGGACATCGACGCGCCGGATCCGTCCGGCCCGCT
90388 C T TCGTCCGTCGATCTCCAGCGAAGGAAGGATCCCACGGAAGTACACAGGAGACGGGCAAGGAGCCCAGAAGGACATATCACCCCCCTTACGAATGGTACGA[C/T]GTGCCACACGGCACGAAATCGCTGGCCATCGTGGTGCAGGACATCGACGCGCCGGATCCGTCCGGCCCGCTCGTGCCGTGGAC
90388 G A GACGGGCAAGGAGCCCAGAAGGACATATCACCCCCCTTACGAATGGTACGACGTGCCACACGGCACGAAATCGCTGGCCATCGTGGTGCAGGACATCGAC[G/A]CGCCGGATCCGTCCGGCCCGCTCGTGCCGTGGACCCACTGGGTCGTCGTGAACATACCGCCTTCCTTGAAAGGGCTGCCCGAGG
90408 GA G AATAAAAAGTAAAATAGAAACCATTCTTTCCAAAACAGAAAGCTCCATCTGTAAAACAAAGTAAAAAGGAACAACGAGAAAAACAAGAATCAGCGTTGGA[GA/G]AAAAAACGAGGGGACAAGTGGGAATAGTCTGGGTATCTACATGGAGCTGTGTTGAGTGTTGTTCGTGCATGGTGTAATGAGCA
90410 A G GCCCAGATTCATCTCCTTTGATCCGCTCAACACATGACTGATATGCACGTAAAGGCCTAACACATCGAGGCTTGCAGGTGTCCTCGTAATATTTCTTCTG[A/G]TCAACAGGCTCCTCATCCGCCATCGCTCAGAAAGACTGAAGTATACTGTTACAGTTGCTTCTCAACCGGTCCTGCAATACAAACAACTA
90434 C T GCCTGCGCAGCAAGAATCATGCTCTGATTCGGCCGACGCCAACCACGACTACGGTTCCTATTTGTAGTATGCTTTACGGAGGTTGATCCACTGTTCGCCG[C/T]CCGCGGACCGATGATCACGGCCTGTTTCGGATGACCCCCACCGCGTCCACTGTTCTGATTTGCGGTATAATTTGGGGATTTTGGTGG
90434 C T GGTATAATTTGGGGATTTTGGTGGAAAATCATCGAAAGGCCCTTCTTGCTTTGTCTCTTCTTTGATATGTACTGGAGCAGCCGGTGGTCCCTTAACTTCG[C/T]TGTCTTCTTCCTTTTCTACTTGTGTCGATTGTTGTTTGAGCTTCCGTTCGCGGTCGCGTTCATGCCTCTCTTTTAGATCTCTCAGTGTAAC
90434 G A TGCTTTGTCTCTTCTTTGATATGTACTGGAGCAGCCGGTGGTCCCTTAACTTCGCTGTCTTCTTCCTTTTCTACTTGTGTCGATTGTTGTTTGAGCTTCC[G/A]TTCGCGGTCGCGTTCATGCCTCTCTTTTAGATCTCTCAGTGTAACAAAATTAGGAGGAATTACTGGACCTTTTTCCATCCTATCAAAATTTT
90460 A G AATCGCAGATGCCTTCTTCAAAGTCCAAGCTCCGAGCCAAATTTATCAGAATCACCTTCTCGGACCCGTACGCCACCGACTCCGATTCCGATTCCGATTC[A/G]GAAGCTTCTCCATCTCGCCCCCGCATAAGGAAGCAAGTGCACATAATAAATCTCCAACAACCTACCTCTGGCCTCCCGTCGGCGCCCTC
90470 TC T GAGATTCCAACGGAGAGCAGTCCGTACGTGCAGTACGACAATCTGGAGGAGTACAAGATGAAGGCGTACGGGGCGCAGGGCCACGAGAAGCCCGTCGATC[TC/T]CCCCCACCACGGCGGCACCACCGATGCCCCCACTCCGTCCGGCGCTGGTTTGACCGACGACAAAGCCAAGGACGCCGTTGAT
90504 G C CGTCTTTTTCACCTCCACTTTCTCTAGCAGTTTCTTCGCCTCTTCCTTTTCTTCTTTCTCTACTAGTTTCTTCACATCTTCGTTTTTCGCTCTCGTCGTC[G/C]TCGTTTCTTTGCTGGACTGAGGGGCAGGCTTCACGTCGTCGGTTTTCGGAACGTCGTCGTCTCCCTGTGTGCGCATAGTTGATTTTTGGTTTG
90516 GCAGGAAA G TTGCTCAATCATAAATGTGATATTCAAGCCAGCAACTGCAAACGGGTACTCCCATGTTGCTCGATGTCCCCCTTCCTTGTTTAGCAACTTTTGAAAAGAA[GCAGGAAA/G]CAGGAAACCTTTTAGCAAAGAAGAGAAGATTCTCCAGTGCAATAAATCCCGCACCCCTGAAATCTGTAGATGGATCTTTTC
90518 G T TCCTACTTCTAGCAAACCCTGCCAGAAAACCAGAAAATAATAGAAAATAAAATAGAATGGGTCTTCTCTCATGGTGGAGAGGCAACAAGTCCCAAGCTCC[G/T]ATTAGCCCTAACAGTAATTCAAACTCAGGCACTTCGAACCCCAACAACGGTACTGCTCTCCACCAGGAAATTTCAAACCTTAACGGC
90518 G A GCACTTCGAACCCCAACAACGGTACTGCTCTCCACCAGGAAATTTCAAACCTTAACGGCGCCGTTGAGGTCCCACGTCGCCGTCCGGATGACGTTACCGT[G/A]TTCGAGTTCGGATCCATATCCGCCGCTGGAGTGACCGCTACCTTAGCTGGGTACTGTCCCGTCTCTGACGATCTCGAGCCATGCCGT
90518 T G AGTTCGGATCCATATCCGCCGCTGGAGTGACCGCTACCTTAGCTGGGTACTGTCCCGTCTCTGACGATCTCGAGCCATGCCGTTGGGAAATTGTTCCTGC[T/G]TCTACTGGTGATACTGATGCTCCTCTATTTCGAATTGTCTTTTAGTTTTGATTTATATTTTGGTCAGTCTGAATTGTGTTTTGATGTGGA
90518 A G TTCGAATTGTCTTTTAGTTTTGATTTATATTTTGGTCAGTCTGAATTGTGTTTTGATGTGGAACAATGGGAATTGAGTTTGGTGATGATTATGTGTGCCA[A/G]AATTTGGTGAATAATGTCGCATTGTATCAATCAGTTTTATTCTGTTAATGAACTTTGTTCGTTAGCATTGCCAAAAAAAAAAAAAAAA
90530 G A CCTGAAAATCCAATGCTTGGTCATCGTACAGTCATTGATGGGAAGTTTAGGTTTTGGCAAACAAGCAGGAAACGAAGGTTTGAAAGATGTTGTTTGGAAG[G/A]GGCGCTCTTGTTCCAAACGAAGTAATCTGCTTGTATCTATAAGAGCATCTTCAATGCCGATGGAATTGGATTGTGAAGTCCACGAC
90546 A G CTTCAAGGCTCGACCTCTTCACTCCATCTCCTGTCAGTTCAGTTAAATGCAGCATGCCATTATTAGTGAAATGCAATGCACAACAAGCAGTTACGACAGC[A/G]AGTTTAGGACAAGGGACTCCTGTGAGACCAACAAGTATATTAGTAGTCGGTGCAACAGGTACATTGGGTAGACAAGTTGTTAGGAAA
90546 T C AAGGCTCGACCTCTTCACTCCATCTCCTGTCAGTTCAGTTAAATGCAGCATGCCATTATTAGTGAAATGCAATGCACAACAAGCAGTTACGACAGCAAGT[T/C]TAGGACAAGGGACTCCTGTGAGACCAACAAGTATATTAGTAGTCGGTGCAACAGGTACATTGGGTAGACAAGTTGTTAGGAAAGCC
90546 G A AAGCAGTTACGACAGCAAGTTTAGGACAAGGGACTCCTGTGAGACCAACAAGTATATTAGTAGTCGGTGCAACAGGTACATTGGGTAGACAAGTTGTTAG[G/A]AAAGCCTTAGATGAGGGTTACGATGTTCGATGTCTTGTAAGGCCTCGTCCTGCTCCTGCTGATTTTCTACGTGATTGGGGTGCAAC
90548 C T GTTGGCCTACTGGCTCTCAAACCCTATTCTTTTTAGGGTTCTTACGAAAGGAATAATCCCCATTACCTTGGAATATCCCTAACAAAATCAGAAGTATTCG[C/T]GCCCAATTTCAGTAGAAATCCAACTTGGAGCTATCGTCAACCGGATCTAGTTATTGAATATGGTATCGGACGCAAGCAAGAAGAAAGC
90548 G T AGAGATATTCATGTAATTTATTTCCCATGTTATTGATTTGTTATGGATTCATTGTTATGAGTTCATCAGCTTGTTAATTGTTTTTAAGCCAGATGCAAGC[G/T]AAGTGAATGATAAACATTCGTTCCTTACCAGTTAGACCGGTTCTCATACGTGTTTTGCAATTAAATGATGTATAAAGGAGTATGTGAGAT
90596 G C AACAGCTCGATCAAACTCGACCACCGATCCTTCAACATCCCCCTGACGGAACAGCACCATGCCACGCCTGACCGCGGCGACCGCATCACTTGCCGCGTTG[G/C]CGCCGGTAATAGCGTCCCATATTGATGCTGCTGCCGTTGGCAGGATGACGCGGCGAGGCAGAGCAAGGGTTCGGTGGAATTTTCT
90596 C T AACAGCACCATGCCACGCCTGACCGCGGCGACCGCATCACTTGCCGCGTTGGCGCCGGTAATAGCGTCCCATATTGATGCTGCTGCCGTTGGCAGGATGA[C/T]GCGGCGAGGCAGAGCAAGGGTTCGGTGGAATTTTCTCGGGTTAGAGTGAAAATGAGGTAGTGATGTGAGCTTGTGTGGCGTGG
90608 T C TTAGACGGACCCAATCCGCAATCCTTTGTGCTAAAACCATAGGTGACTAATTCTTCAACAACGATTCAAGGCCCATCATGCTTTTTGATGGTGTCTGCAA[T/C]CTGTGCAATGGAGGGGTCGGGTTTGTTAGAGGCAACGATCGAAAGAGAAGCATTAGGTATGAATCCTTGCAGAGTGAATCCGGACA
90608 G A AATCCTTTGTGCTAAAACCATAGGTGACTAATTCTTCAACAACGATTCAAGGCCCATCATGCTTTTTGATGGTGTCTGCAATCTGTGCAATGGAGGGGTC[G/A]GGTTTGTTAGAGGCAACGATCGAAAGAGAAGCATTAGGTATGAATCCTTGCAGAGTGAATCCGGACAAACGCTTTTGCAGAGATCG
90608 A C GTGACTAATTCTTCAACAACGATTCAAGGCCCATCATGCTTTTTGATGGTGTCTGCAATCTGTGCAATGGAGGGGTCGGGTTTGTTAGAGGCAACGATCG[A/C]AAGAGAAGCATTAGGTATGAATCCTTGCAGAGTGAATCCGGACAAACGCTTTTGCAGAGATCGGGAAGGTCGCCTGATGATATTTC
90608 A G GATGGTGTCTGCAATCTGTGCAATGGAGGGGTCGGGTTTGTTAGAGGCAACGATCGAAAGAGAAGCATTAGGTATGAATCCTTGCAGAGTGAATCCGGAC[A/G]AACGCTTTTGCAGAGATCGGGAAGGTCGCCTGATGATATTTCTAGTGTTGTACTAGTCGAAAAAGAAAGATCATACATCAAATCA
90608 T C GAGGCAACGATCGAAAGAGAAGCATTAGGTATGAATCCTTGCAGAGTGAATCCGGACAAACGCTTTTGCAGAGATCGGGAAGGTCGCCTGATGATATTTC[T/C]AGTGTTGTACTAGTCGAAAAAGAAAGATCATACATCAAATCAGAAGCAGTGCTAAAGATAATGGAATATATCAATCTCCCTTTTCC
90608 C G GAAGGTCGCCTGATGATATTTCTAGTGTTGTACTAGTCGAAAAAGAAAGATCATACATCAAATCAGAAGCAGTGCTAAAGATAATGGAATATATCAATCT[C/G]CCTTTTCCGCAGTTAGCGCTTTTCTTAAAGATGGTTCCTTTGTTCATAAGGGATTTTGCATACGACAACGTCGCAAATAATCGGTATG
90632 T C CAACAAAAACGTTATAATGCCCTGACGTATCCTCCCTCTGCCCACTTGTGTATGCCCAATTAACTTTTATCGGCTGCCCAAACAAATGCCTTCCATTAAG[T/C]GATACGATTGCAAGTGCAGCAGATCTACGATCAAAATAGTGAATAAAACCATAAGAAGACTTCTCCTTCCTTATTAGCTTGCATCCTTCA
90654 G A TTGCCGCCTGTAAGTGAGGAAGTAGGTGGAGTAAGGCTGTTTGTCGACATATCGGTTCCAAGAAATGTAGGATCATGCATTTCCGAGTTAACTACCGCAC[G/A]CGTATACAACGTGGATGATTTGAAAGAGGTGGTGGAGGCTAACAAAGAAGAAAGGATGAGACGAGCATTGGAAGCTCAAGCGAT
90654 C T ATGCAGAAAGAATCAAAGCAGCTGAAATGGAGAAATGCATTCAGAAAATCGGAGATGAAGCTCTTACTAAGAAAATGAGAAGGGCTATAGAAGATCTTGG[C/T]AATGGTATAGTCAATAAGCTTCTTCGTGGTCCGTTGCAGCATTTGAGGTGCGATGAGAGTGATAATCGAACCCTTGAGGAGACTA
90664 A AATGAAAAATCACCACTGCAAAACCTATTGAGGACTCCTTGAGCGGGTAGACAACATCACACAGGCAAACTTAATTCCAGTGCTCCAAACCTCTGCAGATCATCCCATTTGCC[A/AATGAAAAATCAC]TTTAAGAACAGGTTCCCCTCTGCTGTTGTTGTTAAGCTTTTCCTTGTTCGCAGCTGCTATTTGTGCTTTCGCTGCTTT
90664 C T CTGCCTTCTTTGCGCTGCTTCGGCAGCACGAGCACGAGCTTCCTGGGATTCGATCCGATCCGCTTCTTTCTTCTCTGATTTTGATGGGCCAAAGCATGAG[C/T]AAAATCCCATTAATTGAAAGACTAGCACGATTCCCAAAACTGAAATGGATTTTGCTCAGGTTGGGAAAGGAAAAAATTAACGCGTTTT
90678 T C CAACAGAGATGTCGAACCAAAAGAGAAAGAAGACCAGAAAGCTTCGTGGACATGTCAGCCATGGACACGGTCGTATCGGCAAGCACCGTAAGCATCCTGG[T/C]GGTCGTGGTAATGCTGGTGGCATGCACCATCACAGAATCAATTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGA
90678 C T CTGGTGGTCGTGGTAATGCTGGTGGCATGCACCATCACAGAATCAATTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCA[C/T]TTGAACCGAAACCACAATTTCTGCCCATCAATCAACTTGGACAAGCTGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAA
90678 A G GCTGGTGGCATGCACCATCACAGAATCAATTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCACTTGAACCGAAACCACA[A/G]TTTCTGCCCATCAATCAACTTGGACAAGCTGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAA
90678 C T GCATGCACCATCACAGAATCAATTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCACTTGAACCGAAACCACAATTTCTG[C/T]CCATCAATCAACTTGGACAAGCTGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCC
90678 G A ATTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCACTTGAACCGAAACCACAATTTCTGCCCATCAATCAACTTGGACAA[G/A]CTGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATT
90678 C T TTTCGACAAGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCACTTGAACCGAAACCACAATTTCTGCCCATCAATCAACTTGGACAAG[C/T]TGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTG
90678 A G AGTACCATCCGGGTTACTTTGGCAAGTTGGGTATGAGAAATTTCCACTTGAACCGAAACCACAATTTCTGCCCATCAATCAACTTGGACAAGCTGTGGTC[A/G]TTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTA
90678 A G TGAGAAATTTCCACTTGAACCGAAACCACAATTTCTGCCCATCAATCAACTTGGACAAGCTGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAA[A/G]GCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTACAAATTATTGGGTCGTGGACATTTGCCGAAACA
90678 A G TGTGGTCATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTACAAATT[A/G]TTGGGTCGTGGACATTTGCCGAAACAACCAATCATTGTCAAGGCCAAGCATTTCTCCAAGAAAGCTGAAGAGCGCATTAAGGCCG
90678 T A CATTGGTTGGCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTACAAATTATTGGG[T/A]CGTGGACATTTGCCGAAACAACCAATCATTGTCAAGGCCAAGCATTTCTCCAAGAAAGCTGAAGAGCGCATTAAGGCCGCTGGTG
90678 T C GCGAAAAGAATCGTACAGATTGCAAAGCTGACAAAGAGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTACAAATTATTGGGTCGTGGACA[T/C]TTGCCGAAACAACCAATCATTGTCAAGGCCAAGCATTTCTCCAAGAAAGCTGAAGAGCGCATTAAGGCCGCTGGTGGCGTCTGTC
90678 T C AGGGAAAGGTTCCAGTCGTCGATCTAGTGCAATTTGGATACTACAAATTATTGGGTCGTGGACATTTGCCGAAACAACCAATCATTGTCAAGGCCAAGCA[T/C]TTCTCCAAGAAAGCTGAAGAGCGCATTAAGGCCGCTGGTGGCGTCTGTCTCTTAAGAGCATAAATGTAACAATCGATTACATTTCCG
90678 T C ACAACCAATCATTGTCAAGGCCAAGCATTTCTCCAAGAAAGCTGAAGAGCGCATTAAGGCCGCTGGTGGCGTCTGTCTCTTAAGAGCATAAATGTAACAA[T/C]CGATTACATTTCCGACATGCTGAAGTGTACGATACAAAAATTCCACCTTTGATGTGCACAGTTTTTACGAAAATA
90684 T C GGTGTTTCGATCGCTGACCAAAGTTCTGGTAGTTGGAAACTTGGTCATATCCTTCAAAAAGGCTCTGGTAGAAGGGACATCCTTCAACTTAATGACGACT[T/C]TTCCATCGGCTCGAGCACAGTAAAGTGGATCAGAGAACCTAAATAGCAGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAG
90684 T G TGTTTCGATCGCTGACCAAAGTTCTGGTAGTTGGAAACTTGGTCATATCCTTCAAAAAGGCTCTGGTAGAAGGGACATCCTTCAACTTAATGACGACTTT[T/G]CCATCGGCTCGAGCACAGTAAAGTGGATCAGAGAACCTAAATAGCAGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAGG
90684 C T TATCCTTCAAAAAGGCTCTGGTAGAAGGGACATCCTTCAACTTAATGACGACTTTTCCATCGGCTCGAGCACAGTAAAGTGGATCAGAGAACCTAAATAG[C/T]AGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAGGCTCAAACGTCGCCCACCCACCCGTTCCACTGTTCAGCTGCACGATA
90684 G A TCGAGCACAGTAAAGTGGATCAGAGAACCTAAATAGCAGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAGGCTCAAACGTCGCCCACCCACCC[G/A]TTCCACTGTTCAGCTGCACGATAGTCCTCCCTCCTTTAACCTTCATCATTCTTTCAATGAAGTCGAGTGGGTGACTTTCTTTTAGAAA
90684 G T AGTAAAGTGGATCAGAGAACCTAAATAGCAGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAGGCTCAAACGTCGCCCACCCACCCGTTCCACT[G/T]TTCAGCTGCACGATAGTCCTCCCTCCTTTAACCTTCATCATTCTTTCAATGAAGTCGAGTGGGTGACTTTCTTTTAGAAAGTCCCAAA
90684 T C GTAAAGTGGATCAGAGAACCTAAATAGCAGCCTAGCTGCAGCAGCAGTGACCTCATGGTTCCTAGCAGGCTCAAACGTCGCCCACCCACCCGTTCCACTG[T/C]TCAGCTGCACGATAGTCCTCCCTCCTTTAACCTTCATCATTCTTTCAATGAAGTCGAGTGGGTGACTTTCTTTTAGAAAGTCCCAAAC
90684 G A TAGCAGGCTCAAACGTCGCCCACCCACCCGTTCCACTGTTCAGCTGCACGATAGTCCTCCCTCCTTTAACCTTCATCATTCTTTCAATGAAGTCGAGTGG[G/A]TGACTTTCTTTTAGAAAGTCCCAAACGCCAACAAGTGGGGAGCCTCAATCCAGCCGTCCCTAGGCACTGTGAACTTCAACATGGTCGA
90684 G T GCAGGCTCAAACGTCGCCCACCCACCCGTTCCACTGTTCAGCTGCACGATAGTCCTCCCTCCTTTAACCTTCATCATTCTTTCAATGAAGTCGAGTGGGT[G/T]ACTTTCTTTTAGAAAGTCCCAAACGCCAACAAGTGGGGAGCCTCAATCCAGCCGTCCCTAGGCACTGTGAACTTCAACATGGTCGAATG
90690 A G TGTTGGACTTGGGTAAGCCTAGAGATGGCGACGACGACGATGTTGCGGTGGAGCTGGACCAGGTCTTTCCAAAGATGTCGCCGACCATGGATGTGGGACC[A/G]GGCAGACTGGAAACAGGCTGATGTGTCCATGAAGGTTTCGGGGCGGAGGCGGTGGGGTGTGGGGACCAAGAGGGGGCAGGT
90690 C T GAGCTGGACCAGGTCTTTCCAAAGATGTCGCCGACCATGGATGTGGGACCAGGCAGACTGGAAACAGGCTGATGTGTCCATGAAGGTTTCGGGGCGGAGG[C/T]GGTGGGGTGTGGGGACCAAGAGGGGGCAGGTGAGGATCTGGGTGCAGGAGGGACAGGTTTGTTTAGATCCTTAAGGGGTTT
90694 G C TGGTTAATGCAACCTTGATGAACATAGCAGATAATCCAACTAACGTGCAATTGCCCGGAATGTACAACAAGCAAGAAAATGCTCGTGTCCCTATTATTGT[G/C]ACGGGTAATGATTTTTCGACATTGTATGCTCCTTTGATTCGTGATGGACGTATGGAGAAATTTTACTGGGCTCCGACTAGGGAGGAT
90694 G T GTGTTTGTAAGGGTATTTTCAGGGCCGACAAAGTCAAAGATGAGGAAATTATCAAGCTGGTCGACACCTTCCCTGGTCAATCTATCGATTTCTTCGGTGC[G/T]CTGAGAGCAAGAGTGTATGACGACGAGGTACGCAAGTGGATAGCAGAAATCGGAGTCGACAAGATTGGTAAAAGACTGGTGAACT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
90694 C T GGGCCGACAAAGTCAAAGATGAGGAAATTATCAAGCTGGTCGACACCTTCCCTGGTCAATCTATCGATTTCTTCGGTGCGCTGAGAGCAAGAGTGTATGA[C/T]GACGAGGTACGCAAGTGGATAGCAGAAATCGGAGTCGACAAGATTGGTAAAAGACTGGTGAACTCACGTGAGGGACCGCCGACA
90694 G A ACGACGAGGTACGCAAGTGGATAGCAGAAATCGGAGTCGACAAGATTGGTAAAAGACTGGTGAACTCACGTGAGGGACCGCCGACATTCCAGCAACCAAA[G/A]ATGACATTAGAGAAGCTTCTAGAGTACGGTAACATGCTTGTGCAAGAGCAGGAGAATGTTAAGAGAGTGCAACTAGCCGATAA
90700 T A GGCCTTTTTTTTTTAAACCAAAGGGGAAAAACCCACATTTATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGT[T/A]ACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAA
90700 A G CTTTTTTTTTTAAACCAAAGGGGAAAAACCCACATTTATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATC[A/G]CTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAAT
90700 T TTGAA TTTTTTTTAAACCAAAGGGGAAAAACCCACATTTATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACT[T/TTGAA]TGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAA
90700 A C AAAAACCCACATTTATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAA[A/C]TACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAG
90700 C T CACATTTATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAG[C/T]CCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTT
90700 C A TATTGTTCTCCATTGAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAA[C/A]TTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATA
90700 A T GAATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGC[A/T]GGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTA
90700 G A AATGGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCA[G/A]GCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAA
90700 G T GGGGAAAATCATACAGAATTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGC[G/T]TTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTG
90700 A C TTTATCACTGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATG[A/C]TTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGC
90700 A G TGTTACATTGTCACTGCATCACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTC[A/G]CAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTT
90700 C T ACTTTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTAT[C/T]ACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTAT
90700 C T TTGGAAAATACAAGCTACAAATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCAC[C/T]GCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATG
90700 G A AATACTAGCCCAAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTA[G/A]CATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACG
90700 T G AAACTTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGA[T/G]TAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAG
90700 T G TTAATGATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAA[T/G]TAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAA
90700 T G GATTTTGCAGGCGTTATCACAGCAATCATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAAC[T/G]GGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGG
90700 T G CATGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATC[T/G]TTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTA
90700 T C TGATTAAGTCACAATTGAAATTGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTT[T/C]GATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAG
90700 T C TGTGCTTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATA[T/C]GAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAG
90700 A T TTATCACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGC[A/T]CCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGA
90700 C T ACCGCAGTTGAGCTTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCC[C/T]GTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACC
90700 G T TTAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCC[G/T]GGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACA
90700 G A TAATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCG[G/A]GCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACA
90700 C T ATTTAGCATATGATGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGG[C/T]ATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAA
90700 G T TGATTAATTAACTGGGTAAATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTG[G/T]TGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTT
90700 T C ATTAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTT[T/C]CCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAG
90700 C T TAATAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTC[C/T]GTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCT
90700 T C TAGAACGGCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGT[T/C]TAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGT
90700 C T GCATATCTTTGATCCTGCAAAAATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGT[C/T]CAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGC
90700 A T ATAGTATATGAGCACCCCCGTTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGG[A/T]AAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCT
90700 A C TTTTAGACGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAA[A/C]ATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAAC
90700 A G CGCCGGGCATAGGAAATTTGGTGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCAT[A/G]AAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAACCATTATG
90700 G T TGGTGAGGGCTTCAACTTTCCGTTTAAGGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCC[G/T]GGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAACCATTATGAAATCACTCTCTTTTAGTCCTCT
90700 A G GGTCCAAGGTAGCATCCTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGC[A/G]ATTTCCACACCTTCGTGGATAAATTCTGCAACCATTATGAAATCACTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTC
90700 T A CTTGAGAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCG[T/A]GGATAAATTCTGCAACCATTATGAAATCACTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGC
90700 A T GAGGAAAACCGGGCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGAT[A/T]AATTCTGCAACCATTATGAAATCACTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGCTAAAG
90700 C T GCGACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAAC[C/T]ATTATGAAATCACTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGCTAAAGCGCTCCTA
90700 T G GACTGGACAAAATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAACCA[T/G]TATGAAATCACTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGCTAAAGCGCTCCTA
90700 A G AATCCATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAACCATTATGAAATC[A/G]CTCTCTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGCTAAAGCGCTCCTA
90700 T G CATAAAATCTTTGAGTTTAGTCCCGGGAGCTTGTGATTTTGCTTTAAGGGCAATTTCCACACCTTCGTGGATAAATTCTGCAACCATTATGAAATCACTC[T/G]CTTTTAGTCCTCTAGTAGTCATAGCTGGTGTCCCTATTCGAATGCCTCCAGGGGCTAAAGCGCTCCTA
90708 C T ATGTCTGAGGGGCCTCGACCTCCTTTTTATCCTAATCTGAATGCGGTGAAGGCAAGTATGAGTGGAGAGGAAGGAGACAGAGGAAGGAGATGGGGTGGTG[C/T]TAACTTGGGGATGGAATTGCCAACACCAAAGAATATTCGTTTGGGTTTAGACAAGTATGTCATTGGACAAGAAAATGCTAAAAA
90710 CT C ATTGCCGTCTCTCCCCGCTTTATTCCCTTGCAGCCGGATGACAGCCAACAACGCCTTTCAACGCTGCCTTCATGGTTTGACTAGGGTTCCGACGCTGGTA[CT/C]TTTTTTCGTAGCACAGCGTCAACAGTGCCTTACATCTTCCTCCTTCTGCAGCTACAGCACTCTTCGGTTCATCGACATCTATGGAGGAT
90710 A G ATGGTTTGACTAGGGTTCCGACGCTGGTACTTTTTTCGTAGCACAGCGTCAACAGTGCCTTACATCTTCCTCCTTCTGCAGCTACAGCACTCTTCGGTTC[A/G]TCGACATCTATGGAGGATACCAGGTTGTTAATCGATTTCCTTCTTGCAATTAATGTCACCTGTTGACCTGCGCGTTTTCGGGATAGTTTC
90710 A G GCTGGTACTTTTTTCGTAGCACAGCGTCAACAGTGCCTTACATCTTCCTCCTTCTGCAGCTACAGCACTCTTCGGTTCATCGACATCTATGGAGGATACC[A/G]GGTTGTTAATCGATTTCCTTCTTGCAATTAATGTCACCTGTTGACCTGCGCGTTTTCGGGATAGTTTCATCGGACACATTTACCCACACT
90710 C G TTCATCGACATCTATGGAGGATACCAGGTTGTTAATCGATTTCCTTCTTGCAATTAATGTCACCTGTTGACCTGCGCGTTTTCGGGATAGTTTCATCGGA[C/G]ACATTTACCCACACTTGTCAGCCCTTCTCTGGAGAAACTAATATGGCTTGGTTGCGGTGCTTTATGTTGTGTCTCTCGGTTAGGTCTTCT
90710 G A TACCAGGTTGTTAATCGATTTCCTTCTTGCAATTAATGTCACCTGTTGACCTGCGCGTTTTCGGGATAGTTTCATCGGACACATTTACCCACACTTGTCA[G/A]CCCTTCTCTGGAGAAACTAATATGGCTTGGTTGCGGTGCTTTATGTTGTGTCTCTCGGTTAGGTCTTCTGTCAGTTCGATTCTTCTATTCG
90716 A G AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCT[A/G]TCTCGATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGG
90716 C T AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTAT[C/T]TCGATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCC
90716 G A AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTC[G/A]ATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTAC
90716 T C AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGA[T/C]GATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCC
90716 C T AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCG[C/T]CGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGG
90716 C T AAAGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCGCCGT[C/T]GTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGG
90716 C A AGTCTCCGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCGCCGTCGTC[C/A]TCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCC
90716 G T CGTATTAAGGGAATTTACTGTTTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCGCCGTCGTCCTCATC[G/T]TCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCAC
90716 C A TTATGCTGCTCCGGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCC[C/A]GTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGCT
90716 A G GGTTTCGCTTTCCCAATCTTCTTCGACGAGTCAATTCTATCTCGATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATC[A/G]ACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGCTCTCACCGTCTTC
90716 A G TCAATTCTATCTCGATGATGTCGCCGTCGTCCTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGG[A/G]GTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGCTCTCACCGTCTTCAACCGCACACACTCCAAAACCCTACCCCT
90716 C T CTCATCGTCTTCGCCCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATA[C/T]TGACCGCAGGGTTTGCTCTCACCGTCTTCAACCGCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCC
90716 T C CCTCTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTT[T/C]GCTCTCACCGTCTTCAACCGCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCT
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
90716 T G CTCCCCTTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGC[T/G]CTCACCGTCTTCAACCGCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGC
90716 C T TTCCCGTCTCTCCATCAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGCTCTCAC[C/T]GTCTTCAACCGCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATC
90716 A C CAACGACACGTGTCGGATTTATTGGCACCGGAGTGATGGGCCTACCCATGGCCCAGCACATACTGACCGCAGGGTTTGCTCTCACCGTCTTCAACCGCAC[A/C]CACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATCGGACGTTGTCTTTCT
90716 A C GGTTTGCTCTCACCGTCTTCAACCGCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGC[A/C]TCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAA
90716 C T GCACACACTCCAAAACCCTACCCCTCCTCTCCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATCGGACGTTGTCTTTCTCATCCT[C/T]GGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACAT
90716 C T CCCTCTCCGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCAT[C/T]CTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAA
90716 A C CGCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGAT[A/C]AAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTT
90716 A C GCCGTCTCCGCTTCCTCCCCTGCCGAAGTCGCTGCTGCATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATA[A/C]AGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTA
90716 C A CTGCATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGG[C/A]TCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGG
90716 A C CATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTC[A/C]ATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGG
90716 A G ATCGGACGTTGTCTTTCTCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCA[A/G]TCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGA
90716 G A TCATCCTCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGAC[G/A]ACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGTCTCAGGT
90716 C G TCGGCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTC[C/G]GAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGTCTCAGGTGGAGAT
90716 A C GCTACCCCTCGGACGTCCGCCACGTCATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGA[A/C]CCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGTCTCAGGTGGAGATCGT
90716 G C CATCCTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTAT[G/C]AGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGTCTCAGGTGGAGATCGTGGGGCAAAGAATGGTACACTTTCA
90716 A G CTCGATAAAGACGTCGGGATCGTCGCTGGGATGAAAAAGGGCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGA[A/G]GGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGTCTCAGGTGGAGATCGTGGGGCAAAGAATGGTACACTTTCAATTT
90716 C G GCTCAATCGTCGTTGACATGACGACCTCCGAACCGACACTGGCAAAAGAGGTTTATGAGAAGGTGAAGACTGCTGGAGGTTCTGCGGTGGATGCGCCAGT[C/G]TCAGGTGGAGATCGTGGGGCAAAGAATGGTACACTTTCAATTTTTGCTGGCGGTGATTTGGACGTTGTTAA
90754 T C TAGCATAACGGCGACCAACACCTTTGATTGCTGTCATTGCAATGGTAACCTTACGTTTACCATCGATGTTCGTATTCATGATACGAAGAATATGTTGAAA[T/C]TTATCTGGGATTACCAAAGACATTTTTACTTGTTTCTATTGCAGAAAGCAAATTACAAAAAGCCAGTAGGCCAACAG
90776 T C AACGGACATTTCTTATCTATATAATGTCCCTCAATGGCCTCACGAGGAGTCTTGAATCCTAGACCAACACTTTTAACATGTCGAGGAACCTTTGTTACTT[T/C]CGTAGTACTAAAATTTTTCTTCTTGTTGAGAAATACTGTTGGTTGCTTCTGAAAAGCACGCTCAGTCTGGTCAGCCATCTTGACAGGAAA
AGTCGAACCATATAAAATGGTTTAGGAATGAAGACTTCCATCCTATTGAATCAAGAATCATGCTTAC
90782 A CAAACTGGGTGCACGCTAGCGCCCCGCGTACCCGAGTTCAACTATCACCCCGTACTCCTCCATCGCCACCTAGAGGGAACTGCCGCAACCTTTAGCCTCG[ACTACCACAAAGCAAAACAAAGTCGAACCATATAAAATGGTTTAGGAATGAAGACTTCCATCCTATTGAATCAAGAATCATGCTTAC/A]C
90788 T G AATAAGAAGGGAAAAAAGAAGTTTAAATCAGTGTCTGTGAAGAACCAAATTCGATCTACTCAGCGTATGCTTGATCGCAAGAATCTGCCTTCCGAAATCA[T/G]GGAGGCCCAAGAAAGTAAACTAGAGGAACTCAAGAAGCAGCTCGAGCTTCAATCTCGACTGGCGAAAGAACGGAAAAGACAGTTT
90790 C T TGCACCCGCGGCAGGTCGCCATTTGGTTCCAGAACAAGAGAGCAAGGTGGAAGTCGAAGCAGCTTGAAAGGGAGTACAGTGCTTTGAGAGCTGATTATGA[C/T]GCACTCTCCTCTAAATGCGAGTCTCTTAAAAGGGAGAAGCTAACACTTTCCAAACAGGTGAAGAAATTGGAAGAGCTTGTCGAG
90790 C T CACCCGCGGCAGGTCGCCATTTGGTTCCAGAACAAGAGAGCAAGGTGGAAGTCGAAGCAGCTTGAAAGGGAGTACAGTGCTTTGAGAGCTGATTATGACG[C/T]ACTCTCCTCTAAATGCGAGTCTCTTAAAAGGGAGAAGCTAACACTTTCCAAACAGGTGAAGAAATTGGAAGAGCTTGTCGAGAA
90792 C T CCGTACCCATAGAAGTCAAATCACAAACTATTGCTGAAAAAAAGGCTACTGGCAAAAATCCATCTGGTTTAGGAGCTCCATCCAGTGCTCTCACTTCAAC[C/T]GATGATGCCTATGAAAGACTGATGTCATCTGTTCCAGAATTTTCAAGCTTTGGAAAACTTTTTAAGTCATCTTCTCCCGTGGAGCTGAC
90800 G A AGCTTGGTTTCATAAATCATATCAAAAGCTTCATAAAGTTACCTCCGATTGTCATTGTTTTCCAAAATAAAATATCCCAAAAATGTCAATTCTCACAAGA[G/A]CACCCTCTTCTTCATCGTCTTCCCCTGGCTCGTCTCCCCCTCTCATAATCAAAATACTAAACAAATGCAGGACACGGGTGTTCCTCCTCCT
90800 T C ATAAAATATCCCAAAAATGTCAATTCTCACAAGAGCACCCTCTTCTTCATCGTCTTCCCCTGGCTCGTCTCCCCCTCTCATAATCAAAATACTAAACAAA[T/C]GCAGGACACGGGTGTTCCTCCTCCTAGCAGTCTGCTCTCTCCTCCTCAACTTCTCCTGGAACTTAATCCTCTCTCTCCGCTCGTATTACAAC
90800 A T ATCGTCTTCCCCTGGCTCGTCTCCCCCTCTCATAATCAAAATACTAAACAAATGCAGGACACGGGTGTTCCTCCTCCTAGCAGTCTGCTCTCTCCTCCTC[A/T]ACTTCTCCTGGAACTTAATCCTCTCTCTCCGCTCGTATTACAACTCCGCCGCCCCTTCCTCCTTCTACTCCGTCCTCTACTGCTCCTTGCTCT
90800 T C CTCCTGGAACTTAATCCTCTCTCTCCGCTCGTATTACAACTCCGCCGCCCCTTCCTCCTTCTACTCCGTCCTCTACTGCTCCTTGCTCTACGGAGGCGTC[T/C]TCGGGATCCTTTGGATGGCTGCGGCGCTGGCGTTGGCCGTGCGGGCGACGATGCTGACCTGGATTACGATTTTAGTTCTGCTTGCTTCC
90800 G T CTGGAACTTAATCCTCTCTCTCCGCTCGTATTACAACTCCGCCGCCCCTTCCTCCTTCTACTCCGTCCTCTACTGCTCCTTGCTCTACGGAGGCGTCTTC[G/T]GGATCCTTTGGATGGCTGCGGCGCTGGCGTTGGCCGTGCGGGCGACGATGCTGACCTGGATTACGATTTTAGTTCTGCTTGCTTCCGCG
90804 A G TGAATATTTGTTATCGGATTCATACATGTATGCGCCTTTGCTTGATGATTCCACGAGTTCATTTGCTTGCAGTTTGGGTAAATCCGTCATGGACCTGGAA[A/G]GTTCGCCTACCGGCATTCGCTCATCTCCTCTGAGTATGGGCAAAGGAGCACCTGTGGCTAGGGTGGTGGATAACTGAACCGTTTGCA
90818 T C CTGCATTTGCCAAAGTTGCCGGAGTAATGAAAGCCGCTGGAGGAGTGAAGCTTGGTGCAGCTGCAGCTGCGGTTACAGCTGCTGCTACGGCCGCTGTTTC[T/C]GGAACTAAGAAGGAAGAAGCAAATATGTCCAAGAAATGAACTCACTCCACCTAGTGTTTGTTGTAGATTAGACCCATGATAAGCC
90818 T C GTCCAAGAAATGAACTCACTCCACCTAGTGTTTGTTGTAGATTAGACCCATGATAAGCCCTTTAATATTTGAGCATTTGTGACAAAAACAGGCCTTGGGG[T/C]AAAAGGATTACTTCAGTAGATGTTGTAATTTAATTATTTTGAGCATTTAAAACTGCTGAAATTTTATAGCAGTTCTCTGGCTTCAATGTT
90818 T G GGTAAAAGGATTACTTCAGTAGATGTTGTAATTTAATTATTTTGAGCATTTAAAACTGCTGAAATTTTATAGCAGTTCTCTGGCTTCAATGTTTGGATAT[T/G]TGGGATTCATGTTATGCCATGAACTCATAATGATATATTAAAGGGTCTATAACTTGCTATGCATACATGTACAAGCCATGTTTGTATATA
90822 A T TGTCAAAGAGAGCTACTAAAATACCAAACACCACACTCGCAATCCAACAAAGCGGTTAACAAAAGGCAACACATTTCTTCTTGCAATCCATAGTGCATCC[A/T]CCACCTCCACCACCTCCTCCGTAATTCCTACCTGCCCTACTATACGAAGTAAAGCACTTTGCAGGACACATCAGCTTCCTCTTATAGCA
90822 C T CTTGCAATCCATAGTGCATCCACCACCTCCACCACCTCCTCCGTAATTCCTACCTGCCCTACTATACGAAGTAAAGCACTTTGCAGGACACATCAGCTTC[C/T]TCTTATAGCAAGGCCCCTTTTCCATGCAAACCGTGCTTGGCTGTATTATACCACCGCGTGTATACCCACCACCAGGCCCACTGTAACCCG
90822 A T AGCACTTTGCAGGACACATCAGCTTCCTCTTATAGCAAGGCCCCTTTTCCATGCAAACCGTGCTTGGCTGTATTATACCACCGCGTGTATACCCACCACC[A/T]GGCCCACTGTAACCCGACCCGTATCCGCCGCCCATATTTCCCCAACCGGGGATGTTCAGGTCCGTACCAGGTGGAAGAAAACTGTAAG
90822 G A CCATGCAAACCGTGCTTGGCTGTATTATACCACCGCGTGTATACCCACCACCAGGCCCACTGTAACCCGACCCGTATCCGCCGCCCATATTTCCCCAACC[G/A]GGGATGTTCAGGTCCGTACCAGGTGGAAGAAAACTGTAAGGATCCGGCCCGTTATCCGGGCTCCAGTTTGGTGTTCGGGTGCTGGA
90830 C T TTTGCAATGTTAAGGCTGGAACTTGCCTCGTGAGCAAGAACAGTCCTCTTGGAGTCCCAGCTCTAGCTCGCAGTCCGGCAAAACCACATTGGGCATTCCA[C/T]GGCAATAACCAGTAGAAGGTCGCACGACTTATTTAATTGGGGACGGAGAAGGTGGCTCCAGTATTTACAGAGGCCGCTTTTATCCT
90830 AT A ACCAGTAGAAGGTCGCACGACTTATTTAATTGGGGACGGAGAAGGTGGCTCCAGTATTTACAGAGGCCGCTTTTATCCTTATTACTATTCTTCGCCCTTT[AT/A]TTTTTATTTCAGTTCACCTTAATGATCTTTGAGACTCTTTGTAAATAGTTATTAGTTTTATATTTCCCTAAACAGGAGTGCTGTATGAAT
90834 C T GGGTGCCTGAGCAAGTTCATGATGGAAATGGATCTTCTCCTCTGATGGAGCTTCATTAGCAGTAAACACCCGACTCGCCACCTGTCTTCTTGGAGCATTG[C/T]CGCCGACGTTAGCAAACTCACCGTACCTGAAAGCGTCCACGATGCTGTTGAACTCGACCGCTGTTCGAATCGGGAATCCTCTTAAAA
90834 GT G CCTGAAAGCGTCCACGATGCTGTTGAACTCGACCGCTGTTCGAATCGGGAATCCTCTTAAAAGAACTGCCCCGCTTGCTTCAAGTAGCTCATCCAACCAT[GT/G]TTTTTTGGGTTGTTATTGCTTCAGTCAGTCGGATGTGGTCGAGCTCTGCTGATGGATTTTGGGTGATGGTCGTGGGTAGTAGGACG
90838 C CG TGGCCTACTGGCTCTCTCTCTCTTAAGAAGTTGTAGCTGGCTCACCGCTGATCTCGCTTAAATCGTGATTAAGTCGGCCAGAGATACCCAAC[C/CG]ATCGTATAATATGGCAAGCTACAAGGATGCAGGAAAGGCCTCGGCTGAGGAGCCAACCATCCATAGAATTAGAATCACTCTGACAAGTCGCAAT
90888 C G GGGGATGCTACTGTTGGCAAACAAAGAACCCTAATTCCCAAATGCTCACCCGCCATCTCTCCACCGCCAACTCATCCGGCGTCACCCTCTACCTCCGCCG[C/G]GCTACCATAATTGACTCACTTCGCCAACGCCTCCTCTCTCCGGACAAGTTCCAACTCCCCTCAGATTCCAACATCGACTCTTTCATCGCC
90888 T C TTGACTCACTTCGCCAACGCCTCCTCTCTCCGGACAAGTTCCAACTCCCCTCAGATTCCAACATCGACTCTTTCATCGCCGCCCAAACCATCCGGTCCGC[T/C]GCCTCCACCTCAGCCGCTTTTACCTTCTTCCGATCTCTTCCCTCTGATTTCCGCGACCGAAAATCAGTTGTCTCTTTATCTATCCTTAAACG
90888 T C CATCAACTTCTAGAAAACCTCCATGTCTCCCCATTGGACCGCCTTCGCTTTTTCTCTGCAGCAGGCGACGTCTCCAACGCCGTGAACGCCTGGCAAGAAA[T/C]TAGATCCGCCGCAGAGGAAGCCAAAAAGCAGGTATGTACTGAGTCATACAATTTGATTATGTCTACTTATTCATCTAATGGGATGGAC
90888 T G GCCTTCGCTTTTTCTCTGCAGCAGGCGACGTCTCCAACGCCGTGAACGCCTGGCAAGAAATTAGATCCGCCGCAGAGGAAGCCAAAAAGCAGGTATGTAC[T/G]GAGTCATACAATTTGATTATGTCTACTTATTCATCTAATGGGATGGACACAGATGCAGTAAATTGTTTCATT
90902 G A GATACAAATCCTTTTATACAGCGGAACATAAAATACAGTTTGAATATAGGAAAATATTACTGTGTTAAAATCTTCAGAGTGCGCATTCTTCGAATCCCCA[G/A]GTTCGCTAATCTTCAAATCACAAGCTGAAATCATTAAATTTGCAACACTTGGGTCTTTAACCGCAGCGAATTATTGCTAAGGACGAAGG
90902 C A ATATAGGAAAATATTACTGTGTTAAAATCTTCAGAGTGCGCATTCTTCGAATCCCCAGGTTCGCTAATCTTCAAATCACAAGCTGAAATCATTAAATTTG[C/A]AACACTTGGGTCTTTAACCGCAGCGAATTATTGCTAAGGACGAAGGAACCAGCAATCGTTTAGGTTCGAGCTTGGTGGCGATGAGATA
90902 T C TTAACAATTTGGTGCTTGGATCTGCGGTGGACGGCGGCTCGAGTCCTGACGCGGTGGTGAAGGCTTTCACTTTGGTTTCTAACGGGTCCTTTGATTTTTT[T/C]CTGGTGGCGCTGGCCTCGAGCGCGAGATGGACTAGAGAGGCTCCTCGATTTGAAGTGATGGAGGAAAGTTTAGAGTAGGATTTTGA
90922 T C TTGCAGATACATGGCAATGGTCTTATATCATGCTGGAGATCTGGCTGGTGCCATTACGCAACAACATAAAGAACTTATAATTAACGAACGCTGTCTTGGT[T/C]TCGATCATCCGGATACTGCCCACAGTTATGGAAACATGGCCTTGTTTTATCATGGTCTGTCTCAAACTGAACTTGCTTTACATCATATG
90946 G GA ACAGCTGCAAGATCATATTGTTGCTATGTAAGCCAAATAGAATGCTTGATTTGGCAGAAGTCCAAGATACATTATTATATTCAACAGCATTGTACCAACT[G/GA]AAAAAGAGCTTAAACAACTGTTATTGGAAGATATCAAAAGTACAACTGCAATGCACACACAAATAGATACGGCCCGTTTTCCTTCGA
90946 C T AGCATTGTACCAACTGAAAAAGAGCTTAAACAACTGTTATTGGAAGATATCAAAAGTACAACTGCAATGCACACACAAATAGATACGGCCCGTTTTCCTT[C/T]GAAGTTACCTGGAATGCCTAACCAAGATCAATGCCTCGAAGGGGCATTATCGTCGAGAAGATCGTCGTAGGGGTCGCGACGGCCGA
90946 A T ATTGTACCAACTGAAAAAGAGCTTAAACAACTGTTATTGGAAGATATCAAAAGTACAACTGCAATGCACACACAAATAGATACGGCCCGTTTTCCTTCGA[A/T]GTTACCTGGAATGCCTAACCAAGATCAATGCCTCGAAGGGGCATTATCGTCGAGAAGATCGTCGTAGGGGTCGCGACGGCCGAGAG
90952 C T AACAAGAATCAAAGCAACAATTTATTTCAAATTATAAAATAAGAACAGTCAACCCGGACGATTTTATCTTTTTTTCTTCATTATTGTATTTCTCAATCA[C/T]CACTTAAATAAACAAAAATCCATTATATATTTTCCATAAAGAGATCAATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACC
90952 C G CAAGAATCAAAGCAACAATTTATTTCAAATTATAAAATAAGAACAGTCAACCCGGACGATTTTATCTTTTTTTCTTCATTATTGTATTTCTCAATCACCA[C/G]TTAAATAAACAAAAATCCATTATATATTTTCCATAAAGAGATCAATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACCAC
90952 TA T TCAAAGCAACAATTTATTTCAAATTATAAAATAAGAACAGTCAACCCGGACGATTTTATCTTTTTTTCTTCATTATTGTATTTCTCAATCACCACTTAAA[TA/T]AAACAAAAATCCATTATATATTTTCCATAAAGAGATCAATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACCACAACTAT
90952 T C GGACGATTTTATCTTTTTTTCTTCATTATTGTATTTCTCAATCACCACTTAAATAAACAAAAATCCATTATATATTTTCCATAAAGAGATCAATCACAAA[T/C]AAAAGCGCAAAACATACACAAGCTACTGTACATACCACAACTATAAACCCCCTTTTTTCGTCCTGTGTTCCGGATCTGATAAAAAGGGAGG
90952 AC A CTTAAATAAACAAAAATCCATTATATATTTTCCATAAAGAGATCAATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACCACAACTATAA[AC/A]CCCCCTTTTTTCGTCCTGTGTTCCGGATCTGATAAAAAGGGAGGGTTTGACTCCAAATCGGTATCTAATTACTTAATCCAGTATCTACG
90952 C T TATATTTTCCATAAAGAGATCAATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACCACAACTATAAACCCCCTTTTTTCGTCCTGTGTT[C/T]CGGATCTGATAAAAAGGGAGGGTTTGACTCCAAATCGGTATCTAATTACTTAATCCAGTATCTACGAACACGAACCACATACACCGTAC
90952 G A AATCACAAATAAAAGCGCAAAACATACACAAGCTACTGTACATACCACAACTATAAACCCCCTTTTTTCGTCCTGTGTTCCGGATCTGATAAAAAGGGAG[G/A]GTTTGACTCCAAATCGGTATCTAATTACTTAATCCAGTATCTACGAACACGAACCACATACACCGTACCCGCCGTCGCAGTTCCTTCCA
90952 T A TACATACCACAACTATAAACCCCCTTTTTTCGTCCTGTGTTCCGGATCTGATAAAAAGGGAGGGTTTGACTCCAAATCGGTATCTAATTACTTAATCCAG[T/A]ATCTACGAACACGAACCACATACACCGTACCCGCCGTCGCAGTTCCTTCCACTTCCGTCGCAGAATCGAGCGGCTCCGATGAAGACCGA
90952 C T CCACAACTATAAACCCCCTTTTTTCGTCCTGTGTTCCGGATCTGATAAAAAGGGAGGGTTTGACTCCAAATCGGTATCTAATTACTTAATCCAGTATCTA[C/T]GAACACGAACCACATACACCGTACCCGCCGTCGCAGTTCCTTCCACTTCCGTCGCAGAATCGAGCGGCTCCGATGAAGACCGAACTTCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
90972 A G TATACCTGGAGCTTTAGATTGAGTTCTCTGACAATTTGAAATAGATGCTTATAACCAGCCCAGTTGTATTGCTGGGGCGCATTAGCTTCCACAATTCCCC[A/G]CCAGCAATCAACCATCACACCATCGACCTTTCCGTATTTCAATTTGCTTAACTGCTGCGACAAGCCTTCAGGATCAACCAATTCACACTC
90972 C T ACACCATCGACCTTTCCGTATTTCAATTTGCTTAACTGCTGCGACAAGCCTTCAGGATCAACCAATTCACACTCAGGGCTGATAACACCTAGAGGAAGCA[C/T]AACATAGACTGGGACATAAGGGCTTCCAGCGAAATCTCGCTCCAGTATCTTTGGAGGCTCATCATTTACCAGCTCAGAACCGCCGGCA
90978 C T GCATAAGCTTTTGTTTCAGAAGCAGCAGCAGCATTCCTCCAATAGACAACAGCAGCAAAGAGCAGCCATGCATCCTCTAAGGAAAGAAGAGCAAGAATCG[C/T]CGCCATGATGATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGGTGGAGGAGCATACTGATTAGTATCG
90978 G A TTGTTTCAGAAGCAGCAGCAGCATTCCTCCAATAGACAACAGCAGCAAAGAGCAGCCATGCATCCTCTAAGGAAAGAAGAGCAAGAATCGCCGCCATGAT[G/A]ATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGGTGGAGGAGCATACTGATTAGTATCGAAATACCCTT
90978 T C GAGCAGCCATGCATCCTCTAAGGAAAGAAGAGCAAGAATCGCCGCCATGATGATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGG[T/C]GGAGGAGCATACTGATTAGTATCGAAATACCCTTGATAAGATCCGTAACTCGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGC
90978 A T CAGCCATGCATCCTCTAAGGAAAGAAGAGCAAGAATCGCCGCCATGATGATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGGTGG[A/T]GGAGCATACTGATTAGTATCGAAATACCCTTGATAAGATCCGTAACTCGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGCCAT
90978 C A AGCAAGAATCGCCGCCATGATGATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGGTGGAGGAGCATACTGATTAGTATCGAAATA[C/A]CCTTGATAAGATCCGTAACTCGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGCCATATCCTGGCTGAGGTGGTGGTGGTGGAT
90978 T C TGATGATCATGGTGGTGGTGGGAGTGATGAGCATAAGAAGGAGGAGGTGGTGGAGGAGCATACTGATTAGTATCGAAATACCCTTGATAAGATCCGTAAC[T/C]CGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGCCATATCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATA
90978 CG C GATAAGATCCGTAACTCGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGCCATATCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACC[CG/C]GGGGGTGGGTACGCTTCTTGAGGTGCCTGCTGATAGCTCATTGCTTTCTTTTTTGTTCGTTTTTCCCTTCTTCCTTTCGTTTCCT
90978 T A TCGGCTGAGGTGGCGGGTAAGGCAGAGGTGGGCCATATCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACCCGGGGGTGGGTACGC[T/A]TCTTGAGGTGCCTGCTGATAGCTCATTGCTTTCTTTTTTGTTCGTTTTTCCCTTCTTCCTTTCGTTTCCTTAACCAGTCAACGTTTG
90978 A AT AGGTGGGCCATATCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACCCGGGGGTGGGTACGCTTCTTGAGGTGCCTGCTGATAGCTC[A/AT]TTGCTTTCTTTTTTGTTCGTTTTTCCCTTCTTCCTTTCGTTTCCTTAACCAGTCAACGTTTGTCGCAGACGCTGTAGATGGAACGC
90978 T C CCATATCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACCCGGGGGTGGGTACGCTTCTTGAGGTGCCTGCTGATAGCTCATTGCTT[T/C]CTTTTTTGTTCGTTTTTCCCTTCTTCCTTTCGTTTCCTTAACCAGTCAACGTTTGTCGCAGACGCTGTAGATGGAACGCGTGATCTGA
90978 T C TCCTGGCTGAGGTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACCCGGGGGTGGGTACGCTTCTTGAGGTGCCTGCTGATAGCTCATTGCTTTCTTT[T/C]TTGTTCGTTTTTCCCTTCTTCCTTTCGTTTCCTTAACCAGTCAACGTTTGTCGCAGACGCTGTAGATGGAACGCGTGATCTGA
90978 T C GTGGTGGTGGTGGATAAGGTTGCGGGTGAGAATAACCCGGGGGTGGGTACGCTTCTTGAGGTGCCTGCTGATAGCTCATTGCTTTCTTTTTTGTTCGTTT[T/C]TCCCTTCTTCCTTTCGTTTCCTTAACCAGTCAACGTTTGTCGCAGACGCTGTAGATGGAACGCGTGATCTGA
90982 T C GCTGCTAGTGACTTCTGGCTTCCGCTTTTCATGTATCCCATTACCCCTCCAACTCCAACAAGAGCGGCGTAACCTAATGTCAGCTTCTGAGACATAGACA[T/C]CCCGCTTTTCTTCTTATCTTCTTCCTCGCCTCCACTATCGCCTCCGCTAAATCCGCCTCCGCTGGGACCGCCGCCTCCGCCGAGATTGTC
90982 C T TTCCTCGCCTCCACTATCGCCTCCGCTAAATCCGCCTCCGCTGGGACCGCCGCCTCCGCCGAGATTGTCTGTGTTAGAGACGAAAGAGATGAAGGAAGAT[C/T]TGCAGATCTTAGGCTTAAGAGAGAGTTGGCGAAATGAGACTAGTGAGAATTTAGGACTAGAGATGAGCGAAGACTGGGAATTAAT
90982 A T CGCCTCCGCTAAATCCGCCTCCGCTGGGACCGCCGCCTCCGCCGAGATTGTCTGTGTTAGAGACGAAAGAGATGAAGGAAGATCTGCAGATCTTAGGCTT[A/T]AGAGAGAGTTGGCGAAATGAGACTAGTGAGAATTTAGGACTAGAGATGAGCGAAGACTGGGAATTAATGAGCGTGGTTATAAAT
90984 T C TGACTTTTATAGAAGATTTGAATTTTGTTTTGGGGATTCCAGAGGAAATATATATGAAAAAGTTAAATGAACGCGGGATGAAGAGGCCAACGAGGAGATG[T/C]AGGTTTGACCATTGTCAGAAAACTAATTAATTAGCGTCGTTGCCAGAGGAAGATAACGATCTATATTTCCCAGCCATTGCTGGAGG
90994 G A ATACACTGATTTATTTTATGTCAAATTCTAGCTTATTGATTTATAAGCCAGCAATTTTACACTCGTAGAAAACAATATTTTACACATGCATAGGAGTAGC[G/A]TTTGGTGGTGTATCAATCGAAGCAATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCA
90994 A G ATTTTATGTCAAATTCTAGCTTATTGATTTATAAGCCAGCAATTTTACACTCGTAGAAAACAATATTTTACACATGCATAGGAGTAGCGTTTGGTGGTGT[A/G]TCAATCGAAGCAATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCAACCCTTGTTCCT
90994 T G ACACATGCATAGGAGTAGCGTTTGGTGGTGTATCAATCGAAGCAATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACT[T/G]GCTTGATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACA
90994 G C TGCATAGGAGTAGCGTTTGGTGGTGTATCAATCGAAGCAATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTT[G/C]ATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTG
90994 A G TCGAAGCAATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCAACCCTTGTTCCTTCTCCTCCTCGCT[A/G]TACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTG
90994 C CT AATGATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCC[C/CT]AGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATG
90994 CT C GATCCCTGCTCCCCGTCCCCTTTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCCCAG[CT/C]TATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTAC
90994 G A TTCAGTCCTGCTATTCTCTGCAAACTTCATACTTGCTTGATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCCCAGCTATAATACTCTTCCTCGCTC[G/A]CATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCAT
90994 T A GATGCAACCCTTGTTCCTTCTCCTCCTCGCTATACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTG[T/A]GGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACT
90994 T A CCTCCTCGCTATACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAAC[T/A]GGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAG
90994 A G TATACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGT[A/G]CACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAG
90994 C A ACTCCCAGCTATAATACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACA[C/A]ACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCAC
90994 A G TACTCTTCCTCGCTCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCA[A/G]TCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCC
90994 G C TCGCATTCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGT[G/C]AGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTC
90994 A G TCTTTGATGGTGGCAAAAACATACTGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCC[A/G]GTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTG
90994 T A TGCCCCACTGTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACT[T/A]GTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTGACAATCCCCAAAGATCTACGCGAA
90994 T G GTGGAAAATGCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAA[T/G]AGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTGACAATCCCCAAAGATCTACGCGAAACAAATGGA
90994 A G GCACAAAGGCAACTGGTAATGTACACACCATTATCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTG[A/G]GTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTGACAATCCCCAAAGATCTACGCGAAACAAATGGAATAACTCCA
90994 A T TCATCAATCCCATAAGAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCC[A/T]GTCATTCCATTGACAATCCCCAAAGATCTACGCGAAACAAATGGAATAACTCCAAATACAGCCCCACAAGCTGCTTGTGCGCAGATG
90994 A G GAGTGAGTCCAGTCCCCGAGGAGTACTTTGAACTTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTGAC[A/G]ATCCCCAAAGATCTACGCGAAACAAATGGAATAACTCCAAATACAGCCCCACAAGCTGCTTGTGCGCAGATGGAGAAGCAAACCAT
90994 A G TTGTAAAAAATAGAAGCTGAGTCAATCCAGCACCAAAGTTTCCTCCCGCCCCAGTCATTCCATTGACAATCCCCAAAGATCTACGCGAAACAAATGGAAT[A/G]ACTCCAAATACAGCCCCACAAGCTGCTTGTGCGCAGATGGAGAAGCAAACCATGGCAAATAT
91004 T C CCACCTGGGCCGTAGAAATTGGCGGCGGTGCTGACGTCATAGATGGTGGATTTAATTGACAGGTATATTGGTTTGCTTGGGTCCGATCCGTCGAATTCTT[T/C]CAGCTGTGAAGCGGTGAGCTCCATTTTCCTTTTTGACGAGATTTCCTTGGATCTGATTTTTGTT
91022 C T GCCTGGACGCAATCCCCGGCGGCAGCGTCCTCCCCAAGTCGGGCTTACTCGGCTTAGCCCGTGGAGTTAATGGACTACTGGCGCAAACCGCTTCTCTCTA[C/T]CAGGGTGTATTCTCCTACTGCCTCCCAGGCTACAAATCCTACTACTTTTCCGGCTCGCTAAGACTGGGCCCAGTAAGGCAGCCCAAG
91022 A G GAGTTAATGGACTACTGGCGCAAACCGCTTCTCTCTACCAGGGTGTATTCTCCTACTGCCTCCCAGGCTACAAATCCTACTACTTTTCCGGCTCGCTAAG[A/G]CTGGGCCCAGTAAGGCAGCCCAAGGCCATCCGGACCACTCCGCTCCTATCCAACCCGCACCGTCCTTCCTTGTACTACGTCAATCTCAC
91022 T C AGGGTGTATTCTCCTACTGCCTCCCAGGCTACAAATCCTACTACTTTTCCGGCTCGCTAAGACTGGGCCCAGTAAGGCAGCCCAAGGCCATCCGGACCAC[T/C]CCGCTCCTATCCAACCCGCACCGTCCTTCCTTGTACTACGTCAATCTCACTGGAGTGAGCCTCGGTCGGGTAAACGTTGCCGTACCA
91032 CA C TCTTATACCCATCAAAAGTTTGAGTTTCATTCAAAGCATTTCTGAAACCAAAAGCATTCAATGCGTTGCACCGTGTATCTAGCGCCTGGAAATCCAATTC[CA/C]AAAAAGGAAAACATCGATTTTGACAGGGTGGTCCAAATTGAAATCTGTGTATGCAACATCAAGGTCAGTGAAACCCAGCAGGCATCT
91032
ATCTGTGTATGCAACATCAAGGA GAAACCAAAAGCATTCAATGCGTTGCACCGTGTATCTAGCGCCTGGAAATCCAATTCCAAAAAGGAAAACATCGATTTTGACAGGGTGGTCCAAATTGAA[ATCTGTGTATGCAACATCAAGG/A]TCTGTGTATGCAACATCAAGGTCAGTGAAACCCAGCAGGCATCTCGAGAGCAGGAAGTAGAGCG
91066 A G CCAGGGATCCTCCTTCTGTCTCACATAAACCATGGAGCAATCAAACACCGAGAACAGACCTCCCCAAACAGCAAAGCTTCCACCGACACGCGGCGCGTTC[A/G]TTCGAACGCCATTGACTCCGCCCGCCAGTCTCTCACCATTCGGCGAGTTGTATATCCCTTTTATAAAATGGAAAGCGGATCCGCCAA
91070 C T CTTTGTCATTGAGTCTCTTCCTGCTTCCCTTACGGCCGAAAGTGCCTGAAAAGCGACTGGCAGAGGAGTCCCTGGAGTGGCGGCCAAAGGAAGAAGGATG[C/T]GAAGGAGACTCCATTGGGCTGTTCAACACCGGCGTGGCCTGCATCGACGATGACTTGTCCCCATCATGGGAGTCCCTTGATGGGC
91084 T C CTGTTTTTCCAAGTAGGTTTCCAATCCCAATTCCAACTTCTCAAATCATCATGCAGGAAGGCAACAACGGCTACGCATCTCAGTACTATCCCCATCGCCC[T/C]TATCCTCTTGCTCCGACCCCTAACCCTAATCCAATCGATTTCAATCCTACCCCAAACCCAACTCCAAATCCGATCCATCCCCCTTTCGCCTC
91084 AC A GTTTCCAATCCCAATTCCAACTTCTCAAATCATCATGCAGGAAGGCAACAACGGCTACGCATCTCAGTACTATCCCCATCGCCCTTATCCTCTTGCTCCG[AC/A]CCCCTAACCCTAATCCAATCGATTTCAATCCTACCCCAAACCCAACTCCAAATCCGATCCATCCCCCTTTCGCCTCCGCACCGCCTTACA
91084 AC A CATGCAGGAAGGCAACAACGGCTACGCATCTCAGTACTATCCCCATCGCCCTTATCCTCTTGCTCCGACCCCTAACCCTAATCCAATCGATTTCAATCCT[AC/A]CCCCAAACCCAACTCCAAATCCGATCCATCCCCCTTTCGCCTCCGCACCGCCTTACAACTCTCCGTACCAACACCGTCAATCTGAATACC
91084 C T ACCCTTACCCTAATTACACCGCTCCACCACCTCCTCCTCCTCCTCTTCCCGAGCCCCAATTCCCTCATGATCCGTATTACTCGTACGATTACAACCCTGC[C/T]CCTGCCCCTCCTCCTCCCTACGAAAATCACGCTCAATTCGATCAAGGAAGCGGCGGTGGGTATTTTGGCAGTATTGGAGTTGACGAGCTT
91084 A T GTATTACTCGTACGATTACAACCCTGCCCCTGCCCCTCCTCCTCCCTACGAAAATCACGCTCAATTCGATCAAGGAAGCGGCGGTGGGTATTTTGGCAGT[A/T]TTGGAGTTGACGAGCTTGGCGATGGAAGTGGCATATACGCTTATGATGGAGGTAAAATGGAGCCGTATGGTGCTAGAGGCACTGGA
91116 G GA ATGGATACACTGCGAGGAGTCATCAACGTTTTGAAACCTTTGCAGGCCTTGCATTTTCTCATAGCTGCAGCCGAGCTGCATCTGAGAGTTCATGAATATG[G/GA]AAAAAGCTTGGATGCACAGAGGGCACAATCTCCTTAATTTTATTATGTCAACTTGATATGTACTGTATTAGGTATGCCAGTTGAGTT
91128 GC G TTCCAAGCAAACTGGTTAAGAAACAAGGTCTTTCCATCTGCATCAATCCTGAATGGACCGAGTTCTTCCGAAGCCCCATAAGCGACCGAGGAGCAGCCCG[GC/G]CCCACCATTCAGCCAAAGGACAAGCGGGAAAGAAGCAGAATCTTCCGGAGTTTCGACTAACCAATAAAACAGTGCTCTGCCAGCT
91128 T C CCGGCCCACCATTCAGCCAAAGGACAAGCGGGAAAGAAGCAGAATCTTCCGGAGTTTCGACTAACCAATAAAACAGTGCTCTGCCAGCTGTTTCGTTAAC[T/C]GTAACATAGCCGGAGTATTGCGAAAATTTCACTGGTGGCTGGCCTGGAAGGCTGCTGATTCTGTCATCTTCTTGATTTGCACTGAGC
91136 T C CACTAGTTTAAAATCGAAGAGGATCATCACTTAAAACCACCAACTGCAGCGCCTACCGTTCGCCAGTCGCCACCATCCACCCACCATCGTCACCCTGATT[T/C]CAGGACGAGCTCTCATCCGAAACCGCGTGCCCCTTCTCTCCACCAAAACGCCACAAACTCCACATAACCGAAAATCAATCAACCAACCC
91136 T C TGGATCTCCAACTTCGGCATTTTTCTAAGGTCCTACAGTGAATCATTGCGCCCATTTTTCCTCTCGAAAACCCACCCAAATCTCAGAAATCCAACGTTTT[T/C]ATAAAGATGGGTTGTTTCCATTATTTATTTTCTTTTCTACTTTTGCTTGTCCAGTAGGCCAACAGT
91140 T C TTTATAGTCACATGCCATTCGCCAGCGCCACCAAAGGCATCACCATTACCGCCCCACAGGTCCCATGCCATAATCTCATCTTCAGGAGCACCAACATAGT[T/C]GACTCCGAGTACTTCTGTATTGAACCTTATATTTGGAATAAGGTCAAAATGACGAGCGTAGGAGTAGAGGTAATCCATCACTTGACTA
91140 A C GGAGAACTGATAAGCAATTCTAGGAGTCTGAAGTCGAGTGATTGAGAGTGTATGGGCCCATACCCCTCCAATCGTAGGACCTGCCTCAAAGACGGTGGGA[A/C]TAAAGCCTTTGGCCAGGAGGTGTTTGCAGGTTGTTAGGCCGCTGATTCCAGCTCCCACGATGCATATTCTTTGTTTGTTCATTTTAC
91142 C T TTAAGACCGCATTACACAGCAGTTCTGACATGAAGACATCTAAAGCCCAAGCAAACAAGTAGGCATAACCACCAACAACACAAGAAGCATACCTACGAGT[C/T]CACCACAATCACCATCTCCCCAGAGCTAAACCACCCAGGCTCGCAACAGCCTTACACCCTAAAACACCAAGTCAAACTTCAAATCAG
91174 A C CTATACAAATCAATAAAGAGGGAAGCAGTGTGACATTCAGTAGCCTGCTCTGTCCTAAATAACCAGCTAAAGTGATTGTGCCATCTGCAACGACTCGAGC[A/C]AGTGTTCCTGCCTCGGTTGAAAGCAGACCACCATTGTAGGTCCCACGTGCCAGTCGAGATGACATTACTTCGGACAGCAGTGATAG
91174 A G CATTCAGTAGCCTGCTCTGTCCTAAATAACCAGCTAAAGTGATTGTGCCATCTGCAACGACTCGAGCAAGTGTTCCTGCCTCGGTTGAAAGCAGACCACC[A/G]TTGTAGGTCCCACGTGCCAGTCGAGATGACATTACTTCGGACAGCAGTGATAGATTAACACCTTCGAGCACTTCAGCAGATACAAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
91202 AC A GGTACGGTACCTGTATATCCTTGTCCTTCGTATTGCAGTGTCATAATCTATCCCAGTCCCGACCGCCGCCTCGCTCCCAC[AC/A]CGGGTATCTCCCGCCCAGCCAGCCCTCCTCACCGCACGTACTTGTTCATAAACCTCCTGTGGAAATCCGAGCGCAGCAGATCGTTGATAAACTCCTTCCT
91226 T C AATGGCTACCCCTTCTACCATGGCCACCCAACTTCAGAGCAACTTCATCTCTTCCAGCAGCACCAAAGGCCTCCT[T/C]GTTCCACGTGGCATTTCGGGTCCACTTCTCAGGAACCCAAACCCGAAACGGAGGTCCACCTTCACCGTCAAAGCCATCCAATCAGAAAAGCCCACGTTTC
91226 G A GTCCACCTTCACCGTCAAAGCCATCCAATCAGAAAAGCCCACGTTTCAAGTGGTCCAGCCCATCAACGGCGACCCGTTCATCGGAAGCCTGGAAACCCCC[G/A]TCACATCCTCGCCGCTCATCGCCTGGTACCTATCCAACCTCCCGGCCTACCGCACAGCCGTCAGCCCTCTCCTGCGCGGCGTCGAGG
91226 A G CCTTCACCGTCAAAGCCATCCAATCAGAAAAGCCCACGTTTCAAGTGGTCCAGCCCATCAACGGCGACCCGTTCATCGGAAGCCTGGAAACCCCCGTCAC[A/G]TCCTCGCCGCTCATCGCCTGGTACCTATCCAACCTCCCGGCCTACCGCACAGCCGTCAGCCCTCTCCTGCGCGGCGTCGAGGTAGGT
91226 A G AGCCCATCAACGGCGACCCGTTCATCGGAAGCCTGGAAACCCCCGTCACATCCTCGCCGCTCATCGCCTGGTACCTATCCAACCTCCCGGCCTACCGCAC[A/G]GCCGTCAGCCCTCTCCTGCGCGGCGTCGAGGTAGGTCTGGCCCACGGGTTCCTGTTGGTGGGGCCGTTTGTGAAGGCCGGCCCGTT
91226 T C AAACCCCCGTCACATCCTCGCCGCTCATCGCCTGGTACCTATCCAACCTCCCGGCCTACCGCACAGCCGTCAGCCCTCTCCTGCGCGGCGTCGAGGTAGG[T/C]CTGGCCCACGGGTTCCTGTTGGTGGGGCCGTTTGTGAAGGCCGGCCCGTTGAGGAACACGCCGTACGCCGGGGCTGCGGGGTCGC
91226 G A TGCGCGGCGTCGAGGTAGGTCTGGCCCACGGGTTCCTGTTGGTGGGGCCGTTTGTGAAGGCCGGCCCGTTGAGGAACACGCCGTACGCCGGGGCTGCGGG[G/A]TCGCTTGCGGCAGGTGGGCTGGTTGTGATTTTGAGCATCTGTCTGACGATGTATGGGATCGCGTCGTTCAAGGAAGGGGAAC
91234 T C GATGTGCCACTATTAATGGGATGCTTAATCTAGGCTTTTCTAGGAGAAGTTATCGCCACAGATACACACGTACTCATCCAATCCATGGACAAAGAAGCAT[T/C]CCCATTACAGTTCAAAGCAGCCAAGTGCAGTTAGAAGACATGGAAGATGAAGCATGCGAGCTAGTAAGCGGTGTAGATCTCATAAT
91234 G A ACCGTGTTGCGTGCAATGGCTACAACGTTCTAGTTCCTGACCTCTTTAGAGGTGATCCATGGAGCAAACTTCGACCAGAAAATGAACTAAACCAGTGGAT[G/A]ACAAACCAGACACAGTCTAGGGTATCGATGGACATAGAGACATCGACAAAATGGTTGGTGGACGAATT
91236 A G TCTTTTCTTTCTTGAAGTATGTGTCGTCAAATTTCTCAACATCCACACCAGAGATGTCCACCTTGACTGAGGTTGCAATGACATAGGACTGGACTATACG[A/G]CGCAGAGGAACTCCATTCACCTTGAATGGACCAGTAACAAGAAGCAACCCAGATGGCAACTGCTTCAAAAACACAACTTTCTTGCCCA
91236 C G ATGTGTCGTCAAATTTCTCAACATCCACACCAGAGATGTCCACCTTGACTGAGGTTGCAATGACATAGGACTGGACTATACGACGCAGAGGAACTCCATT[C/G]ACCTTGAATGGACCAGTAACAAGAAGCAACCCAGATGGCAACTGCTTCAAAAACACAACTTTCTTGCCCATGAATCTACCCGCCAGC
91236 A G CAACATCCACACCAGAGATGTCCACCTTGACTGAGGTTGCAATGACATAGGACTGGACTATACGACGCAGAGGAACTCCATTCACCTTGAATGGACCAGT[A/G]ACAAGAAGCAACCCAGATGGCAACTGCTTCAAAAACACAACTTTCTTGCCCATGAATCTACCCGCCAGCAGAATCAACACTGTCCCA
91236 G T GTCCACCTTGACTGAGGTTGCAATGACATAGGACTGGACTATACGACGCAGAGGAACTCCATTCACCTTGAATGGACCAGTAACAAGAAGCAACCCAGAT[G/T]GCAACTGCTTCAAAAACACAACTTTCTTGCCCATGAATCTACCCGCCAGCAGAATCAACACTGTCCCAGGTGTAATACTGTCCCTGA
91236 T C CGTTCTTTGCTTTAATCGCCCACAAACCTCGCTTGTGATACATTTTTGAACGAGAGAATCTTCTGATACCTAGGATCAACTCAGGGTTGCGGGTCACGCG[T/C]GTGGCTTTTCCTTTTCCTGCTGCCATTGAAACAATGTTGGGTGTGATTAGGGTTAAGAGGAATGGAGGCGGCTGGAGAGT
91242 A C CATTTGCATTAGAAGCAGCTGTGGTGAAAAGCACACCAGCAAGACCTAGAAGAGCAGCTCTTCTTCCTTCAATGTTTTTCTCATGCAAATCGATTTTTTC[A/C]ACTTTTTGAGCTCTAATACTCTGCATCCTTTGATTTGCAACCAAGTTCGATGCATTTGAAGGCATGGACATGAGTTTCTTGGTCGATTCA
91262 A G ATACGTGTTAGATAGACAAAATAGAACAAAATAGCAACATGAAAGATAAAGCTACATTTGTACAACTAATTAGTGTATCAAAACTGAAAATTTTATCAAT[A/G]CTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCC
91262 TA T GAAAGATAAAGCTACATTTGTACAACTAATTAGTGTATCAAAACTGAAAATTTTATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTAT[TA/T]AGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTA
91262 T C AGATAAAGCTACATTTGTACAACTAATTAGTGTATCAAAACTGAAAATTTTATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAG[T/C]CATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCA
91262 G C TACAACTAATTAGTGTATCAAAACTGAAAATTTTATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAGTCATTCACAGAGCACGT[G/C]GCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGG
91262 G C TAATTAGTGTATCAAAACTGAAAATTTTATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAGTCATTCACAGAGCACGTGGCCAG[G/C]TCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAA
91262 C T AATTTTATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCC[C/T]CAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCA
91262 T C ATCAATACTGGGAGGTTAGAAGTAAGAGCGTACTATCATAAACTATTAGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAAT[T/C]GAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCATGTCGC
91262 C T ATCATAAACTATTAGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTA[C/T]CCAATATCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGGTCGCTGA
91262 A T AACTATTAGTCATTCACAGAGCACGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAAT[A/T]TCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGGTCGCTGATGATGA
91262 C T CGTGGCCAGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATG[C/T]CACAAACCAGCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGGTCGCTGATGATGAAGCTTGATATCAACATCTCGGA
91262 C T AGGTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAA[C/T]CAGCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGGTCGCTGATGATGAAGCTTGATATCAACATCTCGGATCGCTGTG
91262 A G GTCACAATATTTCGAAACTCCCCCAAATTGAAAATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAACC[A/G]GCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGGTCGCTGATGATGAAGCTTGATATCAACATCTCGGATCGCTGTGAT
91262 G C ATTCATCACCCGTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCATGTCGCTTTGAAGACGCAATCA[G/C]ATCAAAGGGGTCGCTGATGATGAAGCTTGATATCAACATCTCGGATCGCTGTGATTTTAGCATGCGTAGAACGAAGAGAGGCTGGA
91262 T C GTTAGAAAATTAGCTGTACCCAATATCATCTTGCTCATGGAAGAATGCCACAAACCAGCCAAAACCATGTCGCTTTGAAGACGCAATCAGATCAAAGGGG[T/C]CGCTGATGATGAAGCTTGATATCAACATCTCGGATCGCTGTGATTTTAGCATGCGTAGAACGAAGAGAGGCTGGAGCAAAATCGAA
91262 C T GATTTTAGCATGCGTAGAACGAAGAGAGGCTGGAGCAAAATCGAAGTGATTTTGATGGCCGGATGAGGTTGGATCTTCAGTTTTACTTCGGTTCGATATG[C/T]GGTTTAGAGGCTGGATCTATGGTTCAGACATGCTCGAGGCTTGAATCTTCTCCGGACCGTGGTGGCTGGCGGCCGACGGTTAACC
91262 C T GCGTAGAACGAAGAGAGGCTGGAGCAAAATCGAAGTGATTTTGATGGCCGGATGAGGTTGGATCTTCAGTTTTACTTCGGTTCGATATGCGGTTTAGAGG[C/T]TGGATCTATGGTTCAGACATGCTCGAGGCTTGAATCTTCTCCGGACCGTGGTGGCTGGCGGCCGACGGTTAACCTCGGTCGGACC
91262 A G CGAAGAGAGGCTGGAGCAAAATCGAAGTGATTTTGATGGCCGGATGAGGTTGGATCTTCAGTTTTACTTCGGTTCGATATGCGGTTTAGAGGCTGGATCT[A/G]TGGTTCAGACATGCTCGAGGCTTGAATCTTCTCCGGACCGTGGTGGCTGGCGGCCGACGGTTAACCTCGGTCGGACCGCGG
91262 C T CAAAATCGAAGTGATTTTGATGGCCGGATGAGGTTGGATCTTCAGTTTTACTTCGGTTCGATATGCGGTTTAGAGGCTGGATCTATGGTTCAGACATGCT[C/T]GAGGCTTGAATCTTCTCCGGACCGTGGTGGCTGGCGGCCGACGGTTAACCTCGGTCGGACCGCGG
91262 C G TCGAAGTGATTTTGATGGCCGGATGAGGTTGGATCTTCAGTTTTACTTCGGTTCGATATGCGGTTTAGAGGCTGGATCTATGGTTCAGACATGCTCGAGG[C/G]TTGAATCTTCTCCGGACCGTGGTGGCTGGCGGCCGACGGTTAACCTCGGTCGGACCGCGG
91274 C T TAAGGGAGTGCCGGTCATACCCATTGTATAGATTGGTGAGGGAGGAGCTCGGAGCGGGGTATCTGACTGGGGAGGAGGGAACGAGTCCTGGGGAGGTGTT[C/T]GAGAAGGTGTTCGAGGCGGTTTGCAAGGGGAAGGTCGTCGACCCACTGCTAGAGTGCTTGCAGGAGTGGGATGGTGCACCT
91274 G A GGAGGAGGGAACGAGTCCTGGGGAGGTGTTCGAGAAGGTGTTCGAGGCGGTTTGCAAGGGGAAGGTCGTCGACCCACTGCTAGAGTGCTTGCAGGAGTGG[G/A]ATGGTGCACCTGTGCCCATTTGTTAGAGTTACAGTGAGTGAAAATTTATTCTGGTTTGTGAAATAGTAATGTTTATTTGCTGTG
91278 C T CGACATTGAAGAGAAACATCCTGAGCCGAACTGACAGCTTGGGATTTTTGTTTAAGCGGCAAATCCGGTCGTACTCGGCCAGCATGTTTTCCATATCCTC[C/T]TCGTTGGTGACGGAGACGAGGGAATCGAGGTCTTCGCCCGGGAGCTGGTACTTGGCGACAAAGTCGTCGGAGCCGAACAGAGATC
91278 G A TAAATAACGATAAGTAACGGAGCGAGCGATCGACGGCAAGAAGCTTAGATACTCCGCCGACGTAGACGAGGGAATTGTCTGGCAGACGAGGCTGAATCCG[G/A]CCGTTATAGCTGATTATGAGCTTTAAGCGTGGCGGTGGTGATTGGAAGTCGCCGGACAAGACGGCGACGGAGGGATCGTTGTT
91282 C T TAGATGCTTTATCCAGAATAACAAAGGCATTTAACCATTCAGATCCCAAGTTGCTTGAGAAGGCAATTCAGAGAAGCTTTCTTGTATCTGCTGACATGGC[C/T]CATGCTTTACATCCTAATTATATGGACAAGCATGAGGAGAATCATCAACCTAAACTGCATTGTGGTCTGGTCATTAAGCACAATGCTA
91282 G A TTAACCATTCAGATCCCAAGTTGCTTGAGAAGGCAATTCAGAGAAGCTTTCTTGTATCTGCTGACATGGCCCATGCTTTACATCCTAATTATATGGACAA[G/A]CATGAGGAGAATCATCAACCTAAACTGCATTGTGGTCTGGTCATTAAGCACAATGCTAATCAGCGTTACGCCACAAATGCCGTCACTT
91306 T C CTTCAGCTCCATCGTTCTCAACTCCTTCACTTTTCAGTGCTGCCGCACCATCTTCTGCTGCTGCTGCCACCAGTTCTTCTAGTGCAGCAGCAACCTCTTC[T/C]TTTCCTTCATTTTCTTTGCCTACAAGTTCATCTTCTGCTGCCAGCACTTCTTCCTTTTCGTTTGCTAAGAGTACTCAACCATTTGGCATAAGC
91306 C T CTGCTGCCAGCACTTCTTCCTTTTCGTTTGCTAAGAGTACTCAACCATTTGGCATAAGCACTTCTTCGTCAGCTGTTTCTGCTGCTTCTACGCCATCCTT[C/T]ACATCAGCATTTGGTGGATTTGGTAATAATACAGCAAGCTCAACAGCGACTACTCCTTCATCTGGAAGTGGATTG
91352 T A TGGCCTCAACATCTGGGCCAATGCAGTCATCGGCTTTCTCAACTGTGATGCCTAGAAGTTCAGATAGTCTTGGTACAAGAGGTGCCAAGCTGTATTTTGG[T/A]GTAACACCCTTAGGACGTCCCAAGTGACTAGACAAAATAACTTTAGCCCCATTGCTCATCAAATACTTGATGGTAGGTACTGCAGCA
91352 G T CAAGTCAGCCCTGACAAACACTTTCTTCCCTTTCAATTCGGCAGCGCTTAGGTCGCCAACGCTCCTTTTAGCCATGGAGACGACGCCTCTCGGACCTTTT[G/T]TCAGGTGGGTGGAGAAAGCGCGGCACTTGGACGAGACGTGAAGAGAGAGGCTGCAATCGGCGGCGGAGGAGGAGAAGGAGAGG
91356 A G CTCCACTTGGGCCTGGCTCGCTTTCTTCTTCGCCGCCTTCAGTTACTACCGGATCCGGGCCACGGGGTCCGTCGCTAAACCGCACCCGAAGCCCGAACCA[A/G]TTTCTACTTCCAGCACCGGCAACAGCTACGTCAGGTCGGAGAATGCGGTGCGAGTTGAACGGGTGGCTAGGTGCCACGTGGAGGA
91356 A G ACTTCCAGCACCGGCAACAGCTACGTCAGGTCGGAGAATGCGGTGCGAGTTGAACGGGTGGCTAGGTGCCACGTGGAGGATGACGGCGTTACGAAAGGGA[A/G]GTTCACGCTGTACTTCGACTGCACGGAGAGCGAGGGGGACGACGACGAGGCGGTCGACGTGGGGGACGGAAGGGTGGTGG
91356 G C CAGCTACGTCAGGTCGGAGAATGCGGTGCGAGTTGAACGGGTGGCTAGGTGCCACGTGGAGGATGACGGCGTTACGAAAGGGAAGTTCACGCTGTACTTC[G/C]ACTGCACGGAGAGCGAGGGGGACGACGACGAGGCGGTCGACGTGGGGGACGGAAGGGTGGTGGAGAGGATGAAGGAAAG
91356 A C GTTGAACGGGTGGCTAGGTGCCACGTGGAGGATGACGGCGTTACGAAAGGGAAGTTCACGCTGTACTTCGACTGCACGGAGAGCGAGGGGGACGACGACG[A/C]GGCGGTCGACGTGGGGGACGGAAGGGTGGTGGAGAGGATGAAGGAAAGGAGAGGGGATTTGGGGTGGTACCGCCACGTG
91364 CT C GTTTGACCATGAGTGTTACCTCTTGGGAATCCCATTGTATATTTATAGATATCTTGTAAAGAGCAGCATAAAATACTTAGAGGCTTTGAATGGTCAATTT[CT/C]TTTGATTATGCGAAGACGTTCGATGGCTGCATTATTCCTCATATCACAAACAATTGAATACACAGTATCCGTTGGAATAACACCAACA
91364 A G ATGGCTGCATTATTCCTCATATCACAAACAATTGAATACACAGTATCCGTTGGAATAACACCAACAGCGCCATCTTTAATCATATCGATAACAGGTTCCA[A/G]CTTCCACGTGTCAGCTCCCTGTGGGTCCATCTCCACATACAGCATCTTGTCCCCTTTCTTGTTCGGCTGACGCTTAGAAGCGTATTTCAA
91364 G C TGGGTCCATCTCCACATACAGCATCTTGTCCCCTTTCTTGTTCGGCTGACGCTTAGAAGCGTATTTCAAGCGTTTAGGGCTGCGCTTGAGCGCCAATGTG[G/C]TCTGCTTATTTGCAGGCCCGTGATTTGTGCGCGCTGAGAGGGACGCTAAGCGGTTGCTGGCGATGGAAGCGATTGCTTCCAGCAACA
91368 A G TCCACAGAACTTAAAGCTACATGCACAAAAACTACTTTAGTCAACACACATAATCTCTGGATAGACAAATCTATCATCATAAAGAAGAAACTCAGTATTC[A/G]GTTCACTGACATTTCTCAATATACGCTCATTCTTATTAATCAAAGGGAAGGTGTGCTTTCGACGTCCTCAAGTTCACGAAACCAAGCTG
91368 T C ACAGAACTTAAAGCTACATGCACAAAAACTACTTTAGTCAACACACATAATCTCTGGATAGACAAATCTATCATCATAAAGAAGAAACTCAGTATTCAGT[T/C]CACTGACATTTCTCAATATACGCTCATTCTTATTAATCAAAGGGAAGGTGTGCTTTCGACGTCCTCAAGTTCACGAAACCAAGCTGTTT
91368 G A AGTTCACTGACATTTCTCAATATACGCTCATTCTTATTAATCAAAGGGAAGGTGTGCTTTCGACGTCCTCAAGTTCACGAAACCAAGCTGTTTGTTGTAC[G/A]TTTGACGACGGATAGTTGTTGCCATCTCTGTTGTGCTGCTGTGCATTGTTGGACGAGTGCTTACCATTGCCTGCAGGGACAAAGATGC
91368 C T AGTTCACGAAACCAAGCTGTTTGTTGTACGTTTGACGACGGATAGTTGTTGCCATCTCTGTTGTGCTGCTGTGCATTGTTGGACGAGTGCTTACCATTGC[C/T]TGCAGGGACAAAGATGCCGGTTTTTTGATCCGGGCACCAATACTTGTCCGCCTCCGATTCGTACTCTGGCACCACAACTGGACACACT
91368 A ACAG GCACCAATACTTGTCCGCCTCCGATTCGTACTCTGGCACCACAACTGGACACACTTGTTCGTCTATGTTTTTGTCATACAACGACGTCCAGTTAGAATAG[A/ACAG]CAGCAGTCCTCTTAGGTTCAGGGAGCCTACGATTTGAGATCATTTGTTTGCTAGAGCTACCAATGTTCATAAATCTTCTAAGATTA
91376 T C TGGGAGCTTCAACAATGCGACAAGCAACGTTCCATCTGGAAAGTCACTTATGTACTTTGGTCTGCTTCTCGCAAGTGGCATATTTTTCATATTTATAGCT[T/C]TCACGGTTTTCCTTCCTGCCATGGTTCTGGTACCTCAAAAATTTGCTATTTGTTTTACTCTTGGTTGTGCCATGATTGTTGGATCATTCTT
91384 T C CACCTCACGATCGTATCAACAAACACACACGTGTCCTCCTTCGAGTTCCCCTCCGGCACATCGACCACGTAGCTCTCCACCACGGCGG[T/C]GTCGTCACCGCACTTGTGCAGCGTGGTCACAGATCTGTAATTCGTGAGCCGATGCTCGCCTCCGACGACCCTAAAGCTGAGCACGTGCTCGTCGTCGTC
91404 C T GATAAAAATTGATTTTGCTTATTTCCCCAGTTTAAACTTTAAAGCATTCAAAAATAAAACATACAGAAACTCTTGATGCTACAATTACACA[C/T]GACAAATCCCCTCACAAGCTACAAACAACCGTAAAATCACAAAGATTTAGCCGCTGCAACTACGTTCTCCACCGTAATACCATACTCCTTGTAAATAAT
91404 T C TTTAAAGCATTCAAAAATAAAACATACAGAAACTCTTGATGCTACAATTACACACGACAAATCCCCTCACAAGCTACAAACAACCGTAAAATCACAAAGA[T/C]TTAGCCGCTGCAACTACGTTCTCCACCGTAATACCATACTCCTTGTAAATAATCCCAGCAGGAGCGCTAGCTCCGAACTTATCGATCCC
91404 G A TAATACCATACTCCTTGTAAATAATCCCAGCAGGAGCGCTAGCTCCGAACTTATCGATCCCGATTGCCTTCCCTTTACCTCCAATATACTTCTGCCACCC[G/A]AGGGTCGACCCAGCCTCTATACTAACCCTAGCAGTCACAGCTTCCGGAAGCACGCTTTCCTTATACTCGTCATCCTGCTCATCAAACAAC
91420 C G TCAAGAATAAACTCCAGTCCTCCCAGTACAAAGGGGTGGTCCCCCAACCAAACGGTCGGTGGGGCGCTCAGATATACGAGAAGCACCAGCGCGTCTGGCT[C/G]GGCACCTTCAACGAGCAGTCCGCAGCAGCCAAGGCCTACGACGTCGCCGCCCAGCGCTTCCGTGGCCGGGACGCCGTCACCAAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
91420 C T ACGGTCGGTGGGGCGCTCAGATATACGAGAAGCACCAGCGCGTCTGGCTCGGCACCTTCAACGAGCAGTCCGCAGCAGCCAAGGCCTACGACGTCGCCGC[C/T]CAGCGCTTCCGTGGCCGGGACGCCGTCACCAACTTCAAGCCCCTGACCGACGCGGCCGAGCTCGACTTCCTCGGCCTCCACTCCA
91420 G A AGCAGCCAAGGCCTACGACGTCGCCGCCCAGCGCTTCCGTGGCCGGGACGCCGTCACCAACTTCAAGCCCCTGACCGACGCGGCCGAGCTCGACTTCCTC[G/A]GCCTCCACTCCAAATCCGAGATCGTGGACATGCTCCGCAAGCACACCTACCACGACGAGCTCTCGCAGAACAAGCGCAACCAAAT
91420 C T CCAAGGCCTACGACGTCGCCGCCCAGCGCTTCCGTGGCCGGGACGCCGTCACCAACTTCAAGCCCCTGACCGACGCGGCCGAGCTCGACTTCCTCGGCCT[C/T]CACTCCAAATCCGAGATCGTGGACATGCTCCGCAAGCACACCTACCACGACGAGCTCTCGCAGAACAAGCGCAACCAAATCAGGG
91420 A G ACGACGTCGCCGCCCAGCGCTTCCGTGGCCGGGACGCCGTCACCAACTTCAAGCCCCTGACCGACGCGGCCGAGCTCGACTTCCTCGGCCTCCACTCCAA[A/G]TCCGAGATCGTGGACATGCTCCGCAAGCACACCTACCACGACGAGCTCTCGCAGAACAAGCGCAACCAAATCAGGGCGAGCGGAA
91420 A G GGACATGCTCCGCAAGCACACCTACCACGACGAGCTCTCGCAGAACAAGCGCAACCAAATCAGGGCGAGCGGAAAGGACAGCAACTGCGAGGTCAGCAGC[A/G]GCGGCAGCGCCGCGGTCCGGCGTCACCTGTTCGACAAGACGGTGACGCCGAGCGACGTGGGGAAGCTGAACAGGCTGGTGA
91420 C T ACGACGAGCTCTCGCAGAACAAGCGCAACCAAATCAGGGCGAGCGGAAAGGACAGCAACTGCGAGGTCAGCAGCAGCGGCAGCGCCGCGGTCCGGCGTCA[C/T]CTGTTCGACAAGACGGTGACGCCGAGCGACGTGGGGAAGCTGAACAGGCTGGTGATACCCAAGCAGCACGCGGAGAAGCAT
91424 A G GGCCACCAAAATTGCTGAACATGACACAAAGCTGAAGTGCGGTGGAGCCCACTGAGCCAAAGGATTCAGCCATGAGCTCGGCGTACGTAGAAGATACACC[A/G]TATGCAGTGTATTTTAGCATGAACTGAGCAGAAGTGTTGCATAAGAAAGCCATGAGGAGGATCAAGGAGAAAGCAGGGCCGAC
91426 G A TAGTACAAACCACTGGACGCTCAAAATTTTTCCAAATGAATGGCGCTCAAATCAAACAATTTCACAAATCTTCAAAATTTTCGCACCCATGATCATCATC[G/A]CTCAGGAATCCTTCACGCTCAGTACCAACTATAAAGGCCTCGATGCTCCTCCAGGCGACGGACGCCAGCAAGGAGAAGAGAATGATG
91426 G A CACCATAGAAGCAGACCGCCTCCGACTAAACTCATCACCATCAACGTCGTTTTCGCCAATACCGGAATTTCCTTCTCTTTGCCCATCACCTCCATTTTCT[G/A]CAATAATATTTGATGTTGTTGTTTTTTCTTCCTTCTTTGCTTTCTATTTTGGTAGGTGAATGAAGGAGCTGGTTGTTTATGTAATGGGATCA
91428 A G GTGATCACTCGCGTTCCTCCAACAGCTTACGCAGCACTACGCACAGCATTCAGAAAACTGATGTCAAAATACCCAACTTCCCCTGCAGCCTCTATATTAG[A/G]CACATGCTATGACCTAAGTAAATATGGTACCGTATCAATACCAACCGTAGCATTACAGTACGAAGGCGCCACCATGGACTTGGATGTT
91458 GT G CTTAGTTTTTTATGTTCGGTAAATTTCATGAAATGCGATGTTTATTTGGAAGTTGAACCATATGTACGATGGGCATTATGTGCATTTTGCTTATGTTGAT[GT/G]TTTTTTGTCCATGTACGTTAGCCTTTTTAAAGATTTGTAACAAGTTGTAAAGAATGCAAATAGTGTCGTGTTCCATGCTTGGCATTATG
91464 C A CGCTGTCAGCCGAATAAAGAAGCTTTCGATTGTCTGCATGGCACCTGAAGAAGAGAAGATGACTCGACGCTCTCCTCTCGATTTTCCAATTGAATGGGAG[C/A]GACCTAAGCCTGGAAGAAGGCCTGATATATTCCCAAAATTTAGTCCGATGAAAACGCCACTGCCGACTCCTTTACCGGCAGATCCTC
91464 T G ACTCGACGCTCTCCTCTCGATTTTCCAATTGAATGGGAGCGACCTAAGCCTGGAAGAAGGCCTGATATATTCCCAAAATTTAGTCCGATGAAAACGCCAC[T/G]GCCGACTCCTTTACCGGCAGATCCTCCAGAAGAAGACGAAGAAGAGGAAGAAGAGAAGAAAGAGGAGGAGGAAGAGGACCCTGA
91464 G A CGAAGAAGAGGAAGAAGAGAAGAAAGAGGAGGAGGAAGAGGACCCTGAAAAGGAAGAGAATGATAATCCTGAAAAGCAGTAGAACTTGTATTAAGTTTTG[G/A]CAAGTCAGAGTCTGAAGAATTGATGTCTAGCTTGATAATAGGTTTTTTGAGATTTGTTGTGTAATCATGTACCTCACCATCGGT
91464 T C GAAGAGAAGAAAGAGGAGGAGGAAGAGGACCCTGAAAAGGAAGAGAATGATAATCCTGAAAAGCAGTAGAACTTGTATTAAGTTTTGGCAAGTCAGAGTC[T/C]GAAGAATTGATGTCTAGCTTGATAATAGGTTTTTTGAGATTTGTTGTGTAATCATGTACCTCACCATCGGTATTCCGTTTCTAGTT
91464 T TA AAAGGAAGAGAATGATAATCCTGAAAAGCAGTAGAACTTGTATTAAGTTTTGGCAAGTCAGAGTCTGAAGAATTGATGTCTAGCTTGATAATAGGTTTTT[T/TA]GAGATTTGTTGTGTAATCATGTACCTCACCATCGGTATTCCGTTTCTAGTTGTAAATGCAAGACTTTGTATGTGGTTATGTCAAAGT
91480 T C GATGATGGACATGGATGGTGTTCCCAGGCTTTGAGTAAGATTTATGGGTCGGCTATGGGTTTAGTTAGCCATTAGAGAGAGATGAGAGTAAGATGAGTCG[T/C]ATATTGCTCTGTGTGTGTTCCTTGTATTGCGTGTCGTGTGTGTGTTGTGATTTCGATTTGTGTAGTATCTTGGTTCTATTGTTATCGT
91494 G A AATGTTTCTGATTCTGAAAATACTTTTGCTCCATCATTACCACCTATTTCCTCATCCGGAACAAATGATACGTACAC[G/A]TTTCGCTTAGGCCTGAAGCCACTAGAAATCAGTCTGGAGGCAGCTTCCAAGTACTGCATAGAAACACACTTCATGTCCTGCGAGCCGCGAGCGAATATGC
91494 A G TCGGTGTGGGAATTGAGGAGGATGGACGGAAGAGAAGGGTCCGTTCCTGGCCATTTCAGAAGAAGGATGGGCTTATTGGGAACTAGAGTTAGGGTCTGTG[A/G]TTCCAAAGCAGATGGGATTATGGATGTGAGGTAGGAAATCGCTGAGTTGTAGTCAGGATTAGGTTGGGAAGTATTTATGCGGA
91494 C T TGGATGTGAGGTAGGAAATCGCTGAGTTGTAGTCAGGATTAGGTTGGGAAGTATTTATGCGGAGGTATTCTTGGAATCTTTTGATGGCTGATGATGAATC[C/T]AAAGATGTTGACTGGATTGTTATTGGAGAGCTCAGAAAGAAGAAGAAAAGAAGGATGGAGGCTGATTTCTTCATATTTTTCCTGCT
91500 T TA CAATATAACAAAAACAAATAAGCAATGAGCAGCCAGCAATAAAGCATTGCCTTGCTTACATCGTTGGTGGATTCATACAACACCATTATAAAGGCT[T/TA]AAACCCCACCGACGAACAAATAAATAAACAAATAGAAAAGGACAGCAGCAGCATCACAAAGCCAAAAAAAAGCTCACCAATAACGAAAC
91500 CA C ATCGTTGGTGGATTCATACAACACCATTATAAAGGCTTAAACCCCACCGACGAACAAATAAATAAACAAATAGAAAAGGACAGCAGCAGCATCACAAAGC[CA/C]AAAAAAAAGCTCACCAATAACGAAACCCGATAATGGTTATGAAATAATTCATAAAGTGCAGCCACAAAAGCAGAAGAAGAAGCA
91500 C T TGAAATAATTCATAAAGTGCAGCCACAAAAGCAGAAGAAGAAGCACAGCATAGAAATCAAGGCAACGGACTCCACGGCGGAGATCACGGACCAAACCAAA[C/T]TATCCACCAAATTGAACCCCGCATCCAACGGCCGATACAGACGCGAAAAGCTCAGCCAGCTCGGCACCGCAACGCCCAAAGCCG
91500 T C GAAATAATTCATAAAGTGCAGCCACAAAAGCAGAAGAAGAAGCACAGCATAGAAATCAAGGCAACGGACTCCACGGCGGAGATCACGGACCAAACCAAAC[T/C]ATCCACCAAATTGAACCCCGCATCCAACGGCCGATACAGACGCGAAAAGCTCAGCCAGCTCGGCACCGCAACGCCCAAAGCCGG
91500 T C ATTGAACCCCGCATCCAACGGCCGATACAGACGCGAAAAGCTCAGCCAGCTCGGCACCGCAACGCCCAAAGCCGGCAGCTTCAGTCTTTTCCTCGATAAT[T/C]TTTTGCTTATGTTCACTACCTTCGAATCGATCCTTCGTTTTACCACCGACGCCGAAGATAGAATCGATCTTCTTATATTCATGCCTCCC
91500 T C GAACCCCGCATCCAACGGCCGATACAGACGCGAAAAGCTCAGCCAGCTCGGCACCGCAACGCCCAAAGCCGGCAGCTTCAGTCTTTTCCTCGATAATTTT[T/C]TGCTTATGTTCACTACCTTCGAATCGATCCTTCGTTTTACCACCGACGCCGAAGATAGAATCGATCTTCTTATATTCATGCCTCCCATT
91500 A AT CCTCGATAATTTTTTGCTTATGTTCACTACCTTCGAATCGATCCTTCGTTTTACCACCGACGCCGAAGATAGAATCGATCTTCTTATATTCATGCCTCCC[A/AT]TTTTTTATTTTTGTCTCTTTTAGTTTTGTTTTTATTTCCCTCTGTGATTTGTGGCGTGAAAGGGAAATTATTTAGCCAGTAGGCCAAC
91520 C A CACTGTTGGCCTACTGGAACGGCATTTCATTTCTCCCACATCTTCCATTCCGTTATTTCAAACCATGAGAAACAGCAGAACAAACAATCACGACGA[C/A]AAATCAAGAAGCACAGGTAAAGAGGATCCGCTCCGCCATCGATCGCCAGATCGGGTCACCGCCGGCAACCGCAGTCCGATACCGCCGGCG
91520 A G TACTGGAACGGCATTTCATTTCTCCCACATCTTCCATTCCGTTATTTCAAACCATGAGAAACAGCAGAACAAACAATCACGACGACAAATCAAGAAGCAC[A/G]GGTAAAGAGGATCCGCTCCGCCATCGATCGCCAGATCGGGTCACCGCCGGCAACCGCAGTCCGATACCGCCGGCGAACAAAGTGTT
91520 T C TGGAACGGCATTTCATTTCTCCCACATCTTCCATTCCGTTATTTCAAACCATGAGAAACAGCAGAACAAACAATCACGACGACAAATCAAGAAGCACAGG[T/C]AAAGAGGATCCGCTCCGCCATCGATCGCCAGATCGGGTCACCGCCGGCAACCGCAGTCCGATACCGCCGGCGAACAAAGTGTTCAC
91520 C T TCATTTCGCGACACTGGAATCTTAAATCGCGCAACTCCACGCCGTTTCTCAGCTCCTTCGCTCCGTCTGAGATCGCCGCGTTCCTGTCGCTGCTCGTGTC[C/T]CTCTTCTATCTCGCAGCTACTCTTCTTCTATGAGATTGAATCTGCGGTAATTGGTACCCCCAATTTTATTGTTAATTTGCGATGCTGTTGA
91520 A C GCAACTCCACGCCGTTTCTCAGCTCCTTCGCTCCGTCTGAGATCGCCGCGTTCCTGTCGCTGCTCGTGTCCCTCTTCTATCTCGCAGCTACTCTTCTTCT[A/C]TGAGATTGAATCTGCGGTAATTGGTACCCCCAATTTTATTGTTAATTTGCGATGCTGTTGATTTTACTGAGTTATGAATAGTGGATCTGTA
91520 A C TATCTCGCAGCTACTCTTCTTCTATGAGATTGAATCTGCGGTAATTGGTACCCCCAATTTTATTGTTAATTTGCGATGCTGTTGATTTTACTGAGTTATG[A/C]ATAGTGGATCTGTATTTTTTTATAATTTGTCGGTGTTGATTTTACTGGAAATAGAGCCTACCGTCGAAGAATAGATATAGCATGCTGCCA
91536 TA T CAGAGCAACTAACTGAAACTGATAAAACCACAAAAGCAACGGAACTAATTGCATCTACAATCATGCCAGCTGCATAAGCACCAGCAACCAACCCTTCACC[TA/T]AAAAACGTATGCATGCAACACTCAAACGGGCTAAGTATCCATTGTATCCTTGCTTCTGTTCTTTGGGAAATGTTACCTGTCCGGTTC
91548 C T AAGGTTAGGTTGTTTCTCTTTGGACTGTTGTTTGGCCTTGCGGATACCTGGGAGGCCATGCCTGATAATAAGATGGTTGGTAAGGCAAT[C/T]AGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTG
91548 A C TTCTCTTTGGACTGTTGTTTGGCCTTGCGGATACCTGGGAGGCCATGCCTGATAATAAGATGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGAT[A/C]ATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGC
91548 C T GACTGTTGTTTGGCCTTGCGGATACCTGGGAGGCCATGCCTGATAATAAGATGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTC[C/T]AATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTG
91548 T C TGTTGTTTGGCCTTGCGGATACCTGGGAGGCCATGCCTGATAATAAGATGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAA[T/C]CCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCA
91548 A G AGGCCATGCCTGATAATAAGATGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAG[A/G]GTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCA
91548 A G CTGATAATAAGATGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAAC[A/G]ATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCG
91548 T A TGGTTGGTAAGGCAATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAAT[T/A]GCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGA
91548 A G ATCAGGGATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTG[A/G]CTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGT
91548 A G ATCCAGAGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACAT[A/G]CAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAAT
91548 G A AGAAGTTGAAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGC[G/A]AACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATA
91548 G A AAGATAATCGCTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTG[G/A]CAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGG
91548 A C CTTCCAATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCAC[A/C]ATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCG
91548 G A ATCCTAGAAGGTACACTGGTCGACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCC[G/A]TTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATA
91548 C T GACCTAGAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAAC[C/T]GCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAA
91548 T C GAGTAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGA[T/C]GGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGC
91548 G C TAGGAACAATGAGAGAAATTGCTCGAATGACTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGG[G/C]GTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGC
91548 A G CTGACTACATACAAGCGAACTTTGGCAAAGTCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCT[A/G]TACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGA
91548 A G TCACAATTCCGTTTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGA[A/G]ATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAG
91548 T C TTCTGGTACTCCACGGAACCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTA[T/C]GAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGAT
91548 G A CCGCCGATGGGGTGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTC[G/A]TTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATAC
91548 T C TGACATCGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGG[T/C]GAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGG
91548 T C CGCCCGAGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCC[T/C]GATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTG
91548 G C AGGGTTCAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGA[G/C]AACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAACT
91548 T C CAAAATTGCTATACGAAAAGGCAGCAAGCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAG[T/C]GCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAACTATTTCGT
91548 G C GCGAGGATAAAGAAATCATTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGC[G/C]TGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAG
91548 A G TTTTGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGC[A/G]GACTTATACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGC
91548 C T TGTATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGA[C/T]TTATACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGT
91548 A G ATGAAAATATGCTGCATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTT[A/G]TACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
91548 G A ATTCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATG[G/A]ATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTC
91548 T A TCGTTGGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGA[T/A]ACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCTG
91548 T A GGTGCAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTG[T/A]GAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCTGCAGTT
91548 C T CAGGGTGAGCCTGATGAGAACAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAA[C/T]TATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCTGCAGTTTGTA
91548 C T CAGTGCCAGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTG[C/T]AAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCTGCAGTTTGTATGTGTTATAATATGAGATGAA
91548 G A AGAGTTTTGGCTGACATGAGAGCGTGGATCGATAAGAGGGCAGACTTATACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAA[G/A]TTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCTGCAGTTTGTATGTGTTATAATATGAGATGAAATGACTT
91548 G A ACAAAAGGTAATGGATACTGTGAACTATTTCGTTTCAGGCTGTGCAAGGAAGTTGTGAGTGTAGAAAGATGCCTTCGCTGTTCGTTATATGATGTATTCT[G/A]CAGTTTGTATGTGTTATAATATGAGATGAAATGACTTGAATGAACATTAGAGAGTTGAATTA
91554 A T ATCTATCACACTCAACTTGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATG[A/T]GACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTG
91554 G A ATCTATCACACTCAACTTGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCA[G/A]CGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAAT
91554 C T ATCTATCACACTCAACTTGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAG[C/T]GTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATA
91554 A G ATCTATCACACTCAACTTGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACC[A/G]GCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGAC
91554 A G TCAACTTGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGG[A/G]ATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGT
91554 C T TGGTATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGG[C/T]CCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAA
91554 A G ATTAGCAAAAGCCTTCGGGATAGTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCA[A/G]TCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGC
91554 T C GTTCCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTC[T/C]AATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTA
91554 T G CCAGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAA[T/G]GAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTG
91554 A T AGATAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATG[A/T]AACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAG
91554 C G TAAGTTATTATGAGACAAGTATAAATACTCAGCGTTGGGGATACCAGCTATAGATTCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAA[C/G]TGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTG
91554 C T TCAGGAATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAG[C/T]CAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAA
91554 T C ATGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGT[T/C]GAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGA
91554 G C TGGGCCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTT[G/C]AGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAG
91554 T G CCCAATCAGTCTGTTACGGTCGAGTCTAATGAAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGA[T/G]AGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAGACTG
91554 T C AAACTGAGTGGAAGTGCTCCAAGTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAAC[T/C]AGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCC
91554 A G GTGATGAAGGAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTC[A/G]TTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTG
91554 G C GAATAGACCCAGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTC[G/C]AAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAG
91554 A G AGAAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGA[A/G]AGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGG
91554 G A AAAAGTGGTTAAAAGCCAGGTTGAGATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAA[G/A]GTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTA
91554 A T GATAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGAT[A/T]GTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGA
91554 T C TAGTCAAGTTTAGTGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAG[T/C]GTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATA
91554 C G TGAGTTGAGAAAGGAAACTAGGAACAGGGCCTGAAAGGTCATTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGT[C/G]CCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAAC
91554 C T CATTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGT[C/T]AGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCA
91554 G A TTCCAGTCGAAACGGAGAAAGGTGAGACTGGTGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCA[G/A]GTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATT
91554 C T TGAGTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATAT[C/T]TGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGT
91554 G A GTTTAGTGATAGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTG[G/A]CCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTG
91554 T A AGTGTCTGGAATAGTCCCAGTGAGGTTAGTGAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACA[T/A]TGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTC
91554 T C GAGCTTGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACA[T/C]GACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGG
91554 G C TGTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACC[G/C]GCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCC
91554 G A GTGAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCG[G/A]CATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCC
91554 A G GAAACGTTAGAGAAGTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGC[A/G]TTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCA
91554 C T GTCAGGTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGA[C/T]GCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGA
91554 A T GTAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCG[A/T]CCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGACAAG
91554 C A TAGGGAAGGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGA[C/A]CCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGACAAGA
91554 A G GGTCACCAATTGAAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTC[A/G]CAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGACAAGAGGGTATCC
91554 G A AAGGTGATATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGA[G/A]GTTTGCTCTGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGACAAGAGGGTATCCCTGTCATTTTTG
91554 C G ATCTGGCCAGAAACATTGTCGCCGGATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCT[C/G]TGGATCACCCCATGTTATGATTATGTAGGGGTTCCCCATGCCTGACTTTATTGACAAGAGGGTATCCCTGTCATTTTTGTGGCATTTG
91554 T C GATATATCGAGGCCTGTGACATGACCGGCATTGTCACAGTCGACGCCGACCCATTCACAGCAGTCTGAGGTTTGCTCTGGATCACCCCATGTTATGATTA[T/C]GTAGGGGTTCCCCATGCCTGACTTTATTGACAAGAGGGTATCCCTGTCATTTTTGTGGCATTTGT
91558 A G GATCGTAATCATGGCAAAGGCAACCAGGGCAACCAACGAGTTTCCTGAAGATAATGTTTCCAAGTGGATCCCTGCGCCATCTATCAGGATCTCTGCCCTT[A/G]ACCCTCTCCGCCTTCTCCCAACATTGCTGTTTCACGCTGTACGGGAAGCTCCTTGGATTGTTACCATCTTCAACCTCGGAGATGGTGA
91576 T C GCTTCAAGAAACCCGAGCTCCCTCTAAGCGTCGTCTGGACTTCCTTCCATGATTCCGAATCAATAAAAGCTTTCATTTGTAGCAAATCATCAGCGTGGCT[T/C]TTCACTACTGATTCGGCTTCTTCCTTCGTTTGGTCTGGAACGGTCAGGGCGAAGTCGAACGCCGATGCGTCGTCTGAATTCAGGATGG
91604 C T ACCACTGATCCAAAATATCCATAGGAACCACCAATCTACTCCCATCCACCCCACAAAAACTCTGCATGAAATTAAATAAATTCTCCCCGACTCTCATCAC[C/T]ATCTTCTCCACCTTCTTCTCCATCCCCGTATCCACGGCCGCAGGAACCGCCGTCAGATCCTCGACGGAGATCCCAATCTTCGGGGTTCCG
91604 G A AAGTAGGGCTTAGGAGGAAGATGCAGACGTCCTTGATTTGATGGTAGGGGAGTTGGGTTTGTGTGAGGAACGGAGTGAGATCGAGGAGGTAGTGAAGCGG[G/A]TCGATCTGGGTGAAAGTCGTCACGTCGATAGGGTAGCTTTTGTCTGGGAACAGAAGTCCGAACATTTTTAGCTTGATTCTTTTC
91618 C T CGACCTCTCAAAGAAAATCAAGTTCTACGAAAAGGAAAAGCTTCTAGAATTTTTCCAATATGGCAAAGTTCCTCCCGTTTCTACTCCTCCTCTTCATCCT[C/T]TCCACTGCCTTCGCTTCCCACCGCAGCCACAACCACAACCACTTCCTACTCTCCAGCGGCGGTACAATCGCTGATACCCTAGGCGAGGAA
91624 G GTGT TACAGCAAGCAAGCAAAGTTTCGTTACAACATTGAGCACAGTTTGCCACTTAGGTGTTTCGGATCTGGACACGTGCCGCCTCCTCTTGTGATAAACAACC[G/GTGT]CATTAGTATTCGGAGTAGCCGCCGTCTCTTTCGCTTTCTCGGCGGTTAGTCCTTCGTTTGTGACTGTTGTTGTTGTGGCAACGAC
91624 A G TTTCTCGGCGGTTAGTCCTTCGTTTGTGACTGTTGTTGTTGTGGCAACGACTCTTTTCCTTGCGCTTGAAGTGGGTTGAGGATTGTCGTTTGAAGAAGAC[A/G]TGGAACTTTGAAACTCTAAACCCTAATTTCCGGAACCGCTGAGAATTTGAATAAGTGATTTGGGGAATGGTATTACTTTGAGCGCGAA
91662 T A TGTTGCTGGTATACGAAATGAGCAAGCAGGTTTTACCGACCGCGCCGTCGCCCACAGTCACGCATTTGATAAACCTCGACGCGCTCATTTTTCGATAACC[T/A]CCTTGTATGGTCTGCAAATTCAGGATAGATCTTCCGTCTTTTGATTTACGTTATAAATAACTCAAAACAACAAATTAGGAAAACAAACG
91662 T C CCTTGTATGGTCTGCAAATTCAGGATAGATCTTCCGTCTTTTGATTTACGTTATAAATAACTCAAAACAACAAATTAGGAAAACAAACGAAGCTTGATGT[T/C]TTCGTGAGAGAATAGGAAAAAGGCAATGCGCGGTTGAAGCGGTCTCTGTTTGATGCAATTATGTAAAACCAGTAGGCCAACA
91676 A G TCCCGCTAGATGCATATTCTGGGGCCAAATATCCAAATGTTCCCATGACACGCGTGGTCACATGAGTTGCAGCGTCCATAGCTAACCTTGCTAGCCCAAA[A/G]TCAGAAACCTGAGCTTCATATTCGTTATCTAACAAAATGTTGGAGGACTTTATGTCTCTATGAATGATGCGTGGATGACAATCCTCAT
91676 T C ATTCTGGGGCCAAATATCCAAATGTTCCCATGACACGCGTGGTCACATGAGTTGCAGCGTCCATAGCTAACCTTGCTAGCCCAAAATCAGAAACCTGAGC[T/C]TCATATTCGTTATCTAACAAAATGTTGGAGGACTTTATGTCTCTATGAATGATGCGTGGATGACAATCCTCATGCAGGTATGCAATTC
91682 A G TGGCCTTTTTTTTTTTTTTAGATCAAAACTGAAAGTTTAGATGAATAGGTTTGTATACAAATAAATGCTAACAGCATCAAG[A/G]CTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAG
91682 G C TTTTTTAGATCAAAACTGAAAGTTTAGATGAATAGGTTTGTATACAAATAAATGCTAACAGCATCAAGACTAAATGCTACTTGAATACCAGTCAAATAAT[G/C]GACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTC
91682 T G ATAGGTTTGTATACAAATAAATGCTAACAGCATCAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAA[T/G]CCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCAT
91682 A AG AATAAATGCTAACAGCATCAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAA[A/AG]TGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCA
91682 T C AACAGCATCAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTA[T/C]ACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
91682 C T GCATCAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACA[C/T]TTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTG
91682 A G TCAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTT[A/G]TAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCC
91682 T TA CAAGACTAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTA[T/TA]AGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCC
91682 G A TAAATGCTACTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGT[G/A]CTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTT
91682 A C CTTGAATACCAGTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAA[A/C]AGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGG
91682 G A GTCAAATAATGGACTTGTACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCA[G/A]AACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAA
91682 T C ACCATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGG[T/C]ATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTG
91682 T A CATTAGACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTA[T/A]TCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAA
91682 G T GACTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTA[G/T]TCATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATG
91682 C T CTTGATGATCAAAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGT[C/T]ATTTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGT
91682 C T AAATCCGTGCAAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTT[C/T]AAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCT
91682 T C AAAAATAAATGAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTA[T/C]TATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATG
91682 G T GAAAAGTATACACTTATAGAGTGCTTGTAAAAAGACCGTTCAGAACTGTAAAAATGGAGGTATTCTAGTCATTTTTGGTTCAAGCAGGTATTATAACTCT[G/T]CCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATGAACATTCTTTT
91682 C T TTTTGGTTCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTA[C/T]TGTATGAACATTCTTTTGAGAACCCGACTTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTC
91682 A G TCAAGCAGGTATTATAACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATG[A/G]ACATTCTTTTGAGAACCCGACTTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTT
91682 C T ACTCTGCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATGAACATTCTTTTGAGAA[C/T]CCGACTTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCA
91682 C G GCCCTTGAATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATGAACATTCTTTTGAGAACCCGA[C/G]TTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCATCAT
91682 G A AATTTCCAAACTGGCTGAACAAAATGGCCATATCCATTCCTTGAATCATGGTCGGAATAGCTGTACTGTATGAACATTCTTTTGAGAACCCGACTTTTCC[G/A]GATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCATCATGAAGCCT
91682 G A TCGGAATAGCTGTACTGTATGAACATTCTTTTGAGAACCCGACTTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCAC[G/A]TTTGTCATTCCTTTCTTTTCAACGCAATCATCATGAAGCCTACAGCAATCATCAAGATCATCACAGGGCTTTTCTCCGGGACATCCCGACCA
91682 A G AGAACCCGACTTTTCCGGATTTCTTCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCATC[A/G]TGAAGCCTACAGCAATCATCAAGATCATCACAGGGCTTTTCTCCGGGACATCCCGACCATCCAACTCCACAGTACTTCCCATACCTTATACC
91682 A T TCACCTTTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCATCATGAAGCCTACAGCAATCATCAAG[A/T]TCATCACAGGGCTTTTCTCCGGGACATCCCGACCATCCAACTCCACAGTACTTCCCATACCTTATACCAATCGAATTACAATTCTCAGCTACG
91682 A G TTCTTATGCACTTTTTGAATTTTTCATGGCATTTCACGTTTGTCATTCCTTTCTTTTCAACGCAATCATCATGAAGCCTACAGCAATCATCAAGATCATC[A/G]CAGGGCTTTTCTCCGGGACATCCCGACCATCCAACTCCACAGTACTTCCCATACCTTATACCAATCGAATTACAATTCTCAGCTACGCATGT
91688 C T AATCCGGTCCCTGGAGGCTTTGTGCAGGGAGTGGGGTATCATGTGATGCATCATCATCAGCATCCTTCTTCTCAAACTCAGAGCTTTGTGTATGCAAATG[C/T]TGGGTCGGGAACGGATAGCATGGTGCAGCAAGCCCAGGCTCAGGTGTATTACACACATCATGCGTGCACGGAGGCTGATGTGAAC
91688 G A GAGGCTTTGTGCAGGGAGTGGGGTATCATGTGATGCATCATCATCAGCATCCTTCTTCTCAAACTCAGAGCTTTGTGTATGCAAATGCTGGGTCGGGAAC[G/A]GATAGCATGGTGCAGCAAGCCCAGGCTCAGGTGTATTACACACATCATGCGTGCACGGAGGCTGATGTGAACCAGAATAGAGCAT
91690 A T ACCTTCCCAAATTGGTTGAAGGACTGAAGCGTCTTGCTAAATCAGATCCTATGGTACTCTGCTCAATTGAAGAGAGTGGCGAGCACATCATTGCTGGAGC[A/T]GGAGAGCTCCATTTGGAAATCTGCCTTAAGGATCTCCAAGATGATTTCATGGGTGGCGCAGAGATCGTTGTTTCTGATCCTGTGGTT
91690 T C CAGAGATCGTTGTTTCTGATCCTGTGGTTTCTTTCAGAGAAACCGTGCTTGAGAAGTCATGCCGCACAGTGATGAGCAAATCTCCAAACAAACATAACCG[T/C]CTGTACATGGAAGCTCGTCCACTTGAAGAAGGGCTTCCGGAAGCCATCGACGAAGGAAGGATCGGGCCTCGCGATGATCCTAAGAA
91694 A G TCGGTAAGTTCAAGATGGAGATTATTTTTATATGATTATGATGAAGACGATATCAACAAAAACGATGAAGATGAAGACAATGATGATCGTGAGATTCAAT[A/G]TTCAACCCGAATAGCCAATCTGGTGAACCCAAATACTGCTGCCAGTTCTATCAATCTGGAAAATGGGCATCAAATTATCTCAAAAAG
91694 T G ACAATGATGATCGTGAGATTCAATATTCAACCCGAATAGCCAATCTGGTGAACCCAAATACTGCTGCCAGTTCTATCAATCTGGAAAATGGGCATCAAAT[T/G]ATCTCAAAAAGGCAAAACTGACAATGCATCATGCTGTGAGCATATGCACAAATGCCTAAATGGCAACATCACTACTGATGCTTCTGAT
91694 A G AGATTCAATATTCAACCCGAATAGCCAATCTGGTGAACCCAAATACTGCTGCCAGTTCTATCAATCTGGAAAATGGGCATCAAATTATCTCAAAAAGGCA[A/G]AACTGACAATGCATCATGCTGTGAGCATATGCACAAATGCCTAAATGGCAACATCACTACTGATGCTTCTGATTCCCCACAGTTTTGG
91694 C T ACGTGAGTACGAGATTCTGCATCTGACCCAGCCTGAGAAGCCTCCGCTCTGCTACTCTTCAGTCAGCCAGCTGTTGAGATTAGGCGGAAGTTTCCAACCT[C/T]AAACTCTTTGGAAGCACAAGAGGAGCCTACAGAAAAAGGATGGCTTGAGGCGTGGTGCAAGAAAATGAA
91694 C A GTACGAGATTCTGCATCTGACCCAGCCTGAGAAGCCTCCGCTCTGCTACTCTTCAGTCAGCCAGCTGTTGAGATTAGGCGGAAGTTTCCAACCTCAAACT[C/A]TTTGGAAGCACAAGAGGAGCCTACAGAAAAAGGATGGCTTGAGGCGTGGTGCAAGAAAATGAA
91700 G GT CTAGTGTTATATGAAGTTTGAGTTCATGTGGTGTACTTATGCTTTTGATGTTCTTATGGATTTGATGCTGTGAAGTTTGGTGTTCTGTCATAGTTGTAGG[G/GT]AAGTTTTTGTTAAGTTTATTTGAGGGGAACTTTTATTCTGCATGGAGATTGTATGTTGAAGCAATTATATGATATTTGTTACGTTATAT
91744 T A AAAACAGCAGCTCAAAGAGTGAAGCAAAGATTCCTACAATGCCTGCTGGCTTTCCGGGTTCTTTTGACATGTCTGCTTTGTCGGATCTACTAAATGATCC[T/A]TCTATAAAAAATTTAGCTGAGCAAATCGCGAGTGATCCTGTATTTTCCCAGATGGCTGAACAACTTCAACAAGGAGCTCAAAATCCGG
91744 A AC TCAAAGAGTGAAGCAAAGATTCCTACAATGCCTGCTGGCTTTCCGGGTTCTTTTGACATGTCTGCTTTGTCGGATCTACTAAATGATCCTTCTATAAAAA[A/AC]TTTAGCTGAGCAAATCGCGAGTGATCCTGTATTTTCCCAGATGGCTGAACAACTTCAACAAGGAGCTCAAAATCCGGGATCTGATGG
91762 TC T ATCAGCACCAAAAATAATGGTTGGTGCATCAGTAACTAGAGGTATATTCCTTGATATAGCATCCATAAGCACGGTGTTTCT[TC/T]CCCCCAACCTTCACATTGATCTTTAAGGCCACGTTTGCCAGATATTGCTTGTTCATCTTAAAAACATGCTTGGTCAAGCAACATTGTGAAACTATACCAA
91770 A T AACAGCATCAGACCTCACGCCAACATCATACACATACCGACTAGCACAGTACATGCCAGCAGTCGCGACCGCCAACCCAATGGGGTTCACCGACGTGACA[A/T]ACCTAAGTGGAGACGAAGCAAAGGCGGTGACAGCAGCTGTCAGCGATGTGAGTTGCCCGCTCCTAGGGACGTCGTTGGAACCCA
91770 G C TCAGACCTCACGCCAACATCATACACATACCGACTAGCACAGTACATGCCAGCAGTCGCGACCGCCAACCCAATGGGGTTCACCGACGTGACAAACCTAA[G/C]TGGAGACGAAGCAAAGGCGGTGACAGCAGCTGTCAGCGATGTGAGTTGCCCGCTCCTAGGGACGTCGTTGGAACCCAGCCCGGT
91770 G A AATGGGGTTCACCGACGTGACAAACCTAAGTGGAGACGAAGCAAAGGCGGTGACAGCAGCTGTCAGCGATGTGAGTTGCCCGCTCCTAGGGACGTCGTTG[G/A]AACCCAGCCCGGTGGTGATCAGGCCTGTCTTGCAGTACACGGCGAAGTCCTCGCAGTTGTTCTTGAATATGTGGTACGTGCCGA
91770 C T ACCGACGTGACAAACCTAAGTGGAGACGAAGCAAAGGCGGTGACAGCAGCTGTCAGCGATGTGAGTTGCCCGCTCCTAGGGACGTCGTTGGAACCCAGCC[C/T]GGTGGTGATCAGGCCTGTCTTGCAGTACACGGCGAAGTCCTCGCAGTTGTTCTTGAATATGTGGTACGTGCCGAACCCATTATTC
91770 G A ACGTGACAAACCTAAGTGGAGACGAAGCAAAGGCGGTGACAGCAGCTGTCAGCGATGTGAGTTGCCCGCTCCTAGGGACGTCGTTGGAACCCAGCCCGGT[G/A]GTGATCAGGCCTGTCTTGCAGTACACGGCGAAGTCCTCGCAGTTGTTCTTGAATATGTGGTACGTGCCGAACCCATTATTCAGG
91770 G A TTGGAACCCAGCCCGGTGGTGATCAGGCCTGTCTTGCAGTACACGGCGAAGTCCTCGCAGTTGTTCTTGAATATGTGGTACGTGCCGAACCCATTATTCA[G/A]GAGGTAGTTTGCACGATGCAGGACGGTGTCGGGAGTGTCGGAGGATGCCAGGGTGCAGGTGCCGCCTCGGGCTTTGGCCAGGAA
91770 C G AGTCCTCGCAGTTGTTCTTGAATATGTGGTACGTGCCGAACCCATTATTCAGGAGGTAGTTTGCACGATGCAGGACGGTGTCGGGAGTGTCGGAGGATGC[C/G]AGGGTGCAGGTGCCGCCTCGGGCTTTGGCCAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAG
91770 C T TACGTGCCGAACCCATTATTCAGGAGGTAGTTTGCACGATGCAGGACGGTGTCGGGAGTGTCGGAGGATGCCAGGGTGCAGGTGCCGCCTCGGGCTTTGG[C/T]CAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAGCAGGAAGCAGTCCAGGCACGACTTTATC
91770 C T GGGTGCAGGTGCCGCCTCGGGCTTTGGCCAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAGCAGGAAGCAGTCCAGGCA[C/T]GACTTTATCACGCCCTGCGAGTTGCTTTGGTCTCCACATGTAGTGCAAGGGGTTGCTGCGTTCGATGGAGAAGATATGAGGAA
91770 G A CGCCTCGGGCTTTGGCCAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAGCAGGAAGCAGTCCAGGCACGACTTTATCAC[G/A]CCCTGCGAGTTGCTTTGGTCTCCACATGTAGTGCAAGGGGTTGCTGCGTTCGATGGAGAAGATATGAGGAAGCTGTCTAAGAA
91770 C T GGGCTTTGGCCAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAGCAGGAAGCAGTCCAGGCACGACTTTATCACGCCCTG[C/T]GAGTTGCTTTGGTCTCCACATGTAGTGCAAGGGGTTGCTGCGTTCGATGGAGAAGATATGAGGAAGCTGTCTAAGAAGGTTCC
91770 T A TTGGCCAGGAAGAAGGACGGGGTCACGGAGTAGTGGAACAGGTACAGGTTGCACCCCAGCAGGAAGCAGTCCAGGCACGACTTTATCACGCCCTGCGAGT[T/A]GCTTTGGTCTCCACATGTAGTGCAAGGGGTTGCTGCGTTCGATGGAGAAGATATGAGGAAGCTGTCTAAGAAGGTTCCCGTCC
91780 TA T TTAATAATTAAGGTCTAAAGCCTTTTACATCAGAGTACATCAAAACCTGTCTTGCAATAGTAAAGAAGCATAAAGACTTTTTCATAAATTATTCCCCAAG[TA/T]AAAAACAGTAAAGTAGCCATAGCCAAGAAAAGTCCAAGCCATCCATGATGACCTTCAAGCAGAAGAAGTCCGAACTAAACAACAGTA
91786 C T TGCTGGGTAAGCGTGGGGTTTTCATTGTTGAGGGTGATATCAATGATGGTGAGCTTCTTGCCAAGCTTTTCGATGTTGCTGCTTTTACTCATGTTCTTCA[C/T]CTTGCTGCTCAGGCTGGGGTAAGGTACGCAATGAAGAACCCACAATCCTATGTGGCTTCGAACATAGCTGGGCTAGTCAGTCTCTTCG
91786 T C CTTTTACTCATGTTCTTCACCTTGCTGCTCAGGCTGGGGTAAGGTACGCAATGAAGAACCCACAATCCTATGTGGCTTCGAACATAGCTGGGCTAGTCAG[T/C]CTCTTCGAAACAGCCAAATCGATCGACCCGCAACCTGCAATAGTATGGGCCTCCTCCTCCTCGGTCTATGGGCTCAACACAGAAAACC
91786 C A TCTATGGGCTCAACACAGAAAACCCATTCTCTGAGCTCCACAGAACTGACCAACCCGCCTCCCTATATGCTGCCACCAAAAAAGCAGGTGAAGAAATAGC[C/A]CACACGTACAACCACATCTATGGCCTTTCCATAACAGGGCTCCGCTTCTTCACGGTTTACGGCCCATGGGGAAGGCCCGACATGGCT
91802 G GA GTTGGGTTTCTGAGTGTTGTTGTGTCCAAGCTCATTTTGGGCCTCTTCTTCCCCTGGTTTGCCCATCTCACAGTTTCCAGGTCCAGTGTTGCCCTCTTCT[G/GA]CCCCTTGGCCGACCACGTTTCTGGATCTGGTATTATCTCGTGTCTTGAAATATTTTGCATTGAAAGATTCGGCATGCTCCGGATAGTTC
91804 T A GAACTTTTCAATTGTTATGAAGACTAACTGAATGTGACAAGTGCACGATACAGAGTAGCAGTAGACCC[T/A]GGAGACTTTTACGGGACACACTGGCTGTAGTACTGGTTCGAGACCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCGTGCCACCGCACT
91804 C T GAACTTTTCAATTGTTATGAAGACTAACTGAATGTGACAAGTGCACGATACAGAGTAGCAGTAGACCCTGGAGACTTTTA[C/T]GGGACACACTGGCTGTAGTACTGGTTCGAGACCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCGTGCCACCGCACTGTCCGTAGAGGG
91804 G T AGCAGTAGACCCTGGAGACTTTTACGGGACACACTGGCTGTAGTACTGGTTCGAGACCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCC[G/T]TGCCACCGCACTGTCCGTAGAGGGGAGCTTGAGTAGCTTGTGTCTGCGTAGGTGCCGGAGCAGATGTCGGGTTTTGCGGGTTGC
91804 T G GCAGTAGACCCTGGAGACTTTTACGGGACACACTGGCTGTAGTACTGGTTCGAGACCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCG[T/G]GCCACCGCACTGTCCGTAGAGGGGAGCTTGAGTAGCTTGTGTCTGCGTAGGTGCCGGAGCAGATGTCGGGTTTTGCGGGTTGCT
91804 T C CACACTGGCTGTAGTACTGGTTCGAGACCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCGTGCCACCGCACTGTCCGTAGAGGGGAGC[T/C]TGAGTAGCTTGTGTCTGCGTAGGTGCCGGAGCAGATGTCGGGTTTTGCGGGTTGCTCGGTGTGGAAGCGGACTGGGTATATGTC
91804 C T CCTTGCATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCGTGCCACCGCACTGTCCGTAGAGGGGAGCTTGAGTAGCTTGTGTCTGCGTAGGTGC[C/T]GGAGCAGATGTCGGGTTTTGCGGGTTGCTCGGTGTGGAAGCGGACTGGGTATATGTCGAACCGATGTCGCCGACTCGGATGTTG
91804 C T CATGTGCCTGAGGCGCAAACTGTGGGACCAGTCCAGCCCGTGCCACCGCACTGTCCGTAGAGGGGAGCTTGAGTAGCTTGTGTCTGCGTAGGTGCCGGAG[C/T]AGATGTCGGGTTTTGCGGGTTGCTCGGTGTGGAAGCGGACTGGGTATATGTCGAACCGATGTCGCCGACTCGGATGTTGGAGA
91804 A G TGTCGCCGACTCGGATGTTGGAGAAGATGACTTGAGCGTTGGCCTGCTGAGACTCGACGTCGGTGGGTTTACCGGAGGTGGTTGCGCAGGCTCCGCGTGC[A/G]GTTCCGACGCCCGTGCTGTCAGTCGGGTAGGTGGAATCGAGCCAAAGCATGTTCGCGGCGTGGTCGTCCCAGACGCTCATGAC
91804 C G GGATGTTGGAGAAGATGACTTGAGCGTTGGCCTGCTGAGACTCGACGTCGGTGGGTTTACCGGAGGTGGTTGCGCAGGCTCCGCGTGCAGTTCCGACGCC[C/G]GTGCTGTCAGTCGGGTAGGTGGAATCGAGCCAAAGCATGTTCGCGGCGTGGTCGTCCCAGACGCTCATGACGAGAACCATACC
91828 A AG TGTGATTTGGGTTCGGAAGTGGACGAACGGTGTATGAAGAAACTAAGGGAGCTGGAGAATAAGGAAAGGAATGAGAGGAAAGAGAAAAAGGGAAGTAGGA[A/AG]GATAAAACTGACGGCAGAAAGGACCATGGTAGGAAGAAGAAAGAAGAAACTGCTAGCAATCAAAGTAGGAAAGAGAAGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
91838 T C GCGACCGCCTTCTCCTCCTCTGCCCCGACTGCACTAGCCTGCGCCCGTGCGCGTGCTACCACCATCCATCCTCGTCCTCCTCTCCCTCCTCCTTCTCCTC[T/C]TCCGAACGAGTCCGGTACAGCGTTTCCGGCTCGATCGGGTCAGTCGGTCGCGTTTCCAACTTGATCGAGATAGAATCGTCCTTCCAACG
91840 C A GTGACTTACCAGACCTGTTCCTTTTTGTCATACAAAGCAACTGCCTTCCAGCTGCTGTTATCACTAACCTTCGGGGTTTCTCTCTTATCGGTGCACTTGC[C/A]CGCAAATCTATTCCCAAAGACAAACCTGAGAAAGAGGAAGGGAAAGAGAGAGAAGCGGAAGTGGACAGGAAAGAGGACCGAAGTGA
91868 AG A TGAAGGTTAAGCAATAAGTGAGGGGACTTCCTGTAGTCGCTTAAAGGGGAGTTGGTGTCAAGGAGGAGACTGACGAATCGCTATGGTCGGCGTCGACCAG[AG/A]GGGGGGTCGATGGGTGTCCAGGTGACAGCGGAGCGGGGTTAGGCCAGGGAGGTGGTATCACGCATGGATGGAAGAGTGG
91872 A G ATGGTTTTGCGGAAGATTCAGGAATATTGGATCCGGTTCGTAGGGCTGAGTTGAACCGGAAACGGTACGAAGTTGTGAGG[A/G]ATTTAACTTGGGAGCAGGTGCTTATTACAGGAACAAAACACTACAGCGAAGAACTAAGCAGATTCTGCGATGAGAAAATGAGCGAAATAGTCACACAGTT
91872 C T TGCTTACCCTCCAGCGGTAACGGAAATGAGGGTGGAGAAAGGAGTGGCCTATGACAGTAAGTACATGGAGGATGTGGCAGGTGGCAGCCATGGGGTTAAG[C/T]CTACCCCGGTGAGTGTGAAGGCGGTGGTTGCACCAGGGTTTTATTTGTGGAGAGGGAGTTGTGGGGTGGTCAAGTGTAGAGT
91872 C G GCTTACCCTCCAGCGGTAACGGAAATGAGGGTGGAGAAAGGAGTGGCCTATGACAGTAAGTACATGGAGGATGTGGCAGGTGGCAGCCATGGGGTTAAGC[C/G]TACCCCGGTGAGTGTGAAGGCGGTGGTTGCACCAGGGTTTTATTTGTGGAGAGGGAGTTGTGGGGTGGTCAAGTGTAGAGTT
91872 AT A GTGGCCTATGACAGTAAGTACATGGAGGATGTGGCAGGTGGCAGCCATGGGGTTAAGCCTACCCCGGTGAGTGTGAAGGCGGTGGTTGCACCAGGGTTTT[AT/A]TTTGTGGAGAGGGAGTTGTGGGGTGGTCAAGTGTAGAGTTGCATGTGAGTATAGTGATCCCGAGAGTTGCGGCCAGGTGAG
91882 A G TTTTTTTTTTGACAGCTAACAAGGCATAATATTTGTACCTATAAACCACTCAACTAGTCAAGTACCACCAAGCTTTGTGCAC[A/G]CTTATTACAATGATAGAGAGAACCAAAAAACACAATGTGACATCAATAGAATATATGAAACGAAGTATAAAGTGTGGATTAAGACGGGAGCTTTTAAGAG
91882 G A TTTTTTTTTTGACAGCTAACAAGGCATAATATTTGTACCTATAAACCACTCAACTAGTCAAGTACCACCAAGCTTTGTGCACACTTATTACAATGATA[G/A]AGAGAACCAAAAAACACAATGTGACATCAATAGAATATATGAAACGAAGTATAAAGTGTGGATTAAGACGGGAGCTTTTAAGAGGCTGAA
91882 G A CAAGGCATAATATTTGTACCTATAAACCACTCAACTAGTCAAGTACCACCAAGCTTTGTGCACACTTATTACAATGATAGAGAGAACCAAAAAACACAAT[G/A]TGACATCAATAGAATATATGAAACGAAGTATAAAGTGTGGATTAAGACGGGAGCTTTTAAGAGGCTGAAGTGAACTTGAGTGAGAT
91882 G A ATGGCCCAAATGCCCACCACATTTCGCACATGTGATCTCCACCCTCATGCCATCTGGATCAGGAGTGCGATTTATAGCACCAGGAAGTCCCTCATAGAAA[G/A]CTGGCCAACCGCACCCAGAATCAAACTTTGTTGTTGATTTGTAAAGAGGCGTTCCACAGCCAGCACATTCGTATATGCCCTCCTCGTA
91882 C T AATCAAACTTTGTTGTTGATTTGTAAAGAGGCGTTCCACAGCCAGCACATTCGTATATGCCCTCCTCGTAGAATTTGTTATACTCGCCAGTGCCTGGGTA[C/T]TCGGTTCCCTTCATGCGAAGAATGCGAAACTGCTCTGGGGAGAGAACCGCCCTCCATTCCTCCTCCGATTTCGGAACCGAATCCGCCA
91888 G A AAACAACCTGTTTCGTCCCTTTCACGATTTTACCCAGCGTAAGATTAGAATTTGCTTGCTTGTTGTGCTCTGAAATCGCGAATTTTGCGATATCGATTAC[G/A]TGCGGATCGTTTAGATCGCCGATCCAGGTCCAACCGCCGGGGAGAAGACGACGACCGTCGGAGTCGGCAGCCAAGAAGGAAAAGGT
91888 A G TATCGATTACGTGCGGATCGTTTAGATCGCCGATCCAGGTCCAACCGCCGGGGAGAAGACGACGACCGTCGGAGTCGGCAGCCAAGAAGGAAAAGGTGAC[A/G]AGAAGAATCGAGATGAGATAGAGCTTCATATCTTTGATTTTTCAATACTTACTTCACTCGTGGTGGTTTGGTGGATTTTATACAG
91918 A G CCGAGTTATCCGATGGGACGGGATAATAAGCAAGTACTTCAACATCTGTTCCTGCTTCCAGTACAGCTGGTGCACGTATAAATACAGCACGAAAAGTATC[A/G]GGCCCACCTTCCATTTCTACAAGCTTAGGAACTGGAAGCTCGGTTTCAAAGCTCTGAAGCTGACTTCCAAAAAAATTCCTATGGACA
91918 A G AGCACGAAAAGTATCAGGCCCACCTTCCATTTCTACAAGCTTAGGAACTGGAAGCTCGGTTTCAAAGCTCTGAAGCTGACTTCCAAAAAAATTCCTATGG[A/G]CAGTGCAATCCAGACCACCAATTAATTCTTGCCCTCCTAACTTTTGCCCAATGGCATTGTTTGCTAGAAAAATTAACCCTGCACAAGTT
91964 A C TAACCAGATACAAGGACTATCATGAATGAATGTAGTCCACAGAAGTTATCTGCCGATGTACTGATATGCACAAACACAATATTGTGTTCATCCGGAAATA[A/C]AGCAATGAACACAAATTACTATCATTTTATAACTGAAAACAAATTGATGTCAGCTCGCCTCCCAGGACCCTCGACGTGATTTTGAAGA
91964 A G ACTTCCTTCATCTACTCTTCTCCTCTTCCCGATCAACTCTTCTTCTAACATTATACGATACAATCGATCCTATCAGACAGCCCACTCCACCGTTTCAGAA[A/G]CTTCGTGAATCCTTTAGAGGATCGATGGATTTAGGGCCTCTGGTCAAGAGGCAATCAGGCAGCGGCAGGGAAGCGTGCTCCTCCGTGGC
92016 T C CCACCATTAAGTGCTTCATTCTTATTCAATGCAGCAAGACTAATGACTTTAACCCCCATTTTATCTGCTCTCAAAATAGCCAGTTCAATCTGTTTGTTTA[T/C]GCCATCAGTAGCAAATGGCAAGAAATAATGAAAACCAAATCGAGGAACCATCCATGTCTGATGCAGCTTTCCACGTAAATTGTAGAAGG
92020 A AC CATACTCAAACTTCAAACACTAAAAGATCTACTAAATAATATACAATCGTACATAAATAAAATATAATAAGAAAAAAAAACAAGCTCACAGCCTACCAAA[A/AC]CCTCTTTCTGCTGTCTCTTTAACTGAGCCTCTTTACTGTATTTGCGGTGTCGTCGTTCTCTTGCATAGATAACCCAGAATACGAGGGAC
92036 A C CCAGTCCTCTTGCCTCGTGAACGCAATGCTCAATAGCAAGCCTAGCAAGAAGATCATCCTTAGTCCGGATAGCAGAGTCCCAAAGACCGTCATGTGCAGG[A/C]AAAGCCCCATAAAAGGATCCAAGCTCCTTGAGCCTCTCCGCAAGAAGCTTAAAATGGCGGCCTTCATCCTGTGCAACCCTAACAAAA
92036 TA T CAAAGACCGTCATGTGCAGGAAAAGCCCCATAAAAGGATCCAAGCTCCTTGAGCCTCTCCGCAAGAAGCTTAAAATGGCGGCCTTCATCCTGTGCAACCC[TA/T]AACAAAATCATCATAAAATCCTTTGGGTAAACCCTCCTTCGCCCCAAATCTAGCAATGATGTCCCAGGAAAGATCAATCGCCCAGC
92036 C A GCTGTGCAAAGTAGCCTGTCTGCTGCGCAGGCTTCCTCCTTTCCCTAGTTTTGGCATCATATGTGAAGGTACTAGTTTTACTGTAGGAAGACGAGCTGGT[C/A]GATCTGGAGGTAGTTCATCAGAAGAAGAGGATGGAAGGAAAGGAAGGGAAATCTGGCCTTGACGCCATTGGGAGGCTGCGACTTC
92036 C T GCATCATATGTGAAGGTACTAGTTTTACTGTAGGAAGACGAGCTGGTCGATCTGGAGGTAGTTCATCAGAAGAAGAGGATGGAAGGAAAGGAAGGGAAAT[C/T]TGGCCTTGACGCCATTGGGAGGCTGCGACTTCGCCGATTTGGGCTTTGAGGAAAGGATTCGGTTCGTTTAGCACTTCTAACGCT
92036 G A TCATATGTGAAGGTACTAGTTTTACTGTAGGAAGACGAGCTGGTCGATCTGGAGGTAGTTCATCAGAAGAAGAGGATGGAAGGAAAGGAAGGGAAATCTG[G/A]CCTTGACGCCATTGGGAGGCTGCGACTTCGCCGATTTGGGCTTTGAGGAAAGGATTCGGTTCGTTTAGCACTTCTAACGCTGCA
92036 G A GATCTGGAGGTAGTTCATCAGAAGAAGAGGATGGAAGGAAAGGAAGGGAAATCTGGCCTTGACGCCATTGGGAGGCTGCGACTTCGCCGATTTGGGCTTT[G/A]AGGAAAGGATTCGGTTCGTTTAGCACTTCTAACGCTGCATCCACAAGCGTTTTTTGACATGCCACTTCCGCCTCCATGTCTACGA
92048 G A CTTGGTTACTCTAAAGCTCAAATTAAGGCTATCCAGCACTTTGTATGTTGCGAGTATAAAAGACATCAGTGCTTTATTTGTGGAAAGCTTGTCTCTTCCG[G/A]TAAAGCTGCTGGTGCTGAGGTTTTTGCTTGTGTAAATGCAACATGCAGGCATTTCTACCAACTAAAATGCATGTCAGATCGGTTGTTTC
92048 A G TTGCGAGTATAAAAGACATCAGTGCTTTATTTGTGGAAAGCTTGTCTCTTCCGGTAAAGCTGCTGGTGCTGAGGTTTTTGCTTGTGTAAATGCAACATGC[A/G]GGCATTTCTACCAACTAAAATGCATGTCAGATCGGTTGTTTCCTGATGATTCAAACCAAGCAGCTGATTGTGAAAATAAGATCGCTTC
92048 T C TTTATTTGTGGAAAGCTTGTCTCTTCCGGTAAAGCTGCTGGTGCTGAGGTTTTTGCTTGTGTAAATGCAACATGCAGGCATTTCTACCAACTAAAATGCA[T/C]GTCAGATCGGTTGTTTCCTGATGATTCAAACCAAGCAGCTGATTGTGAAAATAAGATCGCTTCTAGGGAATCGTTTACTTGTCCTGCTC
92048 G A AGCTTGTCTCTTCCGGTAAAGCTGCTGGTGCTGAGGTTTTTGCTTGTGTAAATGCAACATGCAGGCATTTCTACCAACTAAAATGCATGTCAGATCGGTT[G/A]TTTCCTGATGATTCAAACCAAGCAGCTGATTGTGAAAATAAGATCGCTTCTAGGGAATCGTTTACTTGTCCTGCTCATAAATGTCAGG
92048 A G TAAAGCTGCTGGTGCTGAGGTTTTTGCTTGTGTAAATGCAACATGCAGGCATTTCTACCAACTAAAATGCATGTCAGATCGGTTGTTTCCTGATGATTCA[A/G]ACCAAGCAGCTGATTGTGAAAATAAGATCGCTTCTAGGGAATCGTTTACTTGTCCTGCTCATAAATGTCAGGTTTGCAAACAAGGAGA
92048 G A GTCAGATCGGTTGTTTCCTGATGATTCAAACCAAGCAGCTGATTGTGAAAATAAGATCGCTTCTAGGGAATCGTTTACTTGTCCTGCTCATAAATGTCAG[G/A]TTTGCAAACAAGGAGAAAATAAAGATGATAAGGCTTTACAGTTTGCTGTGTGCAGGTGGTACCCAAAATCATATCATACGAAGTGCT
92048 GA G TTTGCAAACAAGGAGAAAATAAAGATGATAAGGCTTTACAGTTTGCTGTGTGCAGGTGGTACCCAAAATCATATCATACGAAGTGCTTGCCTAGGAGGAT[GA/G]AAAAAAACAGAATTTGGAATGTAACGGCAACGACGAAGCAAACACGTTAATTGATGAAATCCTGAATTTCTCATGACTTCGTC
92050 T G AAGTTTCGTAGGAATGACCCTGTGCTCGACAGGATTGACGCAGACTTACTGTTTCGCCCTTCGGGCTCCTTTGTGCCTGGCGGATGGTGCGCGGGTGGCG[T/G]AGTGAACGGGTCTGACCCATGTTCGGTTGTGGGGAATAGGACTGATGTTCGTCCTGGGCCAGGTATGGAGCGGGTCTCCCGGTT
92072 G A AATTCTTCGACCACTTAAAGCTTGAACTCGGGCAACTCAAATTTGCAGTATCTAAAACACCGGAGGTGGAGGATAGAATTATTGAGTTGGA[G/A]GCAATGCAGAATGTCTTAACAGAATTAACAGAAGCATACGACAAAATGGAAACTGACTTGGTCTCAACAAAGGATAGGCTTATGAAAATCTTGCA
92072 T C ATAGGAAAACAACTTTACTGGACATGGTTGAGAAGAATGAGCTGACTAGGCCGGTGTTGGCTCTTCTAGATGAGAATATAGCAAGTGCTGTAAAGAATGA[T/C]CAGAAGGAAGCTGCAGCTTTTATGGAGAATGTTCGTTCAATGATGCTGAAGTATATTACTGTCTAATACCAAAGGAGTGATCTTCT
92072 T C CAGAAGGAAGCTGCAGCTTTTATGGAGAATGTTCGTTCAATGATGCTGAAGTATATTACTGTCTAATACCAAAGGAGTGATCTTCTTCTCATGCGTTCTG[T/C]TTTTGCTCAGGCTGTAAAGGCTATTCGGTAACTAATAATTCAAGGTTTTTGTAAGAGATTTGGTTCCCAAGCTTAATCAATTAATTGAG
92078 C T ATACCCAGAAGCCCTAACAACCGTATGAGCCGCCCCTCTAATTCCTCTAGGAGGGTACCTACAGAACCCAACGCATTCCTC[C/T]GCCATCTCGGCGCTCTCCACCATCGGAAAAACGATCCCAGCCGGCCCCAAGTCGAGAACCTTCTTCGTCCAGGTTGCAGAGTGCTCCGGGATCCTGACAA
92078 C T CAACGCATTCCTCCGCCATCTCGGCGCTCTCCACCATCGGAAAAACGATCCCAGCCGGCCCCAAGTCGAGAACCTTCTTCGTCCAGGTTGCAGAGTGCTC[C/T]GGGATCCTGACAACAGCAGGCGTGTTGTTTACCTGCAAAGCGCGCAGGACCTGCAGGCATTCCGTGATGGATCCAGGACCGTGCTC
92078 G A AAACGATCCCAGCCGGCCCCAAGTCGAGAACCTTCTTCGTCCAGGTTGCAGAGTGCTCCGGGATCCTGACAACAGCAGGCGTGTTGTTTACCTGCAAAGC[G/A]CGCAGGACCTGCAGGCATTCCGTGATGGATCCAGGACCGTGCTCGAGATCGACAACAACGAAGTCGTATCCGGCTAGCGAAGCG
92078 A C GCTCCGGGATCCTGACAACAGCAGGCGTGTTGTTTACCTGCAAAGCGCGCAGGACCTGCAGGCATTCCGTGATGGATCCAGGACCGTGCTCGAGATCGAC[A/C]ACAACGAAGTCGTATCCGGCTAGCGAAGCGATCTCGGCAAGCGTAGGTGAAGCGGACAGGAGGAACATGCCGTATAAGGGGGA
92078 A G GGACAGGAGGAACATGCCGTATAAGGGGGAGGAGGATGCGAGGCGGGCTTTCAAAGAGGAGGATGTGCTGGCGGTGATGGATGAGTGAATGGATCTGATC[A/G]GTGGGAAATGCACAGTGGATTTTGGAGAAGACATTAGGGTTTTAGTGGTGGAGAAGGTTGGGGTTTTGTTTGGGGAAATAA
92082 A G ATGAGAAGTTAGCCAATCGTCTTAATCGAGTTGTAGGAGACCTGGGGAGGGAGCCTCTTAAAGTTCTAGTTCAAGTGAATACAAGTGGAGAAGAATCGAA[A/G]TCAGGAGTGGAACCATCTGGCTGTGTAGCCCTTGCTAAGCATGTGAAGCAGGCTTGCCCTAATCTGATTTTCTCTGGCTTAATGAC
92082 G A AGCCTCTTAAAGTTCTAGTTCAAGTGAATACAAGTGGAGAAGAATCGAAATCAGGAGTGGAACCATCTGGCTGTGTAGCCCTTGCTAAGCATGTGAAGCA[G/A]GCTTGCCCTAATCTGATTTTCTCTGGCTTAATGACAATAGGAATGCTGGACTACACTTCAACTCCAGAAAATTTCAAGACCTTATCA
92082 C G AAAGTTCTAGTTCAAGTGAATACAAGTGGAGAAGAATCGAAATCAGGAGTGGAACCATCTGGCTGTGTAGCCCTTGCTAAGCATGTGAAGCAGGCTTGCC[C/G]TAATCTGATTTTCTCTGGCTTAATGACAATAGGAATGCTGGACTACACTTCAACTCCAGAAAATTTCAAGACCTTATCAAAATGTCG
92082 A G CTGGCTGTGTAGCCCTTGCTAAGCATGTGAAGCAGGCTTGCCCTAATCTGATTTTCTCTGGCTTAATGACAATAGGAATGCTGGACTACACTTCAACTCC[A/G]GAAAATTTCAAGACCTTATCAAAATGTCGAAAAGAAGTATGTGAGGCACTGGGCATGACAGAGAGCCAGTGTGAACTTTCAATGGG
92082 A G AGCATGTGAAGCAGGCTTGCCCTAATCTGATTTTCTCTGGCTTAATGACAATAGGAATGCTGGACTACACTTCAACTCCAGAAAATTTCAAGACCTTATC[A/G]AAATGTCGAAAAGAAGTATGTGAGGCACTGGGCATGACAGAGAGCCAGTGTGAACTTTCAATGGGGATGTCAGGTGATTTCGAGCT
92082 A G GCCCTAATCTGATTTTCTCTGGCTTAATGACAATAGGAATGCTGGACTACACTTCAACTCCAGAAAATTTCAAGACCTTATCAAAATGTCGAAAAGAAGT[A/G]TGTGAGGCACTGGGCATGACAGAGAGCCAGTGTGAACTTTCAATGGGGATGTCAGGTGATTTCGAGCTTGCGATCGAAATGGGAAG
92082 T C AGAAAATTTCAAGACCTTATCAAAATGTCGAAAAGAAGTATGTGAGGCACTGGGCATGACAGAGAGCCAGTGTGAACTTTCAATGGGGATGTCAGGTGAT[T/C]TCGAGCTTGCGATCGAAATGGGAAGTACTAATGTTAGGATTGGATCTACTATATTTGGTCCTAGGGAATATCCTAAGAAGGACAA
92082 A G GGGCATGACAGAGAGCCAGTGTGAACTTTCAATGGGGATGTCAGGTGATTTCGAGCTTGCGATCGAAATGGGAAGTACTAATGTTAGGATTGGATCTACT[A/G]TATTTGGTCCTAGGGAATATCCTAAGAAGGACAAAGAGGCTCAGTAGATTTATTTCCTGTTCTGCATCTAAATCTACCATTTTATTG
92082 A G CTTTCAATGGGGATGTCAGGTGATTTCGAGCTTGCGATCGAAATGGGAAGTACTAATGTTAGGATTGGATCTACTATATTTGGTCCTAGGGAATATCCTA[A/G]GAAGGACAAAGAGGCTCAGTAGATTTATTTCCTGTTCTGCATCTAAATCTACCATTTTATTGTAATGAAGAAAATAGAGTCCAACAG
92082 T G CTTGCGATCGAAATGGGAAGTACTAATGTTAGGATTGGATCTACTATATTTGGTCCTAGGGAATATCCTAAGAAGGACAAAGAGGCTCAGTAGATTTATT[T/G]CCTGTTCTGCATCTAAATCTACCATTTTATTGTAATGAAGAAAATAGAGTCCAACAGCACTCTTATACACCAATATTTATACAGCATCT
92082 T A TGGTCCTAGGGAATATCCTAAGAAGGACAAAGAGGCTCAGTAGATTTATTTCCTGTTCTGCATCTAAATCTACCATTTTATTGTAATGAAGAAAATAGAG[T/A]CCAACAGCACTCTTATACACCAATATTTATACAGCATCTACATGTAATATTTGCTCCTCCATGCCTCTGTTATTCAGTGTTG
92084 T G CATGATCAAAATTTAGAAGTGCACATGCGTGTACATTATATGGTAGAGCTACATTGTGTGGAATGAGTGCATGTTCTATTTATTTATAGATGAAGTGTAG[T/G]TGTATTTTGTGCTGGATCATTGTGCATGTATCCTCTTTCTATCTTGCGGCGTTTATCTATGAATCTTTTGTTTAG
92088 A G ACTTTCTTTCTCGCGAAAACATGGAAAGAAGTGATAAAGCAAACTTGGAGTGGCTATCAATGTTTGTAGAAGACTGCTTAAATGGAAGCTTCACTTCCCA[A/G]CCTCCTCCAACCACCCAGCCCCGAAATATCACAACTCAACCCACTACCAACGAAGCCCGAAGCCCACTAAGGGCCCTAAGCCCACTTT
92088 G A ATGTTTGTAGAAGACTGCTTAAATGGAAGCTTCACTTCCCAACCTCCTCCAACCACCCAGCCCCGAAATATCACAACTCAACCCACTACCAACGAAGCCC[G/A]AAGCCCACTAAGGGCCCTAAGCCCACTTTCACTCTCCATCCCATCGAAAGCGAGAACAAAAAGGGCCGTAAAGCCCACCCAAAAAGC
92088 A G TCAGCAGCTACTGGAACACGCCGCTCCTCCCTCAAACCCACTGGCTAGCCGAAAGCGAGCTCCTCGTTTTCCCCAAAAAGGAACGGTCCGGAAGCGACGA[A/G]GGCAAAAAGGACGCTGAGGCGGACGCGGATGAGGAAGCGGACGCGGAGGCGAGCGCGGTGAGGAGGTGCACGCACTGCGGG
92088 A C AGGACGCTGAGGCGGACGCGGATGAGGAAGCGGACGCGGAGGCGAGCGCGGTGAGGAGGTGCACGCACTGCGGGTCCCACAAGACGCCGCAGTGGAGGGC[A/C]GGGCCGCGGGGACCGAAGACGCTCTGCAACGCCTGCGGGGTCAGGTACAAGTCCGGTCGGCTGCTGCCGGAGTACCGGC
92088 C G GGAGGTGCACGCACTGCGGGTCCCACAAGACGCCGCAGTGGAGGGCAGGGCCGCGGGGACCGAAGACGCTCTGCAACGCCTGCGGGGTCAGGTACAAGTC[C/G]GGTCGGCTGCTGCCGGAGTACCGGCCCGCTAAGAGCCCGACTTTTGAAAGCTTTAAGCACTCGAATT
92148 T A GAAAAACTTGACCAAGACGTAACCATTGATATTCCAGCAGAGACCGATGTTGCGGTAGCTATGGATGTTGATCTGAATAAGGAACCAGGTCAACCGACTA[T/A]TCTGGACACAGAAGAAGCTAGCACATCAAATATAGATCTCAACAAGAAAACCGATGAATCCGGTGCTAATCATCTTCCTAAGGAAC
92148 T C CATCAAATATAGATCTCAACAAGAAAACCGATGAATCCGGTGCTAATCATCTTCCTAAGGAACTGCATGAAATGACAGTAAAGGATGATAAAGCTCATGA[T/C]CAAAGTGACAAGGTTGCAGAAACAACAATGTTGAAAGGAAATGGAACAGAGACAGGTCAGATAATCTCAACTACAATTGGTGGGA
92154 C T AATGCAAACAAAACACCGTTTCACGCAGTGAAATCACTGATCACATTTTTTTTCTCTCAGACTTTTCTTTCAGAATTTGGA[C/T]CTTCTACTTCAATCCAAATGCACATCCTTAAAGCTTATCTTCGAACTCAGACAAAGGAGTCATCTGTTCCTTGAGACCTTTCCTTTTCCTAATCTCAGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
92154 G A GCAGTGAAATCACTGATCACATTTTTTTTCTCTCAGACTTTTCTTTCAGAATTTGGACCTTCTACTTCAATCCAAATGCACATCCTTAAAGCTTATCTTC[G/A]AACTCAGACAAAGGAGTCATCTGTTCCTTGAGACCTTTCCTTTTCCTAATCTCAGAGACGATCTTAGAAGCATGAGAGCCTAACTCCATTG
92154 A G GAGTCATCTGTTCCTTGAGACCTTTCCTTTTCCTAATCTCAGAGACGATCTTAGAAGCATGAGAGCCTAACTCCATTGGATCCGAAGCCAGCATATCCCA[A/G]TGATCAAATACACACTGAGGGAAGGCCTGCCCCGAAGTAGCAGCCCTTAAAGTACTGGAAAATCCAAAAGACTCGACAACAGGCAAA
92154 T A GTTCCTTGAGACCTTTCCTTTTCCTAATCTCAGAGACGATCTTAGAAGCATGAGAGCCTAACTCCATTGGATCCGAAGCCAGCATATCCCAATGATCAAA[T/A]ACACACTGAGGGAAGGCCTGCCCCGAAGTAGCAGCCCTTAAAGTACTGGAAAATCCAAAAGACTCGACAACAGGCAAATATGCCTTG
92154 G T TTGGATCCGAAGCCAGCATATCCCAATGATCAAATACACACTGAGGGAAGGCCTGCCCCGAAGTAGCAGCCCTTAAAGTACTGGAAAATCCAAAAGACTC[G/T]ACAACAGGCAAATATGCCTTGATGTTGTAAAGCGGAGTTCCAGGCCTCTGCATTTCCTCAAACACATGCCCTCTTTTCTGATTCAGC
92162 C T CAGGAATCTCTCTGGTAGCTCGTACCGTATCGACAGCTTCCTTATCTAGTATATTCATGATGTGCTTTGCAGTCTTATCAAGCCTCTTGAATTTGATCCG[C/T]TGAGGTTGATGTATATTTGGGGAGGCGGTGGCATTGCCTTCGGTAGAAATCGAGTCAGCACCACTTGATGTTGTCATGGACCTGAGAT
92162 T C CAGTCTTATCAAGCCTCTTGAATTTGATCCGCTGAGGTTGATGTATATTTGGGGAGGCGGTGGCATTGCCTTCGGTAGAAATCGAGTCAGCACCACTTGA[T/C]GTTGTCATGGACCTGAGATTAGTAATGCTTTTCTGCAAATACACATCATTTGATAGTGCCACCACTGGATTATAGAGCAGCTTAGCCT
92164 C T TTAGACTTTGCAGGACATCTCGCGTAGGATTACCAGTTCTGGTGTAGTCATAGGGACCATTCTCTGTAGCTGAAGGCTGATGAAATGTGGATGTCTGATA[C/T]AGAGGGGTACTCATAGCCCCATAAGGATCAAAAGAATTATCAGCGCTTGTCAAAATAGTTGATATACTGGGTTCCCTTAGCTTCAGT
92164 G C CTAGTTTGGAATCGCCCATGAAATCAGTAAGCCCCTCTGCCATAACTGAAGCGCTTAGATCTCTGTCTCTACCTGCTTTGCAAGTCGATTCAAACCTTTT[G/C]GGAGTAGAAAAGAACACCGAGTTTTTTGAAGTTGAGAAAATGCATGAACTTGGTTGAGGCTGAAATCGAGGGAGGAAAGATGAATTT
92164 T A TCAGTAAGCCCCTCTGCCATAACTGAAGCGCTTAGATCTCTGTCTCTACCTGCTTTGCAAGTCGATTCAAACCTTTTGGGAGTAGAAAAGAACACCGAGT[T/A]TTTTGAAGTTGAGAAAATGCATGAACTTGGTTGAGGCTGAAATCGAGGGAGGAAAGATGAATTTACAGCGGTTGCTGACATTGACAG
92168 T TC TCCCTGAAACGTCGCACCACCAATGACCCCCATCAAATCCTCTCCCGCCTCCTCCTTCCTGACCTAACCTCCGCCTTCACTGAGCTCATCCGGCAGGACC[T/TC]CCCCTACTCGCCCTCCCCATCTTAGCTCTCCTTCGCTCTGAACCCAACTACAAACCCAACCTCGTCCTACATTCCCTGCTCATCAAATCG
92232 T TTTAGA AGATGAATGAGGGAAGTGCATTGCTTCTCTCATTTCACTTTGCACAATGCTCCTCACCGCGCTCTTACACACAGGCATGCACGCTTTACAGT[T/TTTAGA]TTAAAATAACAGACACAACGCCTCAACTACAATCAAACTTTTAGTAGCAGGGCAGCACACTTTCTTGGTTGAAAAAAAAAAGTGTAAATATA
92232 T TA GCGCTCTTACACACAGGCATGCACGCTTTACAGTTTTAAAATAACAGACACAACGCCTCAACTACAATCAAACTTTTAGTAGCAGGGCAGCACACTTTCT[T/TA]GGTTGAAAAAAAAAAGTGTAAATATAAACAAATAGGCAAAATATGTAGTCTAACACTAGCACTCAGGTGTAAGCGAATGGTCTCTG
92232 GA G CTTACACACAGGCATGCACGCTTTACAGTTTTAAAATAACAGACACAACGCCTCAACTACAATCAAACTTTTAGTAGCAGGGCAGCACACTTTCTTGGTT[GA/G]AAAAAAAAAAGTGTAAATATAAACAAATAGGCAAAATATGTAGTCTAACACTAGCACTCAGGTGTAAGCGAATGGTCTCTGCCTGA
92240 T C AACCTCGTCGGCCATATGAGAAGGAGCGTCTTGACGCGGAATTGAAGCTTGTGGGAGAGTATGGACTTCGTTGCAAACGTGAGCTTTGGAGAGTTCAGTA[T/C]GCTTTGAGCCGTATTCGTAATGCTGCTAGGGAACTCTTAACTCTGGACGAGAAGAATCCTAAGCGTATTTTTGAAGGAGAGGCTC
92240 CA C TAGGGAACTCTTAACTCTGGACGAGAAGAATCCTAAGCGTATTTTTGAAGGAGAGGCTCTTTTGCGACGTATGCATCGCTATGGGCTTCTTGACGATGAA[CA/C]AAAACAAGCTTGATTATGTGCTTGCGCTTACTGTTGAAAACTTTCTTGAGAGAAGACTTCAAACTCTCGTTTTCAAGTCTGGCATGG
92240 T C TAACTCTGGACGAGAAGAATCCTAAGCGTATTTTTGAAGGAGAGGCTCTTTTGCGACGTATGCATCGCTATGGGCTTCTTGACGATGAACAAAACAAGCT[T/C]GATTATGTGCTTGCGCTTACTGTTGAAAACTTTCTTGAGAGAAGACTTCAAACTCTCGTTTTCAAGTCTGGCATGGCTAAGTCTATTC
92240 T C AAGGAGAGGCTCTTTTGCGACGTATGCATCGCTATGGGCTTCTTGACGATGAACAAAACAAGCTTGATTATGTGCTTGCGCTTACTGTTGAAAACTTTCT[T/C]GAGAGAAGACTTCAAACTCTCGTTTTCAAGTCTGGCATGGCTAAGTCTATTCATCATGCTAGGGTGCTTATCCGTCAACGCCACATCA
92240 T C AAACTCTCGTTTTCAAGTCTGGCATGGCTAAGTCTATTCATCATGCTAGGGTGCTTATCCGTCAACGCCACATCAGTGTTGGAAAGCAAGTGGTGAACAT[T/C]CCATCCTTTGTGGTGAGGGTGGAAAGTGCAAAGCACATAGACTTCTCCCGTAACAGTCCGTTGGGTGGTGGTAGAGATGGAAGGGT
92248 T C AAAAAAAAATCTCAGTACAAGGTCACGAAAGACTGATATCTTTTCTCAAATCACCAAGTTTT[T/C]CAGTTATTTATTAAAGCTTAACGATCATTCAAATAGGTTGTGTCTACAACCATCACATTACAAAAGCATTCCTCACAGCAAACAAGCAAGCTGGAAGTTT
92248 A G CTCAGTACAAGGTCACGAAAGACTGATATCTTTTCTCAAATCACCAAGTTTTTCAGTTATTTATTAAAGCTTAACGATCATTCAAATAGGTTGTGTCTAC[A/G]ACCATCACATTACAAAAGCATTCCTCACAGCAAACAAGCAAGCTGGAAGTTTTATTCAAAACCAAAGTGCTGGTTGGACATGGAAGATT
92248 A G TCAGTACAAGGTCACGAAAGACTGATATCTTTTCTCAAATCACCAAGTTTTTCAGTTATTTATTAAAGCTTAACGATCATTCAAATAGGTTGTGTCTACA[A/G]CCATCACATTACAAAAGCATTCCTCACAGCAAACAAGCAAGCTGGAAGTTTTATTCAAAACCAAAGTGCTGGTTGGACATGGAAGATTA
92248 A G TAAAGCTTAACGATCATTCAAATAGGTTGTGTCTACAACCATCACATTACAAAAGCATTCCTCACAGCAAACAAGCAAGCTGGAAGTTTTATTCAAAACC[A/G]AAGTGCTGGTTGGACATGGAAGATTAGTTGATGTTAAGAAGAGACTCGATCTTGCTGCCAACATGAGCTTCATAGTCTTCGAGACGT
92248 G A ACAAAAGCATTCCTCACAGCAAACAAGCAAGCTGGAAGTTTTATTCAAAACCAAAGTGCTGGTTGGACATGGAAGATTAGTTGATGTTAAGAAGAGACTC[G/A]ATCTTGCTGCCAACATGAGCTTCATAGTCTTCGAGACGTCCCGCCACAGCATCATTTTCCCACCTGATGAGAGTTGGAACGCCCGTG
92248 G A TGATGTTAAGAAGAGACTCGATCTTGCTGCCAACATGAGCTTCATAGTCTTCGAGACGTCCCGCCACAGCATCATTTTCCCACCTGATGAGAGTTGGAAC[G/A]CCCGTGAGCTTGAATTTCGGGTCGGTCCTCCACGGATGGCTAGGATTTCTCCATGTTGGCCTATCACCAACATAGGCTCGAAGGAGC
92270 T A CAGCAGCCACCAGCTTTTGAGCATCCCCAAACCATTTACTCATTAGATTAGAGACCCTAACATTTATAAACACAGCTCCTGATTCTCTAGCTATCGCTTT[T/A]GCTAACATTGTTTTTCCTGTACCCGGAGGTCCATACAGTAAAACCCCCTTTTGTGGACTAAGAAGCTTCCCATAGGAAAATATCTCAGGC
92284 CA C CTACACAATCATGGCCATATTTGAACGATGCTCTTACACAATTCCAGGATCCTGCAGAAGCTGACAAATTAATGAAGATTCAAAGAGACTTGGATGAAAC[CA/C]AAAATAATCTTACATAAAACAATTGACAGTGTGCTTGCTCGAGGGGAGAGGCTTGATAGCTTAGTGGAGAAGAGCTCAGATCTGA
92284 GA G CAATTGACAGTGTGCTTGCTCGAGGGGAGAGGCTTGATAGCTTAGTGGAGAAGAGCTCAGATCTGAGTGCAGCCTCACAAATGTTTTACAAGCAAGCAAA[GA/G]AAAACCAATCAGTGTTGTACAGTACTGTAATAACTGCTGCAGGATTGTATGTGATACAAATTACAGGCTTTATATCTTGAAAATT
92284 G A TGCAGCCTCACAAATGTTTTACAAGCAAGCAAAGAAAACCAATCAGTGTTGTACAGTACTGTAATAACTGCTGCAGGATTGTATGTGATACAAATTACAG[G/A]CTTTATATCTTGAAAATTGCTTTGAAACCGTGTGTGTAAACTTATAATTCTTTGTTGATCCTTTATACGAGTCATATATTGAT
92300 A G ATCGTGGAAGGTGGGTACGTCCATTGCCAGATCTAAGGATAAGTAGCAGCTCTGAGGAAAATTGAAAAGTGATCGTACAGTTTGAGGAGTAAGTAGTAGG[A/G]CGGAATCCTGTGGATCTAAAAGGAGAAGGTAGCAATAGACGAAGAATGGAAGCGTTTGAGCGTATGCTGAATGCAGGAAGAAG
92310 GT G TGGAGAAAGCATTAACAGAGGCAGCAGAGAAGGAAGGAGATAGGATTTCATCAGCGAGGCCAAGCCATTTTAATGAGGCGTGTCCTTTGCAGGAGTTTTT[GT/G]TTAGGTGCCGCTGTTATGGATGTTGGGGCTGAGAAGGAGAAGAAGGAGAAGAGGGCGTCCCTTGTCGAACTGTTTATGATTG
92332 A G CGCTCGAGCTGACCCTTATATCGGCAAAAGATCTGGACAAAGTCAACCTCTTCTCAAAAATGGAGGTCTACGCCATCGCCATGATCGCTGGCGATCCGAG[A/G]TCGAAGAAGAAAACGCATACGGATCGGGATGGCGGCAGGAACCCTAACTGGAACGCAACGTTCAATTTCAACGTCATGGAGTCCG
92332 T G AGAAGAAAACGCATACGGATCGGGATGGCGGCAGGAACCCTAACTGGAACGCAACGTTCAATTTCAACGTCATGGAGTCCGATCTTGAAAGGTGCGTGTT[T/G]CAGGTGGTGTTGAAGGCGGAGAAGGCTTTTGGCGACCGGGAGATCGGTGAGGTTCACGTGCCTCTCAAGGAGTTGTTGAGTGG
92332 C G CAACGTCATGGAGTCCGATCTTGAAAGGTGCGTGTTTCAGGTGGTGTTGAAGGCGGAGAAGGCTTTTGGCGACCGGGAGATCGGTGAGGTTCACGTGCCT[C/G]TCAAGGAGTTGTTGAGTGGATGGAAAAAGGATGTTGGAGTTCAATATTTGAGTTATCAGGTACGAAAACCTTCTGGTAAAGCGA
92332 A G CTTTTGGCGACCGGGAGATCGGTGAGGTTCACGTGCCTCTCAAGGAGTTGTTGAGTGGATGGAAAAAGGATGTTGGAGTTCAATATTTGAGTTATCAGGT[A/G]CGAAAACCTTCTGGTAAAGCGAAAGGCACTCTTAACTTCTCCTACAAGTTCAAAGAACCAATGATGGTGGCTGCTCCTCCGCCTTC
92332 T G GTTATCAGGTACGAAAACCTTCTGGTAAAGCGAAAGGCACTCTTAACTTCTCCTACAAGTTCAAAGAACCAATGATGGTGGCTGCTCCTCCGCCTTCTCA[T/G]GGTGCCGCTCCAGCTTTATACCCCACTCAAGACACAAAGCCAACCAAGATGGCTGAACCCGTAACCACATACCCTGTCACTGGCCCAT
92332 A G GAAAACCTTCTGGTAAAGCGAAAGGCACTCTTAACTTCTCCTACAAGTTCAAAGAACCAATGATGGTGGCTGCTCCTCCGCCTTCTCATGGTGCCGCTCC[A/G]GCTTTATACCCCACTCAAGACACAAAGCCAACCAAGATGGCTGAACCCGTAACCACATACCCTGTCACTGGCCCATCT
92340 C G TATGAGCTTTGGTAACCTTAATGTGAAGAGTACCGCCTCCAAATTCCGACTCGCTCTTATTATGGAACTCCATCCAAGCTTCGTTCTGGTAAAAGCAAGC[C/G]CCTTTCCACTCCAGCGTAGAATTGGGGGAGGAAACGGCACCAACAAAAGTGGGAAGCAGATCCACAGCGCCGCGAAGAGTCGTCAG
92342 A G ACATGGTTGAGAGCCTGCTAGGCCTGGGCTGAAACGCCGCTCTCCTTCTCTGCTGATGAGAGCTAGGTCTAATCAAAGCTGCAAGAGCTCTTTTCACCAA[A/G]TCGCCCTCCACCGTTCCGATCCTAACAAGAGAGTTAGCCATCGCGGATCTCCTCGCATTTAATCTGGTTGATGAATTGCTTATCCTGT
92342 T C TAATCAAAGCTGCAAGAGCTCTTTTCACCAAATCGCCCTCCACCGTTCCGATCCTAACAAGAGAGTTAGCCATCGCGGATCTCCTCGCATTTAATCTGGT[T/C]GATGAATTGCTTATCCTGTTGTTTTGCTGCGAGCTCTGATTCGAAAACCCTTTATGTAAGCTGCAACGGAAGGAACCCGGGTGAGTTG
92342 C T CCGTTCCGATCCTAACAAGAGAGTTAGCCATCGCGGATCTCCTCGCATTTAATCTGGTTGATGAATTGCTTATCCTGTTGTTTTGCTGCGAGCTCTGATT[C/T]GAAAACCCTTTATGTAAGCTGCAACGGAAGGAACCCGGGTGAGTTGTCGGTGAACACATACAGGTCTTTCGCTGAGGGGCAGATGGC
92342 T C ATCTGGTTGATGAATTGCTTATCCTGTTGTTTTGCTGCGAGCTCTGATTCGAAAACCCTTTATGTAAGCTGCAACGGAAGGAACCCGGGTGAGTTGTCGG[T/C]GAACACATACAGGTCTTTCGCTGAGGGGCAGATGGCTTTTTCGCTGGAACGTAGGATATAGAGCGGCCCGGAGAGGTCGGCCGGC
92342 C T TGCAACGGAAGGAACCCGGGTGAGTTGTCGGTGAACACATACAGGTCTTTCGCTGAGGGGCAGATGGCTTTTTCGCTGGAACGTAGGATATAGAGCGGCC[C/T]GGAGAGGTCGGCCGGCTGTCGAGGGAGAACCGGACAGACGCCGACGATGACAACGAACCGGCGAAGTGGACGCGTGTCGGG
92342 G C GGGAGAACCGGACAGACGCCGACGATGACAACGAACCGGCGAAGTGGACGCGTGTCGGGGATGTGGATCTCATGCCGAACGAAGGCGACGATGTTAACGA[G/C]GCCGTGGATGATGCGAAGTGGCTTCCGCTGGAATAGCTGCCGGAGATGGCTGGCGAGCGGGAAAATGAAGTGTAGCTCGAG
92342 T A ATGCCGAACGAAGGCGACGATGTTAACGAGGCCGTGGATGATGCGAAGTGGCTTCCGCTGGAATAGCTGCCGGAGATGGCTGGCGAGCGGGAAAATGAAG[T/A]GTAGCTCGAGAGGACTGGCCCGTTTCTTGCAGATCTGGGATTGGATCTAGAAGAAGACATTATTTTAACTTTT
92366 A G GGACTATTTGATCCAGTATCATTACGATTCGTTTGCCCCATGGGGCCAGATGGTGTCAGCATTCTGGCAGCGGCAAGTGTCTGAAGGTTGAGATCTATGT[A/G]AGCAAGAATTATAGGTTGAGGTTCCATGTCAATCGGAACCATGGAGAGATGACCCTTGATTGCAGTACCACGAAGCTTAACAAGTT
92368 GA G AACGAAACGTTCGGGTGGTATCCGGACGCTTGCTGATCTTAAAAGTGGTTCTGGATCCGACAGCGATGAGGAAGGGCCACAGGAGTATTATACTGGTGGA[GA/G]AAAAAAGTGGAATGCTTGTCCAAGACCCTACCAGAAGAGGAAACCAGGACATTGATTCATTATTCGAACAAGCTAGGCAAATG
92372 A C TTTTACAAAGTTCAAAATTACATTTTAATTAGATTACTCAACCAAGTAAGTTTCTCCAATTCCAAATACAACAAATTATTC[A/C]ATACGTACCAAAGCATTATTCATCACTACCATGAAAAAAGAAAAGAAAAAACAGATCTAAGTAGTAAGAATAGGAGGAAGATAATCCGACTTGGTACCAA
92372 A T TTTTACAAAGTTCAAAATTACATTTTAATTAGATTACTCAACCAAGTAAGTTTCTCCAATTCCAAATACAACAAATTATTCAAT[A/T]CGTACCAAAGCATTATTCATCACTACCATGAAAAAAGAAAAGAAAAAACAGATCTAAGTAGTAAGAATAGGAGGAAGATAATCCGACTTGGTACCAAGAA
92372 GA G ATTTTAATTAGATTACTCAACCAAGTAAGTTTCTCCAATTCCAAATACAACAAATTATTCAATACGTACCAAAGCATTATTCATCACTACCATGAAAAAA[GA/G]AAAAGAAAAAACAGATCTAAGTAGTAAGAATAGGAGGAAGATAATCCGACTTGGTACCAAGAACCCGAGCTTTGGTATCCGGAAAGA
92382 A G TCTCCTGAAAGAGAAAACCAGATGGGTAACATATATAAAAGATTCGCCAAAGCCACCTCCAGTTAGAATAACCTTCACTTTTCCTGTGATCGATGCATCC[A/G]CTTATATTGCCATGGTAGTTGTGGGACCTGGTGAAGTTGATGCAGTCAAAAAGGCACTGGGACCTAGAGATGCTACTTCTGATCTGC
92382 T C TGAAGGCCAAGCGTGAATGTGTTTCGCTGCTTGGAAATAGTTTTGTAGTCTTCAATAAAGTGCTGTTTCTTGAAAACAGTTGCTGGTTTCCGCGATGCTG[T/C]TGTGTTATCGTTCACGCAGTTGGAATATTGCATATGGCTATCAAAGATATGGCTTTGTAGCTAAGACTCTGTTAAGTTGAGCAATCCA
92394 A G ACATAAACTGGCTACTGGACATTTTAATTGAGAAGCAAATTGCAGAGGAATTCGTACGTATATGGGGAAGTGAAAAGGAACTTCTAAGAATCCACAGCAG[A/G]ACATCACCAATGGTGCGTTACGAGCTCAGTCGTATATCGGCAAGCGTGTTTATAGCACTTGGGAAAGGGAAGATTAGGTGCAGTA
92394 A G ACCTGTGGTTTGGAGCAATGGTTTTGGATTTTGGTTGGTTGCAGAGGTGCGGTAAAGGATTGGATGTGAGGGTTCTTGAAGAAGGGTTGGGGCAGGCAGT[A/G]CTTACGCTGCCGTTGAAGCAGCAGCAGGCAATGTTTGTGGAGTGGTTTAGGTGTTTCGGGGTGCAGGGGAGGGAGTGCCCTGA
92398 T TC ACCAGCAGTCCTGTAGCATTCCTCGTGCCCGTGGCGTTCCTCGGCGCATACTTTGCCTGGCGGCACTATCTTGCTCCCTGATTCGCTCCCCTCATATTTT[T/TC]CTACACCTTCATTATGTGTATCTCCACGGCATAATCCATAGATTTTATTTTATGGGTCACCTCCCTGTTGTTGCTTTCCAAAAAAAAAAA
92418 T C ATCGTCGACACTCAAATAATCCCCATTGGCACACTCTGCAGAAGGTTGCAGCTCTTGATTGTCAAGGTAGCTTAAAACTTCAAGGACGGGAAAGCCATCA[T/C]CTGGTTCCATTAGATCATGGATGGAGGTGTCAAGATCACCGAGGTTGCCCCAGTCAAAATCCAAGTCTGCATATTGAATAGAATT
92426 A G GAACACGACAAATGACTGATCCTTGCTTAAAGATACACCATTAGGGAATTGTAGATTCCGTAGAAGAACGGTTGTCACCTTCGTCACTGGGTTATATTTT[A/G]AAAGCCTGCCTGATGGTTCACAAGTAAATACTAGCTGCATGAAGTTCCTTCTCTGAAAGTTGGTGCTACTATCCGTAAAATAGACATT
92426 A T CTTCTCTGAAAGTTGGTGCTACTATCCGTAAAATAGACATTCCCTTCCTCATCAATATCCAAATCATTGGTGAAATTAAATGGTACAGCTTCTGCCTCTA[A/T]TGTTAATTGAGTAGCCAATCCGCCTTCAGGCCCTACCTTTAATAGCCCAAAATATGCATCAGCAATGTACAGATCTCCTGTTTTCTTGTGG
92458 T C CCTTTATGTTCGCTAAAAAAGCACCAAATTGTTCTAAAGTAAGACGACTCCTAGCCTGGCGAAAGAACTCCTTTCCATCTATACGAGGAACACGACCTGA[T/C]GACACAACAGAAGGTGGAGAGCTCGACGCAGATGACTGCTGAGTTGGAGTGTTACTTGATGTAAACGCAGAAGATGCAGAAGAT
92460 C A AAAACGGATCATGTTGGATTCAGACCCGAATGTGAACATATTGTTGCTTGGTGCTGGTGCTGGCTTTGCAATATTGATGGTTTCGGTGCCTAAGAGGTGG[C/A]GACGGATTGAGTCAAGGGCTGTTGTTGTTGTTGTTGTAGGCATTGTTGTGCTTGTTTGATGGGTTTTGCCAAAGGATGTGGATGAT
92468 A T AAAGTTCCGGTCTATCATAACTCAATAAGTTCCTGAAACCCTTACGGTAAATCCCCAAATCTGCAA[A/T]TTGACCAAACATGTCGGAAATACCCGAAGTAAAACTCGGATCGTCGAAGCCAATGATCGCTACACAACAAGAAATGATGGAAAACAAGGTTCCAATCCCG
92468 C T AAAGTTCCGGTCTATCATAACTCAATAAGTTCCTGAAACCCTTACGGTAAATCCCCAAATCTGCAAATTGAC[C/T]AAACATGTCGGAAATACCCGAAGTAAAACTCGGATCGTCGAAGCCAATGATCGCTACACAACAAGAAATGATGGAAAACAAGGTTCCAATCCCGTACCGC
92468 C T TAGTGATGGAGCGGATGCTTCAGATGCAGAAGATTAGGGAAATGGAGGAATTAAAGAAGAAAGGGAAGGTTGGGATGGGGGTCATTCCTGCTACTGCTAA[C/T]GTTTGATTTCTTGGGGAAGGAAGCGCGGCTCCCACCGTTATCTATTCTTACACTTCTTTGTTGCAATTCAGGATGATTTTTCAAGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
92468 G A ATGCTTCAGATGCAGAAGATTAGGGAAATGGAGGAATTAAAGAAGAAAGGGAAGGTTGGGATGGGGGTCATTCCTGCTACTGCTAACGTTTGATTTCTTG[G/A]GGAAGGAAGCGCGGCTCCCACCGTTATCTATTCTTACACTTCTTTGTTGCAATTCAGGATGATTTTTCAAGTGCTGTTCTTGTTGTT
92498 CA C TAATCCTGACCTTCCGATATCATCGCGCTATATGCGTGTACTAATCCTATAATTCCAGTGTGAATTGAAGGAATCCAAATCCATTCACAGAAAAATCAAC[CA/C]AAAAACATCAAAGGATAATTTTTTCTTCTCAAATCTCATTCTTACAATGGCAGGCGCTATTGCGACGGCGATCGGAGACTGCATCATA
92504 T C CAGCGCCAGGAGCTCCACCAGTTCTCTGATACACTGCTGAAATTACCGGATTACAGACTGCCTCAACTTCCTTCAACTTCTCCTCGTAGTCCTCCTTCTC[T/C]GCGTTCTGATTATCGTCCAACCACTCCAAAGCCTCCTTCAAAGCCGCATCGACCTTCTCCTTCTCCTCGCTCTCCAATTTGTCGGCGAGCT
92504 G A ACGTCTCCAGCTGGTTCCTTGCATCTATCCTCTCCTTCACCTTCTTGTCCTCTTCCGCAAATTCCTCTGCTTCCTTCACCATTCTCTCTATCTCTTCCTG[G/A]CTCAGTCTTCCTTTCTCGTTCGTTATTGTTATCTTTTCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTAC
92504 T G TCTCCTTCACCTTCTTGTCCTCTTCCGCAAATTCCTCTGCTTCCTTCACCATTCTCTCTATCTCTTCCTGGCTCAGTCTTCCTTTCTCGTTCGTTATTGT[T/G]ATCTTTTCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTGTTCC
92504 T C TCACCTTCTTGTCCTCTTCCGCAAATTCCTCTGCTTCCTTCACCATTCTCTCTATCTCTTCCTGGCTCAGTCTTCCTTTCTCGTTCGTTATTGTTATCTT[T/C]TCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTGTTCCTCTTGG
92504 G T TGTCCTCTTCCGCAAATTCCTCTGCTTCCTTCACCATTCTCTCTATCTCTTCCTGGCTCAGTCTTCCTTTCTCGTTCGTTATTGTTATCTTTTCCGCCTT[G/T]CCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTGTTCCTCTTGGTGCTGGAG
92504 G A CGTTATTGTTATCTTTTCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGT[G/A]TTCCTCTTGGTGCTGGAGCTATTCCAGACAGATCAAACTTCCCTAGCAGCCTGCAGTCCTTTGTCAGACTTCTCTCCCCCTC
92504 T C GTTATTGTTATCTTTTCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTG[T/C]TCCTCTTGGTGCTGGAGCTATTCCAGACAGATCAAACTTCCCTAGCAGCCTGCAGTCCTTTGTCAGACTTCTCTCCCCCTC
92504 T C TTGTTATCTTTTCCGCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTGTTCC[T/C]CTTGGTGCTGGAGCTATTCCAGACAGATCAAACTTCCCTAGCAGCCTGCAGTCCTTTGTCAGACTTCTCTCCCCCTC
92504 C T GCCTTGCCTGTTCCTTTGTCTTCCGCCTTCACGTTCAATATGCCGTTCGCATCTACCTCGAATGTCACCTCTATTTGTGGTGTTCCTCTTGGTGCTGGAG[C/T]TATTCCAGACAGATCAAACTTCCCTAGCAGCCTGCAGTCCTTTGTCAGACTTCTCTCCCCCTC
92520 G A GTTTATCATGGTGTAATATTTTTGATTTACTGTAGTTTAGATTGGTTATCAGTTTCTGGTCCATGGGGTCGATTTTATCATTTATATGGGTGCTTAAATG[G/A]AGAAGTTACGTTAGATCATTCTAATTAAGTGATGGCGGCAACATAATATTGGGTGAATAATGGATAAAATGATGGACGTGGCGGTTGT
92520 A T GTTAGATCATTCTAATTAAGTGATGGCGGCAACATAATATTGGGTGAATAATGGATAAAATGATGGACGTGGCGGTTGTGTAGCTGTTGTAATAAGCAAT[A/T]TTTTGAGAGTGTATCAATAAGTTTTTGTTGTATCCGCTGTATAAACTTGTTTACCGTGGGTTATTTTGCCTATCGAACGATGATTACT
92522 C T GAGGTGATTTTGAGGATGATGGTGATATGTTGTTGGATATTATGGATGGGGATGATAGTGAAGGCTCAGATGAGTCATATAGCAGTGGAGAAGATGATGA[C/T]GACGACGATGATGGGGACTTCGATGGAGATGGTCTTTTCTATTGAATTTTTTTAGGAAGATCTAGATGTTGTATGGATGTAGAAA
92528 A G AACTGAAGAGCCGATTGTAGAATTCCACTGGTTGGAAGTGAAGCATCGCAAGTGGACAGTGGAGTCGTGACTTGAAGCTTGCAACTACTTAAAAGAGTTG[A/G]TAGGATCGAAGTTATGAAGTTCAGGGATAGGTTGAACTGTCCGTTTGAGTTGGTCCTTGTTGAAGAAACCATGTTGTTTCCGCATA
92528 T C ACTGAAGAGCCGATTGTAGAATTCCACTGGTTGGAAGTGAAGCATCGCAAGTGGACAGTGGAGTCGTGACTTGAAGCTTGCAACTACTTAAAAGAGTTGA[T/C]AGGATCGAAGTTATGAAGTTCAGGGATAGGTTGAACTGTCCGTTTGAGTTGGTCCTTGTTGAAGAAACCATGTTGTTTCCGCATAT
92528 A G TTCCGCATATTAGCTGCACTCCTGCATTTGCAAAGGGAAGTGCACTAACTGTACCAGTACTACCTGTGCTGCAGTTAACAATACCAGCTATGTTAAGTGT[A/G]CCTGACCCAAGTAGCTGGCCTTGTGCAACTACTGTTGCTCCCAGTATGGCAACAGTGAAGAACATAAATGTTTTAGAAGCCATTGGTT
92532 G GT AAAACTCTTCCAAAACCACCACAAATTGCTGTTTGTTTGTAAAGCTGCGGAGACTGTGCTAAGCACGCTGGTTGTCCTTTGTAATCGAGCTTGAATACA[G/GT]CTGCACCACCTTCACTTGCTCCTGCTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAATATACTT
92532 G GT GGTTGTCCTTTGTAATCGAGCTTGAATACAGCTGCACCACCTTCACTTGCTCCTGCTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATA[G/GT]AAATAATCTAAATATACTTTCTACTTGATTTTGGAGTTTGAAGATTGCATGGTTTGCAGGAGTTCGAATGTCAAGGACTCTATTGTTC
92532 A AT ATCGAGCTTGAATACAGCTGCACCACCTTCACTTGCTCCTGCTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAAT[A/AT]TACTTTCTACTTGATTTTGGAGTTTGAAGATTGCATGGTTTGCAGGAGTTCGAATGTCAAGGACTCTATTGTTCAACCTTGTTTCCTG
92532 T TA CCTTCACTTGCTCCTGCTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAATATACTTTCTACTTGATTTTGGAGTT[T/TA]GAAGATTGCATGGTTTGCAGGAGTTCGAATGTCAAGGACTCTATTGTTCAACCTTGTTTCCTGACCAACACGAACAAGCTGCTCCCCTG
92532 A AT CTCCTGCTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAATATACTTTCTACTTGATTTTGGAGTTTGAAGATTGC[A/AT]TGGTTTGCAGGAGTTCGAATGTCAAGGACTCTATTGTTCAACCTTGTTTCCTGACCAACACGAACAAGCTGCTCCCCTGTTTGTTCAG
92532 T TA CTACTAATTTAGGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAATATACTTTCTACTTGATTTTGGAGTTTGAAGATTGCATGGTT[T/TA]GCAGGAGTTCGAATGTCAAGGACTCTATTGTTCAACCTTGTTTCCTGACCAACACGAACAAGCTGCTCCCCTGTTTGTTCAGCTCTTTC
92532 G GA GGAGAGTGGATTCCAGTGAAACCCTCAGCTGATAGAAATAATCTAAATATACTTTCTACTTGATTTTGGAGTTTGAAGATTGCATGGTTTGCAGGAGTTC[G/GA]AATGTCAAGGACTCTATTGTTCAACCTTGTTTCCTGACCAACACGAACAAGCTGCTCCCCTGTTTGTTCAGCTCTTTCTAAATCTTTC
92534 A G TGATCCCAGCCCGATTGTCTGATTGTTCACATAGCTTTGATTCTCTCGTTATCTATGGACTCCTGTGTTCTCAATCTCAAAAGCGGATCCCTCACTTTCA[A/G]TGATGTTAGCAGGTTTTGGTACGATTCTAAACGGGTTTCGGAGTTTAAGGTCCCAAAATTCGTACATGGATGTCGGCCTTTAGTGGTGA
92534 T C GGTACGATTCTAAACGGGTTTCGGAGTTTAAGGTCCCAAAATTCGTACATGGATGTCGGCCTTTAGTGGTGACAGCGGCTGCTGGGAAGAAGAAGAATCA[T/C]GATGGTCATTCCAATTCAGGAAACGATGGAGAAAGTTCAAAGTTTGACGACTCAACTCATCATATTTCACCCGTCAACTGGAGAGA
92534 G A TCGTACATGGATGTCGGCCTTTAGTGGTGACAGCGGCTGCTGGGAAGAAGAAGAATCATGATGGTCATTCCAATTCAGGAAACGATGGAGAAAGTTCAAA[G/A]TTTGACGACTCAACTCATCATATTTCACCCGTCAACTGGAGAGATTTCAGAGCAGAACTTGTGCGCGATGAGCCGCTCAATTCATC
92534 C T GTGCGCGATGAGCCGCTCAATTCATCAGTCACTCCCAAATCACCACTAGGTCCAAAATGGGCACACCCACTATCCGAAATCGAATCGGGCTGCATATTGG[C/T]GGCAACAGAGAAGCTGGACGGTGTCCGCAACTTCGAGAGAAGCGTCGTCCTCCTCCTACGGTTAGGCACCCGTGACCCACGAGAA
92536 CT C AAGGCAGAGAGGTCAACCTCATAGTGGCGTGCGCGTTTGTAGTCTACGTTGCGCATGCCAACCGCGATGTAGGGCTTTCGGGCCGTGCATACTAGCCCGT[CT/C]TTTTTTGGGGTTGCGGGCCTTGAGGCGAGCGACGACCTTTTGCACATTTTGGTCGTGTTCGAGGTTGCGCTGCTTGAAGGATTTT
92536 G T CGCGTTTGTAGTCTACGTTGCGCATGCCAACCGCGATGTAGGGCTTTCGGGCCGTGCATACTAGCCCGTCTTTTTTGGGGTTGCGGGCCTTGAGGCGAGC[G/T]ACGACCTTTTGCACATTTTGGTCGTGTTCGAGGTTGCGCTGCTTGAAGGATTTTGATTCGGAGTAGAGGTCACCGAGGTACGTGAG
92536 G A GCATGCCAACCGCGATGTAGGGCTTTCGGGCCGTGCATACTAGCCCGTCTTTTTTGGGGTTGCGGGCCTTGAGGCGAGCGACGACCTTTTGCACATTTTG[G/A]TCGTGTTCGAGGTTGCGCTGCTTGAAGGATTTTGATTCGGAGTAGAGGTCACCGAGGTACGTGAGGAAGTAGAGTGTGAACGAG
92536 C T AGGGCTTTCGGGCCGTGCATACTAGCCCGTCTTTTTTGGGGTTGCGGGCCTTGAGGCGAGCGACGACCTTTTGCACATTTTGGTCGTGTTCGAGGTTGCG[C/T]TGCTTGAAGGATTTTGATTCGGAGTAGAGGTCACCGAGGTACGTGAGGAAGTAGAGTGTGAACGAGATGGGGAGGACGAGGAAG
92536 G T CGTCTTTTTTGGGGTTGCGGGCCTTGAGGCGAGCGACGACCTTTTGCACATTTTGGTCGTGTTCGAGGTTGCGCTGCTTGAAGGATTTTGATTCGGAGTA[G/T]AGGTCACCGAGGTACGTGAGGAAGTAGAGTGTGAACGAGATGGGGAGGACGAGGAAGATGACTATGATCCATCGGAAGTTTATC
92536 A G TTTTGGGGTTGCGGGCCTTGAGGCGAGCGACGACCTTTTGCACATTTTGGTCGTGTTCGAGGTTGCGCTGCTTGAAGGATTTTGATTCGGAGTAGAGGTC[A/G]CCGAGGTACGTGAGGAAGTAGAGTGTGAACGAGATGGGGAGGACGAGGAAGATGACTATGATCCATCGGAAGTTTATCAGGTA
92536 C T ATTTTGATTCGGAGTAGAGGTCACCGAGGTACGTGAGGAAGTAGAGTGTGAACGAGATGGGGAGGACGAGGAAGATGACTATGATCCATCGGAAGTTTAT[C/T]AGGTAGTCTATCCATACTTTCTCTTTTGGGGGCCGTGGAAGTACCAGTATTTCTGACATGGTGAACTTTGGCTCTTAGGAGCTCA
92536 T C AGAGTGTGAACGAGATGGGGAGGACGAGGAAGATGACTATGATCCATCGGAAGTTTATCAGGTAGTCTATCCATACTTTCTCTTTTGGGGGCCGTGGAAG[T/C]ACCAGTATTTCTGACATGGTGAACTTTGGCTCTTAGGAGCTCAGCTTACTGTTCTTCACACCCCACAACAATCCAGTAGGCCAACAG
92540 T C CATTTCAACAATTCCACCTAGCAAGATGAACAGAGGAGGAAGCAGTGGAGGGGGTCAGAGTTCCTTAGGCTACTTATTTGGTTCTGACGAAGCTCCAAAA[T/C]CTGTTGCAGCTGAGAAACCTGCTGAGAATTCTGCTGCTCCTCCCCCTGTTGAGAAGCTCAAAGAAATTCCCGCAGGCATTCAAGGG
92540 T C GCTACTTATTTGGTTCTGACGAAGCTCCAAAATCTGTTGCAGCTGAGAAACCTGCTGAGAATTCTGCTGCTCCTCCCCCTGTTGAGAAGCTCAAAGAAAT[T/C]CCCGCAGGCATTCAAGGGACAGCTGGAAACAACTATTTTCGAGCCGATGGGCAGAACACTGGAAATTTTATCACTGATCGACCATCA
92544 G A AATGGCGCTTGATGATCTAAATGGAATAACTGGAGAGAACGTTGGAAAGCTGCCAGAGTATCTAGAAGATGCAATGAAAGCTGCATATAACCGCTACATG[G/A]CTTACCTTGAGTCATTTGGTCCGGACGAGGCTTATTTGAGGAAGAAGGTGGAAAGCGAACTCGGAACAAAGATGATACATTTGAA
92548 G A AAGATATTTTGGGGGCAGTCGGAATGGGCGAGGATGGAGTGGACAGCGGCGACCGTGCCACGTAGGTAGGTTTCGTCGAGGGTTATGGCTACGTGGATCA[G/A]GTTAGGGTTGCAGACAATTGAGGGGTGATGGCGTTCGATTTGAATGCAATGGTCGGAGTTGAGGAAATGAGGCGCTTGCTGG
92552 T A GTGCAGTGGTTGTGGGAAGCGACCTCCGCTGATTTAAAATGTTATAAACATGCTCGAATATTGGGCGAACAATGAACATGCATTGCTATTAATGGCTCTG[T/A]TGGATTAATGGCAACAGCAACATCGGTCATCCATCCTAATTTACGAGTGGTTTCGTTCCCTATATCACATGCCAGTTGCCGTAGAAG
92590 A G CCGAGAGTTTCATTATCTACCAAGTAGCTGAGGAGAAGACGTGCATTGTCTCGAGCTTGGTGACCCACTGTTGGGGTTCTCGAGCAACCTAG[A/G]TATGTTGTTGTGGGTCTGCGTAGGTGCGATACTTGGTGTACGATCGTCTTAGTCCTTTGGTTGTCATCTTGAAGGTGTCGAATAGTTGGTTGTGT
92590 T C TGTTGGGGTTCTCGAGCAACCTAGATATGTTGTTGTGGGTCTGCGTAGGTGCGATACTTGGTGTACGATCGTCTTAGTCCTTTGGTTGTCATCTTGAAGG[T/C]GTCGAATAGTTGGTTGTGTGTTTAGTTTTGGGTGGAAGGTAGTTATGTTGTGGCGAGCATGTGTATTCTTTAGGAGTTTGGAATGTG
92590 G GGA TTTGGTTGTCATCTTGAAGGTGTCGAATAGTTGGTTGTGTGTTTAGTTTTGGGTGGAAGGTAGTTATGTTGTGGCGAGCATGTGTATTCTTTAGGAGTTT[G/GGA]GAATGTGATATGCTCCAAGTCGAGCTGTTGTTGTTTGGTCGTGGTTCCGTTGAGGTATGTGCGGTTCGGAATCTTTCTTTCTATTG
92590 T C CGAGCATGTGTATTCTTTAGGAGTTTGGAATGTGATATGCTCCAAGTCGAGCTGTTGTTGTTTGGTCGTGGTTCCGTTGAGGTATGTGCGGTTCGGAATC[T/C]TTCTTTCTATTGGTAATTGTAGCCTCTACACAGCTACCTTCTATTTATTCTCCATTCAAATCTGCTGCTTGTATGCTCTTGGATGTTATA
92590 T C TTTCTTTCTATTGGTAATTGTAGCCTCTACACAGCTACCTTCTATTTATTCTCCATTCAAATCTGCTGCTTGTATGCTCTTGGATGTTATAATTGTTGTA[T/C]GGTGACAGTGCAATGTTTCTTAAATGATGTACGCTTTAGATTATTTTCTAGGCTTTTCTCTGTTCTCATGTGACTGGCCAGCCCCTACGTGG
92608 C A ACTGTTGGCCTACTGGCATGATCGATTAAGCGGACCAATTATACCAGCTTAAGCAGGAAAAAATCGCGAAATAAAC[C/A]AAAGGAAAACCCCAAATCGCAATGCAAAATAACTAGGGTTTGACCTGTCGGTTAACTGTCGTAAGTGCCCTTATCATGTCTAACAATAGACCACAAAGCG
92608 G A TAAGCGGACCAATTATACCAGCTTAAGCAGGAAAAAATCGCGAAATAAACCAAAGGAAAACCCCAAATCGCAATGCAAAATAACTAGGGTTTGACCTGTC[G/A]GTTAACTGTCGTAAGTGCCCTTATCATGTCTAACAATAGACCACAAAGCGACATGCAATTAACCGTCTCCGATCCTTCGCTGACCAA
92608 A C GGTTTGACCTGTCGGTTAACTGTCGTAAGTGCCCTTATCATGTCTAACAATAGACCACAAAGCGACATGCAATTAACCGTCTCCGATCCTTCGCTGACCA[A/C]CAGCACGTCTTCCTCCTCCATGGTTCCGGCGGGGTCGGTGAAAGAAAGCAACGCACTCGTGGAGTACACGAAAACGAAGACGGTTA
92608 G A CCTGTCGGTTAACTGTCGTAAGTGCCCTTATCATGTCTAACAATAGACCACAAAGCGACATGCAATTAACCGTCTCCGATCCTTCGCTGACCAACAGCAC[G/A]TCTTCCTCCTCCATGGTTCCGGCGGGGTCGGTGAAAGAAAGCAACGCACTCGTGGAGTACACGAAAACGAAGACGGTTAAGTTAAG
92608 G T CTTATCATGTCTAACAATAGACCACAAAGCGACATGCAATTAACCGTCTCCGATCCTTCGCTGACCAACAGCACGTCTTCCTCCTCCATGGTTCCGGCGG[G/T]GTCGGTGAAAGAAAGCAACGCACTCGTGGAGTACACGAAAACGAAGACGGTTAAGTTAAGAGAAGACGAAGAGGATCTTGAAGTG
92608 G A CCGATCCTTCGCTGACCAACAGCACGTCTTCCTCCTCCATGGTTCCGGCGGGGTCGGTGAAAGAAAGCAACGCACTCGTGGAGTACACGAAAACGAAGAC[G/A]GTTAAGTTAAGAGAAGACGAAGAGGATCTTGAAGTGAAGCTTCGAAGAATCATCGAGAATGTTCCAGTTAAAGTTAGCAATACTT
92640 A AC TCCCTTCATACAAGCGAGCCCCCCTTTTTTCCACTTCCGTTCATTTTGCCCTCCGCGTTTTGGATTCCAACTGCTAACGGTTTCCAGTACGCCAC[A/AC]CCCCCATGCCTCGCTCAAGTTCACGCAACCGCTTCCCGAGCTAATCTCCAAACTCACACACACCTCGACATTCACCCATCTTCGCTGGTGCTCCC
92648 C T TCCAACATCTAGGGTGCCTTGATAATTCGGCATATTTCGTTTGCTTTTCAATCGATCGATTAAACCAAAAAACATAAAATTATTTAAAACTTACCTTCAT[C/T]TCTGCTTCCGTTCTCGTCCGTTGATTTAATCGACGTTTTTGAGGCGCTTCTAACTTCTATGATGAAAAGACAAATGCTGGATGATTGAAAG
92662 G T ATCATAAAAAATGGCATTCACAACAAAAGCAAGCTGACATTATCCACTGCTCTCAGTGAGACCTGGCCGGTGAAGGAGAGAAGGACCTCGATGCACCACT[G/T]CGACTATGAGCGTAACTCTCCCTCGAGCGCCTCGTATCCCCACCTCCAAAAGAGGAACCTGGGCTGCCTGAATAGGAACCGCTTCT
92662 C T CTGACATTATCCACTGCTCTCAGTGAGACCTGGCCGGTGAAGGAGAGAAGGACCTCGATGCACCACTGCGACTATGAGCGTAACTCTCCCTCGAGCGCCT[C/T]GTATCCCCACCTCCAAAAGAGGAACCTGGGCTGCCTGAATAGGAACCGCTTCTCCTTGAAGGGCTGTAGTAGCTCAAGTAGCTGCT
92662 C T GGTAGGAGAGTAACTCCGTCTTGCTGACCTAGAGTCAAGAGAGCAGGATCTGCGGTACTGCCTTCTTGGTGGCGTCCTTGATCTGTAGCTGCGACGGTAG[C/T]CAGGAGAGTGGGATTGGGATCTATGCCTTCTGTAGTAATACGAGTCCGATCTTGATCTGGATCTATCCCTACGGTAGTATGGAGAG
92662 A G ATCTATGCCTTCTGTAGTAATACGAGTCCGATCTTGATCTGGATCTATCCCTACGGTAGTATGGAGAGTATGACCTCGACCTGTGCCTGCGGTAATAGGG[A/G]GAGTACGACCTCGACCTATGCCTGCGGTAGTAGGAAGAGTATGACCTGGATCGGGATCTGTGCCTGCGGTAGTAGGGGGAGTACG
92678 T C CTACTTACACTGGTTGCGCAAGGGGATTTCAGCGAACTGCAACGAACTGCAATGCACGCGCTCCGCATCCGGGATCGAGTTTTAATCGCCAAAACCAAGT[T/C]TCATCGTAATTCTGATTTATTGCGAGTAGAAGAAACTGAACAAGAAAGGCATGTCGGATTATGAGAAGCAAAGATTATTAAGGATA
92678 A G GATCGAGTTTTAATCGCCAAAACCAAGTTTCATCGTAATTCTGATTTATTGCGAGTAGAAGAAACTGAACAAGAAAGGCATGTCGGATTATGAGAAGCAA[A/G]GATTATTAAGGATACGGGAGAACAAAGAAAGACTGGAAGCATTAGGTCTTCCTAGTCTCTATTCTGCACTTAGCGAGGCTTGTTCT
92678 GA G ATTATGATAATAACGATGATAATGACGATGAAGAATTTGTTGAGGATTCTGCTACTTTTGGACAGAAGGGAAAGAAGAGCATATCAAATGCTTCGTACAA[GA/G]AAAAAATGTCCAAATAAAGGAAGTTTGGAGGATTCTAACCAGTATGACGATGATTTGGCCTTGCAACAGGCAGTAGCTTTATCTC
92690 A G GAAGTGGATTGTATGGTGAAGGTGCGTCCGAACCGTATAAATCCCACTGACCAGTTGTGTTGCCTATATCCTCCAAATCGAAGTATACGCTCTTATCACC[A/G]TATTTAGCAACCACAGCTCCAGCAGACCTGATGTTAGCACGAGCTGCAACTCGACTGCGAACAATGAGTTTAGTGCCGTACAAAGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
92690 G A CGAAGTATACGCTCTTATCACCATATTTAGCAACCACAGCTCCAGCAGACCTGATGTTAGCACGAGCTGCAACTCGACTGCGAACAATGAGTTTAGTGCC[G/A]TACAAAGAGCTGCCACCAAGGCCTTTTACAGTAGTAACAGGCTGTGCAATAGCCATTGTAGTTAGAGAAGCCATTGATGCCAACTAC
92690 C T CAGCAGACCTGATGTTAGCACGAGCTGCAACTCGACTGCGAACAATGAGTTTAGTGCCGTACAAAGAGCTGCCACCAAGGCCTTTTACAGTAGTAACAGG[C/T]TGTGCAATAGCCATTGTAGTTAGAGAAGCCATTGATGCCAACTACTGCTTTCTCCAGTAGGCCAACAGTG
92734 G C TCATTCATGGAAAAGTTTACGATGTGACCACCTTTTTAGAGGATCATCCGGGAGGCGATGAAGTTCTCCTCCAAGCTTCAGCTAATGGAGACGCAACCGA[G/C]TCGTTCGAGGATGTGGGACACAGTTCAACTGCAACTGCCATGATGCAAGGTTACTTCATTGGGTTCCTGGAGGGATACTCTGAAGA
92734 A G GTCGTTCGAGGATGTGGGACACAGTTCAACTGCAACTGCCATGATGCAAGGTTACTTCATTGGGTTCCTGGAGGGATACTCTGAAGAAAAGCCTTCTTCC[A/G]ATGCCAGCAAAGGAAGTAAAACCATTGACAACCTTTTACAGAAACAGAAGCAAGAATCGACTTCTAGCTACTCGGATCTCATTCTGC
92734 C A AACTGCCATGATGCAAGGTTACTTCATTGGGTTCCTGGAGGGATACTCTGAAGAAAAGCCTTCTTCCAATGCCAGCAAAGGAAGTAAAACCATTGACAAC[C/A]TTTTACAGAAACAGAAGCAAGAATCGACTTCTAGCTACTCGGATCTCATTCTGCCTTTGTTCATTCTCGCCATTGCATTTGGTGCTTG
92734 G A AAAAGCCTTCTTCCAATGCCAGCAAAGGAAGTAAAACCATTGACAACCTTTTACAGAAACAGAAGCAAGAATCGACTTCTAGCTACTCGGATCTCATTCT[G/A]CCTTTGTTCATTCTCGCCATTGCATTTGGTGCTTGGTACTACCTCACCTATATCAATGTCAAGGCTTGAACTGTTTGTTTCATTTTTACA
92734 G C TTCTCGCCATTGCATTTGGTGCTTGGTACTACCTCACCTATATCAATGTCAAGGCTTGAACTGTTTGTTTCATTTTTACAGTTATCCGAATAAGTTGCTT[G/C]TGTGTTATTGTTGTTATCTGAATTGGTCTATTTATTTTATATGGGTGTGAAATGAATGTTGCTTTATATTA
92734 T C ATTGCATTTGGTGCTTGGTACTACCTCACCTATATCAATGTCAAGGCTTGAACTGTTTGTTTCATTTTTACAGTTATCCGAATAAGTTGCTTGTGTGTTA[T/C]TGTTGTTATCTGAATTGGTCTATTTATTTTATATGGGTGTGAAATGAATGTTGCTTTATATTA
92738 T G GCAGGTTCTCCTTTGTTGATTTTGGTTTCGTCTTTCTTAGAACTTCTGCTTATTTTGTTGATGTAGTGATCGACCCTTAGTGTAATTGGATTAATTTTTT[T/G]GGCACCCTTTGTTCGTATGGTCGGATCGCTTGTTTTGCTAGAATGCACAGAATCTTTATTTGATATATATCTTTGATTTTGA
92740 G C ATGTTATATCTATCTTCTGTTGAAATGGCGGCGTGACAGTTGTTTAGGCACTACCTTGTTCTCCTTCTGTTATGTAGCTTTTGAAATATTTCTTTAAGCA[G/C]AATCATCGTGTTTGTATATCTTTGATGAGCTGTACCTGCATTTTCACTCCTAATATTTTATAGTGGTTTCTCATGTAAAAAAAAAAAAAAAA
92742 A G CTCAAGTTTTGTCACAAGAGGAAAGGAAGCCAGAGAGGAAGCACTACAGAGGAGTGCGGCAAAGGCCTTGGGGCAAATGGGCATCTGAGATCCGCGACCC[A/G]AAGAAAGCTGCCCGTGTCTGGCTAGGCACATTCAGCACTGCGGAGGACGCCGCCATGGCCTACGATAGGGCTGCCCTAAAGT
92742 A C CTCAACTTTCCAGATAAAGCTCAACAGTACTACAACATCATAAATGACAATACCGCTGCTTCTACACCAAATACTGCAACTGCAAGACATGTAGTTGAGC[A/C]TGTGAGTCAGGCTCAGAGTTCTAGTTCAACGTATCCAGACTTGTTCCAGTATGCTAAGATTCTTCAAAGCGCAGGGGATGATCAGGAT
92746 T C TCGAAATTTCAGGTTTGATTAGATCTTCTACTGAAGTTCAGATTTGCCAGTCGACCAACCCGTCTACCTCTTTGACAAGAACATCAGCGCTTTTGATTAG[T/C]TAATAAATATCATTATTTGTGCATTAAAAATGTTTGTGGATATTACTGAAAAAATTGCACTATAGTTTTTGTGCTTGCAGTTAAGGTTCCG
92746 G A TTTGTGCTTGCAGTTAAGGTTCCGGTGAATTGGCGAAGCTGGAGTCTAAAATGCGACTTCAAATTTGTTGGGTGGTCGCATCTTACAGATCGAGTATGCT[G/A]CCAAAGCCGTCAACAACAGCAGAAGTGGGGAAGCTACAAGTTGTGCTTACTTCGAAGATGATGTTGCCT
92758 T A TCTCGATCTTCAGCCCCGAAACCCTAAAACCCAAAGCAACTGAAGTGCTATTCCTATCCTTCTCCAAACATTTGGAGAAGTACCAATCTTCATCATGCGG[T/A]CCCCAAGTGCGAGCTCCAACCTTGAAATCGATTACGGAAGGATTAACCAGGCCGTAAGTGAGGTCCTCAAGGACGATGTGAGGTAGA
92764 C G ACTACATGCCTTCATCAATTATAACAAACTCATCAATGCTTATACATACACACAGAGACTCTCAAACCTAATCAATCTTCTTAACAGGTCTGGCCTCGAA[C/G]CCACCTCCATCTCTCTTCTCAAGGGAGTAATCCATATGGGTTCCAAATACCTTATCCCAAGTCACAAAGAAAGGCTGCGAGTAATTATAC
92764 A G AATCCATATGGGTTCCAAATACCTTATCCCAAGTCACAAAGAAAGGCTGCGAGTAATTATACTTGTTTCCATACAGCTGATGATGAATATCATGGTAGGC[A/G]CAGTTGTTCCTGAAGAACACATGCAGCAGATTGCCAGGAAGCCACAGTCCACAGTGGTCATCCACAGTTTTGATGGTGGCGAAGGA
92764 G A ACAGCTGATGATGAATATCATGGTAGGCACAGTTGTTCCTGAAGAACACATGCAGCAGATTGCCAGGAAGCCACAGTCCACAGTGGTCATCCACAGTTTT[G/A]ATGGTGGCGAAGGAGAAGAAGAAAACAGCGGTCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTATGGTGTC
92764 A G AGGCACAGTTGTTCCTGAAGAACACATGCAGCAGATTGCCAGGAAGCCACAGTCCACAGTGGTCATCCACAGTTTTGATGGTGGCGAAGGAGAAGAAGAA[A/G]ACAGCGGTCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTATGGTGTCTAGGATAAGCCCCTCGATAGGGTG
92764 G A AGTTGTTCCTGAAGAACACATGCAGCAGATTGCCAGGAAGCCACAGTCCACAGTGGTCATCCACAGTTTTGATGGTGGCGAAGGAGAAGAAGAAAACAGC[G/A]GTCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTATGGTGTCTAGGATAAGCCCCTCGATAGGGTGGTTGTA
92764 G A CACAGTGGTCATCCACAGTTTTGATGGTGGCGAAGGAGAAGAAGAAAACAGCGGTCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTAT[G/A]GTGTCTAGGATAAGCCCCTCGATAGGGTGGTTGTATAGGGCTCCATAGGCATACGGAACTATTAAGCTGTGGTGCTTGGAGTG
92764 C T TTTTGATGGTGGCGAAGGAGAAGAAGAAAACAGCGGTCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTATGGTGTCTAGGATAAGCCC[C/T]TCGATAGGGTGGTTGTATAGGGCTCCATAGGCATACGGAACTATTAAGCTGTGGTGCTTGGAGTGAATGTGCTTGAATAGAAA
92764 C T TCAGAGGGGTCATGTCAGCTGCAAGGAAGGATAGGGCACCCCCTATGGTGTCTAGGATAAGCCCCTCGATAGGGTGGTTGTATAGGGCTCCATAGGCATA[C/T]GGAACTATTAAGCTGTGGTGCTTGGAGTGAATGTGCTTGAATAGAAACTTGTTTATGTGCATGTATCTGTGCATGAAGT
92774 T C AGAACCTTGCAATAAGCAATATGCCAACTGAAGTAACAATCAGAGTGGAAGGGACCCCAAAGCGCAAATGTGACAAGAAAGAGAGATTATAACCAAGAGA[T/C]TGAGCTCTTCTTGCCTGTTCACAGACTATTAGGTTGGCCGCAGAGCCCAACAGCGACAAATTTCCAGCTACTGTGCTTACCCATGC
92774 A G TGCCAACTGAAGTAACAATCAGAGTGGAAGGGACCCCAAAGCGCAAATGTGACAAGAAAGAGAGATTATAACCAAGAGATTGAGCTCTTCTTGCCTGTTC[A/G]CAGACTATTAGGTTGGCCGCAGAGCCCAACAGCGACAAATTTCCAGCTACTGTGCTTACCCATGCTAATATGAGCCATGCTCTTTT
92778 G A AGAAAAGCTCTTCCAACTCGAAGATGTTGCCTTGCCTTCGATGGATCCTGCTTCCGCCTCAACTGCTTATTCGCACCGCGGATCATTAGAGGTCGACTCC[G/A]TAGTTCAACCAATCGCTGACCGGATTCACTTTTCCATGATTGATCCATATCTGACGTCGTCGCTTACTGGAGAACGTTGGCTCTCTGCT
92778 C T GCTCTTCCAACTCGAAGATGTTGCCTTGCCTTCGATGGATCCTGCTTCCGCCTCAACTGCTTATTCGCACCGCGGATCATTAGAGGTCGACTCCGTAGTT[C/T]AACCAATCGCTGACCGGATTCACTTTTCCATGATTGATCCATATCTGACGTCGTCGCTTACTGGAGAACGTTGGCTCTCTGCTAGATCT
92778 T A GCCTTCGATGGATCCTGCTTCCGCCTCAACTGCTTATTCGCACCGCGGATCATTAGAGGTCGACTCCGTAGTTCAACCAATCGCTGACCGGATTCACTTT[T/A]CCATGATTGATCCATATCTGACGTCGTCGCTTACTGGAGAACGTTGGCTCTCTGCTAGATCTTCAGTGCAACCCCGAATCATAAAGCAT
92778 G C CAACTGCTTATTCGCACCGCGGATCATTAGAGGTCGACTCCGTAGTTCAACCAATCGCTGACCGGATTCACTTTTCCATGATTGATCCATATCTGACGTC[G/C]TCGCTTACTGGAGAACGTTGGCTCTCTGCTAGATCTTCAGTGCAACCCCGAATCATAAAGCATCATAGACTGTGACCTTCAACCGAGA
92778 T C CGGATCATTAGAGGTCGACTCCGTAGTTCAACCAATCGCTGACCGGATTCACTTTTCCATGATTGATCCATATCTGACGTCGTCGCTTACTGGAGAACGT[T/C]GGCTCTCTGCTAGATCTTCAGTGCAACCCCGAATCATAAAGCATCATAGACTGTGACCTTCAACCGAGACCTGAATCTTCACCGGATC
92778 C T CATTAGAGGTCGACTCCGTAGTTCAACCAATCGCTGACCGGATTCACTTTTCCATGATTGATCCATATCTGACGTCGTCGCTTACTGGAGAACGTTGGCT[C/T]TCTGCTAGATCTTCAGTGCAACCCCGAATCATAAAGCATCATAGACTGTGACCTTCAACCGAGACCTGAATCTTCACCGGATCCACTTC
92780 C T AATCAAGCAAGGCCCTGAACAAAGAACAATCCGATCTTGTCAAATCCAAGCCGCAGATCGTAGCCATAATCGAAGAGTACGAGAAACTGCGTCAGCCCCT[C/T]CAAGTAGCAGTGCAGGAAGAGTTATCGCAGAAAGACTCAGCTCTGGATGATTTGGTCAGGTTTCTGTATTTCGGGAATTTATTTGA
92780 C T AAGAGTACGAGAAACTGCGTCAGCCCCTCCAAGTAGCAGTGCAGGAAGAGTTATCGCAGAAAGACTCAGCTCTGGATGATTTGGTCAGGTTTCTGTATTT[C/T]GGGAATTTATTTGACGTTAAGAATCAGAATGAGTTCGCGAACGTGATGCTGACTAGGGCTCATGAGAGAGGTTGCTGTTTGACTTA
92784 T C TCAGCACAGTGGAACCGAATTCGCCTCAAGCAGTCGTGTCGCCGCAGGGACCGAAGCCGCCGTCAGGGCCAAAGGCCCTCTTGTTAGCGAGTAAGGCGAC[T/C]CCGGCATCGAAGCGTTCGTCGTTCCAGGCGGGCCATTCTCGAGCGGGGTCGTTGAAGGCGGAGGGAGAGATAAGGGGATGGG
92786 G A CGGCAACAACAGCACCGACAATAACGAGCAATACAATCCCACCAGCACCAATGCTCAACAAGAAATTCTTAAGGGAAGGAGACAAGCTCCTTTCAGCCGC[G/A]TCGGCCACCTCAGGCACCGCTAATGCTGCCACAATCCCTGCTGCATTCGCCAAGTACAAAATAGTGCTTTCTTTCTTTACCAGTGCA
92786 T C CAGCACCAATGCTCAACAAGAAATTCTTAAGGGAAGGAGACAAGCTCCTTTCAGCCGCGTCGGCCACCTCAGGCACCGCTAATGCTGCCACAATCCCTGC[T/C]GCATTCGCCAAGTACAAAATAGTGCTTTCTTTCTTTACCAGTGCATGATAATATTTGGAACGTTGATGACCGCTTGGGTTGGATGAT
92786 G A TCTTTCTTTACCAGTGCATGATAATATTTGGAACGTTGATGACCGCTTGGGTTGGATGATGAAGACGAAGCTGCTGGTGGTTTATACCTTGCAGGTGTCG[G/A]TGTCCGATAATGGGTTACGGTGGATGAACTTGACATGAAAATTGCATGAGTTGACGCCATTGTAATTTGTAGCTGTGTGCCGTTGTG
92786 A T ACCAGTGCATGATAATATTTGGAACGTTGATGACCGCTTGGGTTGGATGATGAAGACGAAGCTGCTGGTGGTTTATACCTTGCAGGTGTCGGTGTCCGAT[A/T]ATGGGTTACGGTGGATGAACTTGACATGAAAATTGCATGAGTTGACGCCATTGTAATTTGTAGCTGTGTGCCGTTGTGTTAGAGCC
92820 C T TGTCCATCTTTCTAGTCTAATAATACCATCCCTTTCTCTGCAGAAATAAAAAAACAGTACAAAATAATGGCTTCTTGCTCTCACAACATCTTCCTAACCT[C/T]CTTCTTCTTCTTGCTCGCCGTATCATCATCTTCGCTTGCTCAGTCTCCTGCTGCAGCGCCCGCTTCTTCACCCAACATCTCGCCGCCTACACC
92820 C T AACATCTTCCTAACCTCCTTCTTCTTCTTGCTCGCCGTATCATCATCTTCGCTTGCTCAGTCTCCTGCTGCAGCGCCCGCTTCTTCACCCAACATCTCGC[C/T]GCCTACACCCAAAATGGCACCTGCTTCGTCACCAGTTTCTTCACCGTCCGCCGCTCCGGTAAACTCGCCCTCTGCTCCGGTAAGCTCACCTC
92820 A G CTTCCTAACCTCCTTCTTCTTCTTGCTCGCCGTATCATCATCTTCGCTTGCTCAGTCTCCTGCTGCAGCGCCCGCTTCTTCACCCAACATCTCGCCGCCT[A/G]CACCCAAAATGGCACCTGCTTCGTCACCAGTTTCTTCACCGTCCGCCGCTCCGGTAAACTCGCCCTCTGCTCCGGTAAGCTCACCTCCTGC
92820 A T CAAAATGGCACCTGCTTCGTCACCAGTTTCTTCACCGTCCGCCGCTCCGGTAAACTCGCCCTCTGCTCCGGTAAGCTCACCTCCTGCTCATGTCTCGGCA[A/T]TGACGCCTTCTTCTATTGCCAACGCACCCGCTGAAGCGCCAACTTCCGCCGTCGGACCTATCATTGCTGGTGGCCGATTTGCTGTTATT
92820 T C CTTCGTCACCAGTTTCTTCACCGTCCGCCGCTCCGGTAAACTCGCCCTCTGCTCCGGTAAGCTCACCTCCTGCTCATGTCTCGGCAATGACGCCTTCTTC[T/C]ATTGCCAACGCACCCGCTGAAGCGCCAACTTCCGCCGTCGGACCTATCATTGCTGGTGGCCGATTTGCTGTTATTTCGTCCGCTCTTTTT
92820 C T CCCTCTGCTCCGGTAAGCTCACCTCCTGCTCATGTCTCGGCAATGACGCCTTCTTCTATTGCCAACGCACCCGCTGAAGCGCCAACTTCCGCCGTCGGAC[C/T]TATCATTGCTGGTGGCCGATTTGCTGTTATTTCGTCCGCTCTTTTTGCTGTCGTGATCTTACTGTAGAATCCTGTCGTGAATGCTTGTTA
92820 A G TCATGTCTCGGCAATGACGCCTTCTTCTATTGCCAACGCACCCGCTGAAGCGCCAACTTCCGCCGTCGGACCTATCATTGCTGGTGGCCGATTTGCTGTT[A/G]TTTCGTCCGCTCTTTTTGCTGTCGTGATCTTACTGTAGAATCCTGTCGTGAATGCTTGTTATCATCCTCTTTCTTCTCTTGTCTATAATAA
92820 A T ATTTGCTGTTATTTCGTCCGCTCTTTTTGCTGTCGTGATCTTACTGTAGAATCCTGTCGTGAATGCTTGTTATCATCCTCTTTCTTCTCTTGTCTATAAT[A/T]ATTATTATTATTTCTGTGGTGACGTACGTAGATTCCTTTAGATCTACGTCCGAGAAGCATTTGTTCATTCTTTGTGATTTATACGATTCCTT
92854 G A TTCCAAATGCGCATTCTAGAACGTTCGGGACTAGGCGAAGAGACCTGCATCCCACCAGCCAACCATTACCTGCCACCTAGACCAAACATGGAACGCGCAC[G/A]TGGCGAGGCTGAACTAGTCATCTTCTCCGCCATAGATGACTTGTTCAAGAAAAGCGGCCTGAAACCTAAAA
92864 CA C AACGTCCCATTTTCTAAACACCATGCATACTCCCTCCATGCGCTATTTCATGTCAAACGCCATCACACCCCATTCCTCTTCTCCCCCTCTAGGCAGTCAC[CA/C]AACCCTAATCTCACACGCGCCTCCTCCAAACAACCCCGACTTCGCCTATCATTTACTGCCGCTACAGGAACTCTGCGACTTTTCCAGCAC
92886 T C TTCAGAATGGTCGCTCCAAAACTGTGGGTTGTCCACCTACTTTCCATCATCAGCCTAATCGCCGCTGCCCGTCTACAATCCGCCGACGGAGCACGCCGCG[T/C]CGCTGCAGGCAAAACCCTTCGTTTTACGAGCGAATCGAGGTTCAAAATCGCGATATTCGCAGATTTGCATTACGGGGAGAATGCTTG
92890 G A AGTTGCTAATAGCAAAACTTTGATATTCAAAGTTCTACTCCATATTTGACATTCCTATCCGCTTCAAGCAAACGTTCTTCAAATCTGCATTAACGGTACT[G/A]AAATTAACAAATCCGCCACTCTTTTCCAATCTGCTCATGTAAATTGCTACCTCTTTTCTAATCATATCCTGCATCATCCCCAAAAACTCATC
92890 C T CATTAACGGTACTGAAATTAACAAATCCGCCACTCTTTTCCAATCTGCTCATGTAAATTGCTACCTCTTTTCTAATCATATCCTGCATCATCCCCAAAAA[C/T]TCATCATCATACGGCGGCTTCTGAGCAACTGCCTGTGGATTCGACATCGACGATGGACTGTTCGATCGATCTCTGGAAATGCTTCCGGGA
92890 A G TCCCCAAAAACTCATCATCATACGGCGGCTTCTGAGCAACTGCCTGTGGATTCGACATCGACGATGGACTGTTCGATCGATCTCTGGAAATGCTTCCGGG[A/G]GTGCTAAGAGTCAAGGCAGTGAAAGTATCCTCCACCTCAGTCTCCATCGGTGGTGATGGCACCTGTGGCTGAGTTGGAGGGTGCG
92892 C T TCTCTTAATACCTTCTCTTGCTCCACTAAATTGGGAGGAATCTCGTCGTAAACGTCCGTGAACAAGTCGCTTAATGGTGGCTTCTCCGCTCTCTCTGCAG[C/T]TTGAATTGCTTGAAGCACCTTTTTCCGAACACCAGCTCTTAATTCGGCTTCGGAGTCATGGTTCCACCACCCGTTTCTTTCTATCCACTTT
92906 T C CAAATATCCTCCTCTTCTTCCATTCATCCCCTTCACCCTCACACTCGTCTCCTTCGCTTAATCTCCTTACCGCCACTGCAGGGCCCCTACCAACAACTAC[T/C]TTATACACAATGCCACTTTTGCTCTTCCCTACAACATAAGCTGATGCTCGCAAGAGCTCTTCTAGTTCTAATGTGAATGAGTTTGATGATAA
92920 A G AAACAAACATTGCAGCCTCCATAAACATCATGCATTAACGAAGGCATTAACAGAACCTTGGGATTCGATGCAGAAAAAACCGAACCAACTCAACGGCGTC[A/G]GCAGTAAGTTCTATATGTTCACTAGTATTTTTGTTTAGAAATGGCAGTTCTAACTAAGAAGTGATAAAAATTCTTTACCAGCCTGTGG
92920 T C CATAAACATCATGCATTAACGAAGGCATTAACAGAACCTTGGGATTCGATGCAGAAAAAACCGAACCAACTCAACGGCGTCAGCAGTAAGTTCTATATGT[T/C]CACTAGTATTTTTGTTTAGAAATGGCAGTTCTAACTAAGAAGTGATAAAAATTCTTTACCAGCCTGTGGCTTTAGGGGGAGCAGGCG
92920 T C TAACGAAGGCATTAACAGAACCTTGGGATTCGATGCAGAAAAAACCGAACCAACTCAACGGCGTCAGCAGTAAGTTCTATATGTTCACTAGTATTTTTGT[T/C]TAGAAATGGCAGTTCTAACTAAGAAGTGATAAAAATTCTTTACCAGCCTGTGGCTTTAGGGGGAGCAGGCGCGGCCGTTTCATCCCA
92920 C T CCCCAGTAGCAGCTGCAGGAACAGGAGCTGGAACTGGTACATCATTCCAATCTGCACCACCACCCCACTGATCTGCTGCTCCCATCCCTTGGTAATCTGT[C/T]ACCGCACCGTAATCAGGAGCAGGCAACACTGCCTCAGCTTCTGCATTTTCCTTTGCTTCATCTGGGTCCCTATAGAAAAACAGATCGA
92920 A G CTGCAGGAACAGGAGCTGGAACTGGTACATCATTCCAATCTGCACCACCACCCCACTGATCTGCTGCTCCCATCCCTTGGTAATCTGTCACCGCACCGTA[A/G]TCAGGAGCAGGCAACACTGCCTCAGCTTCTGCATTTTCCTTTGCTTCATCTGGGTCCCTATAGAAAAACAGATCGACCATCACATCCCA
92928 GA G ACCCCCGGTCTTTACGATGCATGAATCCTCCCTCTTCAGCGACTACGGCTTCGACTCTCAGCTCGACTACTTTCAGGGCAAAGGAGCAACAGGCAAGCAA[GA/G]AAACAAAACGCAGTGACTCTACTCGATTCAAGCTTTCCAAACTGATATCGAAAGACATTGATCGACTGAAGTGTAACAAAAAGAGG
92928 T C TGATATCGAAAGACATTGATCGACTGAAGTGTAACAAAAAGAGGAAATGGTGGGAAAACGCTCTTGGATTCTTGAAAAGAGCCAAGGAAGATGCAGGAAT[T/C]GGTAAAGTTTCGGAATCTCAGGGTACTTTTGTAATTACGGACCAACGGCGAGCGCACCGGTTTATGCGACGGAATCTCATGCGC
92928 G GT CTGAAGTGTAACAAAAAGAGGAAATGGTGGGAAAACGCTCTTGGATTCTTGAAAAGAGCCAAGGAAGATGCAGGAATTGGTAAAGTTTCGGAATCTCAGG[G/GT]TACTTTTGTAATTACGGACCAACGGCGAGCGCACCGGTTTATGCGACGGAATCTCATGCGCGGAGGAGCACAATGTGCAGGA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
92948 TA T TATCCTGGTGATATACTTGTATTTCTTACTGGACAAGAAGAGATTGAATCTGTTGAAAGATTGGTAAATGAGCATGCTCGCCATCTGCCAGATGAAAAAC[TA/T]AAAAATACTAACCATCCCTATATACTCATCTCTTCCGTCTGAGAAACAAATGAAGGTTTTTAAACCGGCACCTTCTGGTACTCGCAAG
92958 C T AAAATTCATGGGGTAAAAGTTGGGGAATGAATGGCTATATGTACATGCTACGCAATAGTGGGAACCCTCAAGGTGTATGTGGCATAAATATGCTAGCTTC[C/T]TATCCTATAAAGACGAGCCCAAACCCTCCTTCCCCTGGCCCTGCACCTACAAAATGCAGTTTTCTAAGTTACTGTCCAGCTGGAAAC
92958 G A CCTATAAAGACGAGCCCAAACCCTCCTTCCCCTGGCCCTGCACCTACAAAATGCAGTTTTCTAAGTTACTGTCCAGCTGGAAACACGTGTTGTTGCAAGC[G/A]TCGTGTTTTGGGTTTCTGCTTTAGTTGGGGATGCTGCGAACTGAGTTCTGCAGTTTGCTGTAAAGATCATCAGTATTGCTGTCCCAGT
92958 G A GCGTCGTGTTTTGGGTTTCTGCTTTAGTTGGGGATGCTGCGAACTGAGTTCTGCAGTTTGCTGTAAAGATCATCAGTATTGCTGTCCCAGTGATCATCCT[G/A]TATGCGATAGCAGTGGAAGGAAGCAATGTCTAAAGGGTAATGGAAACTTCTCTAGAGTTGAAGGGATGGACAGGAAAAGCTCATTT
92962 C T CCGAGCTAAGCGGGTTCAGGTCGCGCGGAGAGTGGACACAGCTTCGATTTGCCATAAAGGCGGCGGCTTGCTGACTTTTGTCGGCGCTGGGTTCGATTGA[C/T]GGTGGCTGGCGAACAGAGAAAGGGACGGAAGGGGTTCGTGGTTGCGGGACCAAAGGCGGCTGCTTAGAGGCGAGAGGAGCG
92962 G T GAGGACGGTCGGAGGACGTTCAATGGAGGTGGATTGGGTTTGCTAGGCCTTGGAGGAGGGTTGACGTGGCCGAGGCGATGATGAAGGCGACTGGCGAACA[G/T]CGATGCTTGGACGATGGACTGATTTTCGGTGGACGCTAGGAATTGAAGGAGGAGCGGAGACTAATTTCTTGATTTGGGAACT
92964 C T GTAAAATTCAGTTGCTATATTTCTATCAAAGTATAACTGGTTCAGATGGACCATTGAACTCAAATATAACTGGTTTACAATGCACAGATTAAGCAGTAAC[C/T]CATAATTGCCCAGCAAAGGCAAAATAGCATTAGTCTCTTGCCACCAATATAAAGCTGTAGTGGAAGCACTTCAAGTTAGCCTCGTGTA
92964 G A TGCCTTGGTGTCCACTTCCAACGAGCGGTGATCACAAGAAGCATTGCTGTCTGAGAAAACAAACCTGAAATCAATCCCAGCCATAATCCCTTACTATACA[G/A]TTTTAGCTTGAATCCGAACAGTACAGCCAGAGGTGTGCCAATGATGTAAAATGCAAATAAATTTGTCCATGCTGCTAAATGTTGCCAT
92964 G A ATCACAAGAAGCATTGCTGTCTGAGAAAACAAACCTGAAATCAATCCCAGCCATAATCCCTTACTATACAGTTTTAGCTTGAATCCGAACAGTACAGCCA[G/A]AGGTGTGCCAATGATGTAAAATGCAAATAAATTTGTCCATGCTGCTAAATGTTGCCATCCACATCCTCTAGCCACCCCCGATAAAACT
92966 T C GCAACAACAATTTCTTGAAGACGCAATCTAAGGCTGATTTTCCACACTACGGTGTTGATTTTCCCCTCTCTAGAGCTACTGGGAGATTCAGCAATGGTTA[T/C]AATGGCGTCGATTTCTTAGCTAAGTATATGGGATTTCGAAGAAGCCCACCGCCTTTTCTTTCAGTTGCAAAGGAGATTAGCCACCAAA
92994 C T TTACCAATTCACTAATTAAGATAATCCCTGTTTAATCATAATAATTAATCCAACGTCCAACCTATAATCATAATAATATTTGACTTAACAAATATGAATG[C/T]GTTTAAATATACTGGACTGATAACATTACTTTAGGTTAGGCACAAAAACATCTTAACTGCAATATAATCTCCTCCATGTCGTTCCATTATCT
92994 T A AACGTCCAACCTATAATCATAATAATATTTGACTTAACAAATATGAATGCGTTTAAATATACTGGACTGATAACATTACTTTAGGTTAGGCACAAAAACA[T/A]CTTAACTGCAATATAATCTCCTCCATGTCGTTCCATTATCTCGCAACAACCCACGCACCACGAAGTTCAACTATGCCTGCACCTATTACCG
92994 C T AACATCTTAACTGCAATATAATCTCCTCCATGTCGTTCCATTATCTCGCAACAACCCACGCACCACGAAGTTCAACTATGCCTGCACCTATTACCGATGA[C/T]CGGAGCCCTATCGTGTTCCACCAGCCGACGCGGCCTAGTCCGTCGTGCCTTCGCCCCAAACCCCAACGAACTCAGCTCAGCCCTTCTCC
92994 T C ACTGCAATATAATCTCCTCCATGTCGTTCCATTATCTCGCAACAACCCACGCACCACGAAGTTCAACTATGCCTGCACCTATTACCGATGACCGGAGCCC[T/C]ATCGTGTTCCACCAGCCGACGCGGCCTAGTCCGTCGTGCCTTCGCCCCAAACCCCAACGAACTCAGCTCAGCCCTTCTCCAAGATTTTG
92994 C A TCAACTATGCCTGCACCTATTACCGATGACCGGAGCCCTATCGTGTTCCACCAGCCGACGCGGCCTAGTCCGTCGTGCCTTCGCCCCAAACCCCAACGAA[C/A]TCAGCTCAGCCCTTCTCCAAGATTTTGACTTCGAACACTGGACAGTCTAGCTAAGATTCTGGCCACCCTCGTACGTATTTTCTGATCAC
92994 A G ACTATGCCTGCACCTATTACCGATGACCGGAGCCCTATCGTGTTCCACCAGCCGACGCGGCCTAGTCCGTCGTGCCTTCGCCCCAAACCCCAACGAACTC[A/G]GCTCAGCCCTTCTCCAAGATTTTGACTTCGAACACTGGACAGTCTAGCTAAGATTCTGGCCACCCTCGTACGTATTTTCTGATCACCTC
92994 CT C CAAGATTTTGACTTCGAACACTGGACAGTCTAGCTAAGATTCTGGCCACCCTCGTACGTATTTTCTGATCACCTCCGTTGGTCTGAAGCATCTCATGGTG[CT/C]TTTTCGATATTATAGTTAAGGAGTTTGATGAATTGATGAATGAATTAGCAAATCGGTGGAGAAGAAGAGTAGGAGTTCGTGGCCATT
92994 A G TTCGAACACTGGACAGTCTAGCTAAGATTCTGGCCACCCTCGTACGTATTTTCTGATCACCTCCGTTGGTCTGAAGCATCTCATGGTGCTTTTCGATATT[A/G]TAGTTAAGGAGTTTGATGAATTGATGAATGAATTAGCAAATCGGTGGAGAAGAAGAGTAGGAGTTCGTGGCCATTGATTTCGTAGTG
92994 T C TCGAACACTGGACAGTCTAGCTAAGATTCTGGCCACCCTCGTACGTATTTTCTGATCACCTCCGTTGGTCTGAAGCATCTCATGGTGCTTTTCGATATTA[T/C]AGTTAAGGAGTTTGATGAATTGATGAATGAATTAGCAAATCGGTGGAGAAGAAGAGTAGGAGTTCGTGGCCATTGATTTCGTAGTGG
92994 T C CTGGCCACCCTCGTACGTATTTTCTGATCACCTCCGTTGGTCTGAAGCATCTCATGGTGCTTTTCGATATTATAGTTAAGGAGTTTGATGAATTGATGAA[T/C]GAATTAGCAAATCGGTGGAGAAGAAGAGTAGGAGTTCGTGGCCATTGATTTCGTAGTGGAGGCGCTGAACAATAATGGTTGACCACA
93000 C T TCTTCTCCTCCCTCATCGCCCAGGGCCTCAAGCTCGCAATCAACCTGATCAACAGCAAGGACGTGGATGAGGCTTTTAGGGTTCACATCAACAAGCGGGT[C/T]CTCAGATTGGGGATGCTCGGATCCGCCGTGGGATCCGTTATGGGCTGCTTGTTTCTGCTGCTGTCGATGGTGAATGTGATCCAGATC
93002 A G CTACAAAGACTCAATCTTTAAGCTGACGTGGACACATTTTAACACGAGCAGGAGCGTACTCCAGGAATCCAGTAGTGAAGAGCACCAACGTTGAAGTACC[A/G]ACTCTAACGGTTCTTTCGTATCTAATTCTAACCCCATATTTTTGAAATTTAGGTACGACCGGTGTACTGCACCACTTTGGCAATTTCA
93002 T C CTGCACCACTTTGGCAATTTCATGACCACTCTGCACTTCGAAATCGCACTGGGCCTTTGGTTTTGAACTTGTGCAAGGAAGTATCCTTTAGCATTCGTTG[T/C]TGCATTTCCATATACTGGTGAGCCTCCACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGG
93002 T C CCACTCTGCACTTCGAAATCGCACTGGGCCTTTGGTTTTGAACTTGTGCAAGGAAGTATCCTTTAGCATTCGTTGTTGCATTTCCATATACTGGTGAGCC[T/C]CCACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGGGCACATAGCCGGGTAGTCTACATG
93002 C T CACTCTGCACTTCGAAATCGCACTGGGCCTTTGGTTTTGAACTTGTGCAAGGAAGTATCCTTTAGCATTCGTTGTTGCATTTCCATATACTGGTGAGCCT[C/T]CACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGGGCACATAGCCGGGTAGTCTACATGA
93002 C T ACTCTGCACTTCGAAATCGCACTGGGCCTTTGGTTTTGAACTTGTGCAAGGAAGTATCCTTTAGCATTCGTTGTTGCATTTCCATATACTGGTGAGCCTC[C/T]ACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGGGCACATAGCCGGGTAGTCTACATGAC
93002 G A TTGTTGCATTTCCATATACTGGTGAGCCTCCACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGGGCACATA[G/A]CCGGGTAGTCTACATGACATACAATACACGACACCTTCTACAGCTGCACTCAGTTTAACCGGTGAAGGAGGCGGAGCCTTAACGGG
93002 G A TTGCATTTCCATATACTGGTGAGCCTCCACGCGTGTTGTTGCACATAACTGTTGCATTGGCACCAGAAAGTGGAGACGCATTCATAGCGGGCACATAGCC[G/A]GGTAGTCTACATGACATACAATACACGACACCTTCTACAGCTGCACTCAGTTTAACCGGTGAAGGAGGCGGAGCCTTAACGGGCGG
93022 TG T GTCGAGATCGGGAAAGTATTGTTGTAATTTCCGAAGTCCACGTCTTTGAAAGTGAAGAGCAAGCGAATGTAAGGGGAGGAAAGGACGCAGAGATTAGGGT[TG/T]GGGGTTAGGGTTTTGTGTCTGATGAGAGACGGCCTGTAAGAGGTTGTTGTCGGAGAGGAGGAAGAAACCAAAGAGGGTCGG
93028 G A CTTGTTGGATCGGGTTAGCAGGAGATAAGCAGATCCGGCTTCGCTTAGGTTCCGATATCTTCACTCTTGAGATTGCTTGAGCAAGTGCATCTACAAAGCC[G/A]TCGTCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCTTGTAACTCAATGAAAGTGCA
93028 G A GTTGGATCGGGTTAGCAGGAGATAAGCAGATCCGGCTTCGCTTAGGTTCCGATATCTTCACTCTTGAGATTGCTTGAGCAAGTGCATCTACAAAGCCGTC[G/A]TCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCTTGTAACTCAATGAAAGTGCAGC
93028 G T TAAGCAGATCCGGCTTCGCTTAGGTTCCGATATCTTCACTCTTGAGATTGCTTGAGCAAGTGCATCTACAAAGCCGTCGTCGTCGTCGCGGTCATCTGAA[G/T]TGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCTTGTAACTCAATGAAAGTGCAGCAAAATTTAATCTAAGAACTGCAG
93028 T C TCTTGAGATTGCTTGAGCAAGTGCATCTACAAAGCCGTCGTCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAG[T/C]GCTTGTAACTCAATGAAAGTGCAGCAAAATTTAATCTAAGAACTGCAGTTTTGTTCTGAGGTTTCGATTTGGCAATCAGTGCCTTTGG
93028 T C GAGATTGCTTGAGCAAGTGCATCTACAAAGCCGTCGTCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCT[T/C]GTAACTCAATGAAAGTGCAGCAAAATTTAATCTAAGAACTGCAGTTTTGTTCTGAGGTTTCGATTTGGCAATCAGTGCCTTTGGCTG
93028 G A AGATTGCTTGAGCAAGTGCATCTACAAAGCCGTCGTCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCTT[G/A]TAACTCAATGAAAGTGCAGCAAAATTTAATCTAAGAACTGCAGTTTTGTTCTGAGGTTTCGATTTGGCAATCAGTGCCTTTGGCTGG
93028 A T CGTCGTCGTCGCGGTCATCTGAAGTGCTACTCGAATTTGAACACGTGAATGTTGGTGATGAGTGCTTGTAACTCAATGAAAGTGCAGCAAAATTTAATCT[A/T]AGAACTGCAGTTTTGTTCTGAGGTTTCGATTTGGCAATCAGTGCCTTTGGCTGGCTTTCTGTGTATAATAGTATCCATGGATGTCTTA
93034 C A AGAGAGAAATCACACGACAGCCGAAGAAAAGAATTATGTAATAAAAAATGGTGTCGGGAGCGCAAAAGGGTAAAATGCACAGGCTGAAGAACGCTCCGCC[C/A]CGTCAATGGCCGATGCGACCGCGCACCCTCACCGTGGAGCAGTTCCGCGATCTCACTCGAAGGAGGGACCTGAAGCAAAATGA
93034 A C GCTCCGCCCCGTCAATGGCCGATGCGACCGCGCACCCTCACCGTGGAGCAGTTCCGCGATCTCACTCGAAGGAGGGACCTGAAGCAAAATGATAACCCTA[A/C]ATCTGGAGCGTCGAAGGAGGAGGGCAAGGGAGAGGGAGAATCAAAGGATCCAGAGGTGGTTGGTGCGGTTCTGGAGGAGAAG
93034 G A CGCACCCTCACCGTGGAGCAGTTCCGCGATCTCACTCGAAGGAGGGACCTGAAGCAAAATGATAACCCTAAATCTGGAGCGTCGAAGGAGGAGGGCAAGG[G/A]AGAGGGAGAATCAAAGGATCCAGAGGTGGTTGGTGCGGTTCTGGAGGAGAAGGGCAAGGATTCGGCTGCTGATTTAGATGAA
93034 A G TGGAGCAGTTCCGCGATCTCACTCGAAGGAGGGACCTGAAGCAAAATGATAACCCTAAATCTGGAGCGTCGAAGGAGGAGGGCAAGGGAGAGGGAGAATC[A/G]AAGGATCCAGAGGTGGTTGGTGCGGTTCTGGAGGAGAAGGGCAAGGATTCGGCTGCTGATTTAGATGAACGCCAAATTTCAA
93034 AG A TTTAGATGAACGCCAAATTTCAAATGCTGATGGAAAGATGGACGTTTCAGAAGTCAGTGGAGTTAAACAATCGGATATAAGAACAAATGATGGGAAGGGG[AG/A]GGTGGTCAGCACATGGACTGCTGAGAAGGAGCAGAGAAGATTAGAAGTAGAGAAGAAACTGGCTGCTGCCCAGGAGAGAAA
93038 A T TTTTTTTTTTTTTTTTCTTTGTTATAAAAACCTCATCACTTCCGCTCCACCACCCAACAAACAAACAG[A/T]AACAAACAAAAATCACAATCGATCCTACAATCCTCTTCCATGAAATCACAAGAAAAAGCACCCACGCACCTTCAGCAATCGAAAAGGCTCAACCGCCAGT
93056
AAGGTTTGGCTATGATTTG A TCAGATCTAGGAAGCCACTTCCTAGATCTCAGACACTGTAATTTTGAAGATCCAATGACCCTTAGATGTTTCTACTTTGAACCATGAAGGAGGCAGTATT[AAGGTTTGGCTATGATTTG/A]AGGTTTGGCTATGATTTGAGGAGCATTGGAATAACGTATCTGCACTACAGGACTTCATGTTCAGTTAAGG
93058 A G GTTCCAATTGGCGAGTGCTACAGCTATTGAGGAGGCTGGTGGGCCCAAGATTCCCATGAAATATGGAAGAGTAGATGTTTCTGCACCTGAGCAGTGTCCA[A/G]TAGAGGGGAAATTACCTGATGCTGGACCACCTTCTCCTGCAGAACATTTAAGAGAAGTATTTTACAGAATGGGACTTAACGATCAG
93058 A G ATGCTGGACCACCTTCTCCTGCAGAACATTTAAGAGAAGTATTTTACAGAATGGGACTTAACGATCAGGAGATAGTCGCATTATCTGGAGCGCATACACT[A/G]GGAAGGTCTAGACCAGAAAGAAGTGGATGGGGAAAACCAGAGACCAAGTATACAAAAGATGGCCCTGGAGCACCTGGTGGACAA
93058 T C CACCTTCTCCTGCAGAACATTTAAGAGAAGTATTTTACAGAATGGGACTTAACGATCAGGAGATAGTCGCATTATCTGGAGCGCATACACTAGGAAGGTC[T/C]AGACCAGAAAGAAGTGGATGGGGAAAACCAGAGACCAAGTATACAAAAGATGGCCCTGGAGCACCTGGTGGACAATCATGGACT
93058 A G CTGGAGCGCATACACTAGGAAGGTCTAGACCAGAAAGAAGTGGATGGGGAAAACCAGAGACCAAGTATACAAAAGATGGCCCTGGAGCACCTGGTGGACA[A/G]TCATGGACTGTTAAATGGCTGAAATTTGATAACAGCTATTTCAAGGATATCAAAGAGGCAAAAGACGAAGATCTACTAATTTTA
93070 A C CACACATAACAGCTTCAGCAGTTTTTCTATACATCTGAAGTCCCTGGCCTTCAGCATTTGAAGTTTCTTTGGAAGCAAAAAAATTTACTCTGGACAACAG[A/C]ACCTGGGTTCCAGCTCTTTTATCATCCCAACTAAACCAAGTCGGTCTTCCCCAATCGGCAAATTTTTGTCCATTTTGCACTGTCACGTAA
93076 T C ACAGTGACTTGGTTCTCATGAGACGTGTCGATTAGAAATATTGCGTACCAGCCGTGATGCAATGCTATAGCAGCGCCATTGAAGGATATGTTGTTCGTTA[T/C]GTTAGTTAAATCTTTCGAGTAATCCACTAGAGGGTCGACCAACCTCATCACCATCTCATCCTGGTTGTAGATCAGTAGAGTTCCATGT
93076 C CCTT TGCACTAATGATCTCGTACCCTCTCAAGTCCAAAAAGCATTCCACTTGGAATGTTTTGTTTAAAAATGGGCTGTAGTAGTGGAAAATGGGCCACTTTCCT[C/CCTT]CTTCTTCTTCTTTGCTTTTTACATGGATCAACAGGGGGCTTTTGCCTACCGGATAGAATGGCGGTTCTGCTTTTTCTATCTCTCTCCA
93080 T C TGCCAATCATATCCTTCAGTTTTGCAACTTCAGAAGCAACTTCTTCACGTATTTGCTTTGCTATTGATTTTCCATCAATAACTTTAGATGA[T/C]GCGTCAGTTGCCACTGCCACTGGAGAAACTGCAAACTTGTTCGAACTCGTCTTAAGTGATCCAAAGACTCTATCTTTACGAGTTAACGATTTAAGTGGG
93080 A C TTCCATCAATAACTTTAGATGATGCGTCAGTTGCCACTGCCACTGGAGAAACTGCAAACTTGTTCGAACTCGTCTTAAGTGATCCAAAGACTCTATCTTT[A/C]CGAGTTAACGATTTAAGTGGGAAACTAGTCGAGCCATTGAAAAGCGAATGGCCATCAAAAGCCTTGCTATTGGATTTCAATAAAAAAT
93088 A G TGCACAGACCGGATGAAATACATTAAATTTACGTCATTTCAAGCGCATACCTTCTCAAAAATCACAACTAATTGTACATTGGTCCTTTTTCTGTTCCTTT[A/G]ATAACCATAACACCTGAGGTCGAGATCCATGATTAAAGCAAAGACCTCATGAACAGTTGAAGGGGCTCAGATCTGAACAGAGGACGGC
GTTATGAAACAATGAAATGATTAGGGAAAAAGATGAAATGTATTAGGAAGCACAAAACTCCAC
93088 A ACACCTGAGGTCGAGATCCATGATTAAAGCAAAGACCTCATGAACAGTTGAAGGGGCTCAGATCTGAACAGAGGACGGCATAGATCTGAGTCTCGTTTGA[ACTAATAAAGTTGAGTTGTTATGAAACAATGAAATGATTAGGGAAAAAGATGAAATGTATTAGGAAGCACAAAACTCCAC/A]CTAATA
93090 AG A CTTCCAGAAGCTGAGATTTTAAATCAACACGGTCAACGCTTGGTCGAACAGATTTGTGTAATATAACAGCAACAGCGAACATTTGTGACTACCAGTGTTG[AG/A]GAACAGTTGATTGTTCTGTTAAGTTTACTATTGTGTTGAGAATATAATTATATGCGCGTTGCTCTATTTGCACATAAACTGTATTAGT
93090 C T CAGAAGCTGAGATTTTAAATCAACACGGTCAACGCTTGGTCGAACAGATTTGTGTAATATAACAGCAACAGCGAACATTTGTGACTACCAGTGTTGAGAA[C/T]AGTTGATTGTTCTGTTAAGTTTACTATTGTGTTGAGAATATAATTATATGCGCGTTGCTCTATTTGCACATAAACTGTATTAGTGT
93100 T C TCAGCTTAATGTACTTCTGTTCAACCTTGAGGATTTCCTCGCTAGCCTGCTCGTTGAGCCTGTCTATTTCATTCTGTACTTCATCTATCTTCTCTATAGC[T/C]TCCTGTAACTCTTTATCGGCATCAGGGCCGATCGACGCACGCTTCGCCTGCTTATTCGTAGTAGCCATGAAATCTGTATAAAATATACGAT
93100 T C AGCCTGTCTATTTCATTCTGTACTTCATCTATCTTCTCTATAGCTTCCTGTAACTCTTTATCGGCATCAGGGCCGATCGACGCACGCTTCGCCTGCTTAT[T/C]CGTAGTAGCCATGAAATCTGTATAAAATATACGATTCCGTCCAACTCAACGCGGACAGCCCGACGTATAGATGCTAATGGATTAGAACTA
93102 A G CACAGATGAAAAGACTCTGATGGCAAGGATCAACTCACTTTGCTGCCTTATACAGCAAGAAGAAGATGGCCAGGACAACACCAAACATGATGATGACAAC[A/G]CTGCTGATAGAGGAAATAATAATAGTAAAGAGGAAGACCCAGTTATGTTGATGAATTTGCCTAGGATTCAGTCGATGCCCAAGTT
93104 G T TGTCTTCAATAACATCAGAAACATATCATGTGATATGTCCAAATGATTAGATAGATTTAATATTTACATTTACATGAAAAAGTTTTGTAGAAGCTTGTCA[G/T]GCCCTGGACTCTTGGAAGTCCGAACCATCTACTTGTCATTTCCAGTTGTGCATGCAGGCCTTCGAGGTGGGAGTTCATGGTGCGGAGT
93104 G A AATAACATCAGAAACATATCATGTGATATGTCCAAATGATTAGATAGATTTAATATTTACATTTACATGAAAAAGTTTTGTAGAAGCTTGTCAGGCCCTG[G/A]ACTCTTGGAAGTCCGAACCATCTACTTGTCATTTCCAGTTGTGCATGCAGGCCTTCGAGGTGGGAGTTCATGGTGCGGAGTCCTCTGG
93104 C CT AAGCTACAGTCATCTGGCTTAAATTTGTACCTTGCTTGCCAAGAGCCCAATCTGCAGAGTCGAAGTATGCGCGCTCGTTGTCCTTTGAGATCAAAGGTTT[C/CT]TTTTTTGGCACAAGCCCACCATATTTTTTTGCCATAGATGCCTCTTGAGAAACATTATCTTCTCCATTGGCTCCTGTCATCCCTTATCTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
93110 G A CATAGATAAGACCATAAGGTATGGGACCGAATTGCCTTGAATCCCTGGATGCATATATATTGTCTCCTTGTACAAAAATATGTCCTTTTGGTACCTTAAC[G/A]GTTTGGACCTTCGTTCCAAGCGCAGGATTGTCCAGAAAACTAATGGAATCCCCCTCGAGTCCTGTCACCCTTTTCGCCACAATCTTCAA
93110 C T TGGACGACACATGCAGTTTTAACAATCAGAGCGGTGCGATTGACGACGTCAGAAGTTATTGCTCGCCATGGAATATGACGGATTCGGGAAGTAAAAGTTT[C/T]GAAGGCAGCTTTGGACATTGATAATTTGGTGAGTTCTTTTCCTGTGTTCAGCTTGCGGTTTTTTCTAAGT
93132 C CG GTTCTTTCATTTCACGAAGAACGCTTTGATGGATAAAGCTACTGGGTATTGATCGAATGATGGCCGTGGAATTTGTTGTTGGGCA[C/CG]TTTTTCAGAGCGGTGCATGCTTCCCATACCGAGCCGGAAAGCTGGGGAATAGCGGTCGATCTTTTGCTGCGGTTGGGTGAATCATAAACAGAGACAGCCT
93132 CA C GAGCGGTGCATGCTTCCCATACCGAGCCGGAAAGCTGGGGAATAGCGGTCGATCTTTTGCTGCGGTTGGGTGAATCATAAACAGAGACAGCCTCTGTTAA[CA/C]AAAGAAAAACTGCAATCAACCACTCGTTTGGCAGATGCACATATGTATTCATAAAGGGTGGGCCCAGCACCAACTGTACTCCCA
93132 A G AATCAACCACTCGTTTGGCAGATGCACATATGTATTCATAAAGGGTGGGCCCAGCACCAACTGTACTCCCATGACATATCAGAAGAAACCCATTGAGCAC[A/G]TTGAAATATGCATTCATGTTCTCTTCCAGATCTTGCATTTGTCGAACTTCCCCATTCCAAAGCATCCCAGCTATTGTGGCTTGTTTGGA
93132 C G ATATGTATTCATAAAGGGTGGGCCCAGCACCAACTGTACTCCCATGACATATCAGAAGAAACCCATTGAGCACATTGAAATATGCATTCATGTTCTCTTC[C/G]AGATCTTGCATTTGTCGAACTTCCCCATTCCAAAGCATCCCAGCTATTGTGGCTTGTTTGGAAACATCATCCCCCAATTTTATAACTTCG
93132 T C TAACTTCGCTCCAACTCACTTTATCGAAAGCTGAATCAGCTGGTTTGTCGAACATTTGAAAAGTTTCGTGAATGTCTTTGATGTGAGACTCGAGTGCTTT[T/C]CTTAAGTGACTTGTTTTGCCTCCTTTCTTCGCCATTTTACTTACTGCGTTTGCTCTTTTGAACAAACTGAATTAACAGCCAGTAGGCCAAC
93154 G A GATGGCTTTGATGCATCCACGTTTGCTCATAATAAGTGCCTTTGTGGTGCGCCCTTGTCTCCTTGCAAGTCTGTGATCACTGATATTTGAATATGTGCAC[G/A]GGGAGAGATCCGTTTGCGGTTTTAAGTATGCAATAATAAATAAAGATGATGTGGTCCTGTGGCCTGTTTCTGATATTGTTGCTTTGTAT
93156 T C TTACTGGACTCACTCCTGGACTTCATGGATTCCATCTTCATGAATTTGGTGATACTACCAATGGCTGCATATCAACAGGACCACATTTCAATCCCAATGG[T/C]TTGACACATGGTGCTCCTGAAGATGAAATCCGCCATGCGGGCGACCTGGGAAACATTGTTGCAAATGCCGATGGAGTGGCAGAGGCG
93156 T C GAGCATTTGTAGTTCACGAGCTAGCAGATGATCTTGGAAAAGGAGGACATGAACTCAGCCTCAGCACTGGGAATGCTGGAGGAAGGTTGGCTTGTGGTGT[T/C]GTTGGATTGACACCAGTGGCATAGTCTCGTGAATTGGAACTTGTGGATAAACCTGCTTTCTAAGTAAGGAAGTTTAAGTGGCAAG
93156 A T TGGAGGAAGGTTGGCTTGTGGTGTTGTTGGATTGACACCAGTGGCATAGTCTCGTGAATTGGAACTTGTGGATAAACCTGCTTTCTAAGTAAGGAAGTTT[A/T]AGTGGCAAGCTTTTCAATGTCTGGCAATCTTTCATGTGCTTGAGATATTTTGTAATGTATCATCTAAATTTCCTTGTATCATTTGGCCG
93156 G A TAAGTAAGGAAGTTTAAGTGGCAAGCTTTTCAATGTCTGGCAATCTTTCATGTGCTTGAGATATTTTGTAATGTATCATCTAAATTTCCTTGTATCATTT[G/A]GCCGATAACATCAGATTTTGGATCGTAATTCTTTTCGAGAATAAAGTTTGTTCCTGCTCAAAAAAAAAAAAAAAAGGC
93160 T C AGTAATAACGCAGAGACTAACCAACAAAACCAATATCCACACTGACACGCTAAAAGCAAGGTCGTAGAGACAGAAGAACACTCACCAGCACGTTGTACGA[T/C]GTAAGATCCACAACCAACACTGGGTCTGCCTTTCGGTATGTGCTCGAGTGACTGAAGCGGCCAGTAGCTAGCAGAAAGACAGATC
93160 AG A GAGAGAGAGGGAAGACGCGGGTCGTACTCACGGAGAAAAATAGAGCTTAGATCTGGTACGGGTAAAAAGCGATACTATGCCACCATGGACAAATATGGGT[AG/A]GGAGGCTAGTGACGAAGAGACGAGGGGGGAAGCAGTGAAATAATCTGAAGGTGTAAGGAGAAAAAATCATACGCGGGAGG
93164 CATGCAAGTG C AAATTATATATAAACGGGTCTTCAGATCTCTCTACACGCCAATACTTACTAATTATCTCAAGCTCAATTAAAAGAAATCACAACGTGCCATGACATG[CATGCAAGTG/C]ATGCAAGTGATGCAACACACCAGCCTTCAAATCATTTATTGGTAGCAGCTGCTTTCTTAACACTAGCCACAGCATTCTGAACT
93164 C T ATTCTGAACTTTCCCTTTAGTACGAGCCACATACTCGTCCTTCTTCTCATGTACAGTGATCTTCTTCTTCCCAGCCGGCTTCTCTGCCTGAGAGGCCGAG[C/T]GCACCTTCTCCGGCACAGGCATGGTCAGAGGCCGCACTTCTGCTTTCGGTGCGACAGGCACCGGAAGCACGACGTCCGTGTGTTCCTTT
93164 A G GGTCAGAGGCCGCACTTCTGCTTTCGGTGCGACAGGCACCGGAAGCACGACGTCCGTGTGTTCCTTTTTCTTCACTGCAGTCATCTCGTGTTTTGGTGCA[A/G]CTGGCTCGGGCAACTTAGCTTGATCAGTTTTGCTTTTGTGGGGTACGGCGCCTGAATTGGTAGTTGCTCCATGCTGCTGGTTATGGC
93164 C T CGGGCAACTTAGCTTGATCAGTTTTGCTTTTGTGGGGTACGGCGCCTGAATTGGTAGTTGCTCCATGCTGCTGGTTATGGCCGTACGAGATGCGACGCAG[C/T]GGCTTCAGAGCAGGTTGGAAGGCGTTGAATATTTTCTCGCACATGCCACCGGGTTGTTGCTGATGAGTTGCTTGCTTCTTCTCCATT
93164 C T GCAACTTAGCTTGATCAGTTTTGCTTTTGTGGGGTACGGCGCCTGAATTGGTAGTTGCTCCATGCTGCTGGTTATGGCCGTACGAGATGCGACGCAGCGG[C/T]TTCAGAGCAGGTTGGAAGGCGTTGAATATTTTCTCGCACATGCCACCGGGTTGTTGCTGATGAGTTGCTTGCTTCTTCTCCATTATC
93168 A G CAAAAAGAATCAGCACCTCGAGAGCTCTCCGGTGTGCGGTGATGACCGTCGATGGTGGTTGCTGGTGGCCGTAATCTTCTTTGCAAGTGGCGTCGGTCGA[A/G]GTGAATTTGGGAGGGCTAGGCGTGATCGAGTTCTACCTGGTTGGCGGCGCAGGACATTGACGTAGTGGCGCTTCTTCTGGCACC
93182 G A CAAGAAACTGAACGAGAACGACCCACGAATGAATCAAAACGAAACACATACTAAAGAAAATGAGATCAAACATGAGCGCCCTCCTCGTAAGAGAAGATGG[G/A]CAAGTAACTGAGCTGATCGCATTAACTGCTTTTCTCTGTTAACTATTGCTTTATATATATACATATATACACATCATTATCAAAAAG
93200 A G AGCTTCAATCGGCGCAGGAATCTTTGTCGTTACTGGAACCGCCGCTCGTGACGCCGGACCTGCTGTTGCAGTTAGCTTTGTTCTTGCTGGTGCTGCTTGT[A/G]TTCTCAATGCTCTTTGCTATGCCGAGCTTTCTTCACGTTTCCCTGCCACTGTTGGTGGTGCATACATGTATTCGTATACTGCATTCAATG
93210 A T CTTCTCTTATGGCGTCAAATGTTTGGAGCACCACTACATATAATGTTGATATTGGGGGGTTCGACAATAATGTTCACTGCTTAGCCAGATGCATCAATGC[A/T]GTCATATCGGGTAGTGAACTTGTTCGAATTGAAAGGACAGAGCAAAAAAGACGATGTCTTTCAAATGACCATTCAACCGGGACAGAA
93210 C A AAAAAAGACGATGTCTTTCAAATGACCATTCAACCGGGACAGAAAATGAAGTTTCTAGTCGTGTGTTAGTTGAAGCAAACATCAAGTCTTCCATGCAACG[C/A]TTTGTTAGATGTGCTGCTGTTGTTTTAAATAGCGATAATAGCAGATCAAACATTGTGCCGAAGCTTATATTCATGGACCAACTCTGCA
93218 T A TTTAAGTTTGCGACGCCATCAAGCGGAACAGTTGACTCTATCTCCTTAGCAAGACAACAAATTTGCAATACTGGCTTTTTTTCCAAGACAGATTCTTCAC[T/A]GCTGGCTTGATTCTCATTTTCAGCACAACCGACACAATTACTGGAGGAGGAAGAAGAGCCAAATTTATCGACATCGTCGGTGTTTGCTC
93220 A T AATAGAATATAATTTGAGAATTGAAGCACAACATTCACGGCGATGCAACGTTCTGGACAATTCTTAGACTGCCACCGCCGACCACCTGCAGCACGCGTCG[A/T]CCAAACTTCCACCGTCCGATCTCAGATTGGCCAATCCAAGGGAGCTACATCGTCCTCTCCCTCTATCACGAAGAAGAAGGCGTGCAT
93220 C T AATTTGAGAATTGAAGCACAACATTCACGGCGATGCAACGTTCTGGACAATTCTTAGACTGCCACCGCCGACCACCTGCAGCACGCGTCGACCAAACTTC[C/T]ACCGTCCGATCTCAGATTGGCCAATCCAAGGGAGCTACATCGTCCTCTCCCTCTATCACGAAGAAGAAGGCGTGCATGTGTTCACCG
93220 G C CGATGCAACGTTCTGGACAATTCTTAGACTGCCACCGCCGACCACCTGCAGCACGCGTCGACCAAACTTCCACCGTCCGATCTCAGATTGGCCAATCCAA[G/C]GGAGCTACATCGTCCTCTCCCTCTATCACGAAGAAGAAGGCGTGCATGTGTTCACCGACGACCCACCCAGGGTCGTTCCGTTGCAGC
93220 G C ATGCAACGTTCTGGACAATTCTTAGACTGCCACCGCCGACCACCTGCAGCACGCGTCGACCAAACTTCCACCGTCCGATCTCAGATTGGCCAATCCAAGG[G/C]AGCTACATCGTCCTCTCCCTCTATCACGAAGAAGAAGGCGTGCATGTGTTCACCGACGACCCACCCAGGGTCGTTCCGTTGCAGCCT
93224 T G CAATTTATATAAGCCTGAATCAAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCAT[T/G]ACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAA
93224 A T ATATAAGCCTGAATCAAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCC[A/T]CCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGT
93224 A G TAAGCCTGAATCAAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACC[A/G]TTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTT
93224 A G GCCTGAATCAAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATT[A/G]GCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTT
93224 A G TGAATCAAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGC[A/G]ATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTT
93224 A C AAACCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGT[A/C]ACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTT
93224 C T CCCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAAC[C/T]ATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCA
93224 A G CCGCTAATCTTCTTCAGGAGCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACC[A/G]TACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCA
93224 G A GCAGGTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATA[G/A]CTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCA
93224 C T GTTTGGAAGCGCCAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTC[C/T]TCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAAC
93224 A G CAGTCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCT[A/G]ACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAG
93224 G T TCTTATGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAAC[G/T]GCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATAC
93224 G A TGTGGAAGCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCA[G/A]TTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAA
93224 A G GCAATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAAT[A/G]TGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGC
93224 T C ATTGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATG[T/C]CTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGC
93224 T G TGATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTC[T/G]AGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGA
93224 A T GATTGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCT[A/T]GGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAG
93224 C A TGTGAATGTTAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGG[C/A]ACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATA
93224 T A TAGGCATTACTCCACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCT[T/A]GTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAG
93224 G A CACCATTAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTT[G/A]TCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGA
93224 T C TAGCAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCT[T/C]GCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCT
93224 A T CAATTGTAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGC[A/T]GCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGG
93224 G T TAACCATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATT[G/T]CCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATT
93224 C T ATACCCAAAAGCTTCGATAGCTCCTCATCGTTTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAG[C/T]AAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCA
93224 A G TTCTAACGGCCAGTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTC[A/G]AGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTG
93224 G A GTTGAATATGTCTAGGCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGC[G/A]AGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGG
93224 C A GCACAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGC[C/A]CCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTC
93224 T A CAATTCTTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCC[T/A]GCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTG
93224 G A TTGTCTTTTTGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACC[G/A]ACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTA
93224 G T TGTTGTCTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTC[G/T]GCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTT
93224 T C CTCTTGCAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTA[T/C]TTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCT
93224 A G CAGCATTGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCC[A/G]GCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGA
93224 T C TGCCAGCAAGTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTT[T/C]AGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
93224 A C GTTCCAGAACCTCGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCG[A/C]GCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCT
93224 G A CGGCAGCAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACC[G/A]ACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTG
93224 A G CAAGATACTCAAGAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGG[A/G]AATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATT
93224 A G GAACGGCGGCGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCC[A/G]GCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTG
93224 A G CGAGATAGACAGGAGCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCT[A/G]CTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGA
93224 C A GCCCCTGCACCGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAG[C/A]CTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATT
93224 T C CGACTCTCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGC[T/C]GCTGCGGATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGG
93224 G A TCTCGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGC[G/A]GATCCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGGGTGAC
93224 T C CGGCGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGA[T/C]CCGATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGGGTGACTGG
93224 G A CGTATTTTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCC[G/A]ATCGCTTTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGGGTGACTGGTCC
93224 T C TTCCAGCCTTTAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGC[T/C]TTTCCTCTTCCTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGGGTGACTGGTCCAGTAGG
93224 C A TAGAAATCGAGCGATTCTACCGACTGGAAATTGTAGGCCAGCCTTGCTACTTCGTGATGTAGCCTTCTTTGCTGCTGCGGATCCGATCGCTTTTCCTCTT[C/A]CTGCCATTGCGAATTTTTTTAAGTTTGAGAATTGGGAGTTTTTGGTGAGATTTGAGATCTGGGTGACTGGTCCAGTAGGCCAACAGTG
93252 AAG A TTGACCTTGTATGTATATTCTGTGTTATCTTCTTTCAGTTTCAGCTCTCTGCTCTAACTGAATTTGCATTCTCAACATATATTATTTGTCCCAAACAGAG[AAG/A]AGAAACCCATGCATGCGCACTCTCCTTGTCCAAACTCTCGCAATATATTATCCATTCATGTTAGCATGCATGGATCAATATAATCCTTCC
93252 A ACCC CCTTGTATGTATATTCTGTGTTATCTTCTTTCAGTTTCAGCTCTCTGCTCTAACTGAATTTGCATTCTCAACATATATTATTTGTCCCAAACAGAGAAGA[A/ACCC]ACCCATGCATGCGCACTCTCCTTGTCCAAACTCTCGCAATATATTATCCATTCATGTTAGCATGCATGGATCAATATAATCCTTCCAAA
93252 TGC T ATACCTCCCTCATGCATGCTGCTACCTTCTCTCGCCTCGCTTCTCTTCTAAGTTCTATATACCAGCTAATTAACTTCCTGCTGCGACATGACATACACAA[TGC/T]GCTCTGCACATGTACACAGAGTACTTACGTACCCTTCATTTTCATCTATAACCAATTTCCTTAATTACCATCCTCATTTTTTTTAAGCAAC
93252 TTACG T CTTCTCTCGCCTCGCTTCTCTTCTAAGTTCTATATACCAGCTAATTAACTTCCTGCTGCGACATGACATACACAATGCTCTGCACATGTACACAGAGTAC[TTACG/T]TACGTACCCTTCATTTTCATCTATAACCAATTTCCTTAATTACCATCCTCATTTTTTTTAAGCAACTTGTCTATTTAACCACAGCACCC
93286 C T GCTTCAGTGATAGACATGTGTACAATGGATGCCAAGAAGAATATAGACTGAATCCGGAAGGAGTGTTCCATGTACCACCGGAGGCGATACACGAGTACTG[C/T]GGAGGACCATGCTTCGAGGAAACGAGGCATGTGCTCAAGTGCATCGACGACATACTTCATACCTTCTTATTTTATAATGGTGCCTC
93286 G A TCTTATTTTATAATGGTGCCTCGCTTGGTGATATCGGTGATACTTTGCAAAGAGGCTGCCATGGTGGCTATCGAGGTGATTATGGGATTTTGGGCATAGG[G/A]GGTGAAGAAGGATACGGTGGATATTACTACGGAAATGCGAAAAAAATTGCTATGTCAACTTCATTGACGGCTATACTGAGTTGTGT
93306 G C AGTTCCTTGCCCACTGCCTGCGTCGCAACTATCAGTTCTCCCTGTTCTGCGCTGACGTCGGCGGGACCCAGTCTTCTT[G/C]TGTGTCTCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTC
93306 T C AGTTCCTTGCCCACTGCCTGCGTCGCAACTATCAGTTCTCCCTGTTCTGCGCTGACGTCGGCGGGACCCAGTCTTCTTGTG[T/C]GTCTCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTC
93306 C T AGTTCCTTGCCCACTGCCTGCGTCGCAACTATCAGTTCTCCCTGTTCTGCGCTGACGTCGGCGGGACCCAGTCTTCTTGTGTGT[C/T]TCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACC
93306 G A AGTTCCTTGCCCACTGCCTGCGTCGCAACTATCAGTTCTCCCTGTTCTGCGCTGACGTCGGCGGGACCCAGTCTTCTTGTGTGTCTCGAATCC[G/A]GTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACCATCCTG
93306 G A CTCCCTGTTCTGCGCTGACGTCGGCGGGACCCAGTCTTCTTGTGTGTCTCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGAC[G/A]TCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACCATCCTGCAATAGGCTCAGAATGTGGAATTTGGTATTGTATATG
93306 A C GCTGACGTCGGCGGGACCCAGTCTTCTTGTGTGTCTCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATC[A/C]TCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACCATCCTGCAATAGGCTCAGAATGTGGAATTTGGTATTGTATATGCTTAGCTAGATG
93306 C T GACCCAGTCTTCTTGTGTGTCTCGAATCCGGTGGCTCCCGTACCTACCTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCG[C/T]CTTGGCTGTCCTTCTTCACCATCCTGCAATAGGCTCAGAATGTGGAATTTGGTATTGTATATGCTTAGCTAGATGCTAATATTTTGGAAA
93306 A AT CTTCATCTGCCTTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACCATCCTGCAATAGGCTCAGAATGTGGA[A/AT]TTTGGTATTGTATATGCTTAGCTAGATGCTAATATTTTGGAAACTTATTCTTCCAACTCAACTCATGCTAACCCCCTCATAATCCTCCAAT
93306 T C TTCTGTTTCCAAGACGTCACCGCCGATCATCTTCCGTTTGCGCCTTGGCTGTCCTTCTTCACCATCCTGCAATAGGCTCAGAATGTGGAATTTGGTATTG[T/C]ATATGCTTAGCTAGATGCTAATATTTTGGAAACTTATTCTTCCAACTCAACTCATGCTAACCCCCTCATAATCCTCCAATCACACATCTATA
93312 A G TGTTTTTCAGCTCTTCACTCAGCCTGAGGCAAGAATTTATGTATCGGTTTCCTTTGGTTGCTGCATCAAGTGCAGCTTCCTGTACAGATCCAGCTATGCC[A/G]CCAAAGCTCTGCATATTTTCTAATGAGGTGCTTGTGACCTCGGAAAGGGCTAAAGAGAGGGATGCGAAGAGAGATGCGTAGCTTTCA
93312 T A AATTTATGTATCGGTTTCCTTTGGTTGCTGCATCAAGTGCAGCTTCCTGTACAGATCCAGCTATGCCACCAAAGCTCTGCATATTTTCTAATGAGGTGCT[T/A]GTGACCTCGGAAAGGGCTAAAGAGAGGGATGCGAAGAGAGATGCGTAGCTTTCAGCGATAGCGATCGAGTCTTTCTCAACGATTTCT
93312 G A CGATTTCTAAAGCTTTAAATATCTCATTTCGACCAGGATTTGACGAGGAGGGATTGGGTTCGGTGGGAGCTGAAGTCCGTTCGGAACAGGTAGGGTTCGA[G/A]CCAGGGTGAATGGGATTCTCTTCCATAGCCCTCCAAAACTGTACAATTAATCGAAGCTGAATTTGTAGCAGCAGGAGAAATTCTTT
93320 G T CTGTTTCCTCTAAGCGTATATACCAGCATTCACCCCCTCCAATTCTCATCGTATCCGCAAATCAA[G/T]CTACCCCAAATTCCATAACCCTACCGACCCCGACATTGTCCGTTGCCTCCTCTACCTCCAACCGTTTCCTTGGCCATAGCCGGCGCCGCCAGTTTCAGCC
93320 A T CCTCCTCTACCTCCAACCGTTTCCTTGGCCATAGCCGGCGCCGCCAGTTTCAGCCCTCCACCTATCGCTCTGCACAGGTGTCCGGCGGTCCCAAATTTCC[A/T]TGACTTGATCGATTCCGGTGGTTACTGTGCTCCGCCTTCAGCCAACGTCTTCTTTGCATGCCACGCCGCCGAACACCTTCCATCTTCGCC
93326 G A TAGTAGTCGTCGTCTTCGCCGTCTATTTTCAGGTCGTTTGTGTACTCTTCGTGTGTTGGAGTCGGAGGACTTTTGACGTCCACCGATTCAACAGTGT[G/A]GATGTCCAAAACAGGTTCGGGTATTTCCCGAGTAGTTGAGCGATTTCTCCCATCTATAGGTTCAACGACGTGGATATCCAGAACGGGTTCG
93326 C T CTTCGTGTGTTGGAGTCGGAGGACTTTTGACGTCCACCGATTCAACAGTGTGGATGTCCAAAACAGGTTCGGGTATTTCCCGAGTAGTTGAGCGATTTCT[C/T]CCATCTATAGGTTCAACGACGTGGATATCCAGAACGGGTTCGGGTACGGTTATTTCTTGAGAAGCAGTGCGAAGTTCTTTGATGGAT
93326 A C GATTAGCGTTGAGTTTCCAGATGATGAAGATGATGGAATTGACGATTATGAGCAGATAAGTCGAAGGAAGTCGAGAAAAATCGGGATAGTTCCAAGTAAC[A/C]GGAAAAGAAAGAGAAAGAACGGATCTTTGGACATGGGTTGAGATCAGGAAAAGCGTCGAAGCGATCCCGACGACAAGGAAGA
93326 A G TAGCGTTGAGTTTCCAGATGATGAAGATGATGGAATTGACGATTATGAGCAGATAAGTCGAAGGAAGTCGAGAAAAATCGGGATAGTTCCAAGTAACAGG[A/G]AAAGAAAGAGAAAGAACGGATCTTTGGACATGGGTTGAGATCAGGAAAAGCGTCGAAGCGATCCCGACGACAAGGAAGAGGA
93326 T A ATTATGAGCAGATAAGTCGAAGGAAGTCGAGAAAAATCGGGATAGTTCCAAGTAACAGGAAAAGAAAGAGAAAGAACGGATCTTTGGACATGGGTTGAGA[T/A]CAGGAAAAGCGTCGAAGCGATCCCGACGACAAGGAAGAGGATTTTGGCAGAAGATACGGCGAAATCCAGGGCGGCTGTCTTT
93326 G A CGAAGGAAGTCGAGAAAAATCGGGATAGTTCCAAGTAACAGGAAAAGAAAGAGAAAGAACGGATCTTTGGACATGGGTTGAGATCAGGAAAAGCGTCGAA[G/A]CGATCCCGACGACAAGGAAGAGGATTTTGGCAGAAGATACGGCGAAATCCAGGGCGGCTGTCTTTTGATGTTCGGGAGACGG
93326 C A GAAGGAAGTCGAGAAAAATCGGGATAGTTCCAAGTAACAGGAAAAGAAAGAGAAAGAACGGATCTTTGGACATGGGTTGAGATCAGGAAAAGCGTCGAAG[C/A]GATCCCGACGACAAGGAAGAGGATTTTGGCAGAAGATACGGCGAAATCCAGGGCGGCTGTCTTTTGATGTTCGGGAGACGGT
93330 TA T CAAACCTTTAAATGACCATTAAGCACAAAAGTGGGAGATCCCATATCCACAACTCATATGAATATAACGTTCTCTCCCCATAAAAATCAAGTGAAAAGGG[TA/T]AACAACGTCTCTTCTATACCCTCTAACTATAAGCATTCTGGGCACGTTCTCAACAAGCAAATCCATGTACTCCATGTAAAAATAAGCA
93340 T TC AAAGATAAACAAGGGGCTAGCGGATAGCAATGTCCACGGACCTAGTCCCCTACTCCTCCACCCCAGGCAAAAGCCCGAACGTCCCTTGG[T/TC]CGGAAATGTTCCGCTCCGCCTCCCTCCGTCAGCCTCCTGACTCACTCCCTCCGACGCGCCCCTCCTCCCCTCCACCCAACGCCACTGCTCAATCCACA
93340 A G TCCCTTGGTCGGAAATGTTCCGCTCCGCCTCCCTCCGTCAGCCTCCTGACTCACTCCCTCCGACGCGCCCCTCCTCCCCTCCACCCAACGCCACTGCTCA[A/G]TCCACATCCAGTCCTTGCTCCTCTACCAAAACGCTATCCCTGGATCCGGAGCCGAAGCTCGCCCTCTACATAGCCATGGCGCACGCACT
93340 T C CGTCAGCCTCCTGACTCACTCCCTCCGACGCGCCCCTCCTCCCCTCCACCCAACGCCACTGCTCAATCCACATCCAGTCCTTGCTCCTCTACCAAAACGC[T/C]ATCCCTGGATCCGGAGCCGAAGCTCGCCCTCTACATAGCCATGGCGCACGCACTCCTCGTCCTCTCCCTCCTAATAACCTACTCACTCTA
93340 C G CCTACTCACTCTACTGCCTCCTTCACTCCTTCCTCAAACCCATCCAGTGGGCCTTTCTTTGCTCAATCCCACTTCGTCAGCTCCATTCCTCCCTCTACTC[C/G]TTCTGGGCTCCGCCCCTTTCCCTCGGCCTCCTCCCTTCTCTCCTCGCCCTACCATCCGCGGTCCTGCGCTCCTCCTCCCACACCCTCTCCGAT
93340 A G TTCTTTGCTCAATCCCACTTCGTCAGCTCCATTCCTCCCTCTACTCCTTCTGGGCTCCGCCCCTTTCCCTCGGCCTCCTCCCTTCTCTCCTCGCCCTACC[A/G]TCCGCGGTCCTGCGCTCCTCCTCCCACACCCTCTCCGATCTCAAATCCATCCTCCTTCGTCGCTCCATCGGATCCTCCTCCGACACCGTCGGC
93340 A C CCTCGGCCTCCTCCCTTCTCTCCTCGCCCTACCATCCGCGGTCCTGCGCTCCTCCTCCCACACCCTCTCCGATCTCAAATCCATCCTCCTTCGTCGCTCC[A/C]TCGGATCCTCCTCCGACACCGTCGGCGGCTTCTCTCGCCTCTTGCGCTGGCTCCTCTCCTTCTTTCTTTTCCTTATTTCTTACGAGAAGTTCG
93340 T A CCTCCTCCCTTCTCTCCTCGCCCTACCATCCGCGGTCCTGCGCTCCTCCTCCCACACCCTCTCCGATCTCAAATCCATCCTCCTTCGTCGCTCCATCGGA[T/A]CCTCCTCCGACACCGTCGGCGGCTTCTCTCGCCTCTTGCGCTGGCTCCTCTCCTTCTTTCTTTTCCTTATTTCTTACGAGAAGTTCGGAATT
93342 G T CACTGTTGGCCTACTGGGTGAATTTTATTTCATTGCTCTTCTTCACCTCCTTTGTCCGCTGTCACT[G/T]GATTTCCCGCCACCAAAACCCTAACAATGTCGGAGAAAAAACGTCGCCTACCAAATCCAAGCGTTGCAGCCGGAAAGAAGCCTAAACTATCCACGTCTAA
93342 GA G ACTGTTGGCCTACTGGGTGAATTTTATTTCATTGCTCTTCTTCACCTCCTTTGTCCGCTGTCACTGGATTTCCCGCCACCAAAACCCTAACAATGTCGGA[GA/G]AAAAAACGTCGCCTACCAAATCCAAGCGTTGCAGCCGGAAAGAAGCCTAAACTATCCACGTCTAAAAAACCTGTATCGCACGCCATGT
93342 A T GAATTTTATTTCATTGCTCTTCTTCACCTCCTTTGTCCGCTGTCACTGGATTTCCCGCCACCAAAACCCTAACAATGTCGGAGAAAAAACGTCGCCTACC[A/T]AATCCAAGCGTTGCAGCCGGAAAGAAGCCTAAACTATCCACGTCTAAAAAACCTGTATCGCACGCCATGTCCCTCAAATCTAAACTCAAA
93342 G T TCCGAGAAGTGTCCGACCGCGATGCCTCCTCCGTCTCTGATGCCATCGAGCGAAATATTCTCCAGATGGCGAAGACTATACTTAATCGTAATGGGTTTTC[G/T]TTCGAAGTTCCTTCCAGATCCTCTGTGAACCAGATGTATGTGAGCGAGTTGGATCGGATTGTTTTGAAAGATAAGAGCTCTAAAAGG
93342 T C AGACTATACTTAATCGTAATGGGTTTTCGTTCGAAGTTCCTTCCAGATCCTCTGTGAACCAGATGTATGTGAGCGAGTTGGATCGGATTGTTTTGAAAGA[T/C]AAGAGCTCTAAAAGGGAGTTTGCTAATTTGAGTACTGTGAGGAAGGCAACTATTACGGCTAGGGTTATGAGTTTGGTTTATGCTGTT
93352 A G ATTCCTCTACTCCAAAATTCATCCTCACGTGGTAGCCTAAGACGTTGAGCTGTAGCTCCTGTGGCTACAATTAGGCTATG[A/G]CATTTTACCTCTCTTTCACTGCTCCTGATTGTAAATGGTCTGGTCATCAAATCAACTGACTCGACATCCTCCTGAAAAAGCTCAGCGCCCCACCTCTCAG
93352 G A CCTCACGTGGTAGCCTAAGACGTTGAGCTGTAGCTCCTGTGGCTACAATTAGGCTATGACATTTTACCTCTCTTTCACTGCTCCTGATTGTAAATGGTCT[G/A]GTCATCAAATCAACTGACTCGACATCCTCCTGAAAAAGCTCAGCGCCCCACCTCTCAGCTTGTCGCTTTATCCTATCCATCAAATCAGGG
93352 G T CAATTAGGCTATGACATTTTACCTCTCTTTCACTGCTCCTGATTGTAAATGGTCTGGTCATCAAATCAACTGACTCGACATCCTCCTGAAAAAGCTCAGC[G/T]CCCCACCTCTCAGCTTGTCGCTTTATCCTATCCATCAAATCAGGGCCAGTTATTCCATCAGGAAACCCAGGGAAATTTTCTACTTCGGTG
93352 C T CGCCCCACCTCTCAGCTTGTCGCTTTATCCTATCCATCAAATCAGGGCCAGTTATTCCATCAGGAAACCCAGGGAAATTTTCTACTTCGGTGGTTGTCAT[C/T]AACTGTCCTCCCGGGACACCGCCCATTTGATATCCCTCAAATACTAGAGGCTTTAAATTAGCTCGGGCTGCATAAATTGCTGCAGTGTA
93352 G A ACCCAGGGAAATTTTCTACTTCGGTGGTTGTCATCAACTGTCCTCCCGGGACACCGCCCATTTGATATCCCTCAAATACTAGAGGCTTTAAATTAGCTCG[G/A]GCTGCATAAATTGCTGCAGTGTATCCAGCTGGACCAGAACCAATGATTACCAAATTCTCAATTCTTTCATTAGAACCTGAGGAAACAG
93352 A G CGCCCATTTGATATCCCTCAAATACTAGAGGCTTTAAATTAGCTCGGGCTGCATAAATTGCTGCAGTGTATCCAGCTGGACCAGAACCAATGATTACCAA[A/G]TTCTCAATTCTTTCATTAGAACCTGAGGAAACAGAAGCATCAGCCTCTACAGCAGAAGAAGACGAAGCGATAAAAGTACGAAGCAAT
93380 CA C GGGGTATGATGATGGTAATGTTGCTTTGATTGCAGCGATAACTTGAGGGTGAATGAGAGTGGTTTCGGTCATGATTTCAGCGGTAACTTGGGTGAACTGG[CA/C]AAAAAAGGGATGAGAGGTAGGAAAGCAGATCTGAAGTGAGAAGGGAATTAAAATAAAGGAGGTGAGAACATCGGTGAAAGC
93384 C A TGAAAGACGGACTGGCGCTAGGATGCGCCTTCAACCACGCCATCCTCGACGGCCACTCCACTTGGCATTTCATGTCTGCATGGGCGGAGCTGACCCGCAC[C/A]CAATCCACCACCATATTGTCCGTCCCCATTCCATTCCACGATCGCTCCAAAGCCCGGGCCACGCGCACTAAATTGGACCTACCCACC
93384 T C CCCAATCCACCACCATATTGTCCGTCCCCATTCCATTCCACGATCGCTCCAAAGCCCGGGCCACGCGCACTAAATTGGACCTACCCACCCAAAAAGCCCA[T/C]GAACTCGCCGACCCGAATGGCCCACCCAAACCCCTCGTCGCCAGAGTCTTCTCCTTCTCTGAATCCGCCCTCGCCCATCTGAAATCTCA
93384 T G CCACGCGCACTAAATTGGACCTACCCACCCAAAAAGCCCATGAACTCGCCGACCCGAATGGCCCACCCAAACCCCTCGTCGCCAGAGTCTTCTCCTTCTC[T/G]GAATCCGCCCTCGCCCATCTGAAATCTCAAGTGAACTCCAAACTTCCACCGAACTCGAAGCCGTTCTCGACCTTTCAGTCGCTCGGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
93384 A G GAACTCGCCGACCCGAATGGCCCACCCAAACCCCTCGTCGCCAGAGTCTTCTCCTTCTCTGAATCCGCCCTCGCCCATCTGAAATCTCAAGTGAACTCCA[A/G]ACTTCCACCGAACTCGAAGCCGTTCTCGACCTTTCAGTCGCTCGGAGTCCACGTGTGGCGATGTGTGTGCCGTGCACGGGGCCTGAA
93384 T G TCGCCGACCCGAATGGCCCACCCAAACCCCTCGTCGCCAGAGTCTTCTCCTTCTCTGAATCCGCCCTCGCCCATCTGAAATCTCAAGTGAACTCCAAACT[T/G]CCACCGAACTCGAAGCCGTTCTCGACCTTTCAGTCGCTCGGAGTCCACGTGTGGCGATGTGTGTGCCGTGCACGGGGCCTGAAGCCG
93384 C G AATCTCAAGTGAACTCCAAACTTCCACCGAACTCGAAGCCGTTCTCGACCTTTCAGTCGCTCGGAGTCCACGTGTGGCGATGTGTGTGCCGTGCACGGGG[C/G]CTGAAGCCGGAAGAGTACACCGTGTTTGCCATATTCATGGACTGTAGGTCCCGTGTTAGCCCTCCTATGAAGGAAGACTACTTCGG
93384 G T TGAACTCCAAACTTCCACCGAACTCGAAGCCGTTCTCGACCTTTCAGTCGCTCGGAGTCCACGTGTGGCGATGTGTGTGCCGTGCACGGGGCCTGAAGCC[G/T]GAAGAGTACACCGTGTTTGCCATATTCATGGACTGTAGGTCCCGTGTTAGCCCTCCTATGAAGGAAGACTACTTCGGCAACTTGAT
93404 AC A AAGCATGGACAGTGAATCTGATTAACCACTGTGTTCTTTTGGCATGAACCACAGACGGCTTTATCTCGATTAGTTGACTCGATCGATGTTGATAAAAAAA[AC/A]CGGGGGGAGAAAATGAATGGAGTGGAACTGATATAAATTGTGATCTAGTAGTAATTAAATGAAACTTCGTTGTGCCAGCTTCAGTT
93416 A G TCCATACACCATGTGTCCAACTCTCCCCATTGGGAAGAACAACTGAATGAGTGCAAACACCATGATTATCATTATACCGGCAAACAGGAACGGGCCGAGG[A/G]AGCTGAAATCGTGCCCTTTCTTCGCCGCCCAGAACGTGTACAGAGTCAGGCTCACCACCACCACTGTTGTCAGAATCGCCGACTCG
93416 C A CCATTGGGAAGAACAACTGAATGAGTGCAAACACCATGATTATCATTATACCGGCAAACAGGAACGGGCCGAGGAAGCTGAAATCGTGCCCTTTCTTCGC[C/A]GCCCAGAACGTGTACAGAGTCAGGCTCACCACCACCACTGTTGTCAGAATCGCCGACTCGAGGATCACTTTTCCGCTTGTAAACGC
93416 A G GCCCTTTCTTCGCCGCCCAGAACGTGTACAGAGTCAGGCTCACCACCACCACTGTTGTCAGAATCGCCGACTCGAGGATCACTTTTCCGCTTGTAAACGC[A/G]CATGTCAATCCAACTGCAAAGCTGATGCACACCGTGAAGATTGCAAGCAGCACTAGGTTCACCGGATGCCACTGGTAGTAGTAATAC
93428 C T AATACACACATGTGACACATACATAATACGACTTCTTGTATTTAAGCAAAGTAGAGTCTCTGAAACTAATATGATACATTACAACGATTAATATGTATAA[C/T]ATAGACAATATAAGAAATACTGTATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTG
93428 A G CATGTGACACATACATAATACGACTTCTTGTATTTAAGCAAAGTAGAGTCTCTGAAACTAATATGATACATTACAACGATTAATATGTATAACATAGACA[A/G]TATAAGAAATACTGTATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTGTCACTAA
93428 T C ATACATAATACGACTTCTTGTATTTAAGCAAAGTAGAGTCTCTGAAACTAATATGATACATTACAACGATTAATATGTATAACATAGACAATATAAGAAA[T/C]ACTGTATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTGTCACTAATAGATCCCTTA
93428 T C TAATACGACTTCTTGTATTTAAGCAAAGTAGAGTCTCTGAAACTAATATGATACATTACAACGATTAATATGTATAACATAGACAATATAAGAAATACTG[T/C]ATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTGTCACTAATAGATCCCTTACCTTC
93428 A G ACATAGACAATATAAGAAATACTGTATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTGTCACTAAT[A/G]GATCCCTTACCTTCATCAAACAGCATAGATTCTGACAACTTGATCAATACCAGCTCTACAAACAGGGCAACCCCAACCCTTGCTTTTAAT
93428 C T GACAATATAAGAAATACTGTATCAACATGGTTGTTTCCTCAGTCCAACCAGACTGCTTCTATATAAGATATACAATGGCAAATGTTGTCACTAATAGATC[C/T]CTTACCTTCATCAAACAGCATAGATTCTGACAACTTGATCAATACCAGCTCTACAAACAGGGCAACCCCAACCCTTGCTTTTAATTTCAT
93428 T C GTCACTAATAGATCCCTTACCTTCATCAAACAGCATAGATTCTGACAACTTGATCAATACCAGCTCTACAAACAGGGCAACCCCAACCCTTGCTTTTAAT[T/C]TCATTCAAACAGGCCATGCAACCGGCCATATGCCCACATGGAATGCATGCTCCTTCCACCCCTGCATCCAAACATATCACACAGGACTCC
93428 T C CCATTTTCATCTTTACCATCCTTAGTCACCTTCTTTCCCTTTTCTTCAACATCGGGCATCTTTAGATCGACTGGGCCAGAATCTATAGTCGGGTACTGAA[T/C]AGGCCCACGGTAGAACGACTCATCGACAGGAGGCGCTGAAGGAACTGTTAAAGCAGGAGGTGCTTCATGGGATGGAGCAACTACAAC
93428 C G ACCTTCTTTCCCTTTTCTTCAACATCGGGCATCTTTAGATCGACTGGGCCAGAATCTATAGTCGGGTACTGAATAGGCCCACGGTAGAACGACTCATCGA[C/G]AGGAGGCGCTGAAGGAACTGTTAAAGCAGGAGGTGCTTCATGGGATGGAGCAACTACAACACCAGTAGGCCAACAGTG
93476 T G TTTTTTTTTTTAGAGGGAAAACCGAAACTGATTGCAGATAAACATACGTATGGACAAAAGTACAACACAGAAAGTTTACGGTTATACATAAGAGTACA[T/G]CCATGACAACATTATTCAGAAGACCAAATACAAAAGATGAACTAAAGTGGAGAAGACGGCACATAGAACGCACGTGCGAATCTTTCTTC
93476 A T TTGCAGATAAACATACGTATGGACAAAAGTACAACACAGAAAGTTTACGGTTATACATAAGAGTACATCCATGACAACATTATTCAGAAGACCAAATACA[A/T]AAGATGAACTAAAGTGGAGAAGACGGCACATAGAACGCACGTGCGAATCTTTCTTCTCCATTACAAGTATGCATTATTACTGGAATG
93476 T C GATAAACATACGTATGGACAAAAGTACAACACAGAAAGTTTACGGTTATACATAAGAGTACATCCATGACAACATTATTCAGAAGACCAAATACAAAAGA[T/C]GAACTAAAGTGGAGAAGACGGCACATAGAACGCACGTGCGAATCTTTCTTCTCCATTACAAGTATGCATTATTACTGGAATGATACC
93476 C G CAGAAAGTTTACGGTTATACATAAGAGTACATCCATGACAACATTATTCAGAAGACCAAATACAAAAGATGAACTAAAGTGGAGAAGACGGCACATAGAA[C/G]GCACGTGCGAATCTTTCTTCTCCATTACAAGTATGCATTATTACTGGAATGATACCATTGTTGTATTGCTCATTTAGAATGTGCAAGA
93476 C T TCTTCTCCATTACAAGTATGCATTATTACTGGAATGATACCATTGTTGTATTGCTCATTTAGAATGTGCAAGATATACAGCCAAATATGCGACGAAACTC[C/T]GTCTCTCCTTTTTTTGGGAAACTTAGTCGCTTAAGGAGAGGTGCGGATTTGGCATCGGTCTTATTCAACATCTCCCACATTATGCGCACA
93476 T C CAAGTATGCATTATTACTGGAATGATACCATTGTTGTATTGCTCATTTAGAATGTGCAAGATATACAGCCAAATATGCGACGAAACTCCGTCTCTCCTTT[T/C]TTTGGGAAACTTAGTCGCTTAAGGAGAGGTGCGGATTTGGCATCGGTCTTATTCAACATCTCCCACATTATGCGCACATCCTCGTACTC
93476 G T TGGAATGATACCATTGTTGTATTGCTCATTTAGAATGTGCAAGATATACAGCCAAATATGCGACGAAACTCCGTCTCTCCTTTTTTTGGGAAACTTAGTC[G/T]CTTAAGGAGAGGTGCGGATTTGGCATCGGTCTTATTCAACATCTCCCACATTATGCGCACATCCTCGTACTCGCAGGTGTTGACTTCAT
93476 A G ATGTGCAAGATATACAGCCAAATATGCGACGAAACTCCGTCTCTCCTTTTTTTGGGAAACTTAGTCGCTTAAGGAGAGGTGCGGATTTGGCATCGGTCTT[A/G]TTCAACATCTCCCACATTATGCGCACATCCTCGTACTCGCAGGTGTTGACTTCATTCTTCAGCTGCATCAATCCAGATTTGCGCATTCG
93476 C T GTCGCTTAAGGAGAGGTGCGGATTTGGCATCGGTCTTATTCAACATCTCCCACATTATGCGCACATCCTCGTACTCGCAGGTGTTGACTTCATTCTTCAG[C/T]TGCATCAATCCAGATTTGCGCATTCGGATTCGGGCAGCAACGCGGATCCAAACCCGCCTCATGGGAGTGATAACTCGAACCCAGACG
93476 C T GCTGCATCAATCCAGATTTGCGCATTCGGATTCGGGCAGCAACGCGGATCCAAACCCGCCTCATGGGAGTGATAACTCGAACCCAGACGTACTTCATACT[C/T]TCGAATCAGAAGGGAAGAGAAGGGAGAAGGAAGAAGAGAGATTAATGTTTAGCGAGAGAGAAAGTAAAGTTAATGAAGGCCACG
93476 G A GCATCAATCCAGATTTGCGCATTCGGATTCGGGCAGCAACGCGGATCCAAACCCGCCTCATGGGAGTGATAACTCGAACCCAGACGTACTTCATACTCTC[G/A]AATCAGAAGGGAAGAGAAGGGAGAAGGAAGAAGAGAGATTAATGTTTAGCGAGAGAGAAAGTAAAGTTAATGAAGGCCACGCA
93478 C T CATCTGATGTTATCGCTGTTCTCTCTACTTAATTATTGTCAATTTTGAGTAGTACGGCTAGATTTGCATCTTTGTTCTAAGGAGTTAGCATTCATTACCG[C/T]GAGAAGCTGGACGATTGGCAGGCAGGAAACAATGTTGTAATGAGATCGAACCAATCAGATTATTATTCGTCATCGATGGATCTACCATC
93480 T C CACAAGCAATCATATCAGGAGAGTGGCCTGATAACTTCTCCTTTCTAAGCTTTGATGACCTTCGCTACTATCTCGAAGCTCAAGAAAATGATGATCATCT[T/C]AACTCTAAGGTAGGACCATCCATGCTGTTAGGGGAAGTGATGTCGACGTCCATAATATCAGCGAGGCCTGACCAGACTTTGGAAGAA
93496 A AC AATCATTCTCTTTCTCTCCATTCTATCCCTAACCTCCCACCTTCCCATCACCAAATCCTCACCGTTCATAGGCGTAAGAGGCGGCATCAACCTGTACTTC[A/AC]CCCTCCCCAGTCCCCACCCTCCATCAACTCCGAATACGACGTCCTCCAGTCCTGGAAGCAGTCCATCACCGACGATCCCAACCGCATTCT
93496 A G ACCGCATTCTGTCCACCTGGGTCGGCCCCGACGTCTGCTCCTACAAAGGCATCTTCTGTTCCATCCCCCAAAACTCCATCCCCTCCTCCTCCTCTTCCCA[A/G]TCTCAAGCCATCCTCGCCGTCGATCTCAACCACGCTAATCTCAAAGGCACTTTAGTCACACAGCTCTGCTTACTCACTCACTTATCCATCA
93496 A G TGCTTACTCACTCACTTATCCATCATCCATTTAAACTCCAACAAATTCTCCGGTTCAGTCCCTGACTGCTTCCAGAATTTACGCTACTTAACAGAACTCG[A/G]TCTGAGCAACAACCAATTCTCCGGCTCTTTTCCGATGTCCACACTCTCGATCCCAAACCTAATCTACTTAGATCTACGATTCAACTCCTTCT
93496 T C ATTTAAACTCCAACAAATTCTCCGGTTCAGTCCCTGACTGCTTCCAGAATTTACGCTACTTAACAGAACTCGATCTGAGCAACAACCAATTCTCCGGCTC[T/C]TTTCCGATGTCCACACTCTCGATCCCAAACCTAATCTACTTAGATCTACGATTCAACTCCTTCTCCGGCCAAATCCCAGACGAGCTTTTCC
93496 A T AATTCTCCGGTTCAGTCCCTGACTGCTTCCAGAATTTACGCTACTTAACAGAACTCGATCTGAGCAACAACCAATTCTCCGGCTCTTTTCCGATGTCCAC[A/T]CTCTCGATCCCAAACCTAATCTACTTAGATCTACGATTCAACTCCTTCTCCGGCCAAATCCCAGACGAGCTTTTCCAAAAAGGGACACTG
93502 G A GTGCTATGTCGCATTTTTAAGAAGAAAAGAAGTGCAAAGGCGAGTGTCGAACAAGAAGGGCATCGTTTCATCGATTTCATGGGCCGAGAAAGGAATGGAC[G/A]ACGCTCTTCCTTGCCGGCTCATTCAGATTCAAGTTGTGTCACGGATCGTGCAGGTGATGAATCGAAGTATGGAGAGGAAATCACA
93502 CT C TCGACATCATATCCATGAGGATGAGATAGTAAAATATTTTAATTGCACTAGCACCACTTTAATTAGTGAGAAGCAATAACCTTTGAGCCTCTTTCTTTTT[CT/C]TTTTTAACTCTTAGGAACTTTGTATAACTTCGTGCTTTCTCTTTTCCCATTGTAATTTCTTGATGCAAAAGAGAGCCTTTAGATATATATA
93516 G T AGGTCAGACGAGATTTTAGGGAGGACGGGGAGGACGTGGGAGAAGTGGACGTGGCGGTGATCGACATAGATTTGAGACGCGGGAAATGTACGCTTGATTT[G/T]GAAGTGGAAGTTAGGGTCAGTGATTTTGGGAGGCCTGGGGTTTTGGATGGGGAAATGGATTTTAAATTTAGAGCAGTCGTCG
93518 C A ATTCTCCTTCGCCCTTCCACGCCGTAATCTCAGCCTCCCCAATGTCTAGTTCTCACTCGTTTGCTTCCTGCGAAAACCTCACCGAGCTCAACGATGCGTC[C/A]GATTTTGACGCTTTATTGTCACCTGATGGTTATATTTCCATTTGCGGTTTCGGTTCTCTTCTCTCTGAGAGAAGCGCCAGGAGCACATTTC
93526 T TA TGGAATACAGTCCATCATCATCAAGCAGTGTGATCTGTACACAATTCTAACAAAATCATTTCAACCTCAGAATATCACAAATGGCCTAAAGCTCCATGTG[T/TA]ATCAACAAAAAACCAAACAAGGACATAATATAAAAACAAAAATAGTAATACAATGCATTACGGTTAAAGGATTAACCTGAATCTGGA
93526 CA C ACAGTCCATCATCATCAAGCAGTGTGATCTGTACACAATTCTAACAAAATCATTTCAACCTCAGAATATCACAAATGGCCTAAAGCTCCATGTGTATCAA[CA/C]AAAAAACCAAACAAGGACATAATATAAAAACAAAAATAGTAATACAATGCATTACGGTTAAAGGATTAACCTGAATCTGGAGGTTGC
93526 TA T GATCTGTACACAATTCTAACAAAATCATTTCAACCTCAGAATATCACAAATGGCCTAAAGCTCCATGTGTATCAACAAAAAACCAAACAAGGACATAATA[TA/T]AAAAACAAAAATAGTAATACAATGCATTACGGTTAAAGGATTAACCTGAATCTGGAGGTTGCGACGACGGTGGAAGAAGGATTCCT
93526 G A AGAAGGATTCCTTTCTGGCCAAAATCGATCTGATCCGATGAAGGTTCAAATCTCTCCGATGACCAACAATTCTCTAACGTAATACTCTGGTGAAGACCTG[G/A]AGCTCTCTGACAATCGGAGCTCTGGCAGCTGGAGATGACGATGGTGAACCCGATTGCAGTGGCGATTGAAGACAAGATCAAATCTC
93528 A G ATAAGCCACAGCTACTGTGTATTCCTCCGAGTGATTGTAAAAGAGAAGTTATGGCTGTTTTAATGAAAAGAGGAACGTAGCTTCCACTGAAGAGTTTCAC[A/G]GTGAGCCAAAACACCACACGAAGAAATGCTTCGCTGCGGCACAAGGTCAGTGCCAGAATATTTGCCATGCAGAACAAGGCAGGTC
93530 C T GGGAAACAAAGAATTATCGAAACGCTTCCATCTAGCAATTGCAAGGAAGAACACTATGATACTGAATCAACGGCTGAGGTTTCACTATCACCAAAAACTT[C/T]GATAGATGCAGAAATTGATGAATTTTTCATCGAAGCCGAGAAAAAAGAAGCCCAAAAATTTGCTAACAAGTATAATTTTGATGTATT
93566 G A GTACGCTCTTAAGTTCAGTCAGATGTTCCATTTGATGCCAACGCCTCAGGGAAGCTTCTATGTGCAGAATGACATATTTCGGTTGAATTATGCTTGATTT[G/A]AAATTTGAGTCGTGTGTTGATTGCTTGCAGAATTGGTTATTTGATGGAGTAAAACGAACCTTGTTATTTTTATTTTGTTCGGCGTTGAA
93566 TTA T GACATATTTCGGTTGAATTATGCTTGATTTGAAATTTGAGTCGTGTGTTGATTGCTTGCAGAATTGGTTATTTGATGGAGTAAAACGAACCTTGTTATTT[TTA/T]TATTTTGTTCGGCGTTGAAAAAACTGTCAGCTGTTGTCTTGTTAATTTAGCCCTCCCATGTCATGCATACTGTATTGTCTTTATCATTA
93566 T A ATATTTCGGTTGAATTATGCTTGATTTGAAATTTGAGTCGTGTGTTGATTGCTTGCAGAATTGGTTATTTGATGGAGTAAAACGAACCTTGTTATTTTTA[T/A]TTTGTTCGGCGTTGAAAAAACTGTCAGCTGTTGTCTTGTTAATTTAGCCCTCCCATGTCATGCATACTGTATTGTCTTTATCATTAAAGAT
93572 G GT TATTCACCAGAGGAGTGGTCGCCAAGCGGGGATGTCTACGTTGGAGGGAAAAGTGGATTAGTTCTGTGGGCAATAACACTTGCAGGATTACTAGCGGGGG[G/GT]CGCCTTGCTTGTCTACAACACTAGTGCTCTTGCTCAGTGATTATTGTGTCTATGGTTATGTATATATGTGTTTATGCATAATGGA
93598 G T AAAAAATTCTGATATGAGAAATGCCATGGGAGACCGCAGAAAGAGAAAGAAAGATGGCTAAACGGGAGACAAGAAGTCGGTATATGCTGATTGCAGCCAG[G/T]CTCTGTTATGTCCGGAAAAGCACTGCAAATGAGTAATATGTATCGCTAATTTTGTGGAATTCATCGAGTATCATCACA
93608 C T CTACCGTCAATCGCTGGTTCAGGCCCGAGGTTTATCCTCTGTTTGCTGCGGTTGGTGCTGCTATAGGAATCTGTGTGTTTTCTCTTGCTCGTAATATTGC[C/T]ATCAATCCTGAAGTCAGGGTAAACAAGGAAGGCAGGGCAGCAGGAGTGCTCGATAACCATGCGGAGGGTGAAAAGTACGCACAACA
93608 G A CTTCGCCGACCCTAAGTGAATTGAATGCAGGGCAGCAACCCTGTAAATTTTTTCCATTCTCATATTATTCTACTGTCATTGCCCTATTGGCTTATTGGGA[G/A]AAATACTGGTAAAATAAGTTTTACTCTGATGTATTATCAGTGATGATCGGTCAGTACTTAACGTTATGGTGTGTGGTTTGCTTAGATTGT
93608 A T CCATTCTCATATTATTCTACTGTCATTGCCCTATTGGCTTATTGGGAGAAATACTGGTAAAATAAGTTTTACTCTGATGTATTATCAGTGATGATCGGTC[A/T]GTACTTAACGTTATGGTGTGTGGTTTGCTTAGATTGTTGAAACTGCTGTGTGCTTTGTGTTTTTGGTAATTTCCTTTCTGTTTTTTATACCC
93608 G C ATTATTCTACTGTCATTGCCCTATTGGCTTATTGGGAGAAATACTGGTAAAATAAGTTTTACTCTGATGTATTATCAGTGATGATCGGTCAGTACTTAAC[G/C]TTATGGTGTGTGGTTTGCTTAGATTGTTGAAACTGCTGTGTGCTTTGTGTTTTTGGTAATTTCCTTTCTGTTTTTTATACCCTTGTTTTGGT
93624 A G CCTTAAAATTCAACAATGCTCTGAAAGTGTTAATGAATAACCTAAGCTTAAGGATGACTGGGATGAAGTACTCAATTGGAAGTTCACATGCAGTCGTTTC[A/G]AACATAATGAAGAACCCACATGCTCTTGGTTTCAAAGAGGTGAAGACAGCATGTTGCGGCTCTGGAAGGTTCAATGCTCAGTCGGC
93624 A G AACAATGCTCTGAAAGTGTTAATGAATAACCTAAGCTTAAGGATGACTGGGATGAAGTACTCAATTGGAAGTTCACATGCAGTCGTTTCAAACATAATGA[A/G]GAACCCACATGCTCTTGGTTTCAAAGAGGTGAAGACAGCATGTTGCGGCTCTGGAAGGTTCAATGCTCAGTCGGCTTGCATGCCAA
93624 C T TCTGAAAGTGTTAATGAATAACCTAAGCTTAAGGATGACTGGGATGAAGTACTCAATTGGAAGTTCACATGCAGTCGTTTCAAACATAATGAAGAACCCA[C/T]ATGCTCTTGGTTTCAAAGAGGTGAAGACAGCATGTTGCGGCTCTGGAAGGTTCAATGCTCAGTCGGCTTGCATGCCAAATGCAACT
93624 T C CTGCTTCTAAGCTTGCGGGCTTAGCTATCTATAATGGTTCTCTTGAGTTTGCAGCTCCTATTAATTTCAGGCAATTGGTCCATGGTTAGTTGTAAACTGC[T/C]GCTTAATAAGATGGTTTTTGTATGTATCTACCCACCTTTGGTGAACTTGTCGGTACAAGTTGTAATTTCAGTGCTGTCTTGGTTTAAGAA
93624 A G TATTAATTTCAGGCAATTGGTCCATGGTTAGTTGTAAACTGCTGCTTAATAAGATGGTTTTTGTATGTATCTACCCACCTTTGGTGAACTTGTCGGTACA[A/G]GTTGTAATTTCAGTGCTGTCTTGGTTTAAGAATGTAAGGTCGTGAGCATGTCCTTTTGGAAGCCAAAAAAAAAAAAAAAAA
93630 T G TTCTTCAAGATAAAATTACTATTTGTCAAGCCTAGCGCGCGCATCCCTACGTCTTCACGTGCCTCTCAACTTTCAAGCTCAAATCTCTAAGATCTGCAAC[T/G]CTCGTATCTAAAATTGCATTGAAGAGGATCACGACATTGACAGGAAGGATGCGATAGCGGAGATGGTGAACTGAATTTCCTGACGAGG
93630 T C CACGTGCCTCTCAACTTTCAAGCTCAAATCTCTAAGATCTGCAACTCTCGTATCTAAAATTGCATTGAAGAGGATCACGACATTGACAGGAAGGATGCGA[T/C]AGCGGAGATGGTGAACTGAATTTCCTGACGAGGTGGGTTTTGCCAGTGCTGGAGAAATTTGCGGTGTGGTGGCTCATATTATGGGT
93630 T C AATCTCTAAGATCTGCAACTCTCGTATCTAAAATTGCATTGAAGAGGATCACGACATTGACAGGAAGGATGCGATAGCGGAGATGGTGAACTGAATTTCC[T/C]GACGAGGTGGGTTTTGCCAGTGCTGGAGAAATTTGCGGTGTGGTGGCTCATATTATGGGTTTCGGGTTGGACACGGTTTGCACTCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
93632 T A TGAAAACTCTCCATCTGATCCTTCAACCTCTTCCTCAACCCACTCACCACCGAAACCCTAGTCCTATCCGTACCGCTCCCAGGCCCGCATCCCTCCACCG[T/A]CCGATTCGACGCGTTGGCCCGATCCAGCGCCTCCAACTTCACCTTCATCACCTTCGCCTTCTTCAGGCAGACTGCCACGTCGGCGTCCAT
93632 C T CCATCTGATCCTTCAACCTCTTCCTCAACCCACTCACCACCGAAACCCTAGTCCTATCCGTACCGCTCCCAGGCCCGCATCCCTCCACCGTCCGATTCGA[C/T]GCGTTGGCCCGATCCAGCGCCTCCAACTTCACCTTCATCACCTTCGCCTTCTTCAGGCAGACTGCCACGTCGGCGTCCATCTTCGACTTG
93632 G C GCCCGCATCCCTCCACCGTCCGATTCGACGCGTTGGCCCGATCCAGCGCCTCCAACTTCACCTTCATCACCTTCGCCTTCTTCAGGCAGACTGCCACGTC[G/C]GCGTCCATCTTCGACTTGAGCGCCTTAATCTGACTCGCGCTGTGCAGCGTTTTCGAGCTCTCGTTCGCTTCGTGCAGCGATCTGTGGAG
93632 A G ACGCGTTGGCCCGATCCAGCGCCTCCAACTTCACCTTCATCACCTTCGCCTTCTTCAGGCAGACTGCCACGTCGGCGTCCATCTTCGACTTGAGCGCCTT[A/G]ATCTGACTCGCGCTGTGCAGCGTTTTCGAGCTCTCGTTCGCTTCGTGCAGCGATCTGTGGAGGAGATCGATTAGTTTCAGCTCCTCTTT
93632 T G AGCTCTCGTTCGCTTCGTGCAGCGATCTGTGGAGGAGATCGATTAGTTTCAGCTCCTCTTTTATGGATTCCACGTCGGAGAAGAACTTGTCCAGGTTGGC[T/G]CCGCCAGACGTGGCCTCTGCACTGCCGAAGCTCGGGTTGCGGGTTAGTTCTGTGGATCGGACGTCGCTGTCGCGGCGCCATGAGTT
93632 A G GCGATCTGTGGAGGAGATCGATTAGTTTCAGCTCCTCTTTTATGGATTCCACGTCGGAGAAGAACTTGTCCAGGTTGGCTCCGCCAGACGTGGCCTCTGC[A/G]CTGCCGAAGCTCGGGTTGCGGGTTAGTTCTGTGGATCGGACGTCGCTGTCGCGGCGCCATGAGTTGGAGAAGAGATTGTTCATTT
93632 G A TGCCGAAGCTCGGGTTGCGGGTTAGTTCTGTGGATCGGACGTCGCTGTCGCGGCGCCATGAGTTGGAGAAGAGATTGTTCATTTGTTGGGCTTTTTCCGT[G/A]TTGTTTCTTTTTTCCCTCAGGAGAGATACTCGGAATCTTATGAAAGGAGAAAGAAGATGAAGGAGAAGGCGTTGGTCAATGGCCG
93632 C CT GCTCGGGTTGCGGGTTAGTTCTGTGGATCGGACGTCGCTGTCGCGGCGCCATGAGTTGGAGAAGAGATTGTTCATTTGTTGGGCTTTTTCCGTGTTGTTT[C/CT]TTTTTTCCCTCAGGAGAGATACTCGGAATCTTATGAAAGGAGAAAGAAGATGAAGGAGAAGGCGTTGGTCAATGGCCGGACGTT
93634 C T CTGCTGTTATAACAGCTGCACTTACTGGCTCGCTTTACTATATCGCAACTGCTCCAAAAGATCCTACATACGTAGTTGCTCCAGTGTTGAGGTCACGCTG[C/T]GGCAAGGCGGATCTCAAGAAGCTTTTTGCAGCCTGGTACGAGCGAAGACAAATGAAGAAGATATATTCTCCCCTTTTGGAGGGGATG
93634 G A GGTCACGCTGCGGCAAGGCGGATCTCAAGAAGCTTTTTGCAGCCTGGTACGAGCGAAGACAAATGAAGAAGATATATTCTCCCCTTTTGGAGGGGATGCT[G/A]GCTCTATATCTTGGCTATGAATGGGTTCGGACGGGTAACATTCTTGCACCGATGATAACACATGGTATATACTCAGCTGTTGTGCT
93660 G C TTGCCTGAGACCAGCCAATTCCGATTCGAGTTTTTGGATTTCTTTGTTCGCTTCTTTAAGCTG[G/C]GCATCGGCGAAACTCGTAAAAGTCAACTTGAAGGCGTCAATTTCCTTGGCCAAGTCTGTAAACTCCTTGTTCATAGCTTTTGCTTCCTTTCCATGGACTG
93660 T C GTTGTCCCCAATGAAGTACTTTATCTGATCCGCCCTCTGGGCCTTGGACAGAGTTGGATCAGCTTGACCAGTAGCCACAGGTAGCATCGTAGTGGCCATT[T/C]GTTCAGATTGGGTTGCAATATTGGCGGCGAGGTCTCTAGAGTCCCAGAGGAGTTTCCTGTATCTTGTCTTGTAACCAGCCCAAGTGG
93662 G A GGGAGGCAGAAAACATATTAATGGCCTCGTCTGTGAAGGTGGAAGGAGCATCGTTGGCGCCAGCTAAGCGTCGAGATCCGTACGAGGTCTTGGGTGTCTC[G/A]AGAGATTCTTCGGATCAGGAGATCAAATCTGCTTATAGAAAGCTTGCTCTCAAGTACCATCCTGATAAAAATGCTAGCAATCCTG
93662 A G AGAAACCGGAGGCATGGATATGGAGATTGACCTGTCCAATCTGGGTACAGTGAACACAATGTTTGCAGCATTATTTAGTAAGTTAGGAGTTCCAATTAAG[A/G]CAACTGTTTCCGCAACTGTTCTAGAAGAAGCTTTGAATGGAACAGTCACAATCAGACCTCTTCCTCTTGGCTCATCATACAGTGGAA
93678 A G TCTTGGATCGCATCAAGAAGGCTTACGATAGGAATGCGGATCTTTCAAATCTCCTTGTAGACCCAGAATTTGCGAAGGAGATAATAGAAAGACAGGCTGC[A/G]TGGCGTCGTGTCATTTGCCTTGCTGTTAACTCCGGCATTTCCACTCCAGGCATGTCTGCGAGTTTAGCTTATTTTGATACATACAGA
93686 T TA CATGTTGAGTCTGTAAGCGGCGGTAGATCTAACCGTGATGACCTGAAAAATTGGGATGCTGAGTTCGTCAAATTCGCTGAAGTTGATAAAGACATGCTTT[T/TA]CGACATGATCTCGGCAGCAGATTCTCTAAACATCCCAAGCTTGGTGGGCCTCCTGTGGCGTACTGTGAGGAAAACAATAAAGGGT
93686 A T TCGCTGAAGTTGATAAAGACATGCTTTTCGACATGATCTCGGCAGCAGATTCTCTAAACATCCCAAGCTTGGTGGGCCTCCTGTGGCGTACTGTGAGGAA[A/T]ACAATAAAGGGTATGACTTCTGAGCAAATGGGCGAATATTTCAACAGAAGAGGAGAAGTAGTTTCGCAGGAAGAGTAAGCAGACC
93686 T A AACAATAAAGGGTATGACTTCTGAGCAAATGGGCGAATATTTCAACAGAAGAGGAGAAGTAGTTTCGCAGGAAGAGTAAGCAGACCGCTCTTGAGAACAC[T/A]CGTCATATGAATAGAATTTAGTTACCAGACTTTGTTGGGTTTAAGAGTGTTTTGGATAGCAGTTGTTGCATAACCATAGTTTTAGC
93686 G A TATTTCAACAGAAGAGGAGAAGTAGTTTCGCAGGAAGAGTAAGCAGACCGCTCTTGAGAACACTCGTCATATGAATAGAATTTAGTTACCAGACTTTGTT[G/A]GGTTTAAGAGTGTTTTGGATAGCAGTTGTTGCATAACCATAGTTTTAGCCTTCGGTATTTTTTGCAATAATATTAAGCTCAGTTCACT
93686 A G AAGTAGTTTCGCAGGAAGAGTAAGCAGACCGCTCTTGAGAACACTCGTCATATGAATAGAATTTAGTTACCAGACTTTGTTGGGTTTAAGAGTGTTTTGG[A/G]TAGCAGTTGTTGCATAACCATAGTTTTAGCCTTCGGTATTTTTTGCAATAATATTAAGCTCAGTTCACTCACGCAATCCGTGATTTAAT
93686 G A TTTCGCAGGAAGAGTAAGCAGACCGCTCTTGAGAACACTCGTCATATGAATAGAATTTAGTTACCAGACTTTGTTGGGTTTAAGAGTGTTTTGGATAGCA[G/A]TTGTTGCATAACCATAGTTTTAGCCTTCGGTATTTTTTGCAATAATATTAAGCTCAGTTCACTCACGCAATCCGTGATTTAATGATGAG
93686 G C GAATTTAGTTACCAGACTTTGTTGGGTTTAAGAGTGTTTTGGATAGCAGTTGTTGCATAACCATAGTTTTAGCCTTCGGTATTTTTTGCAATAATATTAA[G/C]CTCAGTTCACTCACGCAATCCGTGATTTAATGATGAGCAATATGACTACGCTTTTAACTCATGCCCAAAAATTCGTAATTCATTTTAGTTT
93686 A C TTAGTTACCAGACTTTGTTGGGTTTAAGAGTGTTTTGGATAGCAGTTGTTGCATAACCATAGTTTTAGCCTTCGGTATTTTTTGCAATAATATTAAGCTC[A/C]GTTCACTCACGCAATCCGTGATTTAATGATGAGCAATATGACTACGCTTTTAACTCATGCCCAAAAATTCGTAATTCATTTTAGTTTGTTT
93690 T C CGCGAGGCATCTTCTTTGCCTCGGAATCTTCGACGTCCTTCAATTGATAGTAGTGAGGAGCAATTTCAACAAGCCACTCGGGTTTCAATTCAGTGACCTG[T/C]CGCATGTACTCCTTTGTCGTCAAAACAAGCTCATGATAGATGGCCCACCTTGGAAGCTCCTTCGCTAGACCAGAACTTGGATGTATGT
93702 G GCA AAGAAGCAGATTTCTGACTTCGATCGTTTTAAGCTGATGAAGGCCAAGCAAGCGCGTAACCGCCTGGTCATGGTAGAATTTGGCAAGCTGAGGAAGGCAA[G/GCA]AGAAAGCTGGCGTGAAGAAGACCCGCAAGCCAAACAAGAAGGTCCATCGCATCTAAACAAGCTGCAAGAACTGATGTATAGT
93702 CA C GATGAAGGCCAAGCAAGCGCGTAACCGCCTGGTCATGGTAGAATTTGGCAAGCTGAGGAAGGCAAGAGAAAGCTGGCGTGAAGAAGACCCGCAAGCCAAA[CA/C]AAGAAGGTCCATCGCATCTAAACAAGCTGCAAGAACTGATGTATAGTTAGCGGATAACTGTTGAATAGTTAATAGAATGAAA
93726 C CT GTTTTCTTCTCTTCAATTTCAACAACTCGGCCTCGTTCTCAAGCTCCACAAAAACCACTGACATCTTCACTTCACCACAAATCCGGCATCCTCTTTTATT[C/CT]TTCTTCTCCATCATTTACATATGAAATGAATCCTTGTTTGTACTACACAATATGTGCTTGAGTTCTCCATCCAAGATCCACCATTTGTCGTG
93734 T C ACCGTAGACTCCATCAAATGATGTTCCAAGATAGAGACTACGAGAATTGCAAAGGACTTGAGGTTTCTATTGAAAACTTGGTTGATCCGGAGTACACAGT[T/C]GTCAATGTTGAGTGTAGAGATCGACCTAAGCTTTTGTTTGACATCATATGCATGCTCACTGACATGGAGTATGTCGTGTTCCATGGC
93734 A G TCCAAGATAGAGACTACGAGAATTGCAAAGGACTTGAGGTTTCTATTGAAAACTTGGTTGATCCGGAGTACACAGTTGTCAATGTTGAGTGTAGAGATCG[A/G]CCTAAGCTTTTGTTTGACATCATATGCATGCTCACTGACATGGAGTATGTCGTGTTCCATGGCAATGTCTACACTGAAGGAGACTGC
93734 A C GCAAAGGACTTGAGGTTTCTATTGAAAACTTGGTTGATCCGGAGTACACAGTTGTCAATGTTGAGTGTAGAGATCGACCTAAGCTTTTGTTTGACATCAT[A/C]TGCATGCTCACTGACATGGAGTATGTCGTGTTCCATGGCAATGTCTACACTGAAGGAGACTGCGCTCATCAGGAATT
93744 G T GGCCTACCAATGGAAACATTGATATCTTTGACTTGAAGGTTAGATATCGAGAAAATACCCCTTTAATTCTGAAAGGTGTTACTCTCAACATAAAAGGAGG[G/T]GAGAAAATAGGCGTTGTTGGCAGGACTGGCAGTGGTAAATCCACGTTTATTCAAGCATTATTTAGGGTTGTGGAACCATGTGGAGG
93744 A G GTGTTACTCTCAACATAAAAGGAGGGGAGAAAATAGGCGTTGTTGGCAGGACTGGCAGTGGTAAATCCACGTTTATTCAAGCATTATTTAGGGTTGTGGA[A/G]CCATGTGGAGGAAGAATAATTATCGATGATGTCGATATTTGCAAAATGGGACTCCACGATATGCGATCTCGCTTTGGTATTATACC
93744 C T TAGGCGTTGTTGGCAGGACTGGCAGTGGTAAATCCACGTTTATTCAAGCATTATTTAGGGTTGTGGAACCATGTGGAGGAAGAATAATTATCGATGATGT[C/T]GATATTTGCAAAATGGGACTCCACGATATGCGATCTCGCTTTGGTATTATACCTCAAGAGCCAGTGCTTTTGGAAGGAACGGTTAG
93744 A G GAAGAATAATTATCGATGATGTCGATATTTGCAAAATGGGACTCCACGATATGCGATCTCGCTTTGGTATTATACCTCAAGAGCCAGTGCTTTTGGAAGG[A/G]ACGGTTAGAAGCAATATTGATCCTACGGGGAAGTATTCTGATGAAGAGATCTGGCAGAGTCTTGAACGCTGCCAATTGAAAGACGT
93744 A G TATTTGCAAAATGGGACTCCACGATATGCGATCTCGCTTTGGTATTATACCTCAAGAGCCAGTGCTTTTGGAAGGAACGGTTAGAAGCAATATTGATCCT[A/G]CGGGGAAGTATTCTGATGAAGAGATCTGGCAGAGTCTTGAACGCTGCCAATTGAAAGACGTGGTGGCTGCAAAAGCCGAGAAGCT
93744 C T ATTTGCAAAATGGGACTCCACGATATGCGATCTCGCTTTGGTATTATACCTCAAGAGCCAGTGCTTTTGGAAGGAACGGTTAGAAGCAATATTGATCCTA[C/T]GGGGAAGTATTCTGATGAAGAGATCTGGCAGAGTCTTGAACGCTGCCAATTGAAAGACGTGGTGGCTGCAAAAGCCGAGAAGCTT
93748 A G AGTTGTTCACACGCTCGCATTCATCTATCCACTCGCTATATATGTCTACTGGTTCTGTAAGAGCAGTAATGGTAGTGCTGAAATTTTCTTGACAAACCAT[A/G]CAGATGGCTTCCCCAATCAGATTCTTCATATCAATGCGACATTCGACACTGCCACCATGATTGCAGAATGGGCAGCAGAAGGTAGTGT
93748 G A TGTTCACACGCTCGCATTCATCTATCCACTCGCTATATATGTCTACTGGTTCTGTAAGAGCAGTAATGGTAGTGCTGAAATTTTCTTGACAAACCATACA[G/A]ATGGCTTCCCCAATCAGATTCTTCATATCAATGCGACATTCGACACTGCCACCATGATTGCAGAATGGGCAGCAGAAGGTAGTGTCCAG
93778 A T CAGCCTTTTTCTTAAGTGCATCAATCTCACTCTGTAATTTACTCATGCCTGATGATTTCTCTTGAAGGAATGTATCCAAAACAGCAATCTTGTCATCTTT[A/T]ATCTTCAATTCTTTTGTTTTCTCCAAAAGGTTAGATTCTAACGAAGAGATCTTCGACTGAAGCTTGTTGATCTCCAATTTTAAACTCAAATC
93778 T C TGATTTCTCTTGAAGGAATGTATCCAAAACAGCAATCTTGTCATCTTTAATCTTCAATTCTTTTGTTTTCTCCAAAAGGTTAGATTCTAACGAAGAGATC[T/C]TCGACTGAAGCTTGTTGATCTCCAATTTTAAACTCAAATCTGGATCCGCGGGCTCTGAAATCCGCTCTTCAACCTGCGGTTCTGCCCTAAT
93778 C T TCATCTTTAATCTTCAATTCTTTTGTTTTCTCCAAAAGGTTAGATTCTAACGAAGAGATCTTCGACTGAAGCTTGTTGATCTCCAATTTTAAACTCAAAT[C/T]TGGATCCGCGGGCTCTGAAATCCGCTCTTCAACCTGCGGTTCTGCCCTAATTCCAGCTAATAAGACTGAGAAGGCGATCCAAAGCACCAA
93806 C T CTTGTTGGACTTGATGTCAAATGTCTCTGTTGTGGAGTGTTCCCCAATCGGAACCATATGCGGCGAAGCATCTTCAAAGGTGCCGGTATACCTGAACCTG[C/T]GAACGGCCGAACGTTTAGCAGTCCCTGTCAACCACTTCTCCTCCGCTGCCTCCTTAGAAAGTGCCAAGTGAGTCACGCCTCGTTCCTT
93816 G A CGCTTTTATCGTCTTCCCTTCTATCTGAAGAGTTCGAGTCGCAAATTCAACGCCGATCGTAGACTTTGATTCTAAACAAAATTCATTCCTTGTAAATCTC[G/A]ACAAAATGTTTGATTTTCCAACACCTGAATCTCCGATCAATACAATCTTAAACAAGTAATCGTATTCGTGATCCACCCTATGAGCCATAGA
93830 CT C GGAATCATTCCCTCCTCTAGCTCTGTGCCCTCTGTATCTGCCGCTGGGGTTGCACCCCGGTTGTCATCAGGTTGTGTTGCAGCACCTTTTGCCTCATCTT[CT/C]TTTTTTAACACGTTTGTTTTTGTCCACAGGTTTAGCATGGAACTTGGCACGAACTTCCAGTGGCAATAGTTCAGGAGGAACCACTCCTT
93830 CT C ATACTGAGCTTCAATTCCAGCAGATTCATCCATATCCTCAGCAAGTGGTTTCCAATATTCATTGATTGAAGGGGTACGAACACGTTGAGGATCAGTTAAA[CT/C]TAACCAGGATTTTGATCTGCCCATTTCCATAATTGTGCTAGCTCTTTGTTTCCCAGTCTCCATCGTACTTTACGTTTTTT
93830 C T TGAGCTTCAATTCCAGCAGATTCATCCATATCCTCAGCAAGTGGTTTCCAATATTCATTGATTGAAGGGGTACGAACACGTTGAGGATCAGTTAAACTAA[C/T]CAGGATTTTGATCTGCCCATTTCCATAATTGTGCTAGCTCTTTGTTTCCCAGTCTCCATCGTACTTTACGTTTTTT
93852 A T GGCCAGACGGAGTCGGGCCCTCTGGGGAGTGCAGAGGAGGTGAGCCGTATGATGAGGGAGTTGAAGGAGGGGTACGATGGTAC[A/T]TTCATCTGCAGTGGAGGGTACACCCGTGACCTGGGGATGGAAGCAGTCAGGGAAGGAGACGCCGATCTTGTCAGCTACGGTCGGTTGTTCATTTCAAAC
93852 C T AGACGGAGTCGGGCCCTCTGGGGAGTGCAGAGGAGGTGAGCCGTATGATGAGGGAGTTGAAGGAGGGGTACGATGGTACATTCATCTGCAGTGGAGGGTA[C/T]ACCCGTGACCTGGGGATGGAAGCAGTCAGGGAAGGAGACGCCGATCTTGTCAGCTACGGTCGGTTGTTCATTTCAAACCCAG
93852 G A TGCAGAGGAGGTGAGCCGTATGATGAGGGAGTTGAAGGAGGGGTACGATGGTACATTCATCTGCAGTGGAGGGTACACCCGTGACCTGGGGATGGAAGCA[G/A]TCAGGGAAGGAGACGCCGATCTTGTCAGCTACGGTCGGTTGTTCATTTCAAACCCAGATTTGGTTGAAAGGTTTAGACTGGAT
93860 T C TGAACGCTGAAATGGTTTTAGGGCTTTCGATGGTCAGCGTATGCGGGTGGAGAAAAATCAGATCGAGTTTGAAGAAGAGGGTTTTTGGCCTCTTCCCTTT[T/C]TATTCCATTTGATTTTGAGGAGGATAAGAGATCGAGAATTTTTCTCTTTTCTAATCCAGTAGGCCAACA
93870 T C ATCTTGTTTGATTTCTCTTTGGACGAATATACCGACACAAAACACTTAAACATGTCAGAAACACAACACAACTCACATCAAATAATAATAACAACATCAA[T/C]AGAGCGAGAGAACAGTTTATTTGTTGAGTGATTACGTGGGAATTTAGGCTGTCAATTTCCACATTCGAACACATGCATCTTCGCCTGCA
93870 C A GTTTGATTTCTCTTTGGACGAATATACCGACACAAAACACTTAAACATGTCAGAAACACAACACAACTCACATCAAATAATAATAACAACATCAATAGAG[C/A]GAGAGAACAGTTTATTTGTTGAGTGATTACGTGGGAATTTAGGCTGTCAATTTCCACATTCGAACACATGCATCTTCGCCTGCACTAAC
93870 G A ATCAATAGAGCGAGAGAACAGTTTATTTGTTGAGTGATTACGTGGGAATTTAGGCTGTCAATTTCCACATTCGAACACATGCATCTTCGCCTGCACTAAC[G/A]ATGCTGTTGTCATCAACAAAGGCCAGTCCGTACACTCCTCCCAGATGAGCACCTTTCGCTGTTATCCTTTGGCTTGCAGGCTTATCCAC
93870 G A CAATTTCCACATTCGAACACATGCATCTTCGCCTGCACTAACGATGCTGTTGTCATCAACAAAGGCCAGTCCGTACACTCCTCCCAGATGAGCACCTTTC[G/A]CTGTTATCCTTTGGCTTGCAGGCTTATCCACTTCATATATTATCACACTAGTGTCCAGGGATCCAGTGGCTACCTTTTGATTGTCCGGAG
93870 A G CTTCGCCTGCACTAACGATGCTGTTGTCATCAACAAAGGCCAGTCCGTACACTCCTCCCAGATGAGCACCTTTCGCTGTTATCCTTTGGCTTGCAGGCTT[A/G]TCCACTTCATATATTATCACACTAGTGTCCAGGGATCCAGTGGCTACCTTTTGATTGTCCGGAGACCATGCAAGACAGTTTATGCGTGC
93870 T C CTCCTCCCAGATGAGCACCTTTCGCTGTTATCCTTTGGCTTGCAGGCTTATCCACTTCATATATTATCACACTAGTGTCCAGGGATCCAGTGGCTACCTT[T/C]TGATTGTCCGGAGACCATGCAAGACAGTTTATGCGTGCAGTGTGATACAACATGTTTTTCAGCTTCGTCTCTCGAGATGCACGGTCCCA
93872 T G AACTGGTAAAGATTTTTCAACTTCGGTTTTAAGGTCTGCTTTACTAGCTGGAGGAGCTTTCAGAACATCGGGCCTTGGAGCAACCCGACCTGATAATCTA[T/G]GCACTGGAGTAGGTTTTAGCGCTTTAGGTTCAGGTAGAGATCGACCCGATAATTTGGCTGCTTCAGTGGCTGGAGACGATTTTAAAG
93872 T C GGTTTTAGCGCTTTAGGTTCAGGTAGAGATCGACCCGATAATTTGGCTGCTTCAGTGGCTGGAGACGATTTTAAAGCTACAGGTTTGGGTGGAGCTCGAC[T/C]TGAAAAGCAAGGCACGTCAACTTTTGGTCTAGGTATTGCACGGCCTGAACATCTAGCTGGTTCACTAATTGGAAAAGCAGATGCGC
93872 G A GTTCAGGTAGAGATCGACCCGATAATTTGGCTGCTTCAGTGGCTGGAGACGATTTTAAAGCTACAGGTTTGGGTGGAGCTCGACTTGAAAAGCAAGGCAC[G/A]TCAACTTTTGGTCTAGGTATTGCACGGCCTGAACATCTAGCTGGTTCACTAATTGGAAAAGCAGATGCGCCTCTAGGTTTAGGTGC
93872 T C GAGATCGACCCGATAATTTGGCTGCTTCAGTGGCTGGAGACGATTTTAAAGCTACAGGTTTGGGTGGAGCTCGACTTGAAAAGCAAGGCACGTCAACTTT[T/C]GGTCTAGGTATTGCACGGCCTGAACATCTAGCTGGTTCACTAATTGGAAAAGCAGATGCGCCTCTAGGTTTAGGTGCAGGTTGGG
93872 T G TTTAAAGCTACAGGTTTGGGTGGAGCTCGACTTGAAAAGCAAGGCACGTCAACTTTTGGTCTAGGTATTGCACGGCCTGAACATCTAGCTGGTTCACTAA[T/G]TGGAAAAGCAGATGCGCCTCTAGGTTTAGGTGCAGGTTGGGCTGAAAAGGAAGAGGCCCCTTTAGATGGAAGAGCTTGAGA
93874 C T AGATTGCATAGCCACCAGCTCCAGCTGCTAATAGACCAAAGAAGATAACCCATAAAAAGCTCCAGCTTACAACCTCTGTGCTTGCTTCTTTGCTTATGCA[C/T]GTGTCATGCTCCCTCATGTACAATAGATTACTAGGGCAGCCGCACTCGTAACTTCCCCAAGTGTTTCTGCATCTACAGCCTGAGCATTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
93874 C T AAGATAACCCATAAAAAGCTCCAGCTTACAACCTCTGTGCTTGCTTCTTTGCTTATGCACGTGTCATGCTCCCTCATGTACAATAGATTACTAGGGCAGC[C/T]GCACTCGTAACTTCCCCAAGTGTTTCTGCATCTACAGCCTGAGCATTGACAAGCAGTCCTCGCTTTGCATTCATCAATGTCTTCACATGA
93874 G A CAACCTCTGTGCTTGCTTCTTTGCTTATGCACGTGTCATGCTCCCTCATGTACAATAGATTACTAGGGCAGCCGCACTCGTAACTTCCCCAAGTGTTTCT[G/A]CATCTACAGCCTGAGCATTGACAAGCAGTCCTCGCTTTGCATTCATCAATGTCTTCACATGAGTTTACACCATCACCCTTGAAGCCTGGA
93874 G A TGCTTGCTTCTTTGCTTATGCACGTGTCATGCTCCCTCATGTACAATAGATTACTAGGGCAGCCGCACTCGTAACTTCCCCAAGTGTTTCTGCATCTACA[G/A]CCTGAGCATTGACAAGCAGTCCTCGCTTTGCATTCATCAATGTCTTCACATGAGTTTACACCATCACCCTTGAAGCCTGGAGGACATTTA
93874 G A AGCCTGAGCATTGACAAGCAGTCCTCGCTTTGCATTCATCAATGTCTTCACATGAGTTTACACCATCACCCTTGAAGCCTGGAGGACATTTACACCCACT[G/A]GAATTATCTGTGCAGGCACTATATGTCCTCCCGTCTTTGCTCTGGTGCCAGCAACCACCGTTGTTAATTGCACACCTTCCAGA
93878 T G AATCTTCCACCGCCAACTGCTTTCAATCGGCGGTAGGTGCGTCCCAAAGCACGCCAATTCGTTCCATCCCCTCTTCTACCGATTGACCTTTTCCGATCTT[T/G]CCCTTTTTCCATCTTCCCCCTTACAGCCCGTCGTCTTCAAATTCCGTATCAGCAACCCAAAGCGTTTGCTTTGTCCACCTCCTCACATCGAC
93878 T TC ACTGCTTTCAATCGGCGGTAGGTGCGTCCCAAAGCACGCCAATTCGTTCCATCCCCTCTTCTACCGATTGACCTTTTCCGATCTTTCCCTTTTTCCATCT[T/TC]CCCCCTTACAGCCCGTCGTCTTCAAATTCCGTATCAGCAACCCAAAGCGTTTGCTTTGTCCACCTCCTCACATCGACGGCGTCATTGAGG
93878 C A TTTCCCTTTTTCCATCTTCCCCCTTACAGCCCGTCGTCTTCAAATTCCGTATCAGCAACCCAAAGCGTTTGCTTTGTCCACCTCCTCACATCGACGGCGT[C/A]ATTGAGGGAAAATAGCTCCTGCTCCAAAGGCTGTCAGTTAGCCCTACGTTGTTCTCCGACATGTTTTAGGGGAAATAACCACCGTCGCCT
93878 A AC TTGCTTTGTCCACCTCCTCACATCGACGGCGTCATTGAGGGAAAATAGCTCCTGCTCCAAAGGCTGTCAGTTAGCCCTACGTTGTTCTCCGACATGTTTT[A/AC]GGGGAAATAACCACCGTCGCCTATTTGGGATTTCTCTTTGCCTCTTCAACAATGGTTTGCCTCTTCCCATATGGTTGTTTCGAAACGCT
93878 G A CTCACATCGACGGCGTCATTGAGGGAAAATAGCTCCTGCTCCAAAGGCTGTCAGTTAGCCCTACGTTGTTCTCCGACATGTTTTAGGGGAAATAACCACC[G/A]TCGCCTATTTGGGATTTCTCTTTGCCTCTTCAACAATGGTTTGCCTCTTCCCATATGGTTGTTTCGAAACGCTGATGCTTCAACTACAT
93878 T C GGAAAATAGCTCCTGCTCCAAAGGCTGTCAGTTAGCCCTACGTTGTTCTCCGACATGTTTTAGGGGAAATAACCACCGTCGCCTATTTGGGATTTCTCTT[T/C]GCCTCTTCAACAATGGTTTGCCTCTTCCCATATGGTTGTTTCGAAACGCTGATGCTTCAACTACATTCAATTCAATTTGCTGTTGGCTGT
93882 A G CCGCTTGGCCATTCATTTCAGGGTCATCATCATCGTCTTCTTTGTCTTCATCATCTTCATCGCCTGCAAAATCGTCATCGTCGTCATCATCAGCGTCATC[A/G]TCCTCATCGTCGTCATCACCTTCGTCCTCGGAGTCGCCTACATCCTTATTCTCTGTTTCAGCTTTGTTTTTTCGTTTAACAGCGACAGGAAG
93882 GT G CAAAATCGTCATCGTCGTCATCATCAGCGTCATCATCCTCATCGTCGTCATCACCTTCGTCCTCGGAGTCGCCTACATCCTTATTCTCTGTTTCAGCTTT[GT/G]TTTTTTCGTTTAACAGCGACAGGAAGCACCCCAGAGATAACTTGAGCTTCTCCTGTCAGATCATTTTGGCTGGACGAGGCCATCATCAT
93890 T C ACGTCTCTCCTCCAAAGTACTTCTTGTCCCCGAGCTCCGTCTCTAAAACCTTGAGAATGTCGATGTATGCCTTTTTCGCTTCCTCCCTTGCTTCCCCTTT[T/C]TCTTGCCATATCTTCACTCCAGCTCCCCATACCTTGCTCTCAACGTAGTTAGCCCAAAATTTAACTTGGTATTTCTCATAAGGGTTTTTGGGG
93892 A G CAAGAGTTTTCTTGGAGCTCTCACCTCTAAGTCCAGGAAATCTGTTCCTTTTGGCTGTTGGAATTTCTGGCACTCCGGCCGAATCAGCACCTTCAACAGC[A/G]GTGAAATATGCATCCCTTGATATGGCCTGAACTGCTCCAATCCCAGCGGCCTTGACGAAGCTTTCGGCAATCCTATTGACGAGGGGAT
93892 T A CACCTCTAAGTCCAGGAAATCTGTTCCTTTTGGCTGTTGGAATTTCTGGCACTCCGGCCGAATCAGCACCTTCAACAGCAGTGAAATATGCATCCCTTGA[T/A]ATGGCCTGAACTGCTCCAATCCCAGCGGCCTTGACGAAGCTTTCGGCAATCCTATTGACGAGGGGATGCCCAAAATCGAAAAGCCAG
93892 T C TTTCTGGCACTCCGGCCGAATCAGCACCTTCAACAGCAGTGAAATATGCATCCCTTGATATGGCCTGAACTGCTCCAATCCCAGCGGCCTTGACGAAGCT[T/C]TCGGCAATCCTATTGACGAGGGGATGCCCAAAATCGAAAAGCCAGCCCTTTTCCAAGCTCTTCAGCTCATCGAAAAATGTACGGGTT
93892 A G CGAAGCTTTCGGCAATCCTATTGACGAGGGGATGCCCAAAATCGAAAAGCCAGCCCTTTTCCAAGCTCTTCAGCTCATCGAAAAATGTACGGGTTTCGAG[A/G]TTGGTGTTGCTCATCCTGCCTGATGGCGTCAGCGTCAAACAGTATATTTCGAGGAGTGTATTTGATGGATCAAACAAAATAAGGAA
93902 T TA CTGAAAGTAACATTTCAAGTGAAAATAATCAAAGAAATGACAAACAGGGAAAGTCTAATATTCTTAACAATGTTACAGTCAGGGATAATAATAATGGTTT[T/TA]AAATCTTTCAACTCCTTGATAGCGCAACAAGATGGAAATGGGCAGCAAATCACATTCTGGGGAGATGCCACAAAGCCAATTGATGA
93908 C CA ACCACAACAGCAAATAACACATTCAAACCGCAGCCATCACCCAATCATACAAACCACAACACCACACCATACCATTCTCAAGCCTAAAAACTCACTTCAT[C/CA]ACCCAGCAGCGAATTTCTTCGCACCACCCAAAACGCCATCAGCATTCTCATCCTTGGTCTCTGCCTTCTTCGCCTCCTCGGCCTTCGCA
93908 C T CAGCAGCGAATTTCTTCGCACCACCCAAAACGCCATCAGCATTCTCATCCTTGGTCTCTGCCTTCTTCGCCTCCTCGGCCTTCGCACCCGGTTTGAGAGT[C/T]TGTACGTAGGCGCCAGCCTGCTGCGCGCCTGAACACACAGCGTCGCCTGCTTGTTTGCCGAAGCCAGCGGCAGCGTCCATCGCCTTTG
93908 C A TTCTTCGCACCACCCAAAACGCCATCAGCATTCTCATCCTTGGTCTCTGCCTTCTTCGCCTCCTCGGCCTTCGCACCCGGTTTGAGAGTCTGTACGTAGG[C/A]GCCAGCCTGCTGCGCGCCTGAACACACAGCGTCGCCTGCTTGTTTGCCGAAGCCAGCGGCAGCGTCCATCGCCTTTGTTGTTATCTCCA
93908 A G GAGAGTCTGTACGTAGGCGCCAGCCTGCTGCGCGCCTGAACACACAGCGTCGCCTGCTTGTTTGCCGAAGCCAGCGGCAGCGTCCATCGCCTTTGTTGTT[A/G]TCTCCACCACCGTCGTTTGCGCCGTCCCGGCCGCGGCTTGCGCGTTGGTGAAGAAGTTGGATGGTGCTGCAGCCTTTTTGGTATCT
93908 G A CTGAACACACAGCGTCGCCTGCTTGTTTGCCGAAGCCAGCGGCAGCGTCCATCGCCTTTGTTGTTATCTCCACCACCGTCGTTTGCGCCGTCCCGGCCGC[G/A]GCTTGCGCGTTGGTGAAGAAGTTGGATGGTGCTGCAGCCTTTTTGGTATCTTCGCCCTTTGAAAACATTTTTGTTGCCTTTTTTTCCCC
93920 G A TGTGCAACGGCGACGAGTTTTGCGTGGTCGACTCGTCGATTTGGACCGGCGCATTGCCGGATTTGTTACTTACTGGATTTTTATTTGCTCGCTTTTGTTT[G/A]CTTGGAACACAACCTCCCCTTTACCCATTAATTTTCAATTCTAGGTTTAAAGAAGAAGGGCGACTGTATCAGTCTGATTCGGCAATTGA
93920 T TC AGTTTTGCGTGGTCGACTCGTCGATTTGGACCGGCGCATTGCCGGATTTGTTACTTACTGGATTTTTATTTGCTCGCTTTTGTTTGCTTGGAACACAACC[T/TC]CCCCTTTACCCATTAATTTTCAATTCTAGGTTTAAAGAAGAAGGGCGACTGTATCAGTCTGATTCGGCAATTGATACGCTGTCTGTAAG
93920 AG A CGGATTTGTTACTTACTGGATTTTTATTTGCTCGCTTTTGTTTGCTTGGAACACAACCTCCCCTTTACCCATTAATTTTCAATTCTAGGTTTAAAGAAGA[AG/A]GGGCGACTGTATCAGTCTGATTCGGCAATTGATACGCTGTCTGTAAGCAGGGACTAGCGAAACAAATCAACAGTTTAATTTGGATTACA
93926 AT A CCGGCTCACCATTTTGCATGGCCCGCACCATGATGCGTGGAACTCGACCATTACGGGCTCGTCGCTGCATAGGACTAGTTGGTTCCATGAACAAGGATTT[AT/A]TTGTCTCAGGTGTATTTGGATAAGCGTAAGTAACAATCCTTCTCTTAGTTTTCGGATAAATTGAAAGAGAGCAACTAATTGAAGATA
93932 A G ATATCTCTTTCCATTTCTTCTTCTTTTTCCCTGCCACTTTGCTCACAATGCTGCTGCACTTCTTCTTCCTCTTTCT[A/G]ACATCCGTGTCTTTAGCCAGTGCCGCGCCTCATCACCCTGCTGTCACGGTGACTGCTGCAGCGCCTGCTCCTGCTGCGTCCACTACCCCTGCCGACGCTC
93932 A C ATATCTCTTTCCATTTCTTCTTCTTTTTCCCTGCCACTTTGCTCACAATGCTGCTGCACTTCTTCTTCCTCTTTCTAAC[A/C]TCCGTGTCTTTAGCCAGTGCCGCGCCTCATCACCCTGCTGTCACGGTGACTGCTGCAGCGCCTGCTCCTGCTGCGTCCACTACCCCTGCCGACGCTCCGC
93932 T A ATATCTCTTTCCATTTCTTCTTCTTTTTCCCTGCCACTTTGCTCACAATGCTGCTGCACTTCTTCTTCCTCTTTCTAACATCCGTGTC[T/A]TTAGCCAGTGCCGCGCCTCATCACCCTGCTGTCACGGTGACTGCTGCAGCGCCTGCTCCTGCTGCGTCCACTACCCCTGCCGACGCTCCGCCGCCTAACA
93932 CG C ACATCATCGCTCTCATGTCCAAAAAAGGTTGCAAGACGTTTGCGGATCTGTTGACGGCGGGCACCGGGGACGCTGCGAAGACCTTCGCGGATTCGATCGG[CG/C]GGGGGGCTGACGGTGTTTTGTCCGTCTAACGACGCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGCCAAG
93932 A G TTGCAAGACGTTTGCGGATCTGTTGACGGCGGGCACCGGGGACGCTGCGAAGACCTTCGCGGATTCGATCGGCGGGGGGCTGACGGTGTTTTGTCCGTCT[A/G]ACGACGCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGCCAAGACGTCGCTGTTGCTCTACCATGGAGTCCC
93932 C A CCTTCGCGGATTCGATCGGCGGGGGGCTGACGGTGTTTTGTCCGTCTAACGACGCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGC[C/A]AAGACGTCGCTGTTGCTCTACCATGGAGTCCCCGTCTACTACTCGCTGACCATGCTCAAGTCCAGCAATGGCGTGATGAACACGTTG
93932 C T GGGGGCTGACGGTGTTTTGTCCGTCTAACGACGCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGCCAAGACGTCGCTGTTGCTCTA[C/T]CATGGAGTCCCCGTCTACTACTCGCTGACCATGCTCAAGTCCAGCAATGGCGTGATGAACACGTTGGCGACGGACGGAGTGGCGAA
93932 A T CGCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGCCAAGACGTCGCTGTTGCTCTACCATGGAGTCCCCGTCTACTACTCGCTGACC[A/T]TGCTCAAGTCCAGCAATGGCGTGATGAACACGTTGGCGACGGACGGAGTGGCGAAGAACTTCAATTTCACCGTTCAGAACAGTGGC
93932 T C GCGATGAAATCGTTCCTTCCCAAATTGAAAAACCTAACGGCTGACGCCAAGACGTCGCTGTTGCTCTACCATGGAGTCCCCGTCTACTACTCGCTGACCA[T/C]GCTCAAGTCCAGCAATGGCGTGATGAACACGTTGGCGACGGACGGAGTGGCGAAGAACTTCAATTTCACCGTTCAGAACAGTGGCG
93936 G C CCTTTTCAAATTAAGCACTCAATAGATACATACATTCATGAAGCAGTACCTCAGAGTCTCAGACAAGACGATCATAT[G/C]GACATAACGGACAGGTTAGTCTCTGATTCAACCACGGCTTAACACAGTGATAATGAAACTCATGAGAACACGGTGTTTTCAGCACCGTATCTTCCTTCTT
93936 T C ACTCAATAGATACATACATTCATGAAGCAGTACCTCAGAGTCTCAGACAAGACGATCATATGGACATAACGGACAGGTTAGTCTCTGATTCAACCACGGC[T/C]TAACACAGTGATAATGAAACTCATGAGAACACGGTGTTTTCAGCACCGTATCTTCCTTCTTCATCCCACACAAACAAATCGAACAATC
93936 C T GTCTCTGATTCAACCACGGCTTAACACAGTGATAATGAAACTCATGAGAACACGGTGTTTTCAGCACCGTATCTTCCTTCTTCATCCCACACAAACAAAT[C/T]GAACAATCTTTATCATACCCAGTGCCAGTACCATCTTCATCATATGCTACTCTTCCTTGTTTCGTAACAAATATTTCTATTCCGACTCCAG
93936 C T TTAACACAGTGATAATGAAACTCATGAGAACACGGTGTTTTCAGCACCGTATCTTCCTTCTTCATCCCACACAAACAAATCGAACAATCTTTATCATACC[C/T]AGTGCCAGTACCATCTTCATCATATGCTACTCTTCCTTGTTTCGTAACAAATATTTCTATTCCGACTCCAGCGCCCCTAAAGTTCACAATCG
93936 A G GAACAATCTTTATCATACCCAGTGCCAGTACCATCTTCATCATATGCTACTCTTCCTTGTTTCGTAACAAATATTTCTATTCCGACTCCAGCGCCCCTAA[A/G]GTTCACAATCGCCTGATGCGATAGGTTAAAGATGCAGTCTTTGAACAGGTTTACGAAACCCGGATCTGAAATACGAGTGATCGACGTCA
93936 T C ACAATCTTTATCATACCCAGTGCCAGTACCATCTTCATCATATGCTACTCTTCCTTGTTTCGTAACAAATATTTCTATTCCGACTCCAGCGCCCCTAAAG[T/C]TCACAATCGCCTGATGCGATAGGTTAAAGATGCAGTCTTTGAACAGGTTTACGAAACCCGGATCTGAAATACGAGTGATCGACGTCATCA
93936 C T CCTTGTTTCGTAACAAATATTTCTATTCCGACTCCAGCGCCCCTAAAGTTCACAATCGCCTGATGCGATAGGTTAAAGATGCAGTCTTTGAACAGGTTTA[C/T]GAAACCCGGATCTGAAATACGAGTGATCGACGTCATCATCCTCGCCAAAGCATGGAGATGAGAAGCCTCCAGATGTGTGGATCGATC
93936 T C CAAATATTTCTATTCCGACTCCAGCGCCCCTAAAGTTCACAATCGCCTGATGCGATAGGTTAAAGATGCAGTCTTTGAACAGGTTTACGAAACCCGGATC[T/C]GAAATACGAGTGATCGACGTCATCATCCTCGCCAAAGCATGGAGATGAGAAGCCTCCAGATGTGTGGATCGATCGAAGCGGACAGA
93936 A G ATACGAGTGATCGACGTCATCATCCTCGCCAAAGCATGGAGATGAGAAGCCTCCAGATGTGTGGATCGATCGAAGCGGACAGATGAATTTGCCCTGATCG[A/G]TTTTTGTACGGAGATCAAATTCTGGCCTAAAGAGGCACGGCAAGAAAATCCAGATGCGACGATGGAGAAAGAAGCGATTCCGGC
93936 G C CTCGCCAAAGCATGGAGATGAGAAGCCTCCAGATGTGTGGATCGATCGAAGCGGACAGATGAATTTGCCCTGATCGATTTTTGTACGGAGATCAAATTCT[G/C]GCCTAAAGAGGCACGGCAAGAAAATCCAGATGCGACGATGGAGAAAGAAGCGATTCCGGCTGAGTTTGGCGAAGGCGATGGTG
93936 T C CCAAAGCATGGAGATGAGAAGCCTCCAGATGTGTGGATCGATCGAAGCGGACAGATGAATTTGCCCTGATCGATTTTTGTACGGAGATCAAATTCTGGCC[T/C]AAAGAGGCACGGCAAGAAAATCCAGATGCGACGATGGAGAAAGAAGCGATTCCGGCTGAGTTTGGCGAAGGCGATGGTGCTGC
93936 C A GAATTTGCCCTGATCGATTTTTGTACGGAGATCAAATTCTGGCCTAAAGAGGCACGGCAAGAAAATCCAGATGCGACGATGGAGAAAGAAGCGATTCCGG[C/A]TGAGTTTGGCGAAGGCGATGGTGCTGCTTTAATTCTGAACTCGATGTCGCCATGTCGCAGTGAGGCGGC
93936 G A TTGCCCTGATCGATTTTTGTACGGAGATCAAATTCTGGCCTAAAGAGGCACGGCAAGAAAATCCAGATGCGACGATGGAGAAAGAAGCGATTCCGGCTGA[G/A]TTTGGCGAAGGCGATGGTGCTGCTTTAATTCTGAACTCGATGTCGCCATGTCGCAGTGAGGCGGC
93980 C T AGAAATGCTTAATGACCTGCAATATAGGTCACGAGGATTGGAAAAAAGCAGATCGTGATAAACCTCTGATAAGCAGCATATAATGGCGAGAATAATCGTC[C/T]TAGATTTTCCAAAATGAAGCAAAGAGGAAGAACAGTGATTTCATATTGGTTGCCTAGTCCATCTCCCTTTTTAGCATCTCAGCCAGA
93980 T C GATATTATCATTGGATTGTTATTTGTCTAAAATTTGCCTAAGGCGGGAAAGAAGCGAGCAACAGCGAGGGAGAAACCCGAAACGGCTTCCCAAGTGACTG[T/C]TGAGACAATCCTTATTCACTGAACGGTTAGGGTTTACCTGAATTAGCTAGAGAAATATCGTAATCTAGGGAAGCGGGACGGCGAG
93986 T C AACTTTGTTGTTCTTCTACGAGCGTTTTCTGCAAGTCCTTTATCACTTCATCCTTTTGCATAAGCAGTTCGTTCAGGCATTGGAGATCAAAATGTGCACG[T/C]GTGCATGCTTGTTCTTTTTCAACATACAACATTTCCGCCTTTCTAATCGTAGACTGCAGTTGCTCATTGTAAGACTCAAACTCTGATAGTG
93986 GT G TCTTCTACGAGCGTTTTCTGCAAGTCCTTTATCACTTCATCCTTTTGCATAAGCAGTTCGTTCAGGCATTGGAGATCAAAATGTGCACGTGTGCATGCTT[GT/G]TTCTTTTTCAACATACAACATTTCCGCCTTTCTAATCGTAGACTGCAGTTGCTCATTGTAAGACTCAAACTCTGATAGTGGTACTTCCAC
93986 T A TCTTCAATATCACCAGCACCCACGTGCCTCTTACCCTTACCAATGTCACCGTCATGAAAGTTTGAGCTACTCGGTCCAAGGTTTTGATCGACCAAATTCA[T/A]CTGCGGAGAATATGAATGTAGCTCATCATTCGAATAATCATTCTTCTCCTCACAAAAATTCTCTAACTTCATATTAGTCTCATTATTTGAA
93988 C CT ACTGTTGGCCTACTGGATTGAGGAAAGCAAAAGAACCGCAACAGAGAAAAAATGGATCCCTACAAGCATCGCCCGTCGAGTGCTTACAACACTC[C/CT]TTTTTGGACGACGAACTCCGGAGCTCCAGTTTGGAACAACAACTCGTCTTTGACTGTTGGAACTCGAGGACCTGTTCTTCTTGAGGATTACC
93988 C T GAGCTCCAGTTTGGAACAACAACTCGTCTTTGACTGTTGGAACTCGAGGACCTGTTCTTCTTGAGGATTACCATCTTGTTGAGAAGCTTGCACAATTTGA[C/T]AGGGAACGGATCCCAGAGCGTGTTGTCCATGCAAGAGGAGCTAGTGCCAAGGGCTTTTTTGAAGTTACACATGACATTACTCACCTC
93988 C CT TTCTTCTTGAGGATTACCATCTTGTTGAGAAGCTTGCACAATTTGACAGGGAACGGATCCCAGAGCGTGTTGTCCATGCAAGAGGAGCTAGTGCCAAGGG[C/CT]TTTTTTGAAGTTACACATGACATTACTCACCTCACTTGTGCTGATTTTCTTAGGGCTCCTGGTGTACAGACACCAGTCATTGTTCGA
93988 A G ACCATCTTGTTGAGAAGCTTGCACAATTTGACAGGGAACGGATCCCAGAGCGTGTTGTCCATGCAAGAGGAGCTAGTGCCAAGGGCTTTTTTGAAGTTAC[A/G]CATGACATTACTCACCTCACTTGTGCTGATTTTCTTAGGGCTCCTGGTGTACAGACACCAGTCATTGTTCGATTCTCCACCGTCATTC
93988 C T AGGGCTTTTTTGAAGTTACACATGACATTACTCACCTCACTTGTGCTGATTTTCTTAGGGCTCCTGGTGTACAGACACCAGTCATTGTTCGATTCTCCAC[C/T]GTCATTCATGAACGTGGGAGTCCTGAAACATTGAGGGATCCTCGTGGTTTTGCTGTAAAATTTTACACCAGAGAGGGTAACTTTGATAT
93988 T C TTGTTCGATTCTCCACCGTCATTCATGAACGTGGGAGTCCTGAAACATTGAGGGATCCTCGTGGTTTTGCTGTAAAATTTTACACCAGAGAGGGTAACTT[T/C]GATATGACTGGAAACAACTTCCCCGTTTTCTTCATTCGTGATGGAATACAATTCCCAGATATGGTGCATGCTCTCAAACCGAACCCAAA
94022 C CG TGTCTCCAGGAAGACGATAGTGTTCTGCTTGATTGCCACTTCCAGGGCTTCCAGTTGATAGCAGCGAGCTATACTATGAGGATCTGGACTGCCGAGCCTC[C/CG]ATGCTTGTTTGGTGACGATGAGGCTTGATAGTTGAGATCCAACTTCTTTTCTTCCATTATCTATCTTTCTACGTCCGGTAGATTATGA
94024 T A ACATGATCACCGAAGCAGTAGGACAACGACTAAAAGAAATTCAGAATCTCATTTAAACTTACAATCACACAGTAGAAACATTTATTAACTACCACCACCA[T/A]GATTCCGAAACATAAGTACAAAGATGAACATTATTTACCAAGATCCAGCAGCAGGAGCAAAAGAAACCAAATCACGAACCCTAGCCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
94024 G C GAGGGTAACTTTTGCTGCTTCTCATTTTCAGGTTGTAGTGGTGCACACAGAATTTACCCAGATCTTGGATCTCTTTGTTGGATTCGACATTGACGATGAC[G/C]GTTCGGCCGCCAACTCGGCGCTCGCCGTCGCCTCCAATCAGGCGAGAGTGCGACTGGAGCGAAAACAGCAGGAGGAGGAAGAGTA
94058 T TA CAGAACACAAGCATATACCACTTCAGCATGTTCCATGCCTCTCATCACTTGACACCTGTTATTGCAACTGACGATGAGATTGAAGCCGAGGCAAGAGCTG[T/TA]AAAAAATGTCGCAGACCATCTTTGCCCTCTTAATATAGTATTGGATAGAGTAGTACTGACTTCAACTGGCGTTCTTCTTGGGTGCTG
94084 G A CAAATATAAAAACAAATTGACGGTTAACTACTAAAAAAACTATTGCCCCAAAAAATAATAATAACTACACAGACAACCCAGCCAAAAACGCCACACCAGT[G/A]GAAGGCAGCCAAGATGACCCATAAATAAACTGCCCCACCGTAAACTTAACCGCCTCCTCCGGCAAAGTAATAACCCTGTACCCGGGC
94084 A G ACACAGACAACCCAGCCAAAAACGCCACACCAGTGGAAGGCAGCCAAGATGACCCATAAATAAACTGCCCCACCGTAAACTTAACCGCCTCCTCCGGCAA[A/G]GTAATAACCCTGTACCCGGGCCAGGTCACTCTCTTGCCGACAGCTGCACCCGGCCCATAATTCATATACTCCCCATAATACAAAGTG
94084 T C ACGCAAACGTCGCATTCCACTCCAACCACCCAGCCGGGTGCACATGGTCCCCCATGTAACTCATCATGTACACCACCCTCGAATACATCTTCCAAGGTCT[T/C]CCCAAATACGTCGGATACGCCGTTCTCGCCGCCTCCAGATCAGCCGTGGCCACCACTCTGCACGCGTGGATCGAGATCCCCGTGTTCT
94084 A G CATGGTCCCCCATGTAACTCATCATGTACACCACCCTCGAATACATCTTCCAAGGTCTTCCCAAATACGTCGGATACGCCGTTCTCGCCGCCTCCAGATC[A/G]GCCGTGGCCACCACTCTGCACGCGTGGATCGAGATCCCCGTGTTCTGGTTCGGGTCCTTCCG
94088 ACCCCC A CTTGTACTTCCGGTGATTGTGGCACCGGACAGGTATTTTTTGATTCTCATACACATTAACATACATACATTACGTAGATGATTTTACATTCTACGTTATT[ACCCCC/A]CCCCCACACTACAGGTTGCATGCAACAATGCTGGAGGTCGCACCCCTGCCTCGCTTGTAGAATTCAAAGTGAATGGCGACGGCA
94106 G A GTACTTTCCAAATACGCCGAACAGAGAGATCGGCTTAAGAGGGCGCAAAGGCGTGCTTTGGACATCCTCAACACGGTTGGACTGTCCAACTCTGTATTGA[G/A]GCTCATAGAGAGAAGACATCGCACCGACAAGTGGATTGCATACACTGGAATGATTATAACTGTGGTTGTGGTCTATACTTTTTGGA
94106 C G GACATCGCACCGACAAGTGGATTGCATACACTGGAATGATTATAACTGTGGTTGTGGTCTATACTTTTTGGAGGTGGACACACTAGAAAAGTAAAGATGT[C/G]TAAATGTTGAGCATAAGGGTGGAATCAGTTTTCATGTGTAGTATCTGGATTTAAAAATGTCATTGTTTTGGTGAATATTTGCTGACA
94144 G A AGGACTTCATACCGTTTTTTCTTTCGGAGAGTAACATCGAAGACGAGGATGAGAAATCCATTTTGACTAGATTCGAAAAATACTGCAATGAAATAGAGTC[G/A]ACGTCTGCATGGGGCGGTCAGCTTGAGCTCGGCGCTCTCACGCATTGCCTCAAGAAACATATAATCATCTTATCGGGTTCTTTCCCCG
94144 G A ACGAGGATGAGAAATCCATTTTGACTAGATTCGAAAAATACTGCAATGAAATAGAGTCGACGTCTGCATGGGGCGGTCAGCTTGAGCTCGGCGCTCTCAC[G/A]CATTGCCTCAAGAAACATATAATCATCTTATCGGGTTCTTTCCCCGATGTGGAGATGGGAGAGGAGTATAAGTCGGAGAATGAAA
94144 T C GGGGCGGTCAGCTTGAGCTCGGCGCTCTCACGCATTGCCTCAAGAAACATATAATCATCTTATCGGGTTCTTTCCCCGATGTGGAGATGGGAGAGGAGTA[T/C]AAGTCGGAGAATGAAAGAAGCATCATGCTGTCTTATCATCGACATGCGTATGGGCTCGGCGAGCACTACAATTCTATTATTCCTGT
94144 G T ATATAATCATCTTATCGGGTTCTTTCCCCGATGTGGAGATGGGAGAGGAGTATAAGTCGGAGAATGAAAGAAGCATCATGCTGTCTTATCATCGACATGC[G/T]TATGGGCTCGGCGAGCACTACAATTCTATTATTCCTGTGGAGGCGGTAACCACAAGCTCTTGATTCTCTCTGAGCTATATTAGTATTG
94144 C T CTTTCCCCGATGTGGAGATGGGAGAGGAGTATAAGTCGGAGAATGAAAGAAGCATCATGCTGTCTTATCATCGACATGCGTATGGGCTCGGCGAGCACTA[C/T]AATTCTATTATTCCTGTGGAGGCGGTAACCACAAGCTCTTGATTCTCTCTGAGCTATATTAGTATTGTTGCCTGGTGAACTTAATGA
94144 GTAC G GTAACCACAAGCTCTTGATTCTCTCTGAGCTATATTAGTATTGTTGCCTGGTGAACTTAATGAGTTGTATGACATTGGTGATGTTGTAATTGTGCTATAT[GTAC/G]TACTATATGTATAGCATGCCAAATATGAATATGAGTGTGTTGAGTGTCACTGTACTTTGATGCTTCAAATTTTGTTTATGTAGAAAT
94148 A G GATCAAGAAACAATTTAAAAGCATTACCATACAAGACAATGAAGCTATACCTGTTTCTCCTTCTCAACGTTATAGCTTCCTTCATTTCTTTCACCTACTC[A/G]TCAAGAGCAATGCCTCCATCTTCTTTCCAAAAATATAAAACCGTAAACCTTGGTGGTTGGCTTGTTACTGAAGGATGGATCCAACCTAGT
94148 A G TATTGGATGGAACTCAACTGCAAGTTAAGTCCGTAACAGTAAACAAATACCTTTGCGCTGAAAATGGCGGTGGAGACATCATCGTCGCCAATCGATCCTC[A/G]GCTTCTGGCTGGGAAACTTTTAGACTATGGAGAGTCACACAGAACACTTTTCAACTTCGGGTTTTCAACAATCAATTCATAACACTAG
94154 CT C TTACATCACGTCAACACCATGTCTGCAACAGTACGCTGTGTATTGGAAGACGTGTGAAGCATGCTCTTTGTGTCGCTCAAGGCCTATGTAAACTGGTTTT[CT/C]TTGTGGCCCTTGCTGTCAAGCATGTGATGTTGTTTGTAGCACTTTATTATGAAATGTAATTATGTAATCTACTGTTTATTCAGTATATA
94160 T C TGAGTACCACGTGAGGAAGAACTCTCCATACGGGTTGCTCCATCCACCGTTCCGTTGGAAGAACGGCGCTTCTTCAGGCCAGTTGTTGTAGGTACCCGCA[T/C]CCGTTGGGCCTCCATTTCCCCATTCCGGTTTTCCTAACAATTCGGCATTGGCTTTGAGGCTGCTTTTCATGTACTTATCGTAGCATTGA
94174 C CA CAAATTCGTACGTATTCACAAACAACTCATGTCCTCAAAGCACTCAAATATTGGTACAATCACACAATCTTAGGCATGGGTAGAAAAAATCAAACACCAC[C/CA]AAAAGGAAAATAGAAAATCACTTGGAACTTGAAATTCCACAATAGAGTTCAAATTGTAAATTGTAGGTTATACGCAGCTGTTTTGCT
94176 C T TTTGCTTTCGATTTTGGACAACGCTAGCAACCTAGCCTAAATGAAATCCCTTCTTGGAACTACTGTATGCATTCAGGAACCGTTGCTTCCAATAATTGAC[C/T]GCTGTCATAAAACATAATCCACGTGTTCCCGTTCAATACCCCGCTGCTACCTTTGTCACCGCCGCGCCACCCTCCATGATCGACAAGACG
94192 C T ATGCTCAGCCAAAATTGGCCTCCGGTCATGGTCCTATTGTCCTTATCTTGGCACCAACTAGAGAACTGGCTGTTCAAATACAGGAAGAATCTCGTAAATT[C/T]GGTGGCCACTTAACTGTGAGAAGTACCTGTGTTTATGGTGGTACACCTAAAGGTCCACAGATCCGCGAACTTAGAACGGGGGCTGAA
94206 GT G TATTTTGGTGATGATCACAGCAACCTGCAATGTTTCCCTGATCAGAATGTCACTTATCCTTTCTTTGAGAGTGCCATGACGTTGAAGTTCAATGAATTTG[GT/G]TCTTTTCTGAATCATACTCTTAATGGCCCGTGCAGCGTCCTTCAGCAAGCTCTCAGGTGATGATGGACCACAAGATATTGCCTGCGAT
94206 C T CTGAATCATACTCTTAATGGCCCGTGCAGCGTCCTTCAGCAAGCTCTCAGGTGATGATGGACCACAAGATATTGCCTGCGATTTCCTCCCATCAAGCTGA[C/T]AAAGTACTCCATCTACGCACGAGAAGCAGATGAAATGTTCATTCACATCTGTGGAAGCCTCGGTCTCCCCAGCGCTTGCTGCTACTGA
94206 A C GAATGTGCATTCTCCATTTCTCTATCCTTCTCAAGAAACATTGCACGCTCGAATGGATTCATGTTAGCAGTTGACTTGAAAAATTTATCGAAGAACGAAC[A/C]ATCGGCCAACTGGATCTCTGCTACTGCATTTCCAATGGCATGAAGTATCCCAACCGTTCCACAAGCATTGCCTACAGTCTGTTTTAAAA
94216 A G GTTAAAGATAACATTGCCTCTGACGATGCTCATTACACAGCGCAATCCTTGAACCAAACTATAGCTTGCGGCTATTCCATTTGCTATCACCAAAAACACT[A/G]GAGCTTTCATGTCAGTAAACCTGGCCTTCTTCTCAATGGAGAAAATAACCTTAACCTGAGAGTCAGAAGCAATAACAGAGGCAGCAAC
94218 G A CTGGAAAAAACTCATCTAAACCGACCCATAGATTTTATGCTTTCAGATCCTCAACTTTGTATCTCTGACCCAAAACTTCTCACAATTAACTAATTTTGAG[G/A]TCGAACAAATTCAGATATGGAGACTCCTCCAGTTTTTCAGGAGGCACCGAGATGCGACGTATGCAACTGTAGCTTCAACACTTTCCGCC
94218 T C CTCAATTTGGAATATATACTAATGTACGGGTATGCAATGAATGTTTCAACAACTCATCTAGGTCCATCCAAAACGGTTCTCAAAACTCTTCAATTCAATC[T/C]AGTGCTGTAGTAGATAGATTTTCAAAATTAAGTGTCGGGGATGATGCAGTTGTAAATACTTATGCACCTTCAACCGTACCTGTTATTGAA
94224 C T TCGCCCTTCTTTGGTTTCTTAGCCTCAGGCTTCACCGCTGGCGGGGGCGGCCTCTTTCCACCAGATTGGCTCCTAGTTTTCCTTGGTGATGTAAGCGAGG[C/T]GGGAGAGGTAACCGTACCGCTGTTCTTTTTGGGAGCCATTGATTTAATATTTCAAGATGAACCCAAATATTTTTATCCAGTAGGCCAA
94228 C T AAGACAGAATGCTTTATATAGAGGGATGTGCAAATTCAAGGGCAGTGACAATATTTATTCGTGGTGGAAATAAAATGGTGATCGAGGAAACTAAACGTAG[C/T]GTACATGATGCATTATGTGTAGCAAGGAATTTGATCCGCAACAATTCTATTGTTTATGGTGGTGGTTCAGCTGAGATTTCGTGCTC
94228 G A ACCTATTGACACTCTTACTGCAGTCAAAGCTCAACAAATCAAGGAGAAAAATGCTTACCTTGGAATAGATTGCAACGATGCAGGGACGAACAACATGCAG[G/A]AACAGAATGTTTTTGAAACGCTCATTGGAAAGCAGCAGCAAATTCTGCTGGCAACACAAGTGGTTAAAAATGATCTTGAAGATTGA
94238 TA T CGAAATTTGAAAGAATGCTATCATCTCTATGCGCTAAACTCTCTTTCCCAGTAGTTCGCTCCTTCTCTCGTCTCCCAAACCTTAAGAAGAGCCCTTGCTC[TA/T]AAAACCCTAAAAACTCCACTCTTTCTCCAACCATTAGCGCACACCACAACCCTAGCCGAACTCAATTCCTTCGTTACCGACGCCGAAGCC
94242 C T AAAAAGCAAAGATAGCAGTTTTTGCTGGAGGTGTTGATACGTCAGCAACTGATACCAAAGGAACTGTTCTGATTCATAATGCAGAACAGTTGGAAAATTA[C/T]GCAAAAACTGAAGAAGCCAAAGTTGAAGAGCTAATTAAAGCTGTTGCAGAGTCTGGGGCAAAAGTAGTTGTCAGTGGCGCTGCAG
94256 T A CAATCATATTCTACTTGCTATCATCCCCACATCAAGAACATACAGCTTCCACCGCGAGACTCTTTGTCGATCCTGGACATGAATCCCCAAACATCTTCGT[T/A]GATACTGCTACACTGCAGCTTTCTAATCCAACACATGCCTGTTGCACGACTTGACTCACACCATCGCTGCTGCATGATCCATGAACGTAA
94256 G A TAGAAGAAATAAGTTGATTGGGATATGGGCATTTCAGATGAAGCCTTGGCCCAAGTTTACGCTTTGATAACACCGACTTAAATTTAGAAACCCAGGCATC[G/A]ACAGGTGCAGTATGAGATTCTGATACATGTGAGCATAAGATCCCCGTCTGTCTAGTTGTAAATGCTATTTGACTAGGATCACCTCCC
94256 C T TTGGCCCAAGTTTACGCTTTGATAACACCGACTTAAATTTAGAAACCCAGGCATCGACAGGTGCAGTATGAGATTCTGATACATGTGAGCATAAGATCCC[C/T]GTCTGTCTAGTTGTAAATGCTATTTGACTAGGATCACCTCCCATTTCCTCAAACAGCACCAAAATGTTGCCGCTTGATTTAACAAATGA
94256 A G CCGACTTAAATTTAGAAACCCAGGCATCGACAGGTGCAGTATGAGATTCTGATACATGTGAGCATAAGATCCCCGTCTGTCTAGTTGTAAATGCTATTTG[A/G]CTAGGATCACCTCCCATTTCCTCAAACAGCACCAAAATGTTGCCGCTTGATTTAACAAATGATCGAGGAACATGGTACATTTTCTGAG
94260 G C AAGAGGCTGTTGTGATTCTCTACGAGGGGCTATGCATTCACTTGATTTGTTAAAGGCCCTGCACCATAATAAAATGAAAAGACTCTCCATTTTCTCGACT[G/C]TTGAAAATATTTATCCAACCGTTGAATAGATTGAAGTTGAAAACAAATTTCTAAAAGAATATGGATTTTTCACTGGAGGCGATCTCACT
94264 G A GAACATGAAGCCGCCATTGCCGTCGAAGCTGAGCGTCCAGTTGTGGAATTTCCACACCGAACGGCGGTGAGCAATCGTGAGCAACGTGATGCCGCGCGAG[G/A]AGCATTCTTCATACAGCCGTTGTTCGACCTCGACGTCGACGGCGCTGCTGCATTCGTCGAGGATGGCAAATCGGGGTTGGTGGA
94272 C T ACGTCTAGATGATTGAATTTGACCAGAGGAGGAGCTCGAGGCTTGCAAATGGAGGCGCGATCGAGGTACGG[C/T]GCAGGGATTTGGTTTTGGGGATTACGGACGAGCTCTGACCAATGGAGGAGGAATTGGCTTAAGGAGGCACCGTCGGCAGTGCGGTGGTGGCAGGTGAAGC
94272 G A ACGTCTAGATGATTGAATTTGACCAGAGGAGGAGCTCGAGGCTTGCAAATGGAGGCGCGATCGAGGTACGGCGCAG[G/A]GATTTGGTTTTGGGGATTACGGACGAGCTCTGACCAATGGAGGAGGAATTGGCTTAAGGAGGCACCGTCGGCAGTGCGGTGGTGGCAGGTGAAGCCAATG
94272 A T ACGTCTAGATGATTGAATTTGACCAGAGGAGGAGCTCGAGGCTTGCAAATGGAGGCGCGATCGAGGTACGGCGCAGGGATTTGGTTTTGGGGATT[A/T]CGGACGAGCTCTGACCAATGGAGGAGGAATTGGCTTAAGGAGGCACCGTCGGCAGTGCGGTGGTGGCAGGTGAAGCCAATGATGATG
94272 A G TTAAGGAGGCACCGTCGGCAGTGCGGTGGTGGCAGGTGAAGCCAATGATGATGCCACCGCATTTGTAGCGGTTTAGTTGGACCTGAAGTAGTTCTTTGAC[A/G]CCTTCAGTTGGAGGATGCAACTTAGAAAGATCCGACCCACCCTCGAGCGGCATCACCTCCGCCAACGTCAAATCAACTTCCGCCTC
94272 C T TGATGCCACCGCATTTGTAGCGGTTTAGTTGGACCTGAAGTAGTTCTTTGACACCTTCAGTTGGAGGATGCAACTTAGAAAGATCCGACCCACCCTCGAG[C/T]GGCATCACCTCCGCCAACGTCAAATCAACTTCCGCCTCAACGAATCGAACCCCTTCGTTGTTCAAACTAATACAGCCCTCACCGCGCT
94272 G A GAGCCCTAAAGGCGTGCACGGTGGGCACGTGGAGGTCCATGGCGGCGAGGTCGAAGATGGTCAGAGGGACGAGCGAGTTGGTCAGTGGGTGCGGAGGAGT[G/A]GATGGCCATGGTTTTAGAATTGCGCTGCTTGTGATTTCTACTGACATGGCCTTCTTTTCCAGTAGGCCAACA
94278 T C CCATCAAAGTACTCAGAAGAGGACCTGCTTCCATCACAGCCTTCATCAGCTTTCCCTTCTCCGGCAATGCAGCCGCCGCCGCCTCCTCCACCTCCGACGA[T/C]GAAGATGTTGGTGATGACATCATCATCTTTGGCAACGCTTCATGAACGCCATAGTTAGTGGAAATAAGACTTAAGAGGTGGTCACGC
94280 G GC CATCACTCCAACATCCACAATTTCATCATCATCAAGAGGAGCTTCACCATCAGACAACTCCTCGAGATCCGCCAAAAATGAATCAGCTAAATTTGCCATT[G/GC]TTGGCAACGAATCAGATTAACAAAAATGGGAAGGTGCTTCAATTGCTGACTTTCAATTACAGATATGGTTTGGGAATAGTGAATTTC
94282 T C CTCGTGCTGTCGCATTTAGCCAAAGAGACGGAGTTGCAGAAACTGAAAAGAGAGCGAACCGTTCTGATGATGGAAGT[T/C]ATACAGCTGAGGCAACAGCAGAAGAGCTTGAATGAACTGATACTGAAAATGGAGGGGAGAGTGCAATCTACGGAGAGGAAACAGCAGAACATGGTGTCGT
94282 C T GTTCGGGGAAACGACGAAGACTGCCGGATTTCGGAGACATGGAGGAATGCGGAGTTTCGGAACGGCAAAGAAGCATGTTGAAATGCATGGATGAGAGCTA[C/T]GATGCGATTACTGCAGATGTTATATGGGATGAGCTCTCCAACTGTGAATATTTGGGGAATGAATATGACTTGTCGGAGATAGA
94282 G C GGAAACGACGAAGACTGCCGGATTTCGGAGACATGGAGGAATGCGGAGTTTCGGAACGGCAAAGAAGCATGTTGAAATGCATGGATGAGAGCTACGATGC[G/C]ATTACTGCAGATGTTATATGGGATGAGCTCTCCAACTGTGAATATTTGGGGAATGAATATGACTTGTCGGAGATAGATGAGGA
94282 T C GCATGGATGAGAGCTACGATGCGATTACTGCAGATGTTATATGGGATGAGCTCTCCAACTGTGAATATTTGGGGAATGAATATGACTTGTCGGAGATAGA[T/C]GAGGAGGTGGAGGATGTGAAGGAGTTTGTAGAACTTATGGAGTATGATAGTTTCACGATGTAGAGAAGACTAGTGTTATTGTTGT
94282 G A TTACTGCAGATGTTATATGGGATGAGCTCTCCAACTGTGAATATTTGGGGAATGAATATGACTTGTCGGAGATAGATGAGGAGGTGGAGGATGTGAAGGA[G/A]TTTGTAGAACTTATGGAGTATGATAGTTTCACGATGTAGAGAAGACTAGTGTTATTGTTGTATAATTTATTTTTTGTTTGTTCAGAT
94288 CA C TAATAAGTTGGAGATTACAGTCATGGCAAGAGCAAGCGCAGAATTCCCTCCAACAAGATTCGTCAAAGCAACACCACTTGACAACGTTGTAGGCATGCAA[CA/C]AAAAAATTGCCAAACCAATAAAAAATTCTGAAGGGGCCAACTGCACTTTTAAAATCAGCTTTGATAAAACGGGCGTTATAAACAG
94288 C T AACATCCCTGCTGGCCAGGCTTCTGTAGCTGCACCAATTTCCTTGCTTCGCAATGTAAGCCCTGAAATTAAGAATATGCCAAAGGTGCTGAATTTAGACA[C/T]AGAATACTTGTGTGCAAGACATCCAAGAGTAGGATTTACAAGCCCTAGTGCTACACCACTAACAAGAGCGATTGGAAGGAAGTTTGT
94288 G A ACCCAAAATCTAGTAATGTTGATTTCCAACTAACAGAATTAGAAGGATTTGCATTGCCAGTTTGGTATGTTTTGCCGCCATCTTCCTGATCAGATCCTCC[G/A]TTAAGTCCAACTGATTGACAGACGAAAGAAAATTTTCCACTGTGCGATATCTGAGTCGAAGCAGAAAGAAAATAGCCTGCATAGCAGA
94312 T C TAGGCTTCAGAGAAAGAATAAATGATGATGTTACGAAGAACAAAAGAGAAGTTATGGTCTAGGAGGGATTCTGTTCCTGTTAATGCATCAAAAATTTCCA[T/C]ATTAGATTAGTAGCATTTACATATTATTAATGTATTTTGGCTGTAGCATCAAATGTCTGTTAAGCTCAATTTGCGATTTTTGTTGCAAT
94316 G GA TTTTTTGATATTAAATATTAATCATGATATTCCTAATAAATAACTTCACAACTTAAACAGTTCAAAAGATATTGTTCCACATATTACAAGGTATTGAACC[G/GA]AAACCGAAAATGCAATGCAAAGCGTTGGACAATCAAAGTCAAAATCATTTATCTAGAGTGAAAACAACCTTTTGATTTACTTACGCTTT
94316 G A AATACAAGGTCAATGGTTCTTTTCATTCTTGGAGAACTCTTTCTTTAATGTTTGCGACTCTAGCTCTTTTGCAGCAGCTCCCTCTCCTGACTTGGTTGCA[G/A]TTTTGGATTCCTCTTCAAGCCAGTGGCGGATGTGGCGCATGTTTCGCCGGAAAATTGTCGCCGATTGCTTAACGTCTGTGCGTAGAAGG
94316 G A CAGCTCCCTCTCCTGACTTGGTTGCAGTTTTGGATTCCTCTTCAAGCCAGTGGCGGATGTGGCGCATGTTTCGCCGGAAAATTGTCGCCGATTGCTTAAC[G/A]TCTGTGCGTAGAAGGAGAACGGCAGCACTCACAGCTGCTACTGTGAGGACAAAGTTGGTTAGTGCCATTGATCGATTGTTTTTGAAA
94316 T C TTCGCCGGAAAATTGTCGCCGATTGCTTAACGTCTGTGCGTAGAAGGAGAACGGCAGCACTCACAGCTGCTACTGTGAGGACAAAGTTGGTTAGTGCCAT[T/C]GATCGATTGTTTTTGAAATTACAAATCTTCGGTGAACTGAAAACCCTATGCACATGCAACGACCGAAAAATTGAGGAAAAAGAATG
94316 C A CCGGAAAATTGTCGCCGATTGCTTAACGTCTGTGCGTAGAAGGAGAACGGCAGCACTCACAGCTGCTACTGTGAGGACAAAGTTGGTTAGTGCCATTGAT[C/A]GATTGTTTTTGAAATTACAAATCTTCGGTGAACTGAAAACCCTATGCACATGCAACGACCGAAAAATTGAGGAAAAAGAATGCGG
94324 T A CCATGGATTATTGGTTTCGATACTAGACTATTTACCGTTGTCTATTCGGGAGTTGTGTGTACGGGCATTGCTTATTATGTGCAAGGAATTGTTACAAAGG[T/A]GAGAGGTCCGGTTTTCGTTACTGCCTTCCAACCACTGTGTATGATCATAGTTGCTGTTTTGGGGTCGCTCATTCTTTCCGAAGTGATCA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
94324 C A GGTGAGAGGTCCGGTTTTCGTTACTGCCTTCCAACCACTGTGTATGATCATAGTTGCTGTTTTGGGGTCGCTCATTCTTTCCGAAGTGATCACTTTGGGA[C/A]GGGTGTTTGGAGCATTGGTTATAGTGGTAGGACTATATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTCCGAA
94324 T A AGGTCCGGTTTTCGTTACTGCCTTCCAACCACTGTGTATGATCATAGTTGCTGTTTTGGGGTCGCTCATTCTTTCCGAAGTGATCACTTTGGGACGGGTG[T/A]TTGGAGCATTGGTTATAGTGGTAGGACTATATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTCCGAAGACGAT
94324 C A AAGTGATCACTTTGGGACGGGTGTTTGGAGCATTGGTTATAGTGGTAGGACTATATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTC[C/A]GAAGACGATGAGAAAAACTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGT
94324 C T ATTGGTTATAGTGGTAGGACTATATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTCCGAAGACGATGAGAAAAACTCTGGGTTAAAA[C/T]TGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGG
94324 A G TGGTAGGACTATATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTCCGAAGACGATGAGAAAAACTCTGGGTTAAAACTGCCAGTTGC[A/G]GCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATA
94324 A T ATGCCTTGGTGTGGGGCAAAGGCAAAGATGAACTGGGACAGGCCTCCGAAGACGATGAGAAAAACTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACAT[A/T]GAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGC
94324 C A CTGGGACAGGCCTCCGAAGACGATGAGAAAAACTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTT[C/A]AGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAA
94324 T C ACGATGAGAAAAACTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTC[T/C]GGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAA
94324 G A AAACTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGA[G/A]GGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGA
94324 C T CTCTGGGTTAAAACTGCCAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGG[C/T]TGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTG
94324 T A CAGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGC[T/A]TAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTA
94324 T C AGTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCT[T/C]AGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTAT
94324 A T GTTGCAGCCAGTGACATAGAAATACCAACAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTT[A/T]GCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATT
94324 C G CAAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTT[C/G]TATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCT
94324 T G AAGGTCAAAGTTTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTC[T/G]ATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTA
94324 A G TTTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTT[A/G]GTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATG
94324 G A TTAAGGTTCAGAATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTA[G/A]TTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATGA
94324 C T ATTTGATGCTATGTCTGGTTGAAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAG[C/T]TAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATGATGCAATTCAAGT
94324 T A AAGAGGGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGA[T/A]TAGTGCGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATGATGCAATTCAAGTTGCCTTTAATTGAT
94324 G A GGCTGAAAATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGT[G/A]CGCAGTATTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATGATGCAATTCAAGTTGCCTTTAATTGAT
94324 A G AATAATTTTGGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGT[A/G]TTTGTGTTGACTGGTGCGATGTATATCGTCTAATTATTGCATGATGCAATTCAAGTTGCCTTTAATTGAT
94324 G A GGCTTAGCTTGCCAATAAATTGTCAATTTTCTTCTATATGAATTTAGTTATGCTGTAGCTAAGTAATTAAGAATTGGGATTAGTGCGCAGTATTTGTGTT[G/A]ACTGGTGCGATGTATATCGTCTAATTATTGCATGATGCAATTCAAGTTGCCTTTAATTGAT
94326 A G CAAACAATCTAAATTTGAAACATCATTTTAACACAATATGTATGAAAAGAGAATTATATCATCATATGCATTATAACGATGCCGTGTCGGAGGACATAAC[A/G]GTGGTGGTGGTGGTAACAGAAGACGACCTCGGCGTGGTCAGAGCTGGCTTCACCAGAACGACAGACACATCGCTTTTCTTTCTGCGC
94326 G A ACAATCTAAATTTGAAACATCATTTTAACACAATATGTATGAAAAGAGAATTATATCATCATATGCATTATAACGATGCCGTGTCGGAGGACATAACAGT[G/A]GTGGTGGTGGTAACAGAAGACGACCTCGGCGTGGTCAGAGCTGGCTTCACCAGAACGACAGACACATCGCTTTTCTTTCTGCGCTCG
94326 T C CGTGGTCAGAGCTGGCTTCACCAGAACGACAGACACATCGCTTTTCTTTCTGCGCTCGCCTTCAGCTACAAGCTCTTTAGCCACCCACTCGACCTTTTCT[T/C]TGTTCGTCTCCTCGCCGACTGTGCATCCACGGAACATCACGGTCTTCACGTACCGTTCCTTCAGAACAGAGTCCGCGCCAGTTCCGCGG
94328 T C TTCTCTTGCTCTTCATAGGAAAGGAATACAATCACTTGTTTTGGAGAAATCTAGTACAATACGGTCTTCGGGCGCAGCAATTGGTGTTTTTATTAATGGC[T/C]GGCGTGCGCTTGACCAACTTGGAGTTGGTGCAACTCTTCGAACGACAGCTGTTCCTATCTTAGAGATGCACGATGCACTGGTTAGTCA
94328 G A CTTCGGGCGCAGCAATTGGTGTTTTTATTAATGGCTGGCGTGCGCTTGACCAACTTGGAGTTGGTGCAACTCTTCGAACGACAGCTGTTCCTATCTTAGA[G/A]ATGCACGATGCACTGGTTAGTCAAAACAAAACACGAGTGACATCATGCAGGAATGAAGAACTTCATTGCTTGAAAAGAAATGATCTA
94336 T C AATTCTCCACAATTCTACTTTGGTTAGTACATAAAGTTAAACATCCAGTACCATATATATCAGGATTATCTGTATTG[T/C]CAGTGCTCCGAGTACCATAAGGATCAGATATAGTTGCAAGATTCTGGCATCCCACTGCAGTAAATTTGTTGTGCGTGTTTGAAAGTGTGTATCTTTGGCC
94336 C T AATTCTCCACAATTCTACTTTGGTTAGTACATAAAGTTAAACATCCAGTACCATATATATCAGGATTATCTGTATTGTCAGTGCTCCGAGTA[C/T]CATAAGGATCAGATATAGTTGCAAGATTCTGGCATCCCACTGCAGTAAATTTGTTGTGCGTGTTTGAAAGTGTGTATCTTTGGCCCCTTAAGTCCAGA
94336 GT G TAGTTGCAAGATTCTGGCATCCCACTGCAGTAAATTTGTTGTGCGTGTTTGAAAGTGTGTATCTTTGGCCCCTTAAGTCCAGATAACTCTTGTAACGTTG[GT/G]TTGTTTTCTCCATCTGGATAGTGGCAAGAATAGCCAACGTAATTGCAGACGCGCAATTGAGCTTGAGAATGCAACATATCCATTATTT
94336 C T TTGTGCGTGTTTGAAAGTGTGTATCTTTGGCCCCTTAAGTCCAGATAACTCTTGTAACGTTGGTTGTTTTCTCCATCTGGATAGTGGCAAGAATAGCCAA[C/T]GTAATTGCAGACGCGCAATTGAGCTTGAGAATGCAACATATCCATTATTTCGACACCATCAACCGTGCTTGCTGTACCGGTTGCTTCAT
94336 T A TTTCCGGGTAATATTCTGGAGCTGTGTTTGATGCAGCTGAAGGTGAAGTCGTTGCAGCACTTAGCAGCTGAAACAATGTCAAAAATGCAAGAGTTAGTAC[T/A]GTTTTGTAGAGCAGTCTCATTGTTGGTGACATATGAGGCATTGAGACTGATAAAAAGGAAGGAAGATATTGTGTGTGCATATATAG
94362 C T GACCTTCTGTAGTGGAATAATAAAATGGGGAATTAGGGTTTGGTAGCGGCGGAAGACATTGGAATAGATAAAATCCAAAATAAAATGAATGGACATAGGT[C/T]AGAGAGAAAGAGGTGGATGGAAGTGAAGGATGATAGAAGAAAGTCAAGGTAGAGGATTAGGGAGTGAGCAGACGAGAGGAA
94362 A G CTTCTGTAGTGGAATAATAAAATGGGGAATTAGGGTTTGGTAGCGGCGGAAGACATTGGAATAGATAAAATCCAAAATAAAATGAATGGACATAGGTCAG[A/G]GAGAAAGAGGTGGATGGAAGTGAAGGATGATAGAAGAAAGTCAAGGTAGAGGATTAGGGAGTGAGCAGACGAGAGGAAAAG
94362 G A GAATTAGGGTTTGGTAGCGGCGGAAGACATTGGAATAGATAAAATCCAAAATAAAATGAATGGACATAGGTCAGAGAGAAAGAGGTGGATGGAAGTGAAG[G/A]ATGATAGAAGAAAGTCAAGGTAGAGGATTAGGGAGTGAGCAGACGAGAGGAAAAGATCGGTGGAAGAAATAAAGCGGAAG
CAGGAATACTTCAAGACGAGAAAGTAGATGGCAGAACTTCGCG
94366 C CTGCAAGATTGACAAGGAAGGAAAGGCTCGCAAGGTCGTTGGCTGCAGTTGTGTTGTTGTAAAGGATTACGGCAAGGAAAGTCAAGCACTCGACGTTGTT[C/CAGGAATACTTCAAGACGAGAAAGTAGATGGCAGAACTTCGCG]AGGAATACTTCAAGACGAGAAAGTAGATAGCAGAACTTCTCG
94396 A G TACAACAAACAACACACTCAACTATTTGTTATTAATTTTTGCAAACAGAAATTGTACATATCACCATCTTAATGTTGACTGGGCTGATCTTTGAACACCA[A/G]AGTTGTAAGTTTGCAATTTTCCCTTTGTCCATCTATTAGCAGTTCCATATCAGTAGGAGTATTCGTTTCCGCCTCGTAAGCAGGAAGAAA
94396 T C TTTGCAAACAGAAATTGTACATATCACCATCTTAATGTTGACTGGGCTGATCTTTGAACACCAAAGTTGTAAGTTTGCAATTTTCCCTTTGTCCATCTAT[T/C]AGCAGTTCCATATCAGTAGGAGTATTCGTTTCCGCCTCGTAAGCAGGAAGAAAAATGATGAGGATTATTTCAAAAGGCATCCAAATGCA
94396 GA G TGATCTTTGAACACCAAAGTTGTAAGTTTGCAATTTTCCCTTTGTCCATCTATTAGCAGTTCCATATCAGTAGGAGTATTCGTTTCCGCCTCGTAAGCAG[GA/G]AAGAAAAATGATGAGGATTATTTCAAAAGGCATCCAAATGCATCAAAGTACTTCATGCTTAATCTTTGATCTCCCTTGTCCATACGCCT
94396 A G CCATCTATTAGCAGTTCCATATCAGTAGGAGTATTCGTTTCCGCCTCGTAAGCAGGAAGAAAAATGATGAGGATTATTTCAAAAGGCATCCAAATGCATC[A/G]AAGTACTTCATGCTTAATCTTTGATCTCCCTTGTCCATACGCCTGTAGGCGATGACCTTTTGAAGCCCTTGGGGCAAATCGATGGGCA
94396 A T TCCGCCTCGTAAGCAGGAAGAAAAATGATGAGGATTATTTCAAAAGGCATCCAAATGCATCAAAGTACTTCATGCTTAATCTTTGATCTCCCTTGTCCAT[A/T]CGCCTGTAGGCGATGACCTTTTGAAGCCCTTGGGGCAAATCGATGGGCAATTTGGGAAGCAGTCGTAGCCCTAACTCGCCGGTGATA
94396 T C AGTACTTCATGCTTAATCTTTGATCTCCCTTGTCCATACGCCTGTAGGCGATGACCTTTTGAAGCCCTTGGGGCAAATCGATGGGCAATTTGGGAAGCAG[T/C]CGTAGCCCTAACTCGCCGGTGATAGGGTGGGGAAAAAAAGATAGCACAGCAGCGGAGCGAGGGTTCGGCAGGAGCAAATCCGATC
94396 G A TACTTCATGCTTAATCTTTGATCTCCCTTGTCCATACGCCTGTAGGCGATGACCTTTTGAAGCCCTTGGGGCAAATCGATGGGCAATTTGGGAAGCAGTC[G/A]TAGCCCTAACTCGCCGGTGATAGGGTGGGGAAAAAAAGATAGCACAGCAGCGGAGCGAGGGTTCGGCAGGAGCAAATCCGATCGC
94396 C T TCTTTGATCTCCCTTGTCCATACGCCTGTAGGCGATGACCTTTTGAAGCCCTTGGGGCAAATCGATGGGCAATTTGGGAAGCAGTCGTAGCCCTAACTCG[C/T]CGGTGATAGGGTGGGGAAAAAAAGATAGCACAGCAGCGGAGCGAGGGTTCGGCAGGAGCAAATCCGATCGCCTTCGAGTTAGGG
94402 G A ACACGTTGTGCTGGTGTCGAGTCGTAACGAGAAACCAATTAGGCAGAAAACTCTCCGGACAAATCTACTTCCTCTAAGTCTTACCTGTAAAAAGCAAGAT[G/A]GGCGAAGAATCAAAACCAAGCCCTCATCTCGGCTTTGCCGAAAACTTCATGTTGTCCGGAGCTGCTGCCATCATCTCCAAGACTGCC
94412 G A CGTCGAAACGCTGTGTGCTGGAGAGATACCAATCGCAGTACCAGTGCAGTTCGTCTGAGGTGGTGGTCGGCACAATGAGGGATCACGTCGAGTCGGAGCA[G/A]TGCATCGGTGCATGCGGAGTCGATCGTAGCTCGGTGGGGATCTCCTCCGACTCCCTTCTCGAGTCTGGATTCGTTCAGAAACTG
94424 A G GATGTGGGAAAAGAGGAAAATGTTGTTTAGGAAGAAGCGGGCAAAGTCTTCTTGGGTTAGCCAAGCAAAGAGCTGCTTCTTCCTTGTTGGGACTACTAGG[A/G]TTTGGGAACTGCTTTCGAGTATCGCGTCCAAGGCGGCTAGAATGCTTGAATTAGTCTCGACCTTTCGAACCAACGCGTCGCCTTTG
94432 C T CTTCCCGTACGTGTCGCAGACAGCCGTCGTCGGCAGTCCCAGCAGCCAGAGCAGCACCGTCGAGTCGTCCTCGCCTCCTCCGATCCCAGCTGCAGTGTCT[C/T]TGGACCTGGATCTGAGGGTTTCAACTGGCAATTTCAGGCCTGTGTTCTATTTCGATTTGATGGGAAGCGGGTCCGGCTTCGAGAGC
94432 C T CGTACGTGTCGCAGACAGCCGTCGTCGGCAGTCCCAGCAGCCAGAGCAGCACCGTCGAGTCGTCCTCGCCTCCTCCGATCCCAGCTGCAGTGTCTCTGGA[C/T]CTGGATCTGAGGGTTTCAACTGGCAATTTCAGGCCTGTGTTCTATTTCGATTTGATGGGAAGCGGGTCCGGCTTCGAGAGCATGAA
94448 T C CCCGCATCGTCCTCCGACCATCGAAGTGCCATCGGTTGACCCCTGGAAATGCGCTGCTGCCCCTCACGCTCAGCCCCACATCTCGAAAAACTCGAACTCT[T/C]CAACAGTCCTTAAACCTTGTTCGAACGCCAGCATTTCCCGAAGCAATATCAGCCTCCACTGTACATAATTGTCGATCATAACCGTTGGG
94448 G A AACTCTTCAACAGTCCTTAAACCTTGTTCGAACGCCAGCATTTCCCGAAGCAATATCAGCCTCCACTGTACATAATTGTCGATCATAACCGTTGGGATAC[G/A]AGAGGTCACCAAGCTCTACAAAGTTGCTATTGAACAATTCTTGAATCGGTATATGGATGGTGCGAAAATTGGAGAAGAAAAGGGGAA
94452 T C CCAATCCATTGGCGTTGGCATACCTTTCCATGAACCTCATGAACCTATCCCACTCCTGCGGAGTCCTCATTATGTACTTAGCCTCTATCCTCGCCGGTTT[T/C]CCATTCACGAACTTAGCACTCACGTCCACCGATTGAAGAACCCCTTCTTCATCGATCATGTAAAAGCCCGTAATCTCCCCAAGCTCCCCTG
94454 A G AATCTTCTGGTGGCACTTACATCAGTTTCGGCAGGTATGCCTTACAGGCACTCCAGCCTGCTTGGGTCACCGGTAGGCAGATAGAAGCGGGGCGAAGAGC[A/G]ATGTCGCGCCACGCACGTAGTGGTGGAAAGATATGGGTACGGGTTTTCCCCCATAAGCCTATTACAGGGAAGCCTGCAGAGACC
94470 C A GTCCCTTTTCGTGGATCCCTAATCTCTGCCGCCCATTTCCCCCATGGACGGCGCCTGATTCCTCTGTATACGTTTTTACGTGCTTCGCTTCCTGCGACGT[C/A]GCTGGATCCGGATGGGCCTTTAGCCTTCTTACCTCTACCTTGTTGAGCTCGAGGAATCGATTCATTAGCCTCAGAAAATTCAGAAAGAG
94470 C G CCATTTCCCCCATGGACGGCGCCTGATTCCTCTGTATACGTTTTTACGTGCTTCGCTTCCTGCGACGTCGCTGGATCCGGATGGGCCTTTAGCCTTCTTA[C/G]CTCTACCTTGTTGAGCTCGAGGAATCGATTCATTAGCCTCAGAAAATTCAGAAAGAGTGTCAAATTCAGACGACCAGAGATCCCTTTTC
94486 A T TCATTCGCACTGCATCGAAACAGTACTTCATCTGTGCGCCTCGCTTGTACTGTTTTGGCGTTGTTTAGTGGCGTATCCGCGTTTGGAGGTCGTTGAGACC[A/T]GTCACGGCTTGGAAGATTTCTACCTGGGTCTTTTATTTGAGGAAGAGACGATAAAAGAGAGACAAAGTAAGGTAGAGGATAGATTAG
94494 C T CAGAGGCCATTGCAGCAGCAGTTTCTCCAGCAAGATCCGAACCCGGATGATTTGCATCAATTCGGTATGCTTGTCGACTTGTCGTCATTTCTTCAGGTCG[C/T]TGCCAACAATAGTGATCCGTGTTTCCATCTCCAACCTCGCCGTAAAGGACATTAGGCTCAGGGTGGGCTTTGATGAGATAGTCGGTTC
94494 G A CATGGCCCAATTCACCGCTTTGAGCCATTTGCTTGCCGTACTCGACTATGCTCCACGACATCATGGTCAATGTGAATGCCATCGGCAGTCCAAACTTCAC[G/A]TTGTCTCCTGCGTCGTAGTATCCTCCAACTAAATCAATCCCATTAGCCTTGCCATCTTGAAGGCCAGAATTAGCTCTCCAAGTAACCCTC
94498 C T TTTCTCCCTGTAACGGCGATATCTTTAGCATTAAGCAGGATACACATATCCCCATCTTCACGGTAGGGTGTATAAGTAGGTTTATCCTTGCCTTGAACCA[C/T]GGTTGCAATTTGAGATGCCAGCCTTCCAAGTACCTGGCCTTTCGCATCAAACACTCGCCACATCAGGCCTTCTAAATTGATTCTTCTTAG
94498 C T GAACCACGGTTGCAATTTGAGATGCCAGCCTTCCAAGTACCTGGCCTTTCGCATCAAACACTCGCCACATCAGGCCTTCTAAATTGATTCTTCTTAGTCC[C/T]GCTAGCGCTTTCTTCATATTGCCACTACAGGCCAATTTGATTGCCGTTGGATCGAATTTGAGATGCAGTCGGATTTGAGATGCGGCAGG
94498 T G TTAGTCCCGCTAGCGCTTTCTTCATATTGCCACTACAGGCCAATTTGATTGCCGTTGGATCGAATTTGAGATGCAGTCGGATTTGAGATGCGGCAGGTTC[T/G]TTGAAGGAGCGCGAGCCAGCATCACCGGAGGAGGTAGTAGGTGACTGGATTGGATTTGAGAGGAAAGTCACCTGGATCGGATTTG
94498 G A AGCGCTTTCTTCATATTGCCACTACAGGCCAATTTGATTGCCGTTGGATCGAATTTGAGATGCAGTCGGATTTGAGATGCGGCAGGTTCTTTGAAGGAGC[G/A]CGAGCCAGCATCACCGGAGGAGGTAGTAGGTGACTGGATTGGATTTGAGAGGAAAGTCACCTGGATCGGATTTGAGATGTGGCAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
94498 G A CGCTTTCTTCATATTGCCACTACAGGCCAATTTGATTGCCGTTGGATCGAATTTGAGATGCAGTCGGATTTGAGATGCGGCAGGTTCTTTGAAGGAGCGC[G/A]AGCCAGCATCACCGGAGGAGGTAGTAGGTGACTGGATTGGATTTGAGAGGAAAGTCACCTGGATCGGATTTGAGATGTGGCAGG
94498 T C AGATGCAGTCGGATTTGAGATGCGGCAGGTTCTTTGAAGGAGCGCGAGCCAGCATCACCGGAGGAGGTAGTAGGTGACTGGATTGGATTTGAGAGGAAAG[T/C]CACCTGGATCGGATTTGAGATGTGGCAGGTTCGTTGAAGGAGCGCGCGCCAGCGTCACCGGAGGAGGCCGTAGCTGACGGGA
94498 G T CGAGCCAGCATCACCGGAGGAGGTAGTAGGTGACTGGATTGGATTTGAGAGGAAAGTCACCTGGATCGGATTTGAGATGTGGCAGGTTCGTTGAAGGAGC[G/T]CGCGCCAGCGTCACCGGAGGAGGCCGTAGCTGACGGGATTGGATTTGAGAGGAAAGAAACAAATTTGAGTGCTGGATTAAAA
94498 C A GTAGGTGACTGGATTGGATTTGAGAGGAAAGTCACCTGGATCGGATTTGAGATGTGGCAGGTTCGTTGAAGGAGCGCGCGCCAGCGTCACCGGAGGAGGC[C/A]GTAGCTGACGGGATTGGATTTGAGAGGAAAGAAACAAATTTGAGTGCTGGATTAAAATAGGCGATGGCGGAGAAATTTACAG
94498 GA G TCACCTGGATCGGATTTGAGATGTGGCAGGTTCGTTGAAGGAGCGCGCGCCAGCGTCACCGGAGGAGGCCGTAGCTGACGGGATTGGATTTGAGAGGAAA[GA/G]AAACAAATTTGAGTGCTGGATTAAAATAGGCGATGGCGGAGAAATTTACAGAGGACGTAAGAAATACGTTTAAGATATTCGG
94498 C T TGAGATGTGGCAGGTTCGTTGAAGGAGCGCGCGCCAGCGTCACCGGAGGAGGCCGTAGCTGACGGGATTGGATTTGAGAGGAAAGAAACAAATTTGAGTG[C/T]TGGATTAAAATAGGCGATGGCGGAGAAATTTACAGAGGACGTAAGAAATACGTTTAAGATATTCGGTGAAGAATGGGTACGA
94498 A T GAGCGCGCGCCAGCGTCACCGGAGGAGGCCGTAGCTGACGGGATTGGATTTGAGAGGAAAGAAACAAATTTGAGTGCTGGATTAAAATAGGCGATGGCGG[A/T]GAAATTTACAGAGGACGTAAGAAATACGTTTAAGATATTCGGTGAAGAATGGGTACGAGGACGGAGAGATTTGGGGAAGAAG
94498 T TA TAGCTGACGGGATTGGATTTGAGAGGAAAGAAACAAATTTGAGTGCTGGATTAAAATAGGCGATGGCGGAGAAATTTACAGAGGACGTAAGAAATACGTT[T/TA]AAGATATTCGGTGAAGAATGGGTACGAGGACGGAGAGATTTGGGGAAGAAGTTGTATATGCGAAGGATGGAGAAGAATCGG
94500 T C GTTGACTGGCTCCGATCCCCCTCCCGCCTCGACAACCTCCTCTCCCTCCCATACAACCGCGTCACCACTGCTCTAACCAAACACTACAGCCAGAAAAAGC[T/C]ATTCGTCTTCGCCGTCAATCTCCAGATCCCGGGCCGCGAGTGCCACTCCTCTGCCTTCTACTTCGCCACTGACGAAGTCATACAACCCG
94502 GC G AACGACAATAATTAAAGCATACCAAATAACTCAAGCAGCAGCAGGAGCCTCGTTCTCAACACTCTCCACACCCGTCTCATCCGCTTCTTTGTTCACATCC[GC/G]CCCCCTTCCTACTGTTCTTCACAAAATCCATTGTTCTTCGACTGATCTCCTTCGAATACAGCTCTATAACCTTGATCCCATCCTCAATGT
94504 A T AAACAAAAAAAAGGTTGAGAATATATATCAAATAGTACAAAGCAGAGTCAAACGCAAACAGGTAATAATTGAAGATTTTAGCTCATCAACCAAACAAAAT[A/T]AAACAAAAGCATAGTACTTATAATATCTTAGATCTTATCAATGTCTTCATCTTCAAATTCAATGTAGTCATCACCAGCACCATCGTCCT
94504 G A CATCACCAGCACCATCGTCCTCTTCATCCACGCCTGCGATACCTTCATTGAGCCTAGTATTTTCTGGTAGTTCTCCATAGGCTTTGAGTAGCCTAGCTTC[G/A]TCCGGCATGTATTTCAGTATCACATCGGCTTTGTCATCCTGATAATCTCTCAGTCCAACTAGCACAATATCTCCTGCAGCAATCCAGACCT
94504 A G GTATCACATCGGCTTTGTCATCCTGATAATCTCTCAGTCCAACTAGCACAATATCTCCTGCAGCAATCCAGACCTTTTTATGCATCTTGCCTCGAATATG[A/G]CAGAGCCTTTTCGTCCCATCAATACACATCGCCTCACATCTGCCGTTGCCGAGCATCCTCAAAACCTGGGCGTACTCTTGTCCATCTTCTT
94506 G A AATGCCAAGTCAAAACCTCCTTCAGGTGTATCTCCAATGCAGTCGAATACGGCGTCTGCCTCCAAGAAGTCTTCCTC[G/A]GCCGTATAACCGCTCTTTGTAATTATGCATTTCATTCCAGCTGATTTAGCTGCTGCAAGGCCTATTGCGCTATCTTCAACAACTACGCAGCTGGAGGGCT
94506 A T CCTCCAAGAAGTCTTCCTCGGCCGTATAACCGCTCTTTGTAATTATGCATTTCATTCCAGCTGATTTAGCTGCTGCAAGGCCTATTGCGCTATCTTCAAC[A/T]ACTACGCAGCTGGAGGGCTCAACATTTAGAGTGCTTGCAGCAAGCAGATAGATAGCCGGATCAGGTTTCTTGCGAGGAACTACATCAC
94510 A G GTTCCCGACCCCTCTCCTCCGCCTCCATCCTCCGACAATAGCGGAAAAAACGCAAATATTAGTGAAATCCAGATGCACCTGTCACAGTTCCGCCAACAAA[A/G]TCCTTTCCGCAACGCTAAACCTAACTGGGGAACAGTATCAATCCAAGATATCATGAACCGGCGTGCTAATAACCGAAGCACCCAAAA
94510 G A CACCTGTCACAGTTCCGCCAACAAAATCCTTTCCGCAACGCTAAACCTAACTGGGGAACAGTATCAATCCAAGATATCATGAACCGGCGTGCTAATAACC[G/A]AAGCACCCAAAACACAAACGCCAAAATGAATTTTGATGCTATACGCGAGAGCCTGAAGAACTTCAGACCGAACCCACAAAGTTCAAT
94510 A G GTATCAATCCAAGATATCATGAACCGGCGTGCTAATAACCGAAGCACCCAAAACACAAACGCCAAAATGAATTTTGATGCTATACGCGAGAGCCTGAAGA[A/G]CTTCAGACCGAACCCACAAAGTTCAATGAGAGGTTTCAATTTGTTTCCTAACAGAAGAAACCTGGAGACTCCAACTGTTGGGGATT
94562 T G CTAACCGTCACCGACCGCCTCCTTCTTCTTCCTCCTCCAACACGCTTATGCTTCCACCATTCAAAAACACTAAAAGTTCAAACAGTCTCACCTCCCTTCA[T/G]TGCGACCATTTCAACTCGTGTTCGGGCTGCTCGCACGAGCTGGATTTGGATAACCCGCACGTGCTTCAGGAGGCAGCTAAGTTCTTTGG
94564 T G TAACAGAAAAATCGAAATCGCAATCCCCAATTTAAAAAAACGTTTGAACGTCTAGAACCCTAAGAAGGGAGGAGCAGCCTCGCGCAAGGGAAGGCTGGAT[T/G]TCGAGCGCGATGGTGAGCAGCGCTCATGCGCCGGGGAAGCCAGTGGCAGTGCGTTGGATGGGAGGCCGACACCATCATCAAAC
94588 A G CATGTTTGGAGCTATTCCAGCTGCTATGACCTATTACTGGCGGATGAAAATGCCAAAAAACCTCACTTGAGTTCCACGCTGAAGCACAGCGGCTGAATCC[A/G]AGCAGAGACTTCCTCACTTACACCCTAACGCAAAGCCTCAAATCCAAAAAAAGCAGCACTGCCTCAGACGCTACTAGCCAATCTGGC
94598 A T TATCAAGGAAGTAGTCAGATGAGCTGCTTGGCAAAACAGAACTATTTATTTTCTTAACGGCTACCACCTTGCCATTGTTCAATTGAGCTCTGAACACACG[A/T]CCAATAGACCCTTCTCCAATAAGATTGTCTGCGCTAAAACTATTTGTTGCAACCTGCAGATCCGCTACTGAGTACACAGTTGCTTTTATA
94598 T C ACCAATAGACCCTTCTCCAATAAGATTGTCTGCGCTAAAACTATTTGTTGCAACCTGCAGATCCGCTACTGAGTACACAGTTGCTTTTATAGACCCAGAT[T/C]TGTTTTTCTAAAAACAGGTTTGCTAGAAGTGTCCTCTTCACCATATGATTTAAATATAGCAACTGGAGGAGGATTGAAGTCAATAGGAG
94598 G GT CAATAGACCCTTCTCCAATAAGATTGTCTGCGCTAAAACTATTTGTTGCAACCTGCAGATCCGCTACTGAGTACACAGTTGCTTTTATAGACCCAGATTT[G/GT]TTTTTCTAAAAACAGGTTTGCTAGAAGTGTCCTCTTCACCATATGATTTAAATATAGCAACTGGAGGAGGATTGAAGTCAATAGGAGT
94598 T C CAGATCCGCTACTGAGTACACAGTTGCTTTTATAGACCCAGATTTGTTTTTCTAAAAACAGGTTTGCTAGAAGTGTCCTCTTCACCATATGATTTAAATA[T/C]AGCAACTGGAGGAGGATTGAAGTCAATAGGAGTAGCCGGTTCATACATTCTTGAGTTAAATGAAGATGTTTGGACAGGTCTCATTTCTT
94636 C T CAAGGAAGCCAACAAATTTATCCACATATGCATTTTGAATTTGCACATCTGAGAACAGAACTCTCTTCATCTCTCTAGCCTTCT[C/T]CCTCACACCTTCCCCCTCCTCATCGACCATCACAAACTCAACAGCCCTCTTCACATTCTCCTTCGTAAACGACCCGTCACCCTCATCCCGTTCCACCTCC
94636 T C TGCACATCTGAGAACAGAACTCTCTTCATCTCTCTAGCCTTCTCCCTCACACCTTCCCCCTCCTCATCGACCATCACAAACTCAACAGCCCTCTTCACAT[T/C]CTCCTTCGTAAACGACCCGTCACCCTCATCCCGTTCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGG
94636 A G TCTTCATCTCTCTAGCCTTCTCCCTCACACCTTCCCCCTCCTCATCGACCATCACAAACTCAACAGCCCTCTTCACATTCTCCTTCGTAAACGACCCGTC[A/G]CCCTCATCCCGTTCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGGAGAAGCTGGCGATTGCAGCAA
94636 A G TCTCTCTAGCCTTCTCCCTCACACCTTCCCCCTCCTCATCGACCATCACAAACTCAACAGCCCTCTTCACATTCTCCTTCGTAAACGACCCGTCACCCTC[A/G]TCCCGTTCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGGAGAAGCTGGCGATTGCAGCAAGGGGA
94636 T C TAGCCTTCTCCCTCACACCTTCCCCCTCCTCATCGACCATCACAAACTCAACAGCCCTCTTCACATTCTCCTTCGTAAACGACCCGTCACCCTCATCCCG[T/C]TCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGGAGAAGCTGGCGATTGCAGCAAGGGGAAGTCCG
94636 C G AACAGCCCTCTTCACATTCTCCTTCGTAAACGACCCGTCACCCTCATCCCGTTCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATC[C/G]CCTGATCGGAGAAGCTGGCGATTGCAGCAAGGGGAAGTCCGAACCTCAGACTCTCGATCACGGACCCCCACCCGCAGTGCATCAGAAC
94636 G T ACCCGTCACCCTCATCCCGTTCCACCTCCACGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGGAGAAGCTGGCGATTGCAGCAAG[G/T]GGAAGTCCGAACCTCAGACTCTCGATCACGGACCCCCACCCGCAGTGCATCAGAACACCTCCCACCGACCCGTGCCCCAACACCTCCG
94636 G A CGCCGTACCCTCCACCAACCATGATCCTCGCATTCATCCCCTGATCGGAGAAGCTGGCGATTGCAGCAAGGGGAAGTCCGAACCTCAGACTCTCGATCAC[G/A]GACCCCCACCCGCAGTGCATCAGAACACCTCCCACCGACCCGTGCCCCAACACCTCCGTCTGCTGCACCCATCCCCTCACCACCAAC
94636 C T ATGCCCACACGAACGGCACCCTCGCTTCCTCCACCCCGTCCGCAATCCTTTTCACTACTTCTTCGCTGAAGCCCGTTTCGCTTCCAAAAGAGACGTACAG[C/T]ACAGATCTGGGCCTTCTCTTGTTCAGCCACGTAACAATCTCACCCTCCCGATTCTCGACGGGCTCCGGTGGGGGGAGAAGACCCACGG
94638 C T AGATATCTTTATCTGTGAAGGATGGAGCTTTTGTGGTGTGCTTCCATATCTCAAGCTTGACCTCGATGCCTGATGCTGGGTGGCCTTGAGCAATATCAAG[C/T]ACATGTGACGTGATGGGTGGCCGAGATCGAGTGGTGGTTATTGAGGGTGATGAGTTTGAGGATTTATCTGTAGAGGCTTTAGTGTC
94642 A G TTCCTTTTCACTGAATTTTCTCATAATCCATTCTTTAATTCGAAAAACTATCAACACCATTCTCTTCAGCTCTTTGTGCTCAACTTCTTGACCCGTTGTT[A/G]CCGAGCTTTAAGCTCTGATGTGGCCCGTAGCTCATTCTAAGCATGGTGCAGTTCGTATGGGATTTCAGGTAGAGGGAAACCTCGAACTGCA
94642 A G TGTTACCGAGCTTTAAGCTCTGATGTGGCCCGTAGCTCATTCTAAGCATGGTGCAGTTCGTATGGGATTTCAGGTAGAGGGAAACCTCGAACTGCATCGA[A/G]CTCAAAGCGAAGAATGGTGGACCTGAGGCGCATCAGTTGGTGGCGAGAGATCATACTCCGATCAACTATGGTCGACGCAGCAAGG
94642 A G GGCGAGAGATCATACTCCGATCAACTATGGTCGACGCAGCAAGGTATTGGAAGCATCGGTCGTGGGTATTCTGAAACGAAGACATGGAGTTGAGTATTGA[A/G]CCAGTTGTGAGGCTGGCCTGGTATTGGAAGTAGTTGAGCATCAGTTCTGAAGCGGCTGAGTATCGAAGCAGTTGGGTATTGGAA
94652 C T CGGGGGTTGGGTTGAAGATGATGAGAATGGCCGTGCCGCTAAGGGACACCGAGGATGAGAATTTGTTGGATTATTTGGATATTTGTTTGGATTTCATCGA[C/T]GAGGGGAGAAGGGATGGTGGGAGTGTTCTTGTGCATTGCTTTGCCGGTGTTTCAAGGAGTGCTGCTATCATTATTGCTTATCTAA
94674 G T AATGCATGTGCACAATCTTCCAGCATAGTTCAAATGGACGTGGGTACAACCGTACAAGAGCTGCATAACTTGCAGATATATCTCATGACAACAAATTCAC[G/T]TTTACAAGAACGTATTATTTACGTAGAACTTATGCAGCTTATAAAACACACAACTACAGTACTTTTCGAGCAATATACGAAAATGCAG
94674 T A AATAGAGGCTTCTTCAGAAAATGGGCCTCCAAATTGCCCAAAACAAGTTCAGCCATATCAGTCCTAGTCTCCACCGACCCACTCCCAACATGGGGCAACA[T/A]AACAACATTATCGAGGGCAAAAAGTTCTTCAGGCACATGTGGTTCATGCTCAAAAACATCCAGGCCAGCACCACCAAGTCGACCCTC
94674 C T GCACATGTGGTTCATGCTCAAAAACATCCAGGCCAGCACCACCAAGTCGACCCTCAAGAAGCGCTTTCACAAGCTCAGGTTCATCCACGTGAGGTCCCCG[C/T]CCTATGTTTATGAGCACGCCTTTCGAACCAAGAGCATCAATCACTTCCTTGTTGATGATGTG
94686 G A ATCAGATACATGGACATGCAAGGAAAGTATCATTTCAAATTCAACCACCTCCGGCGTCATTGCCAAGAACACAAAGCATGCCAATGACCTCACGAAATTC[G/A]TATACCCCAAGAACAGTGGAAACAGATGGAAGTTTAAAATGGAAGGATCTACTTGCAGACATGGCAGCCGAGCTTGGTGTCTCTGA
94686 G A TGCAAGGAAAGTATCATTTCAAATTCAACCACCTCCGGCGTCATTGCCAAGAACACAAAGCATGCCAATGACCTCACGAAATTCGTATACCCCAAGAACA[G/A]TGGAAACAGATGGAAGTTTAAAATGGAAGGATCTACTTGCAGACATGGCAGCCGAGCTTGGTGTCTCTGACGCTGTCAGTGGCAGC
94686 T C TTCTGCCCAACTTATCTGGAGTGGATCCTACGCCATTTACATATGATTTCGGTGTTAATTGGATGTAGAGTGATAGTGGCAGGCATATTCTAATACTACA[T/C]AGCAGTGTGTTATTTTAGTATATATTTATAGCAGTGCCTTTATGATTTATAGATCTTTCTTGATAAGTTAAGCCGTCTGTAAACTATATG
94688 C T CAGCATTTTCCTGTGTTTTCAAATCAGTTGAAAGAAGCAATCCAACTAGCAGGCTAATAGCTCCACAATTAGCAATCACTATCCTATTATCCATGTTATG[C/T]CTAGCTAGAAGACGAAGCTGTGCTGTGGCATCTCTTTGTATTTCAACTGAATCACTTTTCAAATCTTCGATTAGTTTTCGTGCTTCTGTCT
94690 C A GCCGGAGTCGGGTTGGGTGGGGATGGGAGCGAGGTTAGGGTTTTGACGCAGAGTTTTGGGTAGCGAGCGTTGGAGCAGGAAGCGACGATCGTTCGGTGGG[C/A]TGAAGAAGCTGAAACGAGTCCGGAGAATGATAATGGCAGGACGATGAAGAGGAACATGGATGGAATTTGATTCGCCATTGT
94712 A G TTACTCCCGTCGTCGATCCTTTTTCGTATTCGTTGTAGTAAATTTTGTACCCACCATTGGATCGTGGTTCTGGTTTGTCCATTTTGAGGAAGAGGCCATT[A/G]ATGACAGTTGCACCTGCATCAGAAGCACGTTCCCGAAGGTAGCCATCAAGTACCTCACGTCTAACCATGCCAATATACTCATGCGGCTT
94724 G A GATGGGGAGTGAACGTTCCAACATGAATGACGTTAGTGATGGAGTGTAAGGACCTGGAGGTGAAGCTTCTAATGGCGCAACAAGTGTCTGTGGTGGAGAT[G/A]CAGTGGTCTTAGGCAAAGGAGGAGCATCAACTGAAATTGCTCCAGTAGTCGTTCGAGATATCGGAGGTGGAGATCCAGCTGGT
94744 A G CGTCGTCAGTTAAAACATCGGGTGTGTTTGTTACCCTAATCCCTTTCTCCTTACACTTCTCCAGGTCAATCTTATCCACTCCCACACTATAAGAGGCTAC[A/G]ATCTCAAGTTTCGGCAACATTTCAATCATCTCAGCGTCAGCGCCAATGTTTCTATCGGCTACAATGGCTCGGACGGATTGGCTATGGGTT
94744 A G TCTCCTTACACTTCTCCAGGTCAATCTTATCCACTCCCACACTATAAGAGGCTACAATCTCAAGTTTCGGCAACATTTCAATCATCTCAGCGTCAGCGCC[A/G]ATGTTTCTATCGGCTACAATGGCTCGGACGGATTGGCTATGGGTTTTGAGAAATTCCGATTGTTTCTGGGTTGGGATGTCGTATAACTT
94744 G A CTATAAGAGGCTACAATCTCAAGTTTCGGCAACATTTCAATCATCTCAGCGTCAGCGCCAATGTTTCTATCGGCTACAATGGCTCGGACGGATTGGCTAT[G/A]GGTTTTGAGAAATTCCGATTGTTTCTGGGTTGGGATGTCGTATAACTTGATGAGGTTGCAGCGGTTCGAAAGCTGTTGCTCTAAATA
94744 T A CGGCAACATTTCAATCATCTCAGCGTCAGCGCCAATGTTTCTATCGGCTACAATGGCTCGGACGGATTGGCTATGGGTTTTGAGAAATTCCGATTGTTTC[T/A]GGGTTGGGATGTCGTATAACTTGATGAGGTTGCAGCGGTTCGAAAGCTGTTGCTCTAAATACGAATTTAATTCAAAAGTGGATCAAT
94770 GCA G TCCAAACCAATCCTCAAAATAAGTTATCCCCTCCTTTAATCTCATCGCAGGTCAGCCCTATTTTCCTCTATTGGGAAACAAATCCCAAATAGATCAGCGC[GCA/G]CAACACGAAAGGAGGACATATGAGTGGAACGCAGGTTCTCACGAGTCTAGAAGCCAAGTTTCAAATTTGTTCAATTTTTCTTTGAAC
94774 G A ATTTCAACGGGTGCGACCCAAGGGCCCGTACCCCAATATCGCAGGCGTTGATCTCGTCAACATCTCGGATGCATCCATTGACTAAAATGCCAGCCCACCC[G/A]TTGTTCTGCGCCAGCTGCCCTATGTTACCCCCGACCAACGCACACCTCATGCTGCCTCCGCCATCGACCACGAGCACCCTTCCGTCTC
94774 A G TTCCGTCTCCAGGGGTTTCCAGAAGCTCCCGGACCAGGACATTGTCTTCGAAGACCTTGAGGGTCACTATGGGCCCAGAGAAGGCACGGCATTGCCCGTA[A/G]GATTGGAAGATCGGTTGTAGGACTCGGATGTCCCCTTTGGTTAGAAGGGAGGGGTGAGTGTCACACAAGTCTGCCGTTGCAAGT
94774 T C CACGGCATTGCCCGTAAGATTGGAAGATCGGTTGTAGGACTCGGATGTCCCCTTTGGTTAGAAGGGAGGGGTGAGTGTCACACAAGTCTGCCGTTGCAAG[T/C]GATGCCATTGTTCTGAACCAAATATGATAAAGTGTATCAATAGGAACTCAGCTGCATAAAACCATCAAAATTATATCTTTGGAAAA
94778 AT A CATCCTTTTTAATTTTACAGGCACAAAATGTTTATATAATCCTTCTGTGCTCCCCCATACCTACAACTTCAATTCACGGCAAAGCATATTAACAATTACA[AT/A]TTTTTGGTAATAATAAACTTAGTTTTCATCCACCTTATTTCAATGTACAAAGATTTTTTGTTTTTTTTACATGTTCATCGTTGCAAGAAACT
94786 C T GGTAACAGATTTTTCTTCATATTTATGCTGGCTCACGGGGGCGAGCGGCCCAAAGAGAGCTGAGTGCACGAAGACGGTGGCAATAATCCCCCAAAGATAG[C/T]AAAGCTCTTGCTGCTTGCCGTGTTGTAAGGATTTTGTACATTTGCTGCAGTGTTTGTTGCCTTAAGTGATCTGCCTGAGTAACAAAG
94786 T G TATAATTCACAGCACCTGATACACCTAAAGTATCATTAGCTACCAAAGTCTGGGAAAGAATCCGCTGTAGTTTGTCCATCCCTTGAGAAAGTGCATCTTC[T/G]GCTTGCTGTGACAATTGTTGGAGATTGTGAACTGAAATGCGTTGTTGCTCGGTTAAAGGCTCTAACTCAGGAGACAAAATTTTTAGAA
94792 C T AAAGTGGACACAAGGGTACATATTACTTTGAGTTCTCCAGACCACTGAGGACGATGGACCGATTTCAACAGGATGTGCAATTTGTCATTGGTCAAGCCAG[C/T]AAAATGGGAGTTGCGTTCTGGTACTCAAAGGATGGAGCTCCATGGACTGGATCACAGCACTACTCGGCAAACTGCGATTGGATGC
94792 T C CTTTGAGTTCTCCAGACCACTGAGGACGATGGACCGATTTCAACAGGATGTGCAATTTGTCATTGGTCAAGCCAGCAAAATGGGAGTTGCGTTCTGGTAC[T/C]CAAAGGATGGAGCTCCATGGACTGGATCACAGCACTACTCGGCAAACTGCGATTGGATGCCTATAAAAATCGCTTCTTTTTCAGGAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
94792 G A CAGACCACTGAGGACGATGGACCGATTTCAACAGGATGTGCAATTTGTCATTGGTCAAGCCAGCAAAATGGGAGTTGCGTTCTGGTACTCAAAGGATGGA[G/A]CTCCATGGACTGGATCACAGCACTACTCGGCAAACTGCGATTGGATGCCTATAAAAATCGCTTCTTTTTCAGGAACCTCGTATAAA
94796 C T AAGACTCCAGTCAGTTCAACAACTATTACGGCTATGGGCATCAAGGGTACAGTGCATATGGATACGGCCAACAACCTCAGGATCCAAATATGTATGCCTA[C/T]GGGGCCTATCCAAACTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATT
94796 C A TCCAGTCAGTTCAACAACTATTACGGCTATGGGCATCAAGGGTACAGTGCATATGGATACGGCCAACAACCTCAGGATCCAAATATGTATGCCTACGGGG[C/A]CTATCCAAACTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCT
94796 C T ACAACTATTACGGCTATGGGCATCAAGGGTACAGTGCATATGGATACGGCCAACAACCTCAGGATCCAAATATGTATGCCTACGGGGCCTATCCAAACTA[C/T]CAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCG
94796 A G ACGGCTATGGGCATCAAGGGTACAGTGCATATGGATACGGCCAACAACCTCAGGATCCAAATATGTATGCCTACGGGGCCTATCCAAACTACCAGCAACA[A/G]GTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCGGGTTTGTA
94796 A G CGGGGCCTATCCAAACTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAA[A/G]CTTCGGGTTTGTACCTACATTATGTTTGTGTTAAATTAATATCTAATGTTCATCTCAAAGCATAAACATTTTGATACTTTCGGATGTAA
94796 G T CTATCCAAACTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCG[G/T]GTTTGTACCTACATTATGTTTGTGTTAAATTAATATCTAATGTTCATCTCAAAGCATAAACATTTTGATACTTTCGGATGTAATTTTGTG
94796 T C CCAAACTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCGGGTT[T/C]GTACCTACATTATGTTTGTGTTAAATTAATATCTAATGTTCATCTCAAAGCATAAACATTTTGATACTTTCGGATGTAATTTTGTGGTAT
94796 C T CTACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCGGGTTTGTAC[C/T]TACATTATGTTTGTGTTAAATTAATATCTAATGTTCATCTCAAAGCATAAACATTTTGATACTTTCGGATGTAATTTTGTGGTATGGATC
94796 A G ACCAGCAACAAGTTAATTACCAGCAGCAGCCACAGTGAGCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCGGGTTTGTACCT[A/G]CATTATGTTTGTGTTAAATTAATATCTAATGTTCATCTCAAAGCATAAACATTTTGATACTTTCGGATGTAATTTTGTGGTATGGATCCA
94796 T G GCTGTGTTCTGAATTGGAATCTGATGGGCATTTGTTCTCTTGTAAACTTCGGGTTTGTACCTACATTATGTTTGTGTTAAATTAATATCTAATGTTCATC[T/G]CAAAGCATAAACATTTTGATACTTTCGGATGTAATTTTGTGGTATGGATCCATTATGAGTTTTCTTTTTCAAAAAAAAAAAAGGC
94812 C CT TTCGTTCGTCCATTTGGTCGAACAGGGGCACTCTGCGAACAAGATCAAGGCAGAGATGACGTTTAATATCTCTACGGAGATCCAAAGGAAGCCCTCTAAG[C/CT]AAGGCTTCTTCATCGACACCTTGTGTTGCTACCCACTTGTACTGATCATACCTTCTAATACATTGCTTTAACTCTAATGGAAGCTGTC
94812 TC T ACAGAACCAAGCCAAGAATTGCCAGAACAATTGCAAACAAGTTTTCACCAACGTATGTGCTGGTTTCAAAATCCTGTCCCAGAGAGCTCAAGTTCTTAAG[TC/T]CCCCACCAAAAACAATAGAAGTACTTCTGGAAGAATGGCGAGGAAGTGATGCTGTTGCTAACTGCATCAGCATAGATGCCAACCAG
94816 G C CAAAGTTCTTCATCATTTTGCAGGCTCCGGCAGACTCTCCCATGCCCAAAGGGATCACTGGTAAATTGTCGCAGTTGCATATTTCGACCATGAACCCATC[G/C]GGATCATGAAAGAATAATTGATCCACGAAGATCCCTCCTTCTTCGACTCGCCTTTGGATGTATTTAATGCCCATTTCTTTCAGCTTTTTC
94832 G A CCTGAATGTGTGATGATCAGTCACTAATGCTTATAGTTGATAGTTTCAAAAGGACGGAGAGACCACAAGCTTTGATGATTATGCGCTCCCTATCGATCTC[G/A]ATGCGAAATTGAGATGGTGCCTTATTGTTAGAAAGAGTGGGATCAGTGACAGCATGCATGACTGGCGTCATCACTGGCTTCATACTA
94832 AT A TAATGCTTATAGTTGATAGTTTCAAAAGGACGGAGAGACCACAAGCTTTGATGATTATGCGCTCCCTATCGATCTCGATGCGAAATTGAGATGGTGCCTT[AT/A]TTGTTAGAAAGAGTGGGATCAGTGACAGCATGCATGACTGGCGTCATCACTGGCTTCATACTAAGGGATGGTTGATTATTTAGTT
94836 T C CAGGAGCCTTTTCAATATTTCTTTCCAGCCTCTCTTGTGCTTTAGATTCATCATACATCATGAGAACTTTTGCAATGAAAGCGACGCCGACCGCAACGAG[T/C]ACCATAGGCATAGTTACAGTATCAAGCCACGCAGCGGACTCAGGAACGGGGACGAAAAACTCATCTCGATTCGGATTCCTTTTCCTTC
94850 T TC TGTAGTTTGTACCATCCCGCAAAAGTCTATTTGCCATGCCTAGGACAAAAGAACCCAAACTACATTACAAATACAATCGACTTTATACGCCTTCAACCCC[T/TC]CCCTCCCAGTGGTATTCCTGTTCCGCCTTACATGTGGATCGGCTTAGAGTAAGTCGCCATCGCCGCCTCCTTGAACGCCTCAGCAAGC
94854 T C GTTTAAATACAAGATAAATATATTTACTGGTTAGAAATATGCAGAGTGCGCCGTCTTCGAAATCCCAGCTTTCCCAATCTTCGAATCCTAAACTGTGATC[T/C]TTACAATCTATACTGCTCGGGTCTTAAACAGTGTAGCAACAAAGTGCTGACCGAAAGGGAAAAAGGCAGCTACAGTGTTCGCTGGCCA
94858 C T TTTGCCTTAAATTCAGCCTGGATCGAGGTGAAACCTTATGCTTAGTCCCGCACCTAGATCCTCATGATGCTCAAGGTTGCGTTTCATGGTGGCTAATGGT[C/T]GAAAATGGTGCTATGGACAGTGGAAAATCACCCTATCATAACAATGATAAAATGTTTTTAGGGCATTTGTCCCTTGAACTGCTGCATT
94874 T C TAGCCGAAGTGCTATTGGCCTTGGAGTATCTGCACATGCTAGGCATCATCTACCGTGACCTAAAACCAGAAAACATTCTCGTCCGTGAAGATGGACACAT[T/C]ATGCTTTCAGACTTCGATCTTTCCCTGCGTTGCTCCTTCAGTCCGACCTTAGTGAACTCAAACTCATCCTCCTTCCCTCGCCAAACCTCC
94888 A G GGCAACGCTGCGGTTGTCCTGCAAAATTGTAACTTATACGCCCGAAAACCGAACCCCAACCAAAAGAACATCTTCACCGCCCAAGGAAGGATCGATCC[A/G]AACCAGAATACGGGCATTTCCATTCAGAACTGCAAAGTTGCCGCTGCATCGGATCTTGCGTCCGTGCAGTCCAACTTCAAGTCATACCT
94888 A G TTCACCGCCCAAGGAAGGATCGATCCAAACCAGAATACGGGCATTTCCATTCAGAACTGCAAAGTTGCCGCTGCATCGGATCTTGCGTCCGTGCAGTCCA[A/G]CTTCAAGTCATACCTCGGTAGGCCGTGGAAGATGTACTCGAGGACAGTGTATATAGGGAACGACATAGGGAGTCTTATCGATCCCG
94888 C T AATGGAAAGGGTATAGAGTTATCAGTGCTTCCGAGGCAAGTATGTTTACTGTGCCTAACTTTATAGAAGGGGATAAATGGCTAGGTAGCATTCCCTTCAC[C/T]ACAGGTCTGTAGAATACTATATGTTCTTTTTATTTATTACGTTCTTAGAAGAAAGATGTATCAAATTGGTGTCAGATATATGCACCAA
94890 T C AATATCCTATTAGCTTCACCAAGTTTTTATGCTCCACTACTCCAAGAAATTGTACTTCAGCAAGCCATTGCTTATGCCCCTGCAAGCTTTTTTGATTAAG[T/C]CTCTTAACAGCAACAGGAATTTTATCCCCGATTCCACCGACAGGACGAATAAAACCTTTATAAACACTTCCAAATCCTCCTTCGCCGATCT
94890 CA C GCTGCTCGAATCGTGCGATTTGCATGTGTTGGTATTTGTCGTGAGTGCCGACGAAGTTGAGGATTTTGCTGGTTGGGTTTTGCCGGAGTCTGATTTGAAA[CA/C]AACCGAAACAACTCATGGTGCGGCTGACAGTCTGTGAAATTCGAGAGAAAAGGGAAAGTTGATGATGAATTTTACATGTGCATGA
94902 G A TCTTCTTATATGTCAAGATGAATGAAAGGAGAAATCGAGCTATGTGTAGACTGGAGAGTGTATTAAATTGTGATTGTAGCTGCTGCTTTTATTTACTGTC[G/A]TCCGCATTCCATAAGATGTTGGTTCTCTCGTTGTAATATTTGAACCCTTGGGATTTTCCTGGTTACCTTTTGCGTGGTTGTACTTTTGTA
94904 C CT TAATCAACTAAATGGAAACAAAGGGGTGTTAACTTTGCATAAGTTTCTGTGTTTCGTTATTTTCTTCAAACTTGCTGGTGATGGTTATGATTAGTTTTGG[C/CT]TTTTCCATACCGATAGTAGTGTTAATCAGGTGGGAAACGAATTTCTCATAATCAGCATTATCTTATCCAGACTTAGATTAGCGTAAAAA
94906 GA G TTCTCCCTTCAGCCTTCGTAAAAGAAATCATACAATCGTATTAATCTATAATATCACATAGAATTTGACTTTCAATGCTATCATGAGATTCAAATAGTGA[GA/G]AAAAACAAACGGCGACTTCAACGTCAAGCACAAACGGGACCTTCCGTCCAAGCTCCAGAAACATGGCCATTCCGGCAAACGTAAGCC
94906 C G CATCATCATGAAACCCAAACGTAGTCCTCAAACAAAAGGCCGAGTGAAGATCCCAAGTATCCCTACACTCACAAAATGCACAGCCCATTCCTGTAGTCTT[C/G]CCTCTACTCCCCTTGTTGTCGTTGATCGTCCTCCACACCCTTGACTTGCTGAAATTCTTAAACACTCCCCTGAACAGCATGTACTTCCTT
94922 C T GATGGCAATCACCGCCTATCTGCTGATTCGCATAGTTCTGTGCATAGGCTGCCAAGTTTTGGTCCCAGGACACAGGTCCGACACCAACCTGCCCACGTAC[C/T]GAATTGTGGGCGTTGACATAGTCTTGAGGAGAGTTTTGAGCATTTGCTGATTGAGCTACGACTATTGCCAAGAGGAAAAGAAGTGG
94922 T A TTTGGTCCCAGGACACAGGTCCGACACCAACCTGCCCACGTACCGAATTGTGGGCGTTGACATAGTCTTGAGGAGAGTTTTGAGCATTTGCTGATTGAGC[T/A]ACGACTATTGCCAAGAGGAAAAGAAGTGGCAGAACTGAACAAGTACTGGTCGATCCCATTTCTTTCTCAAAATATTAACCAGTTGAA
94924 A G GTATTCAATGCTTCCTTTAACTTGTTTTGTCTATACAAGCAGTATGCCTTATAGTAATTCAAATCAAGAACAGAACTTTTAAACCCTTGAATTGCTGCTA[A/G]AGCTTTATCCAACTCATCTAATTTAATCAAACCCACAACTTTGCATCTCACAGCATCCTGGTCTTCAGGAGCAATGGCCAAAATCTGATCT
94924 A G TTAACTTGTTTTGTCTATACAAGCAGTATGCCTTATAGTAATTCAAATCAAGAACAGAACTTTTAAACCCTTGAATTGCTGCTAAAGCTTTATCCAACTC[A/G]TCTAATTTAATCAAACCCACAACTTTGCATCTCACAGCATCCTGGTCTTCAGGAGCAATGGCCAAAATCTGATCTGCAACTTTGATAGCA
94924 A G CTTTATCCAACTCATCTAATTTAATCAAACCCACAACTTTGCATCTCACAGCATCCTGGTCTTCAGGAGCAATGGCCAAAATCTGATCTGCAACTTTGAT[A/G]GCACTGCGATATTTCCCATTTCGAATAAAATCCTCAATACTAGAAAATAGATCTTCAATTTGTGGTGGATTTGATGATTTCACATTTGATT
94924 C T ATCCAACTCATCTAATTTAATCAAACCCACAACTTTGCATCTCACAGCATCCTGGTCTTCAGGAGCAATGGCCAAAATCTGATCTGCAACTTTGATAGCA[C/T]TGCGATATTTCCCATTTCGAATAAAATCCTCAATACTAGAAAATAGATCTTCAATTTGTGGTGGATTTGATGATTTCACATTTGATTTTTG
94924 A G TTGATTTTTGTGGCGCCATTCAGATCTAAAATTTAATTTAAGAAAAGCAATAACAGCAGCTATGGAGGTCAGAAGCAGCGGCTAAGGTGTAGGAAGAAGC[A/G]CGAAGGAAGACTGCTAGAATAACAGAAACGCCCCGCAGCCGTGTGGTCAGAAGCAGTCGCGCAGAGTTCGAAAGGTGGAGGAT
94924 A G TTCAGATCTAAAATTTAATTTAAGAAAAGCAATAACAGCAGCTATGGAGGTCAGAAGCAGCGGCTAAGGTGTAGGAAGAAGCACGAAGGAAGACTGCTAG[A/G]ATAACAGAAACGCCCCGCAGCCGTGTGGTCAGAAGCAGTCGCGCAGAGTTCGAAAGGTGGAGGATGGACGGAGGTGTGGAAC
94952 A G TGTTAACTAATTGGGGGTGAATACAGATATCTCTTTTGTTGTGGTTATTTTGGTGAAATAGTTGAAATATGGGGGGTTTATTTAGAGATAGCAGGTATAG[A/G]ATTTACGGGCATCGATTTTTCTTTCCTTTTGGGAATTTCTTTTTTCAGACCAGTGACGTTTTTGTTTTCAAGATGCAAATGATCGTTGG
94954 G A ACCAACCAACATCTGAAAATAATTTTACAGCATAATAAGTTGTTGAATTACTAAGCAAAGAACTCAAGATTGAAGAAGAAGACCCTTTGCAGTGTTTGGA[G/A]TTTGGAATCGTATGGCCTGCAATCCTGGCACAGTGGCACCTACGCCTGCAGGCTATTCCTTTCAAGCGAACCCACAATTTGGATCGC
94954 C CT GCAGGCTATTCCTTTCAAGCGAACCCACAATTTGGATCGCTGTAGTAGCTCGCGATTTGGATTCGATTCTCCGTGACTTTGCATTTTACTGCGATTCGCC[C/CT]TTTTTTCTCGCGATTCACGATTCGCGATTAGGATATTTGGTTATTCCTTAGCAGCGATTCACGATTTGGTCCCCCTGATTTCTCGGTGC
94954 C T AAGCGAACCCACAATTTGGATCGCTGTAGTAGCTCGCGATTTGGATTCGATTCTCCGTGACTTTGCATTTTACTGCGATTCGCCCTTTTTTCTCGCGATT[C/T]ACGATTCGCGATTAGGATATTTGGTTATTCCTTAGCAGCGATTCACGATTTGGTCCCCCTGATTTCTCGGTGCCCTAAGCCGCCGCTTCT
94962 C CA CTAAAGTTCATCGTTTGCTTAAAACTTCAAATACAACAGTTTGCACACTACTAATCACTGCCGATGACTATACATAACAAACAAATGAATTGCTGGAAAC[C/CA]AACCAAGTCTCATATAGACTTCTTAAGTCATTTCAATATCATACACTTGATTATCATTCTGCCTTGGGTTTTCATTATGCCTCGAGTTGT
94962 C T GTCCATCCTTGAGGCCGTACACCCAACCAATAGTTTTAGAGGAGTCAGTGAAGAAGAGGCGGTTGAGTCTGGGTTCAGCAAATATGCCAGTTAGGATGCC[C/T]CCAAGACTACCGGCAACTGCATGAGTGTGGAACACAGCCATGGTATCATCTACATGTTTCATGAATGCGATTTTCTTGTGAAGGAC
94968 C T AGAATGAATAGCTCCTCAATGGTGGCGTCTCTTTGCATGTCCCCATTCATTCAACGCTCACATTAAATCAAAAGCATGCGTCCAAAAGACAGCAACAACA[C/T]AGCGCTGCCAAGCATCCTTCCATGAATGAAGGTCCGCCACTCTGATTCTGCCGAGGCGGAGGCTGCGCATACTGAGGAGGGTATCCA
94968 T C TGAATGAAGGTCCGCCACTCTGATTCTGCCGAGGCGGAGGCTGCGCATACTGAGGAGGGTATCCACCTTGGGGAGGATAGCCCTGTTGAGGGTAACCGCC[T/C]TGTGGAGGGTAACCGCCTTGTTGAGGGTAGCCTTGAGCATATCCCTGGGGCGGGTAGCCTGGAGGAGGATAAGCGTCCTTGGC
94974 T C GCCCCCGCTTCGAACTTCTCAAGCTTCACGTCAAACGCCGTCTTCTCCTCCTTCTTCTCTTCTTCCACGGCCGCTGATGAATCAGATGATGACGAGGAAA[T/C]GGATATAGAGGAGATGTCAGAGGAAGATATTAAGTTGGTGAATCCGAGCTTGTGCCGAAGGAGGATGGTGTAGTCTTCAAGCTCGGG
94974 G A GCTTGTGCCGAAGGAGGATGGTGTAGTCTTCAAGCTCGGGTTTCGTCAGGGAGAGAAGTTCATCGGCGATCCGATGCAGCTTTTGGGTTTGAGGATCGCC[G/A]CTAGAAGTAGCGGTACTAAGGTGGCGGCTGATGATGCGGTGGAAGCCGGTGATTCGCCGCATTTTAGAAAAATCAGCCGGGTTT
94974 A G TGTGCCGAAGGAGGATGGTGTAGTCTTCAAGCTCGGGTTTCGTCAGGGAGAGAAGTTCATCGGCGATCCGATGCAGCTTTTGGGTTTGAGGATCGCCGCT[A/G]GAAGTAGCGGTACTAAGGTGGCGGCTGATGATGCGGTGGAAGCCGGTGATTCGCCGCATTTTAGAAAAATCAGCCGGGTTTTAG
94974 G A GGGAGAGAAGTTCATCGGCGATCCGATGCAGCTTTTGGGTTTGAGGATCGCCGCTAGAAGTAGCGGTACTAAGGTGGCGGCTGATGATGCGGTGGAAGCC[G/A]GTGATTCGCCGCATTTTAGAAAAATCAGCCGGGTTTTAGGGTTTGAGAATGAATCTAGGCAATAGCCAGTAGGCCAACAGT
94974 A G ATCCGATGCAGCTTTTGGGTTTGAGGATCGCCGCTAGAAGTAGCGGTACTAAGGTGGCGGCTGATGATGCGGTGGAAGCCGGTGATTCGCCGCATTTTAG[A/G]AAAATCAGCCGGGTTTTAGGGTTTGAGAATGAATCTAGGCAATAGCCAGTAGGCCAACAGT
94988 T C CCTTCTAGAACCCGATCAACCACCCACGTCTCTAGATTCAATGAAGCCTCTAGAACAAGAGCCCATGCTAGCTGCAAGAATCACCATAGAAGATGGACTG[T/C]GCCTACTACTTACCATAGACGACATAGACCGGCTTCTACAGTCTGGTCAAACACAGGATGGTGGGACCCAACTAAGAAGAAAGCGC
94988 G T TGAAGCCTCTAGAACAAGAGCCCATGCTAGCTGCAAGAATCACCATAGAAGATGGACTGTGCCTACTACTTACCATAGACGACATAGACCGGCTTCTACA[G/T]TCTGGTCAAACACAGGATGGTGGGACCCAACTAAGAAGAAAGCGCCAGGCCCTTCTAGAAGGCCTTGCAGCATCACTCCAACTCGT
94988 C T CCAGGCCCTTCTAGAAGGCCTTGCAGCATCACTCCAACTCGTCGACCCGTTCAACCATTCACCGGGCCTAGGTCCGCAAGACGACCTTGTCTTCCTCCGC[C/T]TGACCTCCCTCCCGAAAGGCCGGAACCTTTTTTCCCGCTTCCTGCTGCTTCTCCATCCAGGAAGTAACC
94992 T C AAAGGAAGCACCTGGAGAAAGTGGAGTGGATATATCAGAGATTCTGGAACGTTCTGCAGAAACCGCAGATGGTCTCTTGAAAATTCGATCGGTTAGCGAA[T/C]GAACTCTGATATTATCATGGTCAAGCATGGTGGACGGTGAACGATTAGCATATGGAACTGGGTTGTGGAGGGCAAGTTCGATGC
95008 CT C GGAGTTGTCTTCGATTCCCCACCACTCTCCACCCTTCCTTTCCGTCGCCAAACTCCATTTTGAAAGTTCTGCTGCAGTTTCATTCTAATTTGGCTGTATT[CT/C]TTTTGGTTTCCACCTTTTTTTACCGTGTTATTATCAGCACCCACACACTACGGTCGGCAAACAACAGGTGGAGCCAGCAGGGCTCCTGTG
95008 CT C TTCCCCACCACTCTCCACCCTTCCTTTCCGTCGCCAAACTCCATTTTGAAAGTTCTGCTGCAGTTTCATTCTAATTTGGCTGTATTCTTTTGGTTTCCAC[CT/C]TTTTTTTACCGTGTTATTATCAGCACCCACACACTACGGTCGGCAAACAACAGGTGGAGCCAGCAGGGCTCCTGTGGCGATTGATCGCCG
95012 C T TTGGTTCCGCAGCAAACAAGAAGGGTACTTCACGAAGCAGCAAAGCTGGCCTTCAATTCCCGGTTGGAAGAATTGCGCGATTTTTGAAGGCGGGGAAATA[C/T]GCTGAGAGGGTTGGCGCTGGTGCGCCGGTTTATTTGGCCGCCGTTCTGGAGTACTTAGCCGCTGAGGTTCTGGAGCTTGCTGGA
95012 C T GTTACCATTGCCAATGGTGGAGTGATGCCAAACATCCATACCCATTTGCTTCCTAAGAAGTCTGGTCCTTCAAAGACTGATGCAGCTGAAGATGAATAAA[C/T]TAGTCTGGTATTTGGAGTTTCAAACTGTAGTGTATGCTTAGATGACTGATGTGGGTGGCTTAATTGTAATGGAAGGACTTTCTACTCT
95012 A G TACCATTGCCAATGGTGGAGTGATGCCAAACATCCATACCCATTTGCTTCCTAAGAAGTCTGGTCCTTCAAAGACTGATGCAGCTGAAGATGAATAAACT[A/G]GTCTGGTATTTGGAGTTTCAAACTGTAGTGTATGCTTAGATGACTGATGTGGGTGGCTTAATTGTAATGGAAGGACTTTCTACTCTTG
95024 A G GGATCGGAATATGGACTCCATCTTCCCTCTGACGGAGAACAGTATGGCGTTGAAGGCCGCAATGGAAGCGAGTGGGGCACCCATGCCTTTGAACAGCCCA[A/G]CAGGGCCCTCGCTGGTTACCGTCTTCCTCACTGCGTCGATTGCACCTGAGTACTTCAGGGACTGCCCGGGCTGTGGAACCGGCTG
95026 A AT GTTGGCCTACTGGGAGAAATGCACAGACTCGTAGCCACCCGCTTCGCCACTGCCTCTTCCGTTGCAGTGGCCATGGCGGGGGCCGCTGGAGGAATGGCTT[A/AT]GCCGACAACTCATCGTCAAGCGGATTTGACCCTGAATCGTTAGAAAGAGGTGCGAAAGCTTTAAGAGACATCAACAGCTCTCCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95034 A AC GGTTTAGCACGAGCTTCACCCATCCCCCCCTTCGCAGCCCCTTCCTTCCCATTTTGATAATTTACTCGGTCTGTTTGATTAATTTGACATTATTGTTATC[A/AC]TTTCTTCCTCCTATTACCATGGAGCTCCGGTTACTTTGTACCTATCTGATCTGACTGTGGTTGCGTTTGGTTATTGATATGGTATTCTGATT
95040 A G AAAGGGAAAATATAGATCAGAAACGCCTTTTCCTGGCCATGCGTTGCTCAGATCTCAGCATCAATTCATCGATCTGATTCATCCAAATTTCTTTGCTACT[A/G]CTGCTCACATCCGTTCCTTCTACCTTCTGCTGAGATTTATCAACTCCTAAACCGATCAATGACAATTCATAATCATACCTTTCCTTTGTCA
95058 CT C AATTCTTGAAAATTCATGGTGCCATTCATATCAAAATCATACATCCTGATCATCTGTTGAACAATTGAGAGAGAAAAAACCAGGTTTCCGACCTCAAGAG[CT/C]TTCTCTGAAGCTGAACAGCGGTAATATTTCCATTATTATTTGAGTCAACTCTTCGAAACCATTCTCTTAAAGCGGCCGTATTATTGTTC
95062 G A GATTAATTTTGTGGTCTGCGCAGAGTGCCTCGATGAGCTTGATATATTCGGCTTCAGTGCAAGTCTCGACGAGGACGCATAAGTGAGCCTGGCGTTTATC[G/A]AGAGCTTTGGCAGCTTCACGGAGGCCTCGAGCCAAACCATCGTGGACGAGGGCATTCTTCAAGACTTGCTGGAGGGCATCCTCAA
95068 G A CAAACAATATGTTGTTCGGCAAAGCTGGCATTTCTGGATGCATTGATTTTGCTCCTCCAGGTACTGGCAGCTGAGATAACGGTGGCAAACTGCCGTAAGC[G/A]CCAGCATAAGGTGCATTCAAACCTGCAGCAGCCTGATTTGCTTCTTGCTCCCGACGTTTTCTCTCAGCTTTATCATCATGACGCTTCT
95068 A G GTCTGATTTAGTCTTGGCATACTGGATCCTCATTGGCTTGTCATAAAATGGAAACCCTTGCATTCGTTTAAGTGCCTCGGTGGCTGAAGCAACATCCTCA[A/G]AAATTACCCATGCTTGTCCTTTATGTTTCAATGTTTTGAATGCCAATACATCTAATATCTTTCCAAACTGGGAGAAAACAGCATTTAATG
95070 T A TCACTGTTGGCCTACTGGCTCGAAAACCCTAAAGCCGCCAGTAAACCGTAGTACTCTGCT[T/A]CCACAATCTTTCAGCTATCTTCAATCTAATTCCTATTACGATGGCAGATGAGGTTGCGGTCGAAACAGTCGCTCCGGCTCTCGGAGAACCCATGGATATT
95070 A G AACCCTAAAGCCGCCAGTAAACCGTAGTACTCTGCTTCCACAATCTTTCAGCTATCTTCAATCTAATTCCTATTACGATGGCAGATGAGGTTGCGGTCGA[A/G]ACAGTCGCTCCGGCTCTCGGAGAACCCATGGATATTATGACTGCTCTACAAGTTGTGTTAAAGAAATCACTGGCTCATGATGGCCTTG
95070 C CA AAGGACTATGGTGAGGAGTCCGAAGGTCTAAACATCGTTCAGAACTACGTGAAGTCTCAATGAGTTAATATTTTAGATGATTTTGATCGTACCAGTTTAA[C/CA]AACAGTGTTGTTAATTTGCTCTTGTAATGTTTGAAGTTTGATGATTTGATGTATTCTGAACTCTATTTGGTATTTTTATGTTCGGTT
95074 C T CAAACCGACGTATGCATTTATAAACAAGGAATGAAGCAGCTGCTCCCACGAATGGAGAGATGACCCATGATGAAGTAACTCGTGCTAATGAACTCCAAAA[C/T]ACAGCACCTATCCCACCATATACGAGGCCGAATCCTACCATGGCTCCCACGATACAGTGTGTAGTTGAAACAGGCCAACCATAAAA
95074 G A CAAGGAATGAAGCAGCTGCTCCCACGAATGGAGAGATGACCCATGATGAAGTAACTCGTGCTAATGAACTCCAAAACACAGCACCTATCCCACCATATAC[G/A]AGGCCGAATCCTACCATGGCTCCCACGATACAGTGTGTAGTTGAAACAGGCCAACCATAAAATGAAGCCACCTGCAACCAGCTACC
95074 C T CGAATGGAGAGATGACCCATGATGAAGTAACTCGTGCTAATGAACTCCAAAACACAGCACCTATCCCACCATATACGAGGCCGAATCCTACCATGGCTCC[C/T]ACGATACAGTGTGTAGTTGAAACAGGCCAACCATAAAATGAAGCCACCTGCAACCAGCTACCAGCAGCAGCAAGAGAACCTAGCAA
95074 G A AGATGACCCATGATGAAGTAACTCGTGCTAATGAACTCCAAAACACAGCACCTATCCCACCATATACGAGGCCGAATCCTACCATGGCTCCCACGATACA[G/A]TGTGTAGTTGAAACAGGCCAACCATAAAATGAAGCCACCTGCAACCAGCTACCAGCAGCAGCAAGAGAACCTAGCAACCCAGCAAA
95082 A G CATTTGCTGAAGCCATTCACCCATTATCGTGCCCTTCATCAACTACCGCCTTCCCTTTCACTACCCTGAACGGACGCCACCAGTAAACTGCCCCCTCTTT[A/G]CCTTGCCACTATCAACCTCAGCCTGCTACCCAAAAAGGATACTTAGTCAGGGTGGTTCATGGTTCAAATGGCTTATTGACTTATGAAGGG
95092 A G ACCCACGTGGATCCCTCAATGTCTCAGGACTTCCACGCTCATGAATGACTGTTGAGAATCGAACGATGAGAGGTGTCTGCACGCCCGGAGAACGAAGAAA[A/G]TCAGCACATGTTAAGTGAGACACATCGTGAGTGACTTCAAAGAAACCTTTTGCACTGGCTCCTCTAGCATGAACAACGCGTTCAGG
95092 A G TAGCATGAACAACGCGTTCAGGAATGCGCTCTCTATCAAACTGCGCAAGCTTCTCAATTAGATGATAGTCCTCAAGGAGGATGGGACCTCTAGATCCAAC[A/G]GTAAGGGATGAATTATTATTCCAAACCGGAGCTCCATAATTCGTCGTCCAGAAGGTCGAATTGAAAGCGCTAGACGGACGATTCTT
95092 G A CAATTAGATGATAGTCCTCAAGGAGGATGGGACCTCTAGATCCAACAGTAAGGGATGAATTATTATTCCAAACCGGAGCTCCATAATTCGTCGTCCAGAA[G/A]GTCGAATTGAAAGCGCTAGACGGACGATTCTTGCAAGGATCCATGGGACAAGAGCGTACCGGAAATGAAAATCCCTTCCGCTTTAA
95100 G A GTTGGGAGAATGGGCCGGATTATGCAAGATTGATAAGGAGGGAAAGGCTCGTAAGGTTGTTGGGTGCAGCTGTGTAGTTGTCAAGGATTATGGTAAGGAG[G/A]GTCAAGCACTTGATGTTGTAACAGAGTACTTCAAGACTCGCAAGTAGTGTTCTGGTCCTACATGTCTCGACGGTGGCAGCTATG
95112 T C CATCAACGGTCCTCCAATACAAGCGATCCTCGAAGGCGAAACGGGACTTCTTCCTCTTGGCCTCAAGTGCAAAGCTTATGCTTCTTGGAATCAAAAACTG[T/C]CTGCTCTTTGCATCCTCCTCGAACTCACATGTCCTATCCTCGTCTATTCTGCTTATCTGCATAGCGCTTCTGCTTCTGGTAACTCTTTCCA
95112 A C CAAGTGCAAAGCTTATGCTTCTTGGAATCAAAAACTGTCTGCTCTTTGCATCCTCCTCGAACTCACATGTCCTATCCTCGTCTATTCTGCTTATCTGCAT[A/C]GCGCTTCTGCTTCTGGTAACTCTTTCCACTCCCCTCGACACGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCG
95112 C T GTCTGCTCTTTGCATCCTCCTCGAACTCACATGTCCTATCCTCGTCTATTCTGCTTATCTGCATAGCGCTTCTGCTTCTGGTAACTCTTTCCACTCCCCT[C/T]GACACGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCGCCTCTTGGATCAGAGCCCGGAGGTCTGCATCGCTTG
95112 A G GCTCTTTGCATCCTCCTCGAACTCACATGTCCTATCCTCGTCTATTCTGCTTATCTGCATAGCGCTTCTGCTTCTGGTAACTCTTTCCACTCCCCTCGAC[A/G]CGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCGCCTCTTGGATCAGAGCCCGGAGGTCTGCATCGCTTGAGC
95112 T C GCATAGCGCTTCTGCTTCTGGTAACTCTTTCCACTCCCCTCGACACGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCGCCTC[T/C]TGGATCAGAGCCCGGAGGTCTGCATCGCTTGAGCTCGGTCTATGGTTGGAAAAGGGATCACATCGTTCCACTCGCTCCGCGCACTTTG
95112 T C TCGACACGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCGCCTCTTGGATCAGAGCCCGGAGGTCTGCATCGCTTGAGCTCGG[T/C]CTATGGTTGGAAAAGGGATCACATCGTTCCACTCGCTCCGCGCACTTTGACATGCCTTTGGTGTACATGTCTCTTGCTTTGAGAACAA
95112 T A CACGCTGCTGCTCTCGACTGGCCCGGCATATGATCGTGATCTTCGAAGTTCCGCCTCTTGGATCAGAGCCCGGAGGTCTGCATCGCTTGAGCTCGGTCTA[T/A]GGTTGGAAAAGGGATCACATCGTTCCACTCGCTCCGCGCACTTTGACATGCCTTTGGTGTACATGTCTCTTGCTTTGAGAACAAATCT
95112 C T GTGATCTTCGAAGTTCCGCCTCTTGGATCAGAGCCCGGAGGTCTGCATCGCTTGAGCTCGGTCTATGGTTGGAAAAGGGATCACATCGTTCCACTCGCTC[C/T]GCGCACTTTGACATGCCTTTGGTGTACATGTCTCTTGCTTTGAGAACAAATCTTCTTAGTCTGCCTCCCTTTTTATCTTTGCTTTTGTTC
95112 T C GTCTATGGTTGGAAAAGGGATCACATCGTTCCACTCGCTCCGCGCACTTTGACATGCCTTTGGTGTACATGTCTCTTGCTTTGAGAACAAATCTTCTTAG[T/C]CTGCCTCCCTTTTTATCTTTGCTTTTGTTCATCTTTCTTATGTTCAATCCAGTAGGCCAACAG
95126 A C TTACATCGTCCAATGGGGGCAATGAATAATAATATGCCTGCATTGCTAAAGTTATCAGGCCATTAACCAAGCAACCAGTGCTTGGGTCTTAACCTGAATT[A/C]TTTTTCAGCATCTGTGGGTCGGTCTGATAGTAAATGACATCACCAACATCACTAACAAAATGATCGACTCTCAAGCTTCTTGCTAACAC
95126 A T GTAAATGACATCACCAACATCACTAACAAAATGATCGACTCTCAAGCTTCTTGCTAACACGCCAATTAGATGGATTGGCAATGGCAAAGATTTCTCAGGC[A/T]CTTTGTAGTATTTTCCTAACACAGGCTTTGCTGCTTTGGTTGCTTCCACAAGATGATAGTGAGGCATTTGAGGGAATAGATGATGAAT
95132 A G GGCCTACTGGTCGGTTAAGGGCTCGAATTAACCCCACAGCCTATCTCAATTCTCCACCAAGCTCTAGTGTGTATCCAGTTGTTGTAGCTGCAAACCCAGT[A/G]GAAAAAATCAATTTGCGATCGGGCTAACAGACGGCAGCATCCAAGTAATAGAGCCTTTAGAATCAGAGGGTAAGTGGGGCACGGAC
95132 G GA GCCTACTGGTCGGTTAAGGGCTCGAATTAACCCCACAGCCTATCTCAATTCTCCACCAAGCTCTAGTGTGTATCCAGTTGTTGTAGCTGCAAACCCAGTA[G/GA]AAAAAATCAATTTGCGATCGGGCTAACAGACGGCAGCATCCAAGTAATAGAGCCTTTAGAATCAGAGGGTAAGTGGGGCACGGAC
95132 G A CGGGGCCTCCTCTTCAGTTAAAGTAGCTGCATCTTCTACCCAGCCGCCGCCTTCAAATACCACAGCAGATCCGCAGTCGAGGTGATGAACGGCTACGATC[G/A]TTTATCAGCTGCTGCCCATACCGATGATAACCTACCAGTTTTAAAATCTCTTCTTTGGAGATGATGTAGCTTTGTATGTGCAGAGAAC
95136 C T GATGAAATTTTTCTTTCCTATTATGTAAGGATTTGATTATCTTGGAGCATAAAGGCAACGAGTAGCCATTCGGATTCTTATGTGCATATCCATTAGTGCC[C/T]TTAACATCCTTTACATCATCAAAGCCGCCAATCAGATGGACATCTAAAGTAGCATCAACTTCATGGTTGGCAAGTAATGACAACATTTGC
95136 G A ATTATCTTGGAGCATAAAGGCAACGAGTAGCCATTCGGATTCTTATGTGCATATCCATTAGTGCCCTTAACATCCTTTACATCATCAAAGCCGCCAATCA[G/A]ATGGACATCTAAAGTAGCATCAACTTCATGGTTGGCAAGTAATGACAACATTTGCGATAAACCTGTGTCGACAACTCCTTCAAAATCCA
95136 A G ATCCTTTACATCATCAAAGCCGCCAATCAGATGGACATCTAAAGTAGCATCAACTTCATGGTTGGCAAGTAATGACAACATTTGCGATAAACCTGTGTCG[A/G]CAACTCCTTCAAAATCCATATGGCTTAACGATGTCATTCCAGTCTCCCGGTTCCTGATTACAAGGCCAACACATGTTGTTGCCTCATCC
95136 G A TGATTACAAGGCCAACACATGTTGTTGCCTCATCCGTGCCCACAAACTTTACTAGATTGGGGTCAACTGTCGCATACTCTCTCTGAAACACGTACACAAG[G/A]TTAACGGGCTCGGATCCTGTAACTTTTCTTTCGGGAGTAGACTTGAGGCGATCCGAAGCAGAAACCAGAGTAGGGTTTCGCAATAAC
95136 G A TACTCTCTCTGAAACACGTACACAAGGTTAACGGGCTCGGATCCTGTAACTTTTCTTTCGGGAGTAGACTTGAGGCGATCCGAAGCAGAAACCAGAGTAG[G/A]GTTTCGCAATAACGAGGTTAGAATTTCATCTGCCGATAGAGAAGAGGCAGCAGTGACGGCAACGCAATCTACGAAGATCATTGAG
95136 G A CAGAAACCAGAGTAGGGTTTCGCAATAACGAGGTTAGAATTTCATCTGCCGATAGAGAAGAGGCAGCAGTGACGGCAACGCAATCTACGAAGATCATTGA[G/A]TAGTTTGACGAGTGCGGGTGGAGGACGAGAATCTGCTGGGTGGATTAGTGCGCTGGGTGTAGTTCAAACTATTTTTT
95142 T G TGCACAATTTTCTTCGTCTTCCCAGTTACTTCTCAGCCACGCGTAAGCTGTAGCAGGCTTTCTGGTTCTGTTGAAGTAATTGCAATGCCTAGGGCTCATT[T/G]CTTGAACCGAGAATCGATCAGACGAACTCACAAGTGTGGTGATATTATCCCATCTTTTCCGTAAACTGTTATAGCCAAACTCATTGAAG
95142 C G TTTCTTCGTCTTCCCAGTTACTTCTCAGCCACGCGTAAGCTGTAGCAGGCTTTCTGGTTCTGTTGAAGTAATTGCAATGCCTAGGGCTCATTTCTTGAAC[C/G]GAGAATCGATCAGACGAACTCACAAGTGTGGTGATATTATCCCATCTTTTCCGTAAACTGTTATAGCCAAACTCATTGAAGTCATGGCG
95160 G GC CGAGCTTGCCGACCGTGTCTTCACTGAGCTCGGAAAGGGTGCTGATGCTCTCGCTGCCGCCAAGGCCCTCGTGAACGCTGAGAAGAACGTCAACCCCTTC[G/GC]CCCAGGACCAACCCACCCTCTGCGACGATGCCAGCCTCCCGGCCAACATTGAGCTCCGTGGCATCACCCCCAAGGTTGACCCCGC
95162 T TC TGTTTCTTCTCTCGAAGTAAACAAATTTATCCCCAAATCGCCTTGGCCTCAACCGAATTTCAGATCGCCCTCTTCAAAAATCGGATCTCCGCTCCTCGTC[T/TC]CGCCTCCTTCTCCACCATCGTCGGCCACCGATTCTCCATCGCCAACACCAATCGAAGCCACCCCTTCCACGAAATCTCGGGATGCTCTTC
95162 C T TCCCCAAATCGCCTTGGCCTCAACCGAATTTCAGATCGCCCTCTTCAAAAATCGGATCTCCGCTCCTCGTCTCGCCTCCTTCTCCACCATCGTCGGCCAC[C/T]GATTCTCCATCGCCAACACCAATCGAAGCCACCCCTTCCACGAAATCTCGGGATGCTCTTCGCCTCCTTCACTGGTTTCCTTAGCTCACCG
95162 C T CCACCCCTTCCACGAAATCTCGGGATGCTCTTCGCCTCCTTCACTGGTTTCCTTAGCTCACCGCTATCAAGCATGAACCCGCCTCTAAAATTCGAAACCG[C/T]TGTTCGCCGCACCAAATCGTTGGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTGCTCCCGGACGATGCTGCACCAACGTC
95162 C T CTTCACTGGTTTCCTTAGCTCACCGCTATCAAGCATGAACCCGCCTCTAAAATTCGAAACCGCTGTTCGCCGCACCAAATCGTTGGAGCCAGCACCTCAG[C/T]AAATCGCTATCACCACCGCTACCTGCTCCCGGACGATGCTGCACCAACGTCATGAGCTCTCGAACCGTTGCATGTCCTAAAAATCGTTG
95162 C T TATCAAGCATGAACCCGCCTCTAAAATTCGAAACCGCTGTTCGCCGCACCAAATCGTTGGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTG[C/T]TCCCGGACGATGCTGCACCAACGTCATGAGCTCTCGAACCGTTGCATGTCCTAAAAATCGTTGTTACACCGTTTTAATGTCCTAAGTG
95162 C T CCCGCCTCTAAAATTCGAAACCGCTGTTCGCCGCACCAAATCGTTGGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTGCTCCCGGACGATG[C/T]TGCACCAACGTCATGAGCTCTCGAACCGTTGCATGTCCTAAAAATCGTTGTTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAG
95162 A G TTCGAAACCGCTGTTCGCCGCACCAAATCGTTGGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTGCTCCCGGACGATGCTGCACCAACGTC[A/G]TGAGCTCTCGAACCGTTGCATGTCCTAAAAATCGTTGTTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAGATTTCAGCTTACA
95162 C T TCGCCGCACCAAATCGTTGGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTGCTCCCGGACGATGCTGCACCAACGTCATGAGCTCTCGAAC[C/T]GTTGCATGTCCTAAAAATCGTTGTTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAGATTTCAGCTTACAAACTGGAGAACGT
95162 T C GGAGCCAGCACCTCAGCAAATCGCTATCACCACCGCTACCTGCTCCCGGACGATGCTGCACCAACGTCATGAGCTCTCGAACCGTTGCATGTCCTAAAAA[T/C]CGTTGTTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAGATTTCAGCTTACAAACTGGAGAACGTGAAGACGCATGACGCATA
95162 T C GCTGCACCAACGTCATGAGCTCTCGAACCGTTGCATGTCCTAAAAATCGTTGTTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAGATTTCAGCT[T/C]ACAAACTGGAGAACGTGAAGACGCATGACGCATATGCGCGCGCAGGCACGACAAAAACCGTAAAACTTTTATTCTTTGAAAAAGTTAT
95162 CA C TTACACCGTTTTAATGTCCTAAGTGTTTCAGATTTAAAGATTTCAGCTTACAAACTGGAGAACGTGAAGACGCATGACGCATATGCGCGCGCAGGCACGA[CA/C]AAAAACCGTAAAACTTTTATTCTTTGAAAAAGTTATGTTACATGTATTGTTTCCGCTGTGAAAAATAATTTGTAAAACTCTGATATTT
95162 T TG GATTTCAGCTTACAAACTGGAGAACGTGAAGACGCATGACGCATATGCGCGCGCAGGCACGACAAAAACCGTAAAACTTTTATTCTTTGAAAAAGTTATG[T/TG]TACATGTATTGTTTCCGCTGTGAAAAATAATTTGTAAAACTCTGATATTTTTGTATAAAATTTATTCCGCTGCAAAAAAAAA
95168 G C CGTCCTCCTTCCTCTCCCTCTTCCTCCCATTCTCCGTCTCCTCCGCCTCGTCCGCCACCACCTCCTTCGCCGCCGTCTTCTCCATTGCGTCCTGGTACCT[G/C]TCCAACATCTCCGTCCTCCTCCTCAACAAGTACCTCCTCTCCATCTACGGCTTCCGCTACCCCATCTTCCTCACCTCCCTCCACATGCTTTCCT
95168 G A GTACCTCCTCTCCATCTACGGCTTCCGCTACCCCATCTTCCTCACCTCCCTCCACATGCTTTCCTGCTCCCTCTTCTCCCTGCTCTTCATCCCCTTCCTG[G/A]CCCTTGTAAAGCCCCAACCCATCTCCTCCCGCAGGCAGTTCCTCAAAATCGCCGCTCTGTCCCTCGTCTTCTGCTTCTCCGTCGTCTGCGGCA
95168 C T CCCTCGTCTTCTGCTTCTCCGTCGTCTGCGGCAACACCTCCCTTAGGTACATCCCCGTTTCCTTCAACCAAGCCATCGGCGCCACCACTCCCTTCTTCAC[C/T]GCCGTCTTCAGCTTCCTCATCACATTCCGCAAGGAATCCGCCATTGTTTACCTGTCCCTAGTCCCAGTCGTTCTCGGGATAGTGTTGGCAA
95168 A G TGGCAAGCAATAGCGAACCCTCTTTCCATCTGTTCGGATTCCTAATCTGCATCGGATCCACAGCGGGTCGGGCTTTGAAATCCGTAGTGCAAGGGATTTT[A/G]CTAAGCTCCGATAACGAGAGACTGAACTCAATGAATTTACTTATGTACATGGCGCCAATGGC
95170 AT A TGTTTCAAGGTAGAATAATGAGCACAAATTTGGCATGGTGTCTTACGAAGGACATCGAACCACCTGTGTGACTCATTTTCAGCTTCTTGCGGTTCTCGGT[AT/A]TTTTTTTCAACTTTTATCTTATTTTTGTGATCATTGTCCCAATAGTTTACCATTCTCCTCCATTGTTCGCTATCCACGCGATCATCTCCAC
95172 A G GGCGGCGACGTCCAACACGGTAGCCGGCACGTTCCAGCACTACATAGAAGTCCATACCATAGATACCAGTAGATGGGTCGTACTTGATTCCAAGATCAAT[A/G]TGTTCTTGAATACCAAAGCCAAAGCAACCAGTATCACTGAAGTTCCTCCTAACCAATTCATACTCCTTCACTTTCAAACCACTCTCCA
95172 C T TAGATGGGTCGTACTTGATTCCAAGATCAATATGTTCTTGAATACCAAAGCCAAAGCAACCAGTATCACTGAAGTTCCTCCTAACCAATTCATACTCCTT[C/T]ACTTTCAAACCACTCTCCAAAAGCTGCATTGCCTTTTCGCCTCTGATTGTCACATAGCACGCAATCTTTTCATTTCTCCTGATCCCAAAAG
95172 G A GAATACCAAAGCCAAAGCAACCAGTATCACTGAAGTTCCTCCTAACCAATTCATACTCCTTCACTTTCAAACCACTCTCCAAAAGCTGCATTGCCTTTTC[G/A]CCTCTGATTGTCACATAGCACGCAATCTTTTCATTTCTCCTGATCCCAAAAGATCGAACAGTATATCTAGCTTTGGAGAACACAGGAGTC
95190 G A CGTTCCCAATTGCATCAATTTTACTCCCTCCATCAACTGACTTCGTCCCTACCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATC[G/A]TAGCTGTCCGACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95190 G A TCCCAATTGCATCAATTTTACTCCCTCCATCAACTGACTTCGTCCCTACCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTA[G/A]CTGTCCGACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTAATG
95190 T C CCAATTGCATCAATTTTACTCCCTCCATCAACTGACTTCGTCCCTACCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTAGC[T/C]GTCCGACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTAATGTG
95190 C G TTGCATCAATTTTACTCCCTCCATCAACTGACTTCGTCCCTACCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTAGCTGTC[C/G]GACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTAATGTGTCTT
95190 C T CATCAATTTTACTCCCTCCATCAACTGACTTCGTCCCTACCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTAGCTGTCCGA[C/T]TCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTAATGTGTCTTTCA
95190 C A CCGTACGCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTAGCTGTCCGACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTT[C/A]GTTATGAAATCGTAGCAAGGAATCAGCAGCGGTTTTAATGTGTCTTTCAGCGTTTCTTCACTTCTAAAGATTTTGCTGAAGCTTTTG
95190 G T GCACGGCACAGGTGGCAGCACATACGTCGCTCATCTTGAAATCGTAGCTGTCCGACTCAACCGCGTCCGATCTGGAGAAAACGAACGGCGATTTCGTTAT[G/T]AAATCGTAGCAAGGAATCAGCAGCGGTTTTAATGTGTCTTTCAGCGTTTCTTCACTTCTAAAGATTTTGCTGAAGCTTTTGGTCTTAT
95190 A T GTGTCTTTCAGCGTTTCTTCACTTCTAAAGATTTTGCTGAAGCTTTTGGTCTTATTCTTTTTGGAGAATAGTCCAAGTAATCCTGGCTTTTCGTTTTTGA[A/T]CATTTTGTTTTTGGTCAGGAATGCAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGC
95190 GT G TCAGCGTTTCTTCACTTCTAAAGATTTTGCTGAAGCTTTTGGTCTTATTCTTTTTGGAGAATAGTCCAAGTAATCCTGGCTTTTCGTTTTTGAACATTTT[GT/G]TTTTTGGTCAGGAATGCAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAAC
95190 A G TAAAGATTTTGCTGAAGCTTTTGGTCTTATTCTTTTTGGAGAATAGTCCAAGTAATCCTGGCTTTTCGTTTTTGAACATTTTGTTTTTGGTCAGGAATGC[A/G]AAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAAC
95190 C T TAGTCCAAGTAATCCTGGCTTTTCGTTTTTGAACATTTTGTTTTTGGTCAGGAATGCAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGAC[C/T]TTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGA
95190 T G GCTTTTCGTTTTTGAACATTTTGTTTTTGGTCAGGAATGCAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCAT[T/G]GCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCG
95190 A G TTTCGTTTTTGAACATTTTGTTTTTGGTCAGGAATGCAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGC[A/G]GCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAA
95190 G A CAAAGGCTTCTTCAGCAGAAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGC[G/A]TCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCA
95190 C T AAAACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGAT[C/T]GTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACA
95190 T C ACAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGT[T/C]GCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCG
95190 G A CAATGGTTTACCGTCAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTT[G/A]CCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGT
95190 A G CAGAGGACCTTTTGGTAAACAGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACC[A/G]GAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATC
95190 A T AGCATTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGG[A/T]TTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCA
95190 A T TTGCAGCGAGAACGCCTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTC[A/T]AGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTAT
95190 A T CTCCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGC[A/T]GTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATT
95190 T C CCGTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAG[T/C]TACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTG
95190 A G GTCGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTT[A/G]CAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGG
95190 A G CGCCGGAACCAGCGGCAGCGTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTAC[A/G]GCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGGG
95190 A G GTCGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCG[A/G]CAGCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGGGTTTTAGGGGTATTGTCAGAA
95190 A G CGAAGAAGTCAGCGATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGAC[A/G]GCGTCAATTGACAAGATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGGGTTTTAGGGGTATTGTCAGAATA
95190 A T ATCGTTGCCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACA[A/T]GATCCGGATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGGGTTTTAGGGGTATTGTCAGAATAGCATTTAACTGGGGT
95190 G A CCGTGGGAAGACCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCG[G/A]ATCTTGCCTCCTCCTCCATTATTGAAATGTTTTGAATTTGGGGTTTTAGGGGTATTGTCAGAATAGCATTTAACTGGGGT
95190 C T CCAGAAATAGATCGAAGGTTGGATTCAAGTCTGGCTATAGCAGTTACAGCAGGTAGTACGTCTTCGACAGCGTCAATTGACAAGATCCGGATCTTGCCTC[C/T]TCCTCCATTATTGAAATGTTTTGAATTTGGGGTTTTAGGGGTATTGTCAGAATAGCATTTAACTGGGGT
95198 G GT TCTTTTCTACATATACACCTTGATTTTGCTGTGCGTGCTCGCCACCAATTTAACCATATCGTCACCTTCTCCTTCAAAGCTTGTCCACAAAATTGGATTT[G/GT]AGCACAGTTGCTTTATTTCTTCATCCACGTCAGATCTGAGTGCTCCTCTCACTTTTAAAGCTTCCTTCTCCACTTCCTCCGTAGTGTCGTGC
95212 C T CAGAAGAATGATTGACTCCAGAAAGTGAAAGACAAACTGCTTTGACAGCCGACCTATCTGAACCCGCCTTCAAAAGTGCTTCCGCCATTATCTTTTCCAA[C/T]GTATCTTTAGCTGCATTTTCGCCAACAGAATTGTGATTGGTGCAGCCAGCGCGAGCACGAGACAGAACAGGAACAGTCGGTGAAGA
95218 AG A ATATTCATATCTTCTATTACATATCGTTGACATCCGGACAGGCTAGTTCAGGTTTATCATAGCCCATCTCCTCAGGGGTAAGAATACCCAGCTCCTTTAG[AG/A]GTGGGGCTGATCTCCTTCAGCATGTACGGCCAGATCTCCTTCACCTTGGGTCCACACTTATCCTTCACTGCCTCAAGGTATCTGACAG
95224 G A CAGATCGACTTCTTGCTGTTAGGAGAGTCATGATAAGGACTCTTAAGTTGCTTTTTTGGGGCATATTCTTACAGGGTGGGTACTCTCATGCTCCAGATAA[G/A]TTAAGTTACGGTGTTGACATGAAACATATAAGGTGGTGTGGTATCCTCCAGAGAATTGCTCTTTCATACTTGGTAGTATCACTCTTTG
95228 GT G ATCTCGCTTTGGTATTTAAGTACACTGCCGTAGTTCCATGTGTACATTATGCAGAGAAAACCCATGGCAAATGCAAGTGGTAGCCAGCCGCCTTCGAATA[GT/G]TTTTGTTAAGACGGCAGAGAGGTAGATGAGTTCTATTGTACCGAATATGGCAGGGAAACATATAGCCAGGAAGAGGTTGGTTTGC
95228 C T ACTTCAGCAATTCCATATGCATTAGCTATATCAGTGGTGCTCCTAAAAGTCGCAACAACAGCAATGCACATGAACATTAGAAACCAGTTGACTACAGGGA[C/T]GTAAATCTGACCCATAAATCTAACAGATGTGTGAATAATTTTCATTCTAGGGAAGCAACCAAGGGCCATGGATTGCTTAATGCAAGA
95240 T C AATTCAAGCCTGATTATCGCTGGTCAAGGTTTCTGTGTCCTGCTCCGAAGAACATGAAGAAGTCGCAC[T/C]TGTCTGCTGCTGGAGATACTCCAAACGAGGCACCTGCTGCATTGAAGCACTTTCCCGCTTTTCACCAGTTCCATTGTTGCTGACATTCTCAGCTTGAGGA
95240 G T AAGGTTTCTGTGTCCTGCTCCGAAGAACATGAAGAAGTCGCACTTGTCTGCTGCTGGAGATACTCCAAACGAGGCACCTGCTGCATTGAAGCACTTTCCC[G/T]CTTTTCACCAGTTCCATTGTTGCTGACATTCTCAGCTTGAGGACCACCAAGTATAATTACATTATTGCCCCCAACAATGCTCCTCCTGT
95240 A T CCTGCTGCATTGAAGCACTTTCCCGCTTTTCACCAGTTCCATTGTTGCTGACATTCTCAGCTTGAGGACCACCAAGTATAATTACATTATTGCCCCCAAC[A/T]ATGCTCCTCCTGTCATGTGATTGGATGATGGAGGACAGGTCAGATGCTGCTGGTAACAAAGTGGGAGATGACCCTGTTGCTCGCTTTAC
95242 GT G GAAGGAGCTGCATTTGGTTTTGGAGAAGCTTGGGGAGAAATGCAGTGTTGAGGATTGCGAAAAGATGATTCGTTCAGTTGATTCCGATGGAGACGGGTTT[GT/G]TTAATTTTGATGAGTTTGTGAAGATGATGTATGACAAGAAAGCAAAACAGAATTAGATAAGCGTCAAGTAATTTAATTTGTGTA
95258 T C GTGCATCCGTTTCACCCGAAAATAACAATAAGGCGAGGAATACTGGCAGCTGAGTGCTCTGACACCATGCAGCAGTTTTTCCAGTTGAGAAGAAAGAAGG[T/C]TAAGAAAGAAGAGACGCCTCCTCCTCCTAGTATGTCAATGTCAGCAGCTCCCGTGAAGCTCTTAGGAAGATTCCACAATTTGTTAG
95258 G A GAGGAATACTGGCAGCTGAGTGCTCTGACACCATGCAGCAGTTTTTCCAGTTGAGAAGAAAGAAGGTTAAGAAAGAAGAGACGCCTCCTCCTCCTAGTAT[G/A]TCAATGTCAGCAGCTCCCGTGAAGCTCTTAGGAAGATTCCACAATTTGTTAGCTGCTATGTTTTGCTTGTAGCTTTTTCTAACTAGC
95258 T C GAAGAAAGAAGGTTAAGAAAGAAGAGACGCCTCCTCCTCCTAGTATGTCAATGTCAGCAGCTCCCGTGAAGCTCTTAGGAAGATTCCACAATTTGTTAGC[T/C]GCTATGTTTTGCTTGTAGCTTTTTCTAACTAGCAGACTAGAGTTGTTTTTTTCTCCACGCTAGTGATGGTATGGATATCAATTCACAGT
95258 TG T GAAGCTCTTAGGAAGATTCCACAATTTGTTAGCTGCTATGTTTTGCTTGTAGCTTTTTCTAACTAGCAGACTAGAGTTGTTTTTTTCTCCACGCTAGTGA[TG/T]GGTATGGATATCAATTCACAGTTTGTGTTTCTGATGTAATTGTGTGATTTTGTTAGATCTCGTGAATTGTGTAAAATTTGTTAAATGTGT
95258 G A GCTTGTAGCTTTTTCTAACTAGCAGACTAGAGTTGTTTTTTTCTCCACGCTAGTGATGGTATGGATATCAATTCACAGTTTGTGTTTCTGATGTAATTGT[G/A]TGATTTTGTTAGATCTCGTGAATTGTGTAAAATTTGTTAAATGTGTCCTAACTTGAATAAATTAACTTCCCGTTTTACAGTACAAAAAAAA
95258 A C GCAGACTAGAGTTGTTTTTTTCTCCACGCTAGTGATGGTATGGATATCAATTCACAGTTTGTGTTTCTGATGTAATTGTGTGATTTTGTTAGATCTCGTG[A/C]ATTGTGTAAAATTTGTTAAATGTGTCCTAACTTGAATAAATTAACTTCCCGTTTTACAGTACAAAAAAAAAGGCCACAT
95280 A C TGCCCGATCTCCCTCGAGATCATGCAGTCGCCAGTCAGTCTCTGCACTGGCGTCACCTACGACCGCTCCTCCATCCAACGGTGGCTCGACTCGGGCAAAA[A/C]AACCTGTCCCGCGACGATGCTCCCTCTGTCCACCACCGATCTGGTCCCTAACCTCACTCTTCGACGCCTGATCAACATATGGTCCGCC
95280 A C GCCCGATCTCCCTCGAGATCATGCAGTCGCCAGTCAGTCTCTGCACTGGCGTCACCTACGACCGCTCCTCCATCCAACGGTGGCTCGACTCGGGCAAAAA[A/C]ACCTGTCCCGCGACGATGCTCCCTCTGTCCACCACCGATCTGGTCCCTAACCTCACTCTTCGACGCCTGATCAACATATGGTCCGCCG
95280 G A CGGCGATTTCTTCGTCGATCAGGATATCGATGATTCCGTCAAAAACTGTTTGGTTTGCGCTTCGGATTTCGCCGGAAACGTTGTTCGTATTGTTTTCGAG[G/A]AACGGCATGGGATCCAGCTGAATCTGAAGGCGCTGGAGATTCTGGATCTGATTCTCGATTCTGATTGGATCGATTCCAAGAGTACAG
95284 A G TGTTAAAGCCTGAGCCACCACCGAAGCCGCCTCGGTTGAACCCACCACCACCAAAACGACCTCCACCGCCGAACGATCCACCAATATAGCCAGAAAACAT[A/G]CTGTCGTTTGCTTCTACGTCCATTTCCGGAAGTTCAGTGAACCTGCAGCCTACATCTTGTTCCACAACTCTAATGATTTTAGTTTGCTC
95284 T A TACTGTCGTTTGCTTCTACGTCCATTTCCGGAAGTTCAGTGAACCTGCAGCCTACATCTTGTTCCACAACTCTAATGATTTTAGTTTGCTCACGAGTGTA[T/A]ATGGCTATCACGGTTCCTTTCTTCCCTGCTCGGCCTGTTCTACCGGATCTGTGCACAAAGCTTTCGGAGTCATTGGGCAGTTCATAGTGT
95294 CA C CGCCATGGAGAGGCGACGATGCGAGTTCCGAAGATTTCGACGGCGCAAAGCTAAAAATGACAAACAACCCTGGTTCCGATCCAGTCATGCACGTGCCTCG[CA/C]AAAAAAACCGTCAACTCCAAAGCCATTGACGATAATTCGACAGTCGAGATTGATCCTGAGCTTCGGTACAGTTTTCAAAGAAACG
95294 A G ATCCAGTCATGCACGTGCCTCGCAAAAAAACCGTCAACTCCAAAGCCATTGACGATAATTCGACAGTCGAGATTGATCCTGAGCTTCGGTACAGTTTTCA[A/G]AGAAACGCTCAGTTTCTTCAGCGAGTTTTTAGCATCGACACCCTTGTAAAACCTCTTCCTCCTGCTATAGGCTACAATGTGTCCCGCAA
95294 T C CAGTTCTTTGATCCAGCTGGAATCGCAGATGCGCAGAGATCTCTTGGGTTAGGGCAAGAAGAGAGAGTCCGCCGTGTTCGTTAAGTCATTATCCTGTAGT[T/C]TGATCTTTGTACCTTCAAACTTGTATCATGCACACCAACACTGCCTATAGCTAAGATATGTGAAATTACAGTTGCTTTCATGTATATG
95304 T G CGATATTCTATATCGTACGATGGTTCGAATGCCTCTTCATCACTGATCACATCCTTTGATCAATTTCATACATCAGAAATTTAGGTATTAGGGTTTCGGT[T/G]TTGTTAGCAAAAACCCAAACCCTACCAAGTGCCAACCAACAATGGATCGTCCTAAACCTCAATCGCCGATCTCCTCCACCACAACCACAC
95304 G A CCTCTTCATCACTGATCACATCCTTTGATCAATTTCATACATCAGAAATTTAGGTATTAGGGTTTCGGTTTTGTTAGCAAAAACCCAAACCCTACCAAGT[G/A]CCAACCAACAATGGATCGTCCTAAACCTCAATCGCCGATCTCCTCCACCACAACCACACCCACGGCTGCTGCTTCTTCTTCTCCGTTCTTA
95304 C T AATTTAGGTATTAGGGTTTCGGTTTTGTTAGCAAAAACCCAAACCCTACCAAGTGCCAACCAACAATGGATCGTCCTAAACCTCAATCGCCGATCTCCTC[C/T]ACCACAACCACACCCACGGCTGCTGCTTCTTCTTCTCCGTTCTTATGCAGCAGCAGATCCGGATACAGTCGATGCTTCTGTCTACCGAA
95304 C T TTTGTTAGCAAAAACCCAAACCCTACCAAGTGCCAACCAACAATGGATCGTCCTAAACCTCAATCGCCGATCTCCTCCACCACAACCACACCCACGGCTG[C/T]TGCTTCTTCTTCTCCGTTCTTATGCAGCAGCAGATCCGGATACAGTCGATGCTTCTGTCTACCGAAGACTTGGCAGCGGATGGAGTATC
95304 C T CTTATGCAGCAGCAGATCCGGATACAGTCGATGCTTCTGTCTACCGAAGACTTGGCAGCGGATGGAGTATCCCGACGACGCTCGCTCCGGCTCCGAAACA[C/T]TCACCCGGAAGTGGTGGAGATCCACCGTGGCGGCGCTGATGAAGGCGAGAGAGTGGTCGGAGATCGTGGCGGGTCCTCGGTGG
95304 C A TGCTTCTGTCTACCGAAGACTTGGCAGCGGATGGAGTATCCCGACGACGCTCGCTCCGGCTCCGAAACACTCACCCGGAAGTGGTGGAGATCCACCGTGG[C/A]GGCGCTGATGAAGGCGAGAGAGTGGTCGGAGATCGTGGCGGGTCCTCGGTGGAAGACGTTCATTCGCCGATTTAACAGAAATA
95304 T G CGGCGCTGATGAAGGCGAGAGAGTGGTCGGAGATCGTGGCGGGTCCTCGGTGGAAGACGTTCATTCGCCGATTTAACAGAAATAGTCCTAGACATGATAA[T/G]AAATTTGGGTATGATCCGTTGAGCTATGCTCTGAATTTTGATGCCAGTCCTGATAGGGATTTCGAATTTCCGACTCAGTATGTTGG
95304 G T GGAGATCGTGGCGGGTCCTCGGTGGAAGACGTTCATTCGCCGATTTAACAGAAATAGTCCTAGACATGATAATAAATTTGGGTATGATCCGTTGAGCTAT[G/T]CTCTGAATTTTGATGCCAGTCCTGATAGGGATTTCGAATTTCCGACTCAGTATGTTGGATCCAGTAAAGGATCAATGGATTTGGCAG
95304 A G AGAAATAGTCCTAGACATGATAATAAATTTGGGTATGATCCGTTGAGCTATGCTCTGAATTTTGATGCCAGTCCTGATAGGGATTTCGAATTTCCGACTC[A/G]GTATGTTGGATCCAGTAAAGGATCAATGGATTTGGCAGCACTGCATCCTGTAAGTGAGAATTCT
95338 G C TCACGTCCGATGTACCGTTATCAAAGAAACCGCCATCAAACCCACCGTCGCCAAGCAAGCCAAAATCAAAATTAAAGTCGTCGCTGATTCCCCAAATCTT[G/C]GCTTCTACGTCATCCACAGAAGCTTCATCCCCAACGTTACCGTTGGCAACAACATTACCGGACGACACATCTGCATCCGCAGGAGGGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95338 G C CAAAATCAAAATTAAAGTCGTCGCTGATTCCCCAAATCTTGGCTTCTACGTCATCCACAGAAGCTTCATCCCCAACGTTACCGTTGGCAACAACATTACC[G/C]GACGACACATCTGCATCCGCAGGAGGGATGCCGAGGTCGTCATCCGAGGCCTCAAGCAAGTACCCGAGATCCGGCTGCACCGAGCTG
95338 A G CTTCTACGTCATCCACAGAAGCTTCATCCCCAACGTTACCGTTGGCAACAACATTACCGGACGACACATCTGCATCCGCAGGAGGGATGCCGAGGTCGTC[A/G]TCCGAGGCCTCAAGCAAGTACCCGAGATCCGGCTGCACCGAGCTGGAGTTAGACTCCGGACCGGACAAGGGATTCACCTCCGAAT
95372 A G CTCGACAAACAGGCCTGTCGTAAGCACCGTGAAGCAGCTTCGATTGGTAGCAGCCGGAGTGATTTCTGGTTGCGGCAGTGCGTGAGCTCAACGGAAACGA[A/G]GACTGGTGAATGCTCAGCACTGGATGGAAGAAGAAGCTTTTTCCCGGTTGTCGACTTCGATCACGGGAAGTGTTGGCAAGGGTA
95372 TG T AAGCACCGTGAAGCAGCTTCGATTGGTAGCAGCCGGAGTGATTTCTGGTTGCGGCAGTGCGTGAGCTCAACGGAAACGAAGACTGGTGAATGCTCAGCAC[TG/T]GGATGGAAGAAGAAGCTTTTTCCCGGTTGTCGACTTCGATCACGGGAAGTGTTGGCAAGGGTACGGATCCGATTGGTCAAAGG
95380 C T GGAAGGTTCAGCAGCACATGGGACCAGCCAGGGCAGTCTTTCAAGGAACAGGAAGGACCCTAGGAGCTGGGCCTTCTGCTGCTTCCAGCACCACGG[C/T]TGCAGTTCCTACACCCGCTGTGTCGCCCATTGCAGTTGATGAGTCTAAACCGACAACTTCTGTGCAGCTTCGTTTAGCTGATGGTTCGCG
95380 G T GACCAGCCAGGGCAGTCTTTCAAGGAACAGGAAGGACCCTAGGAGCTGGGCCTTCTGCTGCTTCCAGCACCACGGCTGCAGTTCCTACACCCGCTGTGTC[G/T]CCCATTGCAGTTGATGAGTCTAAACCGACAACTTCTGTGCAGCTTCGTTTAGCTGATGGTTCGCGCACTGTAGGGCGCTTCAACAC
95380 T A CCCTAGGAGCTGGGCCTTCTGCTGCTTCCAGCACCACGGCTGCAGTTCCTACACCCGCTGTGTCGCCCATTGCAGTTGATGAGTCTAAACCGACAACTTC[T/A]GTGCAGCTTCGTTTAGCTGATGGTTCGCGCACTGTAGGGCGCTTCAACACTGATCATACTGTAGGGCACATTAGGTCCTACATCAGC
95380 T G CTGGGCCTTCTGCTGCTTCCAGCACCACGGCTGCAGTTCCTACACCCGCTGTGTCGCCCATTGCAGTTGATGAGTCTAAACCGACAACTTCTGTGCAGCT[T/G]CGTTTAGCTGATGGTTCGCGCACTGTAGGGCGCTTCAACACTGATCATACTGTAGGGCACATTAGGTCCTACATCAGCAGTTATTCTG
95380 T C CTGCTGCTTCCAGCACCACGGCTGCAGTTCCTACACCCGCTGTGTCGCCCATTGCAGTTGATGAGTCTAAACCGACAACTTCTGTGCAGCTTCGTTTAGC[T/C]GATGGTTCGCGCACTGTAGGGCGCTTCAACACTGATCATACTGTAGGGCACATTAGGTCCTACATCAGCAGTTATTCTGCAAGCAGTG
95380 G A TCAACACTGATCATACTGTAGGGCACATTAGGTCCTACATCAGCAGTTATTCTGCAAGCAGTGGAAGAGCCGTACCAGCTAGGTATTCCCTGCAGACAGT[G/A]GATTTTCCTCCTAAACAGCTTACTGATGATGCTCAAACCATTGAACAAGCTGGCCTTGCTAACTCCGTTGTCGTTCAGAAACTTTGAA
95380 C T TCAGCAGTTATTCTGCAAGCAGTGGAAGAGCCGTACCAGCTAGGTATTCCCTGCAGACAGTGGATTTTCCTCCTAAACAGCTTACTGATGATGCTCAAAC[C/T]ATTGAACAAGCTGGCCTTGCTAACTCCGTTGTCGTTCAGAAACTTTGAATTCATGTGGAGTTTCGACAGAGCGGCTGCTCCCTTGATA
95400 TA T CTGTTAGTAGTAGGACTTCTACTGCTCAGACTCATGAACAGGCTTTTCAGGTTGTGGTATTGCGAGTTTCCATTCATTGCCAGGGCTGTGCTGCCAAAGT[TA/T]AGGAAGCACATTTCCAAGATGGAAGGGGTGACTTCATACAGTGTAGATCTGGAGTCCAAGAGAGTGACAGTAATGGGGCATGTTT
95404 A T TTGCCCTACCCGGCTTGTCCGAAGCCATCACGTTCCTCAACCACTTCACCATAACTATCTCCTCCGTTTCCTGAAAAAAATCATCGGATGGAAATCTACC[A/T]GTCACTATCACTGCAAGAATCACACCAAAGCTGTATATATCGCACTTCGCCGTATATTTAGACGTCTGGTAGTACTCGGGTGCTATGTAC
95406 A G CGGCGTACAACAGATGCGACGCGTCGCATCCGATCTCGAACTACAGCAAAGGGCGCAGCTACGCGTTCGAGCTGAACGAAACGGGGCGGTATTACTTCAT[A/G]TGCAGTCGCGGGTACTGCTACCAGGGCATGAAACTGGCCATAAAAGCCGAGCCGTTGCCACCTTCTCCGCCGCCGACACCGCAA
95406 A G CGTCCGCGGCGGGTCGGTTGGCTGATTTTGGTTGTTGGTGGGTTTGCGTCGTGGTTCGCTTGGTGCTGTTGTAGGGATTGTGTAATTTTTGGACGGTTGG[A/G]TCTTGCTTGTTCATCTCGTGCGATGCGATCTGTTTGTTTTTGTTCTGGGTGCTCTTTAAGTAATGCAGCGAAATCTTTTCGGCAAAAA
95424 T G CTTTTCGACCCATCAATTCGGCAAAAGCAGAGACCAGGTCTCCGCCACGTGCAAGAAAGATGCAATGATCACGATAAGCAGTAATAATAGCATCCTTTTT[T/G]GTGATTGCAGCTTCCATGCCGACGGATACGGCCTCCTGGCCGTCGTACAAGTGGCAGAACCCACGGATGAGCTTGGATTTGTAGAG
95424 C G TAGCATCCTTTTTTGTGATTGCAGCTTCCATGCCGACGGATACGGCCTCCTGGCCGTCGTACAAGTGGCAGAACCCACGGATGAGCTTGGATTTGTAGAG[C/G]GAATCGGATGCAATCTCGAGTCGCCGCATTAGAGACATAGTTTGAAAGAACGACATGAGTTCGGAGGTGGAGGTGGTGACTTGCC
95424 G A CCTTTTTTGTGATTGCAGCTTCCATGCCGACGGATACGGCCTCCTGGCCGTCGTACAAGTGGCAGAACCCACGGATGAGCTTGGATTTGTAGAGCGAATC[G/A]GATGCAATCTCGAGTCGCCGCATTAGAGACATAGTTTGAAAGAACGACATGAGTTCGGAGGTGGAGGTGGTGACTTGCCGAGAGG
95424 T C ACAAGTGGCAGAACCCACGGATGAGCTTGGATTTGTAGAGCGAATCGGATGCAATCTCGAGTCGCCGCATTAGAGACATAGTTTGAAAGAACGACATGAG[T/C]TCGGAGGTGGAGGTGGTGACTTGCCGAGAGGGGGCTTCGCAGTTGTGAGAGGTGAAAGGAACGGAGGTTTCGATTGTTAGGG
95424 C T GCTTCGCAGTTGTGAGAGGTGAAAGGAACGGAGGTTTCGATTGTTAGGGTTTGGTCAGAGGTGGAAGAGAAAGAACGGTTGGCGTAGCGTAGGAGGGAGG[C/T]GGTGGTCGAGATCTGACGGTGACGAAGAGCGGTAGCTGCGGCAGCCATGGCCATTATTCCAGGAAATTTCGCCTTGATGTGA
95424 C T AGTTGTGAGAGGTGAAAGGAACGGAGGTTTCGATTGTTAGGGTTTGGTCAGAGGTGGAAGAGAAAGAACGGTTGGCGTAGCGTAGGAGGGAGGCGGTGGT[C/T]GAGATCTGACGGTGACGAAGAGCGGTAGCTGCGGCAGCCATGGCCATTATTCCAGGAAATTTCGCCTTGATGTGAAGGAGG
95424 G C TGGCGTAGCGTAGGAGGGAGGCGGTGGTCGAGATCTGACGGTGACGAAGAGCGGTAGCTGCGGCAGCCATGGCCATTATTCCAGGAAATTTCGCCTTGAT[G/C]TGAAGGAGGGTTCGGTGAGAAGACTGCCTTTTGTCAGACGATGCTAGAAAGCCTGAAATTAGCAGACCAGGAAAGTGCGGAT
95424 G A TAGGAGGGAGGCGGTGGTCGAGATCTGACGGTGACGAAGAGCGGTAGCTGCGGCAGCCATGGCCATTATTCCAGGAAATTTCGCCTTGATGTGAAGGAGG[G/A]TTCGGTGAGAAGACTGCCTTTTGTCAGACGATGCTAGAAAGCCTGAAATTAGCAGACCAGGAAAGTGCGGATATCAT
95424 T C GGTCGAGATCTGACGGTGACGAAGAGCGGTAGCTGCGGCAGCCATGGCCATTATTCCAGGAAATTTCGCCTTGATGTGAAGGAGGGTTCGGTGAGAAGAC[T/C]GCCTTTTGTCAGACGATGCTAGAAAGCCTGAAATTAGCAGACCAGGAAAGTGCGGATATCAT
95426 G GT ATTGCTTTTCTGTTTTTATTACTCTTTCTTGAAATTTTAACTCCTCCAGCATTGTTATTGCTAGAATCAGCATGATCTGATTGATTTTTGTCAGTACTTT[G/GT]TTTTTTGTTGCAGTGCTCGTTGTTAATTGATTAGCTTGAGGTGGTTTTTTGTATGGCTGAAAGTTAGAAGATGTCTGAGCCTTTTGTACAG
95432 A G AACCAAGTCAAGATGCATCCCCAGTGATACCTATGCTTACACGGCAACAAGCAGACGTCCCTCCCTACTCTTATCTCCTCTTTGCACACCACGCATTCCC[A/G]CCCTTCCTTCTCGCACTCCACCGATGGCAGTGCCACGACAGTGCCTACTGAGGCTGCCACCTCTGATCCTCTTTTTGCCTCCCTGCTCCT
95444 G A ATGCACATTTGGTGTTGATTACTTACTTGCAACACACACACCCGGCTTTGCCTCATTATGACTCGAGCGAATGGGACTGGTTGAGGGGTGCTTTGGCTAC[G/A]GTGGACAGAGATTATGGAATTTTGAATAAGGTTTTCCATAATATAACGGATACTCACGTAGCACATCATTTGTTTTCGACTATGCCAC
95444 A G ACAGAGATTATGGAATTTTGAATAAGGTTTTCCATAATATAACGGATACTCACGTAGCACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGA[A/G]GCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAA
95444 A T TTTTCCATAATATAACGGATACTCACGTAGCACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCT[A/T]GGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAG
95444 G A ATAATATAACGGATACTCACGTAGCACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAA[G/A]TACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAG
95444 A G ACGTAGCACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGG[A/G]ACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTA
95444 C G TAGCACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAAC[C/G]CCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGG
95444 G A CACATCATTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCC[G/A]ATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTAT
95444 G A TTTGTTTTCGACTATGCCACATTATCATGCAATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTG[G/A]AGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATG
95444 G A AATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGC[G/A]CGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTT
95444 C T ATGGAAGCGACTAAGGCGATCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCG[C/T]GTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTG
95444 C T TCAAGCCGGTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGG[C/T]GAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGC
95444 G A GTGCTAGGGAAGTACTATCATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGG[G/A]TAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTC
95444 T C ATTTTGATGGAACCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTA[T/C]AAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGG
95444 T C CCCCGATTGTGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGAT[T/C]TGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACT
95444 C T TGGAGGCGATGTATAGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAAT[C/T]TGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTAT
95444 T A AGAGAGGCGAAGGAGTGCGCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTT[T/A]GGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACT
95444 G C GCGTATGTGGAGAAAGAAGGCGAGAAGGGTAAGGGAGTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCT[G/C]TCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTA
95444 A G GTTTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTT[A/G]AAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACTAGGGCAATTGTTATTTACTTTGATATAGTA
95444 A T TTATTGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAA[A/T]GATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACTAGGGCAATTGTTATTTACTTTGATATAGTAATC
95444 A G TGGTATAAGAATGAGATTTGAGGAATCTGGTGTTGAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGAT[A/G]CTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACTAGGGCAATTGTTATTTACTTTGATATAGTAATCGTA
95444 G A GAGTTTTGGGAAGTCTATTTCTCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGG[G/A]TATGTGAGGGTATTAAGACTAGGGCAATTGTTATTTACTTTGATATAGTAATCGTATTCGTACTTGTTCTATGGAGAAATTGTTTAGTGAT
95444 A C TCTGTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACT[A/C]GGGCAATTGTTATTTACTTTGATATAGTAATCGTATTCGTACTTGTTCTATGGAGAAATTGTTTAGTGATAAATTATGATTGGACTTTTTAA
95444 G A GTCGCCATATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACTAGG[G/A]CAATTGTTATTTACTTTGATATAGTAATCGTATTCGTACTTGTTCTATGGAGAAATTGTTTAGTGATAAATTATGATTGGACTTTTTAAAA
95444 T G TATCTCTCTTTTGTTGTTGATTTAGGTTTAAAGATACTGTCTTAGTATTTTGTTTCCTTCACTTCGTGGGTATGTGAGGGTATTAAGACTAGGGCAATTG[T/G]TATTTACTTTGATATAGTAATCGTATTCGTACTTGTTCTATGGAGAAATTGTTTAGTGATAAATTATGATTGGACTTTTTAAAAAAAAAAA
95448 CA C TTCAGCACATACCAGGATCCTTGAGGACTCGGCATCAAATGAAACATCTGACTAAACTTGAGATGATGCTGCTCGCCGGCAAGCTGAAGCTGGCCGCTAA[CA/C]AAAAACGATGATGCCGCCAGCCGGACCCGACGGCTGACAATCGGTGGTCGAAACGTGATGTTTGCACTGCTGGAAAGGAAGAG
95450 T C ACGTGATGATGAACTACCACCTTTGCGACGCAAGTTCTCCGAGACACCGCTGCTTCTAACTGGCCTAGGCGGAACCCTTTTGCATCTTAGCGGCTCTACA[T/C]CATCAACAGCCTTTGAACAGACTATACTTGCATAAACAGAGAGCGAATCATCTACAACCAGCAGGTTTCTGGCTACATGGACAGCAA
95452 CT C CCAGGTTCCATTGTGCTGAGGCAAGAGATCTAGCAAGCTCTGCATTTGTGGTCTCAAGTTCAGCCATACGAGCAAAGGCTTCCATTCTGGTACTGTTGTG[CT/C]TTTTGTTTTTCGAGATCAACTGCCTCCATAGTTTCAATCATATTTGTTTGCAGCTCTGAAGCCTCTTGAGCTTGTTCTTTAGCTCTCTC
95452 A G CCTTTATCGCCCTCTCAGCAGCCTCCGCAGCCTTTCTCTTAATCATCTCCTCTCTCCTTTTCCTCCTCTCCTCGGCCCTCCTCCTCTCATCCTCAGAATC[A/G]CTGCTCTCTGTCTCTGAATCACTCCCACTGCTCCCAGTTTCTTCCTCTGCTTCTTTCTTCTCTTCATTGCCTATCAATTTTTCCTTACTCGGGGG
95458 G A CAAGAAACCATGCAAAGGGTACCTACTGAAAAACCACCCTTCACCGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCC[G/A]CTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTA
95458 T C AAACCATGCAAAGGGTACCTACTGAAAAACCACCCTTCACCGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTC[T/C]TTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACT
95458 C T AAAGGGTACCTACTGAAAAACCACCCTTCACCGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTA[C/T]GTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCT
95458 C T CTACTGAAAAACCACCCTTCACCGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTA[C/T]GATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATA
95458 C T CACCCTTCACCGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCAT[C/T]GTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCA
95458 T C CGTAGGAGAGCTCAAAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACC[T/C]TTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTT
95458 A C AAAAGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGC[A/C]CTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTG
95458 T C AGGCTATCCCACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACT[T/C]TACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95458 T C CACCCCATTGCTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAAT[T/C]CCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACA
95458 C A CTGGAACCGCTCCGTAATCCGCTCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTA[C/A]CCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGG
95458 C T TCTTTCTCCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTG[C/T]CTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACC
95458 C T CCTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCC[C/T]TTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCT
95458 T C CTACGTATTCTACGATCTAATCATCGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCC[T/C]TATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTC
95458 T G CGTATCCACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGT[T/G]TCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGACGACATCGTAGGGTTTATCCT
95458 G C ACCTTTCTATATCTCGCACTTTACCAAATTCCCAAACTACCCTCCCCTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAA[G/C]CGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGACGACATCGTAGGGTTTATCCTACACACT
95458 T C CTTACCACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTC[T/C]GACTACCAACTCCTCGACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGC
95458 C T ACTACCTTGCCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTA[C/T]CAACTCCTCGACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCA
95458 C T CCTGGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCT[C/T]GACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACAC
95458 C T GGCCCTTATACTGGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGA[C/T]GACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGG
95458 G A GGTACATCCAAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGACGACATCGTAGG[G/A]TTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAA
95458 A C AAGGCTGTTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGACGACATCGTAGGGTTTATCCT[A/C]CACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAAAGGACGAAG
95458 A G TTTCCTAAGCGGCATTTGGGTAATTGCACATGAATGTGGCCATCATGCCTTCTCTGACTACCAACTCCTCGACGACATCGTAGGGTTTATCCTACACACT[A/G]CCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAAAGGACGAAGTCTTCGT
95458 G A CTGACTACCAACTCCTCGACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTC[G/A]AACACAGGGTCATTGGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACACAAACAACCCTA
95458 G A AACTCCTCGACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGG[G/A]TCATTGGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACACAAACAACCCTATCGGTAGGG
95458 A C TCCTCGACGACATCGTAGGGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGGGTC[A/C]TTGGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACACAAACAACCCTATCGGTAGGGTCA
95458 C T GGTTTATCCTACACACTACCCTCCTAGTCCCCTATTTCTCCTGGAAGTACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAAAGGACGAAGT[C/T]TTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACACAAACAACCCTATCGGTAGGGTCATGTTCCTTGTCGTAAGCC
95458 C T TACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACA[C/T]AAACAACCCTATCGGTAGGGTCATGTTCCTTGTCGTAAGCCTCACAATGGGATGGCCCTTGTACCTCCTGTTCAACGTATCGGGTCG
95458 A G ACAGCCATAGGCGCCACCACTCGAACACAGGGTCATTGGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACAC[A/G]AACAACCCTATCGGTAGGGTCATGTTCCTTGTCGTAAGCCTCACAATGGGATGGCCCTTGTACCTCCTGTTCAACGTATCGGGTCGC
95458 A G GGAAAAGGACGAAGTCTTCGTCCCAAAGCCCAAGTCCGCCCTTTCATGGCACTCCAAGTACACAAACAACCCTATCGGTAGGGTCATGTTCCTTGTCGTA[A/G]GCCTCACAATGGGATGGCCCTTGTACCTCCTGTTCAACGTATCGGGTCGCCCCTACCCAAGATTTGCTTGCCACTACGATCCATACGG
95466 T C AGGCACATCCCAACACAAGCAAGAAGGAAAAGAAATCGCTTATTGGGCTCCTCGACCCACGAAAGCTGACAGCGGATGCAGCG[T/C]TGCATGCCATCCACAACGACCGGTTGCCGGTCAGAGCGATCATTCGGATAATCTTCACCGAGCAGTCGAAACTGAACAGAGTGGCCGAGTTCAGCAACAC
95466 C T AGGCACATCCCAACACAAGCAAGAAGGAAAAGAAATCGCTTATTGGGCTCCTCGACCCACGAAAGCTGACAGCGGATGCAGCGTTGCATGCCATCCACAA[C/T]GACCGGTTGCCGGTCAGAGCGATCATTCGGATAATCTTCACCGAGCAGTCGAAACTGAACAGAGTGGCCGAGTTCAGCAACACG
95466 A T TATTGGGCTCCTCGACCCACGAAAGCTGACAGCGGATGCAGCGTTGCATGCCATCCACAACGACCGGTTGCCGGTCAGAGCGATCATTCGGATAATCTTC[A/T]CCGAGCAGTCGAAACTGAACAGAGTGGCCGAGTTCAGCAACACGTCCTTCAATGCAGCTCGAAGCCCGAACATCGGGCTAGAAGC
95466 A G GGTCAGAGCGATCATTCGGATAATCTTCACCGAGCAGTCGAAACTGAACAGAGTGGCCGAGTTCAGCAACACGTCCTTCAATGCAGCTCGAAGCCCGAAC[A/G]TCGGGCTAGAAGCGCCGGGGCGATGTCCTTCTAAGCGCGAGGTTCTAGCGCAGCAGCACGAGGTTCGCAGACTCAGGGATGACG
95466 GT G TTACACGGCTACAGAATCAGTGTAGGGCTCTGCAGGCTCAGGTAGAAAGGTCGGGGACGTTGGAGAAGAAGAGGAGCGGGTTCTTTAGATGGGGCAACCT[GT/G]TTGTTTAGGAACGGCGACGGTGGAGATAGATGGAACAGTGAGTATGATGCTGGGGTTGAAAGGAGGACGCCGAGAACGCC
95476 C T TTAGCCAACATTCAAGCTAAATTAACTCAAAATTTTACAGGTATCCGGCAAGTGTTGAATTCTACCAAAAATAAATCGAAACAAAGCAAAACAAATGGCC[C/T]AAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTC
95476 C A AATTTTACAGGTATCCGGCAAGTGTTGAATTCTACCAAAAATAAATCGAAACAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACAC[C/A]AGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGA
95476 A G ATTTTACAGGTATCCGGCAAGTGTTGAATTCTACCAAAAATAAATCGAAACAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACC[A/G]GCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAA
95476 T C AGTGTTGAATTCTACCAAAAATAAATCGAAACAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGG[T/C]ACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAA
95476 A G AATTCTACCAAAAATAAATCGAAACAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTC[A/G]CCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAG
95476 C T ATAAATCGAAACAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGC[C/T]TTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGAT
95476 C T CAAAGCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTT[C/T]CACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTA
95476 C T GCAAAACAAATGGCCCAAGAGGCACAATCGGAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCAC[C/T]CTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTACGCT
95476 T C GAAACTTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGC[T/C]TGAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTACGCTCACCGGGCATAATGACGACGTAGCCTTCGCA
95476 C T TTCGCCACACCAGCTCTAGTCGCCATCAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAA[C/T]CGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTACGCTCACCGGGCATAATGACGACGTAGCCTTCGCAGAAGT
95476 C T CAGGTACGGTCACCGCACTCTGGCCTTCACCCTTTCCACCCTCCACCGTACCCTCGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAGG[C/T]GTCGCGAGATAGGTGGCTTTACGCTCACCGGGCATAATGACGACGTAGCCTTCGCAGAAGTAGGGCGGTGGCTTTACGTTACCCTC
95476 G A CGCCGCCGCCATCGCTTGAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTACGCTCACCGGGCATAATGACGACGTAGCCTTC[G/A]CAGAAGTAGGGCGGTGGCTTTACGTTACCCTCACCTTTATTCATTTCCGCCGCCTGTGAGCCGGTGCCATCGGTGGTGGTGGAGG
95476 G A GAACCGTCCACCGTGCTGGAAGCAGCAGGCGTCGCGAGATAGGTGGCTTTACGCTCACCGGGCATAATGACGACGTAGCCTTCGCAGAAGTAGGGCGGTG[G/A]CTTTACGTTACCCTCACCTTTATTCATTTCCGCCGCCTGTGAGCCGGTGCCATCGGTGGTGGTGGAGGTGCCGTGGTTTTCGCCT
95476 C G TCGCAGAAGTAGGGCGGTGGCTTTACGTTACCCTCACCTTTATTCATTTCCGCCGCCTGTGAGCCGGTGCCATCGGTGGTGGTGGAGGTGCCGTGGTTTT[C/G]GCCTTGTAGGAACCTGGAAAGGCGCCAGTAGGAGCAGGCGAGGATCAGCAAGGCGCAGGCGATCAGACCGAGCATGGCGGCCA
95476 C T CCGAGCATGGCGGCCAGGCCTCCGACCAAGTAGGGCACTGGCGTCCGCCATGTGTCTGGGCGTAATGGCGGCGGCGGCGTTGGGGTTGGCGGCTTGTTCA[C/T]GACTGGGACCTCTCTCATTATTTTAGGTATTGTGTTTCTTTTTTTGGGGGCTGTGATGATC
95514 T C CGGGCATCATCACAGCCAGTGAAGAGCACACGCGGGTCGGTCGGAGAGAAGGCCAGGGTGCGGACGGGCATGTGGTGCCCTGGGAGGTGGTGAAGGAACT[T/C]CGCACGCTGCACGTCGAAGATGGAGACCGTGCCATCCATCGACCCGCAGGCCAGCCGCTTCCCGTCCGGGCTGAAGGCCACG
95544 A G ATAAGAATAATTATCATGACCGGACCAGACCTCTGTCGAACCATCATTAACCGTGGACCTTCAACCACCACGGCCTAGAGCTCAGTTGAACCTCCTCCAT[A/G]CACTGATCGTTGATTGAACCGCATAACCGAGATCAGACTGCGATTTTAAACCCTGAAAGCCATTTTAGTCGCGATTTTTACTATCCCCA
95544 G A GCGATTTTTACTATCCCCAAATCTAAAAAACCCTAATATCTAAATCTATAACTTCTCCAATCGCGAATTTTTCTTTAATTGAAGACAGTGGCAGAACCCT[G/A]AATCAATCGGAGGCATAGGCGGCAACTGAAGATGTGGAGGTAACGACGGTTGCGACGACAGCGATTGTGGCGGAGTGCTTCAACAAA
95544 C T TCTCCAATCGCGAATTTTTCTTTAATTGAAGACAGTGGCAGAACCCTGAATCAATCGGAGGCATAGGCGGCAACTGAAGATGTGGAGGTAACGACGGTTG[C/T]GACGACAGCGATTGTGGCGGAGTGCTTCAACAAACGATGGCGCAAATGACAACAACCACCCCTTTGTCTGCTTTGTTGACTTATTT
95564 G A CTGTTGGCCTACTGGATTATCACTTTAACTCTGTAATAATTCCAAATCAAACTCGGATCTAATGCTA[G/A]CTTCTACCTCCGCACTGGCCTCCACTTTCATCCCAACCCACCCTCAAATCACTTCCAATCTCTTCACCCCCAAAGCGTCAAGATTTCAAATCAAATCGGA
95564 C T CTGTTGGCCTACTGGATTATCACTTTAACTCTGTAATAATTCCAAATCAAACTCGGATCTAATGCTAGCTTCTACCTCCGCACTGGCCTC[C/T]ACTTTCATCCCAACCCACCCTCAAATCACTTCCAATCTCTTCACCCCCAAAGCGTCAAGATTTCAAATCAAATCGGATGACTTCCCCATTAAATTGAGAA
95564 C T ACTCTGTAATAATTCCAAATCAAACTCGGATCTAATGCTAGCTTCTACCTCCGCACTGGCCTCCACTTTCATCCCAACCCACCCTCAAATCACTTCCAAT[C/T]TCTTCACCCCCAAAGCGTCAAGATTTCAAATCAAATCGGATGACTTCCCCATTAAATTGAGAATATCATGTCAAAGCGCCGCAGCCGCTG
95564 C T CGATAAAGGTGTACCACGTGATGAAGGCGCCTGATTTGGATCTGAACGGCATGGAAGGTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCAT[C/T]TCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGA
95564 A G GGATCTGAACGGCATGGAAGGTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATT[A/G]AGGTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGAATACTTGGATAGTGAATGATTTCGT
95564 G T ATCTGAACGGCATGGAAGGTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAA[G/T]GTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGAATACTTGGATAGTGAATGATTTCGTAGG
95564 G A ACGGCATGGAAGGTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGA[G/A]GGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGAATACTTGGATAGTGAATGATTTCGTAGGCAGTTG
95564 G GA GGAAGGTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAG[G/GA]AAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGAATACTTGGATAGTGAATGATTTCGTAGGCAGTTGTTATTT
95564 C G GTGTGATTAAGCAATATGTCGGTGTGTGGAAAGGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAGGAAAG[C/G]CAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGAATACTTGGATAGTGAATGATTTCGTAGGCAGTTGTTATTTTCTTGGT
95564 T C GGTAAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGA[T/C]GAATTTGAATACTTGGATAGTGAATGATTTCGTAGGCAGTTGTTATTTTCTTGGTGTTTGTAAACCATGCTTTTGGTTGGTATTGGTT
95564 A G AAAAGCATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGA[A/G]TTTGAATACTTGGATAGTGAATGATTTCGTAGGCAGTTGTTATTTTCTTGGTGTTTGTAAACCATGCTTTTGGTTGGTATTGGTTAAA
95564 A G ATCTCAGCGAATTTGCCGTTTAAAGTCGAGTTCTTTATTAAGGTGGAGGGACAGGAAAGCCAGTCAGGTTTTTTGCTCATTTGAAAGAAGATGAATTTGA[A/G]TACTTGGATAGTGAATGATTTCGTAGGCAGTTGTTATTTTCTTGGTGTTTGTAAACCATGCTTTTGGTTGGTATTGGTTAAAGAAAAG
95568 G A GGCAGCTGCAGCTCTGATATTAGGTAACGGTGATAGTAATTTACCCTTTGACCGGTCAACGTCGGTGAAGGGCCCACTTGGCGGTGGTGCTGGGAGGTCC[G/A]GTAGTAGAAGGCAGGGTGGCGGTCTGCCAAGAAGCGCTAGCAGCAGACCCTGCACAGTCGTCGGGGATCCACTTCTTCCTCCTC
95568 A T GTGATAGTAATTTACCCTTTGACCGGTCAACGTCGGTGAAGGGCCCACTTGGCGGTGGTGCTGGGAGGTCCGGTAGTAGAAGGCAGGGTGGCGGTCTGCC[A/T]AGAAGCGCTAGCAGCAGACCCTGCACAGTCGTCGGGGATCCACTTCTTCCTCCTCGCCGCCTTCTTCTCAATCAGGGTAAAGAAA
95568 C T GTAATTTACCCTTTGACCGGTCAACGTCGGTGAAGGGCCCACTTGGCGGTGGTGCTGGGAGGTCCGGTAGTAGAAGGCAGGGTGGCGGTCTGCCAAGAAG[C/T]GCTAGCAGCAGACCCTGCACAGTCGTCGGGGATCCACTTCTTCCTCCTCGCCGCCTTCTTCTCAATCAGGGTAAAGAAAATGGG
95574 TA T AATTCCAAAATAACAACTCTCAAAATCCATAACTGTAAACAGACTTAACAAAGCTCACAAATACAAAATGTAAAAGACAAGCATCCAGAATTTGACTACA[TA/T]AAAATAATGTTACTAGTAAAAGAAACCAAGCACTTTGCCACCGACGTTCTTTCTCCTTGCTTCTTCATGGTCCATGATGCCTGCTGAA
95574 T G TGGCCTGATCATAACCTGGCGCTTGCCACGCTTCTCAGCATTATACATGCTCTTAAGTGCATCATTCAGAACACTGATTCTCACCATCCTTACTAAACAA[T/G]ATTAAACGGGAGAGAAGGGAAATGTGGCGGCTGCTTGAAAACTGAAACCCTTCCAGTAGGCCAACAGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95604 T C CTTCCATAAACTTCGAGTATGAGATATCCCCTGGCTTGAGAGGATTAACCATCAACCCCATAAAGATTTGCCCAGGAACATTTGGACTGAGTGAGACAGA[T/C]GCAACCTTGTAAATCTCATCTACCGTCTCAGCAGGGATGTTGGTCATCTCAAAATATCCACCACGTTGTCCACATTCACCCCAATATCC
95604 T C GCCCAGGAACATTTGGACTGAGTGAGACAGATGCAACCTTGTAAATCTCATCTACCGTCTCAGCAGGGATGTTGGTCATCTCAAAATATCCACCACGTTG[T/C]CCACATTCACCCCAATATCCTTTTGAGACAGTGTGGAAAGATATGAGCTGGACTTCTTTACTAAACGGTAGGCCCATGTCAAACAGTA
95604 T C AGACAGATGCAACCTTGTAAATCTCATCTACCGTCTCAGCAGGGATGTTGGTCATCTCAAAATATCCACCACGTTGTCCACATTCACCCCAATATCCTTT[T/C]GAGACAGTGTGGAAAGATATGAGCTGGACTTCTTTACTAAACGGTAGGCCCATGTCAAACAGTACCTTCCGGGCACTTATAAAAGGTC
95610 T A CTAGTTTTCAATATGAAGAGTGGTTTTACAAACACAGCAAAATACATCACTATATATTTGACGTATCATTTTATATAACATGTTGCCCTCCAAGAGTCAC[T/A]TTATATTGTTGGTATGTCACTAATATTGTTGTCTATCTATGGTTGCTGTCACTTTTTATTATTGCCAGTTTCACTGCTCACCATTAAGACCG
95610 T TG TAACATGTTGCCCTCCAAGAGTCACTTTATATTGTTGGTATGTCACTAATATTGTTGTCTATCTATGGTTGCTGTCACTTTTTATTATTGCCAGTTTCAC[T/TG]GCTCACCATTAAGACCGTCAATCTTCAGTCTCAAAAAATTTACTCACTGTAATATCCTTCTTCCCTGGCTCTCTCATCGTCACTTTCTTCCTC
95610 CA C TGTTGGTATGTCACTAATATTGTTGTCTATCTATGGTTGCTGTCACTTTTTATTATTGCCAGTTTCACTGCTCACCATTAAGACCGTCAATCTTCAGTCT[CA/C]AAAAAATTTACTCACTGTAATATCCTTCTTCCCTGGCTCTCTCATCGTCACTTTCTTCCTCGCCAATATCCGTAACTGCCTCTCTAAACCTTC
95612 A C AATTCTGCCACCTCATCTGGGTTAGGATGCACGCTCACATCACGAACTATGAAAAGAAGATAGTC[A/C]AGCTCGTGCTCTCCCCATTTTCCATCAGAAGGAGCCTTGTATAGAATGCGCCCAATTGGAGTGAACTGATCAACAGGTACCTCATCGGCTGGAATACCAA
95612 A G GATAGTCAAGCTCGTGCTCTCCCCATTTTCCATCAGAAGGAGCCTTGTATAGAATGCGCCCAATTGGAGTGAACTGATCAACAGGTACCTCATCGGCTGG[A/G]ATACCAAGTTCATCTAACAGCTTTCTTTGAGCCGCATTCCTTACTCCAAGAAAATTATCTTCAATAAGTTCAGACTCACGGTAAAGAG
95612 A G CTCCGATTCAATCTTTTCCATCAAATGGCAGTTGTACTTGGAATCATGGCCAACAACTTGGTCGTTTTCATCCACTAGAATACACTCGTCCTCAAACATG[A/G]GGCGCCGCTGAACAGCATCCATGTTCTCATTGTTGGCGGCGACAGTGGAGGAAACGGTGGCTTCTTTTTCCATGCGAACTGAAGAAAC
95620 C T CTTATTAAGTAAGATAACCAAGACACACATGATTAAGTATTTGGTAACCAAACACAAAATATGACATTATAGATAATGGACATGATTGAGTATTTGGTCA[C/T]CAAACACATAATCTGATACTGTAAATAATAGACATGACAAGCTTAAGCATTAAGGACAACCATGTGCTGCTGAACCTTCCTTTCCAACT
95632 C T TGCCGCCTCAGTTGAGAGCTTGTACAAATAAGGAGTCTGATGAGATTGCCCAAATTCAAACGAGAGTAAAAGGGCTCCTTAACAAATTATCCGTATCCAA[C/T]GTGGAATCAATTACTCAAGAAATATCATCAATTTTCCAATCACTTCCTCGTAGTGTTGGCTGCCAAATCGTTGGCGAGGTGGTTGTTG
95652 A AT AGTTTCATTATACAACCAAGCAGCTCCCATAAGTGCATAGGTGCATAACATGGCCTTTCCCATCTGCTTCCAAAAGTAACGATCTTCTTTTCCTAGTCCA[A/AT]TTTTTCTGAGGATCTTCTGAGCTTTTGGAATTTTGAACATTTTTGGCAAACTCGGCAGAGGCGCTGGTCAGTTGGTGATGCTTGATAG
95652 G A CTTTCCCATCTGCTTCCAAAAGTAACGATCTTCTTTTCCTAGTCCAATTTTTCTGAGGATCTTCTGAGCTTTTGGAATTTTGAACATTTTTGGCAAACTC[G/A]GCAGAGGCGCTGGTCAGTTGGTGATGCTTGATAGCGCAAGAACCACAAGATAATGGTGCTCGATAGCAAAAAAGGAGGTGAAGGTGG
95652 A G GGCTAGGGTTGTGTGCGAGATGTGAAGGAACTGCTTGTGGGGATAAAGTCTGTAGGTGGAGGCCAGGCGCAGCGAAGGCGTTGAAGTTGAAGCTCGGGGC[A/G]GCTTAGTGGTGATTATGGAGGTGTCGCGGTAATCGATTTTTCAGGAAAAAGCCGGGGAACGAAATTAAAATTTGGATCCTGT
95652 G C AGATGTGAAGGAACTGCTTGTGGGGATAAAGTCTGTAGGTGGAGGCCAGGCGCAGCGAAGGCGTTGAAGTTGAAGCTCGGGGCAGCTTAGTGGTGATTAT[G/C]GAGGTGTCGCGGTAATCGATTTTTCAGGAAAAAGCCGGGGAACGAAATTAAAATTTGGATCCTGTGAACGCTAGCCAGAAAGC
95666 C G AGCATATTTCTCCACAAGCGGACGGAAGACTGGATCATCGAGAAGAGCCTTGTCAGAAGGTAGTTGAAGAAGCCCATCCTTCTCCCCAGAAAGAAGCTCC[C/G]TGAAGTAAGTGTTGTCAAAGATGAGAGGATTCCGAGTCCAAGCACCCTCAAAGCCTGACCTTTCCTTGTGGCACTTCCCCAAGGTG
95666 C T CCTTCTCCCCAGAAAGAAGCTCCCTGAAGTAAGTGTTGTCAAAGATGAGAGGATTCCGAGTCCAAGCACCCTCAAAGCCTGACCTTTCCTTGTGGCACTT[C/T]CCCAAGGTGTGTCCTCCAGACAGAGCAACGATATCCTTGTCACTCAAACCCATTTGTTCTCCAAAAACTGTTCGAAGGTGGTCGCAAC
95668 CA C AATGAAAGCTGATCAAGATCAACATATGAGGGGCCTTATTGATAAAATGACAAAGATGGAAGCTGAGTTAAAGAATTCCGACTCAATTAAAGCTGATTTG[CA/C]AAAAAACTCACGCTGAAGCACAAAGTGCATTGATGGCTAGACAAGAACTTGCAGCGAAAGCACAGAAACTGAATGAGGATTTAC
95672 T C AGTTGGATGTGGTAGGGTCGCGGCCAGGTTGATGATGTTTAATTTTGGGTTTTATTATATTAGTGAAATCTCCAATCAGGATGAATGTTCAGAGCAAGCT[T/C]ATGTATCTGAAAGACCTGGTGTTATTGTCTCGAATCACGTCTCATATCTTGATATTCTCTACCATATGTCATCATCATTTCCAAGCTTTG
95672 A G ATCAGGATGAATGTTCAGAGCAAGCTTATGTATCTGAAAGACCTGGTGTTATTGTCTCGAATCACGTCTCATATCTTGATATTCTCTACCATATGTCATC[A/G]TCATTTCCAAGCTTTGTAGCCAAGAGATCAGTGGCCAGGCTTCCATTAGTGGGTCTAATCAGCAAGTGCCTTGGTTGTGTCTATGTTCA
95674 T C GTTGCTTGAAAAATGGTCACAAAGCCTCCTGCCAAAATGAAGATTCCGCATGCTCCCCTGATGATAACTCCTCTCACGTACAAGAATCCCTCCATCACCA[T/C]CAACTTCACGGTTTACAAAAACTGGGATTCTTCTTCTCCAAGAAAACTTGCAACTGAGACTGTTTATCACCACGTCTCTCTACTAACCCA
95674 A G TCTCCAAGAAAACTTGCAACTGAGACTGTTTATCACCACGTCTCTCTACTAACCCAAACATCTCTCATCCCCTACCGTTACTTCCTTACCAGTGCCAAGC[A/G]ACGTTCATCCTTTTTATTTTTATTTTGTTTTGATTGCCATATTTCTTTCCAGTAGGCCAAC
95678 C T AAACAAAACAAAACAATGAAATCATCGTCTCCCCCAAGAACATGGAAGTATGCTTCAGTCATCGTAGTATTTCCCATCCTATCCTCCACC[C/T]TAATCTTAATCGTTTACAACTACCCAAAAGACTACAATCCAATAAAAATGCCAGAATACTCGTTCCAGGAGTCGATCCAAGTGCCTAGCGAAAACAACG
95678 T C GGATACGTAGAGTGAAAGTTGGAGGAGACGATGAGGTCGAGGATTGGGTTCAGGTTGGAGGTCGCCCGCTCGGTCTTGCCCTCGCTTCGGACGCTACTTC[T/C]CTTGTTGTTGCTGAAGTCGACAAGGGACTTCTACTGGTAAAAGAAAACAAAGAGATACAACTACTTACAAACGAAGCCGAGGGA
95678 C T AAGTCGACAAGGGACTTCTACTGGTAAAAGAAAACAAAGAGATACAACTACTTACAAACGAAGCCGAGGGACTAAAATTCAAGCTAATAGATGGTGTTGA[C/T]GTTGCTTCAGATGGCATTATCTATTTCACAGATGCTTCTTATAAATACGACTTGCATGCTAACATGTTAGACATACTGGAGGGTCGC
95678 C T TAAAATTCAAGCTAATAGATGGTGTTGACGTTGCTTCAGATGGCATTATCTATTTCACAGATGCTTCTTATAAATACGACTTGCATGCTAACATGTTAGA[C/T]ATACTGGAGGGTCGCCCACATGGAAGAGTTTTAAGTTTCGATCCTTCTACCAATAAAACTTCTGT
95682 G A CAATCCCAACCTCGCAACATGCTCGAGGAGTGGTGGCCCGACCTAATCATGGACGGCACCTTCGAATCCGAACTGCTCCCAACCCTAGATCGGGATCCGA[G/A]CGATCCCGTGGTGGAGAAGGAGACGTACAGCGCGTTCCGAGGGACGGGGATGGATGAGCGGCTGAGGGCGATGGGGATCGAG
95682 T G GCACCTTCGAATCCGAACTGCTCCCAACCCTAGATCGGGATCCGAGCGATCCCGTGGTGGAGAAGGAGACGTACAGCGCGTTCCGAGGGACGGGGATGGA[T/G]GAGCGGCTGAGGGCGATGGGGATCGAGGAGGTGATCGTGGCCGGAGTGATGACGAATCTGTGCTGTGAGACGACCGCGAGG
95684 GGTCCGCCTGCTAAATC
TACTACTTCGTCAGCGGCGTGGCCGACAAGTGTAGAAAAGGCGAGAAGATGATTCTGGTTGTGATGACTCCTAGAGCTGGCCAGAAGCAACCAGTTGCCA[G/GTCCGCCTGCTAAATC]TCCGCCTGCTAAATCTCCGCCTTCCGTGGTTGCTCCGGCTCCGGCTCCTTCTCCGAACACATCTGGTGATCG
95684 C CGGCTCT GAGAAGATGATTCTGGTTGTGATGACTCCTAGAGCTGGCCAGAAGCAACCAGTTGCCAGTCCGCCTGCTAAATCTCCGCCTTCCGTGGTTGCTCCGGCTC[C/CGGCTCT]GGCTCCTTCTCCGAACACATCTGGTGATCGGATTACGCCCGGTCCGGCATCAGCTCCGTCGACGGCGCCTGAACCGAAAT
95692 C T TCTCAAACTCTCAGGCAGCGCTTCAATTGCTTCCTTCTTCAACTTCAGTAGCTGAGTCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTG[C/T]TATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCC
95692 A G TCAAACTCTCAGGCAGCGCTTCAATTGCTTCCTTCTTCAACTTCAGTAGCTGAGTCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCT[A/G]TACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAG
95692 G A TCAGTAGCTGAGTCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTC[G/A]TACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTT
95692 G T TAGCTGAGTCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTAC[G/T]TCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTC
95692 C T GCTGAGTCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGT[C/T]GGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTT
95692 T C TCTCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAAT[T/C]TTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTC
95692 T C TCCACCTTCTGCCTCTCCCTATGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTT[T/C]CTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTCAA
95692 G T TGCTTCCTCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGA[G/T]ACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTCAATTTAGCTTGGTCGATCTCCA
95692 A G TCATCATCACTCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTAT[A/G]TAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTCAATTTAGCTTGGTCGATCTCCAGCTGGCG
95692 C T TCTGCTATACTCCTTCGCCAACCTCCTCCCATCCTCCACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGA[C/T]CTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTCAATTTAGCTTGGTCGATCTCCAGCTGGCGATCTTTGGA
95692 G A CACAGTCAGCTCGTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCG[G/A]CTTTCTTCTTGCTTTTCAATTTAGCTTGGTCGATCTCCAGCTGGCGATCTTTGGAGATGAGGCCAAGCTTCTCACGCTCGATTTCACGAT
95692 C T GTACGTCGGAATTTTCTCGGCATCCACCAGCCCGAGACTTATATAATCCAGACCTGGTGTCCCCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTG[C/T]TTTTCAATTTAGCTTGGTCGATCTCCAGCTGGCGATCTTTGGAGATGAGGCCAAGCTTCTCACGCTCGATTTCACGATCACGCTGCTTCT
95692 A G CCATAACAACTTCATCGCCTTCTTCGGCTTTCTTCTTGCTTTTCAATTTAGCTTGGTCGATCTCCAGCTGGCGATCTTTGGAGATGAGGCCAAGCTTCTC[A/G]CGCTCGATTTCACGATCACGCTGCTTCTGGGTGAGGTGACGGACTGGTGAGGGGGCAGTGAGGCA
95700 CT C ATTTGGCGGATCCCTTTGCTTCATCATGAGGGGAGATCAACTGGCTGAAGGTTGGCCTTTCATCTGAGTTTCCCATAAGTATAACGGTTTTTTGCGGTTC[CT/C]TTTTTTATTCTGGAAATCAATGGGATTTCTTTTCTCTTTAGAGAGAAGATAAAAAATGCTTAGAAGACAACAAATGTACATCCGTCTC
95706 G A AGAGAGAAGGCGATAGTGGTAAATTTGGAACAGATTAGGTGTGTGATTACAGCGGATGAAGTTTTGTTGCTGGATACAATGGATCCGTATGTTATGCAGT[G/A]CGTGGTCGAGCTGCAGAGACGGTTGGTTGCTGGTAATGGGTTGAATGGAGATGAAAGGGATTATTTGCCGTTTGAGTTTAGGGC
95714 A G CAACATCCTTACCATTCCAGTACCAAGGCTGGAGGTGATGACTGGCATCGGAAGAAGGGACCATCACAGAACCCCAGTCCCTCACCCCCGATTTGACCTC[A/G]CGTACTCTTCTACGAACTAGCAAACGAGCCACGTCTTCTCGTCTGTATTCGCATATTGTACGTGCAACGCACATGCAAACAAGTAGG
95718 C T CCCAACTCGTTTCTGCAGCCCTCAACAAATGCTGATACCAAAGAATTTTCAAGTGTGTTCTTCTCATCCGATACATCGATGTATGGAAACGACATTGAAA[C/T]GTTGGAAGTGGTGAACGAGGTCTTTAGCAAGTTCATTAGAGTTGGATCAATGTGAACAGATTTGGATATGTCTGATGACTGTAACTTT
95718 C A AGTGGCGGAAGCAGAGTTCACGAAATCCACCTTATTTGCAGCAAGAAACAAAATGGTCAAAAATACTAATCCAGCTCCTTCCATCTGATCTGATATGTGA[C/A]GAGGAGATCTAGTTTAGGATTTTAGAGAAGCTATGTTGGGCGAAATGCCAATCCCAATCTCAATTAATAAGAAAATATTATAATTTTC
95728 G A TTTTTTTTTTTAAACTTTACAAGCCATCATCCCAAAACCGCCACCACCCACGTTCGTCCC[G/A]TTCAACCTTCACCGAACAACACGTGCAACGCCACTTTTTTGCCAACGGAACATATCGGGCAAGAATCCACCGCCGGCTCGCAATCCAGACACAGGCACAA
95728 CT C TTTTTTTTTTTAAACTTTACAAGCCATCATCCCAAAACCGCCACCACCCACGTTCGTCCCGTTCAACCTTCACCGAACAACACGTGCAACGCCA[CT/C]TTTTTTGCCAACGGAACATATCGGGCAAGAATCCACCGCCGGCTCGCAATCCAGACACAGGCACAAATGCCGACATGGCACAACCACCACCGAC
95732 T C ACATTTGAACTAACCGATACTCACATCAACATGGAGAGAATCATTCAAGGATTCGAATTATATATGTAGTTTGATTTGTAGGATTACTTTGATTTTGTTG[T/C]GATTTTCTGAAGTGGATTTCCGCGTTTGAGAAGAGCGAGACCACGGCTGGTTTCAGGTTTCGAAACAAACGGTTTCCAGTAGGCCAAC
95736 G A GTGTTGGCAACCGATCAAGTATGTCAATCTGTGTGTTTTTATCGTCCTTCAACACCTTATCTGCAGTGTAAAACCCAGCAGGGCCACTGCCAACAATGTC[G/A]TACATGAATTAATCATCTAAGTTGAAAACGATGAAGAGCCCTTGTCGATATGAAATGTTTCATCACATGGAGAAATAATGTGCCTATT
95736 C T CTTCAACACCTTATCTGCAGTGTAAAACCCAGCAGGGCCACTGCCAACAATGTCGTACATGAATTAATCATCTAAGTTGAAAACGATGAAGAGCCCTTGT[C/T]GATATGAAATGTTTCATCACATGGAGAAATAATGTGCCTATTCCTCTTTAGGGTATATTTCTATAATTCAGGGACAAACTTGATAAGAA
95736 A C GCAGTGTAAAACCCAGCAGGGCCACTGCCAACAATGTCGTACATGAATTAATCATCTAAGTTGAAAACGATGAAGAGCCCTTGTCGATATGAAATGTTTC[A/C]TCACATGGAGAAATAATGTGCCTATTCCTCTTTAGGGTATATTTCTATAATTCAGGGACAAACTTGATAAGAATGATTGCTCTCTTAG
95736 C G TGTAAAACCCAGCAGGGCCACTGCCAACAATGTCGTACATGAATTAATCATCTAAGTTGAAAACGATGAAGAGCCCTTGTCGATATGAAATGTTTCATCA[C/G]ATGGAGAAATAATGTGCCTATTCCTCTTTAGGGTATATTTCTATAATTCAGGGACAAACTTGATAAGAATGATTGCTCTCTTAGGCTT
95736 A C AGAGCCCTTGTCGATATGAAATGTTTCATCACATGGAGAAATAATGTGCCTATTCCTCTTTAGGGTATATTTCTATAATTCAGGGACAAACTTGATAAGA[A/C]TGATTGCTCTCTTAGGCTTTTCCACCTACATCAGCAGATTATATGGCACGAGATGGTGCAGATCAGATAAAAGACAGCCTGAAGACGG
95738 A G CCAATGCCAGGAGAGCATCCCCGATCAAAACCGCCACGGGCTCACCATAGACGATGTGGTTGGTCGGACGTCCGCGACG[A/G]AGGTCGTCATCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTC
95738 A G CCAATGCCAGGAGAGCATCCCCGATCAAAACCGCCACGGGCTCACCATAGACGATGTGGTTGGTCGGACGTCCGCGACGAAGGTCGTC[A/G]TCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCG
95738 A T CCAATGCCAGGAGAGCATCCCCGATCAAAACCGCCACGGGCTCACCATAGACGATGTGGTTGGTCGGACGTCCGCGACGAAGGTCGTCATCGTCCA[A/T]GCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCG
95738 G A AAACCGCCACGGGCTCACCATAGACGATGTGGTTGGTCGGACGTCCGCGACGAAGGTCGTCATCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACAT[G/A]GTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGC
95738 C T GCTCACCATAGACGATGTGGTTGGTCGGACGTCCGCGACGAAGGTCGTCATCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCAT[C/T]TCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGACA
95738 A G CGATGTGGTTGGTCGGACGTCCGCGACGAAGGTCGTCATCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCA[A/G]GCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGACACGCTTGCCGCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95738 C T CGAAGGTCGTCATCGTCCAAGCAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGAT[C/T]TCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTT
95738 A C CAGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGG[A/C]GGCGACACAAAGCATCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGAC
95738 G C AGGGTAGATCGTCGTGGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGA[G/C]GCGACACAAAGCATCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACC
95738 C G GGATCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCAT[C/G]GGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAGTGGAACGGCTT
95738 C G TCAAAGACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGG[C/G]CGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAGTGGAACGGCTTCGTC
95738 A G ACATGGTATGGATCATCTCAACGGAGCAAGCAGCAGGCATGGCAGTTGCCTGATCTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGAC[A/G]CGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAGTGGAACGGCTTCGTCTAGGGC
95738 G T CTCCTCCGACTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGG[G/T]TGACCGAGTGGAACGGCTTCGTCTAGGGCTCGGTTAATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGG
95738 T A CTAGCTCGCAGGAGGCGACACAAAGCATCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAG[T/A]GGAACGGCTTCGTCTAGGGCTCGGTTAATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGG
95738 A G TCGGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAGTGGAACGGCTTCGTCTAGGGCTCGGTT[A/G]ATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGGTGACGGCTGCCGTAGCGGGGGATACA
95738 T C GGCCGGACACGCTTGCCGCCAGCGAGGAGGGAGTAGCGCATGGCTTCATGGATGCGCTGCGGGTGACCGAGTGGAACGGCTTCGTCTAGGGCTCGGTTAA[T/C]GGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGGTGACGGCTGCCGTAGCGGGGGATACAGA
95738 G A TGGATGCGCTGCGGGTGACCGAGTGGAACGGCTTCGTCTAGGGCTCGGTTAATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGG[G/A]TAGGGTGACGGCTGCCGTAGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAG
95738 A C CGAGTGGAACGGCTTCGTCTAGGGCTCGGTTAATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGGTGACGGCTGCCGT[A/C]GCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGG
95738 T C GGGCTCGGTTAATGGAAGCGGCCTTCTCGAGCATGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGGTGACGGCTGCCGTAGCGGGGGATACAGATGATGC[T/C]GAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCAAGGA
95738 C T TGTAGGCGTTGAAATCGAAGGAGGTGGGTAGGGTGACGGCTGCCGTAGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTG[C/T]TGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTG
95738 T G GGAGGTGGGTAGGGTGACGGCTGCCGTAGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTA[T/G]AAGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAG
95738 G A TAGGGTGACGGCTGCCGTAGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAG[G/A]ATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAG
95738 G A CCGTAGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAA[G/A]GCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGAAA
95738 A C AGCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCA[A/C]GGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGAAAAGAG
95738 G T GCGGGGGATACAGATGATGCTGAGGTAGTAGGTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCAA[G/T]GAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGAAAAGAGG
95738 G A GTGTTAGAACAGGTTTGGGGTGCTGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGA[G/A]GTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGAAAAGAGGCTGAGGAGAGAGGTTGTTGCCATGGATTCGG
95738 A G TGTTTGGAGAACAGATTATAAGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGA[A/G]GAAGGAGGTGGGAGAGGAAAAGAGGCTGAGGAGAGAGGTTGTTGCCATGGATTCGGGTAGGATTCAAGGGAGAATTGTG
95738 A G AAGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGA[A/G]AAGAGGCTGAGGAGAGAGGTTGTTGCCATGGATTCGGGTAGGATTCAAGGGAGAATTGTGTTTTGATTGAATTGAAATC
95738 A G AGGTGAGGATTTTTTGGGGAAGGCAAGGAGGGAGGAGGATGACATGGTAAGGGATGAGGTGGGAGTAATGGCGGGGAGGAAGAAGGAGGTGGGAGAGGAA[A/G]AGAGGCTGAGGAGAGAGGTTGTTGCCATGGATTCGGGTAGGATTCAAGGGAGAATTGTGTTTTGATTGAATTGAAATCC
95764 T TCG ATGGCGACCAAGTACAGAGCATCCAACTCCAACACCCTCGGGCCCGACGAGTGGCTCTTGGTCAACCACAAGCTCATCTCCGCCGACGGCTCCGCCGAGT[T/TCG]TCGTGCAACCCGACGGCAAGGTCGTCATCTACAAGGACGGCAACCCTATTTGGCAGACCACAGCCCAGCAGCGCTGGGACACC
95784 G A TTACAAAGTTTGGAGATACCTACACAAACTCAGGTCTCAAATCCGCCCGTCTCAAAATCCGCTCAAGCTTCTTAGCAGAAAAAATCAAGCAATCCCATAA[G/A]GCAACCCCAAGCACAATTTCATACACAAAACTAAAGGCAGGGTCATCCCCATTGCTATGCCTGTCTTCCCAATTTGCCCCCTCGTCTCC
95784 CA C AACTCAGGTCTCAAATCCGCCCGTCTCAAAATCCGCTCAAGCTTCTTAGCAGAAAAAATCAAGCAATCCCATAAGGCAACCCCAAGCACAATTTCATACA[CA/C]AAAACTAAAGGCAGGGTCATCCCCATTGCTATGCCTGTCTTCCCAATTTGCCCCCTCGTCTCCACCAAAATTCCATCCTCTTCCACCGC
95784 C T AATCCGCTCAAGCTTCTTAGCAGAAAAAATCAAGCAATCCCATAAGGCAACCCCAAGCACAATTTCATACACAAAACTAAAGGCAGGGTCATCCCCATTG[C/T]TATGCCTGTCTTCCCAATTTGCCCCCTCGTCTCCACCAAAATTCCATCCTCTTCCACCGCCACTGCCGCCGCCTCCAAAAGGTCCGTCG
95784 T C AAGCTTCTTAGCAGAAAAAATCAAGCAATCCCATAAGGCAACCCCAAGCACAATTTCATACACAAAACTAAAGGCAGGGTCATCCCCATTGCTATGCCTG[T/C]CTTCCCAATTTGCCCCCTCGTCTCCACCAAAATTCCATCCTCTTCCACCGCCACTGCCGCCGCCTCCAAAAGGTCCGTCGTCACCGTCT
95784 T G AACTAAAGGCAGGGTCATCCCCATTGCTATGCCTGTCTTCCCAATTTGCCCCCTCGTCTCCACCAAAATTCCATCCTCTTCCACCGCCACTGCCGCCGCC[T/G]CCAAAAGGTCCGTCGTCACCGTCTCCTAGTAACAGATCGTCAGAATCTTCGCCATCATCAAGCGATCGGCGGTGCGTACGACGCTTGCG
95784 A G TAAAGGCAGGGTCATCCCCATTGCTATGCCTGTCTTCCCAATTTGCCCCCTCGTCTCCACCAAAATTCCATCCTCTTCCACCGCCACTGCCGCCGCCTCC[A/G]AAAGGTCCGTCGTCACCGTCTCCTAGTAACAGATCGTCAGAATCTTCGCCATCATCAAGCGATCGGCGGTGCGTACGACGCTTGCGACG
95784 A G CACCAAAATTCCATCCTCTTCCACCGCCACTGCCGCCGCCTCCAAAAGGTCCGTCGTCACCGTCTCCTAGTAACAGATCGTCAGAATCTTCGCCATCATC[A/G]AGCGATCGGCGGTGCGTACGACGCTTGCGACGGACGAGGGCACGTGGAGCGCGCGTGCGACGGAAGGGGTCGGATCGGACGGTG
95784 G A CACCGTCTCCTAGTAACAGATCGTCAGAATCTTCGCCATCATCAAGCGATCGGCGGTGCGTACGACGCTTGCGACGGACGAGGGCACGTGGAGCGCGCGT[G/A]CGACGGAAGGGGTCGGATCGGACGGTGGAAACTGGGCGGTGAGTGGAGAGAAGCGGGAGGATGGATTTTGCTGCTGCGATCG
95784 T C AGCGATCGGCGGTGCGTACGACGCTTGCGACGGACGAGGGCACGTGGAGCGCGCGTGCGACGGAAGGGGTCGGATCGGACGGTGGAAACTGGGCGGTGAG[T/C]GGAGAGAAGCGGGAGGATGGATTTTGCTGCTGCGATCGTGACGGCTGAGATCTCCATTAATAACGCTATAATTCTGATTTTA
95824 C T CCTGTATTAATACCATTGCTCTAAACCCAGATGATATCAAAAAAAGAAGCCGTAATGGATAGTGAGGAAGAAAAGAGTGGAATAACTGAAGTCGATAGCA[C/T]TAATACAGATCAAGGTGAGAATCCCGGCGGTAACACTGAAAAACAACCCACGAATGACCCTGAAGGAGAGAAAAGTGGACCAAC
95834 T C ACTGATCATCCTCGACCATTTGACCTCTGCTACACCTTTTTTTCACCAGCAATATACCCATTGTTTGTCTTCTGCCGGTGACTGCCCCGCCTAGTTTTCA[T/C]CACTGGCTGCAGCCACCAACAAACAAAGTTTCCAGCGAGCCTTCTTGAAATTCTTGATTCAAGATTCGAAGTTCTTTCCCACTATTATATTC
95842 T C AGGGCTAGAAAACAACGATTTCTTGAAGGGCATGGATCCTTATGCTGTCCTCAAGTTTTGCAGCCAGGAGAAAAGGAGCAGCATTGCTTCAGGTCAAGGG[T/C]GTGAACCTGAGTGGAACCAAGTTTTTGTCTTTACCGTCTCTGGCCATGTATCTGATTTCGTCATAAAGCTCATGGACAGCGATGCA
95842 G A AAGTTTTTGTCTTTACCGTCTCTGGCCATGTATCTGATTTCGTCATAAAGCTCATGGACAGCGATGCAGGAAACCAGGATGACTTCGTCGGGGAAGCATC[G/A]ATCGACCTAGAAGCACTGATTTCCGAAGGAAGCCTTCCTCCCACTGTTTACAACGTCGTGAAAGATGACGAGTACAAAGGCGAAATA
95842 CA C TTTCCGAAGGAAGCCTTCCTCCCACTGTTTACAACGTCGTGAAAGATGACGAGTACAAAGGCGAAATAAAAGTCGGATTTACCTTCATACCTGAGGAAAA[CA/C]AAAGAAGAGAACTACGGATATTAAAGATTAATAGATTCAAGTTTTTGGATTATTTATCAATGATGTATGTGTAATTTGTTGCGGTG
95844 C T CACTTAAAGAAACTACAAAAGCATATTGTGGACCAAATAGGGAGCTCAAAGATCATGAAGAAGTGCAGACTCTATATGCAAATGAATGTGGTCAAGCAAA[C/T]CCGTTTACTGTTTTGAAACATAGATTCCTAAATTTCAAAAAGGAAAACTTCATGGAAAATAGGATCCAGTACGAAACTCTTGCTGAA
95844 T G TTTTGAAACATAGATTCCTAAATTTCAAAAAGGAAAACTTCATGGAAAATAGGATCCAGTACGAAACTCTTGCTGAAGGTCAAGCTCCTAAGTTCATGGT[T/G]ATAGCTTGTGCAGACTCCAGGGTTTGTCCTTCCAAAATCCTAGGATTTCAGCCAGGAGAAGCATTTACCCTCCGAAATATAGCAAATT
95852 TC T TAACTCAATGAGCAAAATAACATCCGCAAGGTCGCGACCATCATATCCTAGCCGAAATACATTAGAACAACAGAGAAGAAGACAACCAGGCAGATCAGCC[TC/T]CCCCCACCTCACCGCCAGAAAGCGACGACTTCTCCTCCTTGGAAACCAACCTACGCTGCACACCGCAAGGCGCAGACAATCCCAA
95852 GC G AGATCCGAACTGTTAAAGCAACCTCAACCCACAGACTCAAACAACCGCCAAGCAACAAATCCCCAAGAATACAACCACCACAAACCTTCCTGAACATCAC[GC/G]CCCCCAAACCAAGAAACAAGGCATGCCGATCGGAGAGCAAAGCTCAACCCAGATCTGAGGCCAGGCAGCTCGGCGAAGTTGAAG
95860 G C CTGATCCAGTCTTGCAATTACTTCGCAGATGGTTCCTGGCTATTTCCAAATCGTCAACACAATCCCAAGCATCCGGCACTTGATGTCCCAGATCTGATTC[G/C]CTCTAGCATCGATGCAGCTCAACAACCAGGATTCGATTTTGAAACAATCGTGAGCTCTTTCTCTCTTCAGATCTGGAGCTCAGGAACGC
95860 G GT CAGCTCAACAACCAGGATTCGATTTTGAAACAATCGTGAGCTCTTTCTCTCTTCAGATCTGGAGCTCAGGAACGCTGCGCCTTCTGGGATTTTTTGTAAG[G/GT]TTTGAGATGCAAATCAGACACTTAGGTGTTTTGTCAGGTTAGAGATGGATTTATCGAAGCTTTGAAGCAATTTGTAATTGCAGCGCT
95860 A G ATTCGATTTTGAAACAATCGTGAGCTCTTTCTCTCTTCAGATCTGGAGCTCAGGAACGCTGCGCCTTCTGGGATTTTTTGTAAGGTTTGAGATGCAAATC[A/G]GACACTTAGGTGTTTTGTCAGGTTAGAGATGGATTTATCGAAGCTTTGAAGCAATTTGTAATTGCAGCGCTGCTTGGTTGTACTTGAA
95864 T C CTCCTGTTATATACCGTGACTTAAAGTGCTCTAATATATTGCTTGGAGAAGGGTATCATGCAAAATTATCTGATTTTGGATTAGCAAAGCTTGGGCCTGT[T/C]GGCGATAACACCCATGTATCAACTCGAGTCATGGGGACTTACGGTTACTGTGCACCTGAATATGCAATGACTGGACAGTTGACTAGTA
95878 G A TGAAATGATTGAATTCCATTTTCACTTTGCAATAGCAGCCCAGAAGAGGTGACGTTATAGCTTTCATTTCTTTTCTTGAAAGTGAGCAACATTATCTCAT[G/A]GGTTCGGAGATTTGTATCTTGAAGAAGACTCAATATTAAGGCCAAAATTTCATTGTGATTACCATCTTAATGTTTTATCAAGAACACACC
95878 G A TTAGAATAACCAGCACTCCCATTTGCATCGCCGTATCCACCACCACTCATGTATCCCTGGACAGCTCCTTGATCTGCATTGCCAGCTGGGTTGCTATTAG[G/A]AGCTCCGCCACGACCATATCCATCACCTCCAGCATACCCACCACCATAACCATAGCCCATGTTACCATATCCTGCAGCAGTGTTCTGTG
95878 C A CACCACCACTCATGTATCCCTGGACAGCTCCTTGATCTGCATTGCCAGCTGGGTTGCTATTAGGAGCTCCGCCACGACCATATCCATCACCTCCAGCATA[C/A]CCACCACCATAACCATAGCCCATGTTACCATATCCTGCAGCAGTGTTCTGTGATTGACCGCCTGATGCTCCTGCAGGTCCACCCATAGG
95890 T A TTCATTCATATTACAAGATGAATATTACCTGCTATCAAAATTCAAAACCACCATACATACCTACTATCAAGATGCTTATGGGCTGTTATAAACACAACTG[T/A]AATGACATTGTACTTGGTTGGTAACTTAAAACCAACTTGATATGCCATACAAAGCGCAACAGCAGGGTACAAAAAGAAGAGTAGTTTCG
95890 C T CCATACATACCTACTATCAAGATGCTTATGGGCTGTTATAAACACAACTGTAATGACATTGTACTTGGTTGGTAACTTAAAACCAACTTGATATGCCATA[C/T]AAAGCGCAACAGCAGGGTACAAAAAGAAGAGTAGTTTCGGTCTTTCAGACTTTATAAGAACCATAGAGCGTTAGGCCCTATCGCTTGC
95890 G C ACATACCTACTATCAAGATGCTTATGGGCTGTTATAAACACAACTGTAATGACATTGTACTTGGTTGGTAACTTAAAACCAACTTGATATGCCATACAAA[G/C]CGCAACAGCAGGGTACAAAAAGAAGAGTAGTTTCGGTCTTTCAGACTTTATAAGAACCATAGAGCGTTAGGCCCTATCGCTTGCTACA
95890 C T ACAAAAAGAAGAGTAGTTTCGGTCTTTCAGACTTTATAAGAACCATAGAGCGTTAGGCCCTATCGCTTGCTACAGACGGTATGATTGAAAAAGGCACCTT[C/T]AATCAGAAATTGTTTCTTCTCACGCGATTTCCGGCAGTACTTCTACATCTCTCTGTAACTTTGGGAAGTTCTGGATTAGCTTTCCTTTC
95890 T C GCCCTATCGCTTGCTACAGACGGTATGATTGAAAAAGGCACCTTCAATCAGAAATTGTTTCTTCTCACGCGATTTCCGGCAGTACTTCTACATCTCTCTG[T/C]AACTTTGGGAAGTTCTGGATTAGCTTTCCTTTCTCTCTCTGGTGGTCTTTCCACTATGCTTCCGTTATCAAACAGCTCATTTCCATAGTCC
95890 C G AATTGTTTCTTCTCACGCGATTTCCGGCAGTACTTCTACATCTCTCTGTAACTTTGGGAAGTTCTGGATTAGCTTTCCTTTCTCTCTCTGGTGGTCTTTC[C/G]ACTATGCTTCCGTTATCAAACAGCTCATTTCCATAGTCCTTATTCTCAGCATCCACATAAGAATCCGGAATAACACAAAGAACACCTGGAA
95890 A G CGCGATTTCCGGCAGTACTTCTACATCTCTCTGTAACTTTGGGAAGTTCTGGATTAGCTTTCCTTTCTCTCTCTGGTGGTCTTTCCACTATGCTTCCGTT[A/G]TCAAACAGCTCATTTCCATAGTCCTTATTCTCAGCATCCACATAAGAATCCGGAATAACACAAAGAACACCTGGAATGCCTCCAATTTTAT
95890 A T TAACTTTGGGAAGTTCTGGATTAGCTTTCCTTTCTCTCTCTGGTGGTCTTTCCACTATGCTTCCGTTATCAAACAGCTCATTTCCATAGTCCTTATTCTC[A/T]GCATCCACATAAGAATCCGGAATAACACAAAGAACACCTGGAATGCCTCCAATTTTATTAGCTATTTCCTCATCTATTTCACAACCAAATCC
95890 C T TGGGAAGTTCTGGATTAGCTTTCCTTTCTCTCTCTGGTGGTCTTTCCACTATGCTTCCGTTATCAAACAGCTCATTTCCATAGTCCTTATTCTCAGCATC[C/T]ACATAAGAATCCGGAATAACACAAAGAACACCTGGAATGCCTCCAATTTTATTAGCTATTTCCTCATCTATTTCACAACCAAATCCGAAGA
95892 C T GACTCCCTTCTGGAAAGTCGCTTTTCCAACTGCAGGCAGAAAGGATCTTGTGTGTGCAAAAACTTGCAGCTCAATCAAGTGATGGTTCATCAACAATTCC[C/T]CCAATTCCTTGGTATATAATGACCAGCCCATTCACTGATGATGCCACACGTAGGTTTTTTGCAAGTCACAACTATTT
95904 C T GGTTGAACTTTATACAGTTGATCCCCTTTCGACAATACTGAGGGGGGGAAAGTTGGCGAAGTGGCTTTTCATGAACGAGAACTGTCTTTTCTTTAAAGCA[C/T]TGGATTGCAGTGGGGGAAACAGCGTAAAGGATGCAATTGAAATGGTGTGCGGATACAATGTGGTCACCAAAGAATTAAAGATTTTG
95904 A G ATTGCAGTGGGGGAAACAGCGTAAAGGATGCAATTGAAATGGTGTGCGGATACAATGTGGTCACCAAAGAATTAAAGATTTTGTCTACCGTAGCGGTAGC[A/G]GCACGTGTCGAGACTGATTTTAAGAAGCGAAGTTCCAATGATTTAACAATTAGCTGGGATCACGTGGGTGAGATTTTGGTGGAC
95912 CG C ATAAATAAACATATTTGATATTTATGCAGTAAACAAACTGCTGTATTTCAAAATAAGGACGAGGAACTGTGAATACACAAAGAATTGCCAATTTTGAAGA[CG/C]GGGGGCAAGGAATTAAAATAATAAATTAAGTACCACTCTTTTCAGCAAGGAAGAAGGAATTAAACAAACCAGCCAACATAGACACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
95912 A G GACGGGGGCAAGGAATTAAAATAATAAATTAAGTACCACTCTTTTCAGCAAGGAAGAAGGAATTAAACAAACCAGCCAACATAGACACAGGTAACAAAGC[A/G]ATCAAAGATGCCAATGATTAATCGTGCCCTAGTTGTACTGAAAGAGGTTGCAGCGAATCCTGGAGGTACAGTTGTCATCGCAGTA
95914 G A GGCCGCCGAAGAAGCTGACGCGGCTGCTGAGGCTGTGGCGGAAGAATCAGGAGTGGCACA[G/A]TCGCAATCTTTCAAGGAAGAAAGCAACAAAGTAGCTGATCTCGAAGATCCAGAAAAGAAAGCGCTAGATGAACTCAAACAGTTGATTCAATCTGCCTTAG
95914 C T AAGGAAGTGAAGGCTGAAGAAGAGGCGAAAGCTGAGGATGTGAAAGCTGAAGAACCGGCTAAAGTTGAAGAAGTGAAAGAGGAGAAAGCAGAACTTAAAG[C/T]TGATGAGCCTGCAAAAGTGGAAGAAGCGAAAACAGAAGAACCTGCGAAAACAATTGAAGAATCGAAAACTGTGGAAACAAT
95914 C T AGAAAGCAGAACTTAAAGCTGATGAGCCTGCAAAAGTGGAAGAAGCGAAAACAGAAGAACCTGCGAAAACAATTGAAGAATCGAAAACTGTGGAAACAAT[C/T]GAAGAATCAAAAACTGAAGCAGTGGAGGTCAAACCTGAGGAGGTGAAAACTGAAGTGAAAGAAGCAAAGGCAACTGAGGAGA
95920 GA G GCCGTGACGAGTCAGAGCCGGTTATTGGGCAAGGACCAATAGACCACGAAATAGGGCAACCCAACCCCTTTCTGGGGCAACGACGGGAGTCGGGAGATGT[GA/G]AAAAAAATCAAATCGCGATTCAGATTTCTCCTTTTCCTCCGCACGCACGACGCTGCTCTTTCCTCCGTAACGGCTCGCGACTCG
95920 T C GCAATCTTTAGGCTTGGTTTATAATTTCATTATCGCATCCGTGAATCGGCGATTAACTCTTCCTGAAACAATTTGACAAGGGAAACCCAAAGGCTAGAAC[T/C]GGCCCTGGTGACGACAACCTGAAGATCGAAGGCTGAAGCAACTGGCGACTTCTCAACATTGCTAAGGGTACAGCCGAGCCCGACGG
95930 GT G TAAGAGAATTGAAGCTGTAAATCCTCCTGCTTCATAATTGGGACATCCAAGAACGGCCATGGAAATGAGTTATTGCTGCTCATTACATGCACTTCCTCGT[GT/G]TTTTTTCTTAAATCTTTATGGCGGACGCTGGCGTCTCAGTTTCCCTTTGCAGTAGCGCGTTACTGCTATGTTTTGACCTCTGCAACTAC
95932 C T TACTCAACAGTGATGTGATTAGTGAATACCCTTTTGCTCAACTCATTGACTTTCACAAAGCTCATGGTGGAGAGGCTACTATTCTTGTAACCAAGGTTGA[C/T]GAGCCTTCCAAATATGGAGTGGTGGTCATGAACGAAGAAACCGGAAGCGTCGAGAAATTCGTTGAAAAACCCAAAGTGTT
95944 A G GTCGTTCATCGCAATACGCCTTCTCTCCTGGGAATGCTCAACCAGGTGAAGAGGCTGGTTGTTGTGGAGACGGAGGCCATGTATAATACTCGGAAACAAA[A/G]GGAAGAGGAACACAAAGCTTTACGCCCTCCAATTGTTGTCAGCCATTCTCATCCTCCCTCTGCTCCTGCTGCTCAGTAGGCCGTTTC
95948 T A GTAAGGTAGACAATGATCAAGCTATATACCTAAAAAATATCAAACATATAACTTACCTTCCAAATTATTGGGCTTCCCGGTTGATGAAGAAGATGACACT[T/A]TGTTATGGAACACTCTATCCCTCGCCATCGATGAAATCTGATTGTCCGTTAATTCAACTGCAAAAAAGTTGACTTTGAGATAATTTTAT
95948 G A TATACCTAAAAAATATCAAACATATAACTTACCTTCCAAATTATTGGGCTTCCCGGTTGATGAAGAAGATGACACTTTGTTATGGAACACTCTATCCCTC[G/A]CCATCGATGAAATCTGATTGTCCGTTAATTCAACTGCAAAAAAGTTGACTTTGAGATAATTTTATTTCTCTTGTTGCAACAATTGTGGCA
95948 T A TCAAACATATAACTTACCTTCCAAATTATTGGGCTTCCCGGTTGATGAAGAAGATGACACTTTGTTATGGAACACTCTATCCCTCGCCATCGATGAAATC[T/A]GATTGTCCGTTAATTCAACTGCAAAAAAGTTGACTTTGAGATAATTTTATTTCTCTTGTTGCAACAATTGTGGCAAATCCAAACCCATAT
95948 C A CTGTAAGCTTAAGCCAAACTAAAGATCTTGGACAATGGCAGTTCAGTGAAGCGGGACATGAAAAGACTCTGGCGATTGACTGAGAAATACGGCTGTTGGC[C/A]GGAGGGTCCACCGTAAGTTGGATCGAAGAAGGGGAGGAGTTCAAAGACAGATCTGACAATGGGAAAAGAGGTGCAAAACAGCA
95950 T C CTCCCTCAGGTACAGCCTGACCGCCCTAGACCCAAACGGGTTGTTCTCCGGGTTGCCCCCGTTCTCGTCGTAGGCTGCCCTAAGCCTCCCGATAAGGGCG[T/C]CCAGACTGCCCCAAGCCTGCCGGAGAGGGCAGGGGCACGGCCCCGGCGGGTTGGGCTGCCCGAAGAAAGGGCACATTTGGAGGT
95950 T C GGCAGGGGCACGGCCCCGGCGGGTTGGGCTGCCCGAAGAAAGGGCACATTTGGAGGTGCACCTTCGTCTTCCCGAACTGGTCCAGGTACCTCAAAAACTC[T/C]AGAACGTGCGCCCCACTGCATTGGGAGAGCGCCAATGGCGGCCTGTGGTTTCTTAGGTACTGGTTGAAGGTGTTCCAGTCCCTC
95950 T A GCGCCAATGGCGGCCTGTGGTTTCTTAGGTACTGGTTGAAGGTGTTCCAGTCCCTCCGTTTCTGGGACACGTATCTCGAAGAGGAAGAACTGGTGGACGC[T/A]GACGATGACGATGGCGAGGTCGGGCTTGAATCTTGACCGTCCATCCTGTAGGGCCAGCCTGGATCAAGAATAAAGGAAGGATTG
95956 G T TGATGAAACATTTTATAGCCAATTTTATTAAAAATTTGGTGCAATCTTTTATTTAGTCAGTTC[G/T]GGCAATATGAAATAAGAGTAATTTTTTTACAGGGTTGCTATGCAATCAATTTCAACTCTTGCATCCATGGGCAAAGCAGCCACCTGATAACATGCACGCA
95956 A AG TGATGAAACATTTTATAGCCAATTTTATTAAAAATTTGGTGCAATCTTTTATTTAGTCAGTTCGGGCAATATGAAATAAGAGTA[A/AG]TTTTTTTACAGGGTTGCTATGCAATCAATTTCAACTCTTGCATCCATGGGCAAAGCAGCCACCTGATAACATGCACGCACTGGAAAAGGCTCTGAAAAAT
95956 T C AAAGCATTTTGTTAGCCTTGACAGCCTGAGAATAAGGTCCCAATGCCGCAGGTGCCTTCTTGGTATGAACAGCTTCTTTCTTATCAACAACGGAGGTGGA[T/C]CTAGTAGCATAAGCAAGAGTGAAAAGGACAAAGCAAACTCCAAAAACGGCGGCCAAGGCGACCACCTGACGGCGACGAGGGTTGT
95956 T C ACAGCCTGAGAATAAGGTCCCAATGCCGCAGGTGCCTTCTTGGTATGAACAGCTTCTTTCTTATCAACAACGGAGGTGGATCTAGTAGCATAAGCAAGAG[T/C]GAAAAGGACAAAGCAAACTCCAAAAACGGCGGCCAAGGCGACCACCTGACGGCGACGAGGGTTGTTCATCGGAGATCGGAAGGA
95956 C T TATGAACAGCTTCTTTCTTATCAACAACGGAGGTGGATCTAGTAGCATAAGCAAGAGTGAAAAGGACAAAGCAAACTCCAAAAACGGCGGCCAAGGCGAC[C/T]ACCTGACGGCGACGAGGGTTGTTCATCGGAGATCGGAAGGATTTCACCATCGATTCAGTTGACATACTATTCTTCTGCATAAGTGT
95960 C T ATCGCACTCCTGATCCAGATGGAAGGCGAATAGAAATAACATGTGCAGCGTGTGGGGGGCATTTGGGTCATGTATTTAAAGGCGAAGGATTCGGCACACC[C/T]ACTGATGAGCGCCACTGTGTTAATAGCATCTCGCTAAAATTCGCTTCAGTTTCTTAAAAGATATGCTGCTGTGGTTAAACTTGTAG
95980 T TA GGTTTTGCTAATCAGATTACTACTGTTGATGAAGCCAAAGAGTTCTACCCGCTTTTTGGACTAGGAGCTAACATAGCTCTTATCTTCTCAGGACGTACTG[T/TA]AAAATACTTCTCGAACCTTCGTAAAAATTTGGGTCCTGGTGTTGATGGATGGGCAGTGTCTCTTAAAGGAATGATGAGCATTGTTGT
95980 G C TTAACAAATTTATCCTAAATGATCCGTCCCTCCCGAAACCTCCTCCCAAAAAGAAGAAGCAAAAGGTGAAGTTAGGAATGAAAGAGAGTTTGAAAGTGCT[G/C]GTATCTTCTAGATATGTGAGAGATCTTGCCACTTTAGTGGTTGCATATGGTATCAGTATCAACCTCGTCGAAGTTACGTGGAAATCA
95984 G GT GTGACCGCAGTTTGGCAGTTGTCGGAGGTGTCTTTGTTCCTCAGCGTGAAGGGAATGGTGGCCAATCCTGCGAAATCTTTTGGTGATTTTGTGTTAGGAG[G/GT]TTTTAATGGTAAAGGGAAGAAGAGAGCTGCTACTACTGAAGCTCTTGCTGTTCCTCCTGTTATTGTTCCCGAGCTGCCTCGGGTTG
96004 T C ATAATCATGGCTTTAAAGGCTTATGACCCCAACAAATACTCGTTTGAATGGATGGGATGTAGCACCAATTAAGAGGTTCTCACATACCATCTTGTATAGT[T/C]AGCCTAATTAAACAACAACTATGAATAAACATGCGCGCAATGCCGTTTCATGAACTCAAGCTGGCTTGTTTGTCTTTGATTCCACTGCA
96004 C T CTTATGACCCCAACAAATACTCGTTTGAATGGATGGGATGTAGCACCAATTAAGAGGTTCTCACATACCATCTTGTATAGTTAGCCTAATTAAACAACAA[C/T]TATGAATAAACATGCGCGCAATGCCGTTTCATGAACTCAAGCTGGCTTGTTTGTCTTTGATTCCACTGCACGGTTTACTTCAGGGCTCT
96004 A T AGCCTAATTAAACAACAACTATGAATAAACATGCGCGCAATGCCGTTTCATGAACTCAAGCTGGCTTGTTTGTCTTTGATTCCACTGCACGGTTTACTTC[A/T]GGGCTCTCGACGTCATGCACGGCGTGAGCACGTGTGCTTGTTGTCGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACGGCTAATGG
96004 G A CAACAACTATGAATAAACATGCGCGCAATGCCGTTTCATGAACTCAAGCTGGCTTGTTTGTCTTTGATTCCACTGCACGGTTTACTTCAGGGCTCTCGAC[G/A]TCATGCACGGCGTGAGCACGTGTGCTTGTTGTCGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACGGCTAATGGCACAAGCGATTA
96004 T C TAAACATGCGCGCAATGCCGTTTCATGAACTCAAGCTGGCTTGTTTGTCTTTGATTCCACTGCACGGTTTACTTCAGGGCTCTCGACGTCATGCACGGCG[T/C]GAGCACGTGTGCTTGTTGTCGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACGGCTAATGGCACAAGCGATTACTGCTAGGACAAT
96004 G A CCACTGCACGGTTTACTTCAGGGCTCTCGACGTCATGCACGGCGTGAGCACGTGTGCTTGTTGTCGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACG[G/A]CTAATGGCACAAGCGATTACTGCTAGGACAATGATTACAGAAAGAACTGCAAAGACTGGGCCATATGAACCTTTGCTCTTTGAGTTT
96004 A G TTACTTCAGGGCTCTCGACGTCATGCACGGCGTGAGCACGTGTGCTTGTTGTCGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACGGCTAATGGCACA[A/G]GCGATTACTGCTAGGACAATGATTACAGAAAGAACTGCAAAGACTGGGCCATATGAACCTTTGCTCTTTGAGTTTGTTTGTTGATTTG
96004 T A CGCCTTTTCCTTGCCTAGCTTTCGAGCACATAGACGGCTAATGGCACAAGCGATTACTGCTAGGACAATGATTACAGAAAGAACTGCAAAGACTGGGCCA[T/A]ATGAACCTTTGCTCTTTGAGTTTGTTTGTTGATTTGCTACTGCTAGCGATTGAGGTAGAAGAGAAGACATCGTTATCGCTTCTATGTT
96004 C T AAGCGATTACTGCTAGGACAATGATTACAGAAAGAACTGCAAAGACTGGGCCATATGAACCTTTGCTCTTTGAGTTTGTTTGTTGATTTGCTACTGCTAG[C/T]GATTGAGGTAGAAGAGAAGACATCGTTATCGCTTCTATGTTCAGAATGAATGATAGCTATGTGTGTGTATTAGTGTATATATGTAAGG
96018 A C AGACCCAAAATCAAATGCCAGCAAATGGAAATATCCATCCAGGCATGCCTGCTCCACCTGCCATGTACTTGATTCCACCAGTGCCTTCCCTTGAAGAAGG[A/C]CATGGCATGGCTCCAGTGGCATACCCATATGTTGATCCGTACTATGGAAGTATTTTGGCTGCTTATGGCGGTCAAGCTGTGATGCCC
96026 AT A GACTTCCCTGTTGAGAATTTCTACGTGTCGCCTAGATGTGGATGTGGGGTTGATTGCGTCGACCTGGTAGATTCAATCTGAGGTTGGATGTTGAGGTTTT[AT/A]TTTTTTTCACTTTTAGATTTACTGTTGAATTTATGTCTATGATGATGATGAGACGTTGGATCACTAGTTATAATTCATGATCCTATATA
96026 T A CTAGATGTGGATGTGGGGTTGATTGCGTCGACCTGGTAGATTCAATCTGAGGTTGGATGTTGAGGTTTTATTTTTTTCACTTTTAGATTTACTGTTGAAT[T/A]TATGTCTATGATGATGATGAGACGTTGGATCACTAGTTATAATTCATGATCCTATATATTAAGTTTTATGGTTAATGATTTCTTCATGGG
96026 T G TGTGGATGTGGGGTTGATTGCGTCGACCTGGTAGATTCAATCTGAGGTTGGATGTTGAGGTTTTATTTTTTTCACTTTTAGATTTACTGTTGAATTTATG[T/G]CTATGATGATGATGAGACGTTGGATCACTAGTTATAATTCATGATCCTATATATTAAGTTTTATGGTTAATGATTTCTTCATGGGTATTA
96026 C A TCTGAGGTTGGATGTTGAGGTTTTATTTTTTTCACTTTTAGATTTACTGTTGAATTTATGTCTATGATGATGATGAGACGTTGGATCACTAGTTATAATT[C/A]ATGATCCTATATATTAAGTTTTATGGTTAATGATTTCTTCATGGGTATTATTGCTTTAAAAAAAAAAA
96040 TTCTGGA T CTGTTCATGAAAGGGACAAAAGATTTCCCACAGTGTGGATTTTCCAACACGGTTGTGATGATACTGAAGTCCTTGAATGTTCCATTTGAGACAATGAATA[TTCTGGA/T]TCTGGATCTGGAAAATGAAAATTTGAGGCAGGGGCTGAAGGAGTATTCAAGTTGGCCCACTTTTCCTCAACTTTATATTGAT
96040 G A AAGGGACAAAAGATTTCCCACAGTGTGGATTTTCCAACACGGTTGTGATGATACTGAAGTCCTTGAATGTTCCATTTGAGACAATGAATATTCTGGATCT[G/A]GAAAATGAAAATTTGAGGCAGGGGCTGAAGGAGTATTCAAGTTGGCCCACTTTTCCTCAACTTTATATTGATGGGGAGTTTTATGGT
96040 T A ATATTCTGGATCTGGAAAATGAAAATTTGAGGCAGGGGCTGAAGGAGTATTCAAGTTGGCCCACTTTTCCTCAACTTTATATTGATGGGGAGTTTTATGG[T/A]GGATGTGATATTACTGTTGAAGCATACCAGAGTGGGGAACTGCAGGAAGCAATAGAAAAAGCAATGTGTTCTTAACCAATATCCTG
96052 T C GGTTCCCTGCTGATTCCCATGACACTATCTGGCTCACTGCCACCGTTGAACGAGAGTTCTCTCGCTGCCCAGAATGTGGAAATGTCTACAAGCTCGACTA[T/C]CAGGGACCTGAACACTCCCATGCTCATCACCATTAATATTCACCCTCCTTCGTCAACGTGATAGGATAGAGAGCACCATTGTCCGATA
96070 A G TTTTGAGGGATTTGGCGCGTAGGGTTGGGGCTGATGCATTGTACATGCATAGAGAGGTGAGTAAGGAAGAGGTGAAGGTGGAGGAGAAGGTGGAGAAAGC[A/G]ATGGAGGAGGAAGGGATTGAGGTGAAACATTTTTGGGGGAGTACCTTGTATCATATGGAGGATTTGCCATTTGAGTTGGAG
96072 GT G GCGATGCGTACAAGTCCAATTCCTTCCTCATCTGCACATTGAGACTACTCACTCCGCCGCCCACCGGTGTAGCCAAACCACCCTTCAAACAAACCTTGTT[GT/G]TTTTTTATAGATTCGATCACTTCTTTCGGCACGCATGGGTCCGATCCGTGCACCTCGAATTCTTCAAATTCGATCGGCGCTCTAATCGC
96072 T G CTCATCTGCACATTGAGACTACTCACTCCGCCGCCCACCGGTGTAGCCAAACCACCCTTCAAACAAACCTTGTTGTTTTTTATAGATTCGATCACTTCTT[T/G]CGGCACGCATGGGTCCGATCCGTGCACCTCGAATTCTTCAAATTCGATCGGCGCTCTAATCGCGGAGAAGACTTGAGCAACAGCGTTTG
96072 A G GCCCACCGGTGTAGCCAAACCACCCTTCAAACAAACCTTGTTGTTTTTTATAGATTCGATCACTTCTTTCGGCACGCATGGGTCCGATCCGTGCACCTCG[A/G]ATTCTTCAAATTCGATCGGCGCTCTAATCGCGGAGAAGACTTGAGCAACAGCGTTTGTGACTAACGGACCGATTCCATCGCCTGGGAT
96076 G A CACTTCTTCCAACCACTCAAATGCACACATGTCGTCTCTCTCCATCCCAATTTCCCCAAAACAAAACCTCCATTCCCTCCTAAAAAACCCTGAATCCCTA[G/A]CCCAAATCAAACAAATCCACACGCAAATCATCCGCAAAGCCACCAGCACAGCCTTCTCGTACAACCTTCTAATCCGCGCGTACGTTCTAAT
96076 C T CTTCTTCCAACCACTCAAATGCACACATGTCGTCTCTCTCCATCCCAATTTCCCCAAAACAAAACCTCCATTCCCTCCTAAAAAACCCTGAATCCCTAGC[C/T]CAAATCAAACAAATCCACACGCAAATCATCCGCAAAGCCACCAGCACAGCCTTCTCGTACAACCTTCTAATCCGCGCGTACGTTCTAATCT
96076 A C TAATCTCATCACCCCATCACGCTCGCAGCGTGTTCGTCACGATGCTTCACTCAGCCACACCCGATAAGTTCTCACTGACTTTCTCCATCAACGCGCTCGC[A/C]ACGTTGAAGGATTACGACAACGGCAGGATCTTACACGGGTACGCGTTGAAGCGCGGGCTGTACTGGCATGGCGGGTTGCATCTCGTG
96076 G A CACCCCATCACGCTCGCAGCGTGTTCGTCACGATGCTTCACTCAGCCACACCCGATAAGTTCTCACTGACTTTCTCCATCAACGCGCTCGCAACGTTGAA[G/A]GATTACGACAACGGCAGGATCTTACACGGGTACGCGTTGAAGCGCGGGCTGTACTGGCATGGCGGGTTGCATCTCGTGAACAGTTTG
96076 T G CCCATCACGCTCGCAGCGTGTTCGTCACGATGCTTCACTCAGCCACACCCGATAAGTTCTCACTGACTTTCTCCATCAACGCGCTCGCAACGTTGAAGGA[T/G]TACGACAACGGCAGGATCTTACACGGGTACGCGTTGAAGCGCGGGCTGTACTGGCATGGCGGGTTGCATCTCGTGAACAGTTTGAT
96076 T C ATTACGACAACGGCAGGATCTTACACGGGTACGCGTTGAAGCGCGGGCTGTACTGGCATGGCGGGTTGCATCTCGTGAACAGTTTGATGAGTCTGTACTT[T/C]GGGTGCGGAAGGGTGGAATGTGCGTGGAGCGTGTGGGAGAAGATGAGAGTGAGGAGCGTCGTTTCTTGGACTGCTTTGGTGAA
96076 A G TGTACTGGCATGGCGGGTTGCATCTCGTGAACAGTTTGATGAGTCTGTACTTTGGGTGCGGAAGGGTGGAATGTGCGTGGAGCGTGTGGGAGAAGATGAG[A/G]GTGAGGAGCGTCGTTTCTTGGACTGCTTTGGTGAAGGGGTTGCTGGAGTGTGGCGAGGTGGAGATGGCAGTAAGGGTTTTCG
96076 T C GAGTCTGTACTTTGGGTGCGGAAGGGTGGAATGTGCGTGGAGCGTGTGGGAGAAGATGAGAGTGAGGAGCGTCGTTTCTTGGACTGCTTTGGTGAAGGGG[T/C]TGCTGGAGTGTGGCGAGGTGGAGATGGCAGTAAGGGTTTTCGAGATGATGCCGGCTAGGAATGTGGTTTCCTGGACGGCTGT
96076 A G AATGTGCGTGGAGCGTGTGGGAGAAGATGAGAGTGAGGAGCGTCGTTTCTTGGACTGCTTTGGTGAAGGGGTTGCTGGAGTGTGGCGAGGTGGAGATGGC[A/G]GTAAGGGTTTTCGAGATGATGCCGGCTAGGAATGTGGTTTCCTGGACGGCTGTGATTGATTGGTGTGCTAGGAACGGACGGA
96076 A T GTGCGTGGAGCGTGTGGGAGAAGATGAGAGTGAGGAGCGTCGTTTCTTGGACTGCTTTGGTGAAGGGGTTGCTGGAGTGTGGCGAGGTGGAGATGGCAGT[A/T]AGGGTTTTCGAGATGATGCCGGCTAGGAATGTGGTTTCCTGGACGGCTGTGATTGATTGGTGTGCTAGGAACGGACGGATCA
96078 A T CATCAAACTCAAGCTGGCGACATATACTTGGATCAACCATAGGCGTCCTGGGCTCGGGCCCAGATCTTCTTGGGGCATCTGGGCAGGTCTCAGCAATACC[A/T]GTTAAACGAGGCATCAAAGTTGGTGTCATAAAACCATCATCAGATTTGGCATCGCTAACAATGAGCGAATCACCAATCTGATTCTCT
96078 A C CAGCAATACCAGTTAAACGAGGCATCAAAGTTGGTGTCATAAAACCATCATCAGATTTGGCATCGCTAACAATGAGCGAATCACCAATCTGATTCTCTAA[A/C]ACAAGATCATGAAATTGCTGAAATAGCGACTCATAAATAAGTTCATCCTCAACATCAGCAGCAGACTCCACATCATCTTCTACAGAGC
96078 T C TGATTCTCTAAAACAAGATCATGAAATTGCTGAAATAGCGACTCATAAATAAGTTCATCCTCAACATCAGCAGCAGACTCCACATCATCTTCTACAGAGC[T/C]GCAGCAACTGTCAAAGTTTAATTTACGGCGAGTAGGAATTCTGAACTCCCGTGTGGTCTTCTTAATTGGAGCAAGTGCATAGACTTCA
96082 G A ACTTCGGTCTTTCGAAGCCTCAGGTTGATGGATCTCATGTGTCAAGCATTGTTAGAGGCACTGTTGGTTATTTGGACCCTGAGTATTACATCTCACAACA[G/A]CTAACAGAAAAAAGCGACATCTACAGCTTTGGGGTGATTCTACTGGAACTGATAACAGGCCATGAGCCAATATCAAATGAAAATTTTG
96082 C T CGTTACTGGACGAGGATTACGACATGCAGTCAATATGGAAAATAGCAGAAGTAGCAATTACGTGTGTGAAGCCTCATGGGGTGGATAGACCATCCATATC[C/T]GATATACTGAAGGAGATTCAAGAAGCCATCGCCATTGAGCGTGACTCGATTGCAGGTGCGGAATTGCCCGAAAAATCAAAGAATT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
96088 T C AGGATATAAAGTTAAGGCTCTAGTCAGAAAAGATGACCCAGAAGTAAAAGATATGCTTCCAAGATCAGTGAATATAGTGGTTGGTGATGTAGGTGAACCG[T/C]TGACGCTGAAGGCTGCTGTTGCAGGTTGCAATAAAATAATATATTGTGCTACTGCGCGCTCAACTATTACTGGCGACCTTAACAGG
96088 T C GAAAAGATGACCCAGAAGTAAAAGATATGCTTCCAAGATCAGTGAATATAGTGGTTGGTGATGTAGGTGAACCGTTGACGCTGAAGGCTGCTGTTGCAGG[T/C]TGCAATAAAATAATATATTGTGCTACTGCGCGCTCAACTATTACTGGCGACCTTAACAGGGTCGATAACATAGGAGTGCAGAATG
96092 T A GTGGCCTTTTTTTTTTTTGAAGTGATAAATCAAATTATTAAAACAAAAACAAAAATAAATGAAGGT[T/A]ACATAATTTTTGCCACAACTCCATGTTCATTACCAAATATTATCATAATTTACGGCAGAAAGTCAGACAAACCGAGCGCCCTAGAATCCATAATTACACA
96092 T A TGTTCATTACCAAATATTATCATAATTTACGGCAGAAAGTCAGACAAACCGAGCGCCCTAGAATCCATAATTACACAAGTATGAAACGGATAAACTATCA[T/A]TAAAAATGCAGCCCTTTTCACTGGATGCCATTAATTTCGTATTCATCAACCACGTCCTCGACCTCCTCCTCTTGCATTTCCGGTTCTACC
96092 TA T GTTCATTACCAAATATTATCATAATTTACGGCAGAAAGTCAGACAAACCGAGCGCCCTAGAATCCATAATTACACAAGTATGAAACGGATAAACTATCAT[TA/T]AAAAATGCAGCCCTTTTCACTGGATGCCATTAATTTCGTATTCATCAACCACGTCCTCGACCTCCTCCTCTTGCATTTCCGGTTCTACC
96092 T C TAATTTACGGCAGAAAGTCAGACAAACCGAGCGCCCTAGAATCCATAATTACACAAGTATGAAACGGATAAACTATCATTAAAAATGCAGCCCTTTTCAC[T/C]GGATGCCATTAATTTCGTATTCATCAACCACGTCCTCGACCTCCTCCTCTTGCATTTCCGGTTCTACCAGTTGGTCCAGCCCTTCCACGA
96094 T C TTGGTTTGTTTAGTTTTGGGTTTATTTTCGTTACTTGGTTCTTGTTGGGTGTTCTATGAAATGGTTTGGTGTGCGGTAATGGCTTCTTTCAAGTGCACGA[T/C]GTGTGTTTTCTTGTCTTTTTAACACCATCACTATTGGTCCCTGCTCGTCGGCCATTGTTATGCAACGGCGGAGCTTTTGTGCTGGCTTTTG
96132 G A CACGCCATGACGATGGTTATGGTGATGCCCACCTCTACAATTGACGATCCTCTCAATCGCATCGCTCACCTGCAAGTAGTGACCCACACTGCAGGGAATC[G/A]TAATCGCGCCTTCCTGCTTGAATCCGTACTCCTCCTCCGCCTCCTTCAACAGATCCGTAAACAATGGCTGCTTCAAGTAAGCAATCGG
96162 T C GGAGGCCATCGTTGCGATCGAACTGGACACGGTCTTCGGCGCTGATAGATGACGTGAGGGCGAGTATGATGGTGGCTCCGGATCAACATCTGGTGGTCTT[T/C]GATGTGGCGCTGGACAAGGGATGGGGCGTGGCAGCTTAGATTTGGGTACGGTGTATGGACCGAAGTAGATGGGAACTGGAAT
96168 A G TAATGGTGCCACATTTAGTTTGTCCGTGCATAGCAGCATAGAGTCTTCTCATTAAACTGTCCTGACCACATCCAGGATGATTCTGTTGGAAGAGTGGTAC[A/G]TTGCTATCGAACCAAGTACTAGTGCCAGCATCACACAATGAAGCTACGGCGGCCTTAGCGCAGTTCCATGATCCTTCAGAGTTGCAA
96168 T C TGTTGGAAGAGTGGTACATTGCTATCGAACCAAGTACTAGTGCCAGCATCACACAATGAAGCTACGGCGGCCTTAGCGCAGTTCCATGATCCTTCAGAGT[T/C]GCAAGGATTGGTTCTCTTGCATCGCGCAATCTTTCCCATAAATTGTCTGGTTGTGAAGCACGGAATGGCACGCTCAACGGCGTCCTT
96168 G A AACGGCGTCCTTTTCCTTTACGCATGTGAACTGAATAGCTTTGTTAAGTTTAGTGTATAGAGGCTCGTATTTGTTGATGGCTTCAAACTGGCTACATTCA[G/A]GGTCGTCTAGAAGGGTACGGCCACACTGTAGGAAGCCCTGTGCGGCGCTGCAGATGTCATTGATCGGTGTGTTACGAATTGTATTGA
96186 C T TAGTATGCTACGGACATAGCATATCCTTGTGATGAATATGGTTACAGATTACTGGATGCACCTAAATATTTGGTATAACGTGCCTGAGCTATAATCTTCT[C/T]AGTTGCCTTGTTTTTCAGTTGAACATTAACCACGCCAACTGATTTCCCAGCTCTCAGAACTTTAGCCTCGATTTCAACTTCGTCATCAGG
96186 G A TGCACCCGCTGTATAAAAAGCAGCACCTCCCACCAAATCAACTAAAGATGCAATGGCTCCACCATGCATGAACTTTCCAGCATTGAGAAGACGAAGAGGG[G/A]CGATCAACGAGCAAAGGAGGCGTCCGGGCTCAATGCTGTCAACGGTGATGCCATAAAGAACGAAGGAATCGTAAAATTTTGGGG
96198 A G ACTGTTGGCCTACTGGGTTCTTCATTTATTGCCTGCCTTTCTCGTTTTCCCCACTCCAAACAGATTTTCCCTTTCATTAAAG[A/G]TTCTGCCAGCAATAAATCCTCTATAGCACTTCAGATCAGACAACGGTATTTGTCGTCTTCTTCCAAAATGGAAGAGTCTGGTACCGCGGCGGCTGTTAGC
96198 C T ACTGTTGGCCTACTGGGTTCTTCATTTATTGCCTGCCTTTCTCGTTTTCCCCACTCCAAACAGATTTTCCCTTTCATTAAAGATTCTG[C/T]CAGCAATAAATCCTCTATAGCACTTCAGATCAGACAACGGTATTTGTCGTCTTCTTCCAAAATGGAAGAGTCTGGTACCGCGGCGGCTGTTAGCTCGTCG
96198 C T ATACTATTCCTAGAGAGGTGCTACATGCTTGTTACAGTAAGGTATCACCTTCTGCTCAAGTAGATAAACCAGAGCTTGTCGTGTGGTCAGATTCTGTTGC[C/T]AAAAAGCTTGAATTAGACCCTAAGGAGTTTGAAAGAGAAGATTTTCCTCTTCTGTTTTCTGGAGCTTCACCACTAGTGGGAGGACTAC
96210 GCGAGGAAAA G TTACCCGACTGTCATCAAGATGAACCCAACAGGGTGATTGTGGTCGAGCCATTCTTTCATCATGATCAGTTTTACTTCAGGTCAAAGTCTTGTATATCAT[GCGAGGAAAA/G]CGAGGAAAAAGACCATGCTGCAACAACTATGTGTTGCTGTAACAACAGTGGGGAAGAGGAAGACTCACTGTATTTTGG
96210 GGGAAGA G TTCTTTCATCATGATCAGTTTTACTTCAGGTCAAAGTCTTGTATATCATGCGAGGAAAAAGACCATGCTGCAACAACTATGTGTTGCTGTAACAACAGTG[GGGAAGA/G]GGAAGAGGAAGACTCACTGTATTTTGGTTCAACCCAAAATCACAAGTATTGCACCATGTGGTATCAGCCAGGCTATGCGAT
96228 C CT CCATTCCAAGTCTCTATTCCACCTATTCCACCAGAATTATCAAAGACACCCCCTTCTCCTCGGACATGCCCCTCTCCGCCGCCTCTCCATTTCCTTCTC[C/CT]TTAAAACCCAAACATCTCCGCCGCACAATGACTTCCTCTTCACCCTCTACAACCCTCAAAAAACCCGACCATAACCCTACTTCCAGGCCATC
96228 A G TGGCGGCCAACGACAATAACCCTGAGAAGGCCTTCGATTTCGTTAACAAGATGGTGGAGTTGGGGATGCAGATCAGATTAAGGAGCTACGGACCAGCCCT[A/G]TTTGGTTTCTGCAAAAGATTGGATTATGAAAAAGCTCATGAAATCGAAATCCACATGGAAAAACATGGAATCGTGCCAGAGGAA
96232 A G TCACTGTTGGCCTACTGGGCTGGCCAGCCGCGGAAATCTCCCGACTCAAAGCAAATGGCGTC[A/G]TCTTCCTCTAAACCATTCTACCCCATTTTCTATCCCTCAAAGCGAGCTAAAACCCTATCAACTTCAGCTCCCAATTGCATCTCCACTTCCCTCCCTAAAA
96232 C A CAAAGCAAATGGCGTCATCTTCCTCTAAACCATTCTACCCCATTTTCTATCCCTCAAAGCGAGCTAAAACCCTATCAACTTCAGCTCCCAATTGCATCTC[C/A]ACTTCCCTCCCTAAAACCCCGATCCCCAAGCCTTCAACCTCTGACGCACATTTTTCCTCGGTCGAGGCCCGTAGTTCACCACCGTCGAATC
96232 C T CCCTAAAACCCCGATCCCCAAGCCTTCAACCTCTGACGCACATTTTTCCTCGGTCGAGGCCCGTAGTTCACCACCGTCGAATCTCCCGGGAGATCATAAA[C/T]CAGGAACTGAAATCAAAGAGTTCGTTGAAAAAGCTAAGCGGAACCTTAGTATCTGCAGCGAAAAGATCGAGAAATCAAAAGGTTTGC
96232 C G AAAGGTTTGCATTACGTGAAATTGGAGGAGCTTCTTGTGGAAGAATCGTGGGTGGAAGTGATTTCAGATGAGTTCAATAAACCATATGTAAAAAATTTGT[C/G]TGCCTTTCTGGAGAGAGAGACCCATGGAACTGTTCCGATATATCCACCACAACCCTTAATATTTAATGCGTTAAATTCGACTCCATTT
96232 A G CGTGGGTGGAAGTGATTTCAGATGAGTTCAATAAACCATATGTAAAAAATTTGTCTGCCTTTCTGGAGAGAGAGACCCATGGAACTGTTCCGATATATCC[A/G]CCACAACCCTTAATATTTAATGCGTTAAATTCGACTCCATTTGACAGCGTGAAGGTTGTCATCATAGGGCAGGACCCTTATCATGGAC
96244 G A GTCCAGAGCGAGGGATGCATCTATGGCCGTCGACTCGAATAAGGGATTCGTTCAAGCATTCCTATCTCTCCAAACTCGAATTCAACCTTCATCGCATGAA[G/A]CAGCATCAAAAACAAACCAGAAGCCAAAAAGTCAACCTGAGTAGAGCTCCACTTCTCGACCCCGCTAATAGAGGAGTTGCCGAGGA
96244 CA C GCGAGGGATGCATCTATGGCCGTCGACTCGAATAAGGGATTCGTTCAAGCATTCCTATCTCTCCAAACTCGAATTCAACCTTCATCGCATGAAGCAGCAT[CA/C]AAAAACAAACCAGAAGCCAAAAAGTCAACCTGAGTAGAGCTCCACTTCTCGACCCCGCTAATAGAGGAGTTGCCGAGGAAGATGA
96244 A G CAAACTCGAATTCAACCTTCATCGCATGAAGCAGCATCAAAAACAAACCAGAAGCCAAAAAGTCAACCTGAGTAGAGCTCCACTTCTCGACCCCGCTAAT[A/G]GAGGAGTTGCCGAGGAAGATGATGGAGGTAATAAAAAGCATGGGGCTTGGTGCTTGGAAGCCATACGAGTTGCGGCGAAAGACA
96244 GAT G TGGTGCTTGGAAGCCATACGAGTTGCGGCGAAAGACATGCTTTTTCTCGTCACCTGCTGCTATTGCTGTGGAGCCTGCTGTAATGGAGAGGAAGATCAAT[GAT/G]ATATTTAAGTGGAGACGGAGCTTCTTGCAGATGAATCTCACTGCAGCTGTATCTCTGATGTGTCAAGTAGGATTATTCAATATAT
96244 TA T ATTTAAGTGGAGACGGAGCTTCTTGCAGATGAATCTCACTGCAGCTGTATCTCTGATGTGTCAAGTAGGATTATTCAATATATGTGTCCTCTTGTTTTTT[TA/T]AATTGTTGTGATCAAACTTATAATCGGTTCATCCTCTTAAATGTGAAAAATCACCATTTAGACATCTTGAAAATCGTTGTATTCATGTTC
96252 AT A TTCTCTGTCGTCTTCTTCGGCACGCCATGAGATGCTACCGCACTAAACTGTGATGAACTGGATGTTTGAGTTTTTGTGCTTTCCACAAACTCTGAGCTCT[AT/A]TTTTTTTTACCTGGCCAATATGTCAAAATGCTCATGAAAGGTTCGTATGGAAGCTTCAATGGTGACTGCTATGGTCTTGTGCCACAGCA
96266 G C CGATCGACTCTGTCGAACACGGACGCGTTGTCTGCTCGCTTGCTGTCCCTCCCTGCCTTCGCAATGATAGGAATTACCTGCATGGAGGTGTGATTGCAAC[G/C]TATGTGGATTTGGTTGGGTCTGCTGTGTTCATTGCTTCTGGGTATCCAACAAGCGGAGTCTCTTTGGAGCTCACTGTTTCTCATTTTG
96266 G A ACGGACGCGTTGTCTGCTCGCTTGCTGTCCCTCCCTGCCTTCGCAATGATAGGAATTACCTGCATGGAGGTGTGATTGCAACGTATGTGGATTTGGTTGG[G/A]TCTGCTGTGTTCATTGCTTCTGGGTATCCAACAAGCGGAGTCTCTTTGGAGCTCACTGTTTCTCATTTTGATGCTGCTTTTGTCAGTG
96276 G A CCACGCCCATCATGTGGAGGTACTCCAGTGCCAATATAGTTTCCACTATGTAGAATTTTGCAGAAGAAACGCTGAAGCGCTTGCCAGGCTGCCTTTGCCT[G/A]GCAACATGTAGATCGCCTCCAGAGCAGAACTCCATCACCAAACAAGAATAGTGAGAAGCGTCGAAATCAGCATACAAAGTAGGCAA
96276 A G CCTCAAAATCTCCTTCTCAGTCTCAGCTCTCTGTAGCTTCTTCTTGAATGCTAGTGCCTCTCTATCCACCACCTTCATTGCATAGAGAAGTTTCGGAGAG[A/G]TTGATGGATGTCTGTTGATGTTTCGAAGCGAGCAAAGGTACACATTACCAAGGTCTCCTCCACCAAGCCTGCGTAGAATACAAAAATGG
96276 A T TATCCACCACCTTCATTGCATAGAGAAGTTTCGGAGAGATTGATGGATGTCTGTTGATGTTTCGAAGCGAGCAAAGGTACACATTACCAAGGTCTCCTCC[A/T]CCAAGCCTGCGTAGAATACAAAAATGGTCTAGTCTGATTTGGCCTGAAGAATAAGCACGAATGGAACTGATCGCTTCCCACTCCGTC
96282 T C ACTTAGCAACAAAAGCGACATCCATCAGCGGCCCAGATCGGTACCTCACAACCGGAACAGGCACCCCTTCTTTGTTAAATTCATCCAAGCACGCCTGCAC[T/C]GGAGCAGTCATGTAGGCATCCAAGGCATCCGCCGTCTTCTTATATTCCTTCGCCACCGACGCCTCCTTTGCCTCGCCCAGCCTAGCCT
96282 C G CAGGCACCCCTTCTTTGTTAAATTCATCCAAGCACGCCTGCACTGGAGCAGTCATGTAGGCATCCAAGGCATCCGCCGTCTTCTTATATTCCTTCGCCAC[C/G]GACGCCTCCTTTGCCTCGCCCAGCCTAGCCTCCCCCTCCCCGTAGTACAATGCACATTTATCAATCACGTTATCCACCGCCAACCCGTTC
96282 TC T GCACGCCTGCACTGGAGCAGTCATGTAGGCATCCAAGGCATCCGCCGTCTTCTTATATTCCTTCGCCACCGACGCCTCCTTTGCCTCGCCCAGCCTAGCC[TC/T]CCCCCTCCCCGTAGTACAATGCACATTTATCAATCACGTTATCCACCGCCAACCCGTTCCCTTTCTTCTTCGCTTCTTCATCGATCGAAG
96282 T C CCACCGCCAACCCGTTCCCTTTCTTCTTCGCTTCTTCATCGATCGAAGACTGCAGCCTTCCCGCGCTGGCGCTCAGAATGTCGACCGCAATGGTTGCGAG[T/C]TCGCTGTATTTTGCATCAGCGCTCCTCGGATCTTGCGCAAAGACCTGTTGACACTGAGCGTTGGTTATGAACCCTCCTTCTAGTTTGTG
96282 T C CTTCATCGATCGAAGACTGCAGCCTTCCCGCGCTGGCGCTCAGAATGTCGACCGCAATGGTTGCGAGTTCGCTGTATTTTGCATCAGCGCTCCTCGGATC[T/C]TGCGCAAAGACCTGTTGACACTGAGCGTTGGTTATGAACCCTCCTTCTAGTTTGTGGCACAGTGCTTTCAGGCCTTTGGCGTCTACAC
96282 A G CGCTCCTCGGATCTTGCGCAAAGACCTGTTGACACTGAGCGTTGGTTATGAACCCTCCTTCTAGTTTGTGGCACAGTGCTTTCAGGCCTTTGGCGTCTAC[A/G]CTGACGCTGTGGAAACTTTGTGAGAGGAAGAGGAGTGTGATGATGGCTAGAATCATATTGCTCAGTTTCATTTTTTT
96284 G A AGTTCGATATCGATGCCAATGGTATTTTATCTGTCACTGCTGTGGATAAGGGCACCGGAAAGAAGCAAGACATTACTATCACTGGTGCTAGCACTTTACC[G/A]AGTGACGAGGTTGATAGAATGGTGAAGGAAGCAGAGAAATTTGCAAAGGAAGACAAAGAGAAAAGAGAAGCGATAGACACAAAG
96284 T G GGAGAAACAGCTGAAAGAGCTCGGTGAGAAAATACCAAGTGCCGTAAAAGAGAAAGTGGAATCGAAGCTGAGCGAACTGAAAGACGCAATGTCGAGTGGC[T/G]CGACACAAAGAATGAAAGACGCAATGGCAGCATTGAATCAAGAGATGATGCAGGTTGGACAGTCCATTTACAGTCAGCCAGG
96284 A G AAGACGCAATGTCGAGTGGCTCGACACAAAGAATGAAAGACGCAATGGCAGCATTGAATCAAGAGATGATGCAGGTTGGACAGTCCATTTACAGTCAGCC[A/G]GGTGCTGCACCTGGTGCTGGTCCCGCTGGCCCGGCTGCTGGAGATAGCTCAGGCAACACCGGGGCTCCCGAAGGTGGTGATGT
96286 G A TGCTCCTCTCGATCCCTGTTCTTTTCTTCGTCGCCCCTCGCATTTTGCCGCCAAAAACCCTTCCGCCGATTCCCGATCCCGACGAAATAGACGATCTCGC[G/A]CTTTTCCGCCGCGCCACGTTGGCGTCCACCTCTGCCGTCCGTCGCCGTCAGCCACCGCCGCCGTCTCAACCCAAAATCGCCTTCCTTTTC
96290 T C CTTGTGGAACAAATCATACAGTTGCCGTCGATTCCAGTGGTTCTGTCTACACGTGGGGATTTGGTGGATATGGAAGACTGGGTCATAGGGAACAAAAAGA[T/C]GAGTGGACTCCTCGCCAGGTTGAAGTGTTTCAAAGGAATAACCTTCTACCGCCAAATGCTGTAGTTTCAGCTGGTTCAGTTAATTC
96298 A G CAAAATCGTAAAAATGTGAGATTTTGGCAGCAATATCATAGCTTTTCAGCAATCATCTCATCGCCAGAGAAGGCAAACATCATCTTATTTTTGCATTAAA[A/G]AACTGAAATAGCTTATGCTGTAAAAAGAGAATTGTGGGGATTGCAGCAGGCCCTCTTAAATCAGACAAAGTTTCAATCTTGCAGCATA
96298 T C CAAACATCATCTTATTTTTGCATTAAAAAACTGAAATAGCTTATGCTGTAAAAAGAGAATTGTGGGGATTGCAGCAGGCCCTCTTAAATCAGACAAAGTT[T/C]CAATCTTGCAGCATATATCACCTTTGTTTTAGAAAAGATGTAAGAATCGTGACTGCTTTAGCAAAATTAAAAATAAACAAAGATTATAA
96302 A T GAAATACATACACATACCTACTAAAATACATGGATTCCATCATCCCTTTTATTTTACAGAGTGGCAATGGCATCAACCATGATTTTGACTCCCAAAGGCA[A/T]TGCAGCCGCCTGGTAAGTCGTTCGTGCCGGGCACGGCGACGGAGTATATTTAGCATAGATCTTGTTCACTCTAGCAAAGTCCTTGATG
96302 T C AAATACATACACATACCTACTAAAATACATGGATTCCATCATCCCTTTTATTTTACAGAGTGGCAATGGCATCAACCATGATTTTGACTCCCAAAGGCAA[T/C]GCAGCCGCCTGGTAAGTCGTTCGTGCCGGGCACGGCGACGGAGTATATTTAGCATAGATCTTGTTCACTCTAGCAAAGTCCTTGATGT
96302 A T TACATACACATACCTACTAAAATACATGGATTCCATCATCCCTTTTATTTTACAGAGTGGCAATGGCATCAACCATGATTTTGACTCCCAAAGGCAATGC[A/T]GCCGCCTGGTAAGTCGTTCGTGCCGGGCACGGCGACGGAGTATATTTAGCATAGATCTTGTTCACTCTAGCAAAGTCCTTGATGTCAG
96302 G C AATGCAGCCGCCTGGTAAGTCGTTCGTGCCGGGCACGGCGACGGAGTATATTTAGCATAGATCTTGTTCACTCTAGCAAAGTCCTTGATGTCAGCCAACA[G/C]AATGGTAGTCTTAACAACTGAAGAATAACAGCCACCGGCTGCTTTCAGTATCTCCCCTATGTTCTTCATCACCTGCTCAGCTTGTTCT
96302 C T ACCTGCTCAGCTTGTTCTTCCACGTCCTCAGAAATCACCTTTCCTGTCTCGGGGCAGAGGCCGAGAACACCTGACACGAATACCATGTTGTTAACTTTGA[C/T]AGCCTGAGAATATGGTCCGACTGCTTGAGGTGCTTTATCTGTTTTAATTGCTTCTTTCCCAACAATGGAGAAGGTGGAAGATCGAGCA
96302 C A AGAACACCTGACACGAATACCATGTTGTTAACTTTGACAGCCTGAGAATATGGTCCGACTGCTTGAGGTGCTTTATCTGTTTTAATTGCTTCTTTCCCAA[C/A]AATGGAGAAGGTGGAAGATCGAGCAGCACAAGTGCAGGCTAACGCGGCGAAGAAGATTGGGAGGACAAGTGCTGCCATTTTGGATG
96304 TA T AACACAGATACATGATTCTTGTTAGCAACAGCCAGCTAAACAAAGCCAGTAATCGACAATAGATGCATTAATTAGTTGTTAAAATAATACAAGTTTTTAG[TA/T]AAAAAAACCGACCACCATATCGCTTAACTGCATCACGACTATCGATTGCTTTCCCACCATTGTTGCCGTGGCTAAGCTTTTCCTCAGG
96322 G GT ACGGATGTCGACTTCGATGAAGAAGACATATGGACGATGTCTTCTGAGCACAGCTGGACCAAGCTCAAGTCGAACCGGGTCGACCCGGCCCGTATGAAGC[G/GT]CGCCGTGGAGGGCTTTCGATGACGTTTGACGAGGAGAAGGGTATGACCGTGGCTAGGCGGGGACGCGATGGTCCGACAAAG
96326 G A TGCTACAGAAACTGAGCTCGAGGACCGTAAACTGCGTATAGAGGATGCTAAAAATGCCACTTTTGCTGCTATTGAGGAAGGCATTGTACCTGGGGGTGGC[G/A]CTGCCTATGTTCATCTTTCAAGTTGTGTTCCTGGTATCAAGGATAAGTTGGATGATGCTGATGAACGACTTGGTGCTGATATTATTC
96326 T G GGCTCCTGCATCCCTGATAGCACGCAACGCCGGAGTAGAAGGGGAGGTAATAGTGGAGAAGGTGAAAGAAAGTCCCTGGGAATTTGGATACAACGCGATG[T/G]ACGACAAGTATGAGAACCTTCTAGAAGCAGGAGTCATAGACCCTGCAAAAGTAACAAGATGCGCCCTTCAGAACGCAGCTTC
96332 T A AATTGTGTCATCGGGTGTGCATTAATAGGAAGAGCGTCGATTGCTTTATAAACATAATCTGGAACAGCTGAACGACTTTGCAATTCTGTGGACAAAGCAC[T/A]TACTTGGTTTTTGCTTGGTACCTTCCCGGTCAAAAGAAGCCACAGAAGACCTTCAGGAAGTGGCTCTTCTCCACCAGGAGCAGCTGG
96332 A G CAAAGCACTTACTTGGTTTTTGCTTGGTACCTTCCCGGTCAAAAGAAGCCACAGAAGACCTTCAGGAAGTGGCTCTTCTCCACCAGGAGCAGCTGGTAAT[A/G]ATTTCTGACATTCAGGTATGGAATGACCTCGAAAACGGATACCCTCGTCTGGATCAAGTAATGATGTTTCCCATAGCAATCCGGTCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
96368 A G TGCCGGCGGCGAGGAGGAGGGAGAGGATGATGAGTGCTGCCGGTAATGGGGTCGGCATGGTTGGTCCGAATCCCGGTGTGAAGAAGATGAGGGTTTGCAC[A/G]CAGCAGACCGCGAACTCAAATAATTCGAATTCCAATTGTACAAGGAGTTTTGATACTGCAGGTTCAAGCCATCAAGATGCAAG
96376 A G GTAACATACCTACCAGCACAGTACATGCCAGCGCCAACCACCCCCATGCCAACAGGCCCGGCGGCCAGGATCTTCAAAGAACTGGACACCATGGCAGCCA[A/G]AGGCAGGCCCACGACCGAGGAGGCCTGCCCACTCCTCCCTATCCCTTGCTCATCCTTGCACAGCAGTCCCGTCTTACAATATATGG
96376 C CG GCGGTGGATGACCTGGTCGGGTGGGTCAGAATGGGCTATGGTGCAGGTGCCACCTCTGAGCTTGGACAGGAAGAGGGAAAGGGGCACGCCGTACTCAAAC[C/CG]GGTACAGGGAGCCAGAGCCTAGGAAGCACGTTAGGCAGGACAGGATCACATGGCTGTTTGGGGTCTGGAAGCCGCAGTCC
96382 G A CTCCTCGTCCACGACGTAGTCGAAGAAGCAGAAGCAGAAGCTTCAGCCGTAGTCGTAGCTACAGCCGATCAAGATCCCCTGCGCCAAGAAGAAGAGAGCG[G/A]AGCATAGACAGGGATGACAGGCGGTCAAGAAGCCCCCTGCCGAAGTCGAGAAAATACAGAAGCCCATCACCTGATGGCAGCAG
96388 AT A ATGATGTGGTGGGTTTCTGAGGTTAGTGAGCAGGCTACAACGAGTACATCAGAATTCGAAGCTAGCTCTAAAACACTGGAGTAGTACTGGTATGAGTTTG[AT/A]TTTTTTGGATCTTGTATAGTAGCTGATTGGACACCCGAATGCTTCAGCTCTAGTGGCAATGGCTGCTCCAATTCGACCTAGTCCGA
96388 C G CTCCAATTCGACCTAGTCCGATGATGCCAACCCTTTTGCCACTGAACTTAGAAGTAAGCTTAAAATCGCCTTTCAACTTCCAAGAACCACTCCTAACATA[C/G]CGATCAGCCTCGCAAATCTTCCTCATAACAGAAAGTGCCAACCCAATCGCCAAATCAGCAACATCGTCGGTCAAAACATCCGGCGTGTT
96390 T A GCATTCAGATTGTCTCATGCAGCCGTGTGTAGGTGGGAGGTTGCTGAAGCGCTGTGGGACTGTAGAGGTTGATTCATTCTTTTATCTGTAATTTTCATAT[T/A]TCGTTTCATATAATTTTTTTTTGGGTATGTTATGTGGTGGTTACATATTTATGTTCGTTCTTTGTAAGAATGACTGACTGGATGCAACCA
96390 AT A CTCATGCAGCCGTGTGTAGGTGGGAGGTTGCTGAAGCGCTGTGGGACTGTAGAGGTTGATTCATTCTTTTATCTGTAATTTTCATATTTCGTTTCATATA[AT/A]TTTTTTTTTGGGTATGTTATGTGGTGGTTACATATTTATGTTCGTTCTTTGTAAGAATGACTGACTGGATGCAACCAAAGAAGTATAG
96390 G GTA TGTGTAGGTGGGAGGTTGCTGAAGCGCTGTGGGACTGTAGAGGTTGATTCATTCTTTTATCTGTAATTTTCATATTTCGTTTCATATAATTTTTTTTTGG[G/GTA]TATGTTATGTGGTGGTTACATATTTATGTTCGTTCTTTGTAAGAATGACTGACTGGATGCAACCAAAGAAGTATAGTTTTCATGGTGT
96394 CA C CCTGCTACATGCATTTTACAAACTAAGTCATAACAAAAACAACCTCGCAGTTAACTTGCATGTCATTACGCTGGGTGCAACTTAGAAAATAGAAATGCAA[CA/C]AAAAATAAACCAGTCTAAAACTTAGGCCAATTAGCCACAACAAGCTATCAAGACAGTCTCACTTCAAACAAACAAAATATTCACCGA
96404 A G GTTTGTACGGCCCCCTAGTATTGAAAACACGTCTTCCACCCAATCACGGAACGCTTCTTCCTCGTTCGTCTCTGAACTTACTTGTTCTTTGTCCGAGAAC[A/G]TCTTTGCAGCCATCATTCTCATTATGTCATTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTG
96404 A G CGTCTTCCACCCAATCACGGAACGCTTCTTCCTCGTTCGTCTCTGAACTTACTTGTTCTTTGTCCGAGAACATCTTTGCAGCCATCATTCTCATTATGTC[A/G]TTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAG
96404 C G CTTCTTCCTCGTTCGTCTCTGAACTTACTTGTTCTTTGTCCGAGAACATCTTTGCAGCCATCATTCTCATTATGTCATTCAGTATTATCGTCAAAATTTT[C/G]GACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACAT
96404 T C CTGAACTTACTTGTTCTTTGTCCGAGAACATCTTTGCAGCCATCATTCTCATTATGTCATTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTT[T/C]GTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGA
96404 C G TCTTTGTCCGAGAACATCTTTGCAGCCATCATTCTCATTATGTCATTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCAT[C/G]GACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCA
96404 G A TGTCCGAGAACATCTTTGCAGCCATCATTCTCATTATGTCATTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGAC[G/A]TTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAG
96404 C T ATTATGTCATTCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAG[C/T]CTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGC
96404 T A TCAGTATTATCGTCAAAATTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTC[T/A]GCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCC
96404 A G TTTTCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGC[A/G]GACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCC
96404 C T TCGACTTCATCTCAACCTTTGTAAACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGA[C/T]ACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAA
96404 A G ACTCCCCATCGACGTTGGACTCCTGAAAGAGTGTTCGAACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAA[A/G]AGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTC
96404 T C AACCAAAGCCTGCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAG[T/C]GATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATAT
96404 G A GCAATTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATA[G/A]TTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAG
96404 G C TTCTGCAGTACGAACATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTG[G/C]TTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAG
96404 G A CATCGGCAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAAC[G/A]GTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGG
96404 A G CAGACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAA[A/G]TCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGG
96404 C T GACACATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAAT[C/T]GTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCC
96404 T C CATTAAGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTA[T/C]GAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTT
96404 A T AGAGAATGAGGGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAA[A/T]TTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCT
96404 C T GGGCCAAAAGCTCGGAAGAAGCAAGCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAG[C/T]GAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAAC
96404 G A GCTTTCTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGC[G/A]AATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGA
96404 T C CTCATATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATA[T/C]AGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTA
96404 G A TATTGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGG[G/A]CCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAG
96404 A G TGCGCCAGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCC[A/G]TGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTC
96404 A G AGTGATCCCCATAGTTGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGA[A/G]AGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTT
96404 G A TGGTTGTTCCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTC[G/A]GCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGT
96404 C T CCCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGG[C/T]CCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTG
96404 C T CCAAAACGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGC[C/T]CCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGT
96404 G A CGGTGAAATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTT[G/A]GCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCA
96404 T C AATCGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTAC[T/C]ACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCT
96404 T C CGTATGAAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTAC[T/C]AGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTT
96404 T C AAAATTCCTTAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAAC[T/C]TTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGC
96404 G C TAAGCGAAGGAAACTGAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTT[G/C]CCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGAT
96404 G A GAGGACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGA[G/A]AGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTA
96404 T G GACGGTTAGCGAATATAGGGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAG[T/G]ATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGG
96404 A G GGCCATGAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATC[A/G]TGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGG
96404 T A GAGAAAGAAGACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCAT[T/A]CGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGC
96404 G T GACTTTCTTCGGCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTAC[G/T]GTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTG
96404 G A GCCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCA[G/A]GGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATT
96404 G A CCAAGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAG[G/A]GGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATTTA
96404 C T AGGCCCCTTTGGCTACTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGG[C/T]TCTTTGATGCTTAAAAGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATTTAGAG
96404 A G CTACTAGAACTTTGCGGTTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAA[A/G]AGATGAAGATGGCCTATTATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATTTAGAGAAGACTGCTACTAC
96404 T C TTGCCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTA[T/C]TATTGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATTTAGAGAAGACTGCTACTACTAAG
96404 T C CCAAAACGAAGGGAGAGTATAGGTCCAAGTTTATCATGCATTCGGTTTACGGTGTGGTGCAGGGGCTCTTTGATGCTTAAAAGATGAAGATGGCCTATTA[T/C]TGGAAGAGCTAATGGACTTGGCGGGCTTTTGCCTTTGTTCAAGAATTTAGAGAAGACTGCTACTACTAAG
96422 G T ATGACCCGCTTTCAGAAAACATCGCTAAGCACTGGAAGGCAAATGAAGCCGAGGCTGTCGAAACCGCAAAGGAGTGGACACGCCTATATGCCAGTGGTGC[G/T]TGAGTACATTGAGGCCAATATATGGGGAAAACAATAACAAGTCTGTTATGTGCATCCTGCTTATTATTCTATAAATGAATGTGAAA
96430 T C GCGATGCACGACTCATGGATTTCATGATGCTCGACCTGAGATGGTACGTGCGAGCTGGAAGAGATGGCACTATCTCTCAGGAATGCTCGAGTAGGTTATG[T/C]GCTCGACCACTCAAGGCTGCTCGACCTCTTCATCTTGTTTTGCTCGACCGAGGTATGTTAAAGTGGTGCACGTCAACTTCATGTGAG
96436 T C CAATTTAAAGCAGTTATTTATACAACAAATCATAAATGTTTGAATCAAATGATGCCCATTCATCATCAGCTGAAAAAATTCATTTATGCACCAACTATCA[T/C]CTGAACACCATCTCGGAACTCGCCATTACACCAGTTCCAAACAGAGCCAATCTATCACTATAAACATCCACAAACCCAAACGCATTGGTA
96436 T C ATCCTTCAGCACAGCATCCAGCCACTGCAGCTGCTCTTCCCCCACCCCTCCGTTGTACATCAAAAACCTGGTGTCATTACCCTCCATCCCTTCGGGGCTG[T/C]TCTTGTTTTCATTCGGGTTCCTCTCTTTCAGCAGCCTTTCAGCTCTGGCTCTCTTTGGATGGTCATCTGGCCATGCGAGAGCGCTAATGC
96454 GA G GCATTCAGGCGCACAAGCATGGATCGCTCCGCACAAGGATCGCTCACCAGTGCATGAGGCTCTGCTATTTGAAGCAAAAAGACTAGAGAGAAAGAGAACG[GA/G]AGGAGTGTTTCGATCTCTTGTTCCGCTTCAATCTTCAACATCACATTCCTCTACTTGAAGAAAATGTCTTTGTTTCCAATCATTAG
96454 A G GGCAGACCGTTCTTCTACACAACCCGTTCTTCTACACAACGTCTCATCATTATTTTGCCATAGAAGCACCAAAGATCTCTATTTCAAATACCTAACAAGG[A/G]ACAACTTTTTATAAATAAGTGAACAAAATTTGTGAGTAGAGATTTATGAATCGGTGAGAAGCAAGAAGATAGAGGTTTACATTTATTTC
96462 A G CAAAATTCAATTCAAGGAAAGAAGATGTTGTTGGAGAGACTTATCTGGGGATCCAAATATTCAGGTTTTATTTTAAATGCACAAAATGCTCGGCAGAGTT[A/G]ACTATAAAGACAGATCCTCAAAATTCTGATTATGTTGTAGAATCGGGAGCAGCCCGGAATTATGAGCCTTGGCGGGCAACCGATGA
96462 A G TCAATTCAAGGAAAGAAGATGTTGTTGGAGAGACTTATCTGGGGATCCAAATATTCAGGTTTTATTTTAAATGCACAAAATGCTCGGCAGAGTTAACTAT[A/G]AAGACAGATCCTCAAAATTCTGATTATGTTGTAGAATCGGGAGCAGCCCGGAATTATGAGCCTTGGCGGGCAACCGATGAGGCAGT
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
96464 C T ACGGTTAGCCTTGTCTATGAGGATTGTTGCTGGTTGTTTTCGTGTCTTCCGAGTGGCACCTCGATCTGGTTCTTGGTGTTGTATGTGTTGTTCTTCTCCT[C/T]ATAGTAAGAGGAAAGCTTTATAGTGTTACTCAGCTTTGTGCAGTTTGTGCCATGTGTGAGTGCATTAACGAGATGCTTTGCAAGCTATT
96466 T A GGCATTTAAGGTTCGAGCGTAGTGGGTTTTCTGGAGCTGGAGGATCGCGACTGATGGCGGCGACTGGGACACTTTGTCTCTGGGCGACAGTCAGGTGGGT[T/A]GAGGCGCTGCTCTCGAAGACGTCAGATGATCGTCCAGCAATGGAAATTGAGGTGCGGTGGTGGCTTTGTTAGCTTGAACGAGA
96470 A G GTCCGGCAAGCATCCTAGCAATCTGTATGATCTCAAGATCGATGGATGTACTCTGCTCAAATGGATGCCATAGAATCTGATCCCTATACATCCTCAGCTC[A/G]ATCTGGTTATGGGCAACGGGAAACACATGGCGTGACTCATTATCTCTGGGCCCCCGGTTGTCCGCAGTCCAAAAGCATATACGGGGG
96470 T C TGGTTATGGGCAACGGGAAACACATGGCGTGACTCATTATCTCTGGGCCCCCGGTTGTCCGCAGTCCAAAAGCATATACGGGGGAAAAAGGTCGATGGGT[T/C]AGCAATACGGGTGATAAAATGAAAGTTCCTAGAGTACTCAAAGTACCAATACTGTAACAACTCCCAGAATCCAAATAAAGAAACC
96470 A T GGTTATGGGCAACGGGAAACACATGGCGTGACTCATTATCTCTGGGCCCCCGGTTGTCCGCAGTCCAAAAGCATATACGGGGGAAAAAGGTCGATGGGTT[A/T]GCAATACGGGTGATAAAATGAAAGTTCCTAGAGTACTCAAAGTACCAATACTGTAACAACTCCCAGAATCCAAATAAAGAAACCT
96470 C T TCCAAAAGCATATACGGGGGAAAAAGGTCGATGGGTTAGCAATACGGGTGATAAAATGAAAGTTCCTAGAGTACTCAAAGTACCAATACTGTAACAACTC[C/T]CAGAATCCAAATAAAGAAACCTGAGAATCAGTGATGGTGCACTGCATGTCGAGACATCTGTATAGGTATGCAAGGATAGGTGTGC
96470 G A CGGGTGATAAAATGAAAGTTCCTAGAGTACTCAAAGTACCAATACTGTAACAACTCCCAGAATCCAAATAAAGAAACCTGAGAATCAGTGATGGTGCACT[G/A]CATGTCGAGACATCTGTATAGGTATGCAAGGATAGGTGTGCCCCAATCATATAAAATCGCCCCATCGGCATTTATCTCAGCCGCGA
96470 C A CAGAGTAGTGCTCGAGTATCCTGTCCATAGCCGCACGGATCGCGCTCACTCTAATAGCGCCTTCTTCCTGATACGACGTAGCAGAAACATCCAAATGAGG[C/A]AGTAGATCATGAACAAGTGCACGATCACGCCATCGACCATCGTCACCAGTAGGCCAACAGTG
96508 T TC CGCCACCGTCCTCTGCCGCCTGGAATCCCTCCTCCAACAACAAACCTCCGACCCCACCGCCTCCATCTCCGACTTCTTCGACCTCGCCGCCGGCTCCGGC[T/TC]CCGGTGGCCTCCTCTCCGCCCTCCTTTTCACCCGCAACCCCCACGGCCGCCCTCTCTTCACCGCCCACCAAGCCCTTAGCTTCCTCGCC
96508 C CT ATCCCTCCTCCAACAACAAACCTCCGACCCCACCGCCTCCATCTCCGACTTCTTCGACCTCGCCGCCGGCTCCGGCTCCGGTGGCCTCCTCTCCGCCCTC[C/CT]TTTTCACCCGCAACCCCCACGGCCGCCCTCTCTTCACCGCCCACCAAGCCCTTAGCTTCCTCGCCACCTCCAGCAAAAACACCGTCCTC
96508 C T TCTCCGACCTCACCCTCTGCGACGCCATCAAGCCCCTCCTCATCTCCTGCTTCGACGTAATCACCTCATCCCCCTTCATGTTCTCTCGCTCAGACGCCGT[C/T]GAGTCCGAAACCTACGACTTCCACCTCCGCAACGTCTGCAAAGCCGCCACCAGCAAGCACGCCTTCCCAACCGCCTCCATCAACAAAACC
96524 G T ATACCAGCGTGACGGTCACTGTTGTGGGCGAGAGACGTGCGGCGGCGCCTGATTGCTTGCCCGTTTGGCAGAGTGAGTTGGCCGATACTTCGGGGAAATC[G/T]CTTCCCGGTCTGGTTCTTGCTATTTGAGCTTCTGTTACTTCAGTATGATATATGATAATAAGTAAATAAGTGCTTGCTTGTCCAGTG
96544 T G CCAAATCGTAGCTCGCATCCTGATTAAGGCTCTCATGGCAATGCCTGCACAAGATTTTAGCCTATGCCTATTCTTAATCCCAGAGCAAGTGCAACTGCAA[T/G]AGCAGTTCAAAACTCTGATTATCCTCTCTCACTATCTCGAGACAGCAAAATTTCGGCAATTTTGGGAAGAAGTTTCAAAAAATCGCAGC
96544 A G CTGATTATCCTCTCTCACTATCTCGAGACAGCAAAATTTCGGCAATTTTGGGAAGAAGTTTCAAAAAATCGCAGCATACTTGATGTTGTTCCAGGTTTCG[A/G]CCAAGCAATTCAGCGTTATGCAGTACACGTGCTTTCGTTGACATATCAGAAAGTGCCCAGATCCGTGCTTGCCGAGGCTGTTAATATA
96546 CA C TTCTTCAAGCTAACAAAAGGATCAACATCATAAATCTCGACACTTCCATCACCACCACCTGTGATGAGATGCCTTGGAACCGTCGGAGCAGCCGGAGATG[CA/C]AAAAAAAGAAAGAACATTAACAGGATTCGAAACGAGAATAGACCCGATCTCACAAGAAGTTGACAGATCGTAAAGCTTAATGGAG
96552 G A GACACCGAGTCCGGTCCGGAGTGACGGCGACAACGATCTGGATGATTTTATTGAAGATGATGATGAGGAGGAGCAAGAAGATTTTGAGAAGACGGGGAAG[G/A]GCTATGGGATGGAAAAAGAAGATTTTGGGAAGACAGGGAAGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGG
96552 A G GTCCGGAGTGACGGCGACAACGATCTGGATGATTTTATTGAAGATGATGATGAGGAGGAGCAAGAAGATTTTGAGAAGACGGGGAAGGGCTATGGGATGG[A/G]AAAAGAAGATTTTGGGAAGACAGGGAAGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGGGTGTAAAGAAAGT
AAAAAGAAGATTCTGGGAAGACAGGGAAGAGCTATGGGATGGG
96552 A GTCCGGAGTGACGGCGACAACGATCTGGATGATTTTATTGAAGATGATGATGAGGAGGAGCAAGAAGATTTTGAGAAGACGGGGAAGGGCTATGGGATGG[A/AAAAAGAAGATTCTGGGAAGACAGGGAAGAGCTATGGGATGGG]AAAAGAAGATTTTGGGAAGACAGGGAAGGGCTACGGAA
96552 GA G AGACGGGGAAGGGCTATGGGATGGAAAAAGAAGATTTTGGGAAGACAGGGAAGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGGGTGTAAA[GA/G]AAAGTTAATTTGAAAAAGAGGAATAGAGAGGAGAGAGAAATAGGGGTGGAAGGGAAGGAGAGCCACAGAACTGGTGAT
96552 AT A AAGGGCTATGGGATGGAAAAAGAAGATTTTGGGAAGACAGGGAAGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGGGTGTAAAGAAAGTTA[AT/A]TTTGAAAAAGAGGAATAGAGAGGAGAGAGAAATAGGGGTGGAAGGGAAGGAGAGCCACAGAACTGGTGATAAGGAAGAG
96552 G GA TGGGAAGACAGGGAAGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGGGTGTAAAGAAAGTTAATTTGAAAAAGAGGAATAGAGAGGAGAGA[G/GA]AAATAGGGGTGGAAGGGAAGGAGAGCCACAGAACTGGTGATAAGGAAGAGATGAAAGAGTTAGTGGGATACCGATTGCT
96552 A G AGGGCTACGGAATGGGAAAAGAAGGAAGTTTGAACTCCAAGGGTGTAAAGAAAGTTAATTTGAAAAAGAGGAATAGAGAGGAGAGAGAAATAGGGGTGGA[A/G]GGGAAGGAGAGCCACAGAACTGGTGATAAGGAAGAGATGAAAGAGTTAGTGGGATACCGATTGCTGGTGGTGACTCGGAG
96552 TA T AAGAAAGTTAATTTGAAAAAGAGGAATAGAGAGGAGAGAGAAATAGGGGTGGAAGGGAAGGAGAGCCACAGAACTGGTGATAAGGAAGAGATGAAAGAGT[TA/T]AGTGGGATACCGATTGCTGGTGGTGACTCGGAGGATGATCAAGAGGGTATGAGGACTATGGATGATGACAATTTTATTGA
96552 CG C TTTGAAAAAGAGGAATAGAGAGGAGAGAGAAATAGGGGTGGAAGGGAAGGAGAGCCACAGAACTGGTGATAAGGAAGAGATGAAAGAGTTAGTGGGATAC[CG/C]GATTGCTGGTGGTGACTCGGAGGATGATCAAGAGGGTATGAGGACTATGGATGATGACAATTTTATTGATGATACGGGCG
96558 CA C AGCACTAAGAGCATTCTTCATGATTAAACACCATAGGGAAGACTAAATCAGAAGTTACCTTGGAAGCTAAATTTGGAAAGATCTAATCATCCCCATAAGC[CA/C]AAAAAACGATATTTTTCCTCATATTCGCCATTGAAAAACAAATCGGCTGCAAACCATTTGGGATATCGTACCAAATCTCCTTCCACAA
96558 AT A CATTCTTCATGATTAAACACCATAGGGAAGACTAAATCAGAAGTTACCTTGGAAGCTAAATTTGGAAAGATCTAATCATCCCCATAAGCCAAAAAACGAT[AT/A]TTTTTCCTCATATTCGCCATTGAAAAACAAATCGGCTGCAAACCATTTGGGATATCGTACCAAATCTCCTTCCACAAACCTCATAAAC
96560 T C GGAGTACACTCTGTATGAGGCTCCTCCCACGAGTTCCCATGACAACAGCTGCTGGTTTGATCTTGTCGGCCTCCTTGCATATTGCTTTTCCAGCATGTCC[T/C]TCCACAATCCGAGCAACTGTTCTCACCAAGCACACTTGGAAAGCCTCAACGGAAAGCTTCTCCATCAACTCCTTACTCTTTTCATACACA
96560 G A AGACGGCGTGGACGAGATGAATGGTGTCAGCAAGGCGGCAGAGGTGAGCAAGAGCCCAATCGAACGCGTGTTTGCTGTTAGGACCGTGATCCACAGCGAT[G/A]ATAATGACGCGGCCCCGGCGACGCTCAACCGTTTCTCGTTCGAGTTCTGGTTCGGGTACTACTGGGATTAGGGAAGGCAAGAT
96560 T C CGAACGCGTGTTTGCTGTTAGGACCGTGATCCACAGCGATGATAATGACGCGGCCCCGGCGACGCTCAACCGTTTCTCGTTCGAGTTCTGGTTCGGGTAC[T/C]ACTGGGATTAGGGAAGGCAAGATCACCTCTCTCCAGCTGTACTCTTCTACATCTTCGTTTAAAGTTTCCATCTTTATTATGCAGGAAC
96582 G GA GCCAGAAACAGATGAAGACAGCTATTAACACACCCCTCGCTGAAACCATATTCAAACGAGCCCTTTTATATTCATCTACATTTGCTCTATATATTAAAAA[G/GA]AAAGAAAAAGGTTGGATCTATGTACTTCTTGATGCTTCAGGGCTCTTTGTTTGATAACGTATATTGCATTCGTCATTGCTATTGTTGCA
96582 G GA AGACAGCTATTAACACACCCCTCGCTGAAACCATATTCAAACGAGCCCTTTTATATTCATCTACATTTGCTCTATATATTAAAAAGAAAGAAAAAGGTTG[G/GA]ATCTATGTACTTCTTGATGCTTCAGGGCTCTTTGTTTGATAACGTATATTGCATTCGTCATTGCTATTGTTGCATATTAAAAAAATCGC
96584 A G TCTTTCAATATCTGAGACACAATAAATGCAATTGTATTACCATTTTGACCCCCGACTTGTGTCATCAATCTTGTTTTTACAACATCCAAAGGTGTAGTAA[A/G]ACTTGCAGATATCGCTCCTGCTAGGGCCCCACAACAGACGCTTTCTATTGGCTCAAGGAAACCCTTCTTGGATTTGGATAATACAAATCC
96602 A G TCAATCTGATGGTTGGGGTGTGATGGTCTCTCACCGTAGTGGTGAAACTGAGAACACTGCGATCGCCGACTTGGTTGTCGCCCTCGGAACGGGTCAGATC[A/G]AGACCGGTGCCCCAGCGAGGAGCGAGCGTGTGGCCAAGTACAATGCCCTCCTAAGGATTGAGGAGGAGGTCGCAGGAAACTCG
96602 T C CCTCGGAACGGGTCAGATCAAGACCGGTGCCCCAGCGAGGAGCGAGCGTGTGGCCAAGTACAATGCCCTCCTAAGGATTGAGGAGGAGGTCGCAGGAAAC[T/C]CGATTTACGCTGGGGACAAGGGCATTTCTGCTGGTCTTACCCCACCTGCCTTGCTCAAGAAATAAGCATCACGTCTGTACTACAA
96608 A G GCCAGGTCAAGATCGCTGACTTCGGCGTGGGTAGGATCCTCGCGTGTACGATAGATCCGTGTAAGTCGAGCGTGGGAACCGTTTCGTACATGAGCCCGGA[A/G]AGGATCAACACGGATTTGAACGACGGGGTGTACGACGGATATGCAGGGGATATATGGAGCTTCGGATTGAGTATGCTTGAGTT
96612 T C GACTTTGAGACCCAACCAAATGTCTTTTGGAAAAGCTGTGATCCAATGCGTCCAATTTTTGATGAATTGTCTGATGAGTTACTTTGCACCTTGGCTGAGC[T/C]TGCATCCTTTGCGTCCTTTGACGGATTCTGTTCGGAGTTTCTAACAAATTCAGGGTCTGATATGCTTCTGTTATGGGTAGATGTTGTGT
96636 A G AGAACCAAAAAGCACCAATCCTAGAAATTACATCTGCACTTGAAAATGCATCTTCGTTTATGATGTATTTAGCATCTCTAATAAAATGGATAATTAGGCT[A/G]ATGAGGGAAGCGTGGCATCAAATTGATGGCACAGGGTTCCTAAAAGGACTTGGCCTGAGCTAAGGTAGGATAGCTGCCAGAGAGGA
96636 G C ACATCTGCACTTGAAAATGCATCTTCGTTTATGATGTATTTAGCATCTCTAATAAAATGGATAATTAGGCTAATGAGGGAAGCGTGGCATCAAATTGATG[G/C]CACAGGGTTCCTAAAAGGACTTGGCCTGAGCTAAGGTAGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGA
96636 T C ATTTAGCATCTCTAATAAAATGGATAATTAGGCTAATGAGGGAAGCGTGGCATCAAATTGATGGCACAGGGTTCCTAAAAGGACTTGGCCTGAGCTAAGG[T/C]AGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGGCGCGAAGAGCAGCCAGCGGAGAGAGTTAA
96636 C T TCTCTAATAAAATGGATAATTAGGCTAATGAGGGAAGCGTGGCATCAAATTGATGGCACAGGGTTCCTAAAAGGACTTGGCCTGAGCTAAGGTAGGATAG[C/T]TGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGGCGCGAAGAGCAGCCAGCGGAGAGAGTTAACTGTGAAG
96636 C T AATTGATGGCACAGGGTTCCTAAAAGGACTTGGCCTGAGCTAAGGTAGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGG[C/T]GCGAAGAGCAGCCAGCGGAGAGAGTTAACTGTGAAGATCAACTTGTACACCCTTTGCCTCTTCATATAACCTGCATGAGCACCA
96636 G A GTTCCTAAAAGGACTTGGCCTGAGCTAAGGTAGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGGCGCGAAGAGCAGCCA[G/A]CGGAGAGAGTTAACTGTGAAGATCAACTTGTACACCCTTTGCCTCTTCATATAACCTGCATGAGCACCAAAAATTAAAGTTCCAG
96636 T C GGACTTGGCCTGAGCTAAGGTAGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGGCGCGAAGAGCAGCCAGCGGAGAGAG[T/C]TAACTGTGAAGATCAACTTGTACACCCTTTGCCTCTTCATATAACCTGCATGAGCACCAAAAATTAAAGTTCCAGTAGGCC
96636 A G CTGAGCTAAGGTAGGATAGCTGCCAGAGAGGAGCGGTTGGGGAAGATTGAGAATCACCGACGTTGGCGCGAAGAGCAGCCAGCGGAGAGAGTTAACTGTG[A/G]AGATCAACTTGTACACCCTTTGCCTCTTCATATAACCTGCATGAGCACCAAAAATTAAAGTTCCAGTAGGCC
96646 G GT TTCTCAATTGTTGTTGCAGGGTTACAATACAATACTATGTTCTTCTTTAATGTGGATAAGATTCAGACAAATGATTCCGTTATAGCTCACTATATCATCC[G/GT]TGTACAGGGAAGTATTCATGTAGGTCAAAACAGTGTTGTTGCATGCATGTGTTTGACCCTTGAAAACTGTAAGTCGATAAGGAAAATC
96646 C CA AATTGTTGTTGCAGGGTTACAATACAATACTATGTTCTTCTTTAATGTGGATAAGATTCAGACAAATGATTCCGTTATAGCTCACTATATCATCCGTGTA[C/CA]AGGGAAGTATTCATGTAGGTCAAAACAGTGTTGTTGCATGCATGTGTTTGACCCTTGAAAACTGTAAGTCGATAAGGAAAATCAAACT
96646 AT A CCATGTTCTGCATACAAGCTTGAATTGTATTAGAGAGATAACAGGCAACCGTAGCAAGATTTGATACACCACATCATCATTTACTGACATTCTGATTTTT[AT/A]TTTTTATTTTTGGCTGCGCTATGCTGTTCTCTAATTCAGCTGTCCCCTGCCTCCCTAGTTGAAGACAGCAGCAGGTGGACTGAAGGAA
96646 C CT CAAGCTTGAATTGTATTAGAGAGATAACAGGCAACCGTAGCAAGATTTGATACACCACATCATCATTTACTGACATTCTGATTTTTATTTTTATTTTTGG[C/CT]TGCGCTATGCTGTTCTCTAATTCAGCTGTCCCCTGCCTCCCTAGTTGAAGACAGCAGCAGGTGGACTGAAGGAAGCCAGGCAGCGATT
96662 T TA CAATTGCAATTGTAGTTGGCCTTGTACTTGGAATTGCCTTCTTGATAGCCTTTGCATCTTATCTTAATAAGCGTGAACGCAACAAGTAAATAACACTGAA[T/TA]AAAAAGTAAAAGCAACAGCAATAGCTTTTATGCACAAGGATAGCGCAGATAAAGGTGTCAATATGTATAATTAATGATGGTCCTTTTG
96678 T G ATTAAGTTGTCATAATACATCAATATCGCGTTACAAAATTGCTTATATGCAATTACCATGAACAGTA[T/G]ATTTATTTGTGACCACGGATGGAATGATAGCATTCTCATGTGAAATTGTTTCAAACTTCTTTTAAATACATACCATATATTTCACCAAAAAGTTAGCAGC
96678 G A ATTAAGTTGTCATAATACATCAATATCGCGTTACAAAATTGCTTATATGCAATTACCATGAACAGTATATTTATTTGTGACCACGGAT[G/A]GAATGATAGCATTCTCATGTGAAATTGTTTCAAACTTCTTTTAAATACATACCATATATTTCACCAAAAAGTTAGCAGCTTTCAATGCATCTTACAAATA
96678 C T TATTTGTGACCACGGATGGAATGATAGCATTCTCATGTGAAATTGTTTCAAACTTCTTTTAAATACATACCATATATTTCACCAAAAAGTTAGCAGCTTT[C/T]AATGCATCTTACAAATAAGGGTAGAAATCCAATTCATATATACATGAACATACCGCAGCAGACCATAAAAGCATATCACAAAACTCGTAT
96678 G A AGTTAGCAGCTTTCAATGCATCTTACAAATAAGGGTAGAAATCCAATTCATATATACATGAACATACCGCAGCAGACCATAAAAGCATATCACAAAACTC[G/A]TATATACTTCCACTGTCCAACAAACAAACAAACCAGCTCAGGAACTCGTGTAGCTCTTTCAATCTGCAATATAGCCATAATGCGTTAAT
96678 A G TGACCTAGCCCAGTAGTGTTCTGTTGACCCCTTCCTTTTCTGGATCGATCTCTACGACTTTCCTTGCCGCCGCCAAGTTGATTTTCATCCTCTTTCTCCG[A/G]CTTTTCAAGCAGGCGTGGATCAGATTTTGCCACATGACCATCGGAATTCCTTTCCGCCGTCTTCCTAGATTTCTCTAATTCAGTATCCTTGT
96692 T G TTTCTGCTCCCAGCTACTTTAATCAGAGACATGCTGCCCTTTTCCAGGCTGGCTGTGCCTCAACATCGCCTCCTCAAACCCTACTAAGCTTCCAGACTGG[T/G]TCTTTAGGGTTGGAAGGTTCCGAGAACGATCCTGCAAGCTTCCGAAAGCGGCGTTGGGAGCAGGAGGTTAGTTTGCAGCAGCAACAA
96692 C T ATCAGAGACATGCTGCCCTTTTCCAGGCTGGCTGTGCCTCAACATCGCCTCCTCAAACCCTACTAAGCTTCCAGACTGGTTCTTTAGGGTTGGAAGGTTC[C/T]GAGAACGATCCTGCAAGCTTCCGAAAGCGGCGTTGGGAGCAGGAGGTTAGTTTGCAGCAGCAACAACAGCAGCAGCAGCAGCA
96700 T G TCCATACCCGAACAAGAACCCAAACCAGGATCAATGCCAAGATCCGGGAGATCTTCATGCCGGCCCTCTCCTCCACGATGACCGAAGGCAAAATCGTGTC[T/G]TGGATCAGGTCGGAAGGCGACAAGCTCTCCAAAGGAGAGAGTGTTGTCGTCGTGGAATCCGACAAAGCCGACATGGATGTCGAG
96700 C T CCCTCTCCTCCACGATGACCGAAGGCAAAATCGTGTCTTGGATCAGGTCGGAAGGCGACAAGCTCTCCAAAGGAGAGAGTGTTGTCGTCGTGGAATCCGA[C/T]AAAGCCGACATGGATGTCGAGACGTTTTACGACGGTTACTTGGCAGCCATCATGGTCGATGAAGGTGGTGTTGCTCCGGTCGGTT
96700 GA G CGGTTCTGCCATTGCTTTGCTGGCCGAATCTGAAGCTGAAATCGAGGAAGCGAAATCTAAGGCTGCTTCTTTGGGTTCTTCGGATAATGTTAGCGAAAAA[GA/G]AAAAACCAACTCAGGAAATAGCTGTTGAATCTTCTTCGTCTCCTGAGAAAGTGGTGACATCTGCAAAACCTGCTGCGGCACCAGC
96710 C T AATTCAGATCGAAATACAATCGCAAGCCGGCTCTCTGTTCGACTTCGTGGTACTTTTTCCATTTC[C/T]CTTCATTTCCCACGATGCGTGTTGCTGCTGTTGGATGGAAATTGCAATCGGGTGGACTACAGTTTCGATGATTCAAGTCTGAAGGGACGTCGCTCGATGG
96712 AG A AGGGCTTGCGTTAACAGCAACGATACAAGTAGAATTAACAAGACGATTAAATGGATCGGATCAATTCAATTAGCGACGGCATGAACGCCCAGGAACTCGG[AG/A]GGCGGACCGAGCCATGACCCCTTTGAACTCCTCGAAACTAATGACGCCATCCCCATCCGCATCCACGACCCGCATCATCTCCGTC
96716 T C TCTTTGCCACCCGTCAAGTTCCCTTAATTTAACCGCTATATAACGTCAGCTTCCGGCAAGCTTTGCTGCAATCATCTTGCAGTTCCATTCATCTCTATTC[T/C]TCAACACCTAACTCTTTTAACTGGCACTTTCCAATGGCTGGAAACCTACAGGCGGTGGTCTATCAGAACGCCGCATCTGCCCTTACTCAAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
96746 A G CATTAAAAGCAGCAATCTTGACGCTTACGTTTCAAGAAATACTAACATTGAAACTTCTCAATGCAAACAAGCACTCTAATAAATGCACAACAATAAACTA[A/G]CACAAATACTACTGCAAACAAACGGTCTAATAAATGTTTACTGTTTAATGCAAGCAGAGCACCAGCTTTTTTGAGCAACAATATAGGTC
96752 A T ACCCGTTAGTACACGACGCCCGTTTCAACGATGAAGTCGACCCTGTAGCAATCCAAAACCCGGTTGTACTGACCCCACCACCTGTGTTTACCCACAAAAC[A/T]AACTACGGGTTCAAACCCGCTTTGGTTCGGGTCGAGGGTTTTGATTGTCTCGACCGCGACCACAGCAGGAGTCGCGGAATCGCGGG
96752 A G ACGCCCGTTTCAACGATGAAGTCGACCCTGTAGCAATCCAAAACCCGGTTGTACTGACCCCACCACCTGTGTTTACCCACAAAACAAACTACGGGTTCAA[A/G]CCCGCTTTGGTTCGGGTCGAGGGTTTTGATTGTCTCGACCGCGACCACAGCAGGAGTCGCGGAATCGCGGGTTTTGCTTAGTAGAA
96766 C T TCATACTCCGATACTCTCACCACTTCAAAAGGCTCACCACCTTCTTCCGCTACATCGAGCTTCTTGCCCTCGCCGCCCTCGCCTTCTGGTCCTCCGCCCA[C/T]CTCCCGACCGCCGCCAAATCCTCCTCCGACCTCATCCGCCACGTCATCATCCCCGTCGTCCTCGGCCCCCGCTTCCTCTTCCTCCTCTCCAA
96766 A G ACCACTTCAAAAGGCTCACCACCTTCTTCCGCTACATCGAGCTTCTTGCCCTCGCCGCCCTCGCCTTCTGGTCCTCCGCCCACCTCCCGACCGCCGCCAA[A/G]TCCTCCTCCGACCTCATCCGCCACGTCATCATCCCCGTCGTCCTCGGCCCCCGCTTCCTCTTCCTCCTCTCCAACGTCATCATCGTCTCCC
96766 C G CCCTCGCCGCCCTCGCCTTCTGGTCCTCCGCCCACCTCCCGACCGCCGCCAAATCCTCCTCCGACCTCATCCGCCACGTCATCATCCCCGTCGTCCTCGG[C/G]CCCCGCTTCCTCTTCCTCCTCTCCAACGTCATCATCGTCTCCCTCGTCTTCCTCTCCCGCCAATCCTCCGCTGCCGATTCCACCGACGTCG
96766 C G ATTCCACCGACGTCGCCGCCGCTGCCGCCTTTGTTCCTCCGCCGAACGTCGAAGTTCCCGTATTCGAGGACAAAGAGGTCGTATGCGTGGTGGAGAGGAG[C/G]GATAAGCCCGTGAGGAAGACGTGCAGGAGGACCAGATCGTCGCTTGTGGTGGAGAAGAAGAAGAGATCGCCGGAGCTCCGGCG
96776 A G AGCTGCTGAGTTGCTGGGACGTCTCATAATAAACCCTGACAACGAACCATTTCTTCTTCCTTTTGCACCTCAAATGTACAAGCGCCTAGTCGACCTTTTA[A/G]GCTATCAAGCAGCAGATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGC
96776 C T TAAACCCTGACAACGAACCATTTCTTCTTCCTTTTGCACCTCAAATGTACAAGCGCCTAGTCGACCTTTTAAGCTATCAAGCAGCAGATGCACAAGCTGC[C/T]GCTGTAGGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGTAGATAGACTAC
96776 A T CTGACAACGAACCATTTCTTCTTCCTTTTGCACCTCAAATGTACAAGCGCCTAGTCGACCTTTTAAGCTATCAAGCAGCAGATGCACAAGCTGCCGCTGT[A/T]GGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGTAGATAGACTACTTAAGG
96776 C T TTCCTTTTGCACCTCAAATGTACAAGCGCCTAGTCGACCTTTTAAGCTATCAAGCAGCAGATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTAC[C/T]GAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGTAGATAGACTACTTAAGGTAATAAGGGCTCCACATCCT
96776 T C CACCTCAAATGTACAAGCGCCTAGTCGACCTTTTAAGCTATCAAGCAGCAGATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTACCGAAGTTAA[T/C]GTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGTAGATAGACTACTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGA
96776 G A ATCAAGCAGCAGATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGC[G/A]GTAGATAGACTACTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAG
96776 A G AAGCAGCAGATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGT[A/G]GATAGACTACTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTAT
96776 A G ATGCACAAGCTGCCGCTGTAGGTGCACTTTACAACCTTACCGAAGTTAATGTGGATTCAAGATTGAAGCTAGCTAGTGAAAGATGGGCGGTAGATAGACT[A/G]CTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATCGGAGCCAC
96776 G T AAAGATGGGCGGTAGATAGACTACTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATC[G/T]GAGCCACAAAATAGAACACTTCTTGCTGTTCACGAGACCACATTTTCAGAAATACTATTGTCGGATGGAAGATACTCGGACACGTT
96776 C T TGGGCGGTAGATAGACTACTTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATCGGAGC[C/T]ACAAAATAGAACACTTCTTGCTGTTCACGAGACCACATTTTCAGAAATACTATTGTCGGATGGAAGATACTCGGACACGTTTGCAC
96776 T A TTAAGGTAATAAGGGCTCCACATCCTGTTCCAGAAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATCGGAGCCACAAAATAGAACACTTCT[T/A]GCTGTTCACGAGACCACATTTTCAGAAATACTATTGTCGGATGGAAGATACTCGGACACGTTTGCACGGATATTGTTTGAGCTGACC
96776 A G AAGTGTGCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATCGGAGCCACAAAATAGAACACTTCTTGCTGTTCACGAGACCACATTTTCAGAAATACT[A/G]TTGTCGGATGGAAGATACTCGGACACGTTTGCACGGATATTGTTTGAGCTGACCGCAAGGCCCAACAGTAAACTTGTAAGCGGTCG
96776 G A GCAGAAAAGCAGCAAATATATTGGAGAACCTAGTATCGGAGCCACAAAATAGAACACTTCTTGCTGTTCACGAGACCACATTTTCAGAAATACTATTGTC[G/A]GATGGAAGATACTCGGACACGTTTGCACGGATATTGTTTGAGCTGACCGCAAGGCCCAACAGTAAACTTGTAAGCGGTCGTGCTGT
96776 C G TTCTTGCTGTTCACGAGACCACATTTTCAGAAATACTATTGTCGGATGGAAGATACTCGGACACGTTTGCACGGATATTGTTTGAGCTGACCGCAAGGCC[C/G]AACAGTAAACTTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTTCGTTA
96776 G A ACGTTTGCACGGATATTGTTTGAGCTGACCGCAAGGCCCAACAGTAAACTTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGA[G/A]TGGAAGATTTGATAGTAGTTCGTTATGTAAAAGTGGGATATGAAAAGTAATCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTT
96776 C T GAGCTGACCGCAAGGCCCAACAGTAAACTTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTT[C/T]GTTATGTAAAAGTGGGATATGAAAAGTAATCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTTTTGGTCCATGAATGTGCATTA
96776 A T AAGGCCCAACAGTAAACTTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTTCGTTATGTAAA[A/T]GTGGGATATGAAAAGTAATCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTTTTGGTCCATGAATGTGCATTATAAGGTTAGAAT
96776 G A GCCCAACAGTAAACTTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTTCGTTATGTAAAAGT[G/A]GGATATGAAAAGTAATCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTTTTGGTCCATGAATGTGCATTATAAGGTTAGAATTAA
96776 A T TTGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTTCGTTATGTAAAAGTGGGATATGAAAAGT[A/T]ATCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTTTTGGTCCATGAATGTGCATTATAAGGTTAGAATTAA
96776 A C TGTAAGCGGTCGTGCTGTTTGGGGCATGTGAAGTTAAAATTAGTCAACGAGTGGAAGATTTGATAGTAGTTCGTTATGTAAAAGTGGGATATGAAAAGTA[A/C]TCTGGTTAGTGTGCATTGCTTGTCATAACCCGTGTTTTGGTCCATGAATGTGCATTATAAGGTTAGAATTAA
96784 A G AAAAAAATTCATCCCATATTCCGGCATATTTCCTTCGGATTGGCTTCTGAAAACTTGAAC[A/G]ATATACATTTATGTGAAAAAAGAAATTATACATTAAAGCGCCAATCTAACAAACTAGAAACTACCCACCTAACCCGCACTAGATCCGAAAACAGCAGCCC
96784 A G ACGGAATCGTAATCCCGCCTTGCTGATCGAATCCGAACTCCGCCTCGGCCTCTTTCAGCAGCTCGCCAAAAAGCGGATGGTTGAAATACACGACGGGAAC[A/G]AGATACCGCCGCGGCGGGCCCCACTCATCGCCGTAGCCGCCGACGTAGACCGCCAGGTGCCCTTTCTGCAGCCTCCTCCTTTGCTC
96784 C T AATACACGACGGGAACAAGATACCGCCGCGGCGGGCCCCACTCATCGCCGTAGCCGCCGACGTAGACCGCCAGGTGCCCTTTCTGCAGCCTCCTCCTTTG[C/T]TCGTCTCCATCGTCTCCATAATCGCTGATTCGGCGATAATCGCTTCTGCCCCTTCTGATTATTGTCAATTTACGGGTTAATCGCTTGC
96784 G A CCCCACTCATCGCCGTAGCCGCCGACGTAGACCGCCAGGTGCCCTTTCTGCAGCCTCCTCCTTTGCTCGTCTCCATCGTCTCCATAATCGCTGATTCGGC[G/A]ATAATCGCTTCTGCCCCTTCTGATTATTGTCAATTTACGGGTTAATCGCTTGCTCCAGTCGATGAACTTGGACACGACGGAGTTCTTCTT
96784 C T AATCGCTGATTCGGCGATAATCGCTTCTGCCCCTTCTGATTATTGTCAATTTACGGGTTAATCGCTTGCTCCAGTCGATGAACTTGGACACGACGGAGTT[C/T]TTCTTGAAGAAGAATAAACGTTTGTCGCGTACACAGATTTTGACTAGCCTTCTGCGCAATCGAAAACCGCAGAATTTTTTCATCATTAA
96792 G A CGCTGTTCATACCAGGACATCCTATGGTTAGCAAACAGGAGATGTCATCGTCTATGAGCTTTTCACTACTTTGATGCCTACTCCGAATGAGGAAGCCCGG[G/A]TGAAAAAGCCCAGGTTGAAGTTTTTTGAAATGAAAATCTGGGATAGAGATGGCGTTATTGCCACTACCACCAACACCACAACCACCA
96794 GT G TTAAATAAAATGAATTTTTACATTCATGTTTTATTGAGTGAACTAGCTTAACCGTTTGCTCGGCAGCTTATATTGTTTTGTATTTTATATTGGGATTTTA[GT/G]TTTTTCCTTCAGTACAGTTTTGATTTAGCTTAATTCACAAATTTTATGGTGTCGGATGTACGCCAGAGTTGCTCAAACTTTGAACTCAAAT
96794 G GT AATTTTTACATTCATGTTTTATTGAGTGAACTAGCTTAACCGTTTGCTCGGCAGCTTATATTGTTTTGTATTTTATATTGGGATTTTAGTTTTTCCTTCA[G/GT]TACAGTTTTGATTTAGCTTAATTCACAAATTTTATGGTGTCGGATGTACGCCAGAGTTGCTCAAACTTTGAACTCAAATTTACTCTTTGTAC
96802 A G GGGCTAACCGCTTGACACCAGCAAGGTCCAAACGAACAACTACCCAATCGTTTTGTCGCTTGCCTCCCATGATGTTGGTATAGAAGTCCATGGAATGGTG[A/G]TTCCAGTTCAGAACAGCACCATCCATTCTGGCGCAATCCTTTGCAAGAGCGATCTTTCCAAGTTCACCGAACATTGCTTTACCGACAC
96810 A G TGACAGAAGATCCGGTTTCTCCAGGCGCTAAAAGATACGAAGGGGAAAGCTCGAATTCTCCTGAAGATCTGGACAGCTCTTCTCAGGCAATGAAGAGGCC[A/G]AGGCTGGTATGGACTCCGAATCTGCACAAGAGATTTGTAGACGTTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACG
96810 A G AAAAGATACGAAGGGGAAAGCTCGAATTCTCCTGAAGATCTGGACAGCTCTTCTCAGGCAATGAAGAGGCCAAGGCTGGTATGGACTCCGAATCTGCACA[A/G]GAGATTTGTAGACGTTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACGATTATGCAGTTGATGAATGTAGAGGGGTT
96810 G T AGATACGAAGGGGAAAGCTCGAATTCTCCTGAAGATCTGGACAGCTCTTCTCAGGCAATGAAGAGGCCAAGGCTGGTATGGACTCCGAATCTGCACAAGA[G/T]ATTTGTAGACGTTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACGATTATGCAGTTGATGAATGTAGAGGGGTTGAC
96810 G A GGAAAGCTCGAATTCTCCTGAAGATCTGGACAGCTCTTCTCAGGCAATGAAGAGGCCAAGGCTGGTATGGACTCCGAATCTGCACAAGAGATTTGTAGAC[G/A]TTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACGATTATGCAGTTGATGAATGTAGAGGGGTTGACAAGGGAGAACG
96810 C T CCGAATCTGCACAAGAGATTTGTAGACGTTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACGATTATGCAGTTGATGAATGTAGAGGGGTTGA[C/T]AAGGGAGAACGTTGCTAGTCATTTGCAGAAGTACAGGCTTTTCTTGAAGAGAAAGCATGGATATTCTTGCGAGATCGACTCTGTA
96810 T C TAGACGTTGTAAGTCATATAGGGATAAAGAACGCAGTTCCGAAGACGATTATGCAGTTGATGAATGTAGAGGGGTTGACAAGGGAGAACGTTGCTAGTCA[T/C]TTGCAGAAGTACAGGCTTTTCTTGAAGAGAAAGCATGGATATTCTTGCGAGATCGACTCTGTATCAGATCCTTTGTTTGAATCTAC
96816 C T GCAGATGGTAAATCTGACCCTGCGTCTGCTGTCACGTCCTAGTGTAGAGCATTTACCAACTATTTTTAAGTCTTTGGGAACGGAATATGACGAAAAAGTT[C/T]TGCCGTCAATTGGAAATGAGGTTTTGAAGGCTGTGGTTGCACAGTTTAATGCAGACCAATTGCTGACTGAGAGGCCACATGTGTCTG
96816 A G ACGAAAAAGTTCTGCCGTCAATTGGAAATGAGGTTTTGAAGGCTGTGGTTGCACAGTTTAATGCAGACCAATTGCTGACTGAGAGGCCACATGTGTCTGC[A/G]TTGGTGAGGGAGAGCCTGATCAAGAGGGCTGCGGATTTCAATATTGTCTTGGATGACGTGGCCATTACCCACTTGAGCTATGGTG
96828 A T CAATCTGCTCACTTCTGACCGACCCGAACCCAGATGATCCTTTAGTGCCTGAAATTGCGCACATGTACAAAAATGACAGAAACAAGTATGAGGCAACTGC[A/T]CGTTCCTGGACTCAGAAGTACGCAATGGGGTAGTACAATGTTACTCCAATTTCTGCAACTATATACTCCTCTTAAACCATGTGTTCCT
96828 T A TGCCTGAAATTGCGCACATGTACAAAAATGACAGAAACAAGTATGAGGCAACTGCACGTTCCTGGACTCAGAAGTACGCAATGGGGTAGTACAATGTTAC[T/A]CCAATTTCTGCAACTATATACTCCTCTTAAACCATGTGTTCCTGAACTGAGTATTCTACTTTATTTGGGATGTTTCTGCGTATGATCAT
96828 C T GCCTGAAATTGCGCACATGTACAAAAATGACAGAAACAAGTATGAGGCAACTGCACGTTCCTGGACTCAGAAGTACGCAATGGGGTAGTACAATGTTACT[C/T]CAATTTCTGCAACTATATACTCCTCTTAAACCATGTGTTCCTGAACTGAGTATTCTACTTTATTTGGGATGTTTCTGCGTATGATCATA
96828 A C TGAAATTGCGCACATGTACAAAAATGACAGAAACAAGTATGAGGCAACTGCACGTTCCTGGACTCAGAAGTACGCAATGGGGTAGTACAATGTTACTCCA[A/C]TTTCTGCAACTATATACTCCTCTTAAACCATGTGTTCCTGAACTGAGTATTCTACTTTATTTGGGATGTTTCTGCGTATGATCATATAT
96828 A G GACAGAAACAAGTATGAGGCAACTGCACGTTCCTGGACTCAGAAGTACGCAATGGGGTAGTACAATGTTACTCCAATTTCTGCAACTATATACTCCTCTT[A/G]AACCATGTGTTCCTGAACTGAGTATTCTACTTTATTTGGGATGTTTCTGCGTATGATCATATATTAAATGTGGTTTTGCTGTTTGAACT
96852 T C CATACAACGTTCTCAGCGATGAAAACAGCCGCAAATTCTACGACTGGACTCTTGCACAAGAGGCTGAAAGCAAGCAGGCGCAGAGGATGAGAATGAGGCT[T/C]GAGGATCCTTACGAACAAGATTTGAGAAATTTCGAGTCAATTCCAGACACAGTCGATCGACTGGGTGGCAAAAACATGAAACTTA
96854 G A AGAAACATATAGAGCCGTCTGAGCCTGCTGATGATTCATTTACCATGTCTCCTTTTGGGGTTAGTAAACCGTGCATAGAAGCATTTGGTGGAGCACATTT[G/A]TCATTTCTGAATCCAGAAAGTACTAAAGCATCATTAGATGTGGCTACAATCATGACAGTATGCAATCAGCTTTCAAACAATCCGATCT
96854 T TG,TA TGTCTCCTTTTGGGGTTAGTAAACCGTGCATAGAAGCATTTGGTGGAGCACATTTGTCATTTCTGAATCCAGAAAGTACTAAAGCATCATTAGATGTGGC[T/TG,TA]ACAATCATGACAGTATGCAATCAGCTTTCAAACAATCCGATCTTCTAAATTGTGGGCTACATCCTTTGAAAATCGGCAACGAGAG
96854 A ACAATCCGGTGAAGCATTTGGTGGAGCACATTTGTCATTTCTGAATCCAGAAAGTACTAAAGCATCATTAGATGTGGCTACAATCATGACAGTATGCAATCAGCTTTCAA[A/ACAATCCGGT]CAATCCGATCTTCTAAATTGTGGGCTACATCCTTTGAAAATCGGCAACGAGAGACTTTCCTCGTCGATGCATCGCCAAC
96860 C T ACTGGAACCGGTCGGGTTCACGAATTTGCCTTGGCCGCTGCTTGTTCTGCTTCGTGTGTCTGTTTGAATTGATAGCGCTGACACTAGAGCGCAACTTCTG[C/T]GTTGAAGCCATTGCTGCTCTTGTCCTTTCGTATAACCAACCCGAGAGAAAAATAGCAACAGCAGACGGGAGTTCGAAAATAATGGAG
96860 A G GCTTGTTCTGCTTCGTGTGTCTGTTTGAATTGATAGCGCTGACACTAGAGCGCAACTTCTGCGTTGAAGCCATTGCTGCTCTTGTCCTTTCGTATAACCA[A/G]CCCGAGAGAAAAATAGCAACAGCAGACGGGAGTTCGAAAATAATGGAGGAGGGTTACGTGGGTCTGCCTAAATCAGGCTCGAGACA
96860 C T CTTGTTCTGCTTCGTGTGTCTGTTTGAATTGATAGCGCTGACACTAGAGCGCAACTTCTGCGTTGAAGCCATTGCTGCTCTTGTCCTTTCGTATAACCAA[C/T]CCGAGAGAAAAATAGCAACAGCAGACGGGAGTTCGAAAATAATGGAGGAGGGTTACGTGGGTCTGCCTAAATCAGGCTCGAGACAC
96860 A G TTCTGCTTCGTGTGTCTGTTTGAATTGATAGCGCTGACACTAGAGCGCAACTTCTGCGTTGAAGCCATTGCTGCTCTTGTCCTTTCGTATAACCAACCCG[A/G]GAGAAAAATAGCAACAGCAGACGGGAGTTCGAAAATAATGGAGGAGGGTTACGTGGGTCTGCCTAAATCAGGCTCGAGACACAAAA
96860 T A TAGCGCTGACACTAGAGCGCAACTTCTGCGTTGAAGCCATTGCTGCTCTTGTCCTTTCGTATAACCAACCCGAGAGAAAAATAGCAACAGCAGACGGGAG[T/A]TCGAAAATAATGGAGGAGGGTTACGTGGGTCTGCCTAAATCAGGCTCGAGACACAAAAGAAGGCAAAAAGAGGAAAACATCACG
96860 C T AGCCATTGCTGCTCTTGTCCTTTCGTATAACCAACCCGAGAGAAAAATAGCAACAGCAGACGGGAGTTCGAAAATAATGGAGGAGGGTTACGTGGGTCTG[C/T]CTAAATCAGGCTCGAGACACAAAAGAAGGCAAAAAGAGGAAAACATCACGGAAGAACAGAGAAAAAGAGAGGACCTGGAGCTT
96860 G A AGGAGTTTATCGGTCCTTGCGCGTCTTTGTCGGCGAAAGATTTTACAGAGCCACGTGGCTTATCACGTGCATCTTCTTCTTCCTCTTCGTCTTCCGTCGC[G/A]GTCGCGGATTCTGATGCTCCTGGATCCGCTAGCCCGCCTAGTCAAGCTGCGGGATGGCCTCCAATTGGAAATTTTCGAATTTCCAGCTT
96874 A C GCCTTTTTTTTTTTTTTTCATGATCTTAGCTTCTAAAATTGAAGCGATTGTTCTATTAAATGATACAACATTTGTTTTGACAAATTCAAAC[A/C]GATACAATGTACCGTTGTTCAGAATACAACAGTGGCAGAAAGAGAAATATAATAAGTATAGTTCCATGGCTTATTGCATTCCGTAAACAATAACAAGTAC
96874 C G TTGGGATGTGAAGATTATAAAAATCTAGTATAAGGAGATTTCATTTCACAGGCAGTAAATTCAGCTGGTAGTGTTCATGTCTTCTGGAGCAGCATTACCT[C/G]CGTCTTCAGCGCTAGCAGAAGCATATGCAGATCGACGTGATCTAGCTTGCTGATTTGAGGAGGGCTGCAGTTTTGGGCGAAGAGCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
96874 G A GATCGACGTGATCTAGCTTGCTGATTTGAGGAGGGCTGCAGTTTTGGGCGAAGAGCCTCAAGAGGACCTTTAGGCTTAGGAGTTCCTCCTTGCTTTCCTA[G/A]AGCCCAATCAGCAGAGTCAAAGAAAGCACGCTCATGATCCTTTGAAATGAGTGGTGGCTTTTTGGGTAACATCCCACCATATTTCTT
96874 CT C CAAGAGGACCTTTAGGCTTAGGAGTTCCTCCTTGCTTTCCTAGAGCCCAATCAGCAGAGTCAAAGAAAGCACGCTCATGATCCTTTGAAATGAGTGGTGG[CT/C]TTTTTGGGTAACATCCCACCATATTTCTTTCTGATAACCTGCTCCTCTTCAGCAGGAGAGGGTGCAGAAATCCCTTCATTTTGGTCA
96892 T C ATAAGCGGATGCTGAACAAGCACCTATGCACTACCTATGGCAACCTTAGAAACTATATCCTTGAAAAATCAAGTGGTTGGGGATGGAGAGCCTCTCTTCG[T/C]TAACTTTAACCGCCGACGTCGGCAACGATGGCGCAAAGGATCACTTCCTGACCCACCAACGACCGATTCAACCAAAGAAGGAAATG
96892 C T CTAGAGGAACCAATCATCGCCCTTGGAAACGAAGAGATTGCAGTACCGACAATTGTTTTCGGTCGAAATCAGAAAAGGGAGAATCAAATCCTCCAGTCCA[C/T]CACCACCATTATCAGAAGCCCAAAAACCACGAGAGACGTTAACAGGGAGAGGATGACCAAAACTCCTGACCTTCGAAATAGGAGA
96892 C T TAGAGGAACCAATCATCGCCCTTGGAAACGAAGAGATTGCAGTACCGACAATTGTTTTCGGTCGAAATCAGAAAAGGGAGAATCAAATCCTCCAGTCCAC[C/T]ACCACCATTATCAGAAGCCCAAAAACCACGAGAGACGTTAACAGGGAGAGGATGACCAAAACTCCTGACCTTCGAAATAGGAGAA
96892 T C GTTTTCGGTCGAAATCAGAAAAGGGAGAATCAAATCCTCCAGTCCACCACCACCATTATCAGAAGCCCAAAAACCACGAGAGACGTTAACAGGGAGAGGA[T/C]GACCAAAACTCCTGACCTTCGAAATAGGAGAAAAAGCGCAAACTGGCGAAGTCACAGCCGTATGAAATAAAAAGGGCTCAATTCC
96892 G A TCAGAAAAGGGAGAATCAAATCCTCCAGTCCACCACCACCATTATCAGAAGCCCAAAAACCACGAGAGACGTTAACAGGGAGAGGATGACCAAAACTCCT[G/A]ACCTTCGAAATAGGAGAAAAAGCGCAAACTGGCGAAGTCACAGCCGTATGAAATAAAAAGGGCTCAATTCCAAAAAGCACCACC
96906 C CT CTGTTGGCCTACTGGCTCTATTTTGTTTCCATCTATTTATATTTCCAGCTTTTCCCCAAAATCAACATCGAATGATTTAAAAACCGCTCCCCAGTTTC[C/CT]TTTTTTAATTACAAATCAATTCCTCTAAAATCCTACAATATCGAATTGCAGCCGTGTTCGAAGATTTTGGGACTTGCGAATTAGGGATTTTGA
96914 CG C TCCCGGTCGACCGCTCTTCCTCTTTGTACTACGCGTTCTACGAAGCTCAGGAGCCGGTCGCGTCCATAGCCAAAACACCATTGCTCGTATGGCTGCAAGG[CG/C]GGGCCGGGCTGCTCCTCCATGCTTGGCAACCTATTCGAGATCGGCCCGTACCAGGTTTCTCACCACAACATCACCCTTCACAAGAA
96914 C G TCACCACAACATCACCCTTCACAAGAACCCCTACTCCTGGAACCACCGCTTCGGCCTCGTATTCATAGACAACCCAATCGGCACAGGCTTCAGCGTTGCT[C/G]CATCCAACCGTTCCATCCCTCGTGATCAGCCCACCATAGCTCGCCATCTGTTCATCGGCATCCGCAAATTCATCTCGTCCAACCCGTCG
96918 G A TGGATTCGAAAGCACAGGTGACTGCAATCCATTTGATCATAGGAACTCTTCAGAGAACAACTGTATTTGGGGTTGAGAACAGAGATACTTTAACACATAA[G/A]GCCACAGGGTATTCTGCAAAGTTACTGAAAAAACCAGATCAATGTAGGGCAGTGTACGCATGCTCTCATCTTTTCTGGGTCGATGA
96918 G T AACTGTATTTGGGGTTGAGAACAGAGATACTTTAACACATAAGGCCACAGGGTATTCTGCAAAGTTACTGAAAAAACCAGATCAATGTAGGGCAGTGTAC[G/T]CATGCTCTCATCTTTTCTGGGTCGATGATCAAGATGGAATCAAGGATGGGGAAAGGGTTCTACTTTGTCTTAAACGAGCCTTGAGA
96930 A G CATCAGTGAGAATATGCACTCTGATTCTTTTGGCACCACGTTCACTAGCTCCTTTCAGTAACAACTGTAGCTGATCAAGGCGAGAGTGGACGCCTCCGTC[A/G]CTCAGTAAACCAATTAGGTGCAAAGTATTTGTCTCAAAGGACTGTTTTATGTAGTTAAAGCCTTCTCCCTCATATATCTTTCCAGAAGC
96930 C T CCTAATGCATTGTGACCGACTTCACTATTACCCATGTCATCTTCGGTTGGAAGGCCAACAGCTTTCCCATGAGCTCTTACTAACCTCCACCTTTCCGGAG[C/T]TCCCTTTTTGAATGAATCCATGGTAGGTGTTTCAGCAACATGAATGCAATTATATTTGTCAGGATTTGCTTCTCCCCATCCATCTAACACA
96930 C T ACCTTTCCGGAGCTCCCTTTTTGAATGAATCCATGGTAGGTGTTTCAGCAACATGAATGCAATTATATTTGTCAGGATTTGCTTCTCCCCATCCATCTAA[C/T]ACAATCAAACCGATTGTCTTTCCTTTTGGCAGCTTAGGATGATCTGCCAATTTCCATGAAAAATCTGTGCTTCCCATCTTTCACCCAATAT
96930 C G CCCCATCCATCTAACACAATCAAACCGATTGTCTTTCCTTTTGGCAGCTTAGGATGATCTGCCAATTTCCATGAAAAATCTGTGCTTCCCATCTTTCACC[C/G]AATATATATCTCTTTTCGTTGAAGGGCTGATTATTTTCGTCGAGAATTGACCAATATAGATCTGAGAGAGAAGAACGAAGAGTATTTTTC
96950 A G CTTTCATTCTTCGCTTTAGTTTTGCATTTAGTTCCTTTTCTTTCTCTCGAGCACGCCACAGTTCATTAACCTCTACAGCACGATTTGCTTGCTCGACTCC[A/G]AGAACAGTAGCAGTCAGAAACCTTGAATTGGGTCGACCACGGACATTTGGTCTATGAAGATATGCAAGCACACCTTCTTTATCAGCTTCAG
96950 T C CAGCACGATTTGCTTGCTCGACTCCAAGAACAGTAGCAGTCAGAAACCTTGAATTGGGTCGACCACGGACATTTGGTCTATGAAGATATGCAAGCACACC[T/C]TCTTTATCAGCTTCAGCCTGCAGTCTCCTTGCCTCTTCAACTAACATGGCAGCAAGTCGGTTTTCCGTCTCCAAATCCATTGTTATCTA
96952 G A GCCTCCGTGGAAGACACCTGCAAATACGTAACCGCAACCCGCCCGGACATCGGGCTGGACTTCTGCATAGCAGCACTAAACTCCGACCCGCTAAGCAGAC[G/A]CGGGTCCGACCCGACCCAAATGGCTGTGACCGCGACCAAGCTGTCCATCGCCAATGCCACGAACATAGTGTCCAAAATAACCACG
96952 C T CGCTGATCCAAACTTCCGAGTCCGATCGGCTGTCTAAAGAATGCCTGAGCGCCTGCTCCGAGATTTACGGCGACGCGATAGATCGGCTGGAGGAGGCGGT[C/T]AGAAACATGGATGAGAAGAGGTACGAGGACGCCACCACGTTTCTCAGCGCGGCGTTGGATGCCTCCGATGATTGCGAAGAGGC
96952 C T TTTACGGCGACGCGATAGATCGGCTGGAGGAGGCGGTCAGAAACATGGATGAGAAGAGGTACGAGGACGCCACCACGTTTCTCAGCGCGGCGTTGGATGC[C/T]TCCGATGATTGCGAAGAGGCGTTCGGGGAGGAGGACGTGAAGTCGCCGGTGGGGGAGGAGGACGCGGAGTACGGTAGGTT
96952 G A ATCGGCTGGAGGAGGCGGTCAGAAACATGGATGAGAAGAGGTACGAGGACGCCACCACGTTTCTCAGCGCGGCGTTGGATGCCTCCGATGATTGCGAAGA[G/A]GCGTTCGGGGAGGAGGACGTGAAGTCGCCGGTGGGGGAGGAGGACGCGGAGTACGGTAGGTTGGTCGATATTGCTCTAACC
96952 TG T GAGAAGAGGTACGAGGACGCCACCACGTTTCTCAGCGCGGCGTTGGATGCCTCCGATGATTGCGAAGAGGCGTTCGGGGAGGAGGACGTGAAGTCGCCGG[TG/T]GGGGGAGGAGGACGCGGAGTACGGTAGGTTGGTCGATATTGCTCTAACCATTGTTGCCGCTGCCGCTGCTTGATTTTGTTTT
96952 T C GGGGAGGAGGACGTGAAGTCGCCGGTGGGGGAGGAGGACGCGGAGTACGGTAGGTTGGTCGATATTGCTCTAACCATTGTTGCCGCTGCCGCTGCTTGAT[T/C]TTGTTTTTGTTATTTTGATTTGGTGGAATATATAAATTTTGTCTTTGTGCTTTGTATTTTTCAGTGGGTTTTGTCTTTTAAATTCATA
96988 AT A TACAGTAGAGATAGTAATGGGATTTGAAGAAGAATTTGGCTTCGAGATTCCTGATAGCGAAGCGGATAAGATCAACTCTATTAGCCTTGCCGTTGATTTT[AT/A]TTTCTTCCCACCCTCAAGCAAAATGAACGGCTCGGTTTGTGTTGTAGCAGTTATAAGAGATGCTGCTGTTAGCAAAAAAAGAAAAT
96998 TA T AACAAATTGATTGCATGAACAAGTGATACAATACACATTGAATTTGGAAGCATAAAATTGTACATGTACATGAAGATATGTGCACATAGAATCATAAACC[TA/T]AAAGAAAATGAACTATTGATTACATTTTTGTATCCTTTGAAACTCCGCTGGCTGAAAGCAAATCTATAAAACATACTTGAAAGGAGG
96998 A G GCTGGCTGAAAGCAAATCTATAAAACATACTTGAAAGGAGGAAGAAACTGTATTTTTCCTGCAAAATTTAAACATCTTGATGATGTTTGAGCACCCAACA[A/G]TGATTACTTCCATACAATATCACCCATAAATCTGAGAGCAGGCACCCCTCGTATCTCTACATCAACCAGTGGTGCTTGAATAGTCAAC
96998 A G CAAAATCTGCAGTCTGATGTAGATGGTGGTAAAACCTGATTAACAATAAGCCTCTTGACTGGCACATTTTCTTTCTTCAGTGAAGCACAGAGTCTTGATG[A/G]CTCGTTAATAGCCATGACTGTAGGAATCGTCACAATAATGAATTCAGTTGATTCAGTGTCACGAAATAGCTCTCGCACTTTGACCATC
97002 A G TATATCGTGTTTTATTCCATCTGGTAATAATGCAATACAACATTATCAACCTAATCTCAATCTAATTCTAATTAGCTAATCCTCTTTCTTTCCACCTCTT[A/G]ATCCCGTCCATCCATTTCCGAACCATTCATCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCAATCGAACTCATCAGAAC
97002 C T GTAATAATGCAATACAACATTATCAACCTAATCTCAATCTAATTCTAATTAGCTAATCCTCTTTCTTTCCACCTCTTAATCCCGTCCATCCATTTCCGAA[C/T]CATTCATCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCAATCGAACTCATCAGAACCCTAAAATCAAAATCATCCCCA
97002 A G AATCCTCTTTCTTTCCACCTCTTAATCCCGTCCATCCATTTCCGAACCATTCATCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCA[A/G]TCGAACTCATCAGAACCCTAAAATCAAAATCATCCCCACCCCCACCGCCATTACGAGCCCCAGCACATTCCAATGCAATCCAGCAGCGCCA
97002 G A CCTCTTTCTTTCCACCTCTTAATCCCGTCCATCCATTTCCGAACCATTCATCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCAATC[G/A]AACTCATCAGAACCCTAAAATCAAAATCATCCCCACCCCCACCGCCATTACGAGCCCCAGCACATTCCAATGCAATCCAGCAGCGCCACCG
97002 CCA C CATTTCCGAACCATTCATCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCAATCGAACTCATCAGAACCCTAAAATCAAAATCATCC[CCA/C]CACCCCCACCGCCATTACGAGCCCCAGCACATTCCAATGCAATCCAGCAGCGCCACCGACTTCATCACCGCCTAGAAACACCATGCT
97002 A G TCTCCACCGTCCAATCCAATCCACCGCCCGTACCCAACGCCCAATCAATCGAACTCATCAGAACCCTAAAATCAAAATCATCCCCACCCCCACCGCCATT[A/G]CGAGCCCCAGCACATTCCAATGCAATCCAGCAGCGCCACCGACTTCATCACCGCCTAGAAACACCATGCTCTCGTTGATGACGGGCAA
97002 G C TACCCAACGCCCAATCAATCGAACTCATCAGAACCCTAAAATCAAAATCATCCCCACCCCCACCGCCATTACGAGCCCCAGCACATTCCAATGCAATCCA[G/C]CAGCGCCACCGACTTCATCACCGCCTAGAAACACCATGCTCTCGTTGATGACGGGCAACCCCGCCGCCTGCGGCTCACTTCTCGCGCT
97002 C T ACCCAACGCCCAATCAATCGAACTCATCAGAACCCTAAAATCAAAATCATCCCCACCCCCACCGCCATTACGAGCCCCAGCACATTCCAATGCAATCCAG[C/T]AGCGCCACCGACTTCATCACCGCCTAGAAACACCATGCTCTCGTTGATGACGGGCAACCCCGCCGCCTGCGGCTCACTTCTCGCGCTT
97002 G A ACCCCGCCGCCTGCGGCTCACTTCTCGCGCTTTTAGGGCAGAACGTGATCTCGTAATCCGCCCCTTGCCCGCAGGTGAAGGTGCTGGTACCGTCGTCGTA[G/A]GCGTAGCTGTAAGCCCTGGGACATGCGTTTTTGAATACCTGCGAGTACGAGCTGGGTTTGCAGGTGTTGGGGTTGCCGTACTCGCC
97002 G C TGAAGGTGCTGGTACCGTCGTCGTAGGCGTAGCTGTAAGCCCTGGGACATGCGTTTTTGAATACCTGCGAGTACGAGCTGGGTTTGCAGGTGTTGGGGTT[G/C]CCGTACTCGCCGCTGCAGCAGAACTCGGGAGTGTTGAACGCCTCGCAGGCGCTTTTGCAGGCCACGTTGGCGTCCGCGGCTCTG
97002 T C GTTTGCAGGTGTTGGGGTTGCCGTACTCGCCGCTGCAGCAGAACTCGGGAGTGTTGAACGCCTCGCAGGCGCTTTTGCAGGCCACGTTGGCGTCCGCGGC[T/C]CTGACTTTGAGATCGTTGGGGCAGACGTCGTTCAGATCTACGAGGCAGCCGGTTTTGGTGCAGTTCCCGATGCGTTGGTTGGAAG
97012 T G AGACATGGCCTTCTTTGCCTCAAGCATCTCTCCAGAAGACATCATCATACCCGATCCATCGACGGAGCAACTATGCCTATGCTTACCCTTCACATTTCCC[T/G]CCATTACCGGATCCTGGCTATCGGATCCAGATCCGCTACCCTCCAACCTGCAACCTATCTTCTCTATGTCCATGAACGTGCAGAATAAGT
97030 A G AATTCAATGTAATCAATGGTCCCATTTCCATCTACATCAGCCGCTTCCATGTACTGCCTGACTTCA[A/G]ATTCCGAAAGCTTGGTGCCTAACTTAGGTAGACCAGCTTTGAGTTCTTCAAAGGTTATAGTGCCGCTATTATCAGTGTCCATAGATTTGAACATTTCTTT
97030 C T CCTTCAAAGCAACTTTCTTAAGCTTGTTCATTGCTCTGAACTGCTTCATTCTTGATAGAACAGCGATATCAATAGGTTTATCTGATGCAATTCCATCTTC[C/T]CTGACCCAAGGATGATTTAAAATCTCAGTAGCAGTGAGCCGCTCTTTAGGATCTTGTCTAAGCATCTTCTTAACCAACTCTTTTGCACCAC
97030 C T GATCTGAGGAAAAATCGATGTGCCCTCTTAAAACAGCATCAAAGATTCCCTGCTCATTCTCAGCCCAAAAAGGAGGGACACCCGACAGCAGAATGTAAAG[C/T]ATAACTCCAGCGCTCCAAACATCAGCTTCCAACCCATAGTTCCTCTTCAGTACTTCAGGAGCCACGTAGTAAGCACTTCCAACCACA
97038 T C GCGGTTCCAGGGCTCAGCAGAGGAAAAGAGCACCATGACGAATAAAACGAAGGCGACAGCATCAAACCGCTTCCACTCTCCTTCATCATCTGATCCGACG[T/C]TTCGTTTGCGCTCTTGGCTTCCACTTTAACGGGTTGCGGCGCTGCCACCCTCTCTTTCACCCGCTTCTCCATGCCCGTTAGGCTCTGC
97038 C T GCTTCTCCATGCCCGTTAGGCTCTGCACCAGCCCTCTAAACCCGTGCGGGTCGACCCGGTACACCTTCGGTGGCGCCGGCATGCTTTCGGGCCTCCGCCA[C/T]GGCTTCGCCGGTGGTTTTCTGACGGCGTGGATTGATGACGTGGCTGGTTTGTAATGGTTTGAGTTTGAGTTGGAGTTGGAGTTCGT
97038 T C TAAACCCGTGCGGGTCGACCCGGTACACCTTCGGTGGCGCCGGCATGCTTTCGGGCCTCCGCCACGGCTTCGCCGGTGGTTTTCTGACGGCGTGGATTGA[T/C]GACGTGGCTGGTTTGTAATGGTTTGAGTTTGAGTTGGAGTTGGAGTTCGTTTGGAGAGACGGTGAATAGTCCATGTTCAGTGTTT
97038 G T GCATGCTTTCGGGCCTCCGCCACGGCTTCGCCGGTGGTTTTCTGACGGCGTGGATTGATGACGTGGCTGGTTTGTAATGGTTTGAGTTTGAGTTGGAGTT[G/T]GAGTTCGTTTGGAGAGACGGTGAATAGTCCATGTTCAGTGTTTGGTTAGAAATGGGATGAACTCTGAATGAAGTCCAGTAGGCCA
97046 G A ACCTTCCGGAGATCAAAGGAGATTTACTGTTGAATAATGGTGATGCTGTAGTTACCCTTTTTGAAGCACCTAGAGAAGATAATGATAGTAATGGTACGAC[G/A]ACGGAAAAAGATGTGAATGGAAGGCGGAAGATGAGGCCAGCTAATGGAAGAAGCAAAAGTGAACCGCCTAAAGAACTGCAACTG
97052 A T CTGTTGGCCTACTGGAAGATCCCGCCCATACGTCTGAATTTTTTTCCGCATTTCCCCGAGCAACTTCCTATCAACCTTCTCTGATCGTCAA[A/T]TTTAACAAAGCAGCCCAAAATTCCATGAAATTCAAAGCATTCTTTACTCAAGACGGCATCATTCTTCTAAACAAACGCTTTCTTCCCGCGCTTGATAAAA
97052 A G CCGCCCATACGTCTGAATTTTTTTCCGCATTTCCCCGAGCAACTTCCTATCAACCTTCTCTGATCGTCAAATTTAACAAAGCAGCCCAAAATTCCATGAA[A/G]TTCAAAGCATTCTTTACTCAAGACGGCATCATTCTTCTAAACAAACGCTTTCTTCCCGCGCTTGATAAAATCGGCCGCACGTGCCACCTGC
97052 T C TTCTTTACTCAAGACGGCATCATTCTTCTAAACAAACGCTTTCTTCCCGCGCTTGATAAAATCGGCCGCACGTGCCACCTGCTACTAACCCCGACTCACG[T/C]TATCTTCCTGCACAACCTGATCCACAACGACGGGGTGCAGTCGATCGCGCAGTTCAGCAAAGATTTCCTCTTCAAAGACTACAAAATCT
97052 G A CCGTGGCGGAGGATGACGGTATTCAGATGAAGTTGGTGAAGAAGTTGCCAGTGGGTAACAGCGTGGCGGCGCCGTACTTGAGCTTTGAGACGAAAGGGGT[G/A]AGGAGTGCGGTCGTGCAAGATGTGCCTATTTCAAAGCCTTTAGGAAGGGCGGAGGTAAATGAGCTGCAGGATGCGCTTGATG
97052 C T ATGACGGTATTCAGATGAAGTTGGTGAAGAAGTTGCCAGTGGGTAACAGCGTGGCGGCGCCGTACTTGAGCTTTGAGACGAAAGGGGTGAGGAGTGCGGT[C/T]GTGCAAGATGTGCCTATTTCAAAGCCTTTAGGAAGGGCGGAGGTAAATGAGCTGCAGGATGCGCTTGATGGTGCCCAGGATTT
97052 T C AGAAGTTGCCAGTGGGTAACAGCGTGGCGGCGCCGTACTTGAGCTTTGAGACGAAAGGGGTGAGGAGTGCGGTCGTGCAAGATGTGCCTATTTCAAAGCC[T/C]TTAGGAAGGGCGGAGGTAAATGAGCTGCAGGATGCGCTTGATGGTGCCCAGGATTTGCCTCCTACTTTGGTGCAGGTACCCGA
97052 A G TGCCAGTGGGTAACAGCGTGGCGGCGCCGTACTTGAGCTTTGAGACGAAAGGGGTGAGGAGTGCGGTCGTGCAAGATGTGCCTATTTCAAAGCCTTTAGG[A/G]AGGGCGGAGGTAAATGAGCTGCAGGATGCGCTTGATGGTGCCCAGGATTTGCCTCCTACTTTGGTGCAGGTACCCGACCTTGC
97052 T C GGAGTGCGGTCGTGCAAGATGTGCCTATTTCAAAGCCTTTAGGAAGGGCGGAGGTAAATGAGCTGCAGGATGCGCTTGATGGTGCCCAGGATTTGCCTCC[T/C]ACTTTGGTGCAGGTACCCGACCTTGCCCAATTGCAGAACCTTGTAGATCGACTGAAAAATGTAGGAGATATGCTTA
97056 A G ATGAAATGGTCTTCAGTTATTCATTTGGTTTTATGGAATTTGGTCATTGCTATTATCTGAGAGTTCGAGAATTTGAGCATTTCTTGAAACTGGAGAGGAA[A/G]AAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTC
97056 G A TTGCTATTATCTGAGAGTTCGAGAATTTGAGCATTTCTTGAAACTGGAGAGGAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGA[G/A]TTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATG
97056 C T ATTATCTGAGAGTTCGAGAATTTGAGCATTTCTTGAAACTGGAGAGGAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCA[C/T]AAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAA
97056 A G TGAGCATTTCTTGAAACTGGAGAGGAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCACAAAGATGGAATGGGACTGGCA[A/G]GAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAG
97056 G C GGAGAGGAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGC[G/C]GTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGG
97056 T C GGAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCA[T/C]CGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGGGTGGG
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97056 C T GAAAAAAAGCACATGAAAGACTAGGATATTTGGTTTCAAGACTTTCAGAGTTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCAT[C/T]GGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGGGTGGGA
97056 G A AGTTCACAAAGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCG[G/A]TTTCTGATCGAGGAGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCG
97056 C T AGATGGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGAT[C/T]GAGGAGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCA
97056 G A GGAATGGGACTGGCAAGAGGATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAG[G/A]AGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCAGGG
97056 G A ATGAGAGTCTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGGGTGG[G/A]ATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGACACT
97056 G A CTAGCGGTCATCGGATCAAAGAACGAGACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGGGTGGGATGGTTC[G/A]GCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGACACTCTCACGTG
97056 A G ACCATCAACCAAATGGATGGGAAGCGTGTTCGGTTTCTGATCGAGGAGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATG[A/G]TTTGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGACACTCTCACGTGCAAGCCAAGCCTGGGTCTTCTTTTCTCA
97056 A G GAGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGAC[A/G]CTCTCACGTGCAAGCCAAGCCTGGGTCTTCTTTTCTCAAAAGACTGGCCATTGATTACGTCTACAACTTCCTGAGGAGGAACTG
97056 C T AGAGGGTGGAAAGGGGTGGGATGGTTCGGCCAGAAGTGAAGGAAGAATTGGATGATTTGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGACA[C/T]TCTCACGTGCAAGCCAAGCCTGGGTCTTCTTTTCTCAAAAGACTGGCCATTGATTACGTCTACAACTTCCTGAGGAGGAACTGC
97056 C T TGGTGGAAGCGCGTGAAGCAGGGATAGCCTTTGTATTAGGACACTCTCACGTGCAAGCCAAGCCTGGGTCTTCTTTTCTCAAAAGACTGGCCATTGATTA[C/T]GTCTACAACTTCCTGAGGAGGAACTGCAGAGGACCTGAAGTGGTTTTGAAAGTGCCTCCCGCTTCCTTGCTGGAGGTTGGAATGGT
97056
TCCTGAGGAGGAACTGCAGAGGAT CGTGAAGCAGGGATAGCCTTTGTATTAGGACACTCTCACGTGCAAGCCAAGCCTGGGTCTTCTTTTCTCAAAAGACTGGCCATTGATTACGTCTACAACT[TCCTGAGGAGGAACTGCAGAGGA/T]CCTGAGGAGGAACTGCAGAGGACCTGAAGTGGTTTTGAAAGTGCCTCCCGCTTCCTTGCTGGAG
97056 C T AGCCAAGCCTGGGTCTTCTTTTCTCAAAAGACTGGCCATTGATTACGTCTACAACTTCCTGAGGAGGAACTGCAGAGGACCTGAAGTGGTTTTGAAAGTG[C/T]CTCCCGCTTCCTTGCTGGAGGTTGGAATGGTTTACGTACTGTGACATGTTTATGTCTGTGAGGGGAATACCATGTTTTAGTGGGGTT
97056 G T CTTTTCTCAAAAGACTGGCCATTGATTACGTCTACAACTTCCTGAGGAGGAACTGCAGAGGACCTGAAGTGGTTTTGAAAGTGCCTCCCGCTTCCTTGCT[G/T]GAGGTTGGAATGGTTTACGTACTGTGACATGTTTATGTCTGTGAGGGGAATACCATGTTTTAGTGGGGTTGTTAGT
97056 T C CTGGCCATTGATTACGTCTACAACTTCCTGAGGAGGAACTGCAGAGGACCTGAAGTGGTTTTGAAAGTGCCTCCCGCTTCCTTGCTGGAGGTTGGAATGG[T/C]TTACGTACTGTGACATGTTTATGTCTGTGAGGGGAATACCATGTTTTAGTGGGGTTGTTAGT
97058 GC G GCAGCAGCGCTTTTTCAACGCTGGTCAACTTCTTCTGGCCGCTGCTCCTTTCCACTGGTTTCTTCCTCGTCGCCGTCTTGCTTTTGTTCAAGATCTCCCC[GC/G]CCGCCGGCGTCGGAGTCGGTCGGCGATTCGGTCGGAGAGGAGCTGATTGATTACGTCGCTTATCAACATCACCCCCATCACAATCTGG
97068 A G GGTGTTTCTAGCTGCGATGAGTTTGTTCAGGCTGCTATTGCTGCTGGTGCCGGTCCTGGTCCCAGCGTTTGAGGTGTTCATGTCTTTGTTTTATTGTGGT[A/G]AATTTTTGTAAATTATTTTATTTAAGCAAACATGGGGTTGGTTTTATTCCTCCCTTCCTGTTCTCATGTACAAATATTTAAAGAAAACCG
97068 A AT GATGAGTTTGTTCAGGCTGCTATTGCTGCTGGTGCCGGTCCTGGTCCCAGCGTTTGAGGTGTTCATGTCTTTGTTTTATTGTGGTAAATTTTTGTAAATT[A/AT]TTTTATTTAAGCAAACATGGGGTTGGTTTTATTCCTCCCTTCCTGTTCTCATGTACAAATATTTAAAGAAAACCGTTCGGTTTGTCTTCG
97068 TC T GGTCCTGGTCCCAGCGTTTGAGGTGTTCATGTCTTTGTTTTATTGTGGTAAATTTTTGTAAATTATTTTATTTAAGCAAACATGGGGTTGGTTTTATTCC[TC/T]CCCTTCCTGTTCTCATGTACAAATATTTAAAGAAAACCGTTCGGTTTGTCTTCGTGCGGTGCTACTAGGTGTAATGCAAGCTGATGAGT
97090 A G GCAAGAGTAAGGGGGTTGGCGCAGAGATTTTCGATGGAAGGCCCGTCGTGTCCTGGTGGCGCGACATTGGTGTTTTGGCGTGGTAGGTGCTGCGAGGTAA[A/G]GTTAGAACAGGAGATTGAAGGAGCTACGTGAAGAGCAGCAAGAAGAAGGGTAAACGGGACCAATGAAGTAGCAAAGGAGCA
97094 CA C TTTACACAGCTAATATTTGTGGCATTTCTTAGAAGAAGAAAAAAGAATATTCATATACCCTGCTGAAACAAACAGACATTTCATATATAAATAAATCAAA[CA/C]AAATTAACTGTACAACTCGTTGCATGCCAAAACATTTAAAACGACGCTGTATCATATACCATCATCCAGAGCTTCTCTCCGAATACACA
97094 T A TGTGGCATTTCTTAGAAGAAGAAAAAAGAATATTCATATACCCTGCTGAAACAAACAGACATTTCATATATAAATAAATCAAACAAATTAACTGTACAAC[T/A]CGTTGCATGCCAAAACATTTAAAACGACGCTGTATCATATACCATCATCCAGAGCTTCTCTCCGAATACACACTCTTACAGACGCAGTG
97094 A G GCTCCTCACCAATTTGATTGCCATTGATTTGCATAGAAGAGCTGCTGCTTGATCCAGTAGACGGTGGATGATGTGGTAGAAATGACGGCGGCGAACCTGC[A/G]AACCCAGACCCGGCTCCGGACCCAGACCCGTTAGGAATTGTTCCGCTCCATGAAGCTGCACGGGATCGAGAGAGAGGGCCATTGG
97094 A G TGTTATCCATACTCGGAAATCTTTGCAGTGATAAAGGGGGCGATGATGAAGCGAACTGTGTTTCTTTTGATTCTGATGTTGAAGAATCGGTATTACTTCC[A/G]AGTTCTTGAGCACTTGGTACTGCTGTTACGGAATTGGTATCGTGTTCATTTGAAGGAGGGTGTGCTGTGGGCACAAAGAACTTCGTG
GCATCTCAGTAATCCTCTCCTTCATCTTCCTCATCATCTGACTCTCTGCGCCCACTT
97104 G ACGCACCAGATTAAACATTCAAACATAAACAAACATACAGACACAGTAATACTCAATCAAAATAAACATATCACATAATTCAAGATAAAACTAACACAAA[G/GCATCTCAGTAATCCTCTCCTTCATCTTCCTCATCATCTGACTCTCTGCGCCCACTT]CATCTCAGTAATCCTCTCCTTCATCTTCCTCATCAT
97108 A G TTGAAAGAAAAAAGAGGCGTATGAGATGATGTGAATTGTGCGACAAAATGTTGTTCTACATATAGCATGCATGCATGAAAACTTTGCTAGCATGCAGCAA[A/G]CGCAAGCCTGTAGCCTCCCTCTCCCTTCCCTTTTCACGCAACTCCGCAATGTTTTATCTTTCTCCTTCTTTAACTTCCAAAAGAAAGAA
97120 T C ATAGCTTGGGCCTTGCATTCGTGCTCGCCATCATGCCACTTATTTTGATGTTCCCACTATACCATTATCAACAAAAGCATCCTCTCAATTTTGTCTTTCT[T/C]GGTTTATTCACTGTGTGCTTAAGCCTCAGTGTGGGAGTGGCTTGTGCAAACACTGAAGGGAAGATCGTACTTGAGGCACTGATTTTAACT
97120 C T CCATCATGCCACTTATTTTGATGTTCCCACTATACCATTATCAACAAAAGCATCCTCTCAATTTTGTCTTTCTTGGTTTATTCACTGTGTGCTTAAGCCT[C/T]AGTGTGGGAGTGGCTTGTGCAAACACTGAAGGGAAGATCGTACTTGAGGCACTGATTTTAACTTCTGGCGTTATTGTATCATTAACTGGA
97120 A G TACTTCTACTCACCAGTTTTATCCAGATATTTTTCCCGATGGGGCCAACGTCAGTGGCAGTAATTGGTGGGTTTGGGTCTCTCTTGTTCTCTGCATACCT[A/G]GTGTACGACACGGATAACCTGATAAAGAGATACACATATGATCAATACATATGGGCGTCCGTGGTTCTGTACCTTGATATTCTTAACCT
97120 C T CATATGGGCGTCCGTGGTTCTGTACCTTGATATTCTTAACCTCTTCCTCTCAATCCTGAACATGCTCAAGGGCATGCAGTCTGACGGGTAATTTCATGCT[C/T]TACTCTTCTTGGCCATGTGTGCCTACATATTTGTAAGCTTATTTCAGAAATTATACTTTGAAGTTCGCAGTAGGAAAATGAACCATTACT
97120 A T TGATATTCTTAACCTCTTCCTCTCAATCCTGAACATGCTCAAGGGCATGCAGTCTGACGGGTAATTTCATGCTCTACTCTTCTTGGCCATGTGTGCCTAC[A/T]TATTTGTAAGCTTATTTCAGAAATTATACTTTGAAGTTCGCAGTAGGAAAATGAACCATTACTCCTATGTTTGTGGGCTTATTATACCTTT
97138 T C CGTTCTGCTTTGTTGCGTGTGGACACCTTCAGACTTTCAACGACGCCAGGATAGCTTTGGTGCTCCAATCCAGAGTATTCTCCTTCTGTGTTTTCGCGGA[T/C]AATAGCAAAGTCGACATTGTCGTGGCGAGTGGGGAAACCACGGAGGGACTTGCACAGGACGACAGATGCATAAATGTCGAGTTGTT
97138 A G ACACGTTGTACTGTTCCCATTCAATGGGTGCGTTGACATGCTCAAAGACCTCCTTCACGGAGTCGGTAATTTCGTTTCCAATACCATCACCTGGAATAAG[A/G]GTAACTGTGTAGACCCCACCATACTTGGTCGGCATCCTTTTCGAGACCCTCGGAAAACCTGCTGCGAGGGTTGTCGCAGACCTTAACA
97138 A G ACCTGGAATAAGAGTAACTGTGTAGACCCCACCATACTTGGTCGGCATCCTTTTCGAGACCCTCGGAAAACCTGCTGCGAGGGTTGTCGCAGACCTTAAC[A/G]CCTGCTGGGAAGGCTTGAGAATTGCCGGTTTGGCAGCATTTACAACGGTACTCAGAACCATATGCGGCAGAGGTAGCGGTGGTGG
97152 C T TTAACGTAGTAGAAAGCTACCAATACAAAGTTGGAGATCTGGACAGTTGGGGACTTCCACCTCCTACCAAATCCAACCTCTACTCTTCTTGGTCTTCGAA[C/T]CACCACTTCAAGACCGGCGACTCCCTCATGTTCCTGTACCCGCCGAGCCAGGATTCGGTGCTCCAAGTGACGGAGAAGGCGTACGAC
97152 C T GAGATCTGGACAGTTGGGGACTTCCACCTCCTACCAAATCCAACCTCTACTCTTCTTGGTCTTCGAACCACCACTTCAAGACCGGCGACTCCCTCATGTT[C/T]CTGTACCCGCCGAGCCAGGATTCGGTGCTCCAAGTGACGGAGAAGGCGTACGACTCATGCTCGACGTCCGACCCGATAACGAGAATG
97152 T G GTACCCGCCGAGCCAGGATTCGGTGCTCCAAGTGACGGAGAAGGCGTACGACTCATGCTCGACGTCCGACCCGATAACGAGAATGGACGACGGAAACTCG[T/G]TGTTCAACATCACGGCGCCTGGAAACTACTACTTCGTAAGCGGAGCGAAGGGGCACTGCGAGAAGAAACAGAAGATGGTGATT
97152 G T AGGATTCGGTGCTCCAAGTGACGGAGAAGGCGTACGACTCATGCTCGACGTCCGACCCGATAACGAGAATGGACGACGGAAACTCGTTGTTCAACATCAC[G/T]GCGCCTGGAAACTACTACTTCGTAAGCGGAGCGAAGGGGCACTGCGAGAAGAAACAGAAGATGGTGATTCAGGTGGCATCGGC
97152 A T GAAACTCGTTGTTCAACATCACGGCGCCTGGAAACTACTACTTCGTAAGCGGAGCGAAGGGGCACTGCGAGAAGAAACAGAAGATGGTGATTCAGGTGGC[A/T]TCGGCCGATGGTAAGTTCTTCCCCCCTTCTGCGGATGCGGGTGCGCCTGCTGTTGGGCCTTCTTCCTATTCCAATGCGTTTGGGC
97152 T C TCAACATCACGGCGCCTGGAAACTACTACTTCGTAAGCGGAGCGAAGGGGCACTGCGAGAAGAAACAGAAGATGGTGATTCAGGTGGCATCGGCCGATGG[T/C]AAGTTCTTCCCCCCTTCTGCGGATGCGGGTGCGCCTGCTGTTGGGCCTTCTTCCTATTCCAATGCGTTTGGGCCTATGCCCATGG
97152 T C TGATTCAGGTGGCATCGGCCGATGGTAAGTTCTTCCCCCCTTCTGCGGATGCGGGTGCGCCTGCTGTTGGGCCTTCTTCCTATTCCAATGCGTTTGGGCC[T/C]ATGCCCATGGGCTTGGGTTCTGGTACATCTGCAGCCTGGATTGGAGGCCCACTTTTTGGGTTCATGGGATCCATTGTTGCTGGTGTT
97152 A G TGCCCATGGGCTTGGGTTCTGGTACATCTGCAGCCTGGATTGGAGGCCCACTTTTTGGGTTCATGGGATCCATTGTTGCTGGTGTTGTTATCTGGGCTTC[A/G]CTTTAAGCTTTTATACATCGAATTGTTGTTTTCTGTTGTCACTCACGGTATTCCAAGATTTACTTTAGTCTAAAAAAAAAA
97152 A G GGGTTCTGGTACATCTGCAGCCTGGATTGGAGGCCCACTTTTTGGGTTCATGGGATCCATTGTTGCTGGTGTTGTTATCTGGGCTTCACTTTAAGCTTTT[A/G]TACATCGAATTGTTGTTTTCTGTTGTCACTCACGGTATTCCAAGATTTACTTTAGTCTAAAAAAAAAA
97158 AT A TTAATTGCTTGTTCTCTTGGCCCCTTTTGTCATCTTCTTTTGCTCCAAAACCAACAAGCTGAGGGAATAAATCCATAGATTTTGCAGGACCTGATACTTT[AT/A]TTTTTCTTATCAGCTTCGGAAACATCCACGCCTGTCAATAGATTCATTGTACTCGGTCTTGGATCTGTTTTGCCCATGGAAGCATTAATA
97158 T C GGACCTGATACTTTATTTTTCTTATCAGCTTCGGAAACATCCACGCCTGTCAATAGATTCATTGTACTCGGTCTTGGATCTGTTTTGCCCATGGAAGCAT[T/C]AATACATCTAGCAAGGTTAAGATCTACGGGAGGACGACCTTTCTCTTTGATGAACTGGCTCAAGAGGTTGCATGTCACTGAAAAGCTCG
97158 A G ATCTACGGGAGGACGACCTTTCTCTTTGATGAACTGGCTCAAGAGGTTGCATGTCACTGAAAAGCTCGAAGTTTTACCTGCCGTTGTGTTCGACGACATG[A/G]CACTGATTTTATCTCTCTTCTTCTTGTTTATCTTCTCCTTTTTTTCCGTTCTTCCTTGCGCTTAACCGTGACTTTGAGAGACCTTT
97158 T C TTTGATGAACTGGCTCAAGAGGTTGCATGTCACTGAAAAGCTCGAAGTTTTACCTGCCGTTGTGTTCGACGACATGACACTGATTTTATCTCTCTTCTTC[T/C]TGTTTATCTTCTCCTTTTTTTCCGTTCTTCCTTGCGCTTAACCGTGACTTTGAGAGACCTTT
97162 A G TTGCAGTTGATCTTAGTTTCAACAAGATCGAAGGCCAGTTATCCGAAAACTTTGCAGAGTTTCCATCTCTAGTATCCTTATCCATGAAGTCCAATAGACT[A/G]AGAGGGCAGATTCCGATGAAATATGATAAACTGAAGAGGCTGTTCTTGGATGGAAACTTCTTGAACGGAGAATTGCCTGATGTGTTG
97162 C T AACTGAAGAGGCTGTTCTTGGATGGAAACTTCTTGAACGGAGAATTGCCTGATGTGTTGCTGAAAGGTGAGCTAGTAGCTGGGAGTTTTGGTGATAATTG[C/T]TTACAGAGATGTCCAAAAAGTTTGTCGATATGCTCGCCTGTGCAGAAGCCGGAGTGGATTTGTAAGCAGATTTACGGCATCGGAG
97162 C T TGAACGGAGAATTGCCTGATGTGTTGCTGAAAGGTGAGCTAGTAGCTGGGAGTTTTGGTGATAATTGCTTACAGAGATGTCCAAAAAGTTTGTCGATATG[C/T]TCGCCTGTGCAGAAGCCGGAGTGGATTTGTAAGCAGATTTACGGCATCGGAGGTGGTCAGAAAAGGCCGCACCACCTGGCTCCGA
97162 A G GCTGAAAGGTGAGCTAGTAGCTGGGAGTTTTGGTGATAATTGCTTACAGAGATGTCCAAAAAGTTTGTCGATATGCTCGCCTGTGCAGAAGCCGGAGTGG[A/G]TTTGTAAGCAGATTTACGGCATCGGAGGTGGTCAGAAAAGGCCGCACCACCTGGCTCCGACAAGAGGTTAGTATAGTAAATTTAT
97162 A G AGATGTCCAAAAAGTTTGTCGATATGCTCGCCTGTGCAGAAGCCGGAGTGGATTTGTAAGCAGATTTACGGCATCGGAGGTGGTCAGAAAAGGCCGCACC[A/G]CCTGGCTCCGACAAGAGGTTAGTATAGTAAATTTATGTATGTATTGTATTTATTTGTGCCGCTGTTTTAGAAAGTCTTTGTACTTCA
97178 T C GCGATGGAAATGTTGCCTCCGTGGAGATCGAACAGCGAAGTGGTCGGAGGGTGGTTTTGGTAAGAAAAGGACGCAAGGGATGGAGGTTTGGAGAAACGTG[T/C]AGATTGCTGTGAGAGTAGAAGGGTTTATCAGATGAAGATAATGAGCAGAGCAGGGAAGGAGAAGACAGAAGAGATTGCATT
97194 G A AGCTGTTAGCTCCAGCATGGGCTTAACACCTGCACCATTATTGGAATTCTCTGCAGCAACAGGAACCAAAGACATCACCTTGGGCGCGGAGGT[G/A]GCCTTCGATAGCACTTCCGCATCTTTCAGTAAATACAACGCAGGCATAATGCTAACTAAACCCGACTTCTCTGCATCCCTAATATTGACCGACAA
97194 T C ATGCTGTGGCTGCTGAAATGGTGCACAGGTTCAATACATTTGAAAACAGCTTTACGATCGGAAGCTCTCATAAAATAGATACTGCTACGATGATGAAGAC[T/C]AGAGTTAGCAGCAACGGTAAATTTGGAGTTTTATATCAGCATGAATGGAGGCCAAAATCATTAGTTACTATTTCAGCTGAGTACGAT
97194 T C TTCAATACATTTGAAAACAGCTTTACGATCGGAAGCTCTCATAAAATAGATACTGCTACGATGATGAAGACTAGAGTTAGCAGCAACGGTAAATTTGGAG[T/C]TTTATATCAGCATGAATGGAGGCCAAAATCATTAGTTACTATTTCAGCTGAGTACGATTGTAAGGCGGTCGGTGCTCCTACAAAGGT
97194 G A AGGCCAAAATCATTAGTTACTATTTCAGCTGAGTACGATTGTAAGGCGGTCGGTGCTCCTACAAAGGTTGGTGTTGCTCTTGCTCTCAAATAGGGACGAC[G/A]CATATAAGGCTTGAATTTACTTTTATTATTCTTTTGTTTTGGTGCTTCTGAGTTTTACTGAAAGCATTTGTGTTTTACTTCGCATATATT
97194 C T CATTAGTTACTATTTCAGCTGAGTACGATTGTAAGGCGGTCGGTGCTCCTACAAAGGTTGGTGTTGCTCTTGCTCTCAAATAGGGACGACGCATATAAGG[C/T]TTGAATTTACTTTTATTATTCTTTTGTTTTGGTGCTTCTGAGTTTTACTGAAAGCATTTGTGTTTTACTTCGCATATATTTGTTCGGATAT
97194 T C CTTTTATTATTCTTTTGTTTTGGTGCTTCTGAGTTTTACTGAAAGCATTTGTGTTTTACTTCGCATATATTTGTTCGGATATGCGAGGACTGTGTCCAAA[T/C]TGGTATTACTTTGATGATTATTGTAAACTAGGATGTGAAGGTTTCATATACAATTTTTGTGTGCAA
97200 A T CACAGCCTACTTCAAGTACATGGTGGGTGGACCGGATGTGGCAGTGGAGGAGGTGTTTGAAATGGGAGTAGTCTTTTAGCCATTCATAGTGCTCCTCTAC[A/T]GAAAATCTATTATCCCAATAATGGGGATCTAGGTAGGCAGAAACGGAACTGGGTGCAGGATCAACC
97210 C T TTTCAAACTGAGTTAAATCAACTTGTCCTGTTCGGAGTACATGTGAAAATAGCTCTACTTGCTGACGAAAAGGTGCACTTTGTAACAATTCCAAAATAAT[C/T]TGTGGATTACATGAGCCCTCAGGTAAGTAAGACGAAAGTTCTTGCTCTAATGGCAACATTTCAAGAAGTGGGGAAACCAAATCAGGTT
97222 C T CCAGCAGCAATTGAATCATATAGATCCTTAGTGGCATGACTGTGATTTTTACCTCCAACTGTAATAGCTTCTTCATCTAAGAGACATTTAACTCCACAGG[C/T]AGGTTTCCAGTGGAACTTAACGTAATGAACTTTGCCTTCTTTGTTTATTAGTGTGTATGTGTTTACCCCAAAACCATCCATGTGTCGGTA
97222 A T CAGCAGCAATTGAATCATATAGATCCTTAGTGGCATGACTGTGATTTTTACCTCCAACTGTAATAGCTTCTTCATCTAAGAGACATTTAACTCCACAGGC[A/T]GGTTTCCAGTGGAACTTAACGTAATGAACTTTGCCTTCTTTGTTTATTAGTGTGTATGTGTTTACCCCAAAACCATCCATGTGTCGGTAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97222 G A GATCCTTAGTGGCATGACTGTGATTTTTACCTCCAACTGTAATAGCTTCTTCATCTAAGAGACATTTAACTCCACAGGCAGGTTTCCAGTGGAACTTAAC[G/A]TAATGAACTTTGCCTTCTTTGTTTATTAGTGTGTATGTGTTTACCCCAAAACCATCCATGTGTCGGTAATCCTGTGGGATGCCTAAATCG
97226 G A CCCTCCTTGTTCCCTATCCTTCCATCTTTCAAGTCGATTATTCAATGGATGAAGAAAAAGAATTGAAAAATGAAGAAACTCGAGAGGAGATGCTTTCTAG[G/A]CACAGGCAAGAGATGAAGGAACTCCGGAACAAAGAAATAGCACTGAAAAAAGCTGCTGCAAAAGGTAGCAAAGCAGAGCAAAAGG
97226 T C AAAATGAAGAAACTCGAGAGGAGATGCTTTCTAGGCACAGGCAAGAGATGAAGGAACTCCGGAACAAAGAAATAGCACTGAAAAAAGCTGCTGCAAAAGG[T/C]AGCAAAGCAGAGCAAAAGGCCAAAAAGAAGCAAGTCGATGAAGAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTC
97226 T C GGCAAGAGATGAAGGAACTCCGGAACAAAGAAATAGCACTGAAAAAAGCTGCTGCAAAAGGTAGCAAAGCAGAGCAAAAGGCCAAAAAGAAGCAAGTCGA[T/C]GAAGAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCAGAAGAACTATCCTCATTAGTCAATAACAGCCATCAAGAC
97226 A G AAGAGATGAAGGAACTCCGGAACAAAGAAATAGCACTGAAAAAAGCTGCTGCAAAAGGTAGCAAAGCAGAGCAAAAGGCCAAAAAGAAGCAAGTCGATGA[A/G]GAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCAGAAGAACTATCCTCATTAGTCAATAACAGCCATCAAGACACT
97226 G A AGCTGCTGCAAAAGGTAGCAAAGCAGAGCAAAAGGCCAAAAAGAAGCAAGTCGATGAAGAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCA[G/A]AAGAACTATCCTCATTAGTCAATAACAGCCATCAAGACACTGGTAAAACCAACCTCGACACCCTTGTAATGGCCATAGCTGGCGC
97226 G A CAAAAGGCCAAAAAGAAGCAAGTCGATGAAGAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCAGAAGAACTATCCTCATTAGTCAATAACA[G/A]CCATCAAGACACTGGTAAAACCAACCTCGACACCCTTGTAATGGCCATAGCTGGCGCTTCCATAGCTCCTAACAAAGAGCCCTTCAA
97226 T C AGAAGCAAGTCGATGAAGAGATCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCAGAAGAACTATCCTCATTAGTCAATAACAGCCATCAAGACAC[T/C]GGTAAAACCAACCTCGACACCCTTGTAATGGCCATAGCTGGCGCTTCCATAGCTCCTAACAAAGAGCCCTTCAAGCCTAGCAAAGCC
97226 C T TCTCAAATTTAGTATCTCAACTCGAGAGCAAACAGTCAGAAGAACTATCCTCATTAGTCAATAACAGCCATCAAGACACTGGTAAAACCAACCTCGACAC[C/T]CTTGTAATGGCCATAGCTGGCGCTTCCATAGCTCCTAACAAAGAGCCCTTCAAGCCTAGCAAAGCCGCAAGAAGAAGAGAGAAAAGG
97226 A T ACACCCTTGTAATGGCCATAGCTGGCGCTTCCATAGCTCCTAACAAAGAGCCCTTCAAGCCTAGCAAAGCCGCAAGAAGAAGAGAGAAAAGGGCGCAAGA[A/T]GAAGCCGCTAGAGAACAAAGAATAGAAGAACAAATAAATGGAGTAAGCGACCGCATGATCGAAAACGTACTGCTACAAAAGAAG
97226 T C CTAACAAAGAGCCCTTCAAGCCTAGCAAAGCCGCAAGAAGAAGAGAGAAAAGGGCGCAAGAAGAAGCCGCTAGAGAACAAAGAATAGAAGAACAAATAAA[T/C]GGAGTAAGCGACCGCATGATCGAAAACGTACTGCTACAAAAGAAGCTTGAGCCTCTCAATCTAACCATCAACGAGATCAAGCC
97226 T A GCCGCAAGAAGAAGAGAGAAAAGGGCGCAAGAAGAAGCCGCTAGAGAACAAAGAATAGAAGAACAAATAAATGGAGTAAGCGACCGCATGATCGAAAACG[T/A]ACTGCTACAAAAGAAGCTTGAGCCTCTCAATCTAACCATCAACGAGATCAAGCCCGATGGAAATTGCTTATATAGAGCAGTTG
97226 C G AAGAAGAGAGAAAAGGGCGCAAGAAGAAGCCGCTAGAGAACAAAGAATAGAAGAACAAATAAATGGAGTAAGCGACCGCATGATCGAAAACGTACTGCTA[C/G]AAAAGAAGCTTGAGCCTCTCAATCTAACCATCAACGAGATCAAGCCCGATGGAAATTGCTTATATAGAGCAGTTGAGAATCAA
97226 C T GCCGCTAGAGAACAAAGAATAGAAGAACAAATAAATGGAGTAAGCGACCGCATGATCGAAAACGTACTGCTACAAAAGAAGCTTGAGCCTCTCAATCTAA[C/T]CATCAACGAGATCAAGCCCGATGGAAATTGCTTATATAGAGCAGTTGAGAATCAACTACTCCTTCACCCTCGCAAAATGTCGCAAA
97226 A G GCGACCGCATGATCGAAAACGTACTGCTACAAAAGAAGCTTGAGCCTCTCAATCTAACCATCAACGAGATCAAGCCCGATGGAAATTGCTTATATAGAGC[A/G]GTTGAGAATCAACTACTCCTTCACCCTCGCAAAATGTCGCAAAATTACACTTACCAAGACCTTAGAGCTATGGCTGCAAAGTACATG
97226 A C AAAACGTACTGCTACAAAAGAAGCTTGAGCCTCTCAATCTAACCATCAACGAGATCAAGCCCGATGGAAATTGCTTATATAGAGCAGTTGAGAATCAACT[A/C]CTCCTTCACCCTCGCAAAATGTCGCAAAATTACACTTACCAAGACCTTAGAGCTATGGCTGCAAAGTACATGAGGGAGCATTC
97232 A G CCGAAGGCAGTACTCCATTGCCCGAATTACGGTTCTCAGAAGATATATCAGCCACAAGAGGGGCGACAGCTGCAGCTCCGCCTAATCTGCTCATGCTTAG[A/G]ACCTTGACTTGGAGCTGTAAGAACTTCACGTAGTCGATGATCTCATCCAGCATTGAAGCCTTGTCCGTCTTGTTAGCATTAGGCACC
97238 GA G AGATCTACCTTTTCCGTTGATCGATTTAGTGCAAATTTGTAATGTTCCTTTTCAGCCTCTTTCACTGGCCCGGTTCCTTACTGCCCTGTCTTATGGAAGC[GA/G]ACGCGTTGATGCTCCTGAGCTCAGAGCGAAAGCAATTAACTTGGCGATGCCAGCGCCCGATGTAAGTTCACCCAAAAGTAGTTCCTAA
97244 A G TGGGATATGTAAGTTTGTAATCAATAACCATGACCTTTCTTAAGGTGACAAGGCTAAACAAGCCAAGAAAGCTAACGACAAACATAAAACTAATCATCCA[A/G]CCCAAGGATGGATTTTTAATATCTTCAGCTCTGTTACCAGGATAATCAGCTCCGATAAGCTCATATGTATTCTGATCCATTGATAGCA
97244 T C TCAATAACCATGACCTTTCTTAAGGTGACAAGGCTAAACAAGCCAAGAAAGCTAACGACAAACATAAAACTAATCATCCAACCCAAGGATGGATTTTTAA[T/C]ATCTTCAGCTCTGTTACCAGGATAATCAGCTCCGATAAGCTCATATGTATTCTGATCCATTGATAGCATGTATGATCCAAACCCCCCAC
97244 G A TAAACAAGCCAAGAAAGCTAACGACAAACATAAAACTAATCATCCAACCCAAGGATGGATTTTTAATATCTTCAGCTCTGTTACCAGGATAATCAGCTCC[G/A]ATAAGCTCATATGTATTCTGATCCATTGATAGCATGTATGATCCAAACCCCCCACTAAATGCCAACCCATAGCAAGCCACAACACAAG
97260 T C CTGATTTACTGAGGTTCCATTCGACTAAAAGTGGAGATGAAATGACTAGCCTGAAAGACTACGTAACCAGAATGAAGGAGGGTCAGAAGGATATTTACTA[T/C]ATCACTGGGGAAAGCAAGAAGGCGGTTGAGAACTCTCCGTTTTTGGAGAAGTTGAAGAAGAGGGGATATGAGGTGCTGTTCATG
97268 A G TCGTCATAATACTCCTCTTCAAGCTCCTCTGAAGAGGTAAAGAAAGGCAGCCTCTTATTTGTGCGCTGCTCCATGCCAAACAATGACCTCTCCCCTTGAA[A/G]GAAGAGAGTGTAACCAGGGTTTGAAGAAGAAGAAGAATCGAAAATCAGACGACCAGAATCCATCATTTCAGATCACTCAACAACAGG
97276 A G CAAATGCCTTAGCAAATTTAACCGCAACATGTCCTAACCCACCTAACCCGACAATTCCAATATGTTTTCCAGCCTCATTAAGACCAAAATTCTTCATAGG[A/G]GCAAAAACAGTAATCCCCGCACACAACAGAGGTGCACCCTTATCCAGAGGCAAGTTTTCAGGATATTTTACAACAAAATGTTCGTCGAC
97276 G T CCCCCATAAGTCATAGTGTTGTCTTTGTCAAGGGAGTTGTACGTTAGTATCATTTTTGGGCAGTGATTTTCAAGGTCTTCTTTGCAACTTGGGCAAGATC[G/T]GCATGAGTTCACCAAACATCCAACACCTACTTTGTCTCCGATTTTCACTTTAGCCACCTTGCTCCCAACTTCAGTGACAGTGCCAACAAT
97276 G T CTTTGTCTCCGATTTTCACTTTAGCCACCTTGCTCCCAACTTCAGTGACAGTGCCAACAATTTCATGCCCAGGAAGTACAGGATAGACAGCGTTTCCCCA[G/T]TCATTCTTGATGCAATGAAGGTCAGAGTGGCACACCCCACAATACAAAATCTTTATGGTGACATCTTCATTTCCATTTTTCCTCCTTGAG
97286 C T CACATGAAGTTTTGTTGCTCAATTTTAAGGATCCTTCCATTCAGTCTTTCGTGACCGAGTTGCAAAGAAGAATTAAGCTTCATCATGATGTGAAGGAAAT[C/T]AATGCCGAGAGTGGGATTGAAGGAGAAGAGAAATACCGTGGGTTCAATTCGGATAAAATGAAGGGATTGCCTTTCGAATTTGTTGCT
97286 T C TGTTGCTCAATTTTAAGGATCCTTCCATTCAGTCTTTCGTGACCGAGTTGCAAAGAAGAATTAAGCTTCATCATGATGTGAAGGAAATCAATGCCGAGAG[T/C]GGGATTGAAGGAGAAGAGAAATACCGTGGGTTCAATTCGGATAAAATGAAGGGATTGCCTTTCGAATTTGTTGCTTTAGAAGCTTGT
97286 T C CTCAATTTTAAGGATCCTTCCATTCAGTCTTTCGTGACCGAGTTGCAAAGAAGAATTAAGCTTCATCATGATGTGAAGGAAATCAATGCCGAGAGTGGGA[T/C]TGAAGGAGAAGAGAAATACCGTGGGTTCAATTCGGATAAAATGAAGGGATTGCCTTTCGAATTTGTTGCTTTAGAAGCTTGTTTGGA
97286 G GA CAATTCGGATAAAATGAAGGGATTGCCTTTCGAATTTGTTGCTTTAGAAGCTTGTTTGGAGTCTGCATGTACTTGTTTGGAGACCGAGGCATCAACACTG[G/GA]AAAAAGAGGCGCATCCTGCCTTGGATAAACTGACATCGAAGATAAGCACACTCAATCTTGAACATGTTAGGCAAATTAAAAGTAG
97296 C T AACGTTCCATCATTCCATTATCCCCAAATCAATTTCAAACCCTAGTTAGGAAATGACCCACTTACTCCGCCGTCTTTCCTCCATCTTCACTCAACCTCCC[C/T]ACTCACTCAATCAGACACGCGGTATCCGGGTTGACGTTCCAGACGGCAACCTTGAACGAGCCTTAGCAATATTGCAAAGAAAAATGCAGA
97296 C A AATCAATTTCAAACCCTAGTTAGGAAATGACCCACTTACTCCGCCGTCTTTCCTCCATCTTCACTCAACCTCCCCACTCACTCAATCAGACACGCGGTAT[C/A]CGGGTTGACGTTCCAGACGGCAACCTTGAACGAGCCTTAGCAATATTGCAAAGAAAAATGCAGAGATCGGGAATGGAAAGGTTGATCA
97296 T C TATTGCAAAGAAAAATGCAGAGATCGGGAATGGAAAGGTTGATCAAGAGGAGGGCCGATTACGGGGAGAGGCACATGAAGAATACAGAAAAGAAGGTTCT[T/C]GCCAGAAAGAATCTTGAGCGGCGAATCCAATCTCAAAAGCTTGCCCGGAGTCTGCAGAATATCATTGTTAAGAAGATCAGGAA
97300 T C ACGTGCCCACAAATGATGTTTCTCTAATACAAAGGTATCCTTCATACTGTGGATCCAATAAATGGCCTCATGCATCTTTGCCAGAACTCGAAATCGCATT[T/C]AAGGCACTTGGAAAAATGATGTTGGATGTTGGGCTTATGCTGGCTTTTCATTGTGATCAATATGTATCTAAAACATCACAATTGAAAGA
97300 T A TGTGGATCCAATAAATGGCCTCATGCATCTTTGCCAGAACTCGAAATCGCATTTAAGGCACTTGGAAAAATGATGTTGGATGTTGGGCTTATGCTGGCTT[T/A]TCATTGTGATCAATATGTATCTAAAACATCACAATTGAAAGAGTATGAGGGTCTTGAGAAAATACTTGATCGTTCCAGGTGTCACAAA
97300 A AAGC GCATCTTTGCCAGAACTCGAAATCGCATTTAAGGCACTTGGAAAAATGATGTTGGATGTTGGGCTTATGCTGGCTTTTCATTGTGATCAATATGTATCTA[A/AAGC]AACATCACAATTGAAAGAGTATGAGGGTCTTGAGAAAATACTTGATCGTTCCAGGTGTCACAAAGGCCGATTGTTATATTACTTT
97300 G A CTTTTCATTGTGATCAATATGTATCTAAAACATCACAATTGAAAGAGTATGAGGGTCTTGAGAAAATACTTGATCGTTCCAGGTGTCACAAAGGCCGATT[G/A]TTATATTACTTTCCAAAGCTAAAAAGCCAATGCTTGGAAGATTCAGGATCGGTATCCTCATGGTGTGGTTGGCATACTGACCACGGTT
97306 A AT CAGTATTGCCCATTGCTGTCTGTGCTCTTGCTGATGCCACTGGTTTTATGCCACTGCCAAAAATTAAAGCTCTTGCAAGCAGCGCTGTGTTCTATACGCC[A/AT]TTTTTGAGACAAATTTGGACATGGTTGGGTTTGGTACCTGCATCGAGACAGAACTTTCAATCTTATCTGGAGCGCGGCTATAGCTGTG
97316 A G TTGATGTAACCATGACGCTCTGCATAATCAACGGCACGCAGTTTAGCTGCCCCCTTTCTGTGTTTCGTGTGGGCTTTGAATATACCCCCCGCACCTTTAC[A/G]TTGACTTCTAATTACTCGACCCATTGTTGCGATCTCACGATCACCAAACCGGAAAGCCAGTAGGCCAAC
97322 AT A TAACAAGAACGTAGCAATTACTTCTGCAAAGATCTTTCTTAGTAGAAACTCTTTAGCTAATAACTCCCCAAGTTCAGTCGAAACAGCTGAAATATTACTA[AT/A]TTTTTCTTGGATAACTTTGATCATGAGATGCTGCTGCTGATACACTGCCATTTATATCCAGCGATTTTTGATTACTTGCAATTGATGATC
97328 A G GATAACCGACCACTTTTTGCAGCCAAAGACATCATACCATTTTATTTGGAAAATGCTGCAAAGATATTTCCTCAAAAGAGGCATTTTGCTTCACTGCACA[A/G]TTTCTTCAGCTTCATCCACGGACCAAGATATAACGGCAAGTATTTGCACGCCATGATACAGAAATTACTTGGCAAGACGAAGCTGCAT
97342 A G GTATATATTCTGCGCAGCCTATCCTGTAAAGTACACGAGCATGGATATTTACAGAAAACCCCCCTACTACGGAATATCTTACATATGGTATCCTCTATTT[A/G]CATTATTATCTCCATTAAAGTACGCTCCGCTGCTCCCAGGAGCATTGTACCCTTGCACGAAACCCAAATCATTGGCTTCGCCGGCCACCG
97342 T G CTGCGCAGCCTATCCTGTAAAGTACACGAGCATGGATATTTACAGAAAACCCCCCTACTACGGAATATCTTACATATGGTATCCTCTATTTACATTATTA[T/G]CTCCATTAAAGTACGCTCCGCTGCTCCCAGGAGCATTGTACCCTTGCACGAAACCCAAATCATTGGCTTCGCCGGCCACCGTTACCGCC
97342 C A CTGTAAAGTACACGAGCATGGATATTTACAGAAAACCCCCCTACTACGGAATATCTTACATATGGTATCCTCTATTTACATTATTATCTCCATTAAAGTA[C/A]GCTCCGCTGCTCCCAGGAGCATTGTACCCTTGCACGAAACCCAAATCATTGGCTTCGCCGGCCACCGTTACCGCCTCGTCGTACCGTTCC
97342 C T GTAAAGTACACGAGCATGGATATTTACAGAAAACCCCCCTACTACGGAATATCTTACATATGGTATCCTCTATTTACATTATTATCTCCATTAAAGTACG[C/T]TCCGCTGCTCCCAGGAGCATTGTACCCTTGCACGAAACCCAAATCATTGGCTTCGCCGGCCACCGTTACCGCCTCGTCGTACCGTTCCCG
97362 G A GTTTGGCTATGATGTTGGTGTTTCAGGTGGTGTGACTTCCATGGACGATTTTCTAGTAAAGTTCTTCCCAAAGGTCTACGAACGCAAGCATCAGAAAATC[G/A]TTGAAAGCAACTACTGCAAGTACGACAACCAAGGCCTTCAACTCTTCACTTCATCTTTATACCTCGCTGGACTCACATCAACTTTCTTT
97362 T C ATCAGAAAATCGTTGAAAGCAACTACTGCAAGTACGACAACCAAGGCCTTCAACTCTTCACTTCATCTTTATACCTCGCTGGACTCACATCAACTTTCTT[T/C]GCTTCTTACACCACTCGCACCCTTGGTCGAAGACTGACCATGCTCATTGCTGGCATCTTCTTCCTCCTTGGTGTCATCCTCAACGGCTGTG
97362 C T TTGAAAGCAACTACTGCAAGTACGACAACCAAGGCCTTCAACTCTTCACTTCATCTTTATACCTCGCTGGACTCACATCAACTTTCTTTGCTTCTTACAC[C/T]ACTCGCACCCTTGGTCGAAGACTGACCATGCTCATTGCTGGCATCTTCTTCCTCCTTGGTGTCATCCTCAACGGCTGTGCTATGAACCTCA
97362 C T CCCTTGGTCGAAGACTGACCATGCTCATTGCTGGCATCTTCTTCCTCCTTGGTGTCATCCTCAACGGCTGTGCTATGAACCTCACCATGCTTATCATCGG[C/T]CGTATCCTCCTCGGTTGCGGCGTCGGTTTCGCCAATCAGGCTGTGCCGCTCTTCCTCTCCGAGATAGCCCCTACGAGAATCCGAGGCGG
97362 C T GACTGACCATGCTCATTGCTGGCATCTTCTTCCTCCTTGGTGTCATCCTCAACGGCTGTGCTATGAACCTCACCATGCTTATCATCGGCCGTATCCTCCT[C/T]GGTTGCGGCGTCGGTTTCGCCAATCAGGCTGTGCCGCTCTTCCTCTCCGAGATAGCCCCTACGAGAATCCGAGGCGGGCTTAACATACT
97362 A T ACCCATGGGGATGGAGGCTATCCTTAGCCCTGGCCGGAATACCAGCAATGTTGCTGACGGTTGGAGCGCTTCTTGTGGTTGACACACCAAACAGTTTGAT[A/T]GAAAGAGGCCATGTGGAAGAAGGAAAAGCCGTGCTGAAAAGGATAAGGGGAACCGACAATGTGGACGATGAATTCAATGAGAT
97372 A G CGCCCAAGACATTCCCTTCTCCTCCGCGGCCTCCACCTACGCCACCATCTCCACCTCCACAATCACCAAAGCCCTGCGCACCCGCAAATCGACTTCCGCC[A/G]CGTGGAACGACAAGTTCCTCTTCCGCCTCACCTCCTCCTTCTTCCTCTCCTCCTCCTTCATCATCAAAATCTACTCCCACCGCTCCGCCTT
97374 C T CTGTGGACAGAGTTCTTGGCTCCATGGTAAGGGCTGTATCGAGGGAGAGCTGTACATATGCGCGGGTCAGGCGGGCTCAGCGGCTGAGGAGTTCAACGAC[C/T]GCACTCACGCCTGTGTGGGAGGCAGAGTGGAGAAAACTGACTCCTGCTGAGTGCTACCGTCATCCATGACAACATCGAGAAAA
97386 A T AACTACATTCTGAACTTGCCAATACTGAACAAAGAGCACGTGCAGCAGCTGCTGTAGCTGGGGAATCCAATCGCGTTTCGTTGTATCCACAACTCTATGG[A/T]GGTAGTCAGGTAACATATGGAGGAAGCTCGTATCCAACCACCTATGGATTGTATCAGTCTTCAGCTCCAATGGATGAAGGTAGTCTG
97386 A G TCAGCTCCAATGGATGAAGGTAGTCTGCAACGGTATCAGTCGCCGATTATTGCATCAGCTCCTTACAATACAGGGCCAGTAACTGCAGATGGTGTCTATC[A/G]GTATCCATCATTGGCTATTCGGTCAGTTCCTTACAACACGCAACAAAATCCACCTACCATATGATTTTTGTGGTTATAAGAGAGTGCC
97410 A G TCAGGTAAGCAGTACGCACAGCCTCCCCATGATCCTCAGGGACAGACATGGCATCTCCATACAAGGTGATTACTGTATCAGTCCTATCTTCAGGATCTTT[A/G]GCAACAAGCAAAGAGCATCTAGGATTACCCAATAGATTCTTTGAGTGGACTGCTAAACTACTAATGGCTAATATTGGAGCTCCATCG
97414 G T TTGATTGGCGGTGCCTTGACGGTGGATAACTCACATCACTGGTATGATGTCGTTGTGGGCGGGATAATTGGCGCAGCATGTGCGCTTGCTGCATTCCGGA[G/T]GTCTTTTGCCTCTATTTGGGATCACAGGTTCAATCACATCCCTCTTCCTCGACCAAGCTCTGCATGGAACCCGCTTGTCTCGTCCAGG
97418 G A AGTCCCTGCTGCTTCTCCATGCCATCCCCAAGTACTACAGCCTGTCCGAGTTCAAAAACATCAGCGGCACAGGTCCTGTGTCCACGTTCGGAGGCGGTCA[G/A]TATGCCCTGAACCTGACGGATGCGGCTGGCACGATCAAGATCAACTCGGACTGGGCCGACACGAAGATCGTGAGCAGCGTGGTGT
97418 G A GAGGCGGTCAGTATGCCCTGAACCTGACGGATGCGGCTGGCACGATCAAGATCAACTCGGACTGGGCCGACACGAAGATCGTGAGCAGCGTGGTGTCCAC[G/A]TACCCGGTTGCCGTGTACGAGGTGGATAAGGTCCTGCTGCCCAAGGCCGTGTTCGCCGTGCAGCCCCCTTTGGCTCCTGCTCCG
97420 G A ATCAAGACGGATAGGAGCTAGATTCATCCATATACACACAAACATGTGTGTACTATATACATACATAAATATGCCTCTCTACAT[G/A]GATATATAGAGCCCAATTCATAAATCTACTACATATCATTAAGCCATTCTGCACCGCATTCAAATGGCAGCAACCAAGTCTGATCACTCCTCACTTATCT
97420 T C CCGCATTCAAATGGCAGCAACCAAGTCTGATCACTCCTCACTTATCTACAGAGGCTGACATACAAACGTGGAATACATATAGTCTTAGTACCCTTAATAT[T/C]TACCAGATGTTCATGCGCATACTGCTTATTTTGCAAATAGATAGATAGATGGTAGTCTACTAGTTAATTGGCACTTGTTCTTTTGCAGG
97420 T C AGTCTGATCACTCCTCACTTATCTACAGAGGCTGACATACAAACGTGGAATACATATAGTCTTAGTACCCTTAATATTTACCAGATGTTCATGCGCATAC[T/C]GCTTATTTTGCAAATAGATAGATAGATGGTAGTCTACTAGTTAATTGGCACTTGTTCTTTTGCAGGTGGATCAGGGAATGGAACATGAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97420 T C ATTTTGCAAATAGATAGATAGATGGTAGTCTACTAGTTAATTGGCACTTGTTCTTTTGCAGGTGGATCAGGGAATGGAACATGATGATGCGGGACTTCAC[T/C]GGGTGGATCATTCTTTTTCGAAACAGGTTTGTTGTCACTGACAAGTTGTTCTTTTGCAGGTGGCGTACGTTCACAATGGTGATGACC
97420 C T AGATGGTAGTCTACTAGTTAATTGGCACTTGTTCTTTTGCAGGTGGATCAGGGAATGGAACATGATGATGCGGGACTTCACTGGGTGGATCATTCTTTTT[C/T]GAAACAGGTTTGTTGTCACTGACAAGTTGTTCTTTTGCAGGTGGCGTACGTTCACAATGGTGATGACCAGGTGGGTCATTCTTTCCTA
97440 C G CATTTTGAAAACCAAGCCTACATTAAAAAAAAAATGCATATATATACAAGTTTCAACTCCAT[C/G]GTATACGCCAGTTTAACACAATCCAAAAAGACTCATCAAACAAGGATAGCTACAAGCTCATCCAACGACTTCAAGGTCTTCTCATAGTAAAGGTAAGATT
97440 A AAAAAGATTCATTTTGAAAACCAAGCCTACATTAAAAAAAAAATGCATATATATACAAGTTTCAACTCCATCGTATACGCCAGTTTAACACAATCCA[A/AAAAAGATT]AAAGACTCATCAAACAAGGATAGCTACAAGCTCATCCAACGACTTCAAGGTCTTCTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCT
97440 A G TTGAAAACCAAGCCTACATTAAAAAAAAAATGCATATATATACAAGTTTCAACTCCATCGTATACGCCAGTTTAACACAATCCAAAAAGACTCATCAAAC[A/G]AGGATAGCTACAAGCTCATCCAACGACTTCAAGGTCTTCTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATC
97440 G A AAAACCAAGCCTACATTAAAAAAAAAATGCATATATATACAAGTTTCAACTCCATCGTATACGCCAGTTTAACACAATCCAAAAAGACTCATCAAACAAG[G/A]ATAGCTACAAGCTCATCCAACGACTTCAAGGTCTTCTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATCCAA
97440 C T AAATGCATATATATACAAGTTTCAACTCCATCGTATACGCCAGTTTAACACAATCCAAAAAGACTCATCAAACAAGGATAGCTACAAGCTCATCCAACGA[C/T]TTCAAGGTCTTCTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATCCAACTGGGACATGTTTTCAACCACGTCA
97440 T C TAGCTACAAGCTCATCCAACGACTTCAAGGTCTTCTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATCCAACTGGGACATGTT[T/C]TCAACCACGTCATTAGCGACCTTGACGTAGGACCTTCGACTGCTCTCAGGCACAGTGGCCATGGCGTTCTTCAAATCAGAGTCGAGGT
97440 C T CTCATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATCCAACTGGGACATGTTTTCAACCACGTCATTAGCGACCTTGACGTAGGAC[C/T]TTCGACTGCTCTCAGGCACAGTGGCCATGGCGTTCTTCAAATCAGAGTCGAGGTAGGCGGACTTGAGCCTGATGTAGAACATGACGT
97440 T C CATAGTAAAGGTAAGATTCATACACCTTCGGACTCCTAACATACCTATCCAACTGGGACATGTTTTCAACCACGTCATTAGCGACCTTGACGTAGGACCT[T/C]CGACTGCTCTCAGGCACAGTGGCCATGGCGTTCTTCAAATCAGAGTCGAGGTAGGCGGACTTGAGCCTGATGTAGAACATGACGTAC
97444 A G TGCGACAGAGTCAAGCAACGGGGCGAGCGCGAGTGGGGCAGATACATTGCTTGGGGCGATGCTGGTGATCGCGAGCTGCTTCGCTTACGCGGTGTGGTTC[A/G]TTATTCAGGCGAGGATGAGCAAGACTTTCTCCTCCCCTTACACCAGCTCCGCCATCATGTGCTGGATGGCCTCGGTCGAATGTTT
97444 G T GCAACGGGGCGAGCGCGAGTGGGGCAGATACATTGCTTGGGGCGATGCTGGTGATCGCGAGCTGCTTCGCTTACGCGGTGTGGTTCATTATTCAGGCGAG[G/T]ATGAGCAAGACTTTCTCCTCCCCTTACACCAGCTCCGCCATCATGTGCTGGATGGCCTCGGTCGAATGTTTTGTTTTTGGTTTCGC
97444 C T CCGCCATCATGTGCTGGATGGCCTCGGTCGAATGTTTTGTTTTTGGTTTCGCTGTCGAGCGCAAGGCCCAGGCCTGGGCTTTGGGTTGGGATATCCGGCT[C/T]TACACCGTCTTGTACCTGGGATTGATAGGGTCGGGATTTGCGACGGCGCTCATGTCGTGGTGCATAGAGAAGAGAGGTCCACTATT
97444 G A CATGTGCTGGATGGCCTCGGTCGAATGTTTTGTTTTTGGTTTCGCTGTCGAGCGCAAGGCCCAGGCCTGGGCTTTGGGTTGGGATATCCGGCTCTACACC[G/A]TCTTGTACCTGGGATTGATAGGGTCGGGATTTGCGACGGCGCTCATGTCGTGGTGCATAGAGAAGAGAGGTCCACTATTTGTGTCA
97444 C T GGTTTCGCTGTCGAGCGCAAGGCCCAGGCCTGGGCTTTGGGTTGGGATATCCGGCTCTACACCGTCTTGTACCTGGGATTGATAGGGTCGGGATTTGCGA[C/T]GGCGCTCATGTCGTGGTGCATAGAGAAGAGAGGTCCACTATTTGTGTCAATGTTCAACCCCTTGCTTCTCATCATAGTCGCGGTTT
97444 A G TGGGTTGGGATATCCGGCTCTACACCGTCTTGTACCTGGGATTGATAGGGTCGGGATTTGCGACGGCGCTCATGTCGTGGTGCATAGAGAAGAGAGGTCC[A/G]CTATTTGTGTCAATGTTCAACCCCTTGCTTCTCATCATAGTCGCGGTTTTAGGGTGGGCAGTTCTAGACGAGAAGCTCTACATGGG
97444 C T TCTACACCGTCTTGTACCTGGGATTGATAGGGTCGGGATTTGCGACGGCGCTCATGTCGTGGTGCATAGAGAAGAGAGGTCCACTATTTGTGTCAATGTT[C/T]AACCCCTTGCTTCTCATCATAGTCGCGGTTTTAGGGTGGGCAGTTCTAGACGAGAAGCTCTACATGGGAACGATAATAGGATCGGC
97444 C T TCAGTCAAGATACGAAGTGCGTGAATGACAACGATGAAGAGGGTGACGATTGTAGGAGTATTGGTCTGCCTGTGTATTACAGTCCTGGTAATGAAGGCGT[C/T]GTCGTGCACAAATGATGCAGTTCTGCGACTGAACCTTTAGGAGAAACGGACTTGTGCGAGTTTG
97456 T A GAAGTTGGTAAGACAGACGGTGAAGTTGACAAGGCTGCTGAAGAACTTGGCAAAGCCGATATGGAAGCTGACAAGGTCGGTTTAGAAGCCAAAAAGGTCA[T/A]TGTAGATGCTGACATGGCTGATGTAGAAGTTGAGCAGGCCAATATAGAAGCTGAAGAGGTTGAGAAAGAAGCTGGTAAAGCA
97456 G A AGAAGTGGCTGAAATGGAAGGAGGATCTGTGAAAACTGATTCTGGAGTAGCCTATCAAGATTCTGAAGTCAGAACTGAAGAAGCAGCGGCGAAAATCATT[G/A]AAAGTGCTCCAGAAAATCCTAAAGATACAAGCGAGAAATCTGAGTCTGCTGAAGCAACCAAAGAAGTAGCAACCGACGAGCATA
97474 C T TTCTGCCCTCTGCTAATCTTAATAAAGTGGAACCTTCTCAGGTCAACGCTGCACCAAATGTCGATATACAACCAGCAAATGATCAGAATGTAACATTAAA[C/T]CATTCGAGCGCACCATTTGTGCCTGATGCATCGGCTCAGCAGCAACAGCAAATGAATACAAATATGAGCATGCCTTACCAGGCTGTGC
97474 G A CAACCAGCAAATGATCAGAATGTAACATTAAACCATTCGAGCGCACCATTTGTGCCTGATGCATCGGCTCAGCAGCAACAGCAAATGAATACAAATATGA[G/A]CATGCCTTACCAGGCTGTGCCAAATGCTGCAAACATGGGATGGGGAATGATGGCTGCAGAGACACCACCAATGAACGCGAACATG
97474 A G AGCTGCTAATATGAACATGGGGTGGGGTCCTATGCCAGCTCAGCAAATGGGGAACCCCAACATGAATGTAGGGTGGGTGATGCCAGGTCAAGGAATGCCA[A/G]TGCAGATGAACCCCGGTTGGGTTGCTGCACCAAACCATGGTGATGGCGGTTGGGTTGCACCGCAAGCACCAGGTATTAATGCT
97474 G C ATGGGGAACCCCAACATGAATGTAGGGTGGGTGATGCCAGGTCAAGGAATGCCAATGCAGATGAACCCCGGTTGGGTTGCTGCACCAAACCATGGTGATG[G/C]CGGTTGGGTTGCACCGCAAGCACCAGGTATTAATGCTAGTTCTCAACTGAATCCTAATACTGCACCAGCACCAGCACGCGTTGG
97474 G A GGTCAAGGAATGCCAATGCAGATGAACCCCGGTTGGGTTGCTGCACCAAACCATGGTGATGGCGGTTGGGTTGCACCGCAAGCACCAGGTATTAATGCTA[G/A]TTCTCAACTGAATCCTAATACTGCACCAGCACCAGCACGCGTTGGAATTTGCTTCCAGTTTTCCAAGACTGGCCACTGCAAAAAAG
97478 T A AGAGAACATCGGTCACACCTTTTCCTTCAGTGCCTGGAAGCCATGCAGCAACAAGTGCATCCATGTACCCGACATATGGTTCCATAACAACCGGCCTACC[T/A]GACACAACCACCACCACACATTTCACATTCATGCACACGTTTTTTATCGTTGTCGGACCCGGTTCTGGGATTGTCAAATTAAAATTGTC
97478 C T CACTTGTCTCTGAGTATGGTGTTTCACCAACTACGACAATAGCATAGTCGAAGTTGTTGCTTTTGATGAAGCCAGGGTCTGGATTTTCCGAGGTGATCAC[C/T]GTGGTTGTAGGATTCACCGTTGATTTTATTGCATCAAGAATAGTAGTTCCAACGGTGATTTTTCCACTTGCACCATGCCACTCAATAGT
97478 G C TTGTCTCTGAGTATGGTGTTTCACCAACTACGACAATAGCATAGTCGAAGTTGTTGCTTTTGATGAAGCCAGGGTCTGGATTTTCCGAGGTGATCACCGT[G/C]GTTGTAGGATTCACCGTTGATTTTATTGCATCAAGAATAGTAGTTCCAACGGTGATTTTTCCACTTGCACCATGCCACTCAATAGTCCA
97478 T C TCTGAGTATGGTGTTTCACCAACTACGACAATAGCATAGTCGAAGTTGTTGCTTTTGATGAAGCCAGGGTCTGGATTTTCCGAGGTGATCACCGTGGTTG[T/C]AGGATTCACCGTTGATTTTATTGCATCAAGAATAGTAGTTCCAACGGTGATTTTTCCACTTGCACCATGCCACTCAATAGTCCATCCAC
97478 T C GTTTCACCAACTACGACAATAGCATAGTCGAAGTTGTTGCTTTTGATGAAGCCAGGGTCTGGATTTTCCGAGGTGATCACCGTGGTTGTAGGATTCACCG[T/C]TGATTTTATTGCATCAAGAATAGTAGTTCCAACGGTGATTTTTCCACTTGCACCATGCCACTCAATAGTCCATCCACCGCACTG
97478 A C CATAGTCGAAGTTGTTGCTTTTGATGAAGCCAGGGTCTGGATTTTCCGAGGTGATCACCGTGGTTGTAGGATTCACCGTTGATTTTATTGCATCAAGAAT[A/C]GTAGTTCCAACGGTGATTTTTCCACTTGCACCATGCCACTCAATAGTCCATCCACCGCACTG
97482 A C GGATCATATTCCTATGATTTTTATGTTATTATCAAGCCTAGCAACAATGCAGCTAGTCAGCAAACATAGTACTGAATCAAATCAAGCGATTCATTTTCGG[A/C]CTCTCCATTCTCCAGCATCCAAAGCAGATGCTCGAACAACACCACTTCACATCCTACTACCATCTCCCCTCCTTCGTCTTGCAAGAGCTC
97482 T C AAGAGCTCTCGTACCAAAGGGTGCCCTATGACTTCATGTGATACCATGTACCTACGCCTCGACTTCCCTACATACACAGGGTGCAGCTCGCACGACATGT[T/C]CATGTCTTCATTCTCCGCGGTTGATGTCGTGGCTGTTTGACCCGTTAATGATGGTAGCCGTTTAAGCATTGACCTGAGCTTGCTCAAC
97482 T C CATGTGATACCATGTACCTACGCCTCGACTTCCCTACATACACAGGGTGCAGCTCGCACGACATGTTCATGTCTTCATTCTCCGCGGTTGATGTCGTGGC[T/C]GTTTGACCCGTTAATGATGGTAGCCGTTTAAGCATTGACCTGAGCTTGCTCAACTTCTTTACACCAAACTTTGCCATTTTTTTTATATCC
97490 T C CTTCATCATTCCTGAATAAAATTTGTAGAGCTTGGAAAGAGATTGAACTGCCCAAAATGCATTGGATAGACACGAGCATGCAACAGAGCAAAATATTTCA[T/C]GTAGGTGGTCACAAAGAAATGAAAACTCTCCTTTGAACGAGCAAGACTAGGGAAAAGGAGGCGCAGAAGGGCATGCCATTTGACG
97490 G A ATTGGATAGACACGAGCATGCAACAGAGCAAAATATTTCATGTAGGTGGTCACAAAGAAATGAAAACTCTCCTTTGAACGAGCAAGACTAGGGAAAAGGA[G/A]GCGCAGAAGGGCATGCCATTTGACGTGACTTTCAGGCAGGGCTCAGAGTTGTTAATGCCCGCTACCTGGATGTGGAGGATGGAG
97490 A G AAGAAATGAAAACTCTCCTTTGAACGAGCAAGACTAGGGAAAAGGAGGCGCAGAAGGGCATGCCATTTGACGTGACTTTCAGGCAGGGCTCAGAGTTGTT[A/G]ATGCCCGCTACCTGGATGTGGAGGATGGAGATGTCATTCCTTGGATTATCTTTGAGGTACTACTACAGATAGGGTTATGGACGTC
97490 T TA TTCCTTGGATTATCTTTGAGGTACTACTACAGATAGGGTTATGGACGTCTACCGCGATTGTTGGCAATGGTTGGAATGGTCAAAGCGAGGCTGCACATCT[T/TA]AAAAATGGCATGCTCGATCGAAGATGTTTAGCATTAGGGAAATGAATAAGTTTGGTGTCATTTTGGAAGCTGTTACATTTTATTTAG
97490 AT A AAGCGAGGCTGCACATCTTAAAAATGGCATGCTCGATCGAAGATGTTTAGCATTAGGGAAATGAATAAGTTTGGTGTCATTTTGGAAGCTGTTACATTTT[AT/A]TTTAGTTCACATAAGAGTTTGAAATTGCAAAGCTTGAGTGTAGAATAACTGAAAGATTAGTCCATATTTATAGAGAAAATTGAATGA
97492 CT C TCCTGACAGGGACTAAAATGACAAACTATAATCAGCAACTGGGAGCAGGATCATCATCTTCTTCCTATAGATATCTAAACTTAATTGCATGGGCGGCCTT[CT/C]TTTTTATTCATCAGGCCTTCCGTTTACTTTCATGTTGTGTAACTGGCAATCAATTGTATCTAGCAAAGGCGCAGTTTTGTCATAGATTG
97496 A G CTGTTGGCCTACTGGATATGCTTATATCCCGATATACGAGGATGTGGAGATTGATGGACGGGGAGAGAATGGCATGATCGTGAACTGGTGCAAGCA[A/G]ATCGATGTCCTGAGGCATCCGTCGGTGGGATGTTTTATGATGCACTGCGGGTGGAGCTCGACGCTGGAGAGTTTGTTTAGCGGAGTGC
97496 C T GAGTGCCGGTGGTGGCGGTGCCACAGTGGTTGGACCAGGGGACGAATGCGGCTCTCATGGAGAGGTTGTGGGGGAACGCGGTCTATTGCGAGACGAACGA[C/T]GATGGAATTGTGGAGGGAGATGAGCTGCGGAGGTGTTTGGAATTGGTTTTGGGGAGGGGGAAGAAGGTGTTGGGTTTAGA
97496 G A GTTTTGGGGAGGGGGAAGAAGGTGTTGGGTTTAGAGAGAAGGCTGAGATGTGGAGGAAGAAGGCCGTGGAGGCTTTGATGGAAGGGGGATCGTCGGATCG[G/A]AATTTGAAGACATTTGTTGATGGCGTGTCAAAGTCTCACGTTTGATGGATGGTAGGAGTAGCTAGGTGGAAGAATTTTGCTG
97514 C T TCCTCGACGCCGACAACGACGGAAGGATCAGCCCATCGGACCTGAAATCGGTCCTGAATTCCGGCGACGAGGTCATCAGCTCCATGATGACGGCGGCCGA[C/T]TCCGACCGAAACGGGTTCGTGGATTTGGAGGAGTTCGAGCGGGTTTTGAGGCCTGAACGCGGAAACGAGTTGATGAAGGAGAT
97514 T C CGGAAACGAGTTGATGAAGGAGATGTTTAGGGTGATGGATACGGATGGAGACGGCAAAGTTGGGTTCGTGGATCTGAAGCTGTTTCTGGACCGGGCCGGG[T/C]TGGTTATGTGTGACGAGGAGGTGAGGATGATGATTAGGATGAGCGGCGGGGATGAGTCCGATGGAATTGCCTTTGATGGGTT
97514 G A TGATTAGGATGAGCGGCGGGGATGAGTCCGATGGAATTGCCTTTGATGGGTTTCTTAAGATCCTGACCGTTGATTTTGGTTTGTGATGATTTTATGCGGT[G/A]GAGATTGTGCAACGTTACGGATGAAGAAGAGTGTTTAAATCAATTGAAGTACGTTTTTGGGATGCAAAAACTTCTGAATTTAATGTT
97530 T C CCTTCTTTGAATCCATCGAAAAGCCCCATTTCCTCACCACCGCAACAGCTCAACTGTGCCATCCCCTTCACGCTACTGTGCAAGCCGCGCCCAACCGGGG[T/C]CGTCTCCTATACCACCATCCGCCGACAACGTCCTCAGTTCGCACCCCCATAAATCCCGCGACTACCCCTTCACTCCTCCAGCAGAACTCG
97530 C T TCGCACCCCCATAAATCCCGCGACTACCCCTTCACTCCTCCAGCAGAACTCGCGCACAGCAAGAGGAAGACCCGAAGGCTGTCCGAACACGATGGGAGAA[C/T]TCGATGTATTTAGAGGAATTTTGAAGTAGGGTTTTTCTTTCTCGTTTTCATTTTGCTGAGACCTTGTTTTGTGGCGGCTCCTATCTTA
97542 A G CTACATCAACTTATTTGTCAAATGGGGGTACGATACAGATTCCGCATCCATGGGAATCTTTGATTCATGAGGTTGAGCTTGCTGTTGTGATTGGGAAGAA[A/G]GCCACAGAGGTTAGGGAATCTGCTGCCATGGATTATGTTGGAGGTTATGCTCTTGCACTGGACATGACTGCAAGGGAAATCGAACC
97542 A G CAAAAGGACAAGACACCTTCACTCCAATAAGTTCTGTTTTGCCTACATCTTTGATTAGAGATGCTGATGCCCTTGAATTATGGTTAAAGGTAGACAATGA[A/G]ATCAAGCAAAAAGGCTCAACTAAGGATATGATTTGTAAGATCCCATTTCTTATCAGTCATATAAGCTCGATTATGACACTAATGGAAG
97542 C A CTACATCTTTGATTAGAGATGCTGATGCCCTTGAATTATGGTTAAAGGTAGACAATGAAATCAAGCAAAAAGGCTCAACTAAGGATATGATTTGTAAGAT[C/A]CCATTTCTTATCAGTCATATAAGCTCGATTATGACACTAATGGAAGGGGACGTCATTTTAACTGGCACACCTGAAGGAGCTGGTCCA
97546 A C TTCGAACCTAAACAATGGAAACCTTAGCACCAACTTCCTCAAGCTTCTTCTTGGCTTCCTCAGCCTCCTCCTTACTAACCCCTTCCCTGAACTTCTTGGG[A/C]AGCCCCTCTATCATCTCCTTGGCCTCCTTCAGAGCTAGACCAGTCACTGCCCTTACAACTTTAATGGCAGCAATCCTGGCATTACTCGGCA
97546 A G TACTAACCCCTTCCCTGAACTTCTTGGGAAGCCCCTCTATCATCTCCTTGGCCTCCTTCAGAGCTAGACCAGTCACTGCCCTTACAACTTTAATGGCAGC[A/G]ATCCTGGCATTACTCGGCACTTCATCAATCATCACATCGAACTCTGTCTTCTCCTCCACCACAGCCGGCGCTGCATCTGCGGCCGGAGCA
97546 A G CTTCGATTTTTGGGGCGGTAGCGACGCAGTAGCAAGCGAAATTGGTGGTACGGCGGGATTGGGTTGTGAAAAGCAGGGATTTTGAGGACAGTTTAGTGGA[A/G]ACTGAGGCCGTTTTCGACGGTGAAGGTATGAGTGATAGAGTAGAGGAGATTATTGCTGCCATTTTTTCGTTTCTTTTTGGGGGA
97546 G A TGAGGACAGTTTAGTGGAAACTGAGGCCGTTTTCGACGGTGAAGGTATGAGTGATAGAGTAGAGGAGATTATTGCTGCCATTTTTTCGTTTCTTTTTGGG[G/A]GATGGAGCTGTTATTTGAAATGGAGGAGAGAAGGGAAGTCCAGGAGAAGAGGATCCAGTAGGCCAACAG
97550 A G GCAGATCAAAGATGCCAAACTCACTAGTAGTGAACATCCCATAGCTCTGACCCATAAACCTACTGCAGATAATTCTTCCTCATGGTTGTGCTCAAGATTG[A/G]GCTCATGATAATGATGATGAAATCCAGCAACAGCAAGATCTTCTTCTTCCGCTACTTCCTCCGGAAGTAGTTTCTTCCTACCAGAATGA
97552 TA T CCTGCCGATGGTGTACCCAAAGCAGAAAAAAGTAGACTTGAAGAGTCTGCTCTTAACGAAATGTGTGAAGTCCTAGGTGGAGGGTTAAGAGCTGATGAAA[TA/T]AAAGGATCTTTGGGCTGATTATGAGAACAATGCTTCAATAGAGGCCAACCTTGTGAAGGACTTTGACAAAGTGGAAATGATTCT
97556 A G TTGATTGGGGTGAAGAAGGTACTAGATCAGAAGCTGAAATTGCTGCCCTTCGAACTGCATTTTCTCAAGAAGTAGCTGTTTGGCACAAGCTTGATCATCC[A/G]AATGTTACAAAGTTTATAGGAGCTACTATGGGTGCAACCGGCCTTACTATTCAAACCGAGAATGGTTTGCTTGGCATGCCCACTAGT
97566 A C TTATTATTAGGAGGACGTGACAGTGCACGAACAAATGAGTTGAGAAGCTGCGTAACACCGTTGCCAAACACGATGAGCTTGTCATCAACCACAGCGTTAC[A/C]GACAGCATTATGCAGGCGTCTAATATATATTTCAAGCTCGATAGAGGTATAGTCCCGTGCTCCAGTAGGAAAATAGCTCATTCTGC
97570 C T TCGCACGTTGCATTTACTCAACAGTGGACAAACATCGATGCGTCTACACAAGTATCATTTGGGTTTGAAGTGTGGCACATAGAATTGATCGTAGGTCTTG[C/T]TCTCCTGGTAACATCCAGCCGCTACGTGTTGTTAAAGACATGGCCGGATTTTTCAGAATCTAGTGCAGCTGCAAATGAACAGGTTCTT
97570 A G TGCGTCTACACAAGTATCATTTGGGTTTGAAGTGTGGCACATAGAATTGATCGTAGGTCTTGCTCTCCTGGTAACATCCAGCCGCTACGTGTTGTTAAAG[A/G]CATGGCCGGATTTTTCAGAATCTAGTGCAGCTGCAAATGAACAGGTTCTTACCTGCTTGCAGCCTTTGGACTACCTTGTTGTGGCATT
97570 A G TTGGGTTTGAAGTGTGGCACATAGAATTGATCGTAGGTCTTGCTCTCCTGGTAACATCCAGCCGCTACGTGTTGTTAAAGACATGGCCGGATTTTTCAGA[A/G]TCTAGTGCAGCTGCAAATGAACAGGTTCTTACCTGCTTGCAGCCTTTGGACTACCTTGTTGTGGCATTTTTGCCTGGAATTAGTGAGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97570 A G TGTGGCATTTTTGCCTGGAATTAGTGAGGAGCTGCTATTCCGAGGGGCGCTGCTTCCATCTCTGGGACTTGACTGGAAGAGTGCCCTTGTAACTGGGGCA[A/G]TTTTTGGAGTCCTTCACTTGGGCAGTGGCAGAAAATATTCATTTGCTATATGGGCTACGTTTGTGGGTTTTGCTTATGGCTTGGCAA
97570 A G GCAGTGGCAGAAAATATTCATTTGCTATATGGGCTACGTTTGTGGGTTTTGCTTATGGCTTGGCAACCATCATTTCTTCCACTGCTGTTGTACCCATGAT[A/G]GCTCATTCATTGAATAATCTGATTGGTGGCTTCCTTTGGAATTATATGCGTCCAAAGCAAACAAAGATAGATCAACTCTGATCCTGAAT
97574 A G CCTCCTGGGCCATCATCTTTATAATTCTGTCAGGGTCATGAGGCGCATCGGAAGCAACTAATAGAGCTTCAAGCACGTGATCAGCAGCGATCCTGACATC[A/G]GCAATGAGACGGGAGGCGCGCGACAGTCTTTCCATCGCCGTTGAAACCTGTTTCGGAGGCGCATCAGAAGACGTAGCTTGCGGGG
97574 A T CTGTTTCGGAGGCGCATCAGAAGACGTAGCTTGCGGGGCCGATGCTATTGCTGCTGCCGTCGTCGGCGATTGGGCTCTTAACATTTTCGAAACAACGGAA[A/T]ATTTAATTCTGATATCTGAAGATGGGGTTCTGGTAGACTAACCGGCTGAAATTTCAACGGGGAGATACTGGAAGAAGCAGGAAAC
97582 AG A CATTTGCCGAAGGAACATGGGAGGTATTCGGTGTTTATAATGGAGGATGAGGTCGGAGAAGGGAAGGTGAAGGTGGAGGAGGTTTTGGAGAGATATGGGG[AG/A]GGAGGAAGTGAGAAGGATGATGTGGTGAGGATGATACCGACGTTGGTGTATAGGGATTCGAGGTTTGAGATGGAATATG
97598 A G CATCCTTGAAAGCATTACACTTAAAGCAGCTCGACCTGCTTGCGAAATTGTGGGTCCCACACTGACAGTACCAGTCTCCAAGCCTGACATCTGACCCAGG[A/G]ACAAAGCCATAAGAGGAACCGCTTCGGATGGCACTGAAGTCGCTAACAATCGAGCGAGGATCCCCACATCTCTGACATGACTCTCG
97610 G A TGAAAATCAACTGCTGGAAAATGCTCTTCGCACTTTGCTTCAAGAGCTAGTGTCATCAGCAGTACAATCTGGTGAAAGACTGATGCAATACGGACAGTCC[G/A]TTGATGATGGAGATAACGTTCATGGTCAAATACCACGTCTTCTTGATATCGTGTTGTACCTTTGTGAAAGAGGGCATGTTGAAGGTG
97618 A G TGGCCCGAATTTGCATTTCGAGCGCGGCAATGTAGTCCGTGGTCTCCTCCAGAAGCTTCGGAAACGGAAGTTTCCTGCATCCCGGAACTAGCCTGCTTAA[A/G]ACCTTGGCTTTCTTTTCGATCGGCCGGGCCTTGTTTACCGAGGATTTATGCGGCTTTTTAGTAAGAGTGGTTGGTGGTGACTTTCTCC
97618 G C CTCCTCCAGAAGCTTCGGAAACGGAAGTTTCCTGCATCCCGGAACTAGCCTGCTTAAAACCTTGGCTTTCTTTTCGATCGGCCGGGCCTTGTTTACCGAG[G/C]ATTTATGCGGCTTTTTAGTAAGAGTGGTTGGTGGTGACTTTCTCCTATGGCACTTTTGAGAAGGCGACGGGGCGGAGAGGATGGCA
97618 A T TCCTCCAGAAGCTTCGGAAACGGAAGTTTCCTGCATCCCGGAACTAGCCTGCTTAAAACCTTGGCTTTCTTTTCGATCGGCCGGGCCTTGTTTACCGAGG[A/T]TTTATGCGGCTTTTTAGTAAGAGTGGTTGGTGGTGACTTTCTCCTATGGCACTTTTGAGAAGGCGACGGGGCGGAGAGGATGGCAC
97628 A G CGGCTCCTGGTCTATGGATGACATTTCGGATTCCTCCTCGTTTAGTGGCTGGTGTAAGTTTCTGTCTTGCCTCCATATCTGCTGGGAAAAAGCATAAGAA[A/G]GAGCTCTTTCTCTCTTAAGAGCGGCATCTTTTTTGCTCTGTAGCATAGACTGAATCTCTTCCATTGTGCGAGGGCGATCGTCCCATTCA
97628 C T AGAGCTCTTTCTCTCTTAAGAGCGGCATCTTTTTTGCTCTGTAGCATAGACTGAATCTCTTCCATTGTGCGAGGGCGATCGTCCCATTCATCCGCTACGC[C/T]GCTCGACATAGATCTTCTTTCTGCCATTTCTTGGAAGTACCTAGAGTCCCAAAGAGAAGTATCGCAGTTGCTCAGGGAAGACTTTGTGC
97644 A G GGCTGACTGGACCCAGCACTAGACCTATGGTGGTAATACATCTGCAAGTCCTGAAGTCTCTTGCGCTCTGCCTCAAGCTGGGCCTCTAAATGCGCCTGCT[A/G]CTGTCGTGCCTCCTCTGCAACACGACGTAGCTCACCATCATAGTAATCTAGGCTACGCCTATGCTCTATATAGCCCGTATGCCTAATC
97644 G A CTATGGTGGTAATACATCTGCAAGTCCTGAAGTCTCTTGCGCTCTGCCTCAAGCTGGGCCTCTAAATGCGCCTGCTACTGTCGTGCCTCCTCTGCAACAC[G/A]ACGTAGCTCACCATCATAGTAATCTAGGCTACGCCTATGCTCTATATAGCCCGTATGCCTAATCCCCATCTGCATATCATACAGATCAT
97644 T C GTAATACATCTGCAAGTCCTGAAGTCTCTTGCGCTCTGCCTCAAGCTGGGCCTCTAAATGCGCCTGCTACTGTCGTGCCTCCTCTGCAACACGACGTAGC[T/C]CACCATCATAGTAATCTAGGCTACGCCTATGCTCTATATAGCCCGTATGCCTAATCCCCATCTGCATATCATACAGATCATGATATGAT
97644 C T CGACGTAGCTCACCATCATAGTAATCTAGGCTACGCCTATGCTCTATATAGCCCGTATGCCTAATCCCCATCTGCATATCATACAGATCATGATATGATA[C/T]CTGTGTAGGATCCGGGTAATCGTGATGGGCCGGAGGATGAAACACGTCAACATAACGATCTGATCCAATAGTGGGCACTGAACGAAA
97644 A G CCGTATGCCTAATCCCCATCTGCATATCATACAGATCATGATATGATACCTGTGTAGGATCCGGGTAATCGTGATGGGCCGGAGGATGAAACACGTCAAC[A/G]TAACGATCTGATCCAATAGTGGGCACTGAACGAAAACGCTAGCTGGGTTGGGTAATATCCTCGATAACAGGTGGATGTATGTCGTG
97644 T C TAATCCCCATCTGCATATCATACAGATCATGATATGATACCTGTGTAGGATCCGGGTAATCGTGATGGGCCGGAGGATGAAACACGTCAACATAACGATC[T/C]GATCCAATAGTGGGCACTGAACGAAAACGCTAGCTGGGTTGGGTAATATCCTCGATAACAGGTGGATGTATGTCGTGTCGTATAGC
97644 A G ATCCCCATCTGCATATCATACAGATCATGATATGATACCTGTGTAGGATCCGGGTAATCGTGATGGGCCGGAGGATGAAACACGTCAACATAACGATCTG[A/G]TCCAATAGTGGGCACTGAACGAAAACGCTAGCTGGGTTGGGTAATATCCTCGATAACAGGTGGATGTATGTCGTGTCGTATAGCA
97644 A G TCTGCATATCATACAGATCATGATATGATACCTGTGTAGGATCCGGGTAATCGTGATGGGCCGGAGGATGAAACACGTCAACATAACGATCTGATCCAAT[A/G]GTGGGCACTGAACGAAAACGCTAGCTGGGTTGGGTAATATCCTCGATAACAGGTGGATGTATGTCGTGTCGTATAGCAGATGACC
97656 T C ACGCGGACTCGAGCTGCTCGGAGCATGTGCTGTCGTCGGATTTCACTTCGTGCGACAGGGAGGTGCAGAGCCAGCTGAAGTGGGGGGAGCTCGAAAGAGC[T/C]TTGGCGGTTCCGTTTAACAACGTGAACGCCACTAGCTCGTTTCCGACGTTGGATAACGTGCCGTTATCGGATCCGTTACAGGAC
97656 C T CGGAGCATGTGCTGTCGTCGGATTTCACTTCGTGCGACAGGGAGGTGCAGAGCCAGCTGAAGTGGGGGGAGCTCGAAAGAGCTTTGGCGGTTCCGTTTAA[C/T]AACGTGAACGCCACTAGCTCGTTTCCGACGTTGGATAACGTGCCGTTATCGGATCCGTTACAGGACATATTTATGTATTTGCAAA
97656 C T ACGTACGGCGATGTGCTTGCGAAGGCTGAGACGCTGATTCAGATGAAGTTTGAGATGTAAGAGAGGGAGAGAGATGTTTGTATAGATTGTAGTAGTGGTC[C/T]TGTATATTGATTTCTAATTGATGAAATCGGAGGGCAAATCAATTGGTTATAGTTCAATAGTGTATTTTGGCATGTAGGAATGTTAC
97656 G A GACGCTGATTCAGATGAAGTTTGAGATGTAAGAGAGGGAGAGAGATGTTTGTATAGATTGTAGTAGTGGTCCTGTATATTGATTTCTAATTGATGAAATC[G/A]GAGGGCAAATCAATTGGTTATAGTTCAATAGTGTATTTTGGCATGTAGGAATGTTACTGAACTTGAAGGATGTGATA
97662 AT A TATGCATGTCGTTGTGGTTAGATCATCTTCTCAAGTGGCAGAGAGTATGAAGTAACCGGGAGATGATTATACGTGCAGCGATACATTTGAGAGGAATGTA[AT/A]TTTTTGTGGATATAGAAAATATTTACATTATAGTCAGCTTTTGTTTTGTTTATATGTAATGCTTCGTGTAGTCACAAGAGTAGCATT
97662 GT G AGTATGAAGTAACCGGGAGATGATTATACGTGCAGCGATACATTTGAGAGGAATGTAATTTTTGTGGATATAGAAAATATTTACATTATAGTCAGCTTTT[GT/G]TTTTGTTTATATGTAATGCTTCGTGTAGTCACAAGAGTAGCATTAGAAATATTAGGATTTGCGTGAGAGATACATTTAAAGGATGGT
97670 G C TAAAAGCAAAAGATGTCTTGAAAATCTGCATAGTTGAACCCACCAACTCATCGTTGAAAGGAACAAACTTTGGCTTCCCTTTTGTAGTACCAGAGCTCAA[G/C]GAAAGTGATGTCAATGGAGTTCCAGTTAAAATCGGTGATCGATCTCCATCGATAATCCTTTGTATATAAGGATTCAAGTCATCGTGAG
97670 G T CGATCTCCATCGATAATCCTTTGTATATAAGGATTCAAGTCATCGTGAGACACCAATGGAACACATGCTTTGAAACTTTCAATATCATTTCTATCTCCAA[G/T]ACCCAAATTTTGCAAATACTCAGCGTCTTTATTCATTTCTAATATCTTTTTCAATGTTTCTTTCTGAACTTTTTCTGCATCTTTTGTGATTTC
97670 A G GTATATAAGGATTCAAGTCATCGTGAGACACCAATGGAACACATGCTTTGAAACTTTCAATATCATTTCTATCTCCAAGACCCAAATTTTGCAAATACTC[A/G]GCGTCTTTATTCATTTCTAATATCTTTTTCAATGTTTCTTTCTGAACTTTTTCTGCATCTTTTGTGATTTCTTCAAATTCTTTTATAACCGAC
97670 TCTG T TGATTTCTTCAAATTCTTTTATAACCGACTGAATACAGAAGTTATTCTTTTTGTCTAACATCGCCACAAATAGCTTTAGTTTTGCAGAAATTTGAGAAGG[TCTG/T]CTGAGAACGAAAGGAGAGAGCTTTTAAAGAATCGTCGTCCTCATAATTTGAAGGAGCAGTGATGAGTGATGTGTCCAGTAGGCCA
97672 T TA CATATGCGCTGCCCACGAAAATAAAGACCTGCAGCCTTGTTATAACCTTCACCACTAAAGGATGCACCATCACAGTAGCGAATTTTAACTCGATTCCAGT[T/TA]AAAAAATCTGGATTTTCACTGGCCTTGTTGCTCAGAATGCCAGTAAATTCAATTTGTTTCTCCATGTAGTTTGACGAACCACGACGAG
97678 T C GGGACTCGAACCTCAAGGTGGGCGTCTCATCCGGCATGTGGACCCACAGGTAGTTGGTGATGGCCAGGGTCAGCGCGCCGGAAGGGCAAAAGGTTATTCT[T/C]GGAATTTTGAGCTCTTCGGCGACGTTGTAGGTCCAGCCGAGGAAGAAGTCGGATATGATGGCTACAGGAGGGGCAGAAATGG
97702 G A CACCTTTTGAGGCCAAGCAGGTGGATCCCACTGGAGCTGGCGATAGTTTTCTTGGTGGTTTTGTAGTTGGCTTGGTGAGCGGGCTGAATGTGACAGACTC[G/A]GCTCTCTTGGGGAATTTTTTCGGGTCCCTTACGGTTGGACAGGTTGGAGTTCCAAAGTTTGATCTGAGGATAATGCAGAAAGTTAA
97712 C A TTGATGTTTCGAAACATATCAGCAAACATAGATGGTTTCATAGTATCATCATCACCGGATGAATTTGCAGATTCAAAGCATTCATGTCCGCATGTAGATA[C/A]GACTTCCTCATTTGGCAGAGTAGCTGAGTGCTGCTTGCGGATAAAACTCACGACTTCAATGTTTTTCAGAACAGCATCCCAAACACTCG
97712 C G CGGATCAGATGCAAGTGAAGCGACAACAGACTGAACCTTGGGACATCCCTGCAGCAATGAAAAAGCTTGAACAGCATGTCTTGGCATTGAAGCAGTTAAG[C/G]CTGTACTCCCTGAGCTCAATATTTGACCATCCATCGCCTCTTTCAAATCCTTTATGGCCTCTTTTGCCTCATCCAAACTTGGAGTGGA
97720 C T GGCTTTGAAACTCCTGCCACCACTTACATTTCCGGTGCTCAGGTGAAGGTAGAATGCAGAACAAGGAAAACAGGGACAGAAACATGCAGTTTTGATGGCA[C/T]CACAGATGAAACCGGAACATACACCATCCCAATATCGGACGAACATGAATTTGAAATATGCGAAGCCATACTAGTACACAGTCCAG
97720 C T GCTTTGAAACTCCTGCCACCACTTACATTTCCGGTGCTCAGGTGAAGGTAGAATGCAGAACAAGGAAAACAGGGACAGAAACATGCAGTTTTGATGGCAC[C/T]ACAGATGAAACCGGAACATACACCATCCCAATATCGGACGAACATGAATTTGAAATATGCGAAGCCATACTAGTACACAGTCCAGA
97720 T C CATGCAGTTTTGATGGCACCACAGATGAAACCGGAACATACACCATCCCAATATCGGACGAACATGAATTTGAAATATGCGAAGCCATACTAGTACACAG[T/C]CCAGACAAGGCCTGTGACAGAATTGTGATGGGCCGTGAACGGGCTGAAGTGTTCCTCACGTCCAACAACGGTATGGCAACCGAGA
97720 C G TGAGATATGCTAATGCCTTGGGTTTCAGGAAAGTTACTCCACTTGCCTTTTGTGCTGAGCTTATGAAGCAGTATGAATATGTTGGCTTTTAAGTGGGCGC[C/G]GTTCCTCTGATGTAGTCAAGTTCTTTCCATGTTTAGTATGTACTTACAAGCTCATTTCTTTTGGGGAAATGGGTTGAAATAAGGCAGTA
97722 G GT GATCTGTGTAATAATAATATGTGAAATTTGTGTGGAGATGCTTGTTTTCTCCTGCTGTTGTTGGTTTCTTTTGTTTTATTTTGTTCTCGGTTTTGGTTGA[G/GT]TGATTTATCGCTTGTGCTGTGTAATGTAATAACATGGATATCCTGGAGAATGTTGTTCATCTCTCGTCGGTTTAGCAACGCTTGCTGTAG
97730 G GC CCTGAATCGGTTGTAGTATATGAGAATAATTACGGAAGATCGTACACGTTTAGATATAATATACTGCTCCCTAACGCCGTATGGTATGGGTTCAACCACT[G/GC]CCCCCGGTTTGCTGCTGCCAATGCCACTGGTAATATTTCAGTTATGTAGGAGGACATGGGGGAAATGCAGTGTTGGTTAAGGGGG
97734 T G CGGTTATCTGGTCCAGTCCAGCCCTGAGTTCGAAGAAGGATGCTTTGAATGAAGCAAAATTTGCAGGGAATATCCCAATGGTGAAGAATCTGATGTTTTC[T/G]TCACAGATTCTGTACGATGGGGAGGCGCTGGAGACGAGGGATTATAAGCTGGTCATGGACACTGACTGTGATTTGAAGCTTCTGA
97734 A G TGCAGGGAATATCCCAATGGTGAAGAATCTGATGTTTTCTTCACAGATTCTGTACGATGGGGAGGCGCTGGAGACGAGGGATTATAAGCTGGTCATGGAC[A/G]CTGACTGTGATTTGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGACAGTAAGACTGCAGGCAAGGGGAAGAACTGCTTTT
97734 C T TGTACGATGGGGAGGCGCTGGAGACGAGGGATTATAAGCTGGTCATGGACACTGACTGTGATTTGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGA[C/T]AGTAAGACTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAG
97734 C G GAGGCGCTGGAGACGAGGGATTATAAGCTGGTCATGGACACTGACTGTGATTTGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGACAGTAAGACTG[C/G]AGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGA
97734 A T TCATGGACACTGACTGTGATTTGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGACAGTAAGACTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCT[A/T]GATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGGTGGGGCTTATGGGAACTAC
97734 T C TGATTTGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGACAGTAAGACTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTG[T/C]TGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGGTGGGGCTTATGGGAACTACGTCCTCATTATGCAGA
97734 T C TGAAGCTTCTGAAAGCTGGGAGCGGAGTAGTGTTTGACAGTAAGACTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAA[T/C]GTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGGTGGGGCTTATGGGAACTACGTCCTCATTATGCAGATTAAC
97734 A G GTAAGACTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGG[A/G]AAGGGTGGGGCTTATGGGAACTACGTCCTCATTATGCAGATTAACGGCCAAGCCGTCGTTTATGGGCCTGTCGTTTGGTCTACTT
97734 T C CTGCAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGG[T/C]GGGGCTTATGGGAACTACGTCCTCATTATGCAGATTAACGGCCAAGCCGTCGTTTATGGGCCTGTCGTTTGGTCTACTTCTACTTA
97734 G C CAGGCAAGGGGAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGGTGG[G/C]GCTTATGGGAACTACGTCCTCATTATGCAGATTAACGGCCAAGCCGTCGTTTATGGGCCTGTCGTTTGGTCTACTTCTACTTAAAT
97734 A G GAAGAACTGCTTTTTGAGGCTAGATCATAAAGGGGTGTTGAATGTTCTTGATGATAAGTATAAGAGTCTGTGGAGAAATGGAAAGGGTGGGGCTTATGGG[A/G]ACTACGTCCTCATTATGCAGATTAACGGCCAAGCCGTCGTTTATGGGCCTGTCGTTTGGTCTACTTCTACTTAAATGTATCATATG
97734 G GTAC TATGGGAACTACGTCCTCATTATGCAGATTAACGGCCAAGCCGTCGTTTATGGGCCTGTCGTTTGGTCTACTTCTACTTAAATGTATCATATGTATGTGT[G/GTAC]TTTCCATCATGTTGTGTTGAATAAGAGAATGCTGGAAGTAAGCCGGCTATTCCATGCCTTTGTATTCATTGAATTTGAAGTACGTA
97734 CG C CGTTTATGGGCCTGTCGTTTGGTCTACTTCTACTTAAATGTATCATATGTATGTGTGTTTCCATCATGTTGTGTTGAATAAGAGAATGCTGGAAGTAAGC[CG/C]GGCTATTCCATGCCTTTGTATTCATTGAATTTGAAGTACGTATGTAAGAACATTAATGAGAAAGATGAATTAACGATAAGCTTGTGGA
97734 C T GTCGTTTGGTCTACTTCTACTTAAATGTATCATATGTATGTGTGTTTCCATCATGTTGTGTTGAATAAGAGAATGCTGGAAGTAAGCCGGCTATTCCATG[C/T]CTTTGTATTCATTGAATTTGAAGTACGTATGTAAGAACATTAATGAGAAAGATGAATTAACGATAAGCTTGTGGAAGAGTGAGAAGGG
97736 G T GCGTGTATGCAGAAATGCTCGAACGCCATCTTGAAATCCGGTATGTACGGCTTCAAATCCGCCTTCCACACCTTCCTGCACACCAAGCTCGCCAGAAAGA[G/T]AAGCTGCTCCGACGCCGGCAGCACCAGCGGCCCCAGCGTCGTGATGTTCGACTTCAGCGCCTCCCCCGCTATCGCCATCAGATCCTT
97736 A C CGTGTATGCAGAAATGCTCGAACGCCATCTTGAAATCCGGTATGTACGGCTTCAAATCCGCCTTCCACACCTTCCTGCACACCAAGCTCGCCAGAAAGAG[A/C]AGCTGCTCCGACGCCGGCAGCACCAGCGGCCCCAGCGTCGTGATGTTCGACTTCAGCGCCTCCCCCGCTATCGCCATCAGATCCTTC
97736 G A CGTTCCCTTCCGCGTCCTCCTCCTGGTACACGCACCTGTACGCCTTGTCGTCCGCCCCCTTGTGCGTCCTCACCACGTGGAGGAGTCTGTACTTGGCACG[G/A]GCTCGGTCCTTGCGGCGGTTGGAGAGGAGGATGGCGGCGGCTCCGACGCGGAACAGGCAGTTGGGGAGAAGCATGGCGCGCTGG
97736 T G TGTAGTAGTTGGGGGTTATGATCTCGGTGGAGATGACGAGGGCATTGGAATTGGGGTGGACCTGCAAGAGGTCACGGGCAAGATCGATGGAGATGAGTCC[T/G]GCACTGCAGCCCATGCCGGACAGGTTGAAACTGCGGATGTTGCTGCGGAGTTTGTACCGGTTGACGATCATGGCGGAGAGTG
97736 A G AGTAGTTGGGGGTTATGATCTCGGTGGAGATGACGAGGGCATTGGAATTGGGGTGGACCTGCAAGAGGTCACGGGCAAGATCGATGGAGATGAGTCCTGC[A/G]CTGCAGCCCATGCCGGACAGGTTGAAACTGCGGATGTTGCTGCGGAGTTTGTACCGGTTGACGATCATGGCGGAGAGTGAAG
97738 A T ACAACTGGACAACGCTGCGATCAACTAAGAACTTCCTTAGATGTGAAACAATGAGTTCCACTGCTTTATGCAGACCTTCTGGTTCCCCTTGTATTTCAAC[A/T]ACTCGGTCATCTTCTAATGCAATAGGAGGAACATCTTCAAGAACCCGAATAGTGCAGTTTGACCCTTCTTGCACGGTTTTGATAGTCGC
97738 C T CCCCTTGCTTCCCAATAAGACTTCCAGCTTGTGCAGCAGGCACAAGTAACCTTGTAAAAACCATGTTATTGGGAGGGGCAGGGTTACTAGCGTCATTGTT[C/T]AGACCATCCAGAGTACGTTTATGAACTTTTAGGAGACCATCCATAGCAGGAGAAAATGAAGCATCATGTTCCTCTTTGGCAGAAATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97738 C A TCCCAATAAGACTTCCAGCTTGTGCAGCAGGCACAAGTAACCTTGTAAAAACCATGTTATTGGGAGGGGCAGGGTTACTAGCGTCATTGTTCAGACCATC[C/A]AGAGTACGTTTATGAACTTTTAGGAGACCATCCATAGCAGGAGAAAATGAAGCATCATGTTCCTCTTTGGCAGAAATCATTACAGCT
97738 A T TAAGACTTCCAGCTTGTGCAGCAGGCACAAGTAACCTTGTAAAAACCATGTTATTGGGAGGGGCAGGGTTACTAGCGTCATTGTTCAGACCATCCAGAGT[A/T]CGTTTATGAACTTTTAGGAGACCATCCATAGCAGGAGAAAATGAAGCATCATGTTCCTCTTTGGCAGAAATCATTACAGCTCTTTCC
97738 A G TATTGGGAGGGGCAGGGTTACTAGCGTCATTGTTCAGACCATCCAGAGTACGTTTATGAACTTTTAGGAGACCATCCATAGCAGGAGAAAATGAAGCATC[A/G]TGTTCCTCTTTGGCAGAAATCATTACAGCTCTTTCCTGTGCACCTGGAGGACCATCAAGAATCTTAATTCGTGCTCTGGATTCTTCG
97738 A G GGAGACCATCCATAGCAGGAGAAAATGAAGCATCATGTTCCTCTTTGGCAGAAATCATTACAGCTCTTTCCTGTGCACCTGGAGGACCATCAAGAATCTT[A/G]ATTCGTGCTCTGGATTCTTCGCACATTTTTTTAATAAATTCTCCCTTGCGTCCAATAATGCTACCAACCTTTTGAGATGGAACCAATAT
97740 T C TCTCTCGTTCTCCTCCGCCGCACTCCTCCTCTTTGTCCTTCTCCCTTCTCTCTCTCCTTCTTCGTCTTCCTCTTCCTCTTGTACGCAACAGCCTCCATCC[T/C]CAGATGGTCAAATCTCAGCCATCCATTCCTCAAACACGAATATCAATCTTCAGACCTCTACCACTGAACAGGATATCCAATGGCTGAAATCGC
97744 A G TTAAACCACACAACAAGCCCAAATCCAATCTTCCCGTTGTCCTCTTATTTCAGGAACTTGATTAGGAACCCTTCACGTATTGAACTTCCTTCCCCATCGC[A/G]ATATCACTCAACTATAGCTCGATGAAAGTCGTCCTCTCACCGTCCATCCACAACGTTGACGGCGGATCTGGCCTCGTTAGAACCCATGCC
97756 CA C CCAGACCCTATAAACCAGAAAAGATGAAACCAACTACCATAAGGACCAGAACAACACACCAAAACCAAAATGGCAACACGAACAAACAACTGAAACGACC[CA/C]AAAAAACTCAAACTACAGGGACATTATACACCAAGCAATGTAACGCACGAAGTCGTGAGGTTACCAGTAACACACTACAGTTCTG
97756 T C TGTAACGCACGAAGTCGTGAGGTTACCAGTAACACACTACAGTTCTGTTCGATGAATTGTTTATTGATTACCAGTGAGGCTCTAGAGAGGGCACGAAGTA[T/C]ACCCTGAAGTGGCCGCCGCGATCTGGAGCAGAGGTGTGTTCTGCAAGTAAGGAGTGAGGTTGCGAGGAAGTAGTGAAGTAGATT
97756 A AT GCAGAGGTGTGTTCTGCAAGTAAGGAGTGAGGTTGCGAGGAAGTAGTGAAGTAGATTGCGGTGCGATGGCATGTTGGGAACATATCTGAAACTCAGATCT[A/AT]TTTTAAAAAAGCTTAGATCTAGAAATTTAGAGAGGGAAAAGTAGTGAATACCATGCACGGCGAAAGCATGAGTAGAGAAGTTG
97756 T C CATGTTGGGAACATATCTGAAACTCAGATCTATTTTAAAAAAGCTTAGATCTAGAAATTTAGAGAGGGAAAAGTAGTGAATACCATGCACGGCGAAAGCA[T/C]GAGTAGAGAAGTTGTTTGAGGAAGATGGAAGAGAAAAGAGGATGCATTTGAGTGGAGCGTGAAGAGAGAGAGAGAGAGAGAG
97762 T C TCGGACTTGATGTTGGTTGCTCAATGCTCTCTTGGCTCTTTCGCATTCTCTTCTGAGCTTTCCAAGGGCGCGGTTGTCCTTGCTGATGTCCTTTCCGTGC[T/C]TCTTTTTTATGAGCTTGATGAAGTATTCCATCACTCTCTGATCAAAGTCCTCACCTCCCAAATGAGTGTCCCCATTTGTTGACAGAACTTC
97764 G A GAATCATGCGACATGGCCCGCACCATGGAGCCCAGAACTCGACCAGCACTGGCTTGTCGCATTCCATGACAAGTGATTGCCAAGTGCCATTAGTCACATC[G/A]CGAACATCAACGGCAGTATCTTGTGCCTCACAAACAACGCCGCACCGCTTGGTAGCTGGACCAGATGAAGTCGCTCTTTGATGATG
97776 AT A CTCCATCGTACTTTACGTTTTTTACTGCCTCTTGACCAGCTTTTTTCACAGTCGTCTGCTTCTCAAATGGTTGGCAACCATCTTGTTTCCACCAGACCCA[AT/A]TTTTTTTCTCGTTGCAATATGTGTTCAATACTTTCAAGAAACTCCTTTCCTTTGGGCGGAATAGATTCAATTAATTTCTTGACACGGTCTTC
97778 C T TGAAGGCTCCAGCGTATATTATTGCTTCCAATGCTGGAGTAGAGGGTGCTGTTGTTGTTGGCAAGCTTTTGGAACAGGATAACACTGATCTTGGTTATGA[C/T]GCGGCTAAAGGTGATTATGTTGACATGGTAAAAGCCGGTATCATTGATCCACTGAAAGTTATCAGAACAGCATTGGTTGATGCTGCA
97778 C T AGCTTTTGGAACAGGATAACACTGATCTTGGTTATGACGCGGCTAAAGGTGATTATGTTGACATGGTAAAAGCCGGTATCATTGATCCACTGAAAGTTAT[C/T]AGAACAGCATTGGTTGATGCTGCAAGTGTTTCTTCATTGATGACGACCACGGAAGCTGTGGTGGTAGAACTACCGAAAGATGAGAA
97778 A C TGGAACAGGATAACACTGATCTTGGTTATGACGCGGCTAAAGGTGATTATGTTGACATGGTAAAAGCCGGTATCATTGATCCACTGAAAGTTATCAGAAC[A/C]GCATTGGTTGATGCTGCAAGTGTTTCTTCATTGATGACGACCACGGAAGCTGTGGTGGTAGAACTACCGAAAGATGAGAAGGAAG
97812 A G AAAGAAATACTATGCCATAACGGCGAAAGCTGAGTTAGAGGAAGTTGGATCGGAGAAATGGAAGTGAATGAAGCGAGATTAGGAGGCGAAGGGAGGAGGA[A/G]AAGGAAGAGGTGGGGGAATCGAACGAAGAAAATGGAGGGCTAAAACCCAGTCACCATTGAAACATAACGGAAGCTTTTTTT
97840 TAG T TGGCCTTTTTTTTTTTACTAGACAGTTTCAATCATAATAAAAAAAATCTTGTACATTCGATAGATGGTGACATTCAGATAGAATTGTTACTTTAAAATAA[TAG/T]AGAGAGTATAAATGATTTACTGAAAAACATGAAATGATTAATGATTTAAAGATCAGCCCGGCCGGGGTATCTAGGGAAAGGAATGA
97840 CG C ATAGATGGTGACATTCAGATAGAATTGTTACTTTAAAATAATAGAGAGTATAAATGATTTACTGAAAAACATGAAATGATTAATGATTTAAAGATCAGCC[CG/C]GGCCGGGGTATCTAGGGAAAGGAATGACATCTCGGATATTGTCAAGCCCCGTTGCAAATAAAATCATTCTCTCGAATCCCAGGCCA
97840 G A AATGATTAATGATTTAAAGATCAGCCCGGCCGGGGTATCTAGGGAAAGGAATGACATCTCGGATATTGTCAAGCCCCGTTGCAAATAAAATCATTCTCTC[G/A]AATCCCAGGCCAAAACCACTGTGTTTAACAGTACCAAAGCGGCGAAGATCCAGATACCACTCGTATGGCTCTAGAGGCAACCCTGA
97842 C T AAGCTCTGCCCTTCTTTGCACATTCTAGTAGCTGGACGCAATCGGGAGAAGGGTACTGCTCTAGTCTCAACCCTTGGTGAGAACTCCGAGTTTATCGAAG[C/T]GGACATTGACAATTCAAAAATGTTGGAAGAAGCGTTAAGAGGAGTTGATCTAGTTGTTCATGCGGCTGGACCATTTCAACAAGGAA
97842 A AGTGAGCAATG TTTGTGATGATACAAGCTATGCTACACGAGCAAAGTCTTTACACGAAAAAGCTAAATCTTCTGGTGTGTCGGCTATAACAACTGCTGGAATTTATCCTGG[A/AGTGAGCAATG]TCATGGCAGCTGAGCTAGTTCGTGTTGCAAGAGAAAAAGCTGATGGTGAGCCAGAGAGACTGAGGCACTGGAGGT
97870 G T AATTCCACAACAAAGGGGGCGTACTTATAATCAGCTTTGTATTTGCCTCCGTTTGTGGCCCAT[G/T]CAGACCCATCCCAAATTGTAGCATAAAGCGACATGGGTTTCGATGGGTAGTCGCCTCCCATTGCATCCGAACGAATCACTTCTCTTATCGGGATTTCATC
97870 G C GCATAAAGCGACATGGGTTTCGATGGGTAGTCGCCTCCCATTGCATCCGAACGAATCACTTCTCTTATCGGGATTTCATCGATGTAGAATATGATGGTAT[G/C]GGAAGTCCAAAGGATGGAATATCGATGGGCCTCGGCAGTAGGATCGAACGGGAGAAGATAGCGCTCTTCTCGGCCTCGGCTTGTG
97870 T C AGCGACATGGGTTTCGATGGGTAGTCGCCTCCCATTGCATCCGAACGAATCACTTCTCTTATCGGGATTTCATCGATGTAGAATATGATGGTATGGGAAG[T/C]CCAAAGGATGGAATATCGATGGGCCTCGGCAGTAGGATCGAACGGGAGAAGATAGCGCTCTTCTCGGCCTCGGCTTGTGCTTCCAT
97870 A T CCATTGCATCCGAACGAATCACTTCTCTTATCGGGATTTCATCGATGTAGAATATGATGGTATGGGAAGTCCAAAGGATGGAATATCGATGGGCCTCGGC[A/T]GTAGGATCGAACGGGAGAAGATAGCGCTCTTCTCGGCCTCGGCTTGTGCTTCCATTCCCATAAACGTTGGTTTGAACTCTCCAGTCT
97870 T C TGTAGAATATGATGGTATGGGAAGTCCAAAGGATGGAATATCGATGGGCCTCGGCAGTAGGATCGAACGGGAGAAGATAGCGCTCTTCTCGGCCTCGGCT[T/C]GTGCTTCCATTCCCATAAACGTTGGTTTGAACTCTCCAGTCTTTGCCTTTTATGTTTCCAAGAAATTCAAAGTCCAGTTCATCATGA
97870 G C ATCGATGGGCCTCGGCAGTAGGATCGAACGGGAGAAGATAGCGCTCTTCTCGGCCTCGGCTTGTGCTTCCATTCCCATAAACGTTGGTTTGAACTCTCCA[G/C]TCTTTGCCTTTTATGTTTCCAAGAAATTCAAAGTCCAGTTCATCATGAGTTTTCTCAAACACATCGCCGTTGGATGTATAAAAAGCAA
97870 A G AGTCCAGTTCATCATGAGTTTTCTCAAACACATCGCCGTTGGATGTATAAAAAGCAACAACGACACCAGCAGTGTAATCGGATGGCAACTTAATCGACGC[A/G]CTGAAGAATCCATGGTTGTACATATCCGATGATATAAAACCCGAACCTGAGTAACGATTTAGAACAAGATTGACGTTTTTCCCATCTG
97876 A G TTTCGAGCGAAATTTGGGTCTTCACGTCAGTTCGACTTCCACAAAAACAGACGTAGCTATGCCTTTGGTCTACTGAAGGAGACTTGAGGTGGAAATTAAT[A/G]ATGTACGAGTTGATGGTAGTCTGTGTTGTCTTCTCCATTAGGGACTGTGTGCTACTAGAAAGTATAGCCTAGGCATGTGGATTTGCA
97876 AT A AAGCTAGCTGAGCATTTGTTCCTTCATATTTGTATTAATGTGTAGTTATGAGTTGTTTCCTACAAGTAGTCCCATTACTGCAAAAGTGCTGTCTTCCAAC[AT/A]TTTTAAGACAAAGATTGGTATAAGTACATGTTGAAGGTTTCAAATGCTTCATGTCAGAATTACGGTCTCTAAATCGGCTAGTCAAAACA
97876 GA G CTGAGCATTTGTTCCTTCATATTTGTATTAATGTGTAGTTATGAGTTGTTTCCTACAAGTAGTCCCATTACTGCAAAAGTGCTGTCTTCCAACATTTTAA[GA/G]ACAAAGATTGGTATAAGTACATGTTGAAGGTTTCAAATGCTTCATGTCAGAATTACGGTCTCTAAATCGGCTAGTCAAAACATTTGGTC
97878 G GA AATAACCTAACCCCTCTGTTTCCCTACGTTGCCTTCATAAATAACTGATATTTCGTCGCTAACAGTTTCAAGTAATCAATTCTTTGGCAG[G/GA]AGAAAAGAATGCCTTCTTCTTTGTTCATCCTGGCCAGTCTGCTTCCGTTCATCTTCACCACAGCGCACGGCTACCACCGACATTCAAGGTCAACCGGAT
97878 T TC ATCTTCACCACAGCGCACGGCTACCACCGACATTCAAGGTCAACCGGATGGACCACCGCCCACGCCACATTTTATGGCGGCGGTGATGCTTCTGGAACTA[T/TC]GGGGGGTGCCTGCGGCTATGGAAACCTGTACAGTCAAGGGTACGGCACGAACACGGCGGCGCTGAGCACGGCCATGTTCAACA
97878 C T GCACGGCCATGTTCAACAACGGCCTGAGCTGCGGCTCGTGCTACGAGATCATGTGCGTCGGCGACCGGAAGTGGTGCCTTCCCGGAGCGATAGTCGTGAC[C/T]GCCACCAATTTCTGCCCTCCGAACAACGCCCTTCCGAACAACGACGGCGGCTGGTGCAACCCTCCCCTTCACCACTTCGACCTCGC
97878 T C CCGTCTTCCAGCACATTGCTCAGTACCGCGCCGGCATCGTCCCCGTCGCCTACCGCCGGGTACACTGCAGAAAGAGAGGGGGGATAAGGTTCACGATAAA[T/C]GGGCACTCGTACTTCAACCTGGTTCTGGTAACGAACGTCGGCGGCGCCGGAGACGTGCATGCGGTGTCGGTGAAGGGGTCGAG
97898 A AAC CTCGAAAAAGTGAAAATAGTAGCAAAACGCAGTAACCAACAACATTCATCCAAAGCCAATTTCCCCAAAAAAGGCCGCGTAAACAAGCCTCCCTTTAAAA[A/AAC]GCCTGCCTATAATAATCCTCAAGCAGCAGCAGCAGCAGCTTACCCAAGATACGATCATCGAGACACTAGCAGGTACTCTTATCCT
97900 C T CTTCCAAAATCAGAGGAGACGTCAGGAACTGTTGCTGCGTTGTGTCCGGGGGCGTTTACGAAAATCTGCTCTTCTTCCCTGTTATTCAGGTCATCAAGGA[C/T]AGGTACCCTGGTGTGAAAATCGATATTTTGGCTTCGGCTAGAGGGAAGCAGACTTATGAAATTTGTAAGAATGTGAGGTGGGCGAA
97904 T G CATTAATCTTCTAGTAAGAACTAATACTGCAGTTTGGAGACTGTAAACGAAATATTCTGACATGTGTATTTTGTGGTTTATATGGATCACATAACCTATT[T/G]CCTGAAGCGCTTGGCACCCCTTCTGACATATTATGGTCAGGTTTTTCAGGCACAACTATTTAGATATGTAGCATCCGTCCTCAAGAAATT
97904 A G CAATGCTTTGCGAATCAAAGCAGCATGCTTTCTTTATCTATTTCACAGTTCTCATCCACATTCTGTTGCTATGGCCGTAGATTGCTAGCTTGGACTTCAA[A/G]TATTTCCATTTCAAGGTTGTTGTTTGCATATCTACCGGACTGCTATTAGTAGCAGCATCTCC
97906 T C TCACCTTCGGCCAAATCGCTGAAATCGTCGATAAGGGATCAAGCTCATGTGGAGCTAGTGGAGCACTGTACACGCTGATAATGTGCCTGACAGGCTGCAG[T/C]TGTATATATTCATGCTTCTATCGGAAAAAAATGAGGGGTCAATACTCCTTGCAGGCGAGCCCATGCAACGACTGCCTTATCCATTGC
97906 T C CCTTCGGCCAAATCGCTGAAATCGTCGATAAGGGATCAAGCTCATGTGGAGCTAGTGGAGCACTGTACACGCTGATAATGTGCCTGACAGGCTGCAGTTG[T/C]ATATATTCATGCTTCTATCGGAAAAAAATGAGGGGTCAATACTCCTTGCAGGCGAGCCCATGCAACGACTGCCTTATCCATTGCTTC
97906 C T ACTCCTTGCAGGCGAGCCCATGCAACGACTGCCTTATCCATTGCTTCTGCGAGCCTTGCGCTTTGTGTCAAGAGTTCAGGGAGCTCAAAAGGCGTGGCTT[C/T]AACATGGATGTTGGGTGGCATGCAAACATGGAGAGGCAAGGCAGGGTAGCAGCTGTTATCACAGCCCCTCCGATTGTTCAAGGAG
97906 G C CAAACATGGAGAGGCAAGGCAGGGTAGCAGCTGTTATCACAGCCCCTCCGATTGTTCAAGGAGGCATGAACCGTTAAGTAATATATTTTGGTTGTTATAT[G/C]TATTAAATTTTGTGTATTCTATGGATGGTTGATATATATCTAAGAATTTATATAGCATGTG
97912 C T AAATACAAGTAATGCAAGTTATGTAGCATATGATAATCGATGGGAACAATGATTATTGAAATAGCATAACACGAGGAAACCAACATAACATATGTCGGGC[C/T]AGTGGCTTTCAAAAGTTGGCATTGGTCCAACCAAGGTGTCCTCCAAGCTGCTGATGTTGATAGGGTCCAGCCATCTGCGTAGGACT
97912 T A GCAGCAGGCTGATTCAATCCTAGATTTGCTGGCATGAATGTCTGGAGACCTGGAGACTGCTGCCCTGTCATATTGTAGCATGGAGTTGGTCTGAAGGTTG[T/A]CATTTCTCTTGGATTTTGAATCCATGTTCCATTTTCTGACTGTCCCTGGGGATTTGGAACATAAAGATTGTTGTCCTTGTTATAATTAA
97914 T C TAGGATTAGCAACCGCATTTCGTCTTGGGTTGGAATGTTGTCACGAGTGGAATTCAAGGAGACACGCTCAAAGAGCAGATTTTCCAGTAAACGCTATGGC[T/C]CATCCTTCTGTGTAATTACTATAGTTGTTAAGAGAAAGGCAACAATAAAGAGTGACATCTGTATAGAAACGAAGGTGGTATATTTGT
97916 CA C AAGTCCAAACCCTCATGTATATCAGTAACGTTAGCATAAGACTTTGCAGCAGCACTCTGAACATTAACAATGTGCACAACAGGTGACATGCTGGCATAAA[CA/C]AAGAAATCGCTGATCAGGAGAAAGTGATGTATCTGTAACTGTCCAACGTAAACTCCTCGCAAGGATATCCTTTTGTACTTTCCAATC
97916 G GA TTTCTGACAAAAATGACCACGTCGACACTGGAACTTTCCTACTAGCACGTGTCACATAACGAGTACTCCCACTTGGTTCGGTTTGAAGTTTGGTGAGATG[G/GA]AAAAAATCATGATCTCCATTTAGAGATTCATTGTCCTTTTGTATCCAGGAAGTTCCTTCATCCATCCCTGTGTCACGGGCAGAAGGA
97918 G T GATTTTTATGTTCTCGGCCTCGGAGGAACGGTTGGCCCACGCGACGTAGAAGATATGAGTGACGTCAGACAAAGGGGAAAGGCGATCTAGGGTTTGGCCC[G/T]CGTCAGAGACGTCGCACTGGATGGGGTGGACTCTGGGGTTGTCGGACACATGGGGGCGGCGAGAGACGGCGTAGACCTTCCA
97918 C G GAAAGGCGATCTAGGGTTTGGCCCGCGTCAGAGACGTCGCACTGGATGGGGTGGACTCTGGGGTTGTCGGACACATGGGGGCGGCGAGAGACGGCGTAGA[C/G]CTTCCAGGGACCACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAGGAGGCTGGTGCCGACGATGCCGGTGGCGCCAATTA
97918 G A TGGGGTGGACTCTGGGGTTGTCGGACACATGGGGGCGGCGAGAGACGGCGTAGACCTTCCAGGGACCACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAG[G/A]AGGCTGGTGCCGACGATGCCGGTGGCGCCAATTACTAGAGCGACGGATTGGGGAGGTGGAAGGGTGCTAGGGTTTGAGG
97918 T C GGCGAGAGACGGCGTAGACCTTCCAGGGACCACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAGGAGGCTGGTGCCGACGATGCCGGTGGCGCCAATTAC[T/C]AGAGCGACGGATTGGGGAGGTGGAAGGGTGCTAGGGTTTGAGGAAGAGGATGAATCTAGGGTTTTCCGCGCTGCTCCAATC
97918 C T ACGGCGTAGACCTTCCAGGGACCACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAGGAGGCTGGTGCCGACGATGCCGGTGGCGCCAATTACTAGAGCGA[C/T]GGATTGGGGAGGTGGAAGGGTGCTAGGGTTTGAGGAAGAGGATGAATCTAGGGTTTTCCGCGCTGCTCCAATCGCTCCTGCC
97918 G A GGCGTAGACCTTCCAGGGACCACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAGGAGGCTGGTGCCGACGATGCCGGTGGCGCCAATTACTAGAGCGACG[G/A]ATTGGGGAGGTGGAAGGGTGCTAGGGTTTGAGGAAGAGGATGAATCTAGGGTTTTCCGCGCTGCTCCAATCGCTCCTGCCCA
97918 G A CACCGGGCGTGTCAGCGAGAGGGAGGATGTCGAGGAGGCTGGTGCCGACGATGCCGGTGGCGCCAATTACTAGAGCGACGGATTGGGGAGGTGGAAGGGT[G/A]CTAGGGTTTGAGGAAGAGGATGAATCTAGGGTTTTCCGCGCTGCTCCAATCGCTCCTGCCCACCACCAACTCATGATGATCG
97930 A C CTTATTTTATAACAGCTAACCATATAGCTTTGTACTTTCAATTTTACATAAACATTAGAGCTTATGTAACAATGCACATACAATAAACGCTAAACAAGCA[A/C]GAGCCTTAATTCAACTATGCAAAAGCCATAGTTACGATGAGTCTTTTCTGAATGTCTTTTCTGAATTGGTTGCCAACAATGCAACTTAAG
97930 C T TTTATAACAGCTAACCATATAGCTTTGTACTTTCAATTTTACATAAACATTAGAGCTTATGTAACAATGCACATACAATAAACGCTAAACAAGCAAGAGC[C/T]TTAATTCAACTATGCAAAAGCCATAGTTACGATGAGTCTTTTCTGAATGTCTTTTCTGAATTGGTTGCCAACAATGCAACTTAAGATGAG
97930 A T TGGTTGCCAACAATGCAACTTAAGATGAGTTGCTCATAACCCATTCGACCAATGTGGATACTCCAAATCCAGTTGCCGACTTCTTCTTCTCGTTCCAAAC[A/T]GGGCCTGCCATGTCTATATGCATCCATGCAACCTTCTCATCCACAAATTGTTTCAAGAAAAGTGCAGCAGTGATAGAGCCGCCCTGTCG
97934 T G GACCCACTCCGAGTTTGGAGGAAGCAAAAGAGGCCACCAAGGATTTGAAAGAGGCGATCGACGGGGTGTATTTTACTAATTTGGAAAATTCCATGACTGG[T/G]AGTCAAGTATCGGACTCAGGAAGTACAACCTTGGTTGCTTCAATGCCAAAACATGCTGTTCAAGCTTTTTCTTTGCTGCAGGGATG
97934 C A ACATGCTGTTCAAGCTTTTTCTTTGCTGCAGGGATGTCCCGAGGCCCAGTCTGTTGTTGCTTCAATTGTATCTGACCAGAGTGTCTGGGATGCAGTTCTG[C/A]AAAACAATGAAGTCATGAGTTTTATCAGTAAGCAGCACTCAGCCACTCTGCCAAATGAGGAAGCTGAATTTACAGGCGAAAATGAGT
97934 A T TCAATTGTATCTGACCAGAGTGTCTGGGATGCAGTTCTGCAAAACAATGAAGTCATGAGTTTTATCAGTAAGCAGCACTCAGCCACTCTGCCAAATGAGG[A/T]AGCTGAATTTACAGGCGAAAATGAGTGTTCCGAATCTGTAAATTCCCCCGATGATTACGATGCTACAAAGCCGTCTATGTTTGCTGA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
97934 T C TCTGACCAGAGTGTCTGGGATGCAGTTCTGCAAAACAATGAAGTCATGAGTTTTATCAGTAAGCAGCACTCAGCCACTCTGCCAAATGAGGAAGCTGAAT[T/C]TACAGGCGAAAATGAGTGTTCCGAATCTGTAAATTCCCCCGATGATTACGATGCTACAAAGCCGTCTATGTTTGCTGATATGTTTCA
GGTTTTGAGAAGCCTTTCTATAAATCTTCTGTTAGTAGCATTGACAGTTTGACACCTTCAGCCA
97946 T CAATAGTAGCTCTAGCATTTAGGATTTAGCCTTTAACAATAGCTTCAGCTTCGACCATTCATTTCGTCAGACCATTTGGATCAGCTACACCACTACCACC[TTCCTTCATATGACCAGGTTTTGAGAAGCCTTTCTATAAATCTTCTGTTAGTAGCATTGACAGTTTGACACCTTCAGCCA/T]TCCTTCATATGA
97948 T A GAAGAAAATACAGTGTGAGCTGCACTAGGATATGTACAAGCTCAAAGAAATCATAGTTAAAAAGGACATAATATAAACAGAGCTCAGCTAAAGGCGCTAT[T/A]GTTGAATTTACTACAACTAGGCAAAGCATCCTTTCATAGTCATCACTCATCAGTGCCATCAGCTGCATAGTCATAGTTTTACATATTA
97948 A T TCAGCTAAAGGCGCTATTGTTGAATTTACTACAACTAGGCAAAGCATCCTTTCATAGTCATCACTCATCAGTGCCATCAGCTGCATAGTCATAGTTTTAC[A/T]TATTAGGCTCCTGCCTAAATAATCGGAACCTTTGAGAATCGATGACAACTGGAGCCAGCAGAACATAGAATTGCCTTTCCTAATCCGGA
97948 C T AGGCGCTATTGTTGAATTTACTACAACTAGGCAAAGCATCCTTTCATAGTCATCACTCATCAGTGCCATCAGCTGCATAGTCATAGTTTTACATATTAGG[C/T]TCCTGCCTAAATAATCGGAACCTTTGAGAATCGATGACAACTGGAGCCAGCAGAACATAGAATTGCCTTTCCTAATCCGGACAAACTAG
97950 A G CCTTCCAATCTCAGAAGTTTAGCTAGTAGCAACGATCGAAATAGGAAGCAAGAAGGCGCAAAGGAAAGAGGCGCTGAGGACCTGAGGTGGGGAGTCGTAG[A/G]AGGGCTAAGCAGGAGGTGCGGACGGTCGAGCTTTTTGTCTTTGCTTGAGAGCAGCGACGAAGAGCGTTAGGGTTTTCTTTTAA
97954 T C TTTCGGGTTCCGGGTCCAAAATAGCTGTATCCGATAAATTGGATGACCTAATATGCGAAATGAGCAAATTGGTCAGCAGCGGCATCGCAACTGATGAGGC[T/C]TTAAAATGCCTGTCACAGCTAACGCACTCCAAACACGCTATAAAGCTGATGCTGCATTACGATATTGTCCAAATATTACTGAATATC
97954 T C CTTTAAAATGCCTGTCACAGCTAACGCACTCCAAACACGCTATAAAGCTGATGCTGCATTACGATATTGTCCAAATATTACTGAATATCTTATCACCAGG[T/C]GCAGTTAATCAAAAATCAGCGGAGAAGGCTATAATGGTTCTAGAAGCTTGCGCCAGCTGCACCGCTGGACGCACCTCCATTAACGAGG
97954 A G GGAACCTTTGCTACAACAATAAGAACAATGGCATGGACTTGGAACGGAAAGCGAAGGAGGAGGTGGTGAGGGTAAAGGGCGGAATGGGGAAAGTGCTGGT[A/G]GTGATGCAAGGAGATTGTGGTGGAGTGGTTAGGAAAATGGCTGGTGATTTGCTTAGGGTGTTCAGGGCTGAGAAGATGAGC
97968 C T AACGGTGGGTTTTGTTTCAGACAACAGTAGGCATGGAGGGGACGAAGTGGAATACGGTGACATTCGCGTTTCGCTGTACTACGAACGCAGTCTGATTGCT[C/T]CCACCTCGGTTTATCCAATCGAGCATGGTCCGGGGGAGGAGGTCGCAGAAAGAAAAGCGAGAATGAGGGCAAGCAACATCGAC
97970 A G ATCTTCGCCGCCCGTAGGCTCACCCGACCCGTTTGGACCGGCCGATCGAAATCGATAGTCGATCAAGTGCAGAATGACGCTGGCTGCGAAGCGGGTGGAA[A/G]CGGAAGTGTGGGGATAGGGCCGGTGCCGAAGATGTCGGCGGATCCGTACGAGGATTTCAAAATGTCGATGGTGGAGATGGTG
97984 TC T GCATCCTTTGGGACCAGTGACTGCCCGAATACCTGCTAAAATAGAATCAACTGGAGGAGAGGCGAAAATATCCCCACAGATGGCTGCCGTTAGCATCCCG[TC/T]CCCCAACAAACCCAGCATGGGCAGGTTCATGGCCACTGCCACCACCTGAGATAACAGCAACCTTGTCATAAGTCTTCGGAGAAAC
97984 A T TTAGCATCCCGTCCCCAACAAACCCAGCATGGGCAGGTTCATGGCCACTGCCACCACCTGAGATAACAGCAACCTTGTCATAAGTCTTCGGAGAAACATC[A/T]GCTCGTAGAACTACCTTAATCTGCGGGAAGCCATCTAAATACTGTAAGGCAGGATATGTTTCGGTGAGTCCCTCGATGAATTCAGTC
97990 C T AGATTCCAGGATCTGTTTTTGAGAGATTTCCTCCAGAATTGTTAACCAAGTTGAGCACGGAATGTCTTGCCTTGCAAAATCATATGTTTGGCTTATCACC[C/T]AAGAGGTTGCTAGAAAATGACAAGTTATCAAGATTTTTCAGAATATTGACAACTACTCCAGATGATGAAGGCCAGATTTATGTTTCGAC
97990 T C TATCACCCAAGAGGTTGCTAGAAAATGACAAGTTATCAAGATTTTTCAGAATATTGACAACTACTCCAGATGATGAAGGCCAGATTTATGTTTCGACCGC[T/C]CAAGGGCTTAAATATCCCGTGACAGGCTTCCAGTGGCACCCAGAGAAAAACGCATTTGAATGGGGACCATCATGGATACCCCACAGT
97990 C T CAGGCTTCCAGTGGCACCCAGAGAAAAACGCATTTGAATGGGGACCATCATGGATACCCCACAGTGAAGATGCAATTCAAGTAACTCAACATGTTGCCAA[C/T]TATTTAGTCAGAGAGGCAAGAAGATCTTCAAATCGACCTTCAGATCAGAAAGTCAGGGACAACCTTATTTACAATTACCCTCCTACT
97990 AG A AGTCAGAGAGGCAAGAAGATCTTCAAATCGACCTTCAGATCAGAAAGTCAGGGACAACCTTATTTACAATTACCCTCCTACTTATGGCGGGAAGGCAGGA[AG/A]GGGGGTATGACGAAGTGTACATCTTCAGATAAATCTCAACAGCACGGTGGAAGGCATTCAGATTCTTTGAGCTGGTATGGTACT
97990 G T GATCTTCAAATCGACCTTCAGATCAGAAAGTCAGGGACAACCTTATTTACAATTACCCTCCTACTTATGGCGGGAAGGCAGGAAGGGGGTATGACGAAGT[G/T]TACATCTTCAGATAAATCTCAACAGCACGGTGGAAGGCATTCAGATTCTTTGAGCTGGTATGGTACTAGTCATATTGCATGTCACAG
97990 T C CCTACTTATGGCGGGAAGGCAGGAAGGGGGTATGACGAAGTGTACATCTTCAGATAAATCTCAACAGCACGGTGGAAGGCATTCAGATTCTTTGAGCTGG[T/C]ATGGTACTAGTCATATTGCATGTCACAGTATTGTTCTGATTACAGACTAAAGGGAGACCTGTGTATTCTTGAGCTA
97996 T C GGTACCAACGCCACAGTAATATGGGCCTTGGGGTCCTGGGAAGCCTCCCTTTGGCCAGCCGAATGGAGTGCCATCGCTGTCGAAGAGGGTGTATTCCTGC[T/C]CAAGACCGAACCAGGGCTCGACTTCCTTAGCTTGGTCCATGATCTTCTTGCAGTGGTGACGGTAGTTGGTTCGGTTGGGTGTGCC
98002 G A GGTGGGGACCAGACTGCAGAATCCACGGCCGTTGCTAATTCAAGCAAGCTTCCTGTTGCTAAGGCACAGGTAGTTGGATGGCCGCCTGTTAGATCATTTC[G/A]TAGGGATGCACTCAAAAGGTGTACTTATGTGAAAGTTGCAGTTGATGGAGCACCTTACCTACGAAAGGTTGACCTTGAAACTTATG
98002 T C ATAAGGATGGTGACTGGATGTTGGTCGGAGATGTCCCATGGAAAATGTTCGTTGGCTCTTGCAAACGGCTTCGCCTGATGAAGAGTTCAGAAGCTGGTAA[T/C]CTTGCTCCAAGGGCGTCTCAAGGGAGCACAAACAACACAAGGTGAAACGATCGGAGGCCTTTTTCTTTAATGCTGCTACGTTAAAT
98002 T A AGGATGGTGACTGGATGTTGGTCGGAGATGTCCCATGGAAAATGTTCGTTGGCTCTTGCAAACGGCTTCGCCTGATGAAGAGTTCAGAAGCTGGTAATCT[T/A]GCTCCAAGGGCGTCTCAAGGGAGCACAAACAACACAAGGTGAAACGATCGGAGGCCTTTTTCTTTAATGCTGCTACGTTAAATCAT
98002 C T TCGTTGGCTCTTGCAAACGGCTTCGCCTGATGAAGAGTTCAGAAGCTGGTAATCTTGCTCCAAGGGCGTCTCAAGGGAGCACAAACAACACAAGGTGAAA[C/T]GATCGGAGGCCTTTTTCTTTAATGCTGCTACGTTAAATCATGTACAGGGATTTGTTTGTCATCCTTCTTGTTTTTATCGTGAGTTTTG
98008 G C ATGGTATATCATGTAAGTTAAACAATTGGCATTCCAAAGATTCGGGTCCGGGAGCAAAATGAGTATCCTTCAGTTTTGCTCGAAAAATGAGGTAAACTTG[G/C]CCAATTCGTGGAATATCAATTTGAGCAAATGGTGAAAGCCCTTCTACCTCTGCGCATGCTTCTCCAATGTCTCTCTTGCTGCTCCTTCC
98008 T TC AGTATCCTTCAGTTTTGCTCGAAAAATGAGGTAAACTTGGCCAATTCGTGGAATATCAATTTGAGCAAATGGTGAAAGCCCTTCTACCTCTGCGCATGCT[T/TC]CTCCAATGTCTCTCTTGCTGCTCCTTCCAAAGCAGATTCCCCAATCTCCATAAAACCAGCAGGAAGCGTCCAAAATCCATAAGATGGT
98016 G A GCCGCCGCTTCCCGTGAAGATCGATGAGGACCTTTTCAATTCTATTCTCCAGAGACGTTAACAAATTAGTTTCTTTGAAGATACATAATAAAAGTCGGGA[G/A]GTTACGTATTTCAGATGCCAGTCTCGTAGTGAATAACCAAAATAAACGTATATCAGTCCGTCTGGAGGTTTTTCTCAACCTAGAATAG
98016 G A GTCTGGAGGTTTTTCTCAACCTAGAATAGGATAATGGCTTTTCCCTTTTTACAGTTAATGTAGCGTAATCCTAGCATGTTAATTATGGCGTTGAAAATGC[G/A]TGGATGGATTATAATGTGATGGTAGTCGTAGTAGTCAAACAAGACATTTGGGAGTAAATATATGTATTTGCATCTTTTGATTTGAATCA
98024 TA T TTACAAAAATCATATGTGCTTGTTTTCACCAGAGAAGTTTAATCATTGGAATAGACTTTCTACTAGCACATAAACTAAACATTGCATCTTTCTACATAAC[TA/T]AGAGGAAAAACCCCAAATACGAAGATGAAAAAAAGCTTACACAAACTTTTTCAAACGGAAGATCTACAAATCGGACAGGCCCTAGATT
98024 G A TTCGGAAGTGGCTTCTTCTGCTCCGGCGACGAAGGGCGCGGCCAACGACAAATAGATGGAGGAGCACGACGGCAGCTATGCCAGCAAAGAGGAAGAAGAG[G/A]AAAAGGGCGGTCGCCATTACAAAGGCTTGGAGAAAGAAGGAGAGGACGCGAACACCTCCTTCTGGCTTCGCCGAAGGTGAG
98046 GC G CATTACAGACCATATAGGTGTTAACATATCAACAAACATACATGATTAGATATAACTCTATAGGGCATGGCAGCGTAATATCACACAATAACAGACCCCC[GC/G]CCCAAACATAAAACAAGTGTTCAATAATCAAGTTATAATGTTAATTTATACAAATAAAACATAAACGAGACGCAACTGGCATAGGCA
98046 C T ATGGCAGCGTAATATCACACAATAACAGACCCCCGCCCAAACATAAAACAAGTGTTCAATAATCAAGTTATAATGTTAATTTATACAAATAAAACATAAA[C/T]GAGACGCAACTGGCATAGGCAGAAGTCCATTTTTGAAGCTTTATAAAATCTTAGCTGATTCACTTAAGTTAGTGCGCACTGACAAGGA
98056 CA C ACTATTTTAGTGATGAGAACCTACCCAGTGATAAATTTATGCTGAAGCAAATAAGGAAAGATAAACAAGGATTTGTGTTTATTGGAGTCATTGCATCTTT[CA/C]AAAAAAATGAAAAGACTTGTTAAAGACGTAGCAATGATAGAAGCTGCTCTGAGGACATCAGCTAAGCTGGTTGTTAGTAAGGATGG
98056 G A GATTTGTGTTTATTGGAGTCATTGCATCTTTCAAAAAAATGAAAAGACTTGTTAAAGACGTAGCAATGATAGAAGCTGCTCTGAGGACATCAGCTAAGCT[G/A]GTTGTTAGTAAGGATGGGAAAAAGGTTAAAAGGTTACACCCAGTTCCATTAACTGAAAAAGAAAAGGACACAAAGGTATGTACAAT
98056 GA G TCATTGCATCTTTCAAAAAAATGAAAAGACTTGTTAAAGACGTAGCAATGATAGAAGCTGCTCTGAGGACATCAGCTAAGCTGGTTGTTAGTAAGGATGG[GA/G]AAAAAGGTTAAAAGGTTACACCCAGTTCCATTAACTGAAAAAGAAAAGGACACAAAGGTATGTACAATCATAGCAGAAAATCTCC
98056 TA T CTTTCAAAAAAATGAAAAGACTTGTTAAAGACGTAGCAATGATAGAAGCTGCTCTGAGGACATCAGCTAAGCTGGTTGTTAGTAAGGATGGGAAAAAGGT[TA/T]AAAAGGTTACACCCAGTTCCATTAACTGAAAAAGAAAAGGACACAAAGGTATGTACAATCATAGCAGAAAATCTCCCTGATGATT
98060 C G CCGATCTGATCCTCTTAACGGGCTTGGCCCACTGAACATCATGCAAGCACGGAGACGACGAGGGCCCAATAAGAGGTGACTGGCTGGACATGGGAGATGG[C/G]GGGCACACTCTCTGCTTCTCCCTGTCTTTCCGCTTCCTCCGGCAGAAGACCAGCTCACCCGGATGAGACAGACTGGACTCCAGAG
98068 A G CCCATTTCCAGTCACAATCCAAGCAGCAGATAGGTGGTTATATCACATGCAACAGGCATTAGATACCACTCCCAGCATTGATCCTGATTCCAAAATCAAA[A/G]TGATGAATTTCTTCAGGCACACAGCGTTCTTTCTAGTAGCTGGCAACGAGATGACAAGACAAGCAGAAATTGGCAAACCAGCTGCGG
98078 CA C AATATATTGATTATAAAGGTGACGCTGTAACTGGGTGTTGTTGTTACAGCACTGGCCATTGCATGGCACCAAATGTCATATTTTGCAAACATGATATGAA[CA/C]AAATAAGCTTACTTCCCTCGGTATACTGGCTTTCTCTTCTCTGCAAATGCAGCTAGACCTTCAAGGCGATCTTCGGTATCAAGAAGCT
98080 G A CATCTCCAACGCGTCAAAAACCTCCAACTCGCATGTGCAATAAACCTCTGACTTCATATCTCCTGCACCGCATCGGCTTTCCACCACCAGTGCCAACCAC[G/A]ACTCCACCCTCTTCCTCTCGAGCTCGTCATCACGGCTACCGCAGATCACAACGTCAACTTCGACATCATTGCTAAAGAAAAACGCAAAT
98080 T C AGACAGTCTCCGTCTATACTGGTGTTTTGATTTATAAACGTTTTGCCTTTGAATTGGTTCCTTTCATTCTGTCTCACGGTAATTAGTTTTAATGGTGGTA[T/C]GTAGTTTGGTCTTGAGCAAGGAAATGGGATTAACACTCTATATTTATGCGAATGAAAAGGAGGATAAGTATCACGTATTATCCTACCTTG
98082 AT A TTACAGATGGATGGAATATCCACGATGTGCTAGAAAACTAAGACACCCATCTGACCAGTCTATCGCTACTTACACAGGACATGAAGTCTTACGAACACTT[AT/A]TTCGTTGTTAACTTCTCCCCAGCTTATAGCACTGGCCAGAGATACATATACACGGGATCGCACGATAATTGTGTATACATATATGAT
98082 TA T GATGGAATATCCACGATGTGCTAGAAAACTAAGACACCCATCTGACCAGTCTATCGCTACTTACACAGGACATGAAGTCTTACGAACACTTATTCGTTGT[TA/T]AACTTCTCCCCAGCTTATAGCACTGGCCAGAGATACATATACACGGGATCGCACGATAATTGTGTATACATATATGATGTGATTACTG
98094 T C ACATTTCCCGGAACAAAGCCAAAGAAAGCAGTGGAAAAGAGCTAGTGTATATGATAAGTGCGTCTGAATTTGTTCAATACATGCCAGTATCGCTTTATAT[T/C]TACAAAAGCAGCGGGAAATGAGCATATCTTACGTATTTTTAATGTTGAAATCATAAAAGTGGAAAATTGTACCAGTTCGATTCTTTCC
98094 A G GAACAAAGCCAAAGAAAGCAGTGGAAAAGAGCTAGTGTATATGATAAGTGCGTCTGAATTTGTTCAATACATGCCAGTATCGCTTTATATTTACAAAAGC[A/G]GCGGGAAATGAGCATATCTTACGTATTTTTAATGTTGAAATCATAAAAGTGGAAAATTGTACCAGTTCGATTCTTTCCATTAATTAAC
98096 G A TTACCGTGCTAGCTATTCCTTCATTACTGGACTGGAGTTTTCTTTGCTTTTTATCTCCAGCTTCCCCCTTCGAACTGTCTTGAACTTGAACGCACGTTAA[G/A]GGTACACGGTATCCAGTTTCGCTGCATCGGTATTTCTTATCCTTCTTTTCAGAATAAATGCACGGGATGCAAGGACCAGATGGTGTGCAC
98098 A G CAATATAACCAGGAGGAGCTCCCACTAATCTTGAAACCGCATGTTTTTCCATGTACTCGCTCATATCTATTCTTACAAGTGCATTTTCGGTGTTGAAAAG[A/G]TAACTGGCAAGGGCTTTAGCAAGTTCAGTCTTCCCAACACCAGTAGGACCCATGAACATGAAACTTGCAATTGGACGGTTTGGGTCGG
98098 G A CAAGTTCAGTCTTCCCAACACCAGTAGGACCCATGAACATGAAACTTGCAATTGGACGGTTTGGGTCGGAGAGACCTGCTCTTGAGCGACGTATGGCATC[G/A]GCTACTGATTTTACAGCTATGTCTTGACCGACTACTCTTTTATGCAGTACTTGTTCTAAAGAAACTAACTTGTCTCTTTCGGTCTGTTG
98100 A G ACTGTTGGCCTACTGGCTTCGATCCCAGCTCATCACAACAAGAAGGCGGCGGCGACAGGAAGAATGAGTAGCTTCAGGTTTCACCA[A/G]TACCATGTCGTTGGAAGAGCTCTGCCTACGGCAAAGGATGAAAACCCTAAGATCTTCCGGATGAAGCTTTGGGCTACGAATGAAGTCCGTGCCAAATCT
98100 C T TAAGGTACCAGAGCAGGACAGGGTACCACAACATGTACAAGGAGTACAGGGACACTACCCTGAATGGTGCAGTCGACCAGATGTACACGGAGATGGCTTC[C/T]AGACACAGGGTCCGATTCCCTTGCATTCAGATCATCAAGACGGCAACTGTCCCTGCCAAGCTGTGCAGACGTGAGAGCACCAAG
98100 A G TCAAGTTTCCTTTGACTAACAAGAAGGTCAGGCCACCCTCCAGGAAGCTTAAGACTACCTTCAAGGCTGTCAGGCCTAACCTCTTTATGTAGGGCACTTC[A/G]ATTGCCTTTCAGATTTAATATGCTTATTATTAGTTGTGTTGAATGTTGAACTTTTGTTTTGGGGCATGTCTTTATATTTGGATATTAGAT
98108 A AC ACATATTCACACTCATGTGTAAAAATGACAGCAATATTTAGGGATTCCTGCTCGGATTTCAGCATATCTCCATTCCACTACGGTGCTTTTCCAGAGTATG[A/AC]GGTACTCCCACTCCATGCATCGCACCAGCAGGTCTACCGTCTACTCCATCTTCCAAATGTGCCTCAGGGATGGATAAGTGAAAACTTG
98112 T C AAATACCCAGCTTCTGTGGTGGCGGAAGTGACCTACGACCCGACGCAGATGAACAACGACAAAGACGCTGGATTCCAGATTCTGGCGAATTACATCGGAG[T/C]ATTCGGCCAGCCCCAAAACGCGAAGCCTGAATCGATTGCGATGACTGCTCCGGTTATTACAACTACTGCTCCTGCTGAGAAGATCG
98120 C G TTTTCTATTCCTTGTTGAGACGAAGGCCTTCAATGCCCTCCAGGGCAGAGTCATAATATTTAATGTTGGGTGAGGGTCTTCTTGAGGTAGCTCTCATATG[C/G]TGTTGCTCTGTTGAAGCAATTGGTGTTGAGTCCCGGCTGCTTGAAAAAACAGCTCGTCTTGACGACTCTCCTGACCGCCCCCAATAAT
98120 A C GAGGTAGCTCTCATATGCTGTTGCTCTGTTGAAGCAATTGGTGTTGAGTCCCGGCTGCTTGAAAAAACAGCTCGTCTTGACGACTCTCCTGACCGCCCCC[A/C]ATAATTTGAAGCCATGGCCTCTTTGGTAGACATAGATTCTGTTGCTGGTGGATTCTTCTGTTTTGATAGGCTGCCTCCAATCCCTGTTG
98130 T C CATATGGATCAATATAGGGTGGAGGCGCAATTGACATTTTGCTGGCATCATGTACAAAACTAGACCCAAAGTACAAGTAGAGAGAGGCAGTCAATGCAAC[T/C]GTAATCAAGATCAGAGGCCAAAACGCCAAAAAGAATGTTCCACCAAGTGTCAGAAGCAGCTTCCCTCGCGGAATCAAGCCCTCAA
98136 A G AAAGCAAAGACTGGATAGATGTGAGTATAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAAT[A/G]TTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTG
98136 A G AAGACTGGATAGATGTGAGTATAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGG[A/G]TGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCA
98136 G A ACTGGATAGATGTGAGTATAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATG[G/A]AACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCC
98136 C T TAGATGTGAGTATAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACAT[C/T]CGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGA
98136 A G TGAGTATAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGA[A/G]ACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCA
98136 G A TAGCAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAA[G/A]CGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98136 C A CAGCAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCG[C/A]ACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAA
98136 T A CAACGTCATATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCAC[T/A]GTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATA
98136 A G TATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTG[A/G]CTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCG
98136 C T ATATTGGGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGA[C/T]TTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGT
98136 C T GGCTCCACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTT[C/T]GGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATA
98136 A T ACTGGTTTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATA[A/T]TCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGA
98136 A T TTTGCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTC[A/T]GTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGT
98136 G A GCAGAATATCCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGT[G/A]AACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTT
98136 T A CCAAGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAG[T/A]GTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAG
98136 C A AGCATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGT[C/A]AGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTC
98136 T C ATATACTTCCATCAGCATAAATATTTGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAG[T/C]TTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCAC
98136 G C TGGATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGA[G/C]TATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCT
98136 A G GATGGAACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGT[A/G]TCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGC
98136 A T ACATCCGAGAAACAAAGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATC[A/T]GGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCT
98136 T G AGCGCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCAC[T/G]GCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCA
98136 G A GCACTGTTGGTGACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGC[G/A]TTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCT
98136 G T ACTTGTTCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACAT[G/T]ATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGG
98136 G A TCGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATT[G/A]TTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGA
98136 T C CGGATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTG[T/C]TTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGAC
98136 T C GATAATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTT[T/C]TCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACAT
98136 A C AATCCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTC[A/C]TGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAG
98136 C T CCTCAGTGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATG[C/T]GGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTA
98136 T A TGAACTGAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGC[T/A]CCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCA
98136 G A GAAGTGTCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACT[G/A]ATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACT
98136 A C TCAGTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACC[A/C]GCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACTACGATT
98136 C A GTTTAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGC[C/A]GGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACTACGATTTTG
98136 C A TAAACGTGCCTCCATCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGG[C/A]GGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACTACGATTTTGTAG
98136 A G TCCCAAGGAGTATCATCAGGCCCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCA[A/G]TCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACTACGATTTTGTAGGATTTTTGGCTATG
98136 G A CCAAATATCACTGCGTTCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCA[G/A]TCTCTTTCTTGCAGGCGTCGACATGAGTTAAAATCACTGACTACGATTTTGTAGGATTTTTGGCTATGTTTTCCGGTGCCCTAATTTTGC
98136 C T TCCATAACATGATATTGTTTTCATGCGGAGCTCCACTGATACCAGCCGGCGGATCGCTCTGCAATCTCTTGAAATCTCTCATCAGTCTCTTTCTTGCAGG[C/T]GTCGACATGAGTTAAAATCACTGACTACGATTTTGTAGGATTTTTGGCTATGTTTTCCGGTGCCCTAATTTTGCAATTTGGCCTCTGAGA
98138 T C TTTAGAATAATTTATTATAAATAACAAGCCAAAGGTGGTGGCATCTGAAGCAAATCTAACCAGAACGATATGAGAATTACACGGT[T/C]TTTGCATCATTCAGAGTTGTTATTTCATCAGAAACAACAAAAATCACAAATAAATATTTCTAAACAAATTGCATATCAATCTCTCACATCTTCTTCACGG
98138 CA C ATAACAAGCCAAAGGTGGTGGCATCTGAAGCAAATCTAACCAGAACGATATGAGAATTACACGGTTTTTGCATCATTCAGAGTTGTTATTTCATCAGAAA[CA/C]AACAAAAATCACAAATAAATATTTCTAAACAAATTGCATATCAATCTCTCACATCTTCTTCACGGTGCACTGCACTTGTTCACCTGCA
98138 T C GGAAGGCCGATCATTTTAAGAGTTTGATCCCAGATTGCATAGGAAGTTTCCAGATTGTGCGCTTCTTCAGAAGGGTTCATTGGACTGCAATCATATGCAA[T/C]GTAGGGGCATGCAGGCCATTCATCTGCCTTCAGCGTTTCGCAGTAGTCTGCTATTTGTGGGTCTGTGGCTGCAAATAGTGAACTCCT
98138 T C TTCCAGATTGTGCGCTTCTTCAGAAGGGTTCATTGGACTGCAATCATATGCAATGTAGGGGCATGCAGGCCATTCATCTGCCTTCAGCGTTTCGCAGTAG[T/C]CTGCTATTTGTGGGTCTGTGGCTGCAAATAGTGAACTCCTCGAACCTTCTATGGCATTGAAGATGAAATAGGGGATCAAACGGTATG
98148 CT C ATAGTCTCCTGCGGTGCACGCTTCATCTTATTGGATTCGGGGTTTGGATGGGTCAGGTCCGCCGCGGATGGAGAGCGGTACCGAATGTGGGTCGCCGCTT[CT/C]TTTTTTGGTTGGATCCAGTTTGTTCTTCGGATACCGATCCGAACCCGTTCAGGATCCGAACTGAATTGCTGTACAGTTGTAGTCTG
98150 G T ATGGGCCTGTATGCAGGCCCCATGAACTTCAGGATAGGCGACACCTTGACATGGGCTGGAGGCCCGCATATGTAAGCGGCGGAATACCGATGCTCGGTCC[G/T]GTTGACAACGGCCCTATGCACGACACTATGGAACCGACCATTAGACAATATGTGGCAGAGGTCCCCAACGTTCACCACGAGAGC
98150 T C CCTATGCACGACACTATGGAACCGACCATTAGACAATATGTGGCAGAGGTCCCCAACGTTCACCACGAGAGCACCAGGGATGGGTGGCACGGTAACCCAC[T/C]GGGTCGGGCTCGACTCCTTGTTGGGTCGTAGCACTTGCAGCCCGCTTGTGTTACTTTGGTAAAGTATGGTCAGAAGGCTCGAGTC
98162 G A GTCACCGTCCGCCATCCACGACTGTTACGTCACCAACGACGTCGTCTTCTCCAGTCGTCCTCGTGTTCCCAGCTTTAAAAACGTCAGTTACGGGTACACC[G/A]CATTCGGAACCGCACCGTACGGTCCACACTGGCGTAACCACCGTAAGCTGGTTAATTCCCTGCTCTTCTCTCCTAATCGCCTCCGTTAT
98172 T C GCCCACTCTGGTGCGGCTACTATGGCCGAAGTTGCGTTGTTTGCGTTCTGGCCATTGTATAGTATGTCGTGGAAATAAAGAACCAGTCTTCTGCATGGCT[T/C]TTTCAGTGGCTTTTTGTTGCATGTGGTGAAGGGGGAGAGTAGGATTAGTATGAAGATGGATGTTTGGAAGGTAAAGAGAACTGATT
98208 C T AACACTTCCAGGAACTCGGTTTGGACTATGATTTCTCAAGTAGAAGTAGGTCGAAGGAAGACGTATACTTCATGTCTCATAGAGGGCTCCTGAGAGATGG[C/T]ATCTATATACCAAAACTAGATATGGAGCGGGTTGTATCTATTTTGGAATGGGATAGAGCAGATAAACCTGAACATCGATTAGAGGC
98214 GT G GATAGATGTTGGAGCTGGAGTTATTGATGCTGATTATCGTGGTCCAGTCGGAGTTGTTCTGTTCAACTATTCTGATGTTGATTTTGAAATCAAAAGGGGG[GT/G]TATAGGGTTGCTCAGCTGATTATTGAGAGGATCATGACGCCTGATGTGGTTGAAGTCGATGATCTGGATGCTACTGTCAGAGGTG
98214 G C TGGTCCAGTCGGAGTTGTTCTGTTCAACTATTCTGATGTTGATTTTGAAATCAAAAGGGGGGTATAGGGTTGCTCAGCTGATTATTGAGAGGATCATGAC[G/C]CCTGATGTGGTTGAAGTCGATGATCTGGATGCTACTGTCAGAGGTGAAGGAGGCTTTGGATCAACTGGTGTCTGATTAACTGACTG
98238 T C CAGTTAACCTTCTTAACCAGTATTTTGCATGCCAGCAGCAATACCTTTCATTGTCAAAATAAGTGTATCTTCAAGCCCAGGTGCATACTCGCTTGTTGGG[T/C]TCAGCTTCACTAACTCAGCAGCAGGTTTGCTCGAAACAGAATACTCTTTCGACAGATGCGGCCTTTGTTTCACTTCAAAACTCGGGTCTC
98242 G A TGGCGTGAACTAATCCATTTGTAAGGTAGCGGTAGGTGACAGCTGATGGAGTGAATGGTGCGTTGTCAAGTATCTCACGGTAAATATTCAAG[G/A]CAGTATCTACACGACCAGCATCACAGTGCGCTTTAATCAAGACATTATAACTCACAACATTGGGCAAAACTCCCATTTGCCTAACAAAAAAGCCA
98242 A G TACACGACCAGCATCACAGTGCGCTTTAATCAAGACATTATAACTCACAACATTGGGCAAAACTCCCATTTGCCTAACAAAAAAGCCAAACAAGGTATCC[A/G]CCTCATCGACCCTCCCTTCCTCCAAACACGCCTGCATGACCGCGTTGCATGTGAAGACGGTCGGCCTTACCTTTCCAACACGCATCGC
98254 A G AGTCATCCAGTTCCTTCTTGTTGCCTTGTCGAAATTTACGGTAATTTAGCATATTTTTCAGATTACCTACTAATGGATCAACATATCTATCCATCACCTC[A/G]TCAAGGTCTTCAAATGTTTGGTCATCAATTTGTAATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCAC
98254 T C TGTTGCCTTGTCGAAATTTACGGTAATTTAGCATATTTTTCAGATTACCTACTAATGGATCAACATATCTATCCATCACCTCATCAAGGTCTTCAAATGT[T/C]TGGTCATCAATTTGTAATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCACTATATCCTTATGAGCATA
98254 T C GAAATTTACGGTAATTTAGCATATTTTTCAGATTACCTACTAATGGATCAACATATCTATCCATCACCTCATCAAGGTCTTCAAATGTTTGGTCATCAAT[T/C]TGTAATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCACTATATCCTTATGAGCATAAACCCCATCATG
98254 C T ATGTTTGGTCATCAATTTGTAATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCACTATATCCTTATGAGCATAAAC[C/T]CCATCATGAATTTTTATGGTCAAAGTAAGGAATTTCGGACCTTTAGAACTAGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAAAA
98254 CCAT C TGTTTGGTCATCAATTTGTAATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCACTATATCCTTATGAGCATAAACC[CCAT/C]CATCATGAATTTTTATGGTCAAAGTAAGGAATTTCGGACCTTTAGAACTAGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAA
98254 C T ATGTCTTCCCAATACGAAGTAAGCTGGTAACATCCTTGTGATCTTTTCCACTTTCCACTATATCCTTATGAGCATAAACCCCATCATGAATTTTTATGGT[C/T]AAAGTAAGGAATTTCGGACCTTTAGAACTAGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAAAAACTGCATAGCTTCATCCGCTG
98254 T A TTTCCACTTTCCACTATATCCTTATGAGCATAAACCCCATCATGAATTTTTATGGTCAAAGTAAGGAATTTCGGACCTTTAGAACTAGGCCGAATAATAC[T/A]ATCACCAGCCTCTTTGTCTGATAAAAACTGCATAGCTTCATCCGCTGTCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGTTTGAA
98254 T C CATCATGAATTTTTATGGTCAAAGTAAGGAATTTCGGACCTTTAGAACTAGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAAAAACTGCATAGC[T/C]TCATCCGCTGTCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGTTTGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTC
98254 C T TCGGACCTTTAGAACTAGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAAAAACTGCATAGCTTCATCCGCTGTCAAGTTCTGAAAGCGAGGATG[C/T]ACAATCATCCTGGGTTTGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTCTCTTGTTCATTATGCACATGATCCTCTTCTGGTT
98254 T C AGGCCGAATAATACTATCACCAGCCTCTTTGTCTGATAAAAACTGCATAGCTTCATCCGCTGTCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGT[T/C]TGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTCTCTTGTTCATTATGCACATGATCCTCTTCTGGTTGAATATTGTACCGATC
98254 C T CCGCTGTCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGTTTGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTCTCTTGTTCATTATG[C/T]ACATGATCCTCTTCTGGTTGAATATTGTACCGATCGTTACTATGAATATCACGCGGACCTCGCCAGTAGGCCAACAGTG
98254 A T CGCTGTCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGTTTGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTCTCTTGTTCATTATGC[A/T]CATGATCCTCTTCTGGTTGAATATTGTACCGATCGTTACTATGAATATCACGCGGACCTCGCCAGTAGGCCAACAGTG
98254 A G TCAAGTTCTGAAAGCGAGGATGCACAATCATCCTGGGTTTGAAGTTTTTCTTAGCTAGCTCCTTTGCTTTTCTGGCCTTCTCTTGTTCATTATGCACATG[A/G]TCCTCTTCTGGTTGAATATTGTACCGATCGTTACTATGAATATCACGCGGACCTCGCCAGTAGGCCAACAGTG
98274 G A GACGAACTGGCGGCGTTAGATGGACTCGAGGGTGTCGGGGTTTCCGTCGGAGGACAGGCACGTTGAGGCGGTTCTTCCGGCGGTTGCTGATCGGACAACG[G/A]TGGTCCATGGCGTCAGAGATGATATGGGGGATGAAGTCGAGTGGTTTTGAGAGCAATATGGAACCGAGGGTTGAAGTCGTGA
98282 G A GCCGCACGAACAACCTCATGTGTGGCGCCACCACCAACCCCATCGGTGCCGCCGCCACGACGTTCACAAAAGAGAACTGAGACGGCGGAGGCGGCGCCGG[G/A]AAGTTGGTCTTCGCCTTGTTTCCTCTGAGCGACCTCGCCGCCTGATCGTACGCCACGGCGGCCTCCTCCGGCGTGTCGAACGTCC
98282 A G CCGCCTGATCGTACGCCACGGCGGCCTCCTCCGGCGTGTCGAACGTCCCTAGCCAGACGCGCGTCTTCTTCCACGGATCCCTTATCTCCGCGGCGTAGCG[A/G]CCCCATGGTCTCTTCCTGACACCTCTGTAATGCTGCTGGTGCTGGTGAAGATTAGGGCTTGGGCTGGACATCGATTTTCCCGATTTT
98282 A ATGCTGC CCGGCGTGTCGAACGTCCCTAGCCAGACGCGCGTCTTCTTCCACGGATCCCTTATCTCCGCGGCGTAGCGACCCCATGGTCTCTTCCTGACACCTCTGTA[A/ATGCTGC]TGCTGCTGGTGCTGGTGAAGATTAGGGCTTGGGCTGGACATCGATTTTCCCGATTTTATTTTACCGGTGGTTAGATTAATTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98282 A T TAGCCAGACGCGCGTCTTCTTCCACGGATCCCTTATCTCCGCGGCGTAGCGACCCCATGGTCTCTTCCTGACACCTCTGTAATGCTGCTGGTGCTGGTGA[A/T]GATTAGGGCTTGGGCTGGACATCGATTTTCCCGATTTTATTTTACCGGTGGTTAGATTAATTGGATTTTTGTGT
98284 C T ACCTCGACGAAGAGGATCCTACGGCCAAGAAGCTCAACCGATCGACCCCAGCTTCAATCAGGTCCGTCCATTTAATCCCGCTGCTCATCTTGGTGTCCTT[C/T]CTCATACTTTACCTCATCTCCCACGAACCCTCTGCTTCAGAATTGCCAAAAACCAGAGGGATTGATCGGATTATAGATCGAAAAGTTTC
98284 T TG AAAACCAGAGGGATTGATCGGATTATAGATCGAAAAGTTTCTGTATCGGGAATTATGTCGGCAGCAGCGCTACGAACGAATCGTGGGTTGATGGAAGAGA[T/TG]GGGGGAGAAGAAATATCTTTACCGGCGGCTAGGGATTCATTAAGGAGAATACGTGAGCTGCGCCTGTTGCATTGCTTATTCATA
98284 G C AAGTTTCTGTATCGGGAATTATGTCGGCAGCAGCGCTACGAACGAATCGTGGGTTGATGGAAGAGATGGGGGAGAAGAAATATCTTTACCGGCGGCTAGG[G/C]ATTCATTAAGGAGAATACGTGAGCTGCGCCTGTTGCATTGCTTATTCATATTGGTTTTTTTTTATTCCCCCTTTCCTCCCCTTCTTAT
98284 G C ATCGGGAATTATGTCGGCAGCAGCGCTACGAACGAATCGTGGGTTGATGGAAGAGATGGGGGAGAAGAAATATCTTTACCGGCGGCTAGGGATTCATTAA[G/C]GAGAATACGTGAGCTGCGCCTGTTGCATTGCTTATTCATATTGGTTTTTTTTTATTCCCCCTTTCCTCCCCTTCTTATTTTGGGATTT
98284 C G ATTCATTAAGGAGAATACGTGAGCTGCGCCTGTTGCATTGCTTATTCATATTGGTTTTTTTTTATTCCCCCTTTCCTCCCCTTCTTATTTTGGGATTTTA[C/G]TATGTAAATAATCGAGTATAACCATTATGTTTATAGATTGTGAATTTCTATGAAAAAATCAGTGAACTTTGAGTC
98284 C T AATACGTGAGCTGCGCCTGTTGCATTGCTTATTCATATTGGTTTTTTTTTATTCCCCCTTTCCTCCCCTTCTTATTTTGGGATTTTACTATGTAAATAAT[C/T]GAGTATAACCATTATGTTTATAGATTGTGAATTTCTATGAAAAAATCAGTGAACTTTGAGTC
98292 C T AAGCTCTGTAGTGCAATTGCTGCCGCAGGCTTAATCTCAACCTACACTTCAAGACATGTAGAAAA[C/T]AATCAAGCAGCCGCAGAAACATACTCTATGGTTACCCTCATCGACTGCAGAAAGTTTCTCGACCCAGTTTTAACCGAACGTGATATCGGTTTTTACCATT
98292 C A AAGCTCTGTAGTGCAATTGCTGCCGCAGGCTTAATCTCAACCTACACTTCAAGACATGTAGAAAACAATCAAGCAGC[C/A]GCAGAAACATACTCTATGGTTACCCTCATCGACTGCAGAAAGTTTCTCGACCCAGTTTTAACCGAACGTGATATCGGTTTTTACCATTCTGCCATAATGA
98292 T C AAGCTCTGTAGTGCAATTGCTGCCGCAGGCTTAATCTCAACCTACACTTCAAGACATGTAGAAAACAATCAAGCAGCCGCAGAAACATACTC[T/C]ATGGTTACCCTCATCGACTGCAGAAAGTTTCTCGACCCAGTTTTAACCGAACGTGATATCGGTTTTTACCATTCTGCCATAATGAACACACACACAA
98292 T C TAGAAAACAATCAAGCAGCCGCAGAAACATACTCTATGGTTACCCTCATCGACTGCAGAAAGTTTCTCGACCCAGTTTTAACCGAACGTGATATCGGTTT[T/C]TACCATTCTGCCATAATGAACACACACACAATCCACGGTGAAGACGGACTATGGGACGTGGCTTCGAGAATACACAACGCTTACGAC
98292 G A GGTTACCCTCATCGACTGCAGAAAGTTTCTCGACCCAGTTTTAACCGAACGTGATATCGGTTTTTACCATTCTGCCATAATGAACACACACACAATCCAC[G/A]GTGAAGACGGACTATGGGACGTGGCTTCGAGAATACACAACGCTTACGACAATGCAAAGAAAAACAGAAAACATTTAACAGACATAG
98292 T C ATATCGGTTTTTACCATTCTGCCATAATGAACACACACACAATCCACGGTGAAGACGGACTATGGGACGTGGCTTCGAGAATACACAACGCTTACGACAA[T/C]GCAAAGAAAAACAGAAAACATTTAACAGACATAGGCGAGCTAAACTACCTGATGTGCAAGGCGATAGACAATCCTCATTTGACTCCT
98292 GA G GTTTTTACCATTCTGCCATAATGAACACACACACAATCCACGGTGAAGACGGACTATGGGACGTGGCTTCGAGAATACACAACGCTTACGACAATGCAAA[GA/G]AAAAACAGAAAACATTTAACAGACATAGGCGAGCTAAACTACCTGATGTGCAAGGCGATAGACAATCCTCATTTGACTCCTTCGT
98292 A C CACACACAATCCACGGTGAAGACGGACTATGGGACGTGGCTTCGAGAATACACAACGCTTACGACAATGCAAAGAAAAACAGAAAACATTTAACAGACAT[A/C]GGCGAGCTAAACTACCTGATGTGCAAGGCGATAGACAATCCTCATTTGACTCCTTCGTCGTCTATGAGGACAGCAGTCATATCGGT
98292 G A GGGACGTGGCTTCGAGAATACACAACGCTTACGACAATGCAAAGAAAAACAGAAAACATTTAACAGACATAGGCGAGCTAAACTACCTGATGTGCAAGGC[G/A]ATAGACAATCCTCATTTGACTCCTTCGTCGTCTATGAGGACAGCAGTCATATCGGTGTTTGAAGAACCGGTGGTATATGAATCTTC
98292 G A AACATTTAACAGACATAGGCGAGCTAAACTACCTGATGTGCAAGGCGATAGACAATCCTCATTTGACTCCTTCGTCGTCTATGAGGACAGCAGTCATATC[G/A]GTGTTTGAAGAACCGGTGGTATATGAATCTTCGGAGTTGCATAGTAAGGTTGGTGTGGAGGATTACGTGGGGTGCGCGTCGGTGC
98292 A T AGCTAAACTACCTGATGTGCAAGGCGATAGACAATCCTCATTTGACTCCTTCGTCGTCTATGAGGACAGCAGTCATATCGGTGTTTGAAGAACCGGTGGT[A/T]TATGAATCTTCGGAGTTGCATAGTAAGGTTGGTGTGGAGGATTACGTGGGGTGCGCGTCGGTGCATGGCGTAGGTCCGTCGATCG
98292 A G GGCGATAGACAATCCTCATTTGACTCCTTCGTCGTCTATGAGGACAGCAGTCATATCGGTGTTTGAAGAACCGGTGGTATATGAATCTTCGGAGTTGCAT[A/G]GTAAGGTTGGTGTGGAGGATTACGTGGGGTGCGCGTCGGTGCATGGCGTAGGTCCGTCGATCGCCGTTTTTGATACGATCAGGGA
98292 C T CTCCTTCGTCGTCTATGAGGACAGCAGTCATATCGGTGTTTGAAGAACCGGTGGTATATGAATCTTCGGAGTTGCATAGTAAGGTTGGTGTGGAGGATTA[C/T]GTGGGGTGCGCGTCGGTGCATGGCGTAGGTCCGTCGATCGCCGTTTTTGATACGATCAGGGATGGTAGGCTCGATTGTGCATGCG
98292 G A CTTCGTCGTCTATGAGGACAGCAGTCATATCGGTGTTTGAAGAACCGGTGGTATATGAATCTTCGGAGTTGCATAGTAAGGTTGGTGTGGAGGATTACGT[G/A]GGGTGCGCGTCGGTGCATGGCGTAGGTCCGTCGATCGCCGTTTTTGATACGATCAGGGATGGTAGGCTCGATTGTGCATGCGTAT
98292 T C TATCGGTGTTTGAAGAACCGGTGGTATATGAATCTTCGGAGTTGCATAGTAAGGTTGGTGTGGAGGATTACGTGGGGTGCGCGTCGGTGCATGGCGTAGG[T/C]CCGTCGATCGCCGTTTTTGATACGATCAGGGATGGTAGGCTCGATTGTGCATGCGTATATCCTTCGCCTTTGCATTCCAGGAAGC
98292 T G GGGATGGTAGGCTCGATTGTGCATGCGTATATCCTTCGCCTTTGCATTCCAGGAAGCAGGTTGGTGACCTTGTTGATCACATGGTGAAGACCTTGTGCGA[T/G]GGTTGCGTCTGATTTGTAATTAGTTTTGTATTTGATTTGTGGGTGTAAGAGATCTTGGATTCTGACTAATAATGTTTATAATTTATGC
98300 T C CGTTGTTCCTTTTTCAGTTTCTAAGCCCTCTTCTCACCAACAATGGGCATTGCCATACCATTAACAAGTACCTGAGTGGAGCACTTCTTATAGTTTGCAG[T/C]TTCTCCTGCTGCTTTTCATGTTTCACGGACAGCTACATAGGAAGTGATGGAAAATTATACTACGGAATAGTAACAAAAGGAGGACTATG
98300 T C GGAGGACTATGGTCATTTTCGGATAAGGATGCTAAAAAGGAAGATTTGGCAAAATACAAGCTTAGAATTGGAGATTTTGCACATGCATTCGTCTCCCTAG[T/C]TGTGTTTGTAGTGATTGCTTTACTGGATAATAATACAATGAACTGCTTTTATCCCAAGGCGGATCTGAGGACGCTGATGATGGTTTT
98300 GT G TTTACTGGATAATAATACAATGAACTGCTTTTATCCCAAGGCGGATCTGAGGACGCTGATGATGGTTTTGCCAACGGTGGTGGGTGGGTTGGCCAGTTCC[GT/G]TTTTTGTTATTTTTCCGAACAATCGACATGGGATTGGGTATCCACCACCAACTCAAGATTAAATGAATTATGAACCACAATGGATTC
98310 A G TTCATCTTGTGGAAGCTGAGACCCATGATCAAGTTGACGGGAATCACTGTCCAGTTGTTTACTGTCTTCATCCATGTATCTGAAAATGTCGTTCAGGACA[A/G]AGAAGCCCTTATCTTGAGTAGCCAGGAAAAAGGACTGAGTGAATTTCCTCTTAACATTGTCGTTCTCTGTAAGGTAACCGGTAACAAG
98310 A G TTGTTTACTGTCTTCATCCATGTATCTGAAAATGTCGTTCAGGACAAAGAAGCCCTTATCTTGAGTAGCCAGGAAAAAGGACTGAGTGAATTTCCTCTTA[A/G]CATTGTCGTTCTCTGTAAGGTAACCGGTAACAAGAACGAGAACCCCTCCGTTAAGTGATTCTTGAGCATCCACTGTTTTGATCTCCGAT
98322 A T GATAACTGCTACTACCACAAAGGAAATATCCATTTGCCTACCAGAACCAAACACACCACCCACACAGATATCCAGCATCTCCTCTTCCAAAACCACCGAA[A/T]TCGAATTACCAAAACCGAAGGCAGGCCCTACAAGGTGCAGCACCTGCAACAAGAAAGTGGGGCTAACCGGCTTTGACTGCCGCTGCG
98322 G A ACTGCGGGCAGGGAGGCGATTGCTAAGGCCAACTGTGTCATCAAGGCCGAGAAGCTCGATAAGATTTGAGGTTTGGGAACGAAGAGAGATCGATGGTTGA[G/A]TGGATGAAATTTAGTGGTATGTTTCTATTATTATGTTGTCCTTTGTGTGTCCTAGTTGGTGTGGTTTGTCCACATTATAGAATGGC
98322 A G GTCCTAGTTGGTGTGGTTTGTCCACATTATAGAATGGCTGCCTTGGAAAGAATGGTTCTGCCTGTGTGTTCCTGATAGGGTGTGTGTTATCGGGTTTGAT[A/G]GATGATGTTATCTGATATTGATGAATTTATTTGGGTTTGTAATGTGTTGTAATAGTAACTGGTGGCATTGTTTGTATGGAGTCGTGAA
98338 T C CAGTCATGCTCATCATTCACCCCAGACGGTCAATACATCATATCAGTAGGGGATGACTCCAACGTCTACATATTCAACTCCGACCTCACCACACCACCAT[T/C]GAAGAAAGACCGCCTCTCGAAAGATTTAAAACCCTTGAAATCTATACGCTCCTACGAATTATTCACCTCCAAAAATGCATCGATAGCCA
98338 C T AGAAGCTTTTGGAACCTTCTAGTGATTGTACCCATTGTCATTATCCTAGGCTTACGCATTTATCGGCTACTTGGAATATGGTTATTGTGACTGCTAGCAC[C/T]GATGGGGTCATTAGACCTTTCCATAATTATGGCTTGCCAGTACGACTATGATGAATGAACAGCATTTAATATGAATCAGTGAATAATGG
98338 T C CTGCTAGCACCGATGGGGTCATTAGACCTTTCCATAATTATGGCTTGCCAGTACGACTATGATGAATGAACAGCATTTAATATGAATCAGTGAATAATGG[T/C]CTAATGTAGATGGCATGATTAGTGGGTTTCAGACAACATACTGGAGATAGATAAGGTAATTTTTCTGTATAGATGTGTTGAATT
98378 G A TTCCTTCAATCCGCTCATTCTTCTTGGGTTCATAAGACATGGCGTAAATATCAGCTTCTTTGGACCTCTCAGCGATTAATTGTCCAACCGTTCTACACGC[G/A]TCATCATCGATGAGGGAAGGCAAAGTGTTTCTCAAATCTCTTGCATTTGTGCTCGCAACTGACATCACTTTGCTTGTTCCTCTATGCATTA
98378 CG C CCCTCTGGATCTCCTGGTCCATGCAGCGCAAATGATGCCCATCTGCCGCTGACTAAGTCCGGCAGAAGAGCTGGCATTGAAGTTGAAGGCTAGAGATTTC[CG/C]GAGTTAGGTATAGAAGATGACCACGACAGAGAAGAAGTAGAGGAAGGTAATTTAGTCGTTTGCTTGGGAAGCGAAGAAGAATG
98380 G A TACTACTTTTCTCGCTTTTATAGAGATCTCTGGCATCTGTAGATTATCTTGCAGTAATCTGTTAACTACGTCGAGATCAGGAGAATCATCCTCATGCATG[G/A]CAGCTATCGTATTTGTCCTCAATACAAAAGGAGTAGATATATTACCAATGTTAGTTCCAAAAATATCAGACTCCTCGGCTATTCTGAAAA
98382 C T CAAAAATATACAAGAAAAACAGGTTGCTCGAAAGGTGGTTCCAGCTTGCATGACAAAAAGTTGAAGTTATAAACTGGTACCAAGCAGGCTGATAGTGATA[C/T]AAGTACAGAGACTTGATTGATTTCACCATGAATAAGTGATCAGCCAAATATATACTGATATTAAGGAGCAGAATCCAAAATATTCCA
98382 C T ATCAGCCAAATATATACTGATATTAAGGAGCAGAATCCAAAATATTCCACTAATACGTTTACTTTGCAGCCTTCTGTCTTCTGATCTGCTGAGTTCTAGG[C/T]CTGATACAGAATCTGATCCTTTCAGTCTGCAGAGAAATCTTGATGGTGGGCATAAAGCGATGGAACGCGTGCAAGGCACGTGAATAAG
98390 C CA AATAGTTATTATTGCAACCGGTATTAACTCATGTGGTTACGTATTTAACTCTGAAGGGGGTCATGGAGAGAAAGTATCCACTGTTTGTTCTGAGGTTCTT[C/CA]AAAAATTGGAAGATTTTTTAGAAGAAGATAAAAAGAAAATTAGTAAGAATAATGGCACTACAGTTTCTGGAAGAGTGTCTTCGCTTC
98394 T G CCTTCGAGAATAGTGCATCAACACCTCCTCTTCAATTTGCTAACTCACCTAGATCAGGCACAACCATGGTTAATAATACTCCTTCACCTCAGCAGCAAGC[T/G]CAACATCAACAACAAGCACAAAGACAGAAGTTGATGCAACAGATTCCACAGCAGCAGCAGCAGCAATTGAGGCAGTCTACCTCAGGA
98400 T A AATTCGGGTTGAACATATCATCCGCGAGGAGAATATGATGGCTGCGCAAGAGATTATTGAATTGTTTTGTGAACTAATTGC[T/A]GTTCGTCTATCCATAATCGAAACTCAGAGGGAATGCCCTCTAGACCTCAAAGAAGCCATTTCAAGTGTGTGCTTCGCTGCACCAAGATGCTCAGACTTAA
98400 C T AGAATATGATGGCTGCGCAAGAGATTATTGAATTGTTTTGTGAACTAATTGCTGTTCGTCTATCCATAATCGAAACTCAGAGGGAATGCCCTCTAGACCT[C/T]AAAGAAGCCATTTCAAGTGTGTGCTTCGCTGCACCAAGATGCTCAGACTTAACTGAATTGCAGCAAGTCCAAATGTTATTTGCAGCCA
98410 AT A AGGAACTTCAAGGATGTTTATTTAGTTTATGAACTCATGGACACTGATCTGCATCAAATTATAAAATCTTCTCAGGCACTTTCAAATGACCATTGCCAAT[AT/A]TTTCCTTTTTCAGCTTCTACGGGGTCTTAAATATCTCCACTCAGCAAACATACTTCACAGGGACTTAAAACCTGGAAACCTCTTAATAAA
98416 TA T GTTACAACCAGTAAGCCCTTATCTCATTTCGTTCAGAGTCAACGAAATCCTTTTCAGCCGCCACGAGATAAAAGCAAACCGAAACTCCACCTTTCAAAAA[TA/T]AAAAATAAAAGCAAATGAAATTTCATAAAATTTGATCCTCACATATTCGAACTTGCAGCAAGTGGATCTTCATCTCCAAGGGGTTTCC
98422 T C AGTACTTCAAATGATTGCCTTAAAATTCTTGGACGAAGCGGTGGTGTTGGCGGCAGTTCGTCTTCTGTTAGAGGCTTGGAGTTTAATCTAGACAAGGATC[T/C]GAAGCCCAAGATATGTATCACTTCGAGCACTTCAGCTGGTTTAGAACAAATTCTTCCCTGGCTTTACTACCACAAGGTTATTGGAGTG
98432 G A ATCATGGAAATGCCGAAGATATGGTGAAGCGAAATAAATCGGGGGAGCCATTGCTTGATAGAGACGGAAATATTCAGATTCTCACTTCCCATACCCTTCA[G/A]CCGGTTCCAATAGCTGTAGGCGGCCCTGGACTAGCAGCGGAAGCAAGGTTTCGTAATGACTTGCCAAATGCTGGGCTCGCTAACG
98432 TA T TGTGATGAACCTCCACGGTTTTGAGGCTCCTGATGACTATGAAGCCACTCTTATTGAAGTGGTTGGCAACTAATTTTTATTTGCTCTGCTAATGTTTAAA[TA/T]AAAATCGGTATGGTACCCCTATTGGCATTGTGTGGATCAGCAATTCGTTTTGCTCAGCGAACTGGCATATTTGAATTGTTTGAACTTTT
98432 G A GCAACTAATTTTTATTTGCTCTGCTAATGTTTAAATAAAATCGGTATGGTACCCCTATTGGCATTGTGTGGATCAGCAATTCGTTTTGCTCAGCGAACTG[G/A]CATATTTGAATTGTTTGAACTTTTTGCTGGTGGAAATTATACGACTGCACTTAGGACTAAAAAAAAAAAAAA
98446 T C TCTAAATGGGGGCAGTTTTTAGATAGAGACTGAAGCAGTTCGTCAGTTATCAGTCTACAGCCCAGAAGTTCTAGTTTACTAAGACTGTGACAGCTGGAGG[T/C]GATTGCCATTAATCCTTTGTTGCTTATTTTTCTACAACACGAAACGTTTAATGACTGTAGGGACGACAGGCTTTTTCCAAGGGATACC
98446 AT A AGACTGAAGCAGTTCGTCAGTTATCAGTCTACAGCCCAGAAGTTCTAGTTTACTAAGACTGTGACAGCTGGAGGTGATTGCCATTAATCCTTTGTTGCTT[AT/A]TTTTTCTACAACACGAAACGTTTAATGACTGTAGGGACGACAGGCTTTTTCCAAGGGATACCAATCCAGCATCAGTGATACCTTTACA
98446 A G AGCATCAGTGATACCTTTACAGTTGTGCAAGTCGAGGGTTCTAAGCGACTTGAACCCGGTAGCAACAACAGCAAGATCCGAATCAGATACGCCAGGGTAA[A/G]AGGATCTAGAAGCGCACTGTGAGAGATCGAGTTCTAGGATGTTCGAGAAGCGTACGGCCATCCGGCGAAGCATCGCGTGGCCCG
98446 G A AGAGATCGAGTTCTAGGATGTTCGAGAAGCGTACGGCCATCCGGCGAAGCATCGCGTGGCCCGCACGTGCACGGAGGCGGCGGCGGTCCGAGCTCTGCAA[G/A]TGGAACCATCGCTTGCACACAAGGCCAAAAGTGTCTTTCTCTTCCTGGGATTTGAGCTTGTTCAGAATGAAGAGGAGAGCGTCG
98448 T C CCCTCTCGCGCTTACCACTTCGTCTTGCAGAACTTCGAAGACGACTCCAACCAGCTTGTATAAATCCATTTCTGTCA[T/C]TGCAAATTAGCTGGAGTAAAATTAAAAGAAAATCATGGCAGGAGACGGCGCTAAATGGGATGGCTTATTAAAGTGGAGTCTAGCCCACTCTGATGGTACC
98448 T TA CCCTCTCGCGCTTACCACTTCGTCTTGCAGAACTTCGAAGACGACTCCAACCAGCTTGTATAAATCCATTTCTGTCATTGCAAATTAGCTGGAGTAAAAT[T/TA]AAAAGAAAATCATGGCAGGAGACGGCGCTAAATGGGATGGCTTATTAAAGTGGAGTCTAGCCCACTCTGATGGTACCAAACCTCCTC
98448 C T GAGACGGCGCTAAATGGGATGGCTTATTAAAGTGGAGTCTAGCCCACTCTGATGGTACCAAACCTCCTCGAAATTTGAGCGAGGAGGATCGGAAATGGTT[C/T]ATGGAAGCGATGCAGGCTCAAACGGTTGATGTGATTAAAAGGATGAAAGAAATTACTCTAGTTATGAAGACTCCTGGGGATGTTT
98448 A G TGAAAGAAATTACTCTAGTTATGAAGACTCCTGGGGATGTTTTGGAATCTCAAGGTGTTACTGCGCATGACATTGAAGAAATGTTGGAGGAGCTACAAGA[A/G]CATGTGGAATCTATTGACATGGCTAATGATCTGCACTCTATAGGCGGCCTGGTTCCTCTACTCGGTTATCTGAAAAATGCTAATGCT
98448 C T AACCTCTCATCTCAAATTTCACTTCCGATCCTGACATGTTAGCACGTACAAAAGCTCTTGGTGCAATTTCTTCGCTAATTAGAAACAACAAAGCTGGAAT[C/T]GCTGCTTTCCGTTTATCCAATGGTTATGCTGCACTTAGAGATGCACTGGTTTCTGAGGATGCTCGATT
98470 G A TCAGATCCATCCGCTTCTCATCCGACGGTCGTTTCATGGCCACAGCGGAACCTGCTGATTTCGTGCACGTGTACGATGTAAGTACAGGGTATCACCACGA[G/A]CAGGAACTCGACTTTTTTGGAGAGATTTCTGGCTTATCATTCAGTCCGGATAGCGAGGCTGTTTTCGTTGGTGTATGGGATCGTACA
98478 A G GTTTAAAAGAATGGATTCATCCATAGATATGCCTTCAACACATTACCTGTGAATAGCCTTCAACTGGCGATGACAGCATCTGATTTTGGACCTAAATATT[A/G]ACGCCAGATACTGCTGGAATTTGATTCCTGATGTTTTTCCATATCTGCGGAGCAAATACGTCTAGGTCCATCGTACTGAAGGATATTGG
98478 A C TGGAATTTGATTCCTGATGTTTTTCCATATCTGCGGAGCAAATACGTCTAGGTCCATCGTACTGAAGGATATTGGTTATGCTTTTATGTATATCTGATGA[A/C]ATTGCTCCATGAATCTTCCAACACGAAGGAAGTTCATGGTAACTGTTGTGGAATGTCAAAGCAATAGCTGCACTGATTTTCTTGCTCCT
98478 C T TGATTCCTGATGTTTTTCCATATCTGCGGAGCAAATACGTCTAGGTCCATCGTACTGAAGGATATTGGTTATGCTTTTATGTATATCTGATGAAATTGCT[C/T]CATGAATCTTCCAACACGAAGGAAGTTCATGGTAACTGTTGTGGAATGTCAAAGCAATAGCTGCACTGATTTTCTTGCTCCTATCTTCTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98482 A G AAATAGAAACATACCAAAAAGCTGAAGATGGACAGTCGCGATAGCATCAAACGAGAACAAACTTTGCTACAACAGAGGACACACCACGTTGAGTTGGTCA[A/G]TCCAAGCCTAAGCAAGTCGAAACCTTCCGGGAACCAGAAAGGCCACCATGCCAAGACAAGGAGAGGTAAGGAGTAGCGGCTTCA
98494 A G TTTGCCTCTGAATTGTTTAAGGCTCTCAGAAATGGCGAAACCGCTGCCAAAGTTCATCAACGATCAACTCAACTACCTCTGTAGTAACTCTCCGCTCCAA[A/G]TGAAGGTGGATCAAATTCGGTCAAGCAGCATTAACTCTCGATATTCTGATCATTTTACACTCTCCATACCTTTCTGTCTTGATTACATCA
98494 C T AACTCAACTACCTCTGTAGTAACTCTCCGCTCCAAATGAAGGTGGATCAAATTCGGTCAAGCAGCATTAACTCTCGATATTCTGATCATTTTACACTCTC[C/T]ATACCTTTCTGTCTTGATTACATCAAGTGGGATTTTATGTACGATACGGTGTATCCTTCACGTGCTCCTGATATTGTATTTCCGATTGAAG
98494 C T CAAATTCGGTCAAGCAGCATTAACTCTCGATATTCTGATCATTTTACACTCTCCATACCTTTCTGTCTTGATTACATCAAGTGGGATTTTATGTACGATA[C/T]GGTGTATCCTTCACGTGCTCCTGATATTGTATTTCCGATTGAAGATGAGGAATTTAACCCTCTTGTAGATATTGTTGGAGAAGAGAGAAA
98494 T C TGTATATGGAATACCATAAGAAACGTGCAATGAAGTTAGATGATGATAGATTGCAGTTTGAAGCAAATACAATTCTCACAAGGGAGGGGGTTGAAGTATG[T/C]GTGACGCCTGCTGTGGACGGTGCTGATGGGGCAGGGGCTGTCAAGTTTGTCATACCATTACTGGACAACGTAAACTTGAACAAGT
98498 G A GACCTCAGTAGTTGATCCAGTAGCATCGCTGCAACTGTTTGATGCATTGTTAGCTTTCTTCGAAGATTCGCAATCAATACATTTGCCATCAGTCACGACA[G/A]ATCTGACATAATGTGAATCTGCTGAAAATGTCTTTAGAAATTCATCTTTCTCTAAAAGTGATTCACCAAATATATCCTGAAGAGCATGTT
98500 T C TTGTTCCTCCAAATGTGGCTCGACCTTAGCGTACTTTTGACGTGCAAGATATTTAGTCATTTGCTTCTGGGTGCGCTTCTTGGTCAGCACATCATTCTCT[T/C]CGCCATCCTTGTTCTTAACATCACGCTTACGTCCCAATGGCAGGATGTAATGACTTTCATACCATTGCCGGAATGGTGTGGCATCGATCA
98512 C T AAAAGCTTGGGTTGCTCCCACCATTTCGGGCCTTGAACTTGACGATGGACTTCAGGATTAGTATCGAATCTTCGTTCCGTTGGGTTCTTGTAAGCTTTCG[C/T]CTTTCTGGTTTCTCATCCGTCAGCTTCTGTCTTTTTGCATCATTCTGCATCCCCGCTTCCACATTTGAAGATGGCATTCCGAGATAAAGT
98514 AT A GTGGTTGATGCGTTGGAGATCGTCGTGCCTGATGGAGATGAGGGTGGAATGGTCTGATTTTTGATTGTTGGAGGTGTTTGTGTAAATGTTTCAATGTTTT[AT/A]TTATGGATTGACTGAAGCTAGCTAAGGTTTTGCATGATTTATTTATTCGTGACTTGTTAGAATTTTCCTTTTAGTTGTGTTTCTTGGA
98524 T G CTGCGTCTAACAGGAGAAGCGCTATCATCATCTGAGGGGCTCCTGCTCCTTCGCCTTTCATCTTCGTATTTGCCTCTTCCTCGGCCCCTGGAACGATCCA[T/G]GCTCAAACTACGGCTTCTACTTCGACGGCTATACCTATCCCTGCTACGACTCCGGCTTCGTCTTTTGTAGTCTCTATCACGGTAATCATC
98524 G A CATCACGATGCCGTGGTCTGGGGCTGCGGCTTCTTGACCTCTTAGTCTTGGAAACATCTTCAACAATCCTACCCTGACGAATGCGTTCGGAGTTAGGACC[G/A]TATTTTGCAAACTGAACCATGATGTCTCTACCGTCCACATTTCTCCCATCAAGTTTGTCCACAGCTTTCTGTGCTTCATCAGCGTACTTG
98524 T C TCCTACCCTGACGAATGCGTTCGGAGTTAGGACCGTATTTTGCAAACTGAACCATGATGTCTCTACCGTCCACATTTCTCCCATCAAGTTTGTCCACAGC[T/C]TTCTGTGCTTCATCAGCGTACTTGTACCTCACAAACGCAAACCCTCGCGATTCTCCAGTCCTGCGATCTCGAGGAATGAAAATATCAACG
98524 A G AAATATCAACGACTTTTCCATATTTGTCGAAGAGAGGATACAGATCATCAGCAGAGGTACGGAAAGTAATGTTGAGGACGAGGAGAGAGAAAGTATCCTT[A/G]ATATCGGGAGGTCCAGATCGGCCGAAGTGCGACATCCCGTCCTATATTTTCAACAGAAGGGTTCAGAGAAGGGATAAGAAAGAA
98524 A G GACGAGGAGAGAGAAAGTATCCTTAATATCGGGAGGTCCAGATCGGCCGAAGTGCGACATCCCGTCCTATATTTTCAACAGAAGGGTTCAGAGAAGGGAT[A/G]AGAAAGAAAAGTCGGATGAGGGTTTCGGAGGGAGGATGGAGATGAATGATGATGGGCAATTATCCCAGTAGGCCAACAG
98538 C T GCGGTATAGCTGGGTTGGCGACTGCCCTTGCCTTACAAAAAGTTGGAGTCAAGAGTTTGGTGCTCGAAAGAGCAAACAAACTGAGGTATGAGGGAGCTGC[C/T]ATCTCCCTTTTCCCAAATGCCTGGCGAGCTCTGAAAGCTCTGGATGTTCTACATAAGATTGAACCTCTATATCAACCTTTTCAAATA
98538 T C GCTCTGAAAGCTCTGGATGTTCTACATAAGATTGAACCTCTATATCAACCTTTTCAAATAGGTCAAGTGACAAACCTTGCAGCTGGAACTACGCAACAGA[T/C]TCACTTAGGAAATGGAGTTATGGGTTTGCACAGAAAAGTGCTTATAGACGGGCTAGCAGAAGAGCTACCGCCTGATTGTATAAGATT
98538 G T TTTCTTCCAAACTCGTTTCAATCAAGAACAAAGAGCTTAATGATTCATCCAATGCTACTCACATCGAGCTTGAAGATGGAACCGTTATTCAAGCTAAAAT[G/T]CTGATTGGATGCGAGGGAGTTCATTCTGTAGTAGCCAAATGGCTCGGTCTAAGCACTCCAATTCACTCCGGCCGAGGAGCTTTTCGTG
98538 C G TGGATGCGAGGGAGTTCATTCTGTAGTAGCCAAATGGCTCGGTCTAAGCACTCCAATTCACTCCGGCCGAGGAGCTTTTCGTGCATTGTCTGTGTTCCCT[C/G]AAGGTCATGGATTCAAACATGAAGTTACATTAATGACCAAGATGAGCATAAGAGTCGGATACATTCCTATTTCAGACACAGATGTCT
98538 T C ATTCACTCCGGCCGAGGAGCTTTTCGTGCATTGTCTGTGTTCCCTCAAGGTCATGGATTCAAACATGAAGTTACATTAATGACCAAGATGAGCATAAGAG[T/C]CGGATACATTCCTATTTCAGACACAGATGTCTTCTGGTTCATTACTCATAACATCACGAAGAAAGAAAATGAGCT
98556 T C AGGGGAAGAGTTATGGGATGGGAAAAGGAGAGGGCTCGAGCTCTAAGAGTTTTAAGAGAGAGAAAGGGAAGAAGAGGAACAGGGAGAAGGGAGAAAGAGG[T/C]GATGGGAAGGATAAGTGGAAGGGAAAGGGGAAGGAGGGTGGGAGCGGTGGCGATGGGGCGGAGATGAAGGAGCTGTG
98556 CG C GGATAAGTGGAAGGGAAAGGGGAAGGAGGGTGGGAGCGGTGGCGATGGGGCGGAGATGAAGGAGCTGTGGGATACCATAGCTGGTGGTTCTGAGGATGAT[CG/C]GAAGAAGGTATGAGGACGTTCGATGATGATAACTTTATTGATGATGCTGGTGTGGAACCTGCTAACATATATGGCAGCGA
98562 T C ATCGTTAACCTTTTCGCCTTCGCGTCTCTGCCCGATCAACTGCCAACTGTATTCACCCATCCACCCAATCGGCTGACCACGGCGTTCGCTTCCCCACCTC[T/C]ACAACTTTCCTCATCCCAGCCTCTCTTCCTTCACATATATACAATGGGCTAAATCAACTTTCTTCTAACCTAATCGTTGTTTCCCCCCAGTT
98562 T TA GCTGACCACGGCGTTCGCTTCCCCACCTCTACAACTTTCCTCATCCCAGCCTCTCTTCCTTCACATATATACAATGGGCTAAATCAACTTTCTTCTAACC[T/TA]AATCGTTGTTTCCCCCCAGTTTTTGTTCTCTTCTCCTCGCGTTACGTCCTAGGCTGTTCCAATTTCTCCTCCTATTATCCCTCTCCGAATTTC
98562 TC T CGTTCGCTTCCCCACCTCTACAACTTTCCTCATCCCAGCCTCTCTTCCTTCACATATATACAATGGGCTAAATCAACTTTCTTCTAACCTAATCGTTGTT[TC/T]CCCCCCAGTTTTTGTTCTCTTCTCCTCGCGTTACGTCCTAGGCTGTTCCAATTTCTCCTCCTATTATCCCTCTCCGAATTTCTCAACTGGCCA
98568 G T CTCTCCAGATAAGAAGTATGAGCAGATAAATAGGATAAAAGTAGGGTATTATTGAGCTAGTTCCGCATGGCAAACTGAATGAGAGCGCTAGAAGCAAATC[G/T]CCGAGATAGTTACAGTGCCTTGCAATCCCCCAGTAACCAGAAGCAAGCAGTTTCCCTCCAATGACTCTTGGAGGCCTGCCCCAAAT
98572 A G TTATATACCCCTTTAGTTGCAAAGTCTTGCTTTTCTTCAATTCGGCCAAGTTTTGATTCCAAGGTCTGAACAAC[A/G]ATACGAACAGATTCGACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGA
98572 T C ATACCCCTTTAGTTGCAAAGTCTTGCTTTTCTTCAATTCGGCCAAGTTTTGATTCCAAGGTCTGAACAACAATACGAACAGATTCGACATCACCGTGGAA[T/C]ACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCA
98572 G A AAGTCTTGCTTTTCTTCAATTCGGCCAAGTTTTGATTCCAAGGTCTGAACAACAATACGAACAGATTCGACATCACCGTGGAATACACTTAAATCTCCAC[G/A]CAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTG
98572 G T ATTCCAAGGTCTGAACAACAATACGAACAGATTCGACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGT[G/T]AGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGA
98572 G T AACAACAATACGAACAGATTCGACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACAC[G/T]CATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCC
98572 G C AACAGATTCGACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTA[G/C]TATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGA
98572 T C ACAGATTCGACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAG[T/C]ATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGAC
98572 T C GACATCACCGTGGAATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACA[T/C]GGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAG
98572 A C ATACACTTAAATCTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGA[A/C]GATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGG
98572 T C CTCCACGCAGTCCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCT[T/C]TTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACAT
98572 T C CCCGAAACTTCTTCCTTCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATG[T/C]AAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCAGATCTGTTA
98572 T C TCGTTTCTAAAGTGAGCTGTTTACACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGAC[T/C]GAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCAGATCTGTTATCTTCCAGCCCTTCCA
98572 A G ACGCATCGACATTAGTATCCACATGGTCAATTCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGT[A/G]TTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAAC
98572 G A TCTTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTA[G/A]CAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATA
98572 A G TTGAAGATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGC[A/G]AACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGC
98572 C T ATAAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACAT[C/T]AGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGA
98572 G T AAGTGCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCA[G/T]ATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAAC
98572 T C GCCTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCAGATC[T/C]GTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGA
98572 T A CTTTTTACAGATGTAAGTGATGATGTGACTGAATCCATTTGTTTCCCTACAGTATTGACAGCATCAGAGAAACCACGCCGGGTAGCAAACATCAGATCTG[T/A]TATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGC
98572 C T CGCCGGGTAGCAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAG[C/T]ACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGA
98572 A G GCCGGGTAGCAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGC[A/G]CGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAG
98572 G A GGGTAGCAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACG[G/A]GAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTA
98572 T C CAAACATCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACC[T/C]GAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATT
98572 A T TCAGATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCT[A/T]CCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATT
98572 C A GATCTGTTATCTTCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACC[C/A]GTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGG
98572 T A TCCAGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACCCGTGGATATGAT[T/A]GTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTAC
98572 G A AGCCCTTCCACCATATGTATCCATATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACCCGTGGATATGATTGT[G/A]ACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTG
98572 T C ATCCAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAG[T/C]TGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTG
98572 G A CAACAACCCCAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTG[G/A]AGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAG
98572 C T CAATAACTATTATAGTAGTCGCACCAATAGCACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTG[C/T]CGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGT
98572 T C CCAATAGCACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTA[T/C]TAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAA
98572 T G AGCACGGGAACCTGAGCTACCCGTGGATATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGA[T/G]TATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAG
98572 C T ATGATTGTGACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATT[C/T]TGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTG
98572 T C ACTGATCTGGATGATGCCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTT[T/C]TTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGC
98572 A G CCAAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAG[A/G]CCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCT
98572 C T AAAAGTTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGAC[C/T]CTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGC
98572 G C TTGGAGCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTT[G/C]TAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98572 A T GCTCCTGCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAA[A/T]ATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACG
98572 C T GCCGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTT[C/T]ATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCG
98572 T G CGTAAACTATTAACCTGAGCTATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCA[T/G]AGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCGAG
98572 T C TATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTT[T/C]TAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCA
98572 T C ATTAGATTATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTT[T/C]AGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCAT
98572 T A TATCATTAGGAGCTTTGCTACTTGATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATC[T/A]GATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCATAGCCGCT
98572 T A GATTCTGACCCTTTTTTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACA[T/A]AGCAGACCCAATCAGGCCTGCTCCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCATAGCCGCTGATCAAAACCTAGAGAAATACT
98572 G A TTATCTTGTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCA[G/A]GCCTGCTCCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCATAGCCGCTGATCAAAACCTAGAGAAATACTGGTAAGAAATCAAT
98572 T C GTTGAAGACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGC[T/C]CCGATGACGATAGCGAGCTTTCCCACTGAAATCGCCATAGCCGCTGATCAAAACCTAGAGAAATACTGGTAAGAAATCAAT
98572 G T GACCCTTTGTAAAAATCTTCATAGCACCAGAAATGAGGCTTTTAGCATCTGATAAACCTCCTTCTTTGGACATAGCAGACCCAATCAGGCCTGCTCCGAT[G/T]ACGATAGCGAGCTTTCCCACTGAAATCGCCATAGCCGCTGATCAAAACCTAGAGAAATACTGGTAAGAAATCAAT
98574 A G CGATCAAAAAGTTCACCACCGGAAGCATATTCCATAACGATTGCTAAATGCGTTGGAGTCAAAATCACCTCTTTAAATCTAATAATATTTGGGTGCCTCA[A/G]CGACCTATGATTGATAATCTCACGCTTAACATTTTCGTCTATCTTTTCTCCCCTCTCGATATACTTAACAGCTACAAGCTCCATGCTCTGC
98578 C A GTAGAAGTCAATCACATCGTTTTTACTTTTAACAGACTCATGGGGTTATGATCAACGGGACCATAGAAGTGAAAT[C/A]ATATTCAAAGCGTGGTCAATAATATACATGCACAGCAAAACTTATCGTAAACCCGTACCATTAATTTTCCATCCTCTCCTGTTTACCCTTAACATAATCA
98578 GA G ATATACATGCACAGCAAAACTTATCGTAAACCCGTACCATTAATTTTCCATCCTCTCCTGTTTACCCTTAACATAATCAAGATAATCCTGATAGATGTAA[GA/G]AAACAAAGCCCCAGACAGCCAGCAGCAAAGCCAGAATCTTCACCCCATCCATCCCATCCCCGAAGAACACCACCGCAAACACCGGAAC
98596 A AG TCAAGAAGTCGTACTTTTAGTCGGGCTTGCGCGCACATGCGTCTTCTCGTGCCACTCCTCTCTAGGAGATAAAATCTTTGCATCTGCAACACTTGGGGCA[A/AG]TTTTTGTGGTGACGAACGAGCGGGAACAGAGCAGTGCTTGCTTGTCGATGGGAGCAGATAGTTTCAGCATGCGTCCTAAGGTGGT
98596 G A GAGCAGATAGTTTCAGCATGCGTCCTAAGGTGGTGCTATGGCTGATGTTGCCCCCATTTCCTCTTCTTTTCTTGCAGGTCTCCAGGTTCAACAAGGAGAG[G/A]GCGGTGAGCTTCCAGTAACCGGAGTTGGTGAACAGCGCGGTGCTGACGAACGAAAGCTCAGAAGGGTGCCACAGGTGTGGGCTTC
98596 A G GTGTGGGCTTCGATGTCAGTGGTGCTACGATTAATTTTTGGTTAATCAGGTTTGACAACGAGAAAAACGGAAGGAGGCACAAGTTAATCTATGGGGAAAG[A/G]TGCAGAAGGCGGTAGTGATTATTGCGGTGAAGCTCAGTTCGATTTGCGGTAGGAAGAGCAGCCATTAGATTTTGAAGGAGGAAG
98596 A G ACAACGAGAAAAACGGAAGGAGGCACAAGTTAATCTATGGGGAAAGATGCAGAAGGCGGTAGTGATTATTGCGGTGAAGCTCAGTTCGATTTGCGGTAGG[A/G]AGAGCAGCCATTAGATTTTGAAGGAGGAAGAGGAACAATGAATTTGGGTAAAATTTTGATTTGGGGAATATTGGCTCGTGCAA
98616 T C TCCAGCTTGGGCAACCTGCAACTGTGAAAGTAGCAGCCAATTTAGTTAGATTATTGTCATATCAAAACAAGAATATGCTTCAAACTGGTATGATTGTCGG[T/C]GGTTGGGATAAATACGAAGGCGGTCAGATATTCTCAGTGCCCCTTGGAGGGACCATACTGAAGCAGCCTTTCACAATTGGAGGATC
98616 T C GATTTTTTGACCAAGCATGGAAGGAAGGGATGACCAAAGATGAGGCTGAGAAATTAGTGGTAAAAGCTGTGTCTCTGGCAATTGCACGTGATGGAGCTAG[T/C]GGAGGCGTTGTCCGAACAGTCACAATAAACAGTGATGGGGTAACAAAGAATTTCTACCCAGGTGATTCTCTTCCTCTCTGGCACG
98616 T C TGTCTCTGGCAATTGCACGTGATGGAGCTAGTGGAGGCGTTGTCCGAACAGTCACAATAAACAGTGATGGGGTAACAAAGAATTTCTACCCAGGTGATTC[T/C]CTTCCTCTCTGGCACGAAGAGCTCGAACCTGTTAACTCTCTGCTTGATATGCCTGAGAAAATGGTGGTTGAATAGGGGATATGCTG
98616 C A TGGAGCTAGTGGAGGCGTTGTCCGAACAGTCACAATAAACAGTGATGGGGTAACAAAGAATTTCTACCCAGGTGATTCTCTTCCTCTCTGGCACGAAGAG[C/A]TCGAACCTGTTAACTCTCTGCTTGATATGCCTGAGAAAATGGTGGTTGAATAGGGGATATGCTGT
98618 A G GATGGGTTGCTATATGCGTGCAGGTTCATGGAACCCATAACTGAAGGTGACTATCCTTGGTTTGAAATGTTGAAAGGGTCATTCGACTTCCTTGGTTTGA[A/G]TTATTATACTTCAGACTATGTCAAGAATATATCCTTGTTAGCCAAGGTTAACGCCAGCTATGCTGGTGATATGCATGTAATCCATACA
98624 A G CACTAGCGTTAGGCTCTATTTCCTTCCAGCAAGACGGGAGCTGCAGTGTCTTTCAACTTTGCAGCCATCGACCGATTAGGGTTCCGATGCTGGCGTAGAT[A/G]GTGGGGTGAATAACTTTGCTTACTTACCTCGATACACTGCATAAGCTTCAGCCACATTTTTGGGGTCAGTCTGCCCTTATATATGTGA
98624 TG T CTAGCGTTAGGCTCTATTTCCTTCCAGCAAGACGGGAGCTGCAGTGTCTTTCAACTTTGCAGCCATCGACCGATTAGGGTTCCGATGCTGGCGTAGATAG[TG/T]GGGGTGAATAACTTTGCTTACTTACCTCGATACACTGCATAAGCTTCAGCCACATTTTTGGGGTCAGTCTGCCCTTATATATGTGAT
98624 T C CAAGACGGGAGCTGCAGTGTCTTTCAACTTTGCAGCCATCGACCGATTAGGGTTCCGATGCTGGCGTAGATAGTGGGGTGAATAACTTTGCTTACTTACC[T/C]CGATACACTGCATAAGCTTCAGCCACATTTTTGGGGTCAGTCTGCCCTTATATATGTGATTCCTCTACAACCAGTCAAAAAGCGTCTG
98632 T A TTCATTCGCTTGATTTTATGTATAATACACCCTAAACACATACGTATACAACATATTTATATTTCACAATTTGCACCTATACATACAGAATAAAACGATC[T/A]CGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGG
98632 A AG ATACGTATACAACATATTTATATTTCACAATTTGCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAA[A/AG]GAAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTC
98632 A G ATACAACATATTTATATTTCACAATTTGCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGA[A/G]AAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTT
98632 A AATG ACAACATATTTATATTTCACAATTTGCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAA[A/AATG]AGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCC
98632 A G TTATATTTCACAATTTGCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAA[A/G]TCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAAC
98632 G C TTCACAATTTGCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAA[G/C]AAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCA
98632 A G GCACCTATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAAGAAGCGTGGC[A/G]CACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCG
98632 T C ATACATACAGAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTG[T/C]GAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAA
98632 A G GAATAAAACGATCTCGCTACTTAACCATAAACTTAACCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTT[A/G]GGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACC
98632 A G CCTTACAAAAAGCAAAAGAAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCC[A/G]TTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAAC
98632 A G AAGAAAAAGAACAAAATCAAAGAAGCGTGGCACACTGTGAGCTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATT[A/G]TAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGAT
98632 T C CTCTTAGGATCCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCG[T/C]ATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATCGCCCTGGTAAAACCCGT
98632 A G CCCACATAGCAGGCAGCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGG[A/G]TACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGG
98632 A G GCAAATACTTCCTCCCATTCATCCCCTTCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCC[A/G]AACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCC
98632 T C TCGCATTATAACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGC[T/C]TCCAACCCAGCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAA
98632 A G AACTCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCC[A/G]GCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAATCATTCCAT
98632 A G TCGCACCCGTTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGC[A/G]TTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAATCATTCCATCCA
98632 G T TTACCGGGTCAACCAACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATC[G/T]CCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAATCATTCCATCCACACCAACGT
98632 G A ACACCTTACCCGTATACCCGGGATACGCCCCGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATCGCCCTGGTAAAACCC[G/A]TTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAATCATTCCATCCACACCAACGTCTCCGTTAGGCGCTA
98632 C T CGCTCCCAAACACGCCCGTACAAGCCGATACGGCTTCCAACCCAGCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGC[C/T]AACACAGTAGCCAAATTGATAATCATTCCATCCACACCAACGTCTCCGTTAGGCGCTACTAACGGAGGAGCCTGGGGCCCGTAAATCG
98632 A C ACCCAGCATTCCCATCGCCCTGGTAAAACCCGTTTCCAAACGGATTCGTCACCGTTCCCGCCAACACAGTAGCCAAATTGATAATCATTCCATCCACACC[A/C]ACGTCTCCGTTAGGCGCTACTAACGGAGGAGCCTGGGGCCCGTAAATCGGCTGGTGAAACGGCCA
98634 T C CTATCATCGCTGCGTAAAGAGAGCAGCTCGACCCTTTTATAAAGAGGTTCGTTGCCACGGGACCGACTCGTAGTGGTGCGACGAGCAAGAGGAGAAGATC[T/C]ATTGGTCTCGGTAATGGTAGAGTTGTTAAGTCTTTGAGTAGAAGTGGCTCGAATATTGCTACCACTGCTTGAAAGTGGATCGGAG
98634 G A TGCTTGAAAGTGGATCGGAGTGTACGCCAGAGCTTTTGCGGACTGTAACACCCACAAGTGGATCGGAGTGTACGCCGGAGCTTTTGCGGACTGTAACAGC[G/A]ACAGGAGAGCGCTTCGATCCGGTGCTGTTCCTGGATTGTGATACACCTGATTTTTCTGCATCCACCGTGTTCTTGGAAGATCCACC
98644 G A AAAGCGCGACTATGGCGGCCACTCTTTATTACTGCCCATCTCATCCTAGACTACTCTCAATCTCTGTTCCCTCATCTACACGCCTACAGGTGTCTTTTCT[G/A]GCTCCAATCAAACTCAGACACTCAAATCTCCTTCTTTACCGCCGTCGCCACCCGTCGCTTGCTGGAACTTCCATTTTTTCTGTTGACCTTTT
98644 T C CACGCCTACAGGTGTCTTTTCTGGCTCCAATCAAACTCAGACACTCAAATCTCCTTCTTTACCGCCGTCGCCACCCGTCGCTTGCTGGAACTTCCATTTT[T/C]TCTGTTGACCTTTTACAGGACGGCGGGGCGACTGCTGCTGTGCTGGTTGGAGCTTACTCACTTGTGCTCCTCTTTGATGACCTCACGAAG
98644 A T TGGAACTTCCATTTTTTCTGTTGACCTTTTACAGGACGGCGGGGCGACTGCTGCTGTGCTGGTTGGAGCTTACTCACTTGTGCTCCTCTTTGATGACCTC[A/T]CGAAGCGAAACCTAATCGAACAGAGTTTGAGCAGAAAAGTTGTTCATGTTTTATCAGGTCTTCTATTTATGTCATCGTGGACATTTTTC
98644 G A TTGTGCTCCTCTTTGATGACCTCACGAAGCGAAACCTAATCGAACAGAGTTTGAGCAGAAAAGTTGTTCATGTTTTATCAGGTCTTCTATTTATGTCATC[G/A]TGGACATTTTTCAGTTCCTCGACGGAAGCTCGATGTTTTGCTGCTGTGGTACCTTTAGTCAACTGCTTGAGACTTCTTGTTTATGGGCTA
98644 C T AGGTTTTCTTGATGATCAAAGCCTAATCAAGTCAATTACCCGAGAAGGAAAACGAGAGGAGTTGCTTAGAGGTCCTCTATACTATGTTGTGGTGCTAATG[C/T]TCTGCAGTCTAGTCTTTTGGCGTGATTCACCAGTTGGCATTTTAGTTCTTTCTATGATGAGCGGAGGCGATGGCTTTGCAGATATATT
98644 G T TGATCAAAGCCTAATCAAGTCAATTACCCGAGAAGGAAAACGAGAGGAGTTGCTTAGAGGTCCTCTATACTATGTTGTGGTGCTAATGCTCTGCAGTCTA[G/T]TCTTTTGGCGTGATTCACCAGTTGGCATTTTAGTTCTTTCTATGATGAGCGGAGGCGATGGCTTTGCAGATATATTGGGGAGAAGAT
98658 C T GCTCCTTTACCATCATCCAGATTTGCTGCGCCAACTCAAGCATCACCACTGAGCCTCTCTAAACCACCACTTACCTCATCCACATCAAAGCCGACACCCA[C/T]TGCTGCTCCTCGACCGCTACTTCAGCCGACCACTACTAGATCTGCACCTCTTTTCGGTCCTTCAGTTCGCACAAAAACAGATGTTATTCAG
98668 C T CCTATTCGGTTTCCTCGACCAATCTTAATTCCCGCTCATTCAAAACCCTAGCTTTCTCCTCGAACCTATCACTGTCTTCCTTCCTTAATGGGGCTGAATC[C/T]GTGAAGATGGTAGCGCCTAGCCGACGCGGGCTGATCGTGTGTGAGGCTGCTCCGGCGCAGAAAGCAGATTCTGCATCGAAGAGAGCAA
98668 AC A GAAACACCGGTGCACATAGAAAATCAAGACTTGCAAGGAGGAAGAAGGCTGTAGAGATTCACCATGGGTGGTACACACCTACTGCCGCTTAGGTTGATTT[AC/A]CCCTTCTGTTTATTATGTTTACTTACATTTGATGTATGATTTTTGTGAACCAAATCATTCTTCTGCCCTTTTGTTTCCTTTGCTTTGTC
98674 C T TAGGAAGCTTCCGGCTGGATGGGATCCCACCAGCACCGAGAGGCGTTCCTCAAATCGAAGTCAAATTCGATATAGACGCCAACGGCATTCTCTCAGTCAC[C/T]GCTGTGGATAAAGGCACCGGAAAGAAGCAGGATATTACAATTACAGGGGCAAGTACCCTACCGAGCGACGAGGTGGAGAGGATG
98674 T C CCCTACCGAGCGACGAGGTGGAGAGGATGGTGAGCGAAGCAGAGAGGTTTGCGAAAGAAGACAAAGAGAAGAGAGATGCAATTGATACTAAAAATCAAGC[T/C]GATTCCGTCGTGTACCAAACCGAGAAGCAGCTGAAAGAGCTCGGCGAGAAGGTGCCAGTTCCTGTGAAGGAGAAGGTGGAA
98674 C T AAGCAGCTGAAAGAGCTCGGCGAGAAGGTGCCAGTTCCTGTGAAGGAGAAGGTGGAAGCGAAATTGACGGAGCTGAAGGAGGCTGTAAGTGGAGGTTCTA[C/T]GCAAGCAATGAAGGATGCCATGGCAGCGTTGAATCAGGAAGTAATGCAGTTGGGGCAGTCTCTGTATAACCAGCCTGGTGCT
98676 T A AATCCTCTCCATGGTCTCTTGGAATCATTGTGGCCCTTGCTATCTTCTCTTCAACGAACTTCAGTGTCCCTGTTGGATCATCAGAAGCACCCATAAATGT[T/A]CCTGAGCTTGTTCTCACGCCCTTGGTATTCTCTTCGGTCTCTCCCTTCCTAAGAGCCAGTTTTGATGGTTTAAGTTGTGATTTAGCCTTTC
98676 G A TTAGCCTTTCTAATTATGTTTTCACATTGTTCTGCAGTTGCAAAATTGGGAAAATGGAGTGCCCGTGGTTTCCAACTCAAAACCTGAAAAGGAATAGGAA[G/A]AGGATTGGATTCCCCAGTCTCGCCATGAGGCAGAGCAATTATCGTCTCACTTTCTTCCATCAACCTGACACGTGGCGCCGGATCGACT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98684 TG T AAACACCTTTGGTCTCTGGAAAGTGGAAATGAAGCAGCTGAATTATCTGGTGCTGCAATGCCTTCTGCCCACTTTATTTTATTTTTCTTCTAAAATCCAG[TG/T]GGGGTCGGCCAACCCCACTGGGCCCAAGTTGCGTACGTCATTGTATATAGTTAGCGTCTAAATATATATAGAGCCAGCCATTTAAACA
98694 A G CGTTATTTCTTCTATGATTTATGTTCTGGGGCTAGGGATGCTAACCTTATCATCGGTGATGCCAAAGCTCAATCCATCCAAGTGCGATAACAGATTTAAG[A/G]CCACCACCTGCCCTCCCACATCTTTCCAAGCCGCCTTCTTTTTCTTCTCCATATATCTTGTGGGATTTGCTCAAGGAGGCCATAAACCAT
98694 T C AACCTTATCATCGGTGATGCCAAAGCTCAATCCATCCAAGTGCGATAACAGATTTAAGACCACCACCTGCCCTCCCACATCTTTCCAAGCCGCCTTCTTT[T/C]TCTTCTCCATATATCTTGTGGGATTTGCTCAAGGAGGCCATAAACCATGTGTACAGGCATTTGGTGCTGACCAGTTCGACGAAAACGAC
98694 A G ATCGGTGATGCCAAAGCTCAATCCATCCAAGTGCGATAACAGATTTAAGACCACCACCTGCCCTCCCACATCTTTCCAAGCCGCCTTCTTTTTCTTCTCC[A/G]TATATCTTGTGGGATTTGCTCAAGGAGGCCATAAACCATGTGTACAGGCATTTGGTGCTGACCAGTTCGACGAAAACGACCCAGAAGA
98698 G A GCCATGGCCACGTGTCCGTCCTCTTTTAGTGCATGCCCTTGGTGTACTTTTGGAAATACCAAGATTTGTTTGTTTAGTAAACTTGGGTGCGACAGAACTC[G/A]TTTCATGTGACGTCGCTCTTCCACCTCTACCACGAGGGCGTCCACCACGGGCACGAGATACACGTGCACCACTCGTGCAACGACTTGC
98714 G A ACGATCAAATTATTCAAATATCATCATGACCATGACGAACCTCCTGAGGTGGAATAAAACACTCATTTGACAGTCCCGGCACATTAAAAAGAACGTCATC[G/A]ATCTCCCATATCTCCTCCATCCGGGTTGACTCCTGCACTCCGAACCCGAACCGTACCAAGTTGACAACAGACCTACCGCTATGTGCAA
98714 T C ATCTCCCATATCTCCTCCATCCGGGTTGACTCCTGCACTCCGAACCCGAACCGTACCAAGTTGACAACAGACCTACCGCTATGTGCAATCATAACACCGT[T/C]GACGTCACGATAGTCCTCAATAGAAGATGATATCGTCGTCTCCCAGTACATCACCTCGGCTCCCGGGGTATTGGATCCGGGTCAGCTG
98714 TC T TGACAACAGACCTACCGCTATGTGCAATCATAACACCGTTGACGTCACGATAGTCCTCAATAGAAGATGATATCGTCGTCTCCCAGTACATCACCTCGGC[TC/T]CCCGGGGTATTGGATCCGGGTCAGCTGAGAGTCCTCCAGTTGGACCAGTAACCCGCTTCTTTGGCTGAAGTAACCGATCATTACATG
98720 A G AGGACTGGAAGCTGTGGGAGAAATTGCCATATGTGATTGGATTGGATGGAAGGCCAATGCCTAGAAAGGCGATTAAGACACAGAGAGAAAGCGATGATAA[A/G]TTTTGGGATTTTGCTAGACAGTTCTTTTTGGGACTTTGGGGTTTCAGGCAACGACCTTACCCACCTGGTAGGCCATGTGATGCCG
98726 A G GGTTCCATCAGGGTGGAGGTTTAGCTAACTCATCAAGAAGGCCTGGATTTCGCCTTTATGCAGCTAGCCTAGAGCCACTCATGAATTCTGCTACTCAAAG[A/G]AGCTCCATGAGCAAAGAATTATATGGAGGAAAACTCGGAGATGTTGCTAGAGAGGCCAAAGAGAGATTGGATGAGAAGCTTAGAA
98726 T A CTTCTGATTTTGTTAAAAGGCATAAAAGCATGGGAAATGTAGTAGCTCATTCGGAAGGTTCCAACAACATACAAAGAGAGGTATTTTCGAAGAAAAGTTC[T/A]AGAAAGTTCAAATGGAGCAAACTAGGGTGGAAGGCCTCAGAGCAAGTAGAGTGCGCTGTTTGCCTGGAGAACTTCAAAAACGGAG
98726 T C GAGATATATTGGTGCACCTGTCCTGCGCCCATAGATTTCACTGGAACTGTGCCATGCCATGGATCGAGTCCAGCTCTAGCTGCCCATGTTGTAGGACCTG[T/C]GTCCTTCATGATTGAGTGTTTGATTTGGTTATGTAATTAGTTTGTGAATACTTAATTTATGTTAGTTTTGTGTTTGTGTGAGATATGCA
98726 T C TGGAACTGTGCCATGCCATGGATCGAGTCCAGCTCTAGCTGCCCATGTTGTAGGACCTGTGTCCTTCATGATTGAGTGTTTGATTTGGTTATGTAATTAG[T/C]TTGTGAATACTTAATTTATGTTAGTTTTGTGTTTGTGTGAGATATGCATGATGTCAGGAGATTTTGCTTAAGGATTATGATTGATCATC
98742 C G CACGTGAATCAAGTCATCTTGTGTAACAAGTGGGTAGTCTTTAGCACTCAACAAAACAAACCAATCCCACTGGTCATACAATCTCAACATGGCGGCAGCC[C/G]CTCTCAAGCATGCAGCCAACCCAGAACTTCCCATTTTCGTCATGGCATCTGCCTTCCCCACCACATCAACATTCCCAAAGTCCTTCACG
98742 A G TGTAGTATGCAAAAGAAGGCAGGTGAGTGGGATTATAAAGGAAGCTGGAAATAGGGTTAGGGTTTGGATTAGGGTTGGTGAGTAGGAAGGAAATGACGAA[A/G]AGAAGGAGGAAGGAGATGGCGCAGATGGAGATGATTCGAATAATATGCCGCTCCGGCGACGGTGATGGCGCCATTTGTACT
98742 G T TATAAAGGAAGCTGGAAATAGGGTTAGGGTTTGGATTAGGGTTGGTGAGTAGGAAGGAAATGACGAAAAGAAGGAGGAAGGAGATGGCGCAGATGGAGAT[G/T]ATTCGAATAATATGCCGCTCCGGCGACGGTGATGGCGCCATTTGTACTATAGTCGGGATCAGAACATGACGAATCCGAGGAG
98746 T G TTGTAAACATGAACGCCTTTGACATTATTTCACTTTCCGCTGGATTTGATCTCTCGGGCTTGTTCGTAGAAGGCGATAGAAGGAGAGAAGCCAGATTTAC[T/G]TCTGCCAAGCCAGTAGCAGGTATTATTACGAAGATCGAAGAGGTTGCTAGTAATTTAGGATTCAAAGTGAAGAAGAAAGACGGTGG
98746 C T CCAGATTTACTTCTGCCAAGCCAGTAGCAGGTATTATTACGAAGATCGAAGAGGTTGCTAGTAATTTAGGATTCAAAGTGAAGAAGAAAGACGGTGGGGT[C/T]ATAAAACTCGAAGGTGCAAAAGATGGTAGGAAAGGAGTTTTGGGCATTGATGCCGAAATTTTTGAGCTTACTTCTTCATTTCATTT
98746 T C AAGAGGTTGCTAGTAATTTAGGATTCAAAGTGAAGAAGAAAGACGGTGGGGTCATAAAACTCGAAGGTGCAAAAGATGGTAGGAAAGGAGTTTTGGGCAT[T/C]GATGCCGAAATTTTTGAGCTTACTTCTTCATTTCATTTAGTCGAGATTAGGAAAACAGATGGTGATACATTAGAATATCAGAAGG
98746 C T TTGAGCTTACTTCTTCATTTCATTTAGTCGAGATTAGGAAAACAGATGGTGATACATTAGAATATCAGAAGGTGTGGACTCAGGAGATGAGGCCTGCCCT[C/T]AAGGACATTGTCTGGGAATGGCAAGGAGATCAACCAGCTCAGCCGCAGAACGTTCCAGCTTTGCCGCCACCACCTGCGCCCCAGCT
98746 G A AGAAGGTGTGGACTCAGGAGATGAGGCCTGCCCTCAAGGACATTGTCTGGGAATGGCAAGGAGATCAACCAGCTCAGCCGCAGAACGTTCCAGCTTTGCC[G/A]CCACCACCTGCGCCCCAGCTGGAGCAGCAAGTATAAGTGACTTCCAAGTAGTTTACTTATGTTTTATTTCTCTTCATTATCGCATTC
98752 AT A AAAGAACGAAGATGTTCTACCTCCTAATTATAAAATCCTTAGTTTTACAGATGATCAACAGTCATAAACAACCACATATCTCTAGCCAATAAGAGACTGA[AT/A]TTTTTAGTTTACAAATAACTCTTCCTTAAATCATGAACAGTAATACACAAGACATGCACATACATACAAACATACATAGCTTACTTGGA
98752 G A AACAGTCATAAACAACCACATATCTCTAGCCAATAAGAGACTGAATTTTTAGTTTACAAATAACTCTTCCTTAAATCATGAACAGTAATACACAAGACAT[G/A]CACATACATACAAACATACATAGCTTACTTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTT
98752 C T AGTCATAAACAACCACATATCTCTAGCCAATAAGAGACTGAATTTTTAGTTTACAAATAACTCTTCCTTAAATCATGAACAGTAATACACAAGACATGCA[C/T]ATACATACAAACATACATAGCTTACTTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTTTAA
98752 A T AACCACATATCTCTAGCCAATAAGAGACTGAATTTTTAGTTTACAAATAACTCTTCCTTAAATCATGAACAGTAATACACAAGACATGCACATACATACA[A/T]ACATACATAGCTTACTTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTTTAAGAAACTGGCT
98752 G A ACATACAAACATACATAGCTTACTTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTTTAAGAAACTGGCTTAT[G/A]AGATCAGCAACCAACTTTGGCCTCTCAACATGAGGAAGATGGCCGCAATCTGGTATCTGACACAAAGCTGAATTTGGGAGCTCCTCC
98752 C T ACTTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTTTAAGAAACTGGCTTATGAGATCAGCAACCAACTTTGG[C/T]CTCTCAACATGAGGAAGATGGCCGCAATCTGGTATCTGACACAAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTG
98752 T G TTGGAAGCAACAGTTTGTAAACCTGAAGGTGTGTTGTCTAAAACAGGAACACAGCCTTCTTTAAGAAACTGGCTTATGAGATCAGCAACCAACTTTGGCC[T/G]CTCAACATGAGGAAGATGGCCGCAATCTGGTATCTGACACAAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTGTT
98752 C T AAACAGGAACACAGCCTTCTTTAAGAAACTGGCTTATGAGATCAGCAACCAACTTTGGCCTCTCAACATGAGGAAGATGGCCGCAATCTGGTATCTGACA[C/T]AAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTGTTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAGTGTTT
98752 T C AATCTGGTATCTGACACAAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTGTTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAG[T/C]GTTTTTTGTTTGATCTGATTTATTTGATGGCTGACATTGTATCCACCACTAAACATAAAACTAACAGTTGCATCTTCCCACCAAGGCAATA
98752 GT G ATCTGGTATCTGACACAAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTGTTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAGT[GT/G]TTTTTTGTTTGATCTGATTTATTTGATGGCTGACATTGTATCCACCACTAAACATAAAACTAACAGTTGCATCTTCCCACCAAGGCAATA
98752 T C CACAAAGCTGAATTTGGGAGCTCCTCCTTTAATCTCTGAGCTAAGGTGTTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAGTGTTTTTTGTTTGA[T/C]CTGATTTATTTGATGGCTGACATTGTATCCACCACTAAACATAAAACTAACAGTTGCATCTTCCCACCAAGGCAATAAGCAGTGCAGCCG
98752 A T GCTAAGGTGTTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAGTGTTTTTTGTTTGATCTGATTTATTTGATGGCTGACATTGTATCCACCACTAA[A/T]CATAAAACTAACAGTTGCATCTTCCCACCAAGGCAATAAGCAGTGCAGCCGTCCAATATTTGCCCAATCAATAGAAGTAAAGATCGAGAT
98752 T C TTGTCTATAATTCGATCGTTCTCTCCCCATATGATGAGTGTTTTTTGTTTGATCTGATTTATTTGATGGCTGACATTGTATCCACCACTAAACATAAAAC[T/C]AACAGTTGCATCTTCCCACCAAGGCAATAAGCAGTGCAGCCGTCCAATATTTGCCCAATCAATAGAAGTAAAGATCGAGATTCCACTGAA
98752 A G GGCTGACATTGTATCCACCACTAAACATAAAACTAACAGTTGCATCTTCCCACCAAGGCAATAAGCAGTGCAGCCGTCCAATATTTGCCCAATCAATAGA[A/G]GTAAAGATCGAGATTCCACTGAAGGTCAAGGAATTTGCATAAACCCGCAATGGGATACTCTTCAAAAGAGCTACTCCAGCATATGCT
98752 C T TCTTCCCACCAAGGCAATAAGCAGTGCAGCCGTCCAATATTTGCCCAATCAATAGAAGTAAAGATCGAGATTCCACTGAAGGTCAAGGAATTTGCATAAA[C/T]CCGCAATGGGATACTCTTCAAAAGAGCTACTCCAGCATATGCTATTGCTTTAGGTAATTTTTTGAGATTTCCTGTGCCTTGTGCATAC
98754 T A GCTCCATAACAGCTTCTGTCATATCGTCTACATGAGGAAGATAATCCAACGGCTGAAAATAGGTGATATTTTCTTCAGAATGCGGATCTATCTTGCTTTC[T/A]GATAGCTCTTGAAACAGAACCGAGTAGGCAAACTTTTCAAAATGCATGGAGTCGAGATCATACTGAAGCTCCTGCACTTTTTTGTTTGT
98754 C T TATCGTCTACATGAGGAAGATAATCCAACGGCTGAAAATAGGTGATATTTTCTTCAGAATGCGGATCTATCTTGCTTTCTGATAGCTCTTGAAACAGAAC[C/T]GAGTAGGCAAACTTTTCAAAATGCATGGAGTCGAGATCATACTGAAGCTCCTGCACTTTTTTGTTTGTTGCTCTTGCTTCAAAATTCAG
98754 G A GCTGAAAATAGGTGATATTTTCTTCAGAATGCGGATCTATCTTGCTTTCTGATAGCTCTTGAAACAGAACCGAGTAGGCAAACTTTTCAAAATGCATGGA[G/A]TCGAGATCATACTGAAGCTCCTGCACTTTTTTGTTTGTTGCTCTTGCTTCAAAATTCAGCTTATCGAATAGTGCCTGCCGCTCTTCTAGA
98754 C T AGAACCGAGTAGGCAAACTTTTCAAAATGCATGGAGTCGAGATCATACTGAAGCTCCTGCACTTTTTTGTTTGTTGCTCTTGCTTCAAAATTCAGCTTAT[C/T]GAATAGTGCCTGCCGCTCTTCTAGAGTATTCTGTGCATTAGACAACTCTGAACTGGTAATTTTTAATAAATTTTCCTTCTCCAAGATACTG
98754 C T CTCCTGCACTTTTTTGTTTGTTGCTCTTGCTTCAAAATTCAGCTTATCGAATAGTGCCTGCCGCTCTTCTAGAGTATTCTGTGCATTAGACAACTCTGAA[C/T]TGGTAATTTTTAATAAATTTTCCTTCTCCAAGATACTGCGCTTTAGTTCATCCAGTGCTGCATGCTCGGAGCTTATCATCTTTGTTGATTCC
98754 C A TTAATAAATTTTCCTTCTCCAAGATACTGCGCTTTAGTTCATCCAGTGCTGCATGCTCGGAGCTTATCATCTTTGTTGATTCCTCTTTAAATTTCAGAGC[C/A]CCATCTTTCTCAGCCAATAAATTTTGTAAATCTTCCAATTTCTGACGCAAAAAAATTATTTCCTCGGTGTTCTTTTCAACATTTTCATTATCAT
98756 C T GAATATTTGGATGTTTTGGAATCAGACAGATTTGCATATAAAGATCTTGATGATTTCCCATCTGA[C/T]GATGCCTTTGAAGAGCAAGTTATTACAAGTTTGATTGAGGGGCATGAATCTGATGAAAAGATGATGACATTAGAGCAATATGGAAAGCTAATGGACGAAA
98756 A G GAATCTGATGAAAAGATGATGACATTAGAGCAATATGGAAAGCTAATGGACGAAAAGAAGCAAATTCTCCAGGCTACACTTCAGGAAATTTCTGCTAAGC[A/G]TCAAGAAGAGGAGGACTTCATAAACGAATTTGTGATCATTGAGGCAGAAGATGATGAATTGGAAGCTGATGAATTGGATGACTTC
98756 CT C AAATTCCCTTTCTTTGTTGGGGCTTTTAGATGTAAATAATTTGTCCTGGAACCACAACATAGTCTGCTTGCTCTCACGTAAATCTGAAATTTATTGTTTC[CT/C]TTTAACCGTGCTAGATCGTCAAATTAAAGTACGGTTAAGGGTGTACCTGTGACTTGAACTTGAATAATGATATCTTATTTCTATATAGCA
98764 G A CGTCCGACATTGCACAACCTGCTTGCAACACAAAGCTGATAATACACCATACAAAGGACTTCTCCACCCACTACCAATACATGACCAAGTCTGGAGCGAC[G/A]TAGCGATGGACTTCATCACCCATTTACCACCTTCGGGAGGACAACAATCTGGGTAATGGTGGACAGATTATCCAAGTATGCACACTT
98774 C T AGCTAAAATTTGCAAGAACTCCAAAAAAGAACTGGCAGCAAGCATCAGCTTTGGTATTTTTGCAATAACATGGCTGTTGGAACGTCTAATATTTTTTCCA[C/T]TCTGGATCATCAGAATTGTCTGCATGGAAACTCTGGAACCACTGAAGAAATATAGCAGCCATCCATTTATCTTGTACTGTATATTCAAC
98774 T A ACATGGCTGTTGGAACGTCTAATATTTTTTCCACTCTGGATCATCAGAATTGTCTGCATGGAAACTCTGGAACCACTGAAGAAATATAGCAGCCATCCAT[T/A]TATCTTGTACTGTATATTCAACTCAATCCTTCTGATGCTACTTACCTTGCACATATACTGGTGGAAGCTCATATGCAATAAGATTTTTAA
98782 A G CCCACATACGGCATCATCCCCTCCGCCTTTAACATCTCCCCTTCCTCAGCTTCCAACGACTTTGCCTGCTCCCTTGCTGATGCCACAATCTTCTAGGGAA[A/G]TTATTGAATGCCAGCGTTGTTATATGGTTTGCCACCTCTCCTGTCTGCAGAGTAATCCCAATTCAGCGTCTACCTACATATGTTCATCTTG
98782 G T GTCTGCAGAGTAATCCCAATTCAGCGTCTACCTACATATGTTCATCTTGCAAAGATCCCAGCTTCGTGTACTTCCCAAAATTTTGTGGAGGTGAAAAAGT[G/T]GTTGATTTTGAGGCAGCAAAGGTGCTTAGATTGGCAGGAAAGCTGTCGTTGATTTCGATGGAGAAGGCAGTTCAGTTGGCGAAAAAT
98788 C A AACAGCAACCCAAACCAGAACCAGAGAACCCGCTGACCTCCACTGACATCAACCACCTCCCGAACGAAACCAAAGACCTGGTCCCCATCGACCCATCCGA[C/A]CAGATGACTCGACGTCCCCGGGGCAGGCCCGCTGGGTCCAAGAACAAGCCGAAGCCACCTATAATCATAACCCGGGACAGCGCCA
98788 A G ACCCAAACCAGAACCAGAGAACCCGCTGACCTCCACTGACATCAACCACCTCCCGAACGAAACCAAAGACCTGGTCCCCATCGACCCATCCGACCAGATG[A/G]CTCGACGTCCCCGGGGCAGGCCCGCTGGGTCCAAGAACAAGCCGAAGCCACCTATAATCATAACCCGGGACAGCGCCAACGCCCT
98788 T C CCAAACCAGAACCAGAGAACCCGCTGACCTCCACTGACATCAACCACCTCCCGAACGAAACCAAAGACCTGGTCCCCATCGACCCATCCGACCAGATGAC[T/C]CGACGTCCCCGGGGCAGGCCCGCTGGGTCCAAGAACAAGCCGAAGCCACCTATAATCATAACCCGGGACAGCGCCAACGCCCTGC
98788 T C CGTCCCCGGGGCAGGCCCGCTGGGTCCAAGAACAAGCCGAAGCCACCTATAATCATAACCCGGGACAGCGCCAACGCCCTGCGCAGTCACGTGATCGAGA[T/C]CTCCTCCGGGTCGGACATCAACGAATCGATCTCCACCTTTGCATCCACCCGACACAGAGGCGTCTGCGTCCTGTCTGGCACCGGC
98788 A C CACCTATAATCATAACCCGGGACAGCGCCAACGCCCTGCGCAGTCACGTGATCGAGATCTCCTCCGGGTCGGACATCAACGAATCGATCTCCACCTTTGC[A/C]TCCACCCGACACAGAGGCGTCTGCGTCCTGTCTGGCACCGGCACTGTCACCAACGTTGCCCTCCGCCAGCCTGGCTCCCCTGGCGCT
98788 T C ACGTGATCGAGATCTCCTCCGGGTCGGACATCAACGAATCGATCTCCACCTTTGCATCCACCCGACACAGAGGCGTCTGCGTCCTGTCTGGCACCGGCAC[T/C]GTCACCAACGTTGCCCTCCGCCAGCCTGGCTCCCCTGGCGCTGTCGTGAACCTCCATGGCCGCTTCGAGATCCTCTCCCTCTCCGGG
98788 C A CTCCGGGTCGGACATCAACGAATCGATCTCCACCTTTGCATCCACCCGACACAGAGGCGTCTGCGTCCTGTCTGGCACCGGCACTGTCACCAACGTTGCC[C/A]TCCGCCAGCCTGGCTCCCCTGGCGCTGTCGTGAACCTCCATGGCCGCTTCGAGATCCTCTCCCTCTCCGGGTCCTTCCTCCCCTCCCC
98794 G A GCGGTGGCGTGCACGGATGGGAACAACGGGATACACGTGAGCGAGGGGTACTTAGGGAAGTACGGCGGGGACGTGAAGGTGGAGTTCACGGGGGTGGTGT[G/A]TCATGAGACGACGCACGTGTGGCAGTGGGATGGGGACGGGAAGGCGCCGGCTGGGTTGGTGGAAGGGGTGGCGGACTT
98794 C CG TGGAGTTCACGGGGGTGGTGTGTCATGAGACGACGCACGTGTGGCAGTGGGATGGGGACGGGAAGGCGCCGGCTGGGTTGGTGGAAGGGGTGGCGGACTT[C/CG]GTCAGGCTGAGGGCGGGGTATGAGGCCGGGAACTGGGTGAGGCCTGGGGAAGGGGAGAGGTGGGATCAGGGGTACGA
98796 C T AGGCATGGCCATTCATGCAACCGCAATAACCTGGTATACACTCCACCTACGTACACAAACAAAACGGTGAAAAAATCAGTAAACTTCAGCAATCACAACC[C/T]TGTTTATATCATTCCTCCAAACCCAGAACCCGAACCAACACCTCAAAACCAATATCCTCCAGAACAGAACTCAGTTAATGGGGCTTCC
98798 T C CACCATTAAAAAAATGTCCGAGGGCTAGTCGCATTATTTCAAGCATACAGCTTATGGCAGCAT[T/C]ACTTAATACATTGGATTTAACACCAGTTACAAAACGTGAAGGTAAATAAATATATCCCTATGATGTTATGGTTTCAGAGGTGCACATGTGGGGATGTGAT
98798 G A ATTGAAATCTACTACTTTATCCCTGTGTCCAGCATGCTGAAAGAATAAACCCGGAGGTGTCTTTTGTCCTCTTAATCCAGGCTGTGATTCTGCCTTCCCA[G/A]TCATTTCATGATCCCATATATTTAAGAAACTATCCTCGGCAGCACTACCAAAAACGGATTTCCTGTCGGGGCACCACTGCACAGAAAGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98810 A G CACAATCCGATTGCGGAGTCAAAGATGAAGATCCGAAAACTTTTTCAAGGGGGCTACTACTCCCCTTAGCCTCCTCTCTAGCAGCATCATTGGGCAGTTT[A/G]ACGTTATTATTACCATTACAATTATAGAGCATAATCGGGTCTTGACTGGCAACAGGAGCGTATAATCGCTCCACTATTCCGTCTCTTCT
98810 A G AGATCCGAAAACTTTTTCAAGGGGGCTACTACTCCCCTTAGCCTCCTCTCTAGCAGCATCATTGGGCAGTTTAACGTTATTATTACCATTACAATTATAG[A/G]GCATAATCGGGTCTTGACTGGCAACAGGAGCGTATAATCGCTCCACTATTCCGTCTCTTCTCGATTTGATTTCGGATCGGTGGTCCGAG
98810 G A GCATAATCGGGTCTTGACTGGCAACAGGAGCGTATAATCGCTCCACTATTCCGTCTCTTCTCGATTTGATTTCGGATCGGTGGTCCGAGATCGCAACTGC[G/A]ATTGCGGACTCGATCAGATTCCAAATGTCGACACCAGTTGATTGTAGAATTGATCGCACTTCATCTGCGTCCATTTTTGATGCTTTCTT
98810 A G ATAATCGCTCCACTATTCCGTCTCTTCTCGATTTGATTTCGGATCGGTGGTCCGAGATCGCAACTGCGATTGCGGACTCGATCAGATTCCAAATGTCGAC[A/G]CCAGTTGATTGTAGAATTGATCGCACTTCATCTGCGTCCATTTTTGATGCTTTCTTCTTGTATTTTTTAGGTTTTCTTCGTTTTTGGACTT
98810 T G GGTCCGAGATCGCAACTGCGATTGCGGACTCGATCAGATTCCAAATGTCGACACCAGTTGATTGTAGAATTGATCGCACTTCATCTGCGTCCATTTTTGA[T/G]GCTTTCTTCTTGTATTTTTTAGGTTTTCTTCGTTTTTGGACTTTTTTCAGCTATGTTTTTCGTTAATCCAGTAGGCCAACAGT
98832 T C AATTCAATTTTTTTCAGCTTATATAGGAAAACACGTGTACTAAAGAGCATACATGAATAGGTCTAT[T/C]AATGGGTCGGGTTTGGTCTGGATAGCATAGAACACAAACCTGAGTCCATCTGCAGAAAGCCAAGCCCAACCAGAGCCATTGGGTATTTCAAATCCATTAC
98838 A AC CCACGCCTAAAAGGATATAGAAAACCTAGCTTCTCGTCTAACTGTGCCTCCACCTCGTACGCTTCACTTCTCTCATCTCCAT[A/AC]CCCCGAGTCGCGCTCAGCCTATGCCACCGCCGAAACCCTCAATTCCACCGAGACCCCCATCGCCACTGCCTCGAAGATAGAAGTGCCCCGCATCTCAAAT
98838 AT A TTTCGGCTTCTTTTTTTCGTGATTTGTTGATTTCTACCCATATTGTAGTTAGGTATAAGGGTTGTATTTCAGATCTGCTAGCACTAGTTTCTAAATCATT[AT/A]TTTTTTATTATTTGTTTTTCATACGAAGATCTTCTTACATACTTAGATCCAGATTGTTGTATATTCATGGACTAAAATTGACCCTTGTAATG
98842 G T AATGAAGCAATTGAAGTACTTGACAAACTTCATGAAATGGGGGTCACTCCTAAACTGTTTGAGCAACCAGTTCATAGAGGTAACTGGGAAGGACTACGCC[G/T]TGTGAGTGAAGTTGCAAAGGAAAAATACGGCGTATCTGTTGCTGCAGATGAAAGCTGTAGAAGTGTGGATGATGCACATAGAATT
98844 CA C GGTTTCTCTTCAGCATTTGGAAACTGAAGACGATACACAAGATGGAGAGGAAGAATGAATTGCGTTGCCTTTTAAATTGAAACGTATATCAGTTGTTTAA[CA/C]AAACGTATTTCAGGGTTATTCTGTAGAATTGGGATAAATTGGTGTGCGATGTTCAAGTTTTTGCAATGGGAAAAGATGCTGAAAGT
98848 C CG GGACCCCGTGCTGCAGGGGGTGAGGACAGACAGGCCTACAGGAGGGCCGGTGGTCCCGGGGGTGTCGATAAGAGGGGAGAGGCTGGGGCTGGTGCAGCTC[C/CG]ACAATTCCAATATAGGGGAGGTTTTGGTCGTGGTGGCGGCGCTCCTGAACAGTCTGCCGCTGAACAGGAATAGAATGTGT
98862 C T CATCAGCAGTAGGAGAACCCCAGGACCAAACATCGGTTTCGCAGCTCGTGATGTCGCTTGAAATCACGCTCTGCAAATTGTCAAAGCCAGCATTCATACC[C/T]ACACCCATATCACCCCCTTGAAAATTACCGAGGCACCCTCCATTTTCTTGTATATGATCCATCATATTCATGTCAGCCGTATCAAGGCC
98862 T C GATGGTTTGCATCTGTGAATTGTTTGTAAAGTGCAGCACTTTCTCCTCTCAGCTGATCAACCTGTAGTTCAAGTTGTATTTGTTGAGCTTGCTTCCTCGT[T/C]CTAGAACGTCTAGCAGATTCGCGGTTCGAAATCATCCTTCTCATGCGTTTTATGTCGATGGTGTTAGGATCAGATAGTCCATTTTCGAAT
98866 T C TTGGACTCTCCCATGGATTCCTTTTAGGCCACCTGCAGTCGCTTGGCCTTGATTTTCCTAAGAACATCAGTGTAGTTGCTGTATGCCCCAAGGGCATGGG[T/C]CCATCAGTAAGAAGGCTCTATGTCCAAGGAAAGGAAGTCAATGGTGCTGGCATTAATGCTAGCTTTGCTGTTCACCAGGATGTTGAT
98866 T C GCGAGCGAGGTATTTTGCTAGGCGCTGTTCATGGTATTGTCGAGTCTCTGTTTAGAAGATACACCGAGAATGGAATGGGTGAAGAGCTAGCTTATAAGAA[T/C]ACTGTTGAATGCATCACTGGAATTATGTCAAAGACAATCTCTACCAAGGGCATGCTTTCTGTCTATAACTCATTGTCGGAAGAAGG
98866 G A TTCATGGTATTGTCGAGTCTCTGTTTAGAAGATACACCGAGAATGGAATGGGTGAAGAGCTAGCTTATAAGAATACTGTTGAATGCATCACTGGAATTAT[G/A]TCAAAGACAATCTCTACCAAGGGCATGCTTTCTGTCTATAACTCATTGTCGGAAGAAGGGAAGAAAGAGTTCAACGCTGCATACAG
98872 A G CGGCTGTGCCGATCATCAACTTTCCGTAGATACTATGGCTTTGTCAGGATATACTACAACCGGTGCGATGACTTACAGTTTAATTTTGGCACTAGAAAGC[A/G]ATCCTGGAACAACATATGGGCAATTGCTATATTCGATGCGATCTGTGATTCGTGGCGCCAACACAAACTCCAAGTTGTCCGGCCCAG
98872 T C AACTTTCCGTAGATACTATGGCTTTGTCAGGATATACTACAACCGGTGCGATGACTTACAGTTTAATTTTGGCACTAGAAAGCAATCCTGGAACAACATA[T/C]GGGCAATTGCTATATTCGATGCGATCTGTGATTCGTGGCGCCAACACAAACTCCAAGTTGTCCGGCCCAGTTGCCTCTTTTGCAAGGA
98872 CAT C GGCCATTTCTCTTATAAAAGCATCATCGTCTTGTCTATCAGGCATTTGATTATGTCATAATCCTCACATACTAATCTTTTTTATGTAAAAAGTTGTTTGC[CAT/C]ATATCTGTAATGTAGCTGTAAAGTTAGAGAATCATTTATATGAGAATAATAAGCAGAGAATAACCAATGCTGGACATATTCTCTCCACC
98880 CA C TGTTGCTGTTTCCAGCGTATCAGTAAACTAAAGCTCGATAGCGATGAAATTAGGGCATCATCAATCATTTAGGTGGAATTTTGGGTTCGATATCATTACG[CA/C]AAAAAACAAGGAAAATAAGGTCTGTTCTGAACAAAGATGTGGAGCAGCAGAGAAGTAGAACAAAAATCCGGCAATCGACGTGGTC
98880 GAAC G ACTCCGGCACGACCACATGACGGAGGCCGATTAATTTACTTAACCTTGTAAACCCTAAACTCAACTCCAGTTCCTTTTCCTTTTCGTCTGGTCTGGCGAA[GAAC/G]AACAACACTTCACGGAAGCAATCTGCCATATCGTAAGGAACCGAAACTTCTGATTCGCAAGTGGTCAGTTCATTTAACTGGAGTA
98888 TG T AAGGTCTCGAGGTCATTCGTGTAAAATGGGGAAAGGATAACAGCGGTAAATTCCAATTTGAGGAAATCAAAGGATCAGAAGAAATCATTGAAGCTGATCT[TG/T]GGTGCTTCTTGCTATGGGTTTTCTTGGTCCAGAACCGACAATTGCGGACAAATTAGGGCTAGAGAGGGACCCACGATCAAATTT
98896 G T AACTACATATATGCTCGAGAAAAGCAACGTAGAAAAGTACATTTACCTGAAACCTCTGTTAATTCCCATCCATGCGGTAATTGCTTTCAGAAGCAGAAGA[G/T]GAAGATGAAGGATTGAACGAAGAACTCCTCCTATTACCTCGAAACAAATTACTCAATGACAAAGTAATAGTGGTTTCAGATTCAGGT
98898 A G CACTTCCAGTCTGCCATATTACAAGGGGGAAATGGTCATTTAACTTTCCCTCAGCAACCTCTTCGGCAGCCTTCATTATTGCTTTCCCAATAGTTGGGTC[A/G]AGACCATACTCCATATTCACCTTTGCAGCACATTTCTTCAAAACACCAAAAGCTCTCACAATGGGTTCAGGCATTTGCTCCCGTTCACCT
98898 G A GCATTTGCTCCCGTTCACCTCCAATATCAAAATTCTGCAGCGATCTCTGCGTCTGCGCTCCCCAGAGCTTATCGTTCGGAACACTGATCGGACCGAAAGT[G/A]TCGCGTTCTTCTCTGAACCCCGTCGAGATCCAGCGGAATGATGTCGGACGGCACAACATCTGAGTGGACGAGGTGAGCCGCCTTGAT
98910 G A CTCCTTTTAAACCATTCAAGCTCTATTTGTTGCATCAATTTCCTTCACTTCTATGAAGTGGTTTGCTGATAAAAGCAGCGCATATTTGTTTACCCGTTTC[G/A]TAGTGTTCGTCCACATTCTTTTGCTATAGCGGTAGATTGCTAGCTTGGTCTTCCAGAATTTCAAGGTTGCTATTTCAAATCATTGTCATCGT
98910 T C TCCTTTTAAACCATTCAAGCTCTATTTGTTGCATCAATTTCCTTCACTTCTATGAAGTGGTTTGCTGATAAAAGCAGCGCATATTTGTTTACCCGTTTCG[T/C]AGTGTTCGTCCACATTCTTTTGCTATAGCGGTAGATTGCTAGCTTGGTCTTCCAGAATTTCAAGGTTGCTATTTCAAATCATTGTCATCGTC
98910 GCTATTTCAAAT G TAAAAGCAGCGCATATTTGTTTACCCGTTTCGTAGTGTTCGTCCACATTCTTTTGCTATAGCGGTAGATTGCTAGCTTGGTCTTCCAGAATTTCAAGGTT[GCTATTTCAAAT/G]CTATTTCAAATCATTGTCATCGTCATCCAAGCGGAACATCGTATTGGAGCACGGTATACTGAAATCACGGTAGCTAAG
98910 G A ATTCTTTTGCTATAGCGGTAGATTGCTAGCTTGGTCTTCCAGAATTTCAAGGTTGCTATTTCAAATCATTGTCATCGTCATCCAAGCGGAACATCGTATT[G/A]GAGCACGGTATACTGAAATCACGGTAGCTAAGAATGACTGGTCAAAACTTATAGGGTTGAAATACAGATCTGAAGAACAGAATGCTTC
98910 G A AGAATTTCAAGGTTGCTATTTCAAATCATTGTCATCGTCATCCAAGCGGAACATCGTATTGGAGCACGGTATACTGAAATCACGGTAGCTAAGAATGACT[G/A]GTCAAAACTTATAGGGTTGAAATACAGATCTGAAGAACAGAATGCTTCTTCCAGCGGCAGATCTTTACCATTCAGCCAGCCCCAAAT
98910 C T CGGTAGCTAAGAATGACTGGTCAAAACTTATAGGGTTGAAATACAGATCTGAAGAACAGAATGCTTCTTCCAGCGGCAGATCTTTACCATTCAGCCAGCC[C/T]CAAATCGGAATAGCGGTGTCAGATCCAAAGAAGAGTGGGTACGTGAAAGGGAAATTGTGGTCTGAACGTAACGGCCTCGAGTAGG
98910 T C AGATCTGAAGAACAGAATGCTTCTTCCAGCGGCAGATCTTTACCATTCAGCCAGCCCCAAATCGGAATAGCGGTGTCAGATCCAAAGAAGAGTGGGTACG[T/C]GAAAGGGAAATTGTGGTCTGAACGTAACGGCCTCGAGTAGGTTTAGCGGGTAATTTCGACCGATTACATGAGGATGATGGAATCT
98916 A G AAATCCTAATTTCCTAAAATCGAGCCAAACCCTAAATCCCACAAAACCCAAAGCCCTAACCATCCGTTCCGCAATCAGTCGCACGAAGAAGGAACAAACA[A/G]TCTCCACCGTCCAAACCCACCTCGAGGACTGCCACCTCATCGCCGGAATCCGGTTCAAAGGACTCACCGTCAAAAACTTACAGGAAC
98916 T A CTAACCATCCGTTCCGCAATCAGTCGCACGAAGAAGGAACAAACAATCTCCACCGTCCAAACCCACCTCGAGGACTGCCACCTCATCGCCGGAATCCGGT[T/A]CAAAGGACTCACCGTCAAAAACTTACAGGAACTCCGCCGCAGCCTGCCTCCAACTACCACGCTTCTTGTCGCAAAGAACACTCTTGT
98916 C T TCCACCGTCCAAACCCACCTCGAGGACTGCCACCTCATCGCCGGAATCCGGTTCAAAGGACTCACCGTCAAAAACTTACAGGAACTCCGCCGCAGCCTGC[C/T]TCCAACTACCACGCTTCTTGTCGCAAAGAACACTCTTGTTTACAAGGCGATTGAGAACACGAAATGGGAGGCATTGAAGCCGTGCAT
98916 T C CTGAGGAGATTCCTGAAGGTCTGAAGACATACAGGGCGTTTCAAAGGGAGAAGAAGCTGGAGAACAATGAGTTCACCGGTGCTGTGTTTGAGGGGAAGTT[T/C]TATGGGCCTGAGGAGTTTAAGGCACTTGAGACAATGCCAACCAGAGCAGAAATATATGCAAAGATTTTAGGAGCCATCCAAGG
98918 G A TGCTCCATACCCGTATCCTCCTACTAAAGGAGGAGCCACTTGTGGGTTTATGTATATGTTTGTCCTAGAATTGTTGATTCTAGGGCCAGAACTTCGAGGA[G/A]CAGGTGATCGGAAAGCCTGACCACCGACCCTGCCTCCACTTTTCCCAGCCATGGCTTCTTGCGGAGTTCCTATAATCAATACTCCAGC
98918 T C GCAGGTGATCGGAAAGCCTGACCACCGACCCTGCCTCCACTTTTCCCAGCCATGGCTTCTTGCGGAGTTCCTATAATCAATACTCCAGCAGTCACAGCTA[T/C]GAGTGCCAGCTTCCCCAATTGCCATTTATCTCTGCTCTTGTTCTCCGGTGCATCTGTTTTCTCTTCTGTTTGAATTGATGCACTACGCGT
98918 G A GCAGTCACAGCTATGAGTGCCAGCTTCCCCAATTGCCATTTATCTCTGCTCTTGTTCTCCGGTGCATCTGTTTTCTCTTCTGTTTGAATTGATGCACTAC[G/A]CGTGAGGCGGAACGATTTGACTGTCTTCTTGGTAGGCAACTGCCTGCTGTAATTTAAAGGGATGAGAGTTGCGAAAGGCGAGGATGAG
98918 A G TCCGGTGCATCTGTTTTCTCTTCTGTTTGAATTGATGCACTACGCGTGAGGCGGAACGATTTGACTGTCTTCTTGGTAGGCAACTGCCTGCTGTAATTTA[A/G]AGGGATGAGAGTTGCGAAAGGCGAGGATGAGGACATGGCCATGGCTCAATCTTTTCTCTTCTTCTTGTGTTGGTATTTACTTGTGAAG
98918 G A TTGATGCACTACGCGTGAGGCGGAACGATTTGACTGTCTTCTTGGTAGGCAACTGCCTGCTGTAATTTAAAGGGATGAGAGTTGCGAAAGGCGAGGATGA[G/A]GACATGGCCATGGCTCAATCTTTTCTCTTCTTCTTGTGTTGGTATTTACTTGTGAAGTGAAGGGTGATATTCCTTTATTATAACTGC
98918 A G GCAACTGCCTGCTGTAATTTAAAGGGATGAGAGTTGCGAAAGGCGAGGATGAGGACATGGCCATGGCTCAATCTTTTCTCTTCTTCTTGTGTTGGTATTT[A/G]CTTGTGAAGTGAAGGGTGATATTCCTTTATTATAACTGCATATTTCTTCATCTTCGAGTTTTCCAGTAGGCCAAC
98918 G C AATTTAAAGGGATGAGAGTTGCGAAAGGCGAGGATGAGGACATGGCCATGGCTCAATCTTTTCTCTTCTTCTTGTGTTGGTATTTACTTGTGAAGTGAAG[G/C]GTGATATTCCTTTATTATAACTGCATATTTCTTCATCTTCGAGTTTTCCAGTAGGCCAAC
98932 AT A TACGTTCTGGTGTCGAAGGAGAGCCCGAAGTGCCCTAAGTGCGAGTCGGAGGTGCCTGATGATATTTTTGAGAGGAAGAAGAGACCGAGGATTGACCTTA[AT/A]TTTTTAGGGTAGTTGGTTGGAGGAGTGGTGTTGGGTTTTTTTGATTGGGTTAGTTGTTTTTTTGATTGTAAATGGGGCATTTGG
98934 C A TAATATAATCAGCAAAAGAGGGTAAAAGTCAAAAAATTCAAGAACCCGCAGGGGCAAGCCTAAGCTTCAAATCCAACCCAAACCCGGATCCAATATCCAC[C/A]TCACCCGCATCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGG
98934 A T CAGCAAAAGAGGGTAAAAGTCAAAAAATTCAAGAACCCGCAGGGGCAAGCCTAAGCTTCAAATCCAACCCAAACCCGGATCCAATATCCACCTCACCCGC[A/T]TCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGGTCGAAATCC
98934 C T TAAGCTTCAAATCCAACCCAAACCCGGATCCAATATCCACCTCACCCGCATCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCA[C/T]CCGTCCAAGCAATCACCACCGCCTCGGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGA
98934 A G CCAACCCAAACCCGGATCCAATATCCACCTCACCCGCATCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCA[A/G]TCACCACCGCCTCGGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCG
98934 G A ATCCAATATCCACCTCACCCGCATCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCG[G/A]TCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAAC
98934 C A CCACCTCACCCGCATCCTCATCCTCCGCCACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGGTCGAAATC[C/A]ACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGG
98934 C T ACGTGTCCAAACGAGAAATACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGG[C/T]GGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAACGCGGCCGACTGGTG
98934 A T ACATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGG[A/T]TTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAACGCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGG
98934 T G CATATGCGGGCCCCACCCGTCCAAGCAATCACCACCGCCTCGGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGA[T/G]TGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAACGCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGG
98934 T C GGTCGAAATCCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGG[T/C]GACCGGAACGCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGGCGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGCGTTTCTGG
98934 C G CCACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAA[C/G]GCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGGCGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCC
98934 G T CACCCACCTCGCACCCTTCCCTTTCCCGGCGGGCCCCACCGAGTGAGGATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAAC[G/T]CGGCCGACTGGTGCTGCTGCTGCAGCATCTGGGCGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCCCA
98934 G GT GATTGACGATGCCGCCGCGCGGGTACAAGAACCCACCGGGCGGTGACCGGAACGCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGGCGCGCTTCAGGAG[G/GT]CGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCCCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCG
98934 GT G GGTACAAGAACCCACCGGGCGGTGACCGGAACGCGGCCGACTGGTGCTGCTGCTGCAGCATCTGGGCGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGC[GT/G]TTTCTGGTGACCGCCCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCGTACTTCCTGCCGTCGCCGCCGC
98934 G GT CAGCATCTGGGCGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCCCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTG[G/GT]CACTCGTACTTCCTGCCGTCGCCGCCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTGGAAGCCGAAGAGCTTGAGGGGTTGG
98934 T TA CGCGCTTCAGGAGGCGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCCCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCGTACT[T/TA]CCTGCCGTCGCCGCCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTGGAAGCCGAAGAGCTTGAGGGGTTGGAGTGGGTTGG
98934 G A GCGCCTTTCCTTCTTGTGGGCGTTTCTGGTGACCGCCCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCGTACTTCCTGCCGTCGCC[G/A]CCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTGGAAGCCGAAGAGCTTGAGGGGTTGGAGTGGGTTGGTGTTTGCTGTTTCGT
98934 G GT CCAGCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCGTACTTCCTGCCGTCGCCGCCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTG[G/GT]AAGCCGAAGAGCTTGAGGGGTTGGAGTGGGTTGGTGTTTGCTGTTTCGTGCTGGTCGTCGGATGACATGGTTCGGGTTATATC
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
98934 G GT GCGCCTGGGAGTTGGCGAACTCGCGGCTGCAGTACTGGCACTCGTACTTCCTGCCGTCGCCGCCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTGGAA[G/GT]CCGAAGAGCTTGAGGGGTTGGAGTGGGTTGGTGTTTGCTGTTTCGTGCTGGTCGTCGGATGACATGGTTCGGGTTATATCAGA
98934 T C ACTCGTACTTCCTGCCGTCGCCGCCGCCGCTGCTGCTCGGTTCCGGGTTGCACACGTGGAAGCCGAAGAGCTTGAGGGGTTGGAGTGGGTTGGTGTTTGC[T/C]GTTTCGTGCTGGTCGTCGGATGACATGGTTCGGGTTATATCAGACTGGGAGGGGGGTTTTCGTCTAATGTTTGCTTTTCCAGTAG
98942 A G AACATACAAATCAGTACAATTCCACGCAGGCGCAAGCAAGCAGAGTAGATGTGGAGAGGAGAGAGTGAGTGTGGATCGATTTGAGGGCAGAGAAAGACGG[A/G]AGAGAAGGAGAGGAAGAAATCGAAGAAAACGATGCGCTTTACGCCATTAACGGGATTGTACCGCGTTATCTTTGTTCTAGCCA
98970 A T GAATACTTGTGTCTTTTGCCTTCAAAGTTTCCATCTGCTCTTCAACTCCTTTTGATTTTTCTAACCCAGCATGAACAGCTATCAACTTACAACATTTTCT[A/T]CCTTCGGGAGTATCAATGCGCACATTTTCCTCTTCGTGTACCCAAACTAGATCAACAAGGAACTTTTTATGCTCATCTGGCACTGCTTTCATC
98970 C T GAACAGCTATCAACTTACAACATTTTCTACCTTCGGGAGTATCAATGCGCACATTTTCCTCTTCGTGTACCCAAACTAGATCAACAAGGAACTTTTTATG[C/T]TCATCTGGCACTGCTTTCATCAACTCTGAAGAGCCATGCTGAACTCCATACGATTCAAAAGTAGTGCCCGCATCATAAATGGAGCCCTTG
98970 C T CCCAAACTAGATCAACAAGGAACTTTTTATGCTCATCTGGCACTGCTTTCATCAACTCTGAAGAGCCATGCTGAACTCCATACGATTCAAAAGTAGTGCC[C/T]GCATCATAAATGGAGCCCTTGTAAGGTAAACCTTTTGCTGCATTCCACCTATCCTTGATACAGCCAGCCCACCTCCTCCCTTGGAGGTG
98970 G A TGATACAGCCAGCCCACCTCCTCCCTTGGAGGTGCATCTCCTCATACTTCTCTCCCTTGTACCAACCTTCTCTCTCCTCATTCGCCTCAAACTCCTTCCA[G/A]GTGTCCTTTAGATGTGTCCCATTTGGAGGAGGAGGTAATAGGAGGAGAAAAGCAGAGAAGGCAAAGTCATGGTTGCCTGCAAGAAACA
98970 G A CCAACCTTCTCTCTCCTCATTCGCCTCAAACTCCTTCCAGGTGTCCTTTAGATGTGTCCCATTTGGAGGAGGAGGTAATAGGAGGAGAAAAGCAGAGAAG[G/A]CAAAGTCATGGTTGCCTGCAAGAAACACGTGTCGCTGCCTCGGAAAGAGGGAAGGCAGAGAGAGAAGAAAGGAAATGACATGAC
98970 G A AGAAAAGCAGAGAAGGCAAAGTCATGGTTGCCTGCAAGAAACACGTGTCGCTGCCTCGGAAAGAGGGAAGGCAGAGAGAGAAGAAAGGAAATGACATGAC[G/A]GGTGTCGGGTCCACGGTCACAGTAGTCACCGAGGAAAATGATGGTGGCAGAAGAGAAGACTGTGGACCCCACTGCTGATTC
98970 G A CTGCAAGAAACACGTGTCGCTGCCTCGGAAAGAGGGAAGGCAGAGAGAGAAGAAAGGAAATGACATGACGGGTGTCGGGTCCACGGTCACAGTAGTCACC[G/A]AGGAAAATGATGGTGGCAGAAGAGAAGACTGTGGACCCCACTGCTGATTCAAGCTCTGACCATAGGGATCTAAGTTTCTCTAT
98970 A G GAAACACGTGTCGCTGCCTCGGAAAGAGGGAAGGCAGAGAGAGAAGAAAGGAAATGACATGACGGGTGTCGGGTCCACGGTCACAGTAGTCACCGAGGAA[A/G]ATGATGGTGGCAGAAGAGAAGACTGTGGACCCCACTGCTGATTCAAGCTCTGACCATAGGGATCTAAGTTTCTCTATGTAACC
98970 T C GGAAATGACATGACGGGTGTCGGGTCCACGGTCACAGTAGTCACCGAGGAAAATGATGGTGGCAGAAGAGAAGACTGTGGACCCCACTGCTGATTCAAGC[T/C]CTGACCATAGGGATCTAAGTTTCTCTATGTAACCATGGATGTCTCCCACACAAATTACAGTCTTCTCTGAATCCATGATTTCTATTT
98982 A G TAAAGCAACCATCATGCCTTGCACCACCACAACGTCCAGATCTTCATCGATCATCCATCACCCCCACGCCAGAAAGCACACCCACCACGACCACCCGCTG[A/G]GCCCCACGGAATGCTCCTCCGTCGTCTCCACCACCATCTCCGCCCCGCCCTCCGTCATATGGTCCCTCCTCCGCCGCTTCGACTCCCCT
98982 G C CCTGCCGCCTCCTCGACCCCGCCTGCCCCTTCTCCGTCGGGTCCGTACGCGAGGTCAGGCTGATATCCGGCATACCGGCGGTCTCCAGCCTGGAGCGGCT[G/C]GAGACGCTCGACGACGAACGGCACGTCATCGGCTTCAGGATCGTCGGAGGCGAGCACAGGCTGACCAACTACAGGTCCGTCACTT
98992 A G CAAAGGTCCATGCCTCATGGGCCTCGACTTCTGGATAACTTGCAACCCAGCCAACGTCAACCATGTTTTCAATGCGAACTTTCCAAACTACCCTAAAGGC[A/G]ACGAGTTCCTACAGATTTTCGATATCCTTGGTGATGGCATATTTAATGCCGATGCCGAGTCGTGGAAGGCTCAAAGAAAGAAAGCCC
98992 C T AGAAAGAAAGCCCACGTCGTGATCACAAATCCTAGTTTTCGAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGA[C/T]GAAGTTTGCGGATGAGGAGGTCGTGTTCGACTTGCAAGACGTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGG
98992 G A CCCACGTCGTGATCACAAATCCTAGTTTTCGAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGC[G/A]GATGAGGAGGTCGTGTTCGACTTGCAAGACGTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCA
98992 T C ACGTCGTGATCACAAATCCTAGTTTTCGAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGCGGA[T/C]GAGGAGGTCGTGTTCGACTTGCAAGACGTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCAGG
98992 C T ATCCTAGTTTTCGAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGCGGATGAGGAGGTCGTGTT[C/T]GACTTGCAAGACGTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCAGGGTGTCTGTCTGATGAA
98992 A G TTCGAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGCGGATGAGGAGGTCGTGTTCGACTTGCA[A/G]GACGTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCAGGGTGTCTGTCTGATGAACTTCCGAA
98992 C T GAACCTTTCTCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGCGGATGAGGAGGTCGTGTTCGACTTGCAAGA[C/T]GTGTTTCTACGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCAGGGTGTCTGTCTGATGAACTTCCGAACGT
98992 A G TCGCAGGTTGCACCAAGGAGAAAGTCGACGGTGCGTTGGTCCCGCTTTTGACGAAGTTTGCGGATGAGGAGGTCGTGTTCGACTTGCAAGACGTGTTTCT[A/G]CGTCTCACGTTCGACATGACTTGCAACCTGGTGTTTGGGGTTGACCCAGGGTGTCTGTCTGATGAACTTCCGAACGTTCCGTTCGC
98996 T TG GATGATGAACAGGATGTACCCTAGTAACAGGCTGTACAGTGCTTACGGAGCTGGTCTAGGGCATAGATCGAGTTTTTATGATTCCAGAACCAATGGGAGA[T/TG]GGGGGTATGTAGATACCAAATACAAGCCTGGGGGCAGAGGCAATGGCTTTTATGGTTACCCTAATGAGAGCCTTGATGGCTTGA
98996 T TG GGCTGTACAGTGCTTACGGAGCTGGTCTAGGGCATAGATCGAGTTTTTATGATTCCAGAACCAATGGGAGATGGGGGTATGTAGATACCAAATACAAGCC[T/TG]GGGGGCAGAGGCAATGGCTTTTATGGTTACCCTAATGAGAGCCTTGATGGCTTGAGTGAACTAAATCGGGGTCCTAGAGCCAA
98996 G A TGTACAGTGCTTACGGAGCTGGTCTAGGGCATAGATCGAGTTTTTATGATTCCAGAACCAATGGGAGATGGGGGTATGTAGATACCAAATACAAGCCTGG[G/A]GGCAGAGGCAATGGCTTTTATGGTTACCCTAATGAGAGCCTTGATGGCTTGAGTGAACTAAATCGGGGTCCTAGAGCCAACCGAA
99006 CA C GTAGCACCATCAATGGTTTGATCATCTGCAAAAAGATTTTGAATATAAGGAAGAACCTTTGGCATAGCAGGTAAATCGGCAGCATTTACCGTCATCATAT[CA/C]AAAAGCAATGCATGTTTTATCCTTGTGGCATTCATTGATAACTGGAACTTTTGGGTATCGCTGGCTAAAATGAGTCAGCATAATGCG
99006 A G TGGTGTCCCCAGAATACACAAGCTTCCAGCCCGGTATAGTTTTGCCAGCACTATCACATCTCTCAGCAGCCTTAATGACAACGCCAAAGGCGTCCCTAAT[A/G]GAATGTTCAACATGGACACTGTACAGATATTCCAAACCTGCGGCGTGCAGCTTCTCCTTTAGAACATCTGTTACGACTGTATTTGATTT
99010 G T CAATAGCAACAATTGGAGAGAACATGAAAGTCTCGAGATTTGCTAGGTATAATCTTGGGGAAGGATTAGAGAAGAAAAGTCAGGATTTTGCAGCTGAGGT[G/T]GCAGCCCAAACTGCTGTAAAAGAAACACCTGCAGTTGCTCCAGTTCCACCTAAAGAAGAACCTACTGTTGAGAAGACAGTGCCGG
99014 C T TCTAGCTCTGAGCAGCAACCCAAGGGCTCTAACAAATCCAGAAAGAAGAAGTCTAGAAATTAAGGCTTGTTATGTTTAAGACCTTCATGGTGAAAATATC[C/T]GATTTTTGCTTGTTTATCATTATTTAGTAGTTTTATATGGTCAGAGGGATTTTTGTTATATTATTCCAGAAACTGCGAACATTTGTCTGC
99024 C T GCAGGCGTAATTGAAAGCGAAGGCAGGATAAAATACAGAATGAGCAGGAATGACAAGGAGAGGCTCACAAATGGGATAAGGAGGGCGTTGAGGATACTGG[C/T]GGCGGCAGGGGCATCAGAGGTGGGGACGCATAGGAGCGACGGGCAGAAGCTGAAATGCAGAGGGGTCAAAGAGGAAGAA
99024 GT G GATGGGGAGTTGCAGGATGGGAGTGGACGAGAAAGAGAGCGCTGTGGATGAGAGAGGGGAGACCTGGGAAGCTGAGAATTTGTACGTGTGCGATAGCAGT[GT/G]TTTTTCCTACCGCGCTTGGGGTGAACCCGATGATCACTGTGGAGGCTTTGGCTTACTGCTTAGCTGAAGGAATTGTTCAGTC
99034 T A AAATTGCGATCAATAAATAGCTTTCGAATGCGGATTCCCAATCAAACCAGACCTTATACTGCTGTGCTTGATTCAAATAACTGCTAATTAGTCATGGTCA[T/A]TTCTCAACAACCTGCAAGCCTTGTCTTCAAACAAAAAGTAATTATATACATCATCATTCACTCCTGGATGTCCTTCAAAGCAAATGAAAA
TTTCCTCTGAAAAATGATGGCAAATAAAGGTAAGTTGCAAATTTTCACTTCCATAAAACTAAATTTCAGAACTCCAGCG
99034 C GCTTTCGAATGCGGATTCCCAATCAAACCAGACCTTATACTGCTGTGCTTGATTCAAATAACTGCTAATTAGTCATGGTCATTTCTCAACAACCTGCAAG[C/CCTGAGTTATATTTTTTTCCTCTGAAAAATGATGGCAAATAAAGGTAAGTTGCAAATTTTCACTTCCATAAAACTAAATTTCAGAACTCCAG
99034 G A AAACAAAAAGTAATTATATACATCATCATTCACTCCTGGATGTCCTTCAAAGCAAATGAAAACTAGCTGAGTCAAATCTGTGTCTTCTCTTTGGCTCAAG[G/A]TACCTTGAACATGGTTGAAAACTTTTGCATTATCAGATACCATTTTTAGGGTTTCCGGATCTGTGGCTCGAGAGAGATTGAATCGAAGT
99040 A C CATACCCGATCCCTCTCAATCTACTCCTCAACATCCCCCTCACGCTATCAGGCAACATCCCATACAAATCATCCCTCGCATCAGGTCCTACTGCTCTCGG[A/C]GTCCTTATCATCTTCTCTATTATGGTTATAACACTCGCGTAGTGCATGGCCAATGCCGCAGCCCCCAGCGTCGTCTCCGGTGGAGACGAA
99040 G GC ATACAAATCATCCCTCGCATCAGGTCCTACTGCTCTCGGAGTCCTTATCATCTTCTCTATTATGGTTATAACACTCGCGTAGTGCATGGCCAATGCCGCA[G/GC]CCCCCAGCGTCGTCTCCGGTGGAGACGAAATCATCGACGCTCGTAGCTCAAACAGACCCAACCCACACTTCTTCGTGCACGAGGTAC
99040 C T CATCCCTCGCATCAGGTCCTACTGCTCTCGGAGTCCTTATCATCTTCTCTATTATGGTTATAACACTCGCGTAGTGCATGGCCAATGCCGCAGCCCCCAG[C/T]GTCGTCTCCGGTGGAGACGAAATCATCGACGCTCGTAGCTCAAACAGACCCAACCCACACTTCTTCGTGCACGAGGTACTCAACGGCG
99058 C G TGGCAACCATGGACGAAAGAGCTAACCAGCCTGAACAGCTTTAACATACTTAGAAACGGCCTTCAGACCTTCGGAAGCAGCAAACTTGGCCAGCTCACCG[C/G]TCAGCAGTGGCTTAACCGCTGCCTCAATATCCCAGGAAGATAACGTATCCTTACTCCGTTCAAAGAGAAAAGAGCTACCGTCGGGT
99064 G A CTGGACACTTCTCTCATTAACAAATACTCAACCTTAAGAAGGATTAGAAGAGAGTACAATGGCTTTTAAGAGTACAAAGTCGCTAGCTCTCTTCTTCACC[G/A]TCAACCTCCTCTTCTTCACCCTGGCCACGTCATGCAACACCTGCTCTCCTGCACCAAAACCACCATGCCCGACACCTAAACCCCCTAAGC
99066 A G TGACAAAAATGACTTATGCTCAAGTTGCAGTTTACGGTTTCAGTGACAAAGTAGGACTGCTCTCATTTCCACAAAGGGAAGATGGATTTGAGATGAGCAA[A/G]CCTTACAGTAGCAAAACCGGAGCTATAATAGATGGAGAAGTGAAGAATGGGTTGCTAAAGCGTACACCAAAACCTTAGAAATAAT
99066 A AG TGACAAAGTAGGACTGCTCTCATTTCCACAAAGGGAAGATGGATTTGAGATGAGCAAACCTTACAGTAGCAAAACCGGAGCTATAATAGATGGAGAAGTG[A/AG]AGAATGGGTTGCTAAAGCGTACACCAAAACCTTAGAAATAATAACTGAGCATAAGGATCATGTTTCTAAAATAGCGGAGCTATT
99068 G A GTTGGCCTACTGGAATTAGATCGTCCGGATCTTCTCCTATTCCAATGGCTGCCTTTTGTTTCAGAAAAGAAAGCCTCTCAATCTATCGCCAACTTCTTGC[G/A]CCGTCGCATCTAATGAGATCTTTCTCTTCTCAGTCTTCCAGCCTCGTCGAAATCAAACCTGGCGAAATCGGGATCGTTTCCGGAATCCCT
99068 T C ATTAGATCGTCCGGATCTTCTCCTATTCCAATGGCTGCCTTTTGTTTCAGAAAAGAAAGCCTCTCAATCTATCGCCAACTTCTTGCGCCGTCGCATCTAA[T/C]GAGATCTTTCTCTTCTCAGTCTTCCAGCCTCGTCGAAATCAAACCTGGCGAAATCGGGATCGTTTCCGGAATCCCTGACGAGCACCTCAA
99068 CT C GTTATTATCTATTCTCCAGCTCGAACACCTTCTCAACAGGGATCTGGAAAAGTTGGAAGATGGAAGATCAATTTCATGTCAACTCAAAAGTGGGAAAATC[CT/C]TTTAATGGGGTGGACATCCACAGGAGATCCATATGCTAACGTTGGTGATGCTGGAATGACTTTTGACAGTGAAGAAGCCGCCAGA
99068 C T GATCTGGAAAAGTTGGAAGATGGAAGATCAATTTCATGTCAACTCAAAAGTGGGAAAATCCTTTAATGGGGTGGACATCCACAGGAGATCCATATGCTAA[C/T]GTTGGTGATGCTGGAATGACTTTTGACAGTGAAGAAGCCGCCAGAGCATTTGCCGAAAAGCATGGGTGGATCTGTACGGTGAAAA
99068 G C CAGGAGATCCATATGCTAACGTTGGTGATGCTGGAATGACTTTTGACAGTGAAGAAGCCGCCAGAGCATTTGCCGAAAAGCATGGGTGGATCTGTACGGT[G/C]AAAAAGCGCCACACGCCTCTTCTGAGGGTAAAAGCTTATGCGGATAATTTTAAGTGGAAAGGTCCACCAAAAGCTGAGGAAGCA
99068 T C TCTGAGGGTAAAAGCTTATGCGGATAATTTTAAGTGGAAAGGTCCACCAAAAGCTGAGGAAGCATAAAAGATTTTCTTGCTGATGCGTACATTCTAAAGT[T/C]AGTTCTTTATGAAATGGTCTTTATTTCCAGCATCGTCATTAGATGATCAATTTCACATTTGTGTAAACTCAATAAAACATAACTGATAC
99078 T C CCTTTTTTTTTTTTTAAAACGAAGCAGGACAACACTTAAAGATCTAAAAGCTGGTACATGATACAAATATATAAACTCATAG[T/C]TTGCTCAAATATCATGCAATTTGACAAACCAGGCTGATAAGTGATGATAACAAGGGGAAGAAATACACGGACATAAAAGAATAAACACAATAATTAAATA
99078 C G AGCTGGTACATGATACAAATATATAAACTCATAGTTTGCTCAAATATCATGCAATTTGACAAACCAGGCTGATAAGTGATGATAACAAGGGGAAGAAATA[C/G]ACGGACATAAAAGAATAAACACAATAATTAAATACCGCAACAGCAATTACCAATACTTTCGTATACAACTTCATGCATCTCTGTCCCT
99078 ATAAT A AAACTCATAGTTTGCTCAAATATCATGCAATTTGACAAACCAGGCTGATAAGTGATGATAACAAGGGGAAGAAATACACGGACATAAAAGAATAAACACA[ATAAT/A]TAATTAAATACCGCAACAGCAATTACCAATACTTTCGTATACAACTTCATGCATCTCTGTCCCTCTTGCATTCAGGCGCCATGT
99078 C T TATCATGCAATTTGACAAACCAGGCTGATAAGTGATGATAACAAGGGGAAGAAATACACGGACATAAAAGAATAAACACAATAATTAAATACCGCAACAG[C/T]AATTACCAATACTTTCGTATACAACTTCATGCATCTCTGTCCCTCTTGCATTCAGGCGCCATGTTAGGAAACCTCGTCCTATCCGTAC
99078 A T TGGACCAGTCTGTCTTCTCAAGCCCTCCCCTTGTGGCCCAGTCGTCGGCGTTCCATAAGCTGGAGTAGAGCTTCATGGGCTGGTTGAATGGGAATCTTAC[A/T]CCCAAGTCCTTGCTGTTTTTGAATACCCGGATCGGTATGTTGTCTACGAAGAATACAATCTGGTACATGTTCCACAGAATCGAGTACT
99116 A C GATTCCCCAATCCCCTAACGAACTCCTCCATCTTCTCCACGTCTTCCTTCACCAAACCAT[A/C]TACTTCCTCGCATCCATCATTTCTCCATGCGTTCACCAGCATTCTCGTCGCGACTCCGAAGGGTGATACGCAGTTCACCCTGATTCCGTGTTTGCCTAGC
99116 T C GATTCCCCAATCCCCTAACGAACTCCTCCATCTTCTCCACGTCTTCCTTCACCAAACCATA[T/C]ACTTCCTCGCATCCATCATTTCTCCATGCGTTCACCAGCATTCTCGTCGCGACTCCGAAGGGTGATACGCAGTTCACCCTGATTCCGTGTTTGCCTAGCT
99116 G A GATTCCCCAATCCCCTAACGAACTCCTCCATCTTCTCCACGTCTTCCTTCACCAAACCATATACTTCCTCGCATCCATCATTTCTCCATGC[G/A]TTCACCAGCATTCTCGTCGCGACTCCGAAGGGTGATACGCAGTTCACCCTGATTCCGTGTTTGCCTAGCTCGCAGGCAACGTTTTTGGTGAGCCCTACGA
99116 G A CGAACTCCTCCATCTTCTCCACGTCTTCCTTCACCAAACCATATACTTCCTCGCATCCATCATTTCTCCATGCGTTCACCAGCATTCTCGTCGCGACTCC[G/A]AAGGGTGATACGCAGTTCACCCTGATTCCGTGTTTGCCTAGCTCGCAGGCAACGTTTTTGGTGAGCCCTACGATTGCATGTTTCGACGCA
99116 T C GGGGTCCTAACCCTCCCTGCACTCCTGCCACGCTAGCCATTGACACGATCGTACCCGATCTTCTTGAGATCATCGCACGCCCAGCGTGCTTCATCCCCAA[T/C]GCAGCACCTCGCACGTTCACTTTCATCACCTGGTCGAACTCATCAACGTCAAGCTCAGTGATGGTCTTGGTTTCTGTTGTTTGCCTTCCA
99116 C T GCAGCACCTCGCACGTTCACTTTCATCACCTGGTCGAACTCATCAACGTCAAGCTCAGTGATGGTCTTGGTTTCTGTTGTTTGCCTTCCAAGCACACCAG[C/T]AATATTGCATAAAATATCCAGTTTTCCATGCTGTGCGAGCGTGGAACTTATAAGACGCTCCACATCGATTTCTTGAGAGACGTCGCAAT
99116 G A ACCAGCAATATTGCATAAAATATCCAGTTTTCCATGCTGTGCGAGCGTGGAACTTATAAGACGCTCCACATCGATTTCTTGAGAGACGTCGCAATGATGG[G/A]AAGTTACAAAGGGAGGAAGAGAAGCAGCCAAAGCTTCACCTGCAACGTCGTCGATATCTGCTATGATTACTGTGGCTCCATGCCTTG
99116 A G TATTGCATAAAATATCCAGTTTTCCATGCTGTGCGAGCGTGGAACTTATAAGACGCTCCACATCGATTTCTTGAGAGACGTCGCAATGATGGGAAGTTAC[A/G]AAGGGAGGAAGAGAAGCAGCCAAAGCTTCACCTGCAACGTCGTCGATATCTGCTATGATTACTGTGGCTCCATGCCTTGCAAACAG
99116 A G ATTGCATAAAATATCCAGTTTTCCATGCTGTGCGAGCGTGGAACTTATAAGACGCTCCACATCGATTTCTTGAGAGACGTCGCAATGATGGGAAGTTACA[A/G]AGGGAGGAAGAGAAGCAGCCAAAGCTTCACCTGCAACGTCGTCGATATCTGCTATGATTACTGTGGCTCCATGCCTTGCAAACAGA
99118 C T TCGTCACTACCGCTGCCGCCATCGATGACGTCTCCGACATGTCGATCATCGCTTACGACGAAAAGCACGGATTTGGCGGCATCGAGAGAAGCGAAGAGTC[C/T]ATGCTGCAGATGTACGAGCAGTGGCTCGCGAAGCACGGGAAGCAGTACAACGCGCTCGGAGAGAAGGACAAGAGATTCGAAAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99118 G A CGAAGCACGGGAAGCAGTACAACGCGCTCGGAGAGAAGGACAAGAGATTCGAAATATTTAAGGATAATTTGAAATACATCGACGAGCATAATCAGGCGGC[G/A]GATAGAGGCGAGCATTCGTTTCGGTTGGGTCTGAATAAGTTTGCGGATCTGAGTAACGAGGAGTACCGATCCATTTATTTGGGA
99118 C T TGAAGAGGGAGAGGAAGAGTTTGAGGAGCAATCGGTATAAGGTCACAGACGGTGACAGTTTGCCTGATTCTGTTGATTGGAGGGAGAAAGGGGCTGTGGC[C/T]GCTATCAAAGATCAAGGTGGCTGCGGGAGTTGCTGGGCTTTCTCAGCAATAGGAGCAGTTGAAGGGATAAACCAAATTGTCAC
99128 C CA ATAGGAAATCCATACTACCACAATTACTCACCCCTTACTTCACCCCTGACCTTCAAACTACTCAACAAGTCGAAAGCTTCATACATAACAAGAACATAAC[C/CA]AAAAAAACCAACACAACCGACACAACATTTCACGATGCCAAGCTATAAAATCGATCACTGACTAGATACATAACAGATCTATACCCAT
99130 CCTGAACCATGAATGTAA
C AGCAATTTGGCAAACTCGAATGCTTCTTGCATGCTTTTGCCTGAAGCAACTGCTGCACATATTATGGCGCCAGCAGATGAGCCAGCTAACGGTGTTGTAT[C/CCTGAACCATGAATGTAA]CCGAATGTAATCTTTCTCAATCAAAAGCTGAGAAGCTCCAAGATGATACGGGAACAATAATCCAGCAGCA
99130 C G ATGCTATCCCCCAATCGAACCATACGTGACACGATAGCCATCAGCATATCGCCTGTCACGGTTGCTACGGAAAAAGGTTTGCTACGGTTGTTGCCGCCTT[C/G]TGTGGAGTAACAGAGTCTAGGGCTAGGGATCACATACTGTTGCCGAATAATGCGAGAGATTGCTAGCCTTGAATTTAGGAGAGTTT
99130 G A CGAACCATACGTGACACGATAGCCATCAGCATATCGCCTGTCACGGTTGCTACGGAAAAAGGTTTGCTACGGTTGTTGCCGCCTTCTGTGGAGTAACAGA[G/A]TCTAGGGCTAGGGATCACATACTGTTGCCGAATAATGCGAGAGATTGCTAGCCTTGAATTTAGGAGAGTTTTCGCCATTGTTAACA
99136 T C AAGGCGCCCTCCTGAAAAAGGCACAGCCAAGCGTGCCTCCGGGCTTTGATGCAGAGTCTGCCACAGTTAATAAACCAAAGACAAAGGCAGCAAAAAGAAG[T/C]GAGAAGAGAAAGGAGAAGAAACAACAGGCTGCACTTGCTTCTTCATCTGATCAAAGTGGAAAAGATGCAGATTCTGACCAAATT
99136 T C TGGAGACAGTAGCCAATCAAATTACTAATTTATCCATTTTATCAAATTCCGAAGTTTGCAACCTTTCTTCTGATCAAACTGATGCATCTAAATGCGAGTC[T/C]AAAGGTCAAGATATCGATAAAAGAATCCGTGCACTTAAAAAGAAGATACGGATAGCAGAAGCTCAGCTAAA
99140 C T TTTTTTTTTTAATTTGCAAATATAACTGAATAAACATTAATCTATTAAGATACACCACATTCA[C/T]AGGGTAAGGTACAAAAATAAAATACAGAAATATAATGTTATCAAACAAACAGCATGATTGTCTACATAATCACTATAATCACTATAAGGCTTCAGCGTCG
99140 A C ATTAAGAGCAGTAGCATAGAAGTGCTGCCGCGACGGCAGACTGCCAGATCCATGCTGCTTCTGTTTCTATTTAGTTAGCAGTATCAGAAATCGCTCCCAG[A/C]CGGGATTACAAGTCCAAACAAACTGATTTTGTTTAGCGATTTCTATCGGACGTTGCTATAAAGCCGAAATTGAGTATAT
99148 TG T AAGGCCGGATAATGTTTTCACGCACCCGAGGCATGCGGAGACTCTCAAGTCCGTTGGGATTAATCCACGTGGAGTTTGAGGGAAGCGTCAGCGTGGGGGG[TG/T]GGAAGCTTGAGTGGTTGGTGGTAATTTTTGTGAAGTTCGACCCTCTTCTTTTACTTTCTTTGTATTTTCGCATTTTTGGGTTTCTT
99148 C CT GAGTTTGAGGGAAGCGTCAGCGTGGGGGGTGGAAGCTTGAGTGGTTGGTGGTAATTTTTGTGAAGTTCGACCCTCTTCTTTTACTTTCTTTGTATTTTCG[C/CT]ATTTTTGGGTTTCTTGCCGTAAGATATATATGTAATTTATTGTATGTAGGTAAATAAATTTTGTGTTAATGTAAAAAAAAAAAA
99152 C T CAACCTCACATATAGTTTCTTTAGGATCTCCGACCACCACTTGCGTTGTGACCTTAACATTCTTCTCTTCACATATCTGCAATGCATGCCTAATAATTGC[C/T]GCACTTATCTTCTTCTGATGTGCCTCAATTGCTTCTGTAAACGCAGGCACCTCAATGTTGCTCGGCCCACCAAATGGGATAGCGCCTGGAT
99152 C T CTTCTGTAAACGCAGGCACCTCAATGTTGCTCGGCCCACCAAATGGGATAGCGCCTGGATTTAGTCCAGCAGCAATGGATGGGGGAGACTGAACGTGGAG[C/T]ACGACGAATGATCCCTGATCTGACAGACGGAGATTAAGTAGAGCCCAACGTAGAGCGTTCATGCTCTCTTCGCTTGCGTCCACCG
99156 A C ACATAGCTATATACTGGAAAAGCACAAGATCGATGCACTGTTTGTACAATGCTAAGATGAAGGAAATGGATATCTAAAATTTAATGAAATGAAGTAAAAT[A/C]TGCCTCCATTGTAAATAAAATCATAGCATATACCAAAAGGCTCTGAGTGCAGCCATATACAATACAGTAGAGTACTACCCAGTATAT
99156 A C TGGATATCTAAAATTTAATGAAATGAAGTAAAATATGCCTCCATTGTAAATAAAATCATAGCATATACCAAAAGGCTCTGAGTGCAGCCATATACAATAC[A/C]GTAGAGTACTACCCAGTATATGACGAAGACAATTTGAGACATTCACTCTGGCATCTGCGCAAGCAAATATCATTCCAGTTGGGGACTT
99156 G A ATAGCATATACCAAAAGGCTCTGAGTGCAGCCATATACAATACAGTAGAGTACTACCCAGTATATGACGAAGACAATTTGAGACATTCACTCTGGCATCT[G/A]CGCAAGCAAATATCATTCCAGTTGGGGACTTGGTGCTGATTAACACAAACGGTTCGAGCACAAGCATCAGTGCATGCATCCAGCTCA
99156 A G TCTGCCCGTCTCCTTTTGACTCTAATGGCTTGACCTGTAATCACTGCTGGGATGGCTGCACCTAATAATGTCCACCATATGTCCACCATATTTGCTCACA[A/G]ACAAGCTCGAGATTGACTGACGGTAGTAGGCTGAGAAGCGTCAACGGCAGAGGCAGGCAAGGTCGACAGCAGGACAGGCAAGGTTG
99156 A G ATGGCTGCACCTAATAATGTCCACCATATGTCCACCATATTTGCTCACAAACAAGCTCGAGATTGACTGACGGTAGTAGGCTGAGAAGCGTCAACGGCAG[A/G]GGCAGGCAAGGTCGACAGCAGGACAGGCAAGGTTGACGGCGCGCGCACGCGTGAGCGACGGCGGGCAAACCGAGATGTGGTTT
99162 A G TGCGGTGCGACCTTATCCTATAGCAGCTGCTACTGCAACCAGCAGCATGACTGCCAAAGCTGACAGTGGGGGTTGTAAAATTTTCGGGTTCAACATTAAC[A/G]GCATACCTCCAATATCTGAACCATGTAAGCAGCAGGAACCGGAGGTAATAATACACAATCGAACCTTAGAGCCATCCGCAAGCATC
99162 T C CTATAGCAGCTGCTACTGCAACCAGCAGCATGACTGCCAAAGCTGACAGTGGGGGTTGTAAAATTTTCGGGTTCAACATTAACAGCATACCTCCAATATC[T/C]GAACCATGTAAGCAGCAGGAACCGGAGGTAATAATACACAATCGAACCTTAGAGCCATCCGCAAGCATCAGGTCGTCTGAGTCTGC
99162 G A GCAGCATGACTGCCAAAGCTGACAGTGGGGGTTGTAAAATTTTCGGGTTCAACATTAACAGCATACCTCCAATATCTGAACCATGTAAGCAGCAGGAACC[G/A]GAGGTAATAATACACAATCGAACCTTAGAGCCATCCGCAAGCATCAGGTCGTCTGAGTCTGCTTCAGGTAGCGAGAATGAGAAAA
99162 G T AAGCATCAGGTCGTCTGAGTCTGCTTCAGGTAGCGAGAATGAGAAAAACCTTCAAAATAGTATAAGCGATGCTAAAGATCCTCCAAGAAAGTCATCAGGC[G/T]GTTCAACAAGGAGCTGCACAAAGGTACACAAGCAGGGGATTGCTCTGGGTCGATCAGTTGATCTAACTAGGTTCAATGGGTATGA
99168 C G TTTGATCTTTCTATCCCTTTAACTATTCTTTCCCTTACCCTAGCCACTTCCGATTCGCCCTACTTTTACCTACCGCGTCCTCTCGCTTTGGTTTCTTCTT[C/G]TCAGATCTGACTGTGCTTGCTCCCTCTTCTTCAGTGATTCATGCGGTGGGCCTCTAGCCGGAAGTTGCTTCTCTCGAACACTCGTACATGTCT
99168 G A ACTTCCGATTCGCCCTACTTTTACCTACCGCGTCCTCTCGCTTTGGTTTCTTCTTCTCAGATCTGACTGTGCTTGCTCCCTCTTCTTCAGTGATTCATGC[G/A]GTGGGCCTCTAGCCGGAAGTTGCTTCTCTCGAACACTCGTACATGTCTCCTCGAGATCCACCAGCAGTGCTCCTATATCTCCTGTACTGCC
99168 G T CCCTACTTTTACCTACCGCGTCCTCTCGCTTTGGTTTCTTCTTCTCAGATCTGACTGTGCTTGCTCCCTCTTCTTCAGTGATTCATGCGGTGGGCCTCTA[G/T]CCGGAAGTTGCTTCTCTCGAACACTCGTACATGTCTCCTCGAGATCCACCAGCAGTGCTCCTATATCTCCTGTACTGCCTGAAGCTCACCG
99168 C T CCTACCGCGTCCTCTCGCTTTGGTTTCTTCTTCTCAGATCTGACTGTGCTTGCTCCCTCTTCTTCAGTGATTCATGCGGTGGGCCTCTAGCCGGAAGTTG[C/T]TTCTCTCGAACACTCGTACATGTCTCCTCGAGATCCACCAGCAGTGCTCCTATATCTCCTGTACTGCCTGAAGCTCACCGAAAGGCAAAC
99168 G T CACTCGTACATGTCTCCTCGAGATCCACCAGCAGTGCTCCTATATCTCCTGTACTGCCTGAAGCTCACCGAAAGGCAAACTTCGGTTGTGGATCGCTTGC[G/T]CGACGTTCTGGTAATCTTATTGCTTCACAGTTTTACTGGTGGTATCTTGCGTGGTTTAGTTAGCTGAGGCAAATACTGTAGTGTTTGGG
99172 A G CTGAAGCCGTACTCTTATTTGAAAGAAAACGCCAATCTAAAAGCAGAGAAGAACGCGGTGAATTATGGTTGTCGAGTTAGTTTTGCTGAGCTGATGAAAC[A/G]CATAAGGAATGTATCGCTTGATACATCAGACGAGGAATTTGATGAATGGTTCATGGAATTGGACCATTTCTCGGAGTTCGGGTTCA
99172 C T CCAATCTAAAAGCAGAGAAGAACGCGGTGAATTATGGTTGTCGAGTTAGTTTTGCTGAGCTGATGAAACACATAAGGAATGTATCGCTTGATACATCAGA[C/T]GAGGAATTTGATGAATGGTTCATGGAATTGGACCATTTCTCGGAGTTCGGGTTCAAGGTTGCTCCAGTCAAGGATCACCTTACGCA
99172 G GA TCTCGGAGTTCGGGTTCAAGGTTGCTCCAGTCAAGGATCACCTTACGCAGGTCAGAAATATGCTCTATGATGCTAAGAAGTCTAATGATGAGAGAAACTT[G/GA]AGGTGCGTGCCGCGGAGACTGAAGCTTTGGAGCTGACAGAACGTCGTTCCGAGATGCTTAAGTTGGCGGCTGATGTATCAGTGA
99172 A AT CTCGGAGTTCGGGTTCAAGGTTGCTCCAGTCAAGGATCACCTTACGCAGGTCAGAAATATGCTCTATGATGCTAAGAAGTCTAATGATGAGAGAAACTTG[A/AT]GGTGCGTGCCGCGGAGACTGAAGCTTTGGAGCTGACAGAACGTCGTTCCGAGATGCTTAAGTTGGCGGCTGATGTATCAGTGAG
99182 G C TTGCGATGTATTTCTCCATAGCTTCTTCAGGAGACATGGTACCAAGTTTCTGCCATGCATTCCACTTGGCACGAGCTGTCATTTTAAGTGCAGAAGGTTG[G/C]GGAACGGTACAAGGCCCCTCAGTGGCAATCTTGTAAAACCCATATAATTGCAGTTGCAGATCATTCGAAACTTTAGCCGAATTCCTAT
99182 G A TGTATTTCTCCATAGCTTCTTCAGGAGACATGGTACCAAGTTTCTGCCATGCATTCCACTTGGCACGAGCTGTCATTTTAAGTGCAGAAGGTTGGGGAAC[G/A]GTACAAGGCCCCTCAGTGGCAATCTTGTAAAACCCATATAATTGCAGTTGCAGATCATTCGAAACTTTAGCCGAATTCCTATCCGCAG
99190 C CTT AGAATTGGAAAGAAGTGGCGGAGAAAGTGGAGGAAGTTGAGAGTCAGTACATGAAAGGTGAAGCAAAGGAAGTTGTTGGAAGAAGTAAGAGACTCGAGGA[C/CTT]AAGTTTTTTGGATTGAACTGGGAAAAGGATGATTTTATGGAAGTTTTGAATGAGTGGGCGGAAGCACTGGAAGCAAGGAG
99190 G GT GGAAGTTGAGAGTCAGTACATGAAAGGTGAAGCAAAGGAAGTTGTTGGAAGAAGTAAGAGACTCGAGGACAAGTTTTTTGGATTGAACTGGGAAAAGGAT[G/GT]ATTTTATGGAAGTTTTGAATGAGTGGGCGGAAGCACTGGAAGCAAGGAGAGTGGATTGGCTTGCCCTGCTCGTGAGGATTAA
99190 C T GGACAAGTTTTTTGGATTGAACTGGGAAAAGGATGATTTTATGGAAGTTTTGAATGAGTGGGCGGAAGCACTGGAAGCAAGGAGAGTGGATTGGCTTGCC[C/T]TGCTCGTGAGGATTAAAGAGAGGAGCTTGGACTTGTATTTCAAGGTAGCTGAACTTCTTTTGACTGAAGGATCATTTAGGTCAAA
99216 AAG A TGGTTGTGACTTCCTCGATTTCAGCCATGGTTCCCAATTTGAAGTGAAAGGGGTTGTCGATGAGCGGTGCTGGACTGATCTCGATTATTGCATTCAGAAA[AAG/A]AGAAATGGTATCCAGTATCAAAAACTCTAGCAGAGAAGAAAGCATGGGAATATGCTGAAAAATTCAAAATGGACATTGTGGTTA
99216 GA G CGATGAGCGGTGCTGGACTGATCTCGATTATTGCATTCAGAAAAAGAAATGGTATCCAGTATCAAAAACTCTAGCAGAGAAGAAAGCATGGGAATATGCT[GA/G]AAAAATTCAAAATGGACATTGTGGTTATAAATCCATCCACATGCTTGGGTCCTCTGCTTCAACCTGGTCTTAATGCTAGCTCAGCA
99216 A G CATGGGAATATGCTGAAAAATTCAAAATGGACATTGTGGTTATAAATCCATCCACATGCTTGGGTCCTCTGCTTCAACCTGGTCTTAATGCTAGCTCAGC[A/G]GTCCTTCAACAACTGTTACAAGGGTCTGAGGATACTCACGAGTATCACTGGTTAGGCTGCGTGCATGTTCGGGATGTTGCTTCTGCAC
99216 G A CAAAATGGACATTGTGGTTATAAATCCATCCACATGCTTGGGTCCTCTGCTTCAACCTGGTCTTAATGCTAGCTCAGCAGTCCTTCAACAACTGTTACAA[G/A]GGTCTGAGGATACTCACGAGTATCACTGGTTAGGCTGCGTGCATGTTCGGGATGTTGCTTCTGCACAAATCATGCTCATGGAGACTCC
99216 T C CCTCTGGAAGGCATCTCTGCACCAATGGGATTTACCAGTACAAAGACTTTGCAGAACTTGTTGCAAAGCTGTGTCCAGAATACAATGTTCATAGATTTAC[T/C]GGAGAAACCCAGCCAGGACTTATTCCATGTACAGATGCAGCAAAAAAACTACTTGATCTTGGGCTTGTTTTCACTCCAACCGAGGAGA
99216 CA C AAAGACTTTGCAGAACTTGTTGCAAAGCTGTGTCCAGAATACAATGTTCATAGATTTACTGGAGAAACCCAGCCAGGACTTATTCCATGTACAGATGCAG[CA/C]AAAAAAACTACTTGATCTTGGGCTTGTTTTCACTCCAACCGAGGAGACGATCAAAGAAGCAGTGGCTAGTCTCAAAGAGCATGGCT
99216 C T TACAATGTTCATAGATTTACTGGAGAAACCCAGCCAGGACTTATTCCATGTACAGATGCAGCAAAAAAACTACTTGATCTTGGGCTTGTTTTCACTCCAA[C/T]CGAGGAGACGATCAAAGAAGCAGTGGCTAGTCTCAAAGAGCATGGCTTTATTAGACAGCTTAACCTTCAGGCTTGATTTGTACCACTT
99216 C G ACAATGTTCATAGATTTACTGGAGAAACCCAGCCAGGACTTATTCCATGTACAGATGCAGCAAAAAAACTACTTGATCTTGGGCTTGTTTTCACTCCAAC[C/G]GAGGAGACGATCAAAGAAGCAGTGGCTAGTCTCAAAGAGCATGGCTTTATTAGACAGCTTAACCTTCAGGCTTGATTTGTACCACTTT
99216 G A AGAAACCCAGCCAGGACTTATTCCATGTACAGATGCAGCAAAAAAACTACTTGATCTTGGGCTTGTTTTCACTCCAACCGAGGAGACGATCAAAGAAGCA[G/A]TGGCTAGTCTCAAAGAGCATGGCTTTATTAGACAGCTTAACCTTCAGGCTTGATTTGTACCACTTTTTCATTTTGGCGTTAACCGTAT
99216 C T GCTTGTTTTCACTCCAACCGAGGAGACGATCAAAGAAGCAGTGGCTAGTCTCAAAGAGCATGGCTTTATTAGACAGCTTAACCTTCAGGCTTGATTTGTA[C/T]CACTTTTTCATTTTGGCGTTAACCGTATTTATGTCAAATAAAGTGATGGTGTAACAAAGGGGTGATTAGTAATTATTAGTTATTATCGT
99216 G A ACGATCAAAGAAGCAGTGGCTAGTCTCAAAGAGCATGGCTTTATTAGACAGCTTAACCTTCAGGCTTGATTTGTACCACTTTTTCATTTTGGCGTTAACC[G/A]TATTTATGTCAAATAAAGTGATGGTGTAACAAAGGGGTGATTAGTAATTATTAGTTATTATCGTGATTAATT
99236 A AAGCAGG TCCGTAAAGGTAGGATTGCTGAAGCTGCAAGTAAGTCGAGGAGCCGAAGCCCCGGACCAAGGTCTCGTGATGATTATCACCGTGACAGAGATTACAGGAG[A/AAGCAGG]AGCAGAAGCAGGAGCAGGGAAAGGCGTGGTCGGGGCAGGCACAACGAGAGGGAAAGAGATAGATATCGCCACAGA
99236 A G AAGGTAGGATTGCTGAAGCTGCAAGTAAGTCGAGGAGCCGAAGCCCCGGACCAAGGTCTCGTGATGATTATCACCGTGACAGAGATTACAGGAGAAGCAG[A/G]AGCAGGAGCAGGGAAAGGCGTGGTCGGGGCAGGCACAACGAGAGGGAAAGAGATAGATATCGCCACAGAAGGAGCAGCCG
99236 A T CCGAAGCCCCGGACCAAGGTCTCGTGATGATTATCACCGTGACAGAGATTACAGGAGAAGCAGAAGCAGGAGCAGGGAAAGGCGTGGTCGGGGCAGGCAC[A/T]ACGAGAGGGAAAGAGATAGATATCGCCACAGAAGGAGCAGCCGCAGCTTGAGCCCTGACTATAATAGAGGACGCGGAAGAA
99236 C T GGGAAAGGCGTGGTCGGGGCAGGCACAACGAGAGGGAAAGAGATAGATATCGCCACAGAAGGAGCAGCCGCAGCTTGAGCCCTGACTATAATAGAGGACG[C/T]GGAAGAAGGTATGATGATGTAAGAAGCAGGAGGCGGTCCACTGATAGCTTGTCACCTGTTAAACGTAGTCGTGATTCTAGAC
99236 G A AGGGAAAGAGATAGATATCGCCACAGAAGGAGCAGCCGCAGCTTGAGCCCTGACTATAATAGAGGACGCGGAAGAAGGTATGATGATGTAAGAAGCAGGA[G/A]GCGGTCCACTGATAGCTTGTCACCTGTTAAACGTAGTCGTGATTCTAGACGAAGCGTTTCTCCTCATGATAAAGGTGCTGCCAG
99240 G A AAAATGCAAAACTGATAAAGGAGAGGGATACTCTGGCTGTTACTGCAAAGAAATTGGCTCGAGAATTAGCAAAGTTAGAAACATTCAGAAGACATCTGAT[G/A]CAGTCCATAAGTGAGGATAACTCATCTCAAGCTGAATCTGTTGATATAAGCACATACGAACAAAAAGCTCCTGTTTGGAAAGACAG
99242 A G AGAGAGACGACAGAAAAACTGCACCCACCGTGATTATAGACTTGGCGTTGCTTATTATTTGTAGCTGAAATATTCAAGTATTGTGGTCCTGACTTGAGCA[A/G]AAGTGCACAACGTGAGCCTTAAGTACATAGTACATATCTTATATAATGATGGAACGATCTGTTTCTTATGTCATCCAGGTTGCTTGCA
99256 G GA GGCCCGATTGTATTCACTGCCCTAGACGAACAGTTTTTTTTTTCATTTTTGTTGCCCCATCATGTAAAACAACAATCTTTTCACATGCATAAAATTGTAT[G/GA]AAAGTAAAATGACGGACAACAATGACGGACCCTTTTGTTTGCCTTGGCTGCAGCAGCACTCCTCGGCGGATGCAGACACAACGACGG
99256 G A CTTCCATTCGCCATAGCCTCTTCTCGTTGCAAATTGAAACCTTCGCGTTGAATCAAATTGAATCCCTAAACCCCAAATTGATTGAATCCGAAATCGAACT[G/A]AAACCCAAAACTGATAGAAATTGAAATTGAAATCGAACTGAATTATGCTGCCCTCCTTTGCTCGAGCGGCGAGCCGAAGCCTGTCGCG
99268 A G AGGATGAGAGTGTGACTTTTGCAATGTATGGAGATGGCGCTGCGAATCAGGGGCAGTTGTTTGAGGCATTGAATATGAGTGCCTTGTGGGATCTGCCAGT[A/G]ATACTAGTGTGCGAAAATAACCACTATGGAATGGGAACTGCTGAATGGAGAGCAGCAAAGAGTCCTGCTTATTATAAGCGAGGA
99268 C T TGACTTTTGCAATGTATGGAGATGGCGCTGCGAATCAGGGGCAGTTGTTTGAGGCATTGAATATGAGTGCCTTGTGGGATCTGCCAGTAATACTAGTGTG[C/T]GAAAATAACCACTATGGAATGGGAACTGCTGAATGGAGAGCAGCAAAGAGTCCTGCTTATTATAAGCGAGGAGACTATGTTCCTG
99268 C T CAATGTATGGAGATGGCGCTGCGAATCAGGGGCAGTTGTTTGAGGCATTGAATATGAGTGCCTTGTGGGATCTGCCAGTAATACTAGTGTGCGAAAATAA[C/T]CACTATGGAATGGGAACTGCTGAATGGAGAGCAGCAAAGAGTCCTGCTTATTATAAGCGAGGAGACTATGTTCCTGGATTAAAGG
99268 A T CCTTGTGGGATCTGCCAGTAATACTAGTGTGCGAAAATAACCACTATGGAATGGGAACTGCTGAATGGAGAGCAGCAAAGAGTCCTGCTTATTATAAGCG[A/T]GGAGACTATGTTCCTGGATTAAAGGTGGATGGTATGGATGCACTAGCTGTGAAGCAAGCATGTGCATTTGCTAAAGAACACGCTT
99268 C T CTATGGAATGGGAACTGCTGAATGGAGAGCAGCAAAGAGTCCTGCTTATTATAAGCGAGGAGACTATGTTCCTGGATTAAAGGTGGATGGTATGGATGCA[C/T]TAGCTGTGAAGCAAGCATGTGCATTTGCTAAAGAACACGCTTTGAGCAATGGGCCTATTATCTTAGAAATGGATACATATAGATA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99268 T C TGCTTATTATAAGCGAGGAGACTATGTTCCTGGATTAAAGGTGGATGGTATGGATGCACTAGCTGTGAAGCAAGCATGTGCATTTGCTAAAGAACACGCT[T/C]TGAGCAATGGGCCTATTATCTTAGAAATGGATACATATAGATACCATGGTCACTCCATGTCTGATCCTGGAAGCACATATCGTACCC
99268 G A AGCGAGGAGACTATGTTCCTGGATTAAAGGTGGATGGTATGGATGCACTAGCTGTGAAGCAAGCATGTGCATTTGCTAAAGAACACGCTTTGAGCAATGG[G/A]CCTATTATCTTAGAAATGGATACATATAGATACCATGGTCACTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGAT
99268 T C CTATGTTCCTGGATTAAAGGTGGATGGTATGGATGCACTAGCTGTGAAGCAAGCATGTGCATTTGCTAAAGAACACGCTTTGAGCAATGGGCCTATTATC[T/C]TAGAAATGGATACATATAGATACCATGGTCACTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGA
99268 T C AGCAAGCATGTGCATTTGCTAAAGAACACGCTTTGAGCAATGGGCCTATTATCTTAGAAATGGATACATATAGATACCATGGTCACTCCATGTCTGATCC[T/C]GGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTTTC
99268 C T TGGATACATATAGATACCATGGTCACTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAAT[C/T]GAAAGAGTTAGGAAGCTTATACTTTCTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGT
99268 G A ACCATGGTCACTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAA[G/A]CTTATACTTTCTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTG
99268 C G TCACTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATA[C/G]TTTCTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGC
99268 T G CTCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTT[T/G]CTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAA
99268 C A TCCATGTCTGATCCTGGAAGCACATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTTT[C/A]TCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAG
99268 C T CATATCGTACCCGTGATGAGATCAGTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTTTCTCACGATATAGCTACAGCTGC[C/T]GATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACCAGACCCAT
99268 G A GTGGTGTGAGGCAGGAGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTTTCTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACA[G/A]GCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACCAGACCCATCTGAACTATTTACCAATGTTTACGC
99268 A G AGCGTGATCCAATCGAAAGAGTTAGGAAGCTTATACTTTCTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGT[A/G]GACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACCAGACCCATCTGAACTATTTACCAATGTTTACGCCAAAGGCTATGGTGT
99268 A T CTCACGATATAGCTACAGCTGCCGATCTCAAAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACC[A/T]GACCCATCTGAACTATTTACCAATGTTTACGCCAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTG
99268 C T AAGATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACCAGACCCATCTGAACTATTTACCAATGTTTA[C/T]GCCAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTGTTCTTCCTTGAAGAAGCCTTTTTGTAAAGA
99268 C T GATATTGAGAAACAGGCTAGAAAAGAGGTAGACGATGCTATTGCAAAAGCCAAGGAAAGTCCTCAACCAGACCCATCTGAACTATTTACCAATGTTTACG[C/T]CAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTGTTCTTCCTTGAAGAAGCCTTTTTGTAAAGATG
99268 T A CTCAACCAGACCCATCTGAACTATTTACCAATGTTTACGCCAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTGTTCTTCC[T/A]TGAAGAAGCCTTTTTGTAAAGATGTTTTACGGTTTTTTTCTTTTCCTTTACTGTTTAAAACTTGGAAAATAAATGTCTATGTGCAAATG
99268 A G CAGACCCATCTGAACTATTTACCAATGTTTACGCCAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTGTTCTTCCTTGAAG[A/G]AGCCTTTTTGTAAAGATGTTTTACGGTTTTTTTCTTTTCCTTTACTGTTTAAAACTTGGAAAATAAATGTCTATGTGCAAATGGGTACA
99268 GT G GTTTACGCCAAAGGCTATGGTGTTGAGGTATTTGGTGCAGATAGGAAGGAGGTGAGGAGTGTTCTTCCTTGAAGAAGCCTTTTTGTAAAGATGTTTTACG[GT/G]TTTTTTTCTTTTCCTTTACTGTTTAAAACTTGGAAAATAAATGTCTATGTGCAAATGGGTACAAAGTAGTAGTTTATATATTTTTT
99282 C T TCACTCCTAAGCAACATCACACACACACATAATAATATCGACTTCCTTTTGGAGCACAAACTAAACGACATTTGTCTCTTTACATAAGTAACCCTTAAGA[C/T]TGCTTTCTCTGCTATACAGTATAAATCACTAAATGATGAAATAGCTAAAAGAAAGAAATCAATCATTCTTCTGTTTCATCCCAAGCTCAAC
99282 G GA GAGCACAAACTAAACGACATTTGTCTCTTTACATAAGTAACCCTTAAGACTGCTTTCTCTGCTATACAGTATAAATCACTAAATGATGAAATAGCTAAAA[G/GA]AAAGAAATCAATCATTCTTCTGTTTCATCCCAAGCTCAACGAGCATCGTCAACAAAGCCTCGCACATCTCACTAGAATCGGCTTCCAC
99282 T C GGACTTCTGCATCTCGTCTGGTAACCAAACCATCGCTACTTTCTCCGTATCGGAGCTTTAGATGAAGAGCGGTAATGGCCAAGGCAGCTGCTGCGGGGAC[T/C]ACGATGGGGAATTTAATATCGTCGGATTCCAGTAAGAAGTTGGGTACTGGGATCCATGGGAGTTCGGCGTGAGCAACTAGAGACA
99292 G C CTCCCCATCTTCCTCCCCCAACTCCCCATCCCCTCTATATCCCTGCTCGCTCCCATACCCTGATACATCATTTCCCCCTGCTCCTAGCATCATGACATCA[G/C]CACCACAGTGTCCTACACCTCCAAACACCAAACTCTCTCTACTGCCACCATTACAGCTTTCGCTTGCATCTGATCCCCAGCTTCCTCCGCCCT
99292 A G CAGCACCACAGTGTCCTACACCTCCAAACACCAAACTCTCTCTACTGCCACCATTACAGCTTTCGCTTGCATCTGATCCCCAGCTTCCTCCGCCCTCCCC[A/G]TTAATGAAGAACTCTCCACTCGAGTCCGTTCCCCCTGCCATCAAATGGAAATCGGAGCATGTTCCATACGCGACGGATGCACGGCAGTG
99292 T G ATGAAGAACTCTCCACTCGAGTCCGTTCCCCCTGCCATCAAATGGAAATCGGAGCATGTTCCATACGCGACGGATGCACGGCAGTGTGTGTCGCTGCTTC[T/G]ACCAGAGACTGATCGAGAGGCGGTGCCACGCCGCCGCTTTCGGCGCAACCACTGCCTACGATAGCTATGGTTGGATCTTGGGGAA
99292 G T ATCAAATGGAAATCGGAGCATGTTCCATACGCGACGGATGCACGGCAGTGTGTGTCGCTGCTTCTACCAGAGACTGATCGAGAGGCGGTGCCACGCCGCC[G/T]CTTTCGGCGCAACCACTGCCTACGATAGCTATGGTTGGATCTTGGGGAATCGAGGAGAGAGAGCTTGGAGAGATCGAGATCAGA
99292 CT C AGCTATGGTTGGATCTTGGGGAATCGAGGAGAGAGAGCTTGGAGAGATCGAGATCAGAAGCAGGGTTAGGGTTTGTCGACCGATCGGAGCGGCACGGTTT[CT/C]TTTTTTGAATTAGCGGTTGTACTCGAATCGAATGGTCTCCATGAGTGCAGCTGAAGCGTGCACGATTCTATTTTCGAAGCTAGA
99292 C G CGAGATCAGAAGCAGGGTTAGGGTTTGTCGACCGATCGGAGCGGCACGGTTTCTTTTTTGAATTAGCGGTTGTACTCGAATCGAATGGTCTCCATGAGTG[C/G]AGCTGAAGCGTGCACGATTCTATTTTCGAAGCTAGAGCTTTGGGAGCCATAGAAATTAGAAAGTTATTAAATCCATCAATTGGGGT
99300 T C ACACCCGAACCGCCTCGTACACGAACGGCAACCCGTCCCACCCGTTCTTTCCACTTTCTGGTCCGAACATCGGGTGCGTGCAAACGATCCCAAAATCGGA[T/C]GGAAGGACCTCGAGGAAAAGATTTCTAGGAAATTGTTTGACGGACAAAACGTCTACAAAAATGGTGCCGGGTTTGAGCTTGTGAAC
99320 C T AGAAAGCCTCCGGTTATACCCAATAGGCCCAATATTGCTACCACGAGAATCAACAAAAGACTGCATAGTGTCTGGTTTTCACATTCCTAGTGGCACAATT[C/T]TGCTGACTAATGCATATGAGTTGCACAGAAATCCAGAGTTCTGGGATGAACCTTTGAAGTTTAAACCTGAAAGATTTGAATATATAGA
99328 C A TAAGCATCCTACCATCTACAAAATACTGAAGATCCACAACGGTCAGAAGACCGTAGATCGATTCGAGGAGTACAGGGACCACGTTCGGTACAAAGCCGCC[C/A]GGAACGGCGGAGACGAGCGCGTCCTGGCGGACGGGAACGAACGGCTGAGATTCTACTGCACGACGATGCTGTGCGCGGCGGAA
99328 G A AGCATCCTACCATCTACAAAATACTGAAGATCCACAACGGTCAGAAGACCGTAGATCGATTCGAGGAGTACAGGGACCACGTTCGGTACAAAGCCGCCCG[G/A]AACGGCGGAGACGAGCGCGTCCTGGCGGACGGGAACGAACGGCTGAGATTCTACTGCACGACGATGCTGTGCGCGGCGGAAGG
99328 C T GGGACCACGTTCGGTACAAAGCCGCCCGGAACGGCGGAGACGAGCGCGTCCTGGCGGACGGGAACGAACGGCTGAGATTCTACTGCACGACGATGCTGTG[C/T]GCGGCGGAAGGGTGCAGTCACGTGGGAGCGTGCGGGAATCAGTACTGCAGCACGTGCGGGATCGTGAGGTGCGGGTTTTCG
99328 G T ACGTTCGGTACAAAGCCGCCCGGAACGGCGGAGACGAGCGCGTCCTGGCGGACGGGAACGAACGGCTGAGATTCTACTGCACGACGATGCTGTGCGCGGC[G/T]GAAGGGTGCAGTCACGTGGGAGCGTGCGGGAATCAGTACTGCAGCACGTGCGGGATCGTGAGGTGCGGGTTTTCGGGGAAG
99328 C T GCGGAGACGAGCGCGTCCTGGCGGACGGGAACGAACGGCTGAGATTCTACTGCACGACGATGCTGTGCGCGGCGGAAGGGTGCAGTCACGTGGGAGCGTG[C/T]GGGAATCAGTACTGCAGCACGTGCGGGATCGTGAGGTGCGGGTTTTCGGGGAAGCACGTGGAGATGGACGGGGTGGGGAC
99328 G GT GATTCTACTGCACGACGATGCTGTGCGCGGCGGAAGGGTGCAGTCACGTGGGAGCGTGCGGGAATCAGTACTGCAGCACGTGCGGGATCGTGAGGTGCGG[G/GT]TTTTCGGGGAAGCACGTGGAGATGGACGGGGTGGGGACGCACGAGACGAGCTGGGGCGCGCACGTGTCGCTGCCGGAGG
99330 C T ACAGAACTTACCGTTTAGACTCAGTCCTCTGCATTCATCTCTCTCCTCCTTCATTTCAGGAAGACAC[C/T]TCCAGCAATCGCCCGCAACGTCATACACTTCTGCCGATCTCAAGGCGTTCTTCTGTGCATCGTGGCCTCCAGCTACGAAAACTCTTCCACTGGCTTCCGC
99330 T C ACTTACCGTTTAGACTCAGTCCTCTGCATTCATCTCTCTCCTCCTTCATTTCAGGAAGACACCTCCAGCAATCGCCCGCAACGTCATACACTTCTGCCGA[T/C]CTCAAGGCGTTCTTCTGTGCATCGTGGCCTCCAGCTACGAAAACTCTTCCACTGGCTTCCGCGCAGGCGAAGAAGGACCTCGCGGTCGT
99330 C T GACTCAGTCCTCTGCATTCATCTCTCTCCTCCTTCATTTCAGGAAGACACCTCCAGCAATCGCCCGCAACGTCATACACTTCTGCCGATCTCAAGGCGTT[C/T]TTCTGTGCATCGTGGCCTCCAGCTACGAAAACTCTTCCACTGGCTTCCGCGCAGGCGAAGAAGGACCTCGCGGTCGTCATCGGCTTTCC
99330 T C TCATTTCAGGAAGACACCTCCAGCAATCGCCCGCAACGTCATACACTTCTGCCGATCTCAAGGCGTTCTTCTGTGCATCGTGGCCTCCAGCTACGAAAAC[T/C]CTTCCACTGGCTTCCGCGCAGGCGAAGAAGGACCTCGCGGTCGTCATCGGCTTTCCTTCCCGCCAAATCATCGTCCTCAGATCCAAAA
99330 C G ACCTCCAGCAATCGCCCGCAACGTCATACACTTCTGCCGATCTCAAGGCGTTCTTCTGTGCATCGTGGCCTCCAGCTACGAAAACTCTTCCACTGGCTTC[C/G]GCGCAGGCGAAGAAGGACCTCGCGGTCGTCATCGGCTTTCCTTCCCGCCAAATCATCGTCCTCAGATCCAAAATCCGGACCTCCCTAA
99330 G T CGGACCTCCCTAATCGGATCCAGCGTTTCCGGGTCCCACCCGCCGAGAAGAACCAGATCGGTCCCCACAACCACGGACTGAGTGAACACCGGCACGGAGT[G/T]CAAAACCTTTTGCCACGCTGCGAGCGTGGAGTTGAACAGATTCAGCGAGTATGCAGGCTTTTTCACGGCGATTGGTTCCTTGCAT
99336 C T AAGGTAACTAATCAATCTACAAAAGTACATCGCACAGAAGAGTGGATTGGAACAATATCATCTTTTTGACACATCACACTTTGAAATGCCTAAAACATCC[C/T]AGAATCTTTAGCAATTTGCAGAACTTTGTTCTTTACCATCTAAATGCATAATCATCCAGCTGAGTTCTCATGCAAAATCACATATTCCCG
99340 T A AATGCAACAAGCACTACAAACTAGCATGCCACCAAACTAAAATAGTTAAGAAAGCATTGTCAGCAGGCTGGCCGAAGTTTTCTCAATACTACTCCAAAAC[T/A]TTATTTAAGATTCAGTTCGCCTTTAAGTACCTTTGCTTGCTGGAAACTAATGGTGCATCATATTCTATCAAATATCTTCTACACCCTGAG
CTTTGCTTGCTGGAAACTAATGGTGCATCATATTCTATCAAATATCTTCTAC
99340 T CCACCAAACTAAAATAGTTAAGAAAGCATTGTCAGCAGGCTGGCCGAAGTTTTCTCAATACTACTCCAAAACTTTATTTAAGATTCAGTTCGCCTTTAAG[TACCTTTGCTTGCTGGAAACTAATGGTGCATCATATTCTATCAAATATCTTCTAC/T]ACCTTTGCTTGCTGGAAACTAATGGTGCATCATATTC
99342 G A GCCGTGCACTTGACCTTCCTGTCTATTTTGGCGATGCAGGGAGTCGAGAGGTCCTACATAAAGTTGGGGCAGAAAGAGCTTGTGCTGCTGCAATCACTTT[G/A]GATACTCCAGGTGCAAACTACAGAACTGTTTGGGCATTGAGCAAATATTTCCCAAATGTAAAGACATTTGTCCGTGCGCATGATGTT
99346 A T GAAATCGGAATTGAAGCGCCGTAGTTCTCAGGATTCGACCGTAATTCCTCCCTCCTCAGCCTACACGCTATTCAGAAAAGAGCACGGCGTCGGATTCAGC[A/T]TTTTCAGCCTGATTTCCTCTCAGTCACAACTCCTGCTAGCACGCGGTACTTATTTCGTCTCTAGCAGCCCAAATCTTTCTGCCGGCCCT
99354 G A GTGCAGACTCTTGTGTTGCCTGCAATCCATCAACTTCTTAAAACATGGACGACTTCATTTGGGTTCAAAGAGATGGGCATAGCTGAAAGAGTATAGCTTG[G/A]ATTCACAACATTGATCTTCTTGGATTCAGAGAAAGATCAAGATAGGCACAGCTATAAACAGCGGGAGCATGATCGCGATAGAGAGC
99354 T C AGATGGGCATAGCTGAAAGAGTATAGCTTGGATTCACAACATTGATCTTCTTGGATTCAGAGAAAGATCAAGATAGGCACAGCTATAAACAGCGGGAGCA[T/C]GATCGCGATAGAGAGCATAGGCGCACCGGTGATGACGAACGCAACCATATCTCTCGCGATGATTGACACCATCGGGATCGTTATG
99354 A G ACATTGATCTTCTTGGATTCAGAGAAAGATCAAGATAGGCACAGCTATAAACAGCGGGAGCATGATCGCGATAGAGAGCATAGGCGCACCGGTGATGACG[A/G]ACGCAACCATATCTCTCGCGATGATTGACACCATCGGGATCGTTATGACTCTTCACCTGAAAAGGATAGAGATAGGGTTCACCAT
99354 A C GATCTTCTTGGATTCAGAGAAAGATCAAGATAGGCACAGCTATAAACAGCGGGAGCATGATCGCGATAGAGAGCATAGGCGCACCGGTGATGACGAACGC[A/C]ACCATATCTCTCGCGATGATTGACACCATCGGGATCGTTATGACTCTTCACCTGAAAAGGATAGAGATAGGGTTCACCATTCTTC
99354 T C AGATCAAGATAGGCACAGCTATAAACAGCGGGAGCATGATCGCGATAGAGAGCATAGGCGCACCGGTGATGACGAACGCAACCATATCTCTCGCGATGAT[T/C]GACACCATCGGGATCGTTATGACTCTTCACCTGAAAAGGATAGAGATAGGGTTCACCATTCTTCCAGAAAAAGGAAAGAGCACG
99354 T G CTATAAACAGCGGGAGCATGATCGCGATAGAGAGCATAGGCGCACCGGTGATGACGAACGCAACCATATCTCTCGCGATGATTGACACCATCGGGATCGT[T/G]ATGACTCTTCACCTGAAAAGGATAGAGATAGGGTTCACCATTCTTCCAGAAAAAGGAAAGAGCACGACCATAGTTTTGAGGAATA
99356 A G TGTTGGCCTACTGGGTTCATTTGATCGAATTTCAACTTCAAAACGTTTTTAGCTCATTCCGATCATCCGAGCTTCTGTGCAGAATTTTTCTTCTCAAAA[A/G]ATGGCGTTTCAGAAGATCAAAGTCGCGAATCCAATCGTCGAAATGGACGGTGATGAAATGACTAGGATCTTTTGGAAATCAATTAAAGAC
99356 G A TCAGGAATATATTGAATGGCACTGTATTTAGAGAGCCAATTATCTGCAAAAATGTCCCACGTCTTGTTCCAGGATGGACAAAACCCATCTGTATTGGAAG[G/A]CATGCTTTCGGTGACCAGTATAGAGCTACCGATGTCGTTATTAAAGGACCTGGGAAACTCAAATTAGTCTATGAAGGAGCAGAACAG
99380 T C AGCCCATCCATCTTCCTGTTGTTATTTGTTTTAATGGCTGTAAGCAGACCCAGCGGAATATTCATTTGAAGACCATAACTTATTGAGAAGTATAAAATCT[T/C]CTCATGCATTTGGCCAACATCGAAAAAGTAATGCTGCTTGCTTCTCAGTTAAAAGTGCCAGAAGATAGCAAAACATTTTTTCCATGTTGC
99380 T C CGAAAAAGTAATGCTGCTTGCTTCTCAGTTAAAAGTGCCAGAAGATAGCAAAACATTTTTTCCATGTTGCTTATAAAACTCTCCGTGTGTAGCTCTTATT[T/C]CTGTGAAATCAATGGTTTCCATTATGCTACTGAGGTTACACACTTGAACTAAATATTGCATTTATTGTTCCTGCTATTCTAATTTTGTTTTT
99394 G T TTGCTCGATCGTTTCCAAAATAGTAACTAGGCGTCATAATCTCGGTGGAAACCACAAGAGCGTTTGAGTTAGGGTGCACTTGTAGCAGGTCCCGTGCCAG[G/T]TCTATTGAAATCGGCCCAGCACTGCATCCCATACCCGACAGATTAAAGCTCCGAACACCGCTTCTCATTTTGTACTTGTTGACGATCA
99394 T C GATCGTTTCCAAAATAGTAACTAGGCGTCATAATCTCGGTGGAAACCACAAGAGCGTTTGAGTTAGGGTGCACTTGTAGCAGGTCCCGTGCCAGGTCTAT[T/C]GAAATCGGCCCAGCACTGCATCCCATACCCGACAGATTAAAGCTCCGAACACCGCTTCTCATTTTGTACTTGTTGACGATCATAGCG
99394 T A CACTTGTAGCAGGTCCCGTGCCAGGTCTATTGAAATCGGCCCAGCACTGCATCCCATACCCGACAGATTAAAGCTCCGAACACCGCTTCTCATTTTGTAC[T/A]TGTTGACGATCATAGCGGTAAGAGATGGAGCCGGAGAAAAAATGCTACAATTTAGAACCAATATATCAATGTCCTTTGGTTCAAATTT
99394 GA G GGTAAGAGATGGAGCCGGAGAAAAAATGCTACAATTTAGAACCAATATATCAATGTCCTTTGGTTCAAATTTGGTTTTCTCAATAAGTTTGTCGATGGCC[GA/G]AAAAAATGGCTACTTGAGCCTCCTCGCGTGCGATCTCCAAAGTAGGTCTGGGCGGCAAGTAATGATTGGCGGGAGGTAGGCACG
99394 A AG ACCTTTCTAGAATGCGCGTTTGGAAATGAACCGCCTTGGTGTCCGGGTTTATGAGACGGATGTGCTCCATGAATGTAGCGAAGGGTACGCGGCAACAACT[A/AG]GGGGGTGTGAGTAGCGCATAGTCAACCAGATAGACTTGGCGTGGCCGTGACATGAAGTAGATTATCACAAGCATGAGGGGGA
99396 CA C CAACACTCCAGACACATTCAAATAATACTGTCAAAATATGAAGGGTTCCTACGCCTATTGTACTGTAAAAGGCTCCCATAAGTCCGATCCCATACACCGA[CA/C]AAAAATAGCCTCAGTATCAGGGCTAAAAGACAGACCAGAAATTTCACCAAAGAAATCCAGCTCTTGACACCTTCGATATCCGCTGCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99408 AT A AATCGGGAAGGAAAGCTCCGGAATGTACAAACTCGTCTAGCGCTTGTTGAACGAACGCCTGCTTCCATGCATTTGTTCAACAAACCCCTAGATTATTATA[AT/A]TTTTTTTCCGTTAAAATCCGCTGCATACTTTTCTTCTTTTCCTCACTCTTTCGCGTTTCCAGATTTCCAAACGAGCTTCTCTCCCAAAAT
99412 A G TATGGTTGCAAGAAGAAGACCCCTTCTGCCTGATATGTCCATGAACCTCATGGCAACACCAACTGATGGAAGCATTAGTAATGCTATTAGAGTGCTTATT[A/G]GAATTGATGCAGAGTCAGGGCTGATGCCTACGTCTGGAAGAAGATCTTCTATCCCTGCTCTTTTAAATATTTGAGGAGCATAGTATA
99412 T C CAAGAAGAAGACCCCTTCTGCCTGATATGTCCATGAACCTCATGGCAACACCAACTGATGGAAGCATTAGTAATGCTATTAGAGTGCTTATTAGAATTGA[T/C]GCAGAGTCAGGGCTGATGCCTACGTCTGGAAGAAGATCTTCTATCCCTGCTCTTTTAAATATTTGAGGAGCATAGTATAGAACTCCG
99420 A G AAAGATTAGAAAGAATAGAATTCGGAATCGAAGTCACGCCAGCATTGGTGGCGATGTGGATTTGCTCAGTAATGATGGTGGTGCTGATGACATTGTAAAA[A/G]GCAGCGGTAAAGAAAGTAATGGTGGTGCTGCTAAGGATGTCGTGAACGTGGATCCAGCTCCTATTCGGGAAGATAAGGTTCCCA
99430 T G TGGAAATCATGAAACCACCTCAGAGTGATGATCCAGCTGCAAAGAATTCTCAAATTGTTTTGAAGTTTCTGCCTCTAATGATTGGTTACTTCTCATTATC[T/G]GTTCCATCTGGATTATCAATTTACTGGTTTACAAACAACCTGCTAAGTACAGCACAACAAGTATGGTTAAAGAAACTAGGGG
99438 A G CCACCCCGAAAATCGTCGTCACCAAGGAGCCGCCATCTACCTGCTGTGTCGCCAACACCGCACCACTCGCAGTCAGCAGACTCGGTACTCCGTAACTCCA[A/G]GAAGTCGCCACCGTCTACACCACGTGTGGAACCGCCAGCGTGCACTTCTTCATCTCTACGCTCTATCATCACAGCGACGGACTTGAT
99438 G A CGTCTACACCACGTGTGGAACCGCCAGCGTGCACTTCTTCATCTCTACGCTCTATCATCACAGCGACGGACTTGATGAAGTACATAGTTGAAGCTGAAAT[G/A]GAATTGTTGAAGCCGACAATGACAATCAGCTTTCTTCCAAGACATGTGCATGGGTGTTTATTACCGTCTGTTATTTGGTATCATAACA
99438 C T CCAGCGTGCACTTCTTCATCTCTACGCTCTATCATCACAGCGACGGACTTGATGAAGTACATAGTTGAAGCTGAAATGGAATTGTTGAAGCCGACAATGA[C/T]AATCAGCTTTCTTCCAAGACATGTGCATGGGTGTTTATTACCGTCTGTTATTTGGTATCATAACAAGATCAAAAAATATTTGGAGGTTC
99438 C A CTCTATCATCACAGCGACGGACTTGATGAAGTACATAGTTGAAGCTGAAATGGAATTGTTGAAGCCGACAATGACAATCAGCTTTCTTCCAAGACATGTG[C/A]ATGGGTGTTTATTACCGTCTGTTATTTGGTATCATAACAAGATCAAAAAATATTTGGAGGTTCATAACTTGTTATACTGACAGATTTG
99438 G A CGGACTTGATGAAGTACATAGTTGAAGCTGAAATGGAATTGTTGAAGCCGACAATGACAATCAGCTTTCTTCCAAGACATGTGCATGGGTGTTTATTACC[G/A]TCTGTTATTTGGTATCATAACAAGATCAAAAAATATTTGGAGGTTCATAACTTGTTATACTGACAGATTTGACTTTCATAGTTGTTTAT
99438 G A TGAAGCCGACAATGACAATCAGCTTTCTTCCAAGACATGTGCATGGGTGTTTATTACCGTCTGTTATTTGGTATCATAACAAGATCAAAAAATATTTGGA[G/A]GTTCATAACTTGTTATACTGACAGATTTGACTTTCATAGTTGTTTATTATGTTTTATCTAAAGGATTTGTTATGTTCAGTTGCCTGCAAA
99442 T A AGAGAATCCTTTGTTAGGTCCTTCTTCTTATACGCTAGAGAAACTGGGAGCTCTTAACTGGGATAAAGTGGTGCGTGAGCATGAAGGATGGCGGCTTGTT[T/A]CGTGTATTTGGTTGCATGCTGGGGTTATTCATTTAGTGACAAATATGCTGAGCTTGGTTTTCATTGGTATCCGACTTGAGCAGCAAT
99442 A G GGTGCGTGAGCATGAAGGATGGCGGCTTGTTTCGTGTATTTGGTTGCATGCTGGGGTTATTCATTTAGTGACAAATATGCTGAGCTTGGTTTTCATTGGT[A/G]TCCGACTTGAGCAGCAATTTGGGTTTATTCGAATTGGTGCAGTATATCTTATATCAGGATTTGGCGGCAGCATCCTCTCTACTCTATT
99442 C T CAGGATTTGGCGGCAGCATCCTCTCTACTCTATTTACCAGAAACAGTATTTCAGTTGGTGCATCTGGTGCATTATTTGGACTTCTTGGAGCAATGTTGTC[C/T]GAGCTCTTTACAAACTGGACTATATATACAAACAAAGCTGCCGCTTTACTTACTCTTATTGTGGTCGTCGCAATAAACTTGGCTGTTGG
99470 G A TAGGCAAAAATTGAGCCACTTCAAATAGATTCTTCTTCTTGCTTTTCTTCACCTTCGCAGCCTCTGTCGTGTCCGACGGAACCGGTGCTGAAGATGAAGG[G/A]GACAAAGTACTCAGCATTTTGATTTGAGAGATAGATCTTCGTAATAAAGAGAGAGAAGTCTGGGTTACTGATTTATTCGTCATGGCAG
99520 AG A TAACTCATGATTTTGATTGTCTCCTGGAGATGAATTCTAGGGGTTAAATGCTTTAAAATTTGGTCATCACCATCATCTTTTAGCTTCCTCTTCC[AG/A]GTTTTAATTTTCGGGGTTTTCGATTCTCTGAATACTTGCTCTTCTGTCTTCTATGCTTCCTTAAAGAAACGGGTGTCTCTATTTTGCCACCAACCTG
99520 C T CATCACCATCATCTTTTAGCTTCCTCTTCCAGTTTTAATTTTCGGGGTTTTCGATTCTCTGAATACTTGCTCTTCTGTCTTCTATGCTTCCTTAAAGAAA[C/T]GGGTGTCTCTATTTTGCCACCAACCTGAGAGGAGTCGGCTTCTGCTCCTGTGTCTTCATAAGATTTATAGGACTGTATTTTGTTGTGCCCCT
99520 T A TCATCTTTTAGCTTCCTCTTCCAGTTTTAATTTTCGGGGTTTTCGATTCTCTGAATACTTGCTCTTCTGTCTTCTATGCTTCCTTAAAGAAACGGGTGTC[T/A]CTATTTTGCCACCAACCTGAGAGGAGTCGGCTTCTGCTCCTGTGTCTTCATAAGATTTATAGGACTGTATTTTGTTGTGCCCCTCTGAGTTC
99520 C A GAGAGGAGTCGGCTTCTGCTCCTGTGTCTTCATAAGATTTATAGGACTGTATTTTGTTGTGCCCCTCTGAGTTCACGACATAATTGTAGGAATTAGGGAT[C/A]AAATGTTTAGAATTTTTTTATTAGCATCGGCCTTTAACTTTTGTTTAGCTTTCGACCGCAAACTGTTTTGATCATGTACCTCCTCCTTTGA
99520 A AGT CTTCTGCTCCTGTGTCTTCATAAGATTTATAGGACTGTATTTTGTTGTGCCCCTCTGAGTTCACGACATAATTGTAGGAATTAGGGATCAAATGTTTAGA[A/AGT]TTTTTTTATTAGCATCGGCCTTTAACTTTTGTTTAGCTTTCGACCGCAAACTGTTTTGATCATGTACCTCCTCCTTTGACTGGAAATGG
99526 G A TTTGATTGAGACGGGTGCGTACTCCAAAGAGGCGAGGCGAATTGTTCATGCTGTGCGACGTACAGTCGTGCTACGACGTAAGCTGACATCATCTGTCGTA[G/A]CGAGGTTCCTGTCCACTGTTTTAGTGCCGGGATCGGAGGCTTTTACCAAGCTATCTTCATATACTCCAAAGGAAGATGACCACTCC
99532 AG A TAACTGTTTCAATGTGGACGAGATCATCAGTCTGGCTCTCGAATCACGCCAAAAGGGAAGCGGTGATGGTGATGGTGCTGATGGAGTTGATTGTTTGGTT[AG/A]GGGTAGAAAAATGGAAGGAGGGTGAAGAATGGCATGTGAAGGCGCTTGACACGGTGAGAGCAATGCTAGGCGTTATAGAGGT
99532 GA G TTTCAATGTGGACGAGATCATCAGTCTGGCTCTCGAATCACGCCAAAAGGGAAGCGGTGATGGTGATGGTGCTGATGGAGTTGATTGTTTGGTTAGGGTA[GA/G]AAAAATGGAAGGAGGGTGAAGAATGGCATGTGAAGGCGCTTGACACGGTGAGAGCAATGCTAGGCGTTATAGAGGTAGTGG
99534 T TA TTTTAAATTCTTAGAATGCTCGTACTCATTTATGGTACAAATTACAGAGATAAATTGCATATGATTGCATTGCAATACATACCTGTAGGCAAAAAATATG[T/TA]AAAAAAACAGAGAATCATATAGGTTACAGAGAAGAAACTTGGACAAGCAGCTTATGCAAAGCTTGAGGTTTAGAGAAAAACGGACA
99538 G A TCATTAGAGAATATAGAGGCTTGAAAGAGATGAGGGCTCCAACTAGCCGTGAAAGAGGGGTTTCACCGGCCCAGACTGGTCTATCCAGTAGGCCTTCTTC[G/A]GGTGTAGAGGAGAGTGAAGAAGAAGAAGAAGGCGAAGAAGCATTTGGAGAAGGTAATTGATGCCGTGATTTTCTGAGGTAGCT
99546 CT C TGGAGCTTTCTGTACCTCTTCCGGCCGCCGCACCGGCCGTTGATTATGTTCGGCAGACAGTTCTCTGATGTTGAAACGTTGGGATGTCTGATTTTAACGA[CT/C]TTTTTTTGTGGTATTTCTGACGTCGGTTGGATCGAATTTGATGTCGGCGCTTGCTGTAGGGGCGGGGATCGTGGGTGTACATGGTG
99560 A G TTCAGCTCACACGAGAGCTCAACCACAAATCCGACGGCGAAACAATTCGTTGGCTGCTGGAGCACGCCGAACCGGCGATCATCGCCGCGACGGGCACTGG[A/G]ACGGTACCTGCGATCGCGACGACTGTGGATGGGACTTTGAAGATTCCTACCACAGCACCGGAAAGCGCTTCGGTAGTTTCCTCG
99578 G A AGTCGGATGTGATTGGGAAGCATGTCATTTTGGTCGAAGACATTGTAGACACTGGAAATACCCTTTCACATCTTATATCACATGTGAAATCAAAGGGAGC[G/A]AGATCCATATCTGTGTGCACATTCCTCGATAAAGCAGCAAAAAGACAAGTTCTTCTGCAACTCCCAGGGGAGGGAAAGTTCTACCG
99578 G A GGAAGCATGTCATTTTGGTCGAAGACATTGTAGACACTGGAAATACCCTTTCACATCTTATATCACATGTGAAATCAAAGGGAGCGAGATCCATATCTGT[G/A]TGCACATTCCTCGATAAAGCAGCAAAAAGACAAGTTCTTCTGCAACTCCCAGGGGAGGGAAAGTTCTACCGTGGGTTTGAGTGCCC
99578 C T AAGCAGCAAAAAGACAAGTTCTTCTGCAACTCCCAGGGGAGGGAAAGTTCTACCGTGGGTTTGAGTGCCCAGATTCATTTGTGGTGGGGTATGGAATGGA[C/T]TTTGCCGAGCAGTACCGTAATTTGCCGTATATTGGGGTCCTTAAACCTGAAAAATACTCTTGAGGGTATAGCTTCAGGGTTCATCG
99578 C A TTGCCGAGCAGTACCGTAATTTGCCGTATATTGGGGTCCTTAAACCTGAAAAATACTCTTGAGGGTATAGCTTCAGGGTTCATCGTTGAACAAGTCCATT[C/A]TTTTGTTAGGAAATTTTGTTTTGAGAAGTTTATACTATTTATACTGGCTAGTTTTGGAAAAGATTAAAAAAAAAAAAAGGCC
99586 C T TGGCTTTGCATACAGGCAGCATCGCAACAGAGGCTGCCTCGGCCACTTCTCCGTACCTCAG[C/T]CTCACCACCGGCAGCCTTGTCTTAATCGCTGTTTCTTCATCCTCTATTGCTCCGTTCCCTTTTCCGGTCACTCTTTGTAACTCGTGCTCCACTTTTTTCT
99586 CT C TACCTCAGCCTCACCACCGGCAGCCTTGTCTTAATCGCTGTTTCTTCATCCTCTATTGCTCCGTTCCCTTTTCCGGTCACTCTTTGTAACTCGTGCTCCA[CT/C]TTTTTTCTTTGCGTTTTCGGATTCTGCGACTTCTAGAGACTTCTCCAACCACGTGATTTTATCGGCTATCGCTAATGATTCTTTGCTCAACC
99586 T C TAATCGCTGTTTCTTCATCCTCTATTGCTCCGTTCCCTTTTCCGGTCACTCTTTGTAACTCGTGCTCCACTTTTTTCTTTGCGTTTTCGGATTCTGCGAC[T/C]TCTAGAGACTTCTCCAACCACGTGATTTTATCGGCTATCGCTAATGATTCTTTGCTCAACCGAAAGTAGGTGAAGGAGAGACAGTCAGCGG
99600 G A ATGTAAAAACTACTCAATATTTTAAGTAAGCTAGTACCTCAAGAAGAGAAGCAGCAAACTCCATCTGAAGTTCCTCGTCGATAGTAAAGAAAAGAGGCAC[G/A]TGCACAAAGAGAGATTTAATTTTATGCTCCTCAGCAAATCGAAGAGAGTGGTAGTAAATGTAATTACATACAAATCTTCCAGCATCA
99600 C T GTCTCCCGCACTCGCATAATGCCTCCATCAGAAGGGAAAATAGGAACTCTCTGGGGTTTCCATCCTAGCTCGTCTGGACAGCGAAAAGTAGCCTCGTTTA[C/T]AGCTTGTGTTTCAATAGCGAACCTTGATGCACCACTATTAACACCAAAATGAAGCCAAATAACACGTCCAGTGTCCGGAGAACTGGT
99600 G A TGCCTCCATCAGAAGGGAAAATAGGAACTCTCTGGGGTTTCCATCCTAGCTCGTCTGGACAGCGAAAAGTAGCCTCGTTTACAGCTTGTGTTTCAATAGC[G/A]AACCTTGATGCACCACTATTAACACCAAAATGAAGCCAAATAACACGTCCAGTGTCCGGAGAACTGGTTTCATCAGAATCTACAGCT
99602 G A ATCGGAGGAGTATTTGGGGAAATGCTGCAGCTTGCATTTCCGGTTTCATCCTCTGACCATTTCCATGCTCCATTAGATGGTAATTCAATTGTCCTGTTGA[G/A]TGCTGCAGTTCTTCTGAGCTTTGTTGGAGTTGAAGATTCATCAGAATCCGACCCGTTATGAAGCTCACGACCTGTTTTGGGTTTCAGTG
99604 G T TCAATGTGTATATGTCTGTGTAAACTATTGTAGCATTCTTCAGTCTAGACCTCATTTCATCACACAGAGCAGTCAAACCTTGATTGAATTCCTTTGCAGC[G/T]TTGTTCAATGAAATAATGCATCCATTTGAGTCGATATCGTTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAAGGGA
99604 G A TCAGTCTAGACCTCATTTCATCACACAGAGCAGTCAAACCTTGATTGAATTCCTTTGCAGCGTTGTTCAATGAAATAATGCATCCATTTGAGTCGATATC[G/A]TTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAAGGGACCCGTGTTGTGCACCCAAAATTTTCTGCCACCAGAATCA
99604 A G TCATCACACAGAGCAGTCAAACCTTGATTGAATTCCTTTGCAGCGTTGTTCAATGAAATAATGCATCCATTTGAGTCGATATCGTTGTCATTTTTTCTAG[A/G]TACAACAAGCTTTTCAGGTAGACAACCCAAGGGACCCGTGTTGTGCACCCAAAATTTTCTGCCACCAGAATCATATATTGTCATAAAAG
99604 G A ATTCCTTTGCAGCGTTGTTCAATGAAATAATGCATCCATTTGAGTCGATATCGTTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAA[G/A]GGACCCGTGTTGTGCACCCAAAATTTTCTGCCACCAGAATCATATATTGTCATAAAAGCTAGTTTTATCTCGGAAAGAGCATAAGGGAT
99604 C T TTGCAGCGTTGTTCAATGAAATAATGCATCCATTTGAGTCGATATCGTTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAAGGGACC[C/T]GTGTTGTGCACCCAAAATTTTCTGCCACCAGAATCATATATTGTCATAAAAGCTAGTTTTATCTCGGAAAGAGCATAAGGGATAGTCTT
99604 A G ATCCATTTGAGTCGATATCGTTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAAGGGACCCGTGTTGTGCACCCAAAATTTTCTGCC[A/G]CCAGAATCATATATTGTCATAAAAGCTAGTTTTATCTCGGAAAGAGCATAAGGGATAGTCTTATGTATCACTTCATCAAGCTTCAAGTT
99604 A G GTTGTCATTTTTTCTAGATACAACAAGCTTTTCAGGTAGACAACCCAAGGGACCCGTGTTGTGCACCCAAAATTTTCTGCCACCAGAATCATATATTGTC[A/G]TAAAAGCTAGTTTTATCTCGGAAAGAGCATAAGGGATAGTCTTATGTATCACTTCATCAAGCTTCAAGTTGTGGGCAAAAGCCTTAGCA
99606 C T AAACTTTCACTATCTCACTTCCATTCCCTACTCAGTTGGCCTCTTAGTGTCACTAGAAGAACTCGACATAAGCTACAATAAGATAACACACCTTCCGAAT[C/T]CACTGGCTTGTTTGACAAAGCTTTGCAAGTTCGAAGCAGAAGGAAACCCCATCGTTTTCCCACCTACGGAAGTGGTGGAGCAAGGCGT
99606 C T CAAAGCTTTGCAAGTTCGAAGCAGAAGGAAACCCCATCGTTTTCCCACCTACGGAAGTGGTGGAGCAAGGCGTGGAAGCGGTAAGGCAGTATTTGAGCGC[C/T]AGGATCAACATGGAGGAGAAGGACATTGTTAAGAGCTTGAACAAGAGCAAGAAGAAACCGTGGTTTGTTAAGCTTGCGAGGCA
99606 A G GACATTGTTAAGAGCTTGAACAAGAGCAAGAAGAAACCGTGGTTTGTTAAGCTTGCGAGGCATGGTACGTTTGGGGGCAGGACCGTGCATGATAGCGATG[A/G]GCTTTTGCTTCCGGAACGTCGATCGGTTGACGAGCTTGCTACTCCGAGATATGGGTTGTTTTCTCCTTTGAGGATCTTTTCGCCTA
99606 C T TGTTTTCTCCTTTGAGGATCTTTTCGCCTAAGAGGGTTGGTAAGAAGCTGAGCGTGTAGTGATGCACTTCCATGGTGTTTGGTTTGTTTGTGATGAGGAG[C/T]GTGGGTTGTGTGTATGATATAATGATGTAAATACCATTGTAGGGTACACTCACTGTTGTGTAAGTGGCTATATGTTGACAGGGTATG
99606 A C AGGATCTTTTCGCCTAAGAGGGTTGGTAAGAAGCTGAGCGTGTAGTGATGCACTTCCATGGTGTTTGGTTTGTTTGTGATGAGGAGCGTGGGTTGTGTGT[A/C]TGATATAATGATGTAAATACCATTGTAGGGTACACTCACTGTTGTGTAAGTGGCTATATGTTGACAGGGTATGTGTGTCTGTTTTAG
99606 T A GGTGTTTGGTTTGTTTGTGATGAGGAGCGTGGGTTGTGTGTATGATATAATGATGTAAATACCATTGTAGGGTACACTCACTGTTGTGTAAGTGGCTATA[T/A]GTTGACAGGGTATGTGTGTCTGTTTTAGACTGAAATTCCTAATAAACGCTGAGCTGTTAGAGCTGTTAATATTAAAAAAAAAAAAAA
99630 C G TCAAGCAATAATTAATGGATTGGTATTCATGGCTATCAAACACAAAGCTAGAGCCAACATCAGTCTACAACTACTCCTTAGTATTCGCAGACAACGAGCT[C/G]GAAGAAGAAGACATCGCCCACTTCGACCACGACTTCCTTCAAAGCATGGGCATTTCAATCGCGAAGCACCGTTTGGAGATCCTGAAG
99630 T C ACACAAAGCTAGAGCCAACATCAGTCTACAACTACTCCTTAGTATTCGCAGACAACGAGCTCGAAGAAGAAGACATCGCCCACTTCGACCACGACTTCCT[T/C]CAAAGCATGGGCATTTCAATCGCGAAGCACCGTTTGGAGATCCTGAAGTTGTCGAAAAAGCATAGCAGAAGGAGACGTATGCTATC
99630 A G TCGACCACGACTTCCTTCAAAGCATGGGCATTTCAATCGCGAAGCACCGTTTGGAGATCCTGAAGTTGTCGAAAAAGCATAGCAGAAGGAGACGTATGCT[A/G]TCGTTTCCTCCTATAACAAAAATGTTGGTGGGTGCCTTTAGTAGGTCTAAGCAACGCGTGGTGAGGTACTTTAACACTGCGGTGGT
99630 C T TAGTTGCTGTGACCCCGAGTAAAAAGAAGGGCAGTGATGCAGGGGTGAAAAGGAATAGGAGGGTGGTGGTGGTGAAGCAAGGGAGGTTGCTGATAACTAA[C/T]GGTAGTAAGAAGAATAACGCGGAGTCGAGCCCTATGGTTGGGTATGGTGGTGGTGAAGAAGAAATGAGGTGGGATTGTATG
99630 G A TAAAAAGAAGGGCAGTGATGCAGGGGTGAAAAGGAATAGGAGGGTGGTGGTGGTGAAGCAAGGGAGGTTGCTGATAACTAACGGTAGTAAGAAGAATAAC[G/A]CGGAGTCGAGCCCTATGGTTGGGTATGGTGGTGGTGAAGAAGAAATGAGGTGGGATTGTATGTTTCATGATATGAAGCCTA
99630 A G GGAGGGTGGTGGTGGTGAAGCAAGGGAGGTTGCTGATAACTAACGGTAGTAAGAAGAATAACGCGGAGTCGAGCCCTATGGTTGGGTATGGTGGTGGTGA[A/G]GAAGAAATGAGGTGGGATTGTATGTTTCATGATATGAAGCCTACTTAATGGATTGTTATATATGGTTTGATGTTATATGTATCA
99632 A G TCATCCGAACTGAGTTCTTGAACCATCCTTTGTTTAAAGAATTGCTGGACCAGGCTGAATCCGAGTTTGGATATGCCCGTGATGGACCCATCGAGCTGCC[A/G]TGTAATCTGGACTACTTTGATCAAGTGCTTTCGGATATCTTGGACATTGATGTAAGTTCGCCTGTATGCGGGTTTGGTAGAGGGGCG
99632 T C TGAACCATCCTTTGTTTAAAGAATTGCTGGACCAGGCTGAATCCGAGTTTGGATATGCCCGTGATGGACCCATCGAGCTGCCATGTAATCTGGACTACTT[T/C]GATCAAGTGCTTTCGGATATCTTGGACATTGATGTAAGTTCGCCTGTATGCGGGTTTGGTAGAGGGGCGGTTGGGTTTAGGGTTTTT
99632 A G GGACCAGGCTGAATCCGAGTTTGGATATGCCCGTGATGGACCCATCGAGCTGCCATGTAATCTGGACTACTTTGATCAAGTGCTTTCGGATATCTTGGAC[A/G]TTGATGTAAGTTCGCCTGTATGCGGGTTTGGTAGAGGGGCGGTTGGGTTTAGGGTTTTTGATGTGTCAAGGGTTATGGTTCAGCAC
99632 G A TGATCAAGTGCTTTCGGATATCTTGGACATTGATGTAAGTTCGCCTGTATGCGGGTTTGGTAGAGGGGCGGTTGGGTTTAGGGTTTTTGATGTGTCAAGG[G/A]TTATGGTTCAGCACAGGCTTTAAGGGTGCATGTAAATGTAAACTGCTGCGAGTGTTTGCTTTGTAAATATGGTTTGTGTGTGAAAT
99646 A G TTGTATGTCTTTCAATATTTGCAAAATCGTTATGTTCTTTTGTGTATTGTTAATACATACAGTGTGGAGTTTATGGACCATTGATGTTATGAGTGACCAA[A/G]TCTTGGATTCGTGATAATGTTATCATTTTCGGTAATAAACTTAATGTGGATGTATATTTAGTGCAAAAAAAAAAAAAGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99646 G T TGCAAAATCGTTATGTTCTTTTGTGTATTGTTAATACATACAGTGTGGAGTTTATGGACCATTGATGTTATGAGTGACCAAATCTTGGATTCGTGATAAT[G/T]TTATCATTTTCGGTAATAAACTTAATGTGGATGTATATTTAGTGCAAAAAAAAAAAAAGG
99650 T C TGATAAAACAGATGACTACTTTACCACAGTACCGTGATGTAAGCTGTCAACAGCTTTGTTACATCCCGCCAAGGTGAGGAAACAATTGTTCCAGGACTCT[T/C]GGAAGATTCAGCACTATCTCAGCGAACGCTTCTGGCAAGCTCATGCTTTTTAATGCATCCTCAGCAAATGAAAGAGGTGTTGGAGTA
99650 A G TTGGAGTAGCTTCAGAAATTTCTAAGCCGATTCCACTTTTGTCAAACACACTTATCTTTTTTGAGGGATGAACAGGCCATGCCAAAACTCTGATTCGGGT[A/G]GGCAGTACAGACAAAAGATCCGGATATCTAAGGCTCACAGTAATTTTGCAATCATAGTCTTCCAATGCAAATTCAATTATGTTGAAAG
99662 A AT CGAATGATCTCCAGATCGATGTGGCGTCGAATTATGCTTTTGTACCGTTCACTTTCCTGGCTCTGGAGCCTTTTCTCGAAAACCAACCCATCTTTACTTG[A/AT]TGAATACGCTCCAAAAACGCAATCAAAGGCTGTGAGTCAAACTCAGCCTCTTCCTTATCCTTACCAGCTGACAAAGCCACGGATGTAT
99662 C CA AGATCGATGTGGCGTCGAATTATGCTTTTGTACCGTTCACTTTCCTGGCTCTGGAGCCTTTTCTCGAAAACCAACCCATCTTTACTTGATGAATACGCTC[C/CA]AAAAACGCAATCAAAGGCTGTGAGTCAAACTCAGCCTCTTCCTTATCCTTACCAGCTGACAAAGCCACGGATGTATTCCCACCACTTCC
99662 C T CGGCTAAACAAACTTTGCATCTCGCTGCTTGACTCATTTTCATTTCGGTTGGGATTTGTGTTAACGGATCCAGATCTTGATCCAGTATTAACCTTATTTG[C/T]ATTTGCTTTCGCCTGCTCCTCCAGTTTCTTCCCCGGATCTTCCTTCCTTTCAGTATTATTTGA
99670 A T ATCTGTTTTTCTCTTGCTCTACTAGATATACATGCATCCCAAATGGAGTTTTATCCCCACAAGTTCCATTGCCCAAGAGAAATTTTCTAGTAATTTTCCT[A/T]CCAATTGTAGTATGAGTAGTTGTAGGCAAGGATATACTGATGTTACTGATAAACTCCCAATATCCACTATTCCCTTTAATCACACTTCTCTC
99670 T C CCAAATGGAGTTTTATCCCCACAAGTTCCATTGCCCAAGAGAAATTTTCTAGTAATTTTCCTACCAATTGTAGTATGAGTAGTTGTAGGCAAGGATATAC[T/C]GATGTTACTGATAAACTCCCAATATCCACTATTCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATAC
99670 T A TAGTAATTTTCCTACCAATTGTAGTATGAGTAGTTGTAGGCAAGGATATACTGATGTTACTGATAAACTCCCAATATCCACTATTCCCTTTAATCACACT[T/A]CTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGAC
99670 C T TGAGTAGTTGTAGGCAAGGATATACTGATGTTACTGATAAACTCCCAATATCCACTATTCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGA[C/T]TGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACATCGGCAATCACATTAGATGGCACC
99670 C G GATGTTACTGATAAACTCCCAATATCCACTATTCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCA[C/G]CTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACATCGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAG
99670 A G CCCAATATCCACTATTCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGG[A/G]TCGATGGTGAATGGATCGACATCGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATT
99670 G A ATCCACTATTCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGAT[G/A]GTGAATGGATCGACATCGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATTCATCCG
99670 A G TCCCTTTAATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGG[A/G]TCGACATCGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATTCATCCGACGAGTCG
99670 T C AATCACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACA[T/C]CGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATTCATCCGACGAGTCGGCCGCTA
99670 C T ACACTTCTCTCATCAACAATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACATCGG[C/T]AATCACATTAGATGGCACCGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATTCATCCGACGAGTCGGCCGCTAGAAG
99670 C G ATGTCCAAAATGACTGACTTGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACATCGGCAATCACATTAGATGGCA[C/G]CGGATCATCAACGCTCCTGGAATCCAGAAACGCCACAACAAATTCATCCGACGAGTCGGCCGCTAGAAGAGGCGGAATAAGACAC
99670 G C TGTGCATATACCAATTATCACCTGAAGAGAGTCGAGGATCGATGGTGAATGGATCGACATCGGCAATCACATTAGATGGCACCGGATCATCAACGCTCCT[G/C]GAATCCAGAAACGCCACAACAAATTCATCCGACGAGTCGGCCGCTAGAAGAGGCGGAATAAGACACATCGTGTTTAAAAGATCTA
99686 G A TTCTTTAGTGGGTTGTGACAGCAGAGCTTTGTGCCCATGGAAGACTTTTAAGGAAAACATCGTGGACCCTCATTTGGAACACACATTTGAATCTGTTTGT[G/A]ATATATGAACTCTATATGTTTATGTTTAGTAACCAAAAATAATAATTAGATATCGGACAAGAACAAAAACAGAGTGCAGGGAGCTTGT
99694 T C TATTCGAACCTTTGATCAGCAAATTGGAAGGTTTTATGTCCCGATGGACGATTTGCTGAGAGTGAAGGTAGGATAGCCCGTTCAAGACCTGATAGGCGAT[T/C]TCGGAAAGAGCTGGTTCGGGAAAGGTGAGGTTTCGATCAAGGCTGCCTAGATCCATGTACTCCAGCAGAAGAGCAGGATCGCCAG
99694 A G ATAGCCCGTTCAAGACCTGATAGGCGATTTCGGAAAGAGCTGGTTCGGGAAAGGTGAGGTTTCGATCAAGGCTGCCTAGATCCATGTACTCCAGCAGAAG[A/G]GCAGGATCGCCAGAGTTGGTGTGGAGGACTGCGATGCACTTGACAACGGAGGTAGAGTCAGTGGCGCGGTGGATCTGAATTTC
99694 A G GCCCGTTCAAGACCTGATAGGCGATTTCGGAAAGAGCTGGTTCGGGAAAGGTGAGGTTTCGATCAAGGCTGCCTAGATCCATGTACTCCAGCAGAAGAGC[A/G]GGATCGCCAGAGTTGGTGTGGAGGACTGCGATGCACTTGACAACGGAGGTAGAGTCAGTGGCGCGGTGGATCTGAATTTCGCG
99694 T G AGAGCTGGTTCGGGAAAGGTGAGGTTTCGATCAAGGCTGCCTAGATCCATGTACTCCAGCAGAAGAGCAGGATCGCCAGAGTTGGTGTGGAGGACTGCGA[T/G]GCACTTGACAACGGAGGTAGAGTCAGTGGCGCGGTGGATCTGAATTTCGCGTTTTGAGGAAACGGAATCAGTGTGAAGGACCT
99694 G A GGTTTCGATCAAGGCTGCCTAGATCCATGTACTCCAGCAGAAGAGCAGGATCGCCAGAGTTGGTGTGGAGGACTGCGATGCACTTGACAACGGAGGTAGA[G/A]TCAGTGGCGCGGTGGATCTGAATTTCGCGTTTTGAGGAAACGGAATCAGTGTGAAGGACCTTCAGTGCGTAGATATTGGAAGTT
99694 A G GATCCATGTACTCCAGCAGAAGAGCAGGATCGCCAGAGTTGGTGTGGAGGACTGCGATGCACTTGACAACGGAGGTAGAGTCAGTGGCGCGGTGGATCTG[A/G]ATTTCGCGTTTTGAGGAAACGGAATCAGTGTGAAGGACCTTCAGTGCGTAGATATTGGAAGTTCGTCGGTGGCGGAGCTTGTA
99694 A G GAAGAGCAGGATCGCCAGAGTTGGTGTGGAGGACTGCGATGCACTTGACAACGGAGGTAGAGTCAGTGGCGCGGTGGATCTGAATTTCGCGTTTTGAGGA[A/G]ACGGAATCAGTGTGAAGGACCTTCAGTGCGTAGATATTGGAAGTTCGTCGGTGGCGGAGCTTGTAGACGGTTC
99698 G A TGAACTCTCTGTTCAGAAAAACGCCCAAACGCACGCCCTCGCCCTCCACGGCAGCGCCGGCACCGGCCAACGACTGGAAGCTGATCGCGCATGATCTCTC[G/A]CTGAAGCTTCTCCACGTCAGCCGCCGCCGAGACGAAGCCATTCTGGAAGCTTCCAGACTCAAGCACGCACTTTCCGATCTGCAACT
99698 T A GCGCATGATCTCTCGCTGAAGCTTCTCCACGTCAGCCGCCGCCGAGACGAAGCCATTCTGGAAGCTTCCAGACTCAAGCACGCACTTTCCGATCTGCAAC[T/A]CAAGCTCAAACAATCACAAGTGCAACCAACTTGCAATGGCGATTCGGACAGGACCGATCTGTTCGTGACGGCGGTGAAAGATGCGA
99698 C G CGCATGATCTCTCGCTGAAGCTTCTCCACGTCAGCCGCCGCCGAGACGAAGCCATTCTGGAAGCTTCCAGACTCAAGCACGCACTTTCCGATCTGCAACT[C/G]AAGCTCAAACAATCACAAGTGCAACCAACTTGCAATGGCGATTCGGACAGGACCGATCTGTTCGTGACGGCGGTGAAAGATGCGAG
99698 G A TTTCCGATCTGCAACTCAAGCTCAAACAATCACAAGTGCAACCAACTTGCAATGGCGATTCGGACAGGACCGATCTGTTCGTGACGGCGGTGAAAGATGC[G/A]AGGAAAGCGGTTCGGATGCTGACGCGGGAGATTTCGAGTAGGATCCGACCCGGAAGGATTGCAATGACGATGAAGCTGCCGATA
99702 T C TAGCTTGATTCACAAACATTCCATATTCGATCGTGTAGAAGCAGTTACAGATCTTGAAAAAAATAGCAACTTAACAACCCAATAACACCTTGTTCCTCTT[T/C]ATTGCTGTGCCACCTCAAATTTGATGCTTTGTGGCTATTATGTACTTACTCTAAGCATCTATCGCTCTTCTTCTCAGATGGTGATTAACAT
99706 G GA TGTCTTCCCTTCATTCACCGAAACCCTTTTCCCCTAATTTCGCCATGGCCGCCTTCTCCTCACTGTCAACGTCGTGTTCCTCCTCTCCAATTTGACAGTC[G/GA]ACGAAAACGGTGACTGCTTCCTGGTCCTATTTGCCATCACACCACTCAAGACTAGCGCGTATACCTCCGACAATCGGCGTCGAAGCCAC
99706 TG T ACCCTTTTCCCCTAATTTCGCCATGGCCGCCTTCTCCTCACTGTCAACGTCGTGTTCCTCCTCTCCAATTTGACAGTCGACGAAAACGGTGACTGCTTCC[TG/T]GGTCCTATTTGCCATCACACCACTCAAGACTAGCGCGTATACCTCCGACAATCGGCGTCGAAGCCACCGCACCTCAAACTGTTTATCAT
99706 G A TTCCTCCTCTCCAATTTGACAGTCGACGAAAACGGTGACTGCTTCCTGGTCCTATTTGCCATCACACCACTCAAGACTAGCGCGTATACCTCCGACAATC[G/A]GCGTCGAAGCCACCGCACCTCAAACTGTTTATCATCGAGCCTTCGCAGGTGTGCTAAATCGTAGCAAGTCACCACCGTGGTCCATCCT
99706 C T CAGTCGACGAAAACGGTGACTGCTTCCTGGTCCTATTTGCCATCACACCACTCAAGACTAGCGCGTATACCTCCGACAATCGGCGTCGAAGCCACCGCAC[C/T]TCAAACTGTTTATCATCGAGCCTTCGCAGGTGTGCTAAATCGTAGCAAGTCACCACCGTGGTCCATCCTCCAAGCAACCTCCACCTTC
99726 A G CACCATGTGGAATCCTGCATCAAAAGGATGGGACAACCCCGTACCCGCTATCATTCATGAAGGCAGTGGAGGCATTAATCACCGAGTGCATTGGATCCAC[A/G]TAAGAATCGCTGTCGACCCGTTTAGCGAACCTTCCTTTGATCCTGGGTCGGGTCTCTGCGTAGGCCTTTCTTGAAGCGTAGCGAAT
99726 C T TGTCGACCCGTTTAGCGAACCTTCCTTTGATCCTGGGTCGGGTCTCTGCGTAGGCCTTTCTTGAAGCGTAGCGAATGGTCTTCTCGAACTTTCTATTCTT[C/T]CGCTTCTCTCTGTATCGCATAACTCTTGCTTCTCTGTCCATTGCGTCCATTGGATTTGGCAAAGGTCTACTGTACGGGTTGGATACATCA
99726 T C AGGCCTTTCTTGAAGCGTAGCGAATGGTCTTCTCGAACTTTCTATTCTTCCGCTTCTCTCTGTATCGCATAACTCTTGCTTCTCTGTCCATTGCGTCCAT[T/C]GGATTTGGCAAAGGTCTACTGTACGGGTTGGATACATCAGCTACTGCCATGGAGGTGCTGTTGTCTGGCACCACTCCAGCTTCGGATGA
99730 C T CCTTTCAGATCAAAAGCATCAGCTTCTTCCAACTTTTCCTTGATTTGTTTTGACAGCTCAATGATCTCAGGTGTCCCTGTAACCTCTGCTACAGAAATCG[C/T]CACGGCGGCCTTAGCATCCTCCTCGGCTAAACGCTTAAGGGCTCTTTGAATTTTCCTTTCACACTCCACAATCAGTCTTTCAATTAGATCT
99730 T C TTTGAATTTTCCTTTCACACTCCACAATCAGTCTTTCAATTAGATCTTCAAGTTCAATATCAAAGTTATGACCACCTTTGGACTTTTCTTCTTGATATTC[T/C]TTCCGCAGCTGCAAAGAGTGCACCTTTGGACAAGGGCCCAAATCCATTTTCGTGAGTTGGAACAGATCGTGAGGGCACAACCCAGACAAG
99730 A G CCTTTGGACAAGGGCCCAAATCCATTTTCGTGAGTTGGAACAGATCGTGAGGGCACAACCCAGACAAGTAGAGCTTGCAAACGTCGCGATCGTAATACTT[A/G]CGATTAACTTCACTGACGTCACCGTTGCGGTTGGCACCCATCAGCGCATCCAACTGTTTGCGAATTGCATCCATTAGATGAGTTTGC
99730 G C GTCGCGATCGTAATACTTACGATTAACTTCACTGACGTCACCGTTGCGGTTGGCACCCATCAGCGCATCCAACTGTTTGCGAATTGCATCCATTAGATGA[G/C]TTTGCTTAGGGATTCCGATTCAAAATTGGGGTTTTGCGATGGGTCTGCTTGAATTGTTTGCTTCTTCTATATTAATTGCATTCCTCATCC
99738 G T AGCAGCCCCTTGACGTACTGCTGTGTATACAGGTAAATCGGTAAGGTGCTTTTGTGCATAGATTTGTAGTTGACTCTTGTAAGGTAGCTGACTCACATCG[G/T]GAGAGGGAGGCGGGGGAAGAGTGGGGGCAAAGTGGTCGAAAGCCATCTGAGCAACTTTGTTCTGAGCCTCTTTCGAAGAAGAGG
99738 A T CGCCGCGAGTTACTGTGTAAGTAGGTAAAGACCACTTTTGCTTCTGGCAGAGCTCTTGAAGTTTCGATTTGTACATTGCAGTATTTAGATTCGAAATTGC[A/T]GTATTTTTCTTGAGATATAAAAGGAAGCCGTGGAGAAAAACAGCAGATTCATGTGTTCTGGATGAATGCTCATGTA
99740 A AT ATCTTTGGTTCCATAAAAACAAATAAGAAATCATCAGATGAGTTTAACTAATTTTTTCCAGAATAGCAGATTCACAATTTTAGCTTCTCTTTTTCCCCCA[A/AT]TTTTTCAGAATAGGAGGTTCTCATTTAACTTATACATCATCAAATCCACGCCTATCATTAGATATCGGAGAAGACGGTTGTTCAGGTGAA
99740 G A TTTTCAGAATAGGAGGTTCTCATTTAACTTATACATCATCAAATCCACGCCTATCATTAGATATCGGAGAAGACGGTTGTTCAGGTGAAGAAGAAGGCGA[G/A]TCAGAGACATCAGCTAGAGCTTCAAGCGTGTTGATGACATCGCTGGTGTCGTCTAGATAATATCTAGCCTTGCTTGGTTTTTGACCA
99740 T C CGCTCTCTACCATGGATGATAAGATCTTCTCTGCCGCTACACCTTTACTCACACCCTGAGGTTTGACTTCTACAATAAACTGGCCAGGTTTAACCGTTGC[T/C]GGTTCATTTGCAAGAACACTCTCTAGATGTTCCAGCATCTCTTTTGCTTGTGCAGAACCGAATCCCATATCAGCATCTTTATGATGCCAC
99740 C G CCGCTACACCTTTACTCACACCCTGAGGTTTGACTTCTACAATAAACTGGCCAGGTTTAACCGTTGCTGGTTCATTTGCAAGAACACTCTCTAGATGTTC[C/G]AGCATCTCTTTTGCTTGTGCAGAACCGAATCCCATATCAGCATCTTTATGATGCCACACGAGTGCACTTTCCTTTGTCTCCATGTACGAT
99744 C G GCTGAAACTGCACACCCATCATTCCCATTGCCTGCTGCTGCATGCTATTCTCAATAGGATAACTACTGTTGTATGGAAACTGCGAAGTCTGGGGCATCTG[C/G]AAGTTCATGTGCTGCATGCTTTGGAAATTCGAAAACGAATTTTCATTGCTCATATTGTTATTATGGCCAGGTTTGTTATTGTCTAAAGA
99746 A T GTGTTCAGGGTAGGCAGGACTCTGGCACCACGCAGTTTATTACTGCAGTTTATTACTATGCCCATGCACGGCCATAGCTCCAAATGCACTGCCACTGAGA[A/T]CGAAATGCACCAGTTCTTTAAGGCATGGCCCACCCGGGGATTCATCGATGACCACAGCAGCGATAGGTTTACGCGAGCATGCTTTAT
99748 G A TGCACAATGGACACCTATCCTTGTCGTTTATCATTTCTCCTGTGCCTTTACAGTCATTGCAAGGATGCTGCATCTGCTGAATCATTCCAGGACCCAACTG[G/A]CGAATAGAAACTTTCATACCAGAACCTTGGCAAGATGCACATCTCATTGAAGCACCTGATTTTGATCCTTTACCATTGCATTTTGAGCAG
99754 A G ATTTGAATATGTCCTTCCACAACTGTGGTTCTTTAGAGCCTGGGATTTCCACCTGATGAAATTTCCAAAGCTGCCTTGCAATTTCAGCAGCAATTTTTGG[A/G]TTGCTCATGTCAAGTGGACAAAGTGTACGAGCATTAATGAAAGATTGAACCACGCCATTTTCGAATAGTCCAAGAAGCTCAGCACCAA
99754 C T TGATGAAATTTCCAAAGCTGCCTTGCAATTTCAGCAGCAATTTTTGGATTGCTCATGTCAAGTGGACAAAGTGTACGAGCATTAATGAAAGATTGAACCA[C/T]GCCATTTTCGAATAGTCCAAGAAGCTCAGCACCAAACCCTGCTGCAGACAAGTGTGGTAAAGCCTTCATCTCACGTTCTCGGTCAATC
99754 A G GTAAAGCCTTCATCTCACGTTCTCGGTCAATCACTAAATCTGTGTTTGGACCATATAGTCGTACAGTTAATGAAACTTCATTGCCATCAGCTTCTCTTAC[A/G]GAGACCTTCAGCAATTGATTGGTGATACCACCAGAAACTGTCTCAATGGAAAAACAGGAACCATCAAGATACGACCACTTCTTAAAAAG
99760 CA C GTAATTCAACTAATTATACACTGGCTGTTATCCAAATATATTTACAGAGAATTCGCTACTAAAACAATCAACTATGAATGGTTAAATGCAAAAATAAAAA[CA/C]AAAAAAAGGCTCACGAATAAAGCACTAAAATATGGAAACAGCCCGACCCCACTGCCCCCTCATTTTAATGTAAACATTTATGCACAAC
99760 GC G GCTACTAAAACAATCAACTATGAATGGTTAAATGCAAAAATAAAAACAAAAAAAGGCTCACGAATAAAGCACTAAAATATGGAAACAGCCCGACCCCACT[GC/G]CCCCCTCATTTTAATGTAAACATTTATGCACAACAATAATGCATACTCTACTTATACAATGAAGCACCCAACAAATGACAGGCCACA
99764 T A CTATATAGCTCAATATAGAGACGTACGGAACACAAAATTTGGATGCAACCTGATGAGGCTGACAAATTTATGCCATAAACAAGTACTTGAGATCTTCAAC[T/A]GTGAGCTTCGAAGCACGGCCACCTGCCCCGTCTTCTCCAAATGCAGCGGAAACCATCTTTCTTTTCCTCTCCTGGAGAGCAAGTATTC
99770 G A AAAATCCTACAGAAGTTCGAAATATGGAGTTAACGCTTCTTCTTGCCTGCCTTAGAGGACTTTGATGGGCTGGCAACTATCTGGATGAACAACCCGACAA[G/A]TGCGAGTACTGAAACAAGAGACCCATACTTGGCCAATAGCCTCTTTGCCCATTCAAATTTCTTTTCTGGTGGTCGTTCAGCCAGAATA
99770 C A ATTCAAATTTCTTTTCTGGTGGTCGTTCAGCCAGAATATCTAGTGGCTGAATGGGTGTTGATAATGCTTCCTGAAGTGCGGCCTTTGTGGGAACGCGATA[C/A]TTGATAATGGCAGGAGAGCCTTGAAATACGCCCTTCACTTGGGAATCCAGAACAAGTGAGTGAGAGACAGAGGCGCCACCATCAAG
99770 A G ATTTCTTTTCTGGTGGTCGTTCAGCCAGAATATCTAGTGGCTGAATGGGTGTTGATAATGCTTCCTGAAGTGCGGCCTTTGTGGGAACGCGATACTTGAT[A/G]ATGGCAGGAGAGCCTTGAAATACGCCCTTCACTTGGGAATCCAGAACAAGTGAGTGAGAGACAGAGGCGCCACCATCAAGTCTTTC
99786 C T GCCTAAAAGCCCCATGAGCTCCAACGATCGCCGCACCCAAAGTCAGAGCCGACATCAAAATTGACCCAACCGACGTCAGAAACACGACAAATATCGTCAA[C/T]ACAATTAATCCACCCAACGTTTCCCGATCCGAATATTGCCTGCCGAACATAATCAGCGGCGGATCTGACGGTCTGAAGAGGTACAG
99792 T C AAAATCAAGCAAGCTTTGTACTACCAGCAGTTATTCAAATAACCACTCCACCAGCAAACTCCACTTCCTGTGCAGGGGGCAGTGATGAAACCCAATCTGA[T/C]GCATGAGTTGGAAGAAGACCCAATGTATTGAGCTTCCATAAACCCATACAAAGCCCAGCAAGATTGAGGGCAACGAAGACCAGTTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99792 A G CAGTTATTCAAATAACCACTCCACCAGCAAACTCCACTTCCTGTGCAGGGGGCAGTGATGAAACCCAATCTGATGCATGAGTTGGAAGAAGACCCAATGT[A/G]TTGAGCTTCCATAAACCCATACAAAGCCCAGCAAGATTGAGGGCAACGAAGACCAGTTTAGGTAATAGTGTGTCTACTTTTGAATCT
99792 T C TAACCACTCCACCAGCAAACTCCACTTCCTGTGCAGGGGGCAGTGATGAAACCCAATCTGATGCATGAGTTGGAAGAAGACCCAATGTATTGAGCTTCCA[T/C]AAACCCATACAAAGCCCAGCAAGATTGAGGGCAACGAAGACCAGTTTAGGTAATAGTGTGTCTACTTTTGAATCTTTGTATGGTTCA
99792 A C TTCCAACGCTTTGAAGAGCACTAATCGGCTGCCAAAGAGCTGAAAATGTAATACCAATGCTAAACAAATGCACAGTACTCCCAGACATCCACATCATAAA[A/C]CCCATCATCATTAAATTTTTAAATGGTGCTTGAGCCACTTCCCATGCTTTCTGTGATTTCCATGCAATCTCAGCATCCTTTTTCTGCCGG
99792 G A ATCCTTTTTCTGCCGGCTGGCACTCACATCATCCAGATCTTGCACAGATCGATTGAAGCCGAGAGGATCAGGAACGTCCAGTGACGAGGAGGAAGACGAC[G/A]ACGTAGAGCTATCGGAGAAGTCAACAGCCCATCTTCGAGCCAATCCTTTTCCTTTCTCCATTTCTTCTTAATCTTTGAGTTAAAAGAT
99796 G A GGACTTATAGATGGATGGCCCCAGAAATGATACAGCACAGGCCATACAACCAAAAAGTGGATGTGTACAGCTTTGGCATAGTCCTATGGGAGCTCATAAC[G/A]GGCATGCTCCCGTTCCAGAACATGACAGCTGTCCAAGCCGCATTTGCAGTGGTCAACAAAGGGGCCAGGCCTATCATACCTCCGG
99800 T TC GAGGAGTAGAGTAAAAGGAAACAAAACAGGGACTTCTATCTTTATTTACATAACAGAGCAAGCATTGGCGTTATCATCATTAAACATAGCAGTAGCCTTC[T/TC]CCCCAGCAATACCCGAGTGCCCTCCCCCACCCATCTGATAGTGATAACCACCATACCCGCCTCCCATGACCGAATCATCCGTCCCGT
99800 TC T AAACAGGGACTTCTATCTTTATTTACATAACAGAGCAAGCATTGGCGTTATCATCATTAAACATAGCAGTAGCCTTCTCCCCAGCAATACCCGAGTGCCC[TC/T]CCCCCACCCATCTGATAGTGATAACCACCATACCCGCCTCCCATGACCGAATCATCCGTCCCGTGCTTCCTGTAGTTGTACGAGCTCG
99800 GC G AAGCATTGGCGTTATCATCATTAAACATAGCAGTAGCCTTCTCCCCAGCAATACCCGAGTGCCCTCCCCCACCCATCTGATAGTGATAACCACCATACCC[GC/G]CCTCCCATGACCGAATCATCCGTCCCGTGCTTCCTGTAGTTGTACGAGCTCGTGGACGCGGTCGAGTTCCCAAACGGATTCTCCGTG
99802 GA G CCGGGTTCATTAGCAGCGCTGAACAGCTAAAGGCGAAGGGTATTGCTGAGATCCTGCTTGTCAGCGTTAACGACCCATTCGTGATGAAGGCATGGGCAAA[GA/G]ACCTACCCAGACAACAAGTTCGTGAAGTTCCTTGCTGATGGCTCCGGGAAATACACCCAGGCACTTGGCCTGGAGCTCGACCTA
99802 G T AGAAAGGACTTGGTGTCCGTTCCAGAAGGTTTGCCCTTCTTGCAGATGATTTGAAGGTCAAGGTTGCCAACATTGAACAAGGAGGTGAATTCACCGTCTC[G/T]GGTGCCGAGGAGATCCTCAAAGCTCTTTAAACATCTACTTCTCTTGCTGTCCTTGTATGTGCGACAGTTTTATGCTAACGCTCTCTGT
99802 G A GGAGGTGAATTCACCGTCTCGGGTGCCGAGGAGATCCTCAAAGCTCTTTAAACATCTACTTCTCTTGCTGTCCTTGTATGTGCGACAGTTTTATGCTAAC[G/A]CTCTCTGTCCAATGTGTTTTATGTTCTGTGTTGTTTCAATTCTAAACTGGGCTTTATTTGAATAAGGTTGTGTTGAAATTGGATTATCTT
99802 A G CACCGTCTCGGGTGCCGAGGAGATCCTCAAAGCTCTTTAAACATCTACTTCTCTTGCTGTCCTTGTATGTGCGACAGTTTTATGCTAACGCTCTCTGTCC[A/G]ATGTGTTTTATGTTCTGTGTTGTTTCAATTCTAAACTGGGCTTTATTTGAATAAGGTTGTGTTGAAATTGGATTATCTTTGTTTTTGTTCA
99802 A G AAAGCTCTTTAAACATCTACTTCTCTTGCTGTCCTTGTATGTGCGACAGTTTTATGCTAACGCTCTCTGTCCAATGTGTTTTATGTTCTGTGTTGTTTCA[A/G]TTCTAAACTGGGCTTTATTTGAATAAGGTTGTGTTGAAATTGGATTATCTTTGTTTTTGTTCATGTTATATGGTGTCAAATTGCAGTAA
99808 A G TCCTGCTTCTCCATTTTTTCCCCATTCTTGCCAATAACACTTCTAATAAACTTAATTTCCTTTTTCCCCCCAAGACAGAGCTCCTCTAATGTGCATTCCA[A/G]CTTCCTCTCCTCGGGCGGCAGCTTCCTTAGCAGCTGTCCCGAAAAAGACTTACTGAGTTGTGCCACTTTCGAATAATTTTCTTTTGCAGGGA
99808 A G TAAACTTAATTTCCTTTTTCCCCCCAAGACAGAGCTCCTCTAATGTGCATTCCAACTTCCTCTCCTCGGGCGGCAGCTTCCTTAGCAGCTGTCCCGAAAA[A/G]GACTTACTGAGTTGTGCCACTTTCGAATAATTTTCTTTTGCAGGGATTTTCGAATAATTATAATCCTTAAAGCTCAATGATGCATTTGTAT
99808 T C TTTCTTTTGCAGGGATTTTCGAATAATTATAATCCTTAAAGCTCAATGATGCATTTGTATAGACAAAATCCTTGAAAGTTCTTGTGGGTGAATCTACATA[T/C]TTGGAGGTTAACTTTTCATTCTTCTTTTCATGATTTTCTTCATGCTTACTCTTAGAAAGGTCAAGGAGTCTCTCATAGGCATGAGTAATTG
99816 A G ACAACAAGAAGTCGACCATCTCTTCTCGCGAGATCCAGACCTCCGTTCGTCTGATCCTGCCTGGCGAGCTGGCCAAGCACGCTGTGTCTGAGGGCACCAA[A/G]GCTGTCACCAAGTACTCGTCGTCGACGAAATAAGCTTGTTGGGTTGCATTTGGGGTCTGGCATTTGGTTGGTCATGATGGGGACTG
99838 T C TCTGGTCCAACACCGACAAAGTAACTATGAGTGACCCCGAACCAATGCTCCTCACCACAGATTATGTTGCTTATTCGAATCAGATAACATCACACACATT[T/C]GGGATCGTCCTAAGCTACAAAAACTTCAGACTTGTACTAAGAGACGATTGCAATCTAGTGCTTGAAGACATAAACACATGGGACATAC
99838 C A CCAACACCGACAAAGTAACTATGAGTGACCCCGAACCAATGCTCCTCACCACAGATTATGTTGCTTATTCGAATCAGATAACATCACACACATTTGGGAT[C/A]GTCCTAAGCTACAAAAACTTCAGACTTGTACTAAGAGACGATTGCAATCTAGTGCTTGAAGACATAAACACATGGGACATACTGTGGG
99838 A T CAATGCTCCTCACCACAGATTATGTTGCTTATTCGAATCAGATAACATCACACACATTTGGGATCGTCCTAAGCTACAAAAACTTCAGACTTGTACTAAG[A/T]GACGATTGCAATCTAGTGCTTGAAGACATAAACACATGGGACATACTGTGGGAGACAAAGACGTCAAGCCCTTACCGAGACTGCTACA
99838 T C TATTCGAATCAGATAACATCACACACATTTGGGATCGTCCTAAGCTACAAAAACTTCAGACTTGTACTAAGAGACGATTGCAATCTAGTGCTTGAAGACA[T/C]AAACACATGGGACATACTGTGGGAGACAAAGACGTCAAGCCCTTACCGAGACTGCTACACCCGTTTGGATGACCATGGTGAGTTCTT
99838 A T AGACTTGTACTAAGAGACGATTGCAATCTAGTGCTTGAAGACATAAACACATGGGACATACTGTGGGAGACAAAGACGTCAAGCCCTTACCGAGACTGCT[A/T]CACCCGTTTGGATGACCATGGTGAGTTCTTCATTATGCACAATAGAAGAGATGTACTGTGGAGGACAGGAGTGCGATCTAAAGAA
99840 A T AACAAATAACTGATTTTTGATGAACAAGTTGGTTTGAAGTCGTTTTCTCTTTGAAAGAAACTCAGAAGAGCTAATGGTTGCTACTTTAAAAGAAGTCGGT[A/T]TGCCTGACCATGCGCCTGGATTTGTTGTGGAGACTTGCGGAGCTTCTCTGTTAGATCATGCGCCTGGGTTTGTACCGTACAAGAGCTG
99840 T C TTGGTTTGAAGTCGTTTTCTCTTTGAAAGAAACTCAGAAGAGCTAATGGTTGCTACTTTAAAAGAAGTCGGTATGCCTGACCATGCGCCTGGATTTGTTG[T/C]GGAGACTTGCGGAGCTTCTCTGTTAGATCATGCGCCTGGGTTTGTACCGTACAAGAGCTGTTCTCGGTGCTGCCTCCTCCTCTGGGGT
99840 G A GGTATGCCTGACCATGCGCCTGGATTTGTTGTGGAGACTTGCGGAGCTTCTCTGTTAGATCATGCGCCTGGGTTTGTACCGTACAAGAGCTGTTCTCGGT[G/A]CTGCCTCCTCCTCTGGGGTCCATACCTTCTTGGAGCATGTAAGATCGGAGACAAATGAGCTCATAACATAAGGGTGATGATAATGAT
99840 A G CGGAGCTTCTCTGTTAGATCATGCGCCTGGGTTTGTACCGTACAAGAGCTGTTCTCGGTGCTGCCTCCTCCTCTGGGGTCCATACCTTCTTGGAGCATGT[A/G]AGATCGGAGACAAATGAGCTCATAACATAAGGGTGATGATAATGATGATGACTGTGGTGAAGAAGGCGATAACAAGATTCATTGTT
99840 GAATGTGTACTGTCTTCGGCACTCTGT
G TGTTCAACCCGAGGATCCAACCAAGCTTCCATTTCCCTCTACATTCTTGGTTCTCTATGGCAATAAAGATAGCAAGCTTTTGAAGAAATGTTGAAAAATA[G/GAATGTGTACTGTCTTCGGCACTCTGT]AATATGTTATTTTCTTGATACATGGTTTTCAGACTGTAACAAAATTTTCTAGTTTGTATCTACAG
99844 G T TACCCGTTGTCTTCAACGGTAAGAGGATGTTCACAATCGGGGAATGGCTAAGGAGCGAAGTTGTGAAGGAGCAAGAAGAAGAGCATGGTAGCCCTATCAG[G/T]CTTTGGGTCGGTAGAGGTTTAGCAATTGCTAATCTTATTTTCTGGGGGTTTAATCTCTTCGGCTTTT
99858 A G CCAAGATTATAGCTAATAATATTCCCTCTAAGCTTGTAATGGTTGACAATCATAGCACTCAACGATGGTGTCGGGTTGAACAAACTGCAGTTGACAACCA[A/G]AATCCCGATATCCTTCGGCTTAATCCCAGTCTTCTGCAACAAATCGTCGATGGCACCAAACATAACCATCTCAGCTTCTTTCCTTGCTT
99858 C T GGAGGAACTGCTAAAACAGCTTCCGGAAAGTACGTGTCCTGCCCAAGTCCGGAACGTTCCACAATCTTTCTCTGAAAGGACAAGTTGTCTTCAGTGAACG[C/T]TCCTGCTTGCATGGAGCGTTGCACGAACAGCTCTCTAGTGCATTTCCTTGCGTCTTCCGGCTTGTAGCACGAGTAGTCGAGCAAGTA
99864 A G TCCGCCGCAGCTAAAATCGCACCCAAATCCAAATCGTCTCCCTCTCCCTTTCGCTTCCCCAAACCCATTGCCACGCCTCGTATATTGAGGTCACCGGTTG[A/G]ATCGGTCTGTTGTGTTGAATCTTTGATGCCAATGCATAGCGTGACGGCAGCAGCACTGTTGACTTCCATGTTGTCTGTTACTCGTGGTG
99880 A T GTATCTACGCACCGATTGTGGAACTATTGGGCATAGTGGGAAACGAAGGATTGAAGCAGTCGCAGTGCGAGTGGGCACTGGGCGTTTACCGAAAGTTCGA[A/T]GGAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGAT
99880 A G GGAACTATTGGGCATAGTGGGAAACGAAGGATTGAAGCAGTCGCAGTGCGAGTGGGCACTGGGCGTTTACCGAAAGTTCGAAGGAAATGTGAATCCTTTT[A/G]TAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGCA
99880 A T TCGCAGTGCGAGTGGGCACTGGGCGTTTACCGAAAGTTCGAAGGAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTT[A/T]TGTGGATTTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGC
99880 C G GCGTTTACCGAAAGTTCGAAGGAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCT[C/G]GATGCAATGCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCT
99880 T G CGAAAGTTCGAAGGAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAA[T/G]GCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGCTGC
99880 T A AGTTCGAAGGAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAATGCA[T/A]AGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGCTGCTGCT
99880 A G GAAATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGC[A/G]GTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGCTGCTGCTGTGGTGGCT
99880 G T ATGTGAATCCTTTTATAGAAAACGAGGTCAATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGCAGT[G/T]CAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGCTGCTGCTGTGGTGGCTGGA
99880 T C ATTTTGATGGGATTAGGAGGTGTTATGTGGATTTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTAC[T/C]AGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGCTGCTGCTGTGGTGGCTGGAGTGGTGATTGGGGCCCATGCGGTGGTTGC
99880 C T TTGAAAAGGCTGCTCGATGCAATGCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTG[C/T]GGCTGCTGCTGTGGTGGCTGGAGTGGTGATTGGGGCCCATGCGGTGGTTGCACTGGTAGGCATAGGTCCCACTGTGGTCTGCT
99880 T A AAAGGCTGCTCGATGCAATGCATAGGAGTGCAGTGCAGAAGAGAAGAGTGATGAGATGTGCTACTAGGAGCGCTGCGTATTGTCTGATGGCGTCTGCGGC[T/A]GCTGCTGTGGTGGCTGGAGTGGTGATTGGGGCCCATGCGGTGGTTGCACTGGTAGGCATAGGTCCCACTGTGGTCTGCTGTGG
99886 T C GTCCGCTTCTGTCAAATACTCTCCTCTCACACCCGGCTCCCTCACCTGCTTCAAAAGCTTATAAGTCTCCATCATCCTTCCATTCCAACCATCCACGAAT[T/C]TCTTATCCCTCCTATTATCATTTTCGAGGTTCTTCATGATGTCTTCCTCCTCGTCCATTGCCATAGTAATTTCTCGAGCTGATGGAGGTTTAG
99886 C T GCCAACTGGCTGTTCGCCGTCGAAAAGGGATTTGGTCAGTCCAGTGGACCAGGTGGAGGAGGACTCTTGATCCCAATCTAGAGATGAAGGCGATTGGGAA[C/T]TTTTCGAAGCTGTATTCCAATCTTGATCCCAAGGGTTGCCTCCGTCGCCGCTGTTCGTTGAGAAGGAGGAAGAGACCCTAAAAAT
99890 G A TAAGCACTAGGTCCGTCTAACAAAGAAGCTGCCCACTGACAAAGAAGCGAGGAACCCAGCGGTTACCAAAACAGTCACAGAGGCTATCAGATCCAAAAAC[G/A]GGAGAAAAGCCCAAAACTTCAACAAGGCCACTGACCAGCGAACTCTTCCACGAAACAACTACAGATGAGCACCACAAACACCAAT
99894 T C GCAGCGTGATGGCTTTGGATGAAGACCCGAGCGTCGAGTATGAGCTTGCTGCCCTCAGAGAAGCGGTGGATTCGGGGTGCACTTACCTTTTGTCTCATGG[T/C]GATGTTAGGGCGAAGAAGGATTCTTGGTTTATGAAGAAGCTGGTTATCAATTATTTTTATGCGTTTTTGAGGAAGAACTGCAGGG
99894 GT G GGGCGGGTTCTGGAAATATGAATGTGCCGCATCAGAACATTATACGTGTTGGGATGACCTATTTTGTTTGATGCATTACTGCGCTTTAAATAACCATTTA[GT/G]TTTCTTTAGATGTTGTATTTGAAGAACTATGTTCGTATCATTATTATTACTTGTTACTCATCACATTTATGATGTTTCCAACATTGTCAA
99902 T C GTCGATGTACTCCTTCTCGAACCCGTACACCGAGTTGATCACCATGCCGAAGCACTTGGCCCAGGATTCATTCATCCGGCCTGCTAACCCGTTAACGTCT[T/C]CGATTACCATGAGATTGGACTTGGTCATCTCGATATGGTGCGGCATGCCCGTGATGGCGAAGGGGACGTCGTCGCCTTGCACGGCTT
99902 G A GGCCCAGGATTCATTCATCCGGCCTGCTAACCCGTTAACGTCTTCGATTACCATGAGATTGGACTTGGTCATCTCGATATGGTGCGGCATGCCCGTGATG[G/A]CGAAGGGGACGTCGTCGCCTTGCACGGCTTCGCTTAGCTTGTGGATGGCTATGATGGCTGAAACCATGACGCAGAAGGCATTGCTG
99902 C T TCGTCGCCTTGCACGGCTTCGCTTAGCTTGTGGATGGCTATGATGGCTGAAACCATGACGCAGAAGGCATTGCTGCCGCAGAAGAGGAGCCTAGGGATGC[C/T]TAGATCGGACGTCCACGGGTAGAACACGTCGCTTACTATGAAGTCGGGTTTGTGTAGGGTTACGAGACTTTGGAAAGGCTGTTG
99914 C T GACTCGCCCTGGATGCTGTAGCGCTCGATCGCCTCGCGGCGGAAAGCGTAGATCCAGCCCTGCATGAACCACAGAGACCCGCAGCACGAAGCCGCGTCCA[C/T]CACGTCAACCACCATCAACGACTGGAGGCCGAGCACGCGGTCGCCGTCAATCTTGTTGCCGACGTAGCCGAGCGTGCAGCAAGG
99924 G A TTCGATGTGCAGCAGTTGCACAGTGAACAGCGGCCCATTCGATGCCGTCCAACTGTTCGCTGCTGTATCGAACAGTTCGCTGCTGCTGCAGCGAACGACT[G/A]CTGCAGACAACAACAGTGATGCTGACCAAGCATTTAGTGCATAACCGTTGTAGCAATTTTTATCGACCTAGTTTTACAACGTGACTG
99930 G A AGCATGCTGATCTTCTAAATTCAAATGCCGAAAAAGGATCGCAAAATGACAACAACGCCCCTAAACAAACATCGGCCGATGCTCAAAAACAGTCATTACA[G/A]CCAGAAATGTCAACAGCACGGGCGCCTCCTCCTCCGGTCTCCGCATTCTCTCCGGGCTCAAACTCCCAAAGCCAAGACCGTGGGGA
99936 C T TGGCCTTTTTTTTTTTTGTATAACTATCACCAAAGTCACATTTGTATCAAATCAAACGTAACAAGAATTTCGTAC[C/T]CATATTGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCC
99936 T C TGGCCTTTTTTTTTTTTGTATAACTATCACCAAAGTCACATTTGTATCAAATCAAACGTAACAAGAATTTCGTACCCATA[T/C]TGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTA
99936 C A TGGCCTTTTTTTTTTTTGTATAACTATCACCAAAGTCACATTTGTATCAAATCAAACGTAACAAGAATTTCGTACCCATATTGTATTCCACAA[C/A]AACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAAT
99936 A T TGGCCTTTTTTTTTTTTGTATAACTATCACCAAAGTCACATTTGTATCAAATCAAACGTAACAAGAATTTCGTACCCATATTGTATTCCACAAC[A/T]ACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAAT
99936 A AT TTGTATAACTATCACCAAAGTCACATTTGTATCAAATCAAACGTAACAAGAATTTCGTACCCATATTGTATTCCACAACAACAAAGAGGACGCAAACAGT[A/AT]TTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCT
99936 A AT AATCAAACGTAACAAGAATTTCGTACCCATATTGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGA[A/AT]TTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAAC
99936 G A CGTAACAAGAATTTCGTACCCATATTGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATAT[G/A]TTTGTTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAACCTCATAAC
99936 T G TAACAAGAATTTCGTACCCATATTGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGT[T/G]TGTTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAACCTCATAACAA
99936 G C ACAAGAATTTCGTACCCATATTGTATTCCACAACAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTT[G/C]TTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAACCTCATAACAATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
99936 G A CAACAAAGAGGACGCAAACAGTATTGCCTGTAAAAAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAATA[G/A]CCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAACCTCATAACAATCCTCGACATAATCATAGTCGCCGTCAAAACTAAC
99936 CA C AAAAATATTAAGTCAACTAAGAATTATATGTTTGTTTCATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAAC[CA/C]AAGGAAAAACCTCATAACAATCCTCGACATAATCATAGTCGCCGTCAAAACTAACTCCGTTCCCAAACTCCGTCGACCCGAAAAACGCA
99936 G C ATTCTAAGTCCATTTATTTACACAAATAGCCCTGCTAGCTCGACGTCAAAGATTCCGTCAACCAAGGAAAAACCTCATAACAATCCTCGACATAATCATA[G/C]TCGCCGTCAAAACTAACTCCGTTCCCAAACTCCGTCGACCCGAAAAACGCACCCGTAACGTCATCCTCGAACCCCCAAATCCTCCCGAA
99936 A T TCAACCAAGGAAAAACCTCATAACAATCCTCGACATAATCATAGTCGCCGTCAAAACTAACTCCGTTCCCAAACTCCGTCGACCCGAAAAACGCACCCGT[A/T]ACGTCATCCTCGAACCCCCAAATCCTCCCGAACCCCGCATCATCCTCGCCGCCCGTCGAGAGTCCAACGGCCGGCGGAAGCCCCAAC
99936 G A AAACCTCATAACAATCCTCGACATAATCATAGTCGCCGTCAAAACTAACTCCGTTCCCAAACTCCGTCGACCCGAAAAACGCACCCGTAACGTCATCCTC[G/A]AACCCCCAAATCCTCCCGAACCCCGCATCATCCTCGCCGCCCGTCGAGAGTCCAACGGCCGGCGGAAGCCCCAACTCATCATCGGAAG
99936 A G CACCCGTAACGTCATCCTCGAACCCCCAAATCCTCCCGAACCCCGCATCATCCTCGCCGCCCGTCGAGAGTCCAACGGCCGGCGGAAGCCCCAACTCATC[A/G]TCGGAAGCTTCCAGAAGGTACCCGATGCTAAGGTTCGCATCCGCTTCCTTGCCGGGCGACTCCGAATCGATCTCCTTCTCAAGGCTT
99936 G A CCTCGCCGCCCGTCGAGAGTCCAACGGCCGGCGGAAGCCCCAACTCATCATCGGAAGCTTCCAGAAGGTACCCGATGCTAAGGTTCGCATCCGCTTCCTT[G/A]CCGGGCGACTCCGAATCGATCTCCTTCTCAAGGCTTTTGAACACGTCCGTAATATCAACGTTGCTGTTATCGCAGTCGACGTCTTCG
99936 C T CCGGCGGAAGCCCCAACTCATCATCGGAAGCTTCCAGAAGGTACCCGATGCTAAGGTTCGCATCCGCTTCCTTGCCGGGCGACTCCGAATCGATCTCCTT[C/T]TCAAGGCTTTTGAACACGTCCGTAATATCAACGTTGCTGTTATCGCAGTCGACGTCTTCGTCCTCGAGCATTTGGAACAAGGCGTTCG
99936 G A CACGTCCGTAATATCAACGTTGCTGTTATCGCAGTCGACGTCTTCGTCCTCGAGCATTTGGAACAAGGCGTTCGCTTCCCTGAACCTCTTCGCGTCGAGA[G/A]GCGCGTCCGACTCGTCTCGGGCTCTCTTGTTCGTCGCTGCACAAGACGCGGCCTGGTTTTCCATTGTTTTTGCGATTGAGCAAAGGGA
99936 C T CTGTTATCGCAGTCGACGTCTTCGTCCTCGAGCATTTGGAACAAGGCGTTCGCTTCCCTGAACCTCTTCGCGTCGAGAGGCGCGTCCGACTCGTCTCGGG[C/T]TCTCTTGTTCGTCGCTGCACAAGACGCGGCCTGGTTTTCCATTGTTTTTGCGATTGAGCAAAGGGAACGAGGGTGTTTTTGTAAATA
99936 G C CGCTTCCCTGAACCTCTTCGCGTCGAGAGGCGCGTCCGACTCGTCTCGGGCTCTCTTGTTCGTCGCTGCACAAGACGCGGCCTGGTTTTCCATTGTTTTT[G/C]CGATTGAGCAAAGGGAACGAGGGTGTTTTTGTAAATAAGAAGGTAGCAAGTTAGTTGTGGGATCCAGTAGGCCAACAGTG
99938 G A AGCACTAAATTTACTCAGCTGCAGTTTCAGCTTCAGCTGGAGTCTCCTCCTTGTTTCCAAGCCACTTGGCAAAGCTTTCAAATTCAGTATAGTCGCTATC[G/A]GCGATCATGGTCCTGTAAAACGACTTCCCCGTGGCCTTGATAGCTTTAGCTTCCTCCTTGGTGAGCTTGCTCCTCTTCTTGTTAAGCTTC
99938 C T CTTCAGCTGGAGTCTCCTCCTTGTTTCCAAGCCACTTGGCAAAGCTTTCAAATTCAGTATAGTCGCTATCGGCGATCATGGTCCTGTAAAACGACTTCCC[C/T]GTGGCCTTGATAGCTTTAGCTTCCTCCTTGGTGAGCTTGCTCCTCTTCTTGTTAAGCTTCTCCTTCTTAGCCTTAGCTCCTTGCTCAGCAG
99938 G A GCTCCTTGCTCAGCAGCAAGCAATGCCATCCTCCTTGCAGTCTTTGCATAGGGGTTCAACCTCAAAAGAACATTCAAGTTCTTCAGAGGGTTCTTCTTCA[G/A]TTTCTTCCTCTTAACCTCCTTATTGATCGGTCTGACTACACTTTGCACCTCTTCACTGTTAATAATCCTTCCTAAATCAGCATTCGTCATCT
99938 T C CAGTCTTTGCATAGGGGTTCAACCTCAAAAGAACATTCAAGTTCTTCAGAGGGTTCTTCTTCAGTTTCTTCCTCTTAACCTCCTTATTGATCGGTCTGAC[T/C]ACACTTTGCACCTCTTCACTGTTAATAATCCTTCCTAAATCAGCATTCGTCATCTTACCCCTTGGCAGTATATACCCACTCTTCTTCTCACTG
99938 A G AAGTTCTTCAGAGGGTTCTTCTTCAGTTTCTTCCTCTTAACCTCCTTATTGATCGGTCTGACTACACTTTGCACCTCTTCACTGTTAATAATCCTTCCTA[A/G]ATCAGCATTCGTCATCTTACCCCTTGGCAGTATATACCCACTCTTCTTCTCACTGGGCTTATCAAAAGTTCCAAATACCGAATCAAGCTTTTC
99938 C T AAGTTCCAAATACCGAATCAAGCTTTTCAAATGCAGACTTAGTCCATATAATAAACCTGCCAACATGTCCACCAGGCGCCAGCTTCAACAAATTCAATCT[C/T]TCTACATTGGCTATTTCAACACCTGGAATGTTTCTGAAAGCCCTGGCTATTTTAGAGCCTTCGGTCCCATACACGATCAGTGGCCCCTTT
99938 G C TGCCAACATGTCCACCAGGCGCCAGCTTCAACAAATTCAATCTCTCTACATTGGCTATTTCAACACCTGGAATGTTTCTGAAAGCCCTGGCTATTTTAGA[G/C]CCTTCGGTCCCATACACGATCAGTGGCCCCTTTCTTTTCACATAACGCCTGTTCCTGGCCTTTCCCTTTCCAGGACGGATCTTCACGCTC
99940 A G GACGCTGCCAAGGTTTGGGTTCTCGGGCATTACGCCACAAGAACTGTTACTGCATCCGGGCCGAGGTGGTTGATAGCATTCGCCACAACCGAAACCAGTT[A/G]TGATCAGGCTGCATTGAGGTGTATTGCAATGCACTGGTTTGTAGGAAGACGATAAATATTTGGATTCACAGTCGATCCAGATGTAT
99948 G GT AGTTAGTTTGATGAGGCACAGCAGGCCATCTCGAGAAGTGGACCATTCGGCTAGTGCTGGTATAGTTGTTACTGTTGTTGTGTAATCGCCAGGATTGGTG[G/GT]GGTCGACCGTAGACAGCATGAAAGGGTGATATTCCAATCGCACTATGTTTGGTAGTTTTATACCACCACTCGGCCCATGGGAGGC
99958 G A CCCCAAGCTTTGAGCATACAGGCACAACCGGCCAATGTTCCAACCAGTCTTAAGCAGCGAGCGGAACTAGTTGATGAGATTTGGCATGCAGTCGGAGATC[G/A]TGGATCAGATATTGATTGGTATGTGAAGAGAACAGTGCTTGGTGGCATATATTCAATGTCGGAATTGTACATGGTGACCGATCAT
99958 A G GTCGGAATTGTACATGGTGACCGATCATTCTCCAGAATTCCGCGATACTTGGATGTTCACAGAACGCCGAATCAAAGATGCTTTTGATCTTCAGAAAACC[A/G]TGCAAGAGGCTAAGTACTTGGCAGAAGCTGTTGGTTCTGGCATGGGTAACTCTGTTCAAGGATTCATGAAGAATTTGTTTCAGAGAT
99994 C G AAAAGTTCACTTGCTCGACAAAAGCAATGCTTATCATCAGTTCCAAGATCAACCTCATATGCATTGATATCCGAGAACAGAACCTTCTTTCCAGCTTCCA[C/G]TTCACTAACATCAGAACCAATAGATAATACCTCGCCCATCAAATATCTCTCAAATTTGACAGCTGATTTAGGCAGCAATACTCCACCTGC
99994 G C CCTGCGGTTTTCTCCGGCAAGGGTTCCAGACGAATCAGAACTCTATCAGCTTGCGGAAGAACTTTAGACGGTTCGAATTTCTGAGCCAGAGCTGCTACCG[G/C]GAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAACCTGAGTGAATG
99994 G A AAGGGTTCCAGACGAATCAGAACTCTATCAGCTTGCGGAAGAACTTTAGACGGTTCGAATTTCTGAGCCAGAGCTGCTACCGGGAATGAGCTTTTTTGGG[G/A]GTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAACCTGAGTGAATGAGAAAAGGGAAGGTTTA
99994 G A AGGGTTCCAGACGAATCAGAACTCTATCAGCTTGCGGAAGAACTTTAGACGGTTCGAATTTCTGAGCCAGAGCTGCTACCGGGAATGAGCTTTTTTGGGG[G/A]TGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAACCTGAGTGAATGAGAAAAGGGAAGGTTTAG
99994 G A CGGAAGAACTTTAGACGGTTCGAATTTCTGAGCCAGAGCTGCTACCGGGAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGT[G/A]GAGAAGGGGACAATGAAACCTGAGTGAATGAGAAAAGGGAAGGTTTAGCAGTGAGGATTGAAGACGCCATCAAATTTTCTTCG
99994 A G AGACGGTTCGAATTTCTGAGCCAGAGCTGCTACCGGGAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGAC[A/G]ATGAAACCTGAGTGAATGAGAAAAGGGAAGGTTTAGCAGTGAGGATTGAAGACGCCATCAAATTTTCTTCGCGGGTCAGAAA
99994 C T TCGAATTTCTGAGCCAGAGCTGCTACCGGGAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAA[C/T]CTGAGTGAATGAGAAAAGGGAAGGTTTAGCAGTGAGGATTGAAGACGCCATCAAATTTTCTTCGCGGGTCAGAAAGATGTTTT
99994 G A GCTGCTACCGGGAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAACCTGAGTGAATGAGAAAA[G/A]GGAAGGTTTAGCAGTGAGGATTGAAGACGCCATCAAATTTTCTTCGCGGGTCAGAAAGATGTTTTGAGTTATTTTCCAGTAGG
99994 G A CTGCTACCGGGAATGAGCTTTTTTGGGGGTGACTGAAAATGGGGCGAGAAGGGATAGAGAGTGGAGAAGGGGACAATGAAACCTGAGTGAATGAGAAAAG[G/A]GAAGGTTTAGCAGTGAGGATTGAAGACGCCATCAAATTTTCTTCGCGGGTCAGAAAGATGTTTTGAGTTATTTTCCAGTAGGC
100004 A G CCGAGTGGGCCGGGCCCGTTAGAAGTATGTTTGATGGTTTTAGGTCACCATGGGGTAGGGACCTTTCCTGGTGAAGGTGGTGTAGGCATCGGGCTACGTC[A/G]ATTGCTATTTTTAGCCTCTGAGTTACCGAAAGTCTTGAGTATCTTCTCGGCGTTGACTCGTAAAGATAAAGCGCCAGACTTTCGCC
100004 C T GGGGTAGGGACCTTTCCTGGTGAAGGTGGTGTAGGCATCGGGCTACGTCAATTGCTATTTTTAGCCTCTGAGTTACCGAAAGTCTTGAGTATCTTCTCGG[C/T]GTTGACTCGTAAAGATAAAGCGCCAGACTTTCGCCATAAATGTAATCAGAAACAATAAGCCTTTCTTGCTCCTTTGGCCCCCAATAAT
100004 A G ATCGGGCTACGTCAATTGCTATTTTTAGCCTCTGAGTTACCGAAAGTCTTGAGTATCTTCTCGGCGTTGACTCGTAAAGATAAAGCGCCAGACTTTCGCC[A/G]TAAATGTAATCAGAAACAATAAGCCTTTCTTGCTCCTTTGGCCCCCAATAATAGCCTCTCCAGGGCACGATATTAGGGTGTCTAATGG
100006 G GCTA GCCTACTGGCTTTTGCAGGCGTTTCCCTCTTCCTCCACTTTTCTTTGCATCCCAGCGCCTATGGTCTTATCTCATCAACCATTTACTTCACATCTCTTCT[G/GCTA]ATAAACAAACCTACTATCGTTTTCCGATTATATATAATAAAGGATAGGTTTGTTTTCCATTTGAAGCTCGGCCGTTGATAGAACCTGGA
100006 AT A TATCGTTTTCCGATTATATATAATAAAGGATAGGTTTGTTTTCCATTTGAAGCTCGGCCGTTGATAGAACCTGGATAGTTTACTCTGTTTGAAGAGGCAC[AT/A]TTTTTTTGTTTAGAATCGTACATGCATTGGATACAATGAGATACCAAGAAGCGATCCCGGATTTTCCAGTGCAACCAAATTCTGACCA
100006 T G GAATTTCTAGAACTTCTTCAGGAGAAGAATTTTCGAGTTCAAGAAGAAACCTGAAGATCCAAAAGCGAGCTGCGGGTGTTGCTGGTGCCGAGAAATTTAT[T/G]GCTTCTGCGTCAGAGATGCCACCGCCAACCAATTTGAAAGCTTGCCTTCATTCGAACGGAACTCGTCATGATAGATTTGATAGTCAC
100008 G A CATCTGTTGCTATAATGGAAAGCTCTTCGTTTGTTTGGGCCCTGATGTATTTGTTTGTGAATTTGGTGATAACCCAAGTATTTGTAAGCTTGTCTCTTTA[G/A]GGTTGAATGGATGTGAATATGAGTGGACTCGGCTGGTTGAGTCAGATGGAGACCTTTTGTTAGTTGTTGCATATGACAAACTCTGTCG
100008 C G CTGGAGCTTGGACAGCAGCAGGCCAAGTTGGTGGAGCTGAAATGCTTTGGTGACAGAACATTGCTTGTGGGTTTGGATACTACGTTTTCTCTCCTTGCAA[C/G]CAAGTATCCTGGTTGTAAAAAAATTCTATTTACATACCAGATTTTTTCAGCAGATATGGAACCAAATCTCTTATTCCAGGCCTGTTTA
100008 T TA AGCAGGCCAAGTTGGTGGAGCTGAAATGCTTTGGTGACAGAACATTGCTTGTGGGTTTGGATACTACGTTTTCTCTCCTTGCAACCAAGTATCCTGGTTG[T/TA]AAAAAAATTCTATTTACATACCAGATTTTTTCAGCAGATATGGAACCAAATCTCTTATTCCAGGCCTGTTTATATATGATTGCGAGGA
100010 T C TCATGGGTACCACGAGGAGATCTAGAGTTATTGCTGCTTCTGCTATTCGATCTCTTGGGAGCAACATCCCCAGTTTCCTCGGGAAACGAAGCGGCATACT[T/C]ATCGAGCGAAGGCGAATCCATGGCGGGTGAGGAGGAGGAAGCGGCGGCGATGGATGAACGGAGGCGGCGAGGCGGTGGATGA
100016 CT C CTATTTCTAATTTTGACGAGTTTGTTAGGGTTTTGAAGGAGGAGAAAGGGATTAGGGTTTGTGAGAGGATGCAGCCGGATGGGAAGATTAAGCAGGCTTT[CT/C]TTCTTTGACCCTGATGGGAATGGCTTAGAGGTTAGTACTTTTAATACCCCCCAATCTTGAACAAGCAGTGGCAGGGCAAGGAGA
100030 G A GCAGTCCAGTTTGAATGTTATTCAAAGTCATTGACCTGGTAACCTCCACAGCTTTCGCATGCCTCATCATCTCATCTTCCACTTTTCTTCTACAGGCTGC[G/A]ATTTCTTGCTTCTTTTCTGCTAACGGGTCCCTGGTATCAAACACCTGCCCATCGCCCACATGCCCTGAAGCACCCGAGATCCCGATGCCA
100032 TTCAATCTCAGTC T CTAGTTCGCTCTTTCTGCTCCTCCTCTCCCTCTTCCCCTCCAATCATCAAACCCGTCTCCTATGCTCCCAAACCTAAAGACTCAAATGAAGATCCCAATT[TTCAATCTCAGTC/T]TCAATCTCAGTCTCAGTCTCAGTCTCAACCCCACAGTAGAAATCAAGATACGAGAACAAACTTGACCCGCGAGGATGTC
100032 G A CAATTTTCAATCTCAGTCTCAGTCTCAGTCTCAACCCCACAGTAGAAATCAAGATACGAGAACAAACTTGACCCGCGAGGATGTCCGTTTTGTCAAAGAC[G/A]CTCCCTCCATCTCACCCGTTTCTTACTCATCGAGGGTGGCGCGGCTGCCTGAAGATAGGGTGAGGGAAGTAAGAGATGAGAATGAG
100032 G C AACCCCACAGTAGAAATCAAGATACGAGAACAAACTTGACCCGCGAGGATGTCCGTTTTGTCAAAGACGCTCCCTCCATCTCACCCGTTTCTTACTCATC[G/C]AGGGTGGCGCGGCTGCCTGAAGATAGGGTGAGGGAAGTAAGAGATGAGAATGAGGAGTTGAAGAGGGAAGCGAGGAAGATAGA
100032 G C CGCTCCCTCCATCTCACCCGTTTCTTACTCATCGAGGGTGGCGCGGCTGCCTGAAGATAGGGTGAGGGAAGTAAGAGATGAGAATGAGGAGTTGAAGAGG[G/C]AAGCGAGGAAGATAGAGACTGGGAGAGTGAATAGGTTTGGACTGCAGCAGCAGGAAGAGGAGAACCTTCCGTTTCCAGTTTTG
100032 C A CCCTCCATCTCACCCGTTTCTTACTCATCGAGGGTGGCGCGGCTGCCTGAAGATAGGGTGAGGGAAGTAAGAGATGAGAATGAGGAGTTGAAGAGGGAAG[C/A]GAGGAAGATAGAGACTGGGAGAGTGAATAGGTTTGGACTGCAGCAGCAGGAAGAGGAGAACCTTCCGTTTCCAGTTTTGATCA
100032 G GTGAGAT CTCATCGAGGGTGGCGCGGCTGCCTGAAGATAGGGTGAGGGAAGTAAGAGATGAGAATGAGGAGTTGAAGAGGGAAGCGAGGAAGATAGAGACTGGGAGA[G/GTGAGAT]TGAATAGGTTTGGACTGCAGCAGCAGGAAGAGGAGAACCTTCCGTTTCCAGTTTTGATCAAGCAGGAGAAGCGG
100032 G C AGCGAGGAAGATAGAGACTGGGAGAGTGAATAGGTTTGGACTGCAGCAGCAGGAAGAGGAGAACCTTCCGTTTCCAGTTTTGATCAAGCAGGAGAAGCGG[G/C]AACAGATGATGGCCATGGATCTATCCCAGGCTATTCGTGATGTGAAGGCCAATGCCAAGGCCAAATTTGTTGAAACAGTTGAA
100054 T C GCACAGAAGTTTTGAGTCATTCTTTGTGCTAGTTTTAGCATGCTCCTCCTTCCACTTGGCGTTATCACACTGTGATCACGAGTGGCTACAGAAGATGACA[T/C]AAGAATGGCAAGGCATTCACATTGGCGTTGAAGAGTTGCAATCCAACGTTGTGCACCAAGCCCCATTCCCGATCGTATAAGAGGACG
100056 C A ATGGAAACGGCCATTAAGGACAAAATTCAAGAAGGGATTAAAAGGCAGCAGCAGAGTAGACAACAGAAGAGCCTTTTGAATATCTCAGAAGAGGATGAGC[C/A]AGAAACATCAGAAGCGCCATCCATGTTCATGTCAGAACTGGACTAAGAATTATATAGTGATAGACTGATGATAGTGCTTATATGT
100058 C CA TTTTTTTTTTTTTTAGTACCATAATCACTTCGTTTCCAGTTATTCCCCCCTATAAAGTATCTCGCATGTTCAAAAAATCCGAATCATATTATTCTACAAA[C/CA]AAACAAATCCAAGGGCCAATTAACAAACCACTTCTATTCTAACATTAATGATGTATATTTCACATTTCACGTCAACTTAACACTATGATACA
100058 T C TAGACCATCCTCTAAAACCCAAATCAATTGCAGGTAGACTGGGCTGTATCAGTTGTTACTACCATGCGTATGTATATTACTTTTATGTGCACAATCACTC[T/C]AACTCTTCAGGTGGTAAAGTTGGACTCTTAGAGCACACTGTGATGTTATGAAGCTCCTTCATTTTATCTACAGGGTCACATAGGCCTGA
100058 T C AATCAATTGCAGGTAGACTGGGCTGTATCAGTTGTTACTACCATGCGTATGTATATTACTTTTATGTGCACAATCACTCTAACTCTTCAGGTGGTAAAGT[T/C]GGACTCTTAGAGCACACTGTGATGTTATGAAGCTCCTTCATTTTATCTACAGGGTCACATAGGCCTGAACATCTTGGCATGTCCCAAAC
100060 T C CTAGAGTTAGCAAATCTAGTCCTCCAGCCAATTTGCTTGTAGCCACAGCAGTCTCATTTGAACTTGGAGCGGTTACAAGCGCTAATTCCCAGCCAGTGAC[T/C]CCATGTGCCGAAAAATTAGTTGGTGCAGGGTTTGATGCATCTTCAACAGGTACAATTGCAAGTGCCATAGCATTTTTATTTTCCAATTC
100060 AT A TTACAAGCGCTAATTCCCAGCCAGTGACTCCATGTGCCGAAAAATTAGTTGGTGCAGGGTTTGATGCATCTTCAACAGGTACAATTGCAAGTGCCATAGC[AT/A]TTTTTATTTTCCAATTCCACTGCATCTGCATTTATTTCATCCAACCCCAGCAAATCAATTTCTTTACTGACAGGAACTTCCACTTTCACT
100060 A T ATCTGCATTTATTTCATCCAACCCCAGCAAATCAATTTCTTTACTGACAGGAACTTCCACTTTCACTGGTTCAGGAGGTGGCGTTGGTGCTTTAGGTGCC[A/T]CTTCCTCAACTACTTCAGGAGTTTTAGTATACTCTATTGCCAATACAACTTTCGGCACTTCTTCCTTTATCTGTTCTTTTTGAACTATTGAA
100066 G A AAGAGACTGCTCCAGCAAATCCACTGATGCTAACGCTCTGTCCGTAGTTGATTCTAGTGATTACGGTTACCAGCTCTGAAATCAGCGAAGAAGAAAGCCC[G/A]GCATCTTTCAACTCTGCGTCCAACGTCCGTTGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACT
100066 C T TGATGCTAACGCTCTGTCCGTAGTTGATTCTAGTGATTACGGTTACCAGCTCTGAAATCAGCGAAGAAGAAAGCCCGGCATCTTTCAACTCTGCGTCCAA[C/T]GTCCGTTGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAAT
100066 G A TCTGTCCGTAGTTGATTCTAGTGATTACGGTTACCAGCTCTGAAATCAGCGAAGAAGAAAGCCCGGCATCTTTCAACTCTGCGTCCAACGTCCGTTGAGT[G/A]AGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAATAAAGCATGAATC
100066 G A CTAGTGATTACGGTTACCAGCTCTGAAATCAGCGAAGAAGAAAGCCCGGCATCTTTCAACTCTGCGTCCAACGTCCGTTGAGTGAGTTCATATAATCCGG[G/A]CCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAATAAAGCATGAATCGGTCCAACATTTTCTGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100066 C T CTGAAATCAGCGAAGAAGAAAGCCCGGCATCTTTCAACTCTGCGTCCAACGTCCGTTGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCAC[C/T]GAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAATAAAGCATGAATCGGTCCAACATTTTCTGAACAAATCTATTCATCCGAAACA
100066 T C CCGGCATCTTTCAACTCTGCGTCCAACGTCCGTTGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTG[T/C]GTCTTCCTTATAATAAAGCATGAATCGGTCCAACATTTTCTGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAA
100066 A G TCAACTCTGCGTCCAACGTCCGTTGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTT[A/G]TAATAAAGCATGAATCGGTCCAACATTTTCTGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATC
100066 A G TGAGTGAGTTCATATAATCCGGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAATAAAGCATGAATCGGTCCA[A/G]CATTTTCTGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATCATTCAACAAGCCATATAATTTTCT
100066 T C GGGCCACTTGAGCATTTCAGCCACCGAGTCAAACACTGGCCTGCTTGTGTCTTCCTTATAATAAAGCATGAATCGGTCCAACATTTTCTGAACAAATCTA[T/C]TCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATCATTCAACAAGCCATATAATTTTCTGTAGAAATACGAACTTTTGC
100066 G T TATAATAAAGCATGAATCGGTCCAACATTTTCTGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATCATTCAACAA[G/T]CCATATAATTTTCTGTAGAAATACGAACTTTTGCCATCAGCAGGTTTCAACCCCTTAAAAATGAACTTACTCCCATCCCAAATCCCAAAC
100066 A G TTTTCTGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATCATTCAACAAGCCATATAATTTTCTGTAGAAATACGA[A/G]CTTTTGCCATCAGCAGGTTTCAACCCCTTAAAAATGAACTTACTCCCATCCCAAATCCCAAACCAAGAATCATCATCACTCTTACTGTTAA
100066 T C TGAACAAATCTATTCATCCGAAACAAAGAAAGACCATATCTCCAAAAAATTCTCAAATCATTCAACAAGCCATATAATTTTCTGTAGAAATACGAACTTT[T/C]GCCATCAGCAGGTTTCAACCCCTTAAAAATGAACTTACTCCCATCCCAAATCCCAAACCAAGAATCATCATCACTCTTACTGTTAACACTT
100066 C G ATTTTCTGTAGAAATACGAACTTTTGCCATCAGCAGGTTTCAACCCCTTAAAAATGAACTTACTCCCATCCCAAATCCCAAACCAAGAATCATCATCACT[C/G]TTACTGTTAACACTTAAGTTTAGCAACTTTGCAAATCCCAAAACGTGCAAATTTTTAGGGTG
100068 A G CGCAGTACCACCAGCACCTTGCCGAGACCCTCGACATGGACATGTCGGCCCTACAGTACATGATAAAGGAGTACCCGGGCAACGAGGAGGACAAGATGAG[A/G]TCTGCCATAGGTAGGTTCGGGCTGTCGGGCAAGGCCCAGGTGATGCCCATGAAGAACCTGTCCGATGGCCAGAGGAGCCGTGT
100068 T C AGCACCTTGCCGAGACCCTCGACATGGACATGTCGGCCCTACAGTACATGATAAAGGAGTACCCGGGCAACGAGGAGGACAAGATGAGATCTGCCATAGG[T/C]AGGTTCGGGCTGTCGGGCAAGGCCCAGGTGATGCCCATGAAGAACCTGTCCGATGGCCAGAGGAGCCGTGTAATATTCGCCTG
100068 T C ATGGCCAGAGGAGCCGTGTAATATTCGCCTGGCTGGCCTGGCGGGTCCCAAACATGCTTCTCCTCGATGAGCCCACCAACCATTTGGACATAGAAACAAT[T/C]GACTCATTGGCTGAGGCCCTCAATGAATGGGATGGTGGCCTGGTTTTGGTTAGCCACGATTTTAGGTTGATCAGTCAGGTTGCAAA
100078 G A AAGAACGGGTCATGGTTCTATCCCGGTTCATGTTCTCGACCATCCATAAAAGAAAGAAGTTTTTACGTGGGAATTTCAGATTGCCTTTGTAGACTAGGCG[G/A]AACGATAGCAGATTGCACCAAGGGCATGAGATGAATAGCGGTAGTTGGATTGGGGCGGATGTGAATTTGACAATGGCCCATTGAA
100078 G A TGTTCTCGACCATCCATAAAAGAAAGAAGTTTTTACGTGGGAATTTCAGATTGCCTTTGTAGACTAGGCGGAACGATAGCAGATTGCACCAAGGGCATGA[G/A]ATGAATAGCGGTAGTTGGATTGGGGCGGATGTGAATTTGACAATGGCCCATTGAAGCCCAAGGACGCAGTTCTTGCAAAGAGTGT
100078 AT A TGTATGTACTTGGATTTGAGTGGGCTTGGCTTTTTTTGAAATTTCCCGGTATTGCAGTTGAAGGGAAACTCCAATTTCTCCACATTATGTTCTTAGGACT[AT/A]TTTTTTTGGTTTGACAAAGCAGGTGAACTTTGTGTGATTCTTTCAGCACAATCTGACTGTTGCAAGCAATCCTGATTAATTAGAGATCT
100086 A G GAGCTTCTCAATGAAACTGAGTTAACCGACATATCGCAGTTGTTTGACGGTCCAACTACCAATACTGGGATTGACAATCAAAGCTTATACGGTATGAATC[A/G]GAGAACTTTGAAGAGGCAGAGACTGGAGGAGGATAATTGCCTGCAGGGGCACAAATTAACTAATGTTAATTCTTGGACTGCAGGG
100086 A G GAAACTGAGTTAACCGACATATCGCAGTTGTTTGACGGTCCAACTACCAATACTGGGATTGACAATCAAAGCTTATACGGTATGAATCAGAGAACTTTGA[A/G]GAGGCAGAGACTGGAGGAGGATAATTGCCTGCAGGGGCACAAATTAACTAATGTTAATTCTTGGACTGCAGGGAACTTTTCAAACC
100086 A G GAGGCAGAGACTGGAGGAGGATAATTGCCTGCAGGGGCACAAATTAACTAATGTTAATTCTTGGACTGCAGGGAACTTTTCAAACCAATTAGATTTTGAA[A/G]GCCAGGCATTAATCAATCAGCAGTTGATGTTTAACTCGCAGCTGGATATGCAGCAGAAATGGTTAAGTTAGAAATATATCTGTATT
100090 C G ACCCACTTGAATTCTTGGGATCGACCCTCCTTGCCAAAAACCAAGCATAGACGCCTTCACCAACATGCGCAGCCACAGCTGCTACAAACACCAATCGAGT[C/G]AGCCACAAAGATCGGAACATGAACAAGGCGATGGCCTGCAGATACTTGAGCAGACCTACCGGCGGTAGATATGCTGCAGCAAAAA
100090 T G AATATGATATTGTTTTAGATAAGCCTTCCTGAGGGGTTACCATTGGAACGTACCCTAGCTCTTCCCTTGCCTTTAGATATGAGAAGTAATGCGTCACCCC[T/G]ATCTTGTAAACTTCAGCAGGAAGAAGAAGTGGGTTTGGAAGCCAGCGTCGATTAAGCCATGGATAAAGTAAAGTATAAAAGGCTGAA
100090 A G TGGATAAAGTAAAGTATAAAAGGCTGAAATTACATGCGACAAGGTGACTGCATGGTTAACATCCAATGTAATACTTGGCAACCCATATTCCAGATTTTTA[A/G]GTAGAGGACCGATGATAAAATCAAAAGTATTCACCGGTGATCCATCACAAATGAAGTAAGGTTGTCCAGCAGCAATAGGATGTTTTC
100092 G C CAAAAGTCACTTTGCGAGGGTTATGACTAGTGGGAAGGTCAAGCCTAACACCCATTAGCAACACCATTCTCTGCTACCTTACCTTCTTTTGGTGCAGGAG[G/C]ATTTTCTTCTTTGATTTTGGTACTACCATTCTCAACAATGATGTTATTGTCCTGAACATTCATTGATTCATTCAAGTTCAGAAGTTTTGG
100092 G A TTGCAACCATTACCAGCTTGTGCAGCTGCTGTTGCTTAGCCCGTTTTTCTTGCATTATATTTTCCCTGGTTTCATAGAAGCCAAAATCATCCAGTATCGT[G/A]GTTTTACTGACATGCTCCTTGAAGATTTTGAGCATCTGAACACCCTGCTCAAGTTTTATCTCTTGAGTGTCTCTGCTGTTTGTCACTGGTT
100100 AT A AAACCGTAATAGCCAATGGCGACCGTAGCTAGACTCAGAGGAACAGCAACCGTGCTTCCAAATTCAGCAAACGTCGAACAGGCAAGAAAACGAACCTTCG[AT/A]TTTTTTCAAGATGGCGTGTAGAGCTCTGCCGTCGGTGATGGAGATTTACAATTTACATGATGTCGTCACGATTTCTCAGCTCAGA
100100 C T CAAACATTGTTGACCATGCCAAGCAAAGGCATCATATTCTGGGTCAATACATTCTTGGACGTGAGGTTAAGGATGCGGGGAAAAAAGACGAAGGAAATTC[C/T]GATTTTCTCAAGAAGTTCTATGAGAGCAACTATTTCTGATCAACTTTCAATTGTTCACCTGTGATTTTATATGCATTTATACTCTTCTG
100100 T C CCGATTTTCTCAAGAAGTTCTATGAGAGCAACTATTTCTGATCAACTTTCAATTGTTCACCTGTGATTTTATATGCATTTATACTCTTCTGTTTGTAGTC[T/C]GTCATTTCGCTGAACTCTGCATCAATAAGGTTTATGCTGAATTATTCATCTCGCCGGTTAGAGATGAAAACATTCTTATATGGGTCCGAATA
100100 C G GTTCACCTGTGATTTTATATGCATTTATACTCTTCTGTTTGTAGTCTGTCATTTCGCTGAACTCTGCATCAATAAGGTTTATGCTGAATTATTCATCTCG[C/G]CGGTTAGAGATGAAAACATTCTTATATGGGTCCGAATAGATGCCTTGATATTTACTTTCTTAGTTTGACTTCTTAAATTTAATCACTGTTCT
100106 C T CGGCTCTCTACCAGATCTAGCTTCCTTGTGCTTCCCCATCTTCCAATTCTTTTCTGATTCGATCTATCCATCCTCCCTTTTTGCTTCACATTTCTAGCAT[C/T]TCATCGATGCTTTCCTTTCTCTCCTCCTAGCCCTAGCCCATGCATCCCTTGAATCCACTTATGAGACCTCACAACTTATTTTCCTTGTTGCTTTA
100106 C A GCTTCCTTGTGCTTCCCCATCTTCCAATTCTTTTCTGATTCGATCTATCCATCCTCCCTTTTTGCTTCACATTTCTAGCATCTCATCGATGCTTTCCTTT[C/A]TCTCCTCCTAGCCCTAGCCCATGCATCCCTTGAATCCACTTATGAGACCTCACAACTTATTTTCCTTGTTGCTTTACAGTTAAATGGCCTGAGC
100106 T C TTTCTGATTCGATCTATCCATCCTCCCTTTTTGCTTCACATTTCTAGCATCTCATCGATGCTTTCCTTTCTCTCCTCCTAGCCCTAGCCCATGCATCCCT[T/C]GAATCCACTTATGAGACCTCACAACTTATTTTCCTTGTTGCTTTACAGTTAAATGGCCTGAGCATCTCCTTAGGTTGCTCCAGTATGGTAGGC
100106 A G AGACCTCACAACTTATTTTCCTTGTTGCTTTACAGTTAAATGGCCTGAGCATCTCCTTAGGTTGCTCCAGTATGGTAGGCTTGCTTCAAAGCTTGTTTTG[A/G]CCAGCTAGGAGTCAGTGTTCCCACGGACTTCTCCTTTGTCTGCCCTTATCCCCTCAGACTAGCTTGGTTCCTTGTGCCGAGCTAGCTAGG
100114 G T CCATTCCACTGAGGAGAATGGATAGTAAAAGTCAATTGGACTGTCTTAAACGTGGCATTGAGTTGGTGAAAAAAGGTGCATCCGTATTTTTCTTTCCAGA[G/T]GGCACACGGAGCAAGGATGGCAAATTGGGGTCCTTCAAGAAAGGAGCATTCAGTGTTGCTGTGAAAACTGGTGTGCCAGTGGTGC
100114 C T AACTCAGGTTCTGTGCAAGTTATCATTCACAAGCCTATGATCGGAAAAAATGCTGATGAACTGTGTAGAGATGCTAGAAGTGTAATTGCGGAAACACTCA[C/T]TCTGCATGGTTTTGGAGTGCACAGAAACGAGTAACTCGATCTTAGTTCTGATCAAAGACGT
100118 C T TATACATAGTATCTACATGTTTTGCTATAGTAACCAAACTTTTGGATGTCATTTACAAGTCCTTATCGAGCCCTGATATAAATAGTGGAGGACCTCTTGA[C/T]GTTTCTGGCTCATCTTCTTCCAAGAGATTCATAAGACTCTTTGGTTGTCTAGTCTGTTGCCTTTTAAGCCCCTCTTGAATTTTGTCCTTAAT
100120 T C AACACCCAGAGTGTTCCACAGCTTTATTGTCTTGTCTCTTGATCCAGAAACAATCTGACGATTATCAGCTGAGAAAGCAACGCTCAGTACATCCTTTGTA[T/C]GTCCAACGAACCTACGAGTCGTCTGACCAGTGCTCAAGTCCCATAGACGCAGGGTGCTGTCCCAGGAGCCAGAGAGAGCAAACTGTC
100126 G A TCATGGAAGAAAGAAGCAGGAGATTACACATCTGCAAGGCTGCGTGAAATATTCGAGCAATACGGCAAAATAGAGGATGTCGTAATAAGATCAAAGAAGA[G/A]CAGAGGTTCTGCCCTCATCGTTATGTCCTCCAAAGACGCTGTTGTTGCAGCTGCCTGTGCAATGAGTGGAGGAGGCCTTTCAAAC
100126 T C GAGAAAACTTCAAGAGGCTAGTGAAAAGAGAAAACAAACACAATAGGGTCGGGAAAGAACTCAATATTCATTCATCATCGGGTGAAGGAGACTCGGGTAT[T/C]GCTGTTTAACTGATCTAGCATCATAAGCGGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAA
100126 T A AGGCTAGTGAAAAGAGAAAACAAACACAATAGGGTCGGGAAAGAACTCAATATTCATTCATCATCGGGTGAAGGAGACTCGGGTATTGCTGTTTAACTGA[T/A]CTAGCATCATAAGCGGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTA
100126 G A TAGTGAAAAGAGAAAACAAACACAATAGGGTCGGGAAAGAACTCAATATTCATTCATCATCGGGTGAAGGAGACTCGGGTATTGCTGTTTAACTGATCTA[G/A]CATCATAAGCGGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTAACAA
100126 T C GGGTCGGGAAAGAACTCAATATTCATTCATCATCGGGTGAAGGAGACTCGGGTATTGCTGTTTAACTGATCTAGCATCATAAGCGGTATTATCCCATTTT[T/C]CGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTAACAAATATGGTAAAGATAACATAATATCTGTA
100126 G A GGTGAAGGAGACTCGGGTATTGCTGTTTAACTGATCTAGCATCATAAGCGGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGAC[G/A]GAGTAAACTGAATGAATGTAACAAATATGGTAAAGATAACATAATATCTGTAAGTGGACTCTTCCCTCCGTGGCAGTGCGAAGTAGT
100126 A G ATAAGCGGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTAACAAATATGGTAAAGATAACAT[A/G]ATATCTGTAAGTGGACTCTTCCCTCCGTGGCAGTGCGAAGTAGTTAGTGAATATATATTTAATCATCCGTGAGATACGACTTTCTGTT
100126 T C GGTATTATCCCATTTTTCGAATATTGCTGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTAACAAATATGGTAAAGATAACATAATATC[T/C]GTAAGTGGACTCTTCCCTCCGTGGCAGTGCGAAGTAGTTAGTGAATATATATTTAATCATCCGTGAGATACGACTTTCTGTTTGTGCA
100126 G A TGGACTGAGGTTTGGTACAAAGACGGAGTAAACTGAATGAATGTAACAAATATGGTAAAGATAACATAATATCTGTAAGTGGACTCTTCCCTCCGTGGCA[G/A]TGCGAAGTAGTTAGTGAATATATATTTAATCATCCGTGAGATACGACTTTCTGTTTGTGCAAATCAATTTAAATAAATATATTTGGTA
100126 C T AACAAATATGGTAAAGATAACATAATATCTGTAAGTGGACTCTTCCCTCCGTGGCAGTGCGAAGTAGTTAGTGAATATATATTTAATCATCCGTGAGATA[C/T]GACTTTCTGTTTGTGCAAATCAATTTAAATAAATATATTTGGTACCCATCACTATGATTTTATTTCAAGTGCTTGATGTAATGAGACAAC
100138 C T AACGTGATTGCTATGTTGCTTACATTCAGTGTAACTGCAGAGTGGGTTCTATGTGTCTTCGACATGAAAGAGATATCAAAAGTTGCCCTTGTGGCATCGA[C/T]TGTACAGTATTTGTTAGAAAAGACCTGTCAGATTTTGAAGTTGCTGCAAAATCGTTTGAAAAGGAAACTAATATTGTTGAGATAGTTG
100140 A G AGGAATAGAACAAAAGTTGATAATTCAGGTTGATAAGGCTTATGGCAAGGAAGATGGAAACATCTATTGATTGTATAAGCTGATGATCCTCCTAAGTGTC[A/G]CTTGGGAAATAGTGATTCAGTCTTCTGGTTTATGCTTGAGGCTTCATACATAGAAAGGATGGGATTGGCTCCAGGCTTCAGAGGAA
100140 C CT AGCCCTAATCCCTGGGATTTCTAGTAACCACGGCGCTTTTCGTAGGGTGGGTTTGGATCGGTTAACCTGCCAGCGCTTCCAGAACGACCAGTGTAGCTCC[C/CT]CCAAATGCACCACCCACAGATCCTGCATGGCTACCGTAGCGATCGGGACGACGAACATCATCTATATCATAGCGATCTGAATAAGG
100162 A T CATATAAAGTGGGCCAGGAATATGAAGCTTTATTATGTCTATTTTCCTTCCATTGGCATCGGTGGTATTTGAAAGAACAGATATGGCTTCAACTGCTCGC[A/T]CGTACTGTGGGTCATCTTTGTCATCGGTCCATGATAAAAGCACCACGCCAGGCTTAACAAAACAGCACATATTATCAATATGACCATTG
100170 C T TTCTAGGATCTGTCATACTTTCATTTGCATTTTCTATGTTTAAACAGAGAAAGCTTGTGAAGAGACACGCAGCAGAGATATTCTCATCGGTGATCATCGC[C/T]GCATTGTTCTCTCTTTACTCAACCGCATTCTTAGGTCGCATTGTCGGACTAGAACCTACTTTAACCGTGTCCATTTTACCAAGGTGCATT
100170 C T CAGAGATATTCTCATCGGTGATCATCGCCGCATTGTTCTCTCTTTACTCAACCGCATTCTTAGGTCGCATTGTCGGACTAGAACCTACTTTAACCGTGTC[C/T]ATTTTACCAAGGTGCATTACTGTTGCATTGGCACTAAGCATAGTGTCCTTTTTTGAAGGAGCAAACACATCTCTCACAGCTGCCGTGGTT
100170 C G TGGTTGTTCTGACCGGACTAGTCGGAGCAAATTTTGCTCAGGCAGTCATGGACAAACTTCGATTAGGTGACCCTATTGCTAGAGGAATAGCAACTGCTTC[C/G]AGTGCACATGGATTGGGTACTGCTGCATTGTCTGCAAAAGAACCAGAAGCACTTCCATTCTGTGCCATAGCTTATGCACTCACTGGA
100174 T C GAGACACATATATTTCAGCTAATTCTCTCCAAGCATCATGATCCACCATAAAAATTTCAAGATATTTATTAAGATATTCAACAGCAGCAGATATATTTCC[T/C]TGTGCTTTTGCCATAGCTACCCGTCTTTTATGGATAACTTGATCTAGTGGGTTGTCTTCTAGAAGAATTGCATAAGCTCTATCTGCCTCAG
100174 C A ATTCTCTCCAAGCATCATGATCCACCATAAAAATTTCAAGATATTTATTAAGATATTCAACAGCAGCAGATATATTTCCTTGTGCTTTTGCCATAGCTAC[C/A]CGTCTTTTATGGATAACTTGATCTAGTGGGTTGTCTTCTAGAAGAATTGCATAAGCTCTATCTGCCTCAGCCCATGCACCCTTCGCTTCAA
100174 A G ATATATTTCCTTGTGCTTTTGCCATAGCTACCCGTCTTTTATGGATAACTTGATCTAGTGGGTTGTCTTCTAGAAGAATTGCATAAGCTCTATCTGCCTC[A/G]GCCCATGCACCCTTCGCTTCAAGCAGCATTCCTTCTAGCTTGCCAACTCGTGTACTCCCAGGAAACTGCTTAGAAAGAACATTAATGCAA
100174 G A GCATTCCTTCTAGCTTGCCAACTCGTGTACTCCCAGGAAACTGCTTAGAAAGAACATTAATGCAATCCTTGGCAATATCGACTCGCTGACAATCCATAGC[G/A]GCAACGGCCACCTGCTCATAAAGAGTCCATTCTTCAGCACCGAGTTTAGATCTGGCTTTGGAATCATTCAAAATCGAGAGACCATGCT
100174 C T GAGAGACCATGCTTCAACACTTTGTCAGATCTGCGAGCTTTGAGCTTTTTCACAAGGCAAAGATATTCCCAAGCGCTGCCGCCACCATTATCAACCTCGA[C/T]TTCGAGGCTAGAAAGTTTCGATTCTTCGAGTGCCGATGCCATGAATCGTGAATCCAAGTAGGAAAGAAAGTGCCTGCCGGCTTTATTT
100174 A G AAGTTTCGATTCTTCGAGTGCCGATGCCATGAATCGTGAATCCAAGTAGGAAAGAAAGTGCCTGCCGGCTTTATTTATTCAGATATAATTTTGGAGCAGT[A/G]CTTGAGCAACGGGGTGAACCAAGGTACGGGTGATACGGAGTCAAAATAGAGGGTGGATGCTAGATGGGGGGAGAAGATGGTACG
100188 T C AAACGCCTGCCACTAACGCTTTTGTGTTTCTCCCGACTTTGGTGTTTGTTATCAGCATCTTGAGTGGTGTGCTTGATTTGATTCTAGTCAACTCACCCGA[T/C]TGAAACATAATCGTACTTCCATAAGTGCTCACTGTGTTATCAATTCCAGAGGGTTTTCCATGGATAATCTTTTCGCCTTCATACGCCCATT
100188 G A TGAACCCATGGATTGATGTGTAGATATAAAGAAAGGCAGCAATTCCAGAGGACAACCATATCTTAGCTTCAGGAATATTGTGTTCCTCAACTAATGTGTC[G/A]ATCACTTTATTGCATTGCAATGAGCAAGGCCTAGGAGATGAAGCAAGATTAGAGTTCATTTCACTCAAAGAATTTTCTAGTTTCTTAG
100200 GC G CCTCCCTAAATTTGAATAAAATTCTGTATAGTATAGACATCCAAATGCTCTTCAGGGATTTGACTGCTCCAATTCACCCTCTTTGTCACATCAGCTCCCG[GC/G]CCCCTCGTTCTTATATTCCCCATAAAAAAGGGTATTCAATGCAAAATCTCCACTCCATTCCGACCACCCTTCCGGCCTGATTATCTTCTCC
100200 A G TTATAAACACGGTTCTAGAGTACTCCTTCCATGGTCTTCCAAGGTAAACCTTGTGAATTGCAGGGTTCTGATTGTAGTAACTCCAATAGTCATCGCTTCC[A/G]TTCACGCTACATTTGTAGAACACAAAACCAGTCGACTGGGCCGGGTCTGTTCTTCCATGGGCCGTAACCGTATTTGTCTCCCCTTTTCCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100200 T C TTCTAGAGTACTCCTTCCATGGTCTTCCAAGGTAAACCTTGTGAATTGCAGGGTTCTGATTGTAGTAACTCCAATAGTCATCGCTTCCATTCACGCTACA[T/C]TTGTAGAACACAAAACCAGTCGACTGGGCCGGGTCTGTTCTTCCATGGGCCGTAACCGTATTTGTCTCCCCTTTTCCCGGGTTGAGTTG
100200 A G CTTTTCCCGGGTTGAGTTGGCGAGGCAGTACATAGATCAAGCAATCCTGAAATACCGATGCCGAGTTGCCAAAGATGAAATCCACAGTGCCCGATATTCT[A/G]CAGGATTTGTACAGTTGGCGCAGAGAGTGCGCATAAAGCGTGTCTTGATGACCGAGAAATTCAACAGTTTCAATAATGGAGCGGT
100204 A AT AACTGGATTTCAAGGGCTTATTTCCTGGTTGTTTCTTCCAGCTGTAGCTGCTGGCATTATTTATGATGTGCCGGGTGAATACTTGTACATTGGAGCAGCA[A/AT]TTTTTGTGGTTATATTTTGCGCAATTGAAATGGGAAAGCCTGATAAACCCCATAATTTTGAGCCTCAAATATATAACATGGAAAGTAA
100216 G GA CGATTGGTAAGGGGATGTTCTCCGGAGACGCTCTGGATTTGCTCAAGGGACTGGTGCACTGTGAGATCTCAGGTGAATGCAATTTGTTATCCGATGTAAC[G/GA]AAATAATGGAGAGTAACAAGTGCAAAGTAGGAAATGGGAAAAATGATTATATTCCGACTGTAGTAGAACATCTCAAGCACTTAC
100216 T C TACATTATGATGCTTCGATCTGCAGAACTAAATGGGAGAAAAGTCCGTCAACTCCAGCAGGTGAATACGCGTACATTGAAGTGATCATCGGATCAGACCG[T/C]CTCATTGTCGATATAGATTTCAGAGCCGAGTTCGAAATAGCCAGATCAACAAAATTCTACCGATCCCTGCTTCAGTTCATACCATCCA
100218 A G AAATAATCAATGCTGAACTCCTCCTTCATTAGCACGCTTAAAGATCAAAGCCTGAGCTGCAGCAGCATCATTGGAGGAGATGG[A/G]AGAGGCGAAGGCATCCTTAACCTGCTGGGCACTGAACTGGAAAGTCTTGCATGAAAGAGAGTTGAGAAGGGCTGCTGTTCCTTCACGGTACAATGCACCA
100218 T C ATCATTGGAGGAGATGGAAGAGGCGAAGGCATCCTTAACCTGCTGGGCACTGAACTGGAAAGTCTTGCATGAAAGAGAGTTGAGAAGGGCTGCTGTTCCT[T/C]CACGGTACAATGCACCAACCCCATCGCTTCTGGTGTTTTTAAGGGCATCGGGTATGGTCAAGTTCTTGCCAAATGCTGCACTGCA
100218 G A CCTTAACCTGCTGGGCACTGAACTGGAAAGTCTTGCATGAAAGAGAGTTGAGAAGGGCTGCTGTTCCTTCACGGTACAATGCACCAACCCCATCGCTTCT[G/A]GTGTTTTTAAGGGCATCGGGTATGGTCAAGTTCTTGCCAAATGCTGCACTGCAGGCTGCACCGAACGTCTGGCCTATCGTTCCCCAG
100218 G A AGGTTTAAATGGAGGGAAAGAACCAGGATCAGGCAATGTCGGGCTGGGAACACCTGGAAAATGAGGAATAGTAGGAGTAACTGGAACTGTAGGGACAGGG[G/A]TGACTGGAGGACTAATGATCGGAGTAACTGGAACCGTGGGGACTGGGACGACCGGAGGATTAATGATGGGGGTAACCGGA
100218 T C GGTTTAAATGGAGGGAAAGAACCAGGATCAGGCAATGTCGGGCTGGGAACACCTGGAAAATGAGGAATAGTAGGAGTAACTGGAACTGTAGGGACAGGGG[T/C]GACTGGAGGACTAATGATCGGAGTAACTGGAACCGTGGGGACTGGGACGACCGGAGGATTAATGATGGGGGTAACCGGATG
100220 GT G TCTTTCTTTACAAAGAAAAACAAACAATGATTTCACTCTAGTACGGAAGCTTCTCCTTGTTTTCGAAGTTGAGAGACTCTATGCCTTTGAGAGCAGATTC[GT/G]TAGTTTTTGATCGATGGCATTCTAGCGGAGGAGGAAAACCTGTGCTCTGAAGAAATCGGAGGAGAGTGCCTTTGGGTAGCTGAAAT
100220 T A AGAGACTCTATGCCTTTGAGAGCAGATTCGTAGTTTTTGATCGATGGCATTCTAGCGGAGGAGGAAAACCTGTGCTCTGAAGAAATCGGAGGAGAGTGCC[T/A]TTGGGTAGCTGAAATTCTTTGGAAAGCCACGGCTTCAGGAGTAAGAGGGCGAGCTGGTAATTCAGCTTCAGTGCCATGAAATGCC
100220 T A GCCACGGCTTCAGGAGTAAGAGGGCGAGCTGGTAATTCAGCTTCAGTGCCATGAAATGCCTCTCGGCTGCTGGAAACAGCAGCTCGCCTTGAGGAACTGC[T/A]TGGTCTACCCAAGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACA
100220 T A CGGCTTCAGGAGTAAGAGGGCGAGCTGGTAATTCAGCTTCAGTGCCATGAAATGCCTCTCGGCTGCTGGAAACAGCAGCTCGCCTTGAGGAACTGCTTGG[T/A]CTACCCAAGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAACT
100220 G A TAATTCAGCTTCAGTGCCATGAAATGCCTCTCGGCTGCTGGAAACAGCAGCTCGCCTTGAGGAACTGCTTGGTCTACCCAAGAAAGTGGAACTCGATATC[G/A]TAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAACTACCTGCGTTTATAGCCGGAGATGAAACTCG
100220 C T TGCTGGAAACAGCAGCTCGCCTTGAGGAACTGCTTGGTCTACCCAAGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGC[C/T]GGATTCTTTTGCTTCAACAAACTACCTGCGTTTATAGCCGGAGATGAAACTCGTCTTCTAGAGGAGTCTGCTGCCAACCACCCACTTG
100220 T C GAGGAACTGCTTGGTCTACCCAAGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAAC[T/C]ACCTGCGTTTATAGCCGGAGATGAAACTCGTCTTCTAGAGGAGTCTGCTGCCAACCACCCACTTGTTCTTCCCTCTTCCGCACCTGAAT
100220 C T TACCCAAGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAACTACCTGCGTTTATAGC[C/T]GGAGATGAAACTCGTCTTCTAGAGGAGTCTGCTGCCAACCACCCACTTGTTCTTCCCTCTTCCGCACCTGAATGTCGCTCAGCATTACC
100220 T C AGAAAGTGGAACTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAACTACCTGCGTTTATAGCCGGAGA[T/C]GAAACTCGTCTTCTAGAGGAGTCTGCTGCCAACCACCCACTTGTTCTTCCCTCTTCCGCACCTGAATGTCGCTCAGCATTACCGATGAC
100220 T G CTCGATATCGTAGCCTCTTTTGGAGTAAATGGCTCAGTATTAGCCGGATTCTTTTGCTTCAACAAACTACCTGCGTTTATAGCCGGAGATGAAACTCGTC[T/G]TCTAGAGGAGTCTGCTGCCAACCACCCACTTGTTCTTCCCTCTTCCGCACCTGAATGTCGCTCAGCATTACCGATGACAGGAGGCATAG
100224 A G TGGTCGACCCACCGACAAGCACCACATCATGAACCGAGCTCTTGTCCATCTTGGCATCCCTCAAACACTTCTCAACCGGCTCCATACACTTCCTGAACAG[A/G]TCCATGTTCAGCTCTTCGAACCTGGCTCTTGTTATCGTGGAGTAGAAATCGATGCCCTCAAACAGCGAATCGATCTCTATTGTGGTTTG
100224 G A CAACCGGCTCCATACACTTCCTGAACAGATCCATGTTCAGCTCTTCGAACCTGGCTCTTGTTATCGTGGAGTAGAAATCGATGCCCTCAAACAGCGAATC[G/A]ATCTCTATTGTGGTTTGAGCTGTAGAAGACAAGGTCCTCTTCGCCCTCTCGCAAGCAGTCCTCAGCCTTCTCAGAGCTCTTGGGCTTCC
100224 C T CTTCGAACCTGGCTCTTGTTATCGTGGAGTAGAAATCGATGCCCTCAAACAGCGAATCGATCTCTATTGTGGTTTGAGCTGTAGAAGACAAGGTCCTCTT[C/T]GCCCTCTCGCAAGCAGTCCTCAGCCTTCTCAGAGCTCTTGGGCTTCCGCTTATGTCCTTCTTGTTCTTCCTTTTGAACTCCTGAACGAAA
100224 C T ACCTGGCTCTTGTTATCGTGGAGTAGAAATCGATGCCCTCAAACAGCGAATCGATCTCTATTGTGGTTTGAGCTGTAGAAGACAAGGTCCTCTTCGCCCT[C/T]TCGCAAGCAGTCCTCAGCCTTCTCAGAGCTCTTGGGCTTCCGCTTATGTCCTTCTTGTTCTTCCTTTTGAACTCCTGAACGAAATGATTC
100224 G A CGAATATTCCTTCTTCGATGGTGAGCAGAGACACATCGAATGTGCCGCCTCCAAGATCAAAGATCAACACGTTCTTTTCACCGGAGCTGCTTGCCTTCTT[G/A]TCCAGACCGTAAGCAATGGCTGCAGCAGTTGGCTCGTTGATAATCCTCATTACATTGAGGCCTGAAATGACACCAGCATCCTTCGTGG
100224 G A GACCGTAAGCAATGGCTGCAGCAGTTGGCTCGTTGATAATCCTCATTACATTGAGGCCTGAAATGACACCAGCATCCTTCGTGGCCTGACGCTGTGAGTC[G/A]TTGAAGTAGGCAGGAACCGTCACCACTGCATTTTTTACTGTGGTGCCAAGGTAGGCTTCTGCTATTTCTTTCATTTTTGTCAGAACCA
100238 T C CAGCAGGTGAAACCCCCACCGGACCAGTAGGTGAAACACCCATCGGACTGGCAACCGGGATACCAATAGCTGCACATAAGCTAACATCTGGAGTATCAAC[T/C]TTACAAGCAGTGGGCAATGTAAGGGCCTTGGTAGTATCGATCTCCAGCCCCAAAGGGTTGCCTCCACTGGAGAGCAACTGACATA
100248 T A AGGATGGCGTGATAGGCACGACATGCCCCATACAACCTGGAAGAAACTTCACATACAAGCTGCAAGTGAAAGATCAGATTGGAAGTTTCTTCTACTTTCC[T/A]TCTTTGTATTACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCA
100248 T C TGATAGGCACGACATGCCCCATACAACCTGGAAGAAACTTCACATACAAGCTGCAAGTGAAAGATCAGATTGGAAGTTTCTTCTACTTTCCTTCTTTGTA[T/C]TACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATT
100248 A G GCACGACATGCCCCATACAACCTGGAAGAAACTTCACATACAAGCTGCAAGTGAAAGATCAGATTGGAAGTTTCTTCTACTTTCCTTCTTTGTATTACCA[A/G]AAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTTTACTC
100248 A C AAACTTCACATACAAGCTGCAAGTGAAAGATCAGATTGGAAGTTTCTTCTACTTTCCTTCTTTGTATTACCAAAAAGCAGCCGGCGGCTTTGGAGGCATT[A/C]GAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTTTACTCTTCTTATCGGAGACTGGTACAAGACCAA
100248 A G ACTTCACATACAAGCTGCAAGTGAAAGATCAGATTGGAAGTTTCTTCTACTTTCCTTCTTTGTATTACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAG[A/G]ATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTTTACTCTTCTTATCGGAGACTGGTACAAGACCAATCA
100248 C T AAGATCAGATTGGAAGTTTCTTCTACTTTCCTTCTTTGTATTACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCC[C/T]GTTCCGTTTGATCCACCAGCCGGCGATTTTACTCTTCTTATCGGAGACTGGTACAAGACCAATCATACGAATTTAAGAAAAGCACTGG
100248 T C CTTCTTTGTATTACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTT[T/C]ACTCTTCTTATCGGAGACTGGTACAAGACCAATCATACGAATTTAAGAAAAGCACTGGATGCTGGTAAAATGCTCCCTTTCCCTGACG
100248 C T ACCAAAAAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTTTACTCTTCTTAT[C/T]GGAGACTGGTACAAGACCAATCATACGAATTTAAGAAAAGCACTGGATGCTGGTAAAATGCTCCCTTTCCCTGACGGAATACTAATA
100248 C T AAGCAGCCGGCGGCTTTGGAGGCATTAGAATCCTCAGCAGGCCGTTAATCCCCGTTCCGTTTGATCCACCAGCCGGCGATTTTACTCTTCTTATCGGAGA[C/T]TGGTACAAGACCAATCATACGAATTTAAGAAAAGCACTGGATGCTGGTAAAATGCTCCCTTTCCCTGACGGAATACTAATAAACGGA
100248 A C GCGATTTTACTCTTCTTATCGGAGACTGGTACAAGACCAATCATACGAATTTAAGAAAAGCACTGGATGCTGGTAAAATGCTCCCTTTCCCTGACGGAAT[A/C]CTAATAAACGGACGTGGATCCAATGGTGTATCTTTCACTGTTGACCAAGGCAAGACATACAGATTCAGAATATCAAATGTAGGCCTAC
100248 A C TCCCTTTCCCTGACGGAATACTAATAAACGGACGTGGATCCAATGGTGTATCTTTCACTGTTGACCAAGGCAAGACATACAGATTCAGAATATCAAATGT[A/C]GGCCTACAAAACTCACTTAACATCCGGTTTCAAGACCACAAAATGAAGCTAGTAGAAGTGGAAGGGACCCACACCCTACAGTCGACG
100248 C A AAACGGACGTGGATCCAATGGTGTATCTTTCACTGTTGACCAAGGCAAGACATACAGATTCAGAATATCAAATGTAGGCCTACAAAACTCACTTAACATC[C/A]GGTTTCAAGACCACAAAATGAAGCTAGTAGAAGTGGAAGGGACCCACACCCTACAGTCGACGTACTCCTCCATAGACGTGCACGTA
100248 T C GACGTGGATCCAATGGTGTATCTTTCACTGTTGACCAAGGCAAGACATACAGATTCAGAATATCAAATGTAGGCCTACAAAACTCACTTAACATCCGGTT[T/C]CAAGACCACAAAATGAAGCTAGTAGAAGTGGAAGGGACCCACACCCTACAGTCGACGTACTCCTCCATAGACGTGCACGTAGGGCA
100248 A T ACTCACTTAACATCCGGTTTCAAGACCACAAAATGAAGCTAGTAGAAGTGGAAGGGACCCACACCCTACAGTCGACGTACTCCTCCATAGACGTGCACGT[A/T]GGGCAGTCTGTCTCCGTTCTTCTCACAGCCGACCAACCATCAAAAGACTTCTACATTGCAGTC
100258 C T TCCTTAAAGAAGTAGGCGCCTCCTCCACTCCTCGAGCCCAAAACAAGCCTCCAAACCCCGTAAAGCAGTTAAAACAAACCGTGAGCGACATCAAACACGA[C/T]GTGGAGTCCCAAATTAAGCAAACCAAACAGACCGAAATGCGTGTCCAGAACATCAAAAGGCGGCTCCAGAAACTCCACATAGGCGG
100258 C T ACGACGTGGAGTCCCAAATTAAGCAAACCAAACAGACCGAAATGCGTGTCCAGAACATCAAAAGGCGGCTCCAGAAACTCCACATAGGCGGCCTCAACAA[C/T]GCCATCAACTCCAACACCATCGTGGCCGTCCTCATCGCCACTATTGCCTTCGCCGCCATTTTCACCGTCCCCGCCCAATTCGTCGAA
100262 C G TGGTTTCAACAGTGGCAGTTTTATTAATTCCAACTTCGTAGCACCTAACAACGAAGTTCTCTTTATAAGACAACCCATCCTCCACCAAGCTGCCCATCCT[C/G]AGCTTCCCAGCCACTCCATTCCCTTCCTTCAAAACCGCAGGCGCAGCGACGGCTGAGGCGGCGGAGCACCGCAAAGACGCTTTGTAAC
100262 G T TCCCAGCCACTCCATTCCCTTCCTTCAAAACCGCAGGCGCAGCGACGGCTGAGGCGGCGGAGCACCGCAAAGACGCTTTGTAACATCGTGCACCGGCGAC[G/T]GAACATTGAATTTTATCCGGAACAGGAAGACGCGCGACGTGGGTGGGAGCCACCGCAGCGGGAGGAGTGGGGAGAGTGGATTT
100262 A G GAGCCACCGCAGCGGGAGGAGTGGGGAGAGTGGATTTGAGCATGTGTGATTCAAGATTCGGATCGGAGGTTCTCAACCGCACGATTTTGGTGGAGGAGAA[A/G]GAGGAGGGGTGATGAAAATACACAAATTAATGGTGGAATCGGAATCGGTGGTGAGAACGAAAGGGTAATTAAATGGGAGAG
100262 T C AGTGGATTTGAGCATGTGTGATTCAAGATTCGGATCGGAGGTTCTCAACCGCACGATTTTGGTGGAGGAGAAAGAGGAGGGGTGATGAAAATACACAAAT[T/C]AATGGTGGAATCGGAATCGGTGGTGAGAACGAAAGGGTAATTAAATGGGAGAGCGTGACTGCGGTCGGTCTTTATTTTATTGCG
100266 A C GCTATGGATTTGTTCAGTTTGAGCTTGAGGAGGCTGCTCAAAATGCTATAGAAAAGCTTAATGGCATGTGCCTCAACGACAAGCCAGTTTATGTATCTCG[A/C]TTTCTACGCAAGCAAGAAAGAGATAATGCGGCAAGCACTGCCAAATTTACAAATGTTTTTGTAAAGAATCTTGCTGAATCAACAACG
100278 G A CAAATATTTCTTGGGTGCCATTACCATGGTGCACATCCCAGTCAACAATTAAGACTTTTTTGGCACCTGCACTCTGAGCTGCTAGCGCAGCAACTGCAGC[G/A]TTATTGTGGAGGCAAAAACCCATTGCTTGTTTTATACCTGCATGATGTCCAGGTGGCCTTACAAGAGCAAAACCATTCCTACAGCGTC
100278 C A CAACTGCAGCGTTATTGTGGAGGCAAAAACCCATTGCTTGTTTTATACCTGCATGATGTCCAGGTGGCCTTACAAGAGCAAAACCATTCCTACAGCGTCC[C/A]ATAACAAGTGAGCGAGCAAGATCAGCACAGAAACCTGCAGCGATCCGTGCAGCAGATGCTGAATGGCCATTAGCGTATGTGTCCGG
100278 T G AGCGAGCAAGATCAGCACAGAAACCTGCAGCGATCCGTGCAGCAGATGCTGAATGGCCATTAGCGTATGTGTCCGGAGTAAAATAGCTGGAAAATAACCG[T/G]CTTGTATATTCTACAGTTTCTATATGATCCAATGAATGTACCAACTGCAATTCCTCTCGAGTTATTTCTCTAGCAGGTATCCAGTAG
100278 T G TCCGGAGTAAAATAGCTGGAAAATAACCGTCTTGTATATTCTACAGTTTCTATATGATCCAATGAATGTACCAACTGCAATTCCTCTCGAGTTATTTCTC[T/G]AGCAGGTATCCAGTAGCATTTTGCAGGAAATCCTTCTGCAGAGGCAACACCAGCTGCTACTGCAAGCAGTCGATCTGGTCTCTCTGGGT
100284 C T TACCTTCAGAACCTGATGCATCAAGACTTTGGTTTTCGATTTCAGTAGAATCTGATCCTTTATTGTTGATGGATGTCTCTTCTCCCCAAGAAGATGTTCT[C/T]GCAATAGGCCGATATCCACTGGGTATGTTTACTGACTCTGCTAGAGACGATCTATCATCACTGAGCGACATCATCAATTGCCTCTTGAAA
100284 C T TGATGGATGTCTCTTCTCCCCAAGAAGATGTTCTCGCAATAGGCCGATATCCACTGGGTATGTTTACTGACTCTGCTAGAGACGATCTATCATCACTGAG[C/T]GACATCATCAATTGCCTCTTGAAAGCTTCTAACTTTGATAGTTCTTTCCCCAATTTTTTTGCAGTCAAAGCCAGTGTATCCCTCTCTTTCA
100284 T C TTCTCGCAATAGGCCGATATCCACTGGGTATGTTTACTGACTCTGCTAGAGACGATCTATCATCACTGAGCGACATCATCAATTGCCTCTTGAAAGCTTC[T/C]AACTTTGATAGTTCTTTCCCCAATTTTTTTGCAGTCAAAGCCAGTGTATCCCTCTCTTTCATCAATTTACCATTTTCGTCAGTTGCCTCTCT
100284 G T TCAATTGCCTCTTGAAAGCTTCTAACTTTGATAGTTCTTTCCCCAATTTTTTTGCAGTCAAAGCCAGTGTATCCCTCTCTTTCATCAATTTACCATTTTC[G/T]TCAGTTGCCTCTCTAAGCCTTCTTTCCGAGTTTTCAAACATCTTATCCAAATCCTTGATCTGTTCTTGCAAATCAACAATTCTTTTGTCCTTTTC
100284 T C AGTTCTTTCCCCAATTTTTTTGCAGTCAAAGCCAGTGTATCCCTCTCTTTCATCAATTTACCATTTTCGTCAGTTGCCTCTCTAAGCCTTCTTTCCGAGT[T/C]TTCAAACATCTTATCCAAATCCTTGATCTGTTCTTGCAAATCAACAATTCTTTTGTCCTTTTCTGCATCATTTTGCTTCAATTTCATTATCTCTG
100284 C T GAGATGCGATCGCCATGGACGTGATCTTGCGAGCTAGGTCTAACTGATCGTACGGGTCGGTTGGTATTATTGCCAAAATCTCATCTGAAAGGCCGAAATC[C/T]ATGCCTTTGTGCGCCATTACATCCCTAGCTTTGATTTTCTTTGGAATATTTTCCGAAAAGATTT
100292 T TA TCTGCTCCTTCTTCTGCTCCTGGCCCTTCTCCTAAAGCTTCTGCTCCTTCTCCTTCTCCTGCTTCTGCTCGTAATGTTGCTCCTACTTCTTCACCAACAG[T/TA]GGCTCCTTCAATAGCACCAACTACGGGCTTAGCAGCAGCGCCAGCACCTTCTATAGCACCTAAATCACCAATTGCTGATTCACCGACCAGT
100296 C A CGAAACTACAATTTTAAATGACCTTCTTTCCCATCTACCACCACCACTTGGATGTTTGTTAGCAACTCCATTACTTGCACTACTCAAATTGCCACCATCA[C/A]AACTACCATTTTCATCAATTGCTACTGTATGCCGATGATAAAAGGAGGCAAGAAGAGAGAGCGCACTAGGAGAGTTTTGTTGAATTAGG
100296 A G GATAAAAGGAGGCAAGAAGAGAGAGCGCACTAGGAGAGTTTTGTTGAATTAGGCAAGATAAAGGTTGGTGATGGTTAGAGATTAATGATGAGTAGAAATC[A/G]TTAATTGTGCACCATGAATTTCCTCTTTTATCATACATATACTGAAAGCTCTCCCTACTAGTCCATCTCAAGCGACAAACGGGATG
100298 G A ATCAACTATGTAGAAATACATACATGCCAAAGTTGAAAACAGAGTAAAAACATATAATGTTTAGTACTCAGTTACATTGATAACAAACAATTATTACTCA[G/A]CATCTGTATGGAAACAGAAATTTAGGCAATACAAAAAATATAACACCATCTATATTTATCTTGTAATACAAACGGAAATGAAATCTTTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100298 A G ATCTGTATGGAAACAGAAATTTAGGCAATACAAAAAATATAACACCATCTATATTTATCTTGTAATACAAACGGAAATGAAATCTTTTGAAAGAAGGGAA[A/G]TGCAGGTAGAGTGGAAGTAGCGTGACTATTTAGTAGATTTTGTGGCCATGTACTCTGCGTCGTTCCAACCCATGAACAAAGGTCTGG
100298 T C ATTTAGGCAATACAAAAAATATAACACCATCTATATTTATCTTGTAATACAAACGGAAATGAAATCTTTTGAAAGAAGGGAAATGCAGGTAGAGTGGAAG[T/C]AGCGTGACTATTTAGTAGATTTTGTGGCCATGTACTCTGCGTCGTTCCAACCCATGAACAAAGGTCTGGAGCCTCATCCTTTCCAAGT
100298 G A GAAGTAGCGTGACTATTTAGTAGATTTTGTGGCCATGTACTCTGCGTCGTTCCAACCCATGAACAAAGGTCTGGAGCCTCATCCTTTCCAAGTCTGCATA[G/A]GCTGGGCCTATCGCCCTTAACAGCATCAGCAGAAGCAAATGATTCAAGCAGTGCCATTTCTTCAGGGGTGAGTTTGACAGACAGTGC
100298 C A ATGCTAAATTAACTGTCTTGTACACTGGTTTGGCAAGTGCTTAGGCCTTCACAGAAATAGTTACTTTTCTCAATTCCTCATGTGTTAAAATCACAGGTTA[C/A]TATTCTCACTTTGTCATGCATTGAAATCACCATGATCTTAATTTGGCTAGCCGTTCCATGAACCACTTTACTTTCTCCCCAACCTTAGCAAG
100298 A G GCTAAATTAACTGTCTTGTACACTGGTTTGGCAAGTGCTTAGGCCTTCACAGAAATAGTTACTTTTCTCAATTCCTCATGTGTTAAAATCACAGGTTACT[A/G]TTCTCACTTTGTCATGCATTGAAATCACCATGATCTTAATTTGGCTAGCCGTTCCATGAACCACTTTACTTTCTCCCCAACCTTAGCAAGC
100320 A AT GAAAACATGGCACATTGGGATTTTCCAACTTAATTCTCTCAAGGAATATTCCAATATCTGCAGCAACAGAATCAAGCGAAGGTACAAATCCATGCAATCC[A/AT]CACTACCTCCATGACCTGTCCAGTCCATTGCATAAACTCCAAAGTTGCATGTCATTAGTTGCTTTGCAAAATGTAAGTATCTGCCACT
100320 A G AATCCACACTACCTCCATGACCTGTCCAGTCCATTGCATAAACTCCAAAGTTGCATGTCATTAGTTGCTTTGCAAAATGTAAGTATCTGCCACTGTGCTC[A/G]TTGAGACCATGTATAATCACCAAAATTCCTCTGACATCTCCGTTTCCAATTCCCCACTTCCTACAAAACATCAAATTCCTTCTTTTCCCCTC
100320 CT C TAAGTATCTGCCACTGTGCTCATTGAGACCATGTATAATCACCAAAATTCCTCTGACATCTCCGTTTCCAATTCCCCACTTCCTACAAAACATCAAATTC[CT/C]TTCTTTTCCCCTCAATCAAAAACCAACCTCCACCATCCATCTCCAAGCTCTCCGCTATCACCCTTCTCTTCCTCACATCCTCCTCCTCCAAAC
100320 AAC A ATTGAGACCATGTATAATCACCAAAATTCCTCTGACATCTCCGTTTCCAATTCCCCACTTCCTACAAAACATCAAATTCCTTCTTTTCCCCTCAATCAAA[AAC/A]ACCAACCTCCACCATCCATCTCCAAGCTCTCCGCTATCACCCTTCTCTTCCTCACATCCTCCTCCTCCAAACTCGAACCGAACCGTCCAAT
100320 C T GAACCGAACCGTCCAATAAATCGCCTTTTATCCGGCAAGCGAGGAGACGATAACGTGGCGGCGGAGGTTGTTCTGGTGCGACGGAGGATGGAGTAGAGGA[C/T]CAACGACTGTATGAAAATGAAGAAGTGGAGGAGGATCCTCAAAATAACTATGCAGCGTGCGAAGATTGGAATAATCCGCCCAC
100324 T C AATCAGCAGCCTAGTGGACCGGATCTGGTTCTTTATGGCTCGTTCAAACCGGAGAAGGGAAGCCTCGTCTACGGTTTGGGTAGGGTCGAGGAGTGATCTA[T/C]GATCTGTCAGGATGGAGGATAGGTTCCTCGAAAGATCTACGAAGAGACGGAGCTGCTTGGAGTTTTCGAGCTTAAGTTTGCGGG
100324 G A CGAGGAGTGATCTATGATCTGTCAGGATGGAGGATAGGTTCCTCGAAAGATCTACGAAGAGACGGAGCTGCTTGGAGTTTTCGAGCTTAAGTTTGCGGGC[G/A]TAGGAAGCGTAGGCAGCAGCAAGGGCGGCGTGGTCAGAGAGTTGCTTTCTGATGACGTCAGCACGGGCGCGTACCGGGTCGG
100324 A G GGTTCCTCGAAAGATCTACGAAGAGACGGAGCTGCTTGGAGTTTTCGAGCTTAAGTTTGCGGGCGTAGGAAGCGTAGGCAGCAGCAAGGGCGGCGTGGTC[A/G]GAGAGTTGCTTTCTGATGACGTCAGCACGGGCGCGTACCGGGTCGGAACTGATGGCTAGAAGGGATCTGCGAGCAATGGAAT
100326 A G GCTTGCTGGAATGTGCTTCAGTGGTAAGCCAGCTAAGACAAAGAAGCAAGCTCAAAAAGATGCTGCATTGGCTGCGTGGTGTGCATTGAAACAATTGCCA[A/G]ACATGGTGCCAACAACTTTGTCTTCCTCTTCCTCTTCACAATCAGAACACAAGGCAAACGATGAGCAAGAACAGGCAATTGTTGCA
100326 T C AGTGGTAAGCCAGCTAAGACAAAGAAGCAAGCTCAAAAAGATGCTGCATTGGCTGCGTGGTGTGCATTGAAACAATTGCCAAACATGGTGCCAACAACTT[T/C]GTCTTCCTCTTCCTCTTCACAATCAGAACACAAGGCAAACGATGAGCAAGAACAGGCAATTGTTGCAAAAGTTCTTTCAAGCCTCCG
100326 C T GTCTTCCTCTTCCTCTTCACAATCAGAACACAAGGCAAACGATGAGCAAGAACAGGCAATTGTTGCAAAAGTTCTTTCAAGCCTCCGCCAATCAGAAATC[C/T]ACGGCCAGTCTATTCTACACGTCAACAATAATAACAATAACCATACACAAAGAACAGTTCCATATGCCCACGATATAAACTATTGTGCT
100326 A G AGAACAGTTCCATATGCCCACGATATAAACTATTGTGCTGTGCCTTTCCAAAACTACCCTTACCCAAATTTCCTACCCGACGTCTCAATGCCCCAAATGT[A/G]GCACCATTTCAGTGCTCCTAGGCCCAATATCCTACCCTTCCAAAACTACCCTTTCTACAGCATCAGTCCACTTCCTCAGTTCGAACACCCT
100326 G A TATGCCCACGATATAAACTATTGTGCTGTGCCTTTCCAAAACTACCCTTACCCAAATTTCCTACCCGACGTCTCAATGCCCCAAATGTAGCACCATTTCA[G/A]TGCTCCTAGGCCCAATATCCTACCCTTCCAAAACTACCCTTTCTACAGCATCAGTCCACTTCCTCAGTTCGAACACCCTTCCTATTTTCCGA
100328 C CT GCCTCAGTATCTTATGGAATCTTCATGTGTCTGGAATGTTCTGGAAAGCACCGCGGCCTGGGGGTCCACATCAGTTTCGTCAGATCTGTCACCATGGATT[C/CT]TGGTCCGAAATTCAGTTGAAGAAGATGGAATCTGGAGGGAACGATAAGTTGAATCAGTTTCTGGGGATGTATGGGATTGCCAAGG
100328 A C TGTTCTGGAAAGCACCGCGGCCTGGGGGTCCACATCAGTTTCGTCAGATCTGTCACCATGGATTCTGGTCCGAAATTCAGTTGAAGAAGATGGAATCTGG[A/C]GGGAACGATAAGTTGAATCAGTTTCTGGGGATGTATGGGATTGCCAAGGAGATGGATGTTGTTAAGAAGTACAATTCTAATGCTG
100328 C A GGGTCCACATCAGTTTCGTCAGATCTGTCACCATGGATTCTGGTCCGAAATTCAGTTGAAGAAGATGGAATCTGGAGGGAACGATAAGTTGAATCAGTTT[C/A]TGGGGATGTATGGGATTGCCAAGGAGATGGATGTTGTTAAGAAGTACAATTCTAATGCTGCCTCTGTTTACAGGGATAGGATTCAG
100328 T C CACCATGGATTCTGGTCCGAAATTCAGTTGAAGAAGATGGAATCTGGAGGGAACGATAAGTTGAATCAGTTTCTGGGGATGTATGGGATTGCCAAGGAGA[T/C]GGATGTTGTTAAGAAGTACAATTCTAATGCTGCCTCTGTTTACAGGGATAGGATTCAGGCATTAGCCGAAGGTCGACAATGGAAG
100330 AG A TGGATCCAACGGGCAATACCTTAGTTTGCCCAGTCAGTGGTCAAATATTTGATGGATGGATTGATGAGAATGCAGAACCAGATAATGAGGAAGATATGGT[AG/A]GGGGGTGTTACAGATGATGCTGATGAGCCATTTATGGGTTCTGGACGTGTTGCACGTGCATTTAGTCTTGGTTACAACTGCGCC
100340 GA G TGAATCAAACACTGCAATTCTGCAACTTTCATCACACAAATGATGGAATGAACGGGAAGTCACCGAAGGATCGCTTTTTCTTAGTGCTTTGACCATAAGA[GA/G]AAATCTTCACACTTTCTACAATAGCATTATCATTGAGCTGTTGGACTGTAACAATTTTAGGATGACCAAAACTCAGAAAGTTCTTCCT
100340 T C ACACAAATGATGGAATGAACGGGAAGTCACCGAAGGATCGCTTTTTCTTAGTGCTTTGACCATAAGAGAAATCTTCACACTTTCTACAATAGCATTATCA[T/C]TGAGCTGTTGGACTGTAACAATTTTAGGATGACCAAAACTCAGAAAGTTCTTCCTCGTTTATCTTCTCTGTTCAATCGGATCTATTTGG
100340 T G AACAATGAGGCTGTAGATGCCGCTGACCCTATGAAGAGGAGAACCACCACTTCCATGGTAATGGCACAGCGGACGACCAGTAGCGGTGGTAAAAAGACCT[T/G]GTTTGACGTTGCTCGAGATGGTGCGGCGGGGTGAATATTAGGTATTTAGCGGAGCGGACACAATAGGCAGCAGAGTAAAATTG
100340 G A CCCTATGAAGAGGAGAACCACCACTTCCATGGTAATGGCACAGCGGACGACCAGTAGCGGTGGTAAAAAGACCTTGTTTGACGTTGCTCGAGATGGTGCG[G/A]CGGGGTGAATATTAGGTATTTAGCGGAGCGGACACAATAGGCAGCAGAGTAAAATTGGACATTAGGGTTAAAAACAAAAATAG
100340 CA C GTTTGACGTTGCTCGAGATGGTGCGGCGGGGTGAATATTAGGTATTTAGCGGAGCGGACACAATAGGCAGCAGAGTAAAATTGGACATTAGGGTTAAAAA[CA/C]AAAAATAGGAAAAGAAGAACGAAGGAAAAGAAAATTTAGGAGAAAGAACGAAAGCAGCAGAAAATGGATAGGGCTAGAGTA
100344 C T ATCCCTTCGGATTTGGCGATGGCGAGGCGTCTGATCTCGACGAGGGCGGCAGCGGCCATGGCCAGGATGGAGATGAAGAGGCCGATTCCCATGCGCTGGA[C/T]CTCGCTGAAACCCCTCTCCTTCCCTGTGAAGCGGCGCACGACAGGCACGAGGAGGCTATCGTAGAGTGGAACCCATAGGATGA
100356 GA G TATCATCAAATTAACCACCATCAAAGAACCAAACAAATTCCACAAAACATCCAGCACTCGAGCTCGCACTACCGATCCCAATATACAAACCTTTTATGGC[GA/G]AAAAACACAATATAAAAACATCATCTAGCTAGCGCCGTTATCGCCAGCACTACCTCGCTCAAACAAACCTCCAAAAGGCCAGGCCAT
100356 T A ACCGATCCCAATATACAAACCTTTTATGGCGAAAAACACAATATAAAAACATCATCTAGCTAGCGCCGTTATCGCCAGCACTACCTCGCTCAAACAAACC[T/A]CCAAAAGGCCAGGCCATCATCATAACCCTCCTTCCACCACTCTCCTCCCTCTCAACCACATCCGACGCAGCCCCTCTCTTCACCTCCTGC
100356 A G CACAATATAAAAACATCATCTAGCTAGCGCCGTTATCGCCAGCACTACCTCGCTCAAACAAACCTCCAAAAGGCCAGGCCATCATCATAACCCTCCTTCC[A/G]CCACTCTCCTCCCTCTCAACCACATCCGACGCAGCCCCTCTCTTCACCTCCTGCGCAGGCATCTGGAACCTGCACACAGGGCAGGAGC
100356 T C CAACCACATCCGACGCAGCCCCTCTCTTCACCTCCTGCGCAGGCATCTGGAACCTGCACACAGGGCAGGAGCTGTGCAGCTCCAACCACGGCAGTATGCA[T/C]TCCCCATGAAACAAATGCTTGCACGGCATCATCCTTCCCTCAATTCCCACCTCCATCTCCTCCAAACACACCGAGCAAGTCGACCCAC
100356 T C TCTGGAACCTGCACACAGGGCAGGAGCTGTGCAGCTCCAACCACGGCAGTATGCATTCCCCATGAAACAAATGCTTGCACGGCATCATCCTTCCCTCAAT[T/C]CCCACCTCCATCTCCTCCAAACACACCGAGCAAGTCGACCCACCCTTCTCCACCTTCACCCTCGGCATCCCTTCCACGGCCAACTTCTC
100364 T TA ATAGGATATATTTCACTACTGCTTGTACAAGGTAGAATAGAACTCTACTCGACTTAAAATAAAACACATCCCACCCTACATACGAACTTAATAAACAAGT[T/TA]CGAGAACATTAAACAAACAAGAAACGAACACCATTACATGAACCATTTGCCCGCTTACAACATACGTTGATGCTCTGGATTACAACTA
100364 G C CCCACCCTACATACGAACTTAATAAACAAGTTCGAGAACATTAAACAAACAAGAAACGAACACCATTACATGAACCATTTGCCCGCTTACAACATACGTT[G/C]ATGCTCTGGATTACAACTAACATGAACAAACCAACTTCAGTTTCGCTTTGGAGGAACATACTGCACATTGTTATCAGCACACATGCCCT
100364 C T GATGCTCTGGATTACAACTAACATGAACAAACCAACTTCAGTTTCGCTTTGGAGGAACATACTGCACATTGTTATCAGCACACATGCCCTGGTATTCCTC[C/T]GGGAGTTCCTCGGAGACTGCAAGTGTGTAACATCCAGGGATGAATCGCCCTATTCTCAACCATCGAGCAGCCCAACTTCTGTTTGGAT
100364 T C CCAAAGCTGGTCGGAATCTGAGCAAAGGTTGGCCCTGCCATTCTGTCGTCTTCCTCCATCATATAATCACGGCTGCTTCCTCCTTTTCCGCCCTTCATTG[T/C]GATTTCGCACCTTCTGCTCCTTCCAGGGCGGCCCTGGTAAATGGTAATACGGTGATTTGGGAAAGAATAGAAGAACTCGATGCTGATG
100364 C T AATCTGAGCAAAGGTTGGCCCTGCCATTCTGTCGTCTTCCTCCATCATATAATCACGGCTGCTTCCTCCTTTTCCGCCCTTCATTGTGATTTCGCACCTT[C/T]TGCTCCTTCCAGGGCGGCCCTGGTAAATGGTAATACGGTGATTTGGGAAAGAATAGAAGAACTCGATGCTGATGCTGGAGGAGGATTC
100394 C T CAGCCTACGTTGTCTGCTGCAGCTCTTGCAGAAGCTACGAGGAACACGCTACGAGCACCATCTCTACAAACTCTTCTAGAAGATTTACCTGACCATGTTG[C/T]TCCTCACACTGGTTCAGGAGGTGATTCTGAAGGGAAGAGCGTATCGGACAAAGGTCTGAGAAACAAGAAGATGAAAAATGATATCA
100394 C T TGATAGTTGGTGCTCATGCAATCATGGCTAATGGTGGAGTAATAGCACCAGTCGGGATAAATATGATTGCTCTTGCTGCCAAAAGACACGCTGTACCCTT[C/T]GTTGTTGTTGCTGGTAATCACAAGTTATGCCCTTTGTATCCACACAACCCAGAGGTTTTGCTAAATGAGTTCAGATC
100396 T C AGATGGGCAAGAAAAAATACTGAAACAAATTACCTCAAGATCCCCAACCAGTACTCAGACCTGCACCAAAGCAAGGGTCTTGACTTCTCCCCAAAGCAAA[T/C]CTATTAGAATTATCAAAGATGAAAGATATCAAACTCCCAAGAAAACACACAATAACCCACTTTACACTTCACCAAACACAGCAAGCCT
100396 T C GAAAACACACAATAACCCACTTTACACTTCACCAAACACAGCAAGCCTCACAAGTTACTACAATTACAATGGCACTAGGGTTACAGGGAATCAACCAGCA[T/C]TGCCGAATTACATGACTGCCACTGAGTCCACTAGGGCACGGAGCACCCCGAGGCAGAGGTCATCCACACCAGAACGAGATAGAGCT
100396 A G TGTCTCCGGCATCAGTTTCTGACATCGGTAGATGGATGTTTTGAGTTATGGCCGAGCCTTGCAGGTATTAGCGAAATAATGTATGTTTGTTTAAAGCTTT[A/G]TATTTTAACGTTATTGGGAGTGGGTATTGGGAGCTTATTGGCATTAGAGTGTGCAAGCTTGCTAGTAAATGTTCTATGTGCATGAGTA
100396 T C GTTTCTGACATCGGTAGATGGATGTTTTGAGTTATGGCCGAGCCTTGCAGGTATTAGCGAAATAATGTATGTTTGTTTAAAGCTTTATATTTTAACGTTA[T/C]TGGGAGTGGGTATTGGGAGCTTATTGGCATTAGAGTGTGCAAGCTTGCTAGTAAATGTTCTATGTGCATGAGTATATCAAGTGAATTC
100400 T C GAGGATTTCATGGATGCGGAGGATTACATCAATGATGATGAAAGGTTCAACGTGACGTGGAGGATTATGGAGCTGTTCCCGAAAATTGATGTGGGTCCGG[T/C]CGATGGGTTTGTTAGCATTGATGAGCTGACGGACTGGAATGTGAAGCAGGCATTGAAGGAGGTGTTGCACAGGTCGGAGAGGG
100402 A G AAGAAGCGGTTTATCCGAGATCAGATTGACCTATATTTAAGCGAGTTAGAGAACGAGATTAAGGAAGAAGAAGAAAGCGAGAAAGAAGAAAGCGGGGTGA[A/G]AGAAGAAGAAGAAGACGAAGAGAGTGAAGTGGAAGAAAAAGCAGTGGAGGATGCTAAGGCGACTACAAAGAGAAAATCATC
100402 A G TTTAGCAAACCATGCAGTCTTTCCCCACAACTTGAAGAGTTCATCGGAGAATCTGAGTTAGCCAGAACTGAAGTAGTGAAAAGAATATGGGCTTATATTC[A/G]TGAGAACAATCTCCAAGATCCAAGCAACAGAAGAAAGATTTTATGTGATGAGAAATTGCAAAATCTTTTCAAAGTGAAAAGCATCGA
100406 T C TCGCAGCCTGCTCGCTTCTTCTAAAGGTTACGGAGGTGCGGCTTGGGAAAAGCAGATCAGGAACTCCGCGGCGCCACGTCAGCATGGAAGAATGTCGGTT[T/C]TGGTAACTGGAGCTGCAGGGTTTGTCGGTAGCCACTGCTCTCTTGCTCTTAAAAAACGTGGCGATGGCGTTGTTGGGTTGGATAA
100406 G C CTAAAGGTTACGGAGGTGCGGCTTGGGAAAAGCAGATCAGGAACTCCGCGGCGCCACGTCAGCATGGAAGAATGTCGGTTTTGGTAACTGGAGCTGCAGG[G/C]TTTGTCGGTAGCCACTGCTCTCTTGCTCTTAAAAAACGTGGCGATGGCGTTGTTGGGTTGGATAACTTCAATTCTTACTACGATC
100406 C T ACTCCGCGGCGCCACGTCAGCATGGAAGAATGTCGGTTTTGGTAACTGGAGCTGCAGGGTTTGTCGGTAGCCACTGCTCTCTTGCTCTTAAAAAACGTGG[C/T]GATGGCGTTGTTGGGTTGGATAACTTCAATTCTTACTACGATCCCTCGCTCAAAAGGGCAAGACAGCAGATGCTTAGTAAGAATGG
100408 T C ATTTGGATGGCGTAAAACTCGGCGATGTGCAAGCCACCATAAGTGGAGTTTTCACTGCTGCCTTCTTCTTATTTATATCTCATGCCCGCCCTTTACAGAC[T/C]CTCTCTTCCGCTCGCCCACATCCCAACATATTTTGTGCTTATGTATTCCTTTCCCTAATTGGTCAATTTGCGATGCATCTAACCTTCTTGAT
100416 T C ACAGGAAACCCGCCACGATTGATGACGTCAGCTTACGACGTAGCACGAGCGTATGTCGAACCGCACGAGCGATTCTCCTCACCTCTTTTGAATACGCTCC[T/C]GTCTCGATCAAACTCGCGATCTCCTTCAGATGCTGGAGAGTTGAGACTGAAGGAGAAGGAGACGGATCGGACTGAGGCTGGGGCG
100422 A T GTGGCCTTTTTTTTTTTTACGATGCAATCAACAAAAAATAGTAAACACAAAGAAACTCAATAGTTCATGGCAGGATTCAATTAAAAATGACATAACAA[A/T]ATTCAATGTCTGCAACCTAGAATGAAAATGATATGATTTTAACTCCGGGCAAAACAACATAAACTGCAGTAGTTCCTCAGTTTCTGTAGCC
100422 T C TTTTTTTTTACGATGCAATCAACAAAAAATAGTAAACACAAAGAAACTCAATAGTTCATGGCAGGATTCAATTAAAAATGACATAACAAAATTCAATGTC[T/C]GCAACCTAGAATGAAAATGATATGATTTTAACTCCGGGCAAAACAACATAAACTGCAGTAGTTCCTCAGTTTCTGTAGCCTCTGCTGTT
100422 C T ACACAAAGAAACTCAATAGTTCATGGCAGGATTCAATTAAAAATGACATAACAAAATTCAATGTCTGCAACCTAGAATGAAAATGATATGATTTTAACTC[C/T]GGGCAAAACAACATAAACTGCAGTAGTTCCTCAGTTTCTGTAGCCTCTGCTGTTTCTTCTTCCTCTAGCCTTCTCAAACTTCCTGCCCTT
100422 T A TTCTGTAGCCTCTGCTGTTTCTTCTTCCTCTAGCCTTCTCAAACTTCCTGCCCTTGGATCGCACATAAGGCTTAGTATGACTGTGAGGAACACCTGGTGC[T/A]GGTCCAAAGTGCTTCACTGCTTCCCTTGCATTCTTTGGGCCTCTCAATAGAACCGTGTTCTGTCCAAGTGGGGCACGAAGGGCAAGCTG
100428 G A CACGGCTAGCAGGATTTGACGCCATCATTTTATGTAAGACTATGCTATAATTTTCATTGTGATTGGGTACCGGAGTTGTATCTGGAGATATATTAGTAGC[G/A]CAAGGATTATAAAGTACCAGCTGATTATTAGCATCTGCAATAGAACCATGGCCATTGTTCTCTCCATCAACCACGGCTTTATAAAGAG
100428 TAGC T GAATTTTCACAGTTCTGTTGTTGTGACAGTGGCTCTTTGTCTTGAATTTCAGCGGCAATTGACGATTTTTCATTGGAATAATCCTTACTACTAGTAACCT[TAGC/T]AGCAGCAGTGTCCACAGGCTTTTTAATAATAAGTTTCACTTGTCGTTGTTGAGCAGAGCCATCTTCATTTGCAGCTGATGGAGGATC
100428 C G GCCATCTTCATTTGCAGCTGATGGAGGATCTTGAATATTCGATTGCTTTTGAGTAGACTCAGCCGAATTTTCCATGGGTGATAGGAATATATTTGGTCCT[C/G]AAAGAAGATCAGCAACAGCGTGAAACAACCACCTGATTTGTGATGAGAAATCCCTTATCAGCTAGGTGTATAGCTTAGCCTTGCAGAA
100428 A G CCATCTTCATTTGCAGCTGATGGAGGATCTTGAATATTCGATTGCTTTTGAGTAGACTCAGCCGAATTTTCCATGGGTGATAGGAATATATTTGGTCCTC[A/G]AAGAAGATCAGCAACAGCGTGAAACAACCACCTGATTTGTGATGAGAAATCCCTTATCAGCTAGGTGTATAGCTTAGCCTTGCAGAAG
100428 T A ATTTGCAGCTGATGGAGGATCTTGAATATTCGATTGCTTTTGAGTAGACTCAGCCGAATTTTCCATGGGTGATAGGAATATATTTGGTCCTCAAAGAAGA[T/A]CAGCAACAGCGTGAAACAACCACCTGATTTGTGATGAGAAATCCCTTATCAGCTAGGTGTATAGCTTAGCCTTGCAGAAGGATAAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100428 A G AGCCGAATTTTCCATGGGTGATAGGAATATATTTGGTCCTCAAAGAAGATCAGCAACAGCGTGAAACAACCACCTGATTTGTGATGAGAAATCCCTTATC[A/G]GCTAGGTGTATAGCTTAGCCTTGCAGAAGGATAAAAGAAGAACGAGCATAATCGCAATTGTTTGCTTGCCCAGGGATTTTGCTTTGG
100428 A G GGTCCTCAAAGAAGATCAGCAACAGCGTGAAACAACCACCTGATTTGTGATGAGAAATCCCTTATCAGCTAGGTGTATAGCTTAGCCTTGCAGAAGGATA[A/G]AAGAAGAACGAGCATAATCGCAATTGTTTGCTTGCCCAGGGATTTTGCTTTGGGGCTTTTATCCAGTAGGCCAACAGT
100436 C T GCTTCATCATCTCCAGCTGTGAATCGTTCGTACACATCCCCTGCTTGGTTATATCGTAAGCAACTGAGATTTGGGCAGGCTTTCCCTATAGCTTTGAATA[C/T]TTCAAATGTGCAGAACCCGAAAGTGATATCAAGCTCTTCAAGTTGAGGTTGTTTTCCGGCAATATTAATCAGACCATCATCGCCAATGT
100436 T C CATCTCCAGCTGTGAATCGTTCGTACACATCCCCTGCTTGGTTATATCGTAAGCAACTGAGATTTGGGCAGGCTTTCCCTATAGCTTTGAATACTTCAAA[T/C]GTGCAGAACCCGAAAGTGATATCAAGCTCTTCAAGTTGAGGTTGTTTTCCGGCAATATTAATCAGACCATCATCGCCAATGTTTTCAGC
100436 G A TCCCTATAGCTTTGAATACTTCAAATGTGCAGAACCCGAAAGTGATATCAAGCTCTTCAAGTTGAGGTTGTTTTCCGGCAATATTAATCAGACCATCATC[G/A]CCAATGTTTTCAGCAGATAATAAGTGAAGGCGCTTCAAGCTACTAGTTCTATTAGCAATGTACTCCAAAAGTCCGATCGAACCAAAACC
100436 C T CAATATTAATCAGACCATCATCGCCAATGTTTTCAGCAGATAATAAGTGAAGGCGCTTCAAGCTACTAGTTCTATTAGCAATGTACTCCAAAAGTCCGAT[C/T]GAACCAAAACCTTCGATCCGCAGCTCCTCCATCTGACCTTTACTCCTCTTAACAGCTTCTCTTGCCATTTGTTCCAAATAAGCCTCTCCAT
100436 A G CCTCTTAACAGCTTCTCTTGCCATTTGTTCCAAATAAGCCTCTCCATCTTCTCCTTTTATGTTTTTAAATTCTACCACCTTCCAAATGCAAGGATTGGAA[A/G]AGACATTTCTCCATGTCTTGCAGACCCACTGAGCATGCTGCAGAACGTCTGCTGCTCCAACTTTGGCGAATATTGATGCGAGCAGGTCTCC
100436 A G CCCAGTTGCGTGCTTCTTGACTCATTTCGACTTTAATGGCTGACCCTCTGCGGTTCCCCGACAAACACAAATATGCGTGGCAACAAAATAACGCACCTCC[A/G]CCCAGCGTCCCCGCCTCCCCTCCTTCAAGACATCCGCCACCGCCGAATCACCGTACAGACCCCCCAGACCCGAATTCCCGGCTGTTG
100438 G GC CACAAGCCGAACCCATTCCTGCACAACTCCTGCCGCTCCACCCGCTACCCGGCCTTATGTGAAACGTCGCTCGGCATATATGCACCGACAGTGAGTCACA[G/GC]CCCCCGCCGCCTCGCCCACGCCGCCCTCAACGTCAGCGCTGCCCACGCCGCCGCTGCTTCTTCCTTCGTCCATCGACTCGCCGCTGG
100438 C T ATGCACCGACAGTGAGTCACAGCCCCCGCCGCCTCGCCCACGCCGCCCTCAACGTCAGCGCTGCCCACGCCGCCGCTGCTTCTTCCTTCGTCCATCGACT[C/T]GCCGCTGGCTCCAAAACCACCAAATCCAGATCATCCGTCGCTGTCTCTGACTGCATCGAAACTTTGTCTGACAGCGTTGATCGACTCA
100438 A C AGAGCGCCGATGTCAGAGTTCAGATTCGGAAAAGGATCGTGGCGGTGTCTCAGATCACCAGCAATGCCTTGGCACTGGTCAACCGGTTGGAGTGAAATCA[A/C]TTTGTGTACAAACCAGTAATGTATGTGTTTTTGAGAATTGTATGTAACTGTATTATATAAATAAATATGTAGCAGTCAGGTTTTGGT
100444 A T TTTTTTTTGAGAAGAAGAAAAAATTACATTTATTATGCACTAAAATACCCTTCAGCAGTTTTCCCAAAATAACTCCATTCATGTGGTGACCAAATACAGT[A/T]GTCTTAAAGATAATAGAAACTGAAATTCAAATGGCAAAAGGAGGAAGGTAGATCAATCATTATACTTGAAGTCGTGCTTTCAGCTCTGC
100444 C T TGGATCCATGGATGAGGAGAGCAAGATCTTTGGTCATCTTTCCAGATTCTACAGCTCCAACACAAGCAGCCTCCAGTTTCTCAGTGAACTCTAGAAGTTG[C/T]GCGTTATCGTCCAACTTCGCTCTGTGAGCAAGTCCTCGAGACCAAGCAAAGATTGAAGCAATGCTATTAGTGCTAGTTTCACCACCCT
100450 T C GCATACTCGCCTGCTTAAACGCGTTGGACCCCAAATGGACCGGCTCAAACCCTGCCCACCTGAACCGGCCCTTCCACTGCTCCAGCGGCTCGTGCCGCTC[T/C]GTCCTCTCCGCCCCTTCGCAGGCCACGACGTTGCATATCTGCCGGCCGAGGTACACCTCCGTCATCTGGTCCTGCTGGCCGGATCCG
100450 G A AACCTCTGTATTCAAAATCAACTTGGATCTGCTCGGCTAACTGAGCCAGCTTGAGCCCGACCTGTTGTAAAGCATCGGTGTTATCGGGCGGCGGTGGGCC[G/A]ATACCGGTGAGTCTGAAAGAAGGCGGGCCACCGGGTCTAAGGGCAAGGGCCTGCAACAGGGCAGGCCACTGCATTCCCTGCTTC
100456 A G AACCGCCTTGGAGTACTGGGGTCTCAACAGTCTCCTTCTTCGGCAGAAGCCACGGCGTTTGTTCAGTCTTTCAATCGAGATTTTGTTACTTCTGAAATTA[A/G]ACCCAATTTTGTTGCTGAGGGGTTTATGGAGGCACTGAGCAGGTCCCAGAGAGAGTTTAAGCTGATGTTTGTGTACCTGCATTCGCCT
100456 A T TTCAACGCAAGCCGTTTTCCTTTTTGTGCTGTTGTCTCTGCAGCAGCAAATCAGAGGCTTGCTCTTCTTTCTCAGATTGAGGGTCCGCGGACTCCTGAAG[A/T]AATGCTTAACATTCTCCAACAAATTGTCGAACAATCAGGTACACAACTCGTAACTGCAAGACTTGAGGCCGAAGAGAGAACAAATAAT
100458 A G GTGGTCATGCTGGACCAATTTATTCAGCTAATTTTAGTCCTCTTGGGGACTTTCTTTTATCATCATCTTCAGATTCAACAATTAGGCTGTGGAGCACCAA[A/G]CTGAATGCAAATCTTGTCTGCTACAAAGGTCACAATTATCCTGTCTGGGATGTTCAATTTAGTCCCATGGGTCACTATTTTGCTAGTGCA
100460 T TC CGCCTCATCCTCCTCCTCGTTGCCTTCCTCTCCTTTCGCCTTGAAGGTCATCCATAAATCCTCCATAACCCAAAAACAAGATTCACTCAAACGAGCTCAC[T/TC]GGGAGCTCTCCGTCCTCTCCAATCTCTCAACCCAAAACCCCTTCCTCCCCACTCTCCTAGGCTCCGTCGAAACCCCCTCCTTCCTCGCCTA
100460 G A ACGCTTTCCCTTTCTGCTCCGGAGGCGATCTCAACACCCTCCGCTACTCCCTTTCGGATCGCGTCTTCTCGCCATCCGCCATTCGTTTCTACCTCTCCGA[G/A]CTTCTCATGGCTTTATCTCACCTGCATTCGCTAGGCATTGTCTACCGCGATTTGAAACCTGAAAACGTCCTAATCAAAAGCAATGGCCAC
100460 C T GCCATCCGCCATTCGTTTCTACCTCTCCGAGCTTCTCATGGCTTTATCTCACCTGCATTCGCTAGGCATTGTCTACCGCGATTTGAAACCTGAAAACGTC[C/T]TAATCAAAAGCAATGGCCACATCGTTCTAACCGACTTCGATCTCTCGAAAAAATTGCAGCATCAAAAACTTGCTCGCTTTGCTAAATCGC
100460 CA C CTAACCGACTTCGATCTCTCGAAAAAATTGCAGCATCAAAAACTTGCTCGCTTTGCTAAATCGCCTCCGCCTGCTGCGAGATCCGCTTCCGTTGGCACAG[CA/C]AAAAAAGAACTTTAAATTTTTAACAAAGGCGAAGTCTGCGAGGGTCTCACCTGTAAGCAGGCGCAGCGCTAAAATGTGCGGTAATG
100482 C T TAATGGTGAAACGATTATGACACCTAGATTACAATTAAAATACAAATCATTTAACTACCCCTTTTGCTATGTACTTGGCTTGCCGCAGCTCCTTGCTTGC[C/T]GCAGCATCAAGAAACTATCTGGTTGTTCAATGAAGCAAAATTATCGACCATCAGGGGACAAAAAACGAGCACCATCAGTCGCCAAAGC
100482 C CTATCA TATGACACCTAGATTACAATTAAAATACAAATCATTTAACTACCCCTTTTGCTATGTACTTGGCTTGCCGCAGCTCCTTGCTTGCCGCAGCATCAAGAAA[C/CTATCA]TATCTGGTTGTTCAATGAAGCAAAATTATCGACCATCAGGGGACAAAAAACGAGCACCATCAGTCGCCAAAGCCAAATGGTGT
100482 A G GACCATCAGGGGACAAAAAACGAGCACCATCAGTCGCCAAAGCCAAATGGTGTCTTCCTTCTGCTGCCGCCCTCTCCATACATTTCATTCCATTTTCGTA[A/G]CTCGTTCATACTGGCAGCATCATAAGCAACAGAGGCACCCACCTTAGATTTAGCTTGTATGAAGTCTTCTAAATTAAGGGACCTCAGC
100482 A G GGACAAAAAACGAGCACCATCAGTCGCCAAAGCCAAATGGTGTCTTCCTTCTGCTGCCGCCCTCTCCATACATTTCATTCCATTTTCGTAACTCGTTCAT[A/G]CTGGCAGCATCATAAGCAACAGAGGCACCCACCTTAGATTTAGCTTGTATGAAGTCTTCTAAATTAAGGGACCTCAGCGATGGTGTTG
100482 C T CTCGTTCATACTGGCAGCATCATAAGCAACAGAGGCACCCACCTTAGATTTAGCTTGTATGAAGTCTTCTAAATTAAGGGACCTCAGCGATGGTGTTGTC[C/T]TAATTTCGTTACACTTCTTTTCTTCCTCAATTAGCTCTTGAACCGGTCTATATGCCGCAGCAATACACAGATTCTTCAGATCGCTTCCAG
100482 T C CTGGCAGCATCATAAGCAACAGAGGCACCCACCTTAGATTTAGCTTGTATGAAGTCTTCTAAATTAAGGGACCTCAGCGATGGTGTTGTCCTAATTTCGT[T/C]ACACTTCTTTTCTTCCTCAATTAGCTCTTGAACCGGTCTATATGCCGCAGCAATACACAGATTCTTCAGATCGCTTCCAGAATATCCTTC
100482 T G AGGCACCCACCTTAGATTTAGCTTGTATGAAGTCTTCTAAATTAAGGGACCTCAGCGATGGTGTTGTCCTAATTTCGTTACACTTCTTTTCTTCCTCAAT[T/G]AGCTCTTGAACCGGTCTATATGCCGCAGCAATACACAGATTCTTCAGATCGCTTCCAGAATATCCTTCAGTTGCATTGGCAAGCTCGTCA
100482 C G GTATGAAGTCTTCTAAATTAAGGGACCTCAGCGATGGTGTTGTCCTAATTTCGTTACACTTCTTTTCTTCCTCAATTAGCTCTTGAACCGGTCTATATGC[C/G]GCAGCAATACACAGATTCTTCAGATCGCTTCCAGAATATCCTTCAGTTGCATTGGCAAGCTCGTCATATCTGAAACCTTGTTCCAAATTTT
100482 A G TATATGCCGCAGCAATACACAGATTCTTCAGATCGCTTCCAGAATATCCTTCAGTTGCATTGGCAAGCTCGTCATATCTGAAACCTTGTTCCAAATTTTC[A/G]TTAGAAAGTAAAATTTTCAAAATTTTCCTTCTGTTCTCAGCATCAGGAAGATCAACATATATCCTTCTTGGCAAACGCCGAATTACAGCA
100482 C T CAGATCGCTTCCAGAATATCCTTCAGTTGCATTGGCAAGCTCGTCATATCTGAAACCTTGTTCCAAATTTTCATTAGAAAGTAAAATTTTCAAAATTTTC[C/T]TTCTGTTCTCAGCATCAGGAAGATCAACATATATCCTTCTTGGCAAACGCCGAATTACAGCATCATCCAAGTCAAAAGGACGATTAGTTG
100486 CA C TGCCGTGTTATCGCAACTCGCCGGCTATGTTGTTCTGGGAAGCTTTACCTCTGTCCTGCGATTAACTAAGTAGCTATTTAGCTCACACAAGGACTGATTA[CA/C]AAAAAACGTGAGCTTTGTAGTGAAGCATCTTTAGCTTAGTAAGTGACTTCAGGAAGGTTTGGTTTTCTGTATTGAATAAATGGTTGTG
100488 A G AGATCGACGCAAAGAGGACTCTTAGGGAGATTAAGCTTCTGAGACACATGGATCACGAAAATATTGTAGCAATTAGAGATATAATTCCACCCCCACAGAG[A/G]GAGGCATTTAATGACGTTTACATTGCTTATGAACTAATGGACACTGACCTGCATCAAATAATTCGCTCCAACCAAGGGTTATCTGAA
100500 G T AATTCATCAACTCGCCGGCTTTAACCCTCCAAAACTGACTCTCCCTAAACTTCATCATCCTCTCCAAACATCCCATCAAATTCTCCAT[G/T]GCCATGCCATCCACCATCCTTGACCCATGACCAGGAGATCCAAAAGCCTTCACCACCAATGACCATGGCGACCTGTCTGCGTAAAACACCCTCACCTCCT
100500 G T TGACCATGGCGACCTGTCTGCGTAAAACACCCTCACCTCCTCATCCTCGGAAGCCTGCCCTTCGTCTAAAACAAGCCCAACATTCAACCCTTTAAAAGCC[G/T]CCGACTTTGCAAACTGCGCCCAACCATCTGGGCCGCCTATCTCCTCATCAGGAACTAAACTGATATGAACGTTTCTAAGAGGGACGAA
100500 A G AAGCCTGCCCTTCGTCTAAAACAAGCCCAACATTCAACCCTTTAAAAGCCGCCGACTTTGCAAACTGCGCCCAACCATCTGGGCCGCCTATCTCCTCATC[A/G]GGAACTAAACTGATATGAACGTTTCTAAGAGGGACGAAGTTCTCAACTTCAACCAAATTGCGGATGGCTTCTATGTACTGGATGGCGA
100500 G A ACCCTTTAAAAGCCGCCGACTTTGCAAACTGCGCCCAACCATCTGGGCCGCCTATCTCCTCATCAGGAACTAAACTGATATGAACGTTTCTAAGAGGGAC[G/A]AAGTTCTCAACTTCAACCAAATTGCGGATGGCTTCTATGTACTGGATGGCGATGCATTTATCGTCCTGCGCGCCACGGGCGTATATG
100500 C T CTAAACTGATATGAACGTTTCTAAGAGGGACGAAGTTCTCAACTTCAACCAAATTGCGGATGGCTTCTATGTACTGGATGGCGATGCATTTATCGTCCTG[C/T]GCGCCACGGGCGTATATGTTGCCCGTCTCTGGATCGTGGAAGGCGGAAAATGGAGGATGGGTCCAGAGGGCGGCTTCGGCAGGGA
100500 T G CGTTTCTAAGAGGGACGAAGTTCTCAACTTCAACCAAATTGCGGATGGCTTCTATGTACTGGATGGCGATGCATTTATCGTCCTGCGCGCCACGGGCGTA[T/G]ATGTTGCCCGTCTCTGGATCGTGGAAGGCGGAAAATGGAGGATGGGTCCAGAGGGCGGCTTCGGCAGGGACGGAGTCGATGTGG
100502 G A CACTTTGTTTAAGAAATAGGAATTTGCAGAGTAGGAGTCTGGATTATGTCTGTATGGCAAAGGGCAATGCTAATAAAGATAACGAGGGTTTCTCGTGGGA[G/A]TCATTGAAGAATGCTATGGGAGGTATAGGGAAAGAAGATAATGTTCAAGATTGGGTTAAAAAGCAGATGCGTGAAAATGAATTA
100502 C T ATGTTCAAGATTGGGTTAAAAAGCAGATGCGTGAAAATGAATTAGGGGATGACGGAGGTGATGGATCGCGTCCAGGTGGCGGCAGCGGCGGATTTGGTGA[C/T]GAAGACGATGAGGGGTTCGCTGGAGTTATTGATGAGACTATACAAGTGATATTGGCAGTTATTGGATTTATTTTCGTGTACATT
100502 C T AAAAGCAGATGCGTGAAAATGAATTAGGGGATGACGGAGGTGATGGATCGCGTCCAGGTGGCGGCAGCGGCGGATTTGGTGACGAAGACGATGAGGGGTT[C/T]GCTGGAGTTATTGATGAGACTATACAAGTGATATTGGCAGTTATTGGATTTATTTTCGTGTACATTTACTTGATCAGCGGTGCA
100502 A G CATTTACTTGATCAGCGGTGCAGAGTTAACCAGACTGGCTAGAGATTATATAAGATATCTATTTGGAGCAAGTCCGAGCATGCGATTGATGAAATCAATG[A/G]ACGACTGGAGAAGTTTTGTGAACAAGTTTGCTAGTAAAGTTGATACTAGAGAAGACTGGCTTGAAAGAGCTATAGTTCTTACTCCTA
100502 G A AGCGGTGCAGAGTTAACCAGACTGGCTAGAGATTATATAAGATATCTATTTGGAGCAAGTCCGAGCATGCGATTGATGAAATCAATGAACGACTGGAGAA[G/A]TTTTGTGAACAAGTTTGCTAGTAAAGTTGATACTAGAGAAGACTGGCTTGAAAGAGCTATAGTTCTTACTCCTACATGGTGGCACA
100502 T G TAAAGTTGATACTAGAGAAGACTGGCTTGAAAGAGCTATAGTTCTTACTCCTACATGGTGGCACAACCCCAAGAAATTGGCGTCCGCTGCGAAATCTAAA[T/G]CTAGATACTGAGAGCTAAGTGGTGTTGGCCAAATTTGTTCAGGACAACGGTTGTTTTTCCCCCGTTT
100518 TCA T TCAAGAACAATATAGAACGGCATTCTCAAAGTATTTACAATTGAAAATTAAAGCCCGGCCATTCAATCTCACACTTCTACAACAGCAAAAATAATAGTAA[TCA/T]CACACAAGTGGTGGCTGAATAGCAATTCTTAAGAAAAATAATGAATGGTTAGCAGTAGGAATCATTGTACATTCTGTTTTACCATTC
100518 GA G TTTACAATTGAAAATTAAAGCCCGGCCATTCAATCTCACACTTCTACAACAGCAAAAATAATAGTAATCACACAAGTGGTGGCTGAATAGCAATTCTTAA[GA/G]AAAAATAATGAATGGTTAGCAGTAGGAATCATTGTACATTCTGTTTTACCATTCACCCTTTCCATTTTTGTCAATGCGAAGGCCTTCTA
100518 GAACTGGAC G TTTCTTCTGAGTTGCAGAATTTGAATCAATAGGCGTCATGTCTTGGCTACTAGAAACAGCAACTCGCTTTGAGTATCTGCTTGACCGGCCCAAAAAAGTT[GAACTGGAC/G]AACTGGACAACGCAGCTTCTTTATTGGAGTAATCATTTACTGCTGCATTTTTTTGTTTAGACAAGCTGCCTGAACTTTGAG
100522 C G ATCTAAAGCCCATGCTGAAACATTTACAGCATCCAATTTTTCGGTTGCTCATCAAGATATTTATCATATGGGGGTTGCTTCCCAAAGAACTACTGTCAAC[C/G]CAAGGCAAGTTCAAAGGTCTCTTCAGAAATGGAAAGGCCCTGACAAAATCAGTTTAATTTATGGAGACTGGATTGACGATTTTGAGTA
100522 T G TTCTTCAGTGTTCTCATTTTCTATTTAAGTGGATTTATTAGCGGCATAAGTTGCTCAAACTTGCACTTCTGTTAAGTAGTAGAGGAATTGTCAACTTTTC[T/G]GTCGAATTGTTGTATGGATTTGTTTATTGCTAATTCTGCCTGGGACTCCTTTAACGGTCGATGATCAAAAAAAAAAAAAACG
100526 G GT GCTGCAAGCGGAGTTGGATTAGGATTTGGACTAGTCATGCTTTTGGCTTTTTAATCAGACTCATAGGTGTTTTATTTTGTGTTTGGGTTGATTTCTCAGT[G/GT]ATTTTTGTTTTTCCCTATTTAATTTTATTTTATATTTCCCAAGATTGTATGTACTTGGATGATATTTGTTGAATAAATCTTTTTTTGTGGA
100532 C T CAAGGTGACCAAGCGTCTCAATTGTGAGGCTCAGATCACATCCATTGGCAAAGTATACTTCTGCAAGACTATCAGCTGAAAAACCAGGAAACTGGGATGC[C/T]AGTATCTCAACCGGATCGAACCCTACTTGATCGCCTAACCTAGCATTTGCAAAACCAGCGCTTGAATCTCCATTGTAGTGTTGTGCT
100532 T A GGCTCAGATCACATCCATTGGCAAAGTATACTTCTGCAAGACTATCAGCTGAAAAACCAGGAAACTGGGATGCCAGTATCTCAACCGGATCGAACCCTAC[T/A]TGATCGCCTAACCTAGCATTTGCAAAACCAGCGCTTGAATCTCCATTGTAGTGTTGTGCTTCCATTTCGCTGGCAAGTCTTTGATCTC
100532 T C CAGGAAACTGGGATGCCAGTATCTCAACCGGATCGAACCCTACTTGATCGCCTAACCTAGCATTTGCAAAACCAGCGCTTGAATCTCCATTGTAGTGTTG[T/C]GCTTCCATTTCGCTGGCAAGTCTTTGATCTCCATTTATAAATTTCTTATTCCAGGCGTTGCTCGGTCCAATAGAAGATTTAACTTGAGT
100532 T C AGCATTTGCAAAACCAGCGCTTGAATCTCCATTGTAGTGTTGTGCTTCCATTTCGCTGGCAAGTCTTTGATCTCCATTTATAAATTTCTTATTCCAGGCG[T/C]TGCTCGGTCCAATAGAAGATTTAACTTGAGTACCAAATATCTCATCGGTTATCGACGCATTAAATGTTGATGATTCAGCACCATCTCCTAA
100534 C G AAGCAGAATGAACCTTAGTTACCCAGCCATCCAATTTAACTCCCAAAGATTTAATTTGTGACATTCCCAGAACTCGAGGTTGCACCCATGACACATGTAT[C/G]GTTCCCTCCACCTGATCTATTACGCCTTCTATAAGATGTACCGAAAGACTTTTCATGAGAAGATGTTCCACATCTTCGATTGAAAGCCTA
100534 G T TCCACCTGATCTATTACGCCTTCTATAAGATGTACCGAAAGACTTTTCATGAGAAGATGTTCCACATCTTCGATTGAAAGCCTAGTTTGTTCTGCAATGA[G/T]GCTCAATGGAACAGTTCTGTCTTCAGCAGGCCGACTGAAGATGATCTCCATCAAACAAAGGATGTTGATTTTTTCTAACAGCTTCTTTTC
100534 G C TAAATATTGTCGCCCAGAAGTGCAGACAAGGAAAGGTCAAAAGCCAAATCCAGTTTAAATGCTGCAGACAGAGATTCCACAGCCGTGTAAGCCAAATAAA[G/C]AAGGGCATTTCTGTAGAATTCGGCAAATTCCTGGCGGCATTTGTGATATTGAGATGATACCCAGTAAAAGCTAGCA
100550 T C CTATCTAGAGCTCTCGGATTGTATGAGAATCGAAGATCTTCTTCTTTTGCATCATACTGACTATCTTGTGAAGGAAGAGGAGAATATCCTATGTTTCTTC[T/C]TGTTGCCATAACTAGATACCTAAGATCCTTGTCCTTCGTACCGCAGTTCGGCTTCGGCTTCAAGAATCAAGGCTGGTTCAACACTTCAAC
100552 C G CAGAAGATAAAGAACTCCTTGATTTGTCATCAAGATTGACCGGAGAATCATTGTCTATCACTGGAGATCAAGTTGTGCATATTCAGGCACTTCGAGAACG[C/G]TGGAAAAAATGTGCAGCAAACTCAATACAGCTGCGAGAGCTAGGTCCCCTTCTTAGAGATTATCAACGTCTCATAGTTCAACATCAT
100552 T TCAG CTTCGAGAACGCTGGAAAAAATGTGCAGCAAACTCAATACAGCTGCGAGAGCTAGGTCCCCTTCTTAGAGATTATCAACGTCTCATAGTTCAACATCATG[T/TCAG]AAAGATGATTGGTTCCAGTTTGTCCGACACCTCCTTAAATTCAGGACAGCAAATTCATCGATTTTTTCACGTGAAGAGCTCTTCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100552 AGT A TCGATTTTTTCACGTGAAGAGCTCTTCGCAGCTACGCATGGATGATGTGCCAAAGCTATTGAACGAGTACCAACAGCTAATCTCAAGCTCAAGCTGAAGA[AGT/A]GTGTGTTTATAGTTTATGCATACAAACAGCTATTAAATGAATACAAACAGTCGGAGATTAATTTATCAAGGGAAGTGTTAATGTG
100552 T A TTCACGTGAAGAGCTCTTCGCAGCTACGCATGGATGATGTGCCAAAGCTATTGAACGAGTACCAACAGCTAATCTCAAGCTCAAGCTGAAGAAGTGTGTT[T/A]ATAGTTTATGCATACAAACAGCTATTAAATGAATACAAACAGTCGGAGATTAATTTATCAAGGGAAGTGTTAATGTGAGTAGAGAA
100558 A T TATTGTTGCTTCCGCCTATGAAACAATCCAAGCCACTTGAGCCTAACATCGATATCATCTTTCCCACTCTTATTAGCATCAAGTTCATTCAAGGGCTTCA[A/T]AGCCAGCTCTCTGATCCCATCCTCGACAACAAGTTTCATCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACT
100558 G C ATCCAAGCCACTTGAGCCTAACATCGATATCATCTTTCCCACTCTTATTAGCATCAAGTTCATTCAAGGGCTTCAAAGCCAGCTCTCTGATCCCATCCTC[G/C]ACAACAAGTTTCATCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACC
100558 A T AAGCCAGCTCTCTGATCCCATCCTCGACAACAAGTTTCATCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTT[A/T]AGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGC
100558 A T TCCCATCCTCGACAACAAGTTTCATCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCC[A/T]CCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGA
100558 G C CAAGTTTCATCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTC[G/C]ACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATT
100558 C T TCGGCTCTCTCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGG[C/T]TCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGG
100558 A G TCTCGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCT[A/G]TCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTA
100558 A T CGATCTTAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATC[A/T]TCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGA
100558 T C TAACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCT[T/C]AATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGAATTTTT
100558 A G ACTTTCTCTTGAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTA[A/G]TCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGAATTTTTG
100558 T C GAGGGTTAATCCCCTTTCTGAACTTCTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGT[T/C]TGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGAATTTTTGGAGAGACGA
100558 C T CTCCTTAAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCT[C/T]TGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGAATTTTTGGAGAGACGATGAAGACATGGCGTAAGGAATCGT
100558 C T AAGCACATAATATCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGC[C/T]TTCTCGATGGTGGATTGACATTGATTAAGGTTGGGGTTAGGAATTTTTGGAGAGACGATGAAGACATGGCGTAAGGAATCGTGGTGTT
100558 G C TCCACCTTCCCTCTCTTCGACCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGT[G/C]GATTGACATTGATTAAGGTTGGGGTTAGGAATTTTTGGAGAGACGATGAAGACATGGCGTAAGGAATCGTGGTGTTTGCAATCCAGTA
100558 T C CCCTTGGCTCAAGCCTATCATCGCTTAATCCAGCTGTTTGCGGCGTTGATATTGTTGATGCTCTGAGCCTTCTCGATGGTGGATTGACATTGATTAAGGT[T/C]GGGGTTAGGAATTTTTGGAGAGACGATGAAGACATGGCGTAAGGAATCGTGGTGTTTGCAATCCAGTAGGCCAACAG
100564 G A CCCCACTGCTTCCAGTCAAGGGACTAATATTCCCCATCTTAACCATAGCTGCTGCAAAATCACTAGCGAAAGTGGCACCATTGGCAACATACTGCCTTAC[G/A]ACTGCATCCTGGCTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCC
100564 G A CAGTCAAGGGACTAATATTCCCCATCTTAACCATAGCTGCTGCAAAATCACTAGCGAAAGTGGCACCATTGGCAACATACTGCCTTACGACTGCATCCTG[G/A]CTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGG
100564 G A AAAGTGGCACCATTGGCAACATACTGCCTTACGACTGCATCCTGGCTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCA[G/A]ATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTC
100564 A G AAGTGGCACCATTGGCAACATACTGCCTTACGACTGCATCCTGGCTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAG[A/G]TTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTG
100564 T C CATCCTGGCTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACT[T/C]AATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGT
100564 T C CCTGGCTGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAA[T/C]ATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTC
100564 A G TGCCATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATC[A/G]AGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTA
100564 C T CATTGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAG[C/T]GGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAAT
100564 T C TGTTAAACAACTCTTGATCTGAATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGG[T/C]GCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTG
100564 A C AATGAAGCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCC[A/C]GTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACT
100564 C T GCAGCCCTCTTTGTGCCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAA[C/T]GGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCT
100564 C T CCACCAGATTCCTGTAATAATCGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTG[C/T]CGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGG
100564 G A CGTTCCCAAACCTGGTAGGACTTAATATATCAAGCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGC[G/A]TTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCAT
100564 A G GCGGTGCTAAGTTGCTATCACCTCCAGTAAACGGACATGTCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCG[A/G]AAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACAT
100564 C G TCTGCTGCCGTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACC[C/G]GATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGA
100564 A G GTAGACTTGCAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGC[A/G]GTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCG
100564 A G CAAACCTTGCGTTGATGTCGGTTTCGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCATGTC[A/G]CGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCA
100564 A G CGTTGTAAATGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGA[A/G]AACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTC
100564 G A TGTGGGTTCGAAAGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGT[G/A]ATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTA
100564 C T AGTTGAGGCACTGGGCCTGCCCGATTGAGTGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGC[C/T]AGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCA
100564 G A CGATTGAGTGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGG[G/A]ATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAAC
100564 C A TGGGCACCCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTG[C/A]GTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCAT
100564 G A CCGATAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGC[G/A]GCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGA
100564 C T TAGTGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCA[C/T]TTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCA
100564 A T TGCAGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTT[A/T]GACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGA
100564 C G AGTCATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGA[C/G]TTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCG
100564 C T ATGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTG[C/T]GGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGA
100564 G C TGTCACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGC[G/C]GTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGAT
100564 T C CACGTGCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGT[T/C]GTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATC
100564 C A GCGCTTAGGCCTTTGTTGGAAAACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTG[C/A]ATCTCTCCTTCCTAGTTGTACTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCA
100564 T A ACATTGTGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTAC[T/A]GCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACG
100564 C T TGATTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCA[C/T]GTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTT
100564 T C TTAAAGTCGCCAGCGAGGAGGTGGGGGCTGGGATTTGTGCGTTTGCGGCACTTAGACTTGCGGTTGTTGCATCTCTCCTTCCTAGTTGTACTGCCCACGT[T/C]GGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAA
100564 G A CTGCCCACGTTGGTCCTCCAAGGGCAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAACTTT[G/A]GATTTGATGGCGTCTATGACTTCGAATCCGCGAGCAGAGTTCTTGTTTGGACCTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCG
100564 G A CAACAACTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAACTTTGGATTTGATGGCGTCTATGACTTC[G/A]AATCCGCGAGCAGAGTTCTTGTTTGGACCTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCGTCCAAAAGAATCGATGCATCACAA
100564 G A CTCCATCACGGGAAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAACTTTGGATTTGATGGCGTCTATGACTTCGAATCC[G/A]CGAGCAGAGTTCTTGTTTGGACCTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCGTCCAAAAGAATCGATGCATCACAACCATTA
100564 C G AAGCAAGAGCGAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAACTTTGGATTTGATGGCGTCTATGACTTCGAATCCGCGAGCAGAGTT[C/G]TTGTTTGGACCTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCGTCCAAAAGAATCGATGCATCACAACCATTAACAAAGCAGTCG
100564 C G GAGGATATCGGCACATGAAACGGTAGCCTTGCACGAAGCTTCAACTTTGGATTTGATGGCGTCTATGACTTCGAATCCGCGAGCAGAGTTCTTGTTTGGA[C/G]CTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCGTCCAAAAGAATCGATGCATCACAACCATTAACAAAGCAGTCGTGGAAGAAAA
100564 A G CTTTGGATTTGATGGCGTCTATGACTTCGAATCCGCGAGCAGAGTTCTTGTTTGGACCTGCAGTTTTCTCTCCAGTGAATGTTGCTGTGTCGTCCAAAAG[A/G]ATCGATGCATCACAACCATTAACAAAGCAGTCGTGGAAGAAAAGGCGAAGAATGGAAGCACCCATCCTCGCCTCCTTATTGAC
100568 T C ATTGCTCAGTATCTCAAACGTGTCGCCTATGTTCACGATAAAAGCATTTGGACGAGGTTTTACAGAAACCCATTCATCGTTTTTCTTAATTTGCAAACCA[T/C]GAACTTCATTTATTTGGAGCACTAATGTTAAGGCTGACATATCAGAATGTGGTGTCAAGCCTAACACCTTTTCAGCTTGTGGACACGGC
100572 G A CACCACCACCTACCACTGAGCCATGCTGATGACTGCCAACAATGATGTTTTTGAGGCGTCCAATCGGTCCTACCACACTTTTCATCTTCTCATCGTTGAT[G/A]ATAAGATGTCCACGAAATTCATGGCCATGCCATTTGCCTTTGTGCCACCTCTTTCCCAAAATTACAAGTCCAGTTAATGCAGCAGCAACA
100588 C CA CTATCATACAGTTCAGCTACATTACATTCTTTATTATTTGCAATCTCAAATAAAGCACTAAACTTAACTGCTAAAAATTGCCAAAAGCTAGCAATCAAAC[C/CA]AAAAAGAACACTACTACCATTGCTCACAATTATATGGATACCAAATTTAAAGGACTGGATATTGCTCATAATTTCCTTTTAGTAATAAGA
100594 T C AATCGCAATTGGAGCTGCAATATCACCGATTTCATCAAACTCGGGCACCCAATTCGACATCACTATTCTGATATGGAAAGACCCGAAGCTAGGGCACTGG[T/C]GGATGAGCTTTGGGGACAATGCATTGGTAGGGTACTGGCCATCCGAGCTCTTCACACACTTAGCCGATCATGCTTCTATGGTGGAA
100598 A G ATTTTTCCAAAATGCAGCTAAAAGGTATAATTGGTTCACCTCCATGTTCCTGAACCCAAGCATGAATTTTGGGTAGAAACTTGTTCTTCTTTCGCTGGTA[A/G]TCCTTTTCATTCACATTCACCAAATAGACAACAGGCTTAGCAGTGAGCAACTGTAAGGTATTTAATAACTCGACATCAGCAGTCTTCCAA
100598 C G TCACATTCACCAAATAGACAACAGGCTTAGCAGTGAGCAACTGTAAGGTATTTAATAACTCGACATCAGCAGTCTTCCAATCTCCTAAACGCACATCTTT[C/G]CCTTCTTGGAGCCATGCTTTAATTTTCAAAGAACATTCATGTTCAACTTTAAGCTGCTTGTCATTGCTCCTCTTCATGCTTTTTTCAAGGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100598 A G TTAATAACTCGACATCAGCAGTCTTCCAATCTCCTAAACGCACATCTTTCCCTTCTTGGAGCCATGCTTTAATTTTCAAAGAACATTCATGTTCAACTTT[A/G]AGCTGCTTGTCATTGCTCCTCTTCATGCTTTTTTCAAGGTCTTCCAACTTCCGTTCTATAAATTCTAAATCCTTGAGTCTTAGTTCTGCAGTT
100598 G A CCAACTTCCGTTCTATAAATTCTAAATCCTTGAGTCTTAGTTCTGCAGTTATGGTCTCCAAATCCCTAACAGGATCAACAACATCATCAACATGAATAAT[G/A]TCAGGGTCTTCAAATCCTCTCAGTACGTGAAAAATCCCGTCAACTGCACGGATGTGAGAAAGAAAATTGTTCCCCAAGCCCTGACCCTC
100606 T C AATTCGAGGCAGGGATTTGGTGGCCTCATTCCGAAACTCCCCTAAGGTGCAGCCTCTGGGTTCCCAGCCGGTTTGTT[T/C]GAGTTCGGTGGTTGGCTCTATTGCCTCTGCTAATAGCTCTAAGCGTCGTAGACTCCACAAACGTCATTCGAGGTTTTTTCCGAGGCACTTGCTTCGGTTG
100606 A C TGGCTCTATTGCCTCTGCTAATAGCTCTAAGCGTCGTAGACTCCACAAACGTCATTCGAGGTTTTTTCCGAGGCACTTGCTTCGGTTGGCTCTGTAGTTG[A/C]TGGGTTTAATGGCTCTTCAATGTTAGCTTTTGTGTAGCCTCCTCCTGCGATTACCTTGTCTAACATCTTCTCTTCCCTCTATGTCGAGCTG
100606 T C ATTGATGATTGGTGGGGGCAACTGAGGCAGCTTTTGATTTGGTATCGGTAGACTTGCACAGTTCTATTTTGGTTTCTATGAGTTCGACTGTAGGTAGCTC[T/C]GGCTTGGCTTTGTCGTTTGTAGAGGTTGTTGAAGACTATAGGGCATTGGCAGATCTTTTGTATGGAATTTCTGGCTTTCGATTGGTTT
100608 CT C CCTCCTGCAGTGCCTGCTTCGCACTTTCCAACCCCGCAACATCATTCCACTGCACATTCGGTTTCTCCCTAATAATGGCAGAATTTAATCCCGCCCTCAG[CT/C]TTTTCTTTTTCCTTATCATCGTCTCCATCTCCCTCTCCGCCCTTCCCCTTACTCTTTGGCTTTGTCGCGACAGCCGCATCACCATGTGGGC
100608 GC G CATCATTCCACTGCACATTCGGTTTCTCCCTAATAATGGCAGAATTTAATCCCGCCCTCAGCTTTTCTTTTTCCTTATCATCGTCTCCATCTCCCTCTCC[GC/G]CCCTTCCCCTTACTCTTTGGCTTTGTCGCGACAGCCGCATCACCATGTGGGCCGGGAGCAGGTCCACCTTCGTCCAGCACAGCCCGAATC
100620 GA G AGTTTCATCTCGAGCCACACAATAAAGAATAACCTCCATCATATCACAAGTTGTAAATAGGTACTGTGCTATAGCATATTGTCCAACATAATACGGCTAC[GA/G]AAAAAAACAGTGCAGGTTACCATAATGTACACAAGCAAATGCCAAGCTTTCTGCCTTCCCATGAGAACAACTATCTAGACATGACAT
100622 G A TGTTGTGGGCTGCCACCTGGCTTTATCATGCCACAGGAGATCAGACGTACTTGAATTATGCGACTGTGCAAAATGGAAAGCAGTTTGCAGATTGGGGAAG[G/A]CCAACTTGGTTTAGTTGGGATGACAAGAGGGCAGGAACCCAGGTTCTATTGTCCAGAGTAAACTTTTTTGCTTCTAATCAAGCATC
100628 A G AACAATTGATCATGTCAACTGTGCTCCGAACCATGTTAAAACATACAACCAAAATGTTGAATCATGCAAGTAGATTCACATAGCAATGAACAAGCTGATA[A/G]CTGTACGATCAAAGCGATGCTTAACCACAAAAATACACATTCTTCTCCGGCTTGTGCAAAAACAAATAAGCTACCATGATGCAAATAT
100628 G A TGTGCTCCGAACCATGTTAAAACATACAACCAAAATGTTGAATCATGCAAGTAGATTCACATAGCAATGAACAAGCTGATAACTGTACGATCAAAGCGAT[G/A]CTTAACCACAAAAATACACATTCTTCTCCGGCTTGTGCAAAAACAAATAAGCTACCATGATGCAAATATTCTCCCAGTCAAGTCGCTT
100628 C T ATTCTTCTCCGGCTTGTGCAAAAACAAATAAGCTACCATGATGCAAATATTCTCCCAGTCAAGTCGCTTCTTTCAGCTCAAGTCCTTTAGGGCATATGAA[C/T]AAGGAATCGACACAAAGTCCGCCTTTTATATGAGTGCAATCTATTTGCACCATTGAAAACTTCAGTTTCATTATTTCATCACATTTGTTCA
100628 A G TTATTTCATCACATTTGTTCACGTTAAAATCACCTACATGGTAAAAGATCCAGCATCCCTGCTCTTCTAAGTAGCACTTTGATTGGGATTTCTGACCATC[A/G]GATGTAGAAAGCTGAAATCTTACAGGTTTTAGATCCCAACCGTGGATGTGCTGAGTGTTGCAGGTTCGACGGCCCAGCCGCTTTGTTGG
100638 A G TCCAAAGCTTCTCAGCAAATACGCTGTTAGAGAGAGAAGTATCAAAACTACTAGATAGGTTTTTAGGTTCTCATCGACCTTCACATTGTTAACTACTAGC[A/G]CTTCAAAGCTTCTCAACTACCGACTCGCTATTTAAGCATCATATGAAAGAAGGCGCATCATGGTTGTGTGTTGCACCATCTTCATTGCC
100638 G A GGCGCATCATGGTTGTGTGTTGCACCATCTTCATTGCCTTCTGCTGCATTTTGTCATCACTACTGTTGTGTCTACTGTATGCTTCTTCACTTTCACCTGA[G/A]TACCGCTGCATAGTTGACCACAATAGAAATATGAGGTTAGGTTGAGGAAATAAGAACAAATATCTTTTCTGCATGGCTTATCATTTGTGA
100638 T G CATGGTTGTGTGTTGCACCATCTTCATTGCCTTCTGCTGCATTTTGTCATCACTACTGTTGTGTCTACTGTATGCTTCTTCACTTTCACCTGAGTACCGC[T/G]GCATAGTTGACCACAATAGAAATATGAGGTTAGGTTGAGGAAATAAGAACAAATATCTTTTCTGCATGGCTTATCATTTGTGAGGTGCTA
100638 T C TCACTTTCACCTGAGTACCGCTGCATAGTTGACCACAATAGAAATATGAGGTTAGGTTGAGGAAATAAGAACAAATATCTTTTCTGCATGGCTTATCATT[T/C]GTGAGGTGCTATGATTGTGGAGTTGTCTGTATTATGCAATCCGTGGGTCAAGAATATGAACTGTGAGATTTGCAAAATGCTTTGCAAA
100638 C T GTTGACCACAATAGAAATATGAGGTTAGGTTGAGGAAATAAGAACAAATATCTTTTCTGCATGGCTTATCATTTGTGAGGTGCTATGATTGTGGAGTTGT[C/T]TGTATTATGCAATCCGTGGGTCAAGAATATGAACTGTGAGATTTGCAAAATGCTTTGCAAATTTTTACTGCATGCTGGTAACTATTAA
100638 A G TATCTTTTCTGCATGGCTTATCATTTGTGAGGTGCTATGATTGTGGAGTTGTCTGTATTATGCAATCCGTGGGTCAAGAATATGAACTGTGAGATTTGCA[A/G]AATGCTTTGCAAATTTTTACTGCATGCTGGTAACTATTAACTAAAAACAGCAGAGCAGATTGTGGCAAAGCCGAGGGTAAGAAAGCT
100638 A T GGAGTTGTCTGTATTATGCAATCCGTGGGTCAAGAATATGAACTGTGAGATTTGCAAAATGCTTTGCAAATTTTTACTGCATGCTGGTAACTATTAACTA[A/T]AAACAGCAGAGCAGATTGTGGCAAAGCCGAGGGTAAGAAAGCTTGTAAATCTGCAAAATCACAGTTCAGTGCTCTGGTATGGTATGT
100638 G A TCCGTGGGTCAAGAATATGAACTGTGAGATTTGCAAAATGCTTTGCAAATTTTTACTGCATGCTGGTAACTATTAACTAAAAACAGCAGAGCAGATTGTG[G/A]CAAAGCCGAGGGTAAGAAAGCTTGTAAATCTGCAAAATCACAGTTCAGTGCTCTGGTATGGTATGTGTACAAATTATTGTTTGTTTG
100638 T C TGCAAAATGCTTTGCAAATTTTTACTGCATGCTGGTAACTATTAACTAAAAACAGCAGAGCAGATTGTGGCAAAGCCGAGGGTAAGAAAGCTTGTAAATC[T/C]GCAAAATCACAGTTCAGTGCTCTGGTATGGTATGTGTACAAATTATTGTTTGTTTGTTGATGTTTTTATGCTGAAAGGTCGTGGCTTA
100642 T C TCTTACGCTTCCATGGTCCTTTATATGCTGGATTTGGAACCTTTGGCGCTCTCCAAATGCCATCTTCATCCTCATCCCATGATGCAGGCTTTTTGGCATT[T/C]GGATCAGGAATTTCAGATGGAATCGAGTCATACCCCTCAGGTTTAACAGCATCAGGATTGTCAATGTACTCTCTGTCATCCCAATC
100650 G A ACAAACTGCAAAATTCATCAGAGAAAAGTCGATTTTCTTTTCAGATCGTAGTAAATTAATGGCAAGCGTAAACCCTCTCTACCCAAGCCCTAATTACCCC[G/A]TCCCTCAGTCTCCGCCTCCTCGTCAATCGACGTCAGAAAAGCCGAAGGTTATCTCAGTTCCCGTGAAATTCGCTGATTTAGATGAGAAC
100650 C T AAATTCATCAGAGAAAAGTCGATTTTCTTTTCAGATCGTAGTAAATTAATGGCAAGCGTAAACCCTCTCTACCCAAGCCCTAATTACCCCGTCCCTCAGT[C/T]TCCGCCTCCTCGTCAATCGACGTCAGAAAAGCCGAAGGTTATCTCAGTTCCCGTGAAATTCGCTGATTTAGATGAGAACGTCACGAATA
100650 A C TTTTCAGATCGTAGTAAATTAATGGCAAGCGTAAACCCTCTCTACCCAAGCCCTAATTACCCCGTCCCTCAGTCTCCGCCTCCTCGTCAATCGACGTCAG[A/C]AAAGCCGAAGGTTATCTCAGTTCCCGTGAAATTCGCTGATTTAGATGAGAACGTCACGAATATGGATCGTTCAAACGCTGCGATCAAA
100650 C T CTGATTTAGATGAGAACGTCACGAATATGGATCGTTCAAACGCTGCGATCAAAATCCAGAAATTGTTCCGTGGATTTCTAGTTAGAAGGAATCTGAAAGT[C/T]GTACGCAAAATCGAGGAAGAGCTGAATGAGATCGAGTTGAAATTTAAAAGAGACGGGGACATGGATCGGATTGTCAAGATTGATA
100650 GA G GATCGGATTGTCAAGATTGATAAAGAGCGATTGCTGATCGGTGAGATGTTGATGAGGCTGCTTTTTAGGTTGGATTCGGTGAGAGGAGTTAGGGATTGCA[GA/G]AAAAAGAATAATTCGAAGAGTTATTTCTATTCAGGAGGTTTTGGATTCAATTTCTAGTGGTAATCTAAAACCTGAAATTGAAGAA
100650 G T CTAAAACCTGAAATTGAAGAATCTGGAGTTGTTGTCATGGAAGAAACCGACGCTTGTGGTTGTGGCAATCAAGTTACTGAATCGAACAGCAGTGAAATCA[G/T]GGCTCAAGACGTGAAAGTAGGATCTGAGAACGGGAGTGACAATCGCGATGTGATCATGACTGATT
100660 G A GCTCACTTACAAAACTTATGGGGACAGCTAGAAGGCTTTTAACTCCCTTTTGCCCAAGTTCGATTATTGTCTCATCAGTATATGGCCTGAGCCATTCCAC[G/A]GGACCAACTCTGCTCTGGTAAGCAAGAGTGTAAGCATTTTTAATTCCACGTTTTTCCAGTTCTTCCATTATCAAGTCCACGCATTCCTCC
100668 T G GATCCCTCGCAACTCAGCCAAAGAAGATGGATCCAAGCATCAGAACACCTATTACCCAACTAAGCACACCAACCATCAAAAACGAAGAACAGCCTCCAGT[T/G]GTAATGAAACTTACTACAGCAAAGGGAACCATCCCACCACAATTCGTTCCACCGAGCTCGGCGAAGAATGCTATACTCAATGGAAG
100670 C A CCTCCTCCACCAAATCCAAACCCGAAACCCTAATCCCCATCGGCAAAGGCCACCTCCGCTTTGAGTTCTTCTCCGACGGCTGGGAGGACGTCCACGACCC[C/A]CGCCGCCTCGACCTCTCCCTCTACATGCAACAGCTCAGCACTGCCTGCCCCGTCGAGCTCGGCCATCTCATCCGCCGCCACTCCGACC
100670 C G TAAAACCGTCCCCTTCCCCACCGAATCCAACCCCGACGACCTCCTCCAACTCCCCGGCAACCCCGCACTCACCGCTGCCGAGCTCCCCACCTTCCTCCTC[C/G]AGTCCAACCCCTACGTCGAACTCAGGGATGTCATCCTATCCCAATTCAGCAACATAGAAAAAGCCACATGGGTATTCGCAAACACCTTC
100670 C T TCCTCCAACTCCCCGGCAACCCCGCACTCACCGCTGCCGAGCTCCCCACCTTCCTCCTCCAGTCCAACCCCTACGTCGAACTCAGGGATGTCATCCTATC[C/T]CAATTCAGCAACATAGAAAAAGCCACATGGGTATTCGCAAACACCTTCGAGGAGCTGGAGAGGGAGTCCATCACTGCGATCTCCGCCA
100670 A G TCCAACTCCCCGGCAACCCCGCACTCACCGCTGCCGAGCTCCCCACCTTCCTCCTCCAGTCCAACCCCTACGTCGAACTCAGGGATGTCATCCTATCCCA[A/G]TTCAGCAACATAGAAAAAGCCACATGGGTATTCGCAAACACCTTCGAGGAGCTGGAGAGGGAGTCCATCACTGCGATCTCCGCCAAG
100684 T C TTGGGATCTGGCTTGGCATCTCTTGATTCAAAAAAGCAGAAGCAAAAGCAGTCAAAAAGATCCGTGTGAAATTTCATTGTTTCGCCTAGACAGTCATGGC[T/C]GATCAATCAAATAAGTCTAATAATGTTTTAACAATACAATATGCTGCCTGGCTTTTTTTTGGGTAGCCTAACAGTG
100710 C T ACCACAAAAAGTATGAGACAATTGACAACTTAATGCAAGATGGAAGCGTGCATCGTTTAGCTCGTCAGTATGATTTGCACCTGCAAATGAATGAAGAAGC[C/T]TGACCAGTGTGGTATATAGTAAGTTACATATGTCATGCAACTTAGATGAGGGTATTTTCCTTTTCACTCAGCATGTATGCATTATTTT
100720 T TTGC CTAGAACTACGAATGCCACAACCCATTTCATTGTTTGCGAGCAAGGTTATAGTTTGTGCATTGGTGTCTACTGTGTGCTTCATTGCATGCGAGCCTGCAT[T/TTGC]TGCTGCTGCTGCTGCTGCTTCTGATTCAATTAGAGCTTCTTCCATTGGGTTGAGAGTGGCAACAACATTAAGGAGTTTGGGTTGG
100722 T C CATCAAAGCTCGATAATTTAACAGGGAAGATGATGCATAAGATTTAGATAGCCGCGAAGTATTCTTTGCTGCCCTTTGGATCAGGTTTCATTGACTTATC[T/C]CCAGGCTTCCATCCAGCAGGGCATACCTCGTCCGGGTTTTCTTGCACATATTGCAAAGCCTGAAGTGTCCTCAAGGTCTCATCTACACT
100722 C T TTGACTTATCTCCAGGCTTCCATCCAGCAGGGCATACCTCGTCCGGGTTTTCTTGCACATATTGCAAAGCCTGAAGTGTCCTCAAGGTCTCATCTACACT[C/T]CTACCAATTGCAAGGTTGTTGATGGTTGAGTGCTGAATTACTCCTTCCTTGTCTATAATGAACAGTCCTCTAAGTGCAATTCCCTGATCA
100722 T C GATCAGGAATTAAAACTCCAAAGGATTTTGAAATTGATTTAGTCACATCAGATACAAGAGGGTAGCTTAGGTCTCCAAGTCCACCTGACTTCCTTTCAGT[T/C]TGAACCCAAGCAAGATGCGAGAACACACTGTCGACTGAAACACCTAAAACTTCTGTGTTTATCTTCTCAAATTCAGAATATCGGTCACT
100722 A G TCACATCAGATACAAGAGGGTAGCTTAGGTCTCCAAGTCCACCTGACTTCCTTTCAGTTTGAACCCAAGCAAGATGCGAGAACACACTGTCGACTGAAAC[A/G]CCTAAAACTTCTGTGTTTATCTTCTCAAATTCAGAATATCGGTCACTGAAAGCAGTAATTTCAGTGGGACAAACAAATGTGAAATCCA
100722 G A CAAATTCAGAATATCGGTCACTGAAAGCAGTAATTTCAGTGGGACAAACAAATGTGAAATCCAATGGATAAAAGAACAAGATTACATACTTCTTTCCGAT[G/A]TAATCAGATAGCTTGACATTAATGAACTCCTGATCGAACACTGCCTCAGCTTCAAAATCCGGCGCAACATTTCCAACCAAAGGAAGC
100722 T C AATATCGGTCACTGAAAGCAGTAATTTCAGTGGGACAAACAAATGTGAAATCCAATGGATAAAAGAACAAGATTACATACTTCTTTCCGATGTAATCAGA[T/C]AGCTTGACATTAATGAACTCCTGATCGAACACTGCCTCAGCTTCAAAATCCGGCGCAACATTTCCAACCAAAGGAAGCTCGCTAGCA
100722 C T AAACAAATGTGAAATCCAATGGATAAAAGAACAAGATTACATACTTCTTTCCGATGTAATCAGATAGCTTGACATTAATGAACTCCTGATCGAACACTGC[C/T]TCAGCTTCAAAATCCGGCGCAACATTTCCAACCAAAGGAAGCTCGCTAGCATTAGTAACGAAGCTGTTTCTTCTAGAACAAACTTTGG
100742 CA C CAAACAAGCAAACTTATATGCACTCACCTTATTTGTTCAAATACATCCATTCATATCATAAAACAGACCCCGACTGACAACAAATTTACACAAAAAGGCA[CA/C]AAAACAGTTCAAATTCAATCAAAAGCATTATTCAAACTTCCTCCAAGCAACGACAGCAGACCACCACCATGAACCCTTCCTTCCGGCA
100744 C T CCAGACATTGATTATATTTCTGAAGAAGATATCAATGGACGAGATGATTTTATAGCACATCTTGAGTCCCGTTTCTTGTACCTTGCTGCAGATGCCCAGT[C/T]TACCTTACGTGGCTGGCGACCTTCTTATAGAAATATTTTACTTGGTGTTAGAAGAAAACTGAGTGTTCCCTGTTCAAATAAACTGTCGA
100746 A G TAGGGCTGTCTACTCATGCAGAGAAGTTGCAAATGGACGCGAGTTTAGGCCTTCTCAAGTTGCCCTACAGCCAAGAATTGAAATTGGCGGCGGTGACCTT[A/G]GAAACTCCTATGCACTTGTAATGGTGGACCCAGATGCTCCAAGCCCAAGCAATCCCCATCTAAGGGAATACTTGCACTGGTTGGTC
100772 T TC GCAGTAGCAGCATGGTCACCGCCAGTAATCGCATCGTTATCCACGACCGAAACTGCGTGCCAAGCATGGCTGGTCCAGTCCATCCCCACCGATATGCCCC[T/TC]CTCCCTCCCGTTGCTGACGTCCTCTCCTCCGGGGAGGTACTGAAATGGATGGCTGGAAACGCGACGAAGAGTTTGGATATAATAG
100778 A G TTTGATCAGTTGATTGGGGTCTTTCTGGCTGCAAGTATATGGTTCTTGTTAACCTGCTCGACAAATCAGTAAATTCAAAACTTGAAGGCACAATTGCTAG[A/G]CAAATTCAAGCACAATTCCAAACTTCAGGAAAACAAGCTCTTCAGGAAACATTGAGATCTTGTTTG
100784 G A CCGCGATCGCGATTATGACCATGAACGTGACCGTCATCGCAAGAGGGAACGCGAACGAGAGCGCCCTCATGACAGAGATTTTGTCTACGATGATGATGGA[G/A]TTGCCAAGCGTGATGAGAAGAGGAGCAAGCACAGGTATTATGAAGATGATGATAGAGTTAAGGTTGAACCAGAACATTACGGTG
100784 C T AGATTTTGTCTACGATGATGATGGAGTTGCCAAGCGTGATGAGAAGAGGAGCAAGCACAGGTATTATGAAGATGATGATAGAGTTAAGGTTGAACCAGAA[C/T]ATTACGGTGGAGATGTAGACGTGCGTGAGGAAGGGGAGCATGACTATGGCTACATTAGGCCAGAGCTATAAGAGCATCCTGAA
100784 A T GATAGAGTTAAGGTTGAACCAGAACATTACGGTGGAGATGTAGACGTGCGTGAGGAAGGGGAGCATGACTATGGCTACATTAGGCCAGAGCTATAAGAGC[A/T]TCCTGAATTTCATTTCAGCTGTCTTTCGAAGATTTCCTTTTAATATCTTATGTTGTGTATGCCCTAAATTGAAAAGATCATAACTTA
100784 G A ACGGTGGAGATGTAGACGTGCGTGAGGAAGGGGAGCATGACTATGGCTACATTAGGCCAGAGCTATAAGAGCATCCTGAATTTCATTTCAGCTGTCTTTC[G/A]AAGATTTCCTTTTAATATCTTATGTTGTGTATGCCCTAAATTGAAAAGATCATAACTTATAGTTTGAATCCTAGGGGAGCCTTGTATT
100784 A T TAGGCCAGAGCTATAAGAGCATCCTGAATTTCATTTCAGCTGTCTTTCGAAGATTTCCTTTTAATATCTTATGTTGTGTATGCCCTAAATTGAAAAGATC[A/T]TAACTTATAGTTTGAATCCTAGGGGAGCCTTGTATTTTATATTTATTTTGTTTTGGCAGTAGTAGGATTTCTTCTAAAACCT
100786 G A AAGTCTCTGGCACTCCTGTTGACTGTGTTTCTCTTGCTTTGTCTGGGGCACTGTTTTCTTGGTCCAGGCCTGCTCTTGTTGTGAGTGGAATTAACAAGGG[G/A]TCTTGCTGCGGAAATTATAGTCTCTATTCGGGTGCTATTGCTGGAGCAAGGGAGGCCTTATTGTGTGGGGTACCGTCACTAACAATTT
100786 A G GATTTTCGGGATGCAGTTAATGTTTGTTTGCCACTGATACATGCTGCCATAAAAAACGATGAGACGGGCACCTTCCCAAAAAATTGTTTGCTAAACATAG[A/G]AATTCCCTCCACTCCTTCTGCACACAAGGGTTTCAAGGTGACTAAACAAAGCATGTGGAGGCCTGCACTGAATTGGAAAGCAGTTTC
100794 A G CCGCTGACCGAGCTGCCCAAGCTGCCCGTGCAGCAGCGAGCCTTACTCAGCTTCGGATTGCAGAGCTAGTAACAAAGAGAAACCAGAATGCAACTTCTGA[A/G]ACAAGCCAAAACAAAGAAGCAAAGATTGCAGTAAAACCAGTCTTTGACCAACAGGATTCATTCGATTACACAGATCGTGGAACAT
100794 A G CAGAGCTAGTAACAAAGAGAAACCAGAATGCAACTTCTGAAACAAGCCAAAACAAAGAAGCAAAGATTGCAGTAAAACCAGTCTTTGACCAACAGGATTC[A/G]TTCGATTACACAGATCGTGGAACATACGATGATGGAAACGATTATGTGCATCAGCCTCAGAGATCGGTTTCAATGGAAGATGATC
100794 T G AATGGAAGATGATCCTTATTTTTCGTATCCTAATTTGTTTAATAGACAAAATTCAGGAGCTATTGATCATGAAAGTTCCGTGGATGAACACTCGAAATTT[T/G]ACCAGTAGAATTTGAGTATACCGCATTATGATGTATACTATTATATAGTTTTGTGTTTCCTGTATTGTATTGAGTGTTTGTCAAACTTGTT
100794 G A GTTCCGTGGATGAACACTCGAAATTTTACCAGTAGAATTTGAGTATACCGCATTATGATGTATACTATTATATAGTTTTGTGTTTCCTGTATTGTATTGA[G/A]TGTTTGTCAAACTTGTTCCTGTATATAGATGTATAATTTGGATTTACAGGGTAAATGAATGATTATTCAGGGGTTAATTTGTTATTGTCAA
100800 G A GCCCCGACCTCCTCCCTTCCATCATCGCACATTTCGCCTCCAAATTCCTCCCCGACATCTCCCCTTCCTCCGCCCAATCCACCACCGCCAACTGGCTCAA[G/A]AAGCGCGACCTTCTCGAAAACCTCGTCGGAGCCCTTCCACCTGAAAAGACCTCCATGCCCTCCGACTTCCTCCTCCGTCTCCTCCGCAAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100818 T C TACCTCTTGAAACCACCAGGCATGTTTCAGTAATCAGTATAACGCTATCCAAATTGGAACTGGATAAGGGTGCTGCTGGGTACCAATCTCCTCTCCCTAG[T/C]GACCAAGTGAAACCACTAGCTTTAAACGAGTATGAAGGAGATGCCCCTTCACCAAATCGAGGTAGAGGGCGTGGCGGACGTGGCAG
100818 T C TCAGTATAACGCTATCCAAATTGGAACTGGATAAGGGTGCTGCTGGGTACCAATCTCCTCTCCCTAGTGACCAAGTGAAACCACTAGCTTTAAACGAGTA[T/C]GAAGGAGATGCCCCTTCACCAAATCGAGGTAGAGGGCGTGGCGGACGTGGCAGGGGAAGGGCTCGTGGCGACGGTGGCAATAAC
100818 C T CTGGGTACCAATCTCCTCTCCCTAGTGACCAAGTGAAACCACTAGCTTTAAACGAGTATGAAGGAGATGCCCCTTCACCAAATCGAGGTAGAGGGCGTGG[C/T]GGACGTGGCAGGGGAAGGGCTCGTGGCGACGGTGGCAATAACACAATGGAGTACGGGAATGAGGGTTATGAGATGAGAGATGA
100818 T C ACCAATCTCCTCTCCCTAGTGACCAAGTGAAACCACTAGCTTTAAACGAGTATGAAGGAGATGCCCCTTCACCAAATCGAGGTAGAGGGCGTGGCGGACG[T/C]GGCAGGGGAAGGGCTCGTGGCGACGGTGGCAATAACACAATGGAGTACGGGAATGAGGGTTATGAGATGAGAGATGACGGATA
100822 T C TCTTAGAGCTTTGGCAGTAGCAAAAGCCAAGCTGAAGGAGATTAGAGCTCTCTTTTACAATTATTCTTATAGGCGTCGCATTACTACTGATGCTGAAGAA[T/C]GTCAGAGATTTGCTGAAAAAATTATCGTCCTTCTACTAACTGTTGATGCTATTGAGGGACCGGACTACATGGTTAGGGCAGCGAGGA
100822 G A CTACTGATGCTGAAGAATGTCAGAGATTTGCTGAAAAAATTATCGTCCTTCTACTAACTGTTGATGCTATTGAGGGACCGGACTACATGGTTAGGGCAGC[G/A]AGGAAGTCGATGGTGGAAGAACTAGACTACATGCTGGATACAGTGGACCCTCAGCAAGCAGGCAAACCTGGTTCCCTTAGGCGCA
100822 T TA GGACGATGATGATGGAGACAGCATATGAAGCAACATGTAAGATGAGATTAGTTTCAGACTTGGCACTGTTTCTTTCTGTATTATTATTAGTACTACTGCT[T/TA]TTAGCTGGTGTGTGACCTGTTTTAACTTGTAATAGCTGGATTTTTAATCTTTATTTGCTTTGTAGTAGATGCTTGAAGCAGTGTTTCTG
100822 G A TGGAGACAGCATATGAAGCAACATGTAAGATGAGATTAGTTTCAGACTTGGCACTGTTTCTTTCTGTATTATTATTAGTACTACTGCTTTTAGCTGGTGT[G/A]TGACCTGTTTTAACTTGTAATAGCTGGATTTTTAATCTTTATTTGCTTTGTAGTAGATGCTTGAAGCAGTGTTTCTGTACTTTTAATTGTA
100834 AG A CAGAGGAGGGCACCGATGAAGGCCTTGGAGCGGAGGGCACTGAAAAAGGCCCTGGAGAAAGTACTGGAGCAGGGGAGGGCACCGAAGAAGGCCTAGGAGC[AG/A]GGGGAGGGAACCGAAGAAGGCCTTGAAGCGGAGGGCACCGAAGAAGGCCTCGGCGAAAGAACCGGAGCAGGGGAAGT
100840 G A TTCCTGAAATGGTCAGACTTGCACCAAAAAATGAACACAAGGCAATGTTTAGATCGGAATCGTCTAGGGACTTGGTGAAGCGCATTAAAGAATGTCATAC[G/A]AAGAGAGGTTGAAAAGACAGCTAGTCTTGGAAAGAAAGTTGGAGCCAAGGAGGTGGCCACTACGCGAAGGAGAGGAAGAGTCG
100840 A G GCGCATTAAAGAATGTCATACGAAGAGAGGTTGAAAAGACAGCTAGTCTTGGAAAGAAAGTTGGAGCCAAGGAGGTGGCCACTACGCGAAGGAGAGGAAG[A/G]GTCGAGTGGCATGAGATTGGCTATTAGTTTGCAGGCAAGGCATGGATCAAAGAAAATATGGGAAGATTGAGGAGAGAGGGT
100842 G A CATTGGGAGGTGGACCAAAAATATTATGTCCACATAATTCCATGCATTTTGCCTCAGATTGATGCTTTTGCAGTTTGCCCTCTGCTTCGTTTTCAAGTTT[G/A]CCGCTCATTTCTTTCAGTTTTGTCGCCTCAGACAATGTTATATGCCTCTTTGGTACAACACTCTCATTGCCTCCAAATGAGATTTGACTCA
100844 AG A ATCGTCAAGGTCATCGTCCTCTCCTTCATCGTCCAGGTCATCGTAGAAGTAATGGTAAAGATCTCCAGGCTCATCGTCTGCCTCTTCAGAAAATACGGGT[AG/A]GGGGGTCAAACCAAGTAGCTCTCAGAAGGAGGCAGACGCTCTCCTCGAACATGTAGTCATGGATACAGCCATCAAGGGAGCGATG
100852 T C GGATCTGGTACAGCAACAGAAGGAAAGGTAGATGGTACAGTTGTAGGTGTTGAAGATGTTGTAGGGAGAGAATACTGTGACTGTATAATAGCAGGATCAT[T/C]ATGAATAGAAGATGTTTGAACAGGTGGAGTTGACTTGACCTGTAAATCCTTGATATCACTACCCCGAAAGAGTATGTACTCGTAG
100852 T C GTAAATCCTTGATATCACTACCCCGAAAGAGTATGTACTCGTAGATCTTGTCATTTGCTGGAATTTGTGGACCATCCTTTTTTCGTCCCTCGGTGCCAAA[T/C]GATCGTACGTTTCGAAGTCCAATACTGGACTCTTCGGTATTTATATTATACAAAACCCCTTCGTATCTGATCTCGCACTTTGAAGTTAAGC
100854 G T TGATTTCTGCAAGCAAGGATGAATCTGTGCGGTTGTGGAATGTTCACACTGGGATATGTATCTTAATATTCGCTGGAGCAGGTGGACATCGCAATGAAGT[G/T]TTAAGTGTTGATTTTCATCCCTCTGATATATACCGCATTGCAAGTTGTGGGATGGATAATAGCGTTAAGATCTGGTCAATGAGAGAG
100866 T C AGATAACAAAGTATTACAACAACTCAAGAATTGAGAATGGGATAAAATATACACACAAACACACTCCAAGGAAGCACATAAATAATTCTTCGGAGAGCTG[T/C]ATCTCAACAGAAACCACAACGCACGGCTTGAATCACCTATTCATTTCAACAACAAAAATAAGATGCATATTTTGAGATTTCTATGCTC
100874 G A AAAATATAACAGGAAAGTGAAATGGAAAGTCGTGAAACACCACATGTAACCGAACGTAGGATGCTCCACGAAGGAGATGGATCAACCAAATCCCTAACAA[G/A]TCGAAAATGCCTCCAATAAACCAATAACAGATCCAACAAACCCAAGCTGGCCCGATTCCTCTTGACTCGGGTCAGACAAACGCTA
100874 A G GGATCAACCAAATCCCTAACAAGTCGAAAATGCCTCCAATAAACCAATAACAGATCCAACAAACCCAAGCTGGCCCGATTCCTCTTGACTCGGGTCAGAC[A/G]AACGCTAGACATAAAAACACCCAGCAATGTGACAATCATACTCCCTGGGACACCTAGCTCTGCAAATTATAGGAAATCATTCATCTG
100874 C G CAATAACAGATCCAACAAACCCAAGCTGGCCCGATTCCTCTTGACTCGGGTCAGACAAACGCTAGACATAAAAACACCCAGCAATGTGACAATCATACTC[C/G]CTGGGACACCTAGCTCTGCAAATTATAGGAAATCATTCATCTGGATTCACTAGATTTGAATTGATGAGGCAGAACCACGCTTCACCG
100874 T C GATGAGGCAGAACCACGCTTCACCGGAGAGGCCACCATGCTAAGTAGAAGGAGGGAAGGCTGGTGCAAGATCAGGAAAGAAGAAGGTGACGTGAAGTGGA[T/C]CTGCATAAAAAGGAGGTTTTTGGAGAAGAGGAGGTCGATGGTAATCTCACGCAGGCGAAAGCAGGATCTAGAGGGAGATGG
100874 TA T GCAGAACCACGCTTCACCGGAGAGGCCACCATGCTAAGTAGAAGGAGGGAAGGCTGGTGCAAGATCAGGAAAGAAGAAGGTGACGTGAAGTGGATCTGCA[TA/T]AAAAAGGAGGTTTTTGGAGAAGAGGAGGTCGATGGTAATCTCACGCAGGCGAAAGCAGGATCTAGAGGGAGATGGGAAAG
100880 C T CTTGGGCAAAACCCGATTCTGATGAACCTCCACCTTGGGCTCAGGATTCAGGCGCGGGAACCTCCTCTCAGTCTACTTTTGAGATACCCTTTTATGCATA[C/T]CTATTGGCGTCCGCTATTACAGCCATAGCTGCGATTGGCTCGGTATTTGAGTATGTGAACCAAAAACCTATATTCGGAGTATTGAATTC
100888 G A CGTGGATATTGGGTGACTGTCGCGCGCGAAATACCAGGATACGCTGGGTTCTACTTTGGGTTTGAATATGTCAAGCGACGCTTTCAAGCTACGTACGGCA[G/A]AGACAACGTCCCGGTGTGGGGGCTCCTAGCGAGTGGAGCGTGTGGGGGGATGTCATATTGGCTCAGTTGCTATCCACTGGATGT
100908 G T GAACAGCGATCTCGAACGGGTTGGTGAAGCTGAAAGGGGGCGAGAATAAAGGGAAGAAGCCGGCAGGGCCGAAGACGATAGAGAACGCAGCAACGTGGGC[G/T]CTGCATATGGGGTTGAGTGCGAACATCAGGTATCAGAGCTTGAATGGAGTGGAGTTTGTGCTGGGAAGGATGATGCATCCG
100908 G A CAGCGATCTCGAACGGGTTGGTGAAGCTGAAAGGGGGCGAGAATAAAGGGAAGAAGCCGGCAGGGCCGAAGACGATAGAGAACGCAGCAACGTGGGCGCT[G/A]CATATGGGGTTGAGTGCGAACATCAGGTATCAGAGCTTGAATGGAGTGGAGTTTGTGCTGGGAAGGATGATGCATCCGGTT
100908 GA G GAACAACGTGGCTGGTGGTGCGAGCTTTGTGGCTCTGGGGAGGGCTTTGGGCACGCAGAAGAAGGAGGTGGAGGAGGATGAAAAGGTGGTGGTGTTGAAA[GA/G]ACGAGTGATGTTCCATTTGAGTGTTTTGATTTGAAAAGGATGGCTTCGTTTACGTTAGATGGATTGTTGGGAAGGTACGAG
100910 G T GATGTTGTGCTTGAAACTGGTTGTACTGCCTTACAGATTGCAGAAGATTGAGGAATAGTGGCACAAAGGTACCACACCCACCTTCCTTGAACAATATCTT[G/T]AAGTGATGAGTCGAGTATAGAGCTCTATTTTGATCCTCTGGGACTACAGGCTCCACAAGTCCAGAAATGTTGTTGCAATGGAATATT
100910 T C TGGATATGTAAATAACCCCCTTTGCTTTGACATGTCCACCATGGGCTCCAGGGATCTTGTCGATCTCGAACTCAACACCATCGCGAGTAAGAACGAATAT[T/C]TCTCCAACGAATGGAACAGGAGTTCCGTTTGCAAATAACTGGGGGTTCAGCGCCATCGAATCAACCGAACGAATTAGTCGTGGGGG
100918 A G ACCTAGAGCAACAAGCATTTGATGTCAAGATATTCACATATCAGCGCTTAGATTGGCAGAAGAGAGCATTATCACTGCCAAGTGTTGATTCAAAATACTC[A/G]ATAAGTGAGCAAATGGGGCCAGGACCCAGTTGTGCTTCCACAAATCAAGCCGCTGTGATTGAAGTTCTAGTACCTTCCGTCTTCAGA
100918 G A TTATGCATTGGGTCTACAGCTATCAAACGCTATTCTCAACCGTTTGCAGTAAATGCAAACGTCTTCTGGCGATGGAGAAGTCTCTGGCATTGCTTTTGCC[G/A]CCTATTCGTCGACCATATCAGTATGCAGCCAAAATTTGTAGTGATAACGAAGCATCTTCTTCGGCCAAGGGTTTAAGCCAAGATCAGA
100926 T A TGCTAAATCCCAAAAGAACTGTTTTGCGTCCACAAGATTTCTCAATGGAAGCTAATGATTTAGTTGAACTGCTTGATACTTTGCTTTGAATCTGATCAAT[T/A]GCCTTGCAGAAAACAGAAACAAGATTGGAAGCAGCAAGAAGGCCATGACCACCATAACCTTCAATGGGATCGCCTATACAATCCAAAC
100934 G A AAATTGCTCCAAATTTGCCGAGAATGGAAAAGAAAATCATGAATCCTGCAGATATCTGCACCACTCTTCTGCTTCCTACACGAGTTAGAGCCAATAAACC[G/A]GCATTTTCAACAGATACAGTGGAACCAGTAGCTGTTCCAAACAAACCATCTAACAATACACCAATCCCCTGCCACCCAATGCCTCGGC
100934 G GT AGCATCAAACGTAGGGGCGCCCCATTGAAAAGGATATGGAACTCTAATCCAAGGAGAAGAGCCTACAAGCCCAGATTTATCAGTGCGACAATGCAATTGT[G/GT]TTTTCGGAGCAGCATGCTTATATGCTCCACCAACTGTTAGAAAATATGCATAGAGCCACACTATCGCAACTGAGAAAATGACTGC
100934 A C CATAGAGCCACACTATCGCAACTGAGAAAATGACTGCAAATCGATCAAATACTGGTTTGTCCGATCGAATGGCGTGTGGAATATACTGAGAAAAGACGAG[A/C]AGTATAATTATCATTGGGAGCCCGATCTCAATACATTTAGCAACTCCAGGAAAGCCTAGTTCATATAGCCCAAATCCTGATAAAGCA
100934 T A CCAGGAAAGCCTAGTTCATATAGCCCAAATCCTGATAAAGCAACTAATGGAACAGCTGAAAGCGGACTTAAGAACCTTGTGACATTGCGCCATAGGCCAC[T/A]GAAGCCAACGATGATCTGAAGAGTTGATGCTACAATAAGTGCACCTTGAGTTCCTCGCAT
100938 CA C TATAAGGCTGTATTACCTGATGGTCAAATTGTATCTGTCAAAAGAGCAAAGAAGGATCATTTCTTGCGAGAAGAATTCAATAACGAAGTTGAACTTCTTA[CA/C]AAAAATTGATCACATCAATCTGGTGAGATTACTTGGGTACACAGACAAAGGAAATGAACGCATTATCATTACCGAACATGTTTCAAA
100938 T C TTATCATTACCGAACATGTTTCAAATGGTACTCTTAGAGAGCACCTTGATGGTCAGCATGGGAAAATTCTGGATTTCAATCAAAGACTTCAAATTGCAAT[T/C]GATGTTGCTCATGCCTTGACTTATCTCCATCTATATGCAGAGAAACCAATTATTCACAGAGATGTGAAATCTTCGAACATCATGATAAC
100938 G A AACCAATTATTCACAGAGATGTGAAATCTTCGAACATCATGATAACGGAGAGTTACCGTGCTAAAGTAACGGACTTTGGATTTGCAAGAGTGGGTCCTAC[G/A]GAAGCAGAGCAGACCCATATACTAACTCAAGTGAAAGGGACGGCCGGCTACCTTGATCCAGAGTACCTCAAAACTTTCAAGCTTAC
100940 T C GCCGAAACCGATTCGCCGGAGTAGACATGCGCGTCCGCGTCAAAGGAGGCGGGCATACCAGCCAGATCTACGCTATCAGGCAGAGCATCGCCAAGGCGCT[T/C]GTTGCTTACTATCAAAAATTCGTGGATGAGCAACAGAAGAAGGAGATCAAAGACATTCTTGTTAGTTACGACCGGACTTTGCTTG
100946 G GT AATTACAACTAAACAAATTTCATAATTTACAATGCAGATGTTTTCTTAAAATGTGTTTTGAACTACGTCCTCGAGCACAGAAGCAAAAAAGTTTAGTGCA[G/GT]TTTTACCATTAGGCTGCTGAAGACTCAAAAGAACCCCAGTGTACGAAAACGTGCATAGGATTAGTCCTCATCAGAACTCTCGTAAGC
100952 C T ACTTTTTTCCGTTTAGGAACGACGGCTATAATGTTGTTGTGAACCATCACCCGATTAGAGGAATTCCGGTGTACAATCATAATGTTAATTATATTAATAG[C/T]CATCTTTGTCATGATAATATGAATATGAATAATGGGTTATCGAGGTCTAGGTTTTTGTCGAGAAATAATATGATGTTGGGTAGTAGTAA
100952 A G CTATAATGTTGTTGTGAACCATCACCCGATTAGAGGAATTCCGGTGTACAATCATAATGTTAATTATATTAATAGCCATCTTTGTCATGATAATATGAAT[A/G]TGAATAATGGGTTATCGAGGTCTAGGTTTTTGTCGAGAAATAATATGATGTTGGGTAGTAGTAAGAGAAGCGTGAGATCGCCAAGGA
100952 T C AAATAATATGATGTTGGGTAGTAGTAAGAGAAGCGTGAGATCGCCAAGGATGAGGTGGACTACTTCGCTTCATGCAAGATTTGTTCATGCCGTTGAGCTG[T/C]TAGGAGGCCATGAGAGGGCGACACCAAAGTCAGTGCTCGAGCTCATGGATGTGAAAGATCTGACCTTGGCACATGTCAAATCTCA
100952 A T AGTCAGTGCTCGAGCTCATGGATGTGAAAGATCTGACCTTGGCACATGTCAAATCTCACTTGCAGATGTATAGAACAGTGAAGAGCACTAATGCACCTGC[A/T]GCTTCTTCAGGACAATCAGACAGATTCGAGAGTGGCTCAGCCGGGGAAATATCAGATGACAACTCGATTGAAATGCACAACATTCT
100952 A G AACAGTGAAGAGCACTAATGCACCTGCAGCTTCTTCAGGACAATCAGACAGATTCGAGAGTGGCTCAGCCGGGGAAATATCAGATGACAACTCGATTGAA[A/G]TGCACAACATTCTTGGAGCTCAGTCCCTGATTCAAAATGGATCACAAGTATGTGACTTAAACGATCAAGGGCATAATGATCAGTTC
100952 C T GCACAACATTCTTGGAGCTCAGTCCCTGATTCAAAATGGATCACAAGTATGTGACTTAAACGATCAAGGGCATAATGATCAGTTCGGTCTGTGGAGCAAT[C/T]CGTCAAGGGGTAGCTGGATCAAAGGCAAACAAAGGGATTACTGCACCATTGGGCAAAACAAGAACTGCTATGAGGAAACGCAATC
100958 T C ACCCTGATATTTATAAAAAGGGCCCTGCTTTTGGGATGCCGGGTATTAAGGTGGATGGAATGGATGTTTTGAAGGTGAGGGAAGTAGCAAAGGAGGCAAT[T/C]GGGAGAGCTAGGAGGGGAGAGGGTCCAACTTTGGTTGAATGTGAGACTTACAGGTTTAGAGGACACTCGCTTGCGGACCCTGA
100966 A G CGAGGACAACAGCCACTAATAAGAACAAAGCAACTCCACCAGCAATTATCACTATAATAACCCTAGTTTTTAACTTCTTTGTCGAACTAACTTCATTATT[A/G]CGAGGAAACGAAGGTTGCGAAGAAGAATTAGGTGATAACGGTGAAGGAGGAGCACCAGAACACTGAAGTAGAGGAGGGCCACACA
100966 G T CACTATAATAACCCTAGTTTTTAACTTCTTTGTCGAACTAACTTCATTATTACGAGGAAACGAAGGTTGCGAAGAAGAATTAGGTGATAACGGTGAAGGA[G/T]GAGCACCAGAACACTGAAGTAGAGGAGGGCCACACAGTTGAATATTTCCAACAAATGAATCATTTGAAAATCTTTGAAGGGAAAGG
100966 G A TATAATAACCCTAGTTTTTAACTTCTTTGTCGAACTAACTTCATTATTACGAGGAAACGAAGGTTGCGAAGAAGAATTAGGTGATAACGGTGAAGGAGGA[G/A]CACCAGAACACTGAAGTAGAGGAGGGCCACACAGTTGAATATTTCCAACAAATGAATCATTTGAAAATCTTTGAAGGGAAAGGGG
100978 C G CCGGGAAGAAGTGGCTTCAATGAATCGTACATACCAAAGTAGAGACCACGGTACACAATAATACCAACACATGAAATGTTAAATCCACGGTATAATCCAG[C/G]AATGCCATCACTCTTCAGCGTCTTGCGGTACACATCAATAAGACCATTGAATTGCCTGTCACCACCACCCTTGGCAGCCTTGGCATC
100978 T C GGTACGGGCATAGTCCAAGGAGTAAACAAAGAAAAGGGATGAGGCACCTGCAGCACCACCAGAAGCAAGATTTCCAGCAAACCATTTCCAGTAACCATCT[T/C]TGTCTTTCTTGAAGTTGAAAAGCCTCTTGAAGTAGTCCTTGAAAGCAAAGTTCAGGGCCTGTGTTGGGAAATAACGGATGACATTG
100978 T A AGCAGTCACCGATTCCTTTGTATGGCTTCGATAGACGTCCAGATTTGATCATCTCATCCTGATTTTGAATCAAGAGTTTCACACGCTCAATAGGAGCAGC[T/A]GCCGTTTTTGAGACCGCAGCAGAAACTCCACCCATCAAAAAATCAACAACAAAATTCTTCTCGGCAGGAGCGTGAGCGTAAACTGGAG
100982 A G TCCACATGGGATAGCCCGGGTAACCCACCACAGGCATCATCATCTTGGGCGGTCCTCCTTGCCCTTGCGGCATGGCAAAAGTTCCAGGCATTATTGGAGG[A/G]GGCACAAATGTTGGTTGAGGAGTGTTCAAAAGTTTGATTTGATGCTCTATGTTTTCTTTCTCTTGCTTTAGCCTCTGCTTCTCATTTCG
100986 C A CCATTCATTCATATTCATCAAGCTCAAAAATGCAGATATCATCATCGTCCTATCTCTCCACATTACCCCCATCCTGCAAACTACCACCCGCATCATCATC[C/A]TCGTCCAAATCCTCCATAGACCCTCCAATGATAACAAGAAGACAGCTCGGCCTTTCATTGACGGCAACATTCATGGCAGCACTCGGAACG
100986 C A GCTCAAAAATGCAGATATCATCATCGTCCTATCTCTCCACATTACCCCCATCCTGCAAACTACCACCCGCATCATCATCCTCGTCCAAATCCTCCATAGA[C/A]CCTCCAATGATAACAAGAAGACAGCTCGGCCTTTCATTGACGGCAACATTCATGGCAGCACTCGGAACGGGCACAGCGCCCACCGCGG
100986 G A CGTGGCTGAGGCCGTCACGCGGTTAAGAGAGGCGTCCAATTCGTGGGTCGCCAAGTACAGAAGGGAGAAGTCCCTTTTGGGAAGGGTGTCATTTAGAGAT[G/A]TGTATTCTGCGCTTAATGCCGTTTCCGGCCATTATGTCAGCTTTGGGCCTACTGCCCCCATACCTGCGAAGAGGAAGGCTAGGAT
100986 G A CCGTCACGCGGTTAAGAGAGGCGTCCAATTCGTGGGTCGCCAAGTACAGAAGGGAGAAGTCCCTTTTGGGAAGGGTGTCATTTAGAGATGTGTATTCTGC[G/A]CTTAATGCCGTTTCCGGCCATTATGTCAGCTTTGGGCCTACTGCCCCCATACCTGCGAAGAGGAAGGCTAGGATTCTGGAGGAGG
100990 A G CTTTTAAGATTTGGATTCTGTAATGGACGAGCACTTCTATAGGGATTTTTGAAAGGAGGCAGTTGGCGACTTCATGTTGATTCAATGCTGCTGAACAAGC[A/G]AGCCCACCGAGAAGGTGACTGTCGTCGCAACCTCGGTTTACAAACCAAGAGACAACAGATATTCGACCATGTATTATAGCATTTACG
100990 T C GCAACCTGCAATAACATGAGAACAACTTCTGCACAGTCATATCGAGTAGCTTCTAAAATGCAGTAATTTAGATTGTTAGGTCCCCTTTGCACCAATATAT[T/C]AAGCAAACCTCTAAGAGCAGAAGCTGAAGTATCAGACGCCCAACCCGGATAAAAAGAACATGAGTGAATAATAAGAGTACATGCCCC
100992 C G AAAATTTCATCACTTTCGCTGGTTTGTCACCTGAAAGCACCGTTATTTCTTGGGATAATAC[C/G]GCCACCAGGATTCAGCACCACCAGGAATCTCGGTTGATTGGAACGGGAACATTTGGTTGTGGAACTGTAATTGTTGAGGGAGAAGATTTTATTGCTGAAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
100992 A T CTGTAAATCTCAAGGATTCATAACAGCTCAAAGCAGAAAATCTTCTCAAGAATCAACTGGATATGTGTTTCTGAGATGTGTCATAACCGGAAATGGATCC[A/T]CCTCATATATGCATCTTGGGCGACCATGGGGCCCCTTTGGTAGAGTTGTGTTTGCTTACACATGGATGGATGCATGCATTAAACCTGT
100994 C T AGTCAAAAAAATCGAAGTAAAATCCTGGATAAATGGGACTTATGATTCTTGTTTGTTTCAGAGAAGAAGCATTTTATCTGATGTTCATCAGATGTTTTTC[C/T]ATCTTGCCTTCAAGTTATTAGCAAAGAAGTTGATTGCAGTTTGCAATAATATCCTGCGGTTTACTCAAATGTAGGAGTAAGTTAATATA
100994 G A CATCTTGCCTTCAAGTTATTAGCAAAGAAGTTGATTGCAGTTTGCAATAATATCCTGCGGTTTACTCAAATGTAGGAGTAAGTTAATATAATTTGCAGCA[G/A]TTTATATCAGTGATTATGGATTATCAAGTTGAGGCAATACTGTTTCTTTTTATCTCTTTGTTGTTGGCCGCTGCTGATGCTTTTGAGAGA
100994 C A TGCAGTTTGCAATAATATCCTGCGGTTTACTCAAATGTAGGAGTAAGTTAATATAATTTGCAGCAGTTTATATCAGTGATTATGGATTATCAAGTTGAGG[C/A]AATACTGTTTCTTTTTATCTCTTTGTTGTTGGCCGCTGCTGATGCTTTTGAGAGATGCGTGTTGATCTTTTTTTAGCGAGTGACAGTTTG
101004 C A AAGACTTCTTGATTTAGTGTCTCTATTTTGTTTTGTTCCAAGAGCAAAGTATCTACCATTAGGCCCTATCAGTGCAAAACTCATCGACATATATAGAAAC[C/A]GACACAATATAAGTGCCACATCTGGTCTGAATGATCCAGCTGTTGCTACTGGAATATCGGATCTTATATATGAATCTAAAGAAACACAA
101006 T A ATGTGGTTGCCTCCATAAAACGGGCATCGTTTATTAACGGGTTAGCGGATCTAGCTGGTGGAGATCCGATACAAAAAGGGGAACTAGGTTCAGCTTGGTT[T/A]TCACTGCCCTTTGCTAGAAAAATATTATGAAGTTCGACCGCAGCTTTCAGATCTAAAGCATCCTCTTGGTCACGAGTCTGCCATGAA
101016 T C TTGATGAATCTAACTACCTCCTGTGGAATCAAAGAGGAGGTCAATCAAGTCGTGGAAGAGGAAGAGCTGGGAGATGGAACCCCAACAATAGACCAAAGTG[T/C]CAAATTTGTGACAAACTTGGACACACAGCCAACAGATGCTACTTTAGATTTGACAATAGC
101022 T C ATACATTCCAACGTTTGCTCCATCCACAACGGCGTCAAATGGCCCATGCCGCTCAAGCCATTCCTGAAATTTCACGAAATCAACCTTACGCTCCTGCTCG[T/C]TAGCCAGCTTGGATAACTTCCTAGCAAACTCCTCCGTCTCCATTGGATCAATATCAATGCACGCCAACTTCTCCCCACACTTATTACAAA
101022 T C TTGCTCCATCCACAACGGCGTCAAATGGCCCATGCCGCTCAAGCCATTCCTGAAATTTCACGAAATCAACCTTACGCTCCTGCTCGTTAGCCAGCTTGGA[T/C]AACTTCCTAGCAAACTCCTCCGTCTCCATTGGATCAATATCAATGCACGCCAACTTCTCCCCACACTTATTACAAACTCCCTCACTGCTCA
101026 C G GCATCTTCAAGTTTAATCCCATCATTGCTGATGTCATCTGGACTTAGGCTACTGCTTGGTAACTGTTCAGTTGCACACCCAACTACTTCACCAATTGGAG[C/G]ATTGATCTGAGAAGGTGAACTCAAGTTGGAAAAGACCATATGTGAACTGCTATCTGAGGACCTATGTGCACTTTCGAGTCTCAACACA
101030 G A AAAATATCTCCTTGGACATATGTTAATATATATTCCACAGCTCTGACCCCCACTTCTCCATTCCCCTTTTTCCATAGATATCCTTGAGCTTGAATTGCAT[G/A]TCCACCTCGACGAAGGGTTAGATGGCAAACTGCGCAATAGACCCGACTGGAGAGAACGACGGGCCAACAAAAGAGCTATTTTGGCGCC
101034 C T GTCACCATATTAGGGGAAGCAGCAGAGTAAGTCCCGCTTCTACCATTGATAGGAGTCGTGGTGGTTGGAGTTGATGGAGTGGAGGGAGTAGTAGGAGAGG[C/T]GGTAGAGCCCCCGGATGACGAGGACGACCCTACAGATACAGAGAGCTTCATGCCACCCGTGCAGTGTCCGGGCACCCCACATA
101042 C A GGGTGCACACAGTGCTTATCTCAACCCAGCACGACGAGACCGTGACCAACGATGAGATTGCCAAGGACCTCAAAGAGCACGTCATCAAGCCTGTTGTCCC[C/A]GCCCAGTACCTTGACGAGAACACCATTTTCCATCTCAACCCATCAGGGCGGTTCGTCATCGGGGG
101052 A G AGCTATCTGTGCCAACTGCTCTGATTCCAGCTTCACAACTGAAGAGACGACCGCCACCTCAGTGCCAGTACGCTGATTGTAAATAACCTCGAACTCCATA[A/G]CGATATCTTTGATAATGTCAATCCTGCCCATATCAACCAAAATACTCAAGAAATTCACCATATGTGGCGTCATCTCCTCCGCCTTACCA
101060 CT C GTTCCCATTCTTTTCAACCTATTTTCCATCTTCATGCTTTGTATTGGGCCCTAGCCGAGGTCCTTATCCTATAGTCTTGGTTCAGAATATCTGCCAATCT[CT/C]TTTTTTTACTTGGAGTGCAGAATCGCCTCCACCATGATCTGTTCTGTGTCTTATCCCTATTAGTCGAGTAAGCTGTCTTCTTTCGCTTGTGG
101074 A C GGGAGGATGTTCTATGGACCTGGTGGACCATATGCCTTGTTTGCAGGGAGAGATGCAAGCCGAGCTTTGGCTCTTATGTCATTTGATCCGGTCGACCTCA[A/C]TGGGAATCTTGAAGGTTTAAGTGCATCTGAACTGGAAGTTTTGCAAGACTGGGAGTACAAATTCATGGAGAAGTACGTTAAAGTTG
101074 G A GGATGTTCTATGGACCTGGTGGACCATATGCCTTGTTTGCAGGGAGAGATGCAAGCCGAGCTTTGGCTCTTATGTCATTTGATCCGGTCGACCTCAATGG[G/A]AATCTTGAAGGTTTAAGTGCATCTGAACTGGAAGTTTTGCAAGACTGGGAGTACAAATTCATGGAGAAGTACGTTAAAGTTGGACA
101074 T C TTCATGGAGAAGTACGTTAAAGTTGGACAACTTGTTACCGACAAAACAACCGTTACCAAAAGCGAATTGGTTCAGACTTCCAAACTGGAAAGTGAAGATG[T/C]CAAGTCATGTTCTGACTGACTGCTTCATGGTTATAAACCAAGGCTCTCTCATTTTCTTTTTCTTCTTTTTTCCCTTTTTTTATTAGTTTCA
101078 A G TGGCTGTTGCAAAAATCAAAGAAGGGATTGTCATTGCTGCTTCAAATCCTGAGATTGCATGTGGTATTGTTGCAGGACTAGGGCTTGTGGTGTTAAAGAG[A/G]CCAAGGCGTCTTCTAATTCGAAACACAAGACGGCTCTTCATGAGCGAAGAGTCATTATTGTCTGATGCGGAAGCCAAAGTGAATAA
101078 A T GTCTTCTAATTCGAAACACAAGACGGCTCTTCATGAGCGAAGAGTCATTATTGTCTGATGCGGAAGCCAAAGTGAATAAGCTGCGACAGTCAGTAAACGT[A/T]GTGAAGAATGAAGGCAAAAAGCTTGAGGAAAGGGCACGAAAGGCCGAGGAAGAAATTGAAAGGGGACGCCAGGCTCTAATAAA
101078 T G ATGCGGAAGCCAAAGTGAATAAGCTGCGACAGTCAGTAAACGTAGTGAAGAATGAAGGCAAAAAGCTTGAGGAAAGGGCACGAAAGGCCGAGGAAGAAAT[T/G]GAAAGGGGACGCCAGGCTCTAATAAATGCAGGTCGTGAAATTCGAAGTGAACTACGACTAGCCAGTGGCATTGAAAAAGAAG
101078 G A CGTGAAATTCGAAGTGAACTACGACTAGCCAGTGGCATTGAAAAAGAAGCAATGGGCTTGAAGGACATTATCAGTGAACTGCCGAGGAGAGATGCATCTC[G/A]ATTTCGATCGGAGGTATCAACCCTTGTCTCCCAAGTAAAAAAGGAGAAGAAAGTTCTAACTCGCTCTGCAACAAAGATAATCAAT
101084 AG A TTTGTATCATAAGAAGTACTGGAGAATTATTTAAACAAAGTGGCACATAATAGATGCACGGTATGGTCATAGTCTCATAGATCTGGCAACAATTAATATA[AG/A]GGGCAACATTACGTTGTACACTCAATACAACCCCACCATGATACACAAACAAGCTCCACATCATAGAGAAACATGTTGATCATTGGA
101084 AC A TTAAACAAAGTGGCACATAATAGATGCACGGTATGGTCATAGTCTCATAGATCTGGCAACAATTAATATAAGGGCAACATTACGTTGTACACTCAATACA[AC/A]CCCCACCATGATACACAAACAAGCTCCACATCATAGAGAAACATGTTGATCATTGGAATGAAAAAGATCAGCTCCACAGGAGCATT
101084 G GTA AATTAATATAAGGGCAACATTACGTTGTACACTCAATACAACCCCACCATGATACACAAACAAGCTCCACATCATAGAGAAACATGTTGATCATTGGAAT[G/GTA]AAAAAGATCAGCTCCACAGGAGCATTCCAGCAGCTCCAAGGCAGCGTATAACAAACATAATTTCATTGGTAGAGGGCAATGAATC
101092 T A GTAGTAATACTAACGCTCCATCTTCAGTTGAGAATAAGCAGGTGGTACGTGCAGCAGCTAATGTGCTGCCGGCAATGTGGGCTGTTGGGCCGGCGTCTAC[T/A]GGGGCAGGAGGGGCCTTCTGGATGCTTCCGGTCACTGCTGGAAGCAACGCTCCTACCACCGCAGAAGCGAACAATCCAGCTATG
101092 A G TAATGTGCTGCCGGCAATGTGGGCTGTTGGGCCGGCGTCTACTGGGGCAGGAGGGGCCTTCTGGATGCTTCCGGTCACTGCTGGAAGCAACGCTCCTACC[A/G]CCGCAGAAGCGAACAATCCAGCTATGTGGACGGTGCCTGCGCAGTACAGGAACACCAACACGGTTCAGGCGCCGGTGCAGTTC
101092 A G CAGAAGCGAACAATCCAGCTATGTGGACGGTGCCTGCGCAGTACAGGAACACCAACACGGTTCAGGCGCCGGTGCAGTTCATGTCCAGAATGGGGCTGCC[A/G]AGCATGACGTCCATGTTGAGCCAGCAACCCGGACCTGGTTCCAAATCCCATTTGGGTATCGGGCTCAACGACACCAGTTTCAACA
101092 G C TCCAAATCCCATTTGGGTATCGGGCTCAACGACACCAGTTTCAACATGATAACAGCTCTCAATGCCTACAATAATCATCAGACTTTGGATCAGCATCAGA[G/C]TCAGAGTCACAGTCATGATAGTGCAGATGATCATCACACTAATTCTCAGTAATTATGTTATTACTATTACTATTTT
101100 A G AGTAGAAAAGGCAGAATTTTCCTTACCATCGTCAGAAGCACCATCCTGCGGCATGCTGATTTTCCGGCGGCGGATGAGGTTTACGCCGTCGATCCAGCGC[A/G]CGAGGGCGACGCTAGACGATCGATTTGGATCGTATTCGATGCGCTCGACGATGCCAGTGGACGGAACATTACGCTTTAGATCGAC
101102 T C AAACCGAACTGAAGCTCCCCGTCCTAGCCTTAGTGGACAGTGACCCCTACGGGCTCAAGATATTGTCCGTTTACATGTGCGGCTCGAAGAACATGTCGTA[T/C]GACAGCTCGAATTTGACGACTCCGGACATAAAGTGGCTGGGGGTGAGGCCGAGCGATTTGGACAAGTACCAGATCCCGGAGCAGT
101102 TG T AGTGACCCCTACGGGCTCAAGATATTGTCCGTTTACATGTGCGGCTCGAAGAACATGTCGTATGACAGCTCGAATTTGACGACTCCGGACATAAAGTGGC[TG/T]GGGGGTGAGGCCGAGCGATTTGGACAAGTACCAGATCCCGGAGCAGTGCAGGCTGCCGATGACCGATCAGGATGTGAAGACCG
101102 G A ACGGGCTCAAGATATTGTCCGTTTACATGTGCGGCTCGAAGAACATGTCGTATGACAGCTCGAATTTGACGACTCCGGACATAAAGTGGCTGGGGGTGAG[G/A]CCGAGCGATTTGGACAAGTACCAGATCCCGGAGCAGTGCAGGCTGCCGATGACCGATCAGGATGTGAAGACCGGGAAGGAGCT
101102 C T CTCCGGACATAAAGTGGCTGGGGGTGAGGCCGAGCGATTTGGACAAGTACCAGATCCCGGAGCAGTGCAGGCTGCCGATGACCGATCAGGATGTGAAGAC[C/T]GGGAAGGAGCTGCTGGAGGAGGATTTTGTGAAGAAGAACGAAGGATGGGTGAAGGAGCTGGAGTTGATGGTTAAGACCAGG
101102 A G ATTTTGTGAAGAAGAACGAAGGATGGGTGAAGGAGCTGGAGTTGATGGTTAAGACCAGGAAGAAGGCTGAGATACAGGCGCTTAGCTCCTTCGGCTTTCA[A/G]TATTTGACCGAGGTTTATTTGCCACTTAAGATACAGCAGAAGGACTGGCTGTGAAAGATTGCTGTAACTTTTT
101114 G A TAGAGATCGAGAAAGCTATTAAAAAACCTGATAAGAAGGCAATTCGAACTTCCGTACCTGTTCCGAAGGTGACAGGGGCTGAGCTGGCAAGGAGGAAGGA[G/A]GAAGAGAGGGAGAGGTTGGCAAAGAACGCAGAAGAGGCCAAGAAGAAAGAGAAAAGGATGGCGGATGAGGAAGAGTACGA
101114 G T AGGAGGAAGAGAGGGAGAGGTTGGCAAAGAACGCAGAAGAGGCCAAGAAGAAAGAGAAAAGGATGGCGGATGAGGAAGAGTACGAGAAGGTAGTGCTTGT[G/T]AGCAATACGAATCGGGATGATTCATTGATCGAAGCAAGGTCAGTTGAGGAGGCAATTGCAAAGATTTCGGTTGCAGAAGG
101114 G A GGGATGATTCATTGATCGAAGCAAGGTCAGTTGAGGAGGCAATTGCAAAGATTTCGGTTGCAGAAGGAAGTTTACCACCTGACCGTCATCCCGAAAGAAG[G/A]CTTAAGGCTTCTTTTAAGGCTTTTGAAGAGGCAGAGCTTACCAAACTGAAAGAAGAGAAACCAGGGTTGACTCTTAATCAATATA
101114 A G AGGAGGCAATTGCAAAGATTTCGGTTGCAGAAGGAAGTTTACCACCTGACCGTCATCCCGAAAGAAGGCTTAAGGCTTCTTTTAAGGCTTTTGAAGAGGC[A/G]GAGCTTACCAAACTGAAAGAAGAGAAACCAGGGTTGACTCTTAATCAATATAGGGATTTGATATGGAAGATGTGGAAGAAATCTC
101114 A G TCCTCTCAACCAGGTTGCTGCCGACTGATATGGTGCATCTAAATGTCATGAGGTTATTCACTGTGGTATATGTACATGTGGAACAGGTTCATTTTATTTG[A/G]AATAGTTTGGCAGAGAAAAAGATGCGAGAAGTTGCTTTTAGCTGTGAAGTTGCAAAAATAAGTG
101126 G A TCTGAGTTAACTTGCCCTGGAGATTCTTGTTCAGTGGTTAGTCCCACAACATATGGTTCATTTTCACCATTTGGAGCAGAACTGATAGAATCTGTGTTTG[G/A]GTGCGTCGAAATAACCATAACCTGTGAGGGCCGCTGAGCTCCTGACCTACTTCGTTGTCCTTCTCTTCTAGCGATATGACGTGTTCTTC
101126 T C TTGCTGCAGCTGCTGCCAAATGTTGAATTATCCGTTCTTCAAGTTCACTATCTTGTAAATGTGGTAGCTCAATATCACCTAATGCAGGGTGGTGAAAAAT[T/C]GTAGGCTTTCGAATTTGATTGGACCTGATTTTTCTTTCATTTTCTATGCCTTCAAATAACTCTTGGCTTGTGGGATCTTTCAAACTAATGG
101126 C G CAGCTGCTGCCAAATGTTGAATTATCCGTTCTTCAAGTTCACTATCTTGTAAATGTGGTAGCTCAATATCACCTAATGCAGGGTGGTGAAAAATTGTAGG[C/G]TTTCGAATTTGATTGGACCTGATTTTTCTTTCATTTTCTATGCCTTCAAATAACTCTTGGCTTGTGGGATCTTTCAAACTAATGGGTTGC
101126 AT A TATCCGTTCTTCAAGTTCACTATCTTGTAAATGTGGTAGCTCAATATCACCTAATGCAGGGTGGTGAAAAATTGTAGGCTTTCGAATTTGATTGGACCTG[AT/A]TTTTTCTTTCATTTTCTATGCCTTCAAATAACTCTTGGCTTGTGGGATCTTTCAAACTAATGGGTTGCCAACACATAGGACATTGAGAG
101132 T C GTGCCGCCCTCACCGACCCTTACATCGGCGTTTTCTCCTCTTGGAAAGGCACCGATTGCTGCTCTAACTGGTACGGTGTGAGCTGTGATCCGACAAATGG[T/C]CAGGTAACGGACCTAAACCTCCGGGGAGAATCCACGGATCCAATCCTGACAACCGCTGGCCGATCCGGTCTAATGACGGGTCAAAT
101132 G A GCACCGATTGCTGCTCTAACTGGTACGGTGTGAGCTGTGATCCGACAAATGGTCAGGTAACGGACCTAAACCTCCGGGGAGAATCCACGGATCCAATCCT[G/A]ACAACCGCTGGCCGATCCGGTCTAATGACGGGTCAAATCTCGCCATCCGTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGC
101132 C G ACTGGTACGGTGTGAGCTGTGATCCGACAAATGGTCAGGTAACGGACCTAAACCTCCGGGGAGAATCCACGGATCCAATCCTGACAACCGCTGGCCGATC[C/G]GGTCTAATGACGGGTCAAATCTCGCCATCCGTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGCGGACTGGAAGCAGATATC
101132 C T ATGGTCAGGTAACGGACCTAAACCTCCGGGGAGAATCCACGGATCCAATCCTGACAACCGCTGGCCGATCCGGTCTAATGACGGGTCAAATCTCGCCATC[C/T]GTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGCGGACTGGAAGCAGATATCTGGCGCGATACCGGCCTGCCTCACCCGCCT
101132 G A CGGATCCAATCCTGACAACCGCTGGCCGATCCGGTCTAATGACGGGTCAAATCTCGCCATCCGTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGC[G/A]GACTGGAAGCAGATATCTGGCGCGATACCGGCCTGCCTCACCCGCCTCACCTCCTTACGCCACCTCGACCTGGTCGGCAACCAGCTC
101132 G C TGGCCGATCCGGTCTAATGACGGGTCAAATCTCGCCATCCGTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGCGGACTGGAAGCAGATATCTGGC[G/C]CGATACCGGCCTGCCTCACCCGCCTCACCTCCTTACGCCACCTCGACCTGGTCGGCAACCAGCTCTCCGGCACCATCCCCTCCGACAT
101132 C T GGCCGATCCGGTCTAATGACGGGTCAAATCTCGCCATCCGTCTGCGAGCTAACCTCCCTGTCCACCTTCATCCTGGCGGACTGGAAGCAGATATCTGGCG[C/T]GATACCGGCCTGCCTCACCCGCCTCACCTCCTTACGCCACCTCGACCTGGTCGGCAACCAGCTCTCCGGCACCATCCCCTCCGACATC
101132 C T ACATCGGCAGCCTCAAGTCCCTTACTGTCCTCAACCTCTCCGACAACAAACTCTCCGGCTCCATCCCTCCTTCCATCACCTCCCTTTCCGACCTCCGTCA[C/T]CTCGACCTCAGCGGCAACGAGCTCACCGGTCCCATCCCTTCCAACTTCGGCGACCTCAACATGCTCAGTAGGGCCCTGCTTAACAAAAAT
101132 G C CCTTACTGTCCTCAACCTCTCCGACAACAAACTCTCCGGCTCCATCCCTCCTTCCATCACCTCCCTTTCCGACCTCCGTCACCTCGACCTCAGCGGCAAC[G/C]AGCTCACCGGTCCCATCCCTTCCAACTTCGGCGACCTCAACATGCTCAGTAGGGCCCTGCTTAACAAAAATAAACTATCCGGGTCCATCC
101132 T C CTTCCATCACCTCCCTTTCCGACCTCCGTCACCTCGACCTCAGCGGCAACGAGCTCACCGGTCCCATCCCTTCCAACTTCGGCGACCTCAACATGCTCAG[T/C]AGGGCCCTGCTTAACAAAAATAAACTATCCGGGTCCATCCCAGTGTCCATAACCAGCATGAGACGCTTAGCGGATTTGGATCTTTCTAC
101132 T C ACCTCCGTCACCTCGACCTCAGCGGCAACGAGCTCACCGGTCCCATCCCTTCCAACTTCGGCGACCTCAACATGCTCAGTAGGGCCCTGCTTAACAAAAA[T/C]AAACTATCCGGGTCCATCCCAGTGTCCATAACCAGCATGAGACGCTTAGCGGATTTGGATCTTTCTACCAACGGGTTATCGGGTACAA
101132 C A TCCCTTCCAACTTCGGCGACCTCAACATGCTCAGTAGGGCCCTGCTTAACAAAAATAAACTATCCGGGTCCATCCCAGTGTCCATAACCAGCATGAGACG[C/A]TTAGCGGATTTGGATCTTTCTACCAACGGGTTATCGGGTACAATACCGGAAGGGCTTGGAAACATGCTGGTGCTGTCCACGTTGAAC
101136 C T AAGCAGTAACACCAGATATGGTTCCTTGGGTTCAAGAAACTCAACCGACGGCAGCAGTCCGTTGAAGGTGCAAAGGTCGCGCTTATGCTTTACTACAATC[C/T]GAATGTTTGCATCTAAAAGAAATGTATGACAAACAACAAAGTATTAATGAGAAGCAAGGAAAGGAGATAGAAGAGCTGCGACGTA
101136 T C CTAAAAGAAATGTATGACAAACAACAAAGTATTAATGAGAAGCAAGGAAAGGAGATAGAAGAGCTGCGACGTATGATTCAATCTTCGCAAAACTTGTCAT[T/C]GATTCCTCCATCGCCACCGGAACAACCGTCGTCTACACAAGAAGATATCCTAAACACAAGTCATCAACCACTAACCCAAAATCAGTC
101136 T G GAAAGGAGATAGAAGAGCTGCGACGTATGATTCAATCTTCGCAAAACTTGTCATTGATTCCTCCATCGCCACCGGAACAACCGTCGTCTACACAAGAAGA[T/G]ATCCTAAACACAAGTCATCAACCACTAACCCAAAATCAGTCAACCAATCAACAACAAGCTTCCTCTCAATAGCAAGCTTTCTCTCAAC
101136 A G ATAGAAGAGCTGCGACGTATGATTCAATCTTCGCAAAACTTGTCATTGATTCCTCCATCGCCACCGGAACAACCGTCGTCTACACAAGAAGATATCCTAA[A/G]CACAAGTCATCAACCACTAACCCAAAATCAGTCAACCAATCAACAACAAGCTTCCTCTCAATAGCAAGCTTTCTCTCAACAGCTCCCAA
101136 CA C TCAATCTTCGCAAAACTTGTCATTGATTCCTCCATCGCCACCGGAACAACCGTCGTCTACACAAGAAGATATCCTAAACACAAGTCATCAACCACTAACC[CA/C]AAAATCAGTCAACCAATCAACAACAAGCTTCCTCTCAATAGCAAGCTTTCTCTCAACAGCTCCCAATCCAACAAAATTTATCTTATCCA
101136 A G CATTGATTCCTCCATCGCCACCGGAACAACCGTCGTCTACACAAGAAGATATCCTAAACACAAGTCATCAACCACTAACCCAAAATCAGTCAACCAATCA[A/G]CAACAAGCTTCCTCTCAATAGCAAGCTTTCTCTCAACAGCTCCCAATCCAACAAAATTTATCTTATCCACAATTTGGACCTCTCTATTATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101136 A G CCAATCAACAACAAGCTTCCTCTCAATAGCAAGCTTTCTCTCAACAGCTCCCAATCCAACAAAATTTATCTTATCCACAATTTGGACCTCTCTATTATCC[A/G]CGTCCGTATCATCCGTCGTTATACCCACAAGTGCCTCATCCTACAAGGGACTTTACCTCAACCCTTAATGATATGGATTTTTTACAGTTCAT
101136 G A CCTCTCAATAGCAAGCTTTCTCTCAACAGCTCCCAATCCAACAAAATTTATCTTATCCACAATTTGGACCTCTCTATTATCCACGTCCGTATCATCCGTC[G/A]TTATACCCACAAGTGCCTCATCCTACAAGGGACTTTACCTCAACCCTTAATGATATGGATTTTTTACAGTTCATGGTTCGAGGTTCCACTCC
101136 G A ATTATCCACGTCCGTATCATCCGTCGTTATACCCACAAGTGCCTCATCCTACAAGGGACTTTACCTCAACCCTTAATGATATGGATTTTTTACAGTTCAT[G/A]GTTCGAGGTTCCACTCCAGATAAGTAATTGGTCTTCAAAGTTCACTATATGTAGCATGTTTTCTTTTCAAGTTTGGTTCCATGTATCAATA
101136 T C GTCCGTATCATCCGTCGTTATACCCACAAGTGCCTCATCCTACAAGGGACTTTACCTCAACCCTTAATGATATGGATTTTTTACAGTTCATGGTTCGAGG[T/C]TCCACTCCAGATAAGTAATTGGTCTTCAAAGTTCACTATATGTAGCATGTTTTCTTTTCAAGTTTGGTTCCATGTATCAATAAGAACTCTC
101136 G A TGATATGGATTTTTTACAGTTCATGGTTCGAGGTTCCACTCCAGATAAGTAATTGGTCTTCAAAGTTCACTATATGTAGCATGTTTTCTTTTCAAGTTTG[G/A]TTCCATGTATCAATAAGAACTCTCTGTTCTAGTCCATGTATGATGTTGCTGTATCTAGTTTAGATGGTACAGTCTTTTGTTACTCTTTTGCA
101138 G A AAACCATTCTTGGTCTCTTCCCATACAGTTTTGAGTATCCAAATATGCAAAAGAGAATACATTCTCAATCAACATTTCTATAGCACAATCA[G/A]GACGAATAATATTTCACGGCATAGTAACATCCAATATACTCTTCTTAGAGTTAAAACTGAAGCCCTACATAAACTTGGGGATGTATTCACATCCAAAAT
101138 C T AAACCATTCTTGGTCTCTTCCCATACAGTTTTGAGTATCCAAATATGCAAAAGAGAATACATTCTCAATCAACATTTCTATAGCACAATCAGGA[C/T]GAATAATATTTCACGGCATAGTAACATCCAATATACTCTTCTTAGAGTTAAAACTGAAGCCCTACATAAACTTGGGGATGTATTCACATCCAAAAT
101138 G A TTGGTCTCTTCCCATACAGTTTTGAGTATCCAAATATGCAAAAGAGAATACATTCTCAATCAACATTTCTATAGCACAATCAGGACGAATAATATTTCAC[G/A]GCATAGTAACATCCAATATACTCTTCTTAGAGTTAAAACTGAAGCCCTACATAAACTTGGGGATGTATTCACATCCAAAATGGAGCAAG
101138 T G TCTTCTTAGAGTTAAAACTGAAGCCCTACATAAACTTGGGGATGTATTCACATCCAAAATGGAGCAAGGCGAGGATCTGTTCGCCATGGCAAGCCACTTC[T/G]AGCGCCAAGAGCCTGGCAGTTTGCAGCAGCCACTTTTGACGCAAAAGGCAACATCTTTTCTGGTGCCATCCCTGCACATAAAGCATA
101138 C A CTTTTATGCTTCTCTCAAGCATTACACAACCTTTATCGCCTTGTGTCACAATGATGAACTTAAGATTGGGCAATCTAAGAAACATAGATACTAATGCAAT[C/A]GGGGTGGATGAAGCTTCTGCCCATTGCTGTGGAAAATTTTCAGAGCATACGACGTAGCTTGCTACGTTAAGAAGTTCGTCCAAGCCCT
101176 G C TGTTGGCCTACTGGATATCATTTCTATATACACTCTCTTATCAAAATTTGAAAATAAGCAGAACAATAAATGGCCGAAGTAGAAGCAAAACAGGTGGAGG[G/C]AACTGAAGTTTCTAAAGAGCAGCCGCTACCGACGGCACCACCACTGCCACCAGCTCCTCCTGCAACACCAGTTGTAGCAGATGAAA
101176 A G TTGGCCTACTGGATATCATTTCTATATACACTCTCTTATCAAAATTTGAAAATAAGCAGAACAATAAATGGCCGAAGTAGAAGCAAAACAGGTGGAGGGA[A/G]CTGAAGTTTCTAAAGAGCAGCCGCTACCGACGGCACCACCACTGCCACCAGCTCCTCCTGCAACACCAGTTGTAGCAGATGAAAAG
101176 A G TGCAGAAATATGTGGAAAGACTAGAAAAGAAGAAGGCTGCATATGCTGAGAAATTACAAAACAAGATTGCAATTCTTCACAAAGAAGCGGAAGAAAAGCG[A/G]GCAATGGTAGAAGCGAAGAAGAGCGAAGATTTGCTAAAAGCCGAGGAACTGGCTGCAAAATACAGGGCAACTGGTTCTGTGCC
101188 C T TTGATCTCTTAACTGAAGCAAAATCAATAGAATTGGTGTGACCACTAGATCCAACTGTGTAATTGCCAGAAATGAAAGACTGCTCAAAATAACCTGTAGT[C/T]TCCTCACTGCTATCTCTCATATTGGAGTATTGAGGCAGTGCATTCTGTTTTGAGAAGATCGGTTGGGAATTAAATTGTTTGTTAGGCA
101188 C T GTCTCCTCACTGCTATCTCTCATATTGGAGTATTGAGGCAGTGCATTCTGTTTTGAGAAGATCGGTTGGGAATTAAATTGTTTGTTAGGCAGTCTTTGGA[C/T]GTCAGCTTCGTCCCATGTGGCATGAGATAAAAATCCTGCCGGCATGCTACTATGTCTCAGTAAACCACCGCCGCCAGCGCCGTCAAGA
101188 A G CAGCTTCGTCCCATGTGGCATGAGATAAAAATCCTGCCGGCATGCTACTATGTCTCAGTAAACCACCGCCGCCAGCGCCGTCAAGATTGGACCTCCGATG[A/G]CATGTGGACTCTGAAGCGGTTTGCGATCCCCAAGAGGAGTTGTCCCCGCCGCCAAAAAACCGATTTTTATGCATGTCATTGTTAGCG
101198 C T ACAGGCACCTTTCGCAATGACCACAGCAATCTTGTGGGAACGTTAAGAGGATGATGACTCGTATAATGATCAGCAAAAACCTCGTTAACTTGAAAATAAG[C/T]GCCATTAAGTGGAAAGCTTCCTCTGTTTGCTGTCCGGCATGGGATCAAAATTGTGCCACGGACAGTTCCTGCTTGTGCTTCTCGTTTG
101202 C T CGTCCCCCACTCGGCCAAATTGCTTGCAGAATTTGGGAGTCACCTTGGCATGATGAGGGTGTTGAAGCATTCCCAGCAAGTCATGGTAAACCAGAACCTG[C/T]CCGCTACAAAATGGCCCAGCACCAATGCCAATGGTTGGAACTTGAAGAGCCCGAGTTACTGCAGCAGCTACAGGTGCAGGAACAC
101202 C T GTGCAGGAACACATTCCAAGACAACCGAAAAAGATCCTGCTTCTTGCAATGCCATTGCTGTTTCTACAACCTTCACAGCACTAGAGACAGTTCTACCCTG[C/T]GGTCTAAATCCACCAAGTACACTAATAGCTTGCGGGGTTAGCCCAACATGACCCATTACTGCAATACCGGCTTCCACAATTGCTTTGG
101226 AG A ACTGGAGCATGCATTGGAAATTAGCGAAGTGCATGTGTGAGTGGGAGTGGCTACAGGAGTGAAGTACTCACAGTGTGTAATATGTAAACAAAACGCATGG[AG/A]GGGGGTGCGAAGGCGTGAAGTACCTTGTGGTGTAGCATGCATACACTGTGGAGCGAACATGTGTCTGTAGTAAAAAGAAATC
101236 A G ATAATACAATCATTTATTTATTTTGAAGTCTATAGGTAAAAGCCTGGAGCGAAAACAAAAGCTGCTTCAACTTCTCTTTGGTATCAGCATCAATTAAGTT[A/G]CCATCAGCGTCAAATTTCTGAGGAGGCTCGAATGCTTTCACAAAGAGTTCAGGTTTATTGATGAAGTGAAGGTCTAGAAAAACTCCAA
101236 A G TCACAAAGAGTTCAGGTTTATTGATGAAGTGAAGGTCTAGAAAAACTCCAACTTGGCGGAGATGGTACTGAGATCTTCCTCCTCCAAAGCCGCCTCCTGC[A/G]CTCACAATGGCGGCTGCCTTGTCTGCCCATACATTTGGTGCACGAGATGCCCAATCCATTGCATTTTTTAGCGGACCAGTCAAAGAG
101236 C T CTCCAAAGCCGCCTCCTGCACTCACAATGGCGGCTGCCTTGTCTGCCCATACATTTGGTGCACGAGATGCCCAATCCATTGCATTTTTTAGCGGACCAGT[C/T]AAAGAGTAATTATACTCGGGCGAAGCAAACAAAATACTATCAGCTTCCAGAATCTTCTTCCTGAATACTTCAACTGCCTCCGGAAATGT
101236 C A TCACAATGGCGGCTGCCTTGTCTGCCCATACATTTGGTGCACGAGATGCCCAATCCATTGCATTTTTTAGCGGACCAGTCAAAGAGTAATTATACTCGGG[C/A]GAAGCAAACAAAATACTATCAGCTTCCAGAATCTTCTTCCTGAATACTTCAACTGCCTCCGGAAATGTCCCATTAACTTCAAGATCGGT
101238 A G AAGAAAGCCTTCTGGGAAAGCTAAGGGCACCCTCAACCTGTCTTACAAATTCGGAGATCTAGTCACAGTGCCTACTGCCAGTCCCCCACCAGCTCCAATG[A/G]CAGATCCGTACCCGATCCAGGACACCAAATCTTCCGGGAAACCCGAACCCGTTACCGCATACCCAGCCACAGGTCCATCAGGGTCC
101238 T A GAGATCTAGTCACAGTGCCTACTGCCAGTCCCCCACCAGCTCCAATGACAGATCCGTACCCGATCCAGGACACCAAATCTTCCGGGAAACCCGAACCCGT[T/A]ACCGCATACCCAGCCACAGGTCCATCAGGGTCCTACCCACCTGCAGGATACCCACCTCAACCTGGATATGGGTATACCCCATCCGCT
101238 T A ACCCGATCCAGGACACCAAATCTTCCGGGAAACCCGAACCCGTTACCGCATACCCAGCCACAGGTCCATCAGGGTCCTACCCACCTGCAGGATACCCACC[T/A]CAACCTGGATATGGGTATACCCCATCCGCTCAAGCCGGGTATGGGTACCCTGCACCGGCCGGATACCCCACTTCGCAACCTGGTTAT
101238 C T GGAAACCCGAACCCGTTACCGCATACCCAGCCACAGGTCCATCAGGGTCCTACCCACCTGCAGGATACCCACCTCAACCTGGATATGGGTATACCCCATC[C/T]GCTCAAGCCGGGTATGGGTACCCTGCACCGGCCGGATACCCCACTTCGCAACCTGGTTATGGGTACCAACCCCAGCAACCTGGGTA
101240 C A GCGACCTTTGGCTTCAAAACTGAGTTCAGAAGCTTTTGATCTGTGAATTTTGGTGTGAAAGATAGAACCCATGAAGGAGTTTTTCGACTTTTCAAACCGT[C/A]TTTCTCTTGCTTGACACAAGAGGCTAATCTTTGAAATCCCTCAAGTTGAAAACTAGTGTCTTCCCACATATCTCTAAGGTAACTTGTTTC
101254 T C TTAAACATCTAAAGATGTAAAAGATGTTTCATATGAACATTGTTACTGTAGAGCGTCTCGATCTATAAATTAAACTATTCTAAATATTTGTTCAAACTTG[T/C]TCTTTTGTTAATTTAAATCTGACAGTAAGAACGAAGTAAGCAATATGGAAAAAGTAAGGATTTT
101256 T A AGTCTTTGTGTAATGCGTGCGGGATCAGACATAGGAAGAAGAGGAGAGAAGTGAAAGGAATGTCAGGGATGAAGAAGAAATGGAAGCAGAGGTTTCTGGG[T/A]GAGGAAGAGCAAGCCGCCTTCCTTCTAATGGCCCTATCATCTGGACTGCTGTACGATTGATCTCAGCGTTAGGTCAAAATGGG
101260 C T AGCATTACACGGATTCTTCACTACCTGATTCAAAATCATCTAATGACTTGACTGGTCTTTCACGTGGTGGGCAGCAGATACAGGCATGTCGTGCAGCACA[C/T]ATCAAAGCAATTGAAGTGTTGGTACAGCTGGCTTCACTTCAGACGTCTTTCTTGACACTGGATGAAGCAATTAAGACCACAAATAGG
101262 A T TCGAGTCTTCAGATGCGACGGCTAGGACCCTCTTGCTTGCTATTAATTCTAGGAAGGAGCAAATGAAGAAACCGACAAAGTTGACAATATGCAATGAAGA[A/T]ACCGATTCAAGCACAAGCGGAGATATAATGATTTTCCCAGATATGAAAAGATACAGGCAGATAAGGGCCTGTGATTACAATGCGTT
101262 G A AAATGAAGAAACCGACAAAGTTGACAATATGCAATGAAGAAACCGATTCAAGCACAAGCGGAGATATAATGATTTTCCCAGATATGAAAAGATACAGGCA[G/A]ATAAGGGCCTGTGATTACAATGCGTTTGTTGAACAAGTGCTTGTAAAAGAGTTGGAATGGGAACACCAATCATTTGACAAAATGA
101262 C T AACCGACAAAGTTGACAATATGCAATGAAGAAACCGATTCAAGCACAAGCGGAGATATAATGATTTTCCCAGATATGAAAAGATACAGGCAGATAAGGGC[C/T]TGTGATTACAATGCGTTTGTTGAACAAGTGCTTGTAAAAGAGTTGGAATGGGAACACCAATCATTTGACAAAATGACAGGGTCAT
101262 A G TTGAACAAGTGCTTGTAAAAGAGTTGGAATGGGAACACCAATCATTTGACAAAATGACAGGGTCATTTGTTTTTGTGTGTTCTCACGGAAGTAGAGATAG[A/G]AGATGCGGTGTTTGTGGACCTGACATTCTTAATAAATTTAAGGAAGGGATTAAATCATATAAACTTGAGAGTAGAGTGCATGTTAA
101262 C G TAAATCATATAAACTTGAGAGTAGAGTGCATGTTAAATCATGTTCTCATATCGGTGGCCACAAATACGCTGGAAATGTGATTATTTTTAGTAGGGATACA[C/G]ATGGAGAGATGCATGGACATTGGTATGGATACGTTACTCCAGATGATGTGCCTTCACTGCTTGATGACCATATCAGTAATGGAAATA
101274 CA C GAGGTCACACATCGGTCCCTCATGCGGCACTTCTTGAACACGGTCAAAATTTCGTATGTTGTCAAGCGTATCAATTGACGGAGACAAGCCACCATGTAGA[CA/C]AAAATATTTCAGATTCCACCAGTGCAGTCAAAGGGAAATAATCAAATAGATCCGTGAAGATTTTCCACACGTTTGCATTACCATATT
101274 T C AAAGAGGCTTGCACTGCATAAGTTGAGCAATCTCCTCGTCGAGATTGCCATGGGAGTTCGAATTGATCACACCTGCACTCATCTTTGTCTATACCCCAAA[T/C]TTTCAACAGCAGAACCGGCACTTCGCTCTACAGAAGATTTTGACCGGTGAAATAACCGAGACTGCTGAGAAGGGAAATGGAAGGTTG
101276 A G TTGGGACTGGTTGAAGAGTATGGGAAGTAAGGATCTGGATGTTCCCTGCTTTGTCGAGTAGTGGTTGCCCTGCTTTGGTTCTCTTTACCATGTCTTCAGC[A/G]TTTCCATGATCTGCAGTTACAACATAGATCCCACCAACTTGCTCTATAGCATCAATAATCATCTTAACTGCTTCATCAGCAGCCTTACA
101276 A G TGACACGAACCTGGTCAAATTTCCTGCTGAGAATAGCATCTCTAGCCCTCTCGGCGATTTCTAAAGCCTTCATCTTGGGTTTTACATTAAATGTGATCCC[A/G]CTGTCACTTGGAATTTCAACATACTCCTCCTTGCTTTCATCAAAATATCCAGAACGGTTTCCATTCCAGAAAAATGTAACATGACCAAAT
101276 C T TGAGAATAGCATCTCTAGCCCTCTCGGCGATTTCTAAAGCCTTCATCTTGGGTTTTACATTAAATGTGATCCCACTGTCACTTGGAATTTCAACATACTC[C/T]TCCTTGCTTTCATCAAAATATCCAGAACGGTTTCCATTCCAGAAAAATGTAACATGACCAAATTTGACGGTCTCACTGCAAGCAAAAGTT
101276 G A TAACATGACCAAATTTGACGGTCTCACTGCAAGCAAAAGTTCGCACACCATTTTTGACCAAGTATTCACCGGATGTCCTATCAATCTCAGGAGGAGTAAC[G/A]AGATACTTAGATGGAAGCTTCAATTCACCATCATATTGAAGCATACCAGCATATCGGATCTTTGGTACTCTGACCCGGTCAAACATGT
101276 T C AAGTTCGCACACCATTTTTGACCAAGTATTCACCGGATGTCCTATCAATCTCAGGAGGAGTAACGAGATACTTAGATGGAAGCTTCAATTCACCATCATA[T/C]TGAAGCATACCAGCATATCGGATCTTTGGTACTCTGACCCGGTCAAACATGTTAAAATCTTCATATTCAAGTGCTTTGGCAAGCATAAC
101276 G A CCAAGTATTCACCGGATGTCCTATCAATCTCAGGAGGAGTAACGAGATACTTAGATGGAAGCTTCAATTCACCATCATATTGAAGCATACCAGCATATCG[G/A]ATCTTTGGTACTCTGACCCGGTCAAACATGTTAAAATCTTCATATTCAAGTGCTTTGGCAAGCATAACCATTCGATCTGCACGGAAAT
101276 A G CTCTGACCCGGTCAAACATGTTAAAATCTTCATATTCAAGTGCTTTGGCAAGCATAACCATTCGATCTGCACGGAAATTGATAGTTACAACGGCATCACC[A/G]TCAACAATAGGTCCCACAGCTTTCCCATTCTCATCAACGATGACAAAAGGCGGCAAATATTGATCGCTATTTTTTGGATCTTTCCTTAG
101286 GT G TGCTCTCATATTTCGAGTTGTTTCTTTTCTTTAACGGAACAGGTAGAGGTTTTCCAGGAATTATTTCACCATTTATATATTTATCACCTCCATAGTCTTT[GT/G]TTTTTTACGTCAATATAGGAATCAGGAAGCACCCACAAAACACCTGGTAGCCCTTTGAACTTTTCTGATGTTTCTTCAGAAACTGTGCATT
101302 T G GTGACCGTTGTTGATCTGAGCGGAGGACCAGCGACCAGCACAAGCTGAGTTAGTGATCACCTGCATAGTGCCCTGCTGGAGAGTGGTGGGGAGGGCGCTG[T/G]TAGCGGAGGTACGACCCCAGCCGGTGATGACGCAGTTCTGACCGGAATAATCTCCAGCGTTAGAGGCAGCCATGGTGACGGCT
101302 A G AGTTAGTGATCACCTGCATAGTGCCCTGCTGGAGAGTGGTGGGGAGGGCGCTGTTAGCGGAGGTACGACCCCAGCCGGTGATGACGCAGTTCTGACCGGA[A/G]TAATCTCCAGCGTTAGAGGCAGCCATGGTGACGGCTCTGAGGTTGTTGTTGGTTGTGACTGCGCTGAAGTGAAGAGCGGCCAC
101302 G T TAGTGCCCTGCTGGAGAGTGGTGGGGAGGGCGCTGTTAGCGGAGGTACGACCCCAGCCGGTGATGACGCAGTTCTGACCGGAATAATCTCCAGCGTTAGA[G/T]GCAGCCATGGTGACGGCTCTGAGGTTGTTGTTGGTTGTGACTGCGCTGAAGTGAAGAGCGGCCACATCATTGGGGTATCCCTG
101302 G A TGATGACGCAGTTCTGACCGGAATAATCTCCAGCGTTAGAGGCAGCCATGGTGACGGCTCTGAGGTTGTTGTTGGTTGTGACTGCGCTGAAGTGAAGAGC[G/A]GCCACATCATTGGGGTATCCCTGGTTACCGTTGTTCACGAATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGG
101302 C T TGACGCAGTTCTGACCGGAATAATCTCCAGCGTTAGAGGCAGCCATGGTGACGGCTCTGAGGTTGTTGTTGGTTGTGACTGCGCTGAAGTGAAGAGCGGC[C/T]ACATCATTGGGGTATCCCTGGTTACCGTTGTTCACGAATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGC
101302 T C TCACGAATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTA[T/C]GAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCC
101302 G A CACGAATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTAT[G/A]AGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCG
101302 A C ACGAATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATG[A/C]GGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGC
101302 G T ATCCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGA[G/T]AGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAAC
101302 G T CCGCTGTGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGA[G/T]AGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACAC
101302 C T TGCCTGACGAATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGC[C/T]ACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTG
101302 A G ATGAGCTGAGACTCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCA[A/G]TGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATG
101302 A G TCCTGGTGACACAGGTGCTGCAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGT[A/G]ACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAG
101302 T C CAGGTCGTGTCGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGA[T/C]GAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCC
101302 G T CGGTTCTAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGC[G/T]CCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101302 A C TAACGGTCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACA[A/C]GAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCA
101302 A T TCGTTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTG[A/T]GAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTC
101302 G T TTCCACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGA[G/T]CCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCG
101302 G A CACCAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCC[G/A]CTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTG
101302 A T CAAGGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCT[A/T]ACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAAC
101302 A C GGATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAAC[A/C]CGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACC
101302 G T ATTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACAC[G/T]TAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGG
101302 T C TTGAGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACG[T/C]AGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGC
101302 T C AGTATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAG[T/C]GAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGA
101302 G C ATGAGGAGAGAGCGCCACCACCGCAATGAGCAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGA[G/C]AGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGAGCC
101302 G T CAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGC[G/T]TGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGAGCCAGACAAAGAAGAAGTAGAACTCTCATGATG
101302 G GT CAGCAGTAACGGCCTTGGTGGTTGAGATGAGAGAAGCGCCACAAGAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGC[G/GT]TGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGAGCCAGACAAAGAAGAAGTAGAACTCTCATGAT
101302 C A GAGTGAGAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACAC[C/A]GGCAGAGCCAGACAAAGAAGAAGTAGAACTCTCATGATGAAGCGTTGAACACAAGACCTTTGAGCTGATCAGATGATCTGTAGA
101302 A T GAGCCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAG[A/T]GCCAGACAAAGAAGAAGTAGAACTCTCATGATGAAGCGTTGAACACAAGACCTTTGAGCTGATCAGATGATCTGTAGAAGGTTCT
101302 C G CCGCTAACACGTAGTGAGAGCTGATGGGGGTAGTTAGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGAGC[C/G]AGACAAAGAAGAAGTAGAACTCTCATGATGAAGCGTTGAACACAAGACCTTTGAGCTGATCAGATGATCTGTAGAAGGTTCTTTG
101302 G T AGCGATGTTAGCGTGCTACCTCCAACAACGCGACTGTCAGCTCTCTCGCTGAACACCGGCAGAGCCAGACAAAGAAGAAGTAGAACTCTCATGATGAAGC[G/T]TTGAACACAAGACCTTTGAGCTGATCAGATGATCTGTAGAAGGTTCTTTGGATAATCCAGTAGGCCAACAG
101304 CCTG C CGATTCACAGCCTAAGTTTCTATCGTCCGCAGCGTCCTTGCCTTCCACTTTCTCCCTTTTTGCCATACGGATATCCTTGCCATCGTTGATTCTTTTCTTC[CCTG/C]CTGCTGCTATTTCTTCAACAAGTCGAACCTTCCGCCAGAAAAACCTCAACCTTGGCATGTCTTGAAATCTAGTGGCGGTTGGAGAAGA
101314 C T GTTGGGCTTGATGTTTGTGATCCTTTCTTATCGTTTGAAGGAGTAGTAGAAGCTAAACAAGGCAGACAATTATTTGTCAGAATGCCACAGTTATTCAGCA[C/T]GCCTCCTTCTTCCATTTCAGTTACACCATCCACGGAAGTCCTAGATGTATTATCTACATGTTTTATGCCTTTTTGCTTCAGGTCGACGGA
101314 C T CAGTTATTCAGCACGCCTCCTTCTTCCATTTCAGTTACACCATCCACGGAAGTCCTAGATGTATTATCTACATGTTTTATGCCTTTTTGCTTCAGGTCGA[C/T]GGAATTACCATCTTCATACCGGGCATCTTTCATAGATGATCTAGTAGATATAGATGCAGCTTCATGTCCATGTAAAGAAAATGCATCTTCT
101314 C T TGTCCATGTAAAGAAAATGCATCTTCTAGAACGCTATGATAATCATCCTCACAATCTGATTCCATTGCTCCATTTGAGTCAAACCAAGCCTCGTCAATGC[C/T]GCCTTGAATGTGGAAAGCAGGATTACTGTAGCAAGACCGAAGATCATCCCCATCCTGGTCGGATCTGTTGGCCTCATCAATAGATTTAA
101314 G C GGATCTGTTGGCCTCATCAATAGATTTAAGAGACGAAATCCTATTCTTGACCCTGCGCTTCCTCCTCCATCGCTTTCCTCCCGCCTCCGTCGGGTTCCGA[G/C]ACCTCACTCTAACGCACCCCTGCGGTCGAGACACGCACGTTCCCATCGATCTCCGGAGTGCCAAGTGAGAACGGCAGATTCGTCGTCG
101318 T A TTGCCCATGCAGGGAGAACACCAAATCTCATAGCCTGATTGTGAAACCTTTCGGTGAACCATCCCTCTTGTTCAATAGCAAAAAGAAGCTTGGATTGTTC[T/A]TTTTCCGAAAGAAATTCCTGACACAACCAAAGACCCTTGACTTTCTCAACTGATTCCCAAATGGGGATTTTATCATCTCGCTCAGGAGA
101318 C G AAAAAGAAGCTTGGATTGTTCTTTTTCCGAAAGAAATTCCTGACACAACCAAAGACCCTTGACTTTCTCAACTGATTCCCAAATGGGGATTTTATCATCT[C/G]GCTCAGGAGAGCTGGTATTGAACACTAAATGTTCATCTTCGTTATCATCGCTTTCGGAAGAGTCGCCAAAGGCTATCTGCAGTACATGT
101318 A T GTCGCCAAAGGCTATCTGCAGTACATGTCTTCTCACATCAACGGCGGTGGCAGCTGTGATGGGGGGTGAATGCATCCGTACTTCGTACAGTTGGCTTAAA[A/T]CGACAGTGCTGTGCACCAATGCTCGATTTGCAAGTCTTCCGATATGTAGCGCCGATCACGATAGACGTGAAATTCCCTTTTTGACGC
101322 T C GACATTAAATTTCCAGTTGCTTTGAGCCGTAGTCCCCATAGTTCCAGCAGCATTCCCGTGATAAGAATTTCTTACTGAAATAATATCATGGCAACCAGTA[T/C]AGAGCCTGGCTATCATAAGTGCCAACTCATTTGCTTCTGTTCCAGAATTAGTGAAGAAAACCGTCTTGAGATTCCCAGGCATCTTTGCA
101322 T C ACTGAAATAATATCATGGCAACCAGTATAGAGCCTGGCTATCATAAGTGCCAACTCATTTGCTTCTGTTCCAGAATTAGTGAAGAAAACCGTCTTGAGAT[T/C]CCCAGGCATCTTTGCAGCTAATGCCTCAGCAAAATCTGCAATTGCATGATTTAAATACAAAACAGTAGAATGTTGCAATCGTTCAAGT
101336 C T TTCATGTTTCTGCGGCAGCACTGAAGTGCTCCCACTGTACAGAAACTGCAGCATAAGCATGAACACTTCGTAGCCGACCGAGTTCACCGGAATCACAACT[C/T]CGCCGCCGGCTCCTCTAGGAGACCCCAACGACGAGGTGGCGGACTGCGATTCCACGGGACCGCAGAAGAACTTCCGAAAGAAGAG
101342 CA C CTTAGAACCCGAACTATGTTCAATTATTTCACTTCCAATCAAAACCAATTGTATCAAACCTTGATCCTCCTCAAAGCGACGTACGCCAATATCCTGTACC[CA/C]AAAAAACATCAAAATCAAAGCTCCAACGCTCTCGTAAATACCGACGTGCTTCACAATCTCCTGTTCGTGGATTTGATAATCGCTGTACT
101342 T C TCCTCCTCAAAGCGACGTACGCCAATATCCTGTACCCAAAAAACATCAAAATCAAAGCTCCAACGCTCTCGTAAATACCGACGTGCTTCACAATCTCCTG[T/C]TCGTGGATTTGATAATCGCTGTACTGAACCCCAATAAGAAGTCTATAACAGTAAAATGTGAAGGACGCATACTTCATCCACGTCAGGC
101344 C A GCTTCTCCAGCCAAGTCGTCTCCGGACTCGCGCAAGGCAGTGGCGAGTACTTCACACGTATCGGAGTCGGAACTCCGGCCACCAACGCCTACATGGTTCT[C/A]GACACCGGATCCGACATCGTTTGGATCCAATGCTACCCATGCCGCCGTTGCTACACCCAATCCGATCCCATTTTCAACCCTGCGAAA
101344 T C CCGGCGATTTTTCAGTGGAAACCCTAACGTTCCGCAACGGCCAGCGAATCAGCAAAATCGCCCTCGGCTGTGGTCACGACAACGAGGGCCTCTTCGTCGC[T/C]GCTGCCGGTTTGCTAGGGCTAGGAAGGGGCGGATTGTCTTTTCCCTCTCAAGCGGGAACAAGATTCGGTCAAAAATTCTCCTACTG
101352 C G TTTTGCTGCTTGGTATGGAGCCAAGCTTTTGCAGAGCTTCCTTCAAGTCGTTACTGCTGTTTATTACTGGTATCTTGTGCACTCCTTC[C/G]GCAGCAACAAGAACAGTGATCACAATGTACTCATTGTTGAAACTTCTGGATCTGCCGCTTGATGTTCTCTGCCGCTTGATACTGTTCACATTAACAAGTG
101352 A G CCCATCACCAGCAAGAAGAAACCAGACCCAGCCCCAAACCCAACTCCAACAGCAGGTCCAACATAAAACCCACCTCCACCAAATGGGGTAGGCGCATAAT[A/G]AGGCACCGAGTACGAAAATGCACTTGAAGGTGCAGAATATGAATAAGAGCTTCCTGAATTAGAACGGGACGAAGAAGACGAAAA
101354 T C GCTAAGCTCTTTAATAGGGCCACAACAAGCTCAGAAAATAGTGAACAATGCACTTGTGTTGTTTACTCTAGGAGGAAACGATTTTGTGAATAATTACTAT[T/C]TGCTGCCAAACTCCGCTCGGTCGCAGCAGTATGAACTTCCAGACTACGTTAGATTCGTTATCTCCGAGTACAAGAAAATCCTTCGGAG
101358 G A TAAGCGCCATTGTATGTCTCCAGCCACCGGAAATCTGAGATATGGATCTATCTTTTAAGGCTTCCACCTGATACGGAATCAGATAATCATTGAAATCTCC[G/A]TGCCCTAGCTGGCCATATTTGCTCCATCCATAAGTGTATAAGCTTCCAGTTGAAGATACCGTAATCGTATGCCGCCACCCACATGCAAT
101382 CT C GTAGTGAATTATCTGGGTTGTTTTGGTGCGAAGCAGGAGAAAGAAAATCACGAGAAGGGGAGCCCGGAACAGAGGAGCACCGAAAGGATTAGGCCAGTTC[CT/C]TTTTAAGGCAAAAAAGCTTTGGTCAAACCGATTTTGAAAAGGAGGAGGATACGGGAAGAACGAAGGCCTAGGAATAAATAAA
101392 A C CCGCCTCCCCGTCCAGCGCCATGCACGACACCGCGTCGAAATGCCTCAGCCACACCTTGTTCCGATGCCTCCGCACTTGCACGTAGGCGGACGGGTTCAT[A/C]GAGCTTTTGATGACGTCCTTCAACCGCGGTAAAGTGCCGATTCTTTTGTAGTTCACGGAGTCGTTTTTGTGGGAGAGCTTCCAGATC
101392 T C CCAGATCCGGATTTTGCCGTCTTGGTGGCCGGTGAAGACCCGGTCGCCGGAGACGATTATGGCTTTGACTAGTCCGCTGCCGGATTTGAAGCCGGAGTGT[T/C]CCTGTAGGTTTTTCCATACGCGGATGTTTTTGCTGTCGGATCCGGTGTAGAGCAGCCCGTTAGCCGCTGCGATGGAGTAAAGGTG
101392 G A GTCCGCTGCCGGATTTGAAGCCGGAGTGTTCCTGTAGGTTTTTCCATACGCGGATGTTTTTGCTGTCGGATCCGGTGTAGAGCAGCCCGTTAGCCGCTGC[G/A]ATGGAGTAAAGGTGGCCCTGTTCTCGGATCATGGATCCAATTAGCCCGGTGGAGGGCTCCTTGGAAAGAGGAGCAGTGGTGGAG
101392 G T GCCCGTTAGCCGCTGCGATGGAGTAAAGGTGGCCCTGTTCTCGGATCATGGATCCAATTAGCCCGGTGGAGGGCTCCTTGGAAAGAGGAGCAGTGGTGGA[G/T]TGAGTCCATGGCGATTTTATGTATGGCGATTGGGTGGCGTAGTTAGGAGAGTTTTCCAGGGCAATTTCGTAATTTGAGCGGTCG
101392 A C CGTTAGCCGCTGCGATGGAGTAAAGGTGGCCCTGTTCTCGGATCATGGATCCAATTAGCCCGGTGGAGGGCTCCTTGGAAAGAGGAGCAGTGGTGGAGTG[A/C]GTCCATGGCGATTTTATGTATGGCGATTGGGTGGCGTAGTTAGGAGAGTTTTCCAGGGCAATTTCGTAATTTGAGCGGTCGGAG
101392 T C GAGTAAAGGTGGCCCTGTTCTCGGATCATGGATCCAATTAGCCCGGTGGAGGGCTCCTTGGAAAGAGGAGCAGTGGTGGAGTGAGTCCATGGCGATTTTA[T/C]GTATGGCGATTGGGTGGCGTAGTTAGGAGAGTTTTCCAGGGCAATTTCGTAATTTGAGCGGTCGGAGGAGTAGCCGGGGCTGG
101392 C A GGTGGCCCTGTTCTCGGATCATGGATCCAATTAGCCCGGTGGAGGGCTCCTTGGAAAGAGGAGCAGTGGTGGAGTGAGTCCATGGCGATTTTATGTATGG[C/A]GATTGGGTGGCGTAGTTAGGAGAGTTTTCCAGGGCAATTTCGTAATTTGAGCGGTCGGAGGAGTAGCCGGGGCTGGAGTAGCC
101392 A G AGTTAGGAGAGTTTTCCAGGGCAATTTCGTAATTTGAGCGGTCGGAGGAGTAGCCGGGGCTGGAGTAGCCGGACAGTCGCGGGGAGCTGTCTTCGCTTTT[A/G]GGGTCGGAGGTGGTGAAGAGATTGAGTAATTTGGCCGAAGTTTGTGTTTCTCTCATGGTGTTAACTGAGGAAATAATGAATTGA
101392 A G CAGTCGCGGGGAGCTGTCTTCGCTTTTAGGGTCGGAGGTGGTGAAGAGATTGAGTAATTTGGCCGAAGTTTGTGTTTCTCTCATGGTGTTAACTGAGGAA[A/G]TAATGAATTGAAAAGAACTGAAAAAATATGAGTAATAATGGTATTAGCCAGTAGGCCAACA
101394 T C ACTAATTCTTGTCTGGTATATCACATCGCATTTCGAAGCGACTTCGTATAGATTAGTGCTTTCTTCCCATT[T/C]CACGCCTTTTGATGTCAAGTAGTCCTTGATATCATCCTTCATCTTTACAACATCTGGAGAGACGAAATAAACTTTTACATCGTGGTATAATGCAATGAGA
101394 G A TTACAACATCTGGAGAGACGAAATAAACTTTTACATCGTGGTATAATGCAATGAGATGAGCTAACGATCTAACGGTCCTCCCATTAGCCAGGTCTCCAAC[G/A]AGTGCAAGTTTGATTCCATCCAATCTTCCAATTTCCTTTTGAATTGTGTACACATCCAAAAGAGCCTGAGTGGGATGTTGCCCTGGGC
101394 G A CCAATCTTTTCATTGCAGACTCAAAAGAGAGTCTGGTTCGGGTTGAGGGTTCATAAAATAAGGTAGCCATCAAAAAACCCTTCAGAATTTGACTTCCTGC[G/A]GAATTCTTTTCAATGGATTCCATTTCATGAGCAACTTGGAATATATTATCTAATATATCCCTATCGAATTGTTGAGCTTCAATAACATCA
101394 C T GCCATCAAAAAACCCTTCAGAATTTGACTTCCTGCGGAATTCTTTTCAATGGATTCCATTTCATGAGCAACTTGGAATATATTATCTAATATATCCCTAT[C/T]GAATTGTTGAGCTTCAATAACATCATCAAGTTCAAACTTCTTCCTTGTTGAAAAGGATGGCCTATTTTCAACTAGGGAATAACATTTGCTT
101398 T C TGCCAACTCCACAATTCCTAAACACTGAACAGAAACATATGAATAAACAACTTCCAGTACTTTATACAGGTTGTGAAGTGTGTTGTACTGCTTCAGTTGA[T/C]GGTGCCACTAAAGGCTGTTGTTGTGATTGCTCCATACTCGTGTTCCATGAATGATTGCTTCCATTGAACGACGATGATCTTTTGTCTATG
101398 G A ATGAATGATTGCTTCCATTGAACGACGATGATCTTTTGTCTATGTCGCCATAATCTGGAGATTCGGTGAGTGGCTTTAGAACAGAGGCTTTTTGAAGATC[G/A]GAAAACTGTTTGCTTCCTTCTCCTCCGTAGCTTCCAACACATATTGTATCACCTCGTCCATGCCATACCCCTTCTTGCACGTTGTTCATC
101398 A T TCGTCCATGCCATACCCCTTCTTGCACGTTGTTCATCTCTAGCGTCCTCGATTCCTGGCATAATGCACAGCAAGAACAAATTAGATGATGGATGAAATCA[A/T]CTAGCAGACTGTCCCTTCCCCCAATATTAAACTGCTTCCTGATCCTGTTACGAAAATAGCCACAATAAGCGCCGAATGAGAGAGCAGA
101400 A G TCTCTTGCAATCGGCCGGGATCTTCTAGCTGCTCGAGTGACATCAGCTAACAGAATACGTCTTTGGAACAAAGGTGTCGACTCAGATAATTTTCATCCTC[A/G]ATTTCGCAACTATGAAATGCGAGTAAAGCTAAGTGGTGGAGAACCAGAAAAACCTTTGCTCATTCATGTTGGACGCTTGGGTGTAGA
101404 A T ATGAGAGTGGGAAGCCTTGGCTGTGGTGGGATTATGTGACTGATTTTTCGATCAGATGTCCAATGAAGGAGAAGAAGTATACCAAGGAATGTGCTGATGG[A/T]GTAATCCGATCACTGGGAGTTGATATTAGAAAGGTAAATGATTGTATTGGAGACCCTGAAGCTGATGTTGACAATCCGGTACTTA
101404 A G AGGTAAATGATTGTATTGGAGACCCTGAAGCTGATGTTGACAATCCGGTACTTAAAGCTGAACAAGATTCACAGATTGGTAAAAATTCTCGTGGAGATGT[A/G]ACCATATTGCCCACCCTTGTTATAAATAATCGACAGTATAGAGGCAAGCTTGACAAGGGTGCAGTCCTTAAAGCGATATGTGCAGG
101404 C T CCATATTGCCCACCCTTGTTATAAATAATCGACAGTATAGAGGCAAGCTTGACAAGGGTGCAGTCCTTAAAGCGATATGTGCAGGCTTTGAGGAAACTAC[C/T]GAGCCAGCAGTGTGTTTGAGTGATGATGTTCAGACTAATGAATGCTTGGAAAATAATGGAGGATGTTGGCAAGATAAAGCTGCCAA
101404 T C GTGCAGTCCTTAAAGCGATATGTGCAGGCTTTGAGGAAACTACCGAGCCAGCAGTGTGTTTGAGTGATGATGTTCAGACTAATGAATGCTTGGAAAATAA[T/C]GGAGGATGTTGGCAAGATAAAGCTGCCAATGTTACTGCATGCAAGGACACTTTCCGTGGAAGAAT
101408 A G ACTCACCATCACACACCCTCGTCCCAGCAAAACTAACTGCGACCTGCTTCTCCCCAATACCCTTCTTGTTGGCCTTCATTGGGTGAGACGCCAAAGCCCT[A/G]ACCCCAATATCGCACCCATTGATCTCATCTACGTCCCTGATGCAGCCATTGACAACGATGCCAGCCCAGCCGTTGTTCTGGGCATGCTG
101424 A G GTGCATCAACAGCTGCTAGCTGGTCCAGTCCAATCAAACCCTCTTTTAAAAGATCGATGCATTTTGATTTCAGATTATCTGCATGGGTCAAACAAGAGGT[A/G]TAGTCATTGCGAACAATGGCTGATGAAAGGTTCATGTACTCAGTATTTGCCTCGCCTGCCAAACCATCAGTCAGGTGGCAGATATCCG
101424 T C ATCTGCATGGGTCAAACAAGAGGTATAGTCATTGCGAACAATGGCTGATGAAAGGTTCATGTACTCAGTATTTGCCTCGCCTGCCAAACCATCAGTCAGG[T/C]GGCAGATATCCGGTCCGGGTACAGCTGAATCCGTTTGAGCGGATGGCATGGCTTCAAACACGAGGACTGAGTGATGAGAGATGAG
101424 C T ATGGCTGATGAAAGGTTCATGTACTCAGTATTTGCCTCGCCTGCCAAACCATCAGTCAGGTGGCAGATATCCGGTCCGGGTACAGCTGAATCCGTTTGAG[C/T]GGATGGCATGGCTTCAAACACGAGGACTGAGTGATGAGAGATGAGAGCGCGGCCACTTTCGCTGCAGATGACTGGGTGATGAACT
101424 A G AGTGCGTATTCCTCTATAGTGTAGGCAATGGACATATCCGATACACCAGATTTGGATCCATCATAGTCAATGCCCAGCCCACCTCCAATGTCTATGACAC[A/G]CATTGAAGCGCCTAATCGGACTAGTTCGCAATAAATCTGAGCAGCCTCGACTACTCCATCGGATAATAATGCAGTGGATGGAATCTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101440 G GT ACCTCGCTCATAACTGGTCGGATTTGAATCCGGAACCAGTAGAAGCTGCCATAAGCGACTATTTCAATCTCGATATCGGTTTAGTGGAGATGTGGAGGGG[G/GT]TTTTCGGACGTGGACGAGAGGTTTGCAATGGTGGCAAAACGGCTGGGTGGAGGTGGTGCCAGAGTGATGAGGCAGGATCCGG
101440 G A ATCCGGTAGAATGTTTGTTCGAGTTTCTGTGCAGCTCCAACAATAACATTGGGAGGATTCAGAAGATGGTTGGGGTGCTTTCTTCCTTTGGTAGGATTCT[G/A]GGTTCTGTAGCGGGCTTCCAGTTTCATGAATTTCCATCTCTTGAGAGGTTGGGGACAGTCACCGAGGAGGAGCTTAGACAGGCTGG
101454 T G CCAAGGCACCAGCTTCAAACATCGAGTTCAATGTGGATCCTGACTTTTGCTCCACTTTCAACTTTCAGTCCGATCAGGGCAGTAACTCGATTGACTGTTC[T/G]GACTTTGGCTGGGGAAGTGAGATGGCAAAGACACCTGAGTTCACGTCACTGGCTTCAAATGCTATAATTGAAGAGAATGACTCTGAG
101454 G T TTTGCTCCACTTTCAACTTTCAGTCCGATCAGGGCAGTAACTCGATTGACTGTTCTGACTTTGGCTGGGGAAGTGAGATGGCAAAGACACCTGAGTTCAC[G/T]TCACTGGCTTCAAATGCTATAATTGAAGAGAATGACTCTGAGATCTTTTATGAAGCATTTGGCAATGGCCAGAAGAAGCAGAAGAAT
101454 A G ACTCTGAGATCTTTTATGAAGCATTTGGCAATGGCCAGAAGAAGCAGAAGAATAATGAAGGAGATGCCATATTTGCTAATCAGATATCTGAAGATCCATC[A/G]TCTTATGACTCATACATGAGCTTTTTGCAAGTTCCTGATGTGTCTATTGATGGTTTGTTTGGTAATGAAATCGGTGGTCAGGGCTCTG
101454 C T ACTCATACATGAGCTTTTTGCAAGTTCCTGATGTGTCTATTGATGGTTTGTTTGGTAATGAAATCGGTGGTCAGGGCTCTGATGAAATCTGGGGGTTTAA[C/T]GATGCGTCCATCGTTGGCGGCTACTAAGGTCGCTTGTCAAGATCTGGCTTGGATGGAGTTTTATTTGCAATAAGTTGGTTTGTCGAAG
101458 T C TCAAAAGAATCTACACCAGTACTTTCTTCTTTGGCTCAAGCACTGGTGGGTCGATATCAATACCCATGTTCGCAGCCGTGCCTGCGACAATTCTCATGGC[T/C]GACTCAATACTGGTGCAGTTCAAATCAGGCATCTTTTCCTGGGCAATTGCCCGTAGTTGATCGATTGTTATTTTGCCGACCTTCTCCAG
101458 G A CAATACTGGTGCAGTTCAAATCAGGCATCTTTTCCTGGGCAATTGCCCGTAGTTGATCGATTGTTATTTTGCCGACCTTCTCCAGTTTCGGTTCTTTTGA[G/A]CCTTTCTCTACCCCTGCAGCCTTAAGCAAAAGAACTGATGCTGGAGGAGTCTTCAAAATGAATGTAAAGCTCTTATCATCATAAACAGTG
101458 T A GCAAAAGAACTGATGCTGGAGGAGTCTTCAAAATGAATGTAAAGCTCTTATCATCATAAACAGTGATTTCAACAGGGATAACGTATCCAGCTTTATCAGC[T/A]GTCTTGGCGTTATACTCCTTACAGAAGCCCATGATATTCACACCCTTTGAACCCAACGCCGGGCCAACAGGTGGAGCAGGCGTAGCC
101458 C A GGTGGAGCAGGCGTAGCCTTCCCTGCTTCAAGCGCTAGCTTCACTATGCCCACCACTTTCTTCGCTTTGCCGGCAGGTTTTGGAGGGGCCATGGCTCTGA[C/A]TGTGAGAGTTTTAAGAGAGCGGCATTTACGGATAGAGGGGGTGAGAATAGTAGACGAGAATGGAGAGATGAACGATGAAGAGAG
101464 A ACT TCATATTGCAATATGAAGTTGGAAATTGAAGATCGCCTGCTGACTTAATAACATGTATAAAAGGGACTTCTCATAATATGATTAGGATCGCAGATCCTAA[A/ACT]TCCCTGAGCATCAGGCTTGGCTCTTCACCAAAGCAGCAAAAGCTGCTGCTTAGGGCCCAAGAATATCCAGGGCACCATCTTCGAA
101464 T TC TTGCAATATGAAGTTGGAAATTGAAGATCGCCTGCTGACTTAATAACATGTATAAAAGGGACTTCTCATAATATGATTAGGATCGCAGATCCTAAATCCC[T/TC]GAGCATCAGGCTTGGCTCTTCACCAAAGCAGCAAAAGCTGCTGCTTAGGGCCCAAGAATATCCAGGGCACCATCTTCGAAGGCAAC
101464 G GA ACTTAATAACATGTATAAAAGGGACTTCTCATAATATGATTAGGATCGCAGATCCTAAATCCCTGAGCATCAGGCTTGGCTCTTCACCAAAGCAGCAAAA[G/GA]CTGCTGCTTAGGGCCCAAGAATATCCAGGGCACCATCTTCGAAGGCAACACAGGCAGGAGAGAAAAATAAAATCACGTTACTGCA
101464 G GA CTGAGCATCAGGCTTGGCTCTTCACCAAAGCAGCAAAAGCTGCTGCTTAGGGCCCAAGAATATCCAGGGCACCATCTTCGAAGGCAACACAGGCAGGAGA[G/GA]AAAAATAAAATCACGTTACTGCAAAAAAGAAGCAGCTAATACAGCGATAGAACAACTTGCAATGCCTAGATTGGAATTGGGGA
101470 GA G TCCCCATTCAGCTTCCATATGTTGACACCTGCATCCCATACCTTAGAATCAACATAATTAGCCCAAAATTTAACTTGGTACTTCTCATAGGGATCCTTGG[GA/G]AAAAAAAGGAGCAACATTGTTCCATGCATCATCAATATACTCAACGATCAGAGTAGATTCACAAACTGGCTTTCCATTATGAATCAAAA
101470 A G ACTTCTCATAGGGATCCTTGGGAAAAAAAGGAGCAACATTGTTCCATGCATCATCAATATACTCAACGATCAGAGTAGATTCACAAACTGGCTTTCCATT[A/G]TGAATCAAAACAGGGATCTTTTTATGGATTGGGTTCGATTTAAGAAGCAACTCGCTTTTTTCTTGCAAATCCTCTTCTTTTGTTTCGTAT
101470 C T CTTTTTATGGATTGGGTTCGATTTAAGAAGCAACTCGCTTTTTTCTTGCAAATCCTCTTCTTTTGTTTCGTATTTGATTCCTTTCTCTTCCAAAGCAATT[C/T]TAGCTCTGTGGGCAAACGGGCTCACCCACGTTTCAATCAAAAGTACTTCATTTGCCATGGATCTCGAAACGTTGGGTAGACTTGATTTGAT
101472 T C CTGTGAACGAAGGGTTTGATGGTGGGGAGAAAGCTAGCGTGATGAAGGGAGTGCCTATTATATTGGTACCCAGTGCTTCACAGACATTGATTACTATATA[T/C]AACGTGAAGGAGTTCTTGGAGGATGGTGTTTTCGTTGCGAGTGATGTGAAGGCTAAAGGAGCAGGTGGGAA
101474 G A CTGTTGGTACCTACTTGGGTCATGCTATATACAAGGTCTCATCACTAGAAATTCTACCATGCGATCACACTTTAAATAATTCTTCTCCAGAGCAGAGAAA[G/A]TTGGAAGCCGATCTTTCTAGCCTCCTAAATGCTGCTGAGAAAACGCCCGGTCTATACTTCTCATACAATGCTAACTTAACTCTAAGTGC
101474 A G GGAAGCCGATCTTTCTAGCCTCCTAAATGCTGCTGAGAAAACGCCCGGTCTATACTTCTCATACAATGCTAACTTAACTCTAAGTGCACAGAGACTGCAC[A/G]ATCTTGGTAACGAGTCGAAGTCACTCCCTCTTTGGCAACAGGCTGACCCTAGATTCCTTTGGAATAACTACTTGTTGGAACCGTTGAT
101474 G A GTAACGAGTCGAAGTCACTCCCTCTTTGGCAACAGGCTGACCCTAGATTCCTTTGGAATAACTACTTGTTGGAACCGTTGATTGATAGCAAACTGGATCA[G/A]TACATGCTTCCTGTTATACAAGGAAGTTATCAGAATTTTCATGCAGCGATTGGAACCAATATCGTTGACGTGACGATTATTGCTCGTA
101482 G T TTTCTCCACCACACCGTGCTCCTGAAACGCCTAGCTTGCTTTCTGAAACGCATTGTATTTCCCTGCATATTTGCAGTTTTGTCTACCAATAGATCTAGTC[G/T]GTCTCCTCTTTCAAGAACTTTATCGATGTTCTGAATCATTACATTTCGGACCTGACTCATTTCGCCTTTGAGACGATTCATTCTATCAGCAT
101482 A G TGAAACGCCTAGCTTGCTTTCTGAAACGCATTGTATTTCCCTGCATATTTGCAGTTTTGTCTACCAATAGATCTAGTCGGTCTCCTCTTTCAAGAACTTT[A/G]TCGATGTTCTGAATCATTACATTTCGGACCTGACTCATTTCGCCTTTGAGACGATTCATTCTATCAGCATTAGGGTCATTTGAATAATAAT
101482 T C TCAAAACCCTTGAAAATTCCTCGTTCATTGCATATGCAAGAGCAGTGTGACAAGCACGACCATATTTTTTCACAAATTTTCCATGGATGTCTTCAAGAAA[T/C]GCAAATGGAATTTGTCTGCCGGCGGTATCATCGGCCATGCACAAAACAGTGATCCCGTCCGTACGTTTTACATGAAAAATATGTCGATC
101482 G A CCGTACGTTTTACATGAAAAATATGTCGATCCTGGGAATAGGAGACGTGGCTATCATCCGCCCCCGGAATCTTGTCCAGAATCTGTCTTGCGATAGTGCC[G/A]GCGTTGGATTGGGCGACAGCGGAAAACTCCGCGAGCACTACCGATCCTCTCGCGACAAGCGCGTACAGTATCGCCATCGATTCTCC
101486 C T CTGCCATGCGCATCGCCGCCCTAAGTGAAGCACGTGTCATCTACGTAATGACCCACGACTCCATCGGCCTTGGAGAAGACGGTCCCACCCATCAGCCCAT[C/T]GAACATCTTGTGAGCTTCCGTGCCATGCCCAACATACTAATGCTACGTCCCGCAGATGGTAGGGAGACCGCTGGTGCCTACAGAGT
101486 A G TACGTCCCGCAGATGGTAGGGAGACCGCTGGTGCCTACAGAGTTGCTGTTCTCAACAGAAAAAGGCCATCCATTCTCGCACTGTCTCGCCAGAAGCTTCC[A/G]CATCTGCAAGGCACTTCGGTTGAAGCAGTCGAAAAGGGTGGATACATTGTTTCGGATAACTCGTCCGGAAACAACCCGGATGTTAT
101488 A G AGTAGTTCCAGCAGAGGCGCGCGAGTACGCCCAGGGATATTCCGGCAAAGGCGTAGCCTCCGTAGGCCACGATGTCGAGGAGAGGGGCCTCGCCGCTGCC[A/G]AGGGAGTAGAGCATCCCTTTCAGGAGCATCACTTGGGTGAACCACCCTACTATACCTCTTGTGAATTGTAGGCTTAGTGCTTCC
101488 C T AAGGGGAACAAGACAATTTTTAACTTGTTCCTTACATACTGGTCATTTACTTGAAAATAATATTGTGGGTTGGAGAACCATCTACTAATATTGCTTTGCA[C/T]GAATTCAGAGCTTGAACCCAAAAATTTCTCTCCATACGCGCCCAAGCCTCCTCTAATTAGTCCAGATCCAAGGGTACCAAA
101496 T G GAACATCTCAAACTTGCTTAATTCTAAGCCATTTTCCTTCGCGAAACTAAGAGGGATGTCGCTTTCCTTCTTATCAAGGGTAAAATCTTCGATTTTGTTG[T/G]TTTCGTATGAGCTTTGAAGGAAATTTATGTATGATTTCTCAAATGATGAATGCATAAGCTCACATAGTTTGTCGAGCTTTTTCTGCATATT
101496 G T CAAGGGTAAAATCTTCGATTTTGTTGTTTTCGTATGAGCTTTGAAGGAAATTTATGTATGATTTCTCAAATGATGAATGCATAAGCTCACATAGTTTGTC[G/T]AGCTTTTTCTGCATATTCTGCAGAACTTCGTCCCGAATCTTAACGGATCGCTCCAACCTAACAATCTGTTTCCGCTTAATCCCCTCCTTCT
101496 A G CGATTTTGTTGTTTTCGTATGAGCTTTGAAGGAAATTTATGTATGATTTCTCAAATGATGAATGCATAAGCTCACATAGTTTGTCGAGCTTTTTCTGCAT[A/G]TTCTGCAGAACTTCGTCCCGAATCTTAACGGATCGCTCCAACCTAACAATCTGTTTCCGCTTAATCCCCTCCTTCTCCGCAGCACCAACAA
101496 C T TTCTCAAATGATGAATGCATAAGCTCACATAGTTTGTCGAGCTTTTTCTGCATATTCTGCAGAACTTCGTCCCGAATCTTAACGGATCGCTCCAACCTAA[C/T]AATCTGTTTCCGCTTAATCCCCTCCTTCTCCGCAGCACCAACAATCGCAACCGCAAGAAGCCTCTCCATCGGACTAAACAGCTCCCAAGC
101496 T A CAGCACCAACAATCGCAACCGCAAGAAGCCTCTCCATCGGACTAAACAGCTCCCAAGCTACCGTCTCGTCTTTGCCCAGCCCTTTCCCGACCGATTTTGC[T/A]GACGTGGCCTCTTCAGCCCCGAAGATCGGTCCTTGCAATGAAAGCCAAGCGAGTTTCTTTTTAGCTGGTCGATTCGGCTTGAACGATT
101496 G A AACAATCGCAACCGCAAGAAGCCTCTCCATCGGACTAAACAGCTCCCAAGCTACCGTCTCGTCTTTGCCCAGCCCTTTCCCGACCGATTTTGCTGACGTG[G/A]CCTCTTCAGCCCCGAAGATCGGTCCTTGCAATGAAAGCCAAGCGAGTTTCTTTTTAGCTGGTCGATTCGGCTTGAACGATTTGGTTGA
101500 T G ATTTTCCAACATATAACGACCTTTAAACTCATATCAAATCATATCAAATGGACAATAATATTCAAGCCGTACATTTTCCTATTCCACGAGTATGCACTCA[T/G]CACATGTCCAGCTTCTTTCGCAAATATGTGGAGCTCAAATGATATGCATACCATATAAAACCTGACTTGTTTAGGTATGGACCGTATGGT
101502 A G CTGTAGAACTTATCAAGAAAGAGGAATTCTGATGCACCAGCATCACTGGAATTAGACGGTCTATGAA[A/G]TGGTTGTATCAGCAAGGAAGCAACTCCTTTGGGAAGAATACTTTGAAGCCTGGAATCAGGGATTTGCGGAAAATAAAGCGAATCCTCTAAATCCATAAAA
101502 A G GAGGTTTCGAAAAAGTTTCAGGTACATCCCAATATCCTCGTAAGCACGATACATCTTGAACAACAATCGCCACTGACATGGTGTTCGTATTGCGCAAAAG[A/G]ACATATGTAGCCCACGCCAAGTCTTCTTCCTGCTTTGGTGAAAGATTTTGAGAGATAACGAATATCTGTGTGTTTCCTTCGGGGATAG
101502 T A CTCGTAAGCACGATACATCTTGAACAACAATCGCCACTGACATGGTGTTCGTATTGCGCAAAAGAACATATGTAGCCCACGCCAAGTCTTCTTCCTGCTT[T/A]GGTGAAAGATTTTGAGAGATAACGAATATCTGTGTGTTTCCTTCGGGGATAGACGCACGATCAACTGGATTTGCACCCTTAAGAAACT
101502 T C AACTGGATTTGCACCCTTAAGAAACTTGCCAATATAAGGAAGTGCAGTAGAGAATGCAGCCAAACAGACACCCAAGGCCTCCGTTCTCAATTGCGCTGGG[T/C]TAGGAGAAGAAGCAGAAAGAAAGTGATTTGCAACGATAAGTCCACCAAACGTGACTCCTATCCATCTCGGCAAGTATGACTCGTCA
101504 A G ATATTGTCTGATGCTGGTCTTGGCATGGCTATGTTCAGTCTTGGGCTATTTATGGCATTGCAGCCGAGAATGATAGCATGTGGAAACAAAATTGCATGCT[A/G]CACGATGGCTGTTAGGTTTCTGGTTGGCCCTGCAATCATGGCTGCGGCTTCCTTTGCTGTAGGCCTCCGCGGCGTGCTTCTGCATGT
101504 G C GGTGTTATATTTGGAATGCTGATTGCCCTACCAATAACTTTGGTCTACTACATTGCCTTGGGCTTCTGATACTACTGCAAGTTTTTGACAAGGCCAAGTC[G/C]ACATGCGACGAAAACGAAGATTTATAGGCAGAGAAATTTTTGTGTGAAGGTGGAAAGAAAAATTATATGGTTCGAGTTTGGAATGCT
101520 T C GCATGTCTGCCACAGAACCCTTTCTGTGCTCATAATTTGATTCGTCAATGTCCAAGAGTTCATCCCTATTTGAAGATGAAGAACCATACAAACTTCTCCG[T/C]TCAGCAGCACGGTCTCTATATGTAGCCTGAGAAGTTGATTGCACGGGTGCTTCTGAAAACCTACGCCTTCCACTTCCAGAAGTTACAGG
101526 G C CCTCCAGTTCAGAGATCTCTTCAGAATCATGAGACATCTTCTCCTCAGCCAATCTTTTGAATTGCCGGAACTCCATCTGCGCCTCCGCCTTCTCGCGCTG[G/C]AGACGAAGAATCATAGACATTGCTTCGCTAGCAGCTGTGGCTGAAGCGCTACGCTCCTCTTCCAACTCGCCATACAATTCTTGGATGGA
101526 G A TGACGTCTTTGTCACCATTGTTAACACCGTTGGATACGGCGTTGGAATAGCTGACGTAGTCCTGGTGAAGTTGGTCGAGGCGGCGTTTAAGGGAGCGGCG[G/A]AAGGAGGAAGACGAGGTGGAATGGGGCTCGCAGCAGAGGCATGGGCAAGAGCACGTGCTTCGGTCGTCGGTTTCTTCTGAATC
101526 A G AGGGAGCGGCGGAAGGAGGAAGACGAGGTGGAATGGGGCTCGCAGCAGAGGCATGGGCAAGAGCACGTGCTTCGGTCGTCGGTTTCTTCTGAATCCATTA[A/G]AGAATATAAAAGTAGTAGTATTGCCGCATGAGTTAGGTTTGTTTTGGTTCGTTCTTCTCTTCCGATCTCCCGAGGGGAGAAAAA
101540 T C TTTTTCACTTTACTACCTCACCACCACCATCTTTGCAGACAACTATGGCTGGGAAGGCGGCCATGCCACATTCTA[T/C]GGCGGTGGCGATGCCTCAGGCACAATGGGTGGAGCTTGTGGATATGGAAATCTGTACAGTCAAGGCTATGGAACCAACACTGCAGCGCTCAGCACGGCGT
101540 GA G CACCTCTTCAGCATTTTGATATGGCTGAGCCTGCTTTTCTTCAGATCGCTCAGTATCGTGCTGGAATCGTTCCCGTCTCCTACCGCAGAGTGCCATGTGT[GA/G]AAAAAAGGAGGGATAAGATACACAATCAACGGACACGATTACTTCAACCTGGTGCTGATCAGCAACGTAGGCGGTGCAGGAGATG
101540 C T GCAACGCATACATGACAGGGCAGAGCCTCTCCTTCCGGGTCACCACCAGCGACGGCAAGACCATCACCAGCTACAACGTCGCCCATGCTGGATGGCATTT[C/T]GGCCAGACCTTCGAGGGAAGCCAGATTTAGGGCTAACGGGTTCCGCTTTGGTTGCTGAGGTGGCATTGCATTGCACCCGCTATGA
101542 CT C ACGTAAACATAGCTGATACACAATTCATGTATAGGATTACAAAATAGCATAACAGATACTTGAAAACTGTAGAAAGCCTCTCATTTTTTGGCAGCAAGTA[CT/C]TTTTTTTGGTAGCTTATCGAAAGGAGTAGTTTTAAGCAAGAAAAGCCTAGTCGCCCTCTCAGGCAGAGTTCCACCGCACTTCAGCCC
101546 CAT C CGAGGGGAATCCCGCTGGGGTCGTCCTTATACGCGAAGTAGGAATACGCGTTGATCCAAAATGGGGATCCGGTCTCGGACAAAAAACCCAAAAATTGGGA[CAT/C]ATATAACATCTTCGATATCGGGTTTGAAACACGCCTGCGAAGGAGGGTACGAGCTTCCCAACACCTGCAAAGAATTAGCGCTG
101546 C T AAGTAGGAATACGCGTTGATCCAAAATGGGGATCCGGTCTCGGACAAAAAACCCAAAAATTGGGACATATAACATCTTCGATATCGGGTTTGAAACACGC[C/T]TGCGAAGGAGGGTACGAGCTTCCCAACACCTGCAAAGAATTAGCGCTGGAAACGCGGATGTACGCGTCTAACCCTAATTGAACCA
101546 G T ACATATAACATCTTCGATATCGGGTTTGAAACACGCCTGCGAAGGAGGGTACGAGCTTCCCAACACCTGCAAAGAATTAGCGCTGGAAACGCGGATGTAC[G/T]CGTCTAACCCTAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGA
101546 A G TCGATATCGGGTTTGAAACACGCCTGCGAAGGAGGGTACGAGCTTCCCAACACCTGCAAAGAATTAGCGCTGGAAACGCGGATGTACGCGTCTAACCCTA[A/G]TTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTG
101546 C T AGCTTCCCAACACCTGCAAAGAATTAGCGCTGGAAACGCGGATGTACGCGTCTAACCCTAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTAC[C/T]AAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGG
101546 T C AAAGAATTAGCGCTGGAAACGCGGATGTACGCGTCTAACCCTAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAG[T/C]GTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGT
101546 A G TAGCGCTGGAAACGCGGATGTACGCGTCTAACCCTAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTC[A/G]TCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCAC
101546 C T CGTCTAACCCTAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCC[C/T]ACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACG
101546 T C TAATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATG[T/C]CAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGA
101546 A G ATTGAACCAGGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTC[A/G]GTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAAC
101546 C T GGGCTTGATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTT[C/T]GTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTT
101546 G T GATGGATCGATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGA[G/T]GCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101546 G T ATTTCATGGCGGGTACCAAGGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAA[G/T]GGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGACGGTGACAAT
101546 A G GGCTGAAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTG[A/G]CCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGACGGTGACAATGAGTTCGATGTCGGAGTTG
101546 C T AAATCAGAGTGTGGTCATCGGTGGAGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCA[C/T]TGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGACGGTGACAATGAGTTCGATGTCGGAGTTGGCGAA
101546 G T AGTAGATTTCGTTGCCCACGGCGATGTCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGAC[G/T]ATTTGGGGAACGAGATCGTTTGGGACGGTGACAATGAGTTCGATGTCGGAGTTGGCGAAGGCGGTCAGGACTTTAGGGTTGGT
101546 C T TCAGTGATCTTCGTGGAGGCGATGAAGGGCTTGATGTTGGTGGTGACCCACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGA[C/T]GGTGACAATGAGTTCGATGTCGGAGTTGGCGAAGGCGGTCAGGACTTTAGGGTTGGTATCGTAGATTCTTGTCTTGGTGATTTT
101546 T C CACTGGAGGGCGAATTGCGGATCGACGATTTGGGGAACGAGATCGTTTGGGACGGTGACAATGAGTTCGATGTCGGAGTTGGCGAAGGCGGTCAGGACTT[T/C]AGGGTTGGTATCGTAGATTCTTGTCTTGGTGATTTTGAGGGAGGTTACGAGGGTTCGTACTTGCTCCGGCGAGGGCAGGTTGT
101546 C G GGGACGGTGACAATGAGTTCGATGTCGGAGTTGGCGAAGGCGGTCAGGACTTTAGGGTTGGTATCGTAGATTCTTGTCTTGGTGATTTTGAGGGAGGTTA[C/G]GAGGGTTCGTACTTGCTCCGGCGAGGGCAGGTTGTTTGCTACTTGGCCGTAGTTGATGCCCAGTGTGGAAACTTTCTGTATCAGT
101546 G C AGATTCTTGTCTTGGTGATTTTGAGGGAGGTTACGAGGGTTCGTACTTGCTCCGGCGAGGGCAGGTTGTTTGCTACTTGGCCGTAGTTGATGCCCAGTGT[G/C]GAAACTTTCTGTATCAGTCCCAATTCTGAGTGAAAGAGAAGAAAGGCTACAAAAATGCTGAAAATTCTTGAGAACAAGAGAGCCGC
101546 G T CTTGCTCCGGCGAGGGCAGGTTGTTTGCTACTTGGCCGTAGTTGATGCCCAGTGTGGAAACTTTCTGTATCAGTCCCAATTCTGAGTGAAAGAGAAGAAA[G/T]GCTACAAAAATGCTGAAAATTCTTGAGAACAAGAGAGCCGCCATTGATTGACTCAAAGAGTGTTGATTTCAGTTTTGACTTGCTTGC
101548 AG A GAGGAGGAGAAAAAGAAGAGAGAAGCAGCAAAAGCAGCGGCAGCTGCTCGAGTTCAAGCAAAGTTAGATGCCAAGAAAACTCCAGGCAAGGGAAAAGGGA[AG/A]GGGGAAGTAAACTTTGTCTTCTGTTCAAGTAATATTTTAGTTTGAAGAACCATAACATAACTTCATGGTTTCAGCTGCTATGG
101550 G A AAACCATGAGCTACCAAGATAGGTGACACAAAGTATTGGATAACAAAAAGCAAAATAAATGCAGGAAAGAATGAGTTGCAATGCACATCAAACGAGTATA[G/A]CCATTCAACACGTTGCTCAACCACATGGCTGTTAGGAGTCTCTTCTCTCAAATAAGTATTCGTCAGGAACCAACAACATGTGGCTA
101552 T C TATCTGTACATCTATGCCATCTGCATAAACTTTAACCTTTAAAAAAAGTTCCACGGTGTGATGTAATTTGGCATTTGTTGTCATCGATTGTTTATGTACA[T/C]GCTTGTTGTGCTTTTGTTGTAGCATTTAGAATTTTGTTTGGCTTTGTAGTTTTGGTTACAGCTATTTCAGTGAAAAGCATGTTTTTGTTCAA
101560 A G ATCAGCACGGAGCTGAGTGGTTCTTGTTTGACGATCTGAGGAAGAACGGACGGTCGGGATTGCACTTGGAGGCAGTGGACGATCCAGATGAGGCGGATTT[A/G]TTCTATGTTCCCTTTTTTTCGAGTTTGAGTTTGAATGTGAATCCAATGAGTAGGGAGGCAGGGAAAGCGGTGGAGTATAGTGAT
101560 T G GAGCTGAGTGGTTCTTGTTTGACGATCTGAGGAAGAACGGACGGTCGGGATTGCACTTGGAGGCAGTGGACGATCCAGATGAGGCGGATTTATTCTATGT[T/G]CCCTTTTTTTCGAGTTTGAGTTTGAATGTGAATCCAATGAGTAGGGAGGCAGGGAAAGCGGTGGAGTATAGTGATGAGAAAATG
101560 G T GGGAGGCAGGGAAAGCGGTGGAGTATAGTGATGAGAAAATGCAGGATGAACTGGTAAAGTGGTTAGAAGGGAGTAAATACTGGAAGAGAAACAATGGACG[G/T]GATCATGTGTTCATAGCTCAGGACCCGAATGCACTTTATAGAGTTATCGATAAAGTGAGCAAGGGTGTTCTATTAATATCTGA
101572 T C GAATGGAGCGATATCTAGGGTTTCTATGAGCGTTTCGGTTGGGTCGAGGGAATCAGTTTCATCCGATGCCTTGTTTGCTGATTACAAGCCCAGCACCGCA[T/C]TTCTGTTTCCTGGACAGGGTGCACAAACTGTTGGAATGGGGGCTGCATCCCAGAGTGTGCCTGCTGCTGCAGAATTATTTGAAAAA
101572 T C ATTACAAGCCCAGCACCGCATTTCTGTTTCCTGGACAGGGTGCACAAACTGTTGGAATGGGGGCTGCATCCCAGAGTGTGCCTGCTGCTGCAGAATTATT[T/C]GAAAAAGCAAATGATATACTTGGATTCAATCTCTTAGATGTGTGCACCAATGGTCCAAAAGAAAAGCTTAATTCTACAGTTATAAGC
101572 C T TATACGTCACTAGTTTAGCTGCTGTCGAGGTATTACGTGCACGTGATGGTGGGCTGGATATTATCAACTCTGTAGATGTCACATGTGGTCTAAGTTTAGG[C/T]GAATACACTGCTCTTGCTTTTTCCGGAGCTTTCAGCTTCGAAGATGGTCTGAGACTTGTCAAGCTAAGAGGAGAAGCGATGCAAGAT
101572 C G TCGAGGTATTACGTGCACGTGATGGTGGGCTGGATATTATCAACTCTGTAGATGTCACATGTGGTCTAAGTTTAGGCGAATACACTGCTCTTGCTTTTTC[C/G]GGAGCTTTCAGCTTCGAAGATGGTCTGAGACTTGTCAAGCTAAGAGGAGAAGCGATGCAAGATGCTGCAGATGCTGCGCCTAGCGC
101576 GA G TCTACCACCACCATTATGAGTTCCCCCACCATTGTGTGGTCGTCTATTAAATGGTTTATGAGGACGCTGATGATGATCAGACCCACCATGCGAGTTTGGA[GA/G]AAAACAAACTTCCCTTGGAACTATTATTATTTGTATTCTTGAATGAAAATTCTTGACCCTGACCAACAGGATTATCTGAAAGCTTTTG
101576 C T GGTTTATGAGGACGCTGATGATGATCAGACCCACCATGCGAGTTTGGAGAAAACAAACTTCCCTTGGAACTATTATTATTTGTATTCTTGAATGAAAATT[C/T]TTGACCCTGACCAACAGGATTATCTGAAAGCTTTTGAATTATCTCCACAGGTAGCATTGGTGGTGATGAACCAATCCTCTTTGAGTTGG
101582 A G CAAAGTTGATCCCTTTGAGGTGAGGATGCTTCTTGACGATCATGTTGATAGTTCCACCAACTCCACCTCCTACATCAACTAAGGTGTTAAGCTCCTCAAA[A/G]CCTTTATATGTTTCAAGGACCTTCTTGGTAGTGATTATTGAGTGGTTCCTCATTCCTTCATTGAACACTTTGTTAAATCTAGGGTCTGTG
101582 T C CTACATCAACTAAGGTGTTAAGCTCCTCAAAACCTTTATATGTTTCAAGGACCTTCTTGGTAGTGATTATTGAGTGGTTCCTCATTCCTTCATTGAACAC[T/C]TTGTTAAATCTAGGGTCTGTGCCATGGTATTCAAACGCGGACATTCCATATGCCTTATTGAATGGTATGCCTCCATCAAGGACTGCATCT
101582 AT A TGCCTCCATCAAGGACTGCATCTTTCAAATGATACCAGCTCTCCATGAGGACCTTGTCTTGATTCATCAACCCAAGAGCAGCAATAGACACACCATCTTC[AT/A]TTTTTGGTTAAAAACTTAACAACGGGAGCGGCTCCGTACTTCCTCACTGTTTTACCTTCTTCACTGGTCTCCAACTTACATGTCAAAAC
101582 T A GATTCATCAACCCAAGAGCAGCAATAGACACACCATCTTCATTTTTGGTTAAAAACTTAACAACGGGAGCGGCTCCGTACTTCCTCACTGTTTTACCTTC[T/A]TCACTGGTCTCCAACTTACATGTCAAAACATTATAACTAGCAAGCAGCCTCATTATTCGATCGATCATGACAGGAGCTTGTGGATTCTCC
101582 G A GATCGATCATGACAGGAGCTTGTGGATTCTCCGTAGGCAACTGAGAAGCAATCTCCGATGGCGAAAGGTAAGCATTAGGCCCTGCTTTTGCAATTATTTC[G/A]AAAAGGTCAAGTTCAATTGCTGCTTTTAAAGTCATTGGTAGTACTGAGTAACTGCATAGTTGCATTGCATATAAGCATGCTTCCTCAT
101582 A G TCCGTAGGCAACTGAGAAGCAATCTCCGATGGCGAAAGGTAAGCATTAGGCCCTGCTTTTGCAATTATTTCGAAAAGGTCAAGTTCAATTGCTGCTTTTA[A/G]AGTCATTGGTAGTACTGAGTAACTGCATAGTTGCATTGCATATAAGCATGCTTCCTCATCTGTGGATTGAGGAGCAGGAGTTATGTA
101586 T A GATCCTTACCGGTAAGATCACCAAGCAATGCTCTACAAGGTGACTGAGTAGCATTATTCCCAACATCAAGCAACCAGAATCCCAAGACATAAACACCAAT[T/A]GCTCTTGACCTGATCTTTCCATCCACATCTCCCAGCAACCAACCAATATCTGCAGAATGCCCCACAATTAGTACCGACAATGCAATGG
101596 TA T CACGTAGTAGATTCCCAAACCGAAGATTCCATTCGTGCACTCGATCTAAGAGAAATCGAAATCCCGAACATTGAAACCAAAAATGCTGAATTGGTCGAGT[TA/T]AAAGGAAACAAGATGCTATCAAGGAGATGGAAGATGAAACTTTTGATGCAAAGGGTGACTTTTTAGGGATGTATTGTAGGAGAAT
101596 A G CTATCAAGGAGATGGAAGATGAAACTTTTGATGCAAAGGGTGACTTTTTAGGGATGTATTGTAGGAGAATGGATAGTAAGAACCTATGGAGATATTTGTT[A/G]AATGGAAAATGCAAAGTGGACGAGTTAAGGAATGCGTTTTTAAATTGCGTTGATGGTTGTAGATTGGTTATTGATGCTGTTGATGA
101596 T C GATGAAACTTTTGATGCAAAGGGTGACTTTTTAGGGATGTATTGTAGGAGAATGGATAGTAAGAACCTATGGAGATATTTGTTAAATGGAAAATGCAAAG[T/C]GGACGAGTTAAGGAATGCGTTTTTAAATTGCGTTGATGGTTGTAGATTGGTTATTGATGCTGTTGATGATTTTTTAAGTAATGAAAA
101596 A G TTGATGCAAAGGGTGACTTTTTAGGGATGTATTGTAGGAGAATGGATAGTAAGAACCTATGGAGATATTTGTTAAATGGAAAATGCAAAGTGGACGAGTT[A/G]AGGAATGCGTTTTTAAATTGCGTTGATGGTTGTAGATTGGTTATTGATGCTGTTGATGATTTTTTAAGTAATGAAAAGGTAGGTGA
101596 G A AGGGATGTATTGTAGGAGAATGGATAGTAAGAACCTATGGAGATATTTGTTAAATGGAAAATGCAAAGTGGACGAGTTAAGGAATGCGTTTTTAAATTGC[G/A]TTGATGGTTGTAGATTGGTTATTGATGCTGTTGATGATTTTTTAAGTAATGAAAAGGTAGGTGAGAGCATGAGTGAGAAGTTTTG
101596 G T TTGATGGTTGTAGATTGGTTATTGATGCTGTTGATGATTTTTTAAGTAATGAAAAGGTAGGTGAGAGCATGAGTGAGAAGTTTTGGGTGATTGGAATGCT[G/T]GTGAGGGCATTGTTTGATTCGGAAGGCCATAAAAGGCCAGAAATTTCAAGCACGATTAAGAATCGGGCGGAGGAAGTCCTGTCTG
101596 G A TGATGGTTGTAGATTGGTTATTGATGCTGTTGATGATTTTTTAAGTAATGAAAAGGTAGGTGAGAGCATGAGTGAGAAGTTTTGGGTGATTGGAATGCTG[G/A]TGAGGGCATTGTTTGATTCGGAAGGCCATAAAAGGCCAGAAATTTCAAGCACGATTAAGAATCGGGCGGAGGAAGTCCTGTCTGA
101598 C CT GTAGGTTGATCAATGCCAGAATAAATCAAGCGAAGGTTGTACATGTAAACCAAACTCTCGAAGGGAACTACACGCTTTTCCCTACATATCAATCTAAACG[C/CT]TTTTTTTCCTACATACCAATCGACCCTTGTGGGCAAAAAATGTTTTATAAATATGTATCCAAATGTCCTCAATAGGCCTAGCACTATG
101598 G C AAAGTATAACAGCAGCAGAATCTTTAGCCTTCTTCACACTTGGCATGGGCTCCCCAACACACTCATCCGTCCATCCTCGATCCGAAGTATTAACACGTAC[G/C]GTGTACACAAACCTCTTAGCATGTGCAGGTCCGCCTTCATTTACACACCGATACTGAGGCATCGGCCATTGTTTCCTCAAGCAAATATC
101604 T C AACGGAGGGATAATATCGGACAACGCTAGTACCATTCCCTCTCCAAAGCGACAAGAATCCTTCTTCCTTCATAGTCCTCCCAATACAATCAATCATCCCC[T/C]TGAATTTGATAATCTTCCTGTTATTCAGAATGGCAGCGTTGCTTTCTTGCGTTTGAAGAATCAGTTTTGTCCGCTCTATTGGTGCAACGA
101608 T C ATAACCAGGCAAATAATCAAGTTCAGTTCGGCCTCCATGTGGAGATAGCAAATATGGTTCTTCCTTTCCAACCTTGCAATAACCATTTACTATCTTCATC[T/C]ATGACGAACTCCTTATGATATGCGTCCATGACTTTATCTTTTGCCCTTTTCATTATACCCGGATTCAAAGGAAGTTGGGCAAAGCCAGCC
101610 A G GATCTTAAACACCGATGTGTAGTATCTTTTCATCATACAACAGTGGCACATCGATGGCATAAATGCTCATCGCTTCAATTATTTGTACGTAAGTTTCTAA[A/G]CCTGCATCATTATTAACTATGGATAATAACTGTGAAACGTTCAGTCCTGCAGCCAGAAAGTTGAATTTGATTCTTCTAGCAAACGCATAA
101610 A G ATAAATGCTCATCGCTTCAATTATTTGTACGTAAGTTTCTAAACCTGCATCATTATTAACTATGGATAATAACTGTGAAACGTTCAGTCCTGCAGCCAGA[A/G]AGTTGAATTTGATTCTTCTAGCAAACGCATAATAGCAAACAAAATAATCTCAAAGTTTAGATTTGCCAGTATCAGTTTTAGGCTTCTGCT
101612 A G CACTCCTCCATCTACCAGAAGGACACAACAGACTGAAACTCAAGAAACTGCACCAAAAGTGATGACAAATTTGTCGTACCAAAACTTGGACCATCGCAGG[A/G]TATGGACCAAGACCATCACCAAAATGTAAAACCAACAACGTGAACGTTCTAATCCACACCAATAACTCGAGGAGCAGGCATGGACC
101612 G C GCATGGACCTGCCTTTGGTTTACAAATTAGTAAAAGACAATAAACGCAATAACTACAAGAAGGCTCAAGAGCACTAATGAACAACAAGAAGATCAATACG[G/C]CGACAACCAAAGACTGTGGCAAACAAAGGAGTAAGAAACCAAGGCCCCAAATCGAAGCATAAAAACATATCTGAGAAGGAGCTTA
101612 A C ACAACCAAAGACTGTGGCAAACAAAGGAGTAAGAAACCAAGGCCCCAAATCGAAGCATAAAAACATATCTGAGAAGGAGCTTACTTGACAGCGAGATACT[A/C]TTTGGACTTTGGCACATCTGCCAAAACACAACCAACCCAAAATAGGGTGGTGCGTGCTCAAGAGTGGCGTAGTCAAGCTACAAGC
101612 A G CTAGTCCCTATGGCATAAATAAGACTTACACAGAGAACGAGAGGGTTAGATCTGAAAAGAGATTTGGGTTTCGAATCAAAGACTTCGTTAGCTTCAGTGA[A/G]GAAGCAAGGAGATAAGTTGCAGAAAGGTTAGAAGAGAGCTGTTTGAAAGGGGTGAGGAGAAACAAAGTGAAGAGAGGATTGGC
101614 A G CTTCCATGAAGCAGGCTATGCTTTTTCCACAGCCTGCCCAGCCTGGAGATGCTTTTCATCAGGTTCTGAATGGGCTTGCTAGGAAGCTTCCGCACGATGA[A/G]AGGATGTATTTGAAGCCCGGGCAGAAGGTTCTGAACTGGACTGCAGGGCCTGTCGGTGATTTGAAACCTTGGTAGGGTGTAGGAG
101622 A G CTCCTCCTCCAGTTATGAGGCCGCCCATGCCTGGTCAAATGCCTCCTGGACAAATGCCGCCTGGGTATAGGGGCCCACCTGGACCTGGAGGGCCACCTTC[A/G]TCAATGGGGATGCAGTTTAGACCGCCGCCCGGTGCTCCTTATCAGATGGGACCACCACCACAGTATGGTGGAAGGCCAATGGGTC
101626 GT G CTTGACTGTGGGCCTCCTGAGTTTTTGATGGATGGGGCTGGGGCATCGAGCTCCAGTGATGCTAGGCCCAGGCCTAAGATGTTTAGCAGTAGGAGCATTG[GT/G]TTTTTTTAGCAATAACGCTGTGAGGAGTAGGAGCATGTATAGGAGGAGCGCGGTGCTTACATGCAGGAGAGGGAGTTCGCTTG
101626 C T TTTGGTTGGAGTTGTGAGTTATACTGAGATTATTGCTGCTGTTACTAAGCAGCCTTCTGCTTCTTAGATTTGGTTCTTGTTTGTTTTATTATATATAAAA[C/T]ATAAGCATGTTGATGAACTTAATTTGTGAGACCATTTTGAAGTCCGAGGGTACGCCGCTGAGTTTGTTAGCTTTGATTTGTGTGTTCTTTA
101626 G C AGCCTTCTGCTTCTTAGATTTGGTTCTTGTTTGTTTTATTATATATAAAACATAAGCATGTTGATGAACTTAATTTGTGAGACCATTTTGAAGTCCGAGG[G/C]TACGCCGCTGAGTTTGTTAGCTTTGATTTGTGTGTTCTTTAGATTATATTCCGACTGATGCGATGATGGGCAAAGGTTTT
101630 CA C AAGAGTCACGTTATTCGATTTCATTTTGATTCGATCTACTCTTCGTCTTTATCTTTTAGAGTCTCAAGAACTTGCTAGTTGTAGATGGATAAAG[CA/C]AAAAAACAGTACTGAAATGGAAGAGGGAACACTAGAGATTGGCATGGAGTATAGAACCGTGAGTGGGGTGGCGGGACCACTTGTTATACTGG
101646 A G TGTAAGCAAGACCACGGCATATCTGAAAAGCATAGAGGCGTGCAAAAATGAGAGGCATGTGTTGATTCATTTCGGAATATCGTTTCCTCGTTCGATGGAC[A/G]GTTTCTGGAACATATTCGAGTACAAGATTCAAGTACAGCTCATCCTTTTCAGTTGTTGAGAAGAAGTGATGCTTTAATCGAACTACA
101660 G A ACATACTGTGAACAGAACAGTGCACTAAATTGTAGAAAAGGATGATAACTCTGATATAAAATACATATTCAAGGTATTTCATTATCAACCATAGACACCT[G/A]GTGATATTATTTCTTGTGAGCGCACAATACATAGATTACGAGGGAGCGCTTCATTTTTTGTGCATGTTATCATCTTGGGCAGTACAGG
101660 C A ACTCTGATATAAAATACATATTCAAGGTATTTCATTATCAACCATAGACACCTGGTGATATTATTTCTTGTGAGCGCACAATACATAGATTACGAGGGAG[C/A]GCTTCATTTTTTGTGCATGTTATCATCTTGGGCAGTACAGGTAGAAAGTGCGGAAGATGATGAAATGGCTGCTCGATATGACGAGGTT
101660 C A TGTGCATGTTATCATCTTGGGCAGTACAGGTAGAAAGTGCGGAAGATGATGAAATGGCTGCTCGATATGACGAGGTTCCTAGTTGCACAAGAGCAGGAAC[C/A]GCACCGCCTGCCAATCCTGCGCATGCAGACGAAAAGACAATCACCGGAGGAGCCCCAACGAAATATCGTATCCACATTGGCCCTT
101660 G A CAGTACAGGTAGAAAGTGCGGAAGATGATGAAATGGCTGCTCGATATGACGAGGTTCCTAGTTGCACAAGAGCAGGAACCGCACCGCCTGCCAATCCTGC[G/A]CATGCAGACGAAAAGACAATCACCGGAGGAGCCCCAACGAAATATCGTATCCACATTGGCCCTTTCACATATTTATTTACAATAG
101660 T A ATGACGAGGTTCCTAGTTGCACAAGAGCAGGAACCGCACCGCCTGCCAATCCTGCGCATGCAGACGAAAAGACAATCACCGGAGGAGCCCCAACGAAATA[T/A]CGTATCCACATTGGCCCTTTCACATATTTATTTACAATAGGCATAGCATGATTAAATCCAACAAACACGCATGCTATTCCACCAATT
101660 A G GCATAGCATGATTAAATCCAACAAACACGCATGCTATTCCACCAATTCCAGAGGCAATCATTGATGAGCTATCTCTTATAAAAGGCGAAATAGTCCAACT[A/G]CTTGTTTTCATGTCTTTGGAAAGAGGAGCTGCACAATGATGACAAATTGATGGGTTAGACTGCTGATCTGCCATGTCCACCAATCTAA
101660 G A AATCTAACAAGAAACTCGTTTATTATTCTCTCTTTATCGTTGTTTCTGGACAAGGCAGGTCATACGAGTTTGGGTACTCAAAGTCAACTGCAAAACCAAG[G/A]CTCCTTTGCTCAGCACCGAGAAAAGCTTTGGTTGTCGCAATAACTTGGTCGAGAGGTTCGGGTGCTACTGCAGTTCTG
101664 T C AACCTGTACTCGTCCACGAGATGTGGGATTAAATGTTTCCACACGGATTGGTCCGTGCCGAAACCGTGGGCGAGGACTATGACTTGATCGCCATGGCCGA[T/C]CACTCTGATGTTGTGAGCGTCCTCGAGGACACCCATTTTTTTCTATTTTAGGTTTATGCTAAATTTTTGTGGGTA
101668 C T AGGCCTTAAGATAATCAAATTTCTACATTAAATATGGCATCACTGCCCATCCAAACATTTTCAGTGTCTAAAACGTTTTTCCAGCAAAAAAGCAGCAACA[C/T]AGAAGATTTTCCGATTTAATGCTCTGTATAGAGTCCCATAAATTTCTACTTGTCCTCTGGTTTTATCAAGATTCAATGCACTCCTCATACA
101668 C T ACATTTTCAGTGTCTAAAACGTTTTTCCAGCAAAAAAGCAGCAACACAGAAGATTTTCCGATTTAATGCTCTGTATAGAGTCCCATAAATTTCTACTTGT[C/T]CTCTGGTTTTATCAAGATTCAATGCACTCCTCATACACTTCACCATCTCTAAGATGAACGGCTAGATTTGCTTGAGCATCAGCATCAGAG
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101670 C A CAACTCAGTCGTTAATGGTGGACTCAATGCACTGTGAATCCCCTCACTTTCGAGTGCCGCCTAAATTCAAAGATCCAACGTATGCTGACTTACCAGTTCC[C/A]GATGCCGGAGTTTCCAACTGGCACATAAAGGGAAAGCGAAAAATACCCGATTTGCCGAAAAACCCTTCATATTTCACCGAAGACAACA
101670 T C CCGGAGTTTCCAACTGGCACATAAAGGGAAAGCGAAAAATACCCGATTTGCCGAAAAACCCTTCATATTTCACCGAAGACAACATATTTTCGGATTCATT[T/C]AGAAGAAACAGCATCAAACTACGAAGAATGCTTGCTTTCCACAGGCAAGGAGGCATTTACAACAACTACTCTCCATCATCAGATGAC
101670 T C ACAACAACTACTCTCCATCATCAGATGACGGTCTCCTTCCATACAGCGACATGGCCCCTACATTGATAGATGTGGTGGTGGAGGTTCAGAAGCAAAGCCA[T/C]ACAGGAGAGCACGTGCCCTGGGTCTCCCTTTCGAGCAAGGGCAATCGTGGAAAACCGATTCTTGGGCACCCCATTCAGGTAGAGGT
101674 AT A AAATTTGCGAAAATCAAGCGTAACGTTTTCTGTCTCTTTCTTACCATGCCCAGATCTCCACTCCTACGCAGTACGCGTGATCTTCCCTTCTCTCGATTTT[AT/A]TTTTTCTAACCTAATTTCAGTTACGTCTATGGGATATTGCTCCTTTTCTGCCGGCCCATCCTATTTCTCCTTCTTCCTAAGCCCAAATACGA
101678 G A CGTTGCGGCTAGCGAGGCAGGATATTACCGCGTCGATCGGACGGGAGAGAGTGGAGAGTGTTTGGGTTAGGGTTTCGAGGTTGGTTACGTCGGAGAAGAG[G/A]ACGGTGGATCCGGAAAGCTGGGACTGGGTTTGGGACTTGTCGTTGCGGCCACGGATGCCGCTCCGCTCGCGGGCGACAGAG
101678 A G CGTGGAATCCGCGGGAGACGAGCTCAGAGACGACGAACTTGCCGATGTATCCTGTGGGGCCCACCACCATGACGGTGATGTCTTTTGGAAGCATCGATTT[A/G]AAGGATGGGGTTGGAATAGACAATGTGTTCGACTCTGGTGCTTGGTTTTGGGCTGTGGTGCAGGAAAGTTTGAGGGCCTTCCTG
101684 G A TGTCTTGGACACAGAGAGTAAAAATTGCTGTTGGAGCAGCTAAAGGACTTGAATACCTGCATGAGAAAGCACAACCTCGCCTCATACATCGTGACATCAA[G/A]TCCAGCAATGTTCTTCTATTTGACGACGATGTTGCAAAAATTGCAGATTTTGACCTTTCAAACCAGGCTCCTGATGCAGCTGCACGA
101690 G A AATATCTTTAGTGGATTGAACTTGCAACCTGGATCGAAAAGGAAGTGCATCATCGATACTGATATGCAATGCGAAGCTGCTCCTGCTACAACGGTTGAGA[G/A]TAATTCCATTGATTTGATGAAGACTAAGAGAGCCAGATACTCCCTCTCCCCTAATACCAGCTCTTCTGAGGCGTTTGCAACAGATGA
101690 T A AGTGGATTGAACTTGCAACCTGGATCGAAAAGGAAGTGCATCATCGATACTGATATGCAATGCGAAGCTGCTCCTGCTACAACGGTTGAGAGTAATTCCA[T/A]TGATTTGATGAAGACTAAGAGAGCCAGATACTCCCTCTCCCCTAATACCAGCTCTTCTGAGGCGTTTGCAACAGATGACACTGCATT
101694 A G CATGCCCTAATTTTGGCTTTGAACATACTGATTAGTGGCAGAGAAGACTCGTCATCTTTGAGCATTCAATAACGGGTGGAAAGATAGCGATTTGGGAAGC[A/G]AATTGATTTTGATCAAGTCAAAGGAAATACGTCGGGTTTTCCATTGAAATCGACAGAAGCGAGCGCCCCAACATCTGGCAAGGTGG
101698 CG C TGTTGGCCTACTGGAATTACTTTCCTCACAGAACGCACCAATCTCGACCTGCTAAGATCTAATGGCATCCTCGCACCCAA[CG/C]GGCCGGGGGCCACCACTCACTAGCATTCAGGGTTATGCGACTTTGCCGACCTTCCTTTCACTCTTCGGCCTCCCCTCTCCGTCTCCATCTCTCGGACATC
101698 CG C TGTTGGCCTACTGGAATTACTTTCCTCACAGAACGCACCAATCTCGACCTGCTAAGATCTAATGGCATCCTCGCACCCAACGGC[CG/C]GGGGGCCACCACTCACTAGCATTCAGGGTTATGCGACTTTGCCGACCTTCCTTTCACTCTTCGGCCTCCCCTCTCCGTCTCCATCTCTCGGACATCTTCG
101698 C T CTGGAGGCAGATATGATTTCATTGTGGAACACGATGTGAAGGAGCTTGGAGCTCACACGCTTGTTTGCACTGCTTTATATAATGATGGAGATAGTGAGCG[C/T]AAATATCTTCCTCAGTTTTTTAAATTTGTTGTTGCAAATCCACTCTCCGTGAGAACAAAGGTTCGGTCTGTGAAGGATATTACATTTT
101710 A G TTTACACATTCCGGATTGGCTGCTGCCTAAGGTGACGTCGATCGAAAGGGAGAGGAAGGATGGGAAGCTATGGAAGGAGCTGCAGGAAGGAATCAAACTC[A/G]GCTGGATAATTGTGAACAGGAGATTAGGGCAGGCGGCTAATGTGGCGAGCTGGAGCCCTCTGGGAGGGCAGAGGCACTGGC
101714 G A GAAGGACAAGCAAGCATTTCTCAAGAAGCTTCACAGCCTCTTCATAGGTAAGATCCTCGCGCCATTCGGAGCGAAGAATCGGTCTAGCGAGATGGTTTCC[G/A]AAACCAGTAGCCACGTGATTATCTTCAAAATGAGTGCCAATCATGGTTACCACGCCAAGATACTTCTGCCCATTTTTTACTCCACCAA
101714 C T GTTTACCAATGTGTTTAATTCGCTCCACACTTTTGTAGCGCAATGTAGAACCATAGGAACCTCCCATGTCCGCAGCCAAGATGACTCCATCTTTGTATTT[C/T]ATACCAATAACAGATGTACCAGTGACATAAGGAGATAGTGTCCTCTCCGATCGCCCTTCCGAAATAGCCGTGACAGCACTCGACATAGA
101714 C G GCCAAGATGACTCCATCTTTGTATTTCATACCAATAACAGATGTACCAGTGACATAAGGAGATAGTGTCCTCTCCGATCGCCCTTCCGAAATAGCCGTGA[C/G]AGCACTCGACATAGAAGATCCAAACCGTATTCAAGCGGTGAGAAAATCGAGTAGGGTTGATAGGACAATACTTAAAAGTAAACTAG
101718 T C AATCATTGAATGCCTATCTTCAAAGCTCGCCGTGGCCATAATTTGTATCAGGAAAAAACATATTCTTTATGACATGAAGCAACCCGTCTAAATCTCGAGC[T/C]CCAACTTCCATGATATCCTTTAGTAGTCCACCCTCCATTAATTCATGCTGAAATATTAATATTGTTTCATGCAGTGGTCCCTTCCTATTAA
101718 T C AAAACATATTCTTTATGACATGAAGCAACCCGTCTAAATCTCGAGCTCCAACTTCCATGATATCCTTTAGTAGTCCACCCTCCATTAATTCATGCTGAAA[T/C]ATTAATATTGTTTCATGCAGTGGTCCCTTCCTATTAAAAAAGGCAAGCATGCTTTTAAACCAGGAATTAGTCAGTTCAGCAACAAACTCA
101718 A C AATATTGTTTCATGCAGTGGTCCCTTCCTATTAAAAAAGGCAAGCATGCTTTTAAACCAGGAATTAGTCAGTTCAGCAACAAACTCAAAGTTCTTAATAA[A/C]CCAGCGAGTCCGATCGAATCCCGATTCTAAATCCGAAAACCCCTTCAAAACCTTAAACAGACGGACACCATTTCGTCTGATCTCAGTCA
101718 T C TATTAAAAAAGGCAAGCATGCTTTTAAACCAGGAATTAGTCAGTTCAGCAACAAACTCAAAGTTCTTAATAAACCAGCGAGTCCGATCGAATCCCGATTC[T/C]AAATCCGAAAACCCCTTCAAAACCTTAAACAGACGGACACCATTTCGTCTGATCTCAGTCATCGATCTTCCTCCTCCAATCACGTAATT
101718 T C TCGATCTTCCTCCTCCAATCACGTAATTCCACGCGAAGTCCCATCCAACGGTAAATAACCCTGTACCACCAGTGAGTTTCCTAAACTTCTCGGCTAGCTC[T/C]CGAGCGCGTTCAGCTCCGACAAAGTCGCCGCGAGATTCCCGGGCGGAGGCAACGCGATTAAGAAGAGCATCGGTTAAGGAGATTAGG
GCTGTTATCATCAGAAGCATCTTTTGGCCGTTGTAT
101720 G TCTTCTCTTTATCAGGAGGTCTAAATCTGTTGAACTTCTTGTTAAGTGAAGAGGTAGAAGCAGCTGTCGCGTTGTGCAAAAGATAGAGAACTTCATTGCA[GCTGTTATCATCAGAAGCATCTTTTGGCCGTTGTAT/G]CTGTTATCATCAGAAGCATCTTTTGGCCGTTGTATCTTCCAAGCAGCGTAGTTG
101730 A G GTGGAGATATTGAAGGAGGTGCTGGAAATGGCGGGGGAGGAGAGGGTGGAGACGGAGATGGAGAAGGGGGAGGTGAAGATGGGGATCGAGGAGGGGATAA[A/G]GAAGGAGGATAGTTGGAAGGGGTTTTTCGCAAAAGGGAAGGATTTGGTTGGGTACACGGTTAACGGGTTGAGGAGTTA
101742 C T CCGACCTCCGATTCGGCGTCCTCTTCTCCACCTCCGACGCCTCCTCCTCCGACGTCGGCTGCGTCGCCGAAATCGTCAAGCACGAGAAGCTCTCCGACGA[C/T]CGTTTCTTCCTCATCGCCAAAGGGCAAGAGCGGTTCCGCATCAACCGCGTCCAGCGTACGAAACCCTACTTGGTTGCCGACGTCTCA
101744 A G CGCCATCTTCTTCATCGCTGACGCTCTCGCTCGAGCAGCGATCTGATTCACCATGCACTTCTTCATCAGAAGAGCCAAGGACAAGATAAGGCATCGAGCC[A/G]AAAGCCCTAGCAAGCCTACATGCAATGTGGCCTTCACCATCTCCGTATTCCTCCGCCCTTCTCCTTAATGCCTCGTACATCATTTCAGG
101744 A G ATGCAATGTGGCCTTCACCATCTCCGTATTCCTCCGCCCTTCTCCTTAATGCCTCGTACATCATTTCAGGCTCATGTTGCATGGTCCTCAATACATCCGC[A/G]CTAGCCGGGCCAGATGCAGCCCGTGTCACCGCAAAGCAGTGTGGACCATCGCTCTGCACCACTCTTACCATGCTCGGCCCGCCAAACAG
101744 C T CACCAAGAAACATTCCCAAGTAGTACTTGCCTTCGGTTTCATGAAGTGGTAAGCTATCTTTGCCATTGATGAAGTGGTTGATCTTTCCATCACTGTCGCA[C/T]GTTAAATCCGATAGAATCCCATTCACGTTAGGTTTTTCATCCAAGTGGTGAATCGGAAGAATCGGAAAGAGCTGCCGTATAGCCCAAA
101744 A G GCTATCTTTGCCATTGATGAAGTGGTTGATCTTTCCATCACTGTCGCACGTTAAATCCGATAGAATCCCATTCACGTTAGGTTTTTCATCCAAGTGGTGA[A/G]TCGGAAGAATCGGAAAGAGCTGCCGTATAGCCCAAAAGTCAGGAACAGAAGTGAAGATGGATAAGTTTATGTTGTAGGTTGTGACTG
101746 G GC TCCTTACCCTCCTCAGCACCTTTCCTGTTAATTACGCTCAGCGCCATGCCATCCTCCGTCGACGACGAGTTTTTCGAGTACAACCCTCATCCCTACAAAG[G/GC]CGGTTATGACATCGCCCTCACCTACGGCCAACCCCTCCCGCCTTCCCCATCCACCTGCTACCCCATCTCTCATCCTTCCACTCCAACTCC
101750 G C ATTATCGTAAAAATCTTGTTAGTATCAGAAGAATGCCGTCTCAGAAGCGACCGTTGTCGGAAGACGACCAATCGCCACCGCCGCAGGTGAAGGAGGACAT[G/C]GAAGAAGAGATTGTGGAGCAGAAGCCGCAGAAGCTGAAGCTAGACTCTCCGAAAAAGGAGGAAGATTCGGGCGCTGATGACGA
101750 A T GAAGAGATTGTGGAGCAGAAGCCGCAGAAGCTGAAGCTAGACTCTCCGAAAAAGGAGGAAGATTCGGGCGCTGATGACGACGAAGGTGAAGAAAGCGGGC[A/T]CGAGAAAGATGAATTTGTCTTTGTGAAATTAGCAGATATACGGAAAGAAGTGCAGTGCCCAATTTGCTTAGGGATAATCCGCA
101750 A G AGCTAGACTCTCCGAAAAAGGAGGAAGATTCGGGCGCTGATGACGACGAAGGTGAAGAAAGCGGGCACGAGAAAGATGAATTTGTCTTTGTGAAATTAGC[A/G]GATATACGGAAAGAAGTGCAGTGCCCAATTTGCTTAGGGATAATCCGCAAAACAAGGACAGTTATGGAATGCCTACATCGTTTT
101750 A G AGATATACGGAAAGAAGTGCAGTGCCCAATTTGCTTAGGGATAATCCGCAAAACAAGGACAGTTATGGAATGCCTACATCGTTTTTGCAGAGAATGCATT[A/G]ATAAGTCTATGCGGCTTGGAAATAATGAATGCCCTGCATGTCGAACTCACTGTCCAAGTAGGCGTTCATTAAGGGATGATCCAAAT
101750 T C GGAAAGAAGTGCAGTGCCCAATTTGCTTAGGGATAATCCGCAAAACAAGGACAGTTATGGAATGCCTACATCGTTTTTGCAGAGAATGCATTAATAAGTC[T/C]ATGCGGCTTGGAAATAATGAATGCCCTGCATGTCGAACTCACTGTCCAAGTAGGCGTTCATTAAGGGATGATCCAAATTATGATGC
101766 G A ACGATGCAGGTGATAACGACGACGAAGATGGCGGCAATGATGAAAGGCCAAGCCAGTCAAACATTCCTTTGACTGTTAGTGTTAATAAAGGTCAAGGTCC[G/A]AGTCTGGAGTTCCATTGCACTGCCTATCCTGATGAACTTGTGATTGATGCTATGTCTGTTAGAGAAACACCTAGTGATGAGGAAAT
101766 T C CAAGCCAGTCAAACATTCCTTTGACTGTTAGTGTTAATAAAGGTCAAGGTCCGAGTCTGGAGTTCCATTGCACTGCCTATCCTGATGAACTTGTGATTGA[T/C]GCTATGTCTGTTAGAGAAACACCTAGTGATGAGGAAATGCTTTCATACGAAGGACCCGACTTCAGTGACCTGGACGAAAACCTCCAG
101766 C T GCACTGCCTATCCTGATGAACTTGTGATTGATGCTATGTCTGTTAGAGAAACACCTAGTGATGAGGAAATGCTTTCATACGAAGGACCCGACTTCAGTGA[C/T]CTGGACGAAAACCTCCAGAAAGCTTTTCACAAATATCTTGAGATTAGAGGCATCTCTGCCATCACTACTAATTTCTTGCACGAGTATA
101770 A G GACAAACCCGTAAAAAGGTACAAATCCGATTCCGACCGTCTCCCCTTCATTAAAATCTCCTCCGACACCCGAAACTTCCCATACAAGCATCGCAAAGGCG[A/G]CCGCTCCGCCATCCGCCTCTCCCGAATCGTCTCCGAAACATTCCGCCTCGACCTTCCCAACGTCAGATGGTTCGTCATGGGCGACGAC
101770 C A CATCATATTCTCCTACAACATGGCATACGGCGGCGGCGGTTTCGCCATCAGCGCCCCGCTTGCCTCTTCCCTCTCGAAAATCCAAGACGGATGCCTTTCC[C/A]GGTACCCCGCTTTGTACGGAAGCGACGACAGAATCCACGCGTGCATGGCCGAATTGGGGGTTCCCTTAACAAAGCATCAAGGGTTTC
101770 C T ACGGCGGCGGCGGTTTCGCCATCAGCGCCCCGCTTGCCTCTTCCCTCTCGAAAATCCAAGACGGATGCCTTTCCCGGTACCCCGCTTTGTACGGAAGCGA[C/T]GACAGAATCCACGCGTGCATGGCCGAATTGGGGGTTCCCTTAACAAAGCATCAAGGGTTTCACCAATATGACGTGTACGGAGATCT
101770 A G GCCTTTCCCGGTACCCCGCTTTGTACGGAAGCGACGACAGAATCCACGCGTGCATGGCCGAATTGGGGGTTCCCTTAACAAAGCATCAAGGGTTTCACCA[A/G]TATGACGTGTACGGAGATCTGCTAGGTCTCCTTGCGTCGCATCCTGTGACGCCGTTGATATCTCTGCATCATCTGGATGTGGTGAA
101772 T C CGACTCATGCACAACAAACACAATCAAATCCACCTCCACCGCCAAAAACTCCGGCCTCCGCCTGCGTTGAAGTAGGCAAGTTTGGACTAGAAGAAGAGAT[T/C]GAGCAGCTCAAACGGGACAAAAACATACTAATGCAAGAACTTGTCCGACTCAGACAACAGCAGCAAACAAGCGACCACCAACTGA
101772 TA T AGCAAATGATGTCTTTCCTAGCCAAAGCCATGCAAAGCCCTGGTTTCTTAGCTCAACTAGTGCAGCAAACAGATCCAAGCAGAAGACTAACCGTAGGCAA[TA/T]AAAAAACGAAGGTATCCTAAACAAGACCAAGCAGCAAACGGCAATAGCTCATCATCATCCTCGTCATCATCAGCGGCGCCTGATG
101780 CA C GCTATGGCATCTGATCCAGTAGAAATAAAATTTGATAAACCAGGAAAATGGGTTGCACCATATCCAAAATATGAATCCAATTGGTGGGAAACCTTTTCAC[CA/C]AAAAAGAACAAGCAAAGTTGAAGGATAAATCGCGATTTTCGGCTCTTTGAAGTCCATGTTACTACTTGTACAATATGCAGTAAACTA
101784 C G TGATGTGAAACTACTGAGGGAGAAATGTTCCAATGTGAAGGAAAATAAGGATATAGCTCAGAACGTTTTAGAAGAAGACATGCAAATGCAAGTTAGACTT[C/G]AAATTGTGTATGGAAGATTGAGCATTCGTTCAGTTCGAAGTGCCTTTGAAGAATCTGTGGGAAGCAGAATAAAAAAGTTTAATGG
101790 A G AAACTGCAAGTTTAAGTGGAGCTAACAGCAATATTCCGCAACCTACATTTAACTTAAGCAACCTTATATCTAGCTTCCAAGCCCAAGGACTCTCTGCTAA[A/G]GAAATGGTTGCTCTTAGTGGTGCACATACCATTGGCCAAGCAAGGTGCACAAGCTTCAGAGGGCACGTGTACAATGACAACGACATA
101790 A G ACAGCAATATTCCGCAACCTACATTTAACTTAAGCAACCTTATATCTAGCTTCCAAGCCCAAGGACTCTCTGCTAAAGAAATGGTTGCTCTTAGTGGTGC[A/G]CATACCATTGGCCAAGCAAGGTGCACAAGCTTCAGAGGGCACGTGTACAATGACAACGACATAGACAGTTCATTTGCAAAGATGAGA
101790 G A CATTTAACTTAAGCAACCTTATATCTAGCTTCCAAGCCCAAGGACTCTCTGCTAAAGAAATGGTTGCTCTTAGTGGTGCACATACCATTGGCCAAGCAAG[G/A]TGCACAAGCTTCAGAGGGCACGTGTACAATGACAACGACATAGACAGTTCATTTGCAAAGATGAGACAGTCAAACTGTCCAAGCAGT
101790 C A CCCAAGGACTCTCTGCTAAAGAAATGGTTGCTCTTAGTGGTGCACATACCATTGGCCAAGCAAGGTGCACAAGCTTCAGAGGGCACGTGTACAATGACAA[C/A]GACATAGACAGTTCATTTGCAAAGATGAGACAGTCAAACTGTCCAAGCAGTTCAGGCTCTGGGGATAACAATCTGGCACCGTTGG
101790 A G TAGACAGTTCATTTGCAAAGATGAGACAGTCAAACTGTCCAAGCAGTTCAGGCTCTGGGGATAACAATCTGGCACCGTTGGATCTCCAATCTGCAACTGG[A/G]TTCGACAACAAATATTACCAAAACCTGGTGAATAAGAAGGGCCTGCTTCATTCCGATCAAGAACTGTTCAATGGAGGATCAACAAA
101790 C T CTGGGGATAACAATCTGGCACCGTTGGATCTCCAATCTGCAACTGGATTCGACAACAAATATTACCAAAACCTGGTGAATAAGAAGGGCCTGCTTCATTC[C/T]GATCAAGAACTGTTCAATGGAGGATCAACAAATTCCATGGTTATGGGTTACAGTACAAATCCATCTACTTTTAGCTCTGACTTCGTGG
101790 C T CTGCAACTGGATTCGACAACAAATATTACCAAAACCTGGTGAATAAGAAGGGCCTGCTTCATTCCGATCAAGAACTGTTCAATGGAGGATCAACAAATTC[C/T]ATGGTTATGGGTTACAGTACAAATCCATCTACTTTTAGCTCTGACTTCGTGGCTGCAATGATCAAGATGGGAGACATTAGTCCACTTA
101790 C T CAACAAATTCCATGGTTATGGGTTACAGTACAAATCCATCTACTTTTAGCTCTGACTTCGTGGCTGCAATGATCAAGATGGGAGACATTAGTCCACTTAC[C/T]GGCTCTAATGGCGAGATCAGAAAAAACTGCAGAAAAACTAATTAGCCAGTTTTAATCGTTTTTGCAATTGAATGTCCGCAAGTTTTGTC
101790 C T TGGTTATGGGTTACAGTACAAATCCATCTACTTTTAGCTCTGACTTCGTGGCTGCAATGATCAAGATGGGAGACATTAGTCCACTTACCGGCTCTAATGG[C/T]GAGATCAGAAAAAACTGCAGAAAAACTAATTAGCCAGTTTTAATCGTTTTTGCAATTGAATGTCCGCAAGTTTTGTCCCTTCCAATAAA
101790 A G ACAGTACAAATCCATCTACTTTTAGCTCTGACTTCGTGGCTGCAATGATCAAGATGGGAGACATTAGTCCACTTACCGGCTCTAATGGCGAGATCAGAAA[A/G]AACTGCAGAAAAACTAATTAGCCAGTTTTAATCGTTTTTGCAATTGAATGTCCGCAAGTTTTGTCCCTTCCAATAAACGTCGTTTTTCA
101790 GA G AATCCATCTACTTTTAGCTCTGACTTCGTGGCTGCAATGATCAAGATGGGAGACATTAGTCCACTTACCGGCTCTAATGGCGAGATCAGAAAAAACTGCA[GA/G]AAAAACTAATTAGCCAGTTTTAATCGTTTTTGCAATTGAATGTCCGCAAGTTTTGTCCCTTCCAATAAACGTCGTTTTTCATTGCTCG
101790 C T ATGGGAGACATTAGTCCACTTACCGGCTCTAATGGCGAGATCAGAAAAAACTGCAGAAAAACTAATTAGCCAGTTTTAATCGTTTTTGCAATTGAATGTC[C/T]GCAAGTTTTGTCCCTTCCAATAAACGTCGTTTTTCATTGCTCGATCAGTGCACTCAGTTGTCCCTTTTCTTTCCTTCTTAATTGATTTGTA
101800 TA T AAAATACGAGTTGTTTTTATTTTCAGTCAAAGGAAAACTATCCCCAGGTTGCTTAACATGATGGCATATTTCACGTGCTTTATTCAAATTATCTTTAAAA[TA/T]AAAAAAAGTCACTTCACTACTTTTTCTGAAGGATGACCCAACCTATTATGCCAAATTCCAATGAAGACATGCTTGCAACTGTAATAACTT
101800 C CG CTCTGTGCAGTACCCGCACGCCTTCACCGAGTACTTCCTCATCAACTGTCTCGCACCACTTCGCACTCTACTGTATGCTTTTATGGTTCTCTCTGCCAAT[C/CG]TTTTTATGTCCATCAGTGGTGGTGACAGGGGCGAATGCCTGGTAACAGCCGTAGGGTCATACTGTGAAATTAGGGGTTCAATATCGGA
101808 G A TATCAGCACGTCCAAACACACCACCGTGTCGTACTTGCCTTCCAGGCCCTCCAGATCCTTCACTTCGAACGTGGGGAAGACCGAATCGGGATTTTTCAAG[G/A]CGTTCTCTGCCTTGGATCTGGCTTCCGAGACCATGGCTTCGGAGATGTCGGAGGCGGTGACGACTGCGCCCTCCTGGGCGAGGGGG
101808 T C CCTGGGCGAGGGGGATGGCCAGGCTGCCGGTGCCGCACCCGGCGTCGCAGACGGTGACGCCGGAGAGGGGGCGGTCGTCTTTCAGCATCTGGATGGCGTT[T/C]TCGACTGTTTTGGAGTGGCCCAGGCGGATGTCGAGCTGGACGGTGTTGACGTCTTCGGTGGAGTCGCCGTAGATTTTGCGCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101808 G C TGCCGGTGCCGCACCCGGCGTCGCAGACGGTGACGCCGGAGAGGGGGCGGTCGTCTTTCAGCATCTGGATGGCGTTTTCGACTGTTTTGGAGTGGCCCAG[G/C]CGGATGTCGAGCTGGACGGTGTTGACGTCTTCGGTGGAGTCGCCGTAGATTTTGCGCCAGCGTTGGTAGCCGGTGTTGTTGAA
101808 C G GGCCCAGGCGGATGTCGAGCTGGACGGTGTTGACGTCTTCGGTGGAGTCGCCGTAGATTTTGCGCCAGCGTTGGTAGCCGGTGTTGTTGAAGTAGTTGCG[C/G]ACGACTTCTTTGTCGTCCAGGCCGCCGAGGTCTTGGGACTGCTGCTGACGGCGGCGTTCTGGGTCGGTGAAGGAGATGGCCGC
101808 G C AGTTGCGCACGACTTCTTTGTCGTCCAGGCCGCCGAGGTCTTGGGACTGCTGCTGACGGCGGCGTTCTGGGTCGGTGAAGGAGATGGCCGCGGCAATGGC[G/C]GCGAAGGAGGTGACGGCGATGGCGGAAGTAGGGAGGTCGGTGGGTAGAGCGGAGGTTTTGATTGAGGACCTGCGAGAAGTG
101814 G T TCTCAAATGCAGCAATGGGCATCACAAAATGGTGATTAGGAGGATTGCACAAGCCACCAGCATCAGCCTCCATTCCAAAGTTAGGCGCGCAGTAATTAGT[G/T]GCAGTAACAGTAATACTAGTGCCAGGGATACAGTACTTCAACTCATCTACACATCTAACTTCATAACAACCACCACAGGCTTGACCT
101816 A G TGAAAGAGATACTGGGTGATAAGGTTGAGAAGGTGGTGGTTTCGGACAGGATAGTGGACTCTCCATGCTGTTTAGTGACCGGAGAGTATGGATGGACCGC[A/G]AACATGGAGAGGATAATGAAGGCGCAGGCTTTGAGGGACAGCAGCATGAGCTCGTACATGTCGAGCAAGAAAACGATGGAGA
101818 C A ATCTGAAAATCTTGGGAAGATGCTTGCTCCTTTTTCTCCAAACCAAGGGGTTCTTTCATTCAAGTTTTCTCCGGTCCCTTATCCATCTCAGTATCAAATG[C/A]AGCAATTAGCCAATGCATCTAGTCAGCAGGTACAACTGCAGCATCAACCTCATTTCTTAATCAATAGCCAGATGCAACATCAACAACTAC
101818 A G ACTGTTTTGGCAAGCTCATATAGCACAGTTCAGACAAATTGGGATGCATCATAGCACTTCATCTTCTGCTGCCACCTTAGCCAATAATAGCCAGCCTTCT[A/G]TATTCTCCCTCGTGCCAAATTTCAATCCTCACGTTCATCAACAATTTGTACCCTTGCCTTCTTCTTCACTGTCATCGAGATTGAAGCAGAA
101818 C T AAGATAAGTAATGCAGAGAGTTATAGTATATAGCCCTTGGTGAGATGAAAACCCAAAATTTGAAGCTGATGCTAAACCAGAGGATGAAACAGCTGCATCA[C/T]GGGAATGCGGAAGGCCTGCAAAGCCAAATGGTGAAATGGGTGCGAAGCCGGAAAATGGGGTGGTAGCAACACCAAAATCGAAG
101828 A G GCAGCGGCATTTTGTTTCTATTTCTTGCTAATTCAAGCAATACCTCTCTAGGCGGCGGCTGGGAAAAAGAAAAATTGACCTTTGCCTGAATGGCAAGCCT[A/G]ACATCATCAGGGTCGATGCTAGGCTTGGAGGCATGGTCGGAGTACACCTGAGCGTCGGAAAGGACGTCGTGGACGTAGCGGTAAC
101832 C T AGCCGCAGGTTCCTCTCCCGTAACTGCCCCTGCTACGGCAAAAAGGCCGTGGACATCGAAGAAAAATATTCAGAGCCCAAAAGCCCGGTCAGGCCCAGTG[C/T]CACTAAAGTCGAAAGCCCCGTTTCGGACCACGTAGTGGACGTGACCAAAATCAGGATCTCCACTGGCCTGAACTGGACTAAGGAC
101836 A T ACCATCATCATCAGGCTTTATCCCTAAAGTAGTCCATATGGAACTCTTAGCTGCTTCATCAGGATCATCAATTCTCAATGTTTTCGGCACCCATAAAGAT[A/T]TCTTCTCTGTGGTACCTCCATTGCTATGTATTACTGTTGCTTCATCCCTCGAATGCTTTCCAAGCATGGGAGAATTACTTCCATTATTATCA
101838 C G GATCAGTGTGTCTAAGTCAAGCAAGAGTAAGCAAGCGCCTTCTCCTCCGTGAGTTCTTCAGC[C/G]GTCGCATCCAATTTCTTCCTTGAAAATTCATCAACAGACAGGCCTTGAACAATACTCCATTCACCGTTGCGGCATGTTACTGGGAAAGAGTAGATAAGCC
101838 T C CCATGGAAACCCAAGTGCCCTCTGGAGTTCCTAGCACCCAATCACGAATGTGGTCACAAGCAGAACTGGCTGCAGATAATGCGCTTGAAAGCTTACGAGC[T/C]TTGATAATTGCAGCACCTCGTTGTTGAACAGTTGTGATGAACTCTCCTCTTAGCCAGTCATCATCACCAACAAGTTCACGAACAGGT
101838 A G AGACATTCTTTGACATTACATCTTTCCTCTCCATCCCTTCTTTTCTTGGAAACCCACCAACCATGACAGCAACATTGACTCCAGTACAAGCCTCAACAAC[A/G]TCAGTGGTTGCAACGACTCCTTTAAGTAGAGGAAATGCTGCATCAACCAATTCCATCTTAACACCATTCAATGCCTC
101842 G T ATTCTCCTCTTCCAAACACCCAAACATTCTCTCCTTCTTCTCCATCAACTTGGATTCAGCCTTAGCCTCAGCCATGAAAGAAACTCTGGACGCCTGTGAA[G/T]ATAAACAAATGGAGGGCGAGATGAAGCATTGTGCCACATCATTAGAATCCATGGTTGACTTCACTACCTCGGTACTTAATACCCACAAC
101842 T A AACATTCTCTCCTTCTTCTCCATCAACTTGGATTCAGCCTTAGCCTCAGCCATGAAAGAAACTCTGGACGCCTGTGAAGATAAACAAATGGAGGGCGAGA[T/A]GAAGCATTGTGCCACATCATTAGAATCCATGGTTGACTTCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAA
101842 C G TCTTCTCCATCAACTTGGATTCAGCCTTAGCCTCAGCCATGAAAGAAACTCTGGACGCCTGTGAAGATAAACAAATGGAGGGCGAGATGAAGCATTGTGC[C/G]ACATCATTAGAATCCATGGTTGACTTCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAA
101842 T C CAGCCTTAGCCTCAGCCATGAAAGAAACTCTGGACGCCTGTGAAGATAAACAAATGGAGGGCGAGATGAAGCATTGTGCCACATCATTAGAATCCATGGT[T/C]GACTTCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAACGCGTCAATTCAAGAGTAT
101842 T C CCTCAGCCATGAAAGAAACTCTGGACGCCTGTGAAGATAAACAAATGGAGGGCGAGATGAAGCATTGTGCCACATCATTAGAATCCATGGTTGACTTCAC[T/C]ACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAACGCGTCAATTCAAGAGTATGAATTGACT
101842 G A CCATGAAAGAAACTCTGGACGCCTGTGAAGATAAACAAATGGAGGGCGAGATGAAGCATTGTGCCACATCATTAGAATCCATGGTTGACTTCACTACCTC[G/A]GTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAACGCGTCAATTCAAGAGTATGAATTGACTTCATCT
101842 A G GAAGCATTGTGCCACATCATTAGAATCCATGGTTGACTTCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAA[A/G]ACGCGTCAATTCAAGAGTATGAATTGACTTCATCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGC
101842 G A GCATTGTGCCACATCATTAGAATCCATGGTTGACTTCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAAC[G/A]CGTCAATTCAAGAGTATGAATTGACTTCATCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATAT
101842 C T TCACTACCTCGGTACTTAATACCCACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAACGCGTCAATTCAAGAGTATGAATTGACTTCATCTTA[C/T]CTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAA
101842 G A ACAACCTAGTTTCCGTATCTACCACAACCGATAAAGAAAACGCGTCAATTCAAGAGTATGAATTGACTTCATCTTACCTTAAATCGTCTGGGGATAACAC[G/A]GTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAACGTGTACGACGTTGAGATGGTG
101842 T A GAGTATGAATTGACTTCATCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGC[T/A]TAAAGGGGTGAACGTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACA
101842 A G TATGAATTGACTTCATCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTA[A/G]AGGGGTGAACGTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAA
101842 C T CTTCATCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAA[C/T]GTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCC
101842 A T TCTTACCTTAAATCGTCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAACGTGT[A/T]CGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGAT
101842 T C TCTGGGGATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAACGTGTACGACGTTGAGATGG[T/C]GGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTTAGCAATGAA
101842 A C GATAACACGGTGGTGTGTCATGCACAAACATATGCATATGCAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAACGTGTACGACGTTGAGATGGTGGGAG[A/C]AGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTTAGCAATGAAGATACTT
101842 G A CAGTGTTTTATTGTCATAAGCTTAAAGGGGTGAACGTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATAC[G/A]GATACATCAAAGTGGAATCCAGATAACTTAGCAATGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGTTTGTCATTTCCTTC
101842 A G TGAACGTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTT[A/G]GCAATGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTA
101842 A T CGTGTACGACGTTGAGATGGTGGGAGAAGATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTTAGCA[A/T]TGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAG
101842 G A ATGGGACTAAAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTTAGCAATGAAGATACTTAATGTGAAACCAGGGAC[G/A]GTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGACGTGCTTCTTTCGATGTGCTAT
101842 T A AAGTGAAGGCAGTGGCTACCTGCCATACGGATACATCAAAGTGGAATCCAGATAACTTAGCAATGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGT[T/A]TGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGACGTGCTTCTTTCGATGTGCTATGTTTATGATT
101842 T A ACTTAGCAATGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGAC[T/A]GACGTGCTTCTTTCGATGTGCTATGTTTATGATTTCCAATTCTATGTGTCATGCGTATGTGATATGCATTAGTTTGCTAATAATGTATGT
101842 C T TAGCAATGAAGATACTTAATGTGAAACCAGGGACGGTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGA[C/T]GTGCTTCTTTCGATGTGCTATGTTTATGATTTCCAATTCTATGTGTCATGCGTATGTGATATGCATTAGTTTGCTAATAATGTATGTGTG
101842 A ATC GGGACGGTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGACGTGCTTCTTTCGATGTGCTATGTTTATG[A/ATC]TTTCCAATTCTATGTGTCATGCGTATGTGATATGCATTAGTTTGCTAATAATGTATGTGTGTATAACACCTGAAAGTTGTATATTTTCT
101842 A T GTTCCAGTTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGACGTGCTTCTTTCGATGTGCTATGTTTATGATTTCC[A/T]ATTCTATGTGTCATGCGTATGTGATATGCATTAGTTTGCTAATAATGTATGTGTGTATAACACCTGAAAGTTGTATATTTTCTGCAATTCA
101842 T C TTTGTCATTTCCTTCCCCAGTATGATGTTTTGTGGATGGCTACTTAGTAGGTGACTGACGTGCTTCTTTCGATGTGCTATGTTTATGATTTCCAATTCTA[T/C]GTGTCATGCGTATGTGATATGCATTAGTTTGCTAATAATGTATGTGTGTATAACACCTGAAAGTTGTATATTTTCTGCAATTCAAAAAAAA
101848 A G ATATATCAAGACAGCCAGCAAATGCAAGCATATCCATTTCAAATCTAAGGTGAATTGACATGAAATGCCCTTGTGAACGGAGCTTATTAACTATCTCTTT[A/G]CTCGTTTTTATTATGTGTGGTTTGAATCTTAGAGCATGATAATTCACCCTACATCTTAATCTCTGAAGTTCAGGCTCATCAATCTCCTCA
101848 C T TTCACCCTACATCTTAATCTCTGAAGTTCAGGCTCATCAATCTCCTCAGCCAGTCTATGAGAAAAAGGAGTAAGATATATAGCACCATGCTCTTTCATCT[C/T]TTCTAAAGCAGTTGTGGTGTACCAGCTTAGAGGGGCATCTCTTGGCGGGCGAATCTGAAAAGCTTTGAACTTCTTCTTCTTTCCTCGTTC
101848 A T GTCTATGAGAAAAAGGAGTAAGATATATAGCACCATGCTCTTTCATCTCTTCTAAAGCAGTTGTGGTGTACCAGCTTAGAGGGGCATCTCTTGGCGGGCG[A/T]ATCTGAAAAGCTTTGAACTTCTTCTTCTTTCCTCGTTCATAAACTTCAGGAAGTTTCTCCACAACATTGACATCATATTTCAAGGATTT
101848 C T CAGCTTAGAGGGGCATCTCTTGGCGGGCGAATCTGAAAAGCTTTGAACTTCTTCTTCTTTCCTCGTTCATAAACTTCAGGAAGTTTCTCCACAACATTGA[C/T]ATCATATTTCAAGGATTTGATGAAATGTTCAACATCATAGATTCCTGGAAAACCACTGACATCATGCCAGTAAGAATTAGTGTCTAACT
101874 C A CCCAAGTCATATCCTCTCTCACTACTTCCTTACGTTTCGATGGAGCCATCAATGTTGATGTCACTGAATTCCAAACCAATCTGGTTCCTTACCCGAGGAT[C/A]CACTTTATGCTTTCCTCGTATGCTCCTGTGATCTCGGCGGAGAAGGCCTATCATGAGCAACTGTCAGTGCCTGAGATTACCAGTGCTGTG
101874 T G CTTCCTTACGTTTCGATGGAGCCATCAATGTTGATGTCACTGAATTCCAAACCAATCTGGTTCCTTACCCGAGGATCCACTTTATGCTTTCCTCGTATGC[T/G]CCTGTGATCTCGGCGGAGAAGGCCTATCATGAGCAACTGTCAGTGCCTGAGATTACCAGTGCTGTGTTTGAGCCTTCAAGCATGATGG
101874 TA T GGACCTTGCTGCCTTGGAAAAAGATTACGAGGAAGTCGGTGCTGAGGGTCAAGATGACGACGTCGATGAAGGAGAAGATTATTGATATCCCGAAAGAATA[TA/T]AAAAAAAATCTTTTATTGTGGTTTGCACTTTTGATTCGGTTATGTTTATGTTTAGCTGCTTATAAGGCATGCATGATATCGTAGTC
101884 T C AAGAGGATGAAGATGACGATGAGGAAGATGAGAATGCAATGTCATCTGTTCTTGCGCCAAAGCAAAAGATTGGTGTAAAGGATGAAGCGGTTGATAATAG[T/C]CCTTCGAAAACGTCACCTGCTGGTTCTTCTCGTGCTACTCCATCAAGCACGAAGTCCAAACTAAAGAAGAGGCCTACCCCTGAAG
101890 G A GCTGAGCAGCACCAAGACCAGCCATCCAGCCATCCATAATTGCAGTTGACAAAAGTTCCAGCTGCCCCGTTGTGCCACCAGTTTCGTCACCGCCAGTCAC[G/A]GAAAGAAACTCAAAATTTTCTGCAAGCCATGATCGTATTTGGCGTTGAAGCTCGCCAGCCGGTGTGTGAACAAATAGGGCAGCTAG
101890 T G CACCAGTTTCGTCACCGCCAGTCACGGAAAGAAACTCAAAATTTTCTGCAAGCCATGATCGTATTTGGCGTTGAAGCTCGCCAGCCGGTGTGTGAACAAA[T/G]AGGGCAGCTAGAGATTTATTGCCAATAGCATATGCTTTTGCTTCTTCCGTGATTTCTCTAAGTTTTCCACCAGTTACATGTTGCCTCCA
101890 C T TCAAAATTTTCTGCAAGCCATGATCGTATTTGGCGTTGAAGCTCGCCAGCCGGTGTGTGAACAAATAGGGCAGCTAGAGATTTATTGCCAATAGCATATG[C/T]TTTTGCTTCTTCCGTGATTTCTCTAAGTTTTCCACCAGTTACATGTTGCCTCCAGGTCTCCTGCTCAACCCCGCGAAGCTTCAGCACAA
101896 A G ACTACTGAAAGCATGAGAAGGAAGGAGGCAGGGTTGTCTGCAAAGAGAGCGGAGCAGAGATCGGTGAAGATGGCAGTGCTGAGACCAACGTAGCCTTTCA[A/G]AATTCCCGAAACTGGTCCACGGTTACGGCGAAAGTTACGCATGCAAGTCACGAGTACGGCTGTGTTCATCCATGTTGTGCTGT
101896 A G GTGCTGTTTCCGCCCATACATAGGAAAATGCACATCTGCCAGTACGGCAAAGGGGATATGGACTGCCGCACAACAAGCCATTGAGCTCCATAGCCAACCA[A/G]ACCCTCAATAGACCCAATCAGCAAAATCACCGGAGTCGGAAATCGATCAGAAGCAAGTCCGGCAAGAACGCCAAACGCTTTTCCG
101902 T TC TGCCAAATTGAACATTCATCTCTTGTTACCAAGACTCTGCACTGATTCAAAGTATTGCTTCCAGTTGTCTCAGATCAGAGTCTGAATTCTCAACCTGACT[T/TC]CTTCTTCATAGCTTGGATTTCTATACGCATTTGCAATTGCCTTCCCTTTATCCAAAACAGGCGTTGGCACAGTTTGCAAGAGGCTATCAA
101902 T C CTCTTGTTACCAAGACTCTGCACTGATTCAAAGTATTGCTTCCAGTTGTCTCAGATCAGAGTCTGAATTCTCAACCTGACTTCTTCTTCATAGCTTGGAT[T/C]TCTATACGCATTTGCAATTGCCTTCCCTTTATCCAAAACAGGCGTTGGCACAGTTTGCAAGAGGCTATCAATTGCACTTAAAGCTACAGTG
101904 T C TTTCGCATCTTCTAGCTGGTGCCATGGCGTCGCCAACGCCGAGTCCGCGTGGCGGTCCGATGGTGGCTGTGCCGGTTGTGGCTGTTCCTTGCTTTTTGAC[T/C]CCAGTGACGAATTTGCAGACGCCTAATTTTACTGGTCAGTTTGCTATGACGCATCAAGCTGTTTTGGCTTCAGTTACAGCTCAAGCTC
101910 T A ATTCATATTGAAAAGTGAACCACGGTAAGGTTGCTTCTATTTCCCCAGAGACTGAAAGCATGGATTGACATGACCAAAATTGCTAGAGGCATAAGAATAA[T/A]ATCCCATCACAATCGAAATAACCAACACGACCTCCCTTCAGCCATTGTAATTCACTTTCTGATTTGGTGCGCTCTGATTTTGTTGCTGC
101918 C T ACCCCGACCGCAACCGGTTCCCGGGCTCCGACGAAGCATTTCGAGCGTTGACCGATGCATTCAGCGTCATGTCGGATCCAGTCAGAAGATCCGAAGTTGA[C/T]TCGATTTTCGCAGGGTTTTCAGGGCAAGAAGGCACATTCTGGACCGTCTGTAAGTTTTGCCTACACGCACATCTTTACAGTCGTGCG
101918 A T GCGTCATGTCGGATCCAGTCAGAAGATCCGAAGTTGACTCGATTTTCGCAGGGTTTTCAGGGCAAGAAGGCACATTCTGGACCGTCTGTAAGTTTTGCCT[A/T]CACGCACATCTTTACAGTCGTGCGTACATGAATCAAATGCTCAAATGCCAGAATTGTAAGAAGGCATTTGAGGCCACAGAGGTGGG
101918 A T CGAAGTTGACTCGATTTTCGCAGGGTTTTCAGGGCAAGAAGGCACATTCTGGACCGTCTGTAAGTTTTGCCTACACGCACATCTTTACAGTCGTGCGTAC[A/T]TGAATCAAATGCTCAAATGCCAGAATTGTAAGAAGGCATTTGAGGCCACAGAGGTGGGTACTCCGCCTACTGTGGTGCCGGGTACT
101918 A G AGTTGACTCGATTTTCGCAGGGTTTTCAGGGCAAGAAGGCACATTCTGGACCGTCTGTAAGTTTTGCCTACACGCACATCTTTACAGTCGTGCGTACATG[A/G]ATCAAATGCTCAAATGCCAGAATTGTAAGAAGGCATTTGAGGCCACAGAGGTGGGTACTCCGCCTACTGTGGTGCCGGGTACTGAT
101918 T C CCTACTGTGGTGCCGGGTACTGATAAGTACCATGCAGTTTGGGGTTTCTTTCCTATCGGGTTCGCAAACCCAGGTAGCACAGACGTGGATCAATTTGTAC[T/C]GCTTCAGCCGGATGGAAATGTTAGCGGCGATCGGAAGCAGAACGTAGATGATCGGAGGCAGAATGCGGACATGCCTCCTGGTCAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101938 T C GAGAGGGCAATTCGGTCCATTCACGTCTTGCCACATCATACACCCACAAATCGTTGCGCCTTCCATCCGTCCCACACCCGCCGAAAACGTACACACGGCC[T/C]TCATCTGCGGTCATGGAGTGGTAGCTCCGGTGGGGAGGGCCTGAGGGTAAAAGTGTCCATTCGTCTGTCAAGGTGTCAAAGGAGTA
101938 A G AGGTGTCAAAGGAGTAGAACTCGTCAAGCTCCTTGTGGGAGGCGTCCCGCCCTCCAAAGACATAGATGTTGGTGCCTATTGAGCTCATTGTGACGCCGAC[A/G]CGTGGGGATGGGATTTGGCCAGTGGTGGGTAGGGTAGACCATGTATGGATTTGGAGGTTGAATACATGGAGCTCGTTGTCTACG
101938 A G CCCTCCAAAGACATAGATGTTGGTGCCTATTGAGCTCATTGTGACGCCGACACGTGGGGATGGGATTTGGCCAGTGGTGGGTAGGGTAGACCATGTATGG[A/G]TTTGGAGGTTGAATACATGGAGCTCGTTGTCTACGGGTACACGTGGCGTGAACTCTCCCCCAAATACATAGGCATTGTGGTTTAC
101938 T C GTATGGATTTGGAGGTTGAATACATGGAGCTCGTTGTCTACGGGTACACGTGGCGTGAACTCTCCCCCAAATACATAGGCATTGTGGTTTACTACTGTGA[T/C]TGCGTGAGAGCTTCTTGCGCCTGGTCCGCTCACTCCCTGTGATAGTTTGACCCATTTGCCATCCATTGTTGGTTCTCCCTTCCAATTTA
101940 AACACAAAG A AGATCCATTGTTCTCTAGTACACAGTCCATTTAACATGATACACAGGGCAAATTTATTTAGATAATTACCCTTACTGGCTCATTCATGCCAAACAAAGAC[AACACAAAG/A]ACACAAAGTGCACTGCAAACTTAAAATACACTCATGGTAAGGGAAGCCTCGAATTTAAGTGCATATCATTACATCCTCAAC
101940 C T GAAGCCTCGAATTTAAGTGCATATCATTACATCCTCAACCGTTTACCTTCGGTTCCCAACCAGCAATGACATGGTCTCTTGCAGCTTTAGTCTTTTCAAA[C/T]GATTCACGGCTGAAAAGGAGCTTCATGTAAGCATTGACATTAGGCAAACTTTCTGGAACTTTCCATCCTTTGAAATGATCTAGTGCAATG
101940 T A CAGCTTTAGTCTTTTCAAACGATTCACGGCTGAAAAGGAGCTTCATGTAAGCATTGACATTAGGCAAACTTTCTGGAACTTTCCATCCTTTGAAATGATC[T/A]AGTGCAATGTCAAGATGGTACAGTTTGGGTGCCAAGCTCAAGTCGGCTGCAGATACGTTCTCGCCATTAATAAACGGACCATGAGCCT
101940 C T ACATTAGGCAAACTTTCTGGAACTTTCCATCCTTTGAAATGATCTAGTGCAATGTCAAGATGGTACAGTTTGGGTGCCAAGCTCAAGTCGGCTGCAGATA[C/T]GTTCTCGCCATTAATAAACGGACCATGAGCCTTGAGATGATCATCCAAAGCTTGCAGTTCCGCAAGCAAAGCCTGCTCACTTCCATCG
101940 G C GCAAACTTTCTGGAACTTTCCATCCTTTGAAATGATCTAGTGCAATGTCAAGATGGTACAGTTTGGGTGCCAAGCTCAAGTCGGCTGCAGATACGTTCTC[G/C]CCATTAATAAACGGACCATGAGCCTTGAGATGATCATCCAAAGCTTGCAGTTCCGCAAGCAAAGCCTGCTCACTTCCATCGTTGGGAT
101940 A G TTGGGTGCCAAGCTCAAGTCGGCTGCAGATACGTTCTCGCCATTAATAAACGGACCATGAGCCTTGAGATGATCATCCAAAGCTTGCAGTTCCGCAAGCA[A/G]AGCCTGCTCACTTCCATCGTTGGGATCCTTGCTTTTTAGAAACTTGATAAAAGCAGGAAATATTTTTGACCCAACTGAAGAATATTCG
101940 G A CGGCTGCAGATACGTTCTCGCCATTAATAAACGGACCATGAGCCTTGAGATGATCATCCAAAGCTTGCAGTTCCGCAAGCAAAGCCTGCTCACTTCCATC[G/A]TTGGGATCCTTGCTTTTTAGAAACTTGATAAAAGCAGGAAATATTTTTGACCCAACTGAAGAATATTCGGGTGGGGTAACCAAAGAT
101940 G A GTTCCGCAAGCAAAGCCTGCTCACTTCCATCGTTGGGATCCTTGCTTTTTAGAAACTTGATAAAAGCAGGAAATATTTTTGACCCAACTGAAGAATATTC[G/A]GGTGGGGTAACCAAAGATGGTTCCGGATACTTCTCTTCAATGATTTTAGTAATCACATCAGAATCTGCAATCCATTTTCCTTCTTCATCC
101950 G A CAACGATAGAGGAATCAATCGTATCTACCATGTTAAGTCTGAAGACATTGATCAAATGCAAATAGAGACTAGCACCAATGGGAAACGCAGGAGCAAGATC[G/A]AAGCTTTTAGCGCCTTTCTGTGGAGAATCATTGCAAAAGGTGCGAGGAAGAGAAATGAAGAAGACTGCAATGTATGCAGGATGG
101950 A G GGAGAATCATTGCAAAAGGTGCGAGGAAGAGAAATGAAGAAGACTGCAATGTATGCAGGATGGGCATAGTAGTAAATGGTCGATGCAGATTCCCCCAGGA[A/G]CATTCGATGGACAACTACTTCGGAAACGTACTATCGATACCGTACGGAACAATGAGCATAGATGACCTGGAACAAAACAAGCTC
101950 G C ACTGCAATGTATGCAGGATGGGCATAGTAGTAAATGGTCGATGCAGATTCCCCCAGGAACATTCGATGGACAACTACTTCGGAAACGTACTATCGATACC[G/C]TACGGAACAATGAGCATAGATGACCTGGAACAAAACAAGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGCGA
101950 G C ACGTACTATCGATACCGTACGGAACAATGAGCATAGATGACCTGGAACAAAACAAGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGC[G/C]ATGAAAGCGGAACATTTTCTCGATTTGGTGGACTGGGTGGAGGCCAGAAGGCCAGAGCCGGCAGCGGCAAGGATATACTTGAAC
101950 G A TACTATCGATACCGTACGGAACAATGAGCATAGATGACCTGGAACAAAACAAGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGCGAT[G/A]AAAGCGGAACATTTTCTCGATTTGGTGGACTGGGTGGAGGCCAGAAGGCCAGAGCCGGCAGCGGCAAGGATATACTTGAACGGA
101950 C T TCGATACCGTACGGAACAATGAGCATAGATGACCTGGAACAAAACAAGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGCGATGAAAG[C/T]GGAACATTTTCTCGATTTGGTGGACTGGGTGGAGGCCAGAAGGCCAGAGCCGGCAGCGGCAAGGATATACTTGAACGGAGGTGA
101950 C G AACAAAACAAGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGCGATGAAAGCGGAACATTTTCTCGATTTGGTGGACTGGGTGGAGGC[C/G]AGAAGGCCAGAGCCGGCAGCGGCAAGGATATACTTGAACGGAGGTGACGGTGAGGACGACGGTGTGGCGTTTGTTGTGTCGTC
101950 A G AGCTCAAAGAAACTGCTGAATCAGTACACGATTTCTTAAAAGAAGCGATGAAAGCGGAACATTTTCTCGATTTGGTGGACTGGGTGGAGGCCAGAAGGCC[A/G]GAGCCGGCAGCGGCAAGGATATACTTGAACGGAGGTGACGGTGAGGACGACGGTGTGGCGTTTGTTGTGTCGTCGGGGAGAG
101952 A G ATTACAAACTGGTGTACAACGTCGATGAAACCATCAGCGATGCCGATCCATCATCATTATCTGACATCAAGAAGTTCGCGACTCACATTGCAGTACAGAA[A/G]GAATCGATCTTCCCTACAAACAAGGCGTTCATAACCAGGCAAACGGATCTCGTATCCACATTACAAAAGGTTGGATTCCCCGTCTTCG
101952 A G CCATCATCATTATCTGACATCAAGAAGTTCGCGACTCACATTGCAGTACAGAAAGAATCGATCTTCCCTACAAACAAGGCGTTCATAACCAGGCAAACGG[A/G]TCTCGTATCCACATTACAAAAGGTTGGATTCCCCGTCTTCGTGTATGTGCTTATGAATGAGTTCACATCAACGCCTTGGGATTTCTTCG
101952 T C AAGTTCGCGACTCACATTGCAGTACAGAAAGAATCGATCTTCCCTACAAACAAGGCGTTCATAACCAGGCAAACGGATCTCGTATCCACATTACAAAAGG[T/C]TGGATTCCCCGTCTTCGTGTATGTGCTTATGAATGAGTTCACATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAAT
101952 C A GACTCACATTGCAGTACAGAAAGAATCGATCTTCCCTACAAACAAGGCGTTCATAACCAGGCAAACGGATCTCGTATCCACATTACAAAAGGTTGGATTC[C/A]CCGTCTTCGTGTATGTGCTTATGAATGAGTTCACATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAATACGTACG
101952 A G CCCTACAAACAAGGCGTTCATAACCAGGCAAACGGATCTCGTATCCACATTACAAAAGGTTGGATTCCCCGTCTTCGTGTATGTGCTTATGAATGAGTTC[A/G]CATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAATACGTACGTTCAAGGGGTTGGGGTAGATGGGATAGTTACG
101952 C T CCTACAAACAAGGCGTTCATAACCAGGCAAACGGATCTCGTATCCACATTACAAAAGGTTGGATTCCCCGTCTTCGTGTATGTGCTTATGAATGAGTTCA[C/T]ATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAATACGTACGTTCAAGGGGTTGGGGTAGATGGGATAGTTACGG
101952 T C CATTACAAAAGGTTGGATTCCCCGTCTTCGTGTATGTGCTTATGAATGAGTTCACATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAA[T/C]ACGTACGTTCAAGGGGTTGGGGTAGATGGGATAGTTACGGATTTTCCAGGTACAACTACGAGGTACAGGAAGAACTCGTGTTTAAA
101952 A G AGTTCACATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAATACGTACGTTCAAGGGGTTGGGGTAGATGGGATAGTTACGGATTTTCC[A/G]GGTACAACTACGAGGTACAGGAAGAACTCGTGTTTAAAGATGAAGGGTGATGATGTGCCGATATACATGGCTCCAGTTCTTCCGG
101952 A G ATCAACGCCTTGGGATTTCTTCGCAGATCCAACGGTGGAGATCAATACGTACGTTCAAGGGGTTGGGGTAGATGGGATAGTTACGGATTTTCCAGGTACA[A/G]CTACGAGGTACAGGAAGAACTCGTGTTTAAAGATGAAGGGTGATGATGTGCCGATATACATGGCTCCAGTTCTTCCGGGGGCGCT
101960 C A GACTGCTTGCTTCATAATGGACACCGCTATTGGCTTTGATTTTTCCAGTCTCTAGTACAGCGGCGCAGTCTTCTTCATCTTCCCAGTTACATCTCAGCCA[C/A]GCATAAGCAGTAGCAGGCTCTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACT
101960 A T CTTCATAATGGACACCGCTATTGGCTTTGATTTTTCCAGTCTCTAGTACAGCGGCGCAGTCTTCTTCATCTTCCCAGTTACATCTCAGCCACGCATAAGC[A/T]GTAGCAGGCTCTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACTCACAAGCGT
101960 C T TTCCCAGTTACATCTCAGCCACGCATAAGCAGTAGCAGGCTCTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGA[C/T]CAGATAAACTCACAAGCGTGGTGACCTTAACCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCC
101960 T G AGTTACATCTCAGCCACGCATAAGCAGTAGCAGGCTCTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGA[T/G]AAACTCACAAGCGTGGTGACCTTAACCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTC
101960 C A GCCACGCATAAGCAGTAGCAGGCTCTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACTCACAAG[C/A]GTGGTGACCTTAACCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTC
101960 C T CTCTGATTCGTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACTCACAAGCGTGGTGACCTTAACCCATCTTTC[C/T]CGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAATT
101960 C T GTTTGAAGTAATTGCAATATTCAGAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACTCACAAGCGTGGTGACCTTAACCCATCTTTCCCGTAAAAC[C/T]TTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAATTGCGTTTCA
101960 T C GAGCTCATTTCTTGAACGGAGAATCGACCAGATAAACTCACAAGCGTGGTGACCTTAACCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGT[T/C]CTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGT
101960 T C TCACAAGCGTGGTGACCTTAACCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTT[T/C]ACAATTTTTAGAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATT
101960 T C CCCATCTTTCCCGTAAAACCTTATAGCCAAATTCATTGAAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAA[T/C]TGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCCAAA
101960 T C AAGTTCTCGTGGTGTAGTTCCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTA[T/C]GTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCCAAATCGACTGCCGGCGTGCCCTGTGTACTTTCCAAGTGTA
101960 G A CCTTCTCTTGCAAAATGTCCTTTACAATTTTTAGAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTC[G/A]TAAACATCTTGATTCTTTAAAATTGCCCACCCAAATCGACTGCCGGCGTGCCCTGTGTACTTTCCAAGTGTAAACAGCATGATATCTTCATC
101960 T A CAATTTTTAGAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAAT[T/A]GCCCACCCAAATCGACTGCCGGCGTGCCCTGTGTACTTTCCAAGTGTAAACAGCATGATATCTTCATCTGATTCTTCTACTATAGGCGCAT
101960 A G GAGTTCTGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCC[A/G]AATCGACTGCCGGCGTGCCCTGTGTACTTTCCAAGTGTAAACAGCATGATATCTTCATCTGATTCTTCTACTATAGGCGCATAATGAGGC
101960 A G TGAATTGCGTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCCAAATCG[A/G]CTGCCGGCGTGCCCTGTGTACTTTCCAAGTGTAAACAGCATGATATCTTCATCTGATTCTTCTACTATAGGCGCATAATGAGGCCAATAT
101960 C A GTTTCACGTGAAACGCCCTCGCTGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCCAAATCGACTGCCGG[C/A]GTGCCCTGTGTACTTTCCAAGTGTAAACAGCATGATATCTTCATCTGATTCTTCTACTATAGGCGCATAATGAGGCCAATATGTAGC
101960 T G TGTTTGTTGCTATGTATTTTGTTAATTTGTCGTAAACATCTTGATTCTTTAAAATTGCCCACCCAAATCGACTGCCGGCGTGCCCTGTGTACTTTCCAAG[T/G]GTAAACAGCATGATATCTTCATCTGATTCTTCTACTATAGGCGCATAATGAGGCCAATATGTAGC
101968 C A CAGTGCTCAAACCAGTCAGTAGCCTTCTTCTGAATAGAGTTGCTAATGGAGCGAATCGTGCACCCGGTGGGTTTCCACCCGCAGAAGCATCAACCCGGAT[C/A]CGGTTAAGGTGTGAAGATGGAGAAGAGATTGCTCCTATTGCTCTTAGATTCATTCTTTTCTTCCTTTGTTTTT
101970 A G ACGACCAGAAGCACGGCAAAAACCATCATAAACAGCTGAAAATTTGCAAAGCCTTCTCCTCTTACTTCATCAGCATGCGACTTGCACTTGATGCC[A/G]TTGCCTTCATCCAAATGACATCCATTAGGCATCATGGGTCCGTACAGTGTGAATGCAGTTTGATAGAACCAGAGTCCCTGTAAAGTAATGGA
101970 T C GTTTGATAGAACCAGAGTCCCTGTAAAGTAATGGAAACACCGCTCGCTACATCTACAGTGAAGTTGTCTGAGAGGAAAGAACCGGCAATTGTGGTGGCGA[T/C]GCATAGGCCAACAAGGACCACAAGAAGGAAGTGGTAGTAGCCTTCCAGTCCGGTGTGGGACGTGGAGTGGAAGTAGAACAGGA
101970 C T AACCGGCAATTGTGGTGGCGATGCATAGGCCAACAAGGACCACAAGAAGGAAGTGGTAGTAGCCTTCCAGTCCGGTGTGGGACGTGGAGTGGAAGTAGAA[C/T]AGGAGGTATTCGGCGCTAAATGCCGATGAGGCAATCAGGCATAAGGCTTCTTGAGTCAGTGGGACATATCTGGAATTTTCAGA
101970 A T CAAGGACCACAAGAAGGAAGTGGTAGTAGCCTTCCAGTCCGGTGTGGGACGTGGAGTGGAAGTAGAACAGGAGGTATTCGGCGCTAAATGCCGATGAGGC[A/T]ATCAGGCATAAGGCTTCTTGAGTCAGTGGGACATATCTGGAATTTTCAGAAAGAAGAGCAGCGACACCAAATAGAAAAAACAT
101970 A G GGTAGTAGCCTTCCAGTCCGGTGTGGGACGTGGAGTGGAAGTAGAACAGGAGGTATTCGGCGCTAAATGCCGATGAGGCAATCAGGCATAAGGCTTCTTG[A/G]GTCAGTGGGACATATCTGGAATTTTCAGAAAGAAGAGCAGCGACACCAAATAGAAAAAACATCATCAACATCCCACCATGTTCG
101970 AC A ACGAAGAATTTCAAATGGGTCGAATATAACAACTCAATACACATATCCAGAAACGCACCTCCGGCAACCACATACAGCTCTAGATGCTTCCACCGACCCG[AC/A]CCCCACCGGGTTCCAAACCCGGACCCGAAACGAGCCTGGATCCGATACGAACCGAACAACCGAACACCATATGTGCCATAAACCG
101970 G A CAATACACATATCCAGAAACGCACCTCCGGCAACCACATACAGCTCTAGATGCTTCCACCGACCCGACCCCACCGGGTTCCAAACCCGGACCCGAAACGA[G/A]CCTGGATCCGATACGAACCGAACAACCGAACACCATATGTGCCATAAACCGACGACGAGGAAGAGGCTTCCGGGCAGGGCGTGGC
101974 A G AACATCATCAAGATTCCATTTATCAGAAGCCAATGATCGTGCATTCTCAACACTCGCTTGTTGGTCTGAGTCTTTCCAATCCCAGAGACTTAATGTCTCA[A/G]TATGTGTTAGACACCACAGCTTTTGACATGTTTCCCCAAAGAAGCCGATTTTTGAAACTGACGTCCCCACATTCATCACAGAATCCAAGT
101976 T G TGCTTCAGAGCTTGTTTCCTACTTGCAATTTAATGCCTGGTGCGCAACGTTTGATCAATCATCTCCAATCAAATGGAATTCCCATGGCTGTGGCAACTGG[T/G]TCCCATAAAAGACATTTCGATTTGAAAACTCAAAAGCATGGTGAAATCTTTTCCAAAATGCATCACGTGGTTATGGGAGATGACCCGG
101976 C G GAATGCCTGTAGTTATGGTACCCGATCCGAAATTAGATGCCTCCTATCGAAAAGAAGCAGATGAAGTGCTCGCTTCTTTGCTGGATTTCAATCCAAGCAA[C/G]TGGGGACTACCTCCGTTCCAAGATTGCATGAATTGATATTATGATTATTTGTTGAGAGAAGGGCCATCTCTTATTCCTGTAGAAACAA
101976 G A AAGCAGATGAAGTGCTCGCTTCTTTGCTGGATTTCAATCCAAGCAACTGGGGACTACCTCCGTTCCAAGATTGCATGAATTGATATTATGATTATTTGTT[G/A]AGAGAAGGGCCATCTCTTATTCCTGTAGAAACAAAGAATCTACATTAAATTGGCCTGTCTGACAAGTGACAACAGGTCAATGAACCCT
101976 A G ATTGCATGAATTGATATTATGATTATTTGTTGAGAGAAGGGCCATCTCTTATTCCTGTAGAAACAAAGAATCTACATTAAATTGGCCTGTCTGACAAGTG[A/G]CAACAGGTCAATGAACCCTTCCATCAATTTGTATTCGTTGGGTTGATAATTATCACATTCCAGACATTCACGGTTGTGAAATACTTTGT
101976 A T AATTGGCCTGTCTGACAAGTGACAACAGGTCAATGAACCCTTCCATCAATTTGTATTCGTTGGGTTGATAATTATCACATTCCAGACATTCACGGTTGTG[A/T]AATACTTTGTAGAAACTGGTAAATGTGGTTATTGATCTCATCTGTAACCTAACTATTTTAACATTAGAATCGTCCAA
101976 A G ATTGGCCTGTCTGACAAGTGACAACAGGTCAATGAACCCTTCCATCAATTTGTATTCGTTGGGTTGATAATTATCACATTCCAGACATTCACGGTTGTGA[A/G]ATACTTTGTAGAAACTGGTAAATGTGGTTATTGATCTCATCTGTAACCTAACTATTTTAACATTAGAATCGTCCAA
101976 T G TGTCTGACAAGTGACAACAGGTCAATGAACCCTTCCATCAATTTGTATTCGTTGGGTTGATAATTATCACATTCCAGACATTCACGGTTGTGAAATACTT[T/G]GTAGAAACTGGTAAATGTGGTTATTGATCTCATCTGTAACCTAACTATTTTAACATTAGAATCGTCCAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
101982 A G TTATCATTCGTCCAAACCTGAATGATGTCGCCACAATTGATGATGTAGGAACCGGGCACGGGGTTGACACG[A/G]ACCCACTCTCCTTCTTTTGTCTTGACATCAAGACCGCTGACTCCGTCCACTTCGGCCAGGATGGTTAGGGCACCCTGGTCCTTATGCGGGCCTACTCCCA
101982 T G TTATCATTCGTCCAAACCTGAATGATGTCGCCACAATTGATGATGTAGGAACCGGGCACGGGGTTGACACGAACCCACTCTCCTTCTTT[T/G]GTCTTGACATCAAGACCGCTGACTCCGTCCACTTCGGCCAGGATGGTTAGGGCACCCTGGTCCTTATGCGGGCCTACTCCCAAGGCTAAGTTCGGGTT
101982 G T GCTTAGTTATTGCTATCATCTTCTCGAGCAGGTCTTTGGGCACGCCGTGGTTGATGACCGTGAAGAATCCCCAGACTGTGCATGCATCTTGGATCTGGAC[G/T]ACTAGATCCTTTAAGGATTCGTCTGGTGTGTTTGGGTTTAGGAATAGGGCGAGATCGATCACCGGGATGTCCTTGTATTCCGGTATG
101982 C T AGACTGTGCATGCATCTTGGATCTGGACGACTAGATCCTTTAAGGATTCGTCTGGTGTGTTTGGGTTTAGGAATAGGGCGAGATCGATCACCGGGATGTC[C/T]TTGTATTCCGGTATGTCCGGGTTTGGTAGTTGGTTTTCTGCCTGAATGAAGTGTTGATCGAATTCTAGAACCATTTTATGTATTATTC
101996 A G TCGGACGTGAAATGCTATGCCCATTCTGCGCTGAAGGCTTCCTCCAACAACTCGACGAAGTGGACGATGACCTATCCACACCGTTTGACCTTCTCCAACT[A/G]GACTCCATCCACGATCCCGACCATCCATTTGGCGCGATGCGGGCCCTATCCGCATTCATGAGGCAGCACGCTTCTGGAAGGATCCGC
101996 T C CCGCTGCTCGATCCTCAATAAACGCGATCCCGACGGTCGAGATAAACGGCAGGCATCTCAGAGGAGGAGACTCTCATTGCCCCGTCTGCAAAGAGAGGTT[T/C]GAGCTCGGATGTGAAGTAAGGGAGATGCCGTGCAAACATCTGTATCATTCGGACTGCATCGTGCCTTGGTTGGTTCAGCACAATT
102006 G A TGATAAAGTTCTCATAAGAGTACAAATTCAACTCTCACTGCCATTGTTTTCAGAAAGCAACCCCACCAGCCCTGCTGTGATGAGCCTGAACAGCACAGGC[G/A]CAATGAACGGAAGTAAGACTGAGACATCCACTGATGATGAGCGAATGCCTGCCCGAACAAGTGTGTAAAGATGGATAAGAGTCGCA
102006 A G AGGCGCAATGAACGGAAGTAAGACTGAGACATCCACTGATGATGAGCGAATGCCTGCCCGAACAAGTGTGTAAAGATGGATAAGAGTCGCATAACTTTTG[A/G]ACAGCGTGAGGGGTCAAGGCAGTGCATTGGCTTATGTTCAAGTTCACCAGCCCCTCCTTGTCCGTTTCATTGTTGTTTTGTACCGA
102006 G A TCAGTATTTGTAACTGATTACAATTGCGTGCAATTGCCTGCAGTGCGTTATCTTTTGCAGCACGGACACATCCACAAAGGTTAAGGTTCTTTATGCTGTG[G/A]CAATGATTAGTCAAGTAAGCAAGAGCAGAATCGCTGAAGGTTGAGCAACCACTAATGTTGAGTTTGGTAAGGCGAGGACATCCATGT
102006 T C GTGCGTTATCTTTTGCAGCACGGACACATCCACAAAGGTTAAGGTTCTTTATGCTGTGGCAATGATTAGTCAAGTAAGCAAGAGCAGAATCGCTGAAGGT[T/C]GAGCAACCACTAATGTTGAGTTTGGTAAGGCGAGGACATCCATGTGCCAGCGCAATTAAAGAGCGATCAGTGAGTCTAACG
102010 A G CAAGGCTCCCAACAGTCCTTCGTACCAATGATTTGTTCGTAAGCTCTTGTGGATGAATTTGTGGCATGTGTCCCATACCTGAATCGTCCATGTAGAATGC[A/G]ACAAAGAGAGAATCATTCCTGAGAAAGCAAAATAATAAGGAAGAGTGCGGTCTGGGGCCATAAAATGCCCATCTTCGGTTCGGACT
102010 A G GTGGCATGTGTCCCATACCTGAATCGTCCATGTAGAATGCAACAAAGAGAGAATCATTCCTGAGAAAGCAAAATAATAAGGAAGAGTGCGGTCTGGGGCC[A/G]TAAAATGCCCATCTTCGGTTCGGACTATCTTCGCGACTCCGGGAAACTTCTCGTTTAGCAGTTGAGGAAGCCCAATCGTACCAGG
102014 A C TTCTAAACTTACCAGATGTCGGTGTCCCAACACGGGATGACACTGCAACTGCATCATCCGATCTTGGCACGTGTATCGCTATTGAATGCTTCTCCTTCTC[A/C]TTCTCCGATTGATGTTTCTGGGACCCCCGACCTCCGTTGAAGGAGTTTCCTTCCATCGGCTCCTTCTTCCTAGTAATTTTCGAAGTTCTA
102014 A G ACCCCCGACCTCCGTTGAAGGAGTTTCCTTCCATCGGCTCCTTCTTCCTAGTAATTTTCGAAGTTCTAGGGCTTAATTTGTCTTTATCCACAAGGCAGGC[A/G]ATATTGAGAGCGATAAAATCGGAAGCCCTTTCTGCTTCAGTCGCAATGGCGCTTGATGAGGTCATTGAAGAAACGGGATCTTGAACGG
102032 A G GTAAAGAATTGTATTTCAAGCTCTGTGATTCAGTGCTTATTGACGGCGGCACAAAGGTCTTTTATCTGGAGAAGGCAACTGGAGCAAAATGCTTTGCATT[A/G]GGTGCTAAGGAATTACACATACAACAGGCTGACGATCATATTAATTGGGGTTGGGTTCCTCACCCTACATCGAGGTTCATGTTAGTA
102032 T A TGGAGAAGGCAACTGGAGCAAAATGCTTTGCATTAGGTGCTAAGGAATTACACATACAACAGGCTGACGATCATATTAATTGGGGTTGGGTTCCTCACCC[T/A]ACATCGAGGTTCATGTTAGTAGCAGAGGTACGGTACAGTGGTTCACTAGTACTTGAGTGGTACATCGACTGTAAAGAGCTCTCTCC
102032 T C GGAGCAAAATGCTTTGCATTAGGTGCTAAGGAATTACACATACAACAGGCTGACGATCATATTAATTGGGGTTGGGTTCCTCACCCTACATCGAGGTTCA[T/C]GTTAGTAGCAGAGGTACGGTACAGTGGTTCACTAGTACTTGAGTGGTACATCGACTGTAAAGAGCTCTCTCCGAACACCACATACAA
102032 T C CTGAAGAAGTATCAGTGAAACTTGGAAGTCGAATTTCAAAAGGAAAAGCCTGTCTTCATCCAGACGGAAGCAGCATGAATATATTTAGAAACCCACGCCG[T/C]CAACTGCCTCTAGAAATGCATGTCCCACGGCATAGGTCCGATGGTTGGATGGAACTTGAGCTGGGAGAGTTCTATAACAAAGATG
102032 C T ATCAGTGAAACTTGGAAGTCGAATTTCAAAAGGAAAAGCCTGTCTTCATCCAGACGGAAGCAGCATGAATATATTTAGAAACCCACGCCGTCAACTGCCT[C/T]TAGAAATGCATGTCCCACGGCATAGGTCCGATGGTTGGATGGAACTTGAGCTGGGAGAGTTCTATAACAAAGATGGCAGCGAAGG
102032 T C TGGCAGCGAAGGAGATGTCTGCATGTCCTTTAAGCATGTCGGCAGCATCTGGAGTCGCTGTCTCACTATCCAATGTGTGGAAGTTAGACCAAAGTGATAC[T/C]GTGTTTTATATATAATATGTGTGTATGTTTCAACAACTCTGTTTTAAAGTCAGCTTCCTTGCACACTGGTTAACTGTCTGTCATAAATC
102038 T G TTTCATCTTGATTTTCAGAAGATGGTTTACTAATCATGAGGCTCTTGCTTAAATGGTCTTCAACTGGCTTTTGATTGAGCTCTGCATCATTACTTGTAAT[T/G]GTAGGCAACTGAGGTTCAACTTCATAAGTCAGACTAGTTAAATGGTTATAGACCCGTCTGGCTTCTTTTAGCGTCGGCCTACGAACAGTC
102038 G A ACTGAGGTTCAACTTCATAAGTCAGACTAGTTAAATGGTTATAGACCCGTCTGGCTTCTTTTAGCGTCGGCCTACGAACAGTCAAAGGTATATGACAAAC[G/A]GCATGTCCATGTACATATGACTTTTCAGTATCATAAAGCATTTGACGGTTTTTCGAACCAGCAGAAACAAATATACTTGAAGAAGAAT
102040 C T GGATAAGGAATTTTCAAAATTACAGGCGGGGTGATTTGAATTTGGAAGACAATATATTTGCTTTTCATTTTTGATTTATTGGGGGATTTATTTGATTGAA[C/T]AATGGGGTCTTCGCAAGGGTCCACTCTGACGTCGGCGGCGGCGACAGCTGACGTGAAGGTTGATTTTGTTGATTTGCTGCCGGTTTA
102040 G A GGAAGACAATATATTTGCTTTTCATTTTTGATTTATTGGGGGATTTATTTGATTGAACAATGGGGTCTTCGCAAGGGTCCACTCTGACGTCGGCGGCGGC[G/A]ACAGCTGACGTGAAGGTTGATTTTGTTGATTTGCTGCCGGTTTATGTGAAGGAATTGATTGCTGGCGGAGCTGCAGGTGCTTTTTCC
102040 AC A CTATCCATCGCTAGGATCGGGACCAGTTATAGATTTGTTAGCTGGTTCAGCTTCTGGTGGAACTGCTGTTTTGTGCACATATCCATTAGATTTAGCTCGA[AC/A]CCAAAACTTGCTTATCAGGTTACAAGTAAAAATGGCTCCTTTGACAGACCAAGATCCTACAGTGGAATAACTGACGTTTTCAGGAAT
102040 CA C ATCCATCGCTAGGATCGGGACCAGTTATAGATTTGTTAGCTGGTTCAGCTTCTGGTGGAACTGCTGTTTTGTGCACATATCCATTAGATTTAGCTCGAAC[CA/C]AAAACTTGCTTATCAGGTTACAAGTAAAAATGGCTCCTTTGACAGACCAAGATCCTACAGTGGAATAACTGACGTTTTCAGGAATGT
102040 T C GCTGGTTCAGCTTCTGGTGGAACTGCTGTTTTGTGCACATATCCATTAGATTTAGCTCGAACCAAAACTTGCTTATCAGGTTACAAGTAAAAATGGCTCC[T/C]TTGACAGACCAAGATCCTACAGTGGAATAACTGACGTTTTCAGGAATGTTTACAAAGAAGGTGGAGTACGTGCTTTATATCGAGGAG
102044 G A CTTGTTCAGGCACATGAAACGGCTCATGAGGCCACTTAAGGTTGAGCCTGGTTGCTTCAACTTCCTTGGCACCCAATGCACTCCCATGAACGCTATAAGA[G/A]TTAGCCTTATTTGGTGATCCAAAACCAATGGTAGTTGTTACCTTGATAAGTGTTGGCTTGTCCTTGACAGCCTTTGCTTCTCTGATTGC
102046 A T GTTCATTGGCAGAATCTACAGTTAACCCGATTTTAACAGCATCTGCAATTGTCATTAGTATACAAAGCCTTGTCTCCAGAGAAGCCGACCCTCTTGATTC[A/T]CAGGTGCTGTCGGTTACTCAGTTTCATGGCGGCAACTCACTGGGTGAAGTTCCTGATATTGTTAGCATAGGTGGTACATTCAGGGCCA
102046 A G TTGTCATTAGTATACAAAGCCTTGTCTCCAGAGAAGCCGACCCTCTTGATTCACAGGTGCTGTCGGTTACTCAGTTTCATGGCGGCAACTCACTGGGTGA[A/G]GTTCCTGATATTGTTAGCATAGGTGGTACATTCAGGGCCATGAACAAAAATAACTTCGATGTCCTTAAACAAAGAATAAAGCAAGTT
102046 C T GGAAGAGCATCCCCCGATTCCACCTGCAGTAAATGACAAAAGATTACAGGAAAGGGTGCAAATGCTGTCAGAAGAGATTGTAGGGAAGGAAAACACTAGA[C/T]TGGCTCCACAAATGATGGGAAGCGAGGATTTTGCTTTCTATTTGGAAAGGGTGCCCGGAATATTTATGTTCATCGGCACGGCCAA
102046 CT C GGTTGATTCGGGCCACCCGGTCCACAGCCCGTACTATGCGATCGACGAGGATGCCCTTCCTGTTGGTGCAGCTATGCATGCTGCTTTTGCCCTTGATTTT[CT/C]TTTTTAACTTTGGGCATGAAAGGGAGGTTAGTGTATGTCCATCTGCTGGCTGCATTGTAATTTGTGATGAGTTTTAACCAGTAGAGT
102046 G C CGAGGATGCCCTTCCTGTTGGTGCAGCTATGCATGCTGCTTTTGCCCTTGATTTTCTTTTTAACTTTGGGCATGAAAGGGAGGTTAGTGTATGTCCATCT[G/C]CTGGCTGCATTGTAATTTGTGATGAGTTTTAACCAGTAGAGTAGTTTAAACGTTAGATGAAAAAGTAAAAAATTAATAGCTAGAAAAT
102048 T C CATTGGGCTGGCTGATTCCGAGCGAGACATTTCCACTGGAGACACGGTCGGCAGGGCAGAGTGTGACGGTTTGCGTGAATTTGTTGTTTACGTTTGTGAT[T/C]GCGCAGGCGTTTCTTTCTATGCTGTGCCACTTGAAGTTTGCGATCTTTGCATTTTTCTCGGCTTGGGTGCTGGTGATGTCGTTGTTTG
102048 G A TGGGCTGGCTGATTCCGAGCGAGACATTTCCACTGGAGACACGGTCGGCAGGGCAGAGTGTGACGGTTTGCGTGAATTTGTTGTTTACGTTTGTGATTGC[G/A]CAGGCGTTTCTTTCTATGCTGTGCCACTTGAAGTTTGCGATCTTTGCATTTTTCTCGGCTTGGGTGCTGGTGATGTCGTTGTTTGTG
102050 T G TGGTTGGGACACTGATCGGCGACCCAACACCTGCATTTCCAGGCCCCCCAGCATTCGTTCCCCAGTAATTGTCTCTTTCTGTCTGGGGAGGACCCCATAA[T/G]GAGGTGTCATCTCCGTAGCGTTGGAGTGAGGTTATCATTGACAGGGCGTTGCTTGTTACATTGGTAATTCGGAGTATGAATGACATT
102050 A C TAGTACCATTGACATACTTAAGAGCTGACCAACAATCATATTGATAAAGCAAAGCAGCACTCCCCCAAGCCCTCCCATCGGCTAACCCCCCATCGTTAAC[A/C]GCCCGAGTCGCCGCCGCTAATCTCTTCTCCGAATAGGACAGAAGCAACAAACAATTCTTCGCCGCATTCGTCCTGTTCAGATCGTTTCC
102050 A G AATTCTTCGCCGCATTCGTCCTGTTCAGATCGTTTCCCGTGGAAGCATCCAGAATGCTCTGCGCTTTTTCTTCCGCAGTTTTCAAACTAGCCTGAGATGA[A/G]TCGATTGTGCTGAAAATAAAGTCTTTCGCCTTCGGATTTGCAGGCAGGGTCGAGTTTTGAGCCAAAGTTGATTCGCAGACGGAGGCGT
102050 A G TTTCTTCCGCAGTTTTCAAACTAGCCTGAGATGAATCGATTGTGCTGAAAATAAAGTCTTTCGCCTTCGGATTTGCAGGCAGGGTCGAGTTTTGAGCCAA[A/G]GTTGATTCGCAGACGGAGGCGTATCGTGTGGCTTTACAAGCGTTCTGAATCAATGGAGACGTGGCAAAGGATGACAGGCGGTGGTG
102050 C T CTAGCCTGAGATGAATCGATTGTGCTGAAAATAAAGTCTTTCGCCTTCGGATTTGCAGGCAGGGTCGAGTTTTGAGCCAAAGTTGATTCGCAGACGGAGG[C/T]GTATCGTGTGGCTTTACAAGCGTTCTGAATCAATGGAGACGTGGCAAAGGATGACAGGCGGTGGTGGCGAGCTAAGGCGGATGT
102050 C CGGT CAGGGTCGAGTTTTGAGCCAAAGTTGATTCGCAGACGGAGGCGTATCGTGTGGCTTTACAAGCGTTCTGAATCAATGGAGACGTGGCAAAGGATGACAGG[C/CGGT]GGTGGTGGCGAGCTAAGGCGGATGTTAGGAGGAAGAAGAAAACAAGGACGGAACAATGATAGGCCATTTCGGTAAAGTG
102054 G A AATTCCATCAGCAATTTTTCTCATCACACAATTTTTTCTGCATTCCTTCAAGCATGTGCAAATCATGCCAGAGTTCTGGACTTTTTCGATTACCTCCTCG[G/A]TAACTTTCAAAATTTTCGTCTCCGTTGAGCTCCTTTTGGACAGAGCTTCCTGAAGAAGCTGATGCTGTAGTTCCCAAAAAGCCCTGTTTTC
102060 T C CTAAATGCAAGCGCCATTAATTCACTTATCCTAAAACAATGTCGTCCGCGTCTCCTCCTCCACCCGTCTCCTCCTCATTCTCCCTTTCCTCGTACATCGG[T/C]CTCTCTTTCTCTCTGTTCCTCGCTTCCCTTCCGAGCCACTCCTTGACCCAACTCACCTCCCTCGCGTCCCGCAACCGCATCCTTTCCGTCAAA
102060 A G AAGAGGAGAAGAGACTGCTGGTGAAGATGGAAGAGAAGGAGAGGGAGCTGGAGCGGTTGAGGGGAAGGGTTGAGCAGTTGGAGAAGGAGGTGAGGGAGAG[A/G]GATGAAATGCTTGATTTTATGTCCAGGAAGGATGGATTTGGAAATTATGACGATGAGGATGATGATAAAGAAGTTGGATT
102060 A G GACGATGAGGATGATGATAAAGAAGTTGGATTTGAGAGTAGTGAAATCGGTAATGGGGAAGATACGGCCGATGGCGGTTTTGGATCTTTGGATTCAAAGC[A/G]GTATTTTGAGAGTTTAAGTCAGGGCTTGCAGGGTACGAAGTATGATTCCCTTGAATCTATGTACCATATGAAACACTTTGTGGCA
102068 T C CTGAGGATTGCAGTGAGGAAGAAGTATTGAAGCATATCACACATTTCAATAATGATCCATCAGTTCATGGAATTTTGGTTCAGCTTCCTCTTCCTAAGCA[T/C]ATAAACGAGCACACAATTATTAGTGCTGTCAGTATTGAGAAAGATGTGGATGGATTTAACCCACTAAATATTGGTTGTCTTGCTCTACA
102068 G A GCACACAATTATTAGTGCTGTCAGTATTGAGAAAGATGTGGATGGATTTAACCCACTAAATATTGGTTGTCTTGCTCTACAAGGCAGAGAGCCTTTGTTT[G/A]TTCCTTGTACACCTAAAGGATGCATGGAATTACTGCATCGACACGGCGTTGCAATTAAAGGGAAGAGAGCAGTTGTTATTGGGCGAA
102072 A G CCAAATGGACTGCCACTAGCATATACTGCAGTCCCCTTGCTCCATGTGTATGCCTGCTCAGCCGTACATTCAGACTGTGAAGTAGGGTTTGAGAGAGCCA[A/G]GATTACGGGTCTTTCATTGAAGGCAGCCATGGCCTCAACCACTTCTTGTGTGAATGTTTGACCTACTCCAGATGATCCTATCAGCACC
102072 G A CAAATGGACTGCCACTAGCATATACTGCAGTCCCCTTGCTCCATGTGTATGCCTGCTCAGCCGTACATTCAGACTGTGAAGTAGGGTTTGAGAGAGCCAA[G/A]ATTACGGGTCTTTCATTGAAGGCAGCCATGGCCTCAACCACTTCTTGTGTGAATGTTTGACCTACTCCAGATGATCCTATCAGCACCG
102084 G A CAGCTTTGCATCCAGAGATGGATGCCTGTACTTCTTTGGAAAACGCTCTTTGACAATTGATTTTCTTCCAACAAAATCTGATTCAAACACTCTTGCTTCT[G/A]CACCCTGTTTCAGGAGAACACCATAACCATCATGTTGATTGCGATCAATCTCCATGCCTTTTAGCTTATTCTGCGAGTAGG
102094 GT G TTGTACGCTGCAACTAAAAAAGCAGGAGAAGAAATTGCTCACACGTACAACCACATTTACGGACTATCCATAACAGGCTTAC[GT/G]TTTTTTTACTGTATATGGACCATGGGGCAGACCTGACATGGCTTACTTCTCCTTCACAAAAGACATCCTTAACAAGAAACAGATCACTGTTTTCAAATCG
102096 T C TCCTTCCTTGAACATTGACTGGTCATGTATCTCAGATATGGGAATACATTTTGTGCGCAACTCTTCTCCCACTCCAAGCTGGTCGAGTGCATGCCAACCA[T/C]TAAGGTATATAGAGATTGATGCTCCTGTAGCTCTAAGTGTTTCTGATCTCTCCAGTATCAGACTTTTTAACCCTTTCCTGTGAAGGGCAA
102102 TA T TCAGTAAAACCGATCGACGAATGGCAGCTTAAGCTCTCTCTGCTCACTTTTCTTCGCTGCAATCTCTCCTTACCTTTTTCCGACGAATCCGACCTTTCAA[TA/T]AAATAAACTTCCGAACTTAAACAAGCGCAAGAGAGACGACCCGGTAGCGACTGGAGTGTTGTACTTCAGAAATTTGGAGTTCTTAAAA
102104 C A TCGGATTGTTGCAAAACAGGCAAACTGTATCCACAATACCGTTGTTCTCCACCGGTAACCGATCAGACACGCGCAGTGATGACGATAAATAGCTTTGCTG[C/A]GGGAGGTGATGGCGGAGGTCCATCAGAATGCGACAATCAATACCATAGCGACAGCGAGCTTGTAGTTGCATTATCCACTGGCTGG
102104 A G ATCAGAATGCGACAATCAATACCATAGCGACAGCGAGCTTGTAGTTGCATTATCCACTGGCTGGTATAATGGAGGAAGTCGTTGCCTCAATAACATCAGA[A/G]TCAACGCCAATGGAAGGTCCGTTTTGGCTAAAGTGGTCGATGAGTGCGACTCCGTCCACGGTTGCGATTCTGATCATGATTTTCAA
102104 A G ATCAATACCATAGCGACAGCGAGCTTGTAGTTGCATTATCCACTGGCTGGTATAATGGAGGAAGTCGTTGCCTCAATAACATCAGAATCAACGCCAATGG[A/G]AGGTCCGTTTTGGCTAAAGTGGTCGATGAGTGCGACTCCGTCCACGGTTGCGATTCTGATCATGATTTTCAACCTCCCTGTCCTTAC
102104 C T ACCATAGCGACAGCGAGCTTGTAGTTGCATTATCCACTGGCTGGTATAATGGAGGAAGTCGTTGCCTCAATAACATCAGAATCAACGCCAATGGAAGGTC[C/T]GTTTTGGCTAAAGTGGTCGATGAGTGCGACTCCGTCCACGGTTGCGATTCTGATCATGATTTTCAACCTCCCTGTCCTTACAATGAC
102104 T C ACGCCAATGGAAGGTCCGTTTTGGCTAAAGTGGTCGATGAGTGCGACTCCGTCCACGGTTGCGATTCTGATCATGATTTTCAACCTCCCTGTCCTTACAA[T/C]GACGTCGATGCTTCTCCAGCTGTTTGGAAGGCTCTCAATATTCCGCAATCTCAGATTGGAGACTATGATATTACATGGTCCGATGCCT
102104 A T TTTTGGCTAAAGTGGTCGATGAGTGCGACTCCGTCCACGGTTGCGATTCTGATCATGATTTTCAACCTCCCTGTCCTTACAATGACGTCGATGCTTCTCC[A/T]GCTGTTTGGAAGGCTCTCAATATTCCGCAATCTCAGATTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTT
102104 A G CAATGACGTCGATGCTTCTCCAGCTGTTTGGAAGGCTCTCAATATTCCGCAATCTCAGATTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCAC[A/G]CTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCTCCAAGATAACAATTGAGAGGTCTTTCTGTTATCCGAGGTC
102104 C T TCAATATTCCGCAATCTCAGATTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAA[C/T]GATCAAAATCCTCCAAGATAACAATTGAGAGGTCTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGC
102104 C A ATCTCAGATTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCT[C/A]CAAGATAACAATTGAGAGGTCTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGCGGTCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102104 T C GATTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCTCCAAGA[T/C]AACAATTGAGAGGTCTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGCGGTCG
102104 A G TTGGAGACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCTCCAAGATA[A/G]CAATTGAGAGGTCTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGCGGTCG
102104 T C GACTATGATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCTCCAAGATAACAAT[T/C]GAGAGGTCTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGCGGTCG
102104 T C ATATTACATGGTCCGATGCCTGATTGCACACTATATCTTTTGATATATATTCCTGTACTAGTCCTAACGATCAAAATCCTCCAAGATAACAATTGAGAGG[T/C]CTTTCTGTTATCCGAGGTCAGTTGTCGAAGGACGATCATGTCTGAGGTGGAGATGCGGTCG
102116 CT C CAAACGCGTGTGGTGCCATCTTCAGAGCCAGTAATGACCTGGTTGGTTGATTCACGAGCAGCAATACAGTGCAAGTAGTCTAAGTGGCCCTTGAAAACTA[CT/C]TTTTATTTTTCCACTCTCCATATCCCAACAATATGCACAAGAATCGCCACCAGCTGAGAAAATGCATCCTTCCTGTTCACTGACTGCG
102116 A ACCTTG CACTGACTGCGATGGCATTATTTTCAGGAATAGGGGATAGAGCTCCCCAAGGACCTTCCTGTTGTGGGTTGGCAAAGTCTAGTATGGGTTTCAAATGGCC[A/ACCTTG]CCTTGAAAGTGGCACATCTGAGTTTAATACATCAACCCACTTCCAACCACGAATGTGGCCATCATCCCCACAGCTCAACAAC
102116 A G CATCCCCACAGCTCAACAACAAAGATTCATCTCCACTTCCATAAAATTTCAAATCATACGCAGGGCCTTTATGTCCTTGAATAGTGCAAAATGGTTCCAC[A/G]TATGGATAACCAAGTGCAAACTCATGCTCTCCTTTCTTTCTAGAATGCAAAGTCGGATGAGAAGAATCGATGCAAGAAGAAAGAGAAT
102116 A G TAGATCCATCGCTGGAAGCGCAAACTAGGGTTTCGGGAGTAATAAGGTTTGAAGGAGCGAAGGTAGTTCTGAAAACTGTTCGACAACGAAGCTCTCGATC[A/G]AGCAGAATGTTATTTTTGTAGCATTCTTCGTCCCATTCTCGGACATCGCCAGCTCTTTTACTCCCGCTCTTTTTCGCCATTGATCTTC
102122 G A TCAGCATGCTACGGCAAAGAATTGAAGACCGAGAAATGGATGTGCCCATAATATTGATGGAACGAAAACCTTGATGTATTTGCCATGCCACACAAAGTTG[G/A]CGATTGACATGCTTGCAATGGAACAAGAACCGAAAAAGTAACTGATACTTGGTTAGAGCCTTTCTTGAAATAATTAGGGACAATGG
102122 T C AAAAAGTAACTGATACTTGGTTAGAGCCTTTCTTGAAATAATTAGGGACAATGGCCACTGGATCTTATAGTTGAGGCTGAAAGTTTCTAATCCAGTGATA[T/C]TTACTGGATCCAGCTGATCATCACTTTGAAAAACTGAGTTTTTATAATTTGGAGAATATGTACTCTCAAGGTCTTCAAGTGTAGCCAAT
102122 T C AAATAATTAGGGACAATGGCCACTGGATCTTATAGTTGAGGCTGAAAGTTTCTAATCCAGTGATATTTACTGGATCCAGCTGATCATCACTTTGAAAAAC[T/C]GAGTTTTTATAATTTGGAGAATATGTACTCTCAAGGTCTTCAAGTGTAGCCAATCTCTTGAGCAAAGAAACTCTTTCCACGCAACAAGT
102122 T C CTGGATCTTATAGTTGAGGCTGAAAGTTTCTAATCCAGTGATATTTACTGGATCCAGCTGATCATCACTTTGAAAAACTGAGTTTTTATAATTTGGAGAA[T/C]ATGTACTCTCAAGGTCTTCAAGTGTAGCCAATCTCTTGAGCAAAGAAACTCTTTCCACGCAACAAGTCAACTCCTCATGACAAGGATCG
102122 G A AATATGTACTCTCAAGGTCTTCAAGTGTAGCCAATCTCTTGAGCAAAGAAACTCTTTCCACGCAACAAGTCAACTCCTCATGACAAGGATCGGCGGCGGC[G/A]GCAGTGGTGCGTAAAGCGAGGTCAAGAAGAGACTGCAACTTCTCAACTGATATCTCTTCAGGTCTTTTAGCAAGCTCTTCGCGTGCA
102122 A G AGGTCTTTTAGCAAGCTCTTCGCGTGCAATGTCCATAAAATGAACCAAGAAGTCGCCCTGATCTAACAGAAGATACCGCTTCAAGGATTTAAGCTTTCCC[A/G]TAAGTTCGTACTTGTCTTTTATTAGATTTAAGAGTTCGCCACTTGCAAAATCGTATGCACTTTTAATGCATTCGAGATAATGATGATTA
102126 A AG AATCTTTTTCAAGTCACATTTTATATATCTACAAGCATTTGTACTCTTCACCTACAATTTTAAAAATGGCTGGGCCTTCGTTTACCGGTATCTGTTCTCA[A/AG]TTTTTTAACAGGCTTGGCCCACTGGACCTCTTCATCCGCGGTTGGACTAGCCCACTGACTTGTATGTTGAGCTGGATGCAGCGGCTCTTT
102126 A G TTGGCCTACCGGCGATGTGGGGGCAGGGCGCCTGTCCTGCCTTTTCTTCTTGCAAATGACCAAGTCTCCGGGGTGAGATAAGGATAACGGACTGGGTAAA[A/G]TTTTACTGAAAGAGGATCCTCCACGAGGATTAGGTTTGGAGATCTCAACTTTTGGTTCTGGTTCAATTGTCTTATGTTGCCGCTTGC
102136 G A TCTCCTGCTTCTACGGAAGCAAGTGCACCAAACCCAAAGAAGAGGAGGACGACGACAACCAACAAAACGGCGATTTCGACCCCGAGCTTGTGGCCGAACC[G/A]ATCTCTGCCCGATCAAAATCCTTCGTGGGTACCCACGAGTACCTCGCGCCGGAAGTCATATCCGGGACCGGGCACGGCAGCTGC
102136 C CT CGGAGGTGCCGAGGGATGCGAGGAAGAGGGCAGTGAGGAAGATCGTGATGAGTAGGAGGCAGAGGGAAGAGCCATTTCAGGTTTGTCAGCGAGTTGATTA[C/CT]TTTAGTTTGGATTTGGAGTAGGAAAGTAGTATAAATAGTCTGGATTTGAAGCAAGGAAAAAATAGTAGAAATAGGATGAAT
102136 G GT GTGCCGAGGGATGCGAGGAAGAGGGCAGTGAGGAAGATCGTGATGAGTAGGAGGCAGAGGGAAGAGCCATTTCAGGTTTGTCAGCGAGTTGATTACTTTA[G/GT]TTTGGATTTGGAGTAGGAAAGTAGTATAAATAGTCTGGATTTGAAGCAAGGAAAAAATAGTAGAAATAGGATGAATAATGA
102138 G A ATAACCAGAGATGCCTTTCAAGCCAGTAAGTGTCTTGAATGCTTCAGCTGGAACATCAGCAAAGTAGCTCACAATCAGAGCATCAATACCAGAGAGTGAC[G/A]ATTCCAACTCTGAGTATGCCTTGGTAAATGCTTGCAGCTTGTCGGATTCCAGATCTAGCACAAGAGTGGGCTCATCAAACTGAATCC
102138 G A AATGCTTCAGCTGGAACATCAGCAAAGTAGCTCACAATCAGAGCATCAATACCAGAGAGTGACGATTCCAACTCTGAGTATGCCTTGGTAAATGCTTGCA[G/A]CTTGTCGGATTCCAGATCTAGCACAAGAGTGGGCTCATCAAACTGAATCCATAAAGCACCCGCTGCCTTCAACTCTGAGATAACTTC
102138 C A TCAACTCTGAGATAACTTCCTTGTATACAGGTAACACTTTGTCCAAGAGGGAAAGAGTACAAAATGATTTCTCTACTCCTTTGGCAGGTTTTGAAAGCAA[C/A]AGGTATGACACTGGTCCGACAAGAACTGGAACAGTATTGATTCCAAGCGCTTTTGCCTCCTTGTATTCAGTCACGGCCTTGTGAGAAG
102138 A T GTATCCGGACCCAACTCAGGCACGATGTAATGGTAGTTGGTGTCGAACCACTTGGTCATCTCCATAGCAGGTAGGGTAGCATTTCCTCTTGCCATAGAGA[A/T]ATATGTGTCAAGACCAATTTCTCCTCCACTCCATCCATACCTCTGGGGAACAGCACCAAGCATCACTGTCGTATCAAGAACCTGATCA
102138 A G AGCAGGTAGGGTAGCATTTCCTCTTGCCATAGAGAAATATGTGTCAAGACCAATTTCTCCTCCACTCCATCCATACCTCTGGGGAACAGCACCAAGCATC[A/G]CTGTCGTATCAAGAACCTGATCATAGTATGAAAATGTGTTGCTGGGAATGAATTTAGTTCCAGCAGCAGACATTTGTTTCCAAATGTT
102142 T C CGGCAACTCGCATATCAAGGCCTTGTCTTTCCATTGCCTTGGTCAATTCAGCAACTACATCTTCCCCTACCGTGTCATCAATAGAAAATCCTTTTGTCCA[T/C]TTAATAAGGGTTCCAGATGCAATTGAAGTCTGTTTCACTGGAAATGAAAAGGTAAATCCAATTTCTCTTTGCCTTCCTGGAGGAAGGTGG
102146 TC T ATTCGAGGAGATTGCTAATGTAGATGGTAAGCTGGAAATCAATGCTGCACGATCATACTTTTCAGCAATTTCAGAGGAGGGGTCGTTTGAAAAATGTACT[TC/T]CCATTAACGAACTTGCTGCGATGATCAAGGTTGGTTTCCTCTTGGATTTTGATGATGTTGGTGAATGATTCTTCTTAAAGCTCTTCT
102158 AT A CAAAGCTCACTGTGGATCGCTGAAGAAAATCTACTGCCCAAGATAAACGCGGCTGTAAGTGACCCATTTCGCTTCTAGCTCAGGCCAAAAAAGGCTTTAA[AT/A]TTGCTGTCATTACTTCTAGATTGTCATTTCGCATAATTAATAGCGAAAGAAGTTTATTCTATAATAATCAATCTATGATGTGTAGTTC
102164 C T CGTGGGAGGCTGTTGGGGACGTGGAGTGGATGTACTCGATGCCTTTGGCTGCGGCTAGCGCGATCGCGGAGCGGGTCTCCCAGTTTAGTGGAGTCCGGCC[C/T]GATCCTCTGTTGCCGTGAAGAAGGGAAGACAAACTACCCATGCTCATGTAATCATAGACAAGCAGTCTCTCCTCTTTACTGAAAT
102168 G A GTTACTCTCAGATTGTCCTCAAAATAACTAATAAGTTTTTAAGTACATCTTTCCAAGAGAACAGTTCTAGAAAAGACGTACTACACAGAAATACATCAAC[G/A]AAGAACATTTTATAATTTCGAGTCAAGCACACATCGAAGGCATTCGCCCTCATGCAAAAGGTCAAATGCCTTGTTGATCTCCGAAAAAC
102168 T G TCAACGAAGAACATTTTATAATTTCGAGTCAAGCACACATCGAAGGCATTCGCCCTCATGCAAAAGGTCAAATGCCTTGTTGATCTCCGAAAAACCCAAC[T/G]TGTGCGTGATATACTCATCAACCTTAATCTCCTTTTTCATGTACTTGTCAACAAGCCATGGCACCTGAGAACGGCTTTTAAATCCGCCA
102170 A G TACCCAACAACCAACAACCCCTTTCCCAACTCCAGAACCAGCAACAGCAGTTCCTACCCAACAACGCACAGCCCATTTCCCAGCCTCAGAACCAGCAGCA[A/G]CAGCAGTTCATACCAACGAACTCACAGTATGTTCCGATGCAATCGTACTACCAACTCCCGGTCCAGCAATCTCATTACGTGCCGCAAT
102170 G A CTCAGAACCAGCAGCAACAGCAGTTCATACCAACGAACTCACAGTATGTTCCGATGCAATCGTACTACCAACTCCCGGTCCAGCAATCTCATTACGTGCC[G/A]CAATCTCAGCCGTTTGATCCTTCTGTGCCGATGTACTATGTACCCGTTCGTCAAAACCAGCAGCAGCCCGTTTCTGTACAGGTCCCCA
102170 C T ACGTGCCGCAATCTCAGCCGTTTGATCCTTCTGTGCCGATGTACTATGTACCCGTTCGTCAAAACCAGCAGCAGCCCGTTTCTGTACAGGTCCCCAAGGG[C/T]GGTGCGCCCAAATCCGAGCTGCAGCCCAACATGTACAGGTCGGTTCCACCACCTTCGCAGATGGTCCATATGGCTGCACCAGGAGG
102170 C T AGCCGTTTGATCCTTCTGTGCCGATGTACTATGTACCCGTTCGTCAAAACCAGCAGCAGCCCGTTTCTGTACAGGTCCCCAAGGGCGGTGCGCCCAAATC[C/T]GAGCTGCAGCCCAACATGTACAGGTCGGTTCCACCACCTTCGCAGATGGTCCATATGGCTGCACCAGGAGGTGGATATCATGTGCTG
102178 T C GCGCCTGAACTTATTAGAGAGGTTGCTTTAGACTATATTGAGGCTGGTGCAAATATCATAGCTACGGCGTCTTATCAGGCAACAATTCAAGGTTTTCAAT[T/C]GAAGGGGCTTTCTGTAGAAGAAAGCGAAAATTTACTTAGAAAGAGTGTTCAACTTGCATGTGAAGCAAGGAACATATTTGAAACAAG
102178 A T GTCTGAGTATAGGGGAGATTTCTGCAAATCGCTCACTGTGCAAACTCTGAAAGAGTTCCATAGGAGAAGATTTCAAGTTCTTGCAAAGTCTGGTGCTGAT[A/T]TAATTGCGTTTGATTTGATTCCTAATAAAATGGAAGCTCAGGCTTTTGCTGAGCTTTTGGAGGAAGAAGATATTGACATACCGGCAT
102184 AC A AAACCAGGGCCACATCAACCCCATGCTCCAGTTCGCCAAACGCCTCTCCTTCCACGGCATCAAAACCAGCCTAGCCCTAACCCGCTACATTTCCACCTCC[AC/A]CCCACCCCAAACCCGGCCCAGTTTCCATCGTCACCATCTCCGATGGCTTCGACCAACTCGGCTTCGCGTCCGCTTCCACCATCAAAGA
102184 CCA C GGCCACATCAACCCCATGCTCCAGTTCGCCAAACGCCTCTCCTTCCACGGCATCAAAACCAGCCTAGCCCTAACCCGCTACATTTCCACCTCCACCCACC[CCA/C]CAAACCCGGCCCAGTTTCCATCGTCACCATCTCCGATGGCTTCGACCAACTCGGCTTCGCGTCCGCTTCCACCATCAAAGACTACCTC
102184 C T CCCGCTACATTTCCACCTCCACCCACCCCAAACCCGGCCCAGTTTCCATCGTCACCATCTCCGATGGCTTCGACCAACTCGGCTTCGCGTCCGCTTCCAC[C/T]ATCAAAGACTACCTCGCCCGCTTAGAAACCGTTGGCTCCGAAACGTTAACCGAGTTGATCGAGTCATTCCGGTCGGCCGACGAACCGG
102184 A T ACCCCAAACCCGGCCCAGTTTCCATCGTCACCATCTCCGATGGCTTCGACCAACTCGGCTTCGCGTCCGCTTCCACCATCAAAGACTACCTCGCCCGCTT[A/T]GAAACCGTTGGCTCCGAAACGTTAACCGAGTTGATCGAGTCATTCCGGTCGGCCGACGAACCGGTCCATGTAATTGTATACGATGCGA
102184 T C CTCGCCCGCTTAGAAACCGTTGGCTCCGAAACGTTAACCGAGTTGATCGAGTCATTCCGGTCGGCCGACGAACCGGTCCATGTAATTGTATACGATGCGA[T/C]TTTGCCTTGGGCTTGCGACGTGGGTGGCAAACTCGGGCTGAAAACTGCGGCCTTTTTCACTATGGCCTGTGCAGTCGATTTGATATT
102184 T C AACCGTTGGCTCCGAAACGTTAACCGAGTTGATCGAGTCATTCCGGTCGGCCGACGAACCGGTCCATGTAATTGTATACGATGCGATTTTGCCTTGGGCT[T/C]GCGACGTGGGTGGCAAACTCGGGCTGAAAACTGCGGCCTTTTTCACTATGGCCTGTGCAGTCGATTTGATATTTGCTGAAGCCTGG
102184 C G TCCATGTAATTGTATACGATGCGATTTTGCCTTGGGCTTGCGACGTGGGTGGCAAACTCGGGCTGAAAACTGCGGCCTTTTTCACTATGGCCTGTGCAGT[C/G]GATTTGATATTTGCTGAAGCCTGGGCTGGTAGGATTGTTTATCCTGTTACTGAACCGGTTCTTGTTAAGCCCGGTTTGCCGCTGCTTG
102184 CT C ATATTTGCTGAAGCCTGGGCTGGTAGGATTGTTTATCCTGTTACTGAACCGGTTCTTGTTAAGCCCGGTTTGCCGCTGCTTGAGCCGAATGACATGCCGT[CT/C]TTTTTTATCGGATCCGGCCTGCAGTCCGTACACGCCTATTTTGAGGTGCTTTTAAGCCAGTACAAGAATTTGGAGAAAGCTGATTTA
102184 C CT TTTATCCTGTTACTGAACCGGTTCTTGTTAAGCCCGGTTTGCCGCTGCTTGAGCCGAATGACATGCCGTCTTTTTTATCGGATCCGGCCTGCAGTCCGTA[C/CT]ACGCCTATTTTGAGGTGCTTTTAAGCCAGTACAAGAATTTGGAGAAAGCTGATTTAGTGTTGATCAATTCCTTTTACGAGTTAGAAAC
102184 A C TTATCCTGTTACTGAACCGGTTCTTGTTAAGCCCGGTTTGCCGCTGCTTGAGCCGAATGACATGCCGTCTTTTTTATCGGATCCGGCCTGCAGTCCGTAC[A/C]CGCCTATTTTGAGGTGCTTTTAAGCCAGTACAAGAATTTGGAGAAAGCTGATTTAGTGTTGATCAATTCCTTTTACGAGTTAGAAACCC
102184 A AC TTATCCTGTTACTGAACCGGTTCTTGTTAAGCCCGGTTTGCCGCTGCTTGAGCCGAATGACATGCCGTCTTTTTTATCGGATCCGGCCTGCAGTCCGTAC[A/AC]CGCCTATTTTGAGGTGCTTTTAAGCCAGTACAAGAATTTGGAGAAAGCTGATTTAGTGTTGATCAATTCCTTTTACGAGTTAGAAACC
102184 T C ATTTAGTGTTGATCAATTCCTTTTACGAGTTAGAAACCCAGGAATTTAACATGATGAAATGTATGTATCGAATCAAATCGATTGGCCCTACAGTTCCCTC[T/C]GCATACATGGACAACCGCATTCCAACTGACACCGAGTATGCCATCAACCTCCATCCACCAGACTCCCAATCCTACATCTCCTTTCTCTTC
102184 T C CCAGGAATTTAACATGATGAAATGTATGTATCGAATCAAATCGATTGGCCCTACAGTTCCCTCTGCATACATGGACAACCGCATTCCAACTGACACCGAG[T/C]ATGCCATCAACCTCCATCCACCAGACTCCCAATCCTACATCTCCTTTCTCTTCTCAAAACCAGATTCTTCCGTCATTTACATCTCATTTGG
102186 G A GAGCCAAGACCAAGCTCGAACTCCAATGCCCAGGTGTTGTATCATGCTCGGACATACTGGCAATGGCGGCGAGGGATCTTCTTACAATGGTCGGAGGCCC[G/A]TTCTACAAAGTAGCCCTCGGCAGACTGGACAGTCTAACGTCCACGTCGGCGTCCGTGAAGAAAAGCCTGCCACTCCCGAACATGA
102186 G C ACAGTCTAACGTCCACGTCGGCGTCCGTGAAGAAAAGCCTGCCACTCCCGAACATGACAATGTCCCAAATAATCGATAACTTTGCGTCGAAAGGGTTCAC[G/C]GTTAGGGAGTTGGTGGCCTTATCAGGGGCACACACGGTGGGGTTCTCGCATTGCAAGGAGTTTGCGGATCGTCTTTTCAACTATGG
102186 A G CCGTGAAGAAAAGCCTGCCACTCCCGAACATGACAATGTCCCAAATAATCGATAACTTTGCGTCGAAAGGGTTCACGGTTAGGGAGTTGGTGGCCTTATC[A/G]GGGGCACACACGGTGGGGTTCTCGCATTGCAAGGAGTTTGCGGATCGTCTTTTCAACTATGGGAACAGAGGGCATAACTCGTACG
102186 A C ACGGTTAGGGAGTTGGTGGCCTTATCAGGGGCACACACGGTGGGGTTCTCGCATTGCAAGGAGTTTGCGGATCGTCTTTTCAACTATGGGAACAGAGGGC[A/C]TAACTCGTACGACCCAAGCCTGAACCCGAGGTTCGCGCAGGCGTTGCAGAAGACGTGCGCGAACTACACGAAGGATCCGACCAT
102186 T G CGGTTAGGGAGTTGGTGGCCTTATCAGGGGCACACACGGTGGGGTTCTCGCATTGCAAGGAGTTTGCGGATCGTCTTTTCAACTATGGGAACAGAGGGCA[T/G]AACTCGTACGACCCAAGCCTGAACCCGAGGTTCGCGCAGGCGTTGCAGAAGACGTGCGCGAACTACACGAAGGATCCGACCATG
102186 C T AGGAGTTTGCGGATCGTCTTTTCAACTATGGGAACAGAGGGCATAACTCGTACGACCCAAGCCTGAACCCGAGGTTCGCGCAGGCGTTGCAGAAGACGTG[C/T]GCGAACTACACGAAGGATCCGACCATGGCGGTTTTCATGGATGTGATGACGCCGGGGAAGTTCGATAACATGTATTACAAGAAT
102186 T C TCGCGCAGGCGTTGCAGAAGACGTGCGCGAACTACACGAAGGATCCGACCATGGCGGTTTTCATGGATGTGATGACGCCGGGGAAGTTCGATAACATGTA[T/C]TACAAGAATTTGGAGAAGGGTTTGGGGTTGCTTAAGTCTGATCAGGATTTGATGAGTGATAAGAGGACTGCGCCGATAGTGAGG
102186 T C ACACGAAGGATCCGACCATGGCGGTTTTCATGGATGTGATGACGCCGGGGAAGTTCGATAACATGTATTACAAGAATTTGGAGAAGGGTTTGGGGTTGCT[T/C]AAGTCTGATCAGGATTTGATGAGTGATAAGAGGACTGCGCCGATAGTGAGGCAGTATGCAAGGGATCAGGATGCGTTCTTTAAG
102186 A G CGATAGTGAGGCAGTATGCAAGGGATCAGGATGCGTTCTTTAAGGACTTTACGGCTGCCATGGAGAAGTTGAGTTTGTATGGAGTCAAGACAGGGAAGAT[A/G]GGCGAGGTTAGGAGGAGATGTGATGCTGTTAACAATCTTAGTATGTGATAGAGATTTCCATAGAAGTTTGGTGATTTGTTCGTA
102190 C T CTACAGGCTATTGCGTTTTTATGGGCCCAAATCCAGTGTCGTGGTGTTCCAGAAAACAACCAACAGTCTCTCGCTCCAATACAGAAGCGGAGTACAGATC[C/T]GTGGCTAGCACCACTCTGAGCTCTTATGGATTCAATCGCTACTTCGAGAGCTTCAAATTGATAACCCTAGGAAACCGACAATTTGGTG
102204TCTTCAACAAATTAC T CTTCGCCTTCACCTTGCTGATTTTAGGAAACTCCATTTCCTTTTCGATTTTGTTTGATTTTGGTTCAGACATTTTGTAGCTAATTCAAATCTGAATAAAA[TCTTCAACAAATTAC/T]CTTCAACAAATTACCTCAGTCTGGGAGTAGGTAAAAGGTAGCAACCTTCAAGCAGCAAAGTAGGGCAGCGAGAGG
102208 T G ACTGGAAAAAGAAAATCCATACAATACAATGCCTAACCTGCAAGAAAAAGTAGTCCTTTTCCCGAGCATAGGAATGGGTCATCTGATTCCAAT[T/G]GTCGAACTGGCCAAGTGCTTCACTCAGACGAATTTCTCAGTCACCATCATCGTTGTCACCTCTCCATTCATCCCATCCCTCAACTCATCATACATT
102208 T C AAGTAGTCCTTTTCCCGAGCATAGGAATGGGTCATCTGATTCCAATTGTCGAACTGGCCAAGTGCTTCACTCAGACGAATTTCTCAGTCACCATCATCGT[T/C]GTCACCTCTCCATTCATCCCATCCCTCAACTCATCATACATTTCCAACATCTCCTCCACCTACCCGTCCATCTCCTTCCACCACCTTCCGGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102208 A C TCACCTCTCCATTCATCCCATCCCTCAACTCATCATACATTTCCAACATCTCCTCCACCTACCCGTCCATCTCCTTCCACCACCTTCCGGAAATTCCTCC[A/C]TCAAAACTCCGCACACACAATCGTGTGCTTGCAAACTTCGATATCCTCCGTTTATCGAATCCCCATTTATCCAATTTCCTTTCAGAAGTTCCA
102208 A T CCTCTCCATTCATCCCATCCCTCAACTCATCATACATTTCCAACATCTCCTCCACCTACCCGTCCATCTCCTTCCACCACCTTCCGGAAATTCCTCCATC[A/T]AAACTCCGCACACACAATCGTGTGCTTGCAAACTTCGATATCCTCCGTTTATCGAATCCCCATTTATCCAATTTCCTTTCAGAAGTTCCAAAC
102208 A C TCCCATCCCTCAACTCATCATACATTTCCAACATCTCCTCCACCTACCCGTCCATCTCCTTCCACCACCTTCCGGAAATTCCTCCATCAAAACTCCGCAC[A/C]CACAATCGTGTGCTTGCAAACTTCGATATCCTCCGTTTATCGAATCCCCATTTATCCAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATC
102208 C T TCCTTCCACCACCTTCCGGAAATTCCTCCATCAAAACTCCGCACACACAATCGTGTGCTTGCAAACTTCGATATCCTCCGTTTATCGAATCCCCATTTAT[C/T]CAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATCTTTCTCGACATGTTCTGCACGTACGCTCTTGAAGTAGCACGAGACCTCAACATC
102208 G A TTGCAAACTTCGATATCCTCCGTTTATCGAATCCCCATTTATCCAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATCTTTCTCGACATGTTCTGCAC[G/A]TACGCTCTTGAAGTAGCACGAGACCTCAACATCCCGCCGTACTTTTTCTTCGCCAGCAGCGCTTCTGCACTCATAGCATTCGTTTCAACGG
102208 A G GTTTATCGAATCCCCATTTATCCAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATCTTTCTCGACATGTTCTGCACGTACGCTCTTGAAGTAGCACG[A/G]GACCTCAACATCCCGCCGTACTTTTTCTTCGCCAGCAGCGCTTCTGCACTCATAGCATTCGTTTCAACGGCCACCTTGAAATACTTTGGCC
102208 G A ATTTATCCAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATCTTTCTCGACATGTTCTGCACGTACGCTCTTGAAGTAGCACGAGACCTCAACATCCC[G/A]CCGTACTTTTTCTTCGCCAGCAGCGCTTCTGCACTCATAGCATTCGTTTCAACGGCCACCTTGAAATACTTTGGCCAAACCCAGTTGAAC
102208 G C TATCCAATTTCCTTTCAGAAGTTCCAAACATTCGCGCAATCTTTCTCGACATGTTCTGCACGTACGCTCTTGAAGTAGCACGAGACCTCAACATCCCGCC[G/C]TACTTTTTCTTCGCCAGCAGCGCTTCTGCACTCATAGCATTCGTTTCAACGGCCACCTTGAAATACTTTGGCCAAACCCAGTTGAACTTC
102208 G A TTTATGGAACACATGACCGCCTTGCCGAAGGCAGATGGGATTGTAATCAACACGTTTGAAATGATCGAGAGGGGTGCGGTTCAGGCTTTGAACGATGGAC[G/A]GTGCTACCCGGGTAGGCCCATGCCTCCGGCCTACTGTGTTGGTCCGTTGATTTCCGATGGAGGTTCAGGGATGGGGAAACACAA
102210 G A CAAAAGAGGTGACAAAAAGGGTAGAGATGAACGGAGGGTGGTGGAAGAGTTGGAACTGGAGATCGGAGGGCGATATGCTGCTTAACGGGGCTTACTTCAC[G/A]CCATCTGGCGCTGGATCTTCCGCTAGCTATGCCAGAGCATCGAGTTTGGGTGCCAAATCATCATCTATGGTTGCTTCCATCACT
102210 T C GGGTAGAGATGAACGGAGGGTGGTGGAAGAGTTGGAACTGGAGATCGGAGGGCGATATGCTGCTTAACGGGGCTTACTTCACGCCATCTGGCGCTGGATC[T/C]TCCGCTAGCTATGCCAGAGCATCGAGTTTGGGTGCCAAATCATCATCTATGGTTGCTTCCATCACTTCTGGAGCTGGTGTCCTTG
102210 G A ATCTGGCGCTGGATCTTCCGCTAGCTATGCCAGAGCATCGAGTTTGGGTGCCAAATCATCATCTATGGTTGCTTCCATCACTTCTGGAGCTGGTGTCCTT[G/A]GTTGTCGCAGACGAGCTCAGTGCTAGTGCTAGCTCTATCAATTTATTTCACATATCATAGTATTTTTTTTTTTTAAATTTGATTATTTCCG
102210 GT G ATCTATGGTTGCTTCCATCACTTCTGGAGCTGGTGTCCTTGGTTGTCGCAGACGAGCTCAGTGCTAGTGCTAGCTCTATCAATTTATTTCACATATCATA[GT/G]TATTTTTTTTTTTTAAATTTGATTATTTCCGTATATGCTACACAAATTGATCACACCAAGTTTGCTCACCACTCGCCTCTCCAACCTCCTC
102210 C T CTGGTGTCCTTGGTTGTCGCAGACGAGCTCAGTGCTAGTGCTAGCTCTATCAATTTATTTCACATATCATAGTATTTTTTTTTTTTAAATTTGATTATTT[C/T]CGTATATGCTACACAAATTGATCACACCAAGTTTGCTCACCACTCGCCTCTCCAACCTCCTCCTGCTTACCAAGCGGGTACGAGCAGCGTT
102210 C T TTTTTAAATTTGATTATTTCCGTATATGCTACACAAATTGATCACACCAAGTTTGCTCACCACTCGCCTCTCCAACCTCCTCCTGCTTACCAAGCGGGTA[C/T]GAGCAGCGTTGCTTACTGGATCCACCATCCATGTTAACTTCCTTTCACGCCGTACGTGTATTATATGTTATTTCTGTGTCTCTCTTCCGTAG
102212 A G TAATCCGTGGCAGTCCAGATGTAAAATGGGACAGCATTAAGGGGTTAGAAAATGCAAAGCGTCTTTTAAAGGAAGCAGTAGTCATGCCTATAAAATACCC[A/G]AAGTATTTTACTGGCCTTCTTTCACCCTGGAAAGGTATTTTACTATTTGGCCCTCCTGGTACAGGAAAGACCATGCTTGCGAAGGCT
102218 C T ATAATACTCTATCTGCTTCAAAACTGCTGCACCCATGGCTCCTGGGGATGGAACTGAATGAG[C/T]AGCAACATGAGGAGGAGGTGGTGGTGGTCCCATTACATAGAAAAAAGGAGAAGTCGATCCAGGGAAGCAGAAAGGTGATGTCACAAATGGCCTAACAGGA
102218 A T CCATTACATAGAAAAAAGGAGAAGTCGATCCAGGGAAGCAGAAAGGTGATGTCACAAATGGCCTAACAGGAGGAGGTGGTGGGGCAAATGGACCTGCACC[A/T]GCAGCAGGTGGAGGTGGTCCAACAAACAGACCTGCACCAGGAGGAGGTGGTCCAACAAACTGCACTGCACCAGCAGGTGGTA
102218 G A AGGGAACGTTGGTTTTCCTCGCCCAGAGTCAGGGCTTGAAGAATTAACCTTCAGCTGATTATTCACTGGAACAGGAGCAGGAATTGAAGCTGATCCATCG[G/A]ATTTGACAGCAGATTCTCCCAAAGCAGGCCAAGAATCGGCACCCATAACGTGAGTAGAATCGTTCGCGATGGGATTAGCTTCGTTT
102228 AT A AGCGTGGAAAATGATATTCGCGTCCGACGACACGAATAAAATCTTCAGCGTGCTTTGCTGCGAACGCACCTTTAGGATAAGCGCCGATTCATACAGTTTC[AT/A]TTTTTTGTTCTAGGTAAACTCTTTAGTCCTCGTTCTTCGTGCCTTACTGGATCTGGAACCCTGCGCCGCATCCCATACTGCTCCTTATT
102228 A G ACGCTGAAGACCAACCGCTATTCATTCAAACAATTCCCTTTTCCACATATCCGTTCCTCAGCTACTCTGTAGCACTTCACCATACTGACTTCACTTACCC[A/G]CCACCACACCTCAAGTCTGGCCGGCGGCGTCAATCTGACCACCCATGACCGGCGCCTCAAGCCTCTCTCTCTTCAGTCCTGGCCTCAGGA
102234 C G TATCATCTCGAGTTTCGACAACCGCGTCTCCTTGGCCTCGCCTGGACTATTGGTCCACCTTCTGGTCACAACTTTTCTCCTCTTTCCAAACCCTGAGCTC[C/G]CGTGTCTTCCGTTCGAGCTTCGCCTGTCTTGAAGCAACAAAGCCGCTGTAGTTTTTGCTGGTAAGGTGGGGAGTGCTTTTGCTGCTGAA
102234 A T GCCGCTGTAGTTTTTGCTGGTAAGGTGGGGAGTGCTTTTGCTGCTGAACTAGATACGATGCAGATTGTAGAAAAAAATAGAAGAGCAATGGTGGAGAATT[A/T]GCGCAATTGCGTTTGAGGAAGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCA
102234 G A GCGTTTGAGGAAGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTC[G/A]GTCCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATG
102234 G T CGTTTGAGGAAGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTCG[G/T]TCCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGA
102234 T G GTTTGAGGAAGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTCGG[T/G]CCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAA
102234 T C AAGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTCGGTCCTAGCT[T/C]TGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGC
102234 T C AGAGCAGTTTCTAAGAGTGGTTATCTTTTCTTTTCTTAGTCTGGTATTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTCGGTCCTAGCTT[T/C]GACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCT
102234 T A TTTATATTTGCGGATAAGAGCATCAACAGCTGACCGCTGCTTCGGTCCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGA[T/A]TAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTC
102234 T G GAGCATCAACAGCTGACCGCTGCTTCGGTCCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAAT[T/G]AATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTG
102234 A G GCTGCTTCGGTCCTAGCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGA[A/G]TTAGTTGCTTTTGGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCC
102234 G T GCTTTGACCGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGG[G/T]CTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTT
102234 T C CGATCCGAGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATAT[T/C]GGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGG
102234 C T AGGTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATATTGGTCAC[C/T]GTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGC
102234 T C GTTTAGCCACGCAAGGTGAAATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATATTGGTCACCG[T/C]CGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCC
102234 T C ATCTTTCTCGTGATTAATTTTTGTTTAAATTAATTTACCTCAATATGAATTAGTTGCTTTTGGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTC[T/C]GTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCA
102234 C T AATATGAATTAGTTGCTTTTGGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCA[C/T]CTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTT
102234 T C GGGCTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCT[T/C]GGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTG
102234 T C CTTATATTGGTCACCGTCGATCGGCCCCTCCACCTCTGTCTTTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGG[T/C]GATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTC
102234 A C TTGTTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAG[A/C]AAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAAT
102234 A C TTTATCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAA[A/C]GGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGT
102234 A G TCCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGC[A/G]ACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGTGCCA
102234 A G CCTTCGCTGCACCGTTCCCTTTGCTCCACCTCCAAGCCGCCTTCATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCA[A/G]CTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGTGCCA
102234 G A CATCTTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCA[G/A]TTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGTGCCATGCACCACCTGGAACCGGCAACTTCACCTCACATTTGCTGCTG
102234 A G TTGGTGATGGCCCCACCGAGAACACGAGCTTCAAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTC[A/G]AACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGTGCCATGCACCACCTGGAACCGGCAACTTCACCTCACATTTGCTGCTGACG
102234 A G AAATTCATCTCAGAAAAGGCAACTTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCA[A/G]TAGTGCCATGCACCACCTGGAACCGGCAACTTCACCTCACATTTGCTGCTGACGATAGACCCGGCCACTGCAAGCCCCAAGTGTTA
102234 C T TTAGCTAGGGGTGGCTTTGTTCGGCTCCATCTGTTGATTCAGTTCAAACCTGCAAGTAGAAAAATATGGGGAAAGCAATAGTGCCATGCACCACCTGGAA[C/T]CGGCAACTTCACCTCACATTTGCTGCTGACGATAGACCCGGCCACTGCAAGCCCCAAGTGTTACAGATGCAAAGG
102246 T C TGGATGTGGAGAACAATACCTTGCCGATGCATACATGTGACGACATGGAACTAGACTTAGCATCATCGAGTGAACCACCGGCAACGAGTTTGAAGCTATT[T/C]GGAATGATTTTTGTGATAGAAGATTCGCCAAAGGCATTGAGCTCTATCATAGTAGCAGAACACGAAGATGAATCTTTCACCGATAA
102252 G A TTATTTTTGACATTGATATTCTAGTATTTGGATTTGGGTCGAGAATTTTAGAGATGAGCCTTTTTACGTCGGATGGAAACCAATTTGGGTACTTGAATTC[G/A]GACTTTCCAATCTTTCTATACATCTCCATTAAATTTGAGTCGTGGAAAGGGAGATAACCTGCTAGTAGAACGTATAATATCACGCCACA
102252 T A TCAGACCAAAATCCGAAACCTTCAAATTTCCATTTTCGTCCAACAAAAGGTTTTCAGGTTTCAAATCACGATGATAAACGCCTCTACTATGGCAAAAGCT[T/A]ACGGCACTAATGAGTTGCTGAAAATATTTTCTTGCCACATCTTCTTTGAGTTTCCCTTTAGCAACCTTGTTGAATAGCTCACCTCCTTTAA
102252 AT A GCTGAAAATATTTTCTTGCCACATCTTCTTTGAGTTTCCCTTTAGCAACCTTGTTGAATAGCTCACCTCCTTTAACATATTCAAGAACGAAGTATATTTT[AT/A]TTTTTTGTTGCCATGACTTCATAGAGCTGAACAATATGCGGGTGCCTCACCAATCTCATAATCGAAATCTCGCGTTTGATTTGATCTATAA
102256 T C TTCGCGACTCCTCTCGCTTTTTCTGGGTTGCTTATATCCTATTATACCAAGTACACAATGTATCTGCTCTATCTTGGTGAGCTTATGGTGGAATTAGTGT[T/C]TGGATGGTGAGAGTTTGTTGGGCTTGCTGGATTGTATGCTTGATGGTGTAGCGCTATTAGTCGTCATGTCATAGCTGATAGTGGAGGG
102260 T C TGGCTGTAACAACGATTTGCAGCTTCGCAACGATTCTTGCTTGTCCACCGGCTTTGATTGAGGTGGCTTCTTAGGTGCTGAAGTGCTTTCAGATGTGGAG[T/C]CCTTGTTAGATATTGTTACTGGAAATTATTCATTGCTAGATTGGTGGTCTCTTCAGCATTGTTGTTGAGTTCATTCTCCCCCTGTGTTTT
102262 T C CGGTTGGGTCGTAAACTTTCAATGTTGTTCATGCTTTGTGCTTGTGGAATTTTCTTGGTTCCACTAGCAAGGAGTCAGAGCGAAGTCGTGACTACCGTTC[T/C]GTTATTTGGTGCTCGTATATGTATCACTGGAAGCATCAATACTCTGTATGCATACGCCCCTGAGGTGTATCCAACGTCGGTGAGAAGC
102274 A G GCAGGTTAAGAGAAGAGAACTGCAGCTCGTGGGTGTCAGTTCAATGCTCATTGCTTCCAAATACGAGGAGATCTGGGCTCCTCAGGTAGAGGACTTCATT[A/G]GCATATCGGACAGGGCCTACAACCAGGACCAGATCCTACATATGGAGAAGGCGATCCTGAACAAGCTGGAATGGAACCTGACAG
102282 G A CCATACCACCGTGGGAACCAGCACCCTGGCTCTTAATGTGGTCGACGGCTGCTTGGTTCCAAGAATCCTCTTTGACGATGTTGGTTCCAGGCTCTGGGCT[G/A]CCAAGAGCACCGGCGGAGCCAATGATATAGACGCGCTTGACGGAAGGTGCGTATTTCTTGGCGCTTTCCAAGATCCCTATGGTACC
102282 C T TTAATGTGGTCGACGGCTGCTTGGTTCCAAGAATCCTCTTTGACGATGTTGGTTCCAGGCTCTGGGCTGCCAAGAGCACCGGCGGAGCCAATGATATAGA[C/T]GCGCTTGACGGAAGGTGCGTATTTCTTGGCGCTTTCCAAGATCCCTATGGTACCCTTGATAGCAGGTTGGACGACATCATCTGGGT
102282 A G TGGTTCCAAGAATCCTCTTTGACGATGTTGGTTCCAGGCTCTGGGCTGCCAAGAGCACCGGCGGAGCCAATGATATAGACGCGCTTGACGGAAGGTGCGT[A/G]TTTCTTGGCGCTTTCCAAGATCCCTATGGTACCCTTGATAGCAGGTTGGACGACATCATCTGGGTGCTTGAAAACGAAAGTGACG
102284 T A GTGATGAGAGTCAGAGCTTTTCGCCTGACTTGAAACTGTTTGTAGGAAATTTGCCTTTTTCAGTTGAGAGTGCCGACCTTGCTGGGTTGTTCGACAACGC[T/A]GGGACTGTCGAGATGGTTGAGGTTATTTATGACAAAGAGACCGGTAGAAGTCGTGGCTTTGGGTTCGTGACAATGTCTACTGCTGA
102284 A G GACCGGTAGAAGTCGTGGCTTTGGGTTCGTGACAATGTCTACTGCTGAGGAGGTTGAGGCAGCTGCCCAACAGTTCAATGGCTATGAGTTTCAAGGAAGA[A/G]CATTAAGAGTAAATTATGGGCCACCTCCTCCAAGAGAGGAGCGTGCACCCAGAAGTTTCAGAAGCGGTGGCAGCGGCAATGCTG
102284 C T CCCAACAGTTCAATGGCTATGAGTTTCAAGGAAGAACATTAAGAGTAAATTATGGGCCACCTCCTCCAAGAGAGGAGCGTGCACCCAGAAGTTTCAGAAG[C/T]GGTGGCAGCGGCAATGCTGCTAACTTTGAAGCTGGCAGCAGACTATATGTTGGTAACTTATCATGGGGGGTTGACAATCTTGCCC
102284 C T ATGTTGGTAACTTATCATGGGGGGTTGACAATCTTGCCCTTGAAACTCTATTTAGTGAACAAGGAAAAGTAACGGATGCTAGAGTTGTTATCGATAGAGA[C/T]ACCGGGAGATCCAGAGGCTTTGGCTTTGTTACTTATAGCTCTGCTGCTGAGGCTAATAATGCTATTGCATCTCTTGATGGATCTGAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102284 T C AACAAGGAAAAGTAACGGATGCTAGAGTTGTTATCGATAGAGACACCGGGAGATCCAGAGGCTTTGGCTTTGTTACTTATAGCTCTGCTGCTGAGGCTAA[T/C]AATGCTATTGCATCTCTTGATGGATCTGACTTAGATGGCCGAACTATCCGTGTCTCGATCGCTGAAGCAAGACCACCTAGACGTGA
102292 G A AATTGCAACTGGGTTTTCCAAAGAATTTGGAACCACTCTCAAAAAGGCACATAAATATGTTAAGGACTCTCAGGTTCTAGAAGACTGCCCTGGTGATCTT[G/A]GTCACTGGCACCGCCATATATCTAAGGGTGCATGGCCTTTCTCCACAGCTGATCACGGATGGCCCATCTCTGATTGTACTGCTGAAGG
102292 A G ACGAGTTGACAAGGTCATATGCATGGTTGGAGATCATCAATCCTGCAGAAACATTTGGAGACATTGTTATAGATTATCCATGTGTTGAATGTACATCAGC[A/G]TGTATTCAGGCTTTGGCTTCATTTAGAATGCTATACCCTGGACACCGGAGAGTAGAAATAGAAACGTGCATTACGAAAGCCGTTCAA
102292 T A GGTCATATGCATGGTTGGAGATCATCAATCCTGCAGAAACATTTGGAGACATTGTTATAGATTATCCATGTGTTGAATGTACATCAGCATGTATTCAGGC[T/A]TTGGCTTCATTTAGAATGCTATACCCTGGACACCGGAGAGTAGAAATAGAAACGTGCATTACGAAAGCCGTTCAATTTATTGAAAAG
102296 T C GTACAACATGCAAATTTCAGCTTTCACCAGTTTTAGCTCAGTTGTTCAACGGTGTTTCGGAAGAACTCGGTTCACCAATGGACACAGATGCCAATGACTT[T/C]GATGCCCACGCCTTCGCATTATTCATTGCCTCTTCTTGAATATGAATGCTTTTCTTGCACGGATTCAATCTACTCAAGCTTTGCTTTGCTT
102296 A C CAACGGTGTTTCGGAAGAACTCGGTTCACCAATGGACACAGATGCCAATGACTTTGATGCCCACGCCTTCGCATTATTCATTGCCTCTTCTTGAATATGA[A/C]TGCTTTTCTTGCACGGATTCAATCTACTCAAGCTTTGCTTTGCTTCATGAAGATATGCATGGAAATGATCCCATAATGTAAGTAGACCC
102296 C T AAGAACTCGGTTCACCAATGGACACAGATGCCAATGACTTTGATGCCCACGCCTTCGCATTATTCATTGCCTCTTCTTGAATATGAATGCTTTTCTTGCA[C/T]GGATTCAATCTACTCAAGCTTTGCTTTGCTTCATGAAGATATGCATGGAAATGATCCCATAATGTAAGTAGACCCACGATTTGTATGAGT
102296 T C ATGCTTTTCTTGCACGGATTCAATCTACTCAAGCTTTGCTTTGCTTCATGAAGATATGCATGGAAATGATCCCATAATGTAAGTAGACCCACGATTTGTA[T/C]GAGTCTCCTATAAGCTCTTTCGATGTACGAATTGAGTTTTGGAATAAGGAAGTAGAGTAGTTTTAGTGATACAAAGATGCTAGCTAAGG
102296 A T CATGAAGATATGCATGGAAATGATCCCATAATGTAAGTAGACCCACGATTTGTATGAGTCTCCTATAAGCTCTTTCGATGTACGAATTGAGTTTTGGAAT[A/T]AGGAAGTAGAGTAGTTTTAGTGATACAAAGATGCTAGCTAAGGCTAGATAAGTGTCTTGTTGCAGTATCTTCTCCGGTGAACGAGCC
102296 A G GTATGAGTCTCCTATAAGCTCTTTCGATGTACGAATTGAGTTTTGGAATAAGGAAGTAGAGTAGTTTTAGTGATACAAAGATGCTAGCTAAGGCTAGATA[A/G]GTGTCTTGTTGCAGTATCTTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTT
102296 C T CTCTTTCGATGTACGAATTGAGTTTTGGAATAAGGAAGTAGAGTAGTTTTAGTGATACAAAGATGCTAGCTAAGGCTAGATAAGTGTCTTGTTGCAGTAT[C/T]TTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTG
102296 C G GATACAAAGATGCTAGCTAAGGCTAGATAAGTGTCTTGTTGCAGTATCTTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCAT[C/G]TGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGAGGTTTCATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTA
102296 T C GCTAGATAAGTGTCTTGTTGCAGTATCTTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATG[T/C]ATCAGCTGCTTTGTTGACAGAGGTTTCATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTAGAAAGAAATGAGAGAGCTAAT
102296 G T GTATCTTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGA[G/T]GTTTCATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTAGAAAGAAATGAGAGAGCTAATAGTTCGAGAGCCATGATACCGC
102296 T G CTTCTCCGGTGAACGAGCCCATGAGAATGGGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGAGGTT[T/G]CATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTAGAAAGAAATGAGAGAGCTAATAGTTCGAGAGCCATGATACCGCACC
102296 G A GGCAGTTCTCTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGAGGTTTCATCCAGATCAGCTGACTTAATGCCTGT[G/A]ACATCGCTGTAGAAAGAAATGAGAGAGCTAATAGTTCGAGAGCCATGATACCGCACCCGCATGGTAGAATTTAACAGAAAGAGAGT
102296 G A CTTCTATGGTTTCATCTGGGTTAGGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGAGGTTTCATCCAGATCAGCTGACTTAATGCCTGTGACATCGCT[G/A]TAGAAAGAAATGAGAGAGCTAATAGTTCGAGAGCCATGATACCGCACCCGCATGGTAGAATTTAACAGAAAGAGAGTTGGGAAACC
102296 T C GGAAGGCTTGATGTATCAGCTGCTTTGTTGACAGAGGTTTCATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTAGAAAGAAATGAGAGAGCTAA[T/C]AGTTCGAGAGCCATGATACCGCACCCGCATGGTAGAATTTAACAGAAAGAGAGTTGGGAAACCGTGAACTCCATACCGAGATAAG
102296 T C CATCCAGATCAGCTGACTTAATGCCTGTGACATCGCTGTAGAAAGAAATGAGAGAGCTAATAGTTCGAGAGCCATGATACCGCACCCGCATGGTAGAATT[T/C]AACAGAAAGAGAGTTGGGAAACCGTGAACTCCATACCGAGATAAGACTCTTGGGCGGATAACAGATTCCTCGAACGCAAAATGTC
102296 A G GCATGGTAGAATTTAACAGAAAGAGAGTTGGGAAACCGTGAACTCCATACCGAGATAAGACTCTTGGGCGGATAACAGATTCCTCGAACGCAAAATGTCT[A/G]ATTGAAGGAAATAAGGATGCCATACTATTGAAATTTTGCAGACAAATCTTGGAGAAAGGGCACCATGAGGCATGAAAAAGAACTG
102308 TA T TACATCAGATTGATAGTAAGCAAATGAACCGACAATATCCCAACATAGCACTCCATTAATGCTTTGTCCGGATATGAAAGGATTGCCAGACCTCAAACTT[TA/T]AAAAATTAGATCAATCTAAATTTATGTTTGCTGAAGAAAAAAATACAAATATCGCCATAAGTTCAAATACAATGAAATTTAATCTCTA
102308 GA G ATCCCAACATAGCACTCCATTAATGCTTTGTCCGGATATGAAAGGATTGCCAGACCTCAAACTTTAAAAATTAGATCAATCTAAATTTATGTTTGCTGAA[GA/G]AAAAAAATACAAATATCGCCATAAGTTCAAATACAATGAAATTTAATCTCTAATAATTTAATCCTTCTCTGGAAAGAAAAGCACACGTG
102308 G T CGAAGTCGGGCGATTTAATCAAGGTGGCTCTCTATATTTGTTTTGCTGCTTCAGCCTCTACTCCCGCCTTTCCAACTTCGTCTGTCTTAGTTGCCTCTTC[G/T]GTTTGCACTTCATCATCAGATTCATCAAAATCATCTCCCATGCCTCCCATACCACTCATATCCATACCGCCCATGCTGCTCATATCCATACC
102318 C T ACATCTTCTTCCTTCGAGCTTGCTCTTGAGATTGACGTTGTTTTATAGCATCGATCTCATTTGTCTTTGTTTGTTGATTCTGTTGTTGTTGATGTTGTTG[C/T]TGCTGCTGTTCTTTTAGACGTTTTAGTCTTAAGCGGTCACGCCACATGCGTCTTTCAAGTTCTTCGACATCTAAATCATCATCACTGTCTTCT
102318 A G TGACGTTGTTTTATAGCATCGATCTCATTTGTCTTTGTTTGTTGATTCTGTTGTTGTTGATGTTGTTGCTGCTGCTGTTCTTTTAGACGTTTTAGTCTTA[A/G]GCGGTCACGCCACATGCGTCTTTCAAGTTCTTCGACATCTAAATCATCATCACTGTCTTCTTCATCGGGAAGGGTATCATCGTAATTTGAAG
102318 A G CGCCACATGCGTCTTTCAAGTTCTTCGACATCTAAATCATCATCACTGTCTTCTTCATCGGGAAGGGTATCATCGTAATTTGAAGGGATTGGTTCGGATG[A/G]TTCTACATGGATGGATGAAAAATCAGGAATGAAGGCGGTGGCTTTGTCAAAGCAGTTGGGGTCAAAATGGAGATAACTGAAGTTTG
102318 G A AAAAATCAGGAATGAAGGCGGTGGCTTTGTCAAAGCAGTTGGGGTCAAAATGGAGATAACTGAAGTTTGGAGGGTAGTTCAAGCATTCCATTGCTAAACC[G/A]GCCATTGATTTCGAGTATTTGAGATTAGTAATTTTATGTTGCTTTGAATGATTTGTGCCTGCAATTTTTTCATTTGGTTGTTCTTCCT
102320 G A TAATATCAAGTTGCAAGCGCACAGTATTCTTCTAGCTTAAGAAAATGACTTGAAATACAAATAACCTACACGTACAGCGTGGCACTGGATACTATATATC[G/A]GTGACTGATGCATTTAGTTTCTCATGAGTTGCCGAGGAATGCCGAATTATTGGACCAGAAATTACGTGACTCTCTCAAAGGCGCCACC
102320 G C AATATCAAGTTGCAAGCGCACAGTATTCTTCTAGCTTAAGAAAATGACTTGAAATACAAATAACCTACACGTACAGCGTGGCACTGGATACTATATATCG[G/C]TGACTGATGCATTTAGTTTCTCATGAGTTGCCGAGGAATGCCGAATTATTGGACCAGAAATTACGTGACTCTCTCAAAGGCGCCACCC
102320 C T AGCTTAAGAAAATGACTTGAAATACAAATAACCTACACGTACAGCGTGGCACTGGATACTATATATCGGTGACTGATGCATTTAGTTTCTCATGAGTTGC[C/T]GAGGAATGCCGAATTATTGGACCAGAAATTACGTGACTCTCTCAAAGGCGCCACCCACCTGCATGTGTAACCATTCCGCAGCAGATC
102320 T A ATTGGACCAGAAATTACGTGACTCTCTCAAAGGCGCCACCCACCTGCATGTGTAACCATTCCGCAGCAGATCCTTGCCCTCCGTATTCTCTTGGAGGCCG[T/A]GTGCTGAAGGCTAAACTAGGGTTTTCGTATGCTTGCATTCCAAAATCTTTTTGAGGAAAGCCCTCGATCCCAGAATTGGATTGGGGAT
102322 A G TGCATGATTAAATTAAAGCCCAATTTTTTCTGGACCTTCTGGATTTGGTTCAAGAATATCCATGTCATCATAACATG[A/G]GGAGCAATCCTGATGCAGTAGACAGGAAAGCCGGTGTAAAATTTGAAAGGTCCTCCACTCTTCAAGGTCTTTAAGGCACAATCCAATGAACCAGTATAAG
102322 A T AGGCACAATCCAATGAACCAGTATAAGGATATTTACCAGCTGCATCTGGTTGCATTTTCTGAATTTGGGTTTTCACAAAGTCAAACGGCAAACTACATGC[A/T]GCAGCAAAGAACCCAGAAACAGCACTAGCTCCGACTACAGTGCTTACTTCCCCAAAACCAAGTGAATCTCTGAAAAGCTCGACACTCT
102322 A G GCATACCCATATTAAGTGCCATAGCCCTCACAACAGTGGGGCCTGCCCCTTTCCAAAGTGCAAGAACTCCTTCATCGGCAACAATCCGCGAGAGAGCATG[A/G]AAAGCATTTTTGTAGTGTCTCCTCTGTGCTGCAGGTAATGTCGCATCAGCCTGCATACGTATGAGTGCCAAATCAGCTGGACTGCCG
102322 C G CCCCGATAGCACCAGCAGTCAATCCAATAGCAGCTTTTTGAAGGAGGGGCAGGGGCTTTCCATCATTAGCCTCGATAGCTTTGTTTGTAAGCACTCTGAA[C/G]GATCCAAGTCGAGCAGTTGTGTATGTAGCTTGCCTCAACAAACCAGCAGAAAGTCCCTTGTACAAAGATCCGAAACCTTCTTGCGCG
102330 G C TAGCCTTCAACTTCCCTAGAACAGCGGTCAGGCCAGCTACGGTGCTGGACATGGTAGGGGCTGCCTGCCCTACGAGCCCAAACCCCACTTTCGGGTGGGA[G/C]ACTCTTGAGGACTTGGAGGGCGCCCACCCTTGGGTCGAACTGTATAGGGTTGTTAAACTGACATTGGAGCAGGAAAGACAGAAT
102334 G A AATTCTAATGGTGATGAATCTCCTGGAGATGCTTCTAACCAGCTGGTTCTTTATGATCCTGGGTCTGCTAAAACGACCCAAGATGCAATACCAGTGCCTC[G/A]TGATGATCATCAAGCACCACCCATACAAAATTCTTCTAATCGTGTGACACCTGCAGTTGGAGCTTTCACTGTGCAGTGTGCTGACTGT
102336 C T CTGGAGAGGAGAATGCAATTGCTGGCATTGTCACTGAAAGAGATTATCTTAGAAAAATAATTGTGCAAGGGAGATCATCCAAGTCAACTAAGGTTGGAGA[C/T]ATCATGACTGAGGAGAATAAGCTTATCACTGTTAACCCAGAAACCAAAGTTCTCCAGGCCATGGAACTCATGACAGAAAAAAGAA
102336 GA G ATCCAAGTCAACTAAGGTTGGAGACATCATGACTGAGGAGAATAAGCTTATCACTGTTAACCCAGAAACCAAAGTTCTCCAGGCCATGGAACTCATGACA[GA/G]AAAAAAGAATCAGACACATTCCTGTGATCGATAACAAAAACATGATCGGAATGGTTTCAATTGGAGATGTCGTTCGTGCTGTGGT
102336 A G ATGATCGGAATGGTTTCAATTGGAGATGTCGTTCGTGCTGTGGTGAGCGAACATCGCGAGGAGCTGAACCGGCTTAATGCTTTTATACAAGGTGGCTACT[A/G]ATGCTAAGATGATGATGGCGAAAATAATAAATTAGCTTGGAATGCTTTTCTCAGTTCATGAGTTGTTTATTTCGGTGTATGTGCCTT
102338 G A TAATTAATTCTGTACTCGTAGTAACGGCATCGCTGGCGATTTCTGTCGCTGTGCAAGTGTCGGATGTGAGCCCCGCAGAAGCATTTGTGGTGAAGTCACC[G/A]AGAAGGCTGCAGACAGATGAGCAGGCGACTGTGAAATTATTCCAAGAGAATACGCCGTCTGTTGTTTATATCACTAATCTTGCTGTA
102342 G A CAACTGAATCATACTTCACAACTCCTTCATAATTACCAGTAACATCGGCCAATTCATTGTAATTGGTATCCTTTTTGGTTGCTTCAGCGCTACCTCCTTC[G/A]GCAACTGGATCGGTATTAATGTTTACACCAGCATTTTTCTTACCAGTTGTTTGAGTGTGGTTGTTACTAGGTGGCAGGTTAAGGTTGAAG
102346 T C TTGCCTACAGAATTAGGGTCACCAACAATTCTCAGCGCCCTGTTCAGCTCCTTAGAAGGCATTGGATCATAACAGATGCTAATGGAAAAATTGAAAACTT[T/C]TGGGGTGTTGGTGTAATAGGAGAACAACCTGTCATTCTTCCAAAGACAGGATTTGAGTATTCCTCGGCCTGTCCATTGAGCACCCCTA
102348 A T CCCACTCAACGCGCAGACGGTGCGAAAAGAATCCGTCAGGCCGCCCGGGGAATTCGACATATGGAGCTCCATACAATCACAGATTCAGAAACAAGAATCA[A/T]CGGGCGCAGTTCGGAAACAAGAAGAAACCTACACTCCACTTCCTATCAAACGCTGCACTAGTCTCCTCAACCCGAAAAGCCTCGAG
102348 A T GGCCGCCCGGGGAATTCGACATATGGAGCTCCATACAATCACAGATTCAGAAACAAGAATCAACGGGCGCAGTTCGGAAACAAGAAGAAACCTACACTCC[A/T]CTTCCTATCAAACGCTGCACTAGTCTCCTCAACCCGAAAAGCCTCGAGATATGCACTGAAACCCTTTGCTCTGAAACGGGCTCCGA
102348 C T TTCCTATCAAACGCTGCACTAGTCTCCTCAACCCGAAAAGCCTCGAGATATGCACTGAAACCCTTTGCTCTGAAACGGGCTCCGACGACTTTTTCGAGTC[C/T]GACTTCTTTTCCATCCAGCCTCAAACCATTGCAAGGAACACTGAAAGTCGGTTGTTCTCGAAAACAAGGAAAGACATCAACGTTTCACC
102348 A AC CGAGTAGAAGGTCGTTTGGTAGTGCAGGCTGTGACTGTTCGCGCACAGAACTGCTTGCGTGCAGAGAGACAGAATGGCCGTCTTCTGCTCTCATTTAAAA[A/AC]CGCTACTGATAATTCATGGGGAAGATGATATAGAAGACGAAGCAGAGCCAGAAAATGTAGTGGAAGATACTGAAAATGAACAA
102348 TG T GGTAGTGCAGGCTGTGACTGTTCGCGCACAGAACTGCTTGCGTGCAGAGAGACAGAATGGCCGTCTTCTGCTCTCATTTAAAAACGCTACTGATAATTCA[TG/T]GGGGAAGATGATATAGAAGACGAAGCAGAGCCAGAAAATGTAGTGGAAGATACTGAAAATGAACAAGTAATGCAAAAGGAACA
102352 GA G ACATCGTCCGCCACTGTCCTCGGCCAGCCACTGATATATATAGGACATAGATGATAGAACACTGTATCATTCAAAAAAACAAAACAAAAATGAAAATAGA[GA/G]AAAAAAAATGGAGAATAAGCATTTCCTTATCCTGTCATATCCGGCCCAAGCCCACATAAACACGTCCCTCCACCTCGCCCACCGCC
102352 C T CCTTCTCCACCTCCATCTATGCCCACCGCAAAATGTTCCTAGACATCTCCACACCAAACCAAGAAGTGGCCATAAATTCAGTCACGTATCTCCCATTCAC[C/T]GATGGTTCCGACGATGGTTTCGACCCGAAAACCTCAAACGTATCTGAATTCCTCCAGAAATTCAAAACCATCGGATCCGAATCCATCTCC
102356 T A AGGCAGGTTATAACTATGATGACGAGACATTTGAAAAGGTCTTCAGACGAATTTATTCAACTTTTGGTTCATCAGCACCATATTCTGTGTTTCCTGATTC[T/A]CAGCCTTTTATGAGGTGGGCTCGCAAAAAAGGACTAATTGTTGGAGTAGTCAGCAATGCTGAGTATCGTTATCAAGAAGTCATTCTTCC
102356 A G ATGCTGAGTATCGTTATCAAGAAGTCATTCTTCCAGCCTTGGGTTTGAATAAGGGGTCGGAGTGGGACTTTGGGGTGTTCTCAGGCATAGTTGGCATCGA[A/G]AAACCAGACCCAAGAATTTACGAAATCGCCCTGGAGGAAGCGAACGTGTCAGCAGAAGAAGCATTGCACATCGGGGACAGCATG
102356 C A GAATTTACGAAATCGCCCTGGAGGAAGCGAACGTGTCAGCAGAAGAAGCATTGCACATCGGGGACAGCATGAGGAAAGACTACATCCCAGCTCGAAGCAT[C/A]GGAATGCATGCACTGTTATTGGATCGGTTCAAGACCCCGGAAGCTGAAATTTGGAGAAAATCTGGTGCGCCAGTTTTGACCGAT
102356 T C ACAGCATGAGGAAAGACTACATCCCAGCTCGAAGCATCGGAATGCATGCACTGTTATTGGATCGGTTCAAGACCCCGGAAGCTGAAATTTGGAGAAAATC[T/C]GGTGCGCCAGTTTTGACCGATTTAGCAGCTGCGCAGGAATGGCTTTTAAAGGAGGAGGATGAGG
102360 AG A AAACGAAGGTTAGTTGAGATCTGAAATAAGGGTTTTGAAGCTTAGGCTCCACAATGGCGAAATCTGGGAAGATAAGGAGTGGGGAAAAACGATTAGGGTT[AG/A]GGGGAAATAGAAAGCGAAGTGGAAATGAGATTGAAGGAGGAGATTAAAATGAAAGCAAAGGAGAAAAGGAACGGACCCAG
102366 A G CTTCCAACATCGAACCCTCTTTCACGCTCAGGTTCAATGACTAGCAGAGCAGCTTTTCTCAACTCCTCTAGTGCAAGAAGGCGGTTTTCTACTGAAGACC[A/G]AAAAGCATCATCAATGCGCTTACATGCTGAAAGAAATGGTGAAAAAGAGAAGGGGCACTTTCAGAGCAAAGGCAAAAGTTTTCTGAA
102382 C T CCTGAATATGACTTTGTAACTCTTTGATGTGTTGTACTGCCAAATCCAACATATCCGATGTACTTGTTTGCTTGTCCATGTTTGGAACAAGTTCCTGCAG[C/T]TTTCGCAGCTTCTCACTTATTCTGGTTCTCCTTTCTCTTTCAGCAATGCTTCGAGGATGAGTTGCACAACCACGCTTTGCTCTAACTTTGAA
102382 A G TAAGCTGCGAGTCAAGGTGGTTGTAGAAGTCATCACCACCATCCCTTCTCCTTTTATTTGATGGAGCAGAAAAGGCGATAGAATTTCCTTCATCCCATGA[A/G]CCAATAGAGTAATTACTCGTGATGTAGGATTGATTGCCAGCAGCTTCATCAGAACTATTGCCAAGGCCCTCTGTCATTTCAGGGATGC
102384 T A AATCCACCTCTTCCTCCCTGTGCATGAAGTTCATGGCACCATCATAGTGATTGTTATGATGTGCACATTTTGGTGCATTTACAGGCAACATTAGGTAGTT[T/A]GGCCCAAGCCTGTACCTCTGAGTGTCACCGTATGCAAATATTCTACACTGAAGCATTTTATCATCTGAATAGTAAATTCCAGGCACTACA
102384 G GA AGTGCGATTTACCTTCCTTGTTCACGAAAGTGTAAGTGTTTACTCCAAAACCTTCCATGTGTCGGTAGTCTTGTGGAATGCCGACATCGTCGAAGAGGAA[G/GA]AAAACGTGTGGAGGGTTTCAGGAAGGTGGGAACAAAAGTCGAAGACGCGCCAGTATTCTTGGATATGAGACCTTGGGTTTGGTT
102386 G A CTGTTGGCCTACTGGAATTTTCGTTTCATTGCCCCAAATCGAAATCCCTAATTTTCATTCATCAACATCTCAC[G/A]AAGCTGAAGCTTTCTCCGTCGATGGAGAATAGGGTTACCTGCCGCTAGTCAAAGCAGGTGTCTCGATCCATTCTTTGAACTGCCTCGTTTCATTATCAGA
102386 G A ATCAGAAATAGAAACTCAACGATGGCGGTAAACGAGGATCGAAGAAGGTTTAGTTTTCCGAATCTGAGATTCGTCAGCTCTGCATTGAGGCCAAGCATGT[G/A]TTCATTTCGCAGTCCAATTTGCTTGAGATTCGTGCTCCTATCAAGATTTATGGTACCTACTGCTGTAGCCTTGTGAAAAGGGAAGCA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102386 A G GCTCCTATCAAGATTTATGGTACCTACTGCTGTAGCCTTGTGAAAAGGGAAGCAAATGCCCTGTATTCCTATTCTTTTCTGTAAGTCTTTCTAACCAATT[A/G]TGATGTCAGTAAACCTTAATCTTTTATCTCCTTTTGATGACTGAAAAGGGAAGCAAATGCCCTAGTTTTTTGGAGCAAGGTGTTGTACCT
102386 G T TATCAAGATTTATGGTACCTACTGCTGTAGCCTTGTGAAAAGGGAAGCAAATGCCCTGTATTCCTATTCTTTTCTGTAAGTCTTTCTAACCAATTATGAT[G/T]TCAGTAAACCTTAATCTTTTATCTCCTTTTGATGACTGAAAAGGGAAGCAAATGCCCTAGTTTTTTGGAGCAAGGTGTTGTACCTCTATA
102386 A C GGAAGCAAATGCCCTGTATTCCTATTCTTTTCTGTAAGTCTTTCTAACCAATTATGATGTCAGTAAACCTTAATCTTTTATCTCCTTTTGATGACTGAAA[A/C]GGGAAGCAAATGCCCTAGTTTTTTGGAGCAAGGTGTTGTACCTCTATATGCAGGGATTGTGATAAGGTAGTTTTGTTTTGATGGCAAATG
102386 C T TAACCAATTATGATGTCAGTAAACCTTAATCTTTTATCTCCTTTTGATGACTGAAAAGGGAAGCAAATGCCCTAGTTTTTTGGAGCAAGGTGTTGTACCT[C/T]TATATGCAGGGATTGTGATAAGGTAGTTTTGTTTTGATGGCAAATGTGAACATTTTGATTTGCAATTGTTTGGGAGGATGCTGAAAAAG
102386 G A TTTTTGGAGCAAGGTGTTGTACCTCTATATGCAGGGATTGTGATAAGGTAGTTTTGTTTTGATGGCAAATGTGAACATTTTGATTTGCAATTGTTTGGGA[G/A]GATGCTGAAAAAGTTTGTGATGGTTAAACTTAGTGCATACTATTGCTCTTTTGCTTGTAAGGTTTCAAAAACATTTCCTGATCCGGGAA
102386 C A TTGCAATTGTTTGGGAGGATGCTGAAAAAGTTTGTGATGGTTAAACTTAGTGCATACTATTGCTCTTTTGCTTGTAAGGTTTCAAAAACATTTCCTGATC[C/A]GGGAAAAATGAAGATACATCTACCAAACATTAATGATTCAGATTTCAAGTCTTGGTTCGATCGCAAAAGGAAAATAAAGTGAGGCAAT
102386 G A TTGCTCTTTTGCTTGTAAGGTTTCAAAAACATTTCCTGATCCGGGAAAAATGAAGATACATCTACCAAACATTAATGATTCAGATTTCAAGTCTTGGTTC[G/A]ATCGCAAAAGGAAAATAAAGTGAGGCAATGCATGGACTAGGAATCCCAGATACACGTTCTGGAATATTATCAGTTACTTGGACATACT
102386 GA G CTTGTAAGGTTTCAAAAACATTTCCTGATCCGGGAAAAATGAAGATACATCTACCAAACATTAATGATTCAGATTTCAAGTCTTGGTTCGATCGCAAAAG[GA/G]AAAATAAAGTGAGGCAATGCATGGACTAGGAATCCCAGATACACGTTCTGGAATATTATCAGTTACTTGGACATACTACGTTCAGA
102386 A T AATGAAGATACATCTACCAAACATTAATGATTCAGATTTCAAGTCTTGGTTCGATCGCAAAAGGAAAATAAAGTGAGGCAATGCATGGACTAGGAATCCC[A/T]GATACACGTTCTGGAATATTATCAGTTACTTGGACATACTACGTTCAGAACCTGGAGGAAATACTGATGATAAAAGTGAAGAAACAG
102386 C T ATACATCTACCAAACATTAATGATTCAGATTTCAAGTCTTGGTTCGATCGCAAAAGGAAAATAAAGTGAGGCAATGCATGGACTAGGAATCCCAGATACA[C/T]GTTCTGGAATATTATCAGTTACTTGGACATACTACGTTCAGAACCTGGAGGAAATACTGATGATAAAAGTGAAGAAACAGAATAAGA
102408 C T GTATGATGTAAATCTGCTGGCCTGATTTTAGTGGTAGAATTTGGTTTTTTAGCTCGATACCGACATTTAGCTTTTCAAAATTTTGAAGTTCTTCATTAGA[C/T]TGACTGACTGTTAGTGAACTAATGAATAAGCTCTCGAGTGAAATCAGCACACATAGAACAAGAAGTGACTTTGTCATTTGGATAAGCAA
102412 T C AATGAACAGCAAAAATAAACAACCACCATCGCTGCAAACAGCATAGCTATGCTCGACAGTGATGACCCATACGAGCGGCGTCCAACACCAAGAGACATGT[T/C]AATTACTGATCGAGATCTGAGCCCCAAATACCAGTGAGATTAGCGGTAAAGGAGCACAGAATCGATACCAAAGACAGATCTGCTG
102414 G T TTGGTATGTATAAGTTGCCCAGGAAAGAAGGCAGCACTACCAAACGGAACCATTATCTGGTGTGAGATTTCATCAGGTAGCTTGCGAATGAGTTTCATCA[G/T]ATTTGAATTATCCACGATGAAGGAATTGAGTTGCTGGAGCTCTAATTGGCGATCAAGGATAGCATCTTGGACACGCTTTGATGCCTT
CTAATCATGGACACAGACTCAAAAGCACAGATTCCAACAGTTGTCGAGCAAAGCCAATAC
102414 A GGGAACAGAGAGCCTAAGGTGGTAACTTCACCCTTATTCTCACCAACAACCTTTTCCATCATAATCACACACTCGCCCTCAATTTCTCAAAGTATTTGCC[ACTCAAAACTCAAACTAATCATGGACACAGACTCAAAAGCACAGATTCCAACAGTTGTCGAGCAAAGCCAATAC/A]CTCAAAACTCAAACTA
102428 A G CACTACGCTCTAATTCAGAAATATAATGCAGCTTTCTGACCCTAGATCTCTGTGCCGACTGCCTATTAGCCAAAATCCTCTTGACTCTTTTGGGATCCAT[A/G]GAGCTGGAGGAGCCATCAGCAGCGACGGTAGACTCGCTCTGTACCTCGACGCTGTAGTGATCGGAAGGGGAAGAAGGAGCGGAAGG
102428 T G ACTCGCTCTGTACCTCGACGCTGTAGTGATCGGAAGGGGAAGAAGGAGCGGAAGGTGATCCAGGTGCTGACGTGGCGGTCGACCCAGGAGCTGATGTGGC[T/G]GCGATCCCGGCCACCACATCGTCGGAGAACATGCGCATGAAGTCGTCCTCGAGAACTCCATCGAAGTCAATGCAGGCATCCTC
102428 T G CTGATGTGGCTGCGATCCCGGCCACCACATCGTCGGAGAACATGCGCATGAAGTCGTCCTCGAGAACTCCATCGAAGTCAATGCAGGCATCCTCGAGGAA[T/G]GCGGCGGAGTCGCTGACAGAGCGACGGTGGGACCCGCGTTTGGAGGAGGCGAAGTCCATGAACTCATCGGCCGCCCATGCGTT
102428 T A CCGCGTTTGGAGGAGGCGAAGTCCATGAACTCATCGGCCGCCCATGCGTTGGCGGAGAAGAAAGGGGTGCATTGCCTTCTCTGAACCTGGTTTGGCGCTT[T/A]CGGTGGCAGTTGTGACATGTATGTAATGTATGCGTGTTTGTCTGTTTTATGAAGTCGAAGATTGTGAAAATGTGAAGAACTTCTGC
102438 G A CTAAGAGTTTGATGCCGTATGCCAATGCAAAACGAAAAAGTCACGCAAGGAAGAGCTTAAGTGCAAAAGAAATTATTGAGCGATTGTGGTTGAAAGAAGC[G/A]CATGAAGAACTTCTGGCTTATGAGGCATCGTTGAACGGATCTAAGTTAAAACTTGAGTTGATAAACCAAGAGATAAAACCATATA
102440 G T TGAAGGGTTCAGTGAGTCAAACTGCCCGTGAACCACTAAATGCAGTTTCTGGTCCAGTTCATAGTAAATTTGTTGAGAATTTGCATCAAGGGAAGACACA[G/T]AAGACTGCAGTGGAGAGTGGAGCTAGAAGGATCAGTAAGGCTGGTGCAGGATTTGGAAGGAACATATCTAAGAACTCAGTTGATA
102440 C T CACTAAATGCAGTTTCTGGTCCAGTTCATAGTAAATTTGTTGAGAATTTGCATCAAGGGAAGACACAGAAGACTGCAGTGGAGAGTGGAGCTAGAAGGAT[C/T]AGTAAGGCTGGTGCAGGATTTGGAAGGAACATATCTAAGAACTCAGTTGATATGGCTTTCAGACACATGGACATGAAACAAAGCA
102440 A T TCAAGGGAAGACACAGAAGACTGCAGTGGAGAGTGGAGCTAGAAGGATCAGTAAGGCTGGTGCAGGATTTGGAAGGAACATATCTAAGAACTCAGTTGAT[A/T]TGGCTTTCAGACACATGGACATGAAACAAAGCATTGCAGGCATTACAAACAAAATGATAATTCCTCCTAGCATCCGGTCTAGCTC
102440 T C CAGGATTTGGAAGGAACATATCTAAGAACTCAGTTGATATGGCTTTCAGACACATGGACATGAAACAAAGCATTGCAGGCATTACAAACAAAATGATAAT[T/C]CCTCCTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGA
102440 C T GTTGATATGGCTTTCAGACACATGGACATGAAACAAAGCATTGCAGGCATTACAAACAAAATGATAATTCCTCCTAGCATCCGGTCTAGCTCTAAGCAAA[C/T]GGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATG
102440 T C ACATGAAACAAAGCATTGCAGGCATTACAAACAAAATGATAATTCCTCCTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAG[T/C]AAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCT
102440 G A AAACAAAGCATTGCAGGCATTACAAACAAAATGATAATTCCTCCTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGT[G/A]CAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGA
102440 C CTCT TTGCAGGCATTACAAACAAAATGATAATTCCTCCTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGAT[C/CTCT]TCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGA
102440 G A TCCTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAAC[G/A]ATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGTTTAAATTGGCTACATAATGCTGAA
102440 T C CTAGCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGA[T/C]TCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGTTTAAATTGGCTACATAATGCTGAAGA
102440 A G GCATCCGGTCTAGCTCTAAGCAAACGGAGGCGTCGGTTAAAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTC[A/G]GATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGTTTAAATTGGCTACATAATGCTGAAGATA
102440 G A AAGAGAATAGTAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATC[G/A]AAAGAGGATAAGAATAGTTTAAATTGGCTACATAATGCTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTT
102440 A G TAAGTGCAATGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGAT[A/G]AGAATAGTTTAAATTGGCTACATAATGCTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTTGCCTGAACCTT
102440 T C TGTGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGT[T/C]TAAATTGGCTACATAATGCTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTTGCCTGAACCTTTCAGGCTTA
102440 A G TGATCTCTTCTAATTTGAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGTTT[A/G]AATTGGCTACATAATGCTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTTGCCTGAACCTTTCAGGCTTATA
102440 G A GAGAGCAGCTAGGAAGAACGATTCAGATGCTTATGCAAGTGCTCACTGCGATGCAATGCTATCGAAAGAGGATAAGAATAGTTTAAATTGGCTACATAAT[G/A]CTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTTGCCTGAACCTTTCAGGCTTATAGATGGTTGAGCTTTT
102440 A G GAAAGAGGATAAGAATAGTTTAAATTGGCTACATAATGCTGAAGATAAGTCGGATCAAAGCGTCTTGTTTGATCATGGCGATGCTTTGCCTGAACCTTTC[A/G]GGCTTATAGATGGTTGAGCTTTTATTTTGAAAAGAAGTAATATACAAAATTACACGGTTGACAGTTGGGTTTAGAACCTAAGGATTT
102448 A C TCACATCACCATAACCAGCACCTTGGTCCGCTACAGCATTACCCGGACCACCACCATACCCACCATATCCCTGACTTTGCGGTTGACCAGGCCCACCATA[A/C]CCCGACCCAGGCCCATACCCAATTGGTGCCTGACTGTTCCACGAACTCTTCTGCTGTCCAGACTGCCCACCACTAGCATACCCACCCTG
102448 A G CAAAACCACCTGAACCGTATGTAGGGTACCCACCTCCACCTGCTGCCTGCTGCTGACCATACCTACCTGCACTGTTATCGTAGGACGCTGCCCCGTTGCC[A/G]GGGCCGGCACCGTAAGACTGGTAGGACCCACCGGAAGAGCCGAAGCGGGCTCCACCAGCGCCTGAGCTGGCGTTACCGTCCTTGG
102450 G A CGCAAAAGATAAAACAAGAAGAAGAAGATGACGAAGTGGGTGACGAAATAGTGTACGAGGTGCTGAAACTGAAACAAGAGCAAATATCGATCGACCAAAA[G/A]GTGAAGGAAATGTGGAAAAGGCTGCATGAAACGGAAAGAAAACCAAAGCAAATGCTGGCGTTTCTGGTTAAGTCCGTGGGAG
102450 T C CAAAAGATAAAACAAGAAGAAGAAGATGACGAAGTGGGTGACGAAATAGTGTACGAGGTGCTGAAACTGAAACAAGAGCAAATATCGATCGACCAAAAGG[T/C]GAAGGAAATGTGGAAAAGGCTGCATGAAACGGAAAGAAAACCAAAGCAAATGCTGGCGTTTCTGGTTAAGTCCGTGGGAGAT
102450 A G GTGTACGAGGTGCTGAAACTGAAACAAGAGCAAATATCGATCGACCAAAAGGTGAAGGAAATGTGGAAAAGGCTGCATGAAACGGAAAGAAAACCAAAGC[A/G]AATGCTGGCGTTTCTGGTTAAGTCCGTGGGAGATCCTCAGCTACTGCAGAGATTAATGGAAAAGGAAGGCGGCGAGGAAGAA
102456 T C AGTACACAAAGCCGCAAGGGTTGTATCAGCATCGAGACATAGATCATAAGAAGCTGCGGAAACTTATTCTTGATTCCAAACTAGCTCCTTGTTATCTGGG[T/C]GAGGATGATCCGAGATTCGATCTTGAAGGCTGTCCAATTTGCTTTTTGCATTATCCAAGTCTGAATCGTTCAAGATGTTGCATGAAAG
102460 T TG TAGAAGGAGAACGAGGAGGTGTAGTGTCGATCTCTGTACTTCGAGCTTGAGGAACGATGGGATAACCCCTGTTAAATAAAAATGGAGATTCACTGAAAGC[T/TG]GGGTTTTTTCCGTGGATATGAGATGAGTTCGAACTGTGTTTTGAGAGGAGAAGATGGATTATGTTAGTTCATGCGGCGAATGTC
102472 G A CTGAATTGTTCTCGAAAACTCTTCAGTTTGAACACAAGCTATTCTACTTCGATCTCAAAGAGAACCCTAGAGGGAAATATCTGAAAATCTCAGAGAAGAC[G/A]TCAGCTACGAGATCCACGATTATTGTTCCTGTTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTATGTCAGTACTAGTGACCA
102472 G T CTCTTCAGTTTGAACACAAGCTATTCTACTTCGATCTCAAAGAGAACCCTAGAGGGAAATATCTGAAAATCTCAGAGAAGACGTCAGCTACGAGATCCAC[G/T]ATTATTGTTCCTGTTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTATGTCAGTACTAGTGACCAGGAAGTATTTAGTAAGGA
102472 T C AACACAAGCTATTCTACTTCGATCTCAAAGAGAACCCTAGAGGGAAATATCTGAAAATCTCAGAGAAGACGTCAGCTACGAGATCCACGATTATTGTTCC[T/C]GTTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTATGTCAGTACTAGTGACCAGGAAGTATTTAGTAAGGAGCTAAAGCTTG
102472 T C GGAAATATCTGAAAATCTCAGAGAAGACGTCAGCTACGAGATCCACGATTATTGTTCCTGTTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTA[T/C]GTCAGTACTAGTGACCAGGAAGTATTTAGTAAGGAGCTAAAGCTTGATACTAAGGTATTTTACTTTGATGTTGGTGAGAACAAGAGGG
102472 A G CTGTTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTATGTCAGTACTAGTGACCAGGAAGTATTTAGTAAGGAGCTAAAGCTTGATACTAAGGT[A/G]TTTTACTTTGATGTTGGTGAGAACAAGAGGGGCCGGTTCTTGAAGGTTTCAGAAGCATCTCTTAGCAGAAACCGAAGCACAATAATAG
102472 T C TTAATGGCATAGTTTGGTTTCTTGATCTTTTCAGTTATTATGTCAGTACTAGTGACCAGGAAGTATTTAGTAAGGAGCTAAAGCTTGATACTAAGGTATT[T/C]TACTTTGATGTTGGTGAGAACAAGAGGGGCCGGTTCTTGAAGGTTTCAGAAGCATCTCTTAGCAGAAACCGAAGCACAATAATAGTCC
102472 G A GCCGGTTCTTGAAGGTTTCAGAAGCATCTCTTAGCAGAAACCGAAGCACAATAATAGTCCCTGCTGGAAGCTCTGGTGATGAAGGGTGGACAGCATTTCG[G/A]AACATCCTGCTAGAGGTGAATGAGGAGGCATCACGACTATTCATGAACATGGACGGGTCAGAAAGACTCCCTGGACTTTCAGATG
102472 G A ATTATTCTCCTCCTGAGGAAGTGGCAAGTGGTGTGGGAGCATCTAAAGTAATGAGGGTAGATCAGAAAAGATTTTTCTTTGATTTGGGAAACAATAACAG[G/A]GGCCATTTCTTAAAAATTTCTGAGGTGGCAGGCCCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAG
102472 C A ATTCTCCTCCTGAGGAAGTGGCAAGTGGTGTGGGAGCATCTAAAGTAATGAGGGTAGATCAGAAAAGATTTTTCTTTGATTTGGGAAACAATAACAGGGG[C/A]CATTTCTTAAAAATTTCTGAGGTGGCAGGCCCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAGATG
102472 T C TGGCAAGTGGTGTGGGAGCATCTAAAGTAATGAGGGTAGATCAGAAAAGATTTTTCTTTGATTTGGGAAACAATAACAGGGGCCATTTCTTAAAAATTTC[T/C]GAGGTGGCAGGCCCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAGATGGTTGGTCATTTTGTGGAG
102472 C T TGGGAGCATCTAAAGTAATGAGGGTAGATCAGAAAAGATTTTTCTTTGATTTGGGAAACAATAACAGGGGCCATTTCTTAAAAATTTCTGAGGTGGCAGG[C/T]CCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAGATGGTTGGTCATTTTGTGGAGGTAACAAAAGAT
102472 G T AAGTAATGAGGGTAGATCAGAAAAGATTTTTCTTTGATTTGGGAAACAATAACAGGGGCCATTTCTTAAAAATTTCTGAGGTGGCAGGCCCAGATCGCTC[G/T]TCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAGATGGTTGGTCATTTTGTGGAGGTAACAAAAGATAAAGTTGAAGGG
102472 G A TTTTCTTTGATTTGGGAAACAATAACAGGGGCCATTTCTTAAAAATTTCTGAGGTGGCAGGCCCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACT[G/A]AAACAATTCCATGAGATGGTTGGTCATTTTGTGGAGGTAACAAAAGATAAAGTTGAAGGGTTAACGGGTGCAAATGTGAGGACTCTT
102472 A G TCTTTGATTTGGGAAACAATAACAGGGGCCATTTCTTAAAAATTTCTGAGGTGGCAGGCCCAGATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAA[A/G]CAATTCCATGAGATGGTTGGTCATTTTGTGGAGGTAACAAAAGATAAAGTTGAAGGGTTAACGGGTGCAAATGTGAGGACTCTTGAA
102472 G A ATCGCTCGTCTATCATCCTTCCATTATCTGGACTGAAACAATTCCATGAGATGGTTGGTCATTTTGTGGAGGTAACAAAAGATAAAGTTGAAGGGTTAAC[G/A]GGTGCAAATGTGAGGACTCTTGAATCCACACAGAGATTGTTGAACTGACTTCCCAACTCTTGTTCGTTGTTATTTTATTTTCTGCTTTT
102478 AT A CTCCACTCACTTGCCCTAACGTCATCTCTTCAGCTTGTTTCCCCAAATATTAACCTATTTTCTTAGATCCACATATCCTCTATTTTTTCCTTTGTTTCTG[AT/A]TTTTTTATGGCGACTTTCGCTAAGAGAATGAGGCCTGATGCTTCTAACGGAAACGGAGGATTTGCTGGATCCAAGCGTGTGAAAGGCAGC
102478 T C CAAAATTTTTCAGTACTGCTGGTTGCCCATTTGGTGATGGATGTCATTTTCTACACTATGTTCCTGGTGGATACAGTGCGGTTAGTCAACTGAACAATGC[T/C]GCAAACCACATGCAGTCCCTGCCGGCCCGTGGTCCAATGGGCCCTCCTCCCATGTCCGACTCTCATGGCCCACCCGCAGTGAAAACCA
102478 C T ATGGCGAGCATGAGCTTGGAAATCCTCTGAACCAATTCCATGACATGCCTAGCAACGACTATGATTCAAGGATGGGACCACCGCCATCATCCAACTTTGG[C/T]GGTGGTAGACCGGGTTACCCATACCACGAGCCAAACCCATCTGCATTTGCAGGCCAGAGGATGGGTGGCCCACCAGCACCATCCAG
102478 A G CGCCATCATCCAACTTTGGCGGTGGTAGACCGGGTTACCCATACCACGAGCCAAACCCATCTGCATTTGCAGGCCAGAGGATGGGTGGCCCACCAGCACC[A/G]TCCAGCTTTGGAGCCTCCGCTACTGCAAAAATAAGCGTAGATTCATCTCTTTCTGGCGCTATCATCGGTAAAGGTGGCGTGAACAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102478 G C CTACTGCAAAAATAAGCGTAGATTCATCTCTTTCTGGCGCTATCATCGGTAAAGGTGGCGTGAACACTAAGCACATATGCCGAGTTACTGGAGCAAAAGT[G/C]GCTATTAGGGATCATGAATCTGATTCAAACTTGAAGAACATTGAGCTTGAAGGTACATTTGACCAGATAAATCAGGCAAGTGCCAT
102484 G GT GCGGTAAACGAACCCCAGATTCCACCTGTTCTAGCTCTCTTTGAAGCTCTTTCTGAGTTTGCCTTTCCCTCTCCATCTCAAGATTGAACTGCAGTTCTTA[G/GT]TTTTGCACGTTCAAGCTCGAGTTGCTTCTGCCGGTCCATTGTACGTTCCATTTCTAATTCCCGCTCCCTATCAATCTCTTGAAGAAGCTG
102486 G T CGGTCACGGCAATGATCATCAATACCGTTGTCGCTGATATTACAAATATAGCCAGTGTCAATGCTCCAATGTAAAAAGCTGCTAGGCATGTAAAGAAAAT[G/T]GCCAGGAAACAGCCAACTGCAGCCAAAGATATGAGAGCAGAGATGATAACTGCGTTGATGGTTGCTACCAAAAAGAAGATTGCAA
102486 A G CAAAAAGAAGATTGCAAAGACCAGTAATCCAGACAGAGATAGAAGAACTATGGCCCCAACAGAAATAACAAGGAGAGCACGAAAAGCGCTTCCTTCTCTC[A/G]TCCAATCAAGCAAATCGCGATACAAGTTCGCAGAAGCTTCTCGAAGTTTCGGAGACTGGTCATCGAACGACTTCCTTATCCTTTCC
102488 T C TCTCATCTATGGAGACTAAATCAGCCACAAACCAGTTTGATGAAGCGCTGCATCCTACTGTAGGCGGATTCAGAAAAGTTTGCATAGGAATTATTGATGG[T/C]GAATCCTTGAATGTCACCATCAAGAAAGAAAATTCCATATTAGATGAGATCAGTCCACAGGTGTACTTCCTTGAAACTGTGCCATTTC
102488 A T ACCAGTTTGATGAAGCGCTGCATCCTACTGTAGGCGGATTCAGAAAAGTTTGCATAGGAATTATTGATGGTGAATCCTTGAATGTCACCATCAAGAAAGA[A/T]AATTCCATATTAGATGAGATCAGTCCACAGGTGTACTTCCTTGAAACTGTGCCATTTCAGAGTTTTTGTGCATGGCAAGCATTACCTC
102488 A G CAGTTTGATGAAGCGCTGCATCCTACTGTAGGCGGATTCAGAAAAGTTTGCATAGGAATTATTGATGGTGAATCCTTGAATGTCACCATCAAGAAAGAAA[A/G]TTCCATATTAGATGAGATCAGTCCACAGGTGTACTTCCTTGAAACTGTGCCATTTCAGAGTTTTTGTGCATGGCAAGCATTACCTCCC
102488 T A ATGGTGAATCCTTGAATGTCACCATCAAGAAAGAAAATTCCATATTAGATGAGATCAGTCCACAGGTGTACTTCCTTGAAACTGTGCCATTTCAGAGTTT[T/A]TGTGCATGGCAAGCATTACCTCCCACACTGTTTAAAGAGCAGGAATGGACTGATGCACACAACGTGTTTGATGAAATGAACATACTAA
102488 A G GCAGGAATGGACTGATGCACACAACGTGTTTGATGAAATGAACATACTAAAATGTGAAAGCAAAATTTTTATCTTCGATCCTGGTGGTACATTAAACGTA[A/G]AGAGCATCTCCGACCTTGAGGACAAGGTCGTTTTCGAGCGGTCGGTAGTGATACGGTTTTGGGTAAGCAAGCTATTAACCCATTAC
102488 A G AACGTGTTTGATGAAATGAACATACTAAAATGTGAAAGCAAAATTTTTATCTTCGATCCTGGTGGTACATTAAACGTAAAGAGCATCTCCGACCTTGAGG[A/G]CAAGGTCGTTTTCGAGCGGTCGGTAGTGATACGGTTTTGGGTAAGCAAGCTATTAACCCATTACCCACCTACACATGCAGCTGAACG
102488 C T ACGTGTTTGATGAAATGAACATACTAAAATGTGAAAGCAAAATTTTTATCTTCGATCCTGGTGGTACATTAAACGTAAAGAGCATCTCCGACCTTGAGGA[C/T]AAGGTCGTTTTCGAGCGGTCGGTAGTGATACGGTTTTGGGTAAGCAAGCTATTAACCCATTACCCACCTACACATGCAGCTGAACGT
102488 T A GCAAAATTTTTATCTTCGATCCTGGTGGTACATTAAACGTAAAGAGCATCTCCGACCTTGAGGACAAGGTCGTTTTCGAGCGGTCGGTAGTGATACGGTT[T/A]TGGGTAAGCAAGCTATTAACCCATTACCCACCTACACATGCAGCTGAACGTTGGCACCCAAGCATCAAATGGATAGAAAAAAA
102490 G A TCTAGGAGCCGCAGCCGTTCTTACTCAAGAAGCCGTAGCCGTAGCTTAAGCAGGAGCAAGTCCCCCAAGACAAAATCCCGTTCCAAATCTGGGTCACCTC[G/A]CCCTCGTTCTGCCTTGAAAGAGCATTCTTTGTCTAGATCTCGATCAAGGTCCAGATCTCCTGTTAACTTGAGAGAGAGTACGAGTGC
102490 G A AGCCGCAGCCGTTCTTACTCAAGAAGCCGTAGCCGTAGCTTAAGCAGGAGCAAGTCCCCCAAGACAAAATCCCGTTCCAAATCTGGGTCACCTCGCCCTC[G/A]TTCTGCCTTGAAAGAGCATTCTTTGTCTAGATCTCGATCAAGGTCCAGATCTCCTGTTAACTTGAGAGAGAGTACGAGTGCAGTGGA
102490 T C CGTTCTTACTCAAGAAGCCGTAGCCGTAGCTTAAGCAGGAGCAAGTCCCCCAAGACAAAATCCCGTTCCAAATCTGGGTCACCTCGCCCTCGTTCTGCCT[T/C]GAAAGAGCATTCTTTGTCTAGATCTCGATCAAGGTCCAGATCTCCTGTTAACTTGAGAGAGAGTACGAGTGCAGTGGACAAGAGCCC
102496 G T CCTCGTCCAAAAATATGATACTTGGGGCAGCAAGACGTGCTTTCTGGAATGTCCTACGCAGCAATGCTTCCCCTTCTCCAACATATTTCGAATACAATTC[G/T]GCACCACTCAAAGAAAAAAATGAAGCTTGAGCAGCATAAGCAGCAGCCTTGGCTAGGGTGGTTTTCGAGCATCCTGGTAACCCATGC
102498 C G TGCTGTTATTACCATTATTACTTTCATAGGCCTTGTGCACGAAAATTACGTGCCCTTCAAAATTCTTGTTTGGTTCCTCAATTGCTTTTCGGAAGCCATC[C/G]GCTGTCTTGTACACAAACATTACAAACCCTCTGGGCTTTCCTGTAATCCTGTCTAGTCCCAACGGTCCCTCCTCAATTTCTCCAAACTGAG
102500 G A GCGCCAATAGTCATGTACGGTGTGAGTTGGTTTTGTGAAAAGCAGTCTAAGACTTGATGGCTTTGCAAGATGATGGCCTTGCCCCTCTTCTTCAGCTTCG[G/A]AACCAGGTACATTTTCTAGGAGTGGCGCGGAGAGTAATTTTGGTGTGGAAGACATGTCAGATGTGAAACTGTTTGTTAAGGTCTTTG
102500 T C GAGTTGGTTTTGTGAAAAGCAGTCTAAGACTTGATGGCTTTGCAAGATGATGGCCTTGCCCCTCTTCTTCAGCTTCGGAACCAGGTACATTTTCTAGGAG[T/C]GGCGCGGAGAGTAATTTTGGTGTGGAAGACATGTCAGATGTGAAACTGTTTGTTAAGGTCTTTGAGGTTGAAGATAATAGCAGGTT
102500 C T GGAGTGGCGCGGAGAGTAATTTTGGTGTGGAAGACATGTCAGATGTGAAACTGTTTGTTAAGGTCTTTGAGGTTGAAGATAATAGCAGGTTGATTAAAGG[C/T]TTTGTTAGAAGTCCAAATACCATTGTGCTGAAGAGTACAACAGTGATAGTACTGGTGATCATGATTGCATTGCCTCGCAATTGAGT
102500 A C TGATTAAAGGCTTTGTTAGAAGTCCAAATACCATTGTGCTGAAGAGTACAACAGTGATAGTACTGGTGATCATGATTGCATTGCCTCGCAATTGAGTGTG[A/C]CCTAATCTTGTAAACTGGTTATAGGCAAGAGCAATTGACACAGCGCCTCTCATTAAACCAGCCCACCATATTGTTACTTGTTGCCTGA
102506 TG T AACATCAACAGCTACACTGATGACAGCTTGCAATTGAACGGTGACATCGCTAACGATGGTGGTAGTACCGCTAACAGTGGTTGTGATTTGAGCGGTGAGT[TG/T]GGGGAAATGACAGCAGTGAGTTGGGAGATAACTCCTTCGACGGCTGAAATAAGTTGGCCAAGAACGGCTTGGACTTGAGCTTG
102506 C G CGGAGTTAAGAGCGTCGCTTGCAGCGGCAGTGGCATTCTCAACGGCAGCAGATGCGGTTGCAGTTACTTGAGCAATCAAATCAACGAGAACGGTAAAGGA[C/G]GCAGATATTTGAGCAGTGATTTGTCCGACAACCTTGACGGCTTGGTTGACGGTGGCTTGAACGAGAGCTTGAATTTGGGCTTGA
102520 G A GTGGAAGCCCATATGGATTTGCAATCTGAATTATATCACAATATTCTTCCCCCAATGTCTGCTGCCCAGATCCTGTTGTTAGTATGTAATAAAGCGTCTG[G/A]CCTAATAACTTCACCTCGTTCTGATAAGCCACAGCAAATCTAGTACCGAAGAGGTGACGGAAAGCATCTCGACAGGCGTCGTGAACGT
102522 C A ATAAGACTAAACTGGACCCCAAAGAAGTCGGTGACATTGTAGTTGGCTCCGTTTTAGCTCCTGGTGCTCAAAGAGCAAATGAATGTAGAATGGCTGCATT[C/A]TATGCTGGTTTTCCTGAAACTGTTCCAGTTCGAACAGTAAATCGTCAATGCTCGTCTGGTCTGCAAGCTGTTGCTGATGTTGCAGCC
102522 C T CAATGCTCGTCTGGTCTGCAAGCTGTTGCTGATGTTGCAGCCGCCATAAAAGCTGGTTTTTACAATATTGGTATTGGAGCTGGTTTGGAATCTATGTCTG[C/T]GAATTCAGTTGCGTGGGAAGGATCCATAAACCCAAAAGTGAAACAGTTTCAACAGGCTCAAGATTGTCTGCTTCCTATGGGAATAAC
102522 G A TGCTGTTGAATCTCATCGAAAAGCAGCTGCAGCAGCTGCCTCTGGGAAATTCAAAGATGAAATTGTTCCAGTGACAACAAAGATTGTAGACCCAAAAAGC[G/A]GAGAGGAGAAACAAGTAACTATTTCAATGGATGATGGAATACGTCCTGAGACTACAGTATCAGGTCTAGCAAA
102532 A G TATTGGCCACCAAATACCTCTCGACCGACAAAGCAGCAATGCATCCAGATCCAGCAGCAGTGATAGCCTGTCTCCACTCGTGATCCTGAACGTCACCGGC[A/G]GCAAAGACACCATCCACAGAAGTTTTTGCTGTACCCTCCTTAACCAAGATATATCCTGTACTATCGAGCTCAACTTGACCACCTAGCA
102532 TCTGAAACATTCGCCATAATCAAC
T CTTTCCTGAGTAATATGCCAGACATTTGTCCTTTATTATTGCTGACCACATCCTTGGCCACTGTATTGAAGTGCACCGTCAAATTTGGATTGCTGAATAC[T/TCTGAAACATTCGCCATAATCAAC]CTATCTTGCATAGTCCTTGATGCACGTAGCTGATTTCCACGAACAAGTAAATGTACATGACGTGCAT
102532 T C CATCCTTGGCCACTGTATTGAAGTGCACCGTCAAATTTGGATTGCTGAATACTCTATCTTGCATAGTCCTTGATGCACGTAGCTGATTTCCACGAACAAG[T/C]AAATGTACATGACGTGCATATTTGGTAAGATATAAGGCTTCCTCAGTAGCAGTATCACCTCCACCAACAACTGCAAGAACTTGACCTTT
102532 G A CATGACGTGCATATTTGGTAAGATATAAGGCTTCCTCAGTAGCAGTATCACCTCCACCAACAACTGCAAGAACTTGACCTTTAAATAATGGTGATGCCCC[G/A]TCACATATCGCACATGCACTTATTCCTCTACTCCAAAATTCATCTTCACGTGCCAGTAGGCCAACAGTG
102534 C T CTGTCTCCATTACTCCAGTAAACCCCCAAATCGTTTCCCCCTTTTCACATCGCCCCCCAAAAATCACCCAATGGTGCTAAACATCCTCCTCCTCCACCTC[C/T]TCTTCTTCTTCCTCCTCGCTTCTACAACCGCCATTGAGCCAAAAACAGACCCCTCCGACATCGCCGCGCTGACAGCATTCAAATCCGCGAT
102534 G A TGGTGCTAAACATCCTCCTCCTCCACCTCCTCTTCTTCTTCCTCCTCGCTTCTACAACCGCCATTGAGCCAAAAACAGACCCCTCCGACATCGCCGCGCT[G/A]ACAGCATTCAAATCCGCGATCTCGCCTAAGTCAATCAACCCATGGTCATGCCTCGCCACGTGGGATTTCTCCTCCGACCCCTGCCATCCC
102534 A C TGCTAAACATCCTCCTCCTCCACCTCCTCTTCTTCTTCCTCCTCGCTTCTACAACCGCCATTGAGCCAAAAACAGACCCCTCCGACATCGCCGCGCTGAC[A/C]GCATTCAAATCCGCGATCTCGCCTAAGTCAATCAACCCATGGTCATGCCTCGCCACGTGGGATTTCTCCTCCGACCCCTGCCATCCCGCG
102534 A T CCTGCCATCCCGCGGCTCCTACTCACTTCACCTGCGGCCTCACATGCGCCGCCGTCTACGGCGGAGTCTCCCGCGTCACCGACCTCACCCTCGACCCCGC[A/T]GGCTACTCCGGTACGCTCTCTCCTGCCATTTCCAACCTCACCTTTCTAACCCACTTAAACATGTACGACAACTCCTTTTACGGGAACATC
102534 T C ACTTCACCTGCGGCCTCACATGCGCCGCCGTCTACGGCGGAGTCTCCCGCGTCACCGACCTCACCCTCGACCCCGCAGGCTACTCCGGTACGCTCTCTCC[T/C]GCCATTTCCAACCTCACCTTTCTAACCCACTTAAACATGTACGACAACTCCTTTTACGGGAACATCCCTTTTTCCATTTCGAACCTTGCA
102534 G C GAGTCTCCCGCGTCACCGACCTCACCCTCGACCCCGCAGGCTACTCCGGTACGCTCTCTCCTGCCATTTCCAACCTCACCTTTCTAACCCACTTAAACAT[G/C]TACGACAACTCCTTTTACGGGAACATCCCTTTTTCCATTTCGAACCTTGCAAATTTGGAGATTATTTCAGTCTCTGGCAACAAGTTTTCCG
102534 C T CCGGTACGCTCTCTCCTGCCATTTCCAACCTCACCTTTCTAACCCACTTAAACATGTACGACAACTCCTTTTACGGGAACATCCCTTTTTCCATTTCGAA[C/T]CTTGCAAATTTGGAGATTATTTCAGTCTCTGGCAACAAGTTTTCCGGTTCCGTTCCTGAATCTATATACAAAATTCCAAGCTTGAACGTCCT
102534 C G CATTTCGAACCTTGCAAATTTGGAGATTATTTCAGTCTCTGGCAACAAGTTTTCCGGTTCCGTTCCTGAATCTATATACAAAATTCCAAGCTTGAACGTC[C/G]TCGATCTGTCCAGGAATCAACTGACTGGACGTATCCCCAGTTTTCCAATTGGAATGAAATCGAATATGGTTGACATCGATTTGAGCTAT
102534 T C TTATTTCAGTCTCTGGCAACAAGTTTTCCGGTTCCGTTCCTGAATCTATATACAAAATTCCAAGCTTGAACGTCCTCGATCTGTCCAGGAATCAACTGAC[T/C]GGACGTATCCCCAGTTTTCCAATTGGAATGAAATCGAATATGGTTGACATCGATTTGAGCTATAATCAGCTGTCTGGCGATTTGCCGAA
102534 G A AACTGACTGGACGTATCCCCAGTTTTCCAATTGGAATGAAATCGAATATGGTTGACATCGATTTGAGCTATAATCAGCTGTCTGGCGATTTGCCGAACTC[G/A]CTGCCTCCTAATTTGGTAAGTCTTGCTTTAAGAGGCAATTCAATTTCCGGATATTTACGGAAAACCACTTTTCAATCTTTGAAATACCT
102534 A T CGAATATGGTTGACATCGATTTGAGCTATAATCAGCTGTCTGGCGATTTGCCGAACTCGCTGCCTCCTAATTTGGTAAGTCTTGCTTTAAGAGGCAATTC[A/T]ATTTCCGGATATTTACGGAAAACCACTTTTCAATCTTTGAAATACCTGGAAGTTGTCGAGCTAACTGCAAACAAGTTATACGGGAGAA
102538 G A GTAGCCCAACTACCCCATGTAGATAAGCACAAAACCCAACACACCATTCATTATTCTCCACGTGCCCATCAGCCTCTTATTAGTAGTCGCTATCATCGCG[G/A]ACCTCACCGGGAGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATGCCCTTCCGTGTTCA
102538 A C CCCCATGTAGATAAGCACAAAACCCAACACACCATTCATTATTCTCCACGTGCCCATCAGCCTCTTATTAGTAGTCGCTATCATCGCGGACCTCACCGGG[A/C]GGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATGCCCTTCCGTGTTCAGCGTCTCGATCG
102538 C G CACGTGCCCATCAGCCTCTTATTAGTAGTCGCTATCATCGCGGACCTCACCGGGAGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCT[C/G]AGGTGCGGCAAATGCCCTTCCGTGTTCAGCGTCTCGATCGTCGTCTTCGCCCCCAGATGCGACTTCAGGTACCGGGACACGGATC
102538 C T CTCTTATTAGTAGTCGCTATCATCGCGGACCTCACCGGGAGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATG[C/T]CCTTCCGTGTTCAGCGTCTCGATCGTCGTCTTCGCCCCCAGATGCGACTTCAGGTACCGGGACACGGATCCCGGGATCGACACGT
102538 T C TTATTAGTAGTCGCTATCATCGCGGACCTCACCGGGAGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATGCCC[T/C]TCCGTGTTCAGCGTCTCGATCGTCGTCTTCGCCCCCAGATGCGACTTCAGGTACCGGGACACGGATCCCGGGATCGACACGTCCT
102538 G C CCGGGAGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATGCCCTTCCGTGTTCAGCGTCTCGATCGTCGTCTTC[G/C]CCCCCAGATGCGACTTCAGGTACCGGGACACGGATCCCGGGATCGACACGTCCTTCGCCGTCTGGATCACGCAGCAGGGCACCC
102538 C G AGGCCAGCACGCGGCGGAGCACCGGGACCAGCACCTGCGGCGCGCTCAGGTGCGGCAAATGCCCTTCCGTGTTCAGCGTCTCGATCGTCGTCTTCGCCCC[C/G]AGATGCGACTTCAGGTACCGGGACACGGATCCCGGGATCGACACGTCCTTCGCCGTCTGGATCACGCAGCAGGGCACCCGAACG
102538 A G GTACCGGGACACGGATCCCGGGATCGACACGTCCTTCGCCGTCTGGATCACGCAGCAGGGCACCCGAACGAACTCCAGGATCCCTCTCAGGTCGCTCTTG[A/G]ACACCATCCTCGAGACCCACAGGGATATGTCCGGACGCATGTTGAACAGCGTGATGCTGAACTCCCGCACCGCCGCCGGCACGTC
102538 C T GAGGACCTTCTCGACCTCGCCTCTCTCGAAGCCGCCGTGGTAGCTGCCGTCGTTGAGGAAGCAGGGGGAGATCCCGATCAGGATGAGCTTGTGGAAGAGG[C/T]TGGGGCGGGAGACGGCGGCGAGGAGGCCGACCATGGCGGAGAAGGAGTGGGCGATGAGGGAGCATTTGTCGATGTGGAGG
102540 T C AATTCAAAGAATTGGAAACTGGCTTCAAATTGTGGCTGTCGAAGCAGCCTATGGCTATAGAGGCGGCCGTCGTCACGGTCACCAGCGCCGTCCAGGGCGC[T/C]GCAATTGGCGGACTTATGGGTACGCTAACTCCTCCTTCTGAGTCCATTGCTCCACCGCTTGGTAGCGGGATTAATCCTCAAGCCAT
102540 T A AAGAATTGGAAACTGGCTTCAAATTGTGGCTGTCGAAGCAGCCTATGGCTATAGAGGCGGCCGTCGTCACGGTCACCAGCGCCGTCCAGGGCGCTGCAAT[T/A]GGCGGACTTATGGGTACGCTAACTCCTCCTTCTGAGTCCATTGCTCCACCGCTTGGTAGCGGGATTAATCCTCAAGCCATGGCCTC
102540 A G TCAAGTTGGGTCAGAAGTTCTCTCAGCCACCAACAGAGGATGTCATGTACTCTCGAGCAAGAGGCATGTTGACAAACCTTGGTCTTCAAAATTATGAGAA[A/G]AATTTCAAGAAGGGTTTGCTGACAGATGCCACTCTTCCTCTTCTTACTGACAGTGCACTTAGAGATGTCAAGATACCACCTGGGCCA
102540 A C AAAGCAAGACGCTGAAGATGCTTAGCTCATATAGATCGACGTTCGTTAATGGTTCTACTTTCTTATCCTTAAAGTGTTAGTTAAGATGACAGTTTTCGTC[A/C]TTTTGGAATCAAGTAACTTTTATATGACCAACTGTTGCTGGTTTCTGCTTTGTTAATTTAGGGGGG
102548 G T CATGGCCAACATAATTCATATGCTGGCTTCAGTCTTCTTCATTTTAACATTCACAACGCCATCCCTCTCCTCAAACAACGTCCTTTACTCATCCGACGAT[G/T]TCGTGCTTAAGCAAGGCGACAGTTTGACATACAAAGACTATGCACTGACTCTTCAGGATGACTGTAACCTTGTTCTTTCTGGACCTAATCA
102548 G C TATGCTGGCTTCAGTCTTCTTCATTTTAACATTCACAACGCCATCCCTCTCCTCAAACAACGTCCTTTACTCATCCGACGATGTCGTGCTTAAGCAAGGC[G/C]ACAGTTTGACATACAAAGACTATGCACTGACTCTTCAGGATGACTGTAACCTTGTTCTTTCTGGACCTAATCATGCCGTTCTTTGGCAGA
102548 A C TAACATTCACAACGCCATCCCTCTCCTCAAACAACGTCCTTTACTCATCCGACGATGTCGTGCTTAAGCAAGGCGACAGTTTGACATACAAAGACTATGC[A/C]CTGACTCTTCAGGATGACTGTAACCTTGTTCTTTCTGGACCTAATCATGCCGTTCTTTGGCAGACTCACACTTCACCATTGCTCTATTAC
102548 T C TTTGACATACAAAGACTATGCACTGACTCTTCAGGATGACTGTAACCTTGTTCTTTCTGGACCTAATCATGCCGTTCTTTGGCAGACTCACACTTCACCA[T/C]TGCTCTATTACTCCTGCTATCTCCAGCTTAAATCAAACGGGGAGCTAGTCCTTTTTAACGTCTATCGTTTGTTTCCGCTTGTACTTGGGCA
102548 C T ATAAGCTTCAAGAAAGCTACAAACATTCAGAACCTTCCGAAGGCTCGAAAGTGATCCCGGTAACCGATTCTACTCTTTGGTCGGGGGATATTGCTCCTAT[C/T]GGTACTATTATTGTTAAAGACAACTATGAGTTAGAGCTGGGATGGACTTGTAATTTGACACTTACGGACACGAAGTCCGGCCGGGTG
102548 T A AAGTGATCCCGGTAACCGATTCTACTCTTTGGTCGGGGGATATTGCTCCTATCGGTACTATTATTGTTAAAGACAACTATGAGTTAGAGCTGGGATGGAC[T/A]TGTAATTTGACACTTACGGACACGAAGTCCGGCCGGGTGGTGTGGCACTCGAACAGCACGGATACAACAAGAGATTGCTTTGTGAA
102548 G A TCGGGGGATATTGCTCCTATCGGTACTATTATTGTTAAAGACAACTATGAGTTAGAGCTGGGATGGACTTGTAATTTGACACTTACGGACACGAAGTCCG[G/A]CCGGGTGGTGTGGCACTCGAACAGCACGGATACAACAAGAGATTGCTTTGTGAACTTGGACAGTGATGGGCAGTTGACAGTTAAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102548 C A CGGGGGATATTGCTCCTATCGGTACTATTATTGTTAAAGACAACTATGAGTTAGAGCTGGGATGGACTTGTAATTTGACACTTACGGACACGAAGTCCGG[C/A]CGGGTGGTGTGGCACTCGAACAGCACGGATACAACAAGAGATTGCTTTGTGAACTTGGACAGTGATGGGCAGTTGACAGTTAAGT
102548 A G TTAAAGACAACTATGAGTTAGAGCTGGGATGGACTTGTAATTTGACACTTACGGACACGAAGTCCGGCCGGGTGGTGTGGCACTCGAACAGCACGGATAC[A/G]ACAAGAGATTGCTTTGTGAACTTGGACAGTGATGGGCAGTTGACAGTTAAGTACTTAGGCGGTTCTGTTTTATGGGGCAATGGTG
102548 C T GCTTTGTGAACTTGGACAGTGATGGGCAGTTGACAGTTAAGTACTTAGGCGGTTCTGTTTTATGGGGCAATGGTGCTGGTTCTGATTGGGGACAAGAGTA[C/T]GTTCTTGCGCTTTTGCCTCAAGGACAACTTAAAGTGTATGGTCCTGTTATTTGGACAGCGAGTGATAATTCCTTTGGTAAGGAGCCT
102548 A T CAGTTGACAGTTAAGTACTTAGGCGGTTCTGTTTTATGGGGCAATGGTGCTGGTTCTGATTGGGGACAAGAGTACGTTCTTGCGCTTTTGCCTCAAGGAC[A/T]ACTTAAAGTGTATGGTCCTGTTATTTGGACAGCGAGTGATAATTCCTTTGGTAAGGAGCCTACTATTGCAATGGTGACTGCCTAGTA
102556 AG A GATATCTGGAAGGGAAATACAATCATCTGGGGGACACCGCAGATCCGAAGAACCAAGAGTACGTGAAGATCGTCGGGATGATCGGGAAAAATCAAGGGAA[AG/A]GGGGCAGAGACAGAGAGCGCGATCGTGAGAGAGAAAAATCGCGAGATAGAGATGTACGTGAAGAGAGGCACCGTCACAGG
102558 G A CATCGGTTCTATTTGCAACAGCTCTAGCCAAAAGTGTTTTGCCAGTTCCAGGTGGACCATAACAAAGGACACCCTTAGGAGGGTCAATACCAAGCTTGAC[G/A]AATTTCTCTGGATGCAGCATGGGAAGTTCTACAACTTCACGCATCTTCTCTATCTGTTCTTTACAACCACCAACATCATTGTATGTGAC
102560 A G TTTCTTTTCATACATAATGAGGAGCACAAAAGACTAAGAAAATTAACCTCGTCTTCTATTAATGGATTTGATGCACTTTCCACTTATTTAACGTACATCG[A/G]AGATGTCGTGGTGTCTACCTTGGATAAGTGGTCAAAGATGGATAGCTTCCTTTTCCTAACGGAGATGAGAAGAACAACATTTCGAATTA
102562 G A GTGCTTTGAATGTTGGGGAGTTGGATTTAATTTTGGGGAAATGCGAGCAGTCTAGGGTTCAGTTTATGGATGGTACTATGTGGATGCATCATCCTAGAAC[G/A]GAGAAGATGAAACAGTTTTTGTTGGATCCTGATCAATTTGGACAGCTTAGAATGGTAAACAGCATATTCACCTTCATGGCAGGCTC
102564 T A GCCATGTCCAATTCTGAGCAACACTTGAACCGATAATAGGTCTCTTCTCTGCCGCACTTTCCTCATTTGCCTGATAGAAAGAAGGGTAGGTCCATGATTG[T/A]TGACGATCAGTTGTCATAGATGAGCTGTGTGGATGACCAATCCGAATTGACGAGGAGTGACCAATCCCAGATCTCCTGGAGTCGAAA
102566 A T GATTTTGGTGGTGAAACGAGTGGAGACTGCAATGTAGAAGTCTTTTGCGGGTTGGTCGGCTGTGACCAGAACAGAGACGGACTGGCCCACATGGACATC[A/T]ATGGAGGAGTAGGAGGTTTGCATGGTGTGTGTTCCTTCTACTTCTGCCAGCACCATTTTGTGGTCCTGGAAGCGGATGTTAAGGCT
102566 A G GGAACCTGTAAGTTTTGCCTTGATCAACAGTGAAGAAAGCTCCGTTCGGACCACGGCCGTTGACGAGGATTCCACTGGGGGATGGGATCATTTTACCCGC[A/G]TCCAATGATTGCCTCAAATCCGTATGATTAGCAGTATACCAATCCCCAATAAGAACAGTGAAATCGCCGGCAGGGTCGTCAAAAGG
102568 A G CTTGCTGATCATGACTGCTACACAAACAATAATTTGGGTAACATACCAAGCATGCAGCAGTGTTACTACAATCCAAACGTAATCAATGGAAGCTTGACAC[A/G]GTTGCTGTGGGCCGACAATATTGTGCATGGGATGGATAATTTCTGCAAGACAGGGAATAATCACATGCTCAGCGGCAATAATTCTCA
102568 A G AATAATTTGGGTAACATACCAAGCATGCAGCAGTGTTACTACAATCCAAACGTAATCAATGGAAGCTTGACACAGTTGCTGTGGGCCGACAATATTGTGC[A/G]TGGGATGGATAATTTCTGCAAGACAGGGAATAATCACATGCTCAGCGGCAATAATTCTCATGAAACAGGAATTTATGAATGAGATT
102574 T C TGGAAACTCAATTTATGTTAGTCGAAAGCAAGGATGATGCCGATGAAACCATTTATACTGTGTTTTTGCCTTTGCTTGAGGGTCAATTTCGTGCTGTGCT[T/C]CAAGGAAATGAACAAGATGAGATCGAAATTTGTGTTGAAAGTGGATGTGAAAGTGTGGAAACCAAGCAAGGAAATTATTTAGTGTAT
102576 TA T TTCCTCAAAACCCATTTTTCCATTCTCCCTAATTCAGGTTTAATTAGTTTCCATTCTGGATCGATACTCATTGCAATGTCAATGAACTCTTTGTC[TA/T]AAAAACGGAACTCTAACTTCCAGTCCCCAAGCTGAGGTTGATTTATTTGCTCTTAAACAGTCATATTGATGCAAAGCTTGTACCTTGCGACAAGTT
102576 A G CATATTGATGCAAAGCTTGTACCTTGCGACAAGTTTCACGATGAAACTCTTCTTTATTAGGAGCCTTGTGGAAGTACAAATATCCTCCTAATATTTCATC[A/G]GATCCTTCACCGGATATCACCATCTTTACACCTAATGACTTTATTTTGCGTGACATTAGAAACATGGGAGTACTTGCTCTGATAGTAGTG
102576 T C CAGATCCTTCACCGGATATCACCATCTTTACACCTAATGACTTTATTTTGCGTGACATTAGAAACATGGGAGTACTTGCTCTGATAGTAGTGACGTCGTA[T/C]GTTTCTACATGGTATATCACATCCTCAATTGCATCTATCCCATCCTGAACTGTAAAGTGAAATTCATGATGCACTGTGCCAAGATAATCA
102590 G GA TGTCGATACGCAAGGCATGTCCAACTCGCCTACGCCGCTTGTTCTTTCAGTCTTTCTCATGGTGTTCTCAGTGCCTTGCGGTGAACCAGAAGCAGACCCG[G/GA]CCCACTACTTCCGGCCGAACCCAACGACGCCTGCGACAACGGCGGCAGCATCCTCGCCGCCGACCGACTCCCGGCCACCGCCTCCT
102590 A G GCAGCACCTTCCTCTTCTTGTACTCCTCGTCCGCCCCCACCACCGGCAACGAGCTCGCCCGCTTCAGCTGTCCCACATTCGGCTGTCTTTCCGGCACCAC[A/G]TGGATGTTCATCGCCTCCTCCTTCACTATGCTGTTCACGATCCCACTGTTGAAGAAGTGGTTCGGGTACGCCGAGATCGAAGAGGACC
102594 A G AAGTTTAGCATCATTTGGAGTACACACTTGAAATTTCATAGATCTTAGAGCATATATAGAACTCACTAGAGTTTGGTCGTACTTCAACAAGAGAAGTATC[A/G]GAGTAAATCCCAACTCCCAGAGAAAAGGGATGGTTCAGTAGCGAACCATCCCAATTAGGGAATTACAAGCTTTCTTCCCTCTTTCCTC
102594 G A AACTCCCAGAGAAAAGGGATGGTTCAGTAGCGAACCATCCCAATTAGGGAATTACAAGCTTTCTTCCCTCTTTCCTCGTGGTGCAAACAGTAGGCCGCCT[G/A]CACCCTTAAAAATCTTGGTACACACCTCGACGCCTCTCATCTCTGGCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTC
102594 TA T AGAGAAAAGGGATGGTTCAGTAGCGAACCATCCCAATTAGGGAATTACAAGCTTTCTTCCCTCTTTCCTCGTGGTGCAAACAGTAGGCCGCCTGCACCCT[TA/T]AAAAATCTTGGTACACACCTCGACGCCTCTCATCTCTGGCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTCTATGTTC
102594 C G CCATCCCAATTAGGGAATTACAAGCTTTCTTCCCTCTTTCCTCGTGGTGCAAACAGTAGGCCGCCTGCACCCTTAAAAATCTTGGTACACACCTCGACGC[C/G]TCTCATCTCTGGCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTCTATGTTCACCGTATATGGGCATGGCTCGAAGTTGT
102594 G A AGGGAATTACAAGCTTTCTTCCCTCTTTCCTCGTGGTGCAAACAGTAGGCCGCCTGCACCCTTAAAAATCTTGGTACACACCTCGACGCCTCTCATCTCT[G/A]GCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTCTATGTTCACCGTATATGGGCATGGCTCGAAGTTGTATACATGAATC
102594 T G GCACCCTTAAAAATCTTGGTACACACCTCGACGCCTCTCATCTCTGGCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTCTATGTTCACCG[T/G]ATATGGGCATGGCTCGAAGTTGTATACATGAATCGAGTACGTGTCCAAGGCGAGATTTAGTGATTGCGGCTTCAGGTTAGATGGAGG
102594 TATAC T CACCTCGACGCCTCTCATCTCTGGCCGTTGTCCGTCATCACCACTCGCCAGAATACGATCAAATTCTATGTTCACCGTATATGGGCATGGCTCGAAGTTG[TATAC/T]ATACATGAATCGAGTACGTGTCCAAGGCGAGATTTAGTGATTGCGGCTTCAGGTTAGATGGAGGTGGCCTTTTGTTGTCTAGGT
102594 T G CATCACCACTCGCCAGAATACGATCAAATTCTATGTTCACCGTATATGGGCATGGCTCGAAGTTGTATACATGAATCGAGTACGTGTCCAAGGCGAGATT[T/G]AGTGATTGCGGCTTCAGGTTAGATGGAGGTGGCCTTTTGTTGTCTAGGTAAAGAGCAGCGAGCCTTGATTCAATTTGAAGTAGGGA
102604 C T CGACGTCGTCACAGTAATCGTAGACCAAATGGTTAGCCCTAACCCACATCACCTGGTGCCTCTGATGCACGCTCATCTCCTCCACCACCTCCTCCTCCCC[C/T]CTCTCCTCTATCGCGAAATCCCTGTAGCTCGTCACGAACGGCGCGTGCGACCAGTCCGTCTTCACCCTCCCTCCCTGCGTCGCCCAGTC
102604 G A AATGGTTAGCCCTAACCCACATCACCTGGTGCCTCTGATGCACGCTCATCTCCTCCACCACCTCCTCCTCCCCCCTCTCCTCTATCGCGAAATCCCTGTA[G/A]CTCGTCACGAACGGCGCGTGCGACCAGTCCGTCTTCACCCTCCCTCCCTGCGTCGCCCAGTCGTCCGCGTTCCACAACGAGCTGTACAC
102604 T C TCTTCACCCTCCCTCCCTGCGTCGCCCAGTCGTCCGCGTTCCACAACGAGCTGTACACCCCCATTTCCTGATCCTCCGGAAACGGAATCCTCGTCCTCCC[T/C]CCTTTGTTTTCGTACACTCGAATCGGAGTCTCATCGATGGCGAACACCACGTGTTTCCTCGACCATTCGATCGAGTAGGAGTGGAAATC
102604 T G ACCATTCGATCGAGTAGGAGTGGAAATCCGTGGTCGGATCGAACCACAGATCCATCCTCTGTTCCCTGTTCCCGACGCCGTCGATGTACAGATTGGTCTG[T/G]ACCAAGTAAGGCTCGCCTGTGGTGTTGCCTAGGAATTCGAAATCGAATTCGTTGTGGTTCGGTCCGTCCGACGACATGTAAAACGC
102604 G A CGAACCACAGATCCATCCTCTGTTCCCTGTTCCCGACGCCGTCGATGTACAGATTGGTCTGTACCAAGTAAGGCTCGCCTGTGGTGTTGCCTAGGAATTC[G/A]AAATCGAATTCGTTGTGGTTCGGTCCGTCCGACGACATGTAAAACGCCGTCACCGTTCCGGCGGAGTCTCCGGGAACTAGCTTTATC
102608 CT C AACACATCATTTACACTCTCATTTGGAGTTCCATCATCAGTAGGTGGTGGTTTGATGCCTGGGGATATATTATCTGATAAGTAAACCTCAGAAATTGAAT[CT/C]TTAACTCTCTTCCCTCAAAAGCTCCAAGACCACGAGCATCTAAGAAGCTGTATTCTGGGACTAAATGGCTACGATCGATGCCATTAAC
102608 T C CTTCTTGACCTCGGCAGCCGCCTTAACCGCCTGCTTGATTCCCAAAGCAGACAGCCCGCTGTCGATCGAAGTTTTGGCCACGGGGTTAGTCACAACAACG[T/C]CGTTACTGTCATAGACGGATTCGCCCGAACGTACCAGGTAGTAGCGGTTGACGAGGCGCTGAGGTGGCATTTGGAAGAGACCACG
102608 G A CAACAACGTCGTTACTGTCATAGACGGATTCGCCCGAACGTACCAGGTAGTAGCGGTTGACGAGGCGCTGAGGTGGCATTTGGAAGAGACCACGTGCGTC[G/A]GCGGAGGAAGAAATCGGGACGACGGTGGTTGGAAGGAGTGAGAGGATGAGGCGCCTCGGGATTGCTTTCGGACATATGGGTA
102610 G A TAATTAGTTTGAAGGAAACAGATTGGTGGTTCTGTTGGGGGTTACCTGCAAATTGACAGCTATAAATTTCTTGGACACCCTCCTCTCGGTGATGCACACT[G/A]CATTAAGTCAAAAAAGCCAAGCCCAAATCATGGCCCGTCATCAATATTTTGCTTGCATTCTACATTACTGTAATGATAAACCATTTACT
102616 T A CAGGTCATGTCACCTTATACGAATTTAATGTTGATATCAACCAATGGAGCCGAAAAGATGTTGAGGGATCGCTTTTTGTTGTGAAGAGGAACAAGCAGCC[T/A]AGGTTTCAGTTCATTGTTATGAACAGGAGAAGCACAGAGAACCTCGTTGAGGATCTTTTAGGTGATTTTGAGTATGAGGTTCAGTCT
102616 T C GTGAGTTTGAGGAACTAGAAGCAGTTCCAAGTCTAGATGTGATAGAAGGCCCGCTTGAGCCACAAAGACCTACTTCTACTTCAGTACCTGATGCTTCTGA[T/C]GGCTCATTCTTGAACTTTTTCAATACAGCAATGAACACGGGAAGTGCTTCGAGTACATCTAATGCAGTCCAAAAGCATGCACCACCT
102618 TG T AAGCTAGCAAGGTGGGTTTTAGCAGCTGAGGATATATGTTTCAAAAGTACCGTTTTATCGTACTTTTTCGTTTAGGAAAATGCATACCGATTACAAGGGG[TG/T]GGTGGACTTTATCAGGAACATATGAATGAAGCCCTTGATATTCTGAAAGGTGGAGGCTGGTTGCATACATTTCCTGAAGGAAAAAT
102630 A C TTTCCACCTAAACCCATCGCTCCATTCGTATATCCTCAAATGACCACCGTAGTCCAGCCTCATGTACTGAACCGATGAAGC[A/C]ACTGGCAATGCCAAGCTTACAACCGGTGTACTCGAAGCCCCTACATATACATCCAGGCTCCCATTTCGAAACGTCATACGCGTCGAACTCTTTCCAGCTA
102630 A T TTTCCACCTAAACCCATCGCTCCATTCGTATATCCTCAAATGACCACCGTAGTCCAGCCTCATGTACTGAACCGATGAAGCAACTGGCAATGCCA[A/T]GCTTACAACCGGTGTACTCGAAGCCCCTACATATACATCCAGGCTCCCATTTCGAAACGTCATACGCGTCGAACTCTTTCCAGCTATGGTGTTC
102630 C A TTCCACCTAAACCCATCGCTCCATTCGTATATCCTCAAATGACCACCGTAGTCCAGCCTCATGTACTGAACCGATGAAGCAACTGGCAATGCCAAGCTTA[C/A]AACCGGTGTACTCGAAGCCCCTACATATACATCCAGGCTCCCATTTCGAAACGTCATACGCGTCGAACTCTTTCCAGCTATGGTGTTCG
102630 C T CATCGCTCCATTCGTATATCCTCAAATGACCACCGTAGTCCAGCCTCATGTACTGAACCGATGAAGCAACTGGCAATGCCAAGCTTACAACCGGTGTACT[C/T]GAAGCCCCTACATATACATCCAGGCTCCCATTTCGAAACGTCATACGCGTCGAACTCTTTCCAGCTATGGTGTTCGTAGCAGCTGCCA
102630 T A ATTCGTATATCCTCAAATGACCACCGTAGTCCAGCCTCATGTACTGAACCGATGAAGCAACTGGCAATGCCAAGCTTACAACCGGTGTACTCGAAGCCCC[T/A]ACATATACATCCAGGCTCCCATTTCGAAACGTCATACGCGTCGAACTCTTTCCAGCTATGGTGTTCGTAGCAGCTGCCACATTCTTGTA
102630 C T CATGTACTGAACCGATGAAGCAACTGGCAATGCCAAGCTTACAACCGGTGTACTCGAAGCCCCTACATATACATCCAGGCTCCCATTTCGAAACGTCATA[C/T]GCGTCGAACTCTTTCCAGCTATGGTGTTCGTAGCAGCTGCCACATTCTTGTAGTACATCTGTGAACCAACAAACGCCTGAAACCCGCC
102630 A G TTCCAGCTATGGTGTTCGTAGCAGCTGCCACATTCTTGTAGTACATCTGTGAACCAACAAACGCCTGAAACCCGCCATCCACAACGCTCAGAGATATCAG[A/G]CCCGTACTTGGATTTGTTCTTGAAACGTTAGCTGCAAGCCTTGCCCCCTGCTTTAAGGTCTGTCCTAGAACCAGAGAATCGGTTGGGT
102630 C G CTGCAAGCCTTGCCCCCTGCTTTAAGGTCTGTCCTAGAACCAGAGAATCGGTTGGGTAGTCACCAGACGACCAAATTTTAGCACCTGACGTGGTAGATAG[C/G]GAGAGTTCGCCGATGCTGTTTACGGACATGGCTGACACGGACTTTGCAGAGGTGTTGGTGGACCAAACAAGGGAGCCGTCTGAAT
102630 C T CTGCTTTAAGGTCTGTCCTAGAACCAGAGAATCGGTTGGGTAGTCACCAGACGACCAAATTTTAGCACCTGACGTGGTAGATAGCGAGAGTTCGCCGATG[C/T]TGTTTACGGACATGGCTGACACGGACTTTGCAGAGGTGTTGGTGGACCAAACAAGGGAGCCGTCTGAATCGCGCAGGATCAGATT
102630 G C GTTTCCTTTCAGTAGGAGGGCGCGGATCATTGCGCCATCTGGGTAGTTTATGGTGTTGTTGAGGGTGGGGGTGTTGGTCCATTTTGTGCCTGGGTTTGCG[G/C]TTGGGTAATCGAATGGCTGTGCGGGTATGAGCGGTAGAAGAGCGGTGATGAGTAGGAGCATCATGTTTGATTTCATGTTGCTTGC
102630 G C TCTGGGTAGTTTATGGTGTTGTTGAGGGTGGGGGTGTTGGTCCATTTTGTGCCTGGGTTTGCGGTTGGGTAATCGAATGGCTGTGCGGGTATGAGCGGTA[G/C]AAGAGCGGTGATGAGTAGGAGCATCATGTTTGATTTCATGTTGCTTGCTTGGTTTTTTTGAATGATGTTATCCAGTAGGCCAAC
102636 T A AGTTCCTTGCAAAGTATATTAGATTTTCCAATGATATGTAGCCGCCACCCCTAAAATCAGTTGATGGGTCAATGCCTTGCCAGCCCATATCTTTCCACAA[T/A]TCGGATTTGAGTGGAGGAATTTCTCGTAGAGGATAAGCCAACTTCCAAAGCTGCCTCAAACCATCCTGATGTTCTACTCGAGTACCGTC
102636 T A ATTTCTCGTAGAGGATAAGCCAACTTCCAAAGCTGCCTCAAACCATCCTGATGTTCTACTCGAGTACCGTCAAATGGGACCCCCAATCGTTGTTTCAGGC[T/A]CTGCAATCTTTCTGCCTGCAACGGACTAAGATGAATCTGATTTTCTCCATTACGACTAATTGAATGAAGAGGCCAAAGCCTTCCTACCA
102636 C T CCCCCAATCGTTGTTTCAGGCTCTGCAATCTTTCTGCCTGCAACGGACTAAGATGAATCTGATTTTCTCCATTACGACTAATTGAATGAAGAGGCCAAAG[C/T]CTTCCTACCATCAATCCAGTGCTAAGAACAATATTCGCTAACCATTGAGCCCACTGTGCAATAACATTTGAGAAAATAAATGTCCAATG
102640 T C CTGTCGTTTCAATCATGAATCCCTTAACTATAGTAAAGCGAACTCAGAAGATGAATTCAACCGAAGCGAGGTTGGGGATTTCCGAAGAAGCTTCGTGGCA[T/C]GCGAAATACAAAGATTCAGCTTATATTTTTATTGGTGGAGTCCCTTATGATCTCACTGAAGGCGATTTGCTGGCTGTTTTTGCGCAGT
102640 G A ATTAGAGACAAAGCTACCGGAAAATCAAAAGGGTTTGCCTTCCTTGCTTACGAAGATCAGCGAAGTACAGTTCTTGCTGTAGATAATTTGAATGGTGCTA[G/A]AGTACTCGGCCGAATCGTTAGAGTTGACCACTGTAGCAAATACAAGAAAATGGAAGAGGAAGATGAAGAGGAAGCACAAAAGAAA
102640 G A GGCGAATGTACCCGAGGAGCTTCTTGCAAGTTTTCTCATGATGAGCAGAGAAGTGCAAACACAGGATGGGGTGAACAAGATAAGGAGTCAAGATGGCCTA[G/A]GGATAAATACGTTGGTCCTCCAAAGAGCCATAAGAATTTCCCAGATAAGGACACACGCCCTTCACGATTAGAGAAGACACAGGA
102640 G T GCGAATGTACCCGAGGAGCTTCTTGCAAGTTTTCTCATGATGAGCAGAGAAGTGCAAACACAGGATGGGGTGAACAAGATAAGGAGTCAAGATGGCCTAG[G/T]GATAAATACGTTGGTCCTCCAAAGAGCCATAAGAATTTCCCAGATAAGGACACACGCCCTTCACGATTAGAGAAGACACAGGAT
102640 C T CCCGAGGAGCTTCTTGCAAGTTTTCTCATGATGAGCAGAGAAGTGCAAACACAGGATGGGGTGAACAAGATAAGGAGTCAAGATGGCCTAGGGATAAATA[C/T]GTTGGTCCTCCAAAGAGCCATAAGAATTTCCCAGATAAGGACACACGCCCTTCACGATTAGAGAAGACACAGGATGAATCTAGG
102640 A C AAGGAGTCAAGATGGCCTAGGGATAAATACGTTGGTCCTCCAAAGAGCCATAAGAATTTCCCAGATAAGGACACACGCCCTTCACGATTAGAGAAGACAC[A/C]GGATGAATCTAGGAGATCAAATGATGGTGATAGATACAGAAATTCGAACAGAAGATCCGAGTCAAACCAAGAAGATTATAGAGA
102654 AC A TCAAGCTTATGTCATTCATTGAACACAAACAAACACCTGAAACGGTACAAGCTATAACTCAAGTATGGTGATTTTCAACGCATATTTACATTACAATGGC[AC/A]CCCCATGCTAATTTTTGAAGGACGTAAGTCTGGAAGCTAAAGCCATTTGCCTTACCAATGCCACATAATCACCTTTCTACCTGGATAT
102654 TC T AATCACCTTTCTACCTGGATATTATCAATAAGCAAAGTCTGATGATGTCCAATCTCACCACCATTACTACTCCCAACAGTAACATTTACACTGTTAACAT[TC/T]CCCCCTACCCTCGCTCAACCGCCACATATACCAACTCCCTACACTTCTATAAGGCCTCCACTTCTCGCAAATTTTCTCCATCTGACTAGGC
102666 GC G AAAGAATAACCGATAAATTGCTGGAAACGTTGGAAGAGTTCATGAAAGATCGGGCCAGAAAACCTGTGGAAACACCCAAACAGCTCGAGCCCGCCCCGGA[GC/G]CCCCCCGTCAAAGAAGAAGAACCAGCTGAGGATATGAATGCTATTAAAGCTCTTCCTGCACCGGCTGATTTCGAGCCTGAACCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102676 T C CTTCCAACTACTTGATTTTCTGTGTTGGAGCTCATGATTACTTCTATGATGTATCTGCATTGCTTTGTACGCTGGAAAAATGTGTGATTTGTATCTATTG[T/C]GAAATCTCTCTGTACACATTATATGGTGTAATAAGTTACACAAATGTCTATCTAGATTCATAGTTGTATTTCATTTGTTAGTTTTAGTGTAA
102680 C T TGGCAATCATCATTCTGATCAACATCACCACCAGTTATCATTCAATCATCTAAACAACCTCAATAGAAATCTAAACTGAAACCGATCCAGACAAGGGAGC[C/T]TGTTGAGTCTGAGTGATAAATGGATGCTGCAACAGCTGCGGTGCAGTATACCTCCGATTTGGTTCTTTCTGCAGGCAACAAGCGATGA
102680 A T CAGTATACCTCCGATTTGGTTCTTTCTGCAGGCAACAAGCGATGAAACTCCTAAAATCATTTGATGCCGTTTCAGGTGCCTGTGGTGGATTTGAAAAGCA[A/T]ATAGCACACATCAAACTCGCCCAATCCCCCTGCCCTCTCAAATTCTCACCATACGGAAATTTCCCCAAATAGAACTCCAGCATGCTCAA
102684 A G GCGAAGTGGAATTGAATAGAGCGATAGAGGAGATAAAGGCGAAAACGTGCGAGCTGACGTGTAGGCAGCTGTTGAAAATAAGGAGACTGAGCAAGCTTGA[A/G]GGGTGGAATGTGAAGAGGATCGACGCGACTGAGGCGTTTCAGAATCTGAGCGATAAAGGAACGTGGGACAGAGTGGCGAG
102684 T C AGATAAAGGCGAAAACGTGCGAGCTGACGTGTAGGCAGCTGTTGAAAATAAGGAGACTGAGCAAGCTTGAAGGGTGGAATGTGAAGAGGATCGACGCGAC[T/C]GAGGCGTTTCAGAATCTGAGCGATAAAGGAACGTGGGACAGAGTGGCGAGGGAGCCGAGCGTGAGGATCGTTCGAAAGTTT
102684 A G AGTGGCGAGGGAGCCGAGCGTGAGGATCGTTCGAAAGTTTCTGAAAGGTTCAGGGTCCGTGGCTGCAGTTGCTGTAAGTAATGTGCAGGTTAGCGTGGGA[A/G]CCGCTTTCCAAGTGTCACACTAGGTGATTCGGTGGAGTAACTAAGTGTTGAGAATAGACAGATAGAGAAGAACATCATTCATGA
102686 C T GCTTATCGAAACGTCTTCGAATAGCCTGATCCAGGGCATATGGTGTATTTGTCGCAGCCAGGACAAGAACTTTCTGATCATTGTTTCCTACACCCTGCAT[C/T]TGCACAAGAAGTTCGGTCTTAATCCTTCTAGAAGCTTCACTTTCGTTTCCTTCTCCTCTTTGACCACACAACGAATCTATCTCATCAACAA
102688 C CAT CACATGTGGCCTTTTTTTTGCCTTGTTTAATCGCTCATGAAATTTGATGCACAGCATAAACATTTACACTCTTAAGCTCACATGTCTGAAG[C/CAT]ATAGGCTAAACTGCATGTAACATCACACATGACATGCAGTTTTAGTACATATATAATGTACAGACTACAGACGCTAGCAAGTACCAACTTTTATTTA
102688 A G CACATGTCTGAAGCATAGGCTAAACTGCATGTAACATCACACATGACATGCAGTTTTAGTACATATATAATGTACAGACTACAGACGCTAGCAAGTACCA[A/G]CTTTTATTTAGAAACTTAAGTAGGAGCATGCATACATATTTTCAGAATCAAAATGAGACCACTATGCCAAGGAGAGCCATGAGCTGA
102688 CT C ACATGTCTGAAGCATAGGCTAAACTGCATGTAACATCACACATGACATGCAGTTTTAGTACATATATAATGTACAGACTACAGACGCTAGCAAGTACCAA[CT/C]TTTTATTTAGAAACTTAAGTAGGAGCATGCATACATATTTTCAGAATCAAAATGAGACCACTATGCCAAGGAGAGCCATGAGCTGAG
102688 T G CACATGACATGCAGTTTTAGTACATATATAATGTACAGACTACAGACGCTAGCAAGTACCAACTTTTATTTAGAAACTTAAGTAGGAGCATGCATACATA[T/G]TTTCAGAATCAAAATGAGACCACTATGCCAAGGAGAGCCATGAGCTGAGAAATAAACTGAGGATGTCCAGGCCAGGCAGCTCCAGT
102688 C T ACTGAGGATGTCCAGGCCAGGCAGCTCCAGTCACCAAATTTCCATCAGTGAAACAACGGTCTATTGGGTCAGGTTCTAACCATATTCCTCCTCCTAGAAC[C/T]ACATTTAGCTTCACTGCAGGGTATGCCGTGCATTTCTTCCCCTTAAGAACTCCAGCAGCTGCTAAAATCTGTTGTCCATGGCATATAGA
102688 A G CATCCATGAACTCTTTTACCAATGCTAGTACTTTCTCATTCAACGCAAGATATTCTGGAGCCCGACCACCTGGGACAACCAATGCATCATATTTTGCAGT[A/G]TCCACATCCTCAAAGCTTGCATTTAGTGTGAAGACATGTCCAGGCTTTTCACTGTAAGTTTGATCCCCTTCAAAGTCATGAACTGCTGTG
102688 C T CCATGAACTCTTTTACCAATGCTAGTACTTTCTCATTCAACGCAAGATATTCTGGAGCCCGACCACCTGGGACAACCAATGCATCATATTTTGCAGTATC[C/T]ACATCCTCAAAGCTTGCATTTAGTGTGAAGACATGTCCAGGCTTTTCACTGTAAGTTTGATCCCCTTCAAAGTCATGAACTGCTGTGGCG
102688 A T CTCATTCAACGCAAGATATTCTGGAGCCCGACCACCTGGGACAACCAATGCATCATATTTTGCAGTATCCACATCCTCAAAGCTTGCATTTAGTGTGAAG[A/T]CATGTCCAGGCTTTTCACTGTAAGTTTGATCCCCTTCAAAGTCATGAACTGCTGTGGCGCATTTTTCACCTGTTGGTTTCTTGGGACAA
102688 T C TCCTCAAAGCTTGCATTTAGTGTGAAGACATGTCCAGGCTTTTCACTGTAAGTTTGATCCCCTTCAAAGTCATGAACTGCTGTGGCGCATTTTTCACCTG[T/C]TGGTTTCTTGGGACAAACAGCATCAACTGTGCAACCCAGAGCTTGCAGAGATTGATACGGAACCATAATTTCATAATCTTCCATGAAGT
102696 A G CAAAATTCCCACCTAGCGTGGGATCCACGTAATCTCTCAGCCTTGCTCCTCTAACCCTAGCCGTCATGAACCTTCCATCCGATCCAACGGCCCACAATCC[A/G]CTTATCACTTCATACGCCAACACACCAAAACTGTACACGTCACTCTTCTTCGAGATAATTCCGGTTCTCAAATAATGCGGGTCGGCGTA
102696 G A ATCCACTTATCACTTCATACGCCAACACACCAAAACTGTACACGTCACTCTTCTTCGAGATAATTCCGGTTCTCAAATAATGCGGGTCGGCGTAGCCCGG[G/A]GATCCGGTCAGGTGACCGGACGGTGCGGGTACAACCGCGGCGGAAAAACCCATGCGAGCGGACCCGAAATCGCAAAGCTTCGGGA
102696 G T CTCTTTCCTGCAAGAAAGCGCGGTACAATCTCTCGCTGCTATGCTGCACCTTAAACGCAGCGGGTAGAGTCACCTCCCCCTTTGATTCGGGTAACCGCCC[G/T]ATGTAGACTGTGCTGAATCCGCCCTCTCCGATCACCGCCGACGCCGGGAATTCCCCCGTCATCTTCTCCACCTCCGACCACTTGAACA
102704 A G CGGGAACGATCTCGCTGAAACTTGACACAGCATCCAGTTCCGAGCTCAAATCTGTATCAACTGAGGAGGAAGCATTGCTAGATGTTGCGCGTATTTTAGG[A/G]AAAGACCGCTTTACGTTGAATACAAGGTTCGACTGAGATATCAACCGAAAAGAAGAAATCTTCGGCGACGAGGAAAATAGAGTCG
102704 A G AGATGTTGCGCGTATTTTAGGAAAAGACCGCTTTACGTTGAATACAAGGTTCGACTGAGATATCAACCGAAAAGAAGAAATCTTCGGCGACGAGGAAAAT[A/G]GAGTCGATGATGAAGAAGGCGAAGAGGAGATCGACAAGGACATAATTTATTTGCTTTATTGATTGCTTCAAGCTCT
102704 C A TTGCGCGTATTTTAGGAAAAGACCGCTTTACGTTGAATACAAGGTTCGACTGAGATATCAACCGAAAAGAAGAAATCTTCGGCGACGAGGAAAATAGAGT[C/A]GATGATGAAGAAGGCGAAGAGGAGATCGACAAGGACATAATTTATTTGCTTTATTGATTGCTTCAAGCTCT
102706 C T TCTCAAACATCAACCCGTAGAAAATTTGCCCATCTCGCCTTAAAAGCTGTCCACTGATCTGCAGACCCTGGCCAGTCGATGCTGGCAGTAACACAGGTAG[C/T]GGAGGCCCTGAAGGAGTAGATGGCTCATCACTGGGAACAAGAGCGTTATCCAAACCCATTAAATCACCAAGCAAATCCGGTACTGG
102706 A G ACACAGGTAGCGGAGGCCCTGAAGGAGTAGATGGCTCATCACTGGGAACAAGAGCGTTATCCAAACCCATTAAATCACCAAGCAAATCCGGTACTGGAGC[A/G]GCTGCAGCGGGTGATGCTACTGGCTGCTTAGGGGAAGTATGTGAAACGGTACTTGTACTAGCAGATGCTGGTGCACCATTGATT
102706 A G CTGGCTGCTTAGGGGAAGTATGTGAAACGGTACTTGTACTAGCAGATGCTGGTGCACCATTGATTCCATGGGAAGGTGATTCAGAATATGCAGTTTCTCC[A/G]GTATCTGGAAACTCCTCGTCATCTTGTTTAGGAGTAGTTGACTTTGCACGACTCACAAATGCTTCAGGTGGTTTGTGATAAACTGAA
102706 T C CTAGCAGATGCTGGTGCACCATTGATTCCATGGGAAGGTGATTCAGAATATGCAGTTTCTCCAGTATCTGGAAACTCCTCGTCATCTTGTTTAGGAGTAG[T/C]TGACTTTGCACGACTCACAAATGCTTCAGGTGGTTTGTGATAAACTGAAGAAAGGGTAGCAATATTTCCTAGAAGCTCATCTAGAAG
102706 C T TGTCGGTCTCCACAGTGGCATTATTTAAAACGACCTGAATCATCTGCTGTGGACCTTCAGTTGGTTTTTTAAGAAACAATTTGACAGTTGCAGTGAGCAA[C/T]TGTAATTGTACAAGCGCAGGCTCTTCAGGAAAGCTCTCCAAGAAGCTTTCAAGGAGCTCATCTGCATTGTCAATTCTTTCTGCATATTC
102708 G A GACCAATGCCAACAGGGATGGCTATGGTGCCAATGGTTTTACCTGATGGTCGCATCGGCTATGTTCTACAACAACCAGGAATGCATTCTCCACCACCACC[G/A]CCATCATCAAGAAGAAATGAACGTGGAGGCGGCTCAGGCGATCGTCATTCTCGTGATAGGGACTACGATAGAAGCCAAAGTCGCA
102708 T C TGGCTATGGTGCCAATGGTTTTACCTGATGGTCGCATCGGCTATGTTCTACAACAACCAGGAATGCATTCTCCACCACCACCGCCATCATCAAGAAGAAA[T/C]GAACGTGGAGGCGGCTCAGGCGATCGTCATTCTCGTGATAGGGACTACGATAGAAGCCAAAGTCGCAGATATCGTCCGTACTGAAT
102708 C T TACCTGATGGTCGCATCGGCTATGTTCTACAACAACCAGGAATGCATTCTCCACCACCACCGCCATCATCAAGAAGAAATGAACGTGGAGGCGGCTCAGG[C/T]GATCGTCATTCTCGTGATAGGGACTACGATAGAAGCCAAAGTCGCAGATATCGTCCGTACTGAATTTGTCTTCTCTGCACTGTAATT
102714 CT C TCGTTTATATTTTTTCCTTTTTTTTGTAGGACCGAAGTCCATGCAGGTAATCCCCTTCTTGTTCGCATTCACCTCGTCCAGGCATGTAATTGCCAAATTC[CT/C]TTCGGTTTCTCCCCAACCCGTTCTTCTTCTCTTCGCGTACAGACGTCCTGCCTTCCAACCAACGCGCCCCATCCTTCCCCTGTATTTAGCTT
102714 GT G TATATTTTTTCCTTTTTTTTGTAGGACCGAAGTCCATGCAGGTAATCCCCTTCTTGTTCGCATTCACCTCGTCCAGGCATGTAATTGCCAAATTCCTTCG[GT/G]TTTCTCCCCAACCCGTTCTTCTTCTCTTCGCGTACAGACGTCCTGCCTTCCAACCAACGCGCCCCATCCTTCCCCTGTATTTAGCTTGTCCA
102714 TC T TTTTTCCTTTTTTTTGTAGGACCGAAGTCCATGCAGGTAATCCCCTTCTTGTTCGCATTCACCTCGTCCAGGCATGTAATTGCCAAATTCCTTCGGTTTC[TC/T]CCCCAACCCGTTCTTCTTCTCTTCGCGTACAGACGTCCTGCCTTCCAACCAACGCGCCCCATCCTTCCCCTGTATTTAGCTTGTCCACGTTC
102722 GT G GTTAGTGTCTCTGGATGGGGTTGGTACAGGTTCTTGGTGGTTAGCTGTCTGTGAATAATTGGGGGTCATCTTGATGCTGTAATTTGAAGTTTGTTTAGTT[GT/G]TTTTTGGGTTTACGGTTGTGGTGAGTTTGGTGTGGATGAGCTTTGGGGAGTTCGTGTTTTGTGATGAACTCTTGGGTGCTGCTGCT
102724 C G TGTAGGAATTCACACGGTGATCGACTGTGCAACAGGAAGGCCGGAAGAGCCTATTCGCACGGTAGATTGGGAAGGCAAAGTGGCTTTGATCCAATGCGC[C/G]AAGGCCATGGGGATACAGAAATTTGTTTTCTATTCTATTCACAACTGTGATAAGCATCCCGAGGTTCCTTTGATGGAGCTCAAGTA
102724 G C AGTATTGTACCGAGAAATTCATCCAGGATTCTGGTCTGAATTATGTCATTATTCGGCTATGTGGCTTTATGCAGGGTTTGATTGGACAGTATGCAGTGCC[G/C]ATACTAGAAGAGAAATCAGTGTGGGGAACTGATGCTCCAACTCGAATAGCTTATATGGATACACAGGATATAGCCAGGCTAACTTTT
102724 A T CTCCAACTCGAATAGCTTATATGGATACACAGGATATAGCCAGGCTAACTTTTATGGCGATGCGTAATGAAAAGGTCAGCAACAAGCTCCTGACATTCGC[A/T]GGACCTCGAGCATGGACAACCCAAGAGGTGATTACCCTATGTGAGAGACTTGCAGGGCAAGATGCAAATATTACCACAGTTCCAGT
102726 G A CTGTTCACTGTGGAAGGACTTGCTTCAAACAACTCTTCGGCTTCAACTTTAACTGTTTGCTCGATGCAAGAGTTAACTGAAATCTGGTTGACAGACTTGG[G/A]TGCTAAATCTACTTCAGCAGACTTGTTCGATTCTATTTCAGCATTCTGGGAATCAGAAACTGCAGCAGGCAGCTCAATGGCCACAGGG
102730 A T TACCCATAATTTGGAGCACCATAACCTGAAGATCCATAGGAAGGATAACCACCAGCAGCTGCTTGTGATTGCATGTACTTATTCTGATTGCCTTCGTAGG[A/T]CCCAGAGTTTGCACCAGCACCGCCACCATAAGACTGGTAAGAGCCACTGCCACCGGAACGGCCACCAGAAGCATTATTGGAATTGGC
102730 C T GCATAATTACAGTTTGAAGAACTTCGCCATAATTACTAAAATACTGTTTCATTTTATCTTCGTCGGTTTCCCATGAGATCCCGCCTATGAATAGTTTCCC[C/T]TGATCTGAATCCATAGAGATTGAAATTGATTTGGAACGATGAAATTAGGGTTTAATTTGTCACTCGAGGGCGAAGA
102732 G A CCTTCTTCAACAACCCGGCTATCAGATTTCTAACCGGTAACTCTCCCGGAGAGCACTTTACCGGAAAACACAACTCCTTGTTGATAACATTGCTCAACGT[G/A]GCCTTGTTGGTGGGTCCCACGAACGGAGTCTCCCCGTAGATAATCTCGTACAGGAAAATGCCGTAAGCCCACCAGTCCACGGCGTTCG
102732 G A AAATGCCGTAAGCCCACCAGTCCACGGCGTTCGTGTGCCCGCGCCCGGACGCAACTTCAGGCGAGACGTACTCATGAGTTCCCACGAAGGAATTGGACCT[G/A]GCGGAAACCGGTTCCGCGACGAAGCGGGTCTGCACCGGTTCGGGCTTGGTTCGCGATCTAGACCGGAAGAGGGCAAACTGGCG
102732 G C TGCCGTAAGCCCACCAGTCCACGGCGTTCGTGTGCCCGCGCCCGGACGCAACTTCAGGCGAGACGTACTCATGAGTTCCCACGAAGGAATTGGACCTGGC[G/C]GAAACCGGTTCCGCGACGAAGCGGGTCTGCACCGGTTCGGGCTTGGTTCGCGATCTAGACCGGAAGAGGGCAAACTGGCGACG
102732 C T ACCAGTCCACGGCGTTCGTGTGCCCGCGCCCGGACGCAACTTCAGGCGAGACGTACTCATGAGTTCCCACGAAGGAATTGGACCTGGCGGAAACCGGTTC[C/T]GCGACGAAGCGGGTCTGCACCGGTTCGGGCTTGGTTCGCGATCTAGACCGGAAGAGGGCAAACTGGCGACGTGGCTTTTTCGTC
102736 T TA CAAAGCAAAATGATAAATATCTCCTTTCTCCTCGCCATCGCAACGGTCTTCCTTCCCACGCTGCTCTTCGCAGCCACCGTCTTTCCTCACCACCAAAACC[T/TA]AAAAATGTACAGCTCAACGTAAACTACCACAGCAAGCAGCCTAAACCTTTGTCTACGTCGATAATTACGTCTTCGAAACGATACGAGGG
102736 A G GCCTTCGCTGGCCGAGTGGTGGAGGACGGTGGCTGTTTACTCCGACCAAACGAGTGCGAACGTGACCAGAAGTTTTAAGATTGCGAAGGAGCATTATAAC[A/G]AGGGGATGTCGAGGGGGACTTTTCTCACTAGGTTGGGGATCCAAGAGGTGATTAAGGATTCTGTGGTTGAATTCAATGGCAGCT
102736 G A CTTCGCTGGCCGAGTGGTGGAGGACGGTGGCTGTTTACTCCGACCAAACGAGTGCGAACGTGACCAGAAGTTTTAAGATTGCGAAGGAGCATTATAACAA[G/A]GGGATGTCGAGGGGGACTTTTCTCACTAGGTTGGGGATCCAAGAGGTGATTAAGGATTCTGTGGTTGAATTCAATGGCAGCTTG
102746 G A GAAGGCTGCTCTTGAAAAGAGGAAAGAGAAAGGTGAAGTGACTGCAAAAGCTGTTGTAACTGACGACGACGACGAACTCATAGAAAGGGAGCTTGAGCGC[G/A]GTATCGAGCTTGCTGCTGAAAGCGAAAGGATGGGAAGGAAAGATGCCAATCCCGTTCTGGAGAATGCAGTTGAGGAAGAAGG
102746 A T CGATTTGGGTCAGACTGAGCGAGATGAGAGAGATCGCAAAAGGCAAAGGCTTTAAAACAATGTCATAGATGCTTAGGGTTTAAGAGGTTACACATATACC[A/T]GAAGTGTGCGTTTCTGAGTTGTATATGTATTTGTTAGAGGCTGTGAATACATTTGTATATGTATGAAGATCATATTTGATACATAGA
102752 G C TGGCTTTGCTTTCTATATTCTGGGTTGAAGCATCGTTGTTATTTGGGAAGAGGCGGTCGAGCGTTGTTTCACATTCTTTTATGAGCTTGTTTAAAATGTC[G/C]GTTGTGAAAAATGGTTGCTGCAGCACTTTTTGGATGAAGGGCAGCCTTATTAAAGCACCGGTTCTTTTGTCGTACTTTTTTAGAATCTT
102752 T A TTCTTTTATGAGCTTGTTTAAAATGTCGGTTGTGAAAAATGGTTGCTGCAGCACTTTTTGGATGAAGGGCAGCCTTATTAAAGCACCGGTTCTTTTGTCG[T/A]ACTTTTTTAGAATCTTCACTAGGCCAGTGTAGTTGAGCGCACTGTAATTCTCGAGCAGCACCATTTCACCATGGAAATCAACAATCTCC
102752 A C TCTTTTATGAGCTTGTTTAAAATGTCGGTTGTGAAAAATGGTTGCTGCAGCACTTTTTGGATGAAGGGCAGCCTTATTAAAGCACCGGTTCTTTTGTCGT[A/C]CTTTTTTAGAATCTTCACTAGGCCAGTGTAGTTGAGCGCACTGTAATTCTCGAGCAGCACCATTTCACCATGGAAATCAACAATCTCCT
102752 G A TTTAGAATCTTCACTAGGCCAGTGTAGTTGAGCGCACTGTAATTCTCGAGCAGCACCATTTCACCATGGAAATCAACAATCTCCTTCCAGACCTTCATCA[G/A]ATCTTCTCTACTATCTTCCTCAACTGCTCTCGCAGCTTGATCTAGAAGCACCTTCTGTTTAATAATATACCCTTCTTCCTTATCAGTAAAA
102752 TA T CAGACCTTCATCAGATCTTCTCTACTATCTTCCTCAACTGCTCTCGCAGCTTGATCTAGAAGCACCTTCTGTTTAATAATATACCCTTCTTCCTTATCAG[TA/T]AAAAAACCAATTGAACTTCTCCAGTTCCTTCTCCAAAAGCTCCATAAAAGCCGCTTCCTCTGACGTTATCACTTCGCCTCTGACGTCATATG
102756 GT G AAATGAAGGTGAGAAGAGAGCAGGGACTTAGGGTGAAAGAGTTGATGGAGAAGACTGATTCCAATGATATTGTGGATGACAATCATGAAATGATCTGATT[GT/G]TTTTTGGTAGAAGAAAAGAAAATGTATTCAATCCTTTGTCTTAACCGAGTGTATTTGCAACAGTCCATTATGGTCTTCGAAGAAG
102764 G T AATCAGATTGGAACTCGATTCACTCTTCATATGCATATCGTCCATCGCCATTGTTGTAGCAAGCATATGCTGCTGCTGGAACATCACCTCGTCAGACGTC[G/T]GTACCACCGGAAGCGGAGCCGGCGGAGGCGGCGTCGGAGGTGGGTATCCAGATCCGGCGCTGACACGTGGAGGAATCTTAGTGGT
102764 G A TGCTGGAACATCACCTCGTCAGACGTCGGTACCACCGGAAGCGGAGCCGGCGGAGGCGGCGTCGGAGGTGGGTATCCAGATCCGGCGCTGACACGTGGAG[G/A]AATCTTAGTGGTTGCATCGGGATTCAGAAATCTGGCGAACATAGATTCGGTTTCGGGGCTGGATGGGCGAATCGGAAGGAAC
102768 AT A ACATCCATGAGGCACTATAAAATGTGATCATCAAATTTCCAGGTTTGTCCCCAAGTCATTATCCTCAATGAAACACTAAATAAACCAATTTAAATTACGA[AT/A]TTTTTTAGTCTTTCCTCGACTTGGTATCCAAAACCCAGAGCAATTTCAATGATGCTTCGACGTATAACTCCATTAGGAATAGTTCCCCAC
102768 C CA GTTTTGACTCCACCAGTGCCTCCATGACATGATCAATGTATCTTATTTTGTAAAAGCAACTCAATAAGTGCCAGACCCTACCGCATAAATCTCAAATTAA[C/CA]AAAAAAATGATCATAAGTTAATTCAATAATGTGTTAGTAAAGTGAGAAATGCAATAAATAATTTTTGCCTTGAAGCATAATCCCATTGG
102770 C G GTACCAAGAAAACCCTGGTATTTCATGAAGGTAGACCGCCACATGGCAAACGCACTGAATGGATCATGCATGAGTATTATGTCAATGACAATGAGTTTAC[C/G]CCAGAGATGAAGGACAGCTACGTCCTATGCCGGGTTACCTTCCGGGGTATTTGGGATCCAGTGCATGGATTTGAATTGAATGCACT
102770 C T CAGTGCATGGATTTGAATTGAATGCACTTGATTCAGTTCATGCACAATCTAAATCAGTTGAAACTGAAGAGGAAATTAATGCATGGATCGAGGAACTTAT[C/T]AATCCTGCCTTTACTGGCTGCCCTGTTGGAATTGAACTCAACAGTGTAGATACGGTGGGAAGTAGGTCGATCGTTGAGGCCGCCAAC
102778 AG A GGAATGAGAGAAATGGTCGAGGAGAAAGAGGCACTAGAGCAGCAATTGCAGATAGTTATGATGAACAGCGATGTATTGGAAGGGTGGGTGAGGGAGAATG[AG/A]GGGGAGAAAAGTGCAAGATGCTGTCCAAGTGGATGAGGTGTTTGAAACAGTGGATATGTGTTCGAAACAATTGTTGGAAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102794 A G TCCTCCTTGCATGTTAGTGAAGGTGGAGTTTGTGTGGAATTTGGTTCCAAGGTAAAACCCAAATTATCAATCTTCTTGTTGTGAAGTATTCCTGTTTGAA[A/G]TAAAGTTTGTGCATCGTCACAAACTTCCTTTCCTTCATAAACCACGCCAACTCTAAATCCTTGGTCTATTATAGAACTCACAGCTTCCATA
102794 A G TTCCTTCATAAACCACGCCAACTCTAAATCCTTGGTCTATTATAGAACTCACAGCTTCCATAACTGTCTTCTTAAGTGAGCCCACTGTTGCTGTGTCAGG[A/G]ATATCAATATAAATGTCAGGCACCTTGATAGACTTTACGCTGAATTTCACAAAACATTCTTGAGATTCAAGTAGAGACTTCTGGCCAGAT
102798 T C CCAACACCACCTACACCAACCACACCTCAACCACAAAAGCAAATCATGGTCTCACCTCCAATCACAGACACACCTATGTCATCCCAAGTGGTGGACCCCA[T/C]GTCGGCTAGATGGCCGAAGGCGGAAGTACATGCATTGATACAATTAAGAAGCGAGCTCGACTCAAGGTACCAAGACAACGGTGCAA
102798 C G CAATCACAGACACACCTATGTCATCCCAAGTGGTGGACCCCATGTCGGCTAGATGGCCGAAGGCGGAAGTACATGCATTGATACAATTAAGAAGCGAGCT[C/G]GACTCAAGGTACCAAGACAACGGTGCAAAGGGTCCGCTGTGGGAGGAGATATCCTGCGGAATGCAAAGGCTCGGGTACAGCAG
102800 T TA GGTGAAATTATTGATGTGCGCTTAGCCCAAGATCAAGATGGTAGGTTCAAGGGATTTGGCCACGTTGAGTTTGCTGATGAAGAGTCTGCCCAAAAGGCAA[T/TA]AAAAAGAACAAGGAAGAGCTATTAGGTCGTGAAGTGAAGCTCGACTTTGCTCGTGAACGTGGAGACAGCAAAGAGGATGGTAG
102800 T C CAAGGGGTGATAGCGGTGGCGGTCGACGTGGTGGGGGTCGTGGTGGCGGCAGAGGATTTGGCGGTGGCAGAGGTCGTGGTGGTTTTGGCGGCGGCAGAGG[T/C]GGCGGCTTTGGTGGCGGCGGCAGAGGTCGTGGTGGAGGCGGCAGAGGTCGTGGTGGTGGCAGAGGGAGACGTTGATGA
102806 G C CCGGATCCAGCATTGCCAGGAAATTAAGTAGGAGGCTGTGGAGCAGGAGCAAGAAGGACGAGGGCAAGGTCACGGTGAAGGACATTGTGAGGCTGAACTC[G/C]TTCGAGCTGTACGGAGATAGGGACTCTCTGTTCATGACTTCGCCTGTCGTCAGTAGTTGCAGTAGCTCCTCGGATGGCGGTGA
102806 T A GGTCACGGTGAAGGACATTGTGAGGCTGAACTCGTTCGAGCTGTACGGAGATAGGGACTCTCTGTTCATGACTTCGCCTGTCGTCAGTAGTTGCAGTAGC[T/A]CCTCGGATGGCGGTGACTGTTCGGACTCTCTTGGATCGATTTCCAGTGGCGGATCCGAATGTTTTGGCGGTGGATCCGATTGTTTT
102806 C G GTCACGGTGAAGGACATTGTGAGGCTGAACTCGTTCGAGCTGTACGGAGATAGGGACTCTCTGTTCATGACTTCGCCTGTCGTCAGTAGTTGCAGTAGCT[C/G]CTCGGATGGCGGTGACTGTTCGGACTCTCTTGGATCGATTTCCAGTGGCGGATCCGAATGTTTTGGCGGTGGATCCGATTGTTTTA
102806 A C TCGAGCTGTACGGAGATAGGGACTCTCTGTTCATGACTTCGCCTGTCGTCAGTAGTTGCAGTAGCTCCTCGGATGGCGGTGACTGTTCGGACTCTCTTGG[A/C]TCGATTTCCAGTGGCGGATCCGAATGTTTTGGCGGTGGATCCGATTGTTTTAGCGTGTGTGATTTGGAGTCCAAGAAGAAGGCTCT
102806 G T TTGGCGGTGGATCCGATTGTTTTAGCGTGTGTGATTTGGAGTCCAAGAAGAAGGCTCTGGTTTCTAATGATCTTGGGTGTTCGTTAGAGAATCACGAAGG[G/T]AATGGTTTATCATCTGAACATGCAAGATCTCAATCCGAAGAAGAAAAAGAACAATTAAGTCCCGTATCCGTCATGGATTTTCCCGAC
102806 G A CGGTGGATCCGATTGTTTTAGCGTGTGTGATTTGGAGTCCAAGAAGAAGGCTCTGGTTTCTAATGATCTTGGGTGTTCGTTAGAGAATCACGAAGGGAAT[G/A]GTTTATCATCTGAACATGCAAGATCTCAATCCGAAGAAGAAAAAGAACAATTAAGTCCCGTATCCGTCATGGATTTTCCCGACATCC
102806 T C ATTGTTTTAGCGTGTGTGATTTGGAGTCCAAGAAGAAGGCTCTGGTTTCTAATGATCTTGGGTGTTCGTTAGAGAATCACGAAGGGAATGGTTTATCATC[T/C]GAACATGCAAGATCTCAATCCGAAGAAGAAAAAGAACAATTAAGTCCCGTATCCGTCATGGATTTTCCCGACATCCACGAGGATAAC
102806 A G GTTTTAGCGTGTGTGATTTGGAGTCCAAGAAGAAGGCTCTGGTTTCTAATGATCTTGGGTGTTCGTTAGAGAATCACGAAGGGAATGGTTTATCATCTGA[A/G]CATGCAAGATCTCAATCCGAAGAAGAAAAAGAACAATTAAGTCCCGTATCCGTCATGGATTTTCCCGACATCCACGAGGATAACAA
102806 A T TGGTTTCTAATGATCTTGGGTGTTCGTTAGAGAATCACGAAGGGAATGGTTTATCATCTGAACATGCAAGATCTCAATCCGAAGAAGAAAAAGAACAATT[A/T]AGTCCCGTATCCGTCATGGATTTTCCCGACATCCACGAGGATAACAATGAAGAAAACGACGATGAATACTCAAAAACCTCGCCATAT
102824 C CT AACTTGAAACTCTATTTGAACTCAAAGGTTGGGACGGTTGGTGCATCAAAACCCTCTAAAACCTCAGTTTTAGCACTAGCATGCCCACTTTTCGGTTCCT[C/CT]TTTTTCTTTCCACTAAAGAAACCACCTAACCAAGAAGAACTGCTTGATTCATCAGTTGTCGAGCTCATAGAAGGTCCACTTGCACCAAC
102826 TA T TCTAAGTTTATGCATGCACACAAATGAAGCATGCACTCTGTTCACAATACGCACTTCCAAATCGTTTGAACTAACCATAACAATGACGTATTAAACACCG[TA/T]ACCTCCCCGAGAAAACTTTTGACTATGTAACATTTTGTAAATGAAGTAAATAACAGCAATAATAATGAAAGCCTTCGTAGAATCACAG
102826 T C AAACAAGTTTATTACTTCTTCCATCCATCCAGTCATTCATCAATAAGAAAATTTTGTAGGCAGTTAATTAAAAGTATCATTGCAACTACACTTGAGGCCG[T/C]GAAGAGTCAGCCACTTGTCGAGTTGTTGCATAATCATAGGATCTGGTGTAAGCCGGCTTACTGCCATGGGAACATTCCACATTTGTATT
102826 A T CAAGTTTATTACTTCTTCCATCCATCCAGTCATTCATCAATAAGAAAATTTTGTAGGCAGTTAATTAAAAGTATCATTGCAACTACACTTGAGGCCGTGA[A/T]GAGTCAGCCACTTGTCGAGTTGTTGCATAATCATAGGATCTGGTGTAAGCCGGCTTACTGCCATGGGAACATTCCACATTTGTATTGGC
102826 T C TTTTAGCAATAACAACTTCAGCTCGTAGTTTCTCAACTTCTCTTGCCAAGGATATCAAGTTTCTTTCTAAAATGCACAGCTGCTCCACTTGCTCTTTATT[T/C]GCATCTCTCTCATGCTCAAAAGTAACGCGTAAATTTTGATGCTCCTGCTTTAATTCTTCTAGCTCAGCAAGCAAATTAGGCAATTTTCTGCA
102828 C A TTCGATTGACCCACAAATGCTTCCGTGTGAATGATCTGTCTATGAAGGTTATTTAGCTCAACTCTGTCATTGTCAACTATACCTAAGCAGCCGACACCAG[C/A]CGCAGCAAGATACATGGCAACAGGGGATCCCAGCCCTCCTGCTCCGACAACCAAGATTGATGACCTGGAGAGATTTCTCTGACCATCA
102834 G T CGAGAGATAAAGCTTGGGCTGAAAGGCTAATTGTACTACAAAAACTTGAAGCAGAGAAAATGGCTGCAAAGGCTTGAATACATTATACATCTGCAATAGA[G/T]GATAAGAGTCCAGAGTAGAGCTTTTCGTATTATCAAGTTTTGATATTTGTTACTATTGTTTGTTGTAAGAATCTGTTCGAAAACAAA
102834 CA C ATACATCTGCAATAGAGGATAAGAGTCCAGAGTAGAGCTTTTCGTATTATCAAGTTTTGATATTTGTTACTATTGTTTGTTGTAAGAATCTGTTCGAAAA[CA/C]AAAATATTTTATCTTCTGGCTTGTAAGGCGATGATGCCAGAAAATTGCGTTGTGCTTGCTGTTTTACTGCGTGCTCCTGCTTACCATGT
102834 AT A GCTTACCATGTTTCATCTGTTTATTCAGCAGAAATTCAGAAACAAATTCATACTTACCGTAAATGCTGTTGCGAAGGCATTTTTACTGTATTTACCCAAT[AT/A]TTTTGGTTTACAGTCTCCAGTTGAAGTTATGAAGAACCAACAGCTTAGAATGTGCTTCATGGTTGTTGTCTATATTGGATTTAGCTTTTG
102840 T TG TTGTGGTCGGCTCCGCCAATGCCGACATCTACGTCGAAATCAACCGTCTTCCCAAAGAGGGCGAAACCATTGCTGCCGTCACAGGACAAACCCTAGCTGG[T/TG]GAAAGGGGGCCAATCAGGCATGCTGCGCCGCCAGACTCTCTTCTTCGCCCACATACTTCGTAGGCCAGATCGGAAATGATGCCAA
102846 A G GCATTCATCTTCAACAGACGAACGATTAGCCGAATGGAGATTCACGTCTTAACTGCATTGGAATGGCGAATGCGATCGATTACTCCATTCTGCTTCCTCG[A/G]TTATTTCTCGAATTTCTTCCTTCCTGCTCAGCTTCCGTACGTTTATGCCCTCAAGAACAGATCCGTCCAGTTGCTATTAAAAGCTCAAAA
102846 T C ACAGACGAACGATTAGCCGAATGGAGATTCACGTCTTAACTGCATTGGAATGGCGAATGCGATCGATTACTCCATTCTGCTTCCTCGATTATTTCTCGAA[T/C]TTCTTCCTTCCTGCTCAGCTTCCGTACGTTTATGCCCTCAAGAACAGATCCGTCCAGTTGCTATTAAAAGCTCAAAACAAGAATGAAAA
102846 T C TCTTAACTGCATTGGAATGGCGAATGCGATCGATTACTCCATTCTGCTTCCTCGATTATTTCTCGAATTTCTTCCTTCCTGCTCAGCTTCCGTACGTTTA[T/C]GCCCTCAAGAACAGATCCGTCCAGTTGCTATTAAAAGCTCAAAACAAGAATGAAAATGTGAAGTTCAAGCCGTCATTGCTGGCAGCGTCA
102846 G T TTCCGTACGTTTATGCCCTCAAGAACAGATCCGTCCAGTTGCTATTAAAAGCTCAAAACAAGAATGAAAATGTGAAGTTCAAGCCGTCATTGCTGGCAGC[G/T]TCAGCATTGCTATTAGCCGCAGAGGAACTGTTTCCGATTCAACACTTGGATTTCAAAATGGCCATTTCGAACTCTCAGTTCGTGGATG
102846 A G TGGCAGCGTCAGCATTGCTATTAGCCGCAGAGGAACTGTTTCCGATTCAACACTTGGATTTCAAAATGGCCATTTCGAACTCTCAGTTCGTGGATGATCA[A/G]AAATTATCGGATTCCATGGAGCTGATGAACGACGTCGCTGAAATGGACAGCTACGAGGTAATTTCGAGCTGCGAGACGCCGGTTAC
102846 A G ATCAAAAATTATCGGATTCCATGGAGCTGATGAACGACGTCGCTGAAATGGACAGCTACGAGGTAATTTCGAGCTGCGAGACGCCGGTTACCGTGCTTGA[A/G]CTGGATTACGGTGGACCGAAGTTGAAGAAGCGTAAGGTCGATGATGATACCGTTTTTGAATGATATGTAATAAAAGTACCGGAGG
102850 A C ATCATCATTGAGGAAGAAGCCTCTTAAGCCCAGCCTTCTGTTCAGCACTCAGCCTTGTAGGAAACTTGATATCAAACTTAATCCTCAAATTGCCTTTCCT[A/C]GACGGATCCTTAGGCAGTGGCATTCCTTCACCACGAACGATTTCTTCGTAATCTGGATGAATGATATTATTAATCGGTATCTTAAGGCTC
102850 T C TTGTAGGAAACTTGATATCAAACTTAATCCTCAAATTGCCTTTCCTAGACGGATCCTTAGGCAGTGGCATTCCTTCACCACGAACGATTTCTTCGTAATC[T/C]GGATGAATGATATTATTAATCGGTATCTTAAGGCTCCTTCCATCGAGTGTGGTCAATTGCACAGTGTATCCAGTAAGGGCTTCTAGTAG
102850 A G TGATATCAAACTTAATCCTCAAATTGCCTTTCCTAGACGGATCCTTAGGCAGTGGCATTCCTTCACCACGAACGATTTCTTCGTAATCTGGATGAATGAT[A/G]TTATTAATCGGTATCTTAAGGCTCCTTCCATCGAGTGTGGTCAATTGCACAGTGTATCCAGTAAGGGCTTCTAGTAGAGTGATCTTCTG
102850 A C TATTATTAATCGGTATCTTAAGGCTCCTTCCATCGAGTGTGGTCAATTGCACAGTGTATCCAGTAAGGGCTTCTAGTAGAGTGATCTTCTGAGTTACGAT[A/C]AGATCATTCCCGTCTCGCTTGTAAGTGCTATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAATATTTGGTCGCTCGTT
102850 C T TCCATCGAGTGTGGTCAATTGCACAGTGTATCCAGTAAGGGCTTCTAGTAGAGTGATCTTCTGAGTTACGATAAGATCATTCCCGTCTCGCTTGTAAGTG[C/T]TATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAATATTTGGTCGCTCGTTGCCCTTTTCAGGGAATGTGATCTTAGT
102850 T C AGTAGAGTGATCTTCTGAGTTACGATAAGATCATTCCCGTCTCGCTTGTAAGTGCTATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAA[T/C]ATTTGGTCGCTCGTTGCCCTTTTCAGGGAATGTGATCTTAGTCCCTTTCTTCCACCCTGGCTTTATTTCTATTGTTAGGATCTCTTCCAC
102850 T C CGATAAGATCATTCCCGTCTCGCTTGTAAGTGCTATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAATATTTGGTCGCTCGTTGCCCTT[T/C]TCAGGGAATGTGATCTTAGTCCCTTTCTTCCACCCTGGCTTTATTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACAT
102850 A C CTCGCTTGTAAGTGCTATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAATATTTGGTCGCTCGTTGCCCTTTTCAGGGAATGTGATCTT[A/C]GTCCCTTTCTTCCACCCTGGCTTTATTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACATCGGCAATCTCCCTCGAAA
102850 C T TATGCGGCTTTTCATCGATTATGAAGATGAGGTCAGCTGGAATAATATTTGGTCGCTCGTTGCCCTTTTCAGGGAATGTGATCTTAGTCCCTTTCTTCCA[C/T]CCTGGCTTTATTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACATCGGCAATCTCCCTCGAAATCTTCATTTTCTTAGT
102850 A G CTTTCTTCCACCCTGGCTTTATTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACATCGGCAATCTCCCTCGAAATCTTCATTTTCTT[A/G]GTAGTACCCTTGTACAATTCTTCCAAGCTACAAGGCAAATTGTTCTCAATGGGTGCCGCCTTCTGCTGCCTCATTCCCATTCCCATTCCCTCT
102850 G A CTGGCTTTATTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACATCGGCAATCTCCCTCGAAATCTTCATTTTCTTAGTAGTACCCTT[G/A]TACAATTCTTCCAAGCTACAAGGCAAATTGTTCTCAATGGGTGCCGCCTTCTGCTGCCTCATTCCCATTCCCATTCCCTCTCTAACGCCAGC
102850 T C TTTCTATTGTTAGGATCTCTTCCACTGGTATTGTTTTCCCGCTAACATCGGCAATCTCCCTCGAAATCTTCATTTTCTTAGTAGTACCCTTGTACAATTC[T/C]TCCAAGCTACAAGGCAAATTGTTCTCAATGGGTGCCGCCTTCTGCTGCCTCATTCCCATTCCCATTCCCTCTCTAACGCCAGCACCACCGCC
102852 A G ATACTGTAATGCCAGGAACAAAGGTTGCTGTGATATCAAAATCAGCTTCTAGTGATACACATGTTGCCCCATCAGATGACAAATCAAGCAAACCAACTGA[A/G]TCACCTCCTCCAGAGAAGCCACAAAAAATTGAGAAAGAAAAACCTAAAGCGGAGACTCCTGTTGTAGAAAAACCCAAATCTGCTCCG
102852 G A CATATGCTATGCTGACCACTTTCAATGAAGTTGACATGACAAATTTGATGAAACTCCGTTCAGACTATAAGGATGCATTTGTTGAGAAGCATGGTGTGAA[G/A]TTAGGGCTGATGTCAGGCTTTGTGAAAGCTGCTGTCACTGGACTTCAAAGCCAGCCTATCATAAACGCAGTGATTGATGGTTCTGAC
102854 CA C CCGCTTTGAATCTTCGATGTAACAAATACAAACTATCAAATACTCATCCAAGTCATTTTCAAACAGTTGGTATTGCCAACTTATTACAAAACTACACCAC[CA/C]AAAAAATGTATACGCCTTATTTTCATCCCATCTACCAAAGTCTTGTAATAATGTCACATTTCCCCCACTTTTTAGATTGGTCTAAACTGAG
102854 C CAAAA TCGATGTAACAAATACAAACTATCAAATACTCATCCAAGTCATTTTCAAACAGTTGGTATTGCCAACTTATTACAAAACTACACCACCAAAAAATGTATA[C/CAAAA]GCCTTATTTTCATCCCATCTACCAAAGTCTTGTAATAATGTCACATTTCCCCCACTTTTTAGATTGGTCTAAACTGAGATTTCAAAC
102854 A T ACCAAAAAATGTATACGCCTTATTTTCATCCCATCTACCAAAGTCTTGTAATAATGTCACATTTCCCCCACTTTTTAGATTGGTCTAAACTGAGATTTCA[A/T]ACACTTACAGTTTGCAAGATTGATCTTTTCAGATGGTATGTAATAAATAGACATGTGCGCAGTGAGATTACAGGAAGAACCGTCGCCAAG
102854 G A GTATACGCCTTATTTTCATCCCATCTACCAAAGTCTTGTAATAATGTCACATTTCCCCCACTTTTTAGATTGGTCTAAACTGAGATTTCAAACACTTACA[G/A]TTTGCAAGATTGATCTTTTCAGATGGTATGTAATAAATAGACATGTGCGCAGTGAGATTACAGGAAGAACCGTCGCCAAGTTTTTGTTTA
102854 A C TAATGTCACATTTCCCCCACTTTTTAGATTGGTCTAAACTGAGATTTCAAACACTTACAGTTTGCAAGATTGATCTTTTCAGATGGTATGTAATAAATAG[A/C]CATGTGCGCAGTGAGATTACAGGAAGAACCGTCGCCAAGTTTTTGTTTATACTGGGGTATGAAGCTAGCTAGTGTTGCTTTTCGCTGCC
102854 A G GATCAACTATTTTCTGGAAATTATTAGAATCATGTTCATACACGTCATTGAGTTGAAGTATGAGCTCGTATTGACGAGAGTATCGATCCAATTCTTCTGG[A/G]TTTAATCCAGCTTTGTGTTCATCCAACCACTTTGGATATCTTTCTCCTATTTCCTTCATGGGTTCATGAAGTATCTCTTTAGATAATAACT
102854 TA T TTCATGGGTTCATGAAGTATCTCTTTAGATAATAACTGCTGCATCATTGTCTCCACAATTGATTCCATATCCTCAGAGCCAGCCATCTCTTCAAATTGTT[TA/T]AACAAAATCCTCCATCTCGTTATCAATCCCTGCTCCTCCACCTCCTATGCTACTGACAGATTCAAGCCCCTTTACCGCCTCTTTTGTCTGCT
102856 G T CCAGCTGATTCTCCATCCTCTGGCACCGGAAGTCAAACCAGCAACAACACCACCACCACAAGTAATGTTTCTGGCTATGTAGAAGGCTTCAGTGCAGTGA[G/T]ATCTTTAGGATCGACCTCAACTTCATATATGATAATCCCCTCCCCTAGCCTCCGTTCTCTAACTCCGACTCCATTACAACTGCCAACAT
102862 C T TATTTTTCGTAGTGTCCACGAACATAATGCTCTACACGTATATGTCCATTCACATCGAGTGCTGGACTACCATCATCATTGTATGCTCTTACTTCAAATT[C/T]GACTCTAATGGCTTTACTTAGCAACGAGTATTTTATCTTGCAATCGTCAACTACTGCAAAAAAAGGTACATCACAAGCTTGAGTGTCCAAG
102862 T A GTCCACGAACATAATGCTCTACACGTATATGTCCATTCACATCGAGTGCTGGACTACCATCATCATTGTATGCTCTTACTTCAAATTCGACTCTAATGGC[T/A]TTACTTAGCAACGAGTATTTTATCTTGCAATCGTCAACTACTGCAAAAAAAGGTACATCACAAGCTTGAGTGTCCAAGCTAAAATTGACT
102862 C T TCGAGTGCTGGACTACCATCATCATTGTATGCTCTTACTTCAAATTCGACTCTAATGGCTTTACTTAGCAACGAGTATTTTATCTTGCAATCGTCAACTA[C/T]TGCAAAAAAAGGTACATCACAAGCTTGAGTGTCCAAGCTAAAATTGACTACTTTGATCTGACCTGTCCCATTTTCAATCTCTTTGCTGCCT
102862 A C CTGGACTACCATCATCATTGTATGCTCTTACTTCAAATTCGACTCTAATGGCTTTACTTAGCAACGAGTATTTTATCTTGCAATCGTCAACTACTGCAAA[A/C]AAAGGTACATCACAAGCTTGAGTGTCCAAGCTAAAATTGACTACTTTGATCTGACCTGTCCCATTTTCAATCTCTTTGCTGCCTATTTCGA
102864 G GT TGATTCTGGAGTGGATGGATGAGATTGGCGTAAGTGAATCGAGGCCAAGTTGGTGATCGAAGTGGCGCCGGACAAGATTATCGACAATGGCAACTTCATA[G/GT]TTTTATTGGAAAGATGAAGGGCGGTGGCCCATCCACAATAGCCATCGCCTCCAATTATCATGACCTTCTTTGATTTGGAGTTTGA
102868 T C CATGTGGCCTTTTTTTTATATGTCAAACCTTGAAGAACGTCCGTCCATTTTATTTTTAAAGAGGACTAAATCCAAAAGTTCACTTATTCCATG[T/C]GTCTCCTCAACCTGCGAAGAATTGACTCCATGTTTTTAACAGTCCACACTTATATCAACCTAACGTAAAGTTTATCACACAATAATCCACCATTTTCCA
102868 C G TGCACTATATCAAGCCTCCCGCTGTAGCTCACCGCCACCACCAGATCCAGTTTCGAATTGTTCTTCGTGCTCTCCGTCACCTCCTTCGCAAGCCTCTGCA[C/G]CGTCGCAGGCAATTTCGTCGTCTCTCCTATGATGCACAGCCGTACGTCTTCCTTCAGGAAATCCTTCAAATTTTCCTTGAGGACGTTCTC
102880 CA C TGGAAGATGCCAACACAAGTACGGAAACGACAGAGACTGAGGTTAAATCTGAAGAAAAGGAGCAGGTCGAAGAGTTGGAGAAAGCGGAAGCATCCGAGGA[CA/C]AAAAAAGAGGAGTAAGTGAGAGAAGCAGCAGTATGTTGTATCTGCATTGGAGTTTGATTGTGTGTAAGTTAGTACATTGTGC
102890 T C GTCTGGAAGCAATTTAACCATAACCCATTAATACAGCAAAAAGTATACCACTATTATTGGACAGAGAATTCTAAAACTAATTTTTGGATTGAGATACAAA[T/C]GTAATTGGATGTGAAAGAAAGAAGAAAAGAAGAGAGATGTGCATCCATTGTCAAAAATCACCATCCCAACCCAGCAGCTACAATTCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102908 A T CCACGGATGAAGCAAGGTTAGGGGATACTGATTACTTTGTTGATCAGGGTCAGATTTCTAATACACAAGTTGAAAGTGTGAGGTTAGAAGCTTCAAACGT[A/T]GGACGAGTGAAGAGGAAACTTAGGTCAATTATTTTTGCTTGTTACCCTTGGATTCATGCAACAAATGAAGGATTGTCCTTTGCTTAT
102910 T C TATCATTCTTCTGCAGTGTCCTCCTCTTGTTCTCCTCCGCATGCGCCCAGGACCGATGCGTCAGCTCCAGGATAAACATCTCGCAGGCACGTGCAAATAC[T/C]ACAGGGGCCTCTGCGGCGATCATCCTCACGTCCTCGTCAGCTTTCATGATCTTCTTGATTCGGGCTAAGGGGAGGCTGTGGTTCTTGA
102910 TG T GTTGCTGTTGCTGCTCTTGTTGCTGCTGCTGGTAGAGCTGGTGGTACTGGTAGGGTATGGGGGTGGCTGGAGGGTATGGAGGCACTCCCATTACTGGTGG[TG/T]GGGGGGTTGCCTCCCTGGGTTGGGTCCATTTGTCCTTTACTGTTGCTATACGATATATCTCCAAAATCTTTTCACCAATCCAAATT
102914 A G CTAATTCCAACTTGAACTGAGTAGAAGAAGAATCGTCGAGAGGATCAACAGAAAGCACGACTTTAGCTAAAACAGGGTTGGAGATATCATCAGATGACAT[A/G]GCAGCCTTGTCCGCCGTCGCTTTCCACGACCTCGAAACAACGGGCGGGCATTTCATTAGCCAGACAGAGCGATCCGCTAGTTTTG
102914 T C CATTAGCCAGACAGAGCGATCCGCTAGTTTTGTGTCGAGGATCAGTCTTCCGTCTTCCGTTGACGACATGATTCAGTTGACTTAAAGATTTCCCGGAATT[T/C]GATTTGGGAATTGTTGGGCTAGGGATTTAGTCGGTGCCTTTCATAAACAAGTATAGCATAGAAAAGCTTCGCTTTATCAGGTTGTGTA
102914 G T GAGGATCAGTCTTCCGTCTTCCGTTGACGACATGATTCAGTTGACTTAAAGATTTCCCGGAATTTGATTTGGGAATTGTTGGGCTAGGGATTTAGTCGGT[G/T]CCTTTCATAAACAAGTATAGCATAGAAAAGCTTCGCTTTATCAGGTTGTGTAGGTTGATCCAGTAGGCCAACAGT
102918 T C GAGAATTCCTTAGGCCCAAAGCACTCCAGCACCCGCCCAACAAGCTCGCCGAAGCCCACACTTATCGGGT[T/C]GAAGCCCATGGCTTCGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACCATGGATCGCGTTCATCGAGTACCCG
102918 G A GAGAATTCCTTAGGCCCAAAGCACTCCAGCACCCGCCCAACAAGCTCGCCGAAGCCCACACTTATCGGGTT[G/A]AAGCCCATGGCTTCGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACCATGGATCGCGTTCATCGAGTACCCGC
102918 G C GAGAATTCCTTAGGCCCAAAGCACTCCAGCACCCGCCCAACAAGCTCGCCGAAGCCCACACTTATCGGGTTGAA[G/C]CCCATGGCTTCGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACCATGGATCGCGTTCATCGAGTACCCGCATG
102918 G A GAGAATTCCTTAGGCCCAAAGCACTCCAGCACCCGCCCAACAAGCTCGCCGAAGCCCACACTTATCGGGTTGAAGCCCATGGCTTCGTAGCTCGC[G/A]TAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACCATGGATCGCGTTCATCGAGTACCCGCATGGCTCAAATTCGT
102918 G A CCAACAAGCTCGCCGAAGCCCACACTTATCGGGTTGAAGCCCATGGCTTCGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACA[G/A]AGCCCGACCATGGATCGCGTTCATCGAGTACCCGCATGGCTCAAATTCGTAGTCGCATATCTCCATTTCTGGCATTATTTTCCGGAT
102918 A G CGCCGAAGCCCACACTTATCGGGTTGAAGCCCATGGCTTCGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACC[A/G]TGGATCGCGTTCATCGAGTACCCGCATGGCTCAAATTCGTAGTCGCATATCTCCATTTCTGGCATTATTTTCCGGATCCCGGAGTTC
102918 G A CGTAGCTCGCGTAGCTGAACCCATCCTCCGGAGTAACATGAACGGTCGACAGAGCCCGACCATGGATCGCGTTCATCGAGTACCCGCATGGCTCAAATTC[G/A]TAGTCGCATATCTCCATTTCTGGCATTATTTTCCGGATCCCGGAGTTCTCAGTCATGGTCATAAAGCCGCTGTTTTTGAAGAACACCG
102918 A G TCTCCATTTCTGGCATTATTTTCCGGATCCCGGAGTTCTCAGTCATGGTCATAAAGCCGCTGTTTTTGAAGAACACCGAAGCATTCTCTTTGCTAAGCCC[A/G]GTCATGCACATTTCGAGCGTGAGCATTGGTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCC
102918 C T CTGGCATTATTTTCCGGATCCCGGAGTTCTCAGTCATGGTCATAAAGCCGCTGTTTTTGAAGAACACCGAAGCATTCTCTTTGCTAAGCCCAGTCATGCA[C/T]ATTTCGAGCGTGAGCATTGGTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTT
102918 T A CATGCACATTTCGAGCGTGAGCATTGGTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGG[T/A]TTCCGAAATAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCA
102918 T A ATGCACATTTCGAGCGTGAGCATTGGTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGGT[T/A]TCCGAAATAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCAC
102918 A G TTTCGAGCGTGAGCATTGGTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGGTTTCCGAA[A/G]TAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTA
102918 G A GTTGTTCGGGCTTTTCAGTAGCATAATATATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGGTTTCCGAAATAATGGTTAAGGGTGGA[G/A]ACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTTCACGGATTGTACTTG
102918 C A ATGTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGGTTTCCGAAATAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGG[C/A]GTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTTCACGGATTGTACTTGAAGAGTGAGGCTAGAGGCAAGTTCAAGG
102918 T G GTGCCAGTCTCCGATAATGTAAGCGTTTCCACCCGATTTAAGGTTTCCGAAATAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCG[T/G]GCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTTCACGGATTGTACTTGAAGAGTGAGGCTAGAGGCAAGTTCAAGGAT
102918 C T GGTTTCCGAAATAATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTT[C/T]ACGGATTGTACTTGAAGAGTGAGGCTAGAGGCAAGTTCAAGGATTTTGGGGATTGATAAGAGGAGCTTAGTGGTGCCACAAGTC
102918 T C AATGGTTAAGGGTGGAGACTTCTTCGGAGAAGCTTCTGTGTGGGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTTCACGGATTGTAC[T/C]TGAAGAGTGAGGCTAGAGGCAAGTTCAAGGATTTTGGGGATTGATAAGAGGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGC
102918 T C GGGCGTGCTGGGCTTTTGGGAAGATGAAAGATCCACGAGAGTACTTCACGGATTGTACTTGAAGAGTGAGGCTAGAGGCAAGTTCAAGGATTTTGGGGAT[T/C]GATAAGAGGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGCTTGTAAGGGTAGATGAAGAGGCTTGACTCGGAAAGGACATA
102918 T C CACGGATTGTACTTGAAGAGTGAGGCTAGAGGCAAGTTCAAGGATTTTGGGGATTGATAAGAGGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGCTTG[T/C]AAGGGTAGATGAAGAGGCTTGACTCGGAAAGGACATAGGAGTCAAAGTTCTTGTTTGAGAGGCTCGACACAACGGTGCATCGA
102918 G C TAGAGGCAAGTTCAAGGATTTTGGGGATTGATAAGAGGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGCTTGTAAGGGTAGATGAAGAGGCTTGACTC[G/C]GAAAGGACATAGGAGTCAAAGTTCTTGTTTGAGAGGCTCGACACAACGGTGCATCGAGCAAGGTCTAGGAACGAATCAATTTGG
102918 G A CAAGTTCAAGGATTTTGGGGATTGATAAGAGGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGCTTGTAAGGGTAGATGAAGAGGCTTGACTCGGAAAG[G/A]ACATAGGAGTCAAAGTTCTTGTTTGAGAGGCTCGACACAACGGTGCATCGAGCAAGGTCTAGGAACGAATCAATTTGGGCTCTA
102918 G A GGAGCTTAGTGGTGCCACAAGTCTTGAGAATAAGCTTGTAAGGGTAGATGAAGAGGCTTGACTCGGAAAGGACATAGGAGTCAAAGTTCTTGTTTGAGAG[G/A]CTCGACACAACGGTGCATCGAGCAAGGTCTAGGAACGAATCAATTTGGGCTCTAGAGAGGTTACGGAGACCTTGTTTGTGTGGA
102918 C T GTGCCACAAGTCTTGAGAATAAGCTTGTAAGGGTAGATGAAGAGGCTTGACTCGGAAAGGACATAGGAGTCAAAGTTCTTGTTTGAGAGGCTCGACACAA[C/T]GGTGCATCGAGCAAGGTCTAGGAACGAATCAATTTGGGCTCTAGAGAGGTTACGGAGACCTTGTTTGTGTGGATCAGTTAAGAG
102918 T G AGGCTTGACTCGGAAAGGACATAGGAGTCAAAGTTCTTGTTTGAGAGGCTCGACACAACGGTGCATCGAGCAAGGTCTAGGAACGAATCAATTTGGGCTC[T/G]AGAGAGGTTACGGAGACCTTGTTTGTGTGGATCAGTTAAGAGAGGAGCTTCTGAGAATGTGAGTTCGAGGCGCTTTTCGAAGCC
102918 C G TTGTTTGTGTGGATCAGTTAAGAGAGGAGCTTCTGAGAATGTGAGTTCGAGGCGCTTTTCGAAGCCCTCGAAGCCGATTGGAGATGTGTTGACAGCCATT[C/G]GTTATAGTAATTTAGAGAACACAGTATGACAATAATAATTATCTATATACTACTACTATTACTCAGTTGCTTTTAAGGGTAGTAGCG
102918 A C GTTAAGAGAGGAGCTTCTGAGAATGTGAGTTCGAGGCGCTTTTCGAAGCCCTCGAAGCCGATTGGAGATGTGTTGACAGCCATTCGTTATAGTAATTTAG[A/C]GAACACAGTATGACAATAATAATTATCTATATACTACTACTATTACTCAGTTGCTTTTAAGGGTAGTAGCGATTTCAGGATGGCTTCC
102918 T C TGAGAATGTGAGTTCGAGGCGCTTTTCGAAGCCCTCGAAGCCGATTGGAGATGTGTTGACAGCCATTCGTTATAGTAATTTAGAGAACACAGTATGACAA[T/C]AATAATTATCTATATACTACTACTATTACTCAGTTGCTTTTAAGGGTAGTAGCGATTTCAGGATGGCTTCCTCGCGCAGT
102924 GT G TTGTGAGAACTCGTCTGGCAGCACAGGAGATAATATCCTCAGATTATCCTTCTCAGAGCCATGTCAACTTGTTCACATGAGCTGCTGCAGGTTTAACTGA[GT/G]TTATTTAGACAAACCAGATGTATTATAGAGGGATTTCTCATACGCTTTATTCCATTTGCAAAGATGAAGGGACGAGAGGTTTATACA
102924 C T AATATGGACTATTCAGGACATTTGGTCACATCGTCCGATCCGAAGGCTTTCGTGGGTTGTACAGGGGCATATTGCCCGAATATTACAAAGTCGTCCCCAG[C/T]GTTGGGATTGTTTTCATGACATATGAATCACTAAAGTCGTCTCTATCAAGCTTATGAACTGAGTAAATTAGGCACGAGCACATTTAGT
102924 T C ACAGGGGCATATTGCCCGAATATTACAAAGTCGTCCCCAGCGTTGGGATTGTTTTCATGACATATGAATCACTAAAGTCGTCTCTATCAAGCTTATGAAC[T/C]GAGTAAATTAGGCACGAGCACATTTAGTGGTATTTTGTAGTCTGATATTACATTTTGTCAT
102956 C T CAATTGCTGCGCACATTGTCCCACCAGTTGCCAACATAGGGTCCACAACAAGTAGCCGTGCTCCATCAGGGAATTTATCAGGTAAGTTATTCAGGTATGT[C/T]GATGGCTGAAGTGTTGTTTCATCCCTGCGCATACCCAGATGGTATGTTTTCGTCGCAGGGAGGACAGACGAGGCAAGATCTGCCAA
102956 C T GGAATTTATCAGGTAAGTTATTCAGGTATGTCGATGGCTGAAGTGTTGTTTCATCCCTGCGCATACCCAGATGGTATGTTTTCGTCGCAGGGAGGACAGA[C/T]GAGGCAAGATCTGCCAAAGCTAGACCAGCTCTTAGAATAGGAATAACCAGCACTGGCTCACGTGGATCAACAAATTCAATAGTTGC
102956 C G GAATAACCAGCACTGGCTCACGTGGATCAACAAATTCAATAGTTGCAACACCCATTGGAGACTGAATTTCCCCACTCATTAAAGGCAGCCAGTCTCTTGA[C/G]GCTTCATATATGAGGAGTCTACCAAGTTCTGCCAAAGCATTTTTAAAAACTGCACAGGGGGTCTGCTCATTCCTCAGCACAGAAATCC
102956 C T CACTCATTAAAGGCAGCCAGTCTCTTGACGCTTCATATATGAGGAGTCTACCAAGTTCTGCCAAAGCATTTTTAAAAACTGCACAGGGGGTCTGCTCATT[C/T]CTCAGCACAGAAATCCAATGTTTAATCAAAGGATGCGGGGGCACCATCACCAGCATCCTTTCGTCCGTGGCGACCTTATCCTTCTCCA
102956 C T GCATCCTTTCGTCCGTGGCGACCTTATCCTTCTCCATGGAAGTATCGGATCTCATAGCACAACAAATGCCCCTATTTCTACTTTTCCAAGCCGCCGCGAC[C/T]TTATTTGAAAATGGTATTGATGTAAAGTTGTAAAGGGCAACACAGCTGTGAGGGAGTTTCGGGGAAGAATAAGGTATATGGGGCGAT
102956 G A GTGGCGACCTTATCCTTCTCCATGGAAGTATCGGATCTCATAGCACAACAAATGCCCCTATTTCTACTTTTCCAAGCCGCCGCGACCTTATTTGAAAATG[G/A]TATTGATGTAAAGTTGTAAAGGGCAACACAGCTGTGAGGGAGTTTCGGGGAAGAATAAGGTATATGGGGCGATAAAGGAAGGCGGG
102956 C T AACAAATGCCCCTATTTCTACTTTTCCAAGCCGCCGCGACCTTATTTGAAAATGGTATTGATGTAAAGTTGTAAAGGGCAACACAGCTGTGAGGGAGTTT[C/T]GGGGAAGAATAAGGTATATGGGGCGATAAAGGAAGGCGGGTGTTATATAGGAAAAAGTTGGCCATTGAGAAAAAAGCGGGAGGG
102966 C T TCAACCTGGTTCTTTACTTTATTTATTCTCCTCAATTTGCTCCATCGAAATGTTTGCATGGTTATATTCCAGTATTCTGAAGAAAGCAGTGAATAAGTTA[C/T]AGTAGATGACATATATCTCCTTGGTCAAAAAGTAGAGGCCGTGCTCCAATTTAGGCTAATGCGATACAGATTTTAAATCTTCTGCCATGG
102966 A G TTCTTTACTTTATTTATTCTCCTCAATTTGCTCCATCGAAATGTTTGCATGGTTATATTCCAGTATTCTGAAGAAAGCAGTGAATAAGTTACAGTAGATG[A/G]CATATATCTCCTTGGTCAAAAAGTAGAGGCCGTGCTCCAATTTAGGCTAATGCGATACAGATTTTAAATCTTCTGCCATGGTGTATATGC
102966 G A TTTTAAATCTTCTGCCATGGTGTATATGCTCTGTACGAGAAGACGATTTACTAATGCATCAAGTTGCCGGTTGGGTGCCATTCCAAGCACCGTTGTTGCC[G/A]TTGCTGTCGGTTCTGTTAATGTACTGATAATACTGACGCTCTTTTATGTAAGAAATACCAGACCATACTCCACGTACAGAAAGAATGCT
102966 T C CTCCACGTACAGAAAGAATGCTTACAAAGACCATGCTCCCCATCGTGCATACTACCTCAAGAAATGCCTTGAGAATCCACAAGAAGGCCAGTATAAGAAC[T/C]CCATTAACCGAAAATCTAACCAATTTTGAAGAAAAAGAAGAAGGAAGAACAGATCTCACGGCTTTTCTAGCTCGTCGAGAAATCTTC
102966 A G CACGTACAGAAAGAATGCTTACAAAGACCATGCTCCCCATCGTGCATACTACCTCAAGAAATGCCTTGAGAATCCACAAGAAGGCCAGTATAAGAACTCC[A/G]TTAACCGAAAATCTAACCAATTTTGAAGAAAAAGAAGAAGGAAGAACAGATCTCACGGCTTTTCTAGCTCGTCGAGAAATCTTCCGA
102966 T C GAATGCTTACAAAGACCATGCTCCCCATCGTGCATACTACCTCAAGAAATGCCTTGAGAATCCACAAGAAGGCCAGTATAAGAACTCCATTAACCGAAAA[T/C]CTAACCAATTTTGAAGAAAAAGAAGAAGGAAGAACAGATCTCACGGCTTTTCTAGCTCGTCGAGAAATCTTCCGAAAAACGTTCTCA
102966 G A CAGATCTCACGGCTTTTCTAGCTCGTCGAGAAATCTTCCGAAAAACGTTCTCAATAAATTTTACAAGTAAATCCAAGCTTCTGTCATCTTCTTCTTCTTC[G/A]TCGTCTTCATCATCATCTTCTTCTTCAGCAACCCAAATGCGAGGATCGGGAAAGACAACCACAGCGTCGTTGGGGTAGTT
102974 T C TTGTAGCACATTGGCCTTGGACATTTCTCGTCTTCACACTTATATATCTTTGCATTAGCATATCCAAGTTTGATAGTGATATTCCTCTCCAGTTCATTCT[T/C]AAATCGCACAGTCTGAACACCAGATATTGCTTTCACCACGGTTGACTTTCCATGTGCCACATGGCCAATGGTGCCGATATTAATTGTAGCT
102982 A T TTTTTTTCTTCCCGTTCACCAACAGTTAAAACGATCACAGATTCAAACTCTAAGACTTAACAGA[A/T]ACAGGAATAACCCGAACTTGATCCAAAACAGGCCCACACATAGACCCAATATCACCTCCCTTCTGATGATAGTAAGAACTATAAAACGTAATCCTAGTCC
102982 C T TTTTTTTCTTCCCGTTCACCAACAGTTAAAACGATCACAGATTCAAACTCTAAGACTTAACAGAAACAGGAATAACC[C/T]GAACTTGATCCAAAACAGGCCCACACATAGACCCAATATCACCTCCCTTCTGATGATAGTAAGAACTATAAAACGTAATCCTAGTCCTATCTCCAGTTGC
102982 G A GGGCTCCTTGTGTAAACATACCATTCCCTTTAGAATGAAACTGAACCTTCACGTTAGCAGCTCCGGCAAACGCTTCAACAAGCATAGGCCCATGGCAGTC[G/A]TTCCTCGCGTCTCCAATAACAAATGTCATATTATACACTTTGTTAGGCGCCGTCCTTAAAACCTGAGCTATGGCACTCTCTCTTCCAGC
102982 A G CAACAAGCATAGGCCCATGGCAGTCGTTCCTCGCGTCTCCAATAACAAATGTCATATTATACACTTTGTTAGGCGCCGTCCTTAAAACCTGAGCTATGGC[A/G]CTCTCTCTTCCAGCCACCAGCTCCACTGCATAGTTCCCATAGGGGATGGAAAAATGCTCTTTGTCGACGAACCTGACCGCTTTAAGAG
102982 A G CCTGAGCTATGGCACTCTCTCTTCCAGCCACCAGCTCCACTGCATAGTTCCCATAGGGGATGGAAAAATGCTCTTTGTCGACGAACCTGACCGCTTTAAG[A/G]GACTCCACTATCCACCCTGGCAATGGGGAGGTCTTATCCTCTTGCTTTGGAGGTAACAATATGCCTGAAGTAGAGTTTTTGAAAACAT
102982 A C AGCCCCAGGCATAGGTGTCTGCGCCAAAGCTGGTGTAGAGGGTCTGGAGAGGGAGGTCACCTACAAGGGGAGGGACGGAGACACGTAGGACCTCGTCCTG[A/C]GCGCAGGTCCTGGATGCGCTGAAGGTGAGGGAGTAGAGGGAGCCGGGCTTGAGATTGGAGATGTTCTGAGAGACGGTGGC
102982 G A CCCAGGCATAGGTGTCTGCGCCAAAGCTGGTGTAGAGGGTCTGGAGAGGGAGGTCACCTACAAGGGGAGGGACGGAGACACGTAGGACCTCGTCCTGAGC[G/A]CAGGTCCTGGATGCGCTGAAGGTGAGGGAGTAGAGGGAGCCGGGCTTGAGATTGGAGATGTTCTGAGAGACGGTGGCCTCG
102982 A G GGTCACCTACAAGGGGAGGGACGGAGACACGTAGGACCTCGTCCTGAGCGCAGGTCCTGGATGCGCTGAAGGTGAGGGAGTAGAGGGAGCCGGGCTTGAG[A/G]TTGGAGATGTTCTGAGAGACGGTGGCCTCGTTGCCAAGCCTGATGGCATGGACGCCGTGTGGGACTGGGAAGTACATGCCT
102982 G A CGGAGACACGTAGGACCTCGTCCTGAGCGCAGGTCCTGGATGCGCTGAAGGTGAGGGAGTAGAGGGAGCCGGGCTTGAGATTGGAGATGTTCTGAGAGAC[G/A]GTGGCCTCGTTGCCAAGCCTGATGGCATGGACGCCGTGTGGGACTGGGAAGTACATGCCTCCCGGCTGGGG
102984 G A AACATTCACGAGTATCCAAAGCTATCAGTGTTAGATCAATGGACACTTCGGTTGAAGACGTGGTGATAGTTGGTGCCGGAATTGCTGGTCTTGCAACCGC[G/A]CTTGGTCTCCATAGAAAGGGAATCAAGAGCTTGGTATTAGAATCATCAAGTGAACTAAGAACCACTGGATTTGCTTTTACTACATGG
102984 T A TTGCAACCGCGCTTGGTCTCCATAGAAAGGGAATCAAGAGCTTGGTATTAGAATCATCAAGTGAACTAAGAACCACTGGATTTGCTTTTACTACATGGGC[T/A]AATGCGTGGAGAGCAATGGATGCGCTTGGAGTAGGAAGCTCCCTCAGGAAACACAGCCTACGCCTTCAGTGGGGAACTGCTACAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
102984 C T AGAAAGGGAATCAAGAGCTTGGTATTAGAATCATCAAGTGAACTAAGAACCACTGGATTTGCTTTTACTACATGGGCTAATGCGTGGAGAGCAATGGATG[C/T]GCTTGGAGTAGGAAGCTCCCTCAGGAAACACAGCCTACGCCTTCAGTGGGGAACTGCTACAGCTGCAACTTCTGGAACTTTAACCT
102984 T C CATGGGCTAATGCGTGGAGAGCAATGGATGCGCTTGGAGTAGGAAGCTCCCTCAGGAAACACAGCCTACGCCTTCAGTGGGGAACTGCTACAGCTGCAAC[T/C]TCTGGAACTTTAACCTCTAAACTGGATTTTACAACTCAGGGCAAATGCGGAGAGCATGAAATCCGATGCTTAAAGAGAAATATGC
102984 G A GAACTTTAACCTCTAAACTGGATTTTACAACTCAGGGCAAATGCGGAGAGCATGAAATCCGATGCTTAAAGAGAAATATGCTGCTAGAAGCAATGGAAAA[G/A]GAGTTGCCTCATGGAGCCATAAGGTACTCTTCTAAGATAGTTGCTATCGATGAATTAGAAGAAGAAAATGGAATCAAGATCGTGC
102984 G A GACGTTTAGCGGCAAGAGGTTTCTATTCGTACCCAGATGGACATGATTTTAAGGCTGAATTTGCTCAGTACTTTGGAAAAGGATTCAGATTTGGAGTGTT[G/A]CCATGTGATCATAACAGTGTTTACTGGTTTTTCACTTGGACTCAAAATGTTCAAGACCAAGATGTGGGGAACGATGCCAAGAAGACG
102984 T A CTCAGTACTTTGGAAAAGGATTCAGATTTGGAGTGTTGCCATGTGATCATAACAGTGTTTACTGGTTTTTCACTTGGACTCAAAATGTTCAAGACCAAGA[T/A]GTGGGGAACGATGCCAAGAAGACGAGGCAATTTGTACTGGATACATTAACGTCATCAAAAATACCAAAAAAATAGTGGAAATGGTG
102984 A G GTGTTTACTGGTTTTTCACTTGGACTCAAAATGTTCAAGACCAAGATGTGGGGAACGATGCCAAGAAGACGAGGCAATTTGTACTGGATACATTAACGTC[A/G]TCAAAAATACCAAAAAAATAGTGGAAATGGTGGAGAAGAGTGATATGGGAAGTGTGGTATCATCTCCATTGAAATATAGATGGCC
102984 CA C TTTTTCACTTGGACTCAAAATGTTCAAGACCAAGATGTGGGGAACGATGCCAAGAAGACGAGGCAATTTGTACTGGATACATTAACGTCATCAAAAATAC[CA/C]AAAAAAATAGTGGAAATGGTGGAGAAGAGTGATATGGGAAGTGTGGTATCATCTCCATTGAAATATAGATGGCCATTGGAACTG
103014 C T TGGTAAGGGAGGTAGAAAAGTTGCGAGCAGAGTTGACTAACGCTGCTAACCTTGAGAAAAGTGGTGGACCGTACAATAGCAGTGGTGGCTACAAAGAAAA[C/T]GATTTAACTGGTGGCCAACGGCCTCTTGGTCAAAATGCTTACGAAGAGGCTTATGGGGTCCAGCAGGCTGGTGCAGCAGCTAC
103014 T G GTGGCTACAAAGAAAACGATTTAACTGGTGGCCAACGGCCTCTTGGTCAAAATGCTTACGAAGAGGCTTATGGGGTCCAGCAGGCTGGTGCAGCAGCTAC[T/G]TATGGAGGACCTCAGTCTGGATATGATCCTTCCAAATATACTACAACAACTGGCTATGGGAATACAAAAGGCAGCGGAGGCTCTG
103014 T C ATGCTTACGAAGAGGCTTATGGGGTCCAGCAGGCTGGTGCAGCAGCTACTTATGGAGGACCTCAGTCTGGATATGATCCTTCCAAATATACTACAACAAC[T/C]GGCTATGGGAATACAAAAGGCAGCGGAGGCTCTGATCTTTCTAAAGGCCAAACTGCTCCTGTTTCTGCAAATTATGACGCTGCTATC
103014 C T ATACTACAACAACTGGCTATGGGAATACAAAAGGCAGCGGAGGCTCTGATCTTTCTAAAGGCCAAACTGCTCCTGTTTCTGCAAATTATGACGCTGCTAT[C/T]AAGCCTCAAGCACCTACATCTGCAGCAAACGCAGCAGCTGCTGCTCCTTATGGATCCACACCACAAACCACTTCACCTTATGGGTCAG
103014 T C ATCTTTCTAAAGGCCAAACTGCTCCTGTTTCTGCAAATTATGACGCTGCTATCAAGCCTCAAGCACCTACATCTGCAGCAAACGCAGCAGCTGCTGCTCC[T/C]TATGGATCCACACCACAAACCACTTCACCTTATGGGTCAGGTCAGGCACTCAGCCCTTATGGAGGACCGGCTGGTCAGGCAATGAACC
103014 C A TCAAGCCTCAAGCACCTACATCTGCAGCAAACGCAGCAGCTGCTGCTCCTTATGGATCCACACCACAAACCACTTCACCTTATGGGTCAGGTCAGGCACT[C/A]AGCCCTTATGGAGGACCGGCTGGTCAGGCAATGAACCCTTACGGATCAGGTCAGGCAATGAACCCTTACGCATCGAGTCAGGCAAC
103014 C T CCACTTCACCTTATGGGTCAGGTCAGGCACTCAGCCCTTATGGAGGACCGGCTGGTCAGGCAATGAACCCTTACGGATCAGGTCAGGCAATGAACCCTTA[C/T]GCATCGAGTCAGGCAACAAATCCTTATGGGGCTGCAAGTCAGGCACCCAATGCTTATGGACCTGGACCCACGTCTAATGCTTATGG
103014 G C ACCTGGACCCACGTCTAATGCTTATGGTCAAGGATCAACCCCAAATGCTTATTATGGGTCCATGTCTCAAGCATCCAACCCATACGGGTCAACTCAAGCA[G/C]CTAACCCATACGGGTCATCTCAGGCACTGAATCCTTATGGATCTGCTGCTCAGGCGCCGAACCCGTATGGATCGGGTCAGGCACCGA
103014 A G AGGCGCCGAACCCGTATGGATCGGGTCAGGCACCGAATTCATATGGATCGAATCAAGCACCAAATTCATATGGATCGGGTCAGGCAGCAAACACATATGG[A/G]TCAGGTCAGGCATCAAATCCATATGGGTTGGGTCAGGCACCAAATGCAGCTGGCCCTGGGAATACGCGCAGGTAAGTGGAGTTA
103016 AG A GGTCGGGAGCGAAGCCTCAGGCGGAGTTTCAAACGTCATATTTCAGAACATAAACATATCGAACTCCGGAATCGGCATACACATAAAAACAAACGAAGGC[AG/A]GGGGCGGGTACATCAAAAACATTACAGTCGACAACGTGAATATGTACAAAGTCAGGAAGGGTGTCAGGATTGCAGGCAACGTG
103016 T C TATGGAGTTAAAATTGAACAGGCGGGGACGATCCAAGGGATTAAGGGGTCGCCTTTCAGTGGTATTTGTATACACAATGTGAAGCTTTTGAATGATGGGT[T/C]GACGAAAAAGAAGGTGCCGTGGACGTGTAAAGATGTGAGTGGTTCTGCGGTCGAGGTGGAGCCTGCCATGTGCGATGAGTTGG
103026 A G CTGCTGCGACGCATGCTGCTGGTGGATTCGGAGATTATTACTATGGAAGAAGCGGAATTGGAGGAGGAAGAGGCCAAGCTTATTTGAATCGTCCAGATGG[A/G]AACGAGTTTGCGTTGAAAGAAGCAATTAGACAGTACGGCGCTGATCCTGCGCATCTTTCTACTGTTAGCGGCAGCCATGTGCTTC
103026 C T ATTCCACACCTCAAAGCCGCACACCAAAACCAAAACCGAAACCGAAGAAGAAACCCTCTTCCACAGCCAAAATATTCCACTGTAACGTATGCAATATCGA[C/T]TGCAACAGCGAAACTGTATTCATCACCCACGAACAAGGTAAGAAGCACAAGCTGAACCTCGAAAACCTAAAAAGCTCTATTGCACAG
103026 T C ACCACAAAACCGAAGCAGCTACTACAAAAAAGGGCAAAAACAATAAAAACTTGATCCCTCAGAAAGCTGAAATTTCAATCAAGAGAAAGAACAACAAAAA[T/C]GATGATGATGCACCTGAGGAAGTTTTGGAGACGAAGAAAAGAAAGGTTCTAGATGCTGGAGCGGAGCCCAGTGAAGTGAAGGTG
103026 C G CAGCCAGAAGGTTTTCGAGGCTCATCTTTCTGGGTCCAGGCATCTGGAGAGCCTGAAGAAAATGCAGGCAGCTGGGTAAAGGAAATATCAAGTTGTATCT[C/G]GAACAAATGCTTTAATGAACCTTTTTCTTAAATTTAATGCAGTTTCCGTTTGAATCAATATGATTAGTACCACAACTATCATCTTATA
103026 CT C TTCTGGGTCCAGGCATCTGGAGAGCCTGAAGAAAATGCAGGCAGCTGGGTAAAGGAAATATCAAGTTGTATCTCGAACAAATGCTTTAATGAACCTTTTT[CT/C]TTAAATTTAATGCAGTTTCCGTTTGAATCAATATGATTAGTACCACAACTATCATCTTATATGATATTGTGGAATGTAATGTGATGAT
103026 T C AGGCAGCTGGGTAAAGGAAATATCAAGTTGTATCTCGAACAAATGCTTTAATGAACCTTTTTCTTAAATTTAATGCAGTTTCCGTTTGAATCAATATGAT[T/C]AGTACCACAACTATCATCTTATATGATATTGTGGAATGTAATGTGATGATATTCATTGTGTATTCTTTTGTCCTTTGATTGATTTGCATTA
103028 A G GCTATTAGCATGCGACCTTTTCGTGGCAAGGGCAACTGCGGTAATGCTGGTTGTGTGAGTGATCTGAACCTGGTGTGCCCGGCGGGACTTGCTGTGAAAG[A/G]TGGAGGCAACCGAGTGGTAGCATGCAAGAGCGCGTGCTCTGCGTTTGGATCGCCAAGATACTGCTGCACGGGAAGCTTTGGCAG
103030 A G GCTGTAATGTTATTTTTTCAATCGTTTTCTGCTGGTTTTGCCTTTCCTCTGATCTGTAAGCCTTGATATCAAAATTGAATGGGTGCTCCCCAAAGTTCAC[A/G]GTTACCTCTTCATTCTGGCTGTGAACAGAAACTGTAGGGTATATAGGTCCTTTAATATCTTTTTCAGCAGTTCCAACAAGCTGACCATTCT
103030 A G CAAAATTGAATGGGTGCTCCCCAAAGTTCACAGTTACCTCTTCATTCTGGCTGTGAACAGAAACTGTAGGGTATATAGGTCCTTTAATATCTTTTTCAGC[A/G]GTTCCAACAAGCTGACCATTCTTCGTGAAAAAGAACTGCTGGGATATGTAATTAATGCCAGCACCAACTGTATCTCCAGTTTTATATTT
103030 T C CTTTAATATCTTTTTCAGCAGTTCCAACAAGCTGACCATTCTTCGTGAAAAAGAACTGCTGGGATATGTAATTAATGCCAGCACCAACTGTATCTCCAGT[T/C]TTATATTTGGGGCCAAAAGGATCGACTTTGGTTTTTGGATGATACAGAACGCCATCATCCCCACGATACCCGCAACTATTTGCATCACA
103030 G A AAAAAGAACTGCTGGGATATGTAATTAATGCCAGCACCAACTGTATCTCCAGTTTTATATTTGGGGCCAAAAGGATCGACTTTGGTTTTTGGATGATACA[G/A]AACGCCATCATCCCCACGATACCCGCAACTATTTGCATCACACCCAGGCTGCCGTGTAAGATTATATCCGTGACCAGTAAATCCAATC
103030 G T GCCGTGTAAGATTATATCCGTGACCAGTAAATCCAATCAAAACCTCGCCTTTCTCACCAGCATTCTTAACCGTCATCTCAAAATAATAAGCCACGGTCTT[G/T]GTCGGAGCGGGACAGTCCGACTGTGCTGACCCGACGTCATGGTCATGCTGGGGAATTCCAACATACTTAACTGACATTTTTTCGGGTG
103032 T C AAATGTTCACTAAAGAGTCGGGTAATACTGTTGATGAGGTCAAACTAAGGGTACTTTATGTATCACCTCCTCAACCTCCTTCACCGGTTCATGAAGGTTC[T/C]GAGGAAGGAAATTCTCCCAGGGCTACTATGTCAGACAATGGTCCTGCAACTTCCCTTGAATTTGGCAATGTATCGAGAGCATCTTCTG
103032 T C CTTCCCTTGAATTTGGCAATGTATCGAGAGCATCTTCTGAATCCCAAGAAAAGTCGCCAGAGACAACGCAGTTAATCTCAAGGCTGACCGAGGAGAAGAA[T/C]GCTGCAATTCAACAGAACAATAAGCTTAGACAGGAATTGGAGCTTTTGAGAAAAGAAGCCAGTAAGCAAACCGGTGGTTTCTCTTT
103032 G C AGAATGCTGCAATTCAACAGAACAATAAGCTTAGACAGGAATTGGAGCTTTTGAGAAAAGAAGCCAGTAAGCAAACCGGTGGTTTCTCTTTCATGTTTGT[G/C]TTCATTGTTGTGATTCTCGGAATCCTTCTCGGCTACCTTATGAAGCCCTAATCATTTAGAAGAGCCACAAAATTCTTGAAATGGTAAA
103032 T G GAATGCTGCAATTCAACAGAACAATAAGCTTAGACAGGAATTGGAGCTTTTGAGAAAAGAAGCCAGTAAGCAAACCGGTGGTTTCTCTTTCATGTTTGTG[T/G]TCATTGTTGTGATTCTCGGAATCCTTCTCGGCTACCTTATGAAGCCCTAATCATTTAGAAGAGCCACAAAATTCTTGAAATGGTAAAG
103032 T A AATGCTGCAATTCAACAGAACAATAAGCTTAGACAGGAATTGGAGCTTTTGAGAAAAGAAGCCAGTAAGCAAACCGGTGGTTTCTCTTTCATGTTTGTGT[T/A]CATTGTTGTGATTCTCGGAATCCTTCTCGGCTACCTTATGAAGCCCTAATCATTTAGAAGAGCCACAAAATTCTTGAAATGGTAAAGC
103032 A G AATCATTTAGAAGAGCCACAAAATTCTTGAAATGGTAAAGCGAATGACAGTGTTTTTAGTAGTGTGGTTTGACAAAGCTCTAGTTCGTGGACTGTCAGGC[A/G]ATGTGTGTAGAAGATAATTCATGAATTGTCATCCCGTGCATCTGTATTTAGTCATGCAAAGTCAATCAATTTGGTCTGTTATATCTTC
103034 A G ATGCCTGCATTCCCATTTGCAAGCGAGTTCATCAAATTTTGGAGATTTGCTTCGTTCTCCATTTGTGTGCTCATGCTTGCTTTAGAACTAATGCTAGCGA[A/G]CCCTCCACTGCTAGTGGCACCCATTTGTGCTGCTTTCTGAAGCAATGCAGTTGCAGACATTTGTGGCAAGCACATTTCTTGATTGTTCTG
103034 A G GAACCCTCCACTGCTAGTGGCACCCATTTGTGCTGCTTTCTGAAGCAATGCAGTTGCAGACATTTGTGGCAAGCACATTTCTTGATTGTTCTGCATCGAC[A/G]TGCTGCTGCTGCTGTTGTTATTGTTATTGTTGTTCATGTTGTAAAGTGATGGAACTCCTCCTCCAAACAGGCACATCGGTTCAACCACG
103034 C G CCCTCCACTGCTAGTGGCACCCATTTGTGCTGCTTTCTGAAGCAATGCAGTTGCAGACATTTGTGGCAAGCACATTTCTTGATTGTTCTGCATCGACATG[C/G]TGCTGCTGCTGTTGTTATTGTTATTGTTGTTCATGTTGTAAAGTGATGGAACTCCTCCTCCAAACAGGCACATCGGTTCAACCACGTTTG
103036 G A AATTGGAACCCAATTCAAAACGAGTCAATTGGTAATCACTAATCGATATTTTAGTAACACATGCTAGATCTTCATTATGAGTTCTCTCTTCTATCCTACT[G/A]TCCCATTTTATTCACCAAATCCCCTTTTCAGTTCTTCCATCAAATTAAGATCGACGGCCAAAATTTTCCGCAGCACCATGATGGTCAAGGA
103036 A G TCGATATTTTAGTAACACATGCTAGATCTTCATTATGAGTTCTCTCTTCTATCCTACTGTCCCATTTTATTCACCAAATCCCCTTTTCAGTTCTTCCATC[A/G]AATTAAGATCGACGGCCAAAATTTTCCGCAGCACCATGATGGTCAAGGATTCAAGACCAGTTTCAGGCGAGGTTCACGTTATTATCGGCCC
103036 A T CTAGATCTTCATTATGAGTTCTCTCTTCTATCCTACTGTCCCATTTTATTCACCAAATCCCCTTTTCAGTTCTTCCATCAAATTAAGATCGACGGCCAAA[A/T]TTTTCCGCAGCACCATGATGGTCAAGGATTCAAGACCAGTTTCAGGCGAGGTTCACGTTATTATCGGCCCCATGTTTGCTGGCAAGTCAAC
103042 T C ACCAGGGCACCGCATAGAACAGGTCAGAGTACTCGTTGTCTTTTGTCGCTCTGATTACTTTTCCGTCTGCTAAAACCATCTCTAGGGACACGATGGTGTC[T/C]TGGAACAAACCGTAGATATGGGAGCTGCCCTCAATGCCGTACCCGTTGACCAAGCCACCGATGGTGAGGTCGTCTAGCTCGGACACG
103042 G C GGTCAGAGTACTCGTTGTCTTTTGTCGCTCTGATTACTTTTCCGTCTGCTAAAACCATCTCTAGGGACACGATGGTGTCTTGGAACAAACCGTAGATATG[G/C]GAGCTGCCCTCAATGCCGTACCCGTTGACCAAGCCACCGATGGTGAGGTCGTCTAGCTCGGACACGACGGGTATCGCCAGATTCATA
103042 A G CGTTGTCTTTTGTCGCTCTGATTACTTTTCCGTCTGCTAAAACCATCTCTAGGGACACGATGGTGTCTTGGAACAAACCGTAGATATGGGAGCTGCCCTC[A/G]ATGCCGTACCCGTTGACCAAGCCACCGATGGTGAGGTCGTCTAGCTCGGACACGACGGGTATCGCCAGATTCATAGGGACAGTGAC
103042 T C CTAGCTCGGACACGACGGGTATCGCCAGATTCATAGGGACAGTGACCCGACTGAGCTGGCCCATCTTGACCAGGGGCTCGACCCGGACGACCATGCGGTC[T/C]GTGTCGATCTCGAGGATATCGTAGAAGTCGGAGAGGTCGACCTCGTAGTGACGGGCACGCTTGTAGTCCACGTTTCGCATGCCG
103042 A G GGCCCATCTTGACCAGGGGCTCGACCCGGACGACCATGCGGTCTGTGTCGATCTCGAGGATATCGTAGAAGTCGGAGAGGTCGACCTCGTAGTGACGGGC[A/G]CGCTTGTAGTCCACGTTTCGCATGCCGACCACGATGTAGGGCTTGCGGGCCGTGCATACGAGCCCGTCCCTTTTGGGGTCGCGG
103042 G A CGACCTCGTAGTGACGGGCACGCTTGTAGTCCACGTTTCGCATGCCGACCACGATGTAGGGCTTGCGGGCCGTGCATACGAGCCCGTCCCTTTTGGGGTC[G/A]CGGGCCTTGAGGCGGGATACAACCCTTCGTACCTTCTCCTCATGGTCCTGCTGACGTAGCTTGTGGGGTTTGAGCTCGGCTTTCAA
103042 A T GGGCTTGCGGGCCGTGCATACGAGCCCGTCCCTTTTGGGGTCGCGGGCCTTGAGGCGGGATACAACCCTTCGTACCTTCTCCTCATGGTCCTGCTGACGT[A/T]GCTTGTGGGGTTTGAGCTCGGCTTTCAAGTCGTAGAGATAGGAGATGAAGTGGATGACCGCGGATATGGGAAGGACTATGAACA
103042 C T TGACCGCGGATATGGGAAGGACTATGAACACGATGATTATCCATCTGAAGTCGACCAAATAGTCCACCCATATTTTCTTTCGGATCGGGCGAGGCGGTGG[C/T]GAGTGTAGTTGATCCGACATTGTCATTGTTTATGCTTGGACGCTTTTAATTGAATAGACTCAGAGCAAACCACAAGAAGAAATGCTG
103060 AT A TGAATTTTACTTCGAAGATGGAGCCTTTCCTGAACAAGTTGACTGGATTGGTCAGAAGAATCAAATCGACATAGCAAAATCTGTTGGAGTAAAACAAATT[AT/A]TTTTAGTTGGATCAATGGGAGGAACAGATCTAACAAATCCTCTAAACAGTCTGGGAAATGGTAACATATTGGTCTGGAAGCGCAAA
103064 C T CTTTGCCCTCTAACCGTGTGAAGGGTTACCCTCTTCCTCCTGCAGCCATCGCTTGCAATATGAATGGGAGCAACTACGATTCCGATTCCTCGTTTTCCAA[C/T]GATGGCACTAACAGTGTTAGAAAGAGGGCTAAGGTTTCTAGCTATGCGAAGAAGGAGGATGATGGGATCGTGGAGTTGTCGAAGGC
103072 G A CTCTTGGGGAAGAAGCGCACCCGGAACCTCAACAAACTTGCTAACACCTTTAGCTTCTTTGAGTGCATCCATTTCAGCCTTTGATCTTCTAGGTGCATTC[G/A]TAGTTGATGCGACAAAAGTTGGTACTTTCCCGTCAAGCTCGGAAAATAAAGCAAGAAATTCTTCACGGGATTTTACAGGATCAAGAAG
103072 T C GAACCTCAACAAACTTGCTAACACCTTTAGCTTCTTTGAGTGCATCCATTTCAGCCTTTGATCTTCTAGGTGCATTCGTAGTTGATGCGACAAAAGTTGG[T/C]ACTTTCCCGTCAAGCTCGGAAAATAAAGCAAGAAATTCTTCACGGGATTTTACAGGATCAAGAAGTCCAGTTAGAAAAGCAGCAGGAA
103072 T C CAAAACGAGCACCTTTTCTTTTTGTCAATGCATATCTGCTTTCAATTATGCTTGGTGTTACATTGTTTGGATTTGCATATACATGAGATTTGTATTGTGA[T/C]TGGATAGATTTCTCATTGCTGACTAGTAAGTTGTACATCATCCAACCAATTGCTGGGGCTCTTAACGTGCCTCTTAGAAACCCATACCTTG
103072 A G GAGCACCTTTTCTTTTTGTCAATGCATATCTGCTTTCAATTATGCTTGGTGTTACATTGTTTGGATTTGCATATACATGAGATTTGTATTGTGATTGGAT[A/G]GATTTCTCATTGCTGACTAGTAAGTTGTACATCATCCAACCAATTGCTGGGGCTCTTAACGTGCCTCTTAGAAACCCATACCTTGACTCCA
103072 T C TCAATTATGCTTGGTGTTACATTGTTTGGATTTGCATATACATGAGATTTGTATTGTGATTGGATAGATTTCTCATTGCTGACTAGTAAGTTGTACATCA[T/C]CCAACCAATTGCTGGGGCTCTTAACGTGCCTCTTAGAAACCCATACCTTGACTCCATGGTAGAGTCGCGACCAAAGACGATAGGAAGAG
103072 C T TTGGATTTGCATATACATGAGATTTGTATTGTGATTGGATAGATTTCTCATTGCTGACTAGTAAGTTGTACATCATCCAACCAATTGCTGGGGCTCTTAA[C/T]GTGCCTCTTAGAAACCCATACCTTGACTCCATGGTAGAGTCGCGACCAAAGACGATAGGAAGAGGACCAGCCCAAGTGGGTGCAACA
103072 C T CACCTCCAACTATTACCAATTCGTTACCTGAATTTGACAATGGACTATCAGGAGAATTAATGAACTGGGTCAAAAAGTCTTCCATGACATCAGCATTGTA[C/T]TCAAGTGTTGGTCTATCTGAGTAACCCAATCCAGGCCAATCTACTATTGTAGCATGCCAATTATCTCCACCAGTTCTTGCTACGATATCC
103078 C CT TTTTCCTGCCGTTCTCGGTCTTCAAATAGCTGTTGATTCCAAAGAGTACCTGACTGCTTCTGCTCTACAGTGGAGGTGTT[C/CT]TTTTGTTACCCCATAACAACTTCTTCTTCTGGTCAGTGGACATGTAGCTACTTCCACCAAGGTTCTTATTAACAAGTTCAGCAGCTTTCATTGAAGCAAC
103078 T A TTCTTCTGGTCAGTGGACATGTAGCTACTTCCACCAAGGTTCTTATTAACAAGTTCAGCAGCTTTCATTGAAGCAACTTTAGCAACATTCACGTCACCAG[T/A]GGCCTCAGATTGGTTGGCACTTGGTCCAGCAGTACCTTCCACAGATTTTTCCTCAACACCTTTCAAGCCCATAGGTGGCTTCTCCTCTTC
103080 T C CTCGCCCTTCTGAACTCCATCATGGCTGTAGGATGGACGTGCACCTCGCTGATAAAGTCCCAAATGTTATCTCCCGTGTTGGCAAACAGCGACATGCTCG[T/C]TGGGGTATCCGGCATGAAACAGCCAGTGCCACTCATCCGGCTCACCCAGTCGAGTTCCATGTTGACTTTGAAAGGCCTGTTCTTCCTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103080 CG C ACAGCCAGTGCCACTCATCCGGCTCACCCAGTCGAGTTCCATGTTGACTTTGAAAGGCCTGTTCTTCCTGTTGAACCACGTCCCGATAAAATATTCGGGG[CG/C]GGAGGGTTCTGACCTCGTCCAGAATGTAATAATCTCGAGGGAACGGGGTGGAGTAGTACTCACAGCATTTCCTCGACTCCGAAATA
103080 CG C TGACTTTGAAAGGCCTGTTCTTCCTGTTGAACCACGTCCCGATAAAATATTCGGGGCGGAGGGTTCTGACCTCGTCCAGAATGTAATAATCTCGAGGGAA[CG/C]GGGGTGGAGTAGTACTCACAGCATTTCCTCGACTCCGAAATAATTTTATTTATCAAAGGGGTTAGATTCTCTTTAGTGACCTCTAGG
103084 A G TAATAGAAACATTGAAGGTGAAGGGCAGACGCCCAGTCCTCCTAATATAATCTGCTCTTTCCGACGTTTTCACCGCTTCTTCGTTCATCCTCGCCTCTGC[A/G]TTCGCCCGCTTCTCTTCCGCTATTCTTCGCACTGCCGCAATTTTGTTTGCAAACTTCTCCTGAGCTCGAGCCTTCCTCCTCTCCGCTTTTAC
103084 C T TGAAGGGCAGACGCCCAGTCCTCCTAATATAATCTGCTCTTTCCGACGTTTTCACCGCTTCTTCGTTCATCCTCGCCTCTGCATTCGCCCGCTTCTCTTC[C/T]GCTATTCTTCGCACTGCCGCAATTTTGTTTGCAAACTTCTCCTGAGCTCGAGCCTTCCTCCTCTCCGCTTTTACCTCGATTCTTTTCATCTCC
103084 C A CTCTTCTCTCTTGTACCTTGCCATGTACTTTGCTCTCTCCGCCTCATCCCAAGCCACTGCCCTAGAATCCACAGTACTCGAAACCCTAACCACCTCTCCT[C/A]CATTGACCTTCTCCACACTCCCCGCTCCAATTTCCTGATCATCGTTCCCGGCCCCTTTCCGGTACCTCTCCGGACTGCAAGACCTCGAATCG
103084 T C CGTTCCCGGCCCCTTTCCGGTACCTCTCCGGACTGCAAGACCTCGAATCGATCGGACTCCGCATCCCGCCAGGACTCATCCCTCTGTTAGGCGTCGCCGT[T/C]CTAGACGGCTCCACGCTCCCTATTGGCGTCATCTCCGTCCCCATATCCCTCAACCGCGTCTCCGACATATCCGGCTTGCTCACTCTCCA
103084 C A CGGCCCCTTTCCGGTACCTCTCCGGACTGCAAGACCTCGAATCGATCGGACTCCGCATCCCGCCAGGACTCATCCCTCTGTTAGGCGTCGCCGTTCTAGA[C/A]GGCTCCACGCTCCCTATTGGCGTCATCTCCGTCCCCATATCCCTCAACCGCGTCTCCGACATATCCGGCTTGCTCACTCTCCACATCGA
103084 T C TCTCCGGACTGCAAGACCTCGAATCGATCGGACTCCGCATCCCGCCAGGACTCATCCCTCTGTTAGGCGTCGCCGTTCTAGACGGCTCCACGCTCCCTAT[T/C]GGCGTCATCTCCGTCCCCATATCCCTCAACCGCGTCTCCGACATATCCGGCTTGCTCACTCTCCACATCGATTCTCCTCCTCCGCAGTCG
103084 T C TGTTAGGCGTCGCCGTTCTAGACGGCTCCACGCTCCCTATTGGCGTCATCTCCGTCCCCATATCCCTCAACCGCGTCTCCGACATATCCGGCTTGCTCAC[T/C]CTCCACATCGATTCTCCTCCTCCGCAGTCGATCCTTTTCATCTCCCCTTCGTCGCTCACATTGCTACCGACCGCGGCTATCGTGTTGATGT
103084 T C TAGACGGCTCCACGCTCCCTATTGGCGTCATCTCCGTCCCCATATCCCTCAACCGCGTCTCCGACATATCCGGCTTGCTCACTCTCCACATCGATTCTCC[T/C]CCTCCGCAGTCGATCCTTTTCATCTCCCCTTCGTCGCTCACATTGCTACCGACCGCGGCTATCGTGTTGATGTCGTGGTACAAGCCGAGG
103084 C T TTATCGAGTCCCTCCCTTTCTGCGACGCCGAGTTCAGCAGCCTCCTGTCGTCCGCGTTCGAGTTGCGCGGTTTGTTTTTGCTGTGGTGGCCGTTGTGGTT[C/T]CCGCCGTTGGATAAGCCCGACAGCCATTTCTGCGCGTCGTCCCATTTCGATGGCGTCGGTTTGGATCTGGACCCTACCGTTTTCCGAT
103088 A G TTTAATCGGACACCTATAAAACTTTCTTCCAGGATTTTTTACGGTCTTAGAAGTCAAAACCAAGCAAATTCCAACTCCACAAACGCACATCTTGTCTGCG[A/G]CGTCCTCACCTTCATTCGTATTCCTGGAAAGAGTTCCATCATACTGCTTCTTACTATTAACACTAGTGTTATAACCATAACTATTTTGATG
103090 A G GATCACTAAATACTTTTGTTTCAAGATTTCCCTCTAAGTATAGAATGGACCCAGGCTTCACATGCTGAAGAGCCAGATCACCCAACCTTTCTGGGTACAC[A/G]CTAACTCGATGCCACTGCACAGAGCATCGTTCAGCATATTCTCTCGGCTCTTCATTATCCAATGGCCTACGGTTGTTTCTAATACCTCCA
103090 G A GATTTCCCTCTAAGTATAGAATGGACCCAGGCTTCACATGCTGAAGAGCCAGATCACCCAACCTTTCTGGGTACACACTAACTCGATGCCACTGCACAGA[G/A]CATCGTTCAGCATATTCTCTCGGCTCTTCATTATCCAATGGCCTACGGTTGTTTCTAATACCTCCAGTTCCAACAGAGAACAACACTAC
103090 T C CTACAGTTCTACCGCTCCTTAATTGCTTCTGCACAGGCTTTTGCCCTGCTTTTCCGAGAATTATAGCCTTGTATACACCTGGATCGAGGCCGTTCTCAAG[T/C]ACGCGATCAAATGGAAATTGATTGGTATTTTTGTTAGGGCCGGCTTTCTCGGAGTTGGTAGAATCGGGTTCCGGCTGAAATTCGGGCT
103098 CA C CCACGCCTTCCTTTTCTTCCCTCTCCGAAAATTCATGTCCTGCGAACCTCGCCACCCTCTTCAGCTGCGCGCCAGTGTCCTTCTTCAAGTCTTCATATTT[CA/C]AAAAACAAAACCTTGTTTGGCACGTCGATGCTAGCCTTCCAATACTCCATTACATTGTCCCAGTATGGTCCTAAAGGGTAGACCCCTAAA
103100 C T ATTCAGGGATGGTGGAGGAGACCGAAGAAGTGAGGTTGGAGAACACGATCATGAAGTTCTGCAGAGAAGAGAGCTGACTGATGGCTGGTGCGATCGGGCC[C/T]ATGACGTTGTTGCTGGCTGCGATGACTACGTCGGTCATTCTGTTTAGGGAGTCGCAGGTTACGCCCGTCCATGAGCAGCAGTC
103104 G A CATGTAACCGATACACACATTATATGACATCATCGACCAGCATAGACCTTAACCTCTCTAGGAGGGAAATGGTGATTCTAGGTACTCAGTATGCGGGAGA[G/A]ATGAAGAAGGGTCTCTTTGGTGTGATGCATTATCTCATGCCAAAGCGGCAAATCCTATCCTTGCATTCTGGATGCAATATGGGCAAA
103104 GT G AGAAGGGTCTCTTTGGTGTGATGCATTATCTCATGCCAAAGCGGCAAATCCTATCCTTGCATTCTGGATGCAATATGGGCAAAGATGGTGATGTTGCCTT[GT/G]TTTTTTGGACTTTCAGGTACTGGTAAAACCACTCTTTCAACGGACCATAACAGGCTACTGATAGGTGATGATGAGCACTGCTGGAG
103104 C T CTTGTGATGCCTTCGGAGTTCTGCCTCCAGTGAGCAAACTAAGCTTAGCTCAGACCATGTACCATTTCATTAGTGGCTACACTGCTCTTGTGGCTGGCAC[C/T]GAAGAAGGTATTAAGGAGCCACAGGCAACATTCTCAGCTTGTTTTGGTGCAGCCTTCATTATGATGCATCCAATGAAATACGCTGCTA
103114 C T TGGTCATTGACACCAACATAAAGGGTGTAGCAAATGTTATGCGCCACTTCTTGCCTCTTATGATTGAGCAAAAACATGGTATTATTGTAAACGTATCTTC[C/T]GGATGGGGAAAAGCTGCAGCTGCCAATGTGGCACCTTATTGTGCTTCAAAATGGGCAATCGAAGGTTTAACTCGTGCTGTTGCAAAG
103118 G A TGGTGCGCTGAACCCGAAACTAACATCTCTTGTTGCTGATACGCTAACGGCTGAGAAGGAAAATGAAGCTGTTGTTTGTTGATGTGAAATTGTGTTTGTT[G/A]TGTTGCATTGACTGTTGTATGAATTTGAAAAGATTTTGATCCATGAATGTTCTAACACTTGCTTGGCATTTAGTCTCTGCTTTGGATCC
103118 T A TTGTTTGTTGATGTGAAATTGTGTTTGTTGTGTTGCATTGACTGTTGTATGAATTTGAAAAGATTTTGATCCATGAATGTTCTAACACTTGCTTGGCATT[T/A]AGTCTCTGCTTTGGATCCCTCTTCAGCATACCGGTAACCAAATTTTTGGCAGACTCTGACACATGGTCCCATGGGTCAGAAGGAAATCTG
103118 G A TGCATTGACTGTTGTATGAATTTGAAAAGATTTTGATCCATGAATGTTCTAACACTTGCTTGGCATTTAGTCTCTGCTTTGGATCCCTCTTCAGCATACC[G/A]GTAACCAAATTTTTGGCAGACTCTGACACATGGTCCCATGGGTCAGAAGGAAATCTGAGCTCTGCTGATCTAACAGATTCAAAAATTTG
103118 C A TGCGACTTAGTTTTACCCCAGAATGGAGGCATTCCACAAAGAAGGATGTATAGAATAACTCCAGCACTCCATAAGTCTGCTGCTTCATTATACCCCCCAG[C/A]CAACACTTCTGGTGCTATGTAAAATGGACTCCCTACTGTACCATGCAAGCTCTGCCCAGGCTTGATATATGTTGCTAGACCAAAATCCG
103118 T G CTGCTGCTTCATTATACCCCCCAGCCAACACTTCTGGTGCTATGTAAAATGGACTCCCTACTGTACCATGCAAGCTCTGCCCAGGCTTGATATATGTTGC[T/G]AGACCAAAATCCGCAAGCTTGATCTCTGACAAACTTGATTTTGTTGCCAGCAAAATATTCTCTGGTTTAAGATCCCTATGCACAATTCCT
103118 G C AAATGGACTCCCTACTGTACCATGCAAGCTCTGCCCAGGCTTGATATATGTTGCTAGACCAAAATCCGCAAGCTTGATCTCTGACAAACTTGATTTTGTT[G/C]CCAGCAAAATATTCTCTGGTTTAAGATCCCTATGCACAATTCCTTTCTCGTGACAATACAAAATAACCTCCATTAAATGCTTAAACAGCC
103124 A G CAACAATCAAATTACAACCAAAATTTTCACCAAACCAACTACCATGCCGGATAACTTTGAACCGTCAGGCCTTACTTCCATAACAAAGAAACGTTTTAAC[A/G]GCACATACAGGTACAGGATGTATTTAACTAGAAAAAACCAAAATCATGATGATTTGAGAAAGGAAAAGAAATGGACTAGAAGATCCT
103124 CT C AACGCTGCGTCCTTTTCAGAGAACTCCTAATCTCACTAAGCTTCTCCCGATCATCACGTCTTGCCAACTCAGCTTTCTTCCCATCCTGCCCTCCCACTTC[CT/C]TTTTTTCTTTTTCTTAAAATCATCGCTTGACTGAAGGCACTTAATTGGCCTGACTTTACCAAATCCCCACCATCTTCCCTTCTTTCCAGATTT
103124 C CT CGTCCTTTTCAGAGAACTCCTAATCTCACTAAGCTTCTCCCGATCATCACGTCTTGCCAACTCAGCTTTCTTCCCATCCTGCCCTCCCACTTCCTTTTTT[C/CT]TTTTTCTTAAAATCATCGCTTGACTGAAGGCACTTAATTGGCCTGACTTTACCAAATCCCCACCATCTTCCCTTCTTTCCAGATTTTGAGTTT
103132 C CAAT AAACACCACCATCTAGCAAAGAGCTTCTCACCAGACAGTGACAACCAAAAATTGATGAACCAAGAGTATTGGAAAAATCTGTCAAAATAACATAAGAAAA[C/CAAT]ATCAGACCAACAGGGAAAGGAGTTACCAGCACTGCGAACGCTCTAATCCAAGTTATTCACCCAAAGACCAGGCGAGGATCTGC
103132 C G TTGGAAAAATCTGTCAAAATAACATAAGAAAACATCAGACCAACAGGGAAAGGAGTTACCAGCACTGCGAACGCTCTAATCCAAGTTATTCACCCAAAGA[C/G]CAGGCGAGGATCTGCTTTGAAAATCCGCTTGTTGGAGGCCAAGATACTCACGGCTGACCTTGTGAAGGGCTCAAGTGCATAATGA
103138 A G ATAACAATCAATTGGCAACTTTGCACTTTGTATTCCTTGTTCAGTAGCTTTCTTCATTGTTATCCCTTACCATCTGTTCC[A/G]ATCAACCAACCCACCTATAATATACGTTTTTTTGGATCAAGCTCATCAACTGAAGATTCAGCATCTGCTGTCAGACAGACAAGGTTTTTCCAAGGCTTCA
103138 A T TCCTTGTTCAGTAGCTTTCTTCATTGTTATCCCTTACCATCTGTTCCAATCAACCAACCCACCTATAATATACGTTTTTTTGGATCAAGCTCATCAACTG[A/T]AGATTCAGCATCTGCTGTCAGACAGACAAGGTTTTTCCAAGGCTTCAATGTAAGGTTTACTTTCTTTATCAATGATCCATTTATCAGATCCA
103138 C T TTGTTATCCCTTACCATCTGTTCCAATCAACCAACCCACCTATAATATACGTTTTTTTGGATCAAGCTCATCAACTGAAGATTCAGCATCTGCTGTCAGA[C/T]AGACAAGGTTTTTCCAAGGCTTCAATGTAAGGTTTACTTTCTTTATCAATGATCCATTTATCAGATCCAGGAATTTTTTGTAACTAGATTTC
103144 C A GGAACACGTGGAGATGGTCAGAAGATTCTGAGGCTTTTGAAAGCAGTATACCATCCAAGAAACAGATATCTTTTGCATTTAGATATTGGCTCTTCGCAAA[C/A]TGAGAGAATAGCTTTAGCTAGATCGGTTCAGTCTGAGGCAATATTCAAGAATTTTGGTAATGTTGAGGTTATTGGAAATACATATGC
103144 T C CAGTGCTCCATGGAGCGGCTATTTTGCTCAGAATATTCCAAGATTGGGATTGGTTTATTACATTGAGTGCATCAGATTATCCACTGGTTACGCAAGATGA[T/C]CTTCTACATGTTTTCATGTCTGTGCCACGAGATCTCAACTTTATAGATCATACTGGTGACCTAGGATGGAAAGAGTCTGGGAGGTTTC
103150 A C AAAAGTACTGCTTGCCCATAGACCCGGGCTTGGCCCAATCCTGAAATCTTCTGTGCTCTGCAAAGCCCATGAGCGCCATTTCGAGCACGAATAGAGTGAA[A/C]GGGTCGGCCCAGTAGCTGTAGGTGCCTGCAGGTGGGATGACCCCAGTTTGGAACCATGGAAGGGCTGTTTCTGCAGGGATCAGAC
103150 G A GTCCCAATGGGTCGAATCCAAAATCACCTGGCAAGCTTCCGTCTAAATATGAGAGCGATTGTTTAGATGCAAACCAAAGCTGCCTGTTTGCTCCTTGCTT[G/A]ACAGGAGGAGTGGAAGCAGCTTTAACGACAAAGGAAGCTCGTCGGGAAGTACCAAACGACCTAGAAACAGTACCACCGGTAAGGG
103150 G T CTGGCAAGCTTCCGTCTAAATATGAGAGCGATTGTTTAGATGCAAACCAAAGCTGCCTGTTTGCTCCTTGCTTGACAGGAGGAGTGGAAGCAGCTTTAAC[G/T]ACAAAGGAAGCTCGTCGGGAAGTACCAAACGACCTAGAAACAGTACCACCGGTAAGGGGTCGTCCTCCTAAAAGCTGCCTTCCTGC
103150 T C TTGCTCCTTGCTTGACAGGAGGAGTGGAAGCAGCTTTAACGACAAAGGAAGCTCGTCGGGAAGTACCAAACGACCTAGAAACAGTACCACCGGTAAGGGG[T/C]CGTCCTCCTAAAAGCTGCCTTCCTGCCTCCATTGATGACAGAAGAGCTTGAGTGGTCATTTCTTT
103152 A G TGCGGCACTTAACCCAAGTCAAATCACTACCCGTATCCGCTACTAGCAAAAACTTCTGAGCGGGCGTGCCAACCCGAACCCGAACGAAATACTGACCCGT[A/G]CCCGTGTACGCGCCTGACCTTATCGGCATTGCAAATGATGAAGGCAAAGGAGGCGGCGGTTGAGTGGATCCAGTACATTCAGGGT
103154 GT G TGAAAACGCGTTTTAGCGTCCCATTTCACTACACCATGTACTTATTATGTAAAACACATATTTGTGTGCTCAGACTTCAGTCCGTCTACAAAACTA[GT/G]TTTTTCTTTCCATCCTCTCCTCCATCGTAAGCCTTCTTGTTCCTGGTCGCGCGGGCACACAGACATATCGCTAAGAAACACATTGCATAAACTC
103154 A G CCAGCAAATACAGGGCATAGCCGAAAGTTTGAACAGCTTGTGTCCATGTGTAATATGACGGAGAAGTGGCGTAGAAGAATCGCAATGGCTCTAGGCCGGT[A/G]GCGAGGGCGGTCATGGCGAGGGTAAAGAAGTATATAGCCAAGTACGCTTGTATGAAAATTAAGAAGGTTTGCAAGGACAAATA
103156 T C ACCTAAACCTGCCGTAATCAGCCAACTTCCTCGACCCACTGTGCACCAATCCCACCCCCACCGCACCGTCCGACACGTGTCTCTTGATCTGCGATCTGCA[T/C]GGAGCACGCAGATCCTCTCCGACGACGGTAGCGCTTAAATTGGGCCTCACGAGTGGGCTCAGACAGAAGGCGAAGCTCGACACTCCT
103156 G A GCACCGTCCGACACGTGTCTCTTGATCTGCGATCTGCATGGAGCACGCAGATCCTCTCCGACGACGGTAGCGCTTAAATTGGGCCTCACGAGTGGGCTCA[G/A]ACAGAAGGCGAAGCTCGACACTCCTCTTCCAATCCGCACCGTCGAATTGTTGTTGAACCTCCGTACCGGCGTCGGTTCCGGCCGTC
103156 G A CGTGTCTCTTGATCTGCGATCTGCATGGAGCACGCAGATCCTCTCCGACGACGGTAGCGCTTAAATTGGGCCTCACGAGTGGGCTCAGACAGAAGGCGAA[G/A]CTCGACACTCCTCTTCCAATCCGCACCGTCGAATTGTTGTTGAACCTCCGTACCGGCGTCGGTTCCGGCCGTCTCCATCCAACTGAC
103156 G A CTCTTCCAATCCGCACCGTCGAATTGTTGTTGAACCTCCGTACCGGCGTCGGTTCCGGCCGTCTCCATCCAACTGACCCTTCCGTGGAGTACCCGCTCAA[G/A]CAGCTATCTTCACTGCCTCTAGCCGGCGACATCCCTCTATCGTTGAAGGATCCGTAAACTGATTCCGGCTCATTTGATTTCTTCGATTTC
103156 A G GTACCGGCGTCGGTTCCGGCCGTCTCCATCCAACTGACCCTTCCGTGGAGTACCCGCTCAAGCAGCTATCTTCACTGCCTCTAGCCGGCGACATCCCTCT[A/G]TCGTTGAAGGATCCGTAAACTGATTCCGGCTCATTTGATTTCTTCGATTTCTTCTTCCTGTTGAAGAGTTTCGAGATCCAAGATCTGGA
103156 C T CAAGCAGCTATCTTCACTGCCTCTAGCCGGCGACATCCCTCTATCGTTGAAGGATCCGTAAACTGATTCCGGCTCATTTGATTTCTTCGATTTCTTCTTC[C/T]TGTTGAAGAGTTTCGAGATCCAAGATCTGGACGACCGGATCTCGTCGGATTTGGAATACCCGAAGAGGTTCGGGAACAGCGAGATCTT
103156 T C GGCGACATCCCTCTATCGTTGAAGGATCCGTAAACTGATTCCGGCTCATTTGATTTCTTCGATTTCTTCTTCCTGTTGAAGAGTTTCGAGATCCAAGATC[T/C]GGACGACCGGATCTCGTCGGATTTGGAATACCCGAAGAGGTTCGGGAACAGCGAGATCTTGCTGCTGGTTTTGTAGGTGGGGTTCAC
103156 G C AATACCCGAAGAGGTTCGGGAACAGCGAGATCTTGCTGCTGGTTTTGTAGGTGGGGTTCACCTGAGGTGTTCTGAAAAAGCGGTGGATATGGCAAGGGGG[G/C]AGCGGAGAAGGGAGAACGCTGGGGCGATGCTCCAGCGATCGGCGACCGTCTCGGGCTTCGATCACGGCAAGAAGACGCTCGC
103164 AG A GCCACGTCAGAATAAAGGGGGCTCGTTCTTCTTCAATGGTGGGTTCGGTGTTGGGGGACCGAAGGGTCTGTGAGGTACTAGAGTTATGGAGACTTACCTG[AG/A]GGGGGTAGTTCGAAGAGGCATGGTGACGTCAAGGCAGGACGGGGTTGCTCCAATGATGGGGATTGACGGTAGGGGATGATT
103164 G A GAGGGGGTAGTTCGAAGAGGCATGGTGACGTCAAGGCAGGACGGGGTTGCTCCAATGATGGGGATTGACGGTAGGGGATGATTTTTGATGTTGAGCTGGT[G/A]CCAGTATCTAATGTCGGGTTCAAGGAGGATTGGGAAAATGGTATGCCTGGGAAATAACGGGTGAAGTAACTGATGATGTGGA
103168 A C ATGAAGGGAGGACAGGTGGTTGGTCAGCAGACCCATCTCGCCTTCGTAAGTCTACTTTCATACAAAGTTCAGGAAGCTTGTCGAAACAGAAAAATACAGC[A/C]GCAAATGATTACTCTAATAAAGACGCTATGTTGTCCGGTTCGACATTTATGGGCCGATCAAGTGGATCGTCGAGGAAAGTTGGCG
103168 GT G ATAGAAGGCCTTCGTATTGATAGAAAAGGGAAGTCTGACTGGTAAGAAAACCAGTCCTAAACATTTGACGCACCCTGAAAATTTTACTCAAGGGCAATAA[GT/G]TTTTTCTTATCGTCACTTCTATTAGCATTGTTTACCATAAAAATTGTGATTAAGCTATGTAACTGTGTCATGTTTAAATCTCTCGTGT
103168 A G AATAAGTTTTTCTTATCGTCACTTCTATTAGCATTGTTTACCATAAAAATTGTGATTAAGCTATGTAACTGTGTCATGTTTAAATCTCTCGTGTATACTT[A/G]CTGTGTATGAGAATGCTGTTTTATTCTTCTCAAAGCTGCAAATAGACAAAGCTGGACTTGTAAATTCGAAGGCAACCTGGTCTTTTTGGTG
103172 T C TAGGTTCCTGAATAAGAACATCTTCTTTTACGAAACCCGCAGATTCTAAAAAGACAGGAAAAGTTTTCTTCGAGAATAGCATGCAGAGGTTCAATAGCCT[T/C]AGGAGTTGAATCAGCTCATCCTTTATTTCGGAACCTTTCAGTTGCATACAATTATTTTCCGCAAATTCACTAGAAATTTGAAGATTACC
103172 C T AGTCTCGGAATAAGTGAACCGCATAGTCTCCGCCACCGTCGCTGCTGCTTCCCTCCACGTGGAAGGGGCATGAGCCGGACGCCGCACAATCTTCCTTCGC[C/T]GACCCAGTAACCGCTCCCCTTCCTTCGACCGATCCGCTCCTCCGTCTACATCCACCTCCTCTTTCATCGAAATTCGACGACTTAACACG
103172 C G GTCGCTGCTGCTTCCCTCCACGTGGAAGGGGCATGAGCCGGACGCCGCACAATCTTCCTTCGCCGACCCAGTAACCGCTCCCCTTCCTTCGACCGATCCG[C/G]TCCTCCGTCTACATCCACCTCCTCTTTCATCGAAATTCGACGACTTAACACGAAGTATAGAAGCATTGCCACACCAAGTGCCGTCGCC
103172 C T TGGAAGGGGCATGAGCCGGACGCCGCACAATCTTCCTTCGCCGACCCAGTAACCGCTCCCCTTCCTTCGACCGATCCGCTCCTCCGTCTACATCCACCTC[C/T]TCTTTCATCGAAATTCGACGACTTAACACGAAGTATAGAAGCATTGCCACACCAAGTGCCGTCGCCATTGTTGTCGTTGCCATGTCAA
103178 T C ATTGTTTCATCATTTCCCATTTCTTTGGAACTTTTGAAAACTTCTAGGTGACTGGTACATAGAACTTCCCAATCAACAAGGTACTGTTTCTTTTGTTCAT[T/C]ATAGTTCAACCAATCGCTTGGAGTTTCTACTCCAGTATCCACAAGCTCGTCGTTGTTCAAGTCATTGTTCAGCATGGTAGAGTCCCTGGTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103178 G A TTCTTTGGAACTTTTGAAAACTTCTAGGTGACTGGTACATAGAACTTCCCAATCAACAAGGTACTGTTTCTTTTGTTCATTATAGTTCAACCAATCGCTT[G/A]GAGTTTCTACTCCAGTATCCACAAGCTCGTCGTTGTTCAAGTCATTGTTCAGCATGGTAGAGTCCCTGGTACTTGGGAGAGTAACACCTC
103178 T C TTATTTGTGTTTCGTGAATCAAGCTGATGAGATTCATGCTCGGCAACTGAATTACGACCGCACTGATTACTCCTACCATGAAGCAGCTGTCCAGATTGAG[T/C]CCGAGCTAAATGTAGCCTCTCTCCGCCGTGACCACGACGAGGTTGGTATGGCCGACGCAACCCGGAGCGGCAGTCAGAATCACCGG
103178 G A GATGAGATTCATGCTCGGCAACTGAATTACGACCGCACTGATTACTCCTACCATGAAGCAGCTGTCCAGATTGAGTCCGAGCTAAATGTAGCCTCTCTCC[G/A]CCGTGACCACGACGAGGTTGGTATGGCCGACGCAACCCGGAGCGGCAGTCAGAATCACCGGCCGCGTCAACAGAACGACCAACGC
103178 G A GCTGTCCAGATTGAGTCCGAGCTAAATGTAGCCTCTCTCCGCCGTGACCACGACGAGGTTGGTATGGCCGACGCAACCCGGAGCGGCAGTCAGAATCACC[G/A]GCCGCGTCAACAGAACGACCAACGCCGGGTGATTTCCAAATGTATACGAGCTTCATGCGCTCGTCACGCACCAGATATTTATGAC
103180 C CA TTTTTTAAAGAAGGCCAAAAAAATATTATGTTGCTCATACCAGAAAACTGTACAATACATATGCATTAGACATGCAGAATAATTTCCATCTTAAACTCAA[C/CA]AGTAAGCCCCTGGCACTTCACCGGAATGACACCACTGAACCCTACTCCGGACAGCATACTTCCAACTACCGCTAAATCTCTACAAAAC
103184 C A ATCTGCACCACCACCATAACCACCTCCTCCATAACCACCACCACTTCCTCCATAACCACCGGCACCACTGCCACCATAACCGCCAGCGCCATAACCGCCT[C/A]CAGGGCCACCTCCCCCATAGCCACATAATAGCTGTCACTAGGCTCGCTATAGCCATAGCCCCTGCCTAGGCTACTCCCATACCGACTTG
103184 AC A CACCACCATAACCACCTCCTCCATAACCACCACCACTTCCTCCATAACCACCGGCACCACTGCCACCATAACCGCCAGCGCCATAACCGCCTCCAGGGCC[AC/A]CCTCCCCCATAGCCACATAATAGCTGTCACTAGGCTCGCTATAGCCATAGCCCCTGCCTAGGCTACTCCCATACCGACTTGAATACCC
103184 A AC CTCCTCCATAACCACCACCACTTCCTCCATAACCACCGGCACCACTGCCACCATAACCGCCAGCGCCATAACCGCCTCCAGGGCCACCTCCCCCATAGCC[A/AC]CATAATAGCTGTCACTAGGCTCGCTATAGCCATAGCCCCTGCCTAGGCTACTCCCATACCGACTTGAATACCCGAAGGAGGACTCAC
103184 TC T CATAATCTGCTGCCCTGTTGCTTCCATAACGTCCACCATATCTGATTGGTCCAGAATCTGGGGCACTGCCATAATGGTCTTTAAATCCACCTCTGCCTGC[TC/T]CCCCCTCCCCTGCCCCTTCCGACTGGAGGCTTAGGAGTGCCGTAGTGCTTTGTTGGAGGAGCAAATGAAGGCGCATTTCCAGGTTTCT
103196 A G GAATTAAAAGAGGACCCTTTAAGTTTGAGCAGCCGCTTTTGTGCTGAGTTTCATACCGACATGGCCTATCTTCATTGCTTACCTCCTTCGGTTGAACCAC[A/G]CGTCTCTACTCACATTAACCAGATCATAGACATGATTAAACAGATAATTGATAATGGCTGTGCCTACCGAATTGATGGAGATGTTTACT
103204 A G GCTTCTTCATAAGCAAATTTTTCATACACATCAATCATTTGTAGTGCCTCTGCCTCTGCCTCTTCAAGTGTTGCATGAGCTGTATGGCCCTCTTGCCACA[A/G]AAACTCAAGCGTCCTTATAAATGGTTTGGTCCTCATTTCCCATCTTGTGACATTTGCCCACTGGTTAATCATGAGAGGAAGTTCGCGGTA
103204 T C TTGCCCACTGGTTAATCATGAGAGGAAGTTCGCGGTAACTCTGAATCCACTGTGTAAACATGTGGTTGACAATGGTTTCGCTTGTTGGTCGTACCACAAG[T/C]TTTTCCTCGAGTTCCTTGCCTCCTCCTATAGTAACCACTGCTAGCTCTGGACTAAAACCTTCAACATGGCTAGCTTCTTTCTCAATAAAT
103204 G A GTCCATCGACCGAGGGGTCACCGACTTTCGGTCATCCACCTCCGGAGTTGTCGCCGTTGTCGCTTGGGTACGAAATCTGCAGGGGGGCATGCATGCTGCG[G/A]ACTTTGGTTTGGGGACTGAAGAAGGAAAATTTAGGGTTTTGGAAGGGCAGAAGGGAAACGAGAGGGAGAGGAATTGGAAACAA
103208 C CT AGAAATGGTGTCAGATGAATTACACCTTCCCTTATTTCTTCAGCAATGCATAGGTCCATACTCCAGGAGAAAAGCAAAACTAAATAGCAATGTTCAAAGC[C/CT]TTTTTCATCTTCTCCACTTCCAAGTAAACAGTGGAATAAGGCAAAAACTCAGAGAAATGGTGTTGCATGAGATCATTAATAGCAACG
103212 C T CGAAAACTGAGTTCACCGCCACTGCTTCAGGCTCGGTGTCTCCGTTAGGATCCGACTTGAACATGTAAGGTTCGAGATCCGCTAAACTGCTCGCGACAAA[C/T]CCACGGTATTCAAAATTGACACGAATTGAATCCGCGAGCTGAGCTAGCTTCCATCCGACCTGCTGTAAAGCGTCGGTGTTGTCGGG
103212 A G AAACTGAGTTCACCGCCACTGCTTCAGGCTCGGTGTCTCCGTTAGGATCCGACTTGAACATGTAAGGTTCGAGATCCGCTAAACTGCTCGCGACAAACCC[A/G]CGGTATTCAAAATTGACACGAATTGAATCCGCGAGCTGAGCTAGCTTCCATCCGACCTGCTGTAAAGCGTCGGTGTTGTCGGGTTG
103212 G A CTAAACTGCTCGCGACAAACCCACGGTATTCAAAATTGACACGAATTGAATCCGCGAGCTGAGCTAGCTTCCATCCGACCTGCTGTAAAGCGTCGGTGTT[G/A]TCGGGTTGTGGAGGTCCGATACCAGTTAACCGAAAGGAAGGCGGTCCGCCTGGCCTGACTGCGAGTGCTTGCAGAAGCGCCGGCC
103212 C T AATTCTCTTGCTGAACTGCTTCCGAGCAAGCCATTAGAGTGTGTACTAGTCTGATTCCTGCTTCTTGCGAATCGATTAGGACAAGCGGATGGGAAGAAGC[C/T]TCTGAAGGCGGCTGCGCCAGCGCTGGCCGAGGAACTTGCTGAACCCCAGAGGAGGATGAGGACGAAGATGATGACGCCCTCGTTG
103212 G A GCCATTAGAGTGTGTACTAGTCTGATTCCTGCTTCTTGCGAATCGATTAGGACAAGCGGATGGGAAGAAGCCTCTGAAGGCGGCTGCGCCAGCGCTGGCC[G/A]AGGAACTTGCTGAACCCCAGAGGAGGATGAGGACGAAGATGATGACGCCCTCGTTGTTCTCTGACGCTTATGGTTCCGAGTAGA
103212 A C CCATTAGAGTGTGTACTAGTCTGATTCCTGCTTCTTGCGAATCGATTAGGACAAGCGGATGGGAAGAAGCCTCTGAAGGCGGCTGCGCCAGCGCTGGCCG[A/C]GGAACTTGCTGAACCCCAGAGGAGGATGAGGACGAAGATGATGACGCCCTCGTTGTTCTCTGACGCTTATGGTTCCGAGTAGATC
103212 C T CTAGTCTGATTCCTGCTTCTTGCGAATCGATTAGGACAAGCGGATGGGAAGAAGCCTCTGAAGGCGGCTGCGCCAGCGCTGGCCGAGGAACTTGCTGAAC[C/T]CCAGAGGAGGATGAGGACGAAGATGATGACGCCCTCGTTGTTCTCTGACGCTTATGGTTCCGAGTAGATCCAACTGTCACGGCAG
103212 A AT GACGCCCTCGTTGTTCTCTGACGCTTATGGTTCCGAGTAGATCCAACTGTCACGGCAGTCAGATCGGATCTAAGATCGGAACTGGCGATCATGGAAGAGG[A/AT]TTCATTATTGGGGTAATACCGAAAATCGAATGGATTTAACTGAGAAGAGGAAGAACCGTTTTTCATTACAGGGTTTGGCT
103220 GA G GGCACACTCGGTAAGCTTAACTGATTTCGGCGCCGTAGGTGACGGTATCACCTCTAACACGAAGGCGTTTCAGTCCGCCATTGATCATTTAATGGGGTAC[GA/G]AAAACGAAGGTGGTGGCTTGCTGTACGTCCCCGGGGGTAAGTGGCTCACGGCACCTTTTAATCTCACCGCGAGTCATTTTACTCT
103220 G A AATTGAAGACTGCTACATAGTCTCAGGCGATGACTGCATCGCCATAAAAAGCGGCTGGGACGAATATGGAATAAAAGTGAACATCCCAAGTGAAGACATA[G/A]TAATCCGCCGCCTCACATGCATCTCCCCAACAAGTGCCGTAATTGCCCTCGGATCAGAAATGTCCGGTGGCATCCGGAACGTCCG
103230 T G TTTAGTGGCTTATCTTGTTTCGGGTCCCAAAAAGGTGGAAAACGAATAGTACCTGCAGCCCGTGTGGCCGATGGAAACGCTGCCACAAGCAATGCTCACG[T/G]ACCTCAGTCAACAAACCCATCCAATCAAATCACAAATCAAAACCATTCTCTTCTCGCTCCACCATCGTCTCCAGCATCATTCACAAAC
103230 A G CAAACCCATCCAATCAAATCACAAATCAAAACCATTCTCTTCTCGCTCCACCATCGTCTCCAGCATCATTCACAAACTCTGCTCTTCCTTCAACCGTCCA[A/G]TCACCAAGCTCCTTCATGTCCATGTCAGCAAACTCTCCAGGTGGCCCAACAACATCTACCATGTTCATAACTGGGCCTTACGCACACGAAA
103230 A G CTCACCTTACTACACCATCATCTCCTGAGGTTCCTTATGCGCAGTATCTTTCTTCTGCTGCTAAACAAAACGGAATGCCATATTTTCCTTCATGCTATTC[A/G]GGTGGTACTGATTTACAATCCACTTATCCGCTTTATCCTGGTAGTCCTTCCAGCAGTCTTATATCACCTGCTTCTGGAACCCCTAGAACTGG
103244 C T TTGCTGCCGATGTTAACAAAATATCTCTTAAACATTGGGATCAGGAAGACGTTTTAACCGGTGGCCATGGACTTATGGTGCAGGGATATCATCCAGTAAT[C/T]GAATCCCTTGCAGCAGATCTTGATATCCGTTTGAACCACAGGGTCACAAAAATAGTTCACCACAACAATAAAGTGGTTGTCAATGTG
103244 T C GATATCATCCAGTAATCGAATCCCTTGCAGCAGATCTTGATATCCGTTTGAACCACAGGGTCACAAAAATAGTTCACCACAACAATAAAGTGGTTGTCAA[T/C]GTGGATAATGGATCTGTATTCACAGCTGATGCTGTCATCGTAACTGTTCCTCTTGGTGTTCTCAAAGCAAACCTAATCAAATTTGAGCC
103244 C T ATATCCGTTTGAACCACAGGGTCACAAAAATAGTTCACCACAACAATAAAGTGGTTGTCAATGTGGATAATGGATCTGTATTCACAGCTGATGCTGTCAT[C/T]GTAACTGTTCCTCTTGGTGTTCTCAAAGCAAACCTAATCAAATTTGAGCCTAAACTTCCTGAATGGAAACTCTCTGCTATATCTGATCT
103244 A G TGTCAGACGAAGCAGCAGTAGGTTTTGTCATGTCTGAGCTCAAGAAAATGCTCCCTGATGCTGTAGAACCGGAGCAATATCTGGTGTCAAGATGGGGTTC[A/G]GACATAGACAGCCTTGGAGCATACTCATGCGATTTAGTAGGAAAGCCTGCGGACTTATGCGAGAGGCTTAGAGCTCCTGTAGACA
103252 T G GACTTAGGATTCGGATTATACACATTCTTCAGCAAATCTTGAATCTTGCACATCAACATTTGTGAAGGATCGCCGCTTCCACCACTCACTCCACTGCTGC[T/G]TCCAATTTGAGCAGCAGGAGCACGCTGACTTTCCTGGAGCTTAATTTTCTCAAACAAATACTGCTTTTCAGCTTCAGCCTCGTCCAACCT
103252 C G GCTTAATTTTCTCAAACAAATACTGCTTTTCAGCTTCAGCCTCGTCCAACCTCCTCTTCAGATACATACTTGCGTAGTCTTGTTCGGCTGCGGCTTTCTC[C/G]GACTTAGCAAGCGCAATGCTTTCGAGCCTTTCTGCTTCTTGCCTAGCTTCCGTTGCTTTTAACTGAAACATCTCTGCTTCAGCCTGTTTAAG
103252 A G ACAAATACTGCTTTTCAGCTTCAGCCTCGTCCAACCTCCTCTTCAGATACATACTTGCGTAGTCTTGTTCGGCTGCGGCTTTCTCCGACTTAGCAAGCGC[A/G]ATGCTTTCGAGCCTTTCTGCTTCTTGCCTAGCTTCCGTTGCTTTTAACTGAAACATCTCTGCTTCAGCCTGTTTAAGTCTGACTATGCTTTC
103252 C T CGAGCCTTTCTGCTTCTTGCCTAGCTTCCGTTGCTTTTAACTGAAACATCTCTGCTTCAGCCTGTTTAAGTCTGACTATGCTTTCTAGCTCCTCCACTTG[C/T]TGCTTCTTCCTTTGTCTCTCACGTTTGAGTTCGGTTACTTCTCGGGCTTTGTCTTCTAGCTCACGGTCGCAGGCTTCTAAAGAGAGACGAGC
103258 G T GCAGTATCTGAGAGTACAGGGAGGAGTCCCCCGAGTTTAGGACTTCGTTGCCTACGGATATGGTTGAAATTTTGGTTTTGGGGGTGTAGGGAAGGAAGTT[G/T]GTTGAAACCCACTGGGAGGCAAAGGAAGGAGAAGAGGCGAGGGTGGTGATGTCAGCATTGGAGGTGGCGATGACGAGGCTGA
103282 CT C TGGACACAGTTTCTGGTAATGTGCTTGATTGTTGGGCAACCAGCTAATGCCATGGTAAGCTCCAATTCATCATTAAGCATTTGAATAACTTTTTGCACTC[CT/C]TTTTTCCCCGTTTGCTGCCAAACCAAATACTACAGGTCGCCCAACCAAAACAGCATTTGCTCCAAGTGCCAGTGCCTTAAACACATCAG
103282 A AT TCCATCAACACAGGAATTGCTCCTGAAACTGTTTTGACTATCTCTTCAAGAACAGATATTGGTGCTGGTGAGTAATCAAGCTGTCTGGCACCATGGTTTG[A/AT]TACAATTATTCCTGAAATGCCTGCTTCTATTGCCATTCTAGCATCGTCTGTAGTGAGTATTCCTTTAAGGAGAATCGGCAAGGTTGTT
103282 C CT GCTGTCTGGCACCATGGTTTGATACAATTATTCCTGAAATGCCTGCTTCTATTGCCATTCTAGCATCGTCTGTAGTGAGTATTCCTTTAAGGAGAATCGG[C/CT]AAGGTTGTTTTTGATTTTAGCCATTTTACGTCCTGCCAAGTTAAGGAAGGATCGAAATTTTGATATGTAAATGCTTCAAGACCAGAAC
103282 C T TTTTTGATTTTAGCCATTTTACGTCCTGCCAAGTTAAGGAAGGATCGAAATTTTGATATGTAAATGCTTCAAGACCAGAACCATTATTAGTGCTGACATC[C/T]GCTGATAACAGTTCATAGTTTGCGACTTTTGGTACTATCATTTTGTTCTTGATGTCCTTTTCCCTTTTTCCTAATCTAGGTGTATCAACTGT
103282 G A CGACTTTTGGTACTATCATTTTGTTCTTGATGTCCTTTTCCCTTTTTCCTAATCTAGGTGTATCAACTGTTAGAACAATTGCCTTGAATCCACTACACTC[G/A]GCTCTTTTTACTATTCTTTCAGTGATGTCTCGGTTTTTGAATACGTAGAGTTGAAAAAAGCGAACTGCATCACAGCATGAAGCCACTTCCTC
103282 A G GAAGCCACTTCCTCAAGTGTGCAACTTGATGAAAAGGATAGAACCATCAATGCTTTGCAAGCCGCTGCTGCTCTTGCTGTCGCAACTTCACCTTCAGGGT[A/G]GGCAAGCTTCTGCGATCCAGTTGGGGCGATAAGGATGGGTGAATGAATGTTATATCCAAGTAAATTTGTTGACATATTTATATTTCTG
103290 T G TCGCGCCGCTTGCGATAGGGTTGATCGTGGGTGCGAACATTCTGGTGGGCGGGCCTTTTGATGGAGCGTCCATGAACCCGGCCGTGTCGTTTGGACCTGC[T/G]CTTGTTAGCTGGGAGTGGGCCGGGCATTGGGTGTACTGGGCTGGGCCGCTTGTTGGTGGTGGGCTCGCTGGATTGGTGTACGA
103290 T C GAACCCGGCCGTGTCGTTTGGACCTGCTCTTGTTAGCTGGGAGTGGGCCGGGCATTGGGTGTACTGGGCTGGGCCGCTTGTTGGTGGTGGGCTCGCTGGA[T/C]TGGTGTACGAGCTGTTTTTCATTTCTCACTCCCATGAGATCCTGCCAGCTGGCGAGTACTGATTGGACTCGGAGGTTGAACGGTT
103290 G A TCATTTCTCACTCCCATGAGATCCTGCCAGCTGGCGAGTACTGATTGGACTCGGAGGTTGAACGGTTTGGTTATTTTCGTGCTATGTTGAGTTATATATT[G/A]TATTATGTTTGATTTTTCCCTTTGTTGTATCGCTTTCTGTTTCCTTTTAATTTTGTTTGATTATTGGGAAGTTGTTTCTGTGACTTGTTGCA
103304 G C AGCTTACACGTCATCTTCCTATACAGCTCCTCCAACTCCTTGGTGTACTTCTCGGCACTCTGTCCTACCAAGTCATCCACCTCAAACTCTCCGCTCTCCA[G/C]ATCACAACTCTTCCCATTATTCAAATTATCAACCTCCATCATTTCTGAACCAGACGCCCCACATCCCACCATCCCAAATAATCTGCCTGCTG
103332 T C CAGTGAACTCTTGCTCCATCACACTTCTCAAAAGCAATAATCCATTTTGCTCCATACCAACCTCTTCCTTTTCCTCTTCCTCTTCCTCTTCATTAAACCT[T/C]CGGCTAAAATCGAAAAGAAAAAACCTACACATATACACTTCAGGTTTCCATACGTTTAAGCCCTTACAAAAACCAAATTTATGCAGCAACCA
103332 GA G ATCACACTTCTCAAAAGCAATAATCCATTTTGCTCCATACCAACCTCTTCCTTTTCCTCTTCCTCTTCCTCTTCATTAAACCTTCGGCTAAAATCGAAAA[GA/G]AAAAAACCTACACATATACACTTCAGGTTTCCATACGTTTAAGCCCTTACAAAAACCAAATTTATGCAGCAACCAACTATCGAAACGATCA
103332 A G CTCCTTCGATATTTCCACCCCTTTTTCCTTCTCCTCCGCCTTCGCTTTTCCCTCCGCTTTTTCCTCCAGGACTTCCTTTTCCATTGTTGAGTCCACCTCC[A/G]CCGCCGCCGCCACGTTCTTTGTTTCCTCCCTTGCCGTTTCTTCCTCCATTTCCCGGGGTTCCGCCTGCTAAGCCTTCTGCTGAAAACTTACCTT
103332 C A CTCCTCCGCCTTCGCTTTTCCCTCCGCTTTTTCCTCCAGGACTTCCTTTTCCATTGTTGAGTCCACCTCCACCGCCGCCGCCACGTTCTTTGTTTCCTCC[C/A]TTGCCGTTTCTTCCTCCATTTCCCGGGGTTCCGCCTGCTAAGCCTTCTGCTGAAAACTTACCTTGATCGTTTCTTGATGATTTTTATAGTGTTT
103332 A G TCTTTGTTTCCTCCCTTGCCGTTTCTTCCTCCATTTCCCGGGGTTCCGCCTGCTAAGCCTTCTGCTGAAAACTTACCTTGATCGTTTCTTGATGATTTTT[A/G]TAGTGTTTATAGCTAAAGGTCTTGTTTATAGATAAGATCTTTGACTCCAAACGTTCCTGGTTAACGTGTGTTTGTACATGTTATTCTACTTGG
103332 T A AAGCCTTCTGCTGAAAACTTACCTTGATCGTTTCTTGATGATTTTTATAGTGTTTATAGCTAAAGGTCTTGTTTATAGATAAGATCTTTGACTCCAAACG[T/A]TCCTGGTTAACGTGTGTTTGTACATGTTATTCTACTTGGTTATGCCACATTATTATGTTTGGTTTGATTGCTTGCTTAATTTAGTTTGTGTA
103334 A G TCAAAGAAGGAGAACAAATTGATGAAAGAAAGCTTGAAGAGAAAATAAGAGTCATTCAAAAGGAGAGGGAAGAAAAATTAGCAAACATATTGAAAAATCG[A/G]CTTAATCAATATGTTCAGGGAAACGAGGATACTTTTATTATTCAAGCTGAAGCTGAGATGTCACGACTTTCCAGTGCAGCTTATG
103360 G T TTCATCAGGTTTATTATCGTCTTTTGAAGCTGTAGAATTAGCAGTAGGTTTTCGTCTCTTCCTAGCCCTCTTTGCCTTTTTAATGGGCATGTTCTCTTCT[G/T]TTGGATCAATTTTCACATCTTTCCCTTCATTAACCATTGCTTCACCTTTTTCAATATTGGTAGAAACATCATTGGCACCCGTTCTTCCTTTTCC
103360 T A CCTTCATTAACCATTGCTTCACCTTTTTCAATATTGGTAGAAACATCATTGGCACCCGTTCTTCCTTTTCCACCATCTCCATTGGCCTCCGCTTTCTCCA[T/A]TCTTCCAGCACTCTCTTCTGCTCTATCTGCAGGTTTTTTATTTTCATCTCCATTCAGGTCTTCTTCATTTTGGACTCCTTCACTTTCAACTTCTTC
103362 T A CCTAGGGTTTTGTTTGCAATGGCGGGAAGAAGTGGAGAGATTCTGATGCTGGATGCACCAGCAAACCCCAATAGAGAAGGATGGGCAGTCTCTAACCACC[T/A]GAATGACGTCATAATCGATTCCCTTCCATATATCGATGACGACTATGGCAATCCGCGAGTTAAAGCCGAAGTTGACCGACTAGTG
103362 C T AGCTTAGAATAGAAGCTGCAGAAAGCGGTCTTATATTGGATGCGTCAATGGATGGTACAAAACAATAAGCTCGCAACGGCAAGGTATGGTGGCAGTCTAG[C/T]ATCCAACAGGACATGCACAATGGAAAGACGTTCTATTGATGATTTGTGACAATATCAAAAGAATGTAGTGGCTCTTAAAGTCGGA
103376 T C CTTGACCGTGCACAGGAAAAATTGGCTCCCATTTGTATCAGGACCTGCATTTGCCATGCTTAGTACTCCAGGACCAACATGCTTCAAAGAAAAGTTTTCA[T/C]CAGCAAAACTCGAGCCATAGATGCTCCTTCCTCCAGTTCCATTTCCACGTTCGAAATCACCACCCTGGATCATAAATTCTTTGATTATGC
103382 C T ACAGTGTCTTGTTTGGATTTTCACTGTGTTTCATTCATACAAGGAACAAAAACATGAAACCAAACAATCAAAGCTGCGACATAAAAAACAATCATTGACT[C/T]GTACTACCAATAGTGTCGGCAACCTTCAAGAGCACTTGGCATAATTCCAGTGGCCTGGACAACATGGCCATGTGATCTGCTTCGATCT
103382 C A GAAGCCAAAAACGTAGGACCAAACAGAAGATAGGTTGCCTCACTAGTAGCTTCATCATCTTCTATGAAAAATCCTTGATTATCCATTGCATCATTCTTTG[C/A]CGCCTCTTGCTTGTCATACTGTTGGGCGCAGTGGTAAATGCTGTATGAAAGCTGAGGCAATGAAGCAGCAACAAAGACAGCAGCGTG
103382 C A AATCCTTGATTATCCATTGCATCATTCTTTGCCGCCTCTTGCTTGTCATACTGTTGGGCGCAGTGGTAAATGCTGTATGAAAGCTGAGGCAATGAAGCAG[C/A]AACAAAGACAGCAGCGTGAATTTTATGAGGGAACATCTGCATAGCCTTTGCTATGCTGAGTCCACCCAGGCTGTGTGCTACAAGCAC
103382 C A GCAGCGTGAATTTTATGAGGGAACATCTGCATAGCCTTTGCTATGCTGAGTCCACCCAGGCTGTGTGCTACAAGCACTATTTTTTCTCCGTCGGGGATGG[C/A]GTCCATGGTATCGTACAAAGGCTTTGAGTAGTCGTCGAAGCTTTTCAAGTCTTCGATTCTTGTTGAATTTACGCCTGAAGCGGCAAGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103384 C T GTTGGCAGTATATTTCTGGTAGCTTACCCGATGGGCACGAGCTCAATCGTATCGATAGCCCCGAGGTTCAAGGTATGAAATTTGACCCTGAAGGAAACTA[C/T]GTGCGGACATGGGTACCAGAACTTGCACGGATGCCAAGAGAATGGATCCACCATCCATGGAATTGTCCAAAGTCTGCATTGGAAG
103384 G A CAGAACTTGCACGGATGCCAAGAGAATGGATCCACCATCCATGGAATTGTCCAAAGTCTGCATTGGAAGCTTCGGGTGTGGAGCTTGGAGTGAACTATCC[G/A]AACCCGATTGTGGATTTTGATACAGCAGTGGATAGGCTAGATAATGCAGTTGCCACGATGTGGGAAATAGACCGGGCTGCGCGA
103384 T C GAGAATGGATCCACCATCCATGGAATTGTCCAAAGTCTGCATTGGAAGCTTCGGGTGTGGAGCTTGGAGTGAACTATCCGAACCCGATTGTGGATTTTGA[T/C]ACAGCAGTGGATAGGCTAGATAATGCAGTTGCCACGATGTGGGAAATAGACCGGGCTGCGCGAAACGGATCAACTGAAGTTGTTG
103384 C T TCTGCATTGGAAGCTTCGGGTGTGGAGCTTGGAGTGAACTATCCGAACCCGATTGTGGATTTTGATACAGCAGTGGATAGGCTAGATAATGCAGTTGCCA[C/T]GATGTGGGAAATAGACCGGGCTGCGCGAAACGGATCAACTGAAGTTGTTGACGATAACATGGTGGACCTGAGAATACCGGATGT
103384 C T CGGGTGTGGAGCTTGGAGTGAACTATCCGAACCCGATTGTGGATTTTGATACAGCAGTGGATAGGCTAGATAATGCAGTTGCCACGATGTGGGAAATAGA[C/T]CGGGCTGCGCGAAACGGATCAACTGAAGTTGTTGACGATAACATGGTGGACCTGAGAATACCGGATGTGCCTATAGTGGTTGTG
103384 G A AGCTTGGAGTGAACTATCCGAACCCGATTGTGGATTTTGATACAGCAGTGGATAGGCTAGATAATGCAGTTGCCACGATGTGGGAAATAGACCGGGCTGC[G/A]CGAAACGGATCAACTGAAGTTGTTGACGATAACATGGTGGACCTGAGAATACCGGATGTGCCTATAGTGGTTGTGAGGAGAGAA
103384 G C CTGATCAGAAAGTGCCTTCATTTCGAAATGTCGAATTGAAGAATTTGAAAGTTGATGATACTTCGTCTACTGCCGGGTCATCGTGTGCTAAGAAGAGGAG[G/C]CATTGCCAGAGTCAATGCGCTGTTCCCACTTCATTTTGTTCGTCTTTTTCGTATTCATCGAAGGTGGATGACATGGTCGATGCTTCAG
103384 C T ATGTCGAATTGAAGAATTTGAAAGTTGATGATACTTCGTCTACTGCCGGGTCATCGTGTGCTAAGAAGAGGAGGCATTGCCAGAGTCAATGCGCTGTTCC[C/T]ACTTCATTTTGTTCGTCTTTTTCGTATTCATCGAAGGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATG
103384 A G TGTCGAATTGAAGAATTTGAAAGTTGATGATACTTCGTCTACTGCCGGGTCATCGTGTGCTAAGAAGAGGAGGCATTGCCAGAGTCAATGCGCTGTTCCC[A/G]CTTCATTTTGTTCGTCTTTTTCGTATTCATCGAAGGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATG
103384 GT G TTGATGATACTTCGTCTACTGCCGGGTCATCGTGTGCTAAGAAGAGGAGGCATTGCCAGAGTCAATGCGCTGTTCCCACTTCATTTTGTTCGTCTTTTTC[GT/G]TATTCATCGAAGGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATGGGAACACAACGATGGAAGAGG
103384 C T CCCACTTCATTTTGTTCGTCTTTTTCGTATTCATCGAAGGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATGGGAACACAA[C/T]GATGGAAGAGGAAGACGAAGCCCAGAGTAGCAGCGTCAATGGCTCGAGGCCATCGAAGAAATCTGGGTAAAAGATGGACTGCTAC
103384 C T CGTCTTTTTCGTATTCATCGAAGGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATGGGAACACAACGATGGAAGAGGAAGA[C/T]GAAGCCCAGAGTAGCAGCGTCAATGGCTCGAGGCCATCGAAGAAATCTGGGTAAAAGATGGACTGCTACTGAATTAACAAATAC
103384 A G GGTGGATGACATGGTCGATGCTTCAGTTGTTCATCAATGGCAAGAGATGGATGGGAACACAACGATGGAAGAGGAAGACGAAGCCCAGAGTAGCAGCGTC[A/G]ATGGCTCGAGGCCATCGAAGAAATCTGGGTAAAAGATGGACTGCTACTGAATTAACAAATACATGTGTTGTTTCTTTGTGACAA
103384 G C GTTCATCAATGGCAAGAGATGGATGGGAACACAACGATGGAAGAGGAAGACGAAGCCCAGAGTAGCAGCGTCAATGGCTCGAGGCCATCGAAGAAATCTG[G/C]GTAAAAGATGGACTGCTACTGAATTAACAAATACATGTGTTGTTTCTTTGTGACAAATCGTTTTATTGTAAC
103384 G C TTCATCAATGGCAAGAGATGGATGGGAACACAACGATGGAAGAGGAAGACGAAGCCCAGAGTAGCAGCGTCAATGGCTCGAGGCCATCGAAGAAATCTGG[G/C]TAAAAGATGGACTGCTACTGAATTAACAAATACATGTGTTGTTTCTTTGTGACAAATCGTTTTATTGTAAC
103388 G A GGAAATATAAGAACGGGATATAGGAGAAGAAAAGGAACGCTATATTGAAGATGGTTTTGAAAGATACAAAGCAAGAGAGAAGGGAATTCTTAAAGAAGCA[G/A]GTCTCGAACGGAACTAGAAGAAAGGGAGAAAGGCTGTAACGGGTTCAAAAGGTATTTGTTGGAGCCTGGAGATAGCAGATTT
103388 A G GGTTCAAAAGGTATTTGTTGGAGCCTGGAGATAGCAGATTTAAGGTGGACTTCGGAGATGGCCCCTGAGAAGTTACAGCGTGTTTAGGAAGGCATTCATG[A/G]AAAAGTTCGGTTTTGGTGTGAGCAAACAGCAGGTCATGGGGATGTATTTGGGGGAGATGAGTCCAGGCGGGTGGGCTTTTGAA
103390 G A GTTTGAAGGCCAGTTTATACTTCCCATTTAATCATAATGTGTTGGTTCAGAATCTTACTGTAGCGGAATTCTATAAAGCCTCTGTTCCCGCATCTTCTCA[G/A]GCTTCGTTCCCATATGTTTTTGCCGTCAGCAAATATTTACAGCCTGGAACTTTTGATTTAGTTGGTATCATAGTTTATGAGATTGATCAGC
103390 G A TCCCGCATCTTCTCAGGCTTCGTTCCCATATGTTTTTGCCGTCAGCAAATATTTACAGCCTGGAACTTTTGATTTAGTTGGTATCATAGTTTATGAGATT[G/A]ATCAGCAGCCATATCAATCCACATTTTATAATGGTACAGTTGAAGTTGTTGAGGCTGGAGGCTTGCTAAGCATTGAATCTGTCTTCCTTA
103392 C T CGACGGAAGTCAGGTAATAGGATATAATGGGAAGCCGACTTGGGCGGCGAGTAGTGCACTTTCTGAACCTGCCAATTAAGCTTCTTCTGCCTCCAACACC[C/T]TTCGAATCAATCCAGGAATTTGCGCTCAAAACCATCCCATCTGCCTCCAAAATCGAAATCCGCCGCATCCTCGAATCCTTATATGGAT
103392 G GA ACAAAAAGGCATACATTACTTTGAAAGAACCTCTGTCAATCTCGAAGGATCTGTTTCCGATTCCATGGGTGATGGAAAGCATGAAGCAGAAGATGGAGGG[G/GA]AAAAGAAAAAAGGGAGAAAGACGGAAGTTGAGGAGGGTGAGGAGGGGACAGAGGTTGGACATTGGTTGGATGAGGAGAAG
103392 A G GCATACATTACTTTGAAAGAACCTCTGTCAATCTCGAAGGATCTGTTTCCGATTCCATGGGTGATGGAAAGCATGAAGCAGAAGATGGAGGGGAAAAGAA[A/G]AAAGGGAGAAAGACGGAAGTTGAGGAGGGTGAGGAGGGGACAGAGGTTGGACATTGGTTGGATGAGGAGAAGGGTCGGGAG
103394 CT C AGCGAATACTGAGGACTGCACCACATACATTGTTTCCAGAATCCAGTTGGTCGCCAATAAGTGCAAGGACCAAGTCTTCCCAAAAACGTCCAGAAACTAT[CT/C]TTTTTAAATCGTATTATCCATTTCCCTCCATTGCAATTTGCTGGATCCTCCCATAAAGGTCTAATGCCCTCTTTGAATAGATGCAAATC
103394 G A TTCGCAAGCTTGTCGTTCCTGGTCTCCTGACACCTCTCCGCTTTCCGCGTCGGCTAACGTGGCAGATGATGATCTGGCATCCGCAAGATCTTTTTTCTCT[G/A]CAACTGCGCCCTCCATTTTAACTCCCCCCTTCTTGTTTGAGATTTTGAATTTAGGGTTAAAAGGCTGTGAGGAAAGCAGAAAACGAGGG
103394 TC T CTCCTGACACCTCTCCGCTTTCCGCGTCGGCTAACGTGGCAGATGATGATCTGGCATCCGCAAGATCTTTTTTCTCTGCAACTGCGCCCTCCATTTTAAC[TC/T]CCCCCCTTCTTGTTTGAGATTTTGAATTTAGGGTTAAAAGGCTGTGAGGAAAGCAGAAAACGAGGGTTCCAGTAGGCCAACAGT
103404 C A GCAATCCTTTCGGAAGAGAACCTGGAGTTATACGACCTATAAAATTTCCTGATAAACTCAAAACCCTTAGGTTCACGAATTTGCTAAGCAGTGGAATACA[C/A]ACCAGCCCAAGGTTAACTAATTGTGCAGATGATGATGTGCTAACCAGAGAAGAAATATATTTGTTAGCTATTTCCGTCCCTAGATTGC
103418 C T TTAAGATCGTCTTGATACACCTTGCAACATACTGATTACAGATTCATGGAATCCGCTGTCTATTATAAGTGTCTTCATGCACGAACACAGGCTGCTCGCT[C/T]TGCGCTGGAATTACTGGCTGACCCATCGAAATACCTCGACCACTCTGCTGCGAATCAACCGCCCTCTTGGACATAGAAAGGGTAAAAT
103418 AT A GGATGCTTTGATCCTTGTGGCTTCGGCTAAGAATCCAAGAATGGCGGAGATGATGCCGAGGATTCCAACTATGAAGCAAACTATCATCAGCTTCCTCTCC[AT/A]TTTTTTTAAGGTTTGCCTTTGCTTACAGCAGTCGTCGTGCAGGTAAGTCGTGGAGTTTAAGGCAAGCTTGGTCAAGAAGAGATCAG
103418 GCCTTTGCTTA G TGTGGCTTCGGCTAAGAATCCAAGAATGGCGGAGATGATGCCGAGGATTCCAACTATGAAGCAAACTATCATCAGCTTCCTCTCCATTTTTTTAAGGTTT[GCCTTTGCTTA/G]CCTTTGCTTACAGCAGTCGTCGTGCAGGTAAGTCGTGGAGTTTAAGGCAAGCTTGGTCAAGAAGAGATCAGCAAGTT
103418 G A AATGGCGGAGATGATGCCGAGGATTCCAACTATGAAGCAAACTATCATCAGCTTCCTCTCCATTTTTTTAAGGTTTGCCTTTGCTTACAGCAGTCGTCGT[G/A]CAGGTAAGTCGTGGAGTTTAAGGCAAGCTTGGTCAAGAAGAGATCAGCAAGTTGCAGGAGATTAATCGGACACGAGATGGAATATC
103436 G GA ATCCTCAGTTTCCACATTATCCAACTTTGTATAGTTCTTAAAAGAATGCACAGTACACTTTCCTTCTATAGTATGTGCGCTCTGCATATCATAATGATCC[G/GA]CAAAAACAGCTCCTTTGCTCCATGAAATTGTCTTCTACCTCCCATGCTCTCTTCCGGCCTATAATACCATCTCACTTTAACCTTAACATTA
103436 A G TCACTTTAACCTTAACATTATTCCTATGATCCGCCTCCAACTTTTCCACACGTGCAACGTATGGCGGCTTGTCGGAATCAGAGGGCCGCATCAAAACACA[A/G]TCTCCAACTCTGACGACTTTGTTGGTGCCCTTGATTGTGTAGGAGTCTAGATCTTTCTTTCCGGGCTTGGTCTTTGCCATGAAATTTCTC
103448 G A TTTTCAGATTCGAGTTCGACTCGAAGAGCAATTTGTTGAGATCGTCGATTTTATCGAGATCGGTTTTTATGGACTCGATCTCGGAGAAGAACGTGTTTAT[G/A]TTCGAGCCATCGCTGATGCTGGAGGTTCTTGTCATTTCGGTTTCTGAGAGCCATGATTTGGAAAAGAGGTTGTTCATTTTATCTTCCAG
103450 A G ACCCTCTTCCATTCATAACACTGCAGCAACGTCCCTAAAGCCAGTCCCACAATCTTACGGGCAAGCGCTTCCCCGGGGCACCTCCTCCTCCCCATCCCAA[A/G]AGGCAGCATCTTCTGCTCCAACACCCCGTTTGAATCCTCGAACCTCTCCGGCACAAACTTCTCCGCCTCCTTCCATGTGTCAGGGTCTC
103450 C T GCAGCATTGTTCCCTTCGGGACATCGTAACCTCCAACCGTGCAGTCCTCCGAACTCTCGTGTGGCACCAAGAGCGGTCCAGCAGGGTACAATCGTAGGGT[C/T]TCCGATATGATACATTGGAGGTAGGGAAGGTTTTCTAGGTCAGACTCCTGCAGCAGGTCCTTGTTTCCTACTTTCTCATCTATCTCGG
103454 TA T TACATCCTCATATGTCAAATGTTCACTCAAATCTAATGCAAATGCAGATGCAAACATCTACATGCTCCCAAGCTAAAAACCCAACACTGATGAATCATAC[TA/T]AAAATAACCTACTGTAACTGAAACACAAGCATCTAATCATCTAAATCAGAAACCCTAGATGAATCCATACAGATCAAGAAACCCAAAC
103454 T C ACTTTGGGTTTGCAACTGCTTTGTCATTTGGCTTTGGAGGCCTTCCTCTCCCTTTAGCCTTTGGTGTTGCAACCAACCCATTTTCACCATCTTTTGCCTT[T/C]GCCGGCCTTCCTCGTCCCCTTGACTTGGGTGTTGCACTGATTCCATCCTTTGGTTTTGCTTCCGGGTCTGCACCCGTTTTGCCCTTAGACTT
103454 G A TGTTGCAACCAACCCATTTTCACCATCTTTTGCCTTTGCCGGCCTTCCTCGTCCCCTTGACTTGGGTGTTGCACTGATTCCATCCTTTGGTTTTGCTTCC[G/A]GGTCTGCACCCGTTTTGCCCTTAGACTTCGGAGGCCTTCCACGTGACTTTGGTGTTGCTACCAGCCCATTTTCCGGGTTTGCACCTGTTTC
103454 A G TCTTTTGCCTTTGCCGGCCTTCCTCGTCCCCTTGACTTGGGTGTTGCACTGATTCCATCCTTTGGTTTTGCTTCCGGGTCTGCACCCGTTTTGCCCTTAG[A/G]CTTCGGAGGCCTTCCACGTGACTTTGGTGTTGCTACCAGCCCATTTTCCGGGTTTGCACCTGTTTCACCCTTTGGCTTTGAAGGCCTTCCC
103464 C T TTCCTTCTTCCGTCGTTGAAAGGTGTACCTATAATCCGACCATCGGAAGCGGTCATCCATGTTGCAGTGTCCGCAGTTTGGACGAGACCATGCCGATTCT[C/T]CTATCGCTGTTATGTTCCTAGAATGATGCTACATTTGGTGATGATGCAATCAGACGGTTGGTATGGCTTGGTAGAGTGTGGATTAGTG
103472 A T GTCATTATCTAATTCACGATCTAATTCAGAGTTCTCATTAAAACGAGCGGAAGTGTGCTCGAATGGGGGGAGGCCCTTTTTCGAAACATGAGCATCTAAA[A/T]CAGTGCTCGCCACAGATCTGAATCCAATGGATCTACTCGAACAGCTCCGCCTTCGAAAATCCAAACCCAGCGGTTACATGCAGGAAG
103472 G A GAGCGGAAGTGTGCTCGAATGGGGGGAGGCCCTTTTTCGAAACATGAGCATCTAAAACAGTGCTCGCCACAGATCTGAATCCAATGGATCTACTCGAACA[G/A]CTCCGCCTTCGAAAATCCAAACCCAGCGGTTACATGCAGGAAGAACAATCCCGCAATGAAGCTGACGCGGAAACTTCCGATTGTT
103472 C T GAGATTGGATTGAATCCTTGTCTTGTTGAAGTAGTTGCTGTTCTTGAACCTTTTCTTTCTAAGCATTTTATTATGGTAGTTCCAGTCATTGGGATACTTG[C/T]CAACAAAAATGCATTCACGCCTGTCCTAAATACTTCGGAAGTTGACATGATTTTTGATGTCCCATTAGAAATGTTCCTAAAAGACGAGAA
103476 T C GAAAGGTGGTTGTGGGGATGAAGAAGACACTGGTTTATCATTCTGGGCATGCGCCTACTGGTGCCAGGAGTAATTGGGTCATGCACGAGTACAGATTAAA[T/C]TCTGATTCCTCTTCTACAGCAGATGATCCTCAGGAAACCCTTGTTTTATGCAGGATATTTCAGAAGAATGGTTCTGGGCCGCAAAA
103476 T C AGGAGGAGGAGTGGGCGGACGGTCAGGGTCTTGGTCCTAAAGCAAATGAAGGTGAACTGAATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGC[T/C]CTGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTTCGATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTT
103476 C T GGAGGAGGAGTGGGCGGACGGTCAGGGTCTTGGTCCTAAAGCAAATGAAGGTGAACTGAATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGCT[C/T]TGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTTCGATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTG
103476 G A GGGTCTTGGTCCTAAAGCAAATGAAGGTGAACTGAATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGCTCTGGCTGATGGTCGGGGAAGCACA[G/A]ATATCATTGCAGACTTCGATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTGAATTAGATGAAGGTGTTGATGTAGC
103476 C G CAAATGAAGGTGAACTGAATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGCTCTGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTT[C/G]GATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTGAATTAGATGAAGGTGTTGATGTAGCTGAACCTCAGATTGCGG
103476 A G AATGAAGGTGAACTGAATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGCTCTGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTTCG[A/G]TGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTGAATTAGATGAAGGTGTTGATGTAGCTGAACCTCAGATTGCGGAC
103476 T C ATGGTTTAATACATGCCAATAATATAGAACAGAATCAAGCTCTGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTTCGATGAAAATGTTGGCAG[T/C]CAGGCAAGAAATCCAAGCAATCTTGAATTAGATGAAGGTGTTGATGTAGCTGAACCTCAGATTGCGGACAGTAATATTAAAGCAAT
103476 T C ATCAAGCTCTGGCTGATGGTCGGGGAAGCACAGATATCATTGCAGACTTCGATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTGAATTAGA[T/C]GAAGGTGTTGATGTAGCTGAACCTCAGATTGCGGACAGTAATATTAAAGCAATGTACACCTTTGAAGAACAAGTTGAAAATAACTC
103476 G T TATCATTGCAGACTTCGATGAAAATGTTGGCAGTCAGGCAAGAAATCCAAGCAATCTTGAATTAGATGAAGGTGTTGATGTAGCTGAACCTCAGATTGCG[G/T]ACAGTAATATTAAAGCAATGTACACCTTTGAAGAACAAGTTGAAAATAACTCAAGCCAAAATGATGGATATCTTGAACTAAAGGA
103486 T TA GGAATTGCAACTGCTTCAAGAGCCTGGATCCTACGTTGGTGAAGTTGTAAAGGTTATGGGCAAATCAAAAGTTTTAGTTAAGGTTCATCCAGAAGGGAAA[T/TA]CGTGTTGACATCGACAAGAACATTGATATCGCAAAAATTAGTCCTTCAACTAGAGTTGCCCTTCGCAACGATAGCTACGTTCTTCA
103486 G GT AATTGCAACTGCTTCAAGAGCCTGGATCCTACGTTGGTGAAGTTGTAAAGGTTATGGGCAAATCAAAAGTTTTAGTTAAGGTTCATCCAGAAGGGAAATC[G/GT]TGTTGACATCGACAAGAACATTGATATCGCAAAAATTAGTCCTTCAACTAGAGTTGCCCTTCGCAACGATAGCTACGTTCTTCATTT
103490 A T CATCCTCCTCCCCTATGGTAACCTGAGTGGCAAACCCTTCCAAAAAGGGCAAACTAGCCCTAACCATCTCCTCGGCCTGACTCCACGTCCCATCAAAAAC[A/T]ATAAGCGGCAAATCCCTTTTCGCGTACTCCCTAACATCACGAGCGACCAAGCCCTTATTGGGCATGTTCGGGAACAGAAACAGTGAAG
103502 A G CCTTAGCTTTCGCTGTGGCTTCAGCATATGCTTTTCTTCTTCCATCTTCAGGTATTGCACTGAAAAGTTCACCTACAGACTTTGAAGATGCAGATGGGCT[A/G]GTAGAAACTTCAACAACCTTGTTCTCAGCAACTGTAGTGTCAGAAAAAACATCAGCCACCAATTTTGCAATTTGTGTTTTGGCCACCTTG
103502 GA G ATCTTCAGGTATTGCACTGAAAAGTTCACCTACAGACTTTGAAGATGCAGATGGGCTAGTAGAAACTTCAACAACCTTGTTCTCAGCAACTGTAGTGTCA[GA/G]AAAAAACATCAGCCACCAATTTTGCAATTTGTGTTTTGGCCACCTTGGTTTCGCTAATAACACCTTCCTTTTCAACAACAATGCCAAG
103502 G A AAAAAACATCAGCCACCAATTTTGCAATTTGTGTTTTGGCCACCTTGGTTTCGCTAATAACACCTTCCTTTTCAACAACAATGCCAAGCCCACTAACCTC[G/A]GAATAATCCTCATCAATTGCAGCTTTAATCACTGTATACTTCACCTCCGTGTTCTCCACAATTTTATCCAACAGCCCTCCAATGCTCAGAC
103502 C A GTGATGTCGGGCCATTTTCTGTTGGTCCAATTGTTATGCACAGTTTGGTAGCTGGCCCTATCGCCTTTGCAATTTGTTCAGGTGTAGTGAATGTTGTTTG[C/A]ACCGCATTCAGGCGCTTTGATTCTGCTGGTGAAATAAGCTTATAGGTCGAAGCCAAGCGAGCAAGCTCTTGAGCAGACTCAAGTTCAG
103502 A G TTTGTTCAGGTGTAGTGAATGTTGTTTGCACCGCATTCAGGCGCTTTGATTCTGCTGGTGAAATAAGCTTATAGGTCGAAGCCAAGCGAGCAAGCTCTTG[A/G]GCAGACTCAAGTTCAGGCACCCCTGCCCTAACATTAAACCCTTGCCTGAGCAAAGTCTGAGCAATGCGCACGCCAGCTTGGCCCGTG
103502 C T CTGAGCAAAGTCTGAGCAATGCGCACGCCAGCTTGGCCCGTGGCACCAGCAACAAAAACCGTGTTGGGATCCTTTCTTCTTGCACTAGCAAACAATGAAG[C/T]GGCAGGAGAATTGACCACTGGAATTAAACTCTTTGCATCTGCACTTAACTTTGAAAAATCAAATGAAAATTTTGGCTTGCTCGCGCC
103506 A G GTTAAGTGTCATAACATGTTTAAGTTCACGTAGCGGTTTGTTTACCGCTGACTTGGTTAGCGATCCATCCAAGCCCATCATACAAACCCTCCCCGGTCAA[A/G]GCACAACACGCCTGTATGTGCCAGTCATGGTTCTTGATGCTGTGAAGGGACAGCGCATCGGTGATCTCCGCAGGCGACATTGCATCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103506 G C CGATCCATCCAAGCCCATCATACAAACCCTCCCCGGTCAAAGCACAACACGCCTGTATGTGCCAGTCATGGTTCTTGATGCTGTGAAGGGACAGCGCATC[G/C]GTGATCTCCGCAGGCGACATTGCATCCTTCAAGTCCTGTTTGTTAGCAAAAACGAGCACTACTGCTTGCTCGAGGTCTCCGTGCTGG
103508 A G AACATAGATCATGCTTGCACACAAACAACTTCCGGCGTAGAACATGGATACCAGATAAAACTGGCATATTTGGCCAATAATCCTGAACGATAATGATATC[A/G]GATATCTTTCACCTCTGATTTTCCCTGCGCCTCACATATCTAGTTCTGTCATTGTACCGAGGTCTATCCTGAGCTCTCTGAGGCACAGG
103508 G A ACCGAGGTCTATCCTGAGCTCTCTGAGGCACAGGTTCAACCCTTCTCTGCCGCTCTGGTGACCTCTGAACAATTTGCCCATTCACAAACAACTCGGCGCC[G/A]TAGTCCTTGTTCTCCGCATCTACGTAGGAATCTGGTAGCACAAACAGAACACCAGGAAGACCTTCAAGCTTGTTGGAGGTCTCTTCAT
103508 C G AGAGTATGCCGAATCACCTGACCGGTTCATCCTGCACCGAACCGAAGTCATACGTGTCGGGTTGAAAACGAACGTCATCGCTGCCGGGATCGCGAATCGG[C/G]ATACCGAAGTGGAAGAGGATAGCATTCGCTTTGACAGGAGGCGACATGTTGGAATCAGGGAGATAGAACGAGCAATTGACGTG
103508 C A ATGCCGAATCACCTGACCGGTTCATCCTGCACCGAACCGAAGTCATACGTGTCGGGTTGAAAACGAACGTCATCGCTGCCGGGATCGCGAATCGGCATAC[C/A]GAAGTGGAAGAGGATAGCATTCGCTTTGACAGGAGGCGACATGTTGGAATCAGGGAGATAGAACGAGCAATTGACGTGAGAGC
103514 C T CCTCGCATTTACAAAGATTTCAGTTACGATGACTACAGAAAGCTTCGCCTCTCAACAGGATATAGAGCAGGTGAAGCTCTCTCCCTTTTGTCTAAATAGT[C/T]GTTTGCCTATTTGATATGTGAATGGCATTAGAATGACTAACAAATGGATTAATAAAATAAATATTTCATTTTTAATGCTGATTGTGTTTT
103522 T C ATCGGCGAGCAGGAGGGTATTCATCCCGATAAGACGGTGGTGGCCGCCTTTCAACAGGTGCTCTAGATGGATAGTCAGTAGGAGCTCTACTTCTGGGGGG[T/C]GGCACATCTCGCCTACTGTATTCTCTCTTTGGTATACTTTTTGGATACGCTGGAGCTGGCGGCCTCCTGTCATACGACCGATCAAC
103522 C CT TGGTGGCCGCCTTTCAACAGGTGCTCTAGATGGATAGTCAGTAGGAGCTCTACTTCTGGGGGGTGGCACATCTCGCCTACTGTATTCTCTCTTTGGTATA[C/CT]TTTTTGGATACGCTGGAGCTGGCGGCCTCCTGTCATACGACCGATCAACTGGAGGTAAACGCCTAGGCTTTTCTGGCACATCCATG
103522 C T TTTCAACAGGTGCTCTAGATGGATAGTCAGTAGGAGCTCTACTTCTGGGGGGTGGCACATCTCGCCTACTGTATTCTCTCTTTGGTATACTTTTTGGATA[C/T]GCTGGAGCTGGCGGCCTCCTGTCATACGACCGATCAACTGGAGGTAAACGCCTAGGCTTTTCTGGCACATCCATGTAAGGCCGCTTTT
103522 G A CCTTTTGATGTGGTCTAGATAGTCTAGCCCTAACTTTTACCTTATTATCTCCTTCTCCAAGCTCTTTGTTGTTTATGCCTTCGGCGCACGAAACAGCACT[G/A]TCATGGGTGGCAAAAGTAACAAAACCAAAATCTTTCCTTTTGGCAGATGGCATGTTTCGAGCAAGCTCAACTTTATCAATTGTGCCAAAT
103526 T C CTACTCCTCTGTTCATCGAATGCATCATCTGCTTCTTTAGTGCTGCATCTGCGGCCTGTGGCTTATCCTCCACTGTCTTCACATAAACCCCAGCTCGTTT[T/C]AACTCTGCAGCCAATCCATACCCTTTCTTTGGTGTCAGCAGCTCTCTGGCTGCCTCTACATATTTCACATTCCCACTGATATATCTCTCCTTA
103526 A G TCTTCACATAAACCCCAGCTCGTTTTAACTCTGCAGCCAATCCATACCCTTTCTTTGGTGTCAGCAGCTCTCTGGCTGCCTCTACATATTTCACATTCCC[A/G]CTGATATATCTCTCCTTAAACTTCTGCCTCTTTTTTCCTTTTAAAGACCTCATCCTCCCCAGCTTCTTTTCCCTTTCCCTCTGATGAAGATTTT
103526 T C AAACCCCAGCTCGTTTTAACTCTGCAGCCAATCCATACCCTTTCTTTGGTGTCAGCAGCTCTCTGGCTGCCTCTACATATTTCACATTCCCACTGATATA[T/C]CTCTCCTTAAACTTCTGCCTCTTTTTTCCTTTTAAAGACCTCATCCTCCCCAGCTTCTTTTCCCTTTCCCTCTGATGAAGATTTTTGAAATGCT
103526 CT C CTGCAGCCAATCCATACCCTTTCTTTGGTGTCAGCAGCTCTCTGGCTGCCTCTACATATTTCACATTCCCACTGATATATCTCTCCTTAAACTTCTGCCT[CT/C]TTTTTTCCTTTTAAAGACCTCATCCTCCCCAGCTTCTTTTCCCTTTCCCTCTGATGAAGATTTTTGAAATGCTTCTTCAGATCAAGACTGGTC
103526 G T TTGCATTTCCGGCCGCAAACAGAACATAGGTACGGACTTTCTGGCACCGATAACCCTTTTCTTTCGAGAATTTCTAGGTTGCGTTGCTGCTGGCGCTGTT[G/T]GAGGACCCAGCCTGGGAGGTGAGAGAAGGCATGGCGGTTGGCGTAGGCGGAGATGCCGTCAACGTAGCCGAAGAGGGAGGAAAA
103526 C T GGTTTATTGTCGAGGTCCCAGAGAACGGCGACAAGGGGAGGAGAGGATGTGTAGGTGTTTGTGGATGGGTTTAGGGTTAGGTCGATTTGGGAGGTAGATG[C/T]GGTGGAGACGGCGGCGGGTGGTCGGACGTTTAGTGTTAGGGTTTTCGTGAGAGGGAGGGAGAAGAAGGAAGGAGGAGTTG
103534 A T AGTCATCCGACCATGAAAATGCAGCCTTTCAGAATGCAATGAATCTTGCTGGGACAGAATTTGTTGAGAGTGTTCGTTTTCATGTCAGATCATGGCTGCC[A/T]GCCCGATCAATTGTTCTAGAGTGTTTGGCATCAAGGGAAAATGTTCATACTAGTGGAGAAATTATGGTTCTGAAAAAGTTTTGTCCTT
103544 T G TCCCAGCCACCAACATCTCCATGGTCTTCGCCGGAAACGAGGTTCTCCACTGGGGCGACATGAACATGAAAGCTCATCTCGTTCCCGCCATGCGAACCCT[T/G]AAAACGGCCTTAGTTCTAGAAGGCTTTCGCAACATCAGAGTATCCACTCCCAACTCCTTATCCATCCTCGCCGCCTCCGAACCGCCGT
103544 G T CATCTCCATGGTCTTCGCCGGAAACGAGGTTCTCCACTGGGGCGACATGAACATGAAAGCTCATCTCGTTCCCGCCATGCGAACCCTTAAAACGGCCTTA[G/T]TTCTAGAAGGCTTTCGCAACATCAGAGTATCCACTCCCAACTCCTTATCCATCCTCGCCGCCTCCGAACCGCCGTCGTCCGCCCGATT
103544 T C CGGGCGTGTACGACCCGGTGACGAAGATACGGTACATGAACATGTTCGACGCACAGATGGACGCGGTTCACACGGCAATGAGGAAGCTGGGCTACGGCGA[T/C]GTGGAGATTGTGATTGGTGAAACTGGCTGGCCCACGGTGGGCGAACCGGGTCAGGTTGGGGCGGACCCGGATAGTGCTGCG
103544 C T AACTGGGGCCTGTTCAGACCCGATTTCAGTCCTGTTTATAATGCTGGCGTTCTTCGTGGCGGCGCGAATGTGAAACCGAGTCCAGCGCCATGGAAGAGTG[C/T]GAAATGGTGTGTGGCAAAGAGTGGGAGCAGCAACGATATTCTGCAGTCGAACATAAACTACGTGTGCAGCACAGGCTTGGTCGA
103548 G A CATCAACGACGATTAGAATAATGGTTGGTCGTAACTAGAATGAAGAAACAACCAACATTGGACTACTTTGTCACATAAATAAGAAAATAATAATGATGAT[G/A]ATAATAACTGGCAAAATAATACAATGCACTTTCTAACTTAAGCAAACACCATTAAAAGAAGAAACGTATGTTGGATTCCTTGTTCAGT
103548 A G GTTGGTCGTAACTAGAATGAAGAAACAACCAACATTGGACTACTTTGTCACATAAATAAGAAAATAATAATGATGATGATAATAACTGGCAAAATAATAC[A/G]ATGCACTTTCTAACTTAAGCAAACACCATTAAAAGAAGAAACGTATGTTGGATTCCTTGTTCAGTCTGCAGAATGGGCACGCAGACG
103548 C CTGG TAAGAAAATAATAATGATGATGATAATAACTGGCAAAATAATACAATGCACTTTCTAACTTAAGCAAACACCATTAAAAGAAGAAACGTATGTTGGATTC[C/CTGG]TTGTTCAGTCTGCAGAATGGGCACGCAGACGACTTGCTAAATAATTTCTTAATCTACAGCTTCCACACCAACAGCAAAACTGTGA
103548 T C AGAAACGTATGTTGGATTCCTTGTTCAGTCTGCAGAATGGGCACGCAGACGACTTGCTAAATAATTTCTTAATCTACAGCTTCCACACCAACAGCAAAAC[T/C]GTGATTCCCATTACAACCTCAGTGCTAGACGTTTCTCCGACCCTCCAGCTCTTTGACATGCTCTGAAAGAATCTCCCGGATGTAATTGG
103548 CCCATTACAA C TATGTTGGATTCCTTGTTCAGTCTGCAGAATGGGCACGCAGACGACTTGCTAAATAATTTCTTAATCTACAGCTTCCACACCAACAGCAAAACTGTGATT[CCCATTACAA/C]CCATTACAACCTCAGTGCTAGACGTTTCTCCGACCCTCCAGCTCTTTGACATGCTCTGAAAGAATCTCCCGGATGTAATTG
103548 A T TGTTCAGTCTGCAGAATGGGCACGCAGACGACTTGCTAAATAATTTCTTAATCTACAGCTTCCACACCAACAGCAAAACTGTGATTCCCATTACAACCTC[A/T]GTGCTAGACGTTTCTCCGACCCTCCAGCTCTTTGACATGCTCTGAAAGAATCTCCCGGATGTAATTGGCTATTGCTTTGCATCCCTCTAT
103548 A G GCATGACATTTTCAAATATCTCTATTGGCAATTTTGCATCCATCTGAAGAAGGGTAACTTTATCCATCTTCGCCAGTAGTCCAACTGTGACATCTGGACC[A/G]CCAGCACTGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCCAGCACTGCAAGAAGTTACAATGTCACGCATTGG
103548 A C CTTTATCCATCTTCGCCAGTAGTCCAACTGTGACATCTGGACCACCAGCACTGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCC[A/C]GCACTGCAAGAAGTTACAATGTCACGCATTGGTATTCCTGCATCAGCTAACGCTAGCATTGCAGCATTGATGCATGCTGATCTTGTTCC
103548 T C TCCATCTTCGCCAGTAGTCCAACTGTGACATCTGGACCACCAGCACTGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCCAGCAC[T/C]GCAAGAAGTTACAATGTCACGCATTGGTATTCCTGCATCAGCTAACGCTAGCATTGCAGCATTGATGCATGCTGATCTTGTTCCACCA
103548 A G TCGCCAGTAGTCCAACTGTGACATCTGGACCACCAGCACTGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCCAGCACTGCAAGA[A/G]GTTACAATGTCACGCATTGGTATTCCTGCATCAGCTAACGCTAGCATTGCAGCATTGATGCATGCTGATCTTGTTCCACCATCAGCTT
103548 A C TGTGACATCTGGACCACCAGCACTGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCCAGCACTGCAAGAAGTTACAATGTCACGC[A/C]TTGGTATTCCTGCATCAGCTAACGCTAGCATTGCAGCATTGATGCATGCTGATCTTGTTCCACCATCAGCTTGAAGAACTTGAACAAA
103548 C T TGTCTTCAACATAATTCAGATCTAGTAAAGGAGTAGTACACAGATATCCAGCACTGCAAGAAGTTACAATGTCACGCATTGGTATTCCTGCATCAGCTAA[C/T]GCTAGCATTGCAGCATTGATGCATGCTGATCTTGTTCCACCATCAGCTTGAAGAACTTGAACAAATATGTCGATCTGGGATTTTGGCA
103548 T G TGATGCATGCTGATCTTGTTCCACCATCAGCTTGAAGAACTTGAACAAATATGTCGATCTGGGATTTTGGCATCAAATGAGTAATGATGGCCGCTTCCAT[T/G]GTTTGGCGAATCACCAAGGATATTTCTGTGGAGCGCCTATCACCCTTAGGCCTCCTCATCCGATCTCCTGTACTGAAATTAGCCATGCT
103548 C T TGTCGATCTGGGATTTTGGCATCAAATGAGTAATGATGGCCGCTTCCATTGTTTGGCGAATCACCAAGGATATTTCTGTGGAGCGCCTATCACCCTTAGG[C/T]CTCCTCATCCGATCTCCTGTACTGAAATTAGCCATGCTATACTCACAACGTACCAATGCTTGGTTATTGATTTGTTGGCTCCTATTCTGG
103548 T C TTTGGCGAATCACCAAGGATATTTCTGTGGAGCGCCTATCACCCTTAGGCCTCCTCATCCGATCTCCTGTACTGAAATTAGCCATGCTATACTCACAACG[T/C]ACCAATGCTTGGTTATTGATTTGTTGGCTCCTATTCTGGACCTCTCTAGGTCCGTAGACAGCAGCTATGACCTTGGTATTTCCCATTTCA
103560 C T ACATGCCATATATTATCTAAAATCCATCATCTACGGAAAGATCGAGATATACTTTCTCTATCCCAAGCTGCTTTCAATACATCATAAGATAACTCCTGCA[C/T]GGCTGCCGGAACACTGTGACGCCCGCTTCTATTTCCAGGATCAAAGCCCGGTGTCGAAGTATAATTTGATTCTACTAACATGTCTCCCTC
103560 C A CTCTATCCCAAGCTGCTTTCAATACATCATAAGATAACTCCTGCACGGCTGCCGGAACACTGTGACGCCCGCTTCTATTTCCAGGATCAAAGCCCGGTGT[C/A]GAAGTATAATTTGATTCTACTAACATGTCTCCCTCCAATATTCGTAACACCTGTGACATTTTAGGACGCTGGAGTGGATCGCGTCTGAT
103560 A C TATCCCAAGCTGCTTTCAATACATCATAAGATAACTCCTGCACGGCTGCCGGAACACTGTGACGCCCGCTTCTATTTCCAGGATCAAAGCCCGGTGTCGA[A/C]GTATAATTTGATTCTACTAACATGTCTCCCTCCAATATTCGTAACACCTGTGACATTTTAGGACGCTGGAGTGGATCGCGTCTGATGCA
103560 G A CAGGATCAAAGCCCGGTGTCGAAGTATAATTTGATTCTACTAACATGTCTCCCTCCAATATTCGTAACACCTGTGACATTTTAGGACGCTGGAGTGGATC[G/A]CGTCTGATGCACAATGAGGCTGCATGCAGCATGCAGCAAAGCTCATGTTCCGAGAAATTGTTCCCAAGTCGAGGGTCTATAAGCCCG
103582 T A TCGGAGAATTATCAACAACATCAAATTCATTACCAGAACCCATTCCATTCTCTTCGGAGCTATTTTGTACATTGTCATCTGAATTATCCCCTCTAAAACT[T/A]AAAGGGGCACTGCTGAAATCACCAAACTGCCCCTCGGACATCTGATGAGGCATTATGGAGCAACGACCCCATTGACCCGTCCTTTTTCCA
103582 C T TCAAATTCATTACCAGAACCCATTCCATTCTCTTCGGAGCTATTTTGTACATTGTCATCTGAATTATCCCCTCTAAAACTTAAAGGGGCACTGCTGAAAT[C/T]ACCAAACTGCCCCTCGGACATCTGATGAGGCATTATGGAGCAACGACCCCATTGACCCGTCCTTTTTCCACGACCACGAGTTCGGCCTCT
103582 A G TAAAACTTAAAGGGGCACTGCTGAAATCACCAAACTGCCCCTCGGACATCTGATGAGGCATTATGGAGCAACGACCCCATTGACCCGTCCTTTTTCCACG[A/G]CCACGAGTTCGGCCTCTCTTAGTGAAATTAGATGATGAATCTTTGTGGATAGCAGGATTCGGCTGCATGGTGAACTTGGGCGTTGAA
103582 A G CAAACTGCCCCTCGGACATCTGATGAGGCATTATGGAGCAACGACCCCATTGACCCGTCCTTTTTCCACGACCACGAGTTCGGCCTCTCTTAGTGAAATT[A/G]GATGATGAATCTTTGTGGATAGCAGGATTCGGCTGCATGGTGAACTTGGGCGTTGAAATCGTACCTGCCACACGTGGCATTCTCCCA
103582 C T TGGAGCAACGACCCCATTGACCCGTCCTTTTTCCACGACCACGAGTTCGGCCTCTCTTAGTGAAATTAGATGATGAATCTTTGTGGATAGCAGGATTCGG[C/T]TGCATGGTGAACTTGGGCGTTGAAATCGTACCTGCCACACGTGGCATTCTCCCACCTCTGCTACCAACACCACCACCACGTGGGCGC
103582 A G GCAACGACCCCATTGACCCGTCCTTTTTCCACGACCACGAGTTCGGCCTCTCTTAGTGAAATTAGATGATGAATCTTTGTGGATAGCAGGATTCGGCTGC[A/G]TGGTGAACTTGGGCGTTGAAATCGTACCTGCCACACGTGGCATTCTCCCACCTCTGCTACCAACACCACCACCACGTGGGCGCCCCC
103582 G C ACGACCACGAGTTCGGCCTCTCTTAGTGAAATTAGATGATGAATCTTTGTGGATAGCAGGATTCGGCTGCATGGTGAACTTGGGCGTTGAAATCGTACCT[G/C]CCACACGTGGCATTCTCCCACCTCTGCTACCAACACCACCACCACGTGGGCGCCCCCCACGTCCACGAGGTACACGGTCCTCCACGG
103582 CG C GAACTTGGGCGTTGAAATCGTACCTGCCACACGTGGCATTCTCCCACCTCTGCTACCAACACCACCACCACGTGGGCGCCCCCCACGTCCACGAGGTACA[CG/C]GGTCCTCCACGGCCCATGCGCACACCGCTTCCAGAGTACAGCGACCTCGTTTTGCTTTGGTACTTGACTTGTTCTGGTGTACAGCTT
103584 CT C ACCCTTTCTCCAAACTCTTCGCCCTTAGCAAGTTCATGCCTTGGGCGTAACTGCAGATTTTGGAAGCGTACAGAGCTTGCCTTACATCGTCGATCAGTTT[CT/C]TTTTTATCCACCGATCTTATTTTTGGGGTTTCGAGGCCGGCTTCATCGAGTATTTTGGAAGCGTTTTCACGCTCTTCTTTTAGGGCGCT
103584 AT A CGCCCTTAGCAAGTTCATGCCTTGGGCGTAACTGCAGATTTTGGAAGCGTACAGAGCTTGCCTTACATCGTCGATCAGTTTCTTTTTATCCACCGATCTT[AT/A]TTTTTGGGGTTTCGAGGCCGGCTTCATCGAGTATTTTGGAAGCGTTTTCACGCTCTTCTTTTAGGGCGCTAAGGAATCGGCAGTCGAG
103584 A G TGTCGACAAGTTCACCACTGCTGTGCTCATCTTTGACCTTGAAGATGTCGGCTGTGATCTCGATGAGGAAGCTTTCGAGCTCTCCACGGTTCCATTCTGC[A/G]AAGATGTCTGCGAGTTCTGGGTTGGATAGGCCTCCGACCGTTTTGAGGACATCGTAGGCTTCGGAGATGAGCTGCATGTCGCCGTAC
103586 C T GAATCTTCATCGCCCTGCTGAGAAGAACCATTTTCTTCAGCAACAGAAAGTTGTGAAAATTCTTCCTGAAGAGCGTAAGCCAGAATCTCATCATTCTCTA[C/T]AGAAAAATGATCTGTGCCATAACGACCTTCTCTACTATAGAGTCCATCATAATAGTGGGAATCGTTTTGGTTATATGCTTCACAATAAC
103586 G A TGCCATAACGACCTTCTCTACTATAGAGTCCATCATAATAGTGGGAATCGTTTTGGTTATATGCTTCACAATAACCATGATTAGGAAATGGTTCAACATG[G/A]AGTATATCCATACCCCAGCGAAGAATATCAGGATCCTGGTCATACATAATCATCTGTAGTACTCGAACTCAAAGAAATCCGTCCGCAA
103588 C A AACTCCAAATGTCCTATGGAAGTAAACGCTTCGGCTACCCCATGTAGCGCATACTGTGGCACTAGCCAAAACACCGAAATGGGTAAACCTACATTGCTGG[C/A]CTCGACAAGCCCATGGGCCCTGGCAACGTTTTTACGTTTCACTTCCACAAAGCCAGCGATGAGAGTGGCCAGTGTGGAAATGGCGT
103588 G T AAAACACCGAAATGGGTAAACCTACATTGCTGGCCTCGACAAGCCCATGGGCCCTGGCAACGTTTTTACGTTTCACTTCCACAAAGCCAGCGATGAGAGT[G/T]GCCAGTGTGGAAATGGCGTAGCCTACGCCCATCCTCTGGAGGAAGGAGATGCCACGGGCTGAGCCCGTGTATTTGCGGGTTACAG
103588 G T CGATGAGAGTGGCCAGTGTGGAAATGGCGTAGCCTACGCCCATCCTCTGGAGGAAGGAGATGCCACGGGCTGAGCCCGTGTATTTGCGGGTTACAGGGAT[G/T]AGGATCCGGTCGTAGATTGATATAGTTAGTAGCATTGCTAGCATTGTGAATACTGTCATTGAGCCTGAAGGGATTTGGAAGGAG
103588 C T GAGTGGCCAGTGTGGAAATGGCGTAGCCTACGCCCATCCTCTGGAGGAAGGAGATGCCACGGGCTGAGCCCGTGTATTTGCGGGTTACAGGGATGAGGAT[C/T]CGGTCGTAGATTGATATAGTTAGTAGCATTGCTAGCATTGTGAATACTGTCATTGAGCCTGAAGGGATTTGGAAGGAGGACGAG
103588 T A CCATCCTCTGGAGGAAGGAGATGCCACGGGCTGAGCCCGTGTATTTGCGGGTTACAGGGATGAGGATCCGGTCGTAGATTGATATAGTTAGTAGCATTGC[T/A]AGCATTGTGAATACTGTCATTGAGCCTGAAGGGATTTGGAAGGAGGACGAGTGGGTGATGTGGCGGTCCATGGTGTTGGCTTGC
103588 G C TGCGGGTTACAGGGATGAGGATCCGGTCGTAGATTGATATAGTTAGTAGCATTGCTAGCATTGTGAATACTGTCATTGAGCCTGAAGGGATTTGGAAGGA[G/C]GACGAGTGGGTGATGTGGCGGTCCATGGTGTTGGCTTGCTGGAGGGAGAAGGTGTTTTGTTGGGCTGAGGCGGTGATTACGAG
103588 A G GGATTTGGAAGGAGGACGAGTGGGTGATGTGGCGGTCCATGGTGTTGGCTTGCTGGAGGGAGAAGGTGTTTTGTTGGGCTGAGGCGGTGATTACGAGGAC[A/G]CCTGAGGCCCATATTGGGCCCATTCTGATTATTGACTTTAGCTCCTCCACTCTGTGAACTGTGCTTAGCCTCCAGGGATTTGGG
103588 C A TTGTTGGGCTGAGGCGGTGATTACGAGGACACCTGAGGCCCATATTGGGCCCATTCTGATTATTGACTTTAGCTCCTCCACTCTGTGAACTGTGCTTAGC[C/A]TCCAGGGATTTGGGCTTGTCCCTTTTGTTGCTTGATCCTTTTCTGTTATGATCGCGGCTTTGTCCAAAAATCTCATATGTTTGGTATGC
103588 C A GGTGATTACGAGGACACCTGAGGCCCATATTGGGCCCATTCTGATTATTGACTTTAGCTCCTCCACTCTGTGAACTGTGCTTAGCCTCCAGGGATTTGGG[C/A]TTGTCCCTTTTGTTGCTTGATCCTTTTCTGTTATGATCGCGGCTTTGTCCAAAAATCTCATATGTTTGGTATGCAGAAGCTTCCCACCCA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103598 A C CCAATGTTTCACCGTGTTTTCAAGCCTTTTTTGAGTGCCAAACCTGGTACTTTGCCAAATCTTGTACTTCGGTAAATCTGGTAATTTGCCAAATCCAAGA[A/C]GTGCCAAGCCCGATGCGCACACGTGAACACCATTAACTCGAACACCTTCTTTACCAGAAAGCTGGTCAACCGATCGCGTTTGAGCCTTC
103598 A G CAGGCACAATGGGCTTTTCTTATAAGTCCACGGAATTATATTTCGGTGGTCGGTCGATCGATGTACCTATTGGATTACTCATTGTCCCATTTTTCTGTCT[A/G]TGGCTACTCACCAAGGAATTTGGCACTTAGTGTTTAGACGCGGATCATGTTCAACCGAAAAGATTCCGACAAAACTTGCGGTCTTTGAA
103598 G A TGAACGGATCACGTTCCACCTACTGAAAAGCCGTTCTTCTTTCTAACTTCCCCAAACTGAGTATGGGAACTTTTCGAACCTTCGTCGAAGTGGCCGCCTT[G/A]GTGCGGAGCGCCTCGGCTATAGTGGAAATTTCATTACGTCTCACGTTCCAAGTTCCAGCGTGAATCTTGTGTGCTCGGGCCGAGGTAT
103598 G A GATCACGTTCCACCTACTGAAAAGCCGTTCTTCTTTCTAACTTCCCCAAACTGAGTATGGGAACTTTTCGAACCTTCGTCGAAGTGGCCGCCTTGGTGCG[G/A]AGCGCCTCGGCTATAGTGGAAATTTCATTACGTCTCACGTTCCAAGTTCCAGCGTGAATCTTGTGTGCTCGGGCCGAGGTATGCTGGT
103598 G A CGAAGTGGCCGCCTTGGTGCGGAGCGCCTCGGCTATAGTGGAAATTTCATTACGTCTCACGTTCCAAGTTCCAGCGTGAATCTTGTGTGCTCGGGCCGAG[G/A]TATGCTGGTACACAAATCCTTGGTTGTATTTTATTTACATCATAGACGCAGTTATTTCCATCATCGCCTTCGGAGCGCAAGTTCGGCA
103602 G A GTATCTGATCGAAATTCTTCAAGTCAGGAGATAGTCCTCCATGCATGCATAGTATCTTTTCATCAATCAGTGCAGCAACAGGAAGACAGTTAAAACAGTC[G/A]GTAAAAACTTTCCAAAGACGAACATTGAATCTTCTTTTGCATTCATCATAGAAGCCATATATACGGTTTATCGAAGCACACTCGTGGT
103604 GC G CCTAGTCGTGTAAACCCTTTATTCGGGACCCACGAAGCTAACACGTTTACGCCGGGTGCAAGTATATCAGGTTTCATAATACCCGGTGTGATCGAACCCG[GC/G]CCCCCGTGACGAAAATGGAATGACCTGCGGTGCTGGCTTCGTACCTAGCACGGTCTGTATGAATTTAATGTCGATCGCCAGCCTTC
103612 A G AATCCCCCAGTTTTATTCTCCTTGGGATTTTTTGTAAATGGCAAATTCATCAACCGATTGCGGTGGAGGCTGCAGCAGAGAAGGTGAGGAGGCTGGAAGC[A/G]GAGAGAACTTGCACCAGCAACAAACTGATCAAGAACCGATTTCCAGAACAGCGGGGAAAGGAAAATCTTGTACAGGATGTCTTTA
103612 A G TCACAAAATAGGGGAAACTGAGATGGTAGCCAATGAAGAAGGCCATGATCTTTCTTCTGGCTTCAAGTATGCTTGTATTGGTTATTCCATGTTTTTGGAT[A/G]GCAAGGATATTCTTAATCAGAAGGGAAATAATCAGCCAGAGTTGCCATCTTGCGTTGGTATAGAGATACTGGTGGCTAAACCGTCAT
103616 A G TTCGAACCATAACAGCTCAACAATGGCTAAGAAGAACCCATGCTTGGATTGGCTTTCAATTCAGGTCTAATGTAAGTGAGATTACGCGTTGCTGGAGATA[A/G]TACATTGTTTGTGGTACTAGATGTATGAGGAGAGGGGTCATCTCTCTTCCATTGTAAGCTTCGAGCTCCTGGTTTGATAGTAAGTCG
103616 C T GTAAGCTTCGAGCTCCTGGTTTGATAGTAAGTCGGCCTCTAAATGCACCATGATTGAATCCTCCTCTAGAAAATGCTGTTCTGCTGCCGCTTGATGCAAA[C/T]GGTTGGGCTCGAGCTACACGGGCCCAACTGACTACTTCTGCAGACTCGGTTTTGCGGACTACCTTCAAACTGCGAGACATAAAATAAG
103626 G A CTAGGGTTTGTTCATCATGGTATGGAACGGGCGCGGATCGAGAAGAGAGCTCGACTAGACCCGGGGCGAGACGCTTGAGCTTGAGCCTGCTCTTGGAGGA[G/A]GGGAGGTCGGAGGAAGAGAGGGAGGTGGGACCCACGATGCGGAGGGACAGGAGGGGCATTTGGCTGTTGCTGTCATCTGTG
103626 G T ATCGAGAAGAGAGCTCGACTAGACCCGGGGCGAGACGCTTGAGCTTGAGCCTGCTCTTGGAGGAGGGGAGGTCGGAGGAAGAGAGGGAGGTGGGACCCAC[G/T]ATGCGGAGGGACAGGAGGGGCATTTGGCTGTTGCTGTCATCTGTGGAGTGAGAGGCAGCAAGACGGAGAGCCTCGGAGAG
103630 G A TTTAACACTTTTTATTAGTTCACATCACATCATACTCACCGAAGTTGAGTTAATAGGCAAAATATAACCATTTTGCCTCCTTATAACAGTAAGAATAGTT[G/A]TAATATTTTTGTGGTTCCATGAATTAACATGACTAAGTATTGAAATGTAAACATGATACCAATTTATTTCCAGGAATCATACATCGTACCG
103630 G C AGAATAGTTGTAATATTTTTGTGGTTCCATGAATTAACATGACTAAGTATTGAAATGTAAACATGATACCAATTTATTTCCAGGAATCATACATCGTACC[G/C]GAGGAAACCAACAACGCCCCAACACCAACGCTACCACGATCAAAATACCCAAAACCCCTGATTTTCCACGATAGCAGGCTCTCCCTTCT
103630 GT G CTGAGCTGGCGGAGGACATCGTGCCAGTAGCGTTGGATGCCGATGGCGGTTGGTTGTATGGGACGACGGCAAGCGGGTTGAAGGTTTTGGATCCGTTTGT[GT/G]TTTTTTATGAATCCGTGGCCAAGGTATAGAGTGAGGATTTTGGAGAGGGTGGAGAAAGAGATGACGTGTGCGGGCGGGTGG
103630 T C CGTTTGTGTTTTTTATGAATCCGTGGCCAAGGTATAGAGTGAGGATTTTGGAGAGGGTGGAGAAAGAGATGACGTGTGCGGGCGGGTGGAGCGGGTCGGA[T/C]GTCGCGAATCGTGTGCAGAGGACATTGGGGGCGGCGTTAGGGTTCGAGTGCACTGGGTTAACCAG
103632 A G CTTTCGATTCAATTTTGTCAAATAATTCGCCTCCATCTACGTATTCAAGGACCATGTAAATCTTTGTTTTGCTTGCTGAGACCTCATGTATCCGAACAAC[A/G]TTAGGATGCTTAAGCAACTTCAGCGTATTGATCTCTCTCTTAATCTGGTCGTTGATCTTAAGGGACTGGATCCTCTTCCGATCGAGAATCT
103632 A C CGTCCGCTTTCAACGTGGCGAGCGAACTTCACCTTGCCGAAATTGCCCTCGCCGAGGGTCCTGCCGATCTCGTACTTCCCCAGTCGCATTCCCTTCTCTG[A/C]TGGCGCTTCTTCTCCCGCCATTCGCGTGCGAGGAAGCGAGCAAAAAGTCAAGGGTATACTTGTAAATTTCTTTTCCCCGGTAACAGCT
103640 CA C CAAATAATTACACGCTGCTATCCCAGCACTTTTGACAGCAGTATATATGTGTACCACATTAACTAACATAGAGTCATAGACAAACTAGTTAAAAAGTGAA[CA/C]AAAACCGGGGGGAAAACGTGATGCTGTAGAGACAGCAATAAAGACTTTGGTCAATTCCAAACTTGCGTATCGCAGTGAGCGCAAC
103640 T C AATCCAACGGTAGAACTTCTTTCTCCGCCCACACCCACTTCCCATCGTACCCTCCCGTTACCATGAAACGGAACTGCAACGGCCCCGTTGGAGCCCTGTC[T/C]GTTGTCCAGACCGCACCATGCGCTTTGCTTCTGGTCATGTACCTCCAGTCCGACATGCCGAACCGTGCCACGTCAATCCCCGTTATATC
103640 T C CCAACGGTAGAACTTCTTTCTCCGCCCACACCCACTTCCCATCGTACCCTCCCGTTACCATGAAACGGAACTGCAACGGCCCCGTTGGAGCCCTGTCTGT[T/C]GTCCAGACCGCACCATGCGCTTTGCTTCTGGTCATGTACCTCCAGTCCGACATGCCGAACCGTGCCACGTCAATCCCCGTTATATCGGT
103640 C T TCCGCCCACACCCACTTCCCATCGTACCCTCCCGTTACCATGAAACGGAACTGCAACGGCCCCGTTGGAGCCCTGTCTGTTGTCCAGACCGCACCATGCG[C/T]TTTGCTTCTGGTCATGTACCTCCAGTCCGACATGCCGAACCGTGCCACGTCAATCCCCGTTATATCGGTCTGACCTCCCTGGAACACTA
103642 A G GCTCTGGTTCTTCATCTGGCGAGGAATCAAGTTTCTTGACTGCAACTTGTTGCTCGTCATCCATAACAGCATAATACACTCTTCCATAAGAACCTTCACC[A/G]ACCAAAGACTTTGAGCCAAAATTGTCAGTCTTTTCCTTTAGTACTTCCAAAGATAATTTAGGTACTTCAATAACTATTTCTTTCTTTTCTGG
103642 G GA ACAACATAACCACCTCCGCATGTTTTCTTCTGTTCCAATTTATATACAACTTTTTGCACCTGCGATTAGCTCCTCTTCTTCTTCCTCCACGTTAAGCTGA[G/GA]AATGGAGGAGAGAGAAAGAGAGGAGAAAGAAGCTAGAAAGTTAAAGAATTCGCCGTTTAAAGGAGGGGAGAGGAAAAAATAGCCAG
103646 T C CAACAAGGTTGCCGCTCCTGCCAAGGCTGGTGCCATCGCTAACCTGGATGTCACCGTACCTGCTCAGTGTACAGCTCTCGGTCCTGAGAAAACTTCGTTC[T/C]TCCAGGCTCTGTCCATTCAGACCAAGATTACCAAGGGTACCATTGAAATCTTGAACGACGTGAAGTTGATAAAGATAGGTGACAAGG
103646 G A CTCAGTGTACAGCTCTCGGTCCTGAGAAAACTTCGTTCTTCCAGGCTCTGTCCATTCAGACCAAGATTACCAAGGGTACCATTGAAATCTTGAACGACGT[G/A]AAGTTGATAAAGATAGGTGACAAGGTCGGTGCCTCAGAGGCAACACTACTCAACATGTTGGGTATCTCTCCATTCCAGTACGGACTG
103648 GTCA G GAATAAAAATGGATCAGAATCACAGCAAGAAATGAATGGAATCCAAATACACCACTCTGCACCTTCCCCTCCGAGTTCTTACAGAAAATA[GTCA/G]TCATCATCATACATAATAACAACTACTATATAGTGCCCACAAACTAAAAAAACAATGGAAGAAACACAAGAAGCAAGCCAAAATAATGATGATA
103648 G GA CAAGAAATGAATGGAATCCAAATACACCACTCTGCACCTTCCCCTCCGAGTTCTTACAGAAAATAGTCATCATCATACATAATAACAACTACTATATAGT[G/GA]CCCACAAACTAAAAAAACAATGGAAGAAACACAAGAAGCAAGCCAAAATAATGATGATAATAATGATAATATGTGTCCACTGTCTAC
103648 TA T ATGGAATCCAAATACACCACTCTGCACCTTCCCCTCCGAGTTCTTACAGAAAATAGTCATCATCATACATAATAACAACTACTATATAGTGCCCACAAAC[TA/T]AAAAAAACAATGGAAGAAACACAAGAAGCAAGCCAAAATAATGATGATAATAATGATAATATGTGTCCACTGTCTACGATTTATAACT
103648 A G AGTTCTTACAGAAAATAGTCATCATCATACATAATAACAACTACTATATAGTGCCCACAAACTAAAAAAACAATGGAAGAAACACAAGAAGCAAGCCAAA[A/G]TAATGATGATAATAATGATAATATGTGTCCACTGTCTACGATTTATAACTCTGCCACCATATGCACCCTCTCTAAGCAGCCAACGCAA
103648 A G CATATGCACCCTCTCTAAGCAGCCAACGCAACAGATAGTACCCCAAAAACCAGTCCAAAAATAGTCATTTCCTTCCTCGCTGACCCACTCGTATCGTCAG[A/G]GGCGCCAGGGCCAGGAGACACAGCGTCAGATCCAGTCGGAGCCATCGTCGGAGACGATACAGAACTGACCGTCGACGGAGCAGGC
103648 T TG TTCGGTGGAGCGGTGACTGGAGCGACTGACGTCGGCGGGGATTTGACAGGAGCGGCGGTGGGCGTAGGAGTGGTAACCGGGGTAGCAGGAGGCGACATTT[T/TG]GGGGGCAGAGGCGGGCGACTGGGCGGTGACGATGCAGAAGAGGGTGAGAATAAGGGCGGTGCGAAGATCCATTATTGT
103684 A AG TTTGACGTGCATGACTTTCCAGCTCTTCCTTCCGAAAGCAACGAGCCTTCACTACCAAACAAATATAACCCGTCTTCAAACTTCCTCCAAGGCACCACGG[A/AG]TTTCGCATCAACTGTTCGTAAGCGTTCCTTGCCAGAAGACTCTATAAATCACAAACGCTCAGCTGATAAAAATATGTCTTCACGTAGA
103684 T A CTGCAAGGCTTCCTGTGGCTGTGGAGCAGTTCCTTATAGGAGAAAGGCTTCAGTTTACGCAGCCTCAGCCTGGACTTCTCCGCGTTGCTCTTTAGGTCTT[T/A]TGTCAGAAGTTGTGTAGTGTATTTCTAACTCATATATGTGATCGTAGACATGTAATAGCTAGGATGAATAAGTAATAGTTAACTTACC
103686 G A TGCAAGCTCTCTCCTTTTGATCCTTGTCCGATAAAGGAGGTTCTACACTTTCAACGACTCTATCATCTGAATTTCTCTTAACCAAGGTGTCTTCATCCAT[G/A]GATTCATGTTCTTTATCTTTTGGTGAATCATCAGATGGTAAAGCATAAACCAAAGAGGAAAGAAAAGGATCAGGTGCCACATTTGAAGG
103686 A C AATTTCTCTTAACCAAGGTGTCTTCATCCATGGATTCATGTTCTTTATCTTTTGGTGAATCATCAGATGGTAAAGCATAAACCAAAGAGGAAAGAAAAGG[A/C]TCAGGTGCCACATTTGAAGGAGGAACCATGAAAGAACCTCCAAGAAGAGTTTGAAAATTCCCATCTCGGAGATCCTTCCTTAACAAAG
103686 T C GGCACAAAAAGGGCAAGGAATCTCTGTTTGCGTTTCCTCTCCGCTTCCATCTAAATCTTCGAACTCTAGACATAGATCGTATCGCGACTGAAGAGACGAT[T/C]GATGGCGTTTGGATGCGGCAGACAACCTAGTCCAGGAATCCGATTCCATATTTAAATTAATGTCACGTAGAAACCCTAAATCGATTGC
103692 A G GAAGGCTGGCAGAAAGGTGCATGACGCCACCACAGTTAGCAAAGATTCACTGGCCAAGGTGAGGAAATACAAACGAGGATCATCCAGCCCAAACAAAACC[A/G]AACCTCCACTCTCACCAAAATAATACAGATCAAAAATCCTCTAAAATAGAAAGAACCTCAATCTCATCGAAATGCAAACCAAGGG
103694 A G AACTTAAAGCTAAGTTGCTCAGCTTCTTCAAATGGTTTGACATATAAGGAAGCTGGCGTGGATATTGATGCTGGGTCAGAGCTTGTGAGGCGGATTGCTA[A/G]AATGGTGAAGGGCATTGGAGGATTTGGCGGACTATATGAATTGGGAGATTCCTACCTTGTTGCTGGTACGGATGGTGTTGGGACC
103694 A G AAATGGTGAAGGGCATTGGAGGATTTGGCGGACTATATGAATTGGGAGATTCCTACCTTGTTGCTGGTACGGATGGTGTTGGGACCAAATTAAAGCTTGC[A/G]TTTGAAACAGGAATTCATGATACGATTGGAATAGATTTGGTGGCAATGAGCGTAAATGATATTGTTACATCTGGTGCAAAGCCAT
103694 T C GTACGGATGGTGTTGGGACCAAATTAAAGCTTGCATTTGAAACAGGAATTCATGATACGATTGGAATAGATTTGGTGGCAATGAGCGTAAATGATATTGT[T/C]ACATCTGGTGCAAAGCCATTGTTCTTCCTTGATTATTTCGCTACTAGCCAGCTTGATGTTGATCTTGCCGAGAAGGTAATTAAAGGA
103698 G A TGCTTGTAGGCATCGCTACTCCGATTCCAGGAATAGTTCCTTGATTTTGAGATAATCCTGAGGCGAATGGTCCAGGTGTAGGAGGATCTGCTGCTGAGGG[G/A]AAGCCACTCATCATTCGATTAGAATTAGGATACTGGTCGCCATAACCTGGATTGTAACCGGTGTATCTGTCACTTGCAGTGTCACCA
103710 C T TAAATCCCGAAATGATGAAAAGAGCGTTCTTGAAGCTGTTCAGAAGGTACACGCTATTATCGACAAGGAGGTAGCTTCAGGCATTGATCCTGAAAATATC[C/T]TCATTTGTGGACTTTAGCCAGGGAGGTGCCTTGACACTAGCAAGTGTATTACTTTATCCAAGAAAATTGGGAGGTGGTGCCATTTTT
103710 AC A ATGATGAAAAGAGCGTTCTTGAAGCTGTTCAGAAGGTACACGCTATTATCGACAAGGAGGTAGCTTCAGGCATTGATCCTGAAAATATCCTCATTTGTGG[AC/A]CTTTAGCCAGGGAGGTGCCTTGACACTAGCAAGTGTATTACTTTATCCAAGAAAATTGGGAGGTGGTGCCATTTTTAGCGGATGG
103714 T G TTGATCCTGCAAGAGTATTGGAGAAAGCTTACAATAGGACTAAAAAGGCTGGATCATCAACGGCATGCATCATTGCTCTTCGAGATCAGGGTATTCATGC[T/G]GTTAACTTAGGAGACAGTGGATTCATCGTAGTTAGAGAGGGCTCAACTGTATTCCAGTCACCTTCTCAGCAGCACGACTTCAACTTT
103714 A G TCCAGTCACCTTCTCAGCAGCACGACTTCAACTTTCCCTTCCAGCTCGACGCAGGTGGAATGGGTGATTTGCCAAAAGATGCTCAAGTATTCACAGTGCC[A/G]GTTGCACCTGGGGACGTCATTGTAGCAGGAACTGATGGGCTATTTGACAATCTGTACACCCATGAAGTTGCTGAAGTCATAGTGCAG
103714 T A CTTCTCAGCAGCACGACTTCAACTTTCCCTTCCAGCTCGACGCAGGTGGAATGGGTGATTTGCCAAAAGATGCTCAAGTATTCACAGTGCCAGTTGCACC[T/A]GGGGACGTCATTGTAGCAGGAACTGATGGGCTATTTGACAATCTGTACACCCATGAAGTTGCTGAAGTCATAGTGCAGTCGCTTCAT
103714 T C TTCCCTTCCAGCTCGACGCAGGTGGAATGGGTGATTTGCCAAAAGATGCTCAAGTATTCACAGTGCCAGTTGCACCTGGGGACGTCATTGTAGCAGGAAC[T/C]GATGGGCTATTTGACAATCTGTACACCCATGAAGTTGCTGAAGTCATAGTGCAGTCGCTTCATGCAAATTTGGATCCAGAGAAAGC
103714 C T AGGTGGAATGGGTGATTTGCCAAAAGATGCTCAAGTATTCACAGTGCCAGTTGCACCTGGGGACGTCATTGTAGCAGGAACTGATGGGCTATTTGACAAT[C/T]TGTACACCCATGAAGTTGCTGAAGTCATAGTGCAGTCGCTTCATGCAAATTTGGATCCAGAGAAAGCCGCTCAGAAGATCGGAGC
103714 C G TGGGTGATTTGCCAAAAGATGCTCAAGTATTCACAGTGCCAGTTGCACCTGGGGACGTCATTGTAGCAGGAACTGATGGGCTATTTGACAATCTGTACAC[C/G]CATGAAGTTGCTGAAGTCATAGTGCAGTCGCTTCATGCAAATTTGGATCCAGAGAAAGCCGCTCAGAAGATCGGAGCGCTTGCTCG
103714 A G ATCCAGAGAAAGCCGCTCAGAAGATCGGAGCGCTTGCTCGTGAGCGAGCCTTGGATAAAACGGTAAAATCCCCTTTTGCTGCGGCAGCCGGCGAAGCTGG[A/G]TTTTACTATGCTGGTGGCAAGCTCGACGATATCTCTGTTGTTGTATCTTACGTTGTAGTGGCTGCTGCCTCTGATTCTTGATTGTCA
103714 T C CGCTTGCTCGTGAGCGAGCCTTGGATAAAACGGTAAAATCCCCTTTTGCTGCGGCAGCCGGCGAAGCTGGATTTTACTATGCTGGTGGCAAGCTCGACGA[T/C]ATCTCTGTTGTTGTATCTTACGTTGTAGTGGCTGCTGCCTCTGATTCTTGATTGTCAAGTCCATGTTTATTTATAGTTTTGCATGCTGA
103716 C T TGGAGCTCCGAAACCGATAGGCATAAAGAAGGCATTGGTCTTTTATGCCGGCAAAGCGCCCAAAGGCGAAAAAACAAATTGGATCATGCACGAGTATCGA[C/T]TAGCGGATGTTAACCGATCCGTTAAAAAATTGAATAGCTTGAGGTTGGACGACTTTGTGCTGTGCAGAATATACAATAAGAAAGG
103716 TA T TAAAGAAGGCATTGGTCTTTTATGCCGGCAAAGCGCCCAAAGGCGAAAAAACAAATTGGATCATGCACGAGTATCGACTAGCGGATGTTAACCGATCCGT[TA/T]AAAAAATTGAATAGCTTGAGGTTGGACGACTTTGTGCTGTGCAGAATATACAATAAGAAAGGCGGGCTGGAAAGGCATGTGCCC
103716 A G AGAAGGCATTGGTCTTTTATGCCGGCAAAGCGCCCAAAGGCGAAAAAACAAATTGGATCATGCACGAGTATCGACTAGCGGATGTTAACCGATCCGTTAA[A/G]AAATTGAATAGCTTGAGGTTGGACGACTTTGTGCTGTGCAGAATATACAATAAGAAAGGCGGGCTGGAAAGGCATGTGCCCGAA
103716 C G TGAGGTTGGACGACTTTGTGCTGTGCAGAATATACAATAAGAAAGGCGGGCTGGAAAGGCATGTGCCCGAAATCCCAAACCCGACCCGAGGTTTACCGAC[C/G]CACATTAAGCCCGAGCCCATAGCTTTTCCGCACGTGCCGATGGACATGGTGCATTTTGACGCAGCGGATTCGGTGCCGAGGGTG
103756 C T TTCGTGATCAGTGTGAAGTGAATGCTAAGCTGAAGGCTGTAGTCAAGCAACTTCAAGAAGTGCATAGATCAGTTCAGATTGTCAGAGACAAACAAGAACT[C/T]GCTGAAACTCAAGTGGAGCTCACCAAACTACAAGTAGCACCTAAAGAAACCAACTCTCCTACCCAATCGGAAAAAAGTGACATGTC
103756 G A CAAGTAGCACCTAAAGAAACCAACTCTCCTACCCAATCGGAAAAAAGTGACATGTCCTCATTATCAGCAGCTTCTGAACCTAAGCAACCTGAAATTCCCA[G/A]TCCTCAATTAGCTGTAGCTCTTCCTCAGCAAATCATCCACTCAAACGATCAACAGCCACATTACATTGTAAACCAACCTGTTCCATTCTA
103764 T C AGTCTTGTTTCATCTTACAAAAGCATGTTAGGTGTTGTTGCTGGTATGGTCCGATCCTCTTGTTTGATGCGGTGTTTTCTTAAAGTTTCGAGTTCTAGTT[T/C]GCTCATACAATTTTGCGATCAACAAGAAAATGTTAATGATCTGGGTGATGGTGGAGGGATTCCTGTGTTTTCGAAGTTTTCAGTTTCAAA
103764 G A TTCAAATTTCGAGATATTGGCACAGGAGCTTGTTGATATTTTTCGATTAGAGCTGAACTTAAAGCGGTTGCTTGTAATTGAGTTTCTTAATATTAGTTCC[G/A]ACAAAGAAAGCGAACAGTCTACTGCACTTAGTTGGCATCATCAAATTTATCCTGGAGAATTCAATGATTTGAGAAGGTGCGATATGGT
103768 AC A ACACCACCGACTTAGGCGGATGCTTGTCGAGCCATTGCAGACACGATGCGTCCTCTTTCCAGTAACTAGCCGCCGTATTCGACGTTGCCAAGGCATGAAG[AC/A]CGGGCCGTATTTTATAGATGCGGGGGCATATGAAATTCAGATGCGATATGGCAAGCTCTTCGATCGTGTCCACCGTGTTTAGTAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103768 GT G CGACTTAGGCGGATGCTTGTCGAGCCATTGCAGACACGATGCGTCCTCTTTCCAGTAACTAGCCGCCGTATTCGACGTTGCCAAGGCATGAAGACGGGCC[GT/G]TATTTTATAGATGCGGGGGCATATGAAATTCAGATGCGATATGGCAAGCTCTTCGATCGTGTCCACCGTGTTTAGTATCACAGCC
103768 T A TTAGTATCACAGCCTTAGCATGGTTCAGGTATTTGCTGGTGGTCAGCACGTACTGAAGTGCAGGGTCCTCCGTCGACTTGCATCGTTTGATGAGGCTTGG[T/A]AGGTCTCTTCCTCGGAGAAAAGACTGCATCCCCGGCACGCTTTGTATTGCTTTGTCTTCGTCGCTTCCATCTTGGAAGGGGATCTCTT
103768 T C TCACAGCCTTAGCATGGTTCAGGTATTTGCTGGTGGTCAGCACGTACTGAAGTGCAGGGTCCTCCGTCGACTTGCATCGTTTGATGAGGCTTGGTAGGTC[T/C]CTTCCTCGGAGAAAAGACTGCATCCCCGGCACGCTTTGTATTGCTTTGTCTTCGTCGCTTCCATCTTGGAAGGGGATCTCTTTGCTGT
103770 C T CTTTTGGTATCTTCTTCTCCCTTACATGAACCGCAGCTTGTAGAAGAACAGGTACAACACTGTCAGGGAACATTTCTGGTAGAGTGGATACAAGTTCTTG[C/T]GCCTGATCCAGTTTATTTGTATGAAGAAGCAAAAGTGCACGATTACAATATAAAGCCTCCTTCTGCCTACGAGACAATTTAAAATCAGC
103770 G A ATCAGATGCATCTTTTGTGCCCTTCAAGGCAATAAGGTTATTAGTAGCGATTGCAAGGGTTGATGCATCAGCCACCTTACGGTTGATTACACTCATGTAG[G/A]TGTCAATAGCATCTTGAGTGTTCCCCATTAGCTGGTGGACAAATGCCAGTTGGACATTTATTGGTGCTAGATCAGCTTCTATATCATC
103774 G A GAGTGTCGATACCGTTGATCGGGAAAAAGAGGAGAATTTTGCGGACTGATGGCGGAGTGTTCGTCTTCACTAAAGCGTTTGCTGCCGGAGTGATATTGGC[G/A]ACTGGATTCGTTCATATGCTGCATGATGGTGAGTCCGCACTGAGGAACAGCTGTTTGCCGAAATTCCCGTGGAGGAAATTTCCAT
103774 T G CGTTGATCGGGAAAAAGAGGAGAATTTTGCGGACTGATGGCGGAGTGTTCGTCTTCACTAAAGCGTTTGCTGCCGGAGTGATATTGGCGACTGGATTCGT[T/G]CATATGCTGCATGATGGTGAGTCCGCACTGAGGAACAGCTGTTTGCCGAAATTCCCGTGGAGGAAATTTCCATTTTCAGGGTTTAT
103774 G A CTAAAGCGTTTGCTGCCGGAGTGATATTGGCGACTGGATTCGTTCATATGCTGCATGATGGTGAGTCCGCACTGAGGAACAGCTGTTTGCCGAAATTCCC[G/A]TGGAGGAAATTTCCATTTTCAGGGTTTATCGCGATGGTAGCTGCGCTGCTGACGCTGGTTGTGGATTTTGTTGGAACGCAGTTTTA
103774 A G TCGTTCATATGCTGCATGATGGTGAGTCCGCACTGAGGAACAGCTGTTTGCCGAAATTCCCGTGGAGGAAATTTCCATTTTCAGGGTTTATCGCGATGGT[A/G]GCTGCGCTGCTGACGCTGGTTGTGGATTTTGTTGGAACGCAGTTTTATGAGAAGAAGCATAGGCAGGAGGAGATTGGGATCAAAA
103774 C T GACATGGAAGTGATGACGGTCATGGACATGGGCATGGGCATGGGCATATGCACGACGAGGATGGCCATGTTTCATCTCATGTCAGGCACGTTGTTGTTTC[C/T]CAGATACTGGAGCTTGGAATCGTATCACATTCAGTGATAATAGGATTATCATTAGGTGTATCGCAGAGCCCGTGCACCATCAGACC
103776 C G TGATGCATCGCCACATCAGCGCGCTCAATGACTGGAAGGACGAAATCACCACGGTTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAA[C/G]GATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAA
103776 A G AGGACGAAATCACCACGGTTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAG[A/G]GGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAAC
103776 A T ACGAAATCACCACGGTTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGG[A/T]GGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTT
103776 A G CACCACGGTTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGA[A/G]CGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGAC
103776 G A CCACGGTTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAAC[G/A]TACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCG
103776 T G TTTCCGTGCCACATTCGGAATTCGATTTCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCT[T/G]TCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCC
103776 C T TCGCTTTCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTA[C/T]GGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCT
103776 T C TCAGATCGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAG[T/C]ACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGAT
103776 C T CGGCTAACGATCGAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGAC[C/T]GGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGAT
103776 G T GAGCGGAGAAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTC[G/T]CCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCAC
103776 T C AAGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGA[T/C]GAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGG
103776 G A AGTGGAAGATTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGAT[G/A]AAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGG
103776 T G TTTTCTCCGTAAGAGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTT[T/G]TCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGT
103776 C G AGGAGGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGA[C/G]GCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCAT
103776 G T GGAGGAACGTACCTTTCGATGAGCCCGTCCAGATCTGGGTACGGAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCC[G/T]GGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGC
103776 G A GAAGTACGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTC[G/A]GCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTC
103776 C A CGACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCA[C/A]GTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCG
103776 T A ACCGGAGGCGATTCGCCTTCGATGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACG[T/A]ATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGT
103776 G A TGAAGAACTTTTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGA[G/A]GTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGG
103776 G C TTCGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCG[G/C]CGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGC
103776 G A CGTGGACCGGACGCCGGGAGATCTGGAACTCGAGCCCACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGC[G/A]ACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCC
103776 G A CACCTTCTGATCTGGATATCTCGGCCCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACC[G/A]TTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGG
103776 A G CCACGTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACC[A/G]CGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACC
103776 C G GTATTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGA[C/G]GAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACCTGTT
103776 A G TTGAGGAAATGCCAGTAGGAGGTGCCATCGGCGACCGCGTGGTTGAAGCAGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGA[A/G]GGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACCTGTTCGG
103776 C T AGCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAG[C/T]TGGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTG
103776 T A GCAGGCGAGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGC[T/A]GGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGC
103776 C G AGGAAGAGACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGA[C/G]GTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGAT
103776 C T GACCGTTTTCCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTT[C/T]AGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGT
103776 G A CCAGCTCGGTGACCTGAACCACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAA[G/A]ACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGG
103776 C T CACGACGAAGGGTTCGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACG[C/T]TGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTG
103776 G A CGGTGTGCCCATCATGGTTGACCGCGTAGTTTAGAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGC[G/A]TGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCG
103776 G A GAGGAAACAGCTGGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTC[G/A]ATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAG
103776 G A GCTGGTCGACGTACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTAT[G/A]TAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTT
103776 C T TACTTCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGG[C/T]TGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGA
103776 G T TCAGGGCGAAGACCTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGG[G/T]ACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTAC
103776 T A CTGTTCGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTT[T/A]GGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAA
103776 A G CGGTTTTGACGCTGGTGGCTGATGCGTGGATGAACTGTGCGCCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAA[A/G]CGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGA
103776 G A CCTTGGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGA[G/A]GGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAG
103776 C G GGTTGTTGCAGTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGA[C/G]GATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGA
103776 C T GTCGATTGTTATGTAGTGTCCGGCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGT[C/T]GATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGAGGGGAGAGGA
103776 A T GCTGGGACGGCTGTGGTTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTG[A/T]AAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGAGGGGAGAGGAAGCAGAGGTTGAAGGGAGTG
103776 C T TTTGGAAACGACCGGCGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGAT[C/T]TGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGAGGGGAGAGGAAGCAGAGGTTGAAGGGAGTGAGGTGGTGAGTCGTGC
103776 GT G CGAGTGGGTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAG[GT/G]TCCTTTTTGGATGTAGTGAGGGGAGAGGAAGCAGAGGTTGAAGGGAGTGAGGTGGTGAGTCGTGCGAGGGGGATGCGAT
103776 T C GTAGAAGTGGTGCAGGGCGATGGAGAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTT[T/C]TGGATGTAGTGAGGGGAGAGGAAGCAGAGGTTGAAGGGAGTGAGGTGGTGAGTCGTGCGAGGGGGATGCGATGCTGCTTT
103776 G A GAGGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGAGGGGAGAGGAA[G/A]CAGAGGTTGAAGGGAGTGAGGTGGTGAGTCGTGCGAGGGGGATGCGATGCTGCTTTTATCAAGCAGCTGGAAATTACGGTG
103776 A G GGGACGATTTGAGTCGATCGATTACGGTCTGAATTGAAAATGAGGGAGGGATCTGTGAGAAGAGAAGGTCCTTTTTGGATGTAGTGAGGGGAGAGGAAGC[A/G]GAGGTTGAAGGGAGTGAGGTGGTGAGTCGTGCGAGGGGGATGCGATGCTGCTTTTATCAAGCAGCTGGAAATTACGGTGCG
103778 G GA TTAAGCAACAAAACATAAAGCTCTAAATTTCGGCAGTTCACCTACATATTACAGGTATATCCTAGAATCACCTGTATCCTAATTCCTAACCTGTATCACA[G/GA]ATAAAAACTCATCCAAAATCTTAGAAGCCTCTGTTATTTCAGTAGCGATGGCCTTACTATTGCCAACAACTTTAGATGCAGTAGCTGAA
103778 T TAA TTTGCAGTACGGCGTGCGAGTACTCTTTGCAGCATGTTCATCTTCTCATTTTGAGATAAAAGAGCGGGTTTCTCTTGCTTTTGTTGATTGCACTTATCAG[T/TAA]AAGAAAGAAATTGCAGGCCATTTGGCATATGTGTTGGTATCTTTGGAACATTTACTGTAATGGGCTTCTGAGCAATTATAGACTGAC
103784 A G CAAAATCATAACAGATGAAGCATTATTTTCAATATCAAAGTATTGTAAAAAGCTTGAATGCCTCCGTTTAGAGTCTTGCAATCTACTTTCGGAGAAAGGC[A/G]TCAGTCAAATTTTCACATCTTGTGCCGAACTCAAAGAAATCGATCTCACTGATTGCAACATAAACGATTCTGCATTTGGATCCTTGTGT
103784 C T GTTTAGAGTCTTGCAATCTACTTTCGGAGAAAGGCATCAGTCAAATTTTCACATCTTGTGCCGAACTCAAAGAAATCGATCTCACTGATTGCAACATAAA[C/T]GATTCTGCATTTGGATCCTTGTGTAAAAGCTCCAAGATTAGAATATTGAAGTTGGGCCTTTGTTCCAGCATCACAGATAATGGGCTTGC
103796 TG T ACTGCATTTAAGCATAGCCTTTAATCTCTGCTTGCTGTCCTTATCCCAAAAATTAAATGCACCATCAGAGCCTGCAGTCGTAAAAGTATGATGTACAGGG[TG/T]GGAAGTTCAATGAGTTCACTGAATATATATCATTATTTTCTCTGTGGCATTTGAATGTGAAATTTTTGGAACTTTGTGCTTCGTCTATA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103800 C A TGATGTCCATCATCTGGATTCCATCTTGCAAATGACTCATCAATAGAAGATCACGTGCAATAGAAAATTCATCTGATATCGCATGATGGTAAATATCACA[C/A]AGCATTGCTCTAGCTTTAGTTCTCTCATCTCCAAACTTATAAATGAGAGAAACTAATGTATCCATAAGGGTTCTACTATTTTCAGGAAAT
103800 T C ACACAAGCTCGACTCTTCTCAATGCGACCTTTGCAGCTCCTTTAGAATCCCCTATCCTTTCCAGATAGTTCTGTATATTTTGAGCGACAACAAAGAACAA[T/C]GGTTCATCTCTAAGCCTCTGAACATAATCTTTAGTATGGGGATCAATGCACTGTAAGCTCTTGAAATATTCAATATCAAGCCTTTCAATG
103800 C T CATAATCTTTAGTATGGGGATCAATGCACTGTAAGCTCTTGAAATATTCAATATCAAGCCTTTCAATGAAGTGGACCAAGTTTCCCCAAACTTTAATTGG[C/T]CCCTTGTAATCCACACCCTTCTGTGTTTCATTCTCGTCATGCTCGATAGAATCATCAATAATGATATTTGGATACTTCTCGAGTATATCAA
103806
TTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTCGGTTTGCA
T TGGTTTCGCTTCCAGACCAAATTCTACTTCCTCTACTTCTTTTACTTCGCTTTTCTCTTTTGGTGCTTCTTTTTCCTCTTCTACTTCTGCTTCGGTTTGC[T/TTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTCGGTTTGCA]TCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTGCTCTTTTGGTGGTCCTTCTTT
103806 C T GTGCTTCTTTTTCCTCTTCTACTTCTGCTTCGGTTTGCTTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTGCTCTTTTGGTGGTCCTTCTTTTACTTC[C/T]ACTTCAGTTTGCTCCTTTGGTGCTTCTTTTATTTCTACTTCAATTTTCTCTTCTGGCGCTTCTTTTGCTTTTGCGTCAGTTTGCTCCTCTGGTGCTG
103806 T C CTTCTTTTTCCTCTTCTACTTCTGCTTCGGTTTGCTTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTGCTCTTTTGGTGGTCCTTCTTTTACTTCCAC[T/C]TCAGTTTGCTCCTTTGGTGCTTCTTTTATTTCTACTTCAATTTTCTCTTCTGGCGCTTCTTTTGCTTTTGCGTCAGTTTGCTCCTCTGGTGCTGCCT
103806 G C TTTTTCCTCTTCTACTTCTGCTTCGGTTTGCTTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTGCTCTTTTGGTGGTCCTTCTTTTACTTCCACTTCA[G/C]TTTGCTCCTTTGGTGCTTCTTTTATTTCTACTTCAATTTTCTCTTCTGGCGCTTCTTTTGCTTTTGCGTCAGTTTGCTCCTCTGGTGCTGCCTTTGC
103806 T G CTACTTCTGCTTCGGTTTGCTTCTTTGGTGCTTCTTTTACTTCTACTTCTGCTTGCTCTTTTGGTGGTCCTTCTTTTACTTCCACTTCAGTTTGCTCCTT[T/G]GGTGCTTCTTTTATTTCTACTTCAATTTTCTCTTCTGGCGCTTCTTTTGCTTTTGCGTCAGTTTGCTCCTCTGGTGCTGCCTTTGCTTCTGCTGCC
103806 CT C TCTTTTGCTTTTGCGTCAGTTTGCTCCTCTGGTGCTGCCTTTGCTTCTGCTGCCTCTTCTTCTGCCTTTTCTGCTTCTATATTTTCCCTTGTCTCATCTA[CT/C]TTTTTTCTTGTCAGCGATCGAGACATCTTCAGTCGGAGCAACCTTTTCATTCTCGCTTTGATTTTCATCTGATTTTGCAGACTCCTCCGTGATT
103814 C A TCTGGATTTTCCGAGGTGATCACTGTCGTTGCAGGATTCACCGCTGATTTTATTGCATCAAGAAT[C/A]GTAGTTCCAACGGTGATTTTTCCGCTTGCACCATGCCATTCAATAGTCCATCCACCGCACTGAAAACCCAAGTTATCAGCATGAGTTCCTGCTACAAGAA
103814 G A TCTGGATTTTCCGAGGTGATCACTGTCGTTGCAGGATTCACCGCTGATTTTATTGCATCAAGAATCGTAGTTCCAACGGTGATTTTTCC[G/A]CTTGCACCATGCCATTCAATAGTCCATCCACCGCACTGAAAACCCAAGTTATCAGCATGAGTTCCTGCTACAAGAATCTTAGAAGCTTTCTTCGAAAGTG
103814 T C GATTTTCCGAGGTGATCACTGTCGTTGCAGGATTCACCGCTGATTTTATTGCATCAAGAATCGTAGTTCCAACGGTGATTTTTCCGCTTGCACCATGCCA[T/C]TCAATAGTCCATCCACCGCACTGAAAACCCAAGTTATCAGCATGAGTTCCTGCTACAAGAATCTTAGAAGCTTTCTTCGAAAGTGGAAG
103814 G A TCACCGCTGATTTTATTGCATCAAGAATCGTAGTTCCAACGGTGATTTTTCCGCTTGCACCATGCCATTCAATAGTCCATCCACCGCACTGAAAACCCAA[G/A]TTATCAGCATGAGTTCCTGCTACAAGAATCTTAGAAGCTTTCTTCGAAAGTGGAAGCATCGGTTTTTGGCTTGATTTTCCATTTTTCAAT
103814 A G CTGATTTTATTGCATCAAGAATCGTAGTTCCAACGGTGATTTTTCCGCTTGCACCATGCCATTCAATAGTCCATCCACCGCACTGAAAACCCAAGTTATC[A/G]GCATGAGTTCCTGCTACAAGAATCTTAGAAGCTTTCTTCGAAAGTGGAAGCATCGGTTTTTGGCTTGATTTTCCATTTTTCAATAGCACA
103814 G A AGAATCTTAGAAGCTTTCTTCGAAAGTGGAAGCATCGGTTTTTGGCTTGATTTTCCATTTTTCAATAGCACAAGTGACTTTCTCACTGCTTCTCTTGCCA[G/A]ATCCCTGTGTTCCTGTTTACCGAGTTCCTTAGCTAGGCTTGAATCGGCAAGCGGGTTCTCGAAAAGACCCATAACAAATTTAATACGAAG
103814 A G TAATACGAAGAATTCGTTTTACTGCATCATCGATTCTGCTCATAGGGATTGCTTTGCTCTTCACCAGAGCAGTCAGACCATTGATGAATGTAGGGAAGTC[A/G]TTAGGTACCATTATCATATCAATCCCTGCATTAACCCCAGTGAGAATAGAATATGTGTAATTTGCACCTGGTGGACTGGTTAGTTTATC
103814 T C CTTAAGAGTGTTTTTTAGGAACCCAGTAATGAGATTGCGATTAGCATGCATTTTCACTCCATTCCAACTAGAGTAGGAAACCATGACAGTGGAAACACCC[T/C]TCGCCACAGAGTTGCGATAAGCTGGCATATGAATCTTGAAAAGTCCTTGTTGGCCTATAATTGTATTGTTCTCATTGATGCCCTCATAA
103814 A G TGTTTTTTAGGAACCCAGTAATGAGATTGCGATTAGCATGCATTTTCACTCCATTCCAACTAGAGTAGGAAACCATGACAGTGGAAACACCCTTCGCCAC[A/G]GAGTTGCGATAAGCTGGCATATGAATCTTGAAAAGTCCTTGTTGGCCTATAATTGTATTGTTCTCATTGATGCCCTCATAAGTTCCTCC
103816 A G AATCCAAAATAGAACTCAGATTGCGTCTTTGCCCACCAGATCTAAACTTTATAACCTTACCTTATCACTGAAGAGCCCCACTGATTCAACACGTCAAAGT[A/G]GAAAAACTGCCACAAACTATCTACCGAGCAGTGGAAAGTTTGGTGAAGAAGGACTGGCGCTTGTTATCCAATGGATCTGCCGACGCT
103824 A G CCTCATCGCTCTTATTGTAAAACTTTCTCTCTCCACCACCACCATCACCTCCTCTTCTCCTTACATGCTTACTAACAGGCCTCTCCCTCTTGCCCAACTG[A/G]TTCCTATTGCACTCATAGGATAAATGCCCTTCTTCCCCGCATTCATAGCACCTGCTCTTATCCTTATATATCCTCTTCTTTATAAATTCAGTCG
103828 G A TGTGGAGTCTGCCAGTTATAGATACTAGAATTGTTGTGGTTCACTTGGTTGTAGTCGTTGATCGTCGATGCCCTTCTTTCCAGAGAGGAGGAAGACCCGT[G/A]CGGGTTCGATTTTTGTGTTTTGTTGTGTGATGATTTCGAATTGCTTTTGCCATTGTTGGTCGGTTTCGCATTGTGCTTCTTCTCTGATG
103828 C A GTGGAGTCTGCCAGTTATAGATACTAGAATTGTTGTGGTTCACTTGGTTGTAGTCGTTGATCGTCGATGCCCTTCTTTCCAGAGAGGAGGAAGACCCGTG[C/A]GGGTTCGATTTTTGTGTTTTGTTGTGTGATGATTTCGAATTGCTTTTGCCATTGTTGGTCGGTTTCGCATTGTGCTTCTTCTCTGATGC
103828 A G ATATTGGTCCAGTCCACAAATGTTGCAGCATGTCTCTAGCCTGAAGCCTTCCAAATTCCACATCAGCGTATTTGTAATTCCACACAAGTGATGTCTCGCG[A/G]TGCTCAAAATGAGACCTTGGTGTCCTCTCGGTGAAGTACTCGAATACATGCTTAACACTGTCAACCCAGTCCATGTTTAGATGTTCTGG
103832 G A AATCCTGAAGACAAACTGAGCAGCAATCGATCTTATTCTCTGTTGAAATTTTAATATTTCCAAGTTTGTTAACAGAATCCTTGGACAAGCCACCGCTGCC[G/A]CCTGTCTCGAAAATATCAAGGACTTCGATGAATGAAGTGTCATTCACGGCACTCATCTGACTCTGCACTGCACTTTGAACTGCAGGCCC
103842 A G TGAGCATGCAGAGAATTCCATGGGGACATAACGAAATTGGAAATTCCAGCGGAGGAAAAAAGCAGCCTGTATTGCTGCAACATGGAGTCCTGATGGATGG[A/G]ATGACATGGCTACTAAACTCTCCAAAAGAGTCCCTCGCCTTCATCTTGGCAGATATGGGATATGATGTGTGGATTGCCAACATCA
103842 C T CTCTCGATCCTTCATCATCTGCTTACTGGAACTGGTCATGGGACGAGCTTGTAGCATATGAACTCCCTGCCATTGTAGATTTTGTACACCAGCAGACTGG[C/T]CAGAAAATGCATTATGTTGGACACTCTTTGGGTACGCTGATTGCGCTTGCATCTTTTTCTGAGGAAAGATTGGTAAATAATCTAAAATC
103842 C T TCACATCATTTACAGGAAACAACTGCTGCCTGAATGCATCAACCGTCGAGCTATTTCTGAGATATGAACCTCAACCCACATCGACAAGAAACATGGTTCA[C/T]CTTGCTCAAACATTCAGAGATGGAGTACTGACCAAATACAATTACGAGAGCAAAGTGGCCAACATCGAAAG
103856 T A ATGCAATCGATAAAGTTGGTCCAGATGGTGTCCTTTCAATTGAATCTTCATCGTCATTTGAAACAACTGTTGATGTTGAGGAAGGAATGGAGATTGATCG[T/A]GGCTACATATCTCCCCAATTTGTTACCAACCTTGAAAAGCTGATTGTCGAGTTTGAGAACGTCAAGGTTTTAGTTACTGATCAGAAGA
103856 C T GTGTCCTTTCAATTGAATCTTCATCGTCATTTGAAACAACTGTTGATGTTGAGGAAGGAATGGAGATTGATCGTGGCTACATATCTCCCCAATTTGTTAC[C/T]AACCTTGAAAAGCTGATTGTCGAGTTTGAGAACGTCAAGGTTTTAGTTACTGATCAGAAGATTTCATCGATAAAGGAAATTATTCCTTT
103858 T G CCTCCTCCCTGTCCCCAACCACACGCCTCATCAAACCCTTCAAGCACTCGATGCATGGCTCCGCCCATAAATGCCCCTTAAACGGCCCTTCACCGACCTC[T/G]ACCATCCTCTCGACTTCCAAAGGGTACCCGTTCCCCTCATTCAGATACTCGGTGATGCCCGACCAGTTGGTAGCGATCACTGGCAACCC
103862 CA C TTGGCCTACTGGACAACGAACCATTGTAGTTCCCACTTATTTATTATGCTTGTATAAATTATGCAGTTTCTACCATTCGCGAAATAAATTCATACATTGG[CA/C]AAAAAAATATTAGGGGAAAGCAATGGCAATGGCTTCGGCTTTGCGCAGACTGTCATCTTCTGTTTCGAAGAACAAAACACCCCCTTCT
103862 T C TTATTCCTTCAGAGAATTTCACATCAGTATCGGTCATGCAAGCAGTTGGATCTATCATGACAAACAAATACAGCGAAGGGTATCCAGGTGCTAGATACTA[T/C]GGTGGAAACGAATATATTGACATGGCAGAAACCCTGTGCCAAAAGCGTGCACTTGAAGCTTTCCGTTTGGATCCTGCTAAGTGGGGA
103862 G A GATTGAACGAGACTACTGGGTATATTGATTATGACCAGTTGGAGAAAAGTGCAACTCTCTTCAGACCAAAACTCATAGTTGCTGGAGCTAGTGCATATGC[G/A]CGTCTCTATGACTATGCACGCATACGGAAGATTTGTGACAAGCAAAAATCAATTCTTCTAGCGGACATGGCACATATCAGTGGATTG
103868 CA C CAGGCAGCATTAGATTTTCTAGCCAGTAGGGATGAGATCGACAGATCTAGAATAGTTGTATTTGGTAGATCATTGGGAGGTGCTGTTGGGTCGGTACTAG[CA/C]AAAAAACAATCCGGATAAGGTTTCTGCTTTGATATTGGAAAACACATTCACCTCTATATTAGACATGGCTGGCGTCATGCTACCAT
103878 T G CATGCGGCCCCTACCGCCCCCACAAGCAGGGCAGTACCCTCCGCCTCAAATGCATATGGCATGGCCACCTCAGCCACCCAGTCAGCAGTACCCCCCTCCA[T/G]CTTCCATGCCGCCGCCCCCTCAGCAGTTCAGGCCCATGCCTCCGCCGCCTAACATGCCTCCCCCGCCTCCTCCCAATATGATGCGGGG
103886 GA G GAAAATACAACCGTATAAAGTACAACCACAAATACAATGAACACAAAGAGTACTTAACCACTTAACCATCTCACGTTCATAACACAATTATTCGTAAAAG[GA/G]AAAACAAAAGCTTAAGATAAATTAAAGAGCAAATCTACAGGTCCTTCTTCTTGGCATCCTTGAGCTGCCCCTTTTTGCGGATACCAA
103886 T C GGAGAAGGGAGAGCAGGCACCAAACAGCAGAGTGTGGCCAGTACGGAGTGCATCTGGGTTCATAGCCTATCCATCTTAAGGCGGCTTTGGCGTAGGTGTC[T/C]GATGATGGTACCATGAATGAAGACCTTCTGATTGATGCCATTTTTGTTGCTACATACAAGGGCACCTGGCACTGAACATCTATTC
103886 C T CAGCATGCGTAACCCTAGTAACTCCCTCCACATTTACCTTAATCAAATTCCTCAACAGCTCATCGTCGACTTCGTGAAAATATCGTGCATACGGATACGA[C/T]ACGCCCGCGTTATTGACCAAAACACCCACATCTTTTCCCTTGATAGCATCCTTAATCCTTTCGACACCTTCCACCAAATCGCCTGAAAAG
103886 C T CTTTTCCCTTGATAGCATCCTTAATCCTTTCGACACCTTCCACCAAATCGCCTGAAAAGTCCACAACTACAGTCTCGACTTTAATCCCGCTGTTCTTAGA[C/T]AAAATACTCGACGAAACGTCTTTCAACTTTTCCGGGTTTCTTCCTACTAAAATGAGGTTTAGACCCTTTCTGGCAAACTGGAAAGCAAACG
103888 T C TGAAGTCGGCTAATAAAGAGCTTAAGGGTATGATGAAGACTGTAAAAATACAAGATATCGATAGCATGCAAGATGAAATGATGGATCTTATGGATGTAAG[T/C]ACGGAGATTCAAGAATCTCTTGGTAGAAGCTACAACATTCCTGATGACATCGATGAAGAAGATCTAATGGGTGAACTCGATGCTC
103888 T A CGGACCTTGATGCAGAGCTGAATTTGCCTGCAGCACCTTCAGGAAATGCCATTCCAAACAGGCCTAATGCCCAGGCTGAGGATGAGTTTGGTTTGCCTGC[T/A]GTGCCCAGAGCTTCCTTGCGTGGTTAGAAGTAATATAATTGGTCATGTTCATATATTAAATTCTTTGATCTTGATAGCTAAACTTAAT
103894 C T CCTCCTAAGCCCAACAAACCTCCGACTATACCAGCAAAAACACCGGATATGCAGTATAATACTAACTGATGAATTGTTAAC[C/T]GAGTTTCTGCATCTCCTTTGGAAGCTATGGCACTTTTGCCTGTGTATAAATTTACTGCTTCATACGAGCTTACCCCTACAGCAACTGGAATCTGAAGCAG
103894 T C AAAAACAACCCATACAAAGACGAGAAGACCGAGTTCTTTCCAACAAACATTCTCAAGAATTGGGACCTCTGTTCTCAAGTTTGACTTGACATCTTTGTGA[T/C]TTTCAGGTCCAGCAGGTATAGCTGTGTATTCTATTTCATCACTATTATCTTTTTCTTTAGCAGACTCCTTCAAAGTTATGGTCTCTTTCTT
103894 C T CAGCAGGTATAGCTGTGTATTCTATTTCATCACTATTATCTTTTTCTTTAGCAGACTCCTTCAAAGTTATGGTCTCTTTCTTCCATGTATCAACCCCTTT[C/T]AGAAAGGCTTTCGTTGATGTAAATATGAAGATTATTATTAGCAAAACTGTTACCAGCCAGTCAGGGAATACTACATTGAAGACGACTCCAA
103894 A G CTTTCTTCCATGTATCAACCCCTTTCAGAAAGGCTTTCGTTGATGTAAATATGAAGATTATTATTAGCAAAACTGTTACCAGCCAGTCAGGGAATACTAC[A/G]TTGAAGACGACTCCAATGCTAATTCCGAGCACAAGCATTGGTTGAATCAGAAGAGCCAAGTTGTAGTCGATGATTGGCATATCCAAAG
103894 A T AGTCGATGATTGGCATATCCAAAGTAGGATGTCTAAGCTTAAGATTGTAGTAAACGGTTGAGCCTGCAGCGCCCGTTATCATGCATTTGGACATAGCAGT[A/T]GACGACTTCGGATCAAAGCCAATAATCAAAGCAAGCATTGGAACAAAAATGCCACCACCGCCAACTCCGCCTACACTTCCAAATGCC
103894 C T TGATTGGCATATCCAAAGTAGGATGTCTAAGCTTAAGATTGTAGTAAACGGTTGAGCCTGCAGCGCCCGTTATCATGCATTTGGACATAGCAGTAGACGA[C/T]TTCGGATCAAAGCCAATAATCAAAGCAAGCATTGGAACAAAAATGCCACCACCGCCAACTCCGCCTACACTTCCAAATGCCGCCCCC
103894 T G CCGTTATCATGCATTTGGACATAGCAGTAGACGACTTCGGATCAAAGCCAATAATCAAAGCAAGCATTGGAACAAAAATGCCACCACCGCCAACTCCGCC[T/G]ACACTTCCAAATGCCGCCCCCAAAAATGCAATAACCGTTCCCACTATTATTCTCCATCCGAACTCCATATCCGGCCAAACATGCTGAT
103908 T A GAACAACACAAACTCAACTCCCAGTCAGAAAACAACGCCACATTGCTCATTCCGTCAACCCCCGGTCCCACCACGGAGCCTCCACTCGAAAACAAATCCA[T/A]CCACGACGATCACTACAGAATTTTCGGCGAACATCCCATGCATGAACCACTGACTCCAGACTCCTTTAGCCCAGAGAACGAGGGCAC
103908 T C ACGAGGGCACAAACAAAAGAAAGAGAAGCCACGAAGATTTGGGCGATAGCACGAATCAAGAAGATCCGATGCTTGGCCATCACATTCTCGAATCGGGTAC[T/C]GGCCCTGGATTTCAGGACCCGGGTCTTACTGACTGGTGGGGCCCGATTTGAGTTGCCCTGAATTAGATGCCTCCTGTTGATACTG
103908 C T TACTGGCCCTGGATTTCAGGACCCGGGTCTTACTGACTGGTGGGGCCCGATTTGAGTTGCCCTGAATTAGATGCCTCCTGTTGATACTGTCTGAAGACAC[C/T]GGGCTATATTGGGAATGCTACCCCTGAAGCTGCATTATACACAAATTGTTGGCATAGTTGAGCATAAGAAAATGGTTGACAAATTCG
103912 A G TTGTAAAGGAAAACACAGCATTGAAGGAACAAGTGGCAAAATTACTCCAAGAAGGTGAAATTTGGAAGAGAGCCTTCAAGACTCTACATGGGCAAAAAGA[A/G]GACTTTGAGCGGAGCATCCAAGAATTGCATCAGTTGAGAATGGAGATGTCTCAACGCGATGAGCAGATGAGAAAGCTCCAGGTG
103912 T C GGAACAAGTGGCAAAATTACTCCAAGAAGGTGAAATTTGGAAGAGAGCCTTCAAGACTCTACATGGGCAAAAAGAAGACTTTGAGCGGAGCATCCAAGAA[T/C]TGCATCAGTTGAGAATGGAGATGTCTCAACGCGATGAGCAGATGAGAAAGCTCCAGGTGGAGAACTATCAGTTGAAACTTCGCC
103912 C T AAATTTGGAAGAGAGCCTTCAAGACTCTACATGGGCAAAAAGAAGACTTTGAGCGGAGCATCCAAGAATTGCATCAGTTGAGAATGGAGATGTCTCAACG[C/T]GATGAGCAGATGAGAAAGCTCCAGGTGGAGAACTATCAGTTGAAACTTCGCCTTGTGCAAGAACAGCAACACAACCCCCTGCCTG
103912 G T GGAGAACTATCAGTTGAAACTTCGCCTTGTGCAAGAACAGCAACACAACCCCCTGCCTGGAAGGTTCCATCCTGATATATTTGGGTGATTGCAAATCAAC[G/T]ATATAAATACTTGGGTCTTGTTATGATTCCTATTGTCAGTCCATATGTGATCGTCTATTGAGCCAATCTCCCAGTCAAATTGATTTTTG
103916 G A GATAACATGATTAAGGAACTGAGATTAAAGAAGCAGGAGTTGGCTTCAATAATTAATGAATCTGCAGATGATATATTGAAATCAGTGACAGCTTCTACCA[G/A]AAGTAGCATCGGTGTCTCGGGAAAATGTGATGTGGAATCAATAGACGAGTCAGATAAAACTGATAGAAAAAAGATTTTAATCTCAG
103916 A G AGTTGGCTTCAATAATTAATGAATCTGCAGATGATATATTGAAATCAGTGACAGCTTCTACCAGAAGTAGCATCGGTGTCTCGGGAAAATGTGATGTGGA[A/G]TCAATAGACGAGTCAGATAAAACTGATAGAAAAAAGATTTTAATCTCAGTCCAGGACAAGGATGGACAAAAGCAGTTTCGTATGTA
103918 C T TCTTCTTCTTCTTCTAGCGATGAAGATGAAACCGCATCAGTAGTGGTTCCTGTGACTCCTAGCTTAGTTGTCCCACGCTCGCAAAGGGCAAGCAAGACAG[C/T]GGCACTGACCAAAATGACAGCCAAAATTTCTACACTTGAGTTATCCGACATTGAAGTTGAAGAAGAATCCGATGTCCCCTCCGATGA
103928 C T TACAAATTCCCTCAAATACCCCCATCCTAATTGATGCATACACTTTTCCATCCCAGTTCCTCTTCAGAAAACCCTCTGCCATCTCCAACGCTGCACTGAT[C/T]ACTTCCTCTCTAGTCCCTTTTACACCATCCACCACTCCTTTCTCAAAGGCTTCTGCTGCTTTTACTTTCCTTCCTTTCATCACTATATCCTTTAA
103928 T C GCACTGATCACTTCCTCTCTAGTCCCTTTTACACCATCCACCACTCCTTTCTCAAAGGCTTCTGCTGCTTTTACTTTCCTTCCTTTCATCACTATATCCT[T/C]TAACAACCCTAAATGTTTTATCTTAGCTCCCATGATTTCAATGAAGTAGGGAGGGAACGGCAACTTCATGTCCATCTCCGACATATAAATGA
103928 G A TGACGGCGGCGATGGTTGGCATGGGCAGAGAATATAGATCCGCGACCAGAGGAACGAAAGCGGCAACCATGGAGTGAAGCCGGGCGGCGCGTTCAGGAGA[G/A]GTGGCGGCAGCGGACGCGTAAGCGACGTCGAAGCCGTTGGAGAAGAAATTGCCGTCTGCGCATGTTACGAGAACGTTAGAA
103928 C T TGTTACGAGAACGTTAGAAGAAGACGCTTGAGATCGGATTAGGGCAAGGTTTTGACGGAGGGAGGAGATGAGCGAAGGGGAGAGGCGGTGGTCTGTGGGG[C/T]CGGTAAGGGTTAGGATGAAGATATTGCCGCGCTTTTCGAGGGAACACATACTTTAGGGTTATCTGATTTCGATGAAAACGAG
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
103932 A G TGACTTCCGATGGATTTAGTGATAAAAATGCCGTTTTTAAGAAGCTCAGATCTCGGTCGGAGAACAAGATGTGCTTCGATTGTAATGCGAGAAATCCGAC[A/G]TGGGCGTCGGTGACTTATGGAATCTTCTTATGCATTGATTGCTCAGCTGTTCATCGGAGTTTGGGTGTTCATGTTAGTTTCGTCAGG
103932 G A CTTGGTGTTCGAAAGCTCACAACGAAGCCTAGTGAGAGCCTTTATGACCAGAAGCCTGAAGAGCCAGCACCCGTAGCTGCTTCTTTGACCAGCAGTATCA[G/A]TTCGACAAAAGGACCATCTTATCCTTCTCGATTCGAGTATGTGGAGAATGCACCAAGTAGTGATACTAATTCTGGACACGTAGCAG
103944 T C ATCGCTCAGGGCATGTATTTTGTGTCCTTGCTACTAATTTGGTAGTGATGTTTGTGGATCTCGTTTCCTGTTAGGTGCTGTTGTGTTTGGTCCAAAATGG[T/C]GTATTGGATCATGGTTAATTGGCTTTCTCTGATCGGCAATACATGGAAGCTTTGCTCAAACCCTTGTTTTTCAGTCGAAGCTATACTCAA
103948 C T CCAACTCCAATAGGATTATGTAAATTATACAACAATGGAAGCATGCAAACTAATATGACACATATATAGAAAACACGTACAATTGAATAGATTCAGATTG[C/T]TTACTTCATCATCCTCTTCCTTGCCTACCATACCCACTAGCAGCAGGTGAATTGCCAAAACTACCCTTTGCGCCGGGCACGTTCATCTG
103948 A G ATCCATAACCGCCCGCACTGTTTCCCATATTCACAACATTGCCACCACCACTGTTTGCATTATTATTGTTGCTACTCCCAGTTCCACCTTCTTTATTGCT[A/G]TTCACAGACCCTTCCTTTTCCCCTTCCATTTCCCTGAACTTCTGCAAGTACACCTTCAAAGGCTCCACGTACTCCTCGAATCCGAGGGTCGT
ATTAGGTTTGGGGTGCAAAAATTCTGTGGAATTAGGTTTGGGGTGC,GAAAAATTCTGTGGAATTAGGTTTGGGGTGC
103972 G CAACCATCTGAATGAGCGGTTGATCTTCACCATAATCATTGTCATTTTCTACCTGATTCCTATCATTGCTTGATTCCTCCATTTGTGCCATTGGGACTTC[G/GAAAAATTCTGTGGAATTAGGTTTGGGGTGCAAAAATTCTGTGGAATTAGGTTTGGGGTGC,GAAAAATTCTGTGGAATTAGGTTTGGGGT
103974 A C AGATCGAGAGGATAATTGAAGAGAGGTACGGCAAAAAGATTAGTGATGGCTTGAGGGGAAGATCCAAAATTGGGAGAAGTCATGGTGCTAGAAGTCCTTC[A/C]CGAACAAGGAGGAGGAAATATTTTGATTATGATTCTGATTCCAACTCTGATCATAAATCAAAAAGGCATAGAAGGAGGGATATT
103978 G T TCTCATTCGATCTTCTTCGATTCTCTCAGATCTAGAAGCTTCGATCTCGATTTTAAGCTCGCTGATGATCCTAAGCTG[G/T]CATTGAAGAGATACGATCAGTATTTGTATGACGCGCTCATTGTCTTCTCGCCTTCTGTCAACAAGTTTGGAGGATCTGTAAATCAGGCGGAGATCCTTGA
103978 A G TCGCTGATGATCCTAAGCTGGCATTGAAGAGATACGATCAGTATTTGTATGACGCGCTCATTGTCTTCTCGCCTTCTGTCAACAAGTTTGGAGGATCTGT[A/G]AATCAGGCGGAGATCCTTGATTTCGTGGATTCTGGTCGAGATTTGATTTTGGCAGCGGATTCTTCTGCTTCGGATTTGATTAAGGGGA
103978 G A CTTCTGTCAACAAGTTTGGAGGATCTGTAAATCAGGCGGAGATCCTTGATTTCGTGGATTCTGGTCGAGATTTGATTTTGGCAGCGGATTCTTCTGCTTC[G/A]GATTTGATTAAGGGGATTGCGGCAGAATGTGGTGTTGATTTTGATGAGGATTCAGAAGCAGTGGTGATTGATCACATTGGCTATTCA
103980 G A ATCTCAAAAAGGAAAGAATGAAACTTTGGCTTCAAGACCCGCCCTTTCGGACATAACTAACGATTCACCCATCACCGGTGTAGCAAAGGAAGATTCCATC[G/A]TCAAAACGCCAAACCGGGCACAGGCTTGCAAAAACACACCCGGATCCGGAGAGTCACTGCTCAGAGGACAAGTCAAGAGTTTGCTT
103980 T G TAGACCTACCTGCTCCATCTCCTGTCCAAATGATGGCGCCTACTCCTGCAAATACACCTCAGGTTATTCAGATCCTCGAACCCGTTAAGCCGGAAGAAAC[T/G]TTTATCATTCAAGAAGATGAATCTGCACTCAGCAGAACTTTACTTTTCGATTCGCCCGATTCAGAAAATACTGAAAACACTTCTTCGAT
103980 G A AGCCGGAAGAAACTTTTATCATTCAAGAAGATGAATCTGCACTCAGCAGAACTTTACTTTTCGATTCGCCCGATTCAGAAAATACTGAAAACACTTCTTC[G/A]ATTTCATCGTCGCTGTCATATCAGGGTAGTGGAATGTGTAGTGTTAAGAAATGTGTGGATGAGGATAGCTCTTCTGCGTGGTCTCTTC
103980 G A AAACTTTTATCATTCAAGAAGATGAATCTGCACTCAGCAGAACTTTACTTTTCGATTCGCCCGATTCAGAAAATACTGAAAACACTTCTTCGATTTCATC[G/A]TCGCTGTCATATCAGGGTAGTGGAATGTGTAGTGTTAAGAAATGTGTGGATGAGGATAGCTCTTCTGCGTGGTCTCTTCAGGTTAATGT
103980 G A CTGCACTCAGCAGAACTTTACTTTTCGATTCGCCCGATTCAGAAAATACTGAAAACACTTCTTCGATTTCATCGTCGCTGTCATATCAGGGTAGTGGAAT[G/A]TGTAGTGTTAAGAAATGTGTGGATGAGGATAGCTCTTCTGCGTGGTCTCTTCAGGTTAATGTGAGCTTGGAGGACGAAGATGAAGAG
103980 C T TGGATGAGGATAGCTCTTCTGCGTGGTCTCTTCAGGTTAATGTGAGCTTGGAGGACGAAGATGAAGAGGAAGCAATTACTGATTTCGAGGAGGAAGAGTA[C/T]GATGATTTATGTGATGGGATAAGCAGGATTAGCATGCATGAAGAGATCAAGGTTGAGTTGCCTGAGTTTGAAGGGAGGCATACC
103980 G T TATGTGATGGGATAAGCAGGATTAGCATGCATGAAGAGATCAAGGTTGAGTTGCCTGAGTTTGAAGGGAGGCATACCAGATTTTTGTATGACAGCGATGA[G/T]GAAGAGATTAAAGGGGAAGAATTGGTTGTTCATGACAGGGTCGTGTCGCCAAAAGCAGTTGTTTTGAAAGGGTTGCCTGTGCCT
103980 A G TTAGCATGCATGAAGAGATCAAGGTTGAGTTGCCTGAGTTTGAAGGGAGGCATACCAGATTTTTGTATGACAGCGATGAGGAAGAGATTAAAGGGGAAGA[A/G]TTGGTTGTTCATGACAGGGTCGTGTCGCCAAAAGCAGTTGTTTTGAAAGGGTTGCCTGTGCCTCAAGGGAAGCATATAAGGTTC
103980 T C GTTGAGTTGCCTGAGTTTGAAGGGAGGCATACCAGATTTTTGTATGACAGCGATGAGGAAGAGATTAAAGGGGAAGAATTGGTTGTTCATGACAGGGTCG[T/C]GTCGCCAAAAGCAGTTGTTTTGAAAGGGTTGCCTGTGCCTCAAGGGAAGCATATAAGGTTCCATGAAGAAGAGGAAGATGAAG
103980 T A TTAAAGGGGAAGAATTGGTTGTTCATGACAGGGTCGTGTCGCCAAAAGCAGTTGTTTTGAAAGGGTTGCCTGTGCCTCAAGGGAAGCATATAAGGTTCCA[T/A]GAAGAAGAGGAAGATGAAGATTGCTGAGGAGGATTGGTTTGGTTTCTGTTTCTCTTGTGTTGTTGTCTTGCTT
103982 A G CGAACCTAAAAGTGGTGGACAACTCAGGGGCGAAAAGAGTGATGTGCATTCAGGCACTGAAAGGAAGAAAAGGAGCAAGATTAGGGGACACGATCATCGC[A/G]TCGGTGAAAGAAGCACAGCCGAGAGGCAAAGTGAAGAAAGGGGAGGTGGTGTACGGGGTAGTCGTTCGTGCAGCAATGCAG
103982 C T ACACGATCATCGCATCGGTGAAAGAAGCACAGCCGAGAGGCAAAGTGAAGAAAGGGGAGGTGGTGTACGGGGTAGTCGTTCGTGCAGCAATGCAGAAAGG[C/T]AGATGCGATGGAAGCGAGATCAAGTTTGATGACAATGCGGTTGTTCTGGTTAACAAGCAAGGTGAACCCATTGGGACTCGTG
103986 AT A TTAAAGTTGAGAAAGAAGCCAAATTCGAAGAATGGCTTCGAGATGAACAGTAAATAAATCCAAGCAAGTGCAGTGCTGCTGATGAAATCTCTTAAGAGTT[AT/A]TTTTGTTTGATGTAAAGCATATGAATTGACATGATTTGTTTGTATAATTCTTGGTTGTATTTAAACGACACTATATGAGCCGCTAAT
103998 G C CCAATGAAGGCGGTTTCAGTCCAAGCGGTAGTGGCAACCATGGTTTTGCCAACACGGCTTCTATAGCTGCGTCTATGCTCTCCTTTGATGGTTGAGCATC[G/C]GATTGAGCACGCGGGCTTAAATGTTTTTTCGGAAGAGGTACAATTTCTGGTGGTGGCGGTGGTCGAAAAATAGGATGTGCAGGAG
103998 G GT AGCGGTAGTGGCAACCATGGTTTTGCCAACACGGCTTCTATAGCTGCGTCTATGCTCTCCTTTGATGGTTGAGCATCGGATTGAGCACGCGGGCTTAAAT[G/GT]TTTTTTCGGAAGAGGTACAATTTCTGGTGGTGGCGGTGGTCGAAAAATAGGATGTGCAGGAGGAATTCCAGCAACAGGTTGGGT
103998 A G ATCTCGCTTGTGGTATTAGCGGAGGAGGATAGCATGGCGTTCCTTGAGTTAAAGTCCTTTGGTTATAATGTGGATGATGCTGCCAATAAGTAGGGTCAGC[A/G]GGCACAACAGGTCCATGCACCTGTCGAGGTGGGCCCCATGGAGGCCTGGGCCAGACTGGAACAAGCTGAGGATGCTCCACGGCC
104004 T C AAGATAAACCAAAAGCACACAATGCCCGTCATTTCCCACTCTTCCTTAATTTCTCGCCCACTTTCTCTCTCCT[T/C]CCGATTCTCCCTTTTCCCTTCCAAGCTATCCTCCTCCTCCGTATCATTCCCGACAAATTCATCTACCAAGTCTTTAATTCGCCCCATGAGCTGGCTCGGA
104004 C T CATCTACCAAGTCTTTAATTCGCCCCATGAGCTGGCTCGGAAAACTCGGGTTCATGAGCAAAACATCGTCTTTCTCACCCGATTCGCCGCGTGCGGCGAT[C/T]GCGCAGGGTCCGGACACGGACCTTCCGGAGGCGGGGAAACAGTTCGCGCAATTTGGGGCGGGTTGTTTCTGGGGGGCGGAGCTG
104004 AT A CATAAATTCGTGCCGAACATCTACAATTTAAGCTCTGTATAGCTACTGTAAAGATTCAGTATGTTTTATAGTGTGCTGCCTACTTTTTCTTTTGCAGTTA[AT/A]TTTTTTTTTCAACTGAATTATACCTAATGGTAAATCTTATATGCTTTGTTGGAATCATTTAAGCAGTGTGCCATATGTAAAAAAAAA
104004 C G AATTTAAGCTCTGTATAGCTACTGTAAAGATTCAGTATGTTTTATAGTGTGCTGCCTACTTTTTCTTTTGCAGTTAATTTTTTTTTCAACTGAATTATAC[C/G]TAATGGTAAATCTTATATGCTTTGTTGGAATCATTTAAGCAGTGTGCCATATGTAAAAAAAAA
104006 A C TCACATAATATCCGATCTTATACAAAAGATCACTCGACTGAAATCAAACACTGGCTTTAACAGCATCACTGTACCCATTAATCTTATCATAATACCTACT[A/C]TACAGCATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCAAAACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCT
104006 T C CACATAATATCCGATCTTATACAAAAGATCACTCGACTGAAATCAAACACTGGCTTTAACAGCATCACTGTACCCATTAATCTTATCATAATACCTACTA[T/C]ACAGCATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCAAAACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTG
104006 G A TAATATCCGATCTTATACAAAAGATCACTCGACTGAAATCAAACACTGGCTTTAACAGCATCACTGTACCCATTAATCTTATCATAATACCTACTATACA[G/A]CATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCAAAACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTGCTGC
104006 A G ACACTGGCTTTAACAGCATCACTGTACCCATTAATCTTATCATAATACCTACTATACAGCATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCA[A/G]AACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTGCTGCGTCCTGCGAAGCAGGCAATCCCAAATATATGTTTGTCGCCG
104006 A C CACTGGCTTTAACAGCATCACTGTACCCATTAATCTTATCATAATACCTACTATACAGCATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCAA[A/C]ACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTGCTGCGTCCTGCGAAGCAGGCAATCCCAAATATATGTTTGTCGCCGT
104006 A G TAATCTTATCATAATACCTACTATACAGCATAATCCCACCATATTTGGCTGACCCCTTCACAACAGGCAAAACCTGCGAAACCAAGGTGTTGGGCTCAAT[A/G]TACCCGCTTCCTGCTGCGTCCTGCGAAGCAGGCAATCCCAAATATATGTTTGTCGCCGTCACGCTCGTCGTCCATTTAGTCCAGTAGCT
104006 T C CACCATATTTGGCTGACCCCTTCACAACAGGCAAAACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTGCTGCGTCCTGCGAAGCAGGCAA[T/C]CCCAAATATATGTTTGTCGCCGTCACGCTCGTCGTCCATTTAGTCCAGTAGCTGCTCAGGTTATCCACGCTGCCTGAGGAATACTGGC
104006 C G AAACCTGCGAAACCAAGGTGTTGGGCTCAATATACCCGCTTCCTGCTGCGTCCTGCGAAGCAGGCAATCCCAAATATATGTTTGTCGCCGTCACGCTCGT[C/G]GTCCATTTAGTCCAGTAGCTGCTCAGGTTATCCACGCTGCCTGAGGAATACTGGCATGGCGGATTGTTGTAGAACTGCACCCAAACA
104006 G T CTCAGGTTATCCACGCTGCCTGAGGAATACTGGCATGGCGGATTGTTGTAGAACTGCACCCAAACATAGTCAAACAATCCAGTGTCCAACGCTGTGCTCA[G/T]CTGCGCATCAGGAAATGGGCATTGCGGAGCTGCAGTTAGGTACACTTTTTGCCCATACTGAGTCAGGAACCGGGCAAGTTCGTCAT
104006 T C TGCCTGAGGAATACTGGCATGGCGGATTGTTGTAGAACTGCACCCAAACATAGTCAAACAATCCAGTGTCCAACGCTGTGCTCAGCTGCGCATCAGGAAA[T/C]GGGCATTGCGGAGCTGCAGTTAGGTACACTTTTTGCCCATACTGAGTCAGGAACCGGGCAAGTTCGTCATAGTGACCGGCACCTCC
104006 T G GCGCATCAGGAAATGGGCATTGCGGAGCTGCAGTTAGGTACACTTTTTGCCCATACTGAGTCAGGAACCGGGCAAGTTCGTCATAGTGACCGGCACCTCC[T/G]TGCTCTATGTCGAAATCCACTCCATCCAGAGCAGCAGGTCCCAGAGGTCTAGAAGATGACGTACCTCCTAAATAGCTGTTCCATAG
104006 T C GGAAATGGGCATTGCGGAGCTGCAGTTAGGTACACTTTTTGCCCATACTGAGTCAGGAACCGGGCAAGTTCGTCATAGTGACCGGCACCTCCTTGCTCTA[T/C]GTCGAAATCCACTCCATCCAGAGCAGCAGGTCCCAGAGGTCTAGAAGATGACGTACCTCCTAAATAGCTGTTCCATAGATAATCTG
104006 A G TGAGTCAGGAACCGGGCAAGTTCGTCATAGTGACCGGCACCTCCTTGCTCTATGTCGAAATCCACTCCATCCAGAGCAGCAGGTCCCAGAGGTCTAGAAG[A/G]TGACGTACCTCCTAAATAGCTGTTCCATAGATAATCTGCAACGCTTTGTGCATCTGAAGTGGAAGATAAGGAGTAGCTTCCTGCAC
104006 C T TCAGGAACCGGGCAAGTTCGTCATAGTGACCGGCACCTCCTTGCTCTATGTCGAAATCCACTCCATCCAGAGCAGCAGGTCCCAGAGGTCTAGAAGATGA[C/T]GTACCTCCTAAATAGCTGTTCCATAGATAATCTGCAACGCTTTGTGCATCTGAAGTGGAAGATAAGGAGTAGCTTCCTGCACCGCCG
104006 T G GTTCCATAGATAATCTGCAACGCTTTGTGCATCTGAAGTGGAAGATAAGGAGTAGCTTCCTGCACCGCCGCCAAGGGAAATGAGAACCTTGACATTCATG[T/G]ACTGACAAGACTGGATATCTGAGGACAGTCCTGTGCATCCATTTGAGTCTGGGTTGCAATGGCCGGCCAGGTTGAGCACTGGTGT
104006 C T CTGGGTTGCAATGGCCGGCCAGGTTGAGCACTGGTGTTTGGCCATTGCCGAAGGTGGTAAGGAAGGAGACTATGACGTAGGCGTAGTTTCCGGTTGCGCA[C/T]GTTTCGGCAAGGGTGCCTTCATTGCCGTTTTGACCCCAGTATACGGCGATATTGCCTGCATGTGACAGGGAAGTAACTGATAAGA
104006 A G GGTTGAGCACTGGTGTTTGGCCATTGCCGAAGGTGGTAAGGAAGGAGACTATGACGTAGGCGTAGTTTCCGGTTGCGCACGTTTCGGCAAGGGTGCCTTC[A/G]TTGCCGTTTTGACCCCAGTATACGGCGATATTGCCTGCATGTGACAGGGAAGTAACTGATAAGAGAATGAGTAGTGATGCTATG
104006 G T TGAGCACTGGTGTTTGGCCATTGCCGAAGGTGGTAAGGAAGGAGACTATGACGTAGGCGTAGTTTCCGGTTGCGCACGTTTCGGCAAGGGTGCCTTCATT[G/T]CCGTTTTGACCCCAGTATACGGCGATATTGCCTGCATGTGACAGGGAAGTAACTGATAAGAGAATGAGTAGTGATGCTATGAAAG
104008 G A CTTCGAGAAGGGCAGAATCAGACCTCTGTATGAAGTCATGTCAACTCCTCCATCCCCCAAAGAAAGGGGGAGGCAGAAGGTCAGTCCTGGACCTTCTGGT[G/A]CAAGCAGGAAGCCATCAAGGTCCCTTTCTCCCATGAAGAGCACAACCACTTCCGATACGACGCCGACGATTGCTTCAGAGTGCTTA
104008 A G GGTGCAAGCAGGAAGCCATCAAGGTCCCTTTCTCCCATGAAGAGCACAACCACTTCCGATACGACGCCGACGATTGCTTCAGAGTGCTTAAAAGCAACCA[A/G]TGGAAGCAAGAAGTGGAGACTGAGGGACTTCTCTTGTTTCGCAGCGCGTCGGAAGGTCGTGCCACCGGCAGCAAGGGCAAGGAC
104008 C CT CTCCCATGAAGAGCACAACCACTTCCGATACGACGCCGACGATTGCTTCAGAGTGCTTAAAAGCAACCAATGGAAGCAAGAAGTGGAGACTGAGGGACTT[C/CT]TCTTGTTTCGCAGCGCGTCGGAAGGTCGTGCCACCGGCAGCAAGGGCAAGGACCCTATGCGTAAATTCACAGCTACGCCCTCTT
104008 T A GATACGACGCCGACGATTGCTTCAGAGTGCTTAAAAGCAACCAATGGAAGCAAGAAGTGGAGACTGAGGGACTTCTCTTGTTTCGCAGCGCGTCGGAAGG[T/A]CGTGCCACCGGCAGCAAGGGCAAGGACCCTATGCGTAAATTCACAGCTACGCCCTCTTCTTCTTCCATACATGGGAGCAACAGGA
104008 T C GACCCTATGCGTAAATTCACAGCTACGCCCTCTTCTTCTTCCATACATGGGAGCAACAGGAGGTCCGGGGAAGATTCGAGGAGCTCGAGTTTCAGGTCGG[T/C]GGACAGCGTAGGGTCGTCGATGAGAAGGGCAAAAGTGTCGGCTCATGAAATGCACTACATGTCGAACCGGACCGTGTCGGAGGA
104008 G A GCTCGAGTTTCAGGTCGGTGGACAGCGTAGGGTCGTCGATGAGAAGGGCAAAAGTGTCGGCTCATGAAATGCACTACATGTCGAACCGGACCGTGTCGGA[G/A]GAGATGAAGAAGAAGACCGCTCTTCCTTTCAACAGGCATGGCTTGTTCGGATGCCTGCGTTTCAATCCGGCTGTTAATAGCATTG
104008 C A GAAGGGCAAAAGTGTCGGCTCATGAAATGCACTACATGTCGAACCGGACCGTGTCGGAGGAGATGAAGAAGAAGACCGCTCTTCCTTTCAACAGGCATGG[C/A]TTGTTCGGATGCCTGCGTTTCAATCCGGCTGTTAATAGCATTGTTAAAGGTTTCAACAATGGTGGATGATAGATATCAATATCAAT
104016 T C TCTATGGAGGACTTGGAGCGATAATCTTTGCTGGGTACATAGTTTACGACACGGACAACTTGATCAAACGTTACTCGTACGATGAGTACATCTGGGCTGC[T/C]ATTTCTCTGTACCTCGATATTATCAATCTGTTTCTTTCCTTGCTTTCAATTCTCAGGGCTGCTGATAATTGATCTGTGGCACTCTTAGAA
104022 A G AAAAATCTATTAACGAATCCACAAGAGACAACAGCGAGATCCCATTTCAACTGATCGGTCCCGATCCAGAACGCACGAGCCGCGTGCACGGCAGGAGAGA[A/G]TATAAGCCATGTGATGAAACCAGCAAATAGGGAAACGGGTAGCTTTGAGCGGTCGATTTGGAACGAATTGAAGTTGAATGCAAG
104022 G A GGGGAAACGGAGGAGAGGGAAAAGAGGAAGTAAAAGAAGGCGAAGGAAGAGCAGAGAAAGGGGACAAGAGGGAAGGAGGGAGTGAAAAGAAAGTGAAGAG[G/A]GAGGTTGGAGAGAGAAAGGGACAGGAGGAGGAGAGAGTAGTGGAAGTGAGGGAAGAGGAGGCGGGTAAGGAGGTG
104030 T A ATTTTAAGGCACGGGCATTCTCAACATCAGCAAAAGAGAAGCTGGAGGCAGCTGGTTGCACAATAACTGTACTGCCTGGTAGAAAGAAGTGGGTTAAACC[T/A]TCAGTTGCAAAGAATCTTGCTCGAGCTGATGAATATTTTGCCAAGAAAAGAGCTGCTGCAGCTGCAGCTGCAGATGATGCAAGTT
104030 T TGCTGCA GTTGCACAATAACTGTACTGCCTGGTAGAAAGAAGTGGGTTAAACCTTCAGTTGCAAAGAATCTTGCTCGAGCTGATGAATATTTTGCCAAGAAAAGAGC[T/TGCTGCA]GCTGCAGCTGCAGCTGCAGATGATGCAAGTTCAGGTTCTGCATGAGCCGTTTAATGTTAAATTTCACTGTCTTTTCCCCTTT
104030 A G CTCGAGCTGATGAATATTTTGCCAAGAAAAGAGCTGCTGCAGCTGCAGCTGCAGATGATGCAAGTTCAGGTTCTGCATGAGCCGTTTAATGTTAAATTTC[A/G]CTGTCTTTTCCCCTTTTATTTGCCTGTAGATTACTGAAATCAAGTTGTGGTTTTCAGAAGCATGTTTTGTATTATGTAAATTAGTTTTTG
104030 A T CAGCTGCAGCTGCAGATGATGCAAGTTCAGGTTCTGCATGAGCCGTTTAATGTTAAATTTCACTGTCTTTTCCCCTTTTATTTGCCTGTAGATTACTGAA[A/T]TCAAGTTGTGGTTTTCAGAAGCATGTTTTGTATTATGTAAATTAGTTTTTGTTTATTCTTATGTTAGTTCTTTTGACTATCAACAATCCATA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104032 G GT TTTATTATATTACAGTTTGAGAGGAACATGCCAAGTAGACTTTATTAAAAACATAGTATCTTCGAAAGTGAACAAATTAGACAGTGATCGACTAATTAAT[G/GT]AATACAAAAGCATCATCACTTTCACATATAAGCAATGTATGAGTTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTC
104032 CA C TATATTACAGTTTGAGAGGAACATGCCAAGTAGACTTTATTAAAAACATAGTATCTTCGAAAGTGAACAAATTAGACAGTGATCGACTAATTAATGAATA[CA/C]AAAAGCATCATCACTTTCACATATAAGCAATGTATGAGTTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTCGATAC
104032 T TA GCCAAGTAGACTTTATTAAAAACATAGTATCTTCGAAAGTGAACAAATTAGACAGTGATCGACTAATTAATGAATACAAAAGCATCATCACTTTCACATA[T/TA]AAGCAATGTATGAGTTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTCGATACATGGCCTCCAGAGGAATTTGTTTG
104032 A AT CTTTATTAAAAACATAGTATCTTCGAAAGTGAACAAATTAGACAGTGATCGACTAATTAATGAATACAAAAGCATCATCACTTTCACATATAAGCAATGT[A/AT]TGAGTTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTCGATACATGGCCTCCAGAGGAATTTGTTTGCCCATTGTGA
104032 GTTAA G ATTAAAAACATAGTATCTTCGAAAGTGAACAAATTAGACAGTGATCGACTAATTAATGAATACAAAAGCATCATCACTTTCACATATAAGCAATGTATGA[GTTAA/G]TTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTCGATACATGGCCTCCAGAGGAATTTGTTTGCCCATTGTGAT
104032 T A GCATCATCACTTTCACATATAAGCAATGTATGAGTTAATTAAAGCTTGATCATGACACTCTTCATGTGTTCCCTCGGTCGATACATGGCCTCCAGAGGAA[T/A]TTGTTTGCCCATTGTGATGGCAACGCTCTCCGTCAAGTCTATCATTTCCTCTCCAGTCCTCTTCCAGTCGAAACACTGCACCACCGACCC
104032 G A CCGTCAAGTCTATCATTTCCTCTCCAGTCCTCTTCCAGTCGAAACACTGCACCACCGACCCCAACACCGAACCCACCATTCTCCTTGCAAGAATTTCTCC[G/A]GGGCACTTCATCCTCCCCATTCCAAATATCAGCATTTTGCTTATATCATGCTTCCCACTTTGGAACCTTTCCGGTTCAAATTTCAAAGGCTC
104032 C T TTTCTCCGGGGCACTTCATCCTCCCCATTCCAAATATCAGCATTTTGCTTATATCATGCTTCCCACTTTGGAACCTTTCCGGTTCAAATTTCAAAGGCTC[C/T]ACCCAAGTATCAGGGTCCCTATGGATCCTGTACGCATTGACCAAAAGCATAGTACCTTTTGGAATATTGTACCCTCCTACTACACAGTTTT
104032 T A TCCCACTTTGGAACCTTTCCGGTTCAAATTTCAAAGGCTCCACCCAAGTATCAGGGTCCCTATGGATCCTGTACGCATTGACCAAAAGCATAGTACCTTT[T/A]GGAATATTGTACCCTCCTACTACACAGTTTTGCGACGCTTCATGCGGCACCATCAGCGGGCCTGCTGGCTTTAGTCTAAGGGTTTCGTT
104032 G C TACCTTTTGGAATATTGTACCCTCCTACTACACAGTTTTGCGACGCTTCATGCGGCACCATCAGCGGGCCTGCTGGCTTTAGTCTAAGGGTTTCGTTTAT[G/C]ACACATTGTAGGTATGGTAGATTTTGGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCT
104032 T C CCATCAGCGGGCCTGCTGGCTTTAGTCTAAGGGTTTCGTTTATGACACATTGTAGGTATGGTAGATTTTGGACATCTGATTCTAGCACTAGTCTTTCACT[T/C]CCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTG
104032 C T GGCCTGCTGGCTTTAGTCTAAGGGTTTCGTTTATGACACATTGTAGGTATGGTAGATTTTGGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTT[C/T]TCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTG
104032 C T TTAGTCTAAGGGTTTCGTTTATGACACATTGTAGGTATGGTAGATTTTGGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTC[C/T]GCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCA
104032 T C CGTTTATGACACATTGTAGGTATGGTAGATTTTGGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTT[T/C]AGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCG
104032 T C GATTTTGGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAA[T/C]GTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGT
104032 C A GGACATCTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAG[C/A]GCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTG
104032 T C CTGATTCTAGCACTAGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCA[T/C]TCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTG
104032 C A AGTCTTTCACTTCCTATCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTG[C/A]TGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAA
104032 G T TCTTCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCC[G/T]GCAGCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATA
104032 A T TCTCATCGATCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGC[A/T]GCCAGCATGGTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATG
104032 G A TCTCCGCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCAT[G/A]GTAATGGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATGGTTTTCTTC
104032 T G GCTTGTAGTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAA[T/G]GGCGAATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATGGTTTTCTTCTTCTG
104032 T C GTTTCTTTAGTTTCTCTGGATTGTTCAAAAGCAATGTCAGCGCCCATTCGATCGTGTTTGCTGACGTGTCTGTTCCGGCAGCCAGCATGGTAATGGCGAA[T/C]CCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATGGTTTTCTTCTTCTGTTCGTCT
104032 G A ATCCTTTGATGATTTCATCTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATGGTTTTCTTCTTCTGTTCGTCTGTGCTGCT[G/A]TGTCTTATATCATCTAGCAGTTTCTGGAAGAACTCATTTCTGTACTCGGCTATTGACGCCACCTTCTTCTTCCATCCGTTTAGGTTCAACCA
104032 C T CTGTGTAGTACTTTGGGTCTGTCTTCTGAAGCAAAAGCATGGTTGCCATAATGGTTTTCTTCTTCTGTTCGTCTGTGCTGCTGTGTCTTATATCATCTAG[C/T]AGTTTCTGGAAGAACTCATTTCTGTACTCGGCTATTGACGCCACCTTCTTCTTCCATCCGTTTAGGTTCAACCATCCTAAGAAAGGCAGG
104032 C T TGGTTGCCATAATGGTTTTCTTCTTCTGTTCGTCTGTGCTGCTGTGTCTTATATCATCTAGCAGTTTCTGGAAGAACTCATTTCTGTACTCGGCTATTGA[C/T]GCCACCTTCTTCTTCCATCCGTTTAGGTTCAACCATCCTAAGAAAGGCAGGTAATCTGCTATGTTTGTACGGCC
104034 A G TTCTTGCTCGATTGAGAAGTAGGAGAAATAGGAATTTGAGAAAAGTTGGGGTTTTGACGAATCCCGAGGCAGTGGAGATCGCTATCAAGGAGACGATGAG[A/G]TATGGCTTGTTTTTGGGAAGCTTTGCTGGAACTTATGTTTCCGTTGATGAACTTATTGCCAAGTTGTTGGGGAATAAAAGGACTG
104036 T A CCCTTATAATTCAACAGGCAGTGACAAAAACTGACACAAGCAGGGTCCCGATGCCTAGCAGCAATCAAATCAGCTACCGCTGCTGACAAAACAGTTGGAA[T/A]AGTAGAAAAAATGTTCAAAAACAAATCGTACAAGGAAGTGGATAACAAAGTGGAAGAACACAACTTATTGCCAAGGTGAAAGGAT
104036 G A CCGCTGCTGACAAAACAGTTGGAATAGTAGAAAAAATGTTCAAAAACAAATCGTACAAGGAAGTGGATAACAAAGTGGAAGAACACAACTTATTGCCAAG[G/A]TGAAAGGATAATGACTGGGAGAGAGAAGGGTGAGAAATGATGGTGGAGTACAAGTAACTGGCTAAAGCGGGTTCGGATTCTGC
104044 T C ATTTGATTTTTGAGAAAGAATTTGAATTATCTCATAATTCTAAGAATGCGATTGTTCATTTTACTGGCTACAAATCCATTCAAGACGATGATGTCCCAAG[T/C]GATTTTGATGATTCATCGGAGGAAGAAGATGCAAATCTTGCTTCAAAAACTAATGGTGCTCTCAAGGTAAAGCTTGATGATGTGAAGAA
104058 T C CCAGCAAGATCAGCGACGTGGGCCTGGCCCGCCTCGTCCCTCCCTCCGTCTCCAACGCCGTGACCCAGTACCGCATGACCTCAGCAGCCGGAACCTTCTG[T/C]TACATCGACCCCGAGTACCAGCAGACCGGGCTGCTCGGCTGCAAATCAGATATTTACTCTTTGGGCGTCATGCTGCTGCAGATTATA
104058 A T GGCCTGGCCCGCCTCGTCCCTCCCTCCGTCTCCAACGCCGTGACCCAGTACCGCATGACCTCAGCAGCCGGAACCTTCTGTTACATCGACCCCGAGTACC[A/T]GCAGACCGGGCTGCTCGGCTGCAAATCAGATATTTACTCTTTGGGCGTCATGCTGCTGCAGATTATAACTGCGGATTCGCCTATGGG
104058 G A GTTACATCGACCCCGAGTACCAGCAGACCGGGCTGCTCGGCTGCAAATCAGATATTTACTCTTTGGGCGTCATGCTGCTGCAGATTATAACTGCGGATTC[G/A]CCTATGGGGCTGACGCACAAGGTGGCAAGATCGATCGAGAAGGGGAACTTCGAGAAGGTGCTGGATCCGAGCGTCAAGGACTGG
104062 A G AGGTTTGCTGTCATCTCGGCTGAAACAGGTTCTGTCTGATTATTCTGAAGCTAAAGCACCTTCTGCTGATGGACTACAACCAAGTACTTTGTCCGAAGAA[A/G]CTTATACAGAGTTGGTTCAACGATTAAATGAAGCTCTTTTAAGTTTTATCGAAGGCCCGCCATTTACATTACAGAGATTATGTGAGATC
104062 GT G TCTGAAGCTAAAGCACCTTCTGCTGATGGACTACAACCAAGTACTTTGTCCGAAGAAACTTATACAGAGTTGGTTCAACGATTAAATGAAGCTCTTTTAA[GT/G]TTTTATCGAAGGCCCGCCATTTACATTACAGAGATTATGTGAGATCCTATTAGCTCCAAAAAGTACATATAAAACTCTGTCCAAGCTT
104062 A C TCAACCCTGACCATATGCACTGATCCATATCCAAAATCTGCACATACCACATCAGCAGCCGAATCGAATGATAACCAAGTAGCAGTACCAAACAATAAGC[A/C]AGAAGGCCATTCGTGTGCTTCTGTAACAAATGGCGTAGGAACAGACGCAACAGTTGATGAAGAAATGGTTGAAGCGGAAGCAGATG
104062 A G ATCCAAAATCTGCACATACCACATCAGCAGCCGAATCGAATGATAACCAAGTAGCAGTACCAAACAATAAGCAAGAAGGCCATTCGTGTGCTTCTGTAAC[A/G]AATGGCGTAGGAACAGACGCAACAGTTGATGAAGAAATGGTTGAAGCGGAAGCAGATGATGAATGTGGTCCAGGAGTCGACAAC
104064 A G GGTACACGAACCCGGTTAGGAAGGAGGAGTAGATTAGGTAGGCTACGAATTGGGTTCGTTCGGCGATGGAGCCGGAGGTGATGCCGGCGGCGGCAATGGC[A/G]AAGGCCCATTGGTAGAGGAAGTACGGATAGTCGAAGCTGTCGTTGGGGATGTTGTTTAGGGCGAAGGATTGCTTGCCTATGA
104070 C T TCGGATCTGATGAAGGGGGAGGAGGACGACAGAATGCTGGTGGAGAGAGCAGGTGGGGTCCAGAGTACTGTCGAGCTGATGATGCCGAGGAGCACTGTGA[C/T]GGTAAGGAAGTTGGTCGGACTTGCTACCCATAGACAGCTGTTGTTTGTGCCAGAATTTATTTTAAAGGATGTGCTCAAGAACA
104070 G A CTAACTCCTCTTACTCAGGATGTTTTAATTGTGTGGGGAGAACATGATCGTATTTTCCCACTAAACAAAGCATACGAGGTTCAGAAGCAGCTTGGAGAGA[G/A]CGTGAGAATTGAGATAGTGAAAAATACTGGACATGTACCAAACATTGAACAACCGCAGAGATTTAATGAGATTCTACTCAGTTTTCT
104070 G T TCCCACTAAACAAAGCATACGAGGTTCAGAAGCAGCTTGGAGAGAGCGTGAGAATTGAGATAGTGAAAAATACTGGACATGTACCAAACATTGAACAACC[G/T]CAGAGATTTAATGAGATTCTACTCAGTTTTCTGTTAAATAACACTAAACCTTCGAGTGATTAAAAGTTTATGATTTTGAGTTTGTTCT
104076 C T AATCAGACTTGGCACAAGTTCTACTGGCAGCATGCAAAGGACAGCTAAACAATGTAACGCTTGACTGGTCTTCAGGTTCTGCAATGGTTGTAGTAATGGC[C/T]AGTAAAGGTTATCCCAATGCATATGAAAAAGGAACCATAATAAAGAATCTAGAAGAGGCCGAGCTCGTATCTCCTACAGTAAAAGT
104086 CT C GCATTATCAAGCCTTTGAGTATCAGCCAAACTATCTTTTTGCTCCATCATAGTTCTAGGAGTAGAAACAGGAGCGGAATGGATAGGCTTATATGGTACAT[CT/C]TTTTTTTGAAGCTGACATTGCATTCGGTTCTAAGCTGTTTCTATTAGAACTCATTCTTCCATTTTGAAGATCAGGTGAGTACCCAGAG
104086 A T TCCACGAAGCCGTCTCGTCTGGATTTGAGCTCAGATGGATGGTCGGAGCTGGCGACTGAAATTGCAGTTTCAATCAAAGTCCATAGATCTGAACCTGATG[A/T]TCGGAGAATCGAGCGGAGTTCGTCGGCGTCCATTACTGTCGGAGAACTGGTGCTCAGAGGTTACACAAGTTGGAAAAAGAGTGGA
104088 CCTG C TGATACTCCAAATTCTTTTGATGTTGAAGAGCAAACGCTTTTCTCAATATCTGGTTGTCTCGCAACAGGCACTGCAACTGTTCTTTAAGAGATGCAATCT[CCTG/C]CTGCTCCTTTGATGCAGTGGAGTGATCGACGACTCTTCTTCCAAATGCATCCAAAAATTTTATGGTTCGACTTCGAGCATCTTCCAT
104090 T C ATGGTATTATCGGTCCCGATCCTTATTATTTCACTTTTGATCGGTTAGGAGTCCGGGTTCCGACTATTATGGTATCTCCTTGGATTGAAAAGGGTACCGT[T/C]GTACATGGTCCTAATGGTGTACCAACACCAAATTCGGAGTATGAGCATTCATCTATACCTGCAACCGTGAAGAAAATATTTAACTTGCA
104090 T C ATGAGCATTCATCTATACCTGCAACCGTGAAGAAAATATTTAACTTGCAAGCCCCATTTTTGACCAAAAGGGATGCTTGGGCTGGAACATTTGAAGGCAT[T/C]GTGAAAACTAGGACTGAACCCAGAACTGACTGTCCTGTCCAACTACCAACTCCTGTTCAAATAAGGCAAACTGAAGCTAATGAAGAA
104092 A G CTTTATAGGACCTCTGCCCTTCACCAGCCGCAGCATCTGAGGTCAAAATAGGAATTTGATGCTCTTCTCTAGGCTCCACCGCTTCTTCATTTGCAGCCAC[A/G]ATTTCCTGCCAATTAGGAGGCGGCGGCCGAAGCTCCTCCATCCCATGTGCGAAATTGCAGTTTGTTATGTATGGACAAGTCCCTGCAC
104092 C T CTTCTTCATTTGCAGCCACAATTTCCTGCCAATTAGGAGGCGGCGGCCGAAGCTCCTCCATCCCATGTGCGAAATTGCAGTTTGTTATGTATGGACAAGT[C/T]CCTGCACGGAACTTGCAGCATAGTTTTGTTTTGAAGAACATTTTGCCTATAGCTTTTGATTTGCTGTTGGAATCAGTTTGTGGTTGAGT
104094 T A TCAAAATTCGTTTTCCTCCTTTTCAACCTCATAGCCGCGTACGTCGTCCGCGGTGAAATCGACGGGGACATGTCCATCATATCCTACAACGCCGAGCACA[T/A]TTTCAAAGGCCTGGAACGCACCGACGTGGAAGTCCGTCAAATCTACAGTCAGTGGATGGTCCAGCACGGAAAGCAGTACAACGGGA
104094 G A CCGAGCACATTTTCAAAGGCCTGGAACGCACCGACGTGGAAGTCCGTCAAATCTACAGTCAGTGGATGGTCCAGCACGGAAAGCAGTACAACGGGATCGG[G/A]GAGAATGACGTCAGATTCGAGATTTTTAAGGACAATTTGAAGTTCATCGATGCGCATAACAACGAGGGGCATTCCTATCAACTGG
104094 C T ACGTGGAAGTCCGTCAAATCTACAGTCAGTGGATGGTCCAGCACGGAAAGCAGTACAACGGGATCGGGGAGAATGACGTCAGATTCGAGATTTTTAAGGA[C/T]AATTTGAAGTTCATCGATGCGCATAACAACGAGGGGCATTCCTATCAACTGGGTTTGAACAAATTTGCTGATTTGACGAACGAGG
104094 A G TCGGGGAGAATGACGTCAGATTCGAGATTTTTAAGGACAATTTGAAGTTCATCGATGCGCATAACAACGAGGGGCATTCCTATCAACTGGGTTTGAACAA[A/G]TTTGCTGATTTGACGAACGAGGAGTACAGATCTATGTATTTGGGAGTTAAGGGACGTGAAGGTAGACTTAGAAACGGCGAGAATA
104098 A G TACTAACACAGGAGTTATATAACATACTTTCACAAACGTCCTGAACCAGCAAGACAAGAAGCAATGACTCTCACACGATGATCACGCTGAGACTAGACAC[A/G]ACAATGCATAACATGTTGATCAACAACTCCGAAGGCAGACAAAACTAACAGAACCAAAGTCAATACCAACAACAATCACGTCCAGA
104098 C CA CAACGTCTAGATTGTAGCCAACCTATCACATAGAACGCTGGTTATAGTGGTAAACTCCACCATGAGGACAACATACACCCACCCTAAGGAAAAACAGACC[C/CA]AATCCACACAAACCAAAGAAAGGAAGATCCAAAATCACAAGAACCAAAAGAACTACAACAGATGCAGGCCTCTACAGTCTAAAAT
104106 A G TGCCGGACTCGATCATCTTTGATATACGATTCCGGTCTCTGTACGCCATTATCATCAGAATGTATGCAGCTCTCTCCTGACATTCAGGTGAATCGCACCA[A/G]CTCAGTACATCCGTCAAAATTTCAATCCACTCTGGCAATCTGCTAACCGCCCTTCTGCCTTCGGAAAAAGCTACAATGTTTGAAACGAT
104106 T C ATCTTTGATATACGATTCCGGTCTCTGTACGCCATTATCATCAGAATGTATGCAGCTCTCTCCTGACATTCAGGTGAATCGCACCAACTCAGTACATCCG[T/C]CAAAATTTCAATCCACTCTGGCAATCTGCTAACCGCCCTTCTGCCTTCGGAAAAAGCTACAATGTTTGAAACGATCACCAGCATTTTATC
104106 T C GATATACGATTCCGGTCTCTGTACGCCATTATCATCAGAATGTATGCAGCTCTCTCCTGACATTCAGGTGAATCGCACCAACTCAGTACATCCGTCAAAA[T/C]TTCAATCCACTCTGGCAATCTGCTAACCGCCCTTCTGCCTTCGGAAAAAGCTACAATGTTTGAAACGATCACCAGCATTTTATCGCTTAC
104106 C T CACTCTGGCAATCTGCTAACCGCCCTTCTGCCTTCGGAAAAAGCTACAATGTTTGAAACGATCACCAGCATTTTATCGCTTACTTCGCTATCTCCGATCG[C/T]TTGGAAAATGTGCTCCAAGAGCCCCGATTCAACAATAATGGTTACGTTGGTGTCACAGTTCGACAAATTGCACAATGACCGGATGGAG
104108 T C CAGTCCATCGTGTCTGGAATCTCGGCCACATTGTGCATCGCCTCATCCGCATCCTCATTCATGCTGTGCGTTTTTCCAAAGATGTACGTGTTTGATTTAG[T/C]GCTATCATGTTCGGTTTGCATTCAGGGGTTATGGAGTTTGGTGAGCGGGTTGTGTTTGTACGTGGAGAGATTTGTGCCAGAAGGATGT
104112 A G AGTAACTTATTGGTAGCAGAAGAACAAAAACCGCAACCTGGATTTTCAGCTTTCAAGCAAGTCATGCAATCCCACTTAGCACCAACACTATAAGCAGGGC[A/G]AGTGAACGAATCAAACTTTGCCGTTTCAATCGAACTAACAGCAGGAGAGTGCGTGGTAGTGTTCTGAAACACCGCAGTCAGAATAG
104112 A G GGCCGACTCCTGCTAGCAGTCCTCTTCGCACTGTCTTCGTTTTGAAGAGCTTTGAGAAGCTGATTTTCTCAGAGTCGCCTCGTTCTTTGATTTCGGTCTC[A/G]ACTGATTCATGAAGGGAGTTGATTTCGGCTTCTACTTCATTGGACGGGTAGATTTTGCGAAGAATCGTTTTGGCTTCTTCTTGCCGGCC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104112 AC A GCTTCTACTTCATTGGACGGGTAGATTTTGCGAAGAATCGTTTTGGCTTCTTCTTGCCGGCCTTTTCGGTATAGCCAACGGGGTGACTCAGGAAGGAAGA[AC/A]CCATGAGTGCGAATTGGATGATGGCGGGAACTCCGGCTATGCCAAGCATCCATCTCCATGTTCCTGGTGCCTTGGTAAAAGCTAG
104112 G A ACTCAGGAAGGAAGAACCATGAGTGCGAATTGGATGATGGCGGGAACTCCGGCTATGCCAAGCATCCATCTCCATGTTCCTGGTGCCTTGGTAAAAGCTA[G/A]ATTGATGAGATAAGACAAGAACTGTCCGCCGGTGATGAGAAACCCGTTAAGGCTGACTAGTGCTCCCCTGATCCTCGCAGGAGAG
104114 A G TGGTAGGTGCCATCCCTATGGGGTTGGAGGGACAGCTGGCACACTGGTATGTCTGCTTCGGGATACATGAGCATGAGTGGTACCCATGCACCATGGTCCA[A/G]TCCTCTTTTGCTGTCCTCCTTCACACGGCTGAATCCAGATTTTAGGAGTAGGTCTTTAACTCTCTGTGCAAGGTCAGGTGCACCTGC
104114 A T GGCACACTGGTATGTCTGCTTCGGGATACATGAGCATGAGTGGTACCCATGCACCATGGTCCAATCCTCTTTTGCTGTCCTCCTTCACACGGCTGAATCC[A/T]GATTTTAGGAGTAGGTCTTTAACTCTCTGTGCAAGGTCAGGTGCACCTGCTGCAGGATACTTGATCTGATACATGGATTTTGGAAATC
104114 T C CTGGTATGTCTGCTTCGGGATACATGAGCATGAGTGGTACCCATGCACCATGGTCCAATCCTCTTTTGCTGTCCTCCTTCACACGGCTGAATCCAGATTT[T/C]AGGAGTAGGTCTTTAACTCTCTGTGCAAGGTCAGGTGCACCTGCTGCAGGATACTTGATCTGATACATGGATTTTGGAAATCCATAAA
104114 A C CGGGATACATGAGCATGAGTGGTACCCATGCACCATGGTCCAATCCTCTTTTGCTGTCCTCCTTCACACGGCTGAATCCAGATTTTAGGAGTAGGTCTTT[A/C]ACTCTCTGTGCAAGGTCAGGTGCACCTGCTGCAGGATACTTGATCTGATACATGGATTTTGGAAATCCATAAAAATCATAGATAGTTT
104118 G A AGAGGTCGTTGCGGTTTCCATTGGCCCCACACAGTGCGTGGATACTTTGAGGACAGCGCTGGCAATGGGGGCTGACAGGGGAATTCATGTGGATTCAGGT[G/A]CAGCGAAGGTGGACCCACTTTGTGTTGCCAAAGTTCTTAAGAGTTTGGTTGAGGTTGAGAAGCCTGGGTTGTTCATTCTTGGCAA
104118 T C CCAAAGTTCTTAAGAGTTTGGTTGAGGTTGAGAAGCCTGGGTTGTTCATTCTTGGCAAGCAGGCTATTGATGATGACTGCAATCAAACCGGTCAAATGGT[T/C]GCTGGACTTCTTAAATGGCCACAGGGAACCTTTGCCTCAAAGGTTATTTTGGACAAGGAGAAGCATGTTGCAACTGTGGAAAGAGA
104118 C G GGTTGAGGTTGAGAAGCCTGGGTTGTTCATTCTTGGCAAGCAGGCTATTGATGATGACTGCAATCAAACCGGTCAAATGGTTGCTGGACTTCTTAAATGG[C/G]CACAGGGAACCTTTGCCTCAAAGGTTATTTTGGACAAGGAGAAGCATGTTGCAACTGTGGAAAGAGAGGTTGACGGTGGCCTTGA
104118 T A ACTGCAATCAAACCGGTCAAATGGTTGCTGGACTTCTTAAATGGCCACAGGGAACCTTTGCCTCAAAGGTTATTTTGGACAAGGAGAAGCATGTTGCAAC[T/A]GTGGAAAGAGAGGTTGACGGTGGCCTTGAGACCATATGCCTAGATCTTCCAGCAGTAATTACGACTGATTTGAGATTAAACCAGCC
104122 T C GAGGCAGGACCGAGGATGAGGATGAAAAGCTGAAGTGTGAACTATTGGCTGATGAAAAACAGCGTGCTGAACACATTATGCTTGCTGATCTGGGTAGAAA[T/C]GACGTTGGAAAAGTTTCAAAACCAGGTTCGGTGAATGTGGAGAAGCTCATGAATGTTGAAAAATACTCTCATGTGATGCACATC
104126 A AG ACTAAACCCTTCAATGCTTCTAAGGCACCATGGAATCTAACAGAACCTTTCAAGCTTTCCCATGCTAGAAAACGAAGGTCGTCTTGCAAATCCCTTTTGT[A/AG]GTGGGGCTTTTCAGCAAAGTGCCTCTTAAGGCTAGTACTGCCCTTGGAGCTCCACTTGGTCTCATCAGTATGAAATCTGCCATGGCTG
104132 C G GAAGATCGAAAGAAGAGAATGCAGCCATCAAAATACAGACCGCTTTTAGAGGTTATTTGGCTAGAAGACAATTGCGGGCGTTGAAAGGATTAGTCAGACT[C/G]AAGACGTACACCAATAGCAATGTTGTCGTGCGCCAGTCTGCAGCTACATTGCGTTGTTTAAACACAATGGCAAAAGTTCAAGCAC
104132 T G AAAATACAGACCGCTTTTAGAGGTTATTTGGCTAGAAGACAATTGCGGGCGTTGAAAGGATTAGTCAGACTCAAGACGTACACCAATAGCAATGTTGTCG[T/G]GCGCCAGTCTGCAGCTACATTGCGTTGTTTAAACACAATGGCAAAAGTTCAAGCACAGATATATTCGAGGAGAATCAGAATGTCTG
104132 A G TAGAGGTTATTTGGCTAGAAGACAATTGCGGGCGTTGAAAGGATTAGTCAGACTCAAGACGTACACCAATAGCAATGTTGTCGTGCGCCAGTCTGCAGCT[A/G]CATTGCGTTGTTTAAACACAATGGCAAAAGTTCAAGCACAGATATATTCGAGGAGAATCAGAATGTCTGAGGAGAATCAAGCTCT
104134 T C TGTTCAGCTTCTCGGTCAGTCCGATCTTTGAATCCAGGTTTGCTATGGTGGCGGAGGCGTTTGATGTTAGTTTGTGCCGCTCATCGAATGCTTTTGCATG[T/C]GTTAGGGCGTCTTTGCCGAGTACGAAGCCTTTCGCTAGCATTGTGCTCATCATGTCTTCTGCCTTTTGGATTGTTGACTCTGCTATGTT
104134 G A CATGTCTTCTGCCTTTTGGATTGTTGACTCTGCTATGTTGTTTTCATCTACCGCAGAAGATTTGTAAGCTTCGGGCGGAAGTTGATAATGTTCTTCCAGC[G/A]TTACAGTGACAGAAAGATCAACTATAGTGGCCCCCGTAAGAAGCACTGCTGTATCTGCTCCCTGTGAATCCTTGAACGTGATATATGCA
104138 CA C TGTATTTGATGATACATTTTGGGAAAACTTAGATGTAGTTATTAATGCATTGGATAATGTGACAGCTAGAATGTATATGGATTCTAGGTGTTTGTATTTC[CA/C]AAAAACCTTTATTGGAGTCAGGAACTTTAGGAGCCAAGTGTAACACACAAATGGTAATACCACATCTCACTGAAAACTATGGTGCTT
104146 C T CGGACCTCCGTTTGGGTCTTCCCGGATCCGACAGCCCGGAGCGAGTTAACGGTTCTGGTTTAACTCTCGGTATCAATGTGAAAGGGTTCGGGTCCGGTTC[C/T]AAAAGAGGCTTTAATGACTGTGTTAGTGGATCTCCTAAATGGGTTTTCAGTGGATCTGAGGTTGAGCTCTTTTCACCCAAGAAAGG
104146 A G TGTTCACTGAAACCTGTAGGAGGCTTCGAATAATGAAAGGTTCAGACGCAATCGGACTTGCTCCAAGGGCAAGCGAGAAGAGCAAGAACCGAAACTGACC[A/G]CCATTCCCGTGTTTTCAAGAGACGTCCAAGGCCAAATGGTTTGAAGGGTTATTGAAAATTGTGTTGCTAGTATATTCCTTCTTGGT
104158 A C AAAATCTAAGAAAAGCAGAAAGCCGTACAAATCTGAATGCCGGGGCCTGGGGCGCACACAATTTACACACTGGGAACAGGCATCGCCTTTCTCCGG[A/C]TAACACGTGGCAGTTTCAGTCCACAACACTGCCTCTGCTACTCTGTAAACGCCTTCGTCGGCCCCGATCTCGGTTCCTTTGCTGAATGGCT
104158GGGTTCCTCTAAACAG CCTTTTTATCACGTTTTGATTCTTGGTTTGCCTCTTTCTTTGTTCTACGCTTGGCTCTCTAAGTGGCTGCTTATGAAAGGATATGTTGATACTCTTTCTG[GGGTTCCTCTAAACA/G]GGTTCCTCTAAACAGGAAGCAGTGTCTCATGTTGGTAGCAGCAGGATCATTATCGCACTTTTTCTTGGATCATTTAT
104162 G A AGCAGCAAGCTTTGATGCAGCAAGCTCTTCTCCTTCAGCAGCAGCAGCAGTCTATCTACCCTCAGATTGAGCCAATTCCTAGTGGAAATTTGCCTGTTGG[G/A]TTTGATCCAAACACTTGCCGCAGCGTGTATGTAGGGAACATTCACAGCAGTGTAACTGACACGCTGCTTCAAGAAGTTTTTCAGACTG
104162 T C CTGTTGGGTTTGATCCAAACACTTGCCGCAGCGTGTATGTAGGGAACATTCACAGCAGTGTAACTGACACGCTGCTTCAAGAAGTTTTTCAGACTGCTGG[T/C]CTTATCGAAGGCTGCAAACTAATAAGAAAGGATAAGTCATCCTATGGGTTTGTTGATTATTTTGATCGCAGATCTGCTGCACTTGCAA
104162 C G GCAAAAGTCATGTGGGATCAGAATACTGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTTCGGAATGAGCAGGATGCACAAAATGCCATTAATGAACAAA[C/G]CGGTAAGTGGCTTGGTAACCGTCAGATAAGGTGTAACTGGGCAACAAAGGGGGCTGGAACTAATGATGCTCAGAGTTCAGATTCA
104162 C T CAAAAGTCATGTGGGATCAGAATACTGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTTCGGAATGAGCAGGATGCACAAAATGCCATTAATGAACAAAC[C/T]GGTAAGTGGCTTGGTAACCGTCAGATAAGGTGTAACTGGGCAACAAAGGGGGCTGGAACTAATGATGCTCAGAGTTCAGATTCAA
104168 T C CCCACCTTTTCCAAATGCAAACAGAAGTATATAGCTTCCACCGAGAAGTACAAGTAGTAGAGAGGCAAGCCAGTGCACCGTTTCCTCACCAGCAATTGTG[T/C]TGGCCATGGTTACTGCAGTAATGCCAAGAAGAGATGTTGACATCACATGCAGTACAGCTCCAAATGTAGTAACGAGGAGCGTTCTG
104168 CT C CGAATGCAGCAACGATACTGTTGCGATTCCTCCAATTTTCGGCAGATCTTCGAATCCGATCCCTTCCATTTACGCTGTTTTTCCAAAAAATCCAAACTTT[CT/C]TTCCTTGAACTGAGGTATTATGCCAACTTAGGGCCGGTGAGTGAGATCTGAGAAGGGGAAACGAAGAACGAATGAGTGAGTAGACA
104172 C T CAGCTTCGAATGGTGGGACACCATATAGAAATTCGTAGCAAAGAATGCCTAGAGTCCAGTTATCAACAAAATGATCATGTTCTTTTTTCTCCACCATTTC[C/T]GGTGCCAGATAATCTATAGTGCCACACATTGTGTGTCTCTTTGCATTTGACTGCACAGCCCAGCCAAAATCCGCAATTTTTAAACGACC
104172 T C AATCTATAGTGCCACACATTGTGTGTCTCTTTGCATTTGACTGCACAGCCCAGCCAAAATCCGCAATTTTTAAACGACCCTCAACATCCAGCAATAAGTT[T/C]TCTGGTTTGATGTCTCTATGAATCACATTCTTTTGGTGGCAATAGGCCAACGCGCCTGCTAGGCTTGCAACGTACGTTGCAGCACGCTT
104172 C T AGCCAAAATCCGCAATTTTTAAACGACCCTCAACATCCAGCAATAAGTTTTCTGGTTTGATGTCTCTATGAATCACATTCTTTTGGTGGCAATAGGCCAA[C/T]GCGCCTGCTAGGCTTGCAACGTACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACCGCGAGC
104172 G A AACGACCCTCAACATCCAGCAATAAGTTTTCTGGTTTGATGTCTCTATGAATCACATTCTTTTGGTGGCAATAGGCCAACGCGCCTGCTAGGCTTGCAAC[G/A]TACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACCGCGAGCTGCATACTCAAGAACCAGAA
104172 T G CCTCAACATCCAGCAATAAGTTTTCTGGTTTGATGTCTCTATGAATCACATTCTTTTGGTGGCAATAGGCCAACGCGCCTGCTAGGCTTGCAACGTACGT[T/G]GCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACCGCGAGCTGCATACTCAAGAACCAGAAAAATAC
104172 T C TCTTTTGGTGGCAATAGGCCAACGCGCCTGCTAGGCTTGCAACGTACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAA[T/C]TCACCGCGAGCTGCATACTCAAGAACCAGAAAAATACGCGTCTCATCGTGAAACCAAGCAAAAAGGCGAAGGACGTTAGGATGATC
104172 G A GGTGGCAATAGGCCAACGCGCCTGCTAGGCTTGCAACGTACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACC[G/A]CGAGCTGCATACTCAAGAACCAGAAAAATACGCGTCTCATCGTGAAACCAAGCAAAAAGGCGAAGGACGTTAGGATGATCAAGTC
104172 C T CAACGTACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACCGCGAGCTGCATACTCAAGAACCAGAAAAATACG[C/T]GTCTCATCGTGAAACCAAGCAAAAAGGCGAAGGACGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCA
104172 A G ACGTTGCAGCACGCTTTTCAGAGAAATGGCCAAGATTTTTCAAAAACTTGTACAATTCACCGCGAGCTGCATACTCAAGAACCAGAAAAATACGCGTCTC[A/G]TCGTGAAACCAAGCAAAAAGGCGAAGGACGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAAT
104172 C T AAAAACTTGTACAATTCACCGCGAGCTGCATACTCAAGAACCAGAAAAATACGCGTCTCATCGTGAAACCAAGCAAAAAGGCGAAGGACGTTAGGATGAT[C/T]AAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAAGATAACCTTGAGTGCG
104172 G A CAAAAAGGCGAAGGACGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAA[G/A]ATAACCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGA
104172 A C AAAGGCGAAGGACGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAAGAT[A/C]ACCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTC
104172 C T GGCGAAGGACGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAAGATAAC[C/T]TTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTCGAA
104172 G C CGTTAGGATGATCAAGTCCGTGTTGAATTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAAGATAACCTTGAGTGC[G/C]ACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTCGAAGTCGGATAG
104172 A G TTTCAATCTCTCTTCTCAAATGCGCATGAAATCGATACTTCTCCAGTTTTTCCTTGAAGATAACCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACG[A/G]GCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTCGAAGTCGGATAGTCTCCACTCCTCTTCACTGCTCATTTCTT
104172 G A ATCGATACTTCTCCAGTTTTTCCTTGAAGATAACCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTC[G/A]CCAATGAACCTGCCGATCTCGAAGTCGGATAGTCTCCACTCCTCTTCACTGCTCATTTCTTGCTAAGTGTCGGATTGAAATTTGGGAAC
104172 T G TAACCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTCGAAGTCGGA[T/G]AGTCTCCACTCCTCTTCACTGCTCATTTCTTGCTAAGTGTCGGATTGAAATTTGGGAACTAGGGCTGGAGTTTGGAGAGGATTTGGG
104172 T G CCTTGAGTGCGACTATGTACCCGCTCTGGATTTCACGAGCAAGATAAACTTTGCCGAACTTGCCCTCGCCAATGAACCTGCCGATCTCGAAGTCGGATAG[T/G]CTCCACTCCTCTTCACTGCTCATTTCTTGCTAAGTGTCGGATTGAAATTTGGGAACTAGGGCTGGAGTTTGGAGAGGATTTGGGC
104174 G A TCTCTGGGTAGCGATCTTCGTCATATTCACCCTTAGTAATGTGCAAATCGGGACACAATCCCTTTAAGTAATCATGAATCTCCTTAATACAAAGGTTTCC[G/A]GTACATATAATGTGTTGGATTTTCCCTGGCACGAGCATAGACTTGAACTTAGCTGGCAAATCAGCTGCTCTATGAGGAATGTGAAGATC
104178 AGAGACATGTGACAGTACAACTTAGG
A AATCCAAGAGTACAGTAAGCATAGGGATGGCGCATCACCATCACAAACAGTGCACACACCAGTTTGTGAGAACATACCCAGATCATCCATCTCC[A/AGAGACATGTGACAGTACAACTTAGG]GAGACATGTGACAGTACAACTTAGGGAGACAGGAAAGTAACATAGTAGGAACCATAACAAAGCAAA
104178 C T AAAAACATAAGACTGATCACATTGGGTTCGTGACAGGAAGGAAATGATAAACTCCACCAACCTATAGGCAAAGGCTAGAGCCGAAGCTTCTCATATATTG[C/T]CAAAGGAGATGAAGAGAGCAACAAACCAGATCACCACATCGCGAAACACAACCAGTGACCAGCTCAAAGATGACATAGCGTGATA
104178 T C CGAAGCTTCTCATATATTGCCAAAGGAGATGAAGAGAGCAACAAACCAGATCACCACATCGCGAAACACAACCAGTGACCAGCTCAAAGATGACATAGCG[T/C]GATACCATGGCCAAGTTAAGAGGCCGAGAATCCCCTGAACACCACAAAACTGCATAAAATAACCACAGCTCCAATCTGAAACACAC
104178 A T GAAGAGAGCAACAAACCAGATCACCACATCGCGAAACACAACCAGTGACCAGCTCAAAGATGACATAGCGTGATACCATGGCCAAGTTAAGAGGCCGAGA[A/T]TCCCCTGAACACCACAAAACTGCATAAAATAACCACAGCTCCAATCTGAAACACACGCTCAGAGAAATACACACACCGAAGCTTC
104178 C T AACCAGATCACCACATCGCGAAACACAACCAGTGACCAGCTCAAAGATGACATAGCGTGATACCATGGCCAAGTTAAGAGGCCGAGAATCCCCTGAACAC[C/T]ACAAAACTGCATAAAATAACCACAGCTCCAATCTGAAACACACGCTCAGAGAAATACACACACCGAAGCTTCGACCAGACAGTCGA
104178 A T TAAAATAACCACAGCTCCAATCTGAAACACACGCTCAGAGAAATACACACACCGAAGCTTCGACCAGACAGTCGAACCACCAGACAGTTGCAGAAGTCAG[A/T]AAACAAAAACAAGCTACAAACCAGCAGCGATAAATCGCTCTATTCCAAGATCTTGACTCATCAGAGCAGGCCTTGGAACTGCCTTTG
104178 CA C ATAACCACAGCTCCAATCTGAAACACACGCTCAGAGAAATACACACACCGAAGCTTCGACCAGACAGTCGAACCACCAGACAGTTGCAGAAGTCAGAAAA[CA/C]AAAAACAAGCTACAAACCAGCAGCGATAAATCGCTCTATTCCAAGATCTTGACTCATCAGAGCAGGCCTTGGAACTGCCTTTGGG
104178 A G GGAACTGCCTTTGGGAGTATCTTACCGTGTTAACCGAAGACAACATACCTGCCATTTAAGTGGGCTCAAGAGCATCGTCGTAGTGCAGTTCTAAACTTCG[A/G]CAGAAAAGAAACTGGGTTTCTAGAAGAGAAGCAGTTTGAGTATTCAAGGAAAGGAAACGCACGTTACCCAAAAAAGATGAAGATC
104178 A T TACCGTGTTAACCGAAGACAACATACCTGCCATTTAAGTGGGCTCAAGAGCATCGTCGTAGTGCAGTTCTAAACTTCGACAGAAAAGAAACTGGGTTTCT[A/T]GAAGAGAAGCAGTTTGAGTATTCAAGGAAAGGAAACGCACGTTACCCAAAAAAGATGAAGATCTGAAATAGATCTGAAATTAGAAA
104178 A G TAAGTGGGCTCAAGAGCATCGTCGTAGTGCAGTTCTAAACTTCGACAGAAAAGAAACTGGGTTTCTAGAAGAGAAGCAGTTTGAGTATTCAAGGAAAGGA[A/G]ACGCACGTTACCCAAAAAAGATGAAGATCTGAAATAGATCTGAAATTAGAAAAGGAGGTAACGCACGCTGGCACGCTCGGTTAC
104178 T A TAACGCACGCTGGCACGCTCGGTTACGTGGACATGGAAGAAAGCTTGGAAGAAATGGAGGAAGCGATTTGACTGAGGACATGAGAGAAAGGGAGATACAG[T/A]AGAAAAAGAATGGGAAAGAAGCGGATGAAGAAAAGGGGAGACCAAGTCCCCATGGCCAACGTAACACGACCGGCTTTTGAC
104180 A G TATCATTTTTCCCACACCAGGTGATCCAACAAATATAATTTTGTCAACTGAGGAAACAAGAGCTTGTCCAGTTTCAGCAAACCCTGTAATCACATGAACT[A/G]GATTTTCTGGAGCACCAACAGCAGCTAAAGCAGCTTGAATGATTCTCAGATAAAAGCATCCTGACCAACTGGCATTTTCTGAAACTTTA
104192 G A CCCTTCCCCATCATCTCCATTACATACTTCCTCGCCTCCTCCATCTTCCCGTCCCTACTGAGCCCCTTTATCAGCACCCCGTAAGTATAAACATTCGGCA[G/A]CACCCCACACGTCAGCATCCTCTCGAACGACCTAATCGCCTCCTTCGAGTGCCCTCCCGCGTTCGCGTAGGCCTCGATTACGGCGGTGTG
104192 G A GCATCGTGCCTTTGTCTTTGATCACCGCGAACAGATCTAGGGCTTCGTGGGTTAGTCCGTCTTTGGATAAGGCGTCGAACATTTTGATGGCGCTGTTTGT[G/A]AGGCCTTCGGATCGCATGTTGTGGAAGACTTCCTGAAGATTGGATGGGTCTTTTGGATTTCTGATGGCGGGTTTTTTGTTGAAAGGG
104192 GT G GCGTCGAACATTTTGATGGCGCTGTTTGTGAGGCCTTCGGATCGCATGTTGTGGAAGACTTCCTGAAGATTGGATGGGTCTTTTGGATTTCTGATGGCGG[GT/G]TTTTTTGTTGAAAGGGTCGTATGGTGGCGGCAGCTCCGATGGTGGGATGGTTTTAGGGTTAGGGTTAGGGTTTTTTGAGGAATC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104192 T A ATCGCATGTTGTGGAAGACTTCCTGAAGATTGGATGGGTCTTTTGGATTTCTGATGGCGGGTTTTTTGTTGAAAGGGTCGTATGGTGGCGGCAGCTCCGA[T/A]GGTGGGATGGTTTTAGGGTTAGGGTTAGGGTTTTTTGAGGAATCTTCGTCGTCGGACCAATCGAATGAGGCGGTGGTGTTGGTGA
104192 T C GGTGGGATGGTTTTAGGGTTAGGGTTAGGGTTTTTTGAGGAATCTTCGTCGTCGGACCAATCGAATGAGGCGGTGGTGTTGGTGAAGGAGGTGGAGAGGG[T/C]GCGGACGGAGGTAGGGAGGAGCTGGTAGCGGCACTTGATGGAGTGGCGGTAGATGGATAAGAAGGTGCTGGAGATTAATGA
104192 G A GTGGGATGGTTTTAGGGTTAGGGTTAGGGTTTTTTGAGGAATCTTCGTCGTCGGACCAATCGAATGAGGCGGTGGTGTTGGTGAAGGAGGTGGAGAGGGT[G/A]CGGACGGAGGTAGGGAGGAGCTGGTAGCGGCACTTGATGGAGTGGCGGTAGATGGATAAGAAGGTGCTGGAGATTAATGAT
104192 C T GGTTAGGGTTTTTTGAGGAATCTTCGTCGTCGGACCAATCGAATGAGGCGGTGGTGTTGGTGAAGGAGGTGGAGAGGGTGCGGACGGAGGTAGGGAGGAG[C/T]TGGTAGCGGCACTTGATGGAGTGGCGGTAGATGGATAAGAAGGTGCTGGAGATTAATGATGACGCCATTAAGGGTTTTTTGA
104192 A G TTGGTGAAGGAGGTGGAGAGGGTGCGGACGGAGGTAGGGAGGAGCTGGTAGCGGCACTTGATGGAGTGGCGGTAGATGGATAAGAAGGTGCTGGAGATTA[A/G]TGATGACGCCATTAAGGGTTTTTTGAGAAGACTAAGGAGAGTACTTAAGATGGACCAAGATTTTAGAGCGGACAAAAAATC
104198 GA G CTTTCCACAGGGTTTTATTCAACCACATAAACTTGATCAAAAATAAGGATCACGTATCTCACAAACAATCTCTTTTTATAATTTGACCCAAAAAGGGAAG[GA/G]AAAAAAGGAAATAGCTGACTCATCAAAACAAGCACGAAGACGACAACCGCTGCCAAAAATTAATAATACTTGCTCTGGAATCGACCA
104206 C T GGCTAATGGGCCCTTCTTTAAGCCCATCAAGTTCATAGAGGACTCCATTTACTGGAATATAGCTTATGAAGTGGTACACTTCGTCATCTTTATCAGCGGC[C/T]TTTTGCTCTTCAGGTACGAATGGTTCAGGCCTTGCAAAGCTGTTATGGGCGGTCCGGATCGCTTCACTGTTATTGATTGCTAAGCCTTT
104206 AG A GCTTCACTGTTATTGATTGCTAAGCCTTTGAGGTCAGAAGGGAAGTTTTTGGTGAACTCTTTGAGGTTTGATAGCTCAGGGCCTATGTCGATGTCAGGGG[AG/A]GTTGAGTAAGATGGAAAGAATAGCTTGGGTTGCACAAGCATTATTTATGACCTGACTAGCAAAGAAAAGGTTGGGGTTTGGCTCT
104208 T TG CACTGCTAGGGGTTCGGCAGGGTGGTTCCACGTGAGGTGTGATGTTAAAGGAAGTGAATAAAGAAGGGGGAGTGTTTGGGATGGATACGTGAGTGGTGCA[T/TG]GGGGGATTTTGGTGTGGCCGACGTGAATCGATGGCGTTGGTTTAAAACAAAGTGGTGAAGCAGCGTTTGGTATTTAAAAGA
104238 C T TCAACGTCGTGGAAGTGGAGAAAGTTGGCCTCTGTTGATGTGGGGCCCATTGAGCGGTCGCGGGCCTGGCGGTTGTGGGTGGAGGATCCGATGTAGTGGA[C/T]GGGTATGGAACGAGAGGAGAGGCGGAGGGCAAGGTGGAGGAGTTGGTTGAGGTGGCCTTGGGCTGGGAGAGGGAGGATCG
104254 T C CGACATCACGTGCAACGGTTGCACGCAGTATCTCTTCACCGCGCCCAGTGGCTGAGACAGCACATAGAGAATTGGCGTACGTGCCTGCACCAATGACTGG[T/C]GTGTCACCAATTCGGCCCACCATTTTGTTTACGAGCCCACCTGTGGATGTCGCTGCTGCTAGGTTTCCTTTGCTGTCGATCGCAACA
104254 A G CACCAATGACTGGTGTGTCACCAATTCGGCCCACCATTTTGTTTACGAGCCCACCTGTGGATGTCGCTGCTGCTAGGTTTCCTTTGCTGTCGATCGCAAC[A/G]CATCCCACTGTTCCGATTTGGCTGTCACCATTTTCTGTTTTTGCTGTGTGAGGTGTCACTGGCGGAGTGAAATCTATCTGGACCCGGTT
104254 G A AACGACATCAAGGGCTGATTTGCCATCAGATGTGAGGGCGTCGACGCCGAGGTCAAGACATTGTCGAAGCGCCGCCTCGCGAGGAAGGCGACGATCAGGC[G/A]GTAAGTTGAATGGGATATCACCTGCTCCACCATGTAACGCAATCGCCCATCTTCCCATTAAATTAAACTAAGGACAATCTGGTTA
104258 A T ATCAAACTACTACTCTGATGCCTTCTGGCTTAATTAACGGGGAAGAAGCGAGACCTAATCCGCCATACAAATGGCAAAGGGTATTGCTTAAAGTGAGTGG[A/T]GAAGCACTTGCTGGAGACAATAAGCAAAACATCGATCCAAAGGTCACTATGTCAATTGCTCGGGAAGTAGCTTCTGTAACTCGGCT
104258 A G TGAATGCAATATTTCTGCAAGCAACAATGGAAAGCATCGGCATTCCGACTCGTGTTCAAACCGCATTTAGGATGTCAGAAGTTGCAGAACCTTACATAAG[A/G]AGAAGAGCTGTGAGGCATCTGGAGAAGGGTAGGGTCGTCATTTTTGCTGCTGGAACAGGGAATCCATTTTTCACAACAGACACTGC
104258 G C GAGCTGTGAGGCATCTGGAGAAGGGTAGGGTCGTCATTTTTGCTGCTGGAACAGGGAATCCATTTTTCACAACAGACACTGCTGCAGCTCTTCGTTGTGC[G/C]GAAATTAATGCAGAAGTTGTGCTTAAAGCAACAAATGTTGATGGTGTGTACGACCAAGATCCTAAAGAAAATCCAAACGCTCGCCT
104276 C T TTCCAGGCACTGCTTCCATGTCCAGTTTCAGGGTGGTAGCAGTAGGCAGTGAGTATGTCGCAGTTACTGTTACATCTCCAGGATAACCTTCTTCGCCGTC[C/T]TTGCTGTGATACTTGAAGGTGATTGATGGCTTTTCACCGCCATTGATTTCAGTAACATCCCATATCACTTTGTCATATCCCCTATGACCA
104280 G A TGTAGCACAGCAAAGGCAAGAGAAAGAAGACGAAGAAGAAAAACAAGTCCAGCAAAAAGCCCGAGAAATAGAAGCATTCGATCAACAAAACCACGGAGCC[G/A]TCCCGCAGTACAATGACAGAAGCCACAACAACGAACATTCCGGAAGCTTCCACGGAGCGAACAGCGTGAAAACAACTTCATTC
104280 C T CAGACGCTCCCATCAAAGTCGAGGCCCCTTCGTCCTTCACTACATGTCCTGAAGGCAGAGAGAAGCTGAAACTAAAGCAGCTGTTTCCAATCCATTTAAC[C/T]GAAGAAGAGGGAGGTAAAAATGGTGGAAAAAAGAAATCAGAGCTGGAGAGGAGTTACATTTGCCCGAGCTGCAAGGTGACGCTTA
104280 A G TCCTTCACTACATGTCCTGAAGGCAGAGAGAAGCTGAAACTAAAGCAGCTGTTTCCAATCCATTTAACCGAAGAAGAGGGAGGTAAAAATGGTGGAAAAA[A/G]GAAATCAGAGCTGGAGAGGAGTTACATTTGCCCGAGCTGCAAGGTGACGCTTACAAACACACTTGCTTTGGTGGCGGTGAGCAC
104280 C T ATGTCCTGAAGGCAGAGAGAAGCTGAAACTAAAGCAGCTGTTTCCAATCCATTTAACCGAAGAAGAGGGAGGTAAAAATGGTGGAAAAAAGAAATCAGAG[C/T]TGGAGAGGAGTTACATTTGCCCGAGCTGCAAGGTGACGCTTACAAACACACTTGCTTTGGTGGCGGTGAGCACGTGCGGGCAT
104280 G A TGCGAAGCGACAAGGTCTGCTTGGTGTGCGGTAGGGGCTGCAAGGAGAAGTGTCTGGTGGCGCTGGAGAAGGGTGGGACTGGATTTGCTGGCCATGACGA[G/A]AATTTGGAGGCCAAGGATTTTAAGCATTTAGGCAGTGGATCTGGTTTGGGTTTGGTCCGGCCCGCTCAGAAAACTTGATG
104280 T C GAAGCGACAAGGTCTGCTTGGTGTGCGGTAGGGGCTGCAAGGAGAAGTGTCTGGTGGCGCTGGAGAAGGGTGGGACTGGATTTGCTGGCCATGACGAGAA[T/C]TTGGAGGCCAAGGATTTTAAGCATTTAGGCAGTGGATCTGGTTTGGGTTTGGTCCGGCCCGCTCAGAAAACTTGATG
104282 G A CATCAGCCGCTCCGTTCCCTCCCTCAAAGCATCCCACAGCTCCAGGGTTTCCATACATAGCGGCTTTACTTCTTCACTTTCAACTGTTTCCACGATTGCA[G/A]TGTCTGGAATTTCATCAACCAATGGTCTTTTGTACCTACCATATGGATCAAAATCGTCGGGTAGGTGATCTTCATTGGCATCTATGATCT
104286 T G ATAAGACTACTTTGCAGACACGCCGTGCCCTCTTTTCTGTTCTTTCCAGGTTCATCTTCTTCTACAATTTAGATCACATGCTTGAAGTTTTCCTCGAACA[T/G]TATCCTACTCCTAACAATGCTTTCCTGGTTGGTGGTGCAGCAGATTTCTTTGTGATTGAGCTTACTGATCAGCTACAAAAGTTAAAAATAG
104286 A G TGCTTGAAGTTTTCCTCGAACATTATCCTACTCCTAACAATGCTTTCCTGGTTGGTGGTGCAGCAGATTTCTTTGTGATTGAGCTTACTGATCAGCTACA[A/G]AAGTTAAAAATAGAACCGGTACTGCTACATTATCTCTCTCGTATGCGAGTCCTTCAAGGATGGGAGCTGAGGATGACAACAAGCACAA
104286 G T ATCCTACTCCTAACAATGCTTTCCTGGTTGGTGGTGCAGCAGATTTCTTTGTGATTGAGCTTACTGATCAGCTACAAAAGTTAAAAATAGAACCGGTACT[G/T]CTACATTATCTCTCTCGTATGCGAGTCCTTCAAGGATGGGAGCTGAGGATGACAACAAGCACAAGACTGAAGGCGTGTCTGTACAGC
104286 G A CTGTACAGCTTTACATCTCCAGGAGGTCCCATGTATCCAACTAGAGCTGTTCGTCATGCAGCCTGGGATACGCTAGACTTCCTCTTTCCTGTTGGGCGTC[G/A]CCCACGACATATGATAAGCCTCTTTTTCCGGCTGCTCTATCCTTGGTACTGGCCTTCTTCGTGTTGGAATTTCGTCACAACCTGCATCTC
104290 A C TTTCAGGGAACTAGGCATTCCAGCTTTTGGATTTTCTCCAATGGCAAACACTCCTATTTTACTACATGATCACAATGAGTTTCTGGACAAAGATGAGTAT[A/C]TTAAGGGAATTGGGATATATGAGTCAATTATTCGAAAGCTTGCATCTCACAGTAATGATGAATTTGACAAAGAAACAAGAGCAGAACT
104290 T C CATGATCACAATGAGTTTCTGGACAAAGATGAGTATATTAAGGGAATTGGGATATATGAGTCAATTATTCGAAAGCTTGCATCTCACAGTAATGATGAAT[T/C]TGACAAAGAAACAAGAGCAGAACTATAGGGAGCATTCAGTTTCATTACACACAAGTTCCGTTCTAGTTCATCCTTGGTATTCAAAGG
104290 A G TTCTGGACAAAGATGAGTATATTAAGGGAATTGGGATATATGAGTCAATTATTCGAAAGCTTGCATCTCACAGTAATGATGAATTTGACAAAGAAACAAG[A/G]GCAGAACTATAGGGAGCATTCAGTTTCATTACACACAAGTTCCGTTCTAGTTCATCCTTGGTATTCAAAGGCAGCAGTTGCAATATT
104310 T C CCATACCACCAGCCACCACAATATCATTGATACCAAGTTGAATACTTTGTGCAGCAAACATAGTGGCCTTCATTCCTGCTGCACAAACTTTATTTATTGT[T/C]GTACAAATAACAGAATTAGGAATACCAGCGCCTAATGCTGCCTGTCTAGCAGGAGCCTGACCCAAATTAGCACTCAGTACGTTCCCAAA
104310 G A CACAAACTTTATTTATTGTTGTACAAATAACAGAATTAGGAATACCAGCGCCTAATGCTGCCTGTCTAGCAGGAGCCTGACCCAAATTAGCACTCAGTAC[G/A]TTCCCAAAAAATACTTCTTGCACACTTGTGGGATCAACATTTGCTCTTCTAAGAGCACATTGAATTGCAATGGATCCAAGTTTGGTGGC
104312 G A CCAAACACAGCTCAAAATATTCTTCACAAATCAATTCGCTCAAAACCACAAATAAACGAACAACGATGACGTCAGGGTCTAGGCTGCCGTCGTGGAAGGA[G/A]AGAGAGAATAACAAGCGCAGAGAACGAAGACGACGCGCCATCGCAGCCAAAATCTATTCGGGGTTGCGCATGTACGGCAACTTCA
104312 A G CCACAAATAAACGAACAACGATGACGTCAGGGTCTAGGCTGCCGTCGTGGAAGGAGAGAGAGAATAACAAGCGCAGAGAACGAAGACGACGCGCCATCGC[A/G]GCCAAAATCTATTCGGGGTTGCGCATGTACGGCAACTTCAAGCTACCGAAACACTGCGACAATAATGAAGTTTTGAAAGCTTTG
104312 A G CCAACTCCCTCATTCCATGGTTGAAAAACCTATCGTCGTCGTCTTCCCCGTTCATGCACAACGGGTCCTTGAGCGCCCCCGTCACGCCTCCGTTAAGCTC[A/G]CCGAACATCCACTCTCCTAGACTCGACATTAAAAACGAACCCCGGTGGGCTTCCGGGTCCCAGTACTCGTATCTGCCGTCCTCATCCAC
104312 T C GGGTCTTCGAGGATGTGGACCCCAGGCCAGAGTGGGATGTGCTCGCCTGTTCTGATCGAGCCTGCTGGACCCAGAGACTTGTGTATGGTTGATTCCGGGG[T/C]GGAGGAGTTTGCATTTGGGAGCAGTTTGGTGAAGCCGTGGGAAGGAGAGAGGATTCATGAGGAGTGTGGGGATGATCTGGAG
104314 G A CTGTTGGCCTACTGGAACAAAAACCTAGCTCTCACAGGGTTTCCTTACTTCCGCGGCGCAAATCGTAATCGCA[G/A]TCAAATCACAAACTCTAATAGTATAAGGATTTCATTCTAATGGCGGGAGGTCAGCAAGCAGCAGCCAATCTCCTCACAAACCTAGCGAAAGCAGCCTTCG
104320 A G TACGCTTCCTGAGAGGGCGGTCTAGTGGGCTTGGGCTCCTACGCCGTGGAGAACGGTCATGTGGGCTCAAACTTCTGCGTCGTGGAGAGCGATCACGTGG[A/G]CTCAAACTTCTGCTTCTACCATAGCTTGGACTCCTGCGATACCTAGGAGGAGTTCTACTACGACGACGGCCATTGCCTACTCCTCC
104320 TCTG T TGAGAGGGCGGTCTAGTGGGCTTGGGCTCCTACGCCGTGGAGAACGGTCATGTGGGCTCAAACTTCTGCGTCGTGGAGAGCGATCACGTGGACTCAAACT[TCTG/T]CTGCTTCTACCATAGCTTGGACTCCTGCGATACCTAGGAGGAGTTCTACTACGACGACGGCCATTGCCTACTCCTCCAGAACC
104320 A T CACGGTTTCGACACTCACGAGCAAAATGACCCGACTCGCCACACTCATAACATTTCAAATCGCCTCCACCACCTCGGCCACGACCACGATCATCGCGGTC[A/T]CGACCACCACGACCACCACCTCCACTGCCACCATTTCTAGAGTTATGAGAAAGTTCAACTCTCCATCCATTTTTACCATCCAAGTCACG
104320 A G GGGCATCTCTGCGGTCATCAAATTCAATAAAAGCATAGCCTGGTGGCTTTCTAGCAACCCAAACACTTCGAATAACGCCGAATACACGAAATTCATCCTC[A/G]AGCTCACGTTCAGATACACGTGGATCCAAATTACCAACAAAAACACGAGACATTGTCCTCCCTTAAATCTGGTTGAAAAGGTAGATTT
104320 T C ACTTCGAATAACGCCGAATACACGAAATTCATCCTCAAGCTCACGTTCAGATACACGTGGATCCAAATTACCAACAAAAACACGAGACATTGTCCTCCCT[T/C]AAATCTGGTTGAAAAGGTAGATTTAAAATCTTGAATAGGAGGCTGGAATTGGGGAAGAAA
104326 A C AAGGTGGATGCCCTTTCGCTGGTGCCCCACTAGAGCTCTCAAACAACTTACTCTCCACATTACACGTCTGCACATCATAAAGCAAAACCTCACGCCTAGA[A/C]GCTTCAGTAGAGAGCGCAGCAAACATAGAACCTGAATGATTAAACCTAGCATACTTGCATCCTTCAAACGAATGTGAAGGACCAGTA
104326 T C GTGGATGCCCTTTCGCTGGTGCCCCACTAGAGCTCTCAAACAACTTACTCTCCACATTACACGTCTGCACATCATAAAGCAAAACCTCACGCCTAGAAGC[T/C]TCAGTAGAGAGCGCAGCAAACATAGAACCTGAATGATTAAACCTAGCATACTTGCATCCTTCAAACGAATGTGAAGGACCAGTAGAC
104326 G C TGATTAAACCTAGCATACTTGCATCCTTCAAACGAATGTGAAGGACCAGTAGACAAAGCAGAGGCATCCCATAACTTCACATCATACACAGTAGAAGAAA[G/C]TATCAACTGAGTCCCACTAGAAGACGCAGACTCTATAACAGATACAGGCCATTGATGACACAGATGACTCTCCAAAACATTCCCAGT
104326 C T AGGCATCCCATAACTTCACATCATACACAGTAGAAGAAAGTATCAACTGAGTCCCACTAGAAGACGCAGACTCTATAACAGATACAGGCCATTGATGACA[C/T]AGATGACTCTCCAAAACATTCCCAGTGTTCAGATCAAAAAGTTTCAGATCTCCAGAGTGGCTCCCAGTAGCAATTTGCCACGTATCAC
104330 G A CCCTCCTTCCAGTTCTTCCTCGTGGAATCCCCAAAAGAAGCTACGCCTGCTGCGTACAATTCGTTCTTCACGCACTGATTCTCAATCATTTTGCCCACCC[G/A]TCCGTGAGCCGTCGCTCGTATAAACCGCTTCATCGCCATTTGATTCAGTAATACATCAGCTCCCTTATCGATCTTCGCAAATAAGATAATG
104330 T C GAAGTCTGTTTCTTAGCCACTATTTCCCGTGGGCTGCACGGGCTGGCCTGAAGTGCACTGACTTGATGACTGTGTACTATGAGAAGCATTTTGATGAGGA[T/C]TTGGAGGGTGTTAGAAGGAAATGGGGGATTTTGCCTTGTCCTAAACCTAACATGAAAAGCTGATGGTAGCTTGTTTGTTCACTTAGT
104336 T C ACCGTCGATCCGCAATGGAGTATCCCCCGATAATTTCCTCCGCGGTCGAGCTGCAGCCGTGTTTTGATAACGTCGATCGGTTGCAGGCAGCAGGCTTCCA[T/C]TACTCCGCCAAGGGATCCCGAAAGCGCTCGAACGTGTGGTGGGATCGATTGCCTATTTTTGTTGTTTTGTGGAGAAGTGGTGGTAA
104336 C T TTTCCTCCGCGGTCGAGCTGCAGCCGTGTTTTGATAACGTCGATCGGTTGCAGGCAGCAGGCTTCCATTACTCCGCCAAGGGATCCCGAAAGCGCTCGAA[C/T]GTGTGGTGGGATCGATTGCCTATTTTTGTTGTTTTGTGGAGAAGTGGTGGTAACTTCACCGCTTGCTCCATTGGGAGGTGACATGA
104344 CA C CTGAACTAGACAAATACATCCATGGCAGCAACAGGAGCACTGTTGTTCTATCCACGGGTAGGGTACACACTTTTGTAATATCCGCATTGGATGAATCCGG[CA/C]AAAGAAAAGTGCACAGGTGGAGACTACTTCGAAACGGATCTTTCCGGAACTTTCTGGAAGTCCAGACCTCCGGTCACCGACCATG
104346 A G ACTCTCGGGTGATGATCACTGGGGGCTTGGGCTTGTTCTTGGATCCCGCAGGCCGGCCTCTTGGACGTCGGCCCATGACATCGGTTCCTCCGCTGTGCGG[A/G]TTGCCTGGAGAGCCATCCAGGTCTCCGTAAGGATTGATGCTGTTGTTGTTGTTATTGTTGTTGTTGCTGTTGTTGTTATTGTTTTCAT
104346 G GT GATTGCCTGGAGAGCCATCCAGGTCTCCGTAAGGATTGATGCTGTTGTTGTTGTTATTGTTGTTGTTGCTGTTGTTGTTATTGTTTTCATCTTCATCAGA[G/GT]TTGTTGTTTTGGTTGTGGTGCTGGAGCTGAAGGTCAGGATGGTGGTTTAGTTGATGGATGTATCTCGATGCTGTGCCTAGATCCAAG
104352 T C GTTCTCTTTCTCTCATTGCTTCTTCCGAGAAGTACTCCCCATTCTGCACCAATGTTTCCAGATAAGCCCTGCGGCGATTCTTCACAGCAACAGACCTCGA[T/C]TTGACAAGTTTAGGATTAGGATTAGGATCAAGAATGACACTGAGCCTTGATAGATGAAATTGGATGGAGTAATCATAAGGAAGCTGCT
104352 G T CTCTTTCTCTCATTGCTTCTTCCGAGAAGTACTCCCCATTCTGCACCAATGTTTCCAGATAAGCCCTGCGGCGATTCTTCACAGCAACAGACCTCGATTT[G/T]ACAAGTTTAGGATTAGGATTAGGATCAAGAATGACACTGAGCCTTGATAGATGAAATTGGATGGAGTAATCATAAGGAAGCTGCTGCA
104360 C CG TCGTCGAGTTCTTCCATGACGAGTAGAGAGCGAGATCGTGAGCTTCTGATTCCTGTCTGTGACGCCATCACCGAAGATGACCGCGACTCCAATAAAGCCT[C/CG]CGCCGCCGCCATCCAGCACCACTCAGGAAGAGAGGCATTTTCTAAAGTAGTGCGGAGTTGGGCATCCAAGAAGTTTATGACGGG
104360 T TG CTTTTCTCCAATATACGCTCAGCTTGGGATCAATATATTTGGACTTGGTTTCATAACTTCCATTTTGTTCATCTTCTTGGTTGGAGTATTTATGTCATCA[T/TG]GCTAGGTGCGTCTGTTCTTAGTCTGGGAGAGTGGTTTATCAAAAGGATGCCATTTGTAAGGCACATTTACAACGCATCTAAACAGATTA
104368 T A CGTCGTATGCGCAGATTGAGCTATCGCAAACTGAGGTCGTTGTTGTATTGCCAATAAACAAGCTACCACATTTAGCTGCAGGACAGGAAGCACTCAGCTG[T/A]ATCATTTGGGTTGGGCGGCAATCCAATTGCCATGACATGGAGCTGCAGCTACATTGAATGCAATTGTTGGCAGTGAAGACATAACT
104368 T A GGCAGTGAAGACATAACTACCATTTGGAACTAGCAGATTGTTGTCACGAGATGTGTTGCTTATTGAAGATGAACATGCTTTCAAAGGCACATCAAGAGGC[T/A]GTCCAGCCATCAACTCTTTGGGATCCTTCAACCCATTAACCTCCAACAGGACCTTCTCATCAACCCCAAACCTATCCCCAATCCCACC
104368 A T CAAGAGGCTGTCCAGCCATCAACTCTTTGGGATCCTTCAACCCATTAACCTCCAACAGGACCTTCTCATCAACCCCAAACCTATCCCCAATCCCACCCAA[A/T]GTAGCTCCCATTTGCACAACCAGTCCAAAATGGACCACCTTCATCCCATCCACCTCATCGCACCCGCAAGGAAGCGGTATCTTCAGCTCC
104368 T C ATCCCATCCACCTCATCGCACCCGCAAGGAAGCGGTATCTTCAGCTCCTGCCCCGTCTCAATCAGATTCGGATTCGTAATATTATTGAAAGCCGCGATTT[T/C]CTGATAAGTCACCAGACCGCCGAACACCGTACGCGCGATGTAGTCGAGACCGTCCCCAGTCTTGACTTTGTACATCGGAGGCCGACTG
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104368 C G CACCCGCAAGGAAGCGGTATCTTCAGCTCCTGCCCCGTCTCAATCAGATTCGGATTCGTAATATTATTGAAAGCCGCGATTTTCTGATAAGTCACCAGAC[C/G]GCCGAACACCGTACGCGCGATGTAGTCGAGACCGTCCCCAGTCTTGACTTTGTACATCGGAGGCCGACTGGGGACGCCGGTGCCGT
104368 A G CAATCAGATTCGGATTCGTAATATTATTGAAAGCCGCGATTTTCTGATAAGTCACCAGACCGCCGAACACCGTACGCGCGATGTAGTCGAGACCGTCCCC[A/G]GTCTTGACTTTGTACATCGGAGGCCGACTGGGGACGCCGGTGCCGTTGGCGGTGCAATGGCAGGCGAAGCGGATGCGGACGGTG
104368 G A TTGACTTTGTACATCGGAGGCCGACTGGGGACGCCGGTGCCGTTGGCGGTGCAATGGCAGGCGAAGCGGATGCGGACGGTGGAATTGGGCGGGAACTGGT[G/A]TGAGAGGGGAGTGTTCAGAGGGAGGCTGTTGGCAGAAAGGAAGGCGCGCATGGAGTTGACGTTGAAAAGGGTTTTGATGT
104374 G A CTGTTGGCCTACTGGAAATTAATCAGAAATTAAAAAAGATAAAAATGCCATGTTGTTCTCTTCTATCTTCAAACCCTCCGTCTCT[G/A]ACTTCATCTAACGCATCAAAATCTATCACTTTTCTCCCGCCATCCTACCTCCCGATCTCAAAATATCCCAATGCTATTCCTTTGTTTTCGATATCATGTC
104374 G A TGAAAAGCTTTTTCAGGGGAAAGAACTTGAGTTCTATAAATGGGAAGGAGATGTCCCAACGTTGTTGAGTGATGTGAGGGATAAACTAAACAAGCTTGGA[G/A]AGCATTGGTCTCGTGATGTTAAAAATCAATGTTTAAGAGAAGCTGCCAAGGCATTTCGGTATTCCGGCCAGATTGTTCGCCTTATA
104374 G T GGCCAGATTGTTCGCCTTATAATTACATAGGCAAAGTTCCCTTTTCCATTCAGATTGACAATGATGTTAGTAAATTTGGAGAACTGATGTTAGTAAATTT[G/T]GAGAACGCAAGAGTTATTGTTTTCAAAAGCAGTTTGGAGACATCAACTTGGTTGTTTTTGTTTT
104380 G GCATT TACATTTAATGAAATGGTAATACACTCATGCGTCCATACCCTTCCTTCTAGGCTAGCAAAGAGCATTCAAGACATTAGTTCATGATCTTTTGTTTGATCT[G/GCATT]CATTCATTCATTCTTTCCAAAAACACCATGAGATTAGTTTCACATGGAAGCGATCTGGTAAAAAATGATGTGCAAAAGTCTAGGAA
104380 A T CTGGTAAAAAATGATGTGCAAAAGTCTAGGAAAAGGTTCTGATTACAGAATATGAGTTAACAGTAGACGACAATTGTCCGAGAGGGACAATAAGAGGCGG[A/T]AGTTCCGAGAATCTGCCAATATGGCCAGATAGAAGATTAAAGGAAGTTCCAGTGTCAGGACATCACCAATGTACTGTAGGCAGT
104380 A T GACAATAAGAGGCGGAAGTTCCGAGAATCTGCCAATATGGCCAGATAGAAGATTAAAGGAAGTTCCAGTGTCAGGACATCACCAATGTACTGTAGGCAGT[A/T]GCATTTCTAATTGGCTCATAGATGGTGCCAGATATTTTAGATGGAGGCCAATATCGAAATACAGATCTCCCAACAATATTCTTTATA
104380 C T CCCAGTTATGAGAGTCGATGCTGTCGTTTCGATTATCACCTAGCACAAAGACACATCCGTCCGGTACTACCACTGGCTTCATCTCATAAGCAGGTGGCTC[C/T]AATATGTAGTCTTCTTCTTGAGCAATTCCATTAACATATAGTTCCCCATTGCGAACTTCAACATAATCTCCAGCTGTCGCAACGACTCTT
104380 T A CGATGCTGTCGTTTCGATTATCACCTAGCACAAAGACACATCCGTCCGGTACTACCACTGGCTTCATCTCATAAGCAGGTGGCTCCAATATGTAGTCTTC[T/A]TCTTGAGCAATTCCATTAACATATAGTTCCCCATTGCGAACTTCAACATAATCTCCAGCTGTCGCAACGACTCTTTTGATGAAGACATCA
104380 A G CACCTAGCACAAAGACACATCCGTCCGGTACTACCACTGGCTTCATCTCATAAGCAGGTGGCTCCAATATGTAGTCTTCTTCTTGAGCAATTCCATTAAC[A/G]TATAGTTCCCCATTGCGAACTTCAACATAATCTCCAGCTGTCGCAACGACTCTTTTGATGAAGACATCACCAGACTTGTATCCTTTTTCC
104382 T C TCGCCTTCTTCACATTCTCAGGCAGTCTCAACGTATATCGCTCCATATCCTCTCCATGTCCCCTTCCTGCATGCCCAATCGTATATGACCTGAACTGTCT[T/C]CCTCTTTTCACACTCACAAACCGCTCTAACTCTTCCATCTCTTGCCTCCTCCCTTCGTCATCTTCGATCTCGATCACTACTTTGTCATCACTGT
104382 A G TACTTTGTCATCACTGTCTTTGCTTTTGACGGGCTCAGTCAAATTGCACCTGCAGACCGGGCACGTGACATGTGCGGCGAGCCAGGCATCGATGCAGTCT[A/G]CATGGAACGCGTGGCTGCAGTTGGGAAGCAGGCGTAGAGTTTCACTGTCTTCGAAATCGTTTAGGCAGACCGCGCATTCGAGTGTG
104382 T A ACTTGGAAAGGTTGTGATGTTTGACTTGGGAGTAGATTAAGGTGGGGAAGGAAGAGAGTGTTTCGGGGGTTAGGCCATGACGTTTGGTGGAGAGAGTGAG[T/A]GTAGGGGATGGAGTGGGAGAAGTGGAGTTCGTGGCGATGCACTGACGGAAGTAGACGGAGAAGAAGGTGAGGAAGACAAA
104382 T C GGGGATGGAGTGGGAGAAGTGGAGTTCGTGGCGATGCACTGACGGAAGTAGACGGAGAAGAAGGTGAGGAAGACAAAGGCGGAGATTAGGATGATGACGA[T/C]GAGGATCGACGGTAGTGAGTTCATCTTTGCATTTTGGAGGGTGGGGTGGTTGTTTGGGGTTGGAGGCGTTTGGGCGGTGG
104382 TG T CGGAAGTAGACGGAGAAGAAGGTGAGGAAGACAAAGGCGGAGATTAGGATGATGACGATGAGGATCGACGGTAGTGAGTTCATCTTTGCATTTTGGAGGG[TG/T]GGGGTGGTTGTTTGGGGTTGGAGGCGTTTGGGCGGTGGAGGTACCGGAGGTGATGGTAAGGAAGAGGAGGAGGAGGAG
104382 T C ACGATGAGGATCGACGGTAGTGAGTTCATCTTTGCATTTTGGAGGGTGGGGTGGTTGTTTGGGGTTGGAGGCGTTTGGGCGGTGGAGGTACCGGAGGTGA[T/C]GGTAAGGAAGAGGAGGAGGAGGAGGCGGCTCTGGAAATGCATTTTTGTGTTTGTGAAAATCCAGTAGGCCAAC
104392 A G GGGTACGAGATAACACTCAACGTTGCCTCCTTCTCTGGCTGTTCCTCTTCCCTCAGTTTGATTCTGCTGCCAGCAACAAACTGGAAGTTGCTTCTGCATT[A/G]TTGGTAAGGGTTTTTAGGTTTCTGCTTAGTGTATGTTATGCGATGTTTGAGTCTGTTGGGTTGTTCATAACCTTGGTTACCTGAGAGTTG
104394 G A CACAAGCTGTTTTGGATCACTTGAGCATAACCGCCCTTCGGCAATTAATTCTTTGCTCCCACTCCAATCGTACAGCTTGCATTTCTTCTCTGTGCTACTA[G/A]TTTCACCCGCGCGTAAAACAACTCTATTAGCTGGCCACGCTACTATATGATCCTCGGCATCTCCAATATACGTCAAATTAGGTGTAGGCC
104398 GA G CCAATAGCATGGGGTCTACCCAACTACTTAGTAGATCAACTTCAGGCATTACAACTGATCTCCCTGAGAGACCAGATCAAGCTGACTGTCAATACTACAT[GA/G]AAAAAAGGTAGCTGTAAATTTGGTACTTCTTGCAAATACAATCACCCAAAAGGAAGGCGTTTCGAGAGTCTTGCTACTGTTGGACC
104398 T A AGACCTGGGAATCCTGTCTGCAATTTCTACGCTATATATGGCACCTGTGGATACGGTCTCGGTTGCAAGTATGACCACCCATTCATGGGATATTACAACT[T/A]TGCCACACCCGCTGTCTCCATGCCAGATGCTTGCCTCTTCCCTCAAAATCAGAGTACCAAGCAAACTGGGAAATCACCCAACTCGAAC
104398 T A CTATATATGGCACCTGTGGATACGGTCTCGGTTGCAAGTATGACCACCCATTCATGGGATATTACAACTTTGCCACACCCGCTGTCTCCATGCCAGATGC[T/A]TGCCTCTTCCCTCAAAATCAGAGTACCAAGCAAACTGGGAAATCACCCAACTCGAACAACAGGGAAGCAAAATCAGAAATTGATTGTA
104398 T C GCCTCTTCCCTCAAAATCAGAGTACCAAGCAAACTGGGAAATCACCCAACTCGAACAACAGGGAAGCAAAATCAGAAATTGATTGTAATGATGAGACTAA[T/C]GGTGAATCAACCCCTGCTCAACATCCCGTGGAATAAATTATAAATCTCATTCTTCATACATTTCTGCTTGAATTTTTTAATGCCTGAAA
104400 A G TGAATCTTTCTTCGTCATAAAAGGTAGCACGAACTACTCTACCACCAAAAAATCTCCCATCCAGATCAACAAGTGCTTTTGTGGTCCATTCCGACCTCTC[A/G]AATTGCACAAATATTCTAACTGCTTCATCAACCGGAAAATTGGGCTCTGTGATTTCGAAAATTAAAACACGTGTTACCGTGCCATACTTC
GACAAGCCGAAACGCGAATCAATTCAAGCAGAGGACGTTGCTGCTC
104404 G AGCTAAGCTCTTCCATGTGCCACCTCAGGCGCTTCCACGTAGACACCATGAATTAAAGGCCAATGCTGACGCTGACAAAGCAGACTACCTGCCCCGTCGA[GACAAGCCGAAACGCGAATCAATTCAAGCAGAGGACGTTGCTGCTC/G]ACAAGCCGAAACGCGAATCAATTCAAGCAGAGGACGTTGC
104408 T C TACCGGTGCCTGCCTCGCCTTTCGTTCTAATCATGGCCGCTCCTTCGCTTATCCTGCGCAGAGCTTCACCAAGCGATGTAGCTCCACAAACAAATGGGAT[T/C]CGGAAATTATGTTTGTTGATGTGATGGTCTTCGTCTGCGGGTGTAAGAACCTCAGATTCGTCGATATAGTCGATTCCGATGGCTTGTA
104408 G A CTCCTTCGCTTATCCTGCGCAGAGCTTCACCAAGCGATGTAGCTCCACAAACAAATGGGATTCGGAAATTATGTTTGTTGATGTGATGGTCTTCGTCTGC[G/A]GGTGTAAGAACCTCAGATTCGTCGATATAGTCGATTCCGATGGCTTGTAGAATCTGGGCTTCCACGAAATGGCCTATCCGCACTTTCG
104408 C A GTAGCTCCACAAACAAATGGGATTCGGAAATTATGTTTGTTGATGTGATGGTCTTCGTCTGCGGGTGTAAGAACCTCAGATTCGTCGATATAGTCGATTC[C/A]GATGGCTTGTAGAATCTGGGCTTCCACGAAATGGCCTATCCGCACTTTCGCCATGACAGGGATCGTCACGGCTTCTACGATTTCTTTG
104414 A G AATGGATTGCTGGTGCTATGACTCTTTCCGCTGCAGCTTACACGCTTCAAGGTCAGGAGGTGCATGCAGCGGAGCTTGAGCGCACTTTCATTGCAATAAA[A/G]CCTGATGGAGTTCAAAGAGGATTGATCGCTGAAATTATATCTCGTTTCGAGCGCAAAGGCTACAAACTTGTTGGCGTCAAATTGGT
104414 T C GGTTCCAACCAAGTGAGTTGGTTTCTTTCACAAGCAATGCAGAGAAGTGGGTCTATGGAGAGAACTGATGTTCGACAGATCTTCATCAACCTTTTCCATG[T/C]TATTTTTCAATTAACTGTTTAATTCTTGCTGCTCCAAAATTTTCCTGTGGAGCAGATAATAAAATGTAATTCTGCAAATGGACTACTTAT
104416 G T ATTGCACCAGAAATAATCTCAGTCAGCTCAGTAGTGATCGATGCTTGACGAGTCCTGTTATAGGTGAGAGTTAGCCTGTCAAGCATCTCCCCAGCATTTC[G/T]GCTAGAACTGTCCATGGCTGACATTCTTGCTCCCAGTTCACTGCAAGCATTTTCTAGCACGGCATTGAACATAACACAAGAAAACTGG
104416 A G AAGAAAACTGGAACTCAGCAAGATTTTGAAGTATTTCAGATTTTGTTTCGCCTCCTTCAATCTCATATGCACCCAGATCACCAAGCTTACCCCCAGACTC[A/G]GATTCTCTTTCAATTATCTCAGGTGATAGTATCGTTGACACTGTTGGAAAGAACTGAACAACAGATTGGAACCTGTTGTACACAACCCT
104416 A G TGCCTTGGTGATCTTTTGGATATTCTTTACACTTTTCATACGATTTCTGACAATTTGGGTTGAAATTGATCGAGCACCTAATGGACATGATTCCTCAGAT[A/G]TGACAGAGGATCTTGCAAAGATAGTAGGATTAGGCGTGAGAATGAGACGCCTCCCTTCTCTTCTCATAGCCGCCATCGCCATAGCTATA
104418 G T ATAAAAACTTCTTCAAATACCCATAAACGATCGAGTCATCGATTGCCAGTGTTCTTTAGCCAATCGAACCCTCTCTGTTCTTTCTCTTTGCAGCCTCTCC[G/T]CCCAGTAATCTGGACAGCTTTTGCTCAATAGCATGTTTAGCTCCCCCATAGCTACAGCCCCATTGAATACCCCCACCCTACGACACAGAGG
104418 T G TCCGCCCAGTAATCTGGACAGCTTTTGCTCAATAGCATGTTTAGCTCCCCCATAGCTACAGCCCCATTGAATACCCCCACCCTACGACACAGAGGGCATT[T/G]GGCTTTAGGATTAGCTGACTTTAAACCATAAACGATGGGAGCAGATGCTGCAGAAGTACAGCACGAGAAGCAAAATATATGGCCACA
104418 T C TAAGCGTCTCGATGTGCAAAGCCTGAGCTTGTGTTCTGAATTCCTGTCCTTGCTTAGAATAGTGAAGCTTGTCATATTTCTTCAAAATTTTCCTCATGGC[T/C]ACAGAGTTGATTATGGCATAGGCAACTAGTTCTCTTCCTTCTTGTACTAGGCTTTCGTGATCTTTATGCATGTTGACTTTAAAGCAAGAC
104418 A G TAGTTCTCTTCCTTCTTGTACTAGGCTTTCGTGATCTTTATGCATGTTGACTTTAAAGCAAGACAAAGATTTCCTAAAATTAGAAGTTAAATGAAACTCG[A/G]GTAATTTCTGTGCTCGTTTGTTGAAACAGCTGGAAACCGTCGACATCTCCTGGAGCAGCTCAGGGAAAAAACTTCCATCGCAAACTGAG
104418 T C GGAGCAGCTCAGGGAAAAAACTTCCATCGCAAACTGAGCAGCGTTCGGGGCAGGAATGACTCGAATCAGCTTCTACAGTATTTTGATCAATTTGATGAAT[T/C]TCGTTTCTACATTTCTTCAGTATTTTCTTTAATTTCTTCAATTCAACACCAGGCAGCTCCTTTTCTTTACCCTGCATGAACTGTTCGTAT
104418 T C TTCGGGGCAGGAATGACTCGAATCAGCTTCTACAGTATTTTGATCAATTTGATGAATTTCGTTTCTACATTTCTTCAGTATTTTCTTTAATTTCTTCAAT[T/C]CAACACCAGGCAGCTCCTTTTCTTTACCCTGCATGAACTGTTCGTATCTCTTACAAAATTTCATCTTTTCTATGATTTCTTTTACGTTAAACAG
104420 A G GGTGATTGGATTTGGGGTTGTTTCGTTTGTAGAAGAGGTTCTGAGCCATGCGTCGATTGCGGCGGCGGGCGTTGAGCTTCGCTTGACGGCGAATTTCGGA[A/G]TTGCCTTCGATTCTGCCTCCGGTTGACGGAGGGTTCTTTTTGCGGCCGGCGGAGGGCGGCGGAGGAGGAAGGGTGGTGGGTTG
104424 A G TTTCGGTCTATATGCACCATGCAGACTTAAGCACTGCATCATCAACCGCACCATGTCCCTCATTCCTTCAGAGGTATAACTTCTGTGCATTCGCCTGTCA[A/G]CGAAAGTATCCGCACCAATATGTGCTTCTGCCTGATATATCAATATCGTTCTACACATTAAATACTAGTATCAAAATGTTACTACCAGTG
104428 T C TATGCTACAATGGTCAAGATCATGAAAGAGAATCCTGCTCCTATTTCAGTTCCGGCGCCTGTTTCCACAAGGCCCGCACCTAAGAATCGTGAAAAACGTT[T/C]TAGTGTTGCACCTGTTGCAAGTCAAGTGTCTGCGACTAATGGATCTAATGTCATTGATAATAAAAACTCTCAAGACACAGAAGCTGAT
104436 G A AAAACAAAACCCCAATAATTCTTTCCACTCAATACAAATGGCTGAAGTGCACCAAAGTAACATCTCCAGCCTTAGCCTTCATTTGGAACACAGG[G/A]AAATTCCAAGCAGCCTCAGAACAAGGTTACCTAAACCTATCGTCTATAGTACGGCAGCAATCCTGTTTTAGGATCCCCAGGGCTTGATTGGCTC
104436 T C TTAACCCCCATTCTCTGCAATGCAGACTGCTGTGCTTGATAGTTCCCAATCACACTCGGGCTCATGGCGTTCACTCCGTATAAACTTGGTGTCGCACCAC[T/C]ATTCCCTCCATATAGACCATGCATCGCATTACTTACCTCCTGAGGGCCAGGGGTCACAGCCTTATTCAACCCCTGACCCAAAAAAGAAG
104436 G T GGTACCGAACAACACAAAGCCATAACCTTTGCATTGACTGGTGACGCGATCCAGGACCGCCTTGCAGTCCTCGATGGGGCCGTACTGTTTAAAAGCGTCG[G/T]TGAGAGTCTGAGTAGTACAGTCCCAACCAAGACCGTATACAAAGATCCTGCGATGCGAAGGGTCGGACTCGGATGATTTAGTGAT
104436 C T CCGCCTTGCAGTCCTCGATGGGGCCGTACTGTTTAAAAGCGTCGGTGAGAGTCTGAGTAGTACAGTCCCAACCAAGACCGTATACAAAGATCCTGCGATG[C/T]GAAGGGTCGGACTCGGATGATTTAGTGATTTTTGAGCGGAGGCTGGGGTGGCGAGGCAGGTATTCCGTTAGGAGCTCGACCAGC
104436 C T AGCGTCGGTGAGAGTCTGAGTAGTACAGTCCCAACCAAGACCGTATACAAAGATCCTGCGATGCGAAGGGTCGGACTCGGATGATTTAGTGATTTTTGAG[C/T]GGAGGCTGGGGTGGCGAGGCAGGTATTCCGTTAGGAGCTCGACCAGCTGCTCTTTTGTGAAGTGGGTGATTATGTGTTTCAGGG
104448 C CA AGAACAATGGTTTATATAGAGCTACATAATATTCAATAGTACATTTGAGTTAATAACAAAACCTCAGTATATAAATATACTACAGAAAACACTACAACTC[C/CA]AAAAAATACATCTCATAAAGCAAGTTCCACACCATAGAAACAACAAAACAAAATTGATCCAAAAAACACAGCAGCTTTCAGGCAACTT
104448 TTGC T AGGCAACTTAAGCTAACATAAATAGAATAAATATTTGAATGGAGAAGGAAGATGATCATTCGCCATTAAGAGACAACGAAGCCATCTGACTGTGAGGTAT[TTGC/T]TGCTGCTGCTGCTGCTGCTGAGCTACATCTTTAAGAACTTCCATTGCTTCGCCAACTTTTGCTTTCAAAGACTCAGGTGATTCGA
104448 G GA GCCATTAAGAGACAACGAAGCCATCTGACTGTGAGGTATTTGCTGCTGCTGCTGCTGCTGAGCTACATCTTTAAGAACTTCCATTGCTTCGCCAACTTTT[G/GA]CTTTCAAAGACTCAGGTGATTCGAGTAGATGCAACACTTCAGTTTGATCCATCTCAAGTAGCATTCCAGTAACTTTGGCAGCATGATC
104466 T C CATGCCTCATGATTATTTCCTATAGGTAGCCAAACAGTACAAATGGATTTACTAAATTGGGAAATCTACATATAGAACCGATAAATAAAGCTTTCAAAAG[T/C]AGTGAATTGGAAAATGTGAAAGCTAGAATAGAGTCAGGGTAGCAGAATATACTGAGGCATTTCATGCTCAAACTCATGTGTTACGCT
104466 T C AACCGATGAAGGGATGCTTTTCTCGCAATTGGAAGGCCTGATGAAGTAGCAGCCGGGGTAGGCCGAGGAGGGAGTGCTGCTTGCACAGTTGGCAAAGGAG[T/C]GGATGTCAAAGGCAATGGAGAGACCGGTGGCACAAAATTAGTATCCTTCTTGGTATTTGCACATCCTTTGCCTGCAAGCATCAT
104466 A T ATGAAGTAGCAGCCGGGGTAGGCCGAGGAGGGAGTGCTGCTTGCACAGTTGGCAAAGGAGTGGATGTCAAAGGCAATGGAGAGACCGGTGGCACAAAATT[A/T]GTATCCTTCTTGGTATTTGCACATCCTTTGCCTGCAAGCATCATCAAATCATTTGCCTTGTCCTCGGGAAAGTCATCAAAAACCA
104472 T A TATCGTCATCGCTACTTTCAGTAGCATCACGTTCCATCTGCACGTTGGGTTCCCCGAAATATTCTCAGTCCATTCCGAATTACTTTCCAAACTCGTCAAA[T/A]TGCTCTCTTCCTGCGTCAAACAAACTGCGGCGCGGTTGCGTCTTGATGGCTCTAGCAGGTACGTATGATGTGGAACTGGATGGTTCAAA
104472 T C ATCGTCATCGCTACTTTCAGTAGCATCACGTTCCATCTGCACGTTGGGTTCCCCGAAATATTCTCAGTCCATTCCGAATTACTTTCCAAACTCGTCAAAT[T/C]GCTCTCTTCCTGCGTCAAACAAACTGCGGCGCGGTTGCGTCTTGATGGCTCTAGCAGGTACGTATGATGTGGAACTGGATGGTTCAAAT
104472 C T TTCCATCTGCACGTTGGGTTCCCCGAAATATTCTCAGTCCATTCCGAATTACTTTCCAAACTCGTCAAATTGCTCTCTTCCTGCGTCAAACAAACTGCGG[C/T]GCGGTTGCGTCTTGATGGCTCTAGCAGGTACGTATGATGTGGAACTGGATGGTTCAAATCCTGATATTGTGGGAGAAAACGATTTATTG
104472 A G CATCATGAAGAATTAATCAGAGTTGGAATCCAGCCTTCTTTAAGAGGTCGTACACTTGGTACTCGATTCCCTTATGTAATATTCTGCGCTCCTCCGTCAA[A/G]GACTGATGATTATCCTGGTGATATTAGATTAGCAGCATCACATTGGAGTGGTGATGGCTGTTTCGTATTTACTTCGAGCACTGGTGTAT
104472 G C TGCGCTCCTCCGTCAAAGACTGATGATTATCCTGGTGATATTAGATTAGCAGCATCACATTGGAGTGGTGATGGCTGTTTCGTATTTACTTCGAGCACTG[G/C]TGTATATGATCGCAACGATAATGGGCATTGTGATGAGGATACTTCAATCGTGCCGCTTGGTAAAACCCCTCGGATAGATGTTCTTCTG
104472 G A AGATAGAGGTGCACATACCTACTGGTTGGAGAAGGGAACAGTTCCTCAACGTCCTGATCATGTAGTCAATCTGATTCACTACGAGGACGCCGCCTCACTT[G/A]CGGTTGCTATAATGAAAAAGAAGTTCCACGGTCGAACATTTTTAGGCTGCGACAATCATCCTTTATCCAGGAAAGAAATAATGGATA
104472 A G ACCTACTGGTTGGAGAAGGGAACAGTTCCTCAACGTCCTGATCATGTAGTCAATCTGATTCACTACGAGGACGCCGCCTCACTTGCGGTTGCTATAATGA[A/G]AAAGAAGTTCCACGGTCGAACATTTTTAGGCTGCGACAATCATCCTTTATCCAGGAAAGAAATAATGGATATAGTGAACAAAAGTGG
104472 A T TTCACTACGAGGACGCCGCCTCACTTGCGGTTGCTATAATGAAAAAGAAGTTCCACGGTCGAACATTTTTAGGCTGCGACAATCATCCTTTATCCAGGAA[A/T]GAAATAATGGATATAGTGAACAAAAGTGGGAAATTCAGCAAAAAGTTTCAAGCCTTCACAGGAAATGATGGTCCATTGGGGAAAAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104474 C A ACTCCTGGCTAACAACACCAGCAGCTCCAATTTTTTGGTTAATTTCTGCAATAATGGCAGTTGGGCCAGCAATTAAAGAAGTTCCAGAATCTGCAATGGC[C/A]GCACATCCTCCCGCACAAAAGCCTGTAGACTGACCGCCAACAAGAACATCTCCCATGTTGAACTGCCAGTAACCCTTCTGAGAAACAG
104474 GA G TCGCTCCTGTTCCGTAATGAATTGCCGCTGCCTTCCCATTCTTATGATATGTCGAGGATCGGGTTGATCTGTACTTTGAATGAAGGAGACAGGAAATCGA[GA/G]AAAAAACATTTGGAAGAGGGGACCCACAAATTAGAGCTGCCAGTGTCAAATATAACTGTAAACTTCTGTGGGGGAGAACCGATGC
104474 TG T TGTACTTTGAATGAAGGAGACAGGAAATCGAGAAAAAACATTTGGAAGAGGGGACCCACAAATTAGAGCTGCCAGTGTCAAATATAACTGTAAACTTCTG[TG/T]GGGGGAGAACCGATGCCTATTTCCCCGAAATACTGAGCATTCATATAATTCTTAAGGGCGACGATATCGGTCGGGTCGGAATCA
104476 AG A ATTACATAGTCGATGCAACTTCAGAAGAGGAATCTCAAATGAGCTCGGCTCTCACAGTATCTGTCAATAGGCACGGACAAATATGTGGGATTACTAAAAG[AG/A]GGGGGTGCCGGTCTGGATCCAAGTGTTATACTAGATATGATTTCAGTTGCAAAATCAGTGAGCCAACACTTCATATCTGTAATCG
104476 T A GCTCGGCTCTCACAGTATCTGTCAATAGGCACGGACAAATATGTGGGATTACTAAAAGAGGGGGTGCCGGTCTGGATCCAAGTGTTATACTAGATATGAT[T/A]TCAGTTGCAAAATCAGTGAGCCAACACTTCATATCTGTAATCGATTCCGAGATTGCTGCTGCTGAGGCTGCTGAAGCTGATTTATAA
104486 AG A AACTCTTCCCTCCACCCTTGCTTTTCGGTGAACTATTTCCACCGTTAGAGTTATGACCAGGATTAGTTTTACGGCCTGCTGGAGGAGTTGAGAACGGTGG[AG/A]GGGGGAGGTGCAGGACCCAAACTCCATGAATTACCATCAGTCTGAAGATTGTTTATCTTTTTTAGTTGGTCAGGGATCCATCCAGA
104486 T A ATCCAGAAAAACGGTTGTTTCCTAAATTTAGATCAGTGAGCGGAAGACCAATAAGGGCATTTACAGAACCAGTCAACTGATTGTTCTGTAAATAAAGTGC[T/A]GTCAGTCTTGATAGACTGCTGAAACTCTGGGGGAGATCACCAGTAATTGCATTGAAGGAGATATCCATAGTTTTAAGGTTGGAGAG
104488 CG C CTAATGTAATGCCTCAAAGTATAAAACGACCAACGACCCAATTCAGGCATAGGCATTACAAGTTGAACATTTGCGGATATTAACTGCTTGAAATCTTTGT[CG/C]GGGAGATCCAATAACAACTCTGTAACCCTTTTGTAAAACTTGTTCTGTAAGAGTGGCAATCACATCATCTGCTTCATAGCCACTGAGC
104494 C T CTCAAAACCCATGCGCCGTAGCCGTCGTCGAAATGAACCCGGACGGCAGTCACAAGCTCGTTGGCGAAATATCCGCGTACAAGCTCTGGAAATGCGACTA[C/T]CCAGCCGCTGCATGGGCCATGGAGAACCTAACCGCTCGTCAGTTCGTGATGGGCTCCGACGATAACGACGGCTGCTCTGGTATGG
104498 T C TTAGGTTTCAAAAGCAACAAAGAGACGTGTACCAAAACGGCATTGCAAATTACAATTTTGGTACAAGTGCAATCTTCAATTCATTAAATACTCGGTTCCA[T/C]AATATAAGAAGCAAACGATGTGTGCATTCACCAATAAGTTAGCGAACACAAATTACCTATCCTCTTATACTAAACAACAAATAATGCAG
104498 A C TCAAAAGCAACAAAGAGACGTGTACCAAAACGGCATTGCAAATTACAATTTTGGTACAAGTGCAATCTTCAATTCATTAAATACTCGGTTCCATAATATA[A/C]GAAGCAAACGATGTGTGCATTCACCAATAAGTTAGCGAACACAAATTACCTATCCTCTTATACTAAACAACAAATAATGCAGTTACATT
104498 T C GCAGTTACATTTGACTTTGTATTCAAATGTGTAATAGGAGAAGGATGTTATTTCAATATTGGCAAGAACATATCTAGCAGTTCCAGTAGTCTCAACTGGT[T/C]GACGCTTTCTGGCGCTTTTGAATGTCAAAATGGACATCAATGAGATCAGTTATGCCGGCTGTAATCCGTTGCCCAGCTTTTACAGGGC
104498 C T GTTACATTTGACTTTGTATTCAAATGTGTAATAGGAGAAGGATGTTATTTCAATATTGGCAAGAACATATCTAGCAGTTCCAGTAGTCTCAACTGGTTGA[C/T]GCTTTCTGGCGCTTTTGAATGTCAAAATGGACATCAATGAGATCAGTTATGCCGGCTGTAATCCGTTGCCCAGCTTTTACAGGGCCAA
104498 A G TATTTCAATATTGGCAAGAACATATCTAGCAGTTCCAGTAGTCTCAACTGGTTGACGCTTTCTGGCGCTTTTGAATGTCAAAATGGACATCAATGAGATC[A/G]GTTATGCCGGCTGTAATCCGTTGCCCAGCTTTTACAGGGCCAACACCCTGTGGAGTACCAGTTAAAATGACATCTCCCTCCAACAGTG
104498 C T GGACATCAATGAGATCAGTTATGCCGGCTGTAATCCGTTGCCCAGCTTTTACAGGGCCAACACCCTGTGGAGTACCAGTTAAAATGACATCTCCCTCCAA[C/T]AGTGTCATTATTGAACTTATATGACTGATAAGAAAAGGAATCTTAAAGATCATATCTTTAGTTGAACCTTTTTGCTTGATTTCGTCATC
104498 G A CTGTAATCCGTTGCCCAGCTTTTACAGGGCCAACACCCTGTGGAGTACCAGTTAAAATGACATCTCCCTCCAACAGTGTCATTATTGAACTTATATGACT[G/A]ATAAGAAAAGGAATCTTAAAGATCATATCTTTAGTTGAACCTTTTTGCTTGATTTCGTCATCTATCTTAAGCCACAATTCAAGATTATCA
104498 T C GACATCTCCCTCCAACAGTGTCATTATTGAACTTATATGACTGATAAGAAAAGGAATCTTAAAGATCATATCTTTAGTTGAACCTTTTTGCTTGATTTCG[T/C]CATCTATCTTAAGCCACAATTCAAGATTATCAGGATCTTTGATCAATGACTTGGGCAAAATTTCACTGATTGGGGTGAAGGTGTCTTGTC
104498 G A TGATAAGAAAAGGAATCTTAAAGATCATATCTTTAGTTGAACCTTTTTGCTTGATTTCGTCATCTATCTTAAGCCACAATTCAAGATTATCAGGATCTTT[G/A]ATCAATGACTTGGGCAAAATTTCACTGATTGGGGTGAAGGTGTCTTGTCCTTTGGCGACAGTCCATGGAAGACCTGCAGACTTAGCAGA
104498 A T ATGACTTGGGCAAAATTTCACTGATTGGGGTGAAGGTGTCTTGTCCTTTGGCGACAGTCCATGGAAGACCTGCAGACTTAGCAGAAGCTTGGATTTCTCT[A/T]GCAGTCATATCCAATGCAAGTGCATAACCGCCAACATATTCCATGGCGATTGCTTCTGGAACTTCGGTAGCTTTCTTCCCAATCACAA
104500 G T ACTCGTGTGCCTGTAATCGTGGAACATATCGATAGCAGCCTGGAGATCAAACGACCAAGTTACATGTTCTCCTTCCTTCTTCAGGTTGCTGCCTATCCAT[G/T]CTGAAAGAGATCTGGAAAATCCAAGTGCAACCATGCGGTCTACGACCCACTTTCGAGATGGAAGTGGCGTGGGTAAACTTTGTAGAG
104500 C CT CATGCTGAAAGAGATCTGGAAAATCCAAGTGCAACCATGCGGTCTACGACCCACTTTCGAGATGGAAGTGGCGTGGGTAAACTTTGTAGAGTGTGCAAAA[C/CT]TTTTTCCACTTCTCCATCGCTGTCATCCTGATTCACCTCTCCAGGGACAGAGTCTAACACCCAAATCTGTTTAGGCAACACAGCAG
104500 T C TTCGAGATGGAAGTGGCGTGGGTAAACTTTGTAGAGTGTGCAAAACTTTTTCCACTTCTCCATCGCTGTCATCCTGATTCACCTCTCCAGGGACAGAGTC[T/C]AACACCCAAATCTGTTTAGGCAACACAGCAGATTCTCCATAGTCACCACGGGCACAACTTGCTGCGTAGGCTAAGGCAACTTTTCCAC
104500 G A ACGAAAGCAGTTGAACTGGAAGGCTTTTCAGACGACGAAATTTCCTCATAAGCTAGTGTCTCTATATTTCTATACTCCGATCGCTTCACTAAACTAAAGG[G/A]CAACTGGTTCGAAAATAGAAGACGGGATCGAAGAGCAAAATTCGACAGCGTTTTCGCCATAATTTTTTTATCAATCCACGGATGTGTT
104528 G A AAAATTTAAATTTCAAAAACAAGAACATTCATCATCACAACTCTCCACGAACAACATCACGATTTATTAACCGCGACAGGGGGCA[G/A]CCCAACGCTTCGATTAGCGCAAAACTGCTCGCCGCCGCCGCCGCCGCCATGGACGACGAAATGACCAACCTGCCCCTCCCCCTTGACCAGATTCTCGCCG
104528 T C AAAATTTAAATTTCAAAAACAAGAACATTCATCATCACAACTCTCCACGAACAACATCACGATTTATTAACCGCGACAGGGGGCAGCCCAACGCT[T/C]CGATTAGCGCAAAACTGCTCGCCGCCGCCGCCGCCGCCATGGACGACGAAATGACCAACCTGCCCCTCCCCCTTGACCAGATTCTCGCCGCA
104528 TCGC T AAAAACAAGAACATTCATCATCACAACTCTCCACGAACAACATCACGATTTATTAACCGCGACAGGGGGCAGCCCAACGCTTCGATTAGCGCAAAACTGC[TCGC/T]CGCCGCCGCCGCCGCCGCCATGGACGACGAAATGACCAACCTGCCCCTCCCCCTTGACCAGATTCTCGCCGCACAGAAACTCCT
104528 C A TATTAACCGCGACAGGGGGCAGCCCAACGCTTCGATTAGCGCAAAACTGCTCGCCGCCGCCGCCGCCGCCATGGACGACGAAATGACCAACCTGCCCCTC[C/A]CCCTTGACCAGATTCTCGCCGCACAGAAACTCCTCACTGTACCTCCTCTCCACCTCCCTCTCAAAATCATGCACGATAACATCCGTCT
104528 C T TAACCGCGACAGGGGGCAGCCCAACGCTTCGATTAGCGCAAAACTGCTCGCCGCCGCCGCCGCCGCCATGGACGACGAAATGACCAACCTGCCCCTCCCC[C/T]TTGACCAGATTCTCGCCGCACAGAAACTCCTCACTGTACCTCCTCTCCACCTCCCTCTCAAAATCATGCACGATAACATCCGTCTTCC
104528 A C CGAAATGACCAACCTGCCCCTCCCCCTTGACCAGATTCTCGCCGCACAGAAACTCCTCACTGTACCTCCTCTCCACCTCCCTCTCAAAATCATGCACGAT[A/C]ACATCCGTCTTCCCCTTTCCCCTCCTCGCCATCACCGCTGCCGTGAATATCGCCGCCATCCTCCCCGGTGACTCATCCGAGTACCCCCTCG
104528 C T TCCTCGCCATCACCGCTGCCGTGAATATCGCCGCCATCCTCCCCGGTGACTCATCCGAGTACCCCCTCGGTCCATCCACGATTATCACATCCCAGTCCAC[C/T]TCATAAAGTTCATTCGGCAGATCGTTAATCGCCAGCCGACACTCCGAGAACAGCAGATTCTGAACAGGCCTGCAGTCGCCGTTCACCT
104528 T C ATCACATCCCAGTCCACCTCATAAAGTTCATTCGGCAGATCGTTAATCGCCAGCCGACACTCCGAGAACAGCAGATTCTGAACAGGCCTGCAGTCGCCGT[T/C]CACCTTCGATTTCGCTTCCGATACGAGCTCGTCCGCTTCCTTCACCTTCGTCGAGTACGCCACGTCGTACGCTTCGATGTTGGGATGC
104528 C T TACGCCACGTCGTACGCTTCGATGTTGGGATGCTTGTCCTCGAAGTGTTTAATGTAGTACTCGTTCTCGTCCAGGATGACGGTCCTGCCGCCGTGGTTGA[C/T]GGATTTCCACAAGAGGGTCTCGGGGCCGAGGCCGAAGATGAGGAGGTTGGAAGGAGATCTGCGGCGGAGGAGGGAGGCGATGG
104528 A G CGGCGGACATGCTGCCGGCGGAGGCAGAGGCGGTGGTGGCGTAGTGGAGGAGGGAGTCGTAAATCGGGAGAGGGAGGGAGGTCTGGGGAAAACGGGGATC[A/G]GGTTTGGGGCTGGACAGGGAAGCGCGGTTGTTAGAGGAAGAAAGGAAGGTGAAGAAGGAGGCGAAGGAGAAGAAGGT
104528 A G AGGTGAAGAAGGAGGCGAAGGAGAAGAAGGTGATGATGAAGATGAGGAAAATGCGAGAGGAGGAGGAGAAGATGAAGTTTTGCTTGTGGAGAGAAGGCTG[A/G]AGAAGGATTAGTTTAGTGTTGCCGTTCATTGCGGTCTTCATTTTTAATTAGGAGTATTATATATGGTTTAATGGATATTTTTCG
104534 A G GCTACAGAAGAGAAGGGGTTAGTCCAGCTGAGAAGGTACAAAAAAGATCACCCATTTGCGCAGCTATCTGGATCCGATAACATAATAGCGTTCACGACAG[A/G]AAGATACAAGGACCATCCTTTAATAATTCGTGGACCTGGGGCAGGTGCAGCGGTCACTGCTGGTGGTGTATTTAGTGATATATGC
104546 A C TTTGTGTCAAATGATTTGAGATATTTAGACTTGTGTTCATGGAAAAGACTGAGAAATGTGTCCATCAGGCCTTCGACTAAGATACCAAGTATTTTCTCTA[A/C]CAATGGTTTGGCACCAGCAAATACCTCGGCGTGCACAGCCACAAGACAATGCAACAATTCCAGAGTTGCATCCCGGATACCCTTCACT
104554 A G AAGCCTGTTGAAGCTGATGTCTATGTAAGTGAGGTTTTTACCAAGGCAATCGGGTACAGGACCCGTGAGCTGGTTCTGGGCCAAACGGATTTGGGTCAGC[A/G]TGGGGAGGCGGCAGATGGACTTGGGTATGCGGCCCGTTAGGAGGCTGTTTTGGTCGATCTGAAGGAGGGTAAGATGGTGGAGT
104554 G C GAGGCTGTTTTGGTCGATCTGAAGGAGGGTAAGATGGTGGAGTTTGCCTATGGTGTGAGGAATGGTGCCTGTGAGTCGAGTGTTGTGGGATATGATTAGG[G/C]TTTCGAGCTTGGAGAGCTGGCCTATGGAAGGAGAGATCGGGCCATTGGCTTCGGTGAACTGAATGAGAAGGAAGTTGACTCTG
104554 G A GAGTTTGCCTATGGTGTGAGGAATGGTGCCTGTGAGTCGAGTGTTGTGGGATATGATTAGGGTTTCGAGCTTGGAGAGCTGGCCTATGGAAGGAGAGATC[G/A]GGCCATTGGCTTCGGTGAACTGAATGAGAAGGAAGTTGACTCTGCCGCTGGTGGGGTCGCATATGATTCCAAACCATGCACAG
104554 A G TGCCTATGGTGTGAGGAATGGTGCCTGTGAGTCGAGTGTTGTGGGATATGATTAGGGTTTCGAGCTTGGAGAGCTGGCCTATGGAAGGAGAGATCGGGCC[A/G]TTGGCTTCGGTGAACTGAATGAGAAGGAAGTTGACTCTGCCGCTGGTGGGGTCGCATATGATTCCAAACCATGCACAGCAGTC
104558 T C TCAGAAAAATGTAGAAAAATAGTGAAGTGCCATGCAACTTGATCCACAAGATAGAAGCAATATAGACATGACTAAGAATCAAGCCATCAACAGACGCAGG[T/C]CTGGCCCAAAGGCAAGACGGATGAGACATTTGTCTAGGGCACTGTCACCAGAGGCGGTGAAGAGCACCAGCAAGTAGCCAATGC
104558 A G GCAACCTGGGTTCAATTCCTGGCACTTCTCCTATAAAGTTGCCGAGGGCACCAAATACTTACGGGTCGCCACTGAACAGACGTTACTATAACTTGTTCTT[A/G]CTAAGCAGAAGAACTAGCCTGACGAAGTGCAGATAGCCACATCGCTCATCAAATCACCTCAAGCTTCCACATCTACAAAACCAGAGA
104558 A G GGGTTCAATTCCTGGCACTTCTCCTATAAAGTTGCCGAGGGCACCAAATACTTACGGGTCGCCACTGAACAGACGTTACTATAACTTGTTCTTACTAAGC[A/G]GAAGAACTAGCCTGACGAAGTGCAGATAGCCACATCGCTCATCAAATCACCTCAAGCTTCCACATCTACAAAACCAGAGATCCCCTCT
104564 G A TGAATGTTATTTCTGGAGATCCCAATAAACAGTCTAAGCAGAGGTCACCATCACCAGTGGTAAAGAGGACTTCGGAGTCGAATAATAATGCGTCTCTTGG[G/A]AACTTTACCAAGTATGTTCCTAACCGAAAGTGGACAGATGGGAGCTTTTCTTGGTCATCAATTCCGTCATCTCTATCAAAGCTGGGG
104564 A G AAAGAGGACTTCGGAGTCGAATAATAATGCGTCTCTTGGGAACTTTACCAAGTATGTTCCTAACCGAAAGTGGACAGATGGGAGCTTTTCTTGGTCATCA[A/G]TTCCGTCATCTCTATCAAAGCTGGGGAAGGAAGTACTGAAATATAGAGATTCTGCACAACAAGCAGCTATTGATGCTATACAAGAG
104564 C T TGGGAACTTTACCAAGTATGTTCCTAACCGAAAGTGGACAGATGGGAGCTTTTCTTGGTCATCAATTCCGTCATCTCTATCAAAGCTGGGGAAGGAAGTA[C/T]TGAAATATAGAGATTCTGCACAACAAGCAGCTATTGATGCTATACAAGAGGCAACGTCTGCTGAAAGCTTGATCCACTGCTTAAGCA
104564 A T TTGGTCATCAATTCCGTCATCTCTATCAAAGCTGGGGAAGGAAGTACTGAAATATAGAGATTCTGCACAACAAGCAGCTATTGATGCTATACAAGAGGCA[A/T]CGTCTGCTGAAAGCTTGATCCACTGCTTAAGCATGTATGCAGACCTATGCTCATCAGCTAAAGTGGACAATCCACAGCCAACAATAG
104564 C G TCATCAATTCCGTCATCTCTATCAAAGCTGGGGAAGGAAGTACTGAAATATAGAGATTCTGCACAACAAGCAGCTATTGATGCTATACAAGAGGCAACGT[C/G]TGCTGAAAGCTTGATCCACTGCTTAAGCATGTATGCAGACCTATGCTCATCAGCTAAAGTGGACAATCCACAGCCAACAATAGAACC
104564 T C ATTCTGCACAACAAGCAGCTATTGATGCTATACAAGAGGCAACGTCTGCTGAAAGCTTGATCCACTGCTTAAGCATGTATGCAGACCTATGCTCATCAGC[T/C]AAAGTGGACAATCCACAGCCAACAATAGAACCAATTCCTCTCCTTCCATGCCTGCCTCGCTTCTTCTTCTCAGATTTCCAATTCCCTGCT
104564 AC A TACAAGAGGCAACGTCTGCTGAAAGCTTGATCCACTGCTTAAGCATGTATGCAGACCTATGCTCATCAGCTAAAGTGGACAATCCACAGCCAACAATAGA[AC/A]CCAATTCCTCTCCTTCCATGCCTGCCTCGCTTCTTCTTCTCAGATTTCCAATTCCCTGCTCAAATCAGTCTCCTTTTCTCATTCCAACAC
104566 C A GATTGCTAAGCACGGGAGGTTGAAGGAGCACTGTGCTAGAAATTACTTTAGGCAGCTTGTTTCTGCTGTTGATTTTTGTCATAGCCGTGGAGTTTATCAC[C/A]GAGATCTGAAGCCAGAGAACTTGTTGCTTGATGATCAAGGAAATTTAAAGATAGCTGACTTTGGTCTTAGTGCATTTGCTGGAGAAG
104566 A G GCCGTGGAGTTTATCACCGAGATCTGAAGCCAGAGAACTTGTTGCTTGATGATCAAGGAAATTTAAAGATAGCTGACTTTGGTCTTAGTGCATTTGCTGG[A/G]GAAGATGGTTTGCTCCATACGAGATGCGGGACTCCAGCATACGCAGCACCTGAGGTTGTTGAAAAGAAAGGTTACGATGGTGCTA
104566 T C ATGGTTTGCTCCATACGAGATGCGGGACTCCAGCATACGCAGCACCTGAGGTTGTTGAAAAGAAAGGTTACGATGGTGCTAAGGCTGATATATGGTCCTG[T/C]GGAGTCATCTTGTATGTTTTACTCGCTGGTACTCTTCCATTTCAGGATGACAATCTTGTGACCATGTACCGAAAAATTCATAAAGGC
104566 T G GATGCGGGACTCCAGCATACGCAGCACCTGAGGTTGTTGAAAAGAAAGGTTACGATGGTGCTAAGGCTGATATATGGTCCTGTGGAGTCATCTTGTATGT[T/G]TTACTCGCTGGTACTCTTCCATTTCAGGATGACAATCTTGTGACCATGTACCGAAAAATTCATAAAGGCGACTTCAAATGCCCTTCA
104566 C T TACTCGCTGGTACTCTTCCATTTCAGGATGACAATCTTGTGACCATGTACCGAAAAATTCATAAAGGCGACTTCAAATGCCCTTCATGGTTCTCTTCCGA[C/T]GCTCGTCGCCTAGTCACCAGACTCCTCGACCCAAACCCGAAAACCCGTATTTCGATTGAAAAA
104568 T C ACGAAATGCGCAAGCGTGCCGAGCTGAAGGCGTCCATCTCGGAGCTCGAGAAGCCATGGGAGCTGGTGGAGAAGGCGCCTGTTTTGTTTTCCATCAAGGC[T/C]GATGATCAGGTCAAGGCTTTGGCCGACAGGTTCCAAAAGCCTGGTGGGTTCGACATGTGGTCTCCTCGCGACGGGCCTCAGATA
104568 T A AGCTCGAGAAGCCATGGGAGCTGGTGGAGAAGGCGCCTGTTTTGTTTTCCATCAAGGCTGATGATCAGGTCAAGGCTTTGGCCGACAGGTTCCAAAAGCC[T/A]GGTGGGTTCGACATGTGGTCTCCTCGCGACGGGCCTCAGATACTGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAA
104568 T A TCGAGAAGCCATGGGAGCTGGTGGAGAAGGCGCCTGTTTTGTTTTCCATCAAGGCTGATGATCAGGTCAAGGCTTTGGCCGACAGGTTCCAAAAGCCTGG[T/A]GGGTTCGACATGTGGTCTCCTCGCGACGGGCCTCAGATACTGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAAGGT
104568 G T CGCCTGTTTTGTTTTCCATCAAGGCTGATGATCAGGTCAAGGCTTTGGCCGACAGGTTCCAAAAGCCTGGTGGGTTCGACATGTGGTCTCCTCGCGACGG[G/T]CCTCAGATACTGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAAGGTTTTTCCCAAAAGGGGTTGTACATAGCGTGAAA
104568 C T GTTTTCCATCAAGGCTGATGATCAGGTCAAGGCTTTGGCCGACAGGTTCCAAAAGCCTGGTGGGTTCGACATGTGGTCTCCTCGCGACGGGCCTCAGATA[C/T]TGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAAGGTTTTTCCCAAAAGGGGTTGTACATAGCGTGAAACCGTACGGG
104568 G GT GGTTCCAAAAGCCTGGTGGGTTCGACATGTGGTCTCCTCGCGACGGGCCTCAGATACTGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAAG[G/GT]TTTTTCCCAAAAGGGGTTGTACATAGCGTGAAACCGTACGGGATTCATAGTGTTGACGATGATGATTCTATCATGAACTTTGATG
104568 C T GCGACGGGCCTCAGATACTGGATACTAGTACCAGTCGTGTGGCTTTTTCAAATAGCGGAAGGTTTTTCCCAAAAGGGGTTGTACATAGCGTGAAACCGTA[C/T]GGGATTCATAGTGTTGACGATGATGATTCTATCATGAACTTTGATGATTGGATTAGTAGAGGTGCAGGTGGGGTTAGGAAGAGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104568 T C GACGTGTTCGATTGAATGCCGATGAGAAAGAAGGCTGTATAGATGTTAAAGGTACTGTTACAGATATTAAGGACGATAACCAGAGAAGCACTGAAAATAG[T/C]GGTAGGAGAGCTGGTAGAAATAGGATTAACAGAAATCGAGAAAATAGTCAATTGGGTTCAAATTCAAAGAAGCTTGGGGAAAGC
104568 T G ATAACCAGAGAAGCACTGAAAATAGTGGTAGGAGAGCTGGTAGAAATAGGATTAACAGAAATCGAGAAAATAGTCAATTGGGTTCAAATTCAAAGAAGCT[T/G]GGGGAAAGCAATGGACGTAGCGGCCAAGATATTTCATGTAGTTCAGATTCAGATGTCATCTTGAAGAATAAATATAAAAATAAAG
104570 CT C AAATGTACAAAATCGACGACCATTTGGCCTGTGCCGTAGCAGGCATCATGTCCGATGCCAACATCCTAATCAACACAGCCCGTGTCCAGGCCCAAAGATA[CT/C]TTTTTTTCTTACCAAGAGCCCATGCCAGTAGAACAGCTGGTCCAAGCTCTGTGCGACACCAAGCAAGGGTACACTCAGTTTGGCGG
104570 C T ACATCCTAATCAACACAGCCCGTGTCCAGGCCCAAAGATACTTTTTTTCTTACCAAGAGCCCATGCCAGTAGAACAGCTGGTCCAAGCTCTGTGCGACAC[C/T]AAGCAAGGGTACACTCAGTTTGGCGGACTACGTCCGTTTGGCGTCTCCTTTCTATTCGCGGGCTGGGACAAAAACTATGGGTTTCAG
104570 G A TCAACACAGCCCGTGTCCAGGCCCAAAGATACTTTTTTTCTTACCAAGAGCCCATGCCAGTAGAACAGCTGGTCCAAGCTCTGTGCGACACCAAGCAAGG[G/A]TACACTCAGTTTGGCGGACTACGTCCGTTTGGCGTCTCCTTTCTATTCGCGGGCTGGGACAAAAACTATGGGTTTCAGCTTTACATG
104570 T C AAAGATACTTTTTTTCTTACCAAGAGCCCATGCCAGTAGAACAGCTGGTCCAAGCTCTGTGCGACACCAAGCAAGGGTACACTCAGTTTGGCGGACTACG[T/C]CCGTTTGGCGTCTCCTTTCTATTCGCGGGCTGGGACAAAAACTATGGGTTTCAGCTTTACATGAGCGACCCAAGCGGCAATTACGGA
104570 C T CCAAGCAAGGGTACACTCAGTTTGGCGGACTACGTCCGTTTGGCGTCTCCTTTCTATTCGCGGGCTGGGACAAAAACTATGGGTTTCAGCTTTACATGAG[C/T]GACCCAAGCGGCAATTACGGAGGCTGGAAAGCTGCTGCTATCGGTGGTAACAATCAAGCGGCACAAAGCATGCTGAAGCAGGATT
104570 T C AGCTTAGTAGGGAGGAAGCTGTTGAGCTAGCCCTGAAGGTTTTAAGCAAGACCATGGACAGTACTAGTCTTACTGCTGAGAAGCTTGAGCTTGCAGAAGT[T/C]TATTTGTTGCCTGAAGGCGAAGTTATGTACGAGGTTTGTTCACCTGATAAACTTGGCAAGTTGCTGGTTAAATCCGGAGTTACTCA
104570 T C AGCTAGCCCTGAAGGTTTTAAGCAAGACCATGGACAGTACTAGTCTTACTGCTGAGAAGCTTGAGCTTGCAGAAGTTTATTTGTTGCCTGAAGGCGAAGT[T/C]ATGTACGAGGTTTGTTCACCTGATAAACTTGGCAAGTTGCTGGTTAAATCCGGAGTTACTCAGCCAGCAGCAGAAGCAAGTTAAGG
104570 G A TGCAGAAGTTTATTTGTTGCCTGAAGGCGAAGTTATGTACGAGGTTTGTTCACCTGATAAACTTGGCAAGTTGCTGGTTAAATCCGGAGTTACTCAGCCA[G/A]CAGCAGAAGCAAGTTAAGGAATCATTAAAGTGGAAGTTTGATTGATTGAACCGAATGGTTATTTAAACTGTATTTGGTCATTTGAGC
104570 G A TTATGTACGAGGTTTGTTCACCTGATAAACTTGGCAAGTTGCTGGTTAAATCCGGAGTTACTCAGCCAGCAGCAGAAGCAAGTTAAGGAATCATTAAAGT[G/A]GAAGTTTGATTGATTGAACCGAATGGTTATTTAAACTGTATTTGGTCATTTGAGCCATGGTTAGACCTATTATTATGCTCTGTTCACT
104570 T C AGCAAGTTAAGGAATCATTAAAGTGGAAGTTTGATTGATTGAACCGAATGGTTATTTAAACTGTATTTGGTCATTTGAGCCATGGTTAGACCTATTATTA[T/C]GCTCTGTTCACTTTTTCAGCCTCCATCTGCTTTCTCATGGTTATATTTCGGTTAAAGGTAGTAAAAAAATATTGGTTCCTCTGTATTTGTT
104570 G A GAACCGAATGGTTATTTAAACTGTATTTGGTCATTTGAGCCATGGTTAGACCTATTATTATGCTCTGTTCACTTTTTCAGCCTCCATCTGCTTTCTCATG[G/A]TTATATTTCGGTTAAAGGTAGTAAAAAAATATTGGTTCCTCTGTATTTGTTAACTCCCTACCATGTTGATGCATGCAACAATTACTGTTTTT
104570 A G CTGTATTTGGTCATTTGAGCCATGGTTAGACCTATTATTATGCTCTGTTCACTTTTTCAGCCTCCATCTGCTTTCTCATGGTTATATTTCGGTTAAAGGT[A/G]GTAAAAAAATATTGGTTCCTCTGTATTTGTTAACTCCCTACCATGTTGATGCATGCAACAATTACTGTTTTTATATGATAATTCTTGGACTC
104570 A C CATTTGAGCCATGGTTAGACCTATTATTATGCTCTGTTCACTTTTTCAGCCTCCATCTGCTTTCTCATGGTTATATTTCGGTTAAAGGTAGTAAAAAAAT[A/C]TTGGTTCCTCTGTATTTGTTAACTCCCTACCATGTTGATGCATGCAACAATTACTGTTTTTATATGATAATTCTTGGACTCAAAAAAAAAAA
104574 A T ACTGGTGTGATTCTGTTCGTAAATTGGCTGACAAAAGTGCACAAACTATGATATGTCCAAGCAGTGGAGTGCATATCGTACTTCCTGATTATTATTCTCC[A/T]GAAGGAATGGGACTAATTGTCCCTAAAACGAAAGATGGTCGTGTTGTGTTCATGTTGCCTTGGCTAGGGAGGACCGTTGCAGGAACC
104580 C CT ACACCACCAAAAATATCGGCACATAGTGCCACTTGTCGTTCTTGAAGTAAAACCCAAAACCCGCCGTCATCGCACTAAGCATGAACCCTAGCAAGTTCAT[C/CT]TTCACAGGATCGGCTTGCACGAGCAATTGAATTGGGTGGAATGCCGGTAGGGAAATCGATGCAAACACGAAGTAAACCGTCCAAA
104588 A G TACTAAATTTTGATTCAATTCCAATCGGTGTATTACATGTTGCAAGCAACAAATTCACCATAATACATTTCCATTACACACGCTTATAATT[A/G]TAGTATATATATATATGTATGCATAGTAATTAAAATGGAGTATGCATGCCCACAAGTGAAAGATGGAGGCATTTCATTATTGTGCAGGTTCAACCTCCG
104588 A T ACACGCTTATAATTATAGTATATATATATATGTATGCATAGTAATTAAAATGGAGTATGCATGCCCACAAGTGAAAGATGGAGGCATTTCATTATTGTGC[A/T]GGTTCAACCTCCGTATCTGCTTTTGCATGATTCAGGGGGCACTTCTTCCATGATACCTGCACCTCTTGTTGTATTCAAATATTGCCTTAT
104588 T G GGAGTATGCATGCCCACAAGTGAAAGATGGAGGCATTTCATTATTGTGCAGGTTCAACCTCCGTATCTGCTTTTGCATGATTCAGGGGGCACTTCTTCCA[T/G]GATACCTGCACCTCTTGTTGTATTCAAATATTGCCTTATGGTTGTTTTTCTATCTCCCAGGAATGTATGGTCTAGGAAATTATCATACA
104588 G A CATGATTCAGGGGGCACTTCTTCCATGATACCTGCACCTCTTGTTGTATTCAAATATTGCCTTATGGTTGTTTTTCTATCTCCCAGGAATGTATGGTCTA[G/A]GAAATTATCATACACTTGTTCCCCTTGACTTTTCGCTGCTAGAACACAGTGCTTAAGGTAAACTCTGCATGGTAAAACATCATCTCGCCAT
104588 T C TTGTTGTATTCAAATATTGCCTTATGGTTGTTTTTCTATCTCCCAGGAATGTATGGTCTAGGAAATTATCATACACTTGTTCCCCTTGACTTTTCGCTGC[T/C]AGAACACAGTGCTTAAGGTAAACTCTGCATGGTAAAACATCATCTCGCCATATCTTATGTACCCCGTATTGCCCACATCTTTTGTATAAAAT
104588 C G AATTATCATACACTTGTTCCCCTTGACTTTTCGCTGCTAGAACACAGTGCTTAAGGTAAACTCTGCATGGTAAAACATCATCTCGCCATATCTTATGTAC[C/G]CCGTATTGCCCACATCTTTTGTATAAAATTTCTTTACTGCCTTTGCATCTGATATGAAAATACTCTTCGTCTGTGCTACTAGAACACACAAC
104588 C T ACACTTGTTCCCCTTGACTTTTCGCTGCTAGAACACAGTGCTTAAGGTAAACTCTGCATGGTAAAACATCATCTCGCCATATCTTATGTACCCCGTATTG[C/T]CCACATCTTTTGTATAAAATTTCTTTACTGCCTTTGCATCTGATATGAAAATACTCTTCGTCTGTGCTACTAGAACACACAACAGCTGGAG
104588 A G CTTGTTCCCCTTGACTTTTCGCTGCTAGAACACAGTGCTTAAGGTAAACTCTGCATGGTAAAACATCATCTCGCCATATCTTATGTACCCCGTATTGCCC[A/G]CATCTTTTGTATAAAATTTCTTTACTGCCTTTGCATCTGATATGAAAATACTCTTCGTCTGTGCTACTAGAACACACAACAGCTGGAGTCC
104588 T A TACTGCCTTTGCATCTGATATGAAAATACTCTTCGTCTGTGCTACTAGAACACACAACAGCTGGAGTCCCATGTGGTTTTCCATTAAAATCTTCAGGATA[T/A]ACGGCTAAAAATCTGTACTCATTCTCCCGTTCAATAAAGGCTGGCACCTCTTCTAATCTGATCTCAAAAACTGTTACAATCAGAGTTTCA
104588 C G AAACCAGAGACTTCCCCGGTTTCCTGATTCGCCAACCCAAGTCGAAAAAAGACAGACCCAACACCTGCGTATAGTCGGCGAAAGCCTCTAAGAACTCCAA[C/G]TCTGAAATTCCTTACTTCCGAAAACGTGCTTCTAGCGCTTTTCTCAGAGAGAAGTGAACCAAAACCGCAAATGGAGACATAGCCATC
104588 C A TTTCCTGATTCGCCAACCCAAGTCGAAAAAAGACAGACCCAACACCTGCGTATAGTCGGCGAAAGCCTCTAAGAACTCCAACTCTGAAATTCCTTACTTC[C/A]GAAAACGTGCTTCTAGCGCTTTTCTCAGAGAGAAGTGAACCAAAACCGCAAATGGAGACATAGCCATCTGGAGAAGACAGAGCTTTG
104588 A C AACCAAAACCGCAAATGGAGACATAGCCATCTGGAGAAGACAGAGCTTTGAAATCAGAGAGGTCGTTGAGCTCAACGTGGCCGTCTGAATGTCTACTGAA[A/C]GCAGGCATGGTTCAAGGATTTTCTTTTTCTGCTCTTCTTCCTCCTTCTCCTCCTTTTAAGGTGAAGAACTTGCCCTTGTTCACAAGCT
104588 A G GAGGTCGTTGAGCTCAACGTGGCCGTCTGAATGTCTACTGAAAGCAGGCATGGTTCAAGGATTTTCTTTTTCTGCTCTTCTTCCTCCTTCTCCTCCTTTT[A/G]AGGTGAAGAACTTGCCCTTGTTCACAAGCTCTTCTAAGTTAAGAACTTTCCCTTGTTTCTTTAAGTAATTAAGAACTTGTCATTTTTCTTCC
104590 C T TCAGCAACTGGAGCTGTTTAACGAATACAAGAAGAAGGTAGTAGCAATCGTAGGAGCTGAGAGAGCAGCCACAATATTTTCAAAAAGTTTATATGTAGTA[C/T]GTGCAGGTAGTGATGATGTGGCAAACACATACTTCCCTACACCATTCAGAAAAACAGTTTATGATATCCCTTCCTACTCCGATCTGT
104600 A G CGCAGAATCTCATCCGTCGGTGTGTTCTACGCCAACGTTTCAGGCTCTATACCATCCTTCGTCAGCGATCTTTCTGCCTTAACCTCCATCAACTTCTACA[A/G]TCTGCCTAATTTGACAGGCACCATTCCTTCTTCGATCACTAAGCTCGCTTCCCTTACCCAAATCACAATAGCAAAGTCAGGCCTTTCGGGT
104600 T C AGCTGAAGAATCTGAGGCTTTTGGATGTCAGCTATAATAAGTTGTGTGGAGCTATACCGTATATGAAGGCGTTTAGCGAGCTTCCGTTGGCGTTTCAGCG[T/C]AACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGAT
104600 G A TGTGTGGAGCTATACCGTATATGAAGGCGTTTAGCGAGCTTCCGTTGGCGTTTCAGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAA[G/A]GCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTAT
104600 A G AGGCGTTTAGCGAGCTTCCGTTGGCGTTTCAGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGT[A/G]CGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATG
104600 C G GGCGTTTAGCGAGCTTCCGTTGGCGTTTCAGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTA[C/G]GCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGT
104600 T C AGCGAGCTTCCGTTGGCGTTTCAGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTG[T/C]GGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTT
104600 T C TGGCGTTTCAGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATA[T/C]ATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTA
104600 C T AGCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCT[C/T]AGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATT
104600 A G GCGTAACAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTC[A/G]GCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATT
104600 AT A CAAGTGCCTGTGTGGAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTT[AT/A]TTTTTGTTTTGAAATTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATTATCTGT
104600 A T GAGCGCCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAA[A/T]TTTGTGCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATTATCTGTTTTACTTAGATCTTTT
104600 T G CCCTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTG[T/G]GCTTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATTATCTGTTTTACTTAGATCTTTTAGTGC
104600 C T CTTGTCTCCATGCAAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTG[C/T]TTTATCTTCTACCACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATTATCTGTTTTACTTAGATCTTTTAGTGCAG
104600 C T AAGAAGGCTGCTGGGGTTCGGAGAGTTGTACGCCTTGTGGCATGAGGATATATGAATCTCAGCTTTATTTTTGTTTTGAAATTTGTGCTTTATCTTCTAC[C/T]ACTGTTACTGCCTCATGTTGTCATTTATCTTATCTTATTAGAGATGATTATCTGTTTTACTTAGATCTTTTAGTGCAGCATGTAATA
104606 T TCAGTTTGGTTTCGCTGGTTTCATTCTTCGTATCTTTCTCCGCCTCGCTAGTTATCGTTGGTGCCATTCTTCGCCTCAATCAGGGTGTTGTGCTTTGCTTCTATCAATA[T/TCAGTTTGG]CAGATTGGGCGAGGCATCCTAAGAGGAGGAGAGAGGACATTAAGAAGGAGAAAACTACTGAATTTTATGTCTGTAATTCAG
104606 T C CCACCATCAACCCAACAACAAATCTCTGTATCCTACCTTCTAGGATTTACCATCGCTAACGTAGTCGGTCTCAAATACTAATCCGCCGCATAAATAACCG[T/C]GAACTAGCCTGCCTCTTCCGAGAACCTTTAAACCAGTACGACCCAAACGCCATCAAGGTTCTCAACACTCGCTCTGTCCAAGTAGGCCA
104608 G T TGAAATGGCTGAAATGTCCAAGCTTGTTGCACTTGTTCCATACTACATTGACCTTATCGGACGCTACAAATTAAGCTCTCAGGCACGGTCCAAAACTGAA[G/T]CAGCAAGATTGAAGTTGGTGCAAGAGGCCTATAAGGAACTACAACATGCAAGGCAGGAAGCAATACAGAGGAAGAAGTTGGAGAA
104610 A G CCTTATCGGAAAACTTCTGCCTCTGAACAGCAACTGAATCAAAGGGCGTTGGCAAGTCTTTAGCGTCTGAAGCGGAAGAAATTCGACCATCACGCCTACC[A/G]AGTGGAACTGACCAACTAGGCCCATTTGTCAGATCCACGGAATCACGTGCTGCTAGTGCCAGTATATCTGCACAAGATACAACCCC
104610 C G GCTGCTAGTGCCAGTATATCTGCACAAGATACAACCCCTGGACATGCAGCTTCTACCTGAGACTTCGCATCGTCTATAACTTCGAATCCTCTGAGGCCTC[C/G]GTTTGGTAACGCAGTTCTTTCAGACGATGGACCGGATATCAGTATCGACCCATCACAACCCTGAACAAAGCAGTCATGAAAGTGCAG
104610 T C ATCAGTATCGACCCATCACAACCCTGAACAAAGCAGTCATGAAAGTGCAGTCTAAGCACTCCAGGAGCTACAGTAAAGTCATTGTCGAAATGCTTCTGAA[T/C]AGTGGATCGAACAATTGCTTCGACCTTCGGACAAGAGGAAGCATAAAAGTCAGTTTGCAGTTGTGCATGAGAGGAGGATACAGTG
104616 A G CGATCTTGTTCTTGACATGAAGAACCTTCAAGTTCGGATGCCCTTTCACCTTCTCATTGAACTCCTTGTTCCCTATTTGTGGGCTTCCAAACACCACTGC[A/G]CATACAGGGAAGGCAGCCAGGCCATTTTCAACTATATCGAAAGCACTCAGCACGGCCAAGCTAGCGCCTAAGCTGTGCCCTACACATAT
104616 C G GAGGGATGGGGACGAGTTCGGGGTGGAAGACGTCAGCCCACTCGAGGTCGCGGATGGTGCCACGCCATGCGATGTAAATGTCGCGTCTTCCTGTGGCAAG[C/G]GAAGATTTGTCTGAAGAGACGGCGATGTAGCCGATCCAGTTGGATTCCCTGCTCCAGGCTTCACGGGAGAGGGAGAAGAGGA
104620 C T GCAAAGCTTCAGTATCTATGTGATGCCCGAATGAACGACTATAAGCACTGACCAGCAGTGAATTTCTCTTTCAAACGAAGCTACGACACAATCGACAGTG[C/T]GAGATGACAATAGACCTACCCCAGATTAGCATTACCATTTGCAAACCAACTGTGGTAATAAAAGCATTAAAACGTATTGAAAATCAA
104622 C T TATTAATATTATTACTATACATGTGATGATTCATGGACGACTGTCCATATGATAGAGGGGATGAAACAGTCTGAATTTGCTCTATCAAATTCTGCCTGTA[C/T]CGCTCGAGTGTCAAATTAACATCAACATCCCGGAAACTTAACGACGACTTCAATCGACTGTTGGGTAACTGAAGTGCTGGAATTTGGG
104622 C G GCGCGTTCTCGCCTGGATGGACGAAAGGGCACTCCGTCCAGTCGTGGGAGTAAGCCCTGGAGCAGGGCTTCACCTTGAACGTGTACATACGGAACTCGTC[C/G]GTGCCGTACAGCCCGTTTTTGATGTCCGGTAACGTCAGATCCAACGGGTACTCTTTCTTCTTGCTTTCGATCGCAGCGGTGGATTT
104622 C G GGCACTCCGTCCAGTCGTGGGAGTAAGCCCTGGAGCAGGGCTTCACCTTGAACGTGTACATACGGAACTCGTCCGTGCCGTACAGCCCGTTTTTGATGTC[C/G]GGTAACGTCAGATCCAACGGGTACTCTTTCTTCTTGCTTTCGATCGCAGCGGTGGATTTAGGGCTGGATTCCAGATCTGGAAGATT
104622 C A CCGTCCAGTCGTGGGAGTAAGCCCTGGAGCAGGGCTTCACCTTGAACGTGTACATACGGAACTCGTCCGTGCCGTACAGCCCGTTTTTGATGTCCGGTAA[C/A]GTCAGATCCAACGGGTACTCTTTCTTCTTGCTTTCGATCGCAGCGGTGGATTTAGGGCTGGATTCCAGATCTGGAAGATTGTGAGC
104622 C T TCCAGTCGTGGGAGTAAGCCCTGGAGCAGGGCTTCACCTTGAACGTGTACATACGGAACTCGTCCGTGCCGTACAGCCCGTTTTTGATGTCCGGTAACGT[C/T]AGATCCAACGGGTACTCTTTCTTCTTGCTTTCGATCGCAGCGGTGGATTTAGGGCTGGATTCCAGATCTGGAAGATTGTGAGCTGA
104622 T C GCTTCACCTTGAACGTGTACATACGGAACTCGTCCGTGCCGTACAGCCCGTTTTTGATGTCCGGTAACGTCAGATCCAACGGGTACTCTTTCTTCTTGCT[T/C]TCGATCGCAGCGGTGGATTTAGGGCTGGATTCCAGATCTGGAAGATTGTGAGCTGAAACCGAATCTGCAGGAAGGAAATCGGAGAG
104622 A G TACGGAACTCGTCCGTGCCGTACAGCCCGTTTTTGATGTCCGGTAACGTCAGATCCAACGGGTACTCTTTCTTCTTGCTTTCGATCGCAGCGGTGGATTT[A/G]GGGCTGGATTCCAGATCTGGAAGATTGTGAGCTGAAACCGAATCTGCAGGAAGGAAATCGGAGAGACAGCGGATTGCCTCAAAACG
104622 A G CGATCGCAGCGGTGGATTTAGGGCTGGATTCCAGATCTGGAAGATTGTGAGCTGAAACCGAATCTGCAGGAAGGAAATCGGAGAGACAGCGGATTGCCTC[A/G]AAACGGGTTTTGGCGCCGCCTGCAGCGGCGAGATCGAAAGCGGTGGCGCCGTCGGTTTCGGATCGGGAGTTGACGTCGATTTC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104630 A G AGAAAACAACGGAAAACATGAAAGATTCTAGTCAAACAAAGATAAACCCAGGTCCTCATCCGATTCCTCTTCCGGCTCCTCTTTCTTTTCCTCTTCCTTC[A/G]CAGCAGCTGGTGCAGCAGCACTACCTGCAGCCGCAGCTGGCGCAGACGTCTTAGCAAACTTGCTTGGATCCTTGAGGTACTCTTTGAC
104630 A G ACTTGCTTGGATCCTTGAGGTACTCTTTGACCTCCTCGGCCTGTGGGAAGGAGTACTCGGTGACAACAGCTAGAGCAAGGACATTCTTATAAGCATTAAT[A/G]AACATATGGGGAGCAGCAGCAGTGGTAGGGTAGGAGAGCGCTAGTGAAAGGGAAGCCACCATGGAAACACCAGCTGCAAACTTC
104630 T C GGAGCAGCAGCAGTGGTAGGGTAGGAGAGCGCTAGTGAAAGGGAAGCCACCATGGAAACACCAGCTGCAAACTTCTCAACTAGGTCGTCCTCTGTTAAAT[T/C]CAGAACCTCCGGGCTGAACACGGACCCATTGTCATACACCGAAAGGACAACAAGACCATATGAAAACGGCCTTATTCCAAGTTTG
104630 C A GGTAGGAGAGCGCTAGTGAAAGGGAAGCCACCATGGAAACACCAGCTGCAAACTTCTCAACTAGGTCGTCCTCTGTTAAATTCAGAACCTCCGGGCTGAA[C/A]ACGGACCCATTGTCATACACCGAAAGGACAACAAGACCATATGAAAACGGCCTTATTCCAAGTTTGGCAAGAAGGGCAGACTCTG
104630 G A CCGGAGCAATAAGTCCAACACGTGCAGGAGCTCCAACCTTGTATTTAGCAACTTCGTCGCTGACTTCCTTCAAATCTCCCTTTGTGAAAATCAAACCAAC[G/A]TTTCCCACTAGTAAAGGAAGCAGATTCAGATAATCTTTGTTTCCAGTTTTCTCAACTTGCACACGAATGCAACGCCTGATCAGAGTGTT
104630 A G CACGAATGCAACGCCTGATCAGAGTGTTCTTCCCCATCAGAATAATAGAATGGCCTCTCAATCCTCTTCGAATATTCTGCAGCTGATTCGATCCGACATT[A/G]TCGGCACCAACGATCAGCACTTTATCGTACTCTTCCAACAGCTGGCAAAGCTTTTGATCGTACCTTTCCTTCTTCTGGAACTTGGTCAGT
104636 C T TACCGGTAACACTCAAAGTAATCTTCCCTTTACCAGAAGAAGGATCCTTAATGTTCTCCTTACTCAACTCTTCTTCATCTCCCCTTCCTCCTGCTGGCAA[C/T]GCCACAGCATTGTCATACCCAGTTGACCCACCCCTACCCTTTGGGTCTAGGAAGGATGACCCTCTGTAGCTAGGAACCAAGAAGTCCCCT
104636 T A TAGCTCCCGTTGCGAGCAAAGCAGAGGTAGCAAGAGCAAGCCCTGCAAGTTTTGCAGCATCTGCACATTTCTGAGCTACATCTTTAATATCTGCATGGAG[T/A]GAGCAAGTGATCCTTGCATTTGATTCAAAACCAAATGCTTTCGACAAGTGAGAGTTTGAAGACTTGAGCTGTTGTCCGAACTTAGCA
104640 G GA TTTTTTTTTTTTTGAAAATTAAAATGGCTATCAATTGAATAAAAGCATCAGTTAACATATTACACAGTGAGAAACTGAACGAAGATTAGTAAG[G/GA]ATTGCTAAACGCATGGTCATTCTGCACCATACCGTATGAAGCAATCCCTTCTTTGAGTATCTTGAACCAAGGCTAAACCACAAAAGAAAACTCAC
104640 T C TCTGCACCATACCGTATGAAGCAATCCCTTCTTTGAGTATCTTGAACCAAGGCTAAACCACAAAAGAAAACTCACTAGCGAGAATGACAAAAGATCAGCA[T/C]GAGTAGGAAACATATACCCTAATCAGGTAGAAGCATCAACAAATTCTTCTGAATTTTAAAAGGGCGCGATGTGCAATCTTCTTCGTCG
104640 T C CAACAAATTCTTCTGAATTTTAAAAGGGCGCGATGTGCAATCTTCTTCGTCGATAGCTTGAATGCTGTCACTGGTAGCTCTTTTATATGGTAGCAACAAA[T/C]TGGGCTTTCTATCCTGAGAATCAGAAAACAGATCTAACAACACATTCGGCCTCGACCTCTTGAGCTCTCTACCATTAGAATTTCCTCCGA
104640 C T TTGTTTACTTCATCATCATCTTCTTCTTCCGTGCCTGAAGAACAAGAGCAGGAGCTCTCCACCGGCGGCTTCACCTCTGTTTCAGGCACAACCTGCTCAT[C/T]TCCTTCCTCCTCCTCCTCCTCGCTGTCGTCCTTTTCCTCATACTCATCTCCTCCAACCTCGCCGTCTACATTCTTGTTGTCGTTTCCGATCGT
104640 T A AGAACAAGAGCAGGAGCTCTCCACCGGCGGCTTCACCTCTGTTTCAGGCACAACCTGCTCATCTCCTTCCTCCTCCTCCTCCTCGCTGTCGTCCTTTTCC[T/A]CATACTCATCTCCTCCAACCTCGCCGTCTACATTCTTGTTGTCGTTTCCGATCGTGTTTGTTTTGCCGTCCAGGCACCCATGACATAGAGA
104652 T C TGATTCCAGCTACCGCTCGCGATAGCACTGCAAACGGTGTTATTTTGAGACTCTCTTGAAGCATTATGTATGGAAGACCCGGAGCTTCTTTCTCAATTAC[T/C]GATTTCGTGGCTTCGGGAGTGACGTCTCTGGGAGTGAAGCCAGTACCACCTAGCGTGAGGATAAGGTCGACATTATCTATGTCACTC
104652 C T CAGCTACCGCTCGCGATAGCACTGCAAACGGTGTTATTTTGAGACTCTCTTGAAGCATTATGTATGGAAGACCCGGAGCTTCTTTCTCAATTACTGATTT[C/T]GTGGCTTCGGGAGTGACGTCTCTGGGAGTGAAGCCAGTACCACCTAGCGTGAGGATAAGGTCGACATTATCTATGTCACTCCACTTCT
104652 C T GATTTCGTGGCTTCGGGAGTGACGTCTCTGGGAGTGAAGCCAGTACCACCTAGCGTGAGGATAAGGTCGACATTATCTATGTCACTCCACTTCTTCAGAG[C/T]ATCAGAAATCTTATCTACTTCGTCAGGAACAACAGCAGACGCAAAAACGTAAGCTCCACCCAGCTTTTCTGATGAAGAGTTGATCAC
104652 G T GAAGCCAGTACCACCTAGCGTGAGGATAAGGTCGACATTATCTATGTCACTCCACTTCTTCAGAGCATCAGAAATCTTATCTACTTCGTCAGGAACAACA[G/T]CAGACGCAAAAACGTAAGCTCCACCCAGCTTTTCTGATGAAGAGTTGATCACGAATATTGCTCTTGGGCCGCTCCTGTCAGGGCCTG
104652 C G TCCACTTCTTCAGAGCATCAGAAATCTTATCTACTTCGTCAGGAACAACAGCAGACGCAAAAACGTAAGCTCCACCCAGCTTTTCTGATGAAGAGTTGAT[C/G]ACGAATATTGCTCTTGGGCCGCTCCTGTCAGGGCCTGCACCTGATGCAACCGTGTCACTCACAGTAAGAATTGCTACTTTGACACTTT
104652 C T GATGCAACCGTGTCACTCACAGTAAGAATTGCTACTTTGACACTTTCAGCACCTTTTATTTGCATACTTTCCATCGGCTTGCTGACTTTTACATTGTCGC[C/T]TTTACAAAGGGGTACGGTAGAATCATCACACGTCTTTATAGTACTTATAGGAAAACTGCTAATGTCAGAAATCAATACAGCCTGGACTAC
104652 A G TTTCCATCGGCTTGCTGACTTTTACATTGTCGCCTTTACAAAGGGGTACGGTAGAATCATCACACGTCTTTATAGTACTTATAGGAAAACTGCTAATGTC[A/G]GAAATCAATACAGCCTGGACTACTGCTCCTGCAGGGAGTATCTCTCCTGTAGCCGGCAACTCTAATAATGCATTAGCAGATTTCATACT
104652 G A TACAAAGGGGTACGGTAGAATCATCACACGTCTTTATAGTACTTATAGGAAAACTGCTAATGTCAGAAATCAATACAGCCTGGACTACTGCTCCTGCAGG[G/A]AGTATCTCTCCTGTAGCCGGCAACTCTAATAATGCATTAGCAGATTTCATACTAAGAAGGCGACTGCTCATTTGTTTACCAGTGCTCT
104652 C T TAATAATGCATTAGCAGATTTCATACTAAGAAGGCGACTGCTCATTTGTTTACCAGTGCTCTCAGCAATAAAACCAGGTTTTCCAGTTGCATTAGAAAAA[C/T]CCCATCTTACTATGGCACGTTGATATTCGGGCCGAGCCGGGTCTGTCTTTATAGAATTTGTGATACAGGCATGCACTCTTTGGAGATGA
104652 T C TGTTTACCAGTGCTCTCAGCAATAAAACCAGGTTTTCCAGTTGCATTAGAAAAACCCCATCTTACTATGGCACGTTGATATTCGGGCCGAGCCGGGTCTG[T/C]CTTTATAGAATTTGTGATACAGGCATGCACTCTTTGGAGATGAGGATTTGACCAGCCAGAAAGAAGACGAATGGCAGGAACAGCAA
104660 T G AGGTTACAGCGTCTGCTGAAAAGATCAGAGCGGCGACTCATGGAGTGATTTCATATGCAGAAAGGACTAGTTTGCTGGCGATACGTACGTCGTTTTATGG[T/G]ATAATGAGGAGGTATAATAGCTCTGGGTCTGTAAGGGTGGCTCCATGGGCCACGTTTGGGCTCAGTTTGCTGGCCTGTTCTGGGC
104660 T C AAAAGATCAGAGCGGCGACTCATGGAGTGATTTCATATGCAGAAAGGACTAGTTTGCTGGCGATACGTACGTCGTTTTATGGTATAATGAGGAGGTATAA[T/C]AGCTCTGGGTCTGTAAGGGTGGCTCCATGGGCCACGTTTGGGCTCAGTTTGCTGGCCTGTTCTGGGCTTGTTAAGTATGGAGATG
104660 G C ACGTACGTCGTTTTATGGTATAATGAGGAGGTATAATAGCTCTGGGTCTGTAAGGGTGGCTCCATGGGCCACGTTTGGGCTCAGTTTGCTGGCCTGTTCT[G/C]GGCTTGTTAAGTATGGAGATGGCATTGAGTGTGCTGCTGAGTCGGTTCCTTTTGTTTCTACAGTTGCTAGTTTGGGGCGTGGGATT
104660 A T CAGGAAAAGCTGCTTGCGCTTGCTAGTGGTAGGAAGAAATAATGATCTTTTTTATTCTTCATATAATTTTCTTTTTCTGGGTCACACTTGGGTCTTTGAA[A/T]GTTGATCATACTAACATGAATGATTGAGGTATATGGGGTTATATAGTTTTCTCATTTTTATGTCTTCTTCTGTACTTGTTTGTAAGTTTGT
104662 T C ACAGTGGCATGAGGCAACATCTCCATTACCTTCTCCCTCTGAATCATCAGCTTCTTCATCTCATTTTCCAAGGACTCAATTCTCGCAGTTCCACTTACAC[T/C]ACTGATCCTCTTGCTAAGCTGTCCATTTCAGATCCTTAACTGTGCATTCTCGAGGCGGAGAAGCTCAGCCTGCCTAGCGGCATCTTGGAG
104662 G A ATCTCATTTTCCAAGGACTCAATTCTCGCAGTTCCACTTACACTACTGATCCTCTTGCTAAGCTGTCCATTTCAGATCCTTAACTGTGCATTCTCGAGGC[G/A]GAGAAGCTCAGCCTGCCTAGCGGCATCTTGGAGATGGAAAAGGCAGAGGTCATAGCAGTTGGAGAAATCCTGATGTTGCAGGCGGAG
104662 G T CAAGGACTCAATTCTCGCAGTTCCACTTACACTACTGATCCTCTTGCTAAGCTGTCCATTTCAGATCCTTAACTGTGCATTCTCGAGGCGGAGAAGCTCA[G/T]CCTGCCTAGCGGCATCTTGGAGATGGAAAAGGCAGAGGTCATAGCAGTTGGAGAAATCCTGATGTTGCAGGCGGAGTCCAGCAAGA
104662 TCGTAC T CTCAGCCTGCCTAGCGGCATCTTGGAGATGGAAAAGGCAGAGGTCATAGCAGTTGGAGAAATCCTGATGTTGCAGGCGGAGTCCAGCAAGATAAAGGCGA[TCGTAC/T]CGTACATTTTCTAGTTCTTTCTCGCATGCATCATCACACAATTTCGGTTTCTCTTCTAAAGGCAAACCAGCTGAATGCACTT
104670 G A CGAGAAAAGGGTAGGTCAAGAACTCAAAGTCTTCTAGGAACGGATGGAGGTGGTATGCTGTTTCTGCATACATCCATGTTTCATGTAAGGGCATGAGGTA[G/A]GGTATGCATGCTAGGGTACGCCAGAACCAGCGAGGCTTTTTGGTCATTTGAGGGTATCTGAAGCTGTATGGCACGTCTTTTGAAG
104670 A G CTAGGAACGGATGGAGGTGGTATGCTGTTTCTGCATACATCCATGTTTCATGTAAGGGCATGAGGTAGGGTATGCATGCTAGGGTACGCCAGAACCAGCG[A/G]GGCTTTTTGGTCATTTGAGGGTATCTGAAGCTGTATGGCACGTCTTTTGAAGCTTTTGGGATCAATGTTGTTGGCGAGCGAGGCC
104670 T C CTCCAATTTCCTTGGAGCCACATACAAGTCTTTAACACTCAGTGTTTTAAAGGGCTTTGACTTACAAAAGAAGTTAGTGTAAGAAGAGTTGTATGCTCCT[T/C]GACAAGTCCATGGTTGCTTTATTGTCCAAGTTGCCATGCATGCATTGAGATTCATATCATATGTCTTCCAATTCCGGATTCAATTTCCGA
104672 TC T AAGAGGAAAACACCTCCAAATCATCATCAGTGAACGTTGTCAATGCTTCAAAGCCTTCTAAAAGCATCAAGATTGAGAAGTCAAATTCAAATTCAAACCC[TC/T]CCAAAACTGACATTGATGCCAAAATGCGGCGACCCGGGTCGAGACAAACTTAGAGAAATACTTGCAGATGCATTTTCCAAAGTATA
104672 A G AGCGTGCTAATAAAGAGATTAAAGATAAAGCGTTGAACGAATGCGAAAGAGGAGCTGCTCCGCTTGCTTCTACTGATCAGTTTAAGTGTGGGAGATGTGG[A/G]CAAAGGAAGTGCACTTATTATCAAATGCAGACTAGATCCGCCGATGAGCCCATGACTACATTCGTTACTTGCGTTAATTGCGACAA
104674 AT A ACTGACCTGGAAGGCCCTAATCCGTCTACTGTTTCTACTGCTGAAGGTATTACACATTACATTATTGTATTTCATTATTGACTGATTAATGTGTGGTTGG[AT/A]TTTTTTTGTTGTTGCCATCTACGAGGTAAATTGAATCTTGGGTGACAGAAATGCAGCAACGGTGTGATCCTTGCAACCAGAATTGATA
104676 T C AAATATAAACAGTTTTAGGTACAGGTGTTTCCACTCGCTGAGTGTGGTGGTAATGGCATTCTAACTCTGGCAAGCTCTGCAGCAGCACGTGCGGCAGCTG[T/C]AGCCCGATCAGCTGCAGCAATGGCTGCTCGTGCCATCTCCATAACATCAGAAGACTTCTCTTTTAGTGTAGGTTTATCATCTTCTAAG
104676 A G GATTATAATTTTTGATCATCGGAGATGATTCAGCCTTGTTTGGAGATGGTAGGTGTAACGATGGCTTTAGTAGAGAATCTTGTGCAGCCATGGGAACTGA[A/G]CCATCCAGCAAGTCCTCGTGTTTTTTGCTGAAGTCCGCCTCAGTGTTCGATGAGTCCCAATCCAAGTGATACTCCTTAGCAATTCCCT
104676 T C TTGCTGAAGTCCGCCTCAGTGTTCGATGAGTCCCAATCCAAGTGATACTCCTTAGCAATTCCCTTCAACGTTCTCAGTTTCACTTCGGACGAAGGTGCTT[T/C]TGGAGACAGTTTCTCAATTATAAGGCGGTTAACGTTACTATCAGGACGTAGTTCAGAAGCAGCTGCCACAAATTCCTTTCCATACTTCA
104676 A G TTGGATCAACTCAGGCAAATCTGAACATCTAGGAGATGCAAATATGATGCTAGAAACAGCCTCTTGCAATTCCATGGGGCAATCCTTTTGAGCTTCAAGA[A/G]TAGGAACACGTGCAAGAACAAATTCACAAAATAACTCTATAATCTCATAAGCAGCCATTATGTTCTCTTCTCTTATGATATGCTCCACC
104678 AT A TCTGTACTCTCAACTAAAGCAATATTTACAGAGGGAAACTCAAAGCAACAAGCCGCAGCTTCAAGCAATTGTTCCTTCAGCAACATTCGCTGGAGCATTA[AT/A]TTAGTTTCATACTTTGCCCAGCCGAGCTTGTGAAGTGTAGAATGCAAGTTCAGGGAAGGGACATGGCGGTTTCACAATATGTCAAG
104678 AAGTGT A GGAAACTCAAAGCAACAAGCCGCAGCTTCAAGCAATTGTTCCTTCAGCAACATTCGCTGGAGCATTAATTAGTTTCATACTTTGCCCAGCCGAGCTTGTG[AAGTGT/A]AGTGTAGAATGCAAGTTCAGGGAAGGGACATGGCGGTTTCACAATATGTCAAGTACTCGGGACCTCTTGATTGTGCTATTGC
104678 G A TGCTGGAATGGCTTTTTGGACAGTTGTTTTGCCATTTGATGTTGCAAAAACTGTAATACAAACTGCACCAGATCCAAATGCCGATCGCAATCCCTTTAGG[G/A]CATTATACTCGATCTATACAAGGGTAGGGATGAGGGGCTGCTATGCTGGCCTTGGACCAACATTAGTCAGAGCATTTCCTGCAAATG
104680 T C AGATCAATGAATTAAAGACCGAGAAGAATGAACTTCGAGATGAAAAGCAAAGGCTAAAACAAGAGAAAGAGAATCTGGAGCAACAGCTGAAGCTTTTAAG[T/C]GCTCGTCCAACCTTTATGCCTCCTCCATTAATGCCTGCAGCATTCGCTTCTCCAACTCAGGGTCAATCAGCTCCATCAAAGATGATG
104680 C T AGCAAAGGCTAAAACAAGAGAAAGAGAATCTGGAGCAACAGCTGAAGCTTTTAAGTGCTCGTCCAACCTTTATGCCTCCTCCATTAATGCCTGCAGCATT[C/T]GCTTCTCCAACTCAGGGTCAATCAGCTCCATCAAAGATGATGATGCCTATAATGGGCTACCCTGGCTATCCCATGTGGAGTTTCATGC
104680 A T TAATGGGCTACCCTGGCTATCCCATGTGGAGTTTCATGCCCCCTTCCGTTACCGACACTTCTCAAGATGTCGAGTCCTGCCCACCTGTTGCTTAAGCTCA[A/T]TTCTCTCAAGCTTCCCATTGGAAGAAAAGGGGGGAAAAACTTGAATTATGACATTGTTTGTTAGCATTGCCTTGGGTTTAACTTTCTGT
104682 T C ACTGATACGTAAAAGTCGGTCCAGCACAAAAATCAATATATATGATCTGCAGATTAAAATAACAATAATGTCGGCAAGTTAACTGTTTGGATACAATCCT[T/C]GCGCATCCAGAGACACAAATGAAAAAAATACAACAGAAGGCCTTGTAAAAAACCCATCAGTAAAATAATACAAACTCCAGTAAAAAC
104682 GA G CAGCACAAAAATCAATATATATGATCTGCAGATTAAAATAACAATAATGTCGGCAAGTTAACTGTTTGGATACAATCCTTGCGCATCCAGAGACACAAAT[GA/G]AAAAAAATACAACAGAAGGCCTTGTAAAAAACCCATCAGTAAAATAATACAAACTCCAGTAAAAACCGACGGCACGTGAAATGAG
104682 TA T ACAATAATGTCGGCAAGTTAACTGTTTGGATACAATCCTTGCGCATCCAGAGACACAAATGAAAAAAATACAACAGAAGGCCTTGTAAAAAACCCATCAG[TA/T]AAAATAATACAAACTCCAGTAAAAACCGACGGCACGTGAAATGAGTATCAGGTTCACATTAACAAGCGCAGGATCAGCTATTTGA
104682 G A CAACCCCAACCTTCGTAGGAGAACCAAATGCTTTTGCGTCGTACTCAGCTGAAATTGTTATCAATGATTTTGGTCTCCATTCATGCTGACATAAAACTCC[G/A]TACTTACCATTACTGCTGAATCTAGTTTTCATCATCGTCCTTGAATCGAGCAAATGAGAGCTTCCAATCATAAAACTATTCTCAAATGTG
104688 A G TGCAAATATTCAACATTAATAGATAAAATAATCAGCATTTCAAACTCAAAAGCTGTAGAAACGATATACTGAAAATGCAGTAGTATCAAAACTAAACACT[A/G]TCTTCTTCAGAACGTACTAACATGATGGAGAGATCTATCAAATGCAGAAGTAAAACGGTCACATGAACATTACTTAACTACAGGTAAA
104688 T A ATTTCAAACTCAAAAGCTGTAGAAACGATATACTGAAAATGCAGTAGTATCAAAACTAAACACTATCTTCTTCAGAACGTACTAACATGATGGAGAGATC[T/A]ATCAAATGCAGAAGTAAAACGGTCACATGAACATTACTTAACTACAGGTAAAGATATCATCAGCAGGTACTCCCATCCGTCTTCTTCA
104688 C T TAAACGGCTTTTTACCTTTAGTGACCCTGGCTATTGCTATCAACTCTTCTAGCAGTTCTTCCAAATGCCACAAAGGCCATTGTGTTGGACCATCTACTGG[C/T]GCGTTCAGTGGATCATCGTGAACCTCCATGAAAATTCCATCAACTCCAACTACAACTGCAGTACGTGCAATGCACGGTATTAGCTCACG
104690 AT A GATGTGGAGATAATGAAGCAGAAGAACGGATTGAGCAGAGGATTTGGTTTTGTTACTATGAGCTCTTGGGAGGAGGCACAAGCTGCAGTAGACAAGTTTA[AT/A]TTCTTATGAATTGATGGGGAGGACCATCAGAGTTGAATTTGCAAAGAACTTCAGACCACCTGCTCCTCCTCCGCCGCCTGACAC
104690 G T CATCAGAGTTGAATTTGCAAAGAACTTCAGACCACCTGCTCCTCCTCCGCCGCCTGACACACCTAAACCAGGGGGTTATAAATTATATGCAGCAAATTTA[G/T]CATGGAAAGTGAGGTCTGCTAACCTCAAAGAAATTTTCTCTGAAAAATTTAATCCAGTATCTGCACGTGTGGTGCTTGATAGTACAAC
104690 T C GGTTATAAATTATATGCAGCAAATTTAGCATGGAAAGTGAGGTCTGCTAACCTCAAAGAAATTTTCTCTGAAAAATTTAATCCAGTATCTGCACGTGTGG[T/C]GCTTGATAGTACAACTGGGAAATCCGCTGGTTATGGATTTGTAGGTTTTGCCACGGTGGAAGAAGCCAAAACTGCTATTTCTGAAATG
104690 A G TGAAAAATTTAATCCAGTATCTGCACGTGTGGTGCTTGATAGTACAACTGGGAAATCCGCTGGTTATGGATTTGTAGGTTTTGCCACGGTGGAAGAAGCC[A/G]AAACTGCTATTTCTGAAATGAATGGAAAGGAATTGATGGGGAGACCTCTACGTTTGAAAATGAGTGAAAAGGCAAATGACGTACC
104710 AGG A ATAAAAACAGTGAAGTTTTTTTTTATTCCAACATGTTTTGTCACACAACAACATAAAAACAAGTTCTGCAATAACTCATACAATCTAGAAGAA[AGG/A]GGATGAAAAATACACTCACTTGCAGGTTAAACTTTATAACCTCAGAGCTTAGATGCAGCTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATC
104710 T C ACACAACAACATAAAAACAAGTTCTGCAATAACTCATACAATCTAGAAGAAAGGATGAAAAATACACTCACTTGCAGGTTAAACTTTATAACCTCAGAGC[T/C]TAGATGCAGCTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATCCAATTTGATCATTTGAACTGGAAGCAGATCACCGGAGCTATCA
104710 G C AAACTTTATAACCTCAGAGCTTAGATGCAGCTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATCCAATTTGATCATTTGAACTGGAAGCAGATCACC[G/C]GAGCTATCACCAGCACCGAATGCTTGAACAATAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTACATTAGCAGATGAATTGAT
104710 T C TGCAGCTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATCCAATTTGATCATTTGAACTGGAAGCAGATCACCGGAGCTATCACCAGCACCGAATGCT[T/C]GAACAATAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTACATTAGCAGATGAATTGATAACAGGTAGAGTGAAGGTAATTCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104710 A T AGCTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATCCAATTTGATCATTTGAACTGGAAGCAGATCACCGGAGCTATCACCAGCACCGAATGCTTGA[A/T]CAATAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTACATTAGCAGATGAATTGATAACAGGTAGAGTGAAGGTAATTCTTTC
104710 A G CTTCTTTATCAGCAAACCAGTTAAGTTCTCCATCATCCAATTTGATCATTTGAACTGGAAGCAGATCACCGGAGCTATCACCAGCACCGAATGCTTGAAC[A/G]ATAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTACATTAGCAGATGAATTGATAACAGGTAGAGTGAAGGTAATTCTTTCAG
104710 C T TTGATCATTTGAACTGGAAGCAGATCACCGGAGCTATCACCAGCACCGAATGCTTGAACAATAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTA[C/T]ATTAGCAGATGAATTGATAACAGGTAGAGTGAAGGTAATTCTTTCAGGTGGTGGCTTTGGTGAGTCCTTGATGAAAGTTATCCAGTG
104710 T C TAACATCAGATTTACCAACACCAGTTGCCACAAGTGCTACATTAGCAGATGAATTGATAACAGGTAGAGTGAAGGTAATTCTTTCAGGTGGTGGCTTTGG[T/C]GAGTCCTTGATGAAAGTTATCCAGTGTTCCTTTTCATTTAAAAGAGGGTGGCCAGGAAACAGAGAAGCAATATGACCATCAGGCCC
104710 A G TGATAACAGGTAGAGTGAAGGTAATTCTTTCAGGTGGTGGCTTTGGTGAGTCCTTGATGAAAGTTATCCAGTGTTCCTTTTCATTTAAAAGAGGGTGGCC[A/G]GGAAACAGAGAAGCAATATGACCATCAGGCCCCATCCCTAATAGCATCAAATCAAATTTCGGGTAGCTTGTTATTGAGGAAAGCTG
104710 A T TGACTAATTGTTTTAAGCAAGCTTCATAGTCCTCTGCAGCGCCTTCAGCTGGCAGAGCATCATTTATGGCATAAACATGGCCTGGTGGGATAGGAACCTT[A/T]GATAGGAACCCATCATATGCCAATTTGTAATTGCTATCGGCATGATCTTTTGGAACAACTCTCTCATCAACCCAAAACACATGCCATTT
104710 C A AGGAACCTTAGATAGGAACCCATCATATGCCAATTTGTAATTGCTATCGGCATGATCTTTTGGAACAACTCTCTCATCAACCCAAAACACATGCCATTTA[C/A]TCCATTCGATAGAGTTAACATATGGACCTTCTGTCAACTTCCTGAGCGCTTTGACGAGAGATCCGCCGGAGATAACGACAGTAAAAGA
104714 G T TGATTAAGATTTTAACCTACAATGTTTGGTTTCGCGAAGACATAGAAGTGCATAAGAGGATGAAAGCTTTGGGTGATCTCATTCAGCAGTACTTGCCTGA[G/T]ATTATTTGTTTCCAAGAGGTGACGCCATGCATTTATGAATTATTTCAAGATTCAGCATGGTGGAGTATGTATAAGTGTTCCCTTACAA
104714 G A TTTCGCGAAGACATAGAAGTGCATAAGAGGATGAAAGCTTTGGGTGATCTCATTCAGCAGTACTTGCCTGAGATTATTTGTTTCCAAGAGGTGACGCCAT[G/A]CATTTATGAATTATTTCAAGATTCAGCATGGTGGAGTATGTATAAGTGTTCCCTTACAAGGAATATGGTGGATTGCAGGCCATATTT
104714 T C TTGGGTGATCTCATTCAGCAGTACTTGCCTGAGATTATTTGTTTCCAAGAGGTGACGCCATGCATTTATGAATTATTTCAAGATTCAGCATGGTGGAGTA[T/C]GTATAAGTGTTCCCTTACAAGGAATATGGTGGATTGCAGGCCATATTTTTGCATGCAGATGAGCAAATTCAGCGAAACATCATTCAAG
104714 C T TTTGTTTCCAAGAGGTGACGCCATGCATTTATGAATTATTTCAAGATTCAGCATGGTGGAGTATGTATAAGTGTTCCCTTACAAGGAATATGGTGGATTG[C/T]AGGCCATATTTTTGCATGCAGATGAGCAAATTCAGCGAAACATCATTCAAGTGCAAACAATTCAACAACTCGGTAATGGGGAGAGAA
104714 G T TCACTCAAGCGAAAGAATCGATCGAAACACTAAAAAATACCCAAATGTCGTATTTGGAGGCGATATGAACTGGAACGACAAACAGGATGGCGATTTCCCT[G/T]TGACGAGCGGATGGATCGATGCATGGTACGAGCTTAAAAGAGGCGAAAATGGATGGACATACGACACGGTTTCGAACAAAATGC
104714 T A CACTAAAAAATACCCAAATGTCGTATTTGGAGGCGATATGAACTGGAACGACAAACAGGATGGCGATTTCCCTGTGACGAGCGGATGGATCGATGCATGG[T/A]ACGAGCTTAAAAGAGGCGAAAATGGATGGACATACGACACGGTTTCGAACAAAATGCTGACCGGGGGCCGGAAGTTTCAGACG
104716 G A AAGCTCTTTCGCTTCCCCATTTTCCGCAGCCAACTTCTCAGTTCAAATGAGCACTTCAAAATCAAATGCACGACAAACCGATACGTCAAGTCTTGAACCG[G/A]ATGACAGTAGGAAGAAGAAAATATTCGTGGCTGGTTCAAGTGGCAGAACAGGGAAGAAGATCGTGGAGAAACTGCTCTCAGAAGGG
104716 C G CTTTGGACTGACATTAATAGCAAAACTTCAGGCAGAAAATTATACTAGGAAATCCGGTATTGATTTCACTATAGTAAGACCTGGTGGATTAAAAGATGGT[C/G]CCCCAACTGGAAATATTATCATGGAACCTGAGGATACCCTATCTGAAGGTTCTATATGCAGAGAACAAGTGGCAGAGGTGGTTGTTG
104716 A G TCACTATAGTAAGACCTGGTGGATTAAAAGATGGTCCCCCAACTGGAAATATTATCATGGAACCTGAGGATACCCTATCTGAAGGTTCTATATGCAGAGA[A/G]CAAGTGGCAGAGGTGGTTGTTGGAGCATTGTCATGTGCAGAAGCATCATACAAAGTAGTTGAGATTGTTGCACGCAGTGAAGCTC
104716 A C AAGTGGCAGAGGTGGTTGTTGGAGCATTGTCATGTGCAGAAGCATCATACAAAGTAGTTGAGATTGTTGCACGCAGTGAAGCTCCCAGACTTCCTGTTCA[A/C]GAATTATTTACTGCCATCAAATAGCGCTGAACCTGTGCATTGACATTGACTAATATCTACGGTCTGCCAGAAGACATCTTTATGACT
104716 C T GTGCAGAAGCATCATACAAAGTAGTTGAGATTGTTGCACGCAGTGAAGCTCCCAGACTTCCTGTTCAAGAATTATTTACTGCCATCAAATAGCGCTGAAC[C/T]TGTGCATTGACATTGACTAATATCTACGGTCTGCCAGAAGACATCTTTATGACTTCTGGCTGCTGTGCTGTAAGGATATACCTTTATTG
104716 G A TTGCACGCAGTGAAGCTCCCAGACTTCCTGTTCAAGAATTATTTACTGCCATCAAATAGCGCTGAACCTGTGCATTGACATTGACTAATATCTACGGTCT[G/A]CCAGAAGACATCTTTATGACTTCTGGCTGCTGTGCTGTAAGGATATACCTTTATTGTTAGGGTTATTCAATGTTAATAGTTGTTCACGG
104716 T A TGTTCAAGAATTATTTACTGCCATCAAATAGCGCTGAACCTGTGCATTGACATTGACTAATATCTACGGTCTGCCAGAAGACATCTTTATGACTTCTGGC[T/A]GCTGTGCTGTAAGGATATACCTTTATTGTTAGGGTTATTCAATGTTAATAGTTGTTCACGGTATCAAAACAAACGTCTTCTATTTCATGA
104716 A T TGCATTGACATTGACTAATATCTACGGTCTGCCAGAAGACATCTTTATGACTTCTGGCTGCTGTGCTGTAAGGATATACCTTTATTGTTAGGGTTATTCA[A/T]TGTTAATAGTTGTTCACGGTATCAAAACAAACGTCTTCTATTTCATGAGGAGGATGCGATTTATAAATGTCCGTAACCCCCACTCATCCA
104716 C CA CTGCCAGAAGACATCTTTATGACTTCTGGCTGCTGTGCTGTAAGGATATACCTTTATTGTTAGGGTTATTCAATGTTAATAGTTGTTCACGGTATCAAAA[C/CA]AAACGTCTTCTATTTCATGAGGAGGATGCGATTTATAAATGTCCGTAACCCCCACTCATCCAAGCAGCGAGTGAGGGTTTATAATAA
104726 A G GCACAGTCCTCAAACTAAAACTCTGATTGTAACTCGAAAGCGCCCTCTGCAGCTCCTTGTCATCAATGAACCCACTACCATCAGAATCAGCTGCCTGAAA[A/G]CACGCCACAACGTTCGGATCCGTCCCAGGCGGGAAGGCAGACGGCACTAACGCCGCAAAGGGGCTTCCGTACGGCGCTGGGGCCG
104726 GT G CGCCAGGATGTGCACCGTAGGCCGGTTGGGGTGGGGCGTAGCCTCCGTAAGGAGCTGGCGGGGCGGTAGGGTAACCGCCGTAGCCAGCGGATGCGGGGTT[GT/G]TTTTCCTTGGGGGGCTTGTTGGGCTTGCCGCCTTCGGCGCCGTACGGGTTGGAGGGAGCTGGAGCGCCAGCGTAGTAGGG
104728 TA T AGTGAAACATACGGTTCTAGTGATTCCAATGATGAACCGACAAGTGTAGACAGCATCCAACAAGAATCTACGGATGAAGCCTCTGATCCAAATGAAGGGA[TA/T]AAAAAAGAGTACTGTAAAGCTTTTTATAGGTGGAGTAATTCATAATAAGGAGGATGTTTTATCAAAAACTTATGTACGTCTCCCTG
104732 A G ACGTATATCTTAGAGGCAAGAATGCCTGATGGGGAGGTCACTACAACTGCTGGTGAAAGGCTGCGGCCATGGGCTTGCCCCTGGTTCTATATAATATAAA[A/G]GCATGTGCCACAGCAAGTGTAGGTCGTTGGTACCAACTTGGAGGTTAAACCGTCGGTCTTCGATGATTTGTCAGGCGCCGGAAAA
104732 G C GTGAAAGGCTGCGGCCATGGGCTTGCCCCTGGTTCTATATAATATAAAAGCATGTGCCACAGCAAGTGTAGGTCGTTGGTACCAACTTGGAGGTTAAACC[G/C]TCGGTCTTCGATGATTTGTCAGGCGCCGGAAAACGTGGGACTGCGGTCCGCGCGCGGCCGGCTTGTGTGAGCTGTGAGGGACGC
104734 TA T GTTGAATTAGTTAAAAACATGCTATGTGACTCGTTAGTGCATGCCTCATCGTGTAACAACTCTAAAATTCAAGTGATTTTTACCTCCACCATTTGCAAAG[TA/T]AAAAACGAATTGAATTTGAATATGGTCTTAATAGAAAACCAAACCAAGCAGTGTTTGACCAAAAATATCCCTGAAATTGGTTAATATA
104734 G T TACCTCCACCATTTGCAAAGTAAAAACGAATTGAATTTGAATATGGTCTTAATAGAAAACCAAACCAAGCAGTGTTTGACCAAAAATATCCCTGAAATTG[G/T]TTAATATACTTTACCGTGCATGTGCATATAAATCATACTGCGACCATATGGTATCCAGAGGGCACGGCCGACGCTCATCCAACCGAAC
104734 T C CCATGCTGATTCCACCTGTGGTTGATTGCCGCCACGTTTCCTGCGAACACCAGCAAATACGGCGGGAGAGACCCTAATTCGTATATCCTGCCGCCACCTG[T/C]CCTTTGGATCTCCATCCATTTCTCTATCTCCTTCGTGAAATCGAATCTCCTCCATCGGTCCAAATCTATCACCATCACCCCGGTGTTAAA
104734 G A TCTCCATCCATTTCTCTATCTCCTTCGTGAAATCGAATCTCCTCCATCGGTCCAAATCTATCACCATCACCCCGGTGTTAAAATAGCACGGGTTTCGCCC[G/A]GTGAACGTACTGGTCAGCTTCGAATCCGACCAGAAGCGATCCGTAAAGTAATTTGTAAAATTCGCGTGGCAGTATTCCGGCGCTCCGAC
104734 C G GATCGGAGTCCAGGTAGATGACCCGATTCACGCAGGGTTCTAGGATTTCAACCAGGTAATTCCTCGCGTAGTTCAATGGCTGCTCCAAAGCTTGACGGAT[C/G]GAAGAAGATATCAGGTTCCGGACTCGATCCGGGTCGAAATAGTAGACATTGAACCGGAGTTTCGGGAAAGTGGAACGGATTAGG
104744 T C CAAAACTCACCATGAATCGAACTGGTACCTTTGGAAGTACGAATCTGCTGCAGTCGCTTTCTGAGAAAAATGGCTGTGTGGGTGTTGATAACTGTAACAC[T/C]GATTCTCACAATCAGCAGAATGTATATGGTTTGAACATAGATTCTTCTTCTTCGATGTTTTCCAACGCAGTGCCGAGCATAGCAGGCA
104744 C T TTGGAGATGACCCGTGGGAAGCATTTATGAACAATGTTTGGTACATCAAAATACTTTCACCTGAAGATTTACAGAGAATGGGGAAGGCAGGAGTTGATTC[C/T]TTCTCTTAGTTCTCTTCCACTCAGAAGAACCCAAAGAGGCTGGGTATGTGTGCCTTCATGTGCTTCTACCACGGTTGTATGATTTCAT
104744 G GAGTAC TTTGGTACATCAAAATACTTTCACCTGAAGATTTACAGAGAATGGGGAAGGCAGGAGTTGATTCCTTCTCTTAGTTCTCTTCCACTCAGAAGAACCCAAA[G/GAGTAC]AGGCTGGGTATGTGTGCCTTCATGTGCTTCTACCACGGTTGTATGATTTCATGTTAGTTGTGGATATTGCGGTAAAAATCTAG
104744 G GT TGTTAGTTGTGGATATTGCGGTAAAAATCTAGCTTCTACTAGCTAAGCTTCTTATTGTTGTAATGTGTTCTTATTAGTGTTCGGATGAATACTTTCACGG[G/GT]ATTATTTCTGTATCTTATTGGAATTCAGTATTCCTCTAACTAGTTATTGTGACTGTAGGATCATTAAGTCCCAAGTATTTTTTTGGAT
104746 C T ATCAAATGTTGGCCCTTCCCCACTCAGCCTCATGACAGCTAGATTTCCAAGGAAAGTTTTTGCATGCGTCTTGACGAATGCGTAGAAGTCAACTACCTCG[C/T]CCGGCAATCCAAAGTGTCGAGCTTTCCTCAGTTCAAAGTTGAGGAAAGCAGCGTCTTGTGATTGATCATATTGAGTGTAATCAGACGT
104748 A G GCGACCTCAACCCAAACCAAGACCTTAACTTATGGGCCCCGATTCTTCTCGGGATGATAAACAATGGCATGAGAAGACGAAGGCCATTCAACAGAGAAGA[A/G]GCAGCCTCAGAAGAGGATTACGACTTGATATCTCAATTGAGGAGACGCCAGAGAGCATCAGCCATCCTAGAAGTGCTCAACGACA
104748 T C TCGGACTTGGAGAAGTAGGGAGAGAGATGCCTTGTAAGCATATGTTTCATGATGGGTGCATATTGCCATGGCTTGATATGCATAGTTCTTGTCCGGTATG[T/C]AGGTTTCAGATGCCTGTTGAGGGGAGGGAAAGTGAGAAGGAAGGTGCTAATGAAGGAGAAAATGGTGGTAATGGCAATGATAAT
104748 T C TTGATATGCATAGTTCTTGTCCGGTATGTAGGTTTCAGATGCCTGTTGAGGGGAGGGAAAGTGAGAAGGAAGGTGCTAATGAAGGAGAAAATGGTGGTAA[T/C]GGCAATGATAATGGAGCTAGTAATGGTGATAATGGAAGGAGGTTTTGGCCTGTGCCTTGGCTTTTAAATGGGTTGTTTTCTGTGT
104752 A G GTTGGCTAACCCTACTTTTGTGGATTCCGTTCTAGATTGAGACTTCGAAGAGTTTATTGTTTGCGGCTCGTTCCTCAAAGCATGCCCGTCGTTCGAAGAT[A/G]TCGCGACCTCCCTATTGGCTGTTGCCATAGGTCCGATGTCAGTAGTTTTGTCTAGGTTTGACTGAGATTCAGATCTACGTTTACTCGCT
104752 T C GTTTTCTTCTTCGCTGGTTTCCAACTTCTCACCACGTTGGAGAGCCGATGGTCCAACGGTGTCACTGGTGGTGGGTGAGCAGCTTGCTCCGGCTGTCGTT[T/C]GAGCGAAACAGGAGTTGACTGCCGGTTTTGTTCCTCGACTGCTTTTCAAGTGCTCGCAAGCGGCTCCGATATCGGCAACCCATGATT
104756 A G TAAGGCGATTCACTTTGTCAGGAAACTGCTCCTGAACGAAATGAGTTCCTCCAGGAATAAACTCTATTTTCGAATCAGGTACGTAATTCTTCATTGCTTC[A/G]CTCCTAACATATTCTTCCATTCCCGAAAACTTGAGAATGTAGTCATTTTCTCCCATTATGACCATAGCCGGAACCTCGATCTTAGTATCG
104756 C T GGTACGTAATTCTTCATTGCTTCACTCCTAACATATTCTTCCATTCCCGAAAACTTGAGAATGTAGTCATTTTCTCCCATTATGACCATAGCCGGAACCT[C/T]GATCTTAGTATCGGCTCTTTCTGGAAAATTATCGAGTGCCCTATAAGGGATCTGCATAGGAGCTACAAATCCGGACTTTTCATATAGAGA
104756 C T TTCTGATTACCGTTCCTGTGTCAAAACGAGCGAAATCTGCTTCAGCTCGTCCTGGTTCCCGCCATCGGCTTATGTAGAAGCCTTTTGGAGGTTGGGACAC[C/T]GTGGAGCTTATTATGGGTGAGAAAGGCACACCAATGGTTATGATGCCGAGTACTCGATCAGGGTAGTCTACAGCTAAATCAAATACA
104756 C T TTTGAATCCAGCTTCAGCTGTTGCCACCATTTGATGCCTCCATGAATACCAGATCTCTGGAAACCCATGCAGGAACACAACTGCTCCTTTTTCCCCTTCC[C/T]CGGTATGTGCTATGTGAAGGTTGATTCCTCTTATGAATAGATGAGAATGGGTTATCTTCTTATTCCACTCCATTGCCCTCTCATCTGATTT
104758 C T GCGGTGGAATGGAACGGGAAAAAGTCGAGGAGAAGGATAAAACAGGAGAAAAAGGAGAAGAAGAGTAGCAAAGAGGAGATCAGAAATCATAGCAATCGTA[C/T]TGGCTTTGAAAATAGCCATCACCGTGATGAATTTGGACACGATGAGGATGACGCATGGTATGGTCGTCATGATGAAGAATCA
104758 G A CGTCTTGACGTGGATAGAATGTCATATGAGGAGTTGCTCGAGCTTGGTGATAGAATTGGGCATGTCAGCACTGGCTTGAGAGAAGAAGAAATATCATGCT[G/A]TCTGATCAAAGTGAAAATACCTCTTGATGCTAAATATCAACTCTTCTCCAATGAAAAAGACAAGAAATGCAGCATTTGTCAAGAAG
104758 T C ATGCTAAATATCAACTCTTCTCCAATGAAAAAGACAAGAAATGCAGCATTTGTCAAGAAGAATTTGAAGTGAATGATGACATTGGGAAACTGGAGTGCCG[T/C]CATAGTTACCATATGCACTGCATCAAGCAATGGCTGCTTCAGAAGAATGCTTGCCCTGTATGCAAAACAACAGTAACCAAATCAAAA
104758 A G GAATGATGACATTGGGAAACTGGAGTGCCGTCATAGTTACCATATGCACTGCATCAAGCAATGGCTGCTTCAGAAGAATGCTTGCCCTGTATGCAAAACA[A/G]CAGTAACCAAATCAAAAACCTAAAGCAAACTCCCTGTACATGGGTACCTATATTCATACTATGAAGTTGAAGAATGAGTCGCAAGTT
104758 A G ATGGGTACCTATATTCATACTATGAAGTTGAAGAATGAGTCGCAAGTTCTTATGTGTATATAAATACTTTGTTTTAGTATCATAATGTGTGCTCTGAATG[A/G]TTTTCTCAAGAACTCTTACGGTTTGTACAGTCTTTTGTGTGATTACGGTCTGAATGTTATCAAGCGGGAAACTAAATCGTTATAGATTTA
104766 A T AAAATTTAATCGCCTCAAATCCACCAGCTTTAGGAAAACCAAAATAGTATATGACATTGTATATGGTTCCCCATAGATTCATTCCTAGCATTATTTCCCA[A/T]GCGCTTGTTTCTTGGTACCGTGCTTTAATGGAATCCTGTGTAGAGTTTGTGAAACCATCAAGTGCCAAGTTCAGAAAACACAACCCATAT
104766 C T TTGTGAAACCATCAAGTGCCAAGTTCAGAAAACACAACCCATATCCAAGTGGAGCATTTGGATGAGCAAGTTTGCTCATGGTTTTTGAACTAGTCTTTGT[C/T]AACGCAAATGCAGAAACCCCGCCAGCAACAAGGAAGGTGCATACATATTCAGGCAATGTATATTTGACACCATAATAAAAAGCACCC
104766 GC G CAAAACCTGAGCTGGATAGCTAATATATTTCAATGCCTGGATACCCATAGCTGGACCAACCGTATTTGAAATGCTTGCTAGCCAATAGCTTCGCAAAGGT[GC/G]CCCCCTTCCCCTTTGAATTACTTGGCCAAATTGCCAACATAATAATCGACCAAATCAAGCAGACTACATTCTGCGCCAGATTCAAAA
104766 A G CCAGATGCTCGAACCTCTTCCCATCCGGACCAAATTTCTTAGTAGATACAGTCTCCTGAAGAACGCCCTGTGTTATATAAGAAGTCCAGATTCCGGCGAC[A/G]CAAAAGATGAGGATAAACACACGCCCAAATCCGCCTGCTTCCATGCTCCACGTAGTTGAGGTTACGAATCAGCTAAATTCCGTCCAAA
104766 C T TGTTATATAAGAAGTCCAGATTCCGGCGACACAAAAGATGAGGATAAACACACGCCCAAATCCGCCTGCTTCCATGCTCCACGTAGTTGAGGTTACGAAT[C/T]AGCTAAATTCCGTCCAAATCCCCGCAAACGCCAGAAATCAGGGATGCTGCTGATGAGATCGTCCGTCCTAGCTTCTTCCGCCCTTGA
104766 A C AAAGATGAGGATAAACACACGCCCAAATCCGCCTGCTTCCATGCTCCACGTAGTTGAGGTTACGAATCAGCTAAATTCCGTCCAAATCCCCGCAAACGCC[A/C]GAAATCAGGGATGCTGCTGATGAGATCGTCCGTCCTAGCTTCTTCCGCCCTTGATTTTAGATCCGCACTTTGCACTGCACCCAGTAGG
104768 T A CACCTCCTCAACCTGGGTCAATGTTAGGTCTCACTTCCGTAGATAGGGTTTATGCATCTGATCCGAAGTCTGCTCTTGCATTACAAAAATTAGTTCAGGC[T/A]GCTGTGTGGTTTCTTGGTGAAAATGCAAATTATGCTGCTTCTGAGTATGCATGGGAATCTGCAACACCGCCTGGTACAGCTTTGATGA
104774 G T GCACCTCAAAATGGTGATAGCTTTTCAAAACACTTTGATCAGTGGCTTGAACAGCAGCAGCATGACCTCCGAGCCCTTCTGGCTGCAGTGTCTAACCACC[G/T]TCCACTTACAGATGAGGAAGAGAGCAACCAAATCCTTCCACTTATTGATCGTGCAGTTTCAAACTACGAAAACTACTACAGGCACAAA
104774 TGAG T GTGATAGCTTTTCAAAACACTTTGATCAGTGGCTTGAACAGCAGCAGCATGACCTCCGAGCCCTTCTGGCTGCAGTGTCTAACCACCGTCCACTTACAGA[TGAG/T]GAGGAAGAGAGCAACCAAATCCTTCCACTTATTGATCGTGCAGTTTCAAACTACGAAAACTACTACAGGCACAAATCTACCTTTG
104774 C T CAGCAGCATGACCTCCGAGCCCTTCTGGCTGCAGTGTCTAACCACCGTCCACTTACAGATGAGGAAGAGAGCAACCAAATCCTTCCACTTATTGATCGTG[C/T]AGTTTCAAACTACGAAAACTACTACAGGCACAAATCTACCTTTGCAAAACGTGATGTAAAACCAATGTTCTCTCCTTCTTGGACTTCCA
104774 G A CACATGATTTATCGGGCATTTCCCCCTCCCAGCTGCAGCAGATTGATCGATTACAAAGAGAAACGATAAAGCAGGAGCAAGAGATATCAGAAGAAGAGGC[G/A]AAAGCACAAGAAACAGGGGCAGACACACAGATGGTTGAGCTAGTGAACATGATCACAGAGAGTGGTGGCAATGGAGGGGATGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104774 A T CAGATTGATCGATTACAAAGAGAAACGATAAAGCAGGAGCAAGAGATATCAGAAGAAGAGGCGAAAGCACAAGAAACAGGGGCAGACACACAGATGGTTG[A/T]GCTAGTGAACATGATCACAGAGAGTGGTGGCAATGGAGGGGATGAAGAAGGCGCTGAAATGCTGAAACCACAAATTGAAAA
104774 G A GTGGTGGCAATGGAGGGGATGAAGAAGGCGCTGAAATGCTGAAACCACAAATTGAAAACAGTGAGGAGAAAATGGAACAAGTGCTGCAGAAAGCCGATCG[G/A]CTTAGATTGGATACTCTGAAAGGAATCATTGACATACTGAAACCTTTCCCATTTTCTAATTGCAGCCGCAGAGCTGCATTTGAG
104774 T TTGCAAGCAACAAATTGAAAACAGTGAGGAGAAAATGGAACAAGTGCTGCAGAAAGCCGATCGGCTTAGATTGGATACTCTGAAAGGAATCATTGACATACTGAAACCT[T/TTGCAAGCA]TCCCATTTTCTAATTGCAGCCGCAGAGCTGCATTTGAGGATTCACGAGTATGGGAAGTGCAAGGATGGACGGGCTGC
104774 T C AGGAATCATTGACATACTGAAACCTTTCCCATTTTCTAATTGCAGCCGCAGAGCTGCATTTGAGGATTCACGAGTATGGGAAGTGCAAGGATGGACGGGC[T/C]GCACATGCTTCTTAAGTACTACTGCCTACTTCCTTTATGTTCTGCATTTTTATGGAGTTTTTTTAATGTCTGTTTCTCTTGAAAATGTGG
104774
ATAAGTAGCAGTGTGTTGGGATA GTACTACTGCCTACTTCCTTTATGTTCTGCATTTTTATGGAGTTTTTTTAATGTCTGTTTCTCTTGAAAATGTGGTTTCTTTTTGTAGCAGTGTGTTGGG[ATAAGTAGCAGTGTGTTGGGAT/A]TAAGTAGCAGTGTGTTGGGATTAAGTATCTGTGTGTTGTTCTCGTAGTAGAACTTTGTTAGGATATGTT
104780 A G AAATAACTACTTCCAAAACACCATTCCTTCCAACCTCACAACACAGCCACCAGGTGCCTGCAAATTGACTTGGACAAATTGCTTAGGATCTCTCATACTC[A/G]TTCACCGCTAACCAGTCGAACTAAATAACCATCACCAAATAACCAAAGCCACAGACCATACAAATTGATACAACGTCTAATCTGAAAGT
104790 C A GGATCTGGTTGAGATAATTTCGGCACCTCAATTTCAGCTTTCCAAAGTTGAATTACCTCCCGAGGTTGAGCAGCCTGCAAGTCAGGATAAATGGCCAACT[C/A]AAATTTTTGAGGCCTTGTAGGATTACGATAGTCACAGGGTATGACCACTGCCCATATTTTCCTTTGCACCCATTGTGGAGCAAATGCT
104800 C A CTTCAGCCGAAAGAGCTTCAAAAAGAGGATGTTCCTCCATGCACGATCTCATCCAGATACCGAGTTCTTCGACATCGGTGACTGTATATATAATGCCGCC[C/A]ACTTCAAGTGTGTATGCGTATTCATCCAGCAGTTGTATACTGATAACTCTACGTCTGTGATTCTTTTCTTTGAAATGCGGATCCGGGAA
104800 G T TGTTCTCGTATTGACCAGGGTTAGTGGCCCTTAATGCCAGTATTCTTTCTTTCACATATTCTGTCACCTTGTCTCTGAGCTCCATCCCTATCATTAGTGT[G/T]TCTGGGAAAAGAGTAGACAAACTAACCAGCAAACCACCAAATCCACATCCAATATCAGCAAATTTTATTTTTGGAAGTGGCTTAATATTAT
104800 G A AGCTCTAGCTCTGTAGAAGCGTTTCCTAGGAAGACGCTTAGATTGTCCATTCCCTTGCTTCTCGTTGTTATTTTCTGACATGAGCATGATAATCAATCCT[G/A]AATTGTACTGGTGGAACACTGCTTCAGGTGCGAGACAATATTATGAGAGCACAAACTACCTTCTTTACTTTTGGGACGCCTGTTCAAAG
104804 CT C GGGTTTGCTGTATGCGCTCTGGACCATCAAGGGCATGGGTTCTCCGATGGCCTTTATGCTCATGTTCCTGATATCAACCCTGTTGTTGATGATTGCGTCT[CT/C]TTTTTTTAACTCCTTCAGACAAAGATACAGTCCACAAGTTCCTGCATTTTTGTATGCGGAGTCCCTTGGTGGTGCTATTGCACTTCTGA
104804 A G TGTCAGTGGTTGCCAAATTAGTGCCCACATGGCAGGTCGTCCCTACTAAAGGGTCTATACCCCAGGTTTCCTTTAAGGTGGAATGGAAGAGGAAGTTAGC[A/G]GTGGCAAGCCCAAGAAGGAAGCAAACAAGACCACGAGCAGCCACAGCACTAGAGCTGCTACGAGTGTGCAGAGAAGTCCAAGAC
104804 A T AAGGGTCTATACCCCAGGTTTCCTTTAAGGTGGAATGGAAGAGGAAGTTAGCAGTGGCAAGCCCAAGAAGGAAGCAAACAAGACCACGAGCAGCCACAGC[A/T]CTAGAGCTGCTACGAGTGTGCAGAGAAGTCCAAGACAACTTCAATAACATAACAATCCCAATGCTCATTGTCCATGGAGGTGAG
104806 T A GATCTAACCCTTTTATTAAAAAACTGCTTCTAGTTTTCAGATCTGTCCACTTCCCTATCTACCCCTCTTTCTTCAATCCACACCGCAAGCACTCATTTCA[T/A]CGCATCTACACTTAGTCTTCCCCTCAGATCTATATGCGGTGGCCTTACTGGAAACTACTTGCTTACTGTCTCCAACCGGCAGTAGGTGCGTT
104808 C A CAGCAATCGTAGTTCCAGCAGGCGATGTTACAGCATCTTTCAGTTGACCTGGATGCTTTCCTGTATTTTTAACCATTGATGCTGCACCTAAAACAGTCTG[C/A]GATGCAAGACCAAGAGCAAGATCACGAGGTAGACCAGCAGCTACACCACCATCCGCTAAGGCTTCTATTGCTAAGAACACATATGCA
104808 A G CCATGTTTCCTGCGCCTATAAACCCTAATTTGAATGCATCCGTTGAGCTTATAGCCGCCGCCATTGCTCTAAATTCAAGAACCCTAGTTAAGACTTAATT[A/G]TCGAGTTTAGATCTTGCAGGAAGTCCAATAGATTTGTCTTTCAAGCACACCCTGAAAATCAAAGTGGCTTTGTTACGTCCAAAAACCAC
104818 T A AATGAGTGAGGATGATAGTGTAGAGAAGGAAGATGAAACACTGAAGGACATAGCTGATACCAAAGAATCCGATGACGAAAATTCAGATGTGAATGACTCA[T/A]TGCCAAATGAGTTGGCAGAGTTTGGTGACTTTATCTTGAGAATCAAATCAGTTTTTAAGTGCAGGATTTGCCCAAAAGTTCTTTGT
104818 G A AAAGACAGTGGTCGCAAGCGACAAGATATAAGAAGAAAAAGGAAACAACTTCAGCAGCTGAAGAAAAAAGCCAAAGAACATGTCGTAAATCATGAGAAGA[G/A]CTCTGATGGGCCAGCTAAAAACGGGAAGAAGTCTGAAGTACTCACCGAAGTTCCTAAGAAATCCGAAAAACCAGACAAAAATC
104818 G A AAAAGCCAAAGAACATGTCGTAAATCATGAGAAGAGCTCTGATGGGCCAGCTAAAAACGGGAAGAAGTCTGAAGTACTCACCGAAGTTCCTAAGAAATCC[G/A]AAAAACCAGACAAAAATCCTAAGAAATCCAAAAAAACGGACAAAAATCCTAAGAAAAACAGCGCAAAAATAAAACAGAAGTCTA
104818 T TA AGAAATCCGAAAAACCAGACAAAAATCCTAAGAAATCCAAAAAAACGGACAAAAATCCTAAGAAAAACAGCGCAAAAATAAAACAGAAGTCTAATATTTT[T/TA]CTCTGAAGTGGCTGTTAAACTGTTACGAGGTTGGATGTGATGTTTAATAGGCTGGATTTTGGTCAATAATTTTACCCTGC
104832 G A CCGGTGGCGCTCCGGCCAACGTGGCAATTGCTGCATCTCGGCTTGGCGGAAAATCTGCGTTTGTGGGAAAGATGGGGGACGATGATTTTGGTCACATGTT[G/A]GATGAGACGTTGACAAGCAATGGAGTTTGTAACGATGGCGTCGTGTTTGATGAAAACGCAAGGACAGCTTTGGCTTTTGTTAGTT
104832 GT G CGATGATTTTGGTCACATGTTGGATGAGACGTTGACAAGCAATGGAGTTTGTAACGATGGCGTCGTGTTTGATGAAAACGCAAGGACAGCTTTGGCTTTT[GT/G]TTAGTTTGAAAGACGATGGCGATAGAGAGTTTATGTTTTATCGCCATCCCAGCGCCGATATGCTGTTGCGAGATGATGAGCTTGA
104832 TA T TCACTGCTATCTTATGATCCAAACTTGCGTCTTGCTCTTTGGCCCAATGAGGAAGAAGCAAAGAAGCAAATAACAAGTATTTGGAATGAAGCAGATATTA[TA/T]AAAAATAAGTGATTCGGAGCTAGAGTTTTTGACTGGTCATGAAGGAGTTAATGATGATGTTGTAATGTCATTATGGCATTCAGGAT
104838 G A AGGTATTTGTATGGGGCTTCCGCCATACAACAACGCCAATTAAACTGTTGTCGATATTTGAGTGAAGAGCAGCAGTGTAATTGCTTGGGAGGCGACTTTC[G/A]AGCATTTTGATGGTGTCTGGATGTGAAGGACAGAGGTAAAGTTCAACACCTGGCGCAGGTTCTGCGAATCCTACTCTTTGGTCTGC
104846 G A TGGACTTGATCTTGACCTGCCCGATGCAAGTGACTTTAGGCGACGAAGGTTCAGCCGTTTCTACAGAAGCGGACTTGCGGCGAGAGGAGGGGAACATTGG[G/A]GATTGGACGCCGGCGGAGGAGGATTTAAGGCTGAGGCGACGGCTGAGGGAGGCTGAAAGGGAAGGATTGCGGCTGGGGCTA
104848 G A ATTGTCCGATTGCAGTAGTAATGCAATTAGAACATTCCTTTGCATCTAGGTCCCCTACACACTGGGCTGCTGCCTGCACATATCCTGCTGCTCCAATTCT[G/A]TAAGTACCTCCAGTGCCTCCTGATACCACAATCGCCTGAAGAGCTTCATCCCTCATTCCTATAAGGTTTGGATCATACCCGTTGGATGG
104850 T C TCCTCTTATGGCAGAACAAACAAACATGAAACCCACACTCACAAGGTAGAAAACTTGAATCGGTTAAGTCTAAATCTTCATAACATATAGGGCACGACGA[T/C]TGTGGAGGTGCATTGAAAGTCCTATGGTTCATTATATTAGGCAAGCTCTGAGGGCGGAACTCGTCGTTGGGCCTCCATGTTCTTGAA
104850 A G AGAACAAACAAACATGAAACCCACACTCACAAGGTAGAAAACTTGAATCGGTTAAGTCTAAATCTTCATAACATATAGGGCACGACGATTGTGGAGGTGC[A/G]TTGAAAGTCCTATGGTTCATTATATTAGGCAAGCTCTGAGGGCGGAACTCGTCGTTGGGCCTCCATGTTCTTGAATTGGCCTTACAA
104850 G A TTAAGTCTAAATCTTCATAACATATAGGGCACGACGATTGTGGAGGTGCATTGAAAGTCCTATGGTTCATTATATTAGGCAAGCTCTGAGGGCGGAACTC[G/A]TCGTTGGGCCTCCATGTTCTTGAATTGGCCTTACAAGACTCGTGCTTTGTATCTTCGAATGAGTCGGTGGACATTGGGCTGTGAGCA
104850 G A TTGTATCTTCGAATGAGTCGGTGGACATTGGGCTGTGAGCATGATGCTGACTGCTGTTTGGGGATGTTGAGAGAGCATCAGCAATGGTTTCCCAGTCATC[G/A]AGTTCGTCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTCGAGAATACGATCCGACGCTGCTTCCGGTACAGCTGCTGGCGATG
104850 G T TGCTGACTGCTGTTTGGGGATGTTGAGAGAGCATCAGCAATGGTTTCCCAGTCATCGAGTTCGTCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTC[G/T]AGAATACGATCCGACGCTGCTTCCGGTACAGCTGCTGGCGATGCTACTGCTGTTGTTGGTGGCGGGATCGTTGTTTTTACAGTTGTTG
104850 C T GGGGATGTTGAGAGAGCATCAGCAATGGTTTCCCAGTCATCGAGTTCGTCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTCGAGAATACGATCCGA[C/T]GCTGCTTCCGGTACAGCTGCTGGCGATGCTACTGCTGTTGTTGGTGGCGGGATCGTTGTTTTTACAGTTGTTGTGTGTTGGTGATTCT
104850 C T ATGGTTTCCCAGTCATCGAGTTCGTCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTCGAGAATACGATCCGACGCTGCTTCCGGTACAGCTGCTGG[C/T]GATGCTACTGCTGTTGTTGGTGGCGGGATCGTTGTTTTTACAGTTGTTGTGTGTTGGTGATTCTAAGTCGCTGTTTTCGAGATTGGTCA
104850 T TTGA GAGTTCGTCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTCGAGAATACGATCCGACGCTGCTTCCGGTACAGCTGCTGGCGATGCTACTGCTGTTG[T/TTGA]TGGTGGCGGGATCGTTGTTTTTACAGTTGTTGTGTGTTGGTGATTCTAAGTCGCTGTTTTCGAGATTGGTCAGTTCTTCATGGTCC
104850 C T TCTCCTTCGTAATCTTCTTCTGCATCGCTGACGCTTCGAGAATACGATCCGACGCTGCTTCCGGTACAGCTGCTGGCGATGCTACTGCTGTTGTTGGTGG[C/T]GGGATCGTTGTTTTTACAGTTGTTGTGTGTTGGTGATTCTAAGTCGCTGTTTTCGAGATTGGTCAGTTCTTCATGGTCCAAAGTTGGTG
104850 A G TACTGCTGTTGTTGGTGGCGGGATCGTTGTTTTTACAGTTGTTGTGTGTTGGTGATTCTAAGTCGCTGTTTTCGAGATTGGTCAGTTCTTCATGGTCCAA[A/G]GTTGGTGCGTTTGAATATGAACGCTCTTTTTTCGTTGTTGATTTGCTTTGGGAACTGCGTTGAAGGGGTGAGGTGGGAGAGACCGGG
104850 CT C TTGTTTTTACAGTTGTTGTGTGTTGGTGATTCTAAGTCGCTGTTTTCGAGATTGGTCAGTTCTTCATGGTCCAAAGTTGGTGCGTTTGAATATGAACGCT[CT/C]TTTTTTCGTTGTTGATTTGCTTTGGGAACTGCGTTGAAGGGGTGAGGTGGGAGAGACCGGGATGGATGCCCTTTCTTCGTTTCCCTTC
104850 C T GAAGGGGTGAGGTGGGAGAGACCGGGATGGATGCCCTTTCTTCGTTTCCCTTCTTAACTTGAGATAACCATTGCTCCCTTCTCGCATCAAGCTTGCACTG[C/T]TTCAACCGCGCGCTCCTATTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACA
104850 A G AGACCGGGATGGATGCCCTTTCTTCGTTTCCCTTCTTAACTTGAGATAACCATTGCTCCCTTCTCGCATCAAGCTTGCACTGCTTCAACCGCGCGCTCCT[A/G]TTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATT
104850 C T TAACTTGAGATAACCATTGCTCCCTTCTCGCATCAAGCTTGCACTGCTTCAACCGCGCGCTCCTATTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAAT[C/T]GCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATTATAGAGAAAGAAACTGATACGAAATTGCGAGACGA
104850 C A TCAAGCTTGCACTGCTTCAACCGCGCGCTCCTATTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTA[C/A]GACAGACCTTAAGATCAAAAATTATAGAGAAAGAAACTGATACGAAATTGCGAGACGATTCGGACTAGCAGAAAAATTAGCGGTGAGA
104850 G A GCTTCAACCGCGCGCTCCTATTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAA[G/A]ATCAAAAATTATAGAGAAAGAAACTGATACGAAATTGCGAGACGATTCGGACTAGCAGAAAAATTAGCGGTGAGAGAAATAGCATATA
104850 T C CGCTCCTATTCGACCTCTTTTTCTTCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATTA[T/C]AGAGAAAGAAACTGATACGAAATTGCGAGACGATTCGGACTAGCAGAAAAATTAGCGGTGAGAGAAATAGCATATATACTATTTTGAC
104850 T C TCCCAATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATTATAGAGAAAGAAACTGATACGAAAT[T/C]GCGAGACGATTCGGACTAGCAGAAAAATTAGCGGTGAGAGAAATAGCATATATACTATTTTGACCTGCCCTTGGTATAGAATTTTCTT
104850 G A ATCTCTCTCGCAATCGCAGGCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATTATAGAGAAAGAAACTGATACGAAATTGCGA[G/A]ACGATTCGGACTAGCAGAAAAATTAGCGGTGAGAGAAATAGCATATATACTATTTTGACCTGCCCTTGGTATAGAATTTTCTTTAATC
104850 A G GCGCATCAAAATTTTCATTGGCCATTACGACAGACCTTAAGATCAAAAATTATAGAGAAAGAAACTGATACGAAATTGCGAGACGATTCGGACTAGCAGA[A/G]AAATTAGCGGTGAGAGAAATAGCATATATACTATTTTGACCTGCCCTTGGTATAGAATTTTCTTTAATCCAGTAGGCCAACA
104858 T A GAGGTCGTCGTGTAGAGTGGCCGCCGAGGAACGTTTTGTACAGGTACTGTGCCGTTTTCCTTGCATTTTCCGCGGATGCGAGGGAGTAGTTCCCTACTCC[T/A]CCTCCGATCGAAAGCAGTACCTTGATGCCCATGGCCTGACAAGCAGTGATATGGCTACTAAGGCCAACACAGCCATTAAAGCTCGG
104858 C T AGTGGCCGCCGAGGAACGTTTTGTACAGGTACTGTGCCGTTTTCCTTGCATTTTCCGCGGATGCGAGGGAGTAGTTCCCTACTCCTCCTCCGATCGAAAG[C/T]AGTACCTTGATGCCCATGGCCTGACAAGCAGTGATATGGCTACTAAGGCCAACACAGCCATTAAAGCTCGGGTCACAGTGACCGGC
104860 A G CCTCTGCCCTCCCTTCTACTACGCCTACGGCGACGGCAGCCTCGTCGCCCACCTTAGGCGGGGCCCGCTCTCCCTTTCTTCCTTCCGGTTCCGCAACTTC[A/G]CCTTCGCCTGCTCCCACTCCGCCCTCGCCGAGCCCATGGGCGTTGCCGGGTTCGGGCGCGGGGCCCTCTCCCTGCCCAATCAGCTTCA
104860 A G TTCCGCAACTTCACCTTCGCCTGCTCCCACTCCGCCCTCGCCGAGCCCATGGGCGTTGCCGGGTTCGGGCGCGGGGCCCTCTCCCTGCCCAATCAGCTTC[A/G]GGCCCTCGTTCCCGATTTAGGCAACCGATTCTCCTACTGTTTGATTTCTCACTCTTTCAAACAGAGTCGATTGATCAAGGCCAGCCCTT
104872 TATG T CATTGTATTTGTTTGGGTCAGGACCGGTTGAGTTTAGTCAGAAGATTGTGGCAATAAATTACATTATTATGGATAAATTATGCCTCTTTAGATGATCTGT[TATG/T]ATGAACCAGTTTCAGTGTCCTTTTCATCGATTTTAAAGAATGTGTTTATTGTTTTATTGCAAGTACTGAGGCTATAAACTTTTGTATT
104872 G A GAACCAGTTTCAGTGTCCTTTTCATCGATTTTAAAGAATGTGTTTATTGTTTTATTGCAAGTACTGAGGCTATAAACTTTTGTATTATTGTCCTAGTCCA[G/A]CGTGCATTTCTGGTGGATTATTTGTTTGGAGAAAAAAAGCTTGTAACCTGTACTTGTGTATTGATTTTTTGTTGTAA
104882 T G CGCTCTTACAGATATGCTGTGGCACTTCGGTCAGAAAAGGGGAGCTCAACAAGTAGTGCTTGAAGGAGTACAGCGTCAAGTGTGGGAGAGTGCATGGAGT[T/G]AATTCTGCTTAGATTTGCACCTCATGTCATCAGGTGCTGCACAAGCTATGCTTCATGCTTGGCTCCTAAGCGTTCGTACGATTGTT
104890 T C GACTTTTGCTGGCTCGACGTGTTTTGAAGAAACTTGAAATGGACGAGGAGTACGAGGGTAATGTTGAGGCTACTGGAGAAGATTATTCAGTAGAGCCTGC[T/C]GAGAGCAGAAGGCCATTCCGCTGTGTTCTTGATGTTGGTCTTATTAGGACCACCACAGGCAACAGAATCTTTGGTGCTCTCAAGG
104902 TA T TAGAGAGATACACAAAAACGAAGAAAAGCACATACTCTGGATTTGAGCTGTTCCGTATCAAAGAAAGGGACATTCCAATTGAAGTGTTAGAGCTTGATAA[TA/T]AAAAATGATAAGGTCATAGCATTTGCATGGGAACCGAAAGGTCATAGGTTTGCCGTGATCCATGGGGATGGCCCACGCCCTGAT
104908 A G ATGTGACATGTGACAAGCAAAAGTTGGTTATTGGAACTCTGTCTTCTGAAAAGTGTGCCCAGATTTCTTATGACTTAGTGTTCGAGAAGGACTTTGAATT[A/G]TCTCACAGTTCGAAGAATGCTAGTGTTTACTTTACTGGCTTCAAGTCGATTGTTCCTACCGATGATGAATTTCCAAGTGATTCTGATGT
104908 C T ACGATGATTCTGAAGATGAAGATTTTGAGGATGATGATGACTCTCATGACGGTAGCTCTGATGATGAGGACATGGTGGAAGCTGGGAAGGGAAGCGATGA[C/T]GACGACAAAGACGACGATTCTGAGGACGAGGATGACGATTCTGAGGACGAGAATGACGATTCTGAGGACGAGGAAGAAACAC
104908 A G CTGGGAAGGGAAGCGATGACGACGACAAAGACGACGATTCTGAGGACGAGGATGACGATTCTGAGGACGAGAATGACGATTCTGAGGACGAGGAAGAAAC[A/G]CCCAAGAAGGCTGCTTCCAAGGACAAGAAGAGGCCAGCTGAGCCTGTAACAAAAACTGCTGTTTCTGAGAAGAAGGCTAAGC
104914 G A AGCCGGAACTGAAGAAACCCGATAAGATTTTGCCGTGCCCGAGATGCAACAGCGGGGACACGAAGTTCTGCTACTACAACAACTACAACGTGAACCAGCC[G/A]CGCCACTTCTGCAAGAACTGCCAGCGGTACTGGACGGCGGGCGGCACCATGCGCAACGTCCCGGTCGGGGCAGGCAGACGAAA
104914 C A CTTCTGCAAGAACTGCCAGCGGTACTGGACGGCGGGCGGCACCATGCGCAACGTCCCGGTCGGGGCAGGCAGACGAAAGTCCAAAAACGTCCCACCAAAC[C/A]ACTACCCGCACATCGCCGTGCCCGACCCTTCCCGCCCCGTGAAGGGCGGCACAATCCTCAGTTTCGGGACGTATCCATGGGGAC
104914 T C TCCCACCAAACCACTACCCGCACATCGCCGTGCCCGACCCTTCCCGCCCCGTGAAGGGCGGCACAATCCTCAGTTTCGGGACGTATCCATGGGGACCCGC[T/C]TGCTGGGGCTACGGTCCTGTGCAGTGGGTTCCGTCCCCCGTTGTCATGACTCCTTCTGGGTCGGGCACCAGCACTGTTTGCTCTGGG
104914 T C CTGTTTGCTCTGGGTCCATTTCGCCTTTGGGGAAGCGCTCGAGGGAAGGGGAGAGCGAGGACGGAAGAGGGAACTTGTGGATGCCGAAGACGCTGAGGAT[T/C]GACGACCCAGAAGAAGCGGCGAAGAGCTCGTACTGGGCCACGATGGGATTCGATAAGTCGGAGCATGGACTTTTTAAACCGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104916 T C GATCCAATAAGCTACTAACTAGAGGTAGTATCCGGGTCTTATATCGCTTTACCCCCTCTTCATACCCGATATCCATCAAGAATTCTGGTACATTCTCCGC[T/C]GTGTACGTCTTCCCATAGTACGTGTTAACAACAAGTGCTTTGGATTCGAATAGTTTTGGAGATGGTAAAAGCCACATGTTGCTCTCAGA
104916 T C CTACTAACTAGAGGTAGTATCCGGGTCTTATATCGCTTTACCCCCTCTTCATACCCGATATCCATCAAGAATTCTGGTACATTCTCCGCTGTGTACGTCT[T/C]CCCATAGTACGTGTTAACAACAAGTGCTTTGGATTCGAATAGTTTTGGAGATGGTAAAAGCCACATGTTGCTCTCAGAGCTACGCTGTTC
104916 C T GTAACGGGTTGACAATGGGTATGCCCAAAGTGGATCCAGACCCATAAGTGAGCATTTGCATGACCGTACCTCCCCAAGGAGCAGAGAGGGTGATCAAGTG[C/T]TTTACGTGCTTGGCACGCCATGAGGGATCGATACGTGTGAGTAGTTGGTGTGCATAGAGGCTACCAAGGCTGTGGGCTAGGAGG
104916 A C AGAGGCTACCAAGGCTGTGGGCTAGGAGGATAACGGGTTTGAACCCATTGGATGTGTATGCGGATTCTATTAGCTGCTGGAGGTCTTGGAGGTATTTGGA[A/C]CCAACCTGGGTTGGGTGGTTAGGTGCGGCTAGACCATATCTGAAGTCGTAGGGAGCACCAAAGAGGTTCCGGCCATCTTCGTAC
104918 C T TGAAATCTGCTACTGGCAATTTCAGACCTGATAGCATTCTCGGTGAAGGAGGATTTGGTTATGTTTTTAAAGGATGGATAGAAGAAAATGGAACTGCTCC[C/T]GCCAAACCAGGAACTGGAATTACTGTTGCCGTGAAAAGTCTTAAACAAGATGCTCTTCAAGGTCACCGCGAGTGGGTGGCAGAGG
104918 A G TTCTTGATTCGGAATACAATGCAAAGCTATCAGATTTTGGCTTGGCAAAAGCCGGACCTCAAGGAGATATGACTCATGTCTCTACCAGAGTTGTCGGCAC[A/G]TATGGTTATGCAGCTCCAGAATACGTTATGACAGGGCATTTGACATCCAAGAGCGACGTCTACAGTTTCGGAGTAGTACTGCTAGAG
104918 A G GGAGATATGACTCATGTCTCTACCAGAGTTGTCGGCACATATGGTTATGCAGCTCCAGAATACGTTATGACAGGGCATTTGACATCCAAGAGCGACGTCT[A/G]CAGTTTCGGAGTAGTACTGCTAGAGATGTTAACCGGGAGAAGATCAATGGACAAGAGGCGACCAAAAGGAGAACACAATCTAGTG
104918 A G TCTACAGTTTCGGAGTAGTACTGCTAGAGATGTTAACCGGGAGAAGATCAATGGACAAGAGGCGACCAAAAGGAGAACACAATCTAGTGTCATGGGCAAG[A/G]CCTCATCTAGGCGACAGGCGCAGGCTTTATCAACTAGTGGACCCTCGACTACAGTACAGTTTTTCAATGAAAGGAGTTCATAAGG
104924 A G TTGCGAACTTGGTCCGGACACAAGTCCCGGTCTAGAGCCCTGGGCAGATGTGGCCTGATTCGGTCCCTGAGTTGACGGGTCGTTCATGGCAGCATTCACT[A/G]GCTCGTCTGATAGGCTGTCTTCACTCATATTCGAACTATACTACAACTTAACAAAGCCGATCGCCTTTGTTGTTGTAGATGAAATTTG
104924 T C GGTCTAGAGCCCTGGGCAGATGTGGCCTGATTCGGTCCCTGAGTTGACGGGTCGTTCATGGCAGCATTCACTAGCTCGTCTGATAGGCTGTCTTCACTCA[T/C]ATTCGAACTATACTACAACTTAACAAAGCCGATCGCCTTTGTTGTTGTAGATGAAATTTGAGCAATTGTTATGTAGTAAGGAAAGAG
104924 A G GTCACTTAAGGGCTTATTCAACTTGTGTGGTGTGAATATCTCGTCACTTAACAGCAGTGCTCCATTATCGGCTAACTTGTAACTTACGCTGGTTCCTCCG[A/G]GCGAAGGTTTGATATCGACTTGCAGCTGCAGGGCGGTACTAGCCGGTTTACCTAGTATGTCCATTGGCATGTGTAGGCTTGACCCATT
104928 G A CGCATGGCCAAAGCACCGAACCCCTAAACCGCGGCCATCAGTTATCAGCACAAGCGAAGATTCGCAAAAGAGAGGGACCTCGAAAGCAGTTCGCTCGTTC[G/A]TCAGTCCTCACGAATCGCTTGGCGAACTCCGACTGCCTCTACGTCGTCACCCTGAACTCCGCCACCAACATAACCACCACAGTTAC
104928 CT C CTGCTGTTGATGCTTTTCTGTCTTTCGAGATAGGAAGGAAGTTGTATGCCATGCGTAGTCCTACATCCGCTTCCACTTCTGCTCGTTGACTGTCTCCTTT[CT/C]TTTTGTTCCAAGGTTCTCCATGTTAAAGAGAGCTGTTGCCATGATGTAGCGACTTTCCTGTAATTTTATAGCGTTGTTGAATGTAATGTA
104932 C T CCCTGCACAATCCATCCACATTATCTCCTCCTAAACCGTGTTGATTCCATTTGTGCTCCACCGCCTTCACCTCGCCGGCGAACACCAGCAGAAACGGCGG[C/T]AGCGACCCGAGCTCGTAGATCCGATCCTTCTTCTTCTGCACCTCCATCCAGTACTCCAGCTTCTTCGTGTACCCTCCCGCCCTCCACTTC
104932 T C TCTTCTGCACCTCCATCCAGTACTCCAGCTTCTTCGTGTACCCTCCCGCCCTCCACTTCATTAGATCCATCACCATCACACCCGTGTTGAAGTAGCACGG[T/C]TTCTTCGTGCGGGATTCGAACACTTTTACGTAGTCGGGGTTGGACCAGAAGGCGTTGGTGAAGTAGTAGGTGAAGTTGGCGTGGCAGT
104932 T G GCTTCTTCGTGTACCCTCCCGCCCTCCACTTCATTAGATCCATCACCATCACACCCGTGTTGAAGTAGCACGGTTTCTTCGTGCGGGATTCGAACACTTT[T/G]ACGTAGTCGGGGTTGGACCAGAAGGCGTTGGTGAAGTAGTAGGTGAAGTTGGCGTGGCAGTACTCGGGGGCGGCGAGGACGGTGT
104932 G C TCACCATCACACCCGTGTTGAAGTAGCACGGTTTCTTCGTGCGGGATTCGAACACTTTTACGTAGTCGGGGTTGGACCAGAAGGCGTTGGTGAAGTAGTA[G/C]GTGAAGTTGGCGTGGCAGTACTCGGGGGCGGCGAGGACGGTGTGGGACGAGAGCGGCGTGTTCCAGAGGTGGATGACGTCGTC
104932 G A CGGAGGAAGAGATCTTGTCGCGGACGAGGGTGGGATCGAAGCGGTAGATGCGGAAGGAGAGGGAAGGGAAGGTGGAGAGGAGGATGGGTCGGAGCTTGCG[G/A]GGGGAGATGGCGAGGAAGTGGAAGGAGAGGTTCTGGGGGCAGGACGAGTGCTGGAGGAGGGAGAGGATTCCGGCGA
104932 G A TGCGGGGGGAGATGGCGAGGAAGTGGAAGGAGAGGTTCTGGGGGCAGGACGAGTGCTGGAGGAGGGAGAGGATTCCGGCGAGGCTGCCGCGGAGGTAAGT[G/A]GCGTCGAGGGTCATGGCGATGTGGATTGTCGGAGAATGGCGGCAGGAAGGCGGGTTACGGAAGGCAGGGGCTTCGGA
104932 T G AGGAGAGGTTCTGGGGGCAGGACGAGTGCTGGAGGAGGGAGAGGATTCCGGCGAGGCTGCCGCGGAGGTAAGTGGCGTCGAGGGTCATGGCGATGTGGAT[T/G]GTCGGAGAATGGCGGCAGGAAGGCGGGTTACGGAAGGCAGGGGCTTCGGAGAATTGGGGGATGGGCGGGGATGCAGCG
104932 T TG GCTGCCGCGGAGGTAAGTGGCGTCGAGGGTCATGGCGATGTGGATTGTCGGAGAATGGCGGCAGGAAGGCGGGTTACGGAAGGCAGGGGCTTCGGAGAAT[T/TG]GGGGGATGGGCGGGGATGCAGCGGAGACGGAGGTCAGGAGGAGGGAAACAAACACCGAGAGCAGCAACGCCATTGTTG
104934 AC A TAAAGGTTACCAGAATTTGTATTGCCTTATGCAACAAGTTTGAAAACTATTTCATCATAGGGCAGAGTTCTTATAGGAATAA[AC/A]CCCCAACCCCAGCTTTCCTGCCCAACCTACCAGCATCAACATACTGCACAAGAAGTGGGCATGGACTGTACTTGCTATCTCCCAGCCCATTATGAAGCAC
104934 C T TTGTTCCTAACACCATTGCCGCATCGATGTCTTCTTTGGTGGCCACGCCCGTGTATAATGTGTGAAATGCTTCATTTATCATGGGCATGAGTATTCTGTT[C/T]ACTATAAAACCTGGGTAGTCCAAGGAGCATACAACGATTTTTCCCAATCTTTCTGCCAATGCTTTTATAGTATCAAAAACCTCATCGGAC
104934 G A CCAATTTCATTATAGGAGGAGGATTCATAAAATGCATGCCTATCACCTGGGACGGACGACTGGTTGCAGAAGCAATTCGGGTTATTGAAATCGAACTAGT[G/A]TTTGATGCTAAAATAGCAGAAGTCTTTGTGATTTTATCAAGTTCTGAAAATACTTTCTTCTTTATTTCCTCCGACTCAACAATAGCCTC
104934 C T CCTATCACCTGGGACGGACGACTGGTTGCAGAAGCAATTCGGGTTATTGAAATCGAACTAGTGTTTGATGCTAAAATAGCAGAAGTCTTTGTGATTTTAT[C/T]AAGTTCTGAAAATACTTTCTTCTTTATTTCCTCCGACTCAACAATAGCCTCAATTACGACATCTGCATCCCTCAGATCTTCCATGCTAGT
104934 G C GACTCAAAGCACCAGTTCCTAATTCCTTAGATAATTGACCTTTGGAAATAAAACGATCGATTGAAGAAGATATTGATCGAGTGGCGTTTGAAAGAGCTTT[G/C]GGATCCGAATCGTGGATCCATACGTCGAACCCAGCGACGGCGGCAAGTTGAGCGATGCCTGAACCCATCTGACCGCCGCCGATTAC
104934 A T AAATAAAACGATCGATTGAAGAAGATATTGATCGAGTGGCGTTTGAAAGAGCTTTGGGATCCGAATCGTGGATCCATACGTCGAACCCAGCGACGGCGGC[A/T]AGTTGAGCGATGCCTGAACCCATCTGACCGCCGCCGATTACGCCGATTGTTTTCAGATTATTCGCCATCGGAAAATGAAATACTTT
104938 C T TGCTCAGCAGTTTGCAATTTTTGGAGTATTTGATGGCCATGGTGGGGATGCAGCTGCCAAAACTGCTAGCAAGATGTTGCCTGAAAAGGTAGCTGAGATT[C/T]TTTCGATAACGGAGAACAGAGAAAGTGTTGTTTCCTCGTGCAATGCTACAGATGTCCTCAGGGATTCTTTTCACCTTACTGAGGCAG
104950 T C AGTTTATTCAATCCATTAGGAGTCTTCACATAGTCTTCAATGAAGATAGTAACGACTTCAGAAGTGTTGTTTTCAAGAAAAGTCTGAATTTCTTTGAGGA[T/C]GTTGGCTGCCGGTTGAAAGGCAGTAAAATTGTAGCAATTTCCACCGAAGGAGTGGCACAACCAAATGTCATTTTGGAAGTCGTACATG
104950 G A ATTCAATCCATTAGGAGTCTTCACATAGTCTTCAATGAAGATAGTAACGACTTCAGAAGTGTTGTTTTCAAGAAAAGTCTGAATTTCTTTGAGGATGTTG[G/A]CTGCCGGTTGAAAGGCAGTAAAATTGTAGCAATTTCCACCGAAGGAGTGGCACAACCAAATGTCATTTTGGAAGTCGTACATGTCCAG
104952 T C TAAAACTACACTACCTTAGAACGGTTTACTACTTCAAACATAGCGAGGTCATAGAGAACTTAGGCATTGTTCAAATAAAAGAGCCTATGTTTCTGATGCT[T/C]GATGTCTTCCCAGAAGCAGCGGGGAGGATAAGAAGGCATGAGTCGGGTAGGCCTCATCTGAAGTGTAACGATAGTGGAGTGAGGA
104952 T C TTGTTCAAATAAAAGAGCCTATGTTTCTGATGCTTGATGTCTTCCCAGAAGCAGCGGGGAGGATAAGAAGGCATGAGTCGGGTAGGCCTCATCTGAAGTG[T/C]AACGATAGTGGAGTGAGGATAGTCGAAGCCAAATGTAAGGTTACCATGGATGAATATCTTAAAATGGAGAATGAGGCAGATAGG
104952 T G TCCCAGAAGCAGCGGGGAGGATAAGAAGGCATGAGTCGGGTAGGCCTCATCTGAAGTGTAACGATAGTGGAGTGAGGATAGTCGAAGCCAAATGTAAGGT[T/G]ACCATGGATGAATATCTTAAAATGGAGAATGAGGCAGATAGGTGTAAGAATGTTGTGTATGATAAAGTCATCGGTCCTGATCT
104962 A G GAGGAAAGTCGCTTGCTTTTGTTGGCGATTCGGTTGGTAGAAATCAAATGCAGTCCTTGATGTGCCTATTAAACAGAGTAACATATGCAGTGGATGTATC[A/G]CCAACAGCAGATGAAAAGTCGAAAACCTGGTCATACCCAACCCACAACTTCACCCTAGCAAACTTCTGGTCGCCCTACCTAGTTGAA
104964 A G GTGCGAACGAAGAAGGAGGAAGCTTATGAACGAGTGATAGAGCTGCACAGGGAGATAAGGGAAGCGGGGTACGTACCTGATACGAGCTATGTGCTGCATG[A/G]TATCGATGAGGAGGCGAAGGAGAAAGCGCTTATGTACCATAGCGAGAGGCTGGCGATAGCTTTTGGGCTTGTAAGCACCAAG
104980 A G GGAAAATTCTAGCAATCCATTTCTTGGAGACAGTAACATGCAAACTATGAGGCAATGTAGTCCCAATTTATTCAGTTTGAGTGAGCAAACATCAAAAAAG[A/G]AGCGAGGTCGGCCAAGAAAATACGTGACAGACGGAAATGTGGCATTGCAAGTTTCTCCTATTTCATCGAATCCAGGTTTATCAAATT
104992 C A AGAGTGCAGATTAGTACCTTAGCTGTGAAAGATAACATGATTGTTGCTGGTGGATTTCAAGGAGAGCTTATCTGCAAGCATCTGAATCAACCTGAAGTAG[C/A]CTATTGCGCTAAAGTAACCAGTGGCAACAATGCCATCACAAATTCAGTGGATATATACCGGACTGCAGGTGGCTCAACTCGAGTGA
104992 T C GCGCTAAAGTAACCAGTGGCAACAATGCCATCACAAATTCAGTGGATATATACCGGACTGCAGGTGGCTCAACTCGAGTGATGGCTGCCAACAATGACTG[T/C]TGTGTACGGATTTATGATGCTAATAGCTTCACCTTGTTGAATCAACTTTCATATTCCTGGTCTGTAAATGGCACATCGGCCAGTCCG
104992 A G TCAAATCCGATTACGCTTGTGCTCAGGAAATCGACATATTTGGTGAAATTGCAGGTATTTCTTTCAGTCCTGATGCTGAAGCGATCTTTATTGGGGTTGC[A/G]GATAGGACTTACGGTAGCGTGTTGGAGTTTAGGAGGAGGCATCAGTTTAATTATTTGGACTCCTTTATATGAGCTTTATAGGGTTTGT
104996 A AC CAAGCCGTTGTTCTCTTCCTCCTCTTCTTCCGCCGCCATGTCCACCGCTCCCACCTCGACAATCGAACACGTCGTCCTGTTCAAAGTCAAACCCTCGGCC[A/AC]CGAGTCCCAGGTTTCCTCCATGATCTCCAGCCTCCAATCCTTATCCTCCCTCTCCCTCACCTCCTTCCTCACGGCCGCCCCTATCCTTCGC
104996 C CT AAGCCGTTGTTCTCTTCCTCCTCTTCTTCCGCCGCCATGTCCACCGCTCCCACCTCGACAATCGAACACGTCGTCCTGTTCAAAGTCAAACCCTCGGCCA[C/CT]GAGTCCCAGGTTTCCTCCATGATCTCCAGCCTCCAATCCTTATCCTCCCTCTCCCTCACCTCCTTCCTCACGGCCGCCCCTATCCTTCGCC
104996 T C ACGAGTCCCAGGTTTCCTCCATGATCTCCAGCCTCCAATCCTTATCCTCCCTCTCCCTCACCTCCTTCCTCACGGCCGCCCCTATCCTTCGCCGTTGCTC[T/C]GCTGCCGCCGATGAATTAGGGTTTACTCACCTCCTTCACTCTCGTTACCCATCTAAATCTAATCTGTCCACCTACTCTGCTCATGAAGATCA
104996 C A GCTCTGCTGCCGCCGATGAATTAGGGTTTACTCACCTCCTTCACTCTCGTTACCCATCTAAATCTAATCTGTCCACCTACTCTGCTCATGAAGATCATGT[C/A]TCGGTTGTTAAGAACTACATCCTTCCTATAACTGATGACATCATGGCCGTCGACTGGGTCTCCGACCAGGAATCTTTGGCTGTTCCTGAG
104996 T C ATGAAGATCATGTCTCGGTTGTTAAGAACTACATCCTTCCTATAACTGATGACATCATGGCCGTCGACTGGGTCTCCGACCAGGAATCTTTGGCTGTTCC[T/C]GAGGCAGGGAAGGTTTTGAGGGTCACGATCGTGAAAGCAAAGGAAGGGGTGTCTGCGACTGAGGTTACGAATATGATTGGGGAGA
104996 T G TCTCCGACCAGGAATCTTTGGCTGTTCCTGAGGCAGGGAAGGTTTTGAGGGTCACGATCGTGAAAGCAAAGGAAGGGGTGTCTGCGACTGAGGTTACGAA[T/G]ATGATTGGGGAGACGGATGTGGCAGGAAAGGCAGAGCAGGTTAGTTTTGGGGAGAATTTCTCACCTGCTAGGGCTAAGGGCTA
104996 T C TGTGTTGGATTATGTTGTGCCTAGCAGTACCGGCACTGCTTCCCTTTGATTGCATTCCTTAAGTTTTTTGGAATTTTGCTGCAGCATGGATTTAGACTTA[T/C]AAAGTCAGCTCACGTTAACTACAAATTGCTACTCTATAACGTTGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGG
104996 G A TTGGATTATGTTGTGCCTAGCAGTACCGGCACTGCTTCCCTTTGATTGCATTCCTTAAGTTTTTTGGAATTTTGCTGCAGCATGGATTTAGACTTATAAA[G/A]TCAGCTCACGTTAACTACAAATTGCTACTCTATAACGTTGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAG
104996 A G GGCACTGCTTCCCTTTGATTGCATTCCTTAAGTTTTTTGGAATTTTGCTGCAGCATGGATTTAGACTTATAAAGTCAGCTCACGTTAACTACAAATTGCT[A/G]CTCTATAACGTTGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCA
104996 T C CCTTTGATTGCATTCCTTAAGTTTTTTGGAATTTTGCTGCAGCATGGATTTAGACTTATAAAGTCAGCTCACGTTAACTACAAATTGCTACTCTATAACG[T/C]TGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTG
104996 T C ATTCCTTAAGTTTTTTGGAATTTTGCTGCAGCATGGATTTAGACTTATAAAGTCAGCTCACGTTAACTACAAATTGCTACTCTATAACGTTGTATGGAGT[T/C]GGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACG
104996 C T TCACGTTAACTACAAATTGCTACTCTATAACGTTGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACT[C/T]GGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTACTGCAATA
104996 A G AATTGCTACTCTATAACGTTGTATGGAGTTGGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTT[A/G]AAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTACTGCAATATATGTGATATATAA
104996 C T GGGCTCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATG[C/T]GGCACTACAACTTTGCACAGGAAGATGCTTAACTACTGCAATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAA
104996 A G TCTGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGC[A/G]CTACAACTTTGCACAGGAAGATGCTTAACTACTGCAATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTT
104996 T C TGTTATAATATAATTTGCTCATGCTGTGTGGAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCAC[T/C]ACAACTTTGCACAGGAAGATGCTTAACTACTGCAATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTTGA
104996 C T GAGAGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTA[C/T]TGCAATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTTGATTGTTCTGTGAAACCAAAATTG
104996 C T AGTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTACTG[C/T]AATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTTGATTGTTCTGTGAAACCAAAATTG
104996 A G GTGAAGTCTACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTACTGC[A/G]ATATATGTGATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTTGATTGTTCTGTGAAACCAAAATTG
104996 T C TACGGACTCGGCTTGATCAGTTAAAGCTTGAGGGAAGACGGATGCTGGGATGCGGCACTACAACTTTGCACAGGAAGATGCTTAACTACTGCAATATATG[T/C]GATATATAATGAAATGTGAGTAAGATTATTATTTGTAAAAGTTGATTGTTCTGTGAAACCAAAATTG
104998 G A ACATCCACTGAACATAGTCCGTCAGCCCAGCCGACCCCAAACACCACCTGCTCTCCGGCAGCCCAAACCTCTTCCTCATCTCTATCCTCCAAAACCCACC[G/A]TACAACAATCCACACACGCACAACACGACCCCCGCACACCACATCACCTCATCGATCATATCGTTCCGTATCTTCATCGCCGTGTTGCTA
104998 G A TAAACAGATGCAGGTACATGTTTCCGAACCCGAGCCTTTCCATGTTCCACCCGAACACGCAGCACGTGCAGAAGCAGGAGAGGTAACCAACTGTCACGTC[G/A]TCGGAGCAGTCCATCAGCCCACCAACCCACTCCGGCTGACCCACCACGACCATCCCGGTAGTCCTCAAAGTTTGCAACGCCTCGTA
104998 T C GCAGGAGAGGTAACCAACTGTCACGTCGTCGGAGCAGTCCATCAGCCCACCAACCCACTCCGGCTGACCCACCACGACCATCCCGGTAGTCCTCAAAGTT[T/C]GCAACGCCTCGTAGTACTCCCCCGCCGAGTCTATGGGCTCGTACTCCCGTCCAAGCGGGCTGTACAGGGTGTATGCCCCAGCGAGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
104998 T C CGACCATCCCGGTAGTCCTCAAAGTTTGCAACGCCTCGTAGTACTCCCCCGCCGAGTCTATGGGCTCGTACTCCCGTCCAAGCGGGCTGTACAGGGTGTA[T/C]GCCCCAGCGAGGACCGGAGCGATGGTGCCGAGGGCAAAGAACACGGCCTCTGGAAATTCTGGTCTATCGGATTCAGCGTACCCCC
104998 A T GTCTATGGGCTCGTACTCCCGTCCAAGCGGGCTGTACAGGGTGTATGCCCCAGCGAGGACCGGAGCGATGGTGCCGAGGGCAAAGAACACGGCCTCTGGA[A/T]ATTCTGGTCTATCGGATTCAGCGTACCCCCAGTACAGGCCGCAGAGGACATACTGGGCCACGCAGGTTAAATGCAGCAAGAAG
105012 T C ACCGCTGCCTTGCTCTTCATGATTGCCAATTCTCCGTAAACTTGCTAACAGGAAAGCGGCAGGAGAATAAGGTGGCAATGAGAAAGAGGCGGCCAGAAAG[T/C]TTCGGTGCAAAAAGAGTAGATAAAGAGCACGAGTAAAGAGAGAGTCCGGCCTTGATAATGTTTGTCTTCGGAGGAGAGGGCAG
105014 G C CATCTAAAGAATAATATCAGTGTATAAGTATGAAATCTACCTGAAATAAGACTGAACAAAGATTCGATGTTGATGTATCGGCAAGCATTAAGATTAAGAT[G/C]CAAGAAGTATATTTGTGGCTACAGTGATGTCGTTCCTAGCTTGGATCAAAGCCTGTCGTGCCGAATTTCTATCAAACCCCATTGACAC
105014 G A CACAAGTGTAGCAATGGAATCCTCTGCTGGTTCTGGAACTGATGCCCTTGTTGCCGATGGATGGTTCTCCGCTTGACGACCGGTATTAGGTATATTTCTC[G/A]GACCTCTCCTGGCTGATGTTGTTCGCGTGACAGCTGACGAGCTTCCTGAGGCCCATGCTAAGCGTGCAAAAAAAGATGATATGGATT
105014 G C AATGGAATCCTCTGCTGGTTCTGGAACTGATGCCCTTGTTGCCGATGGATGGTTCTCCGCTTGACGACCGGTATTAGGTATATTTCTCGGACCTCTCCTG[G/C]CTGATGTTGTTCGCGTGACAGCTGACGAGCTTCCTGAGGCCCATGCTAAGCGTGCAAAAAAAGATGATATGGATTTCGGAAACTTTG
105014 CA C TCCGCTTGACGACCGGTATTAGGTATATTTCTCGGACCTCTCCTGGCTGATGTTGTTCGCGTGACAGCTGACGAGCTTCCTGAGGCCCATGCTAAGCGTG[CA/C]AAAAAAAGATGATATGGATTTCGGAAACTTTGCACTTCGAACATGGAAGACATTGGCCCGATACAATATGCCAGCAAGTACACCAC
105014 G GA TGGAACTTCGAAGAAACCGGAATATCAACATAGAAAGGGATAAATGAAGCAAATATTAAACCATATGGCCCAGATGCTAGTATGACTGATGAATCTTTAA[G/GA]AAAAACAATGCCAAAGCTTGAAGAAGAAATGACATGACTAGCGAGAACAGAATAAATACTGAATATTTGTTGGACCCAATCTGTC
105014 A G GAAGAAACAATTCTCCATAGCCTGAACTGTTTGAAAATTTCCTCATAAGATAGCCCAAGCTTAAAAGCACGACTTCTGATCCCAAATATAACCGTAAGGA[A/G]GCCACTTGCTATTACAAAAGTTCTTGTAATCGGAGCATTATGGAATCCGGACGGACCGCCGTGCATCTTTGGAGCGAGGGCGGAGA
105018 G A CCGCCGTAAAATCCACCATCCTCTTCGTTCTGACAATCTACGTCGCTACGTCGGCACCTACATTGCCTTCTACCGCCGTCAGTTCGAACTCCGTTCTGGT[G/A]GCCCTTCTGGACTCCACCCACTACACAGAGCTGTCTGAACTGATCGAGAAGCACTTCTTCTACCAACTCTAGAAAACGAAATCGCAGTC
105018 G GA CGTCGGCACCTACATTGCCTTCTACCGCCGTCAGTTCGAACTCCGTTCTGGTGGCCCTTCTGGACTCCACCCACTACACAGAGCTGTCTGAACTGATCGA[G/GA]AAGCACTTCTTCTACCAACTCTAGAAAACGAAATCGCAGTCCGCAACCTCACGATTTTCGCGCCAAAGAATGAAGCTCTGGAACGCG
105018 A C TTGCCTTCTACCGCCGTCAGTTCGAACTCCGTTCTGGTGGCCCTTCTGGACTCCACCCACTACACAGAGCTGTCTGAACTGATCGAGAAGCACTTCTTCT[A/C]CCAACTCTAGAAAACGAAATCGCAGTCCGCAACCTCACGATTTTCGCGCCAAAGAATGAAGCTCTGGAACGCGACCTTGACCCTGAGT
105018 C A GCCTTCTACCGCCGTCAGTTCGAACTCCGTTCTGGTGGCCCTTCTGGACTCCACCCACTACACAGAGCTGTCTGAACTGATCGAGAAGCACTTCTTCTAC[C/A]AACTCTAGAAAACGAAATCGCAGTCCGCAACCTCACGATTTTCGCGCCAAAGAATGAAGCTCTGGAACGCGACCTTGACCCTGAGTTC
105018 C T CGCCAAAGAATGAAGCTCTGGAACGCGACCTTGACCCTGAGTTCAAACGCTTCCTCCTCGAACCCGGCAATTTGAAGTCGCTCCAATCGCTCCTCCTCTA[C/T]CACGTCATTCCGTCCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAA
105018 T C ATGAAGCTCTGGAACGCGACCTTGACCCTGAGTTCAAACGCTTCCTCCTCGAACCCGGCAATTTGAAGTCGCTCCAATCGCTCCTCCTCTACCACGTCAT[T/C]CCGTCCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCC
105018 C T ACCCTGAGTTCAAACGCTTCCTCCTCGAACCCGGCAATTTGAAGTCGCTCCAATCGCTCCTCCTCTACCACGTCATTCCGTCCAAACTGCATTTCGGTCT[C/T]CTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCGACCGGACGA
105018 A G CTCCTCGAACCCGGCAATTTGAAGTCGCTCCAATCGCTCCTCCTCTACCACGTCATTCCGTCCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTA[A/G]CAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCGACCGGACGACGTAGTCAGACCTGACGGC
105018 A G CCTCGAACCCGGCAATTTGAAGTCGCTCCAATCGCTCCTCCTCTACCACGTCATTCCGTCCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTAAC[A/G]GCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCGACCGGACGACGTAGTCAGACCTGACGGCGT
105018 C T TTCCGTCCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGT[C/T]ACCCGACCGGACGACGTAGTCAGACCTGACGGCGTCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTC
105018 A G CCAAACTGCATTTCGGTCTCCTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCG[A/G]CCGGACGACGTAGTCAGACCTGACGGCGTCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAA
105018 C T ATTTCGGTCTCCTCCAAAACCCTAAACTTAACAGCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCGACCGGACGA[C/T]GTAGTCAGACCTGACGGCGTCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAAAGACGCAG
105018 T C GCAACCACAAATCCTTATCTGGGCACGAAATAAAGTTAGATCCCGCTGCTGTCACCCGACCGGACGACGTAGTCAGACCTGACGGCGTCATCCATGGAAT[T/C]GACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAAAGACGCAGTCTAGCATCAATCGCTGCAGTCTTACCTACTGG
105018 C T TCACCCGACCGGACGACGTAGTCAGACCTGACGGCGTCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAAAGACG[C/T]AGTCTAGCATCAATCGCTGCAGTCTTACCTACTGGGGCGCCATTAGTAGATCCACGCACTCACAGACTGAAGAAGCCAGCTCCGC
105018 T C CCCGACCGGACGACGTAGTCAGACCTGACGGCGTCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAAAGACGCAG[T/C]CTAGCATCAATCGCTGCAGTCTTACCTACTGGGGCGCCATTAGTAGATCCACGCACTCACAGACTGAAGAAGCCAGCTCCGCCGG
105018 G T TCATCCATGGAATTGACCGGATCTGGATTCCCAGATCGGTACAGGAGGACTTCAACAAAAGACGCAGTCTAGCATCAATCGCTGCAGTCTTACCTACTGG[G/T]GCGCCATTAGTAGATCCACGCACTCACAGACTGAAGAAGCCAGCTCCGCCGGTTTTACCTGGATCTGCACCTGTCCTACCGATTTAC
105018 C T CAGATCGGTACAGGAGGACTTCAACAAAAGACGCAGTCTAGCATCAATCGCTGCAGTCTTACCTACTGGGGCGCCATTAGTAGATCCACGCACTCACAGA[C/T]TGAAGAAGCCAGCTCCGCCGGTTTTACCTGGATCTGCACCTGTCCTACCGATTTACGATGCTTTGGCTCCTGGTCCGTCCATTGCGC
105018 G C TCTAGCATCAATCGCTGCAGTCTTACCTACTGGGGCGCCATTAGTAGATCCACGCACTCACAGACTGAAGAAGCCAGCTCCGCCGGTTTTACCTGGATCT[G/C]CACCTGTCCTACCGATTTACGATGCTTTGGCTCCTGGTCCGTCCATTGCGCCGGCGCCAGCCCCAGGACCGGGATCCGGAGCCCACC
105018 T G CATCAATCGCTGCAGTCTTACCTACTGGGGCGCCATTAGTAGATCCACGCACTCACAGACTGAAGAAGCCAGCTCCGCCGGTTTTACCTGGATCTGCACC[T/G]GTCCTACCGATTTACGATGCTTTGGCTCCTGGTCCGTCCATTGCGCCGGCGCCAGCCCCAGGACCGGGATCCGGAGCCCACCATTTC
105018 A G CATTAATCCTGTACGGAGGGTACAACGAGTTTGCGGATATTTTAGTGAACCTGACCTCATTAGCGACGGAGATGGGGAGGCTTGTTTCGGAGGGGTACGT[A/G]TTGACTGTGCTGGCGCCGAACGATGAGGCGATGGCAAAGCTGACGGCGGAGCAATTGAGCGAGGAAGGGGCGCCGGAGCAGA
105022 C A TGAGTGCATGGAAGATCTTTCTTCTGAGCAAAATAAGTTCCAATATTACTACCGGAACCTTCAAAGGCAGCAAGCACAGCAGCAGGCCTGGCTACAAAAA[C/A]GGAGGATGGAGAACATGGCAAGAAAATCTGCCGGAGAAGAGCCATTGCCAGAGGAGGATCCTTCATTTAAGCCATTGCCAGAGCC
105022 CA C ACTACTGTAATCAAATTAACGGGGTCGCTGGACAAAGTTTTAGTAAGCTGTATTTGATGAAGGCAATTCAAGATAATTGATGAATTTTAAGCTATTGTCA[CA/C]AAAAAGAACTGATTTTTGATTTAAGCTTAAATCTTGATGCTACTTCTGTTTAACATTCTTGTACTTTTTAGTATGATTATTTTTCCCTTG
105024 A G CTAACGACTGTGCTTTTAGGTCTTCAATTGGATTTCCAGTATTATATTCAGCTTGCTCTAAATAATCAGCAGCCTTTGTCACTGCACGAAGAACAAACAA[A/G]AATGTGAAGTACATGTTTCCAACTCGATCAGGATATTGTAGAACACGATCAAATAACAATTTAGGATTTGGACCCCATATGTTTTTAGC
105024 T C GATAGCCCGAGGCTATATGAACAGTGATAGAGGAATGGAGACCAGAAATCAACTTATAAAGTACCCTTTTTTCCGGACAAAATTCTCCAGAAGGATACTT[T/C]GGACAATTTTCAGTGTAAATGGCATCCCATATCCTCCTAGCTGATGGACCCACATAACCCGTATAGCGCTCAGGGTTTAGCTGGAGA
105024 G T CATCCCATATCCTCCTAGCTGATGGACCCACATAACCCGTATAGCGCTCAGGGTTTAGCTGGAGATTCACATAAGTCGTCTCAGCATTATCAGTCTCGTC[G/T]TCATATGTCCATGGATTATCCACTTCAACCCATCCTCTAAAAGCTTTGCTATCAAGGGTGCGATCAACAGCAGCTTCCGATTTCCCTTCT
105024 G A CACACCATAATTTTACCTTGAAATAACGGAAGAAAGGAGTAGCGACCAGGTCCTGTAAGATGGGATTAAGGATATGGTGATTCAATGAATCGGCGGTCTC[G/A]TAATCACAGGTACAATCTTCAACCAGCCCAGAGTACCTTCTAGAACCCGGAGGGCACTGATAAGTTGATTTATTATGAAAATATAT
105028 A AAAATG TACGGTAGTGATGACCATCAGGCAGTCGAGAACAATTGCTTCACCATTTTGCTTGAGATTGATCACCACTAACTAGAAAGTTAAAACAACTACAGACTCA[A/AAAATG]AAGGAGCAAACACCAGACGTCCACAAACAATAGTTACAATACCCAAAATACACATAGAAAACATTTTCCATAACACACTACAA
105028 AACAATAGTT A CGAGAACAATTGCTTCACCATTTTGCTTGAGATTGATCACCACTAACTAGAAAGTTAAAACAACTACAGACTCAAAAGGAGCAAACACCAGACGTCCACA[AACAATAGTT/A]ACAATAGTTACAATACCCAAAATACACATAGAAAACATTTTCCATAACACACTACAAACATCACAGTTAACCAACAAGA
105028 A C TAACCAACAAGACGCCTGTCGTTTCGACGTTGAATATCAAGAAACCAGAATTGACCCAACACCACTCGCACTGACACGAATTCCACCAGCTCTCACCTAG[A/C]AGAGATCGACCATAGTTTTTGGTATATAAGGAAAATACATACCGGATCTGGGATAGTCGCAAACCAAATCCAATTACGAGAAGTTGC
105028 G C TTGACCCAACACCACTCGCACTGACACGAATTCCACCAGCTCTCACCTAGAAGAGATCGACCATAGTTTTTGGTATATAAGGAAAATACATACCGGATCT[G/C]GGATAGTCGCAAACCAAATCCAATTACGAGAAGTTGCCGCCTCCATAGCAGCTCCACGCCGATTACCACTACTGCATCCAAACAAGTC
105028 T C AACAAGTCAAAACCTTGAAAATCGAAAAGACTAAAAAGGCCACCACGCTCAAATATAGGTAGGAAAAGCAGTGCAAGAGGGAAAAAGTTTTTGAGGCAAA[T/C]TAGGCAAGCAATGGACGATGACGTGATAAAAGGGTTCGAATCGAAAGTTAAAACTAGGGTTCTCTTACTTTTCATGCAGGAGAA
105028 C T ATTAGGCAAGCAATGGACGATGACGTGATAAAAGGGTTCGAATCGAAAGTTAAAACTAGGGTTCTCTTACTTTTCATGCAGGAGAAAGCAAAAGCTAGGA[C/T]GATGAGAGGAAAGTTGAGGCGGAAGCGGAAGGGATTAGAAGTGCGAGACAAGAGAACTGAAGAAAAGGATGAAGAAAAAGAA
105034 T C CACGAAACTGTGGCTGTGGCTGTGGCTGTAAATTGCTAGTGCCAGCAAGAGACTCCACCGAGTAATAAAACGCCCGTGGTGGAGGTGAACCAGCTCGTGC[T/C]CCACCCTGGCTGCTCAACTGAGTGCCAGAAATACCAGGAATATCATGCCCTCTTATAGGGCTGTAAACAGTACCATAAGGCCCAG
105054 G A ATTTTTACCCGAAAATCTGCATGTAAAGAGTTTGAAATTGGATTGTGCTAGACTTGATGATGCGGCGATTGATATTCTAGCAAGACCATCTTTGACTGAA[G/A]TTCATTTACATAATTGTGAGAACTTCAATGGAAAGTTGATATCTGAGCTTGGGAACAAGTGTCATGAATTGAGGAGTTTGTATGTGAG
105054 G A CTCATTGGCTGAACGTAGAAGGAAAGTACTACAGTTTGCTGATCTGGATAAAGTGCTCAGGGGTTGTCCCCAGTTAGATTCGTTGAGCTTGGCTTTCGAC[G/A]TTTCAAGGTTTGAAGACCCGAACTTCGCTGTAAACTGGGCAGTTGCTTCATCCAAACTTCAATCTCTCGAGATTGGCTACATTCCCAC
105054 T C AACGTAGAAGGAAAGTACTACAGTTTGCTGATCTGGATAAAGTGCTCAGGGGTTGTCCCCAGTTAGATTCGTTGAGCTTGGCTTTCGACGTTTCAAGGTT[T/C]GAAGACCCGAACTTCGCTGTAAACTGGGCAGTTGCTTCATCCAAACTTCAATCTCTCGAGATTGGCTACATTCCCACGTCAATGTTAA
105054 G A GGAAAGTACTACAGTTTGCTGATCTGGATAAAGTGCTCAGGGGTTGTCCCCAGTTAGATTCGTTGAGCTTGGCTTTCGACGTTTCAAGGTTTGAAGACCC[G/A]AACTTCGCTGTAAACTGGGCAGTTGCTTCATCCAAACTTCAATCTCTCGAGATTGGCTACATTCCCACGTCAATGTTAATCGAGCTCC
105054 T C TGAGCTTGGCTTTCGACGTTTCAAGGTTTGAAGACCCGAACTTCGCTGTAAACTGGGCAGTTGCTTCATCCAAACTTCAATCTCTCGAGATTGGCTACAT[T/C]CCCACGTCAATGTTAATCGAGCTCCTTGACCATATCATCCTAACCGCTGACGTGCTAGTGCCTGGTAACCCTTTAAAACCTTCAACCTTC
105054 G A CTGGGCAGTTGCTTCATCCAAACTTCAATCTCTCGAGATTGGCTACATTCCCACGTCAATGTTAATCGAGCTCCTTGACCATATCATCCTAACCGCTGAC[G/A]TGCTAGTGCCTGGTAACCCTTTAAAACCTTCAACCTTCCCTTCTCTTAAAAAACTATGCCTCTCAGTTGACAACATCTCCGACTCCATAGT
105054 C T CGTGCTAGTGCCTGGTAACCCTTTAAAACCTTCAACCTTCCCTTCTCTTAAAAAACTATGCCTCTCAGTTGACAACATCTCCGACTCCATAGTCGACAAA[C/T]TATCAACTGGCCTTAGCAACCTCACACACCTCGACCTAAAGGATGCACCCTACACCGAACCATCCCTTAACTCTGATCTCACAAACAGCG
105054 G T GCCAGGAGTTCCTATTCACCCACTTCAGACGCGTGAACGATCAAGGTGTCCTTCTAATGGTAGAAAACTGCCTAGAATTAGAAAGCGTAAGCCTAGGCGG[G/T]TTCTGCAGGGTCACAGATGCCGGATTCAGAGAATTCGCTCACAGATGCCCGAAACTCAAAA
105060 T C TACTCCTAGATCGATTTCCCCTATTTCTTGAATTTCTAAAACTACTGAACACTTTACTAAAGATACATGAACTCCACCATTTCCCTTCTCGTCTATTGAA[T/C]TCTTCATATTCATCCGCACCATTGTCGTCGCTTCCGTACTCAATAACATAATCTCCTAGCACCACACCATGTGGTACTTCCGCATGAATCGTG
105064 C T CAGTTCAAAGCTATCCAGAGGACATACCAGTTCTTTGTAAAGTTTTATGGCTCCATTTTGAGGCAGGTGATAGACCTCTTCACATGTGTTACAATACAGC[C/T]GTGTTGGTCTACTAGATATGTACTTCATATAACGTGTACATTTTCCACATTTGCTGAGCAAACGTCCTGAATCTGATAATGGTGAAAAT
105064 T A AAGAAAACTTCCGAGTGAACTGCAGAAGAGCATGCTGCACGACACGAACATGGTCGGCTTGACCTTTGGCTATCAGAGTTATTTGCTGTTCAATAAAACT[T/A]CGTATGTCAGGTAAGCAAAGGTCTGGATCTATGCATTGGTATCCTCTTATCAGAGTAGTTCCTAGGGTAGTTGGTACCAATCTCCTT
105066 T C TGTTGTGTGGTTTAGGTTCGGCAAGAGCTGTTAACCGGCGGTACATAAGTGATTGCGTACCTCAGAAAATACGCTTGCAAGCATCAGCAGGTTTTGTTAG[T/C]GCAAGTGCACTTGGAATGGCTTGTGGGCCTGCTCTTGCTGGTGTGCTTCAGACAAATTTCAGGATATATGGAGTTACAATAAATCAA
105066 T C ACATAAGTGATTGCGTACCTCAGAAAATACGCTTGCAAGCATCAGCAGGTTTTGTTAGTGCAAGTGCACTTGGAATGGCTTGTGGGCCTGCTCTTGCTGG[T/C]GTGCTTCAGACAAATTTCAGGATATATGGAGTTACAATAAATCAAGATACTTTACCTGGATGGGTCATGGCAGTAGCTTGGTTTTTG
105066 G A CTGGATGGGTCATGGCAGTAGCTTGGTTTTTGTACTTGGTCTGGTTGTCGATATCTTTCAAAGAGCCAGTTCGTGACACATATGATGTTCAAATACCGCA[G/A]GAGGGTGCAGTTGCTGGAATCAATAATGACGATCAAATTGAGAGCGGTATGGTACAACCTCTTCTTTTGACCTCATCGGAGGAAAAG
105066 G A TTTTGACCTCATCGGAGGAAAAGAAAGATGAAGATGATGACGATGACCTTGATGATGATGAAGCTGCAGATTCCCGCAAACCTGCAAATTCTATTGCTTC[G/A]GCATACAGACTGCTTACACCATCTGTGAAGGTACAATTGTTGATATATTTCATGCTCAAGTATGCAATGGAAATTTTACTTTCAGAAT
105070 CA C ACTTAGCAACTGGATCAATTTCATGACAAAGAGTGCATGCAGTTTCTTTGTGAGGCATTGTGACACTGAACCCAGCGAAGTCGGGAGAAGCATACGTACC[CA/C]AAAAAATTAGAAAGATCATCAACTAAAAATGGCACATAAACTGCATTGAGATTAAGTCCCTTGAATGATGCATTGTGTAATAATGG
105070 G A TGGCCTGTATCTGCTTTATTCTGTACACATCCAATAAATCTGACATAGTAGGCTGACCTGGAGCAGATTCTTTTCCTTTGCTAAGTGTACCAAATGTGAG[G/A]TACCCACCAAATTTTGGGGATAACAATCGAGAGATAAGTCCTCTTTCACCCATACATAAGCCTATTATGGGGACCTGACAGTGCACCAG
105084 T C CTGAAAACGACCCAAGAAGAGATGAACTGAAACAACTAAAGAAAACGAAGGAAGAGATCGACATGCTTGCTCACAAACAAGTCCGGCGCTTACTCTGGTC[T/C]GGACTAGGGTTTCTGATAGTCCAAATCAGTCTTTTCTTCAGATTGACATTTTGGGAATTTTCATGGGATGTCATGGAACCTATTGCA
105084 GA G TATTGCTTGGGTATGCCTACTTTCTTTTCACTTCCAGAGATCCAACATACCAGGATTTAATGAAGAGGCTATTCTTATCGAGACAGAAGAAGCTATATCA[GA/G]AAAAAAGGGTTTAACTTGGATAGGTACCTGGAGTTGCAGAATCATTGCAAGTGCCCTTTGGATGGAGAAAGTGCTCTTCATGTGAT
105084 AT A GGTACCTGGAGTTGCAGAATCATTGCAAGTGCCCTTTGGATGGAGAAAGTGCTCTTCATGTGATCCAGGAAAAGGAAAAACTGATATAGCCGTATGCCTT[AT/A]TTTTTTCTAGTTTAAAGTACCTGCCGGATATTTTACTGAGCATCTGGGTACACACTTCTTTTTTTTTAATTGATAATATAGCATCTAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105086 C T TATACAGCCCCTCGGGGCTCGAAGAACCTCTACTAGGAGTGCAAGTAACTGAATTGCTCGATGGAATTTTCATCGGGGGCTCTTTGAATCATAGCGC[C/T]GGAGACGGCAACACATTTTGGCAATTTTTCAACACTTGGTCGCGTGTCTGCCGAAACAACTGCAGCAACGAAAAACCGGAGGCTACTTT
105086 C T ACAGCCCCTCGGGGCTCGAAGAACCTCTACTAGGAGTGCAAGTAACTGAATTGCTCGATGGAATTTTCATCGGGGGCTCTTTGAATCATAGCGCCGGAGA[C/T]GGCAACACATTTTGGCAATTTTTCAACACTTGGTCGCGTGTCTGCCGAAACAACTGCAGCAACGAAAAACCGGAGGCTACTTTAAA
105086 A G ATCATAGCGCCGGAGACGGCAACACATTTTGGCAATTTTTCAACACTTGGTCGCGTGTCTGCCGAAACAACTGCAGCAACGAAAAACCGGAGGCTACTTT[A/G]AAATTTGACCGGTGGTTTCCAAATTCAATCCCCACTCCAGTTCTTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCA
105086 A G CACATTTTGGCAATTTTTCAACACTTGGTCGCGTGTCTGCCGAAACAACTGCAGCAACGAAAAACCGGAGGCTACTTTAAAATTTGACCGGTGGTTTCCA[A/G]ATTCAATCCCCACTCCAGTTCTTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTC
105086 CT C CACTTGGTCGCGTGTCTGCCGAAACAACTGCAGCAACGAAAAACCGGAGGCTACTTTAAAATTTGACCGGTGGTTTCCAAATTCAATCCCCACTCCAGTT[CT/C]TTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTCCGATTTTCCTCAGATTATGT
105086 T C ACCGGTGGTTTCCAAATTCAATCCCCACTCCAGTTCTTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTT[T/C]TTCCGATTTTCCTCAGATTATGTGAAAGGACTGAAGGCGAAGGCGAACGAGGAGATGGGTACTAGCAACATATCTTCGCTACAAGCA
105086 A G ATTCAATCCCCACTCCAGTTCTTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTCCGATTTTCCTC[A/G]GATTATGTGAAAGGACTGAAGGCGAAGGCGAACGAGGAGATGGGTACTAGCAACATATCTTCGCTACAAGCATTGGTGGCATACATG
105086 G A CCACTCCAGTTCTTTTTCCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTCCGATTTTCCTCAGATTATGT[G/A]AAAGGACTGAAGGCGAAGGCGAACGAGGAGATGGGTACTAGCAACATATCTTCGCTACAAGCATTGGTGGCATACATGTGGAAGTCA
105086 A G CCTATAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTCCGATTTTCCTCAGATTATGTGAAAGGACTGAAGGCGA[A/G]GGCGAACGAGGAGATGGGTACTAGCAACATATCTTCGCTACAAGCATTGGTGGCATACATGTGGAAGTCAATTACGTGCGCACGTA
105086 G A TAGAGAAATACCCTGAGATTAGGAAGCCGAGCTCAAGCTATAATCCAGAGTGTTTTTTCCGATTTTCCTCAGATTATGTGAAAGGACTGAAGGCGAAGGC[G/A]AACGAGGAGATGGGTACTAGCAACATATCTTCGCTACAAGCATTGGTGGCATACATGTGGAAGTCAATTACGTGCGCACGTATCTC
105086 CG C GAGATGGGTACTAGCAACATATCTTCGCTACAAGCATTGGTGGCATACATGTGGAAGTCAATTACGTGCGCACGTATCTCATGTGCACGTGCACAAGGGG[CG/C]GGAGGGTGAGAGTTCCTGTTGGTTTACGGCATCCTTTCGAGCAAAAGTCATTCCTCAACTCCTAGACACATACGTAGGAAATTCC
105086 G A CTAGTTCGCCTAGGTTTGATGTGTATGGAAATGACTTCGGATGGGGGAAGCCGATTGCTGTTCGAAGCGGGCCAGGGAACAAGGTTGAAGGGAAACTCAC[G/A]TTGTTTCCAGGTATGGAGGGTGGGATCGATATGGAGGTCACATTGCCCAAACATGCGATGGAAACTTTGCTTCAAGATGAAGAT
105086 CTGGCTCAG C AAGATGAAGATTTCATGGATCATGTTCTGTGATCTGTAGTTGTGGCCTGGTGAAAGCTACATATCACGAGTCTTGTTCCCTAATAATAACTGAAGCCTCA[CTGGCTCAG/C]TGGCTCAGTGGCACTCTACAACAGATGGACAACTATTGTGAGAAGCAATAGCACATGTTCATGAGTGCATCATGTCTAA
105104 AATCTTTCTGATAGCTTCGAGT
A AGTAATAGACTTGCCAATAACCAAGATTTTAGCAGGCACCGGTCAAATAAGGAATGAAGTGGATTCTCCTTGTCTAAGTAACTCGTCTGATAGCCTCGAG[A/AATCTTTCTGATAGCTTCGAGT]ATCTTTCTGATAGCTTCGAGTATCTTTCGAGTACCTTTTCTTCCTCAATTGGCTTTGCCAAGTGAAGA
105104 T A TAATAGACTTGCCAATAACCAAGATTTTAGCAGGCACCGGTCAAATAAGGAATGAAGTGGATTCTCCTTGTCTAAGTAACTCGTCTGATAGCCTCGAGAA[T/A]CTTTCTGATAGCTTCGAGTATCTTTCGAGTACCTTTTCTTCCTCAATTGGCTTTGCCAAGTGAAGATCCATTTATGCTGAATATGAATC
105106 G C AAGCTGAGTATGATGAGTATGCAGCTACCAATGCAAGCGGTGCTGCGTTTTGTCGTTCTGCAGCTCTAATTCTTATGGCCCTTTTGTTAATGAGACATGC[G/C]TTGACCCTTTCCAATGGTGACGATGATGACGATGCTTCTGCATATTTTTCTCTCTTTTTATTACGTGCTGCTGGATTTCTACTACCGTGC
105122 C A TATGAGCCTCGAAGACAACGGTGACAGTGGAGACAACAACGGTGGTGTTGGTCAAGGTGAAGATGGTCAAGGTGTAGGTGGTGATGGTGTTGGACAGAGG[C/A]GGCGGCGGCGGCGTAGGAGAAGCAGGGTTAGGTCGGTCCCTGGTTCAAGTGATTTATGATATATACATGTACACATATATCCA
105130 T C TATTTGCATGATGTTCCATACTTGCAACTACCGTTTTTCATGTAGAATTGACATTCAGGTTGATCAGGCCGCTCTGGTAGATCTGTAGTACCACTTGAAG[T/C]GAACTTGTTAAATGTTTGGGTGGATCCGGCACTATCAATTGTTGGAAATTGGGGAACAGAACCCATGTAAGTGTTCCAAGTCTGTTGC
105130 C T ATGTTTGGGTGGATCCGGCACTATCAATTGTTGGAAATTGGGGAACAGAACCCATGTAAGTGTTCCAAGTCTGTTGCATTGGCAGAGAACATTGAGATGA[C/T]GGATGCACAAAAGGCACATAACCAGCGGCATCTTGCAATGTTGGATTAGATAGGTAGGGCCTAACTAGCGGCATGGATGGAAATC
105130 C T GTTGGAAATTGGGGAACAGAACCCATGTAAGTGTTCCAAGTCTGTTGCATTGGCAGAGAACATTGAGATGACGGATGCACAAAAGGCACATAACCAGCGG[C/T]ATCTTGCAATGTTGGATTAGATAGGTAGGGCCTAACTAGCGGCATGGATGGAAATCCTCCAAACATTGGGAAATTGGACGGAAG
105130 A G CAGAACCCATGTAAGTGTTCCAAGTCTGTTGCATTGGCAGAGAACATTGAGATGACGGATGCACAAAAGGCACATAACCAGCGGCATCTTGCAATGTTGG[A/G]TTAGATAGGTAGGGCCTAACTAGCGGCATGGATGGAAATCCTCCAAACATTGGGAAATTGGACGGAAGTGCGATTGCTGGTCCTG
105130 T C TGCATTGGCAGAGAACATTGAGATGACGGATGCACAAAAGGCACATAACCAGCGGCATCTTGCAATGTTGGATTAGATAGGTAGGGCCTAACTAGCGGCA[T/C]GGATGGAAATCCTCCAAACATTGGGAAATTGGACGGAAGTGCGATTGCTGGTCCTGTTGATCCATAGGCAGCAGATGGTCCATA
105132 A G ACATTTCTTAACATGTATAACATGTAAAACTTGATATCAGCTTGCCCCAGTTTGCACCATAGGGAAAAAAGCCCAGTCTTTATTAGGCACTGCCTCCACT[A/G]CAGCCCCATCCGAATTACTGAACTTGAACTCTTTACTTGCAGCAAGCTCACCAGAACTCTCGATCCTCTCAACCAACTCATCATGGTTAA
105132 G A TTTCTTAACATGTATAACATGTAAAACTTGATATCAGCTTGCCCCAGTTTGCACCATAGGGAAAAAAGCCCAGTCTTTATTAGGCACTGCCTCCACTACA[G/A]CCCCATCCGAATTACTGAACTTGAACTCTTTACTTGCAGCAAGCTCACCAGAACTCTCGATCCTCTCAACCAACTCATCATGGTTAATCT
105132 T A TGTTATTGAAATTATTATTGCAGAGTGGTGCTTCAGGCAGGATGGCCGAGATTTGACCATCAAGAATGGACCCGTTCTTTCTGGAATGGAAGTCCATGTC[T/A]GGAGGGAACGGAGAAGACGCACCGGAGCAAACAGAGCTTGGTGAGATCAGGTGACCGATAGGGCTATCCGGGTACCAAGGGTAG
105132 CT C AGAAGACGCACCGGAGCAAACAGAGCTTGGTGAGATCAGGTGACCGATAGGGCTATCCGGGTACCAAGGGTAGGAGCTGTACTCGTTGGTTTTGCCTTCG[CT/C]TTTTTTTACGATTGGACTCGAAGGAGGAGAGAAGCTGAGCGAATGGGACTTCCGGAGAGGAAGGAGTGGTGAGTTGGACGGA
105132 A G TGGCTGGTGAAAGGGAGTGGATGCCTCCGGGCGATTGGGTTGAGGAAGGGGGTTCTGAGTTTAGGAAGGAAGCGGGCGAGGAAGGTGGCACGATGAATGG[A/G]AGGGTTAGCGTTTGTGTTGCTGTAGGGTGTTGTGGAACGGAAGGATCTGGTCTTGAAGGAGTTGGTTCAGGGGCTAATGAT
105134 A G AAAGTACAACAGATCTGAGTACCAAAATCAAAACATTCAAATCTTCAATTCCTAACCCAAAGCA[A/G]AAGAAATCACCAATCTGAACCAACTGGAAAAGGCTCCAAGGCATCCAGTTTCCCATGAACATAGAAATCAACAACAGCTCTCATTCTGTGAACCTTATTA
105134 G A GGTTGTCGTGCCCATCGCTCATGGACTCCACGTCGCAGTCTCTGTAGAGGTGGTGGAACGGGTTTTGAAGGTAGATGATGTCGACGTCGGAGAGCAGGAC[G/A]CTGTACCCTAGCTGTAGGAACTCCCTAAGGACGCGGAACTTAAGGCCGGAGACAGCGTGGTTGGAGCCGGTTTTGGCGACGGA
105134 G A AGACAGCGTGGTTGGAGCCGGTTTTGGCGACGGAATCGAGTCGGTCGTTGTCTAGGACCTTCCGGTAGACGGGGACGTCGTTTTCGGTGCAGAGACGTTC[G/A]ATTTGGTCGTCAAGGGCGACGACGAGGTAGTTTTGAATTTTGATCCGTTTGATGCTTTCGAACCAGAGGATGAGCATGTCTTTGA
105138 A G CCGCAATAGCAAGGATATCAGCACAGGAGACTATGCCTGGACATTGGTTTTCAACCGCGGATTTAATGTTATCTACTACACCAAATCCACGAGCTGAGTT[A/G]CTATTCGGAAGTGCACTCTTCTCGCTTTGTATGTTTGTGGCATCATCTAACAAAATTGATCCATCGCAACCTTGGACAAAGCAGTCAT
105138 C T TAGCAAGGATATCAGCACAGGAGACTATGCCTGGACATTGGTTTTCAACCGCGGATTTAATGTTATCTACTACACCAAATCCACGAGCTGAGTTACTATT[C/T]GGAAGTGCACTCTTCTCGCTTTGTATGTTTGTGGCATCATCTAACAAAATTGATCCATCGCAACCTTGGACAAAGCAGTCATGGAAGT
105138 G C GACATTGGTTTTCAACCGCGGATTTAATGTTATCTACTACACCAAATCCACGAGCTGAGTTACTATTCGGAAGTGCACTCTTCTCGCTTTGTATGTTTGT[G/C]GCATCATCTAACAAAATTGATCCATCGCAACCTTGGACAAAGCAGTCATGGAAGTGAAGGCGGATTAGGCTTCCGTAGATTCTTGGGT
105138 G A TGTTATCTACTACACCAAATCCACGAGCTGAGTTACTATTCGGAAGTGCACTCTTCTCGCTTTGTATGTTTGTGGCATCATCTAACAAAATTGATCCATC[G/A]CAACCTTGGACAAAGCAGTCATGGAAGTGAAGGCGGATTAGGCTTCCGTAGATTCTTGGGTCAGAGCTATGTGCCTGCTGAACAACGC
105142 T C GATTCCTAAATTTCATTCATCATTGTTCGATATCACTTCATTAAACTTAAGAAACAGCTGTGTATCCGAAGAAGAAGAACTCAGCGATGCCATGGAGCAG[T/C]TCAATGCGTCACTGCTTCTAAGGTTGGCGTACTGATCAACATAACTAGCAGTCGAGTGCTGAGGTGTCATATGTGGTGGCGTGGTGG
105150 T G GAGTTCAGCTCCTCGACGGACCTCGTGTTATCATTTAACCACCAACAATCTTTAAGTATTCGTGCTGCCTCTGAATACAGTTGCAAGTGAAAATCGGGAG[T/G]TAAATGTGCCAAAAGAAGCCCGCATGCTTGAATCATTAAGCAAGAAAGTTGTTGGCAGGAATACCCACTTTTTGCAACAAAGTTTGCA
105150 T C AGTGAAAATCGGGAGTTAAATGTGCCAAAAGAAGCCCGCATGCTTGAATCATTAAGCAAGAAAGTTGTTGGCAGGAATACCCACTTTTTGCAACAAAGTT[T/C]GCAAAACTAGCTCCACTTGCTGCTGAATTTGCATGACTTGCACTGTATGCCTCAGTACCAGCACCAGAAGGCGAATTTGGTAGACCT
105154 A G TGCATGGCACTTTGACTTTATCAAGCATATCTCTGCAGTCACTCGAAAATACAATTTTTGCCAAGGATAAAGCTACTTCGGGAATCATCTTCTTCAAATC[A/G]TTTTTAAATTTCTCAATAGAGAGTGGATGGTTATTTCCAACGACTTGTTTTGTGAAGTCTTCAACCCATGTTAGATAATTGATCTTCATTG
105156 AG A CTTCTTTAGCTCTAAGCTACTTCATTTGAAACGGTCATTTTACATGGAACTATAGATGAGTCCAAAGCAGCTTTTTCCGAAAATGAAACAAGAACGTTAA[AG/A]GGGGCTAGAAAAACGAGTCTATTTACATACGAACTATAGATGCTGCATATCTTCTGTTTCGGAGAATGTTTCTGAGAAAGGACTACA
105156 GA G GCTCTAAGCTACTTCATTTGAAACGGTCATTTTACATGGAACTATAGATGAGTCCAAAGCAGCTTTTTCCGAAAATGAAACAAGAACGTTAAAGGGGCTA[GA/G]AAAAACGAGTCTATTTACATACGAACTATAGATGCTGCATATCTTCTGTTTCGGAGAATGTTTCTGAGAAAGGACTACATCTTTTTG
105156 GA G GCTACTTCATTTGAAACGGTCATTTTACATGGAACTATAGATGAGTCCAAAGCAGCTTTTTCCGAAAATGAAACAAGAACGTTAAAGGGGCTAGAAAAAC[GA/G]AGTCTATTTACATACGAACTATAGATGCTGCATATCTTCTGTTTCGGAGAATGTTTCTGAGAAAGGACTACATCTTTTTGCAAGCAT
105156 TA T AAACGGTCATTTTACATGGAACTATAGATGAGTCCAAAGCAGCTTTTTCCGAAAATGAAACAAGAACGTTAAAGGGGCTAGAAAAACGAGTCTATTTACA[TA/T]ACGAACTATAGATGCTGCATATCTTCTGTTTCGGAGAATGTTTCTGAGAAAGGACTACATCTTTTTGCAAGCATCGCAGTGGCTGC
105156 A G TAGATCGAACTGCTGCCTCGTGTAGTTGAAGCAGCTTCTCGTTAGTAAGCTTCTCCAGAGAAAGTGCAAGCTCCATTGCATATAGCGCATCGCCTTTCTC[A/G]GAGTGGTCATATTCAGACAAGGGTGTCATTATTGACTGAAGCTTCACTCTACCCCCTCTTCTGTTCTGATACTCCATTAGTTTCTCGGC
105156 G A AATATTACCGCAGCCAAGGGCTTGCTATTCGCGGAAGCCATAGCCAAAACTCCATACGAAATGCCAGTTTTGTACTTCCCCGCATTCAAACACGAAGACG[G/A]CCAATCCCCGATGGAGATCTCATGACTTTTTGGAGAGAGGAGCAACGAAAGGGAAGAAACTGTAGATTTGAGAAGCATATTTCAAA
105156 A T AGCCAAGGGCTTGCTATTCGCGGAAGCCATAGCCAAAACTCCATACGAAATGCCAGTTTTGTACTTCCCCGCATTCAAACACGAAGACGGCCAATCCCCG[A/T]TGGAGATCTCATGACTTTTTGGAGAGAGGAGCAACGAAAGGGAAGAAACTGTAGATTTGAGAAGCATATTTCAAATTTTCTTTAAAT
105165 A AG TGTCCAATCTTTTTCCAGCAGACATTTAACTCTTGAAGAGCTTTCAGAACCTCCGTCATAATTTCACGAGGATGAGCACGGGACTGCAGTCCAAGAGCCC[A/AG]TTTTTTTTCAGCGGGAACATTCAGCCGTGTATTTATTTGATGATCCATGTATCCTGGTGCCATTCTATGAGCAACTGAAGGTGCAGG
105165 A G CAATTAGCTGTGTTTTGTCAAAGCCCATTTTAACTACTTCACGGAGAATTTCCTCATCGATTTTCTTAGCTTGCTGCATCGTATCAGGTGGAGGCACAGC[A/G]AGATAACGAGGAAGATGAGATTGAAACCATGGATGTTCATGGATCTCACGAATGGTCATTCGTTTCATAGGATCGACAACTAGCATCC
105169 T A CTTGTAGAAACGTTCTCGAGCTCGCTGCTGAGGTACGTGTACCTGTGAAGAACACGTATGTGTATGCATTTGCTGAGCATGGAAATGATCTGGGCAGTTC[T/A]AAAGACCTTAAAGGAAACCCTACAGAATTCTTCAGACGTGCTGGCCATGGGTCGTCATATGGTGTTGGAGCTAAGCTTGGTTTAGT
105179 A G GTTCACAAGGAGGGGACTCGAAGAGCCTCAAACTAGCCTTGTCCAAGAGAAGTCAACTCAAAGTCACAATTCTTGAAGCTGACAATATTGTTCGAAGGAC[A/G]TAAAAGCCTGCCTCGGTATCACCTTTGAAAAGACACTTCGGTCCGTGAGGCGCAGGCTATTGGCTTACGATGGAAGAGAAGCTTT
105205 TA T AAAAAGAATTAACCAACACCATATCAGCTTTCTCCAAATTCTTATACTGGTTCAAAACCAAGTGCAAGTAGGCCGGGTATGGACCAGGCACCGGATCCGA[TA/T]AAAAAAGATGGCATGTCCCTTGGTTCGAATAGGGGCATACCTGGTTTAACAAGGATTGATTCAGTAACAGGGTATTTTATCCGGCC
105207 C T GTATGCCCTACAATTCAGAAAGAGAGGTAAAAATTTGAAAAGAGTCAAGTTACAAACACTTGGATGCAAATTTCAAAAATATCGGTTCTCAAGCAACTGA[C/T]TGGAGAGCTTTGTCGAAGTTCTCTTCTGCAGCAGTTGCACGCTTCACCAGCAAATGATCAGGATGCGAGAGTTTCAGTTGGCTGAGG
105211 G A TTAATGCCGCGGTTGGTCAAGTCGAGAGGCTTGCTCTTGAAAACGACTATTATCGTCGTAGGATGGCTATTTTGCGACGTCAGGAGCTACTCAGGCAGCA[G/A]TTGCAAGCTGCTCGTTTTTTCGAATTGAAGAGGCAGCAGTTGATAAAGATGCAGCAGCAACAATATGCCAACGCCGTTTGGGAAAA
105211 T C CAGGCGAAAGTCTGTCACTAAGCGAGTGGCCCCCACTGCAGAAGCAGAATCCGAAGAAAGCGCTTAATGGATCTGGTATGACTGCCGTTTTCCTTGACGC[T/C]GGCAGGAGGCAGTCGACTGGTACGGGCGTTTTCTTACCACGGACTGCTGGTGCCCGTTGCTCTGAACCAAAAAGGAAACCAGGTT
105211 A C TGCTGGCAATGATGAATTAGAAAATTACTATCGGCCAAAGAGGAATTATAATCACGCAGCTGTAGCACCAGCTTCGAGCTCAGAGATTTTAAAACTGCCT[A/C]AGGAGTGGACCTACTAATTTCGTGGTTCAGATTCGCAGTCCGTTGATTAGAACAAATTTAGTAAAATTCGTATAGCGTTGAAAGAAT
105211 G GTT GGACCTACTAATTTCGTGGTTCAGATTCGCAGTCCGTTGATTAGAACAAATTTAGTAAAATTCGTATAGCGTTGAAAGAATATTATGGTTCTGAAGAAAA[G/GTT]TTAGGTTTTAGGGTATTTGTTTGATTAATTTGATTCTCTGGGGTGGAAGAATAATAATGTTTGGCAGGTAATGGATAAAGATGAAA
105213 T G CTTCCATTGTAGCTCGTTTTCCTTTAAAAGTAGAATAACCATAGCTGAATCCTATACTTCTGTTCCCAGTAATAAAACTAAAGCCGCCGCCACTGTAGAT[T/G]GCACCGGGAACCGATGGCTGTGTCATCGGAAACTGAACAGCATTCCTCGGAGGCAGTGACCGTATGGTTTCTATATTCGGGCAAAAAA
105215 A C TGTTCCGAAATATTCTGTGAATATATTTCAGATTGAAAAGAGCGACTAAGTTATAGTTCTCAAAGGAAGAATCTGTTACAGTGGCATTAGCATTTGCCAC[A/C]AGAATTTGTGACTTTTCTAGAGCTTTTATTCGTACTCCTAATATGAGCTTTGGAAGTAGCTCTGCCGCTACAGGTACTCGTGCTGCTAG
105215 G A CCCTTCCAAACATAAAATGGATTTGCCCGACAGCCCCTACACGGCCTGTGAAAATTTTTGGTGGATTCCCTTGCACTGCATGGTTTGATGTTGGACAACT[G/A]ACAGAGGATGGTCCTGATGATGTTGAGGGTTTGGATGCTTCAGCAGCACATGTTGCGAACCTTCTATCTACAGAACCTGCTGACATTA
105215 G A ACTGACAGAGGATGGTCCTGATGATGTTGAGGGTTTGGATGCTTCAGCAGCACATGTTGCGAACCTTCTATCTACAGAACCTGCTGACATTAAACTTGGT[G/A]TTGGTGGGTTCAGTATGGGTGCTGCAACGGCGCTGTATTCCGCTACGTGTTATGCTCATGGGAAATATGGAAATGGTAATGTGTAT
105215 C A AGGAGGGCTGCCACCATTCCCCTTCTTCTCTGTCATGGAAAAGATGACGATGTTGTCATCCATAGACATGGTGAAAAATCTGCCGAGGCACTGAAATCTA[C/A]TGGATTCAATAATGTCATGTTTAAATCTTACAGTGGGCTAGGGCATCACACAATACCTAGAGAGATAGATGATGTATGCCAGTGGCT
105215 T G TCAATAATGTCATGTTTAAATCTTACAGTGGGCTAGGGCATCACACAATACCTAGAGAGATAGATGATGTATGCCAGTGGCTTTCTACTAATTTAGGTCT[T/G]GAATCCTAACTCTGAATATTGTTATGGAGCCAGAGATCTCAAATATTTGCATTTGTACTAAGATTGGGGACGTGTTCATTATGAAATAA
105217 T G AAAATCCTGGCTCGACAGGTAATTTAATCTATTGTAACTTACATCGTCACAAATATGTCAT[T/G]ATTTTAGTTATGGTGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105217 G T AAAATCCTGGCTCGACAGGTAATTTAATCTATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATG[G/T]TGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATT
105217 A G AAAATCCTGGCTCGACAGGTAATTTAATCTATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGT[A/G]AGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATC
105217 T G AAAATCCTGGCTCGACAGGTAATTTAATCTATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGTAAGTAGCA[T/G]CATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTC
105217 G A AAAATCCTGGCTCGACAGGTAATTTAATCTATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGTAAGTAGCATCATAT[G/A]CATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCA
105217 ACGCG A ATTTAATCTATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACAC[ACGCG/A]CGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGG
105217 T TGC TATTGTAACTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCAC[T/TGC]CTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCA
105217 T G CTTACATCGTCACAAATATGTCATTATTTTAGTTATGGTGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAG[T/G]AAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAAT
105217 A G TTATGGTGCAGTAAGTAGCATCATATGCATTCAATCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTA[A/G]CCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAAC
105217 C T TCTTTATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGG[C/T]TTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTT
105217 G C ATTTGTTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTG[G/C]ACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTG
105217 G T TTACACACACGCGCACTCTTTCAGTAAAGACGGGTTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACAT[G/T]CTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCG
105217 A C TTTATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGC[A/C]CGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCC
105217 A T ATTGAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACG[A/T]CCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACG
105217 A G GAGTAATTTTCAAGTAACCATTGGTGATCATCCACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACC[A/G]AAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACGATG
105217 C G CACTCCAAACTCCAATGGCTTTGGACATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTT[C/G]GTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCA
105217 T C CATGCTTCAAAGTCCAATAAGACCACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTG[T/C]ACTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTA
105217 G A ACCCGAAACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTC[G/A]CCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAAC
105217 G A AACTAGCACGACCAAAAACATCCATCATAGCATCCGCTAGTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCAC[G/A]ATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAG
105217 T A GTCTTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAA[T/A]TCCGCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAA
105217 C G TTTCGTAGTCTTCCTTGCTCGCGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTC[C/G]GCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACAT
105217 G A CGTTCTGTACTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAAC[G/A]AAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAAC
105217 G A CTTGCCATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAACGAAGTCAAT[G/A]TTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCA
105217 T C ATTCCGCTACCCACTCGCCCACGATGACTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTG[T/C]TGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCAAACTGA
105217 T G CTAGAGGACCGTTGGATATAGACACAGCATTCAATTCCGCAGCTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCT[T/G]GAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCAAACTGAAGAAGCTCTGTGGAGTCTGCAGACAG
105217 G A CTCGAGTATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGT[G/A]AACCCGCTTGCAAACTGAAGAAGCTCTGTGGAGTCTGCAGACAGTCTATTCGACATGATCACATATGCACTAGAAGTGTATTTTCGA
105217 G A TATTGTAAACGAAGTCAATGTTCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCC[G/A]CTTGCAAACTGAAGAAGCTCTGTGGAGTCTGCAGACAGTCTATTCGACATGATCACATATGCACTAGAAGTGTATTTTCGAACCGCA
105217 T A TCTGTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCAAACTGAAGAAGCTC[T/A]GTGGAGTCTGCAGACAGTCTATTCGACATGATCACATATGCACTAGAAGTGTATTTTCGAACCGCATTGTAGCCCAGTTGGTAGTAC
105217 G A GTTGAACCGAAAGGTTATCGAAACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCAAACTGAAGAAGCTCTGT[G/A]GAGTCTGCAGACAGTCTATTCGACATGATCACATATGCACTAGAAGTGTATTTTCGAACCGCATTGTAGCCCAGTTGGTAGTACTTC
105217 C T AACTGCTTGAGAAGAGGTTGTAGTAATGAACATCTATCACAGAGCCTGTGAACCCGCTTGCAAACTGAAGAAGCTCTGTGGAGTCTGCAGACAGTCTATT[C/T]GACATGATCACATATGCACTAGAAGTGTATTTTCGAACCGCATTGTAGCCCAGTTGGTAGTACTTCTTCAGATTGTCTAGAGGCACT
105217 G A ACAGTCTATTCGACATGATCACATATGCACTAGAAGTGTATTTTCGAACCGCATTGTAGCCCAGTTGGTAGTACTTCTTCAGATTGTCTAGAGGCACTCC[G/A]GGTGCCATGGGTTCATTTAGCAATTCTACTGCTAATAGGCTACTCCGATTGGCATATCTATTGGCAAGGAAGTCAATGACTGTAACAG
105217 A G TGATCACATATGCACTAGAAGTGTATTTTCGAACCGCATTGTAGCCCAGTTGGTAGTACTTCTTCAGATTGTCTAGAGGCACTCCGGGTGCCATGGGTTC[A/G]TTTAGCAATTCTACTGCTAATAGGCTACTCCGATTGGCATATCTATTGGCAAGGAAGTCAATGACTGTAACAGTTTGAGCTATGTTAT
105217 T C AGCCCAGTTGGTAGTACTTCTTCAGATTGTCTAGAGGCACTCCGGGTGCCATGGGTTCATTTAGCAATTCTACTGCTAATAGGCTACTCCGATTGGCATA[T/C]CTATTGGCAAGGAAGTCAATGACTGTAACAGTTTGAGCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCAC
105217 T C TTGTCTAGAGGCACTCCGGGTGCCATGGGTTCATTTAGCAATTCTACTGCTAATAGGCTACTCCGATTGGCATATCTATTGGCAAGGAAGTCAATGACTG[T/C]AACAGTTTGAGCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAG
105217 A T GCACTCCGGGTGCCATGGGTTCATTTAGCAATTCTACTGCTAATAGGCTACTCCGATTGGCATATCTATTGGCAAGGAAGTCAATGACTGTAACAGTTTG[A/T]GCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATG
105217 G A TATTGGCAAGGAAGTCAATGACTGTAACAGTTTGAGCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCC[G/A]TTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAA
105217 A T TAACAGTTTGAGCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATG[A/T]AGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATG
105217 C T TGAGCTATGTTATCATCAGTTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTA[C/T]AATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGA
105217 C T TTTTACCCCAGTCCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTA[C/T]TTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCAC
105217 T C CCTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCA[T/C]GTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGG
105217 G A CTGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCAT[G/A]TGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGT
105217 T C TGGGAGCCATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATG[T/C]GAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGTA
105217 G A CATCTCTTGATGCACTGTGTTCGTTTCCGTTTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGC[G/A]TTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGTATTCTCACT
105217 A G TTTGTGACCCAGGCGCAGCATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGAC[A/G]TAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGTATTCTCACTCCATTTAACCCGTTTTCTGAAATGAATTTG
105217 C T CATGAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGA[C/T]GGATCGCTAGCAATCCACCATCCAACAGGTATTCTCACTCCATTTAACCCGTTTTCTGAAATGAATTTGAAGTCATTTTCCACTATGA
105217 A G GAAGATCTACAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGG[A/G]TCGCTAGCAATCCACCATCCAACAGGTATTCTCACTCCATTTAACCCGTTTTCTGAAATGAATTTGAAGTCATTTTCCACTATGAAAC
105217 A G CAATGACACCTAGGTTGTACTTTTCTGCCCATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGC[A/G]ATCCACCATCCAACAGGTATTCTCACTCCATTTAACCCGTTTTCTGAAATGAATTTGAAGTCATTTTCCACTATGAAACTGTTCCAGT
105217 A G ATGTGAAGGCGTTATCGAGAGCCTGAAGAGACCCACCGACATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGTATTCTCACTCC[A/G]TTTAACCCGTTTTCTGAAATGAATTTGAAGTCATTTTCCACTATGAAACTGTTCCAGTGCTCTTGCATAACAGCTTCAGCCTTGTCGG
105217 C T CATAAGGCCATGGTGGAGACGGATCGCTAGCAATCCACCATCCAACAGGTATTCTCACTCCATTTAACCCGTTTTCTGAAATGAATTTGAAGTCATTTTC[C/T]ACTATGAAACTGTTCCAGTGCTCTTGCATAACAGCTTCAGCCTTGTCGGGTCCATAGCCATTAGTGACTTGAAACTCACCTTGCAGCTG
105219 A T TTTTTTACACTTCACCGAGTTTACCCACATGAACCTTTGGGTTACAGCATTACAGTGGTGTAAAAATTCGTATAATCCCCTAATATCTACATATCCCATG[A/T]TGGGATTAAAACCCAAATGCAGATCGTGCCAATGCCTCGCCAAATTTCACCTCCAAAACTCAAACCAAATCATAACTTAAATGTGCATGG
105219 A T CTTCACCGAGTTTACCCACATGAACCTTTGGGTTACAGCATTACAGTGGTGTAAAAATTCGTATAATCCCCTAATATCTACATATCCCATGATGGGATTA[A/T]AACCCAAATGCAGATCGTGCCAATGCCTCGCCAAATTTCACCTCCAAAACTCAAACCAAATCATAACTTAAATGTGCATGGAAGGAGTA
105219 C T ACACACCATTCCAACTCTTAGAGGATATGTACCCAGTAAGCAAAGGCCCAATAGCAGCCCCAGCTGACCCGGTACCATCTATGATTGCCGTCACTGTGGC[C/T]AAAGCCCTCGAGTTCCCATTTAGCGAACTGTGGGTGCCCAAATCTGCCGAAACCGCAGTGGTTATAAGTGCATATGGGCCATTGACT
105219 G C CTGCCGAAACCGCAGTGGTTATAAGTGCATATGGGCCATTGACTAACATCCCGGTTATGAACATGAGGATAACGTTGTGCGTTAAAGATATCGATCCATA[G/C]GCACGGTACAAGAATAGGGATGGGATTGCTAAGTACATGAAACTTGCTGCTGTTAGTGCACGTGCATCTAACCGGTCTGAGATGTG
105223 A G GTACCCAGAGCAGCTTGTGTCTGAAGCCCACGATGCAGGAGTTATGGTTATCCATCAGCTTGGCAGCTATGAAAATGCAGAGAAAGCCAAAATTGCTGGA[A/G]TAGATGCAATTATAGTTCAAGGTCGTGAGGCAGGAGGCCATATAATTGGTCAGGAGGGAGTGATATCATTAGTACCAAAGGTTG
105223 A G TACACAAATGTATTTGGTCGATCGAGGTGGCCAGGTGCCCCACATCGTGTTTTGAATACACCATTTTTCAGCGAATGGAAACATCTTCCCGATCATGAAA[A/G]CGAGGATAATCAGCATGTCATTGGTCATACATTTATTCATGGAAGAAAAAAGGATATACATCGCTTTGCTGGCACAGTACCAAATGC
105223 C T TTATTCATGGAAGAAAAAAGGATATACATCGCTTTGCTGGCACAGTACCAAATGCGACAACAACAGGTGATGTTGAAAGCATGGTAATGTATGCTGGTTC[C/T]GGTGTCGGGCTTATCAAGGAGATTCTTCCAGCTGGTGAAGTAGTGAAAAGATTAGTTGCGGACGCAAAACAGATTATCCAACAGCA
105235 A G ATTCTGCGGCGTGGTAGAGTTCTGTTACGCTTTGCTTCCGCCCTACTGCTTATTAACTAACTCCAGTTTCTTGCCAAAGGCCTCTAGTGTAGAATTCTAC[A/G]TACCATTAGCCCTATTCATTATTTACAATATCTCAACGCTCGGTGATTCCCTTGAATGTGGACTGACATTCCGTACATGGTGGAATAATC
105235 C T TTCTTGCTCGGTTTCCTATCTGTGGTTCTTAAATACTTGGGGCTTTCGGAAACAATATTCGAAGTTACTAAGAAGGATCAGAAGGAATCTTCTGATAATG[C/T]GGAAGGAGGTACGAATGCGGATATTGGCAGGTTCACATTCAACTCGTCGACAATCTTTGTGCCTGCAACTGCGCTTTTGCTAGTACAC
105237 A G AGAGAAAATAAGAGGTTTTAGATCTAGCAGAAACAAGATATAGAAATTAGCTTTAGGGCTTCACCCACGCAAACGAAAGCAAGGCGGAGAGGAACAGATA[A/G]AGAGAGAGGTGGATCGATTAGCTAAGAATTGGAAAAGGAAGCGTTGAAGAAGGAGATTGCAAGGAACGCGATGAAAAGAAAG
105241 T C GTTGGCCTACTGGTGATAACAATATAACTAAAGGGCTTGATAGGGATGTTAAGATCGAGCCCGTGTTTGTAAATTCCAAACTTAAACTGTCTG[T/C]TGACTTTGAGAACCGAGTTAAGATTGCAAGCGATGGGTTAGAAAAGGGAAACTTACCGGTTATGTCTTCTGAAGGAACAGGAGGAGCTTATTT
105241 T C ACAATATAACTAAAGGGCTTGATAGGGATGTTAAGATCGAGCCCGTGTTTGTAAATTCCAAACTTAAACTGTCTGTTGACTTTGAGAACCGAGTTAAGAT[T/C]GCAAGCGATGGGTTAGAAAAGGGAAACTTACCGGTTATGTCTTCTGAAGGAACAGGAGGAGCTTATTTCATGCAAGATGAATCTGG
105241 A T ATTCCAAACTTAAACTGTCTGTTGACTTTGAGAACCGAGTTAAGATTGCAAGCGATGGGTTAGAAAAGGGAAACTTACCGGTTATGTCTTCTGAAGGAAC[A/T]GGAGGAGCTTATTTCATGCAAGATGAATCTGGTAACTATGTTGGTGTGTTTAAGCCAATCGATGAAGAACCGATGGCTGAAAACAA
105241 G A TAAGATTGCAAGCGATGGGTTAGAAAAGGGAAACTTACCGGTTATGTCTTCTGAAGGAACAGGAGGAGCTTATTTCATGCAAGATGAATCTGGTAACTAT[G/A]TTGGTGTGTTTAAGCCAATCGATGAAGAACCGATGGCTGAAAACAATCCACGTGGTTTACCTGTGACGTTGAATGGAGAAGGGTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105241 T C TGAATCTGGTAACTATGTTGGTGTGTTTAAGCCAATCGATGAAGAACCGATGGCTGAAAACAATCCACGTGGTTTACCTGTGACGTTGAATGGAGAAGGG[T/C]TGAAAAGGGGCACTAAGGTTGGTGAAGGTGCACTTAGGGAAGTTGCCGCTTACATTCTTGACCATCCAATTGGTGGAGCTCGAAA
105241 T C GTGTGTTTAAGCCAATCGATGAAGAACCGATGGCTGAAAACAATCCACGTGGTTTACCTGTGACGTTGAATGGAGAAGGGTTGAAAAGGGGCACTAAGGT[T/C]GGTGAAGGTGCACTTAGGGAAGTTGCCGCTTACATTCTTGACCATCCAATTGGTGGAGCTCGAAACCAGTCCATTCTTTCTGATG
105241 A G TTCTTGACCATCCAATTGGTGGAGCTCGAAACCAGTCCATTCTTTCTGATGAAATTGGTTTCTCAGGGGTTCCTCCTACTATGATGGTTAAGTGTTCAAA[A/G]GGCGTTTTTAACAGTGGGGAAAATGGATATAAGATAGGGTCTCTGCAGATGTTTGTGAACAATAATGGAAGTTGTGAGGATATGGGT
105241 T C TCTCTCTACTCAATGCTCTCGCACTCTTCGCATCTCAACCATGCTTTTGAAGAAAGGAGCGAAGAGAGGTCTGTCTCCTTATGCAATCGGAAGCATACTA[T/C]GCAGGGAAACACTGAACAAAGAATCGAAGATAGAGGAGATGGTTGGTGAGGCAATGGATTCGGTTCTTCCAGGCACCAGTGAAGCT
105249 A G AATTTCATGAAAATGTGCCTTCAGTTGATCATGAAGCCTCTACAAAATCAAGTTTAACTGCGGCTACTATTAACACTCTTGCTAAAGAATTTGAGCTTGA[A/G]GATTACTACAACGCGGCTAAGAAAATGTCTGCCACTGAATCATCACCATGCGAAGAAGCTTGTTCTACTTCCAAAGAGCCCGAAGACG
105251 G C ATGTTTCCCATGTTGAAACAAAGAAACCTAAATATATCAAGACTACTGCATCGGAAAGTGGTCTTTTTGACCATTTGATTAACATATGGGAATTTAATCC[G/C]GGCCCTGTTCCAGGAACGTGCGATCTTCATTTCCTGGTGGATTTCAAGTTTCAGTCACCTTTGTATCGCCAGGTGGCATCAATGTTCTT
105255 T C ATAGGGGAAGCTGTACTCAGTCTCTACTCGGTGAGCTATTTTGAAAATGTTTGCATTCTTGGTTCTTTGGTTTGGTTGTGTTGGGTTAGATTGTACAGCT[T/C]GATATTCAATGTTTTCTGTTGGTGTCGTCTTGCTGGTGTTAAGTCATTGACAAGGGGTGCGTTTGGATTGTAGTTGTTTTAGTTGTAAG
105259 C T TTGAAACCGCACCAAGAGAAGTTTTGGAAAACAATGGGTTTAAACTAGGGAAAAGATTTGCTGCTGCATTAAACAAACTGACAGGCAGGCCCGCAGAAGA[C/T]AATATTGCTTGGTTTATGCTCGAAGCCATCAGAGGGTTAATTTCATTTCTCTCAGGATGGTTGTACCGGCACGTAGTGCTATACTTG
105259 A G TTAACATATAATGTGCACAATCCTTTTCTCCTGGTCTTTGTGGATATAAAGGTAACTGGCTTGAGGATTCAATTCTAGGGTGTTTGAACATAGAAGTTGA[A/G]GATAATAATGCATTGTGTCCAATAGTGTTAAGGCCTCCAAGATCAGCCTGACTGTAGAGAGCATCAGCAGATCGTTTAGCCCCTAGAC
105267 A AC TTATCCACTGTGTTTTTATTTGTTTCTTGATTGTCACTCCTTTAATTTATTGTAAGTAGTGACAAGTCATTATGTATGTTTTTTGATGCTTGGTTTAGCA[A/AC]AAAGACACTGACTATCCAAATTTTGAGGTAATAGCATAATCCCAAAAAGGCCAAAACATGCGTACTCATATACACGTGTGTATACATTTG
105267 CA C ATTTGTTTCTTGATTGTCACTCCTTTAATTTATTGTAAGTAGTGACAAGTCATTATGTATGTTTTTTGATGCTTGGTTTAGCAAAAAGACACTGACTATC[CA/C]AAATTTTGAGGTAATAGCATAATCCCAAAAAGGCCAAAACATGCGTACTCATATACACGTGTGTATACATTTGTATATGTATACGCACA
105269 C CAG AGATTTACCAATAGGCAGTGGTCTAACTGTGACAGTCCCATTCAGAGCATCTTCAAGAACATTAACCGAGATCGTAGTTTTTATCGGAACCCCAAGCTTA[C/CAG]AACAATGCTGCAAACATTGTGTTTACTGTACCAAGGTTGGACAAATCAATTTCCCTATCCATGCCTTCACTGTCTAAAGCATCAAAG
105269 A G ACAACAATGCTGCAAACATTGTGTTTACTGTACCAAGGTTGGACAAATCAATTTCCCTATCCATGCCTTCACTGTCTAAAGCATCAAAGCCAGCACTATC[A/G]TACTTCCGTCTTTTCTCTGGATCAGATAAAATGCTATACGAAAGTGCAATTTCTTTAAAGCGCTCCGAAGCTTCACTATTACTCGCATTT
105269 T C TTGTGTTTACTGTACCAAGGTTGGACAAATCAATTTCCCTATCCATGCCTTCACTGTCTAAAGCATCAAAGCCAGCACTATCATACTTCCGTCTTTTCTC[T/C]GGATCAGATAAAATGCTATACGAAAGTGCAATTTCTTTAAAGCGCTCCGAAGCTTCACTATTACTCGCATTTTTATCAGGATGGTACTT
105277 A G CCAAGCCCATATACCATCTCGCTCTCCCATTCGTTCAATGCATTCAATCCTAAAGCCAAACAAAGCGTTAATATCTGCTGCCTCATGGTTACCACGAATC[A/G]AATGTACATTGTGAGGATGCTCAACCTTCAGTGCAAGGAGAAGTGAAATAGTTTCCAGACTATGTTGCCCCCTATCAACATAATCTCCT
105287 T C CGGTAGCAATGTGCATTCAAGCTGCTGCCGCAAGGTTTAGTTTCCCAGGTTCTGGTTCATTATATTTCTCAGTTGGTGGAATGTTGATGTTCGTTTTGGC[T/C]TTCGCATTGGGAGCTGGCCCAGTCCCTGGTCTTCTGTTGCCCGAAATCTTTCCAAATAAAATCCGTGCAAAGGCTATGGCTCTATGCAT
105287 CT C TGGTCTTCTGTTGCCCGAAATCTTTCCAAATAAAATCCGTGCAAAGGCTATGGCTCTATGCATGTCTGTTCACTGGGTGGTGAATTTCTTTGTTGGTTTG[CT/C]TTTTTTTGCGTCTCCTGGAGCTTTGGGGTGCACAAATTTTGTATACCATTTTCGCATCATTTTGCCTTGTAGCAGCCATATTTGCAAAGA
105287 T C AATATAGTTGAGTCCAGATTGCTCGTTGCAGCGTTCATTATACTAATACAAGTTTATGCAGTATATACATATGTCCATTCCTTGGATGCTCCTTTTGTGT[T/C]GAGAAAACACAATTGTGGATGTGTTTATGTATCATTGATTGTTTATACTTGTATAAAAGAGATCGTTTGACATCAATTACCATCATGTAAT
105295 T A CCGAATTGACACCTACAGCTGCATTAGTTTGACTCCCGAAAACACATGGCTTCTTCTCATCTTTAATCAATCTAATAGGCTGCAGTTTTCCATTTTCATT[T/A]TTTATAGGGAAAAGATACCATTCTCCATTTAGAGCACGCTCCAGTGCATCATCATCTTCAAACCATTTTTGCAACATGTCATCTGCCCTGTC
105301 A G CCAATAGGCATTCCGTCAATCGAAACATCAATGAACACATTCTTCGTTGTCGGCTTATTCCCAGCACATATGCTGGGGTCGGACGGGACGGTACTACTAG[A/G]CTCGATTTCGGCCGAAGAAGAGAGTACAGGGAGTAAGAGAGGGGTGATAATAGCAAGAGAGCGTCTTGATATGTTGAATGTGAAC
105311 T C CACAATGCCCTGTACTGGTTTTTATTAATTCCAAGAGTGGGGGTCAGCTGGGCGGCGAGTTGCTCCTTTCATATCGCAAGCTTCTCAACCAGGAACAGGT[T/C]TTTGATCTGGGATCCACTGATCCTGGAAAGGTATTGCATAAGCTTTATGGCAATTTGGAGAAGCTGAAGTCCCGTGGTGATGCTGTT
105313 C T GGTGGTTACAGGAACAACAACGAGGCGGTGAACGGAATATGGAGGAGGCTTAATCGTGAGTTTGGCTTGGAGGCTTGGGCTTCAGATTTCGTCTACTCGT[C/T]TACTTGAGGTAAACAGGATGAATGAAGAGAGAGGGGCTTCTTCCCCTTTTCATTTGATTTTCCCCTT
105321 G A ACCAGTATCATTTTTCATGCCAATTTACAGCTGATCTCATTGCCATGAATCGGTCAGATTTCATCATTACAAGTACATTTCAAGAAATTGCTGGAAGCAA[G/A]GACACAGTGGGACAATACGAGTCCCATACGGCGTTCACACTTCCAGGGTTGTACCGAGTAGTTCATGGAATCGATGTCTTTGATCCCA
105321 T G TTCACCCTGAAATCGAGGAGCTTTTGTTCAGTGATACTGAAAATACCGAACACAAATTTGTTCTGAAGGACAAGCACAAACCGATCATATTTTCAATGGC[T/G]AGGTTAGACAGGGTGAAGAACATCACAGGGCTAGTTGAGCTGTATGGAAAGAATAAACGACTAAGAGAGCTAGTTAATCTAGTGGT
105321 C T TAGTTAATCTAGTGGTTGTGGCTGGAGACCATGGAAAAGAATCAAAGGACAAGGAAGAACAAGCTGAGCTTAAAAGGATGTACAGTCTCATAGAGGAGTA[C/T]AAGTTGGACGGCCAGATTCGGTGGATCTCGGCTCAGATGGACCGTGTCAGAAATGGGGAGCTGTATCGCTGTATCTGTGATACC
105321 T C TGACATGTGGATTGCCCACATTCGCCACCTGTTATGGTGGACCTGCTGAAATCATAGTGCATGGAGTTTCCGGATTTCATATCGATCCATACCAAGGGGA[T/C]AAAGCTTCTGAGCTTCTAGTGAGTTTCTTTGAGAAATGCAAAGAAGACCCTAAGCATTGGGAGACGATCTCTAATGGAGGACTGAAA
105321 T C TTCATATCGATCCATACCAAGGGGATAAAGCTTCTGAGCTTCTAGTGAGTTTCTTTGAGAAATGCAAAGAAGACCCTAAGCATTGGGAGACGATCTCTAA[T/C]GGAGGACTGAAAAGGATAGAAGAAAAGTATACTTGGAAGCTGTATTCAGAGAGGTTGATGACTTTGGCTGGTGTTTATGGATTTTG
105329 C T ATTCTCGAGAGCTTAGCGCTGAGGAGGTTAGGCAGAGGAGACTAGAGAGGTTTGCTCGATGAGAAGAATGACAATTGTGTTGATTATTCCTTGTAATTTG[C/T]GTTGAAGATGATGGTGAGCAAATCATATATGGTAAACACTGTAAGATTTTTATCTTTGATTGGTTTACTTACTGGTAAAAAAAAAAA
105347 A C CAGAGTGGCTCTCACAACAGTCATTTGTTATTCAGCACTCAGTCACACCTGACATTGCAGTTCATGGGTTACCTGTCGATAATTTTTCTGGATCAGGAAG[A/C]GGTGGGGTCAACCTATGCCGCACTTCAATTGGTGTCGATCTCAGTGAACCAGCTACTTCTCATTGGAACACTACTACTAGTCTGAAGT
105347 T C GAGAAGGCGCTGTTGGCTCAGGAAGGTCATGCTTAATTTTAAACAGCGAGGTTACGATACCTTTGACAAAGGAGCTGGAAGGGGCGGTTTTCATGGACTG[T/C]GGAACCGACATGGGCTCTGCTCATCATGTACCTGGTAATCCTGCCCTTAGGCAAGGCAAACCTGGATATGGAGTTGGGTTTGGGT
105351 T C GCGATAATAGATTCCTACCGTCATTCCAAACTGAGAATTGTGTTTTCACATCAAGTACCTTCCCATCTACTAGAGGTATTTTAGAAGGCTGACCAAGGAT[T/C]TAAACATAAACAGAGTGAACTTCAATCTTGGCTGGGAAAACTTACTGGAAAAAACTTCCCTTTGTAGATCTAAGCAAGCCATGACTTAA
105351 T C TGAACTTCAATCTTGGCTGGGAAAACTTACTGGAAAAAACTTCCCTTTGTAGATCTAAGCAAGCCATGACTTAACAGATCTGACTTAGCATAACAATCGG[T/C]TGAGAGGAAAAAAAGCTTCAGCATGAGCTGTCGTAAATTAAAACCGATTACGCCAAAGCCCCGATTCCCTGATGTCTTGATTCTTGCA
105355 CT C CTTTTTATTGTAACTTGTAGCTGTAGGAGTGCATCTTCAACCCGCATACCTCGCACAAGTTTAGCCACCAGATTGACTTTCTTAGGACTCTGTTTTATTC[CT/C]TTTTTTAATCGCTTGAACAGATGATTTTTTGATAATATCTTTTCCATTTGCTTTTCCATCTCCTGATACTGGCATGAGAGGAGACGAAACT
105355 C G GACTCTGTTTTATTCCTTTTTTAATCGCTTGAACAGATGATTTTTTGATAATATCTTTTCCATTTGCTTTTCCATCTCCTGATACTGGCATGAGAGGAGA[C/G]GAAACTGGCTCCATGTTTGAGACATCTGTTGAAAATTTTCTTGAACTGAAATACCCCAAGTGTTGTAGAGTTTGATAACTAGATAGCTTGA
105355 G A CATTTGCTTTTCCATCTCCTGATACTGGCATGAGAGGAGACGAAACTGGCTCCATGTTTGAGACATCTGTTGAAAATTTTCTTGAACTGAAATACCCCAA[G/A]TGTTGTAGAGTTTGATAACTAGATAGCTTGAAACTTCTAGTAGAGAGATCAGCAACTTCAAGCTTTGCAATTTTACCTTGCAATCCTGA
105355 G C TGCCCAATTTTGTTGGGAACATTACGAATGGCTAGTCGCATAAACCTTTGCCATCCAGCCATCTCTCCAACCAAAATCAAGCTGTAACTTTGAGCAATAC[G/C]CGTTTGATTACACTGAAATCGAAAACCTTTTATTAAGCTGAAGTTTTGATTGAACAGTAGTACCTTTAAATTCTCCTTTTCTTTTCCAGTA
105359 GA G AATTCAAAAATTCAAGAGAATGGAAATCTATTTAATCTTCCGTTAAGTATCTGTTCCTCCTCGCACCAAAGGCAAGCCTT[GA/G]AAAAAATCTGAGAGTAGGCTTTAATGCCTGTGAGAAATTTAATGTATGTTGGCCTCATAAATTGTCTAATGGGAACTGATCTTATTGCAGGAACGAGGTA
105359 A G ATCTGCATCGGATGTTTCTGTCAAAGGCTTGTAACTGTAAGCATTTGATCCAGCATTGTTAATCCAAATGTCAATATAACCAAACTTGTCTTGAGCAAAC[A/G]ATACAAGTTCCTTAACATCTTTTCCATCTCTAACATCGCATGTGGTTCCCCAAACACGATGCTCTCCAAATTCTTCCTTCAAATTCCGAGT
105359 T C AATTCCTTTTGTTGAACCAGTGATTAAGACATTGTACGGTGGAACCATGGACTCAGATGATGTTTCGGAGGAGGATTCTGCGAAGATTCTATTCAAGTTC[T/C]CGTTTTGATGCTGTTGACGATTCTTTTTGTGAGAAAAACGTCCCCAAGAAAACCACAACGCGAAACGGAAAGTTTTGCTCGATTGTGA
105359 C CT TTAAGACATTGTACGGTGGAACCATGGACTCAGATGATGTTTCGGAGGAGGATTCTGCGAAGATTCTATTCAAGTTCTCGTTTTGATGCTGTTGACGATT[C/CT]TTTTTGTGAGAAAAACGTCCCCAAGAAAACCACAACGCGAAACGGAAAGTTTTGCTCGATTGTGAAGCATTTTGATTGAACGCAGA
105359 A G GATGATGTTTCGGAGGAGGATTCTGCGAAGATTCTATTCAAGTTCTCGTTTTGATGCTGTTGACGATTCTTTTTGTGAGAAAAACGTCCCCAAGAAAACC[A/G]CAACGCGAAACGGAAAGTTTTGCTCGATTGTGAAGCATTTTGATTGAACGCAGAGTGCAGCTTATAGTGATAACAGGGGAGTGAGA
105359 T C CTTTTTGTGAGAAAAACGTCCCCAAGAAAACCACAACGCGAAACGGAAAGTTTTGCTCGATTGTGAAGCATTTTGATTGAACGCAGAGTGCAGCTTATAG[T/C]GATAACAGGGGAGTGAGAATATCGAGCAGCGGAGGAGGAGAGTGCGGGATATGAAGCACTCATAGCCATTGAGAGTCGTTTAGA
105361 G A TTTCTAAAATCTTGAAGGGTTTCTTCAGACCAGCATTTTCAGGTCTATCAAGTTCATAGATTATAGAACCATTCATACCACCTGAATTGTCGTCTATATC[G/A]TAAGTTCCCGCATCATGAAACACCATTCGAAGCACACCAGCAGCTTTTGCCTTAGACAATACATTTCTAACTTCACTTTGAATTAATGAAA
105365 A C TCAGTGGGAAGTCTTTGATTAAGCAAGATTTCAAGACGTCAATATTACGGCAAGCAAATTTTAAAGGTGCCAAATTATTGGGTGCAAGCTTCTTTGATGC[A/C]GATTTGACTGGTGCCGATCTTTCTGATGCTGATCTTCGCAGTGCAGATTTGTCCTTGGCAAATTTTACCAAGGTAAATTTGAGTAATG
105365 T C TTAAGCAAGATTTCAAGACGTCAATATTACGGCAAGCAAATTTTAAAGGTGCCAAATTATTGGGTGCAAGCTTCTTTGATGCAGATTTGACTGGTGCCGA[T/C]CTTTCTGATGCTGATCTTCGCAGTGCAGATTTGTCCTTGGCAAATTTTACCAAGGTAAATTTGAGTAATGCAAATCTTGAAGGCGCAT
105365 C T ATTTGACTGGTGCCGATCTTTCTGATGCTGATCTTCGCAGTGCAGATTTGTCCTTGGCAAATTTTACCAAGGTAAATTTGAGTAATGCAAATCTTGAAGG[C/T]GCATTAACCACTGGGAACACATCTTTTAAGGGTTCAAACATAAATGGAGCAGATTTCACTGATGTGCCATTGCGAGATGACCAGCGGG
105365 A G AGCGGGAGTACCTCTGTAAAATTGCAGATGGTGTAAATCCAACAACGGGAAATCCAACAAGGGAGACATTGCTGTGTAAGTAACAGTGAACTGAAAATCA[A/G]ATAAACAAGAAGATAGGTTGCCTCTGATGCATCTGAATTTTCTCCAGCTCGGGCGACTAAGTCCCACCTCTTTCCTGATGATATTTG
105365 A G GCGGGAGTACCTCTGTAAAATTGCAGATGGTGTAAATCCAACAACGGGAAATCCAACAAGGGAGACATTGCTGTGTAAGTAACAGTGAACTGAAAATCAA[A/G]TAAACAAGAAGATAGGTTGCCTCTGATGCATCTGAATTTTCTCCAGCTCGGGCGACTAAGTCCCACCTCTTTCCTGATGATATTTG
105365 C T CAACAAGGGAGACATTGCTGTGTAAGTAACAGTGAACTGAAAATCAAATAAACAAGAAGATAGGTTGCCTCTGATGCATCTGAATTTTCTCCAGCTCGGG[C/T]GACTAAGTCCCACCTCTTTCCTGATGATATTTGGTAAAAGATGGTCGGTCAACAAAACCAGTTGGAATACAGTAATTGTTAGTTTGG
105365 A C AGGGAGACATTGCTGTGTAAGTAACAGTGAACTGAAAATCAAATAAACAAGAAGATAGGTTGCCTCTGATGCATCTGAATTTTCTCCAGCTCGGGCGACT[A/C]AGTCCCACCTCTTTCCTGATGATATTTGGTAAAAGATGGTCGGTCAACAAAACCAGTTGGAATACAGTAATTGTTAGTTTGGATAGT
105365 A T CATTGCTGTGTAAGTAACAGTGAACTGAAAATCAAATAAACAAGAAGATAGGTTGCCTCTGATGCATCTGAATTTTCTCCAGCTCGGGCGACTAAGTCCC[A/T]CCTCTTTCCTGATGATATTTGGTAAAAGATGGTCGGTCAACAAAACCAGTTGGAATACAGTAATTGTTAGTTTGGATAGTGTTATAAG
105365 C T TAAAAGATGGTCGGTCAACAAAACCAGTTGGAATACAGTAATTGTTAGTTTGGATAGTGTTATAAGTTAAGGATCTTGCCTCTTTGTATATTCTACAAAT[C/T]TCTTTAATTAACACATCTCTATATAAAAATTGTCGACGATGATACCGACTGTTTTGTATCATCTACGGCGACCACCAAAATATTTGGTTC
105373 G A CGACCTTGGCGCCATCGTAGCCGTTCTTGATGAGGATCTCAGGCGCCACGTAAGCGGGGGTTCCGCAGAGCGTGTGGAACATCCCATCGGCTCGGGTTTG[G/A]TCCGTGAGGGCGCTGAGCCCAAAATCGGTGACCTTGAGGTCGCCGTGTTCGTCGAGGAGGAGGTTTTCCGGCTTGAGATCGCGG
105373 A G CGTTCTTGATGAGGATCTCAGGCGCCACGTAAGCGGGGGTTCCGCAGAGCGTGTGGAACATCCCATCGGCTCGGGTTTGGTCCGTGAGGGCGCTGAGCCC[A/G]AAATCGGTGACCTTGAGGTCGCCGTGTTCGTCGAGGAGGAGGTTTTCCGGCTTGAGATCGCGGTGGAAGACGCCGCGGGAGTG
105373 G C CGTGTTCGTCGAGGAGGAGGTTTTCCGGCTTGAGATCGCGGTGGAAGACGCCGCGGGAGTGGCAGTAGCCGACGGCGGAGATGAGCTGCTGGAAGAGTTT[G/C]CGGGTTTGGTCCTCCGGGCAGCGGCCGTGTTTGGAGATCTTGGCGAAGAGCTCGCCGCCTTTGGCGAACTCGAGGACGAAGA
105373 C T GGAGGTTTTCCGGCTTGAGATCGCGGTGGAAGACGCCGCGGGAGTGGCAGTAGCCGACGGCGGAGATGAGCTGCTGGAAGAGTTTGCGGGTTTGGTCCTC[C/T]GGGCAGCGGCCGTGTTTGGAGATCTTGGCGAAGAGCTCGCCGCCTTTGGCGAACTCGAGGACGAAGAAGATCTTGGTTTTGG
105375 TC T GCCACGTCTGTTGGTGGTGACTGACCCAAGGACTGATCATCAGCCAGTCAACGAGGCTGCATACGTAAACCTGCCGGTCATTGCTCTGTGTAACACTGAC[TC/T]CCCCCCTCAAGTACATTGACATCGCCATCCCATGCAACAACAAGAGTGTTCACTCTATTGGACTGATGTGGTGGATGCTGACTAGA
105375 T C TGATGTGGTGGATGCTGACTAGAGAAGTGCTGCGTCTGCGTGGTAATGTGAGTCGTGATATGGCCTGGGATGTCATGCCTGATCTCTACTTCTACCGTGA[T/C]CCTGAAGAGACAGAGAAGGAGGAGGTTGTTGCAGGAGACCAGACTAAGGCCAAGGATGAGTATGTGCCAGAGTACAGCGCAGC
105377 G A ATGCCCAGTGCTTTCAAGGCAAGTGTGACATCATAGAAAACCCGAGGCCTTCCTTTTCCAGATAACTCAACAGGATTTGCAATCAAAAGCTCCGTGTCAG[G/A]TCCACGACTAATAATCATAACTCGTAGAGAATGAAGCATTTCCAACTTTAATCTAGAGCATATTGAATTTTGCTTATCTTGATCCACTA
105377 T TA ATCATAACTCGTAGAGAATGAAGCATTTCCAACTTTAATCTAGAGCATATTGAATTTTGCTTATCTTGATCCACTATTTTCTTCCCATCAGCTTGTTGAA[T/TA]AAAAGATCAATTTCACGATAGCCTTTCTTGCCTGGCAGGAATCTTCCATAAGCTATCTTAATAGAGCAATCCTTCATGGTTCTCAGAATA
105379 C A CTGCCCAGTCTTGGGCTTCCAAACGATTTCAATTGCCGCCTTCTCGGGATTTTCACCTTTACGGGTTCCGGGTTTGGGTCCGTAAACAGCAGCCAACACA[C/A]TGGTATTCCCTTGAGACCAACGTGCAGACCCATGAGCGCGATGGTTAAGATTGCGAGAACAAGAGAGAGGTCTGAATTGATTCTGG
105379 C T TTAAGATTGCGAGAACAAGAGAGAGGTCTGAATTGATTCTGGTTTCTTCTATCTAACCTTTCAATTTCCATTGCTCCCATTTATATTTGTTTAGTTTATG[C/T]ACCTGCAACAGAAAGCAACCAAATTCTGCTACAGCTGCAAGCAGCTTCGAAAGGCAGACCAAATCGAAGCAAAATCGGCCGAGTAGAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105379 A T AAAGCAACCAAATTCTGCTACAGCTGCAAGCAGCTTCGAAAGGCAGACCAAATCGAAGCAAAATCGGCCGAGTAGACAACTGACTGGAAACAGAAAACTG[A/T]CGCTAGGAAAGGCCGATGTCGATGAGCGGTTGCTGAGGAATCTAAAGCGATGAGGCAGGGTGGAGGGCTGGACGGAGCTGTG
105383 T C AAATGAACTACTCAGTTGCAGAACTTCATTAGATGGACCAAAATCGTTGATCACGCCATGATTATTACTCAAATGTCCATATCCATCAGTTATTGCCTTG[T/C]ATTGTCTCAAACACTTAAATTGGTTAACCCTATTTCTCGAAATTCTCATAGACTGAAAATTTGCTTGATTTTTCGAAGTCTCATGCCGGGC
105385 T C ACCCACGTTTTAGCCAATGCTTGCGAACCAAGTTGGGTACTCCAGCTGCCGAGATCACGATATCAGCTTTGCTTGTGATCTCTTCTGGATTTCTTGTGAA[T/C]GCGTGCACTGTAAACACGGTTGCATGATGTCTCTGTAGCAGTAAAGAAACAGGCAGACCAACCACCCTGCTTCGCCCAATCACAGCTA
105385 C T TTCGCCCAATCACAGCTACATTTTTCCCCATAAGCTCGACACCAGATCTTAGCAACAACTCCATACACGCTTTTGCTGCACAAGGAATAAATAGAGGTTC[C/T]CCCCCATTCATTGCAAGATTCCCCACATTTAAAGGATGAAACCCATCAACATCTTTCTCCAGCTTAACAGCATTTAATATTTTCTTCACAT
105387 T A GAACACCACGTGTCCTCCTCCCATCTTTCCGACGTTCTCCACGTTCAACTTCACGTCGAACATCGCGTTGCCGCATCCACTTTCGTCTACACTTACCGAT[T/A]TGCAAGTTTGTTTTCGACATGAATGCCCCTCCTCTAGAGATACCGATACCAATTTCGGTGCTTGGGCTAACTTATGAGTGAATTCTCCATA
105387 T C CGGATCCGGTCTCATTCTCATGTCCGTCATTGGTACCTTCTGCACGTACGACTCTGGGTACCAGGTCACTGGAAGTCTTCCACTTGGATTATAGGCACCA[T/C]AGATGACGTCAGCAATAGCAGCACCACCAGCCTCCCCAGGATAGCCGACCCACAAAATACTGGATATCCGATCATCCTCTTTAGCAAA
105387 G A CCTCCCCAGGATAGCCGACCCACAAAATACTGGATATCCGATCATCCTCTTTAGCAAAGCTTATATCAAAAGGTCCTCCAGACATAATAACAAGTATAAC[G/A]GGACCTTTAGCCACTTTAGCGACTTCTGTTATAAGCTGAGTTTGCTGACCTGGCAGTAGCAGACTGACCCTATCAAAGCTTTCACGCT
105387 A C GCTCTGTTGATTGATCTGCACCTACAATCAAGATAGTTGCATCCGACTTAGATGCAGCAGTTTTAGCTGGGTCCAACTGAAGGCTGTTTCCTGTGCAGCC[A/C]ACATTTGCACAACCGGGCTGGAACACGGTGGTGGCACAGGCTGAGAGGCCCTGTAATGGAGTGGTGTACTTGCAAGGTGTACCTTC
105387 A G TTTTAGCTGGGTCCAACTGAAGGCTGTTTCCTGTGCAGCCAACATTTGCACAACCGGGCTGGAACACGGTGGTGGCACAGGCTGAGAGGCCCTGTAATGG[A/G]GTGGTGTACTTGCAAGGTGTACCTTCGTAATTTCCTATCATGGTTTTGGTTACGTTGGCATTGGGCCCGATAACCGCCAAGGTTTT
105389 AC A GCTCACCCGCGAGCTGGGTCACAAGTCCGACGGCCAGACCATCGAGTGGCTCCTCCGCCATGCCGAGCCCTCCATAATCGCAGCCACCGGCACTGGTACC[AC/A]CCCCCGCCTCCTTCTCTTCCTCCACCGGCGCTAGCAACATCAACACCAGCAATATCCATTCTTTATCCCAAAACGCGCCTCCTGTTT
105389 G GACA TTCTTTATCCCAAAACGCGCCTCCTGTTTTCAGCATCCTCGGCAAACGACTCAGAGAAAACGAAATCGATATGGAGCACAACAATAATAACAGCAATAAC[G/GACA]ACAACAACAACAACATCAGTACTGGAAATAGTAACAGTAATAAGATGGTGGTTGGGCCAACGACGCATGGAGGGTTCTGGGCT
105389 TG T CATCTGCGGCGAGGGTGGGGAACTACTTGCCTATGCCTATGAGCCAAGGGCATTTGAATTTATTGGCTTCCTTTTCGGCTGGTCCAGCTAGAGGTGGAGG[TG/T]GGGGGAGCAGATGATGAGAACTGTTGAATTGGGGCTTACTTTTAGGGATTCATTCCAGTCACTTAGGTGTTAGGTTTTGATTTCT
105391 T C CTGTGAGGCAAATGGGTAACTCTAGAGGAGACGTATGCACTATACCAATCTGTAACCGTATGGAACATATTTGCGTATTCAAATCGTGTCACTAGCAGTG[T/C]AGGCTCTTCAATCCACTGCCCACATTCCAAGCTTCCAACACCAACAACGCGAATGGAATCAACCAAATTACGCATGGTATGAACCTG
105391 C G CAGTGTAGGCTCTTCAATCCACTGCCCACATTCCAAGCTTCCAACACCAACAACGCGAATGGAATCAACCAAATTACGCATGGTATGAACCTGAATCCGC[C/G]CGAGAGGCATGTGAGCATTCAAAAAATCTTCATCCACAACTTTAGCGTTCTCATACTCACTCACAACTCCCTCAATCTCGAACGCCCC
105395 C T AGTCTCCCAATCCATTGTCAAGTTGCAGTGTGTCAGGTGCATTGAGGTAAACACAATCAACAAAGCCAGGAAAAGTGACCAATTCCCTTTCCTCTTTACC[C/T]TCCAAAGGATTGGAAGGATCAGGGTCCTTGTTGAGAGTTTTACAGCCTTTTAAGCCTTTGACAGATGCTCCTGACACAGACGCACTGA
105395 T C TTGTAGAAAGACTGTTCGATTGAAGTATGACCTTGTACAGAGCATGAAAACTAAAGTCCCACATTGATCGACTGTAAGAGTCGTCTTTAAGTTCCAAAGT[T/C]ATAGCCACATCACCTTCTTTGTCCTCAGAATCAGTATGAGACCAGATCATATTTCTTCCAAAACCATGCTGTTGAATGGGACCTGGTCC
105395 C T TATGAGACCAGATCATATTTCTTCCAAAACCATGCTGTTGAATGGGACCTGGTCCAAACTGAGGGAAACAATGTGGAATTCCTCCACTGATAGGTTTCTT[C/T]CCATTAAAAACTGCATCCGGTCTGACAAAGAGTAGATCTTTCCCATTTGGAAGCTTCCAAGATGTCACACATCCACCAAACAGATAAA
105395 C G ACCTCGGCAGCGCTGCCACTAGAGGAGGTCAAAGAAACCCTAGAAAGACCGCCATTGCCATCGCCAATCTGCACTCCTGTAGCTACAGTACTTGTATTTT[C/G]ATTCAAGCTGCTAGCGTATGTTCTGCTGCGATTGGGGAGGCGTTTAGGGTTTGAAGAGGATGAAAAGACTGGCCGCATAGAAATG
105395 G A TCTGCACTCCTGTAGCTACAGTACTTGTATTTTCATTCAAGCTGCTAGCGTATGTTCTGCTGCGATTGGGGAGGCGTTTAGGGTTTGAAGAGGATGAAAA[G/A]ACTGGCCGCATAGAAATGCTCGATGCCATTGTTATAAACAAGATGAATTCAATGCTCCGGTATTAATTGGAATATTTATTCTATGCAG
105401 CT C TTTTTTTTTTTTTTTAAACTGAATGAAAGTAAATTCTCTTAGACCAGTTTAGTTATGTTACTAGAATGCACAGAAAGCAGTACATTAGATT[CT/C]TTTTGTTCCATTATTTAAAATCATACACTCAACCAATAAGCTGGAAAATAAAGATTACAACACTTCAGCCTTGCCCCGTCTTTGTTATTAAGTAGAAAAA
105401 CA C AAAGTAAATTCTCTTAGACCAGTTTAGTTATGTTACTAGAATGCACAGAAAGCAGTACATTAGATTCTTTTGTTCCATTATTTAAAATCATACACTCAAC[CA/C]AATAAGCTGGAAAATAAAGATTACAACACTTCAGCCTTGCCCCGTCTTTGTTATTAAGTAGAAAAAGTTCCAACTATGCACATTGACTG
105401 TA T AGACCAGTTTAGTTATGTTACTAGAATGCACAGAAAGCAGTACATTAGATTCTTTTGTTCCATTATTTAAAATCATACACTCAACCAATAAGCTGGAAAA[TA/T]AAAGATTACAACACTTCAGCCTTGCCCCGTCTTTGTTATTAAGTAGAAAAAGTTCCAACTATGCACATTGACTGGACTGGATTTTGGTA
105403 A G CTAATCATAAAATCAAATAATAGCTAAACCAAATAATCATATGGACTTAAAAACACCCACAACAATA[A/G]AATTACAGATTTAACAGTAAATTTAGCACCCTCTCTGGCATCTCAAAGCTTTTCGATTACCAAGAACTATCAAGAACCCACACGACACTCAACAAGCACT
105403 A G CTAATCATAAAATCAAATAATAGCTAAACCAAATAATCATATGGACTTAAAAACACCCACAACAATAAAATTAC[A/G]GATTTAACAGTAAATTTAGCACCCTCTCTGGCATCTCAAAGCTTTTCGATTACCAAGAACTATCAAGAACCCACACGACACTCAACAAGCACTTGAAAGT
105403 G A ACAGTAAATTTAGCACCCTCTCTGGCATCTCAAAGCTTTTCGATTACCAAGAACTATCAAGAACCCACACGACACTCAACAAGCACTTGAAAGTTGAAAC[G/A]CGAAGGAAGAAATGTAGAAATTTACAAACACGATAGTAAATATTAATAAACACAAGGTACAAGATGTAACATTCTTTTATGTATTGAC
105403 C T AGATACCCACTTCTCTTTCAGCTCCATTATGGCCTTGGGTTGAAGGAAGATGATGCTTTGGCAAGGGAAGTTATGCCGCCAGCACTATGATAACGATGAG[C/T]AGAACCACTCCGAAGATCACCAAAAGCAAACAAGTCAAAGATGAATTTGACTTCTGTGTTTTGGCAGCCTTAACAAGTTGACTTTTT
105403 T C AAGGAAGATGATGCTTTGGCAAGGGAAGTTATGCCGCCAGCACTATGATAACGATGAGCAGAACCACTCCGAAGATCACCAAAAGCAAACAAGTCAAAGA[T/C]GAATTTGACTTCTGTGTTTTGGCAGCCTTAACAAGTTGACTTTTTGCTTGAACTGTTGCTGCTAAAGAACTCTCGAAATGGGTGTC
105403 A T ACCAAAAGCAAACAAGTCAAAGATGAATTTGACTTCTGTGTTTTGGCAGCCTTAACAAGTTGACTTTTTGCTTGAACTGTTGCTGCTAAAGAACTCTCGA[A/T]ATGGGTGTCAATGTCATCAATCATGGCTCCCTGATCATGTACCAGTACAGCAAGATCTTTAAAAATTTCATTCACTTCGCCAATCTGGT
105403 T G GCTCTTGAGATTTGTCATAACTGACATCAGCTTCATTTGAAGTATTGCTGGTCTGCTGAGCTGCCTGGGGAACGAAAGGTGCATACGCTGTTTCCCTCTC[T/G]GCAGCAAGTCGTTGTGCTTTTTGAAATTCTTTCAAAACTGCTTCGAAGTCTTTGGCGAGCTTTGCATCAGCAATCTTTTTACTTGCGCT
105403 G A TGGTCTGCTGAGCTGCCTGGGGAACGAAAGGTGCATACGCTGTTTCCCTCTCTGCAGCAAGTCGTTGTGCTTTTTGAAATTCTTTCAAAACTGCTTCGAA[G/A]TCTTTGGCGAGCTTTGCATCAGCAATCTTTTTACTTGCGCTAACTTCAACATGGTGATCTGTTTCACTAGCTTGCTTGAGCTTAGCAGA
105407 C A CGTCTCCATCCTTGTACTTGTTAAAGCTCTTCGACTTCGTAACACACCCGCTAAGTATCTCTGCTTCGGTTTTGATCCCATACTGGTCCATTAAGCAACC[C/A]AGTGTAAAATCATACTGCTCCTTGTGGTTGAAAGCATCGGTAACATGATCCATGAAGCCTTCGACTTCCATGTCGCGGTCGTATGATTTT
105407 G A TCTCCATCCTTGTACTTGTTAAAGCTCTTCGACTTCGTAACACACCCGCTAAGTATCTCTGCTTCGGTTTTGATCCCATACTGGTCCATTAAGCAACCCA[G/A]TGTAAAATCATACTGCTCCTTGTGGTTGAAAGCATCGGTAACATGATCCATGAAGCCTTCGACTTCCATGTCGCGGTCGTATGATTTTTTG
105407 C T CCCATACTGGTCCATTAAGCAACCCAGTGTAAAATCATACTGCTCCTTGTGGTTGAAAGCATCGGTAACATGATCCATGAAGCCTTCGACTTCCATGTCG[C/T]GGTCGTATGATTTTTTGGAGATTGCTTTGGTGAATCCTTCTAAGTAGCTTGGGTTTATGTAGTGGTCTTTTACGGCTCTGAAAAGTTTG
105407 T G GGTCTTTTACGGCTCTGAAAAGTTTGCCTACCACGCCTTTTGATTCGTAGGACGGTTTGTCAGGCTTCTCCATGAAGTCGGGGAACTCTTTGACGTAGAG[T/G]TGGGGTGGGATTTCGGCGGGTATGCCAGTTTTAGGGAAATCAACCGCAATCGAGAATAGTTCTGCGAGCTCCAGGCAGGGTGTGCT
105407 G T CGGCTCTGAAAAGTTTGCCTACCACGCCTTTTGATTCGTAGGACGGTTTGTCAGGCTTCTCCATGAAGTCGGGGAACTCTTTGACGTAGAGTTGGGGTGG[G/T]ATTTCGGCGGGTATGCCAGTTTTAGGGAAATCAACCGCAATCGAGAATAGTTCTGCGAGCTCCAGGCAGGGTGTGCTTTCAGCTTT
105407 G A AGAATAGTTCTGCGAGCTCCAGGCAGGGTGTGCTTTCAGCTTTTAGAGGCTCTATGTCTGCAAAGACTGTGTGTGCGTTTGCGATTATTCCCAGGCTGTC[G/A]TTGACTATGTAGTTTGTGAAGTACTCATGAACTTCCTGAATAGTCACATCGTGATCAAGGTTTTCAGCTGGAGCGGCTGCATATTCCA
105431 C T CCATTGGAAGACCGGCCCACAGTACGTCTGTCCCTGTTGTGTGGGCATTACATAGAGGCGTGTCAAGGAAAAGATCGGCTAAGGCACCACGCCTAATATG[C/T]TCGTTCTTGATCGCTACATCAGTAAATATGATCTGATCATCCTTTACCCCTTGTCTTCTAGCATAGTCACGAAGTCTTCTCTCTCCAGC
105435 TA T TCTCCTCGTACCAGTGGCTCTATAAACCAGCCACTGTAAAAGTCGAAAGCTCTGCCTTTTGCTTCTAAATCTTCTTTGGAATTTGTTGCGGGGAGAAAAT[TA/T]AAAAACTAAGATATTCAGTCCTATGAAGCCTTTTTGATTGGCCTGATAATATTTCTTGTACAAAGAGGCAGCTGAACCGTGTGCAAGC
105441 G T GTTAGACACATTCAAGTACTCAACACCTCCCCCGCTCACAATGTCCAAAATACCCTCAGGAGATAACACACATGAATCAGCTTCTATATAAGCTAATGTT[G/T]GAGAGCATCCCCTAAATCCTGTTCCTGATACGCCTCTACAATATGATATCATCACCGCTTGCAATTTAGTGCATTCTACTGAGAGAGCA
105441 C T TCAGGAGATAACACACATGAATCAGCTTCTATATAAGCTAATGTTGGAGAGCATCCCCTAAATCCTGTTCCTGATACGCCTCTACAATATGATATCATCA[C/T]CGCTTGCAATTTAGTGCATTCTACTGAGAGAGCATGGATACCAGAGTCTGTGATCATAGTGCAATATGAAAGGTTCAAGCTTTTCAATG
105441 A T GTGCATTCTACTGAGAGAGCATGGATACCAGAGTCTGTGATCATAGTGCAATATGAAAGGTTCAAGCTTTTCAATGCATGACATGAATGGGCTAGGCTGG[A/T]TAAGCCAGGGTCTGTGATATTGCATCGGTAAAGAGTTACTTTAACCAAATTAGGACAGCCATTGGCTACTAAGCTTAGTCCGTTATC
105453 A G CACTTACACCTTGATCAACAAAGAAGGAAAAGTTCACTACGTTAAGTTCCACTGGAAACCAACTTGTGGTGTCAAATCTTTACTGGATGATGAAGCTGTT[A/G]TGGTAGGAGGAACTAACCATAGCCATGCTACAAAAGATTTGACTGATTCAATCGCTGCTGGAAATTTTCCAGAATGGAAGTTGTTCA
105453 G A TTGGTCGCCTGGTGCTGAATAAAAACATTGATAACTTCTTTGCGGAGAATGAACAGCTCGCATTTTGTCCTTCACTTGTGGTGCCTGGTATTTACTATTC[G/A]GATGATAAGATGCTGCAAACCAGGATTTTCTCATATTCTGATACCCAGAGGTATAGGCTTGGTCCAAACTATTTGATGCTACCAGCCAA
105453 T C CTGGGTCAGAAGCTGGCGAGTCGCCTCAATGTCAAGCCAAGCATGTAATTTGGAGCATTAATCTGTACTCTACTCCGGAAACAGAAACAGGAAATACCGT[T/C]TGATTTATAGAACTTGAAATGGAGCTTTTGAATTATTCTACCGTACTAATTATGTAATAATAATTTATAAACGTTCCATGTTGGGTTG
105453 C T CATGTAATTTGGAGCATTAATCTGTACTCTACTCCGGAAACAGAAACAGGAAATACCGTTTGATTTATAGAACTTGAAATGGAGCTTTTGAATTATTCTA[C/T]CGTACTAATTATGTAATAATAATTTATAAACGTTCCATGTTGGGTTGATACAAACTTTTGCTGTTATAAAGAGTCAATAGCTAAATACTT
105453 A T TAATTTGGAGCATTAATCTGTACTCTACTCCGGAAACAGAAACAGGAAATACCGTTTGATTTATAGAACTTGAAATGGAGCTTTTGAATTATTCTACCGT[A/T]CTAATTATGTAATAATAATTTATAAACGTTCCATGTTGGGTTGATACAAACTTTTGCTGTTATAAAGAGTCAATAGCTAAATACTTTTTA
105455 A G TTGAATTTTTTTCAACTGAGCCCTCGCTGTGAATCTTAGCTATATGACATGCAAGTCCCATTTTTGAAAAACATGTTTTTGTACTAACAAAATAAAGAGG[A/G]CCATGATTACTGAAGAGACCTGGAACCAACAAATAGACCATCGTGTTAGGCAACTTGTGTTCGTCATTTCTGACATTCTGAAGAATTTC
105455 A G AAAAACATGTTTTTGTACTAACAAAATAAAGAGGACCATGATTACTGAAGAGACCTGGAACCAACAAATAGACCATCGTGTTAGGCAACTTGTGTTCGTC[A/G]TTTCTGACATTCTGAAGAATTTCCATGAAGCGTTGTGTTCCATCTTCAACAGAAGGCATGCCAGGAGCACGCTGCAGCCATCCAATG
105455 G T CCATGATTACTGAAGAGACCTGGAACCAACAAATAGACCATCGTGTTAGGCAACTTGTGTTCGTCATTTCTGACATTCTGAAGAATTTCCATGAAGCGTT[G/T]TGTTCCATCTTCAACAGAAGGCATGCCAGGAGCACGCTGCAGCCATCCAATGTCTTCTGCTGAACCAAGAACAGTTTTCCGTGCTCTA
105455 A G GACCTGGAACCAACAAATAGACCATCGTGTTAGGCAACTTGTGTTCGTCATTTCTGACATTCTGAAGAATTTCCATGAAGCGTTGTGTTCCATCTTCAAC[A/G]GAAGGCATGCCAGGAGCACGCTGCAGCCATCCAATGTCTTCTGCTGAACCAAGAACAGTTTTCCGTGCTCTAGAAATAAGGCCTTGAA
105455 C T TGCTGAACCAAGAACAGTTTTCCGTGCTCTAGAAATAAGGCCTTGAAATAATGATGACCCATTTTGGAATATACTAGTGGAGGCTAAGGCTTGAGATCTA[C/T]TTCCAGCTGAGGTTGAAAATAGAGTATCCCTATTCTCATGCACAGGCTGAGCCGTGTTAGCTTGTTCGGAAACAAAGGTTGTCAATT
105455 A G ACTAGTGGAGGCTAAGGCTTGAGATCTACTTCCAGCTGAGGTTGAAAATAGAGTATCCCTATTCTCATGCACAGGCTGAGCCGTGTTAGCTTGTTCGGAA[A/G]CAAAGGTTGTCAATTCCTGTCCATCGTCTACAGAGCCAGTGAAGCAACCAGTAAAGTAGGAAGTAGTCTGTGCAAGATAATCAGCC
105461 TC T CTTTGCATTCACACCTTTGCAGACATGATCTCCTGCAGAGAAGTCCAAGTTCCAGACACAGCAAACACAAGCCCGACAATCACAATAGCTATATCCGAAG[TC/T]CACGACGAACCAACTCAGCTCATCCCCGAACACCTTCAAATGGAACAAAGCAGGGATCACAAACCCCAGTAAGATGCACACACTGC
105473 C T GACAGGCTCCTCCCATGGTGGATTCCACTACCATCTGCACCTCCTTTTCCAGCGGATACAGCCTCGGAAGAAGAAGTAGGGCCCACATGCGCGGAGGCGA[C/T]GTCATCAGATAGGGAAGGGATGTCGATGTCAGAGAAGTTAAAATCGGGATCAGAGTCAAAAAGCAAGTCGTCGGGGAGGCGGA
105475 CT C TCGGGTTGTTAGAGATTCAAAAACAAGTTTGGGGAAGGGTATTGCATATATATTGTTCAAATCAAGGGACGCTGCAAATACAGTAGTGAGGAGAGGAGGA[CT/C]TTTAAGATCGCGATCGAGTGCTCAGGCTGTGCCATGCAGCTAGAGCAGATACCATGCCACCTAAAAAACCCGAATCTAATTCAA
105475 A AT GTTAGAGATTCAAAAACAAGTTTGGGGAAGGGTATTGCATATATATTGTTCAAATCAAGGGACGCTGCAAATACAGTAGTGAGGAGAGGAGGACTTTAAG[A/AT]TCGCGATCGAGTGCTCAGGCTGTGCCATGCAGCTAGAGCAGATACCATGCCACCTAAAAAACCCGAATCTAATTCAAGGAGGGA
105491 T G TCGATTCCGTTAAAGCGACGGTTCAGATTGCGAGGGTCGAGTTTAACATGAATGATTTGGATGATCGGGAGGTGGTTCCATCGGAAGTGAAGCTGCTGAC[T/G]AGATCGGACGTTGGCAACAGCGCGTTTCCGTCGGTTTCGCCGGATGGAAAATGGGTCGTGTTTCGATCTGGACGGTCAGGGTTT
105491 T C AAGCGACGGTTCAGATTGCGAGGGTCGAGTTTAACATGAATGATTTGGATGATCGGGAGGTGGTTCCATCGGAAGTGAAGCTGCTGACTAGATCGGACGT[T/C]GGCAACAGCGCGTTTCCGTCGGTTTCGCCGGATGGAAAATGGGTCGTGTTTCGATCTGGACGGTCAGGGTTTAAAAATCTGTAT
105491 C A TGGGTCGTGTTTCGATCTGGACGGTCAGGGTTTAAAAATCTGTATGTCATGGATGCGGTTAAGGGTGAGACGGGAAGCATGCGTAGGTTGACGGAGGGGG[C/A]ATGGATCGACACGATGCCGTGTTGGTCGCCGGACGGGGAGTGGATAGCGTTTTCCTCGAACCGGCATAATCCGAAGAACGAGA
105491 G A TTAAAAATCTGTATGTCATGGATGCGGTTAAGGGTGAGACGGGAAGCATGCGTAGGTTGACGGAGGGGGCATGGATCGACACGATGCCGTGTTGGTCGCC[G/A]GACGGGGAGTGGATAGCGTTTTCCTCGAACCGGCATAATCCGAAGAACGAGACGACTTTCAGCGTGTATCTGGTGAAGCCAGA
105493 T C TAGGTATTTGAGTGATAGAGCCCTTCCTCCCTTCTATACGACCAGCACGCTCATATATTGTTGCAAGATCTGTGTACATGTAACCAGGATAACCACGTCT[T/C]CCAGGCACCTCTTCTCGAGCAGCAGACACCTCACGAAGAGCATCAGCATACGAACTCATGTCAGTTAAGATGACAAGGACATGCTTTC
105495 T C CCACTTCATCACATCTTGTCTTCCTTTCCACAAAAACAATGGTCAATGGTTGAGCATAACAGCAACTTTCTGCTTGAGCAGCCTCCTCAACAAGTACAGA[T/C]AGAAGCCGGTCGATCTTCTCATTTTCGGTTATCTTCACCAAATTTTGAGAAACATTTGCTGTAGGGCTGCTTACTTTACCGACTTTAACTT
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105497 G A GTACCGTTTGTCTTTCAGAAGGGTCACGTTAAGTTGGCGTCCGGGTCGGAAGTGTCCGACGCGTCGACGCGGGGCCTGCCAATTCGCCGCTTCCAGACGA[G/A]CAGCTCGAATTGTAGCTTTCATGTTCCCCGTTCATCCTTATACCCCTTTTACACCCTTATGCCCCTTTCGTGTGCCCCTTCTGGATAA
105497 T C AAGGGTCACGTTAAGTTGGCGTCCGGGTCGGAAGTGTCCGACGCGTCGACGCGGGGCCTGCCAATTCGCCGCTTCCAGACGAGCAGCTCGAATTGTAGCT[T/C]TCATGTTCCCCGTTCATCCTTATACCCCTTTTACACCCTTATGCCCCTTTCGTGTGCCCCTTCTGGATAAAATAAAAACTCATTCTCCT
105497 T C TATACCCCTTTTACACCCTTATGCCCCTTTCGTGTGCCCCTTCTGGATAAAATAAAAACTCATTCTCCTTTCACCAATTTTCCCCTTCCCCAACTCCTTC[T/C]GAATATCCCTTCCAAATACCACTTTCTGTTCGAAATCAAACGCACCCTTTTTCAACCTTGAAGTAGGTAGCATGATCAAACATGGAGCATCA
AAGGACGATTGCAGAAGAAAAGGGTAAAACTGCAAGCCAAAATGTTAACATGTTTAC
105497 T TTTATTTGGTAGCAGATTCAAGTTCGAAATTCATCAATCCACATCCACTAAATTTAATGTAGGAGGTAAGTGATGACCCCAATATCCAGTCTCAACTTAT[TCTTAGACGCGAAGGACGATTGCAGAAGAAAAGGGTAAAACTGCAAGCCAAAATGTTAACATGTTTAC/T]CTTAGACGCGAAGGACGATTG
105507 A AC CAAGAGGAGGAGCTCCATCTACAGGGGTGTCACCAAGCACAGGTTGACTGGGAGGTACGAAGCTCATTTATGGGACAAGCATTGCTGGAACAATGTTCAA[A/AC]TAAAAGGGGAAGCAAGTTTATTTAGGTGCATATGATAATGAAGAGGCAGCTGCGCGCACATATGATCTTGCTGCTTTAAAATAT
105513 A AG AGAGATGTCGAGGAGGGGTGAAAGGGTTTTGGAGTATTAAACAGTGGTGGGGTTGCGTTCGATTTTGAAAAGGGGGAGGCGCTGCAAATTTGCGAATTGT[A/AG]GAGGGGAGAGGTTGAATTGATGTACAGGTGAACGATGATTTTGGTCGAGTTTCATTGGTGAACGGAGGGAGTTCAGGTACC
105513 G A TTCGGCTGAGGGAAATTTTTTCTCAAAAAATTAAATCGTCAGTTCCTTCCAAGCCTTCCCCAAGAATAGCTGTTGCCTTCCAAACCGCCGCCTCCTCTCC[G/A]AACCGCCGCCGCCTCTCCAAGCGCTAGCCGTCATCCGACCGATCAACGCTTGAAATCGTGTATTTTGTGTCAAATTTGATCGATCTGTCT
105517 A T GCGCGTACCTCAACTTCATGTTGGACGCTGGCACCTGCGTCCTGTTGGACACTACCGTCGCTGCCACGGGATTCTCTCTAAACTCCCTCAACTGCTCCGC[A/T]CCCATACTCAATGTACCCTGCCCGTCCGCGTCCGTCAGTACCAAACTCTTAATCGTCGGATTGCCCTCAATTATCGGTCTCAACAAATG
105517 G C CCACGGGATTCTCTCTAAACTCCCTCAACTGCTCCGCACCCATACTCAATGTACCCTGCCCGTCCGCGTCCGTCAGTACCAAACTCTTAATCGTCGGATT[G/C]CCCTCAATTATCGGTCTCAACAAATGATGTCTAGTGGAAGCCGCAATCAACGAACTGATTGTCCAAACCACACGGAGTTTGAGTCCTCC
105517 T G GCGGAGGTTTTGGACGTGGGTGAACTTCTTGAGGACCTGAGTGGGGGAGTGGTGGGCGATTTGGGGGAGAACCCCCTTTAGGGTGCGGGATTGATGGAAG[T/G]GTTTGAAGAAGGCGAAGAAGATGAGCTTGAGGAATTGGGAGAGGAGCGACTTGGATTTGCGGGAGGAAGGGTCGACGGAG
105517 A G TTTTGGACGTGGGTGAACTTCTTGAGGACCTGAGTGGGGGAGTGGTGGGCGATTTGGGGGAGAACCCCCTTTAGGGTGCGGGATTGATGGAAGTGTTTGA[A/G]GAAGGCGAAGAAGATGAGCTTGAGGAATTGGGAGAGGAGCGACTTGGATTTGCGGGAGGAAGGGTCGACGGAGTCGTCGG
105517 A G GCGACTTGGATTTGCGGGAGGAAGGGTCGACGGAGTCGTCGGATTGACCGTCGATGGTGAGGACGCGGTCGATCTTGACGTAGACGTCGTGGACGAGGGG[A/G]ACGAGGGCGTTGAAGCGTTTAGAGACGGCGGAGCAGCGGCCGAGGGATCGGACATCGGCGACCTTGTTGAATATGTCGAGA
105517 A G AAGGGTCGACGGAGTCGTCGGATTGACCGTCGATGGTGAGGACGCGGTCGATCTTGACGTAGACGTCGTGGACGAGGGGAACGAGGGCGTTGAAGCGTTT[A/G]GAGACGGCGGAGCAGCGGCCGAGGGATCGGACATCGGCGACCTTGTTGAATATGTCGAGAACGATTGAGTCCGGGATGCGG
105523 A G ACGCCGTCCGCTTCCTCCGTCGCGCCACCGCTCGCCGCATGACCCAACCTTCCCTCGCCGTGCGCGAAGCGGCGGCGGAGCAGCTTGAAGATAGGCAGTC[A/G]GATTGGGCCAATTCCAGGCCTGTTCTGCTTCTCGACGTGTTGTGGAACCTGTCGTTCGTGGCGGTTGCGGTTGGAGTTCTGAGCG
105523 G T TCGCCGTGCGCGAAGCGGCGGCGGAGCAGCTTGAAGATAGGCAGTCAGATTGGGCCAATTCCAGGCCTGTTCTGCTTCTCGACGTGTTGTGGAACCTGTC[G/T]TTCGTGGCGGTTGCGGTTGGAGTTCTGAGCGTGAGCTTGGAGGAGAATCCGAGTGTTCCTTTGCGTGTTTGGATCGTGGGGTAC
105523 C T GTGGAACCTGTCGTTCGTGGCGGTTGCGGTTGGAGTTCTGAGCGTGAGCTTGGAGGAGAATCCGAGTGTTCCTTTGCGTGTTTGGATCGTGGGGTACGCG[C/T]TGCAGTGCGTGGTTCATGTGGGGAGTATTGGGTTCGAGTATTGGAAGAGGAGGGATGGTGGTGGGGCTTTGAATTCCGACTCA
105523 T C TGGCGGTTGCGGTTGGAGTTCTGAGCGTGAGCTTGGAGGAGAATCCGAGTGTTCCTTTGCGTGTTTGGATCGTGGGGTACGCGCTGCAGTGCGTGGTTCA[T/C]GTGGGGAGTATTGGGTTCGAGTATTGGAAGAGGAGGGATGGTGGTGGGGCTTTGAATTCCGACTCATACGATGATGAGAGGTC
105523 C T GTGTTTGGATCGTGGGGTACGCGCTGCAGTGCGTGGTTCATGTGGGGAGTATTGGGTTCGAGTATTGGAAGAGGAGGGATGGTGGTGGGGCTTTGAATTC[C/T]GACTCATACGATGATGAGAGGTCGAGTATCAGCAAACATATGGAATCTGCAAACACAATGTTTTCATTCATATGGTGGATAATTG
105523 C T GTGTTTTGTGTCGCTTTGGCTTGCCTAATTGGTTTTGCCGTATGCTGCTGTCTTCCATGCATAATTGCCATCCTTTACGCTGTGGCAGATCAGGAAGGGG[C/T]ATCTGATGAAGATATTAATCAACTTCCAAAGTACAAATTTCATAAAATTGGGAATCCTGAGAAATTGCCTATTGAGTTATCAGGACCTT
105523 G T TCTGCATAACAGCATATGAGGATGACGTTGAACTGCGAGAATTACCTTGCGGACACCATTTCCACTGCGCATGTATAGACAAGTGGCTCTATATAAACGC[G/T]ACCTGTCCACTCTGCAAGTTCAATATTGTTAAGCACAGCCATGATGGCAGCGAAGAGGTGTAACCGCATGCAAATGATGGTTATGCA
105523 A T GCATGTATAGACAAGTGGCTCTATATAAACGCGACCTGTCCACTCTGCAAGTTCAATATTGTTAAGCACAGCCATGATGGCAGCGAAGAGGTGTAACCGC[A/T]TGCAAATGATGGTTATGCATCCGGGGCATTTGTTTGTTGTTGTTAAATGTATCATAAATATAGCGTTTATGTAGAGCAATGGTGTTC
105523 G T TATAAACGCGACCTGTCCACTCTGCAAGTTCAATATTGTTAAGCACAGCCATGATGGCAGCGAAGAGGTGTAACCGCATGCAAATGATGGTTATGCATCC[G/T]GGGCATTTGTTTGTTGTTGTTAAATGTATCATAAATATAGCGTTTATGTAGAGCAATGGTGTTCATCTCCATGGGGATTCAAACAGTG
105523 G A TAAACGCGACCTGTCCACTCTGCAAGTTCAATATTGTTAAGCACAGCCATGATGGCAGCGAAGAGGTGTAACCGCATGCAAATGATGGTTATGCATCCGG[G/A]GCATTTGTTTGTTGTTGTTAAATGTATCATAAATATAGCGTTTATGTAGAGCAATGGTGTTCATCTCCATGGGGATTCAAACAGTGT
105525 G A CTCGGTGGACCGATTCAAACTCTCCTTGTTGCCTTGCTTGATCCCTGCATTGCCCACGTTTGGTATAGTTGGACATGACTATCAAGTCGTTAGGTGACAT[G/A]ATATCAATACGATGAGCAGAAATACTAGAATAGGGGAACCACTTCTGAGTATTCCACCAATAAGTCAACCAAGGAGCATGATGAGCA
105525 A T ATTCAAACTCTCCTTGTTGCCTTGCTTGATCCCTGCATTGCCCACGTTTGGTATAGTTGGACATGACTATCAAGTCGTTAGGTGACATGATATCAATACG[A/T]TGAGCAGAAATACTAGAATAGGGGAACCACTTCTGAGTATTCCACCAATAAGTCAACCAAGGAGCATGATGAGCAACTCTATATGCCC
105525 C T TGGATGGAAAACTAGGCCACCAGTAGTTAGAAGCTGGTGCTACTAAAGCTGCACCTGAAAGCCTATGAGGTATATATTTCAAGCAACCCCACACAAGTTC[C/T]CCTCCTAATGAAAATCCAACCACAAAGAACTTTCCACCTAGCTCAAAAATATCTGCTATTTCTTCAATATCCCGTGCATTGCTTTTGAC
105525 A G ACCAGTAGTTAGAAGCTGGTGCTACTAAAGCTGCACCTGAAAGCCTATGAGGTATATATTTCAAGCAACCCCACACAAGTTCCCCTCCTAATGAAAATCC[A/G]ACCACAAAGAACTTTCCACCTAGCTCAAAAATATCTGCTATTTCTTCAATATCCCGTGCATTGCTTTTGACAGACCTATGAGGGTGTGG
105525 A G GTGCTACTAAAGCTGCACCTGAAAGCCTATGAGGTATATATTTCAAGCAACCCCACACAAGTTCCCCTCCTAATGAAAATCCAACCACAAAGAACTTTCC[A/G]CCTAGCTCAAAAATATCTGCTATTTCTTCAATATCCCGTGCATTGCTTTTGACAGACCTATGAGGGTGTGGATCACTCTCTCCATACCCA
105525 A G GTATATATTTCAAGCAACCCCACACAAGTTCCCCTCCTAATGAAAATCCAACCACAAAGAACTTTCCACCTAGCTCAAAAATATCTGCTATTTCTTCAAT[A/G]TCCCGTGCATTGCTTTTGACAGACCTATGAGGGTGTGGATCACTCTCTCCATACCCAGGTCTATCAAAAGAGAGCATATAAATACCATAT
105525 C T ATATTTCAAGCAACCCCACACAAGTTCCCCTCCTAATGAAAATCCAACCACAAAGAACTTTCCACCTAGCTCAAAAATATCTGCTATTTCTTCAATATCC[C/T]GTGCATTGCTTTTGACAGACCTATGAGGGTGTGGATCACTCTCTCCATACCCAGGTCTATCAAAAGAGAGCATATAAATACCATATTCAT
105529 C A CTGGCTACTCAATTGGAAAATTTGAAAATTACATGCTTCCAAGTTGTCCCAGTAACAGGTGAATATGATTTACATATTTGTGACCAAAGC[C/A]TTAAGGGTCTTGTACATTATTACAGATTTCATACGTCGTCATCCGGAGCCTACTGTAGGGTCATCGCCCCATACGTTATCCCAAGCGCCGCTCGAGGA
105529 ATGC A CAGATTTCATACGTCGTCATCCGGAGCCTACTGTAGGGTCATCGCCCCATACGTTATCCCAAGCGCCGCTCGAGGACTGAGGAGCTTTAGGACCCTCAAT[ATGC/A]TGCTGCTGCTGCTGCATATTTGGGTGTTGTAGGTCACCAGGTCCTAATTCCTGCGGCTGCTTATTCGCCTTTGTCCTGATCCCTA
105529 C A GAGCTTTAGGACCCTCAATATGCTGCTGCTGCTGCATATTTGGGTGTTGTAGGTCACCAGGTCCTAATTCCTGCGGCTGCTTATTCGCCTTTGTCCTGAT[C/A]CCTAGTATTCTCAGCGCAAATCTTGCAAGCTCACCATATAACATACCCGAACGATCAAATAGCTGTAGAAGGGCAGACATAAACATGT
105529 T A CAAATCTTGCAAGCTCACCATATAACATACCCGAACGATCAAATAGCTGTAGAAGGGCAGACATAAACATGTGAAAAGCCTGCGTGTTCTGATCGATAAG[T/A]ACCGATATCCGTCCAAAGAAATTTACAACCCCGTGCATCACTCGAAGAAAAGATACCCAAAAGCCAGGTGGCGACGGAGGACCACC
105529 A T TACCATAAGGACCGCCCATGGCCATCCCCATTCCCATGCCAGAACCCATCCCCATGCTAGAACCCATTCCCATGCCATAACCACCACCATTATACATGCT[A/T]CCACCATACATTCCCGAGCTTCCATAAAGACCACCTCCATATCCACCTCCTCCATACATGTTATTGCTTGTACCATACATCCCACCTGCAT
105533 G T ATCAAAGCCATCATCACCAACATCTGGATCCTCATCGCTGCTACCAAGATCTCCTAAAAGAAATACATCTAAGTCCAGTTCTGCAGTTGAAGTCTTGCTT[G/T]GCAAATTTGGTACTTTTGCCTCTGGTACTGAAGGAGCTAACACACTTGGATTATCCTTCACCTCACCAATTTGATTTTGTTTCACCGATT
105533 A T GGTACTTTTGCCTCTGGTACTGAAGGAGCTAACACACTTGGATTATCCTTCACCTCACCAATTTGATTTTGTTTCACCGATTGGGTACTTAAACTTTCAT[A/T]ATACTGCTTCTCATAAGGTGATACATAATTGTTTACAAGTATGAAATATATCCGCCAAAATTTCCGCTCCTTCATATATCGTGGGCATAGC
105543 A G CAGGAGTGATGGGCACAGTCAAATGATTATGGCCCATTCCAACAAGACAGACTTTACCAGCAGACCTGGTAGCATTAAGGGCGGTCGACATTGTCTTGCT[A/G]AACCCAGCACAATCAAAGCTCACATCAACGTCTGAACCCATTGCATCTAATATCTTTACCACTTCCTCATCCACTTCCTCGATGTTGG
105543 A C CAACTACAACAATTTTAGGAGAACCAAAAGCACGCGCCGAAAGCTGTGTTACAAGTCCTATAGGACCTGCGCCTATGATGAGGACATTAGTCTCAGGTCC[A/C]ACTTTAGCACGACGGCAAGCATGGATTCCAACACTGAGCGGTTCACACATTGCTCCTTCTTCTAGACTCACATTGTCGGGAAGTTTG
105543 C T ATATCAGGGCAAAGATTGTATCTTCCACCCTTGCAGTATTTACAGTGCCCACAACTAATTCCAGGTTCCAATGCTACACGATCTCCTGGAACTAAAGACT[C/T]CACTTCGCTTCCCACCTCTTCTATTATTCCAGCACATTCATGTCCAATTACCATAGGTTCTTTCACAACGTAATGTGCACATGTCATCGTC
105545 G A GAAGCTGAATTTCCGGAGCAATATCGTCCCATTTGTCGCGCGAAGCTCAGACTGGGAACAGCAGGAAACTTCTATTCAAGACGTCAGTGAGGAAGGCGGA[G/A]GGGGAGAAGTAATCCTGGCTGATGTGAGGAAGGAGCAATCATCTAAACCAAAACAAAGAGAAACCTCTGGAAAAATGAAGTAC
105545 CA C CATCTAAACCAAAACAAAGAGAAACCTCTGGAAAAATGAAGTACTGGAACATAAACCTAGAAGAAATGATGAAATCTGGAGTCCACTTTGGCCATGGCAC[CA/C]AAAAAATGGAACCCAAAAATGGCCCCATACATAGCCTCAAGCCGTAACGGTATCCACATCATAAACCTCGCTAAAACCGCCCGTC
105545 C CA CACATCATAAACCTCGCTAAAACCGCCCGTCTCCTCTCAGAAGCCTGCGACCTACTCTTCAATGCTGCCAGTCAAGGCAAAACATTCCTAATTGTAGGTA[C/CA]AAAAACAAAGCATCCGACTTAGTAGCCTCCGCAGCAATAAGGGCTCGCTGTCACTATGTAAATACAAAATGGCTAGGGGGCATGTT
105545 A C GGGCTCGCTGTCACTATGTAAATACAAAATGGCTAGGGGGCATGTTGACAAATTGGTCCACTACAGAAACCAGGCTTCAAAGGTTCAGAGACTTGAGAGC[A/C]GATCAAAAGACGGGGAAGCTGAGCAGACTTCCTAAAAGAGAAGCTTCTATGCTGAAGAGGAAGTTGGTGACATTGCAGAAGTAT
105545 C T CACTATGTAAATACAAAATGGCTAGGGGGCATGTTGACAAATTGGTCCACTACAGAAACCAGGCTTCAAAGGTTCAGAGACTTGAGAGCAGATCAAAAGA[C/T]GGGGAAGCTGAGCAGACTTCCTAAAAGAGAAGCTTCTATGCTGAAGAGGAAGTTGGTGACATTGCAGAAGTATTTGGGTGGTGT
105545 C T GAGAAGCTTCTATGCTGAAGAGGAAGTTGGTGACATTGCAGAAGTATTTGGGTGGTGTCAAGTATATGACGAAGTTGCCTGATATCGTGATCATTGTTGA[C/T]CAGCAGGAAGAGTATACTGCTATTAGAGAGTGTGCAGTTTTGGGAATCCCAACTATTTGCTTGATCGATACCAACTGTGATCCTGA
105545 C T AGTGTGCAGTTTTGGGAATCCCAACTATTTGCTTGATCGATACCAACTGTGATCCTGAGCTTGCTGATATTTCAATTCCTGCTAACGATGATGCTATTGC[C/T]TCAATTAGGTTGATTCTGAATAAACTAGTTACTGCAATTTGTGATGGTCGTGCTAGCACTGTGAAAAGTCGTTGATTTGAAGTATTTAG
105545 A T GCTAACGATGATGCTATTGCCTCAATTAGGTTGATTCTGAATAAACTAGTTACTGCAATTTGTGATGGTCGTGCTAGCACTGTGAAAAGTCGTTGATTTG[A/T]AGTATTTAGTTTACTGTTTTTGTTTCACGAATTTCCTGCAATTTTTTTGGTGTTGTAATATGAAAATTTGGGTTAATGAAATATT
105551 C T AGTTTTCTCCAGATGCAGAAAACGGATACACGGTTATTATTCAAAAGGCTAGGAAATTTACTGCCACTGATGAAGCTTACGTCAAAAACAGCTTCAAGAT[C/T]GGTGAGCCAGGCAAGGTGGTTCTCACAATTGATAACACTTCATCAAAGAAGAAGAAACTTCTCTTTCGATACAAGGACAATACTGCA
105551 T C CGGTTATTATTCAAAAGGCTAGGAAATTTACTGCCACTGATGAAGCTTACGTCAAAAACAGCTTCAAGATCGGTGAGCCAGGCAAGGTGGTTCTCACAAT[T/C]GATAACACTTCATCAAAGAAGAAGAAACTTCTCTTTCGATACAAGGACAATACTGCAACTGAATCCACCTAAGAGTCACAAAGGGTA
105551 T C TTCAAAAGGCTAGGAAATTTACTGCCACTGATGAAGCTTACGTCAAAAACAGCTTCAAGATCGGTGAGCCAGGCAAGGTGGTTCTCACAATTGATAACAC[T/C]TCATCAAAGAAGAAGAAACTTCTCTTTCGATACAAGGACAATACTGCAACTGAATCCACCTAAGAGTCACAAAGGGTACATTACATA
105551 CT C CTCTTTCGATACAAGGACAATACTGCAACTGAATCCACCTAAGAGTCACAAAGGGTACATTACATATGAAGGAGATGTTTATTTATTTATTTTTGCAGTT[CT/C]TTTTAGTGTATCATCTGGTGGTATCTTGATCCCCTTTTGTGTTCAGTTATATTTGTTTGGTTAAAAAGAACATATTGGTTGTTGTTGATT
105557 AC A CAAGCCTCAAAGAACATGGTACATAAACGAAAAACATGATGATCACAAATTCCTTTTCAAAAACTCCCAAATCCTTCTCTCCATGTAAACCCTATCCTTA[AC/A]CCCCTCTGGGCATATGCCTCTCGTTTGGAAACAGCAGAATCTCATAGTCCTTCTCCGCCTCAATCAACCCATTAACAAGCCTGGCCGTA
105565 TA T TTTGTTCGTTTCTGTACACGCATATTTTATTCCAAACAACAAAAATATAAAATATAGCGGTAGATGCACCTACGACATAGATTAAT[TA/T]AAAAATAAACGTTCAAATTAAGTACAACAATGTGAAGCACTTGATGTCACTAGAATATAGAGAATGAAACTACGTGAAAATTGACCCCTCTTGACGTATT
105565 CT C ATAGATTAATTAAAAATAAACGTTCAAATTAAGTACAACAATGTGAAGCACTTGATGTCACTAGAATATAGAGAATGAAACTACGTGAAAATTGACCCCT[CT/C]TTGACGTATTTTTAGGATAGACGCCAACTAACACTCCATTAATCTAAGCTTGTTGACTTAATCAGACGTAAGAGCTTTGACTTCAACC
105565 G A TAGAGAATGAAACTACGTGAAAATTGACCCCTCTTGACGTATTTTTAGGATAGACGCCAACTAACACTCCATTAATCTAAGCTTGTTGACTTAATCAGAC[G/A]TAAGAGCTTTGACTTCAACCTCCTGTACCAGCATCAGCGATTCAATCTGAATTAACATATGGATTTATGTAGCCATACACTAAATTAGA
105565 T C AACCCAATCACCAGGCAATCCAATTATTCTCTTTACAAGTTTCTTTGTATGGTCACTCGGACACGAAAATATAACCACATCTCCACGGGAAAATTTGTAG[T/C]TCTCAAGGCAGAATTTTTCAACTAAGGCAACATTACCTTTTAAAAATTGGTTTTGACTATCAAAGGTAGGAACCATAGAATTGCCAACTA
105565 A C CGCTGGACTGGAGGATTGTGACGCTAGCTTCGGCGCAGGAGGACAGGAGGAGGCCGAAAGGCCACAGCTAGAGCTTCGGTGTAGTGCGACACTTGATGAT[A/C]GAAAGTTGAGAGTATGGAGCCCTTTTTCTTCCTTCCTTTCTCCTTTCTCGAGGTGCTTGAGGATGCTGAGGAGACGGCAGCGGC
105565 C CT CAGGAGGAGGCCGAAAGGCCACAGCTAGAGCTTCGGTGTAGTGCGACACTTGATGATAGAAAGTTGAGAGTATGGAGCCCTTTTTCTTCCTTCCTTTCTC[C/CT]TTTCTCGAGGTGCTTGAGGATGCTGAGGAGACGGCAGCGGCACTGGACGAGGCGGAGGCAGCTGCAGCCAGCGCAATGGTGGC
105567 GC G GCGAAATGGCAACAGACAAGCTTCCATCTCCTTCCGTACTGGGCAACATGAAAGCCAACCCTTCGTAAGCAATACCACCGGGTCCCATAAATATCGGGCG[GC/G]CCCCACCCAAAATCCGCGTCATGTATAGGCAACCTGGTCCAGCTAGTGATCCCGATATTAGGACATCTAAAAGTATGAGCTCCCCT
105571 G A TGTATTTGTCAAGGTAGAGCTTGAGCATTTTGAAGCGCTCTTCTTCTCCAGGAAGTGGGAACTCCAGGGCTTCATCTATTCGATCAGCAACTGCAGAGTC[G/A]AGGTCGCCAGGTCGGTTCGTGGCAAGAGCAAGAACAATGTCTTTTGATTGGTCGCCCGTTCGAAAGAGGAGGGCGTTCAGTGCACT
105571 C T GCTTGAGCATTTTGAAGCGCTCTTCTTCTCCAGGAAGTGGGAACTCCAGGGCTTCATCTATTCGATCAGCAACTGCAGAGTCGAGGTCGCCAGGTCGGTT[C/T]GTGGCAAGAGCAAGAACAATGTCTTTTGATTGGTCGCCCGTTCGAAAGAGGAGGGCGTTCAGTGCACTTCTTTGAGCTTCGCTCAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105571 A G CCAGGGCTTCATCTATTCGATCAGCAACTGCAGAGTCGAGGTCGCCAGGTCGGTTCGTGGCAAGAGCAAGAACAATGTCTTTTGATTGGTCGCCCGTTCG[A/G]AAGAGGAGGGCGTTCAGTGCACTTCTTTGAGCTTCGCTCATGTATGTTTTGTTGCGCTCGCACAAAAAGGCATCTGCTTCATCGATG
105571 G C CATCTATTCGATCAGCAACTGCAGAGTCGAGGTCGCCAGGTCGGTTCGTGGCAAGAGCAAGAACAATGTCTTTTGATTGGTCGCCCGTTCGAAAGAGGAG[G/C]GCGTTCAGTGCACTTCTTTGAGCTTCGCTCATGTATGTTTTGTTGCGCTCGCACAAAAAGGCATCTGCTTCATCGATGAACAAAAG
105571 T C ATCAAACAGTTGATGTATTTTAGTAACTGCCTGTGAACCTAATGGTGCAACATCTCCACCAGTCATTAGTGCATAATCCAAACCAGATTTGCGAGCAAGT[T/C]CTCTAGCAGCCATAGTTTTCCCAGTTCCAGGCGGGCCATAAAAAAGCATGTTACGGAATGGGGCCTGATGAGCTTTGGTATTGGCAG
105577 C T TGGATCTTCTAGCTCCTTACCAGAGAGGTGGAAAGATTGGACTGTTTGGTGGAGCTGGCGTTGGAAAAACTGTGCTTATCATGGAACTTATTAACAATGT[C/T]GCTAAAGCTCATGGTGGTTTCTCTGTCTTTGCTGGTGTTGGTGAGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGA
105577 T C GAGGTGGAAAGATTGGACTGTTTGGTGGAGCTGGCGTTGGAAAAACTGTGCTTATCATGGAACTTATTAACAATGTCGCTAAAGCTCATGGTGGTTTCTC[T/C]GTCTTTGCTGGTGTTGGTGAGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAG
105577 T G GACTGTTTGGTGGAGCTGGCGTTGGAAAAACTGTGCTTATCATGGAACTTATTAACAATGTCGCTAAAGCTCATGGTGGTTTCTCTGTCTTTGCTGGTGT[T/G]GGTGAGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGA
105577 A C GAGCTGGCGTTGGAAAAACTGTGCTTATCATGGAACTTATTAACAATGTCGCTAAAGCTCATGGTGGTTTCTCTGTCTTTGCTGGTGTTGGTGAGCGTAC[A/C]CGTGAAGGGAATGACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTC
105577 C T TGCTTATCATGGAACTTATTAACAATGTCGCTAAAGCTCATGGTGGTTTCTCTGTCTTTGCTGGTGTTGGTGAGCGTACACGTGAAGGGAATGACTTGTA[C/T]AGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGA
105577 G A TTATTAACAATGTCGCTAAAGCTCATGGTGGTTTCTCTGTCTTTGCTGGTGTTGGTGAGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGA[G/A]AGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCAC
105577 A G GTGGTTTCTCTGTCTTTGCTGGTGTTGGTGAGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAA[A/G]CAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTG
105577 C T AGCGTACACGTGAAGGGAATGACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTA[C/T]GGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAA
105577 T G ACTTGTACAGAGAAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCC[T/G]GGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTA
105577 A T AAATGATTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGC[A/T]CGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGATAACATCTT
105577 T A TTGAGAGTGGTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGT[T/A]GGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGATAACATCTTCCGTTT
105577 A T GTGTGATCAAGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTAC[A/T]GGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGATAACATCTTCCGTTTCACTCAGGC
105577 G C AGCTAGGAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGAC[G/C]GTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGATAACATCTTCCGTTTCACTCAGGCAAATTCTGA
105577 T A GAGACAAACAGGCCGAGAGCAAATGTGCTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGC[T/A]GAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGATAACATCTTCCGTTTCACTCAGGCAAATTCTGAAGTGTC
105577 A G CTCTTGTGTACGGTCAAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACA[A/G]GATGTGCTTCTCTTTATTGATAACATCTTCCGTTTCACTCAGGCAAATTCTGAAGTGTCTGCTTTGTTGGGACGTATTCCATC
105577 T C AAATGAACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTT[T/C]ATTGATAACATCTTCCGTTTCACTCAGGCAAATTCTGAAGTGTCTGCTTTGTTGGGACGTATTCCATC
105577 T C ACGAACCCCCTGGTGCACGTGCACGTGTTGGGCTTACAGGGTTGACGGTTGCTGAACACTTCCGTGATGCTGAAGGACAAGATGTGCTTCTCTTTATTGA[T/C]AACATCTTCCGTTTCACTCAGGCAAATTCTGAAGTGTCTGCTTTGTTGGGACGTATTCCATC
105581 G A TGCCGTTCACCTTCCCTCTATTCCAGTGGTGGCCGGTGTTGAGGACCAGGACACTGAATTTGCGTATGTAGGTTTGGAGAAAGCGAACAGGCCGGTCCAG[G/A]TGCATGGCTACGTTGGTTGATGGGTCGGACGGGTTGATGGGCTCGAGATCGCAGAGGCTGGCGGACCAGTAGTAGAGGACGGT
105585 T C AATCAAACTGCTTTGCCTGGTGATATTGTGAATGGAAATAAAGCAGGCAGTGATGCTGCTCCAAGCAACGGTAAAAAGGATATAGAGGCGCTTAAGGATA[T/C]CTTGAGTGATCTGGAGAGGAAGCTTGAAGATCTGCGGCAGTCATTGTTGAATCCTAAACCTGAACTTGCAGAGATAATGAAAGTG
105587 T C CTCTGGTGAGCGCCATCCAGTCCGCCGGAAACGGTAAATCCAACGCCGCTGCAGCCTGCACCGTCATCACCAGTCTGGTCACCGCCGATGTCAATAAGAT[T/C]ACCGTCGGCTCTCACCCGAACGCCATACAGAGCCTGCTCAGCCTGCTGCTTGTGGAAGGTTCCACTAAGAGAGAAAAGAAGGAATC
105587 G A CCTGCACCGTCATCACCAGTCTGGTCACCGCCGATGTCAATAAGATTACCGTCGGCTCTCACCCGAACGCCATACAGAGCCTGCTCAGCCTGCTGCTTGT[G/A]GAAGGTTCCACTAAGAGAGAAAAGAAGGAATCGTTAACTGCAATTTATGAGCTGTGTAAGTTTCCTGAAAACAGGAAGCGAGTGGT
105589 G A GAATTGCCCATTCTGCTCTAGCCTATGCTATGAATGATGAATTTTCTCGTGTATTACATCAGCAAATGGAGTATTTCTCTAGCAATCCAAGTGTGGATAC[G/A]CTTAATCGAGTGCGAGGAGAAGTTAGCGAGATTCATACCATCATGGTAGAAAATATAGACAAGATATTAGACAGAGGTGAACGCATT
105589 T C GCTTGTTGTGGAGGTATCACTCTTCCTTCATGCCGTTCGTGAAAAGCCTAATCTGCGTTTGTTCTTGGTCAGTGTAAAAAGAATTAGTTTGTTAGCGTGT[T/C]ATTTCCGCCCTTTTATGTATTTTCCCTTTTGCAAGTAAAACAGTAATATAGGATTCTATTCCGAAAGTAAAAAAAACTGTAAATGGGATG
105591 A G ATATGTTCTGGGTTATTCTGGAGGAGTTATGGTTCCTTTGGGATGGACAGGTGGTGTAGTTGGTCTACTTTTGGCAGCTGCTATTTCTCTTCATGCAAAC[A/G]TGCTCATTTCCCATCTTCACGAGTATGGCGGCAAAAGACATATTCGATACAGAGATCTTGCTGGTTTCATATATGGTCAAAAGATGTA
105591 T C GCTGGACAAGCATTAAAGGCCGCATATGTGGTGTATAGAAGTGACGGTGCATTAAAACTTCCTTACTGCATTCTAATTGCTGGATTTGTATGTGCACTAT[T/C]TGCTTTTGTGATTCCTAGTCTATCTGATCTAAGAATTTGGCTGGGCTTCTCGACATTCTTCAGTCTTGTGTATATTGTTATAGCATTTGC
105603 C T CATAGTCATGTGCATCGCTGGACCGTCAATACAACACAAAGAACAACAGATAACACATGCCAACATGGAAAAGAACTGCAGCATCGCAAAATGATCTGTG[C/T]CAGGCATTCACTCAGCGAGCAGGCCTGGTACTGCTTTCGAAATCCATACACAGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGG
105603 T A AGATAACACATGCCAACATGGAAAAGAACTGCAGCATCGCAAAATGATCTGTGCCAGGCATTCACTCAGCGAGCAGGCCTGGTACTGCTTTCGAAATCCA[T/A]ACACAGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGGCTCAGGAGCATCACATAACTCTACAGTTACAGCGTTGTTGAGTGGCA
105603 C T AACACATGCCAACATGGAAAAGAACTGCAGCATCGCAAAATGATCTGTGCCAGGCATTCACTCAGCGAGCAGGCCTGGTACTGCTTTCGAAATCCATACA[C/T]AGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGGCTCAGGAGCATCACATAACTCTACAGTTACAGCGTTGTTGAGTGGCAGCCT
105603 T C CCTGGTACTGCTTTCGAAATCCATACACAGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGGCTCAGGAGCATCACATAACTCTACAGTTACAGCGTTGT[T/C]GAGTGGCAGCCTAGCTACGGGGTTGATGATGAAGAACCACATCAACTCCAAATAAAAGAAACAAATTGGATCTGAAAGCACTGCA
105603 G T TACTGCTTTCGAAATCCATACACAGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGGCTCAGGAGCATCACATAACTCTACAGTTACAGCGTTGTTGAGT[G/T]GCAGCCTAGCTACGGGGTTGATGATGAAGAACCACATCAACTCCAAATAAAAGAAACAAATTGGATCTGAAAGCACTGCAAAACC
105603 G A TCCATACACAGAAGGCAGTGGGCATGGCTATCTAAGAGGAGGGCTCAGGAGCATCACATAACTCTACAGTTACAGCGTTGTTGAGTGGCAGCCTAGCTAC[G/A]GGGTTGATGATGAAGAACCACATCAACTCCAAATAAAAGAAACAAATTGGATCTGAAAGCACTGCAAAACCTAGACCAGAATCAC
105603 T C CAAATAAAAGAAACAAATTGGATCTGAAAGCACTGCAAAACCTAGACCAGAATCACTACTACAAATCTACTGTACCACAACCTCCAACGAAGAGTGGGCC[T/C]AGGAGCATCGAACGCCGGCGCCAGGAGAGTTGTGCCATAGATCTGAGAAATGAAGCATAGGCTTTGATTTAGAGGTTCGTGCTCG
105603 G A ATAAAAGAAACAAATTGGATCTGAAAGCACTGCAAAACCTAGACCAGAATCACTACTACAAATCTACTGTACCACAACCTCCAACGAAGAGTGGGCCTAG[G/A]AGCATCGAACGCCGGCGCCAGGAGAGTTGTGCCATAGATCTGAGAAATGAAGCATAGGCTTTGATTTAGAGGTTCGTGCTCGATT
105605 T C CCATGCAATTTGTATGTTAACCGCCGCCCACGTTCTCCAATTCGACGAAAAATACCTCAATATTCTATTAAGCTTCTCATTCGAGAACTGATACCTGAAA[T/C]GCTCTGTTATATATTTAAGATGCACGGCATCTAACCCAAAAGCTTCGGTTGTTTCTGCACATTCGAATGTAGCTGATGAAGCAGGAAGA
105605 TG T GTTGCCTTCTCTTCATCCACCATTCCATGTCGCGACATCTCACTTGCTTCTTTCTCTTCCTAGCCATAACCGCATGCAAGAACACCTGAATATTACCAAT[TG/T]GAACAAAGTGAAGAGCATCAAACCACTCAGAACAATGATGATACTGAACATCACTTCTAGCCAGTGACTAGTTGGTGCAAGATCATTTC
105611 A G CGTTGAACAGAAACAACCTCAGTCTCACCGCGTGCTTAGCGTTACTCAGGCGGCAGATCCTCTCATATTCCGCCACCATATTCTCCAGATCCTCATCATT[A/G]GTGACAGATATCAAAGAATCCAGGTCTTCCCCAGGGAGCTGGTACTTGGCAACGAAATTATCGGAGCCAAAGAGCGCCCGAAGCTTG
105611 G A AATTATCGGAGCCAAAGAGCGCCCGAAGCTTGGCGACGAAGGCAGGGAACCGAAACGACCGGTCAATGGCAAGGAGCTTGTTGTCGCCACCGACGTAGGC[G/A]AGGCAGTTATCCTGCTGCCGCGGCTGGATCCGGCCATTGTAGCTGACCATCAGCCTAACCCTAGCCGGCTGCGGTGGGATTTC
105619 T C GACCCCACTTGACATCTGATACATCCGAGCCTGCTCCTCTATCAACGTCTGTGAACTGCCGATAGGAAACTGCTGTCTGGCCCTTCTATCATCTTTCACA[T/C]CTATTACATCTGCAGCAATGCTTCCAGGACCAGCATTCAGATCAAGGCCTTGTCCTACTCCACCCCACCTATTTCTATCAGAACCTTCAG
105623 A G GGTTTAAAATAAAAAGTCGAGCAAGGTCACTCTACTATTTGCCAATGGAAGCACTACTATGCCAAGCGATAGGAG[A/G]CCCAACGCTCCCGCTCACCAGTTCATCGCCAATTACCATCTCCAAATCGTACCCCGTTCCTGCTCTTTCGTCTCCAACTTCCGTTAAAGTTAAAATTCAT
105633 A C CTTCCTTACCACCGCGGGGACCACGTCCACCTCGCCCGCCACGTCCTCCACGACCGCGGCCACGACCACGACCGCCCCTGCCTCGCTCGCCCGATCCAAA[A/C]CCTCCGCGAAATCCTCCACGAGGTGCAGCGTCAGCCATGTTTACTTGGAAAAAGCCAGTAGGCCAAC
105637 G A AACTCCCTGTTATAATCTTCCTCCCCAGCATAATCATAGGCGTGATAAACTGCATTGGCTGGGAGATAACGCCCATCATGATCAACTTCCCATCAACTTT[G/A]AGCAAGGCCAAGTAAGGCTCCAATGGATGGAACGCGGGCACCGTGTCAATAATGTAGTCCAAACTATCAATCGCGCTAGCCATTTGA
105637 G A TTGGCTGGGAGATAACGCCCATCATGATCAACTTCCCATCAACTTTGAGCAAGGCCAAGTAAGGCTCCAATGGATGGAACGCGGGCACCGTGTCAATAAT[G/A]TAGTCCAAACTATCAATCGCGCTAGCCATTTGAGCCTCGTCTGAGCTAACCAAATAGGCATCTGCGCCCAAATGATCCATTGCTTCC
105637 G T ACAGTCACATGGTGCCCCATTGCCTTTGCGATTTTCACTCCCATATGCCCCACACCTCCCAGTCCTAAAATTGCTCCTTTCAGGTTAGGTTCAGTTAGCT[G/T]GAAATGACGAAGCGGGCTGTATACTGTTACTCCTGCGCATAGTAATGGGGCTGCCTGCTCTGGGGCCAGACCTGCTGGGACTTTTACC
105637 T A TTGCGATTTTCACTCCCATATGCCCCACACCTCCCAGTCCTAAAATTGCTCCTTTCAGGTTAGGTTCAGTTAGCTGGAAATGACGAAGCGGGCTGTATAC[T/A]GTTACTCCTGCGCATAGTAATGGGGCTGCCTGCTCTGGGGCCAGACCTGCTGGGACTTTTACCACAAACTTTTGGTCGACGGTCATGG
105637 T C CCAAGATGGTTCTTGGTTTGATGAATATCCGTGTGGCAAACTCCACAATACAACACTTTGATCACCACATCTTCTTCTCCTGTTGTCCTTAAAGTGTAAG[T/C]GTAGGGAGAGAGAACACCAGATGCATCTTTTGCAGCCCAACCAGTCACAGTTCTTCCTGTAGAAACGCTTCCCATTTTTTTTCAACGTTC
105637 A G ACAACACTTTGATCACCACATCTTCTTCTCCTGTTGTCCTTAAAGTGTAAGTGTAGGGAGAGAGAACACCAGATGCATCTTTTGCAGCCCAACCAGTCAC[A/G]GTTCTTCCTGTAGAAACGCTTCCCATTTTTTTTCAACGTTCTCAGGATCAAGAAATGATGAGAGAAGAGGAACAGTTCGACCTTTTGCT
105641 C T GTAATAATTTAAATGAAGGAAATTCAGATGACAAAGCTGATGAAAAAAGTACCTCATGCAGTGATGCTGGTTCTAATGCGAAACTAGGCATTGACAAATC[C/T]ATCTTTATCAAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTC
105641 T C ATTTAAATGAAGGAAATTCAGATGACAAAGCTGATGAAAAAAGTACCTCATGCAGTGATGCTGGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTT[T/C]ATCAAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAG
105641 C T TAAATGAAGGAAATTCAGATGACAAAGCTGATGAAAAAAGTACCTCATGCAGTGATGCTGGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTTTAT[C/T]AAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAA
105641 G A AGCTGATGAAAAAAGTACCTCATGCAGTGATGCTGGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTTTATCAAGCCGAGAACATTTCATTTAACC[G/A]TTGTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATT
105641 T A CTGATGAAAAAAGTACCTCATGCAGTGATGCTGGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTTTATCAAGCCGAGAACATTTCATTTAACCGT[T/A]GTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGG
105641 T G TGGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTTTATCAAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGT[T/G]CTGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTCAGGCTTCAGGG
105641 C T GGTTCTAATGCGAAACTAGGCATTGACAAATCCATCTTTATCAAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGTT[C/T]TGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTCAGGCTTCAGGGA
105641 A T CCATCTTTATCAAGCCGAGAACATTTCATTTAACCGTTGTTATGCTGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAAAT[A/T]TCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTCAGGCTTCAGGGACTGGAATGCATGCGAGGTTCGCCGGCTAAA
105641 C T TGAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGT[C/T]AGGCTTCAGGGACTGGAATGCATGCGAGGTTCGCCGGCTAAAGCGCGTGTGGTATATGCTCCAGTTGAAGAAATTGGTGCAGAGG
105641 A T GAAACTGTGGAATAAAGATCGTTCTGCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTC[A/T]GGCTTCAGGGACTGGAATGCATGCGAGGTTCGCCGGCTAAAGCGCGTGTGGTATATGCTCCAGTTGAAGAAATTGGTGCAGAGGG
105641 G A GCAGCAGCTACTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTCAGGCTTCAGGGACTGGAATGCATGC[G/A]AGGTTCGCCGGCTAAAGCGCGTGTGGTATATGCTCCAGTTGAAGAAATTGGTGCAGAGGGTCGATTGTTAAATGCTTGTAAGGTT
105641 G A CTGAAGTTCTGCAGAAAATATCTTCTGAAGTTCATGAGGCATTGGACAACCGACCTGTTTCTGTCAGGCTTCAGGGACTGGAATGCATGCGAGGTTCGCC[G/A]GCTAAAGCGCGTGTGGTATATGCTCCAGTTGAAGAAATTGGTGCAGAGGGTCGATTGTTAAATGCTTGTAAGGTTATCACTGAAGC
105641 T A TGCGAGGTTCGCCGGCTAAAGCGCGTGTGGTATATGCTCCAGTTGAAGAAATTGGTGCAGAGGGTCGATTGTTAAATGCTTGTAAGGTTATCACTGAAGC[T/A]TATATTGAAGCAGGACTTGTCCTACAAAAGGATGCCCATCAAACACTGAAACTTCATGCGACAATTATAAATGCTGGACACAGGAA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105641 G C TCCTACAAAAGGATGCCCATCAAACACTGAAACTTCATGCGACAATTATAAATGCTGGACACAGGAAAAGGAGCTATAAACATAAGAAACGTGATACTTT[G/C]GATGCACGAAACATCTTCTCCAAATATGGCTCGGAGAACTGGGGAGAGTATATAATCCGAGAAGCGCATCTTTCAGAAAGATTCAA
105641 C T AGAAACGTGATACTTTGGATGCACGAAACATCTTCTCCAAATATGGCTCGGAGAACTGGGGAGAGTATATAATCCGAGAAGCGCATCTTTCAGAAAGATT[C/T]AAGTACGATGAAAATGGGTACTACCACTGTTGTGCTTCATTGCCATTCCCTGACCGCGTGCAAGTTGAATAATATC
105645 G T CTCGTCTTCAACGCCGAATGTAAAGCTTTTACATCCGATTCAGAAACAATAAATTGGATAATGAATTCCTGCATTTTGAGCTACTGCGCTCCAGAAACTT[G/T]TAGTACGCTCAACTAGATATGGAATAATTATATATGGAATGTAGAGTAATTGCGCAAAGCTCAGAACCTCAACACTGCTGTCAAATTGA
105645 A C TTTACATCCGATTCAGAAACAATAAATTGGATAATGAATTCCTGCATTTTGAGCTACTGCGCTCCAGAAACTTGTAGTACGCTCAACTAGATATGGAATA[A/C]TTATATATGGAATGTAGAGTAATTGCGCAAAGCTCAGAACCTCAACACTGCTGTCAAATTGAGGAATGGTGGTATAGTCGATATCCTT
105645 C T AGCTACTGCGCTCCAGAAACTTGTAGTACGCTCAACTAGATATGGAATAATTATATATGGAATGTAGAGTAATTGCGCAAAGCTCAGAACCTCAACACTG[C/T]TGTCAAATTGAGGAATGGTGGTATAGTCGATATCCTTTTGGGAAGGAACCGTTATCTCCTTCATTAGGAAACCAAGACTCTCCAAAA
105645 A T GAGTAATTGCGCAAAGCTCAGAACCTCAACACTGCTGTCAAATTGAGGAATGGTGGTATAGTCGATATCCTTTTGGGAAGGAACCGTTATCTCCTTCATT[A/T]GGAAACCAAGACTCTCCAAAATTTCACAAGCAATATCTTTCAAATCAGGTAAAACTGCACAAAGGACAGAGAAATAGCCAGAGAGAA
105645 G A AGGAAACCAAGACTCTCCAAAATTTCACAAGCAATATCTTTCAAATCAGGTAAAACTGCACAAAGGACAGAGAAATAGCCAGAGAGAAGAGCTTTCTCGC[G/A]GCCTTCAGCATTTCTGAATGTGTGCATACCCAACATGAAGGCATATGGAACTGATTCATCATTGTCGGGTACATAAATTTCAACAGG
105645 T A AAACTGCACAAAGGACAGAGAAATAGCCAGAGAGAAGAGCTTTCTCGCGGCCTTCAGCATTTCTGAATGTGTGCATACCCAACATGAAGGCATATGGAAC[T/A]GATTCATCATTGTCGGGTACATAAATTTCAACAGGGTTCGGTAAAGATATATTGGTTCTGATCCTTGGTACAGTAGTTGTTCTCAAG
105645 T C CTGCACAAAGGACAGAGAAATAGCCAGAGAGAAGAGCTTTCTCGCGGCCTTCAGCATTTCTGAATGTGTGCATACCCAACATGAAGGCATATGGAACTGA[T/C]TCATCATTGTCGGGTACATAAATTTCAACAGGGTTCGGTAAAGATATATTGGTTCTGATCCTTGGTACAGTAGTTGTTCTCAAGCAG
105645 A G CTGATTCATCATTGTCGGGTACATAAATTTCAACAGGGTTCGGTAAAGATATATTGGTTCTGATCCTTGGTACAGTAGTTGTTCTCAAGCAGAGCTGCTT[A/G]TCCGAAGTTTGGAATGAGCCAGATGACAGTGCCATTTGTGAAGGAGACTTCTTGCTTGACATGATCGATGCCTAGCTCCCTGGCAGT
105645 T A CAACAGGGTTCGGTAAAGATATATTGGTTCTGATCCTTGGTACAGTAGTTGTTCTCAAGCAGAGCTGCTTATCCGAAGTTTGGAATGAGCCAGATGACAG[T/A]GCCATTTGTGAAGGAGACTTCTTGCTTGACATGATCGATGCCTAGCTCCCTGGCAGTGATTATGAACTGTTTCCTTTACCTCTGAGTC
105647 A T ACTGCCTATTTGCAAGAATCCTTTTAGCCCTTTTGGGATCCAGCAGCGCCAGCTCAGCAAGCTTATCCGCCTCCATAGCTTTTTTTGTATAGTCAGACGA[A/T]ATCGAATTAGAAGGCGAAGTCTGTCCGCTTCTCAAGTGCTTATTATCACTGTTGTGCTCGTTTAGTTCATCGAAGAAAGCCGCGTCAAC
105649 C CA TTCCATAGCTATGTATACTGTCGTCTATACATTACATTTCTGGACAAAGTGCCACTAATTACCTCGAATTGTATGGTTTCCAAACTACAAACAGATGAAT[C/CA]AAAACTGCACCAACAAAAAACCAAAAAAAACTTAAAAAGAGCATTTCAAATGACTATTACAAAAATCACAAAGGACGCAAATCTAAAC
105649 C CA GTCTATACATTACATTTCTGGACAAAGTGCCACTAATTACCTCGAATTGTATGGTTTCCAAACTACAAACAGATGAATCAAAACTGCACCAACAAAAAAC[C/CA]AAAAAAAACTTAAAAAGAGCATTTCAAATGACTATTACAAAAATCACAAAGGACGCAAATCTAAACAAACATAATAATGTCTCTCTTC
105649 T G CGAATGTGAAACTTGGGCCAGAAGCAGTAGGGTTCTGCGGTTGCCCAAATGCAGGAAACGTCGGGGTTGGGGTCGGAGCTTGATTTGTTGCATCAGTCAT[T/G]GTGTCCTCCACGCTCATCTGATCGTTGTTCGGAGAGTTTGCACCAAATCCGAAAGTCGGAGTCGTAGATGATGATGAGTTGAATG
105651 A T AGATCCAGATCTTTCCATCTTCTCAGCTCCAGAGGTGGAGTTTCTCGCGGAAGACGAAATTGTAGAAATTGTCCCCAACATTAGTATGAAAGATCTCAAT[A/T]TGATATGTGGTGACTTCGGTCCTTTCATGCCACAAATTGCTACTAAGGTCCCACTTTGGCTAGCAGTAGCTTTGAAGAAGCGTGGAAA
105653 C CG TCTGGCTCTACCATCCAAAATTCTGCCAAATGTCGTGATGTGTGAGAATGTTCAGCTCTAAAAGTTGGTCCAAAAGTGTAAACATTTCCCAAGGCACAAG[C/CG]ATATGTCTCAACTTGAAGTTGACCAGACACGGTTAAAAAGGCCTGTCGGCCAAAAAAATCACGAGAATAATCCATCTTCCCATCCTT
105653 GT G TATTAAATCTTTCTTGTAGCTTGGATAAATTTTCTTTTGACTTGTTGAGCTCAGCCACTGAAGCAGTGATTGCTTCTTTTCCTGCTTTTGACACTTTAAG[GT/G]TTTTTTACTGCATTTCCTAATTCAACCACAGCTTTCTTAGCATCCTCTATTTCTGACTCTGTTGGTGCAGGATTCTCCTTCAGATCTTTTTCC
105653 G A CAGGACCAACCTCCAAAACCTTAGCAACCTTCAACTCCACGCTCTGTTTAGCCCCTTCCGGCGGCTTCTTCAAATTACCCTCCACAAATACACAAGTTCC[G/A]GTCGGAGTCAGCTGCGATAGAGGATGAACGTCTGCGTCGACAATGACCTGAAGATTCGCGAGGCACGACCCGTCATTGAGTTCGAGA
105653 T A GACCCGTCATTGAGTTCGAGAAACGCGAAAGTACCCTTGCCTTGTTCTCTGCCTGTTTTGACCCAACCACCAACAGTGACAGTCTGGTCGATAAGGTCGG[T/A]TGGGTTCGACAAGATTGATCGGATGAAGGTCCGCTTTAAAGAGGGTTCTAGATCTAGGGTTTCAGCTTCCATGATTTTAGGAGATTC
GTTAGCCATAACACATTATCATGTCTTGGTTTCAAAATACACAAATAAACCAGA
105657 G AATAACATAGAGGTAAACTGCAACATCATGCGCCTAAATTTACAAGCCACATAGACTTTTCATACATTATTAGTAATAAAACCCTCCGAGTCATTCCTTG[GCGCTGTTAGCCATAACACATTATCATGTCTTGGTTTCAAAATACACAAATAAACCAGA/G]CGCTGTTAGCCATAACACATTATCATGTCTTG
105657 A G TGTCGTGGAGGTACACGATGTCCAGAGTACAGCTCTTCGGGCTTACCGGGTACCTGTGCTCTGGTGGCGTCGATGATCGGCAGTAGATCAATATCACTCT[A/G]AATATTCGACCCTGTTGCTTTGATCTTTTTGCTTCGTAGGCTGCTTTTTGGAGTAGTAGAGTGAGATCTGCTCTTCCATAAGATGAAT
105657 T A CCAGAGTACAGCTCTTCGGGCTTACCGGGTACCTGTGCTCTGGTGGCGTCGATGATCGGCAGTAGATCAATATCACTCTAAATATTCGACCCTGTTGCTT[T/A]GATCTTTTTGCTTCGTAGGCTGCTTTTTGGAGTAGTAGAGTGAGATCTGCTCTTCCATAAGATGAATCTGATGATTTTATGGTCTGCAG
105657 T C AATATTCGACCCTGTTGCTTTGATCTTTTTGCTTCGTAGGCTGCTTTTTGGAGTAGTAGAGTGAGATCTGCTCTTCCATAAGATGAATCTGATGATTTTA[T/C]GGTCTGCAGTGCTGAAACCGCATCTCCAACATTATTACTAAACGCTCTGCGCTCCCAGATGTGATCTTTGCCAAGAGTAGAGAAAGAGA
105657 G A TTTTTGGAGTAGTAGAGTGAGATCTGCTCTTCCATAAGATGAATCTGATGATTTTATGGTCTGCAGTGCTGAAACCGCATCTCCAACATTATTACTAAAC[G/A]CTCTGCGCTCCCAGATGTGATCTTTGCCAAGAGTAGAGAAAGAGAAACGATGGTCAGAGTCAATGGTGAGTTTGGCGTGAACAAACA
105657 A G ATGATTTTATGGTCTGCAGTGCTGAAACCGCATCTCCAACATTATTACTAAACGCTCTGCGCTCCCAGATGTGATCTTTGCCAAGAGTAGAGAAAGAGAA[A/G]CGATGGTCAGAGTCAATGGTGAGTTTGGCGTGAACAAACATCATCACCGCTTGTTTAACAGATTCTAAACGAGTAACTGGTCCGCCA
105657 C T AACGATGGTCAGAGTCAATGGTGAGTTTGGCGTGAACAAACATCATCACCGCTTGTTTAACAGATTCTAAACGAGTAACTGGTCCGCCAATTTTGGGATT[C/T]GCCTTCATTTCCACTTTGGTTTCAACATCGACGTCTAGGCAGAAGAGTATGTCTTCTTTGTTGTACGGTTGCGGGTTCAGAGTGAAAA
105663 C CG ATATCATTCTGTTATAACTCTCACCCAAGCTTTTTCACACAAAAAATCGCTGAATAGTTCATTCTCTTTGTCAAAGAGAACTTCATCTTGTTCTGTCCGT[C/CG]GGGTTTTTAATCTGGTCGGCTATATAAGATGTGAAGCGGTTGGGGAAGGGCCCGGAACCAGTACAGTGTACGAAGGCGTGTACGGTC
105663 A G CTCTTTGTCAAAGAGAACTTCATCTTGTTCTGTCCGTCGGGTTTTTAATCTGGTCGGCTATATAAGATGTGAAGCGGTTGGGGAAGGGCCCGGAACCAGT[A/G]CAGTGTACGAAGGCGTGTACGGTCCCTGGTCAGTTGATTCTTCAGATATCCGCGAGGTAGTATCATATCGATCTGGACTGGTAACC
105663 C T CATCTTGTTCTGTCCGTCGGGTTTTTAATCTGGTCGGCTATATAAGATGTGAAGCGGTTGGGGAAGGGCCCGGAACCAGTACAGTGTACGAAGGCGTGTA[C/T]GGTCCCTGGTCAGTTGATTCTTCAGATATCCGCGAGGTAGTATCATATCGATCTGGACTGGTAACCGCTGCTGCATCATTTGTAATT
105663 C G TTGCTTCATCCACTGCATTCCTACCTGAAGGCAATATTTTGAAAGATGTTCTAAAACAAAACATTGACTTACTGTACATAACTGGTGCTGGTGGTCTTGG[C/G]TTATCCTTGCTCCTAATTCATATATACGTTACTCCAATTAAACGCTTCATTCAAGCACTATGGGGACTTGGCATGTTGGGGTCTATTGCT
105663 A C ACATTGACTTACTGTACATAACTGGTGCTGGTGGTCTTGGCTTATCCTTGCTCCTAATTCATATATACGTTACTCCAATTAAACGCTTCATTCAAGCACT[A/C]TGGGGACTTGGCATGTTGGGGTCTATTGCTACATATTTTGCATTTGCTCAGCCAGTTGGTGAAAGTTTGGTGCAGTATGTGGTAGATAA
105663 A G AAAGTTGGAAGCTGGTGTACTGACATTTATCATCCCTACCCTTCTCCTTGGTCATTTGTCTGGACTAATGAGTGACGGAGTAAAACTTGGTCTGTTGGGC[A/G]TTTGGATGGCTCTCTTTGTTGTATTTGCAGCAAGGAAATTCCAACAACCGATTAAGGACGATATCGGTGACAAATCTGTATTCATATT
105663 T G GACAAATCTGTATTCATATTCAATGCTTTGCCTGAAGATGAAAGAAATGCTTTAGTCGAGAAACTCAAGCAACAAAGTCGTCAAGAACTTGACTGAGATG[T/G]TGGAAACTTACCTGCTGTAAACGGAAGTAGCTGTTACTTATTAGAAGCATATAGAATCCTCAGGTGTTGTAGCAGTGAATTTTCATA
105663 C T ATGCTTTGCCTGAAGATGAAAGAAATGCTTTAGTCGAGAAACTCAAGCAACAAAGTCGTCAAGAACTTGACTGAGATGTTGGAAACTTACCTGCTGTAAA[C/T]GGAAGTAGCTGTTACTTATTAGAAGCATATAGAATCCTCAGGTGTTGTAGCAGTGAATTTTCATATCCCTAGCTTAACGTTACATCGA
105673 AC A AAAAAGGTATACAACAAGGGCTTTAAAAACCATTCATTTCGAGAAGGTAAGTCCTCCTTTTAACCAACGCCTTAACCGCATCCCTAA[AC/A]CCTCCCATCAAACGCCCCACAAACAAAGGCCTCGGCCTCCTTCCTACTACAACCCACGCCACCATCCGAAGGCCTAATCGTCACCAAAGTCGCCCCTTCC
105673 CA C TATACAACAAGGGCTTTAAAAACCATTCATTTCGAGAAGGTAAGTCCTCCTTTTAACCAACGCCTTAACCGCATCCCTAAACCTCCCATCAAACGCCCCA[CA/C]AAACAAAGGCCTCGGCCTCCTTCCTACTACAACCCACGCCACCATCCGAAGGCCTAATCGTCACCAAAGTCGCCCCTTCCATCCCCATC
105673 T C AAGTCGCCCCTTCCATCCCCATCCCATCCGACAACTCCAAATTAGGGCAGTACCTCAACTTCATATTCGAAGGAGGGACATGAGTCCTGTTCGAAGAAGC[T/C]GAAGATGCATACAGCTGATTCTCCCTAAACTCCTCCAACTGCCCTGCCCCCATCACAAGCATCCCCTGCCCATCTGCATCGGTCAGCA
105673 C T AATTAGGGCAGTACCTCAACTTCATATTCGAAGGAGGGACATGAGTCCTGTTCGAAGAAGCTGAAGATGCATACAGCTGATTCTCCCTAAACTCCTCCAA[C/T]TGCCCTGCCCCCATCACAAGCATCCCCTGCCCATCTGCATCGGTCAGCACCAGGCTTCTCAGTGTGGGATGCTCCTTGACTATCGATC
105673 C T CCCTAAACTCCTCCAACTGCCCTGCCCCCATCACAAGCATCCCCTGCCCATCTGCATCGGTCAGCACCAGGCTTCTCAGTGTGGGATGCTCCTTGACTAT[C/T]GATCTCAACAAATAATGCCTAGTGGAAGCAGCGATCAGGGAGCTAATAGTCCAAACAACCCTTAATTTCAAACCGCCGTTAGTGTAAA
105673 G A TCCCCTGCCCATCTGCATCGGTCAGCACCAGGCTTCTCAGTGTGGGATGCTCCTTGACTATCGATCTCAACAAATAATGCCTAGTGGAAGCAGCGATCAG[G/A]GAGCTAATAGTCCAAACAACCCTTAATTTCAAACCGCCGTTAGTGTAAAACGACTCTGGTATGTTCCCGTTATCCTCCAAACTCGATT
105673 G T GGACTTGGGAAGGAGAATGATGGGAGACTTGAGGGAACAAGGGCTTGTTTGCTCCGTTCGACGTGCAACGGAGGTTGTGGAACGGTTTGAGGAAGGTGAG[G/T]AGCATGAACTTCACGATGTGGGACAACAAGTTTCTAGGCTTTAGCGCTGTCGAGGTTGAGGTTTCATCTGGGTCGGGGTCGGA
105677 TA T TCAATTGTAACAAAATCATTACTCACAAGTCACCACCACAACAAAAGAATACATGCTCCCCGTCATTATTCAGATAACACTGCTCGGCTGCATATGAAAT[TA/T]ACTTGCTTGACTACTTTGTTACATAACTGATTCAAAAATGCAGTAAAAAGTAGAATATATATTCATACCACTACCCTATTTTTTGACAAT
105677 A T CAACAAAAGAATACATGCTCCCCGTCATTATTCAGATAACACTGCTCGGCTGCATATGAAATTACTTGCTTGACTACTTTGTTACATAACTGATTCAAAA[A/T]TGCAGTAAAAAGTAGAATATATATTCATACCACTACCCTATTTTTTGACAATACCAAGCTTCTGAAGAGCTAATTGAATGTCATCGACAT
105677 T A AACAAAAGAATACATGCTCCCCGTCATTATTCAGATAACACTGCTCGGCTGCATATGAAATTACTTGCTTGACTACTTTGTTACATAACTGATTCAAAAA[T/A]GCAGTAAAAAGTAGAATATATATTCATACCACTACCCTATTTTTTGACAATACCAAGCTTCTGAAGAGCTAATTGAATGTCATCGACATC
105677 AC A ATTCAGATAACACTGCTCGGCTGCATATGAAATTACTTGCTTGACTACTTTGTTACATAACTGATTCAAAAATGCAGTAAAAAGTAGAATATATATTCAT[AC/A]CCACTACCCTATTTTTTGACAATACCAAGCTTCTGAAGAGCTAATTGAATGTCATCGACATCGTATCCACCTTCAGTTTTGACATTATTT
105677 C G ATCAAATGCCACGACGTCTTCTATAGGGTAGCCTCTAGCGTGTAATTCTTTAACCGTAGTTTCACAAGCACCCTTCAGTATAACAGTTTTGTGCACCCCA[C/G]CAAGCAGTCCATCGTAGTCTGTATCACCGGTCTCGCCAACAAATACGACCATGTTTGATAGCTCTACGCCCCACCTTACGTGCAAGTAC
105677 A G CGACCATGTTTGATAGCTCTACGCCCCACCTTACGTGCAAGTACCTGAGTGCCTGTGAACGAGATGCTAATACAGGAATGACATGGAGCTTGCTACCGTC[A/G]CGGCTATAGATAACATGGCACCGCAAAGCTTGAATCCTTACCAATTTCCGAAGTTCCTTTACAGAAGGAACCAGAGTTGGATTCAGC
105689 TCAGGAAAATAAATACTATGGCTG
T ATCCTAACGCGCTCCAGAAATTGTGTCGAATCGAGAAACGAAATTTGAAACCGCGTCTTCCCCGATCTCTCGCCTCAGCGCCTTCACGTCAGTCCTCAAC[T/TCAGGAAAATAAATACTATGGCTG]CAGAGATGAAGAGGGTGGTCATTGTCGGTGGAGGAGTCGCCGGAGCTTTGCTTGCCAAATCTC
105689 AG A GACATGCAGATCCAGTTCCAAAAAACATCAAGGATAGGCTAGACGAGTTTGAACAAGACAATCATAAAATAAAGTCATCAAAATCTATATTAATCATCGG[AG/A]GGCGGTCCAACCGGTGTCGAACTAGCAGCAGAGATAGCTGTAGACTTTCCAGAAAAGAAGGTCACTCTGGTACATAAAGGTCCA
105689 G GA TGATTGGTTAACATCCAGGAAAGTTGAAGTTCTATTAAATCAGGCAGTTAGTCTTGATTCTGATTCGGAGCATTCAAGTGTTTATACCACATCACGCGGT[G/GA]AAAAAATTACAGCGGATGCTAAATTTCTCTGTGTTGGGAAAACATTAGGTTCATCATGGCTTCAGGAGACTATGTTGAAGGACTGT
105691 C T CGTGTCCCGGTCACTATATTTGCACCCGTCTCAAGTTGCTTCTTGATAAAGCTTGGCAGATATTTTGGATGGTGAGACAGATCCGCATCCATGATAACAA[C/T]AAAATTTCCAGATGCATGCTTTAGCCCATGATAGTAAGCAGTTCCCAGTCCAAGCTTCCTAGGTCTTGCTCTCAACAGGACGCGGTCT
105691 C T CAACAAAATTTCCAGATGCATGCTTTAGCCCATGATAGTAAGCAGTTCCCAGTCCAAGCTTCCTAGGTCTTGCTCTCAACAGGACGCGGTCTTCTCCATA[C/T]ACTTGTTGCAACTGCTTCACAATATCTTGAGTCCCATCCGGACTTCCATCGTCCACAATGATAACCTCAAAATCAACATTCTGAAGATGC
105691 TCTGCACTGAAA T ATTCTGAAGATGCTTGAAGAGTAGATAGATAATAAGGGCTATATTGAGACGTTCATTGTACGTAGGGATTATTATGCTGTACTTGTTTTCCTGCTCCATA[TCTGCACTGAAA/T]CTGCACTGAAACACTGAGAAGGAGCAGCTCGAGGTTGACGACGAGGACTGAGAAGCGTCGACGGCAGATTGGGTC
105691 G A GAGACGTTCATTGTACGTAGGGATTATTATGCTGTACTTGTTTTCCTGCTCCATATCTGCACTGAAACACTGAGAAGGAGCAGCTCGAGGTTGACGACGA[G/A]GACTGAGAAGCGTCGACGGCAGATTGGGTCGGAAATTGGTGTAGGCGCAGGCAACGGCAGGCCAGGTCGACGGCAGGTAGGCG
105691 TAGGCGCAGGCAACGGCAGGTGA
T TTCCTGCTCCATATCTGCACTGAAACACTGAGAAGGAGCAGCTCGAGGTTGACGACGAGGACTGAGAAGCGTCGACGGCAGATTGGGTCGGAAATTGGTG[T/TAGGCGCAGGCAACGGCAGGTGA]AGGCGCAGGCAACGGCAGGCCAGGTCGACGGCAGGTAGGCGAGATCACGCGGAAAGTAG
105693 C T TCCTGAAGATCCATCATTGCCATATATCTTTGTAAAGGAACTTGATACTGTCTAAGACTGTGCATCATCTTCTTTACCTGAAGTTCTTGAGAGATAGCTA[C/T]TGGAGGTAACAGACCTTTGAGGTAGTGAGCTTCTCTCTCTTTTTCTGTAAATGCTAGGCCTTTGTTGTGTCTCGGATCTCTTAACAAATT
105697 T A CCCCTTTCGCCCTCATTCAACATCCGCTACTGCGCCTGTTCTTTCTCCACGAAAGCATCTGTTTCCCAACAGCC[T/A]AATGCATCAATCAACGATGTAGTAGGTGACGGGCTTCCAGGGCGAGTTGGATTCTTAGGGCTTGGAATCATGGGTTCTCCAATGGCACGAAATCTTTTGA
105697 C T TCAACGATGTAGTAGGTGACGGGCTTCCAGGGCGAGTTGGATTCTTAGGGCTTGGAATCATGGGTTCTCCAATGGCACGAAATCTTTTGACAGCTGGATA[C/T]GACGTTACAGTCTGGAATCGAACCAAAAGCAAGTGTGATCATCTTGTTGATCTTGGTGCCAAGTATGAAGTTTCACCAGCAGAAGT
105697 C T AGTTGCATCTTCTTGCAATGTGACATTTGCTATGCTGGCTGATCCGAAAAGCGCTGTTGAAGTTGCATGCGGAACAAATGGAGCTGCTGAAGGGTTGAGT[C/T]CAGGAAAAGGGTATGTTGATATTTCTACTGTTGATGCTGATACATCTAAATTCATCAACGAACAAATTAAACAGACAGGGGCATCAT
105697 T C TATTTTTAACTGCTGGGGACGAGCATTTATACCATACCGTCGCACCGTTCTTAGATGTTATGGGGAAGTCGAGATTTTACCTTGGTGAAGTTGGTAACGG[T/C]GCCGCTATGAAGCTTGTCGTCAATATGATCATGGGAAGTATGATGGCATCTTTTTCGGAAGGGCTTCTGCTTAGCGAGAAGGTAGGG
105697 C T TTTACCTTGGTGAAGTTGGTAACGGTGCCGCTATGAAGCTTGTCGTCAATATGATCATGGGAAGTATGATGGCATCTTTTTCGGAAGGGCTTCTGCTTAG[C/T]GAGAAGGTAGGGTTGGACCCAAAAGTCTTGATAGAGGTCATTTCTCAAGGAGCTATAAGTGCACCAATGTTTTCTCTCAAGGGTCCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105697 G A GGTTAAATCGCAATACCCTACTGCATTTCCTCTAAAGCATCAACAGAAGGATATGAGGCTTGCGTTAGGATTAGCTGAATCAGTTTCTCAGCCTACTCCA[G/A]TTGCAGCAGCGACAAATGAGCTTTACAAGGTAGCAAAATCTTATGGCCTCAGCGACCATGATTTTTCTGCTGTGATCGAAGCTTTAAA
105703 GT G TATGGAACAGAAATCCACTGTGTGTCACAATTGCAATCTCCTTCTCTGGTCGTGTCCACAACCAGTCAATAAACTTCATTCCTCTAGCAGCAACTTCGGA[GT/G]TTTTTTTCTCTTATATCAGCTTGCCACAAAACATCTTCGTCATTTTCTATAAGAGAAAAATCAATTGCAGGAAAAAGTGGCTTATATTC
105703 A G TTGCCACAAAACATCTTCGTCATTTTCTATAAGAGAAAAATCAATTGCAGGAAAAAGTGGCTTATATTCTTGAATACTTCTTCGTTTATCGCACGGATGA[A/G]CTCCCAGGTGTTCTCGGCAAGCTTCAACTGCCATAAAAGGTGGACAGTTTAAACTAGAAATTGCATAATGGTCACTGTTCCCAGCATTT
105703 T C ACGATGCAATGGAAACATACTGGATCCTACAGCACTCATATCTGATAAAGAAGAAGATGACGCGTAATCTGCTGCGGCCGTTGCGACAGTGGTGGTTGAA[T/C]GGAAGGACGAGGGAGAACAAGGGGGGAATTTCAGATGATTTAAGTGATCAGCAGAAAGATTTCCGTTAGGAGAAGTGCTGTTAT
105703 G A GCTGCGGCCGTTGCGACAGTGGTGGTTGAATGGAAGGACGAGGGAGAACAAGGGGGGAATTTCAGATGATTTAAGTGATCAGCAGAAAGATTTCCGTTAG[G/A]AGAAGTGCTGTTATTGAAGAAGAAAAATGGGGTTATTGGATTCGTGGGAAAGGAGCCGTGGCATTTT
105709 GT G ACCAAGAAATACAACAAGAAGAAGCGTGGAAAGAATTGCATTGATATTGGAGTTCGAACGCTAATCATTGTAAAAAGTTCACAAAGCCACACAAGAGTCA[GT/G]TTACCAAAAATGCAAGAAGCTGATCATCGTAGAACTCAAACAGGAAGAACAGAATGCCAATCATTATCGGAACAAAAACTAATG
105709 T TA CAACAAGAAGAAGCGTGGAAAGAATTGCATTGATATTGGAGTTCGAACGCTAATCATTGTAAAAAGTTCACAAAGCCACACAAGAGTCAGTTACCAAAAA[T/TA]GCAAGAAGCTGATCATCGTAGAACTCAAACAGGAAGAACAGAATGCCAATCATTATCGGAACAAAAACTAATGACTCGATTACAT
105709 CA C AAAGTTCACAAAGCCACACAAGAGTCAGTTACCAAAAATGCAAGAAGCTGATCATCGTAGAACTCAAACAGGAAGAACAGAATGCCAATCATTATCGGAA[CA/C]AAAAACTAATGACTCGATTACATGAACAAAGATTAGCTGGAAAGTGGGAAGCTGGTGACGTGCATGGTGTTGTAACTGCACTGT
105727 GT G ACCTTGCTTGAAGAATTCTCCCTTGCAGATGTACGATTATCGCTAGTACCAAATATGGATGACACCCAACTTGAACCACTTGCGGACCCTGCTGACCCTG[GT/G]TCTTTCATTGTCTGCAATGGGCCGAGCAGCCTGATCAGTAGCTATCCCATTTGCAGCAGACCGCCCTAAAATAGCTCGAGATTTTGT
105727 G C AGCAGCCTGATCAGTAGCTATCCCATTTGCAGCAGACCGCCCTAAAATAGCTCGAGATTTTGTAGTTCTCTCAGAAGACTGAAGCTTATCTAAATCAATG[G/C]CATCCTTTGATTTATGCATGGCTGCTGTTAGCCTGGAAGATTTGACTTGCTGCTGTGCCAATTCAATGGCCTTGTTTCCACCAATGAAG
105737 A G ATAGTGGATCTCCTGATGATCTATTCAGGAAGGAGATAGCCAAGTATGATCACATATGTGAAGAAATTGCTCAGAATATCGAAGCTCAGGAGAACTTGCT[A/G]CTGGAGATACAAGCACAAAATGATGAATTTGCTGCTGTCTTCAACTTGGAGGACTACAAAGTGTCAAAGGGGAAATGCTACCAACA
105737 G C TGGATCTCCTGATGATCTATTCAGGAAGGAGATAGCCAAGTATGATCACATATGTGAAGAAATTGCTCAGAATATCGAAGCTCAGGAGAACTTGCTACTG[G/C]AGATACAAGCACAAAATGATGAATTTGCTGCTGTCTTCAACTTGGAGGACTACAAAGTGTCAAAGGGGAAATGCTACCAACAAATA
105737 C T CTGTAGCAAAATATAGGGAGATTAAAGATAACATCAACGAAGGTTTGAAGTTCTACGTCACTCTTCAGGATGCGATAACAAATGTAAAACAACAATGTAG[C/T]GACTTTATAATGACAAGAACTATCCAATGCCGTGAAATGATGGAAGACGTGCAACGTAAAATTTCGGGTCTGAACTTCAATACAAG
105737 G T CCCATGGGCATGATTATGGACAGCCTGCCTATCCTGGGTGGCGTGGGCAGTACTATAATGCACATCAGCCTCAGCCTGGACAGCAGCCGCCTCCTCCACC[G/T]TACAGTGTGCAGCCCCCTTATCAGTCTCAACAGAGCGGGTACTACAGGCCACCTCAATAGTTTTGTATTACTTGGTTGGTTTGTTGA
105737 T A TGCCTATCCTGGGTGGCGTGGGCAGTACTATAATGCACATCAGCCTCAGCCTGGACAGCAGCCGCCTCCTCCACCGTACAGTGTGCAGCCCCCTTATCAG[T/A]CTCAACAGAGCGGGTACTACAGGCCACCTCAATAGTTTTGTATTACTTGGTTGGTTTGTTGATATAAAATTCTTTGTTTAGATTATGT
105739 GT G GGATAAATATTCATTCAAATCATCCTCCTCTCCAGTAATTGCAAAACCGTTAATGTCATTTACGTCACCGTCATCATCATCTTCGTCGTTCAAAATGCCA[GT/G]TAACCATTGCTCTTAAACCCATCTTCATCAAAAAAAGCTCGTAAATACAACACCGAACAGCTATCCATAGAAGAGCCGCGCGAAAGCTG
105745 A G CATCGGACTCTTCCCTATCATCCGACATAGAAGAAGAAGCAAACGAAGTCGATATGGAGAGCTCTCTCATGCTCAAATCCTTTGCCATTTTCCTCCTCTT[A/G]AACCTTCTCCAAGCCGCCTGTATAAAGCAAGCAGCCCACGTTCGCCAGTGGTGGGAGTAAAACCGAAAGGTGTGCTGAAGCTTCTTG
105745 A G CATGAGGTAGTTGTCTATGTTTCATCCATTCTTCCGTATCCCTTCGCTTTAATCGCCATTCTTCTAGTCTCACGGTTATAGATTGCAAATATGTCTGCAT[A/G]TTTCCAATTAAGTGTGCAAATAGAACAAGCCCAAGAATAGCAATGAGGATGGCAAATGATGTTTCACCAATAAAAGTGCTTGTCTGCAAA
105757 A G CCTACCACATGCACATAAACCTAGAGCTTCTGGAAGCCACCCACCTCATCTGCGCAATGCTCCTAGAAGTCCCCAACATCGCGTCAACCTCCCATGACTC[A/G]AAGCGCAAGGTCATAAGCAAAACCTTCCGGCGCCACCTAGAAATAAGCGAACGTCAGACCTTCGTGGGCCCACCTGAAAATGTACGG
105757 A G TCGTGGGCCCACCTGAAAATGTACGGGACCATGTCATGTGTGCAGCCCGTGCGCTTTCCAAAGGCGATTACGTCAAATCCTCTGCCACCCTCAGGTCCCT[A/G]GACACCTGGAAGCTTCTAAGAAACCCCGACTCCGTGCTCTCCATGCTCGATTTCAAACTCAAAGAAGAAGCGCTCCGCACCTATCTC
105757 C A ATGTCATGTGTGCAGCCCGTGCGCTTTCCAAAGGCGATTACGTCAAATCCTCTGCCACCCTCAGGTCCCTAGACACCTGGAAGCTTCTAAGAAACCCCGA[C/A]TCCGTGCTCTCCATGCTCGATTTCAAACTCAAAGAAGAAGCGCTCCGCACCTATCTCTTTACATACTCATCCTGCTATGAAACTCTGAG
105757 C T CCTGGAAGCTTCTAAGAAACCCCGACTCCGTGCTCTCCATGCTCGATTTCAAACTCAAAGAAGAAGCGCTCCGCACCTATCTCTTTACATACTCATCCTG[C/T]TATGAAACTCTGAGCATTACCCAGCTCACGGCAATGTTTGACTTACCCGAGCCTCAAGTGCACAGCATCGTAAGCAAAATGATGGTTAA
105757 T G TTCAGGGCTTGCTGTTCCAGATGTCTGACAAGCTCAACATACTTGCTGAGAGCAACGAGAGGGCGGCTGAGGTGAAGACAGGTGGTGGGCTTGATGGGCT[T/G]CCGCCTAGGCGAAGAGGGGACGGTCAGGATTACATGGGTAAGTGGCAGGACAACTTTGCGAGCTCCAACCAGGGTAGGCAGG
105757 G T GGCTTGATGGGCTTCCGCCTAGGCGAAGAGGGGACGGTCAGGATTACATGGGTAAGTGGCAGGACAACTTTGCGAGCTCCAACCAGGGTAGGCAGGGTGG[G/T]ACCCGTTATGGAACGGGTAGTACCCGGATCAACTATGGTGGGACCCGAAGCGGGCAAGCGGGTAGAGGTGGGTATGCAGGT
105757 A G TCAACTATGGTGGGACCCGAAGCGGGCAAGCGGGTAGAGGTGGGTATGCAGGTTCTAGGTATCAGGATGCTTATGGGCAGAGAGCTGGTTATCAAAGTGG[A/G]TCTGCGAGAGGCGGGCAAATGGATGGTTCACGGATGGTTAGCCTGAGCAAGGGAGTCCGGATTTAGTCGAAGACAAGGAACT
105757 G A CACGGATGGTTAGCCTGAGCAAGGGAGTCCGGATTTAGTCGAAGACAAGGAACTGTTTGAAATTAAAATTTGAAGAGTAGTTTTGAGGGCTTTATCATCT[G/A]TTGTTTTGGTATCTGGTACTATTACCTTATTTTTTTGAGACCTATTTATGGATGCTCGTACTGAACTTGTTTTGTATTTTGGAAAATTA
105761 G A CACTCATAGCATCCACAGAGGCTGATGGAACTAGTGATGACATGGCCATTGTTGATTGGCTACCTGATCCTCTAGGACCCATTGAGAAGTTCCCTTTACT[G/A]TCAGTATTGCTGCTTGGGGGTATTGGTGGCAGCCCTGCTGGAGGGGATCCAATAATGCGATGAATAGACCTATCAATTGATGTGAA
105763 G A GTATCCATCCTCTAGTTTTGTTTCATCGAATCCTTCATCTCCTACGTTTAGCCTTGTATCGCCCAGTTCAGGTGCATTTGGGTTTTCAAATAGCGGAATC[G/A]TGAGTGAGGGGTCTTCGAGGATGTGCACACCAAGCCAAAGTGGGATGTGCTCTCCTAACAATGCTGGAGATGTTCGTATGAAGTCGGA
105765 A G GACAAGATTTTGGTGAAGCTTAGTAATAGTTATGACCAAATGATCGAGAAAGATGTAAAAGATGTACCTGAAATTCAAACTACTCCAATTTCCTTACCTC[A/G]AAATGCAACCAAAGTGCCACAAACTGAGTGCTCTAGAGCAACTGCAACCGCTACCACGTGTAGATCGAGAAGGCGGAGTCATAATG
105767 TA T AACATGGAAATTAGAAACATACTTCAACTTGTTATCTTGAAATGGTGAATCTGCAAATTTTCAACTCCAAGTTTCTGAAAATTACTGTTTCTCCTGGACT[TA/T]AAAGAAACGGCCAAAGGTGAACTTGCTGTATTTGGCCGGATCAACGTCAGTCACCAACTCTTCCGCAGGCTTCATCACCGTGTGACAT
105767 G A GAATGAGGTCTCCTACATTGATGACATAAGAATTTGGAGCAGGATTTATGCGAATCCATTCACCATCGGACTTCCTTTTGACATCGAGACCGCTAACATC[G/A]TCTTGTGCGAGGATTGTAATTGCTCCTTGATCTTTATGAGGGCCAACACCTAGAGCAAGATTGGGAGAAGGACAAGGAGGATAATG
105767 A G TTATGCGAATCCATTCACCATCGGACTTCCTTTTGACATCGAGACCGCTAACATCGTCTTGTGCGAGGATTGTAATTGCTCCTTGATCTTTATGAGGGCC[A/G]ACACCTAGAGCAAGATTGGGAGAAGGACAAGGAGGATAATGGTTGAATCGTATTCGACTGCTCGAGTCTTGGTTGAAGTACTTGTTT
105767 T C TTGAGATCAACTCAAGCAGCCTGAATGCTAGGACTTCTACTGCTTTTGCATATTCCATGCATGTTTCTCTCATATTCTTAGGATATTCCGGCCACCGATT[T/C]ACCACCTCCTCGATCTTGACCTCTCCCTCGTTACTCGTGACCGGAACCGTTATCGCTCCCCTCGATGTAAAATCGAAAGTCTCCTTCCAAT
105767 G A ATATTCCATGCATGTTTCTCTCATATTCTTAGGATATTCCGGCCACCGATTTACCACCTCCTCGATCTTGACCTCTCCCTCGTTACTCGTGACCGGAACC[G/A]TTATCGCTCCCCTCGATGTAAAATCGAAAGTCTCCTTCCAATCCCTAACATTCTTCGTGTTCTCCGCATCATAATACCCAAGAAAATTGTCT
105767 C T AGAACCCCCAAACTTTACATGCATCTTCTACTTCCTTTACCAGATCTACTAATTTTCTTGAATTGTTGTCTGGATCGATTAATGGTTGTAAATCGATTAC[C/T]GGTATTTGTTTTAGTTCGGGTATGTTGAGGTTTGGTTTTTGGTTTGAGATTTGGATGAATGATT
105775 T C AAAATTTCACTTATGAGCAGTTGAGTGTTATAGGGCATGAGCTTAAAGAGAAGATAAATGAATCCACGGACTTTGAAAACAGCGATTTTGAAACAATAGT[T/C]GATGAAATCAAATCAGCAAACAAGAAATATGAATCGGATTGGGTGGGAAATGACAAGTGTGAGCCATGGTGGCGTGTAACCGATC
105777 G C AGCACTTCCTCATCGGCGGATCCTCCTCCTCCGTAATTTCATCCGTCTCCGACGCCGGAATAATCCAAACTCTAACAGACTCGTCCAGCTTTGGATCTGT[G/C]TCCTCCGTTGCCGTTGACTACATCCGTCGCCGACTCATCTCCGCCGGCAGTGCATCTTCTATCATCATCTCCTCCTACGATCTACGTTCCC
105777 T C TCTATCATCATCTCCTCCTACGATCTACGTTCCCCTACTCCACACCGTCTCATTTTCTCATCCCCGATTTCAGTTGCTTCAGATTCCGCCGTTGCTGCTG[T/C]TGATGTTTCTGCCGGTACAGGTGATGCGTATATTGCTACTGCTGCAGGCGAGATATTCAAAAGTGATCTCTTTGGAAATATATCGAACTTG
105777 C T CGTCTGAGTTAAGCATGGAAAAAGTGAGAATGAGAAGGGATGGAGCAGTGGTTACAGGTGGAAAGACAGCGAGGTGGTTAAAAAGCCAGGATGGATGGGC[C/T]GAAATGGCAGTTTATGACGAGTTCAGTGTATCAGAAAGAGAGAGAATTGTTGATGTTGCCGTTAGAGATAGGAGCAGTGTTT
105777 T C TGGAAAAAGTGAGAATGAGAAGGGATGGAGCAGTGGTTACAGGTGGAAAGACAGCGAGGTGGTTAAAAAGCCAGGATGGATGGGCCGAAATGGCAGTTTA[T/C]GACGAGTTCAGTGTATCAGAAAGAGAGAGAATTGTTGATGTTGCCGTTAGAGATAGGAGCAGTGTTTATGTTTTAGTGGAGA
105777 G A GGGCCGAAATGGCAGTTTATGACGAGTTCAGTGTATCAGAAAGAGAGAGAATTGTTGATGTTGCCGTTAGAGATAGGAGCAGTGTTTATGTTTTAGTGGA[G/A]AAGGAAGAGGAAGATGGAAGCAGGAGCAGCAGGATAGAGGAGGCGGAATGGGGAAGAGAAGGGGAGGGAGAGATGGTGTG
105777 C T TCAGTGTATCAGAAAGAGAGAGAATTGTTGATGTTGCCGTTAGAGATAGGAGCAGTGTTTATGTTTTAGTGGAGAAGGAAGAGGAAGATGGAAGCAGGAG[C/T]AGCAGGATAGAGGAGGCGGAATGGGGAAGAGAAGGGGAGGGAGAGATGGTGTGGGTTTTGGTGTTGGTTGGGTTGGCCATG
105779 G A AACAGCTGTTCGAGCGGTTATTCAACGGACAGCTCAACGAGCTGGCGGCGGCCAGAGCCGACGCCTTTGCGGAAGTTCAGTAATCCGATCAGAGGTGGGA[G/A]TGGATTATCGGGTTTTTCGGTCTGCTTGAGCCCGCTTGTGAGGCCCAGTGGCACAAAATTTAACGGGGATGAGGTGCTTGGAAC
105783 C T TCTTCTTCCCCAACTCTGCCTCGGCGTGCCCATTACACTTCACTTCTTCGTTCTCTCCTTCACTCAAAGCACGTCTCCTAAGTTCCTCCACCACCTTCCT[C/T]ATCGCGAAATCCGCATCGCATCCGTCACACCCCATAAATATCTCTGCTATATCTGCCGGCGTAACCCTAACTCCCTTGATCAAATCCTCCACC
105783 G C CTTCCCCAACTCTGCCTCGGCGTGCCCATTACACTTCACTTCTTCGTTCTCTCCTTCACTCAAAGCACGTCTCCTAAGTTCCTCCACCACCTTCCTCATC[G/C]CGAAATCCGCATCGCATCCGTCACACCCCATAAATATCTCTGCTATATCTGCCGGCGTAACCCTAACTCCCTTGATCAAATCCTCCACCTCC
105783 T C CTCCTTCACTCAAAGCACGTCTCCTAAGTTCCTCCACCACCTTCCTCATCGCGAAATCCGCATCGCATCCGTCACACCCCATAAATATCTCTGCTATATC[T/C]GCCGGCGTAACCCTAACTCCCTTGATCAAATCCTCCACCTCCTTCATCCCCTCATACCCTTCCTCAACCTCCAAATAATTCTTCGCCAGAAC
105783 A G TCCGCATCGCATCCGTCACACCCCATAAATATCTCTGCTATATCTGCCGGCGTAACCCTAACTCCCTTGATCAAATCCTCCACCTCCTTCATCCCCTCAT[A/G]CCCTTCCTCAACCTCCAAATAATTCTTCGCCAGAACCTTAAACCCTTCCATCCCACAGTACCCCAGATTGATCTTTCGATCCATCCTACCTG
105783 T C TCCCCTCATACCCTTCCTCAACCTCCAAATAATTCTTCGCCAGAACCTTAAACCCTTCCATCCCACAGTACCCCAGATTGATCTTTCGATCCATCCTACC[T/C]GGCCTCAGCATAGCCGGATCCAACTTCTCCGGATGGTTCGTCGTGAATATCATCAGCCTTTCGCCTACGCACGACGACCACAACCCATCCA
105783 G A CCGGATCCAACTTCTCCGGATGGTTCGTCGTGAATATCATCAGCCTTTCGCCTACGCACGACGACCACAACCCATCCACGAAATTCAAAACCCCCGACAA[G/A]CTCACCGAACTCATAAGCGGCATCAATTGATCCTTCCTACCCGAATCCGCCTCCAAATTTGGGTTCCCGTTCTTACCAGAACTAACGCC
105783 C G CAACCCATCCACGAAATTCAAAACCCCCGACAAGCTCACCGAACTCATAAGCGGCATCAATTGATCCTTCCTACCCGAATCCGCCTCCAAATTTGGGTTC[C/G]CGTTCTTACCAGAACTAACGCCAGCGTTGCGGTCGGAGAGGTCAAGTGAGCAGTCGACGTCTTCCACCACGATGACCGATTTGGTGG
105785 TA T TTCTTGAAATGATTGATAATGGACAAGGGGTGGATGTGAAGGGAATTTCTGACAAATTACTAGCAAGACATTTGAAGAAGCTTTTCAGGTCGTTAAAACT[TA/T]AAAAGAACCGGTAGTGGAGTTTACATGTTGCCGACACATGGCCATTCTACCTTACAAATCATCAGACCAATATTGTGTGCCTGTCT
105785 C T CTTGCTCAAAGATGCTGACGTAGAAGCGGACGATGGTTTGCTTATAGGACCTCCTCCCCCATCAATGGTTGCCGAAGTAGAATCAGCAAATGAAGCCGAG[C/T]GTTTTGAAGAGGTGGCTCGAATTGCTGGTGCCGAAGCTGAAAAACCGTACGATGTTCTAGGAGTGAATTGGAAAATGTCCTCTGA
105785 A G GAAGCTGAAAAACCGTACGATGTTCTAGGAGTGAATTGGAAAATGTCCTCTGATAATATCAAGAAAAAGTATTGGAAATTGTCACTTATGGTTCATCCAG[A/G]CAAATGTTCTCATCCACAAGCACATCAAGCATTTGTAAAACTGAATCAAGCTTTCAAGGACCTGAAAGATTCAACCAAGAGAAATGC
105785 T C TTGGAAATTGTCACTTATGGTTCATCCAGACAAATGTTCTCATCCACAAGCACATCAAGCATTTGTAAAACTGAATCAAGCTTTCAAGGACCTGAAAGAT[T/C]CAACCAAGAGAAATGCAATTGATGAGAAAATCAGACTCAAAGAAGAACAAGAAGCATTCAAGATTGAGCTGAAAGAGCTTCGTGAAG
105785 A C ATTGAGCTGAAAGAGCTTCGTGAAGCTGCAAAATGGAGGAAATCTCAAGGTATATCAATGGAAGGCGATGAGGAACTTCTTGCTGTCGCTGATGAGGTCA[A/C]AAAAGAAGCACCAAACAAGAGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGA
105785 CA C GAGCTTCGTGAAGCTGCAAAATGGAGGAAATCTCAAGGTATATCAATGGAAGGCGATGAGGAACTTCTTGCTGTCGCTGATGAGGTCAAAAAAGAAGCAC[CA/C]AAACAAGAGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGAACATTCAGCAAA
105785 A G GCTTCGTGAAGCTGCAAAATGGAGGAAATCTCAAGGTATATCAATGGAAGGCGATGAGGAACTTCTTGCTGTCGCTGATGAGGTCAAAAAAGAAGCACCA[A/G]ACAAGAGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGAACATTCAGCAAAACC
105785 A G GGTCAAAAAAGAAGCACCAAACAAGAGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGAACATTCAGCAA[A/G]ACCACCAAGGAAGGGCGTGGTGACGCTAGCGCGTGGACTGATACACCACTTGATAATGCCCAAAAAGCAAAACAGAATTATTTG
105785 G T CACCAAACAAGAGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGAACATTCAGCAAAACCACCAAGGAAG[G/T]GCGTGGTGACGCTAGCGCGTGGACTGATACACCACTTGATAATGCCCAAAAAGCAAAACAGAATTATTTGGAGGCATACAACAA
105785 G A AGATGAATGGATGACCACTCTACCCCCTGAGAAGAAGGCTGGTGGAGTGAGCATGCAGTCAAGAACATTCAGCAAAACCACCAAGGAAGGGCGTGGTGAC[G/A]CTAGCGCGTGGACTGATACACCACTTGATAATGCCCAAAAAGCAAAACAGAATTATTTGGAGGCATACAACAAAACAAAAGCAA
105791 G A TTTCTTGTAATAAGTCTGCCTTGTACAATTGAAGTCGCTCTTTTGCTCCATCCAATGATAGTAGATGTTCCGTTCTCTTTGGATCAGCAGGGTCCCTGAC[G/A]GATGCTCTAACAGTATAACCTCGATGAAGCAGAAGCTTAACGAGCCATGAAGCGACGAAGCCTGATGCTCCAGTCACGCACACCGTCT
105793 T G GCCGTGCGACAACTTCAGATCTCCTCTCATACATTTCTTCAGGCACTTCATCGGTATGATAAAGAGTCTTGTGAATATCCATGGCATAATCAACCATATT[T/G]GTTTTGCTTAATAATTGAATCTTGGCCTTCAAGATGTCGTCATCTTTGTAGAAGCCACGCTCTTGAAGGAACTCGAGCAAGGGGAAGAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105797 G GGGGTACATA TGCTCCGCCTGTGAGCTGCTGCGTTGCGATGGTACAGTTGGGCCTGGTGGAAGCCCCGATGAGAATGGAGAAACCACATTAGATGCTTTAGTAATGGATG[G/GGGGTACATA]GACAACCATGGAGGTTGGTGCTGTGGCAGCCATGAGATACGTAAAGGATGCCATTAAAGCTGCAAAGTTGGTTAT
105797 T G CGGTTGGGACCTCTACTAATGGCGCCACGTTCAAAATTCCTGGTAGAGTGGGGGATGGGCCGATAGCTGGATCTTCGTCCTATGCAGACGACGAAGTTGG[T/G]GCATGTGGTGCTACAGGAGATGGCGATATCATGATGCGCTTTCTTCCATGCTATCAAGTTGTGGAGAGCATGAGGCAAGGGATG
105799 T A GCAGCATTAGCATGTTACAATATAAAACAGCTTCAGGATGATACAATCTGTATTTATTGTGATTCAATTTGTTACCTTGAACTTACGGATACCTTTCGGC[T/A]TTATTGTAAGCAACGTAGATACCCGACTAGTATAAAACTGCATCAAGATCATGCAAAGGACTTATTGAACCTATTCAGCCGAGATAAGC
105799 G A TACAATATAAAACAGCTTCAGGATGATACAATCTGTATTTATTGTGATTCAATTTGTTACCTTGAACTTACGGATACCTTTCGGCTTTATTGTAAGCAAC[G/A]TAGATACCCGACTAGTATAAAACTGCATCAAGATCATGCAAAGGACTTATTGAACCTATTCAGCCGAGATAAGCATCTATAGTTTGGAA
105799 T G CGGATACCTTTCGGCTTTATTGTAAGCAACGTAGATACCCGACTAGTATAAAACTGCATCAAGATCATGCAAAGGACTTATTGAACCTATTCAGCCGAGA[T/G]AAGCATCTATAGTTTGGAAGAGGGCTTTGAACCACGACTTGCTATAAATTTCTGCATTGCTGTAAATTGCTCGGGCGTCATCTCTTCA
105799 G C GGACTTATTGAACCTATTCAGCCGAGATAAGCATCTATAGTTTGGAAGAGGGCTTTGAACCACGACTTGCTATAAATTTCTGCATTGCTGTAAATTGCTC[G/C]GGCGTCATCTCTTCATAAAAGCTATGACCTCTTTCCTTCTCAAGGGCAAGGGCATGTTTGAGGTCCAATTTGAACCCGTCATTGATAAC
105799 A G TTGAACCACGACTTGCTATAAATTTCTGCATTGCTGTAAATTGCTCGGGCGTCATCTCTTCATAAAAGCTATGACCTCTTTCCTTCTCAAGGGCAAGGGC[A/G]TGTTTGAGGTCCAATTTGAACCCGTCATTGATAACGGACTTGTACTTAAGCACCATATCCTTGTTATTTCGACAAATAAGTTGTGCAATC
105799 T C CTTCTCAAGGGCAAGGGCATGTTTGAGGTCCAATTTGAACCCGTCATTGATAACGGACTTGTACTTAAGCACCATATCCTTGTTATTTCGACAAATAAGT[T/C]GTGCAATCTCCTTAGCTTTCTTCAGAACATCCTCATTTTCAACGACATGGTTCACTAGTCCCCATTTCTCTGCCATGTCTGCGGTTATGG
105799 T C CATCCTCATTTTCAACGACATGGTTCACTAGTCCCCATTTCTCTGCCATGTCTGCGGTTATGGGCATGCCTGTGTATGATACTTCACGTGCTCTGTTTGG[T/C]CCAATAACTCGTGATAGTTTTTGCGAAAGTCCCCATGATGGAAATATCCCGAATTTGGAATGACTATCAATGAACTTGGCATCCTTGCCA
105799 T C CAGCAACCAAGAAATCACAAGCCAACGCGATTTCGAATCCAGCAGTGACCGCGAACCCGTTAATAGCGCCAATGACCGGTTTCCTGCACCTCTCCAGCTG[T/C]ACAACCGGATCCGTATCCTCGTTCTTGACGTCACCTTTGAACACGTCCTTTGCCGCCGTCAAGTCGACGCCGGAACAGAACGCTCTT
105799 A T CAACCGGATCCGTATCCTCGTTCTTGACGTCACCTTTGAACACGTCCTTTGCCGCCGTCAAGTCGACGCCGGAACAGAACGCTCTTCCTTTTCCAGTAAT[A/T]ATTATGACAGTGACGCACGGGTCGTCGTTTAGAGATCTGATGGCATTTGCAAGGGAGGAGATCATGGATTTGGTTAGTGAGTTGAGG
105799 G A TAATAATTATGACAGTGACGCACGGGTCGTCGTTTAGAGATCTGATGGCATTTGCAAGGGAGGAGATCATGGATTTGGTTAGTGAGTTGAGGGATTTGGG[G/A]CGGTTTATTGTGATGTACCCGATAGAGGACTCGATCTGGGTTTGGATTAAAGGTTCCATTGACGTTGACTGGTTTGGGTACGGAA
105799 G T CATGGATTTGGTTAGTGAGTTGAGGGATTTGGGGCGGTTTATTGTGATGTACCCGATAGAGGACTCGATCTGGGTTTGGATTAAAGGTTCCATTGACGTT[G/T]ACTGGTTTGGGTACGGAAACTTGTTCCGATGTGTTACTTTGATTCAGAGGAGGAAGAAGCAGC
105801 G A CCATGGTCCAATGTTTCGGATGCGGGTTCCCTTCTTTATCGGGTTGGATTCACAGACGATCTGCCTGAAATTCCTGACTGGATTTCGGATTCCGGTAAGG[G/A]CTTTCTGAGCAAGTGTTTGGTGAAGGACGCTGCCAATAGGTCTGCCGTTGGCGAGTTGTTGATGCATCCTTTCTTAACGGACGCAGA
105801 T C TTCTTTATCGGGTTGGATTCACAGACGATCTGCCTGAAATTCCTGACTGGATTTCGGATTCCGGTAAGGGCTTTCTGAGCAAGTGTTTGGTGAAGGACGC[T/C]GCCAATAGGTCTGCCGTTGGCGAGTTGTTGATGCATCCTTTCTTAACGGACGCAGATTTGGAAATCCAGTACAAGCGGGTTACGCCG
105803 T C GTACCCAGCCGAAGCGGGGAGAGTAGTTGTCAGGCCTGTTGGAGCAGGGCCAGCTGTGGTAGTGCTTGTTTTGGTAGTCGTTGTCTTGGTGGTTGTAGTC[T/C]TTGTCGTTGTGGTCTTTGTCGTTGTGCCTCCACCAGAGCCGCCAGTAGTGGTTTGTCCAGAGCTAGGCGGCAGGCACTGATAATA
105803 A G ACCACTCGTTAATTACGACGCAAACGAGTCCAGAGTCACAGGTTCCGGTGATGCCGTCAATTCCACCACACTGGTAATAGATGGGGATGGCCAAGGCCGC[A/G]GGAAGAGAAACAAGAGCGAGGAGCGCAGAAGTGAGCTTCATGTTTACAGTGAGTTGAAGGCAACTTGTCTGATCCAGTAGGCCA
105803 A G TACGACGCAAACGAGTCCAGAGTCACAGGTTCCGGTGATGCCGTCAATTCCACCACACTGGTAATAGATGGGGATGGCCAAGGCCGCAGGAAGAGAAACA[A/G]GAGCGAGGAGCGCAGAAGTGAGCTTCATGTTTACAGTGAGTTGAAGGCAACTTGTCTGATCCAGTAGGCCAACA
105807 C T GAGTTACTGTTCTGGTGGATGAAACAATACGAGTCGCGATTCACGGAGGCGAGGTGGGGACGTTGTAGTGGATCCGGGTTTGGAGTTCGTGCGAAGAGAA[C/T]GGAGTAGAGGCTAGAATGTCGGCAACAGTGAGAAATTCGAGGCATAGTTTGTTTCAGGAAAATGTGGTACTGTGTGTTTAGGA
105807 A G GTCTCATTCCTGAAAGAAGAAGATGATTAACCGAAAAGAAACAGTGATCGTAGGGGGTATTGATGGGTGTATGGTGCGGTGTCTGTTGTAGGAGATTAGT[A/G]AAGGTTTAATACGTGGATTTTAAAGAAGTAGAAAGAAATAGAAACCATTAAGAATGAATTGGTTCGGCAATTTGGTACTTTGTGA
105809 C T CCATCCCCAAGTATATACATTGCCACCAGAAACTGCTGCTGTATGCTTCCAGCCACAAGATACCTCAGATACTGGAAATTTAAACAAGGAACTCTTGATA[C/T]TTTCAGGAGCTTGAACCATGTCAACGGAACCAAGACCCAGACAGCCATTTTCATTAGAACCCCATGTGCATATGCTCCCATCACTTGCT
105809 A T AAGATACCTCAGATACTGGAAATTTAAACAAGGAACTCTTGATACTTTCAGGAGCTTGAACCATGTCAACGGAACCAAGACCCAGACAGCCATTTTCATT[A/T]GAACCCCATGTGCATATGCTCCCATCACTTGCTATTACGCAGGTGTGATAGCCGCCACAAGCAACATTCCTAGAATATGGAATCTCTT
105809 A G TGAATGTAACATTCCGGCAGCAACTTTCTCAACCTTAATCCCTTCAAAAAATTTGATTAGCCTTGGAGTATATTCACTTGAGCTCAATGAGAAGCCTAAG[A/G]CACTAGACTGATGTCCATGACCAAGCCTACCAGAGTCGCCTGCTCCCCAACTCAAAACACTGCCTTCATCTGTTAGGGCAACTGAGTG
105809 AG A CCCAACTCAAAACACTGCCTTCATCTGTTAGGGCAACTGAGTGTTCTGCACCAAGTGCTACCATTTTAACATTCATGCCTGCCAAGGACTCAATCTTGGT[AG/A]GGGGTAGATACTGTACTCTTTGACTTTTTGCCAAGACCAAGCTGCCCACTCGAATTTTTCCCCCAAACATAAAGCTCTCCATCATCCGT
105815 A G TGCAGCAATGCTACTAAAAGTGAGGAACGGTCCTCCACCTCTGGTTGTTGCCCTGAAACCACTCATAGAGAAAGATGGGAGTTCCATCATGAACTCCTCC[A/G]TGCGCATCGTCTCCATGGAAAGCATCAAAGTTGAAGCGGATGTTGTTCACCATTCTTATGCAACGGAAGCCGTCCCCCAAGTCGTTG
105815 C T TTTGGCTAATGTCATTGATCTTCCTTATGGTACGGAAGCCATCTCCAAGATCCTTACTTTCACTCCAAAGGACTGACGCATCAGGGAAGCTAGGATCATA[C/T]GGAACTAACCGAACTTGCTCATGTGGTCCACAAGGATGTTGTATAGCTTGCCCGGTAGCTTTGTTTACAAGAGCAAAGCTTGGAAACC
105819 C T CAAGCATCTGAAATGCATTGACATTGCTTTTGATGCCAAAGTTGAATATACGTTTGCAGAGTTATCTCCTGCTGTTGCTTCGAAGCCAGATACTACCAAT[C/T]TCATTTGTTCGCAATACCTTCTGTATCTTCTGTGTACCTCTTCTAGCATGGACTGAAGTTTTGCCTTTCTACTATGAAGTTCAACAAGATC
105819 G A TTGCTTTTGATGCCAAAGTTGAATATACGTTTGCAGAGTTATCTCCTGCTGTTGCTTCGAAGCCAGATACTACCAATCTCATTTGTTCGCAATACCTTCT[G/A]TATCTTCTGTGTACCTCTTCTAGCATGGACTGAAGTTTTGCCTTTCTACTATGAAGTTCAACAAGATCCAAAGAATAGAGGGACGAAGAA
105821 A G TCGCTGCTAAATTAGACCTTTCGGATTCAGATTCAGCTTCAGGTTCTTGATTCTGTAACCCTTCAATAATAATTTTACTCAATTCCTCGGATGGTCGAAA[A/G]CCACAGCAAAGAAGATCTAAAAGAAGACTGAGAGCAAAAACCGAGTTGCGATCATGCTTCAAAACATCAGTGCAAATTTCAAAGATTC
105821 A G TTCCTCGGATGGTCGAAAACCACAGCAAAGAAGATCTAAAAGAAGACTGAGAGCAAAAACCGAGTTGCGATCATGCTTCAAAACATCAGTGCAAATTTCA[A/G]AGATTCGACTATCGGCTAGCATAAGGTTGGTTTGGTTTTGGTACAAGCCTCGTAGGTATCTCCAAGGGCTTTCGTTCGATGGATTT
105821 A G TGAAGCTGATTTCTGATTCTCGCATTGCTTCGAGACCTCCTAGAAGTGGAGATTTTGTGATTACGAAGTACCTCTGATTCCAGGCTGAGTTGTTAAATAT[A/G]TCGTCTTTGAGAAGCTTGTCACAGTAGCCAAGCTCGTCTTCCCATCCACCCAACGCTTGAAGAACCCACTGTCTATGTGACCAAGCATG
105821 A G CATGATAGTTTTTTGCATCAAGAGAAAGCACTTTCATGGTAAATTCTAACTCATGCTTCACTGCTTTTTGTCCTATTTTCTCAGCTAGCCATCTTCTGTG[A/G]TGCCAAATCTGATAATTTTTGGAGTTTTTTGTGGCAACATCATCAATAAAATCCCTCTCAGAATATAAATCAGCCTCCAATGCCTCCAATAC
105821 C T TTTAAAAGAATAGTTTCGGCAGTAAGACTCAGAGATCTAGGGCTTCTTTCGTCCGCAAAATAAACGGCGCGGAAGTAATCCATCGTTTCTCGAAACTCCG[C/T]TCGATAAGCGATGGCCACCACAGGATTTGGACCGTCATTCTGAGGGATTGGTGTAACGTCCGACCACTCCGGTCGTCGGCTTATCGG
105839 A T ATAGTCGTACAGAGTTCTGATTTGCTGGGAATACTGCTGAACAAGAACATCAGCGTATTGTTCAGGTGTGTACTGTTGACTAGTTGAGTAAATGTTTGGC[A/T]TGAAATAATTGTTCAAGTAGTCATTGCTTCCCATGCCAACAGAAAATATACACTTGCTTAGATAGTTGGCGGTTGTGTCTTCATCTCCT
105839 G A TGATTCTGGATCCCAGTTGCTGTCCAGTTTCCTCTCTAATTCCTGCTGCCGCAGAAGCAAAATTAACACCGGTAAGGAGTTGATTCTCGTTCGCGTTTGC[G/A]TATGGCGGGATGAAATTCTCGAACCCCAGAAGTTTCGAAATAACATCAACGGTTGTCATGCCATTGCTGAACCTCCCAGTCGGGCCAT
105843 T C TTCGGCAGTTCTTTAGTCAAGTTAGCAACAGCTATACTTTTTTCATGGAGAAGGAGATTGAAGACTTGTGCAGATCATGTGGTCTAATTAATTATACCAG[T/C]AAGGTTGAAAAGGCCTTCATAATGTTCTCTGCTCAGAAGCCATGATAGCCAGATGATTTTTCTTATAGATTATACATAGACCACACATT
105845 T C TACAGATTTAAGGCCGACGGCCAATTGCCTTCCCACACATAAGTGCATTATCAGGCATAGCATACTCATTAGAAAAGCTTTGTTCAGAAGTCCAAACCCT[T/C]ATGTAAAACTGTTGGCCAAGGTATTGCCTTGCCCACATTGCTGATCTTACATTCCACATTCCCTGGTTATCTAGTGATACCAGTATGGC
105845 A G AGTCATGAAGTCCGAATTTAAGAACAGGGGTTCCCAGAACATAGGTGTTAACCATCGAATCCGTAGCTGGTAAGCTATCGTAAGTAAAAACTCCGTTGAT[A/G]TTCAAACTGTCAGCTAGTTTTAATGGTGTATCGGGCACAACATAAGATACGCCATTAACAGCATAACGTGGTTTGTTATCGATAACT
105845 G A GAGAGTTCGAATTACTGTAATGGAGGATAGAGGTTGCAGTTAACTGTTTTCTTTGGAAGCGAGAAGTTGCAATAATGTAGTAATCTTTCGGGGTTTGATC[G/A]AAGGTGACTAGTACAGACATGGACTGCCCAACGTGAAGGTCGAGTGAGTCGTAAACGTTTTGAATTGTGTGTGAACCCTCGACTTC
105845 A G GGTTGCAGTTAACTGTTTTCTTTGGAAGCGAGAAGTTGCAATAATGTAGTAATCTTTCGGGGTTTGATCGAAGGTGACTAGTACAGACATGGACTGCCCA[A/G]CGTGAAGGTCGAGTGAGTCGTAAACGTTTTGAATTGTGTGTGAACCCTCGACTTCCACGAGTTTTAGAAGGTGGTTCTGGATTCTG
105847 C CAAGTA GCCCTAGAGAAATCTTCCAGATTTTATCTGAAAAATCATGGATTTGGGAGAAAATTTAGCTTCTATAAACAAATTTGGGAATAAAAGTGCCAACAGATGA[C/CAAGTA]AAGATACGCAATTTGCAAAATCCTTCCGCAGGAAAGACAAATTTTGATAAACGCAAATTGATGTTTATAACAACAAATGAGA
105849 G A AGAGAAAATCATAGAACTCACCATACGAGAAAATCCAAGAGTAGATGTCGTGCCTATTTTGCTACGAACAGTCTCTTGCGGTGGAGACGGCCAGGGAGAT[G/A]CAAGCAAATTGGGAGGAGAGAAAAATAGCAGCTTTGATTTTTAGATCTAAGACAAGAACGATGGGATTGCGTGGAAGGTCACCT
105849 A G ATGCAAGCAAATTGGGAGGAGAGAAAAATAGCAGCTTTGATTTTTAGATCTAAGACAAGAACGATGGGATTGCGTGGAAGGTCACCTCCATTGAAAAGGA[A/G]GGAAGAAAGCTGGGGTAAAACGCGGTTGCGAAGTGAGGAATAAAAGTGAAGAGACAAAGAGATGAAGGAGAAAAGATCGGC
105857 A G TTTCACCACCGGCCTTCAGCTCAGAGTTACGATAACCACACAATTCACAAGAGCTTGCCATTATAATAACTTCTCGAAAATATGGGATTCTCGTTGCATA[A/G]AAGCGGGTTTCACATGCAGCTCCACATGCCCCACATGTAGAAGGAAGAGTGTCAACCTCTTCTGGAGCTGCATATCTATAAAGTTTAG
105857 T C CGGGTTTCACATGCAGCTCCACATGCCCCACATGTAGAAGGAAGAGTGTCAACCTCTTCTGGAGCTGCATATCTATAAAGTTTAGAAACATCATCAGTGT[T/C]GGACTGAGCAATCGACCGGTAAGCTGAGACAGCTCCAACTGAACCATGTGGAACATTTGGAGAAGATGAATCAACTTCTGGGACTG
105857 G A GGGTTTCACATGCAGCTCCACATGCCCCACATGTAGAAGGAAGAGTGTCAACCTCTTCTGGAGCTGCATATCTATAAAGTTTAGAAACATCATCAGTGTT[G/A]GACTGAGCAATCGACCGGTAAGCTGAGACAGCTCCAACTGAACCATGTGGAACATTTGGAGAAGATGAATCAACTTCTGGGACTGA
105857 C G CAGCTCCACATGCCCCACATGTAGAAGGAAGAGTGTCAACCTCTTCTGGAGCTGCATATCTATAAAGTTTAGAAACATCATCAGTGTTGGACTGAGCAAT[C/G]GACCGGTAAGCTGAGACAGCTCCAACTGAACCATGTGGAACATTTGGAGAAGATGAATCAACTTCTGGGACTGAGGTGGGAATAG
105857 A G ATCTATAAAGTTTAGAAACATCATCAGTGTTGGACTGAGCAATCGACCGGTAAGCTGAGACAGCTCCAACTGAACCATGTGGAACATTTGGAGAAGATGA[A/G]TCAACTTCTGGGACTGAGGTGGGAATAGTAAGATAGCCTAACTCAATTTGCTGTTGCTGTGTCCTTTCATAAAATCGAACAGATAA
105857 G C GTTGGACTGAGCAATCGACCGGTAAGCTGAGACAGCTCCAACTGAACCATGTGGAACATTTGGAGAAGATGAATCAACTTCTGGGACTGAGGTGGGAATA[G/C]TAAGATAGCCTAACTCAATTTGCTGTTGCTGTGTCCTTTCATAAAATCGAACAGATAACAATGGATCGGAAGATGGGGCCAATGG
105857 A G AACCATGTGGAACATTTGGAGAAGATGAATCAACTTCTGGGACTGAGGTGGGAATAGTAAGATAGCCTAACTCAATTTGCTGTTGCTGTGTCCTTTCATA[A/G]AATCGAACAGATAACAATGGATCGGAAGATGGGGCCAATGGGTTCTCAATGTAGCTATTTCCAGCTGGATCATCAAGTATGAAAGT
105859 CA C TTGGCCTACTGGTCTCACTATGTTCTTGGATGGAGTTTTGTCGTGAACGGAACTAATGCGCCGTTGCTCAACTATGCGTTGCTTCCTTCTGTTCCCGTTA[CA/C]AAAAACTAAAGGTAGGTCGAAGGCTTTCGCGATATGGTTCCCGATTGGGTCAGTCATCTTCATATCAATAGTTGTTATATCCATATTA
105859 CT C CCACAGACAACGCATGTGGTCGGGACTATGGGCTATCTCGCACCTGAACTTGTAAGGATTGGAAAGGCGACTACTGCGACTGACGTGTACGCTTTTGGAG[CT/C]TTTTTTGTTGGAGGTTGCTTGTGGAAGAAGGCCGGTTGATCTCGGTGTGGGCGTAGAAGAACATATGCTGGTGAGCTGGGTGCT
105859 G A ATCTCGCACCTGAACTTGTAAGGATTGGAAAGGCGACTACTGCGACTGACGTGTACGCTTTTGGAGCTTTTTTGTTGGAGGTTGCTTGTGGAAGAAGGCC[G/A]GTTGATCTCGGTGTGGGCGTAGAAGAACATATGCTGGTGAGCTGGGTGCTCAAGTGTTGGCAGAGAGGGGCAATTTTGGAAGCG
105863 G T TCGTTTTGATGAGGCCACAACCCACTAAGCCAGCAACTACACCGGAGTTGGGCCCGGCCCATGCGGATAGGATGAATAGGGCGACTTTGCCATAGTTGTA[G/T]GCCATATTCATGTCAGTAAGCCCTGCCCCATATGCATTGCAAAACGCTAATACTGGTGCGAAAATGTAAGAGACTACCACGTAGTA
105869 T C GGAAAATGGCTCCTTGTGGGACCTCCTTCATGGTCCATCAAGGAAAGTGATGCTTGATTGGGACACACGCCTAAAGATAGCAGTAGGTGCTGCACAAGGG[T/C]TAGCATACCTTCATCATGACTGCAATCCTCGTATAATTCATAGAGACATAAAGTCCTCGAACATTCTTCTTGATGGGGACTTTGAAC
105875 TG T TGGATTTCACAAAATTCAGATCACCAGGGACGATACTACGTTCGATGCTTATGTAGTTGGCAAAGAAAATGCACCAGGTATAGTAGTACTCCAAGAGTGG[TG/T]GGGGAGTTGATTTTGAAGTTAAGAACCATGCAAAGAAAATTGCAAATCTCGGTTCAGGTTATAGAGCTTTAATTCCAGATTTGTAT
105875 T C CAGGTATAGTAGTACTCCAAGAGTGGTGGGGAGTTGATTTTGAAGTTAAGAACCATGCAAAGAAAATTGCAAATCTCGGTTCAGGTTATAGAGCTTTAAT[T/C]CCAGATTTGTATCGAGGAAAAGTTGGTTTGGATGTTGCTGAGGCTCAGCATTTGATGGAAGGACTCGATTGGCAAGGTGCTGTGA
105875 G A AGAAACTGAAGTCTTCAGGGGTTCCGCATGAGGTTCACATATATCCTGGAATTGGGCATGCTTTCATGAACGTGTCTGAACAAGGTCTCAAAAGGCGCAA[G/A]GATATGGGAATGCAAGATGAGGATTTTTCTTCTGTCGAATTGGCTTGGTCACGCTTCGAAGCCTGGATGGCTAAATACCTATCTGC
105879 A G TTGCCGCGAGCGTGAGCATATAAAGCCATCCTTTTTCTGATAGGAGCTTGTCCGCAATAGGAAGTATGCGATCGATTACTTTTCGACCATTCTCGCCACC[A/G]GCCCATGATGAAGTTATTCCTTCTTGACCAACTTCGCCATCTGGGGTTGGCACGTATGGTGGATTCACCACTATAACATCAACCAAGC
105889 C T TTTTTCTTTGATGCTGCTATCCAAGGTATATAAAAATTTCAAGGGCTCAGATTGTTGATCGCATGCTCTTTGAACTGCTATACCAAGAT[C/T]AACCGCTCCTTTTCCACCATGGGCATGATGGCTGCAAACAACTGCATCAAAAGCACCAGCTGCTAAAGCAGCACTCTTCACAGCACTCATTTCAGCATCC
105889 T C CTTCCACCAAAGCAACATTTTCAGACACATAAGCATGGTCCAAAGGCCTTCCAGCCACAACCTCTGGGCCTCCACCATGCATCTTAAGAGCCCTTATAGT[T/C]GCCACAATAATCGCACATTGAGGCTTCAAACCACTGTACCTACATTTAATATTCATAAATTTCTCTGTTCCGATATCTGCACCGAAACCT
105889 T C GCATCTTAAGAGCCCTTATAGTTGCCACAATAATCGCACATTGAGGCTTCAAACCACTGTACCTACATTTAATATTCATAAATTTCTCTGTTCCGATATC[T/C]GCACCGAAACCTGCTTCGGTCACCACAAACCCACCTTTCCCTACCAACTTAAGCGCTATCTTATCCGCCACAATCGAAGAGTTCCCATGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105889 C T CAATCGAAGAGTTCCCATGTGCAATGTTAGCAAAGGGACCTGCATGCACCAGAACCGGAGTTCCTTCTAGGGTTTGCATCAAGGTTGGATTGATAGCGTC[C/T]TTCATTAGCACCGTGAGAGCCCCACCTATCCCAAGGTCATCAGCGGTAATCGGGTCACCAGCCTTGCTATTTCCTATGACCATTTTG
105889 A C CGGGTCCTTGCCCGATGGTGATTTTTCTGAGGAATCGGTCGTTCACGTCCATGACTCTTCTGAATGTGATAGAAGATGGATCAATGTCTAACCTAACAAA[A/C]TTTTTGATCTCTTCAGGGGTTAAGTCGTTAGGATTTGTTTTTGAGATTCCTAGTTTTTTTAGGCGGGTGAGCATTACATTTGCGAACGT
105889 A G TTTTTAGGCGGGTGAGCATTACATTTGCGAACGTTCGGTTCCCTTCTTTGTTGGGAGGGCAAAGGCGGTTGAAGAGGCCTTTGTCAGATTGGGTGGATTC[A/G]TGGAAGATACGAGCATCGATGGCTGCCGCAAGAAGGTTATTGGCGGCTGTGATAGCATGAATATCGCCCGTGAGATGGAGGTTG
105891 G A AAAGGCGGCGGCGAGGACGGCTAAGCAGTAGTATAGCCAAAGAGAGGAGAAATACGAAGAACAAAGGAATGAACGATCCTCCGTGTTGGCCGCCAGAATT[G/A]GGTTTGTAGTAATGGATTTGCTTGTTCCCGTCACAATAACGCCCACCGTGTGGTAAATTGTGTGTGTTGTCTCCGACGTGCGGT
105899 C CT TGTTGGCCTACTGGAAAATCAGGACCGAGGTTATACTCCTATGGCGACTGGGTAGCCGCTTTCTTCATCTTCGACTCTTCTTCCAGC[C/CT]TAACACCCTTCGTCCTTTCTCTTTCACTTCTATTTCTTGTCTCCTCCCTCTTGCCTCCTCTTCCTGCTTCCGTCTACCCAGCTTTCATCGTAGTAGCTAT
105899 TC T ACCCTTCGTCCTTTCTCTTTCACTTCTATTTCTTGTCTCCTCCCTCTTGCCTCCTCTTCCTGCTTCCGTCTACCCAGCTTTCATCGTAGTAGCTATTAGC[TC/T]CCCCAAACCCTAACTCAGATCGAGATCCAAATTTTTCGTGCTCCTTTCAATCCGTTCTGCCTGGCCGATCCCCATCGTCCGACTACCTATTTT
105899 T A CCTCTTGCCTCCTCTTCCTGCTTCCGTCTACCCAGCTTTCATCGTAGTAGCTATTAGCTCCCCAAACCCTAACTCAGATCGAGATCCAAATTTTTCGTGC[T/A]CCTTTCAATCCGTTCTGCCTGGCCGATCCCCATCGTCCGACTACCTATTTTCCTTACCCCTTCTAGTTCCACCGCCTTTACTCGCGATGTTTC
105903 G GT TGTCGGAGCAAATACCATCAATAAATCCTCTACGGTTAGAATTTCATATGCATTGATGCTCATCCTTGCAACCTTTGCTACCATTGTCTCTTTTATTTGA[G/GT]TTTTTTTAAGCAATTTTGTTTTTAGTTAGTTCAAGTTTTAGGTATGTGTTCACCTTTGGATGTGTTGCATTGTTAAGGTAGAAGAGAGAT
105903 GT G CAATAAATCCTCTACGGTTAGAATTTCATATGCATTGATGCTCATCCTTGCAACCTTTGCTACCATTGTCTCTTTTATTTGAGTTTTTTTAAGCAATTTT[GT/G]TTTTTAGTTAGTTCAAGTTTTAGGTATGTGTTCACCTTTGGATGTGTTGCATTGTTAAGGTAGAAGAGAGATTTTAGGGCTTGGTTTGCTT
105903 A C TTGATGCTCATCCTTGCAACCTTTGCTACCATTGTCTCTTTTATTTGAGTTTTTTTAAGCAATTTTGTTTTTAGTTAGTTCAAGTTTTAGGTATGTGTTC[A/C]CCTTTGGATGTGTTGCATTGTTAAGGTAGAAGAGAGATTTTAGGGCTTGGTTTGCTTCCACTTTTGTAGTTACTGTTGTTGTGTTTTATGGT
105903 C T TGATGCTCATCCTTGCAACCTTTGCTACCATTGTCTCTTTTATTTGAGTTTTTTTAAGCAATTTTGTTTTTAGTTAGTTCAAGTTTTAGGTATGTGTTCA[C/T]CTTTGGATGTGTTGCATTGTTAAGGTAGAAGAGAGATTTTAGGGCTTGGTTTGCTTCCACTTTTGTAGTTACTGTTGTTGTGTTTTATGGTT
105905 G A TCTTCTTGAATGAATCTACTCCTTCCGCTTCTAGAATCTGGCCAACTTCCTCCCAGTTGATGCCAAGTTTCTCTAGTGCGCTGTAAATGCCTTCTGCTTC[G/A]GATATATTTTGGTCGATGGTTCTTGAGACATGACCATGATCGATGAAAGCTTGCAGAGCTTGGTCGGGCATTGTTGAGACAGTGTCAGG
105905 C T GAGTATCAACACGGCTAACAAAGAAGGAAGCCACACTTGTAAGCTTAGAGAGGTCGCTGAGCCCAGATGATTCAAGGCCATCCAAGTATGCATCAATGAC[C/T]GCTTCATATCTTGAAAGCGAGAAAATTAACGTTACATTGACGCTTATGTTATTTGCAATAACTTCTCTGATGGAAGGGACACAATCA
105909 A AG CATAATATTTGATTTCATACACAGCTTCGTATGTACAAAACAACAGTAGCATCACGAATTTACACTATGAACAATTGAAGAGAGT[A/AG]AGAGAAGAAAGCTGAAAATCCACAGAACAAAGTTTTATATGCACATCAAAATCAAAAATCCCGATTTCTCCCAAACTACACATTTGATATTTTAGCCAAC
105909 G T GACATTCTAACCTCAATCAGCCCTCTGTACAAATCCCCAATTCTCAATTCAATCTTCCCGACCCCACTCTCCAACTCCACCACTCTCGTCTTCAACTCCC[G/T]CACCAAATCCCTAATTTCACCTCCTCCCTCCTCGCTCAGCGACCTTCTCAACCTCTGTGCACCTTCCACCACCTGTCTCAGCTCCTCCAACAC
105909 T A TGTACAAATCCCCAATTCTCAATTCAATCTTCCCGACCCCACTCTCCAACTCCACCACTCTCGTCTTCAACTCCCGCACCAAATCCCTAATTTCACCTCC[T/A]CCCTCCTCGCTCAGCGACCTTCTCAACCTCTGTGCACCTTCCACCACCTGTCTCAGCTCCTCCAACACCGCTCCGTCCTTCCTCCTCTTCTCG
105909 G C TCTCAATTCAATCTTCCCGACCCCACTCTCCAACTCCACCACTCTCGTCTTCAACTCCCGCACCAAATCCCTAATTTCACCTCCTCCCTCCTCGCTCAGC[G/C]ACCTTCTCAACCTCTGTGCACCTTCCACCACCTGTCTCAGCTCCTCCAACACCGCTCCGTCCTTCCTCCTCTTCTCGAACTCCTCCTTCACCTC
105909 T C CACTCTCCAACTCCACCACTCTCGTCTTCAACTCCCGCACCAAATCCCTAATTTCACCTCCTCCCTCCTCGCTCAGCGACCTTCTCAACCTCTGTGCACC[T/C]TCCACCACCTGTCTCAGCTCCTCCAACACCGCTCCGTCCTTCCTCCTCTTCTCGAACTCCTCCTTCACCTCCTTCTGCACTTCCCAAATCACCC
105909 T C CCCCGCGCCTGGATCTGAACGACAGCGAGATGTTCGCCGTCATAATGGCGACCAACGCAATCGCCTGCGACCCAACCAGACATTCGTTTTTCCTCCCGTC[T/C]TCCTTCACCGCCACCATCCTCTCTCCCAGCTTCCTCAATCCCGACCCGCACGTGTCGAAATCCGCGCACCGCTTCTCGGAGCACGCGC
105909 C T ACCCAACCAGACATTCGTTTTTCCTCCCGTCTTCCTTCACCGCCACCATCCTCTCTCCCAGCTTCCTCAATCCCGACCCGCACGTGTCGAAATCCGCGCA[C/T]CGCTTCTCGGAGCACGCGCACGCCTCGAGGGCGTGCTTCGCGCGCGTGGCTAGAAACTCCGTTGGCCGGTTCTCGCCTTCCAGGTAATG
105909 T C ATCCTCTCTCCCAGCTTCCTCAATCCCGACCCGCACGTGTCGAAATCCGCGCACCGCTTCTCGGAGCACGCGCACGCCTCGAGGGCGTGCTTCGCGCGCG[T/C]GGCTAGAAACTCCGTTGGCCGGTTCTCGCCTTCCAGGTAATGTAGAGCGCTGTTGATTGAGTTCGTGTACGATTGGATTTCCTCGAT
105909 T C CCTCGATCCGTTTTTGTACGGCTTGGCACGCGTCGAGGAGCTCGATCGTGTCGTCGACGTAGTTTTCGGGCGAGATGGACGCGTCGTCGTTGATGGATTT[T/C]GTCGCGAGTTGTTGAGATGAGACCGCTGTGGATAAGGTTTGAGAGAGCCAGGAGGCTGTGGAGTAGAGGTTGGGTTGGGTGCGG
105913 C T TTTCAACGCCTTGATTACAAGCATAGACTAACGCATCTGCAAGTGTAAGCCTTCCCTCAGCATCAGTGTTATTTACTTCAATTGTCTTTCCATTAGAAGC[C/T]GTGACAATGTCACCAGGTCTCATGCCAGTACCACTTATCATATTTTCACAAGCAGCAACTATAAAATGTACCTCAACCCCAGAAGGCTTA
105913 A G CAGTAAACACATCACTATATAAAGAAGCAACTTTTGAAGCCTCCTCCGCCAGCACACCAGGGGTAAGGACGTTAGCTGGTGCATTTACAAGCTCTTTTCC[A/G]AGGATTACCCCAGAACATACATCATTAGCATACTTGAATTTCTTGTCCAACTGTGGACCAGAACCCAGACCAGCAATATCGACAGATT
105915 A G TTGCCTTCTCACAGAAGACAGACAGCGCACTTACTGTCTCTAACGTAAGCTTTGGCACGTATACTACACTTCGTAATCCAAATGCTGAAGCCTGCTTAAC[A/G]TTGTCATAAACACTTGCTGGGTTGGTAAAATCTACCACCACACCAGTTGCTTTAGATTGTGATATGGAACCCAAAACCATAGTTAGATC
105915 T C CAGCAATAGCAGCTCTGCCAATATCTGTTGTCGCACCGTTGATCACGACTTTGATATTATTGCTTTGTAAAGGCTGCACTGTGCATGAAATGGTAAAATT[T/C]ACGGTGCTGGTAGAAGTGGTTATTGGTCTAATACTATTGCCCCTTCCCCTGGCAGCGAGTTGATGTGAGGAAGAGTAACAAAGAGAG
105915 T C TTGTAAAGGCTGCACTGTGCATGAAATGGTAAAATTTACGGTGCTGGTAGAAGTGGTTATTGGTCTAATACTATTGCCCCTTCCCCTGGCAGCGAGTTGA[T/C]GTGAGGAAGAGTAACAAAGAGAGGCCATTTCAGTATTTGATATCGTATGAAAGTGGTGTTCGTCCGTTATCCAGTAGGCCAACAGT
105917 A G GGGAATTGTCTCCGAACTTTCCGACGAGGTTGGCTACGCTGTTCAGCGTAACAATGAGTTCAACGGCGCCGCAAACACAGCACCAGCTGGTACTTTCACC[A/G]CCGCTCCATATAGCTACAGCCTTCTTAGCACCTCCCAAGTGAAGAGCTCCGTAATCGCCAACGCCGGACCCAAGTTGACTTGGTCAT
105921 C T ATGGAGATAATTTACAATTCAAGCCGTACAAAGATAATATCTCTAATATTATCCTGTACAGTTACGAAATAGTCGAAAATCAGCCGAAATTGTACTCGCA[C/T]CCATTCAAGCGAGATAGGATCTCACTGCAGCTAGGTCGTTCGTTTGGTTCTGCCCAGCAATCAGCAATTAGCTTTCCAATGGGTCCATC
105929 A T GATTTGAGGAGGGTCATGTTGGATGAGGCGAGGTCGGCGCTGCCACCCAGGAAGCCGGGGAGGACAG[A/T]TGCAAGGGCATTTAGGCATTGTTGGGACAGGTTTCTTGTCGCGTCCGCTGGGCTTTCTGGGGTATATGTCGGAAGAGCCTTTTCCCAACCGGCAGGCAGT
105929 C T GGAGGGTCATGTTGGATGAGGCGAGGTCGGCGCTGCCACCCAGGAAGCCGGGGAGGACAGATGCAAGGGCATTTAGGCATTGTTGGGACAGGTTTCTTGT[C/T]GCGTCCGCTGGGCTTTCTGGGGTATATGTCGGAAGAGCCTTTTCCCAACCGGCAGGCAGTTCTCCGGTTACAATAGATTTCAAT
105929 G A GGGCATTTAGGCATTGTTGGGACAGGTTTCTTGTCGCGTCCGCTGGGCTTTCTGGGGTATATGTCGGAAGAGCCTTTTCCCAACCGGCAGGCAGTTCTCC[G/A]GTTACAATAGATTTCAATTCGGCTGCTTCCTCTGCGTACTTCTTCTCATACTCTGCAAACTTGGCATTCCACTCGGCTTCGAGAGCAG
105929 G A ATGAGTTTGCTTTGTTTGGTGATCCATAACCAATGGTAGTGGTAACCTTAATCATAGTTGGTTTATCGGTAACTGCCTTTGCTTCCTTGATCGCTGCTCG[G/A]ATTTCGTCATAGCCAGTGTTTCCATTCTTTACCCAAAGAGTATGCCACCCAAGAGACTCAAAACGAGCACTGACATCTTCAGTAAATGC
105929 A G TAACCTTAATCATAGTTGGTTTATCGGTAACTGCCTTTGCTTCCTTGATCGCTGCTCGGATTTCGTCATAGCCAGTGTTTCCATTCTTTACCCAAAGAGT[A/G]TGCCACCCAAGAGACTCAAAACGAGCACTGACATCTTCAGTAAATGCAATCTCTGTGTCTCCATCAATTGAAATATGGTTATCATCATAG
105929 C A GAGACTCAAAACGAGCACTGACATCTTCAGTAAATGCAATCTCTGTGTCTCCATCAATTGAAATATGGTTATCATCATAGAAGGCAATTAGCTTTCCAAG[C/A]CCCCAATGACCAGCAAGCGATGCTGCTTCATTTGAAATTCCCTCCATGTTGCAACCATCTCCAACGATCACATATGTGTAGTGATCAAC
105929 T C CATCTTCAGTAAATGCAATCTCTGTGTCTCCATCAATTGAAATATGGTTATCATCATAGAAGGCAATTAGCTTTCCAAGCCCCCAATGACCAGCAAGCGA[T/C]GCTGCTTCATTTGAAATTCCCTCCATGTTGCAACCATCTCCAACGATCACATATGTGTAGTGATCAACGATTTCAGCATCAGGTTTATTG
105931 A G AGTACCATGGCACATTGAAGGTGGTATGCTTTTGTTGGAACTAAACAGATTGTTGCGTCCCGGTGGTTACTTTGTGTGGTCTGCTACACCTGTGTACCAA[A/G]ATCTTCCAGAAGATGTTGAAATTTGGAAAGCCATGAGTGCATTGACAAAATCAATGTGTTGGAAAATGGTGAAGAAAACAGAGGAT
105931 T C AAGCTTGCATGCACAAAGTGCCAGTAGACCCATCAGTTCGTGGGTCGCAGTGGCCAGAGAAATGGCCAACAAGAGCTGAAGCCACTCCGTATTGGTTAAA[T/C]GACTCCCAGATTGGTGTTTATGGTAAACCTGCTCCTGAAGACTTTGAAGCAGATTATAAACATTGGAAAAGAGTTGTTAACAAATC
105931 A G GTACCATAACTGGTGTGAATCATTCAGTACTTATCCTAGAACATACGATCTTCTCCATGCTGATCATTTATTTTCGAAGCTCAAAAAGAGGTGCAAGTTA[A/G]TACCTGTAATTGCTGAAGTTGATAGAGTCCTCAGGCCTGAAGGGAAACTTATAGTAAGAGATGATGCAGAAACACTAGCTGAGATAG
105931 A C TCCATGCTGATCATTTATTTTCGAAGCTCAAAAAGAGGTGCAAGTTAATACCTGTAATTGCTGAAGTTGATAGAGTCCTCAGGCCTGAAGGGAAACTTAT[A/C]GTAAGAGATGATGCAGAAACACTAGCTGAGATAGAAAATATGGCAAAATCATTGCATTGGGAGGTAAGAATGACCTACTCAAAAGA
105937 C CT CGCTTGCTCCTCTCCCTCACTTTGCTTTCCTTCACTCTCCTTATCGTTCCACACTCTCTCTTCTCCGATATGCCTTGCTTTTGTCTGCATGGTCGAAGCC[C/CT]TAAAACATATTTCTCAGATCTCGATTTGTCAGATCTGAAACCCCTTATTTATCTTCCAAAGTTCCCTCCTTTATTCTGATCTGCCTCCCCTTCT
105937 T C TCATTGCTAGGTGATTTTTTGTCCTACTTTTGTCTGACCCTGGTCAGGTATTGGGTGTGTTGGTGCTTGTTGGGACATTTTGCGTTGGTTTCGATCGTGG[T/C]GTTTAGTGATTGTTCTGGTTGTGGTTTGGCTTGTTGGGTGATGGAAGTTTTGCCTCCTTTCGCGGAGCTTCCAGTGTACTCTACGTGGT
105939 T A ACAAACTCAAAATTGAATCCTAAAAATGCAATCAGCCAGCGTCTTCCACCCCATCCCCGTTAAATTTCCATTAAAATTCCAAAGTGGTCGCTCCTTCCTA[T/A]ACCCTAATCCCCCGATTCTGAAAACGGCTTCAAAATCAAAACCCCGCCGTCAGAAGCTTTCAAACATTTCCTGCATCAGTAACAGCAACG
105939 A G GGGTGGGCCCTAGGTCGGTTGGGGTATGCTTGCTGACGTCGTCGTTCGTCGGAATGGCGTTTACTATCCAGTTCGTGAGGGAGTTTACGAGGCTCGGTCT[A/G]CATAAGTCGGTTGGAGGTGTGTTGGCCTTGGCATTTGCCAGGGAGTTGAGTCCTGTGGTCACCGCTGTGGTTTTTGCTGGTAGGG
105939 C A GTGCAATGATTAAATCACAGGTATTTGGTGGAATAATAGCGGTTGTTAGCTGTGCTTGGGGAGTGACTACGATCGGTGGTGCCAAGGGTGTCGGAGAGTC[C/A]ACGACCTCCGCTGTGGTTATTTCTCTCGTTGGAATATTTATTGCGGACTTTGTTTTGTCTTGCCTGTTTTTTCAGGGTGCTGGTGAT
105943 A G ACGACAAGTGTGCCCCATGCATGGAAACGATGACGGGTTGAGTGGGCTGGATGAGTCGAGCCTGAGCTTTGACGAGGCATATTACAGGAATCTGATGGAG[A/G]AGAAAGGGTTGCTGCATACCGATCAGGAGCTGTACAGAGGGGACGGAGGGGAGGTGGATGAGCTGGTGGAGTTTTATAGCG
105949 T C TATTTTGCTAGTAATGATGCAGCTATAAATATGTTTCGACATTCTCAAGGGACCGCTGAATTGCAAGTTGTTCCAGTACTTTTCCAAAATAGTCTGCAAC[T/C]ACAAAAAGGTGACCCTGGAGTGAAACTTGAAGATATATTTGGCGTGGAGCCTATGAAAGTGAATAGTCCTGCATCCAACTCTGAAATT
105953 CA C TAAGAATCCGCAGATCTGTGAGGTTCCTTGGCAATTTCAACATCCGATCATCATCAGCTTTCGGCATAGTGAACAATACACAAACTAGACCAACGGAAAA[CA/C]AAAACGAAAATCGAAATAGCAGCTGCCATTTCCGTTCGAGATAATGGAAACTTAGCGTCGGTCTTCGACTTCTTGCCCGTAGGAGA
105955 T C CTTAACTTTTCTTCCTTCCTTTTTCATTTCTGACATTTTCTCCCTTCCAACTTCAGATTCTTCTTCATCAATTCTTTCTTCTCCACAAAATCACCCTATA[T/C]TCTTTCCTCTTTCAACTTTTACCGTTATCATCTTAGCGTCGTTGTTCCCCTATTTCAGATCTAGTTGTTCCTTTTCTTTTCTTGCTTATCAGATCTGA
105955 A G TTCCTTTTTCATTTCTGACATTTTCTCCCTTCCAACTTCAGATTCTTCTTCATCAATTCTTTCTTCTCCACAAAATCACCCTATATTCTTTCCTCTTTCA[A/G]CTTTTACCGTTATCATCTTAGCGTCGTTGTTCCCCTATTTCAGATCTAGTTGTTCCTTTTCTTTTCTTGCTTATCAGATCTGAAATCTCATCTTTCA
105955 A G TTTCATTTCTGACATTTTCTCCCTTCCAACTTCAGATTCTTCTTCATCAATTCTTTCTTCTCCACAAAATCACCCTATATTCTTTCCTCTTTCAACTTTT[A/G]CCGTTATCATCTTAGCGTCGTTGTTCCCCTATTTCAGATCTAGTTGTTCCTTTTCTTTTCTTGCTTATCAGATCTGAAATCTCATCTTTCAACTACT
105955 G A ACCCTATATTCTTTCCTCTTTCAACTTTTACCGTTATCATCTTAGCGTCGTTGTTCCCCTATTTCAGATCTAGTTGTTCCTTTTCTTTTCTTGCTTATCA[G/A]ATCTGAAATCTCATCTTTCAACTACTTGTGCTTTTTTGTCAAAACCTAGCCTTATCGTCACTCCACCTTCTCCGTACTCCCTAACCTCTTCCATGT
105955 C T CAGATCTAGTTGTTCCTTTTCTTTTCTTGCTTATCAGATCTGAAATCTCATCTTTCAACTACTTGTGCTTTTTTGTCAAAACCTAGCCTTATCGTCACTC[C/T]ACCTTCTCCGTACTCCCTAACCTCTTCCATGTCTTGTGCGCCACCTATTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTC
105955 C T CTTTTCTTTTCTTGCTTATCAGATCTGAAATCTCATCTTTCAACTACTTGTGCTTTTTTGTCAAAACCTAGCCTTATCGTCACTCCACCTTCTCCGTACT[C/T]CCTAACCTCTTCCATGTCTTGTGCGCCACCTATTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCC
105955 A G TCATCTTTCAACTACTTGTGCTTTTTTGTCAAAACCTAGCCTTATCGTCACTCCACCTTCTCCGTACTCCCTAACCTCTTCCATGTCTTGTGCGCCACCT[A/G]TTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATT
105955 C G ACCTTCTCCGTACTCCCTAACCTCTTCCATGTCTTGTGCGCCACCTATTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTAC[C/G]CGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGG
105955 T C TCTTGTGCGCCACCTATTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGG[T/C]TGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGG
105955 T C CTATTCCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTG[T/C]ATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGG
105955 C G CCGTGGTCTCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATAT[C/G]AACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTG
105955 C T TCTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGC[C/T]AGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATT
105955 A G CTCTCTTCAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCC[A/G]GTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATTG
105955 T C CAGATCCTTGTTGTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGG[T/C]ATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATTGGAGTTTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
105955 T G GTTTTCACACGATCTCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGG[T/G]GAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATTGGAGTTTTGGATTTTTGGT
105955 G C TCTCCTTACCCGTGTCCCCACCGAAAGGCTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGG[G/C]TTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATTGGAGTTTTGGATTTTTGGTTGAGTGACTCGATT
105955 T C CTGGCCTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTA[T/C]AGGGCATTTAGTTGGACTTGGCATCATTGGAGTTTTGGATTTTTGGTTGAGTGACTCGATTTGGGTCTACTCTGTGTGGTGGTATGATT
105955 C T CTTCTGGTTGTGGATTGTTGTATATCAACATGCCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGG[C/T]ATTTAGTTGGACTTGGCATCATTGGAGTTTTGGATTTTTGGTTGAGTGACTCGATTTGGGTCTACTCTGTGTGGTGGTATGATTAAGTT
105955 GGATTTTTGGTTGA G CCAGTTAGGTATATGTTTTGGTGAGTTTTCTGTGGGTTTGGTAAGTATTTGAACTGACCTTTATAGGGCATTTAGTTGGACTTGGCATCATTGGAGTTTT[GGATTTTTGGTTGA/G]GATTTTTGGTTGAGTGACTCGATTTGGGTCTACTCTGTGTGGTGGTATGATTAAGTTTGTGCTGAGATTTTAGATG
105955 G T ATCATTTTTCTGGCTAGATCTGGTTTTTGAGGTGGTTGGTTCGGAGATAATAGTGTGCCTTTCTTCATTTCACCACTTTATCCTAGTTTAGCAATCAAGT[G/T]GAAGCTATAGTCTAGACTTTGTTGGATTTTGTGGATGGTCTATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGG
105955 A G GGAGATAATAGTGTGCCTTTCTTCATTTCACCACTTTATCCTAGTTTAGCAATCAAGTGGAAGCTATAGTCTAGACTTTGTTGGATTTTGTGGATGGTCT[A/G]TCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGGTAGGTCTGTGGGGAACTATGCCTTTTGGTGGTGTTGTTTCTG
105955 GTGCA G CTTTATCCTAGTTTAGCAATCAAGTGGAAGCTATAGTCTAGACTTTGTTGGATTTTGTGGATGGTCTATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTG[GTGCA/G]TGCATGCTGCTGGGTAGGTCTGTGGGGAACTATGCCTTTTGGTGGTGTTGTTTCTGCTCGACGCTTGCCATGGTGATGGTTCTG
105955 G C GAAGCTATAGTCTAGACTTTGTTGGATTTTGTGGATGGTCTATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGGTAGGTCTGTGG[G/C]GAACTATGCCTTTTGGTGGTGTTGTTTCTGCTCGACGCTTGCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCA
105955 G A AGTCTAGACTTTGTTGGATTTTGTGGATGGTCTATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGGTAGGTCTGTGGGGAACTAT[G/A]CCTTTTGGTGGTGTTGTTTCTGCTCGACGCTTGCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATT
105955 T G TGGATTTTGTGGATGGTCTATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGGTAGGTCTGTGGGGAACTATGCCTTTTGGTGGTG[T/G]TGTTTCTGCTCGACGCTTGCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCT
105955 T G TATCTTTGCCTGCCACTTTCTCGGCCGGTGGGTGGTGCATGCTGCTGGGTAGGTCTGTGGGGAACTATGCCTTTTGGTGGTGTTGTTTCTGCTCGACGCT[T/G]GCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCT
105955 G A GTAGGTCTGTGGGGAACTATGCCTTTTGGTGGTGTTGTTTCTGCTCGACGCTTGCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCA[G/A]TGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCTATTGGTTTCAAGACAGTTTTTTCTGGGGATTTTAGTGCTTTTTCATTGAT
105955 A G TGCTCGACGCTTGCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCT[A/G]TTGGTTTCAAGACAGTTTTTTCTGGGGATTTTAGTGCTTTTTCATTGATCTTTCATGGGAATATGCTGCCTTGTTGCATGTCAAGATGTT
105955 A T GCCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCTATTGGTTTCAAG[A/T]CAGTTTTTTCTGGGGATTTTAGTGCTTTTTCATTGATCTTTCATGGGAATATGCTGCCTTGTTGCATGTCAAGATGTTACTGTATGCAAT
105955 C G CCATGGTGATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCTATTGGTTTCAAGA[C/G]AGTTTTTTCTGGGGATTTTAGTGCTTTTTCATTGATCTTTCATGGGAATATGCTGCCTTGTTGCATGTCAAGATGTTACTGTATGCAATG
105955 T C GATGGTTCTGTCGCAATGGTTACTTGGTATGAGAACGCAGTGCTATTTTTGTTCCCTGCTCTTACCTTGATGTGATGTCTATTGGTTTCAAGACAGTTTT[T/C]TCTGGGGATTTTAGTGCTTTTTCATTGATCTTTCATGGGAATATGCTGCCTTGTTGCATGTCAAGATGTTACTGTATGCAATGGTTTGTTT
105955 T C TTCAAGACAGTTTTTTCTGGGGATTTTAGTGCTTTTTCATTGATCTTTCATGGGAATATGCTGCCTTGTTGCATGTCAAGATGTTACTGTATGCAATGGT[T/C]TGTTTACTGTGTCAGAGTTCTTTATTTGGCTGCAGTGATGAATTGTTGTATTATTTTCTTCTCTGTTCTTGTTCACGTAAAGCTGGGTAGC
105959 GC G TATCCAAAACGCGACCAAGCATCAACCGTGTGTTCTGCAGGGCAATCTGCCGCTCAGACAAACCCCCATCATTACCAACCACGCCGCTTCCTGCTACGGG[GC/G]CCCCCACCCATATACTCAAAGGCCCGCTCCGGGCCTTGAACGAACTCTGAGGCATAAGCATCTTCTCTGTCAACCCAGACCCACTA
105959 T TG AAGCATCAACCGTGTGTTCTGCAGGGCAATCTGCCGCTCAGACAAACCCCCATCATTACCAACCACGCCGCTTCCTGCTACGGGGCCCCCACCCATATAC[T/TG]CAAAGGCCCGCTCCGGGCCTTGAACGAACTCTGAGGCATAAGCATCTTCTCTGTCAACCCAGACCCACTATTGATATCCCCAAAGCC
105959 G A TCTGAGGCATAAGCATCTTCTCTGTCAACCCAGACCCACTATTGATATCCCCAAAGCCCAACCCTCCGCCCAACTCATCAAAATGGCCCCCACCCGACCC[G/A]CTGCAGCTCTGCAGGAGCGCTTCCAGAACGCTCAGCGCCTCCCAGCACAGAGTGCTCTCCACCAGCTGTGACACGATTGCATACACAT
105959 T C CCAACTCATCAAAATGGCCCCCACCCGACCCGCTGCAGCTCTGCAGGAGCGCTTCCAGAACGCTCAGCGCCTCCCAGCACAGAGTGCTCTCCACCAGCTG[T/C]GACACGATTGCATACACATGTGGGCTCTGAGCCGCATCCACCGGAGTCTGCTGCAGGAGTGCCTTCAGCAGTAGCAGAATTACCCT
105959 G A GAAACCACTCCATGCATATCATAGGAGAAACTCTTGCAAAAAGATCATCAGTAGTCGAAATCTCCCTTCTAGAATATGATAGAAAGACCTGTGCTAAGTC[G/A]TTGAGGGATTTCACACGGCACCATGAAGATATATTGGAAGCTACCACACACGCTTTTGGAAAATCTGAAAAGTCGGGTGAGAGCTG
105959 G C ACTCCATGCATATCATAGGAGAAACTCTTGCAAAAAGATCATCAGTAGTCGAAATCTCCCTTCTAGAATATGATAGAAAGACCTGTGCTAAGTCGTTGAG[G/C]GATTTCACACGGCACCATGAAGATATATTGGAAGCTACCACACACGCTTTTGGAAAATCTGAAAAGTCGGGTGAGAGCTGAAGCCC
105963 AG A GGAGAAAGAGATGGGTAGAGGAAAGAAAGAAAAGAAGAGGGCAAACGAGGAGTTGGATAAAGTTGCGAATTTGGAGAATGGGAAGGAAAAGAAGAAGTTT[AG/A]GGGCGATTGACGTTGCACCGGCCCATGCCACCAAGGAGGTTTATGCTTCAATTTTTACTAGTTCAAGGAAAGGGGAGATTA
105973 T G TATCCGCCGTATACTACCTTTCCTCCGCCTTCACCGGTGATCTATTCCTCGACTCCTCACCAACCCTAACTTTGGCCTCCGCCATCGATCCCCAAACCCT[T/G]CTCCCAATCCCCTTCTCGCTGTCCCCAACCCACCCCTTGCCCCCCAACCAAACTCTAACCCTAACCCTAAAAAATCAGCAATCGTTTCAGCT
105973 AC A CTTCACCGGTGATCTATTCCTCGACTCCTCACCAACCCTAACTTTGGCCTCCGCCATCGATCCCCAAACCCTTCTCCCAATCCCCTTCTCGCTGTCCCCA[AC/A]CCCACCCCTTGCCCCCCAACCAAACTCTAACCCTAACCCTAAAAAATCAGCAATCGTTTCAGCTTACGTTCACAACCTCCCCTGCCTCTTT
105973 GC G ATCTATTCCTCGACTCCTCACCAACCCTAACTTTGGCCTCCGCCATCGATCCCCAAACCCTTCTCCCAATCCCCTTCTCGCTGTCCCCAACCCACCCCTT[GC/G]CCCCCCAACCAAACTCTAACCCTAACCCTAAAAAATCAGCAATCGTTTCAGCTTACGTTCACAACCTCCCCTGCCTCTTTCGCCTTGCAGT
105973 G A ACCACCCGTTCGTGTACACACAGTGTCAGTCAGTGCACGCTCGTTCCATTTTCCCATGCCAGGACACTCCAGCAGCACGTGTGAAGTACGGCGCGTTGCT[G/A]AACATCCCGTCTGAATTGTCCTCTGTGATGTCAGCTTCTAAAACAAACAGGAGGGATCCACGATCTAACGAGGCACGTGGTGCGTG
105973 A G CGGCGCGTTGCTGAACATCCCGTCTGAATTGTCCTCTGTGATGTCAGCTTCTAAAACAAACAGGAGGGATCCACGATCTAACGAGGCACGTGGTGCGTGC[A/G]ATGATGCAGTATGGTGCGCACCTGGAAGGATGGTGGAAGAGTTTGTGATGGAGCAGCCGATACCTCCTTATCTGTTTGCATTTGC
105973 A G ATTGTCCTCTGTGATGTCAGCTTCTAAAACAAACAGGAGGGATCCACGATCTAACGAGGCACGTGGTGCGTGCAATGATGCAGTATGGTGCGCACCTGGA[A/G]GGATGGTGGAAGAGTTTGTGATGGAGCAGCCGATACCTCCTTATCTGTTTGCATTTGCAGTGGGAGAGATTGGAGTGAGGGAGG
105973 G A GATGGAGCAGCCGATACCTCCTTATCTGTTTGCATTTGCAGTGGGAGAGATTGGAGTGAGGGAGGTGGGACCAAGAAGTAGGGTTTATGTGGAAGGAGGT[G/A]TGGAGGTTTTGGATGCTGCAGAGAGGGAGTTTAAGGGGACGGAGGAGATGATCAAGGTGGGCGAGAGTCTGTTTGGGAAGT
105973 G T CTGCAGAGAGGGAGTTTAAGGGGACGGAGGAGATGATCAAGGTGGGCGAGAGTCTGTTTGGGAAGTATGAGTGGGATAGGTTTGATCTGCTAGTCTTGCC[G/T]CCTAGTTTCCCTTATGGTGGGATGGAGAATCCGTGTATGGTGTTTTTGACTCCATTTGTTATTAAAGGGGATGGGACTGGAGCA
105977 A G ACCCACAAAAGCGAGCAAATCGAAGTAAGAAGCAAAGACCAGACTATGATAATGGTTGGAGCTCTATCTTGCTTGCCCAACATTCCCTTTATGAATGGAT[A/G]TAAATGCACTATAACCCAAAATGAGAAGAACAGTTTGCCAAACAATGGCCCCCATGACTCGTATCCGTTGTTAATGGCGTTTGATAT
105993 T C TCCTTTGACTCTCACTGATACATCCAACAAGATAAAGAAGGGAACACAGGGTGACGCCACAGTGTTGGGGCCTACAATTATGGCTTGTGTGCCTGCTATC[T/C]TGGACCGTGTCAGAGATGGCGTAAGGAAAAAGGTTGATGCAAAAGGTGGGTTAACGAAGAAACTATTCGACATAGCATATGCACG
105993 T A CTGCTATCTTGGACCGTGTCAGAGATGGCGTAAGGAAAAAGGTTGATGCAAAAGGTGGGTTAACGAAGAAACTATTCGACATAGCATATGCACGTAGGCT[T/A]TCAGCAATTAATGGAAGCTGGTTTGGGGCATGGGGTTTGGAGAAAGTGTTATGGGATGTTCTTGTGTTCAGCAAAGTTCGAGCAA
105993 GA G AAGGTGGTTACAAAACTGAGGATAGACCAATGCCTCGTGGTGAAATAGTTATTGGAGGTCCTAATGTTACCGCTGGATATTTTAATAATGAGGAAAAAAC[GA/G]AAAGAAGTATATGAGGTTGATGCAAAAGGGATGAGGTGGTTTTATACTGGTGACATTGGGCGTGTGCATCCGGATGGCTGCCTT
106001 G C TGCTTTGGATGAAACCACTTCGTGCGAGTATAGAGATTTACCCGAGCCCTTAAGGCTTCCGGGTTATGGGCCGCTGCATGGGGAGGATTTCATCAGCCCG[G/C]TTCAGGACAGAAAGAACGAAGGTTACAGTAGAGTTGTTCGTATGGCTAAAAGGTATAGAGAGCTGGATGGCATTCTGGTTAACAG
106001 A G AAACCACTTCGTGCGAGTATAGAGATTTACCCGAGCCCTTAAGGCTTCCGGGTTATGGGCCGCTGCATGGGGAGGATTTCATCAGCCCGGTTCAGGACAG[A/G]AAGAACGAAGGTTACAGTAGAGTTGTTCGTATGGCTAAAAGGTATAGAGAGCTGGATGGCATTCTGGTTAACAGTTTCAACTTTA
106001 G T CCCGAGCCCTTAAGGCTTCCGGGTTATGGGCCGCTGCATGGGGAGGATTTCATCAGCCCGGTTCAGGACAGAAAGAACGAAGGTTACAGTAGAGTTGTTC[G/T]TATGGCTAAAAGGTATAGAGAGCTGGATGGCATTCTGGTTAACAGTTTCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCT
106001 G A GTTATGGGCCGCTGCATGGGGAGGATTTCATCAGCCCGGTTCAGGACAGAAAGAACGAAGGTTACAGTAGAGTTGTTCGTATGGCTAAAAGGTATAGAGA[G/A]CTGGATGGCATTCTGGTTAACAGTTTCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTG
106001 A G GACAGAAAGAACGAAGGTTACAGTAGAGTTGTTCGTATGGCTAAAAGGTATAGAGAGCTGGATGGCATTCTGGTTAACAGTTTCAACTTTATGGAGGGTA[A/G]TGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACCGCTAGGCGAGTTTAGTCCAACT
106001 G A AGCTGGATGGCATTCTGGTTAACAGTTTCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTT[G/A]ATCGGACCGCTAGGCGAGTTTAGTCCAACTGGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTC
106001 G A GCATTCTGGTTAACAGTTTCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACC[G/A]CTAGGCGAGTTTAGTCCAACTGGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTC
106001 C G CATTCTGGTTAACAGTTTCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACCG[C/G]TAGGCGAGTTTAGTCCAACTGGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCA
106001 A G TCAACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACCGCTAGGCGAGTTTAGTCC[A/G]ACTGGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCATTTGGAAGTGGTGGGA
106001 T C ACTTTATGGAGGGTAATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACCGCTAGGCGAGTTTAGTCCAAC[T/C]GGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCATTTGGAAGTGGTGGGACGC
106001 G A ATGCTGCTGAAATATTGGCTAGTTCAGATAGAGAAGGGTTGCCTCCAGTTCACTTGATCGGACCGCTAGGCGAGTTTAGTCCAACTGGAGGAAGATCGGA[G/A]TGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCATTTGGAAGTGGTGGGACGCTGTCTTCAAAACAGA
106001 T C GACCGCTAGGCGAGTTTAGTCCAACTGGAGGAAGATCGGAGTGCATGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCATTTGGAAG[T/C]GGTGGGACGCTGTCTTCAAAACAGACAGAAGAGCTAGCACTTGGCCTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAGA
106001 C T TGGATTGGCTAAACAGGATGCCCCATGGCTCGGTTCTGTACATCTCATTTGGAAGTGGTGGGACGCTGTCTTCAAAACAGACAGAAGAGCTAGCACTTGG[C/T]CTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAGAGCACCTAGCGATTCTGAAAGCGGAGCCTATTTTGGATTTGAAAACA
106001 A G ACATCTCATTTGGAAGTGGTGGGACGCTGTCTTCAAAACAGACAGAAGAGCTAGCACTTGGCCTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAG[A/G]GCACCTAGCGATTCTGAAAGCGGAGCCTATTTTGGATTTGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAAT
106001 C T TTGGAAGTGGTGGGACGCTGTCTTCAAAACAGACAGAAGAGCTAGCACTTGGCCTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAGAGCACCTAG[C/T]GATTCTGAAAGCGGAGCCTATTTTGGATTTGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAATCAACCAAAG
106001 T C CAAAACAGACAGAAGAGCTAGCACTTGGCCTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAGAGCACCTAGCGATTCTGAAAGCGGAGCCTATTT[T/C]GGATTTGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAATCAACCAAAGATGTTGGGATGGTGGTCCCAGACT
106001 T C CAGACAGAAGAGCTAGCACTTGGCCTGATGGAGAGCAGGCACAGGTTTCTTTGGGTGATAAGAGCACCTAGCGATTCTGAAAGCGGAGCCTATTTTGGAT[T/C]TGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAATCAACCAAAGATGTTGGGATGGTGGTCCCAGACTGGGC
106001 A C TTCTTTGGGTGATAAGAGCACCTAGCGATTCTGAAAGCGGAGCCTATTTTGGATTTGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGA[A/C]TCAACCAAAGATGTTGGGATGGTGGTCCCAGACTGGGCTCCACAGGTGGATGTATTGGGCCATGGGGCGGTTGGAGGATTCATGA
106001 T A TCTTTGGGTGATAAGAGCACCTAGCGATTCTGAAAGCGGAGCCTATTTTGGATTTGAAAACAAGGACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAA[T/A]CAACCAAAGATGTTGGGATGGTGGTCCCAGACTGGGCTCCACAGGTGGATGTATTGGGCCATGGGGCGGTTGGAGGATTCATGAC
106001 G A ACCCCTCGGAATATTTACCGAAGGAGTTCTTAGAATCAACCAAAGATGTTGGGATGGTGGTCCCAGACTGGGCTCCACAGGTGGATGTATTGGGCCATGG[G/A]GCGGTTGGAGGATTCATGACACACTGCGGATGGAACTCGGTTCTCGAGAGTGTGATGAATGGAGTGCCGATGATTGCTTGGCCG
106001 A G AGGAGTTCTTAGAATCAACCAAAGATGTTGGGATGGTGGTCCCAGACTGGGCTCCACAGGTGGATGTATTGGGCCATGGGGCGGTTGGAGGATTCATGAC[A/G]CACTGCGGATGGAACTCGGTTCTCGAGAGTGTGATGAATGGAGTGCCGATGATTGCTTGGCCGTTGTTCGCCGAACAAAGAATG
106003 A C GGAACTCTTTGCTAACGTTACGTCAGGTGTTCTGCGAGTTCGCACTAACCATACATACCCCCTCTCTCAAGCTGCAAAATGCCACGCTGATCTTGAGGCC[A/C]GGAAGACCTCAGGCTCCGTTCTTTTGATTCCAGATGAAGAACTGCACTCATAATTGTACATAAACAGTGGTATTTGGCAGAACTATTC
106003 G A TACGTCAGGTGTTCTGCGAGTTCGCACTAACCATACATACCCCCTCTCTCAAGCTGCAAAATGCCACGCTGATCTTGAGGCCAGGAAGACCTCAGGCTCC[G/A]TTCTTTTGATTCCAGATGAAGAACTGCACTCATAATTGTACATAAACAGTGGTATTTGGCAGAACTATTCTTGTGTAATCTAAAATGTA
106003 C G CATACATACCCCCTCTCTCAAGCTGCAAAATGCCACGCTGATCTTGAGGCCAGGAAGACCTCAGGCTCCGTTCTTTTGATTCCAGATGAAGAACTGCACT[C/G]ATAATTGTACATAAACAGTGGTATTTGGCAGAACTATTCTTGTGTAATCTAAAATGTATCAAAGACTGTAATATGTAAAATAAGCAGG
106003 A T TTCTTTTGATTCCAGATGAAGAACTGCACTCATAATTGTACATAAACAGTGGTATTTGGCAGAACTATTCTTGTGTAATCTAAAATGTATCAAAGACTGT[A/T]ATATGTAAAATAAGCAGGTGAGTGGTTTACTCGAATGTCGCTCTTGTGCTTGAATGTGATGTAATACTATCGTCAAATTGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106007 G A TGCAGAGAAAAGGTAGATCAAGTACAGTACCACTATGGCAAGCATCTATAAATGCATGGAGCTTAACTCCGCGAGGAAGTGGTCGGACAATAGCTACATT[G/A]ATATCATCGTCAACAATCATTCCTTGTGTTTCAAAATCTAGTGGGCATAGAGTTTCATCAAATCCATCTGCCTCTTCATAGCTCCTTT
106015 A G AAGTCGATATTTACAAATTCGATCCTTGGAATCTTCCAGATAAAGCTATGTTTGGCGACAAAGAGTGGTACTTCTTCACACCGAGAGATCGGAAGTATCC[A/G]AACGGAGTCAGACCGAACCGGGCTGCGGGTTCCGGGTACTGGAAGGCTACCGGAACCGATAAGCCCATCGTGACGACTATTGGAA
106015 G A ATCCTTGGAATCTTCCAGATAAAGCTATGTTTGGCGACAAAGAGTGGTACTTCTTCACACCGAGAGATCGGAAGTATCCAAACGGAGTCAGACCGAACCG[G/A]GCTGCGGGTTCCGGGTACTGGAAGGCTACCGGAACCGATAAGCCCATCGTGACGACTATTGGAAATGAGAACATCGGTGTAAAG
106015 C T ACATAGGAAAACCTCCTAAAGGTGTGAAGACTAACTGGATCATGCATGAATATCGCCTTACTGAAAGCAATATAAAGAGCAGTAACAGTATTACTAGACC[C/T]ACAAGGATCAGAAATTCTTCCATGAGGTTGGATGACTGGGTGCTGTGCAGAATTTATCAGAAGGGAGGCCAAATGAAAGAAGATT
106015 G A GGTTGGATGACTGGGTGCTGTGCAGAATTTATCAGAAGGGAGGCCAAATGAAAGAAGATTCAGTTGAGAATGAAAGTTCATTCGAAGACAACAAGCTTGA[G/A]ATTCAAAGATCGTTTTCTTTGTCGGAGCTTTTGAACGAAGCAGACTTCTCACTGTTGTCGAGATTTATAGAAACTCCGGTGGATGC
106021 T C CGGAAATGTAATCATAGCAACAGCATTAGAAGATCGTACCATTGCTCTGAGAGATCTGATAAAGGAGACCATGTCCCAATCCATATCGGTATATCCACAA[T/C]GAGGGGCACAAAGTGATTGTATGGCAATTCGACCAGCATTACTTCCATCATTCCTCGGAAGTGAAGTTAAGAAATTGAAACAACGAT
106023 GA G TCAACCTCACCATGTCCTTCGGCTACTTCTTCAGCGACTGCTGCACGGACCACAGCTGCTCCTACTCGTGTGGTGATACTACGAATACCTGAGATGGAAG[GA/G]AAAAAGAATCCCCTTTTGGATCTCTTCTTCAGTCATGTAAGATGAAAGGCATTCAGCTGCAGCTTGAAGCATGCCATCTGTTATACG
106029 G GA AGAAGATTATACCAGCTTAATGCACCAGCGTTTAAAATACACATCAAAAAATTGAACTCACACATCTAGCAGAAGATATATTAACATGATAATGGAGGAA[G/GA]AAAAACAAGCCAAGTACAAATCCAAGTGTAAAAAAAGACCAATTCAACAAGGCATAAGAGAAGTAAACCACTACCAATAATAAAA
106029 A T TCATCGATGCTCCGACCTGATGCGGATGCTGCTGCCTTTCCACCACCAGAGTATCTCCTCCGCCCGAGCCATTGTTTTCCATCTCTGATGACTCTTTTTC[A/T]GATTTCTGTCGCTTTGTGAAGAAGGTTAAGAGAACGGAAATAGTTGCGGCAACCGCTACTACAACGGAGATGGAGGTGTACATGTGGT
106029 G GT ATGCTGCTGCCTTTCCACCACCAGAGTATCTCCTCCGCCCGAGCCATTGTTTTCCATCTCTGATGACTCTTTTTCAGATTTCTGTCGCTTTGTGAAGAAG[G/GT]TTAAGAGAACGGAAATAGTTGCGGCAACCGCTACTACAACGGAGATGGAGGTGTACATGTGGTAAACGATGAAGTAGACATTGGAG
106029 G C TTTCCATCTCTGATGACTCTTTTTCAGATTTCTGTCGCTTTGTGAAGAAGGTTAAGAGAACGGAAATAGTTGCGGCAACCGCTACTACAACGGAGATGGA[G/C]GTGTACATGTGGTAAACGATGAAGTAGACATTGGAGATCTAATCCAATTTAAGGGTTAGGGTTTTGTGAAGAGAAGGACGGTTTTA
106049 A C GTAAAAACTATAAAAATGTTTCTTCTCCTTCTACCTAATAGTCAGCAGTAAGGAAATTTCCAGGCAAGGATACCTTTTCGCCCAATTTAAAGGGAGGAAG[A/C]CCTTTATAAGGGCACCCGCTGCATCTAAAAGCATCGCCAAGCCCACAACTGCCGCATGAAGACTTAGGGTTATATATCTGCTCAGTAG
106049 C G AAGCATCGCCAAGCCCACAACTGCCGCATGAAGACTTAGGGTTATATATCTGCTCAGTAGTAAGCCCCAGTTTAACTGTTTTCTCTTCTTCCTCCGCTCG[C/G]CCACAGGTGCAGTTCTTGCATGCTTTCCTTGTACTTCCCACTCCACAGTCCACAGCAACTGGAAGTTGTGGTTTTTTCAGGTCTTCCTCA
106049 A G GTGGTTTTTTCAGGTCTTCCTCAGTTAACAAGCTATCTTCATCAATTAAATCTGAATCATCATCAAGTTGAAGCTGGATTTTTGGAACAGTTTTGGTGTT[A/G]TTCTTGAGGGAGAATGATGACCCTGCTTTCCATGAAGCCTTCTTGCCCTTGATCGTAATGTAACGGGCACTTTCAATTTGCAAGAACGCT
106049 T C CCAGTGTAGATTGTTGCTCATTAGAATTATCACTGGATGCCAGTGGCATTTGAAATAGAATATTTCCACCAGGTTTTAAGATTCTGCCAAATTCTTCGAT[T/C]AAATCTTTTGTGACTAGGTCAACAGTCCTTGTGACTGAAATAATAAGTTCAACCGACGCGGCGTTGATTGATAACTTTTCACCCAAAAA
106049 G A TATTTCCACCAGGTTTTAAGATTCTGCCAAATTCTTCGATTAAATCTTTTGTGACTAGGTCAACAGTCCTTGTGACTGAAATAATAAGTTCAACCGACGC[G/A]GCGTTGATTGATAACTTTTCACCCAAAAACTGTGCTTGAGTGACAATAAGAACTTCACTCCCTGAAAATTTTCCGCCTGAGAAATCATTA
106049 C T GTCAACAGTCCTTGTGACTGAAATAATAAGTTCAACCGACGCGGCGTTGATTGATAACTTTTCACCCAAAAACTGTGCTTGAGTGACAATAAGAACTTCA[C/T]TCCCTGAAAATTTTCCGCCTGAGAAATCATTAATGGCAGATAGAATTTGGTCACTTGGGATTGCAACAGTATCAGCAAGAAAAACAGC
106049 G T GCGCGACAATCTACAACGGGAAGAGCCATGGATCAGAAGAAGGAACAGAGAGTTGCGCTCTTCTTATTCTTGCGATGAAATGATTGAAGAAAGGAGGAGC[G/T]GGGAAGCGCTTTCGGTAAAGCTAGGTATCGCTGAGAAGTTCGAAATTGCAAGCTCCGATATTTTAGTCACAAATTAAATTCCAGT
106051 A G GTTTTGTTGAATATTTCCGACTTGCAACACCGGAGCTAGAGTATGGAAGAATGAACATCGGAAGCAGGCCTTCAAAGAGAAAGCCAAGCGGTGGCATTGA[A/G]TCGCTACGTGCGATTCCATGGATTTTTGCGTGGACACAGACAAGGTTCCACCTACCTGTGTGGCTTGGTTTTAGAGCAGCATTCAA
106053 T C TACATATGATACTATAATTCAGAGTTCATCGTTAACTTGTAAATCGCTTAGAGGTACACTAGATCCTGATTTCATAGCAGCAGTTATTTTTCTCTGTAAT[T/C]TGAGTAAACCGACTCTTTTTGAAACCACATATAGCACAGCAGACATGAAAATAAGAAATCCAATGACCATGATCAGCCTATCCATCACAT
106055 G A GCTATTGAGCTACCCTAACCCAAAGAAGTATCCAAGCACCTCTACTCACAAGCAGAATCCCAAAAAATCCAAAGCAGACACCAAGTACTACTAATAAGTC[G/A]AGTTCCGAAATGCACCGCACCAGTGACGAAACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTA
106055 A G CCAAAGAAGTATCCAAGCACCTCTACTCACAAGCAGAATCCCAAAAAATCCAAAGCAGACACCAAGTACTACTAATAAGTCGAGTTCCGAAATGCACCGC[A/G]CCAGTGACGAAACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTACCTGGATTAGCCGCGAAGT
106055 A G ATCCAAGCACCTCTACTCACAAGCAGAATCCCAAAAAATCCAAAGCAGACACCAAGTACTACTAATAAGTCGAGTTCCGAAATGCACCGCACCAGTGACG[A/G]AACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTACCTGGATTAGCCGCGAAGTGGATAGTGCC
106055 T A CACCTCTACTCACAAGCAGAATCCCAAAAAATCCAAAGCAGACACCAAGTACTACTAATAAGTCGAGTTCCGAAATGCACCGCACCAGTGACGAAACCCC[T/A]TCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTACCTGGATTAGCCGCGAAGTGGATAGTGCCATTGTCA
106055 G A CACCAAGTACTACTAATAAGTCGAGTTCCGAAATGCACCGCACCAGTGACGAAACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGC[G/A]AGTAGTTACCTGGATTAGCCGCGAAGTGGATAGTGCCATTGTCAGAAAGGTATCCGCAGAGATCTACAGAGGAGAGATGAGGTTG
106055 T C CAAGTACTACTAATAAGTCGAGTTCCGAAATGCACCGCACCAGTGACGAAACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAG[T/C]AGTTACCTGGATTAGCCGCGAAGTGGATAGTGCCATTGTCAGAAAGGTATCCGCAGAGATCTACAGAGGAGAGATGAGGTTGAG
106055 G A CGAGTTCCGAAATGCACCGCACCAGTGACGAAACCCCTTCCACCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTACCTGGATTAGCC[G/A]CGAAGTGGATAGTGCCATTGTCAGAAAGGTATCCGCAGAGATCTACAGAGGAGAGATGAGGTTGAGGAAATGGGGAAAGAGGA
106055 T A CCATCGTGACCAATAGTTGAAGAACAAGCGACGAAGCGAGTAGTTACCTGGATTAGCCGCGAAGTGGATAGTGCCATTGTCAGAAAGGTATCCGCAGAGA[T/A]CTACAGAGGAGAGATGAGGTTGAGGAAATGGGGAAAGAGGAACTCATAAATGATTTTTAGGTTTAGCTTAGATCTAGAGGCGA
106055 G A GATAGTGCCATTGTCAGAAAGGTATCCGCAGAGATCTACAGAGGAGAGATGAGGTTGAGGAAATGGGGAAAGAGGAACTCATAAATGATTTTTAGGTTTA[G/A]CTTAGATCTAGAGGCGAAAAGTTGAGTTTTGGGAAAACCCACGCGTGACGAAAGCTTGGTAGGGAGAAAGGCAGAGATGCGAG
106055 A G TTGTCAGAAAGGTATCCGCAGAGATCTACAGAGGAGAGATGAGGTTGAGGAAATGGGGAAAGAGGAACTCATAAATGATTTTTAGGTTTAGCTTAGATCT[A/G]GAGGCGAAAAGTTGAGTTTTGGGAAAACCCACGCGTGACGAAAGCTTGGTAGGGAGAAAGGCAGAGATGCGAGAGACGAATG
106055 G A TCCGCAGAGATCTACAGAGGAGAGATGAGGTTGAGGAAATGGGGAAAGAGGAACTCATAAATGATTTTTAGGTTTAGCTTAGATCTAGAGGCGAAAAGTT[G/A]AGTTTTGGGAAAACCCACGCGTGACGAAAGCTTGGTAGGGAGAAAGGCAGAGATGCGAGAGACGAATGGTGATTTTTGGAGG
106059 A G GCCGCCTCTCCTCCGTCCTTGCCCCGAGGTGGGAGGAAGACATGGACGACTTGTCTCGAGCTCGCTCCACGCCCGGGTATTTATGGCGCAAGGATGAGAA[A/G]TGGCTTGCTGTCACCACCGTGTCTAATGGAGATGGACTTCAGACGTTTCGTACAAGGCCAAAGATCGATTGCCAAATTAATGAAC
106061 A G CGTACGTCAACCTTGCGATATTCGATCCCAAGACGTCGCGCGGGTACGTGAGGGGGTTGATCGGGGAGGCGGCGGAGAGGTTGGTGCATTTGTTTTGCGT[A/G]GTCGATAGGCAAAGGATCATTCACGATGATTTGCTGTTTAGGTTTGGGGACGAGGAGTTGACTGATTTTTTGCAGAAATCGGAG
106069 A G CAAAAAATTCGTATTTTGTACGACGACCCTGATTTGACCGACTCATCAACCGACGAAGATGACGACGGGAGACACGTTGCAAAGCGCAAACGGGTTGTGA[A/G]AGAGATACCCGTTCGTGTGTACCAGGCCCGGCCTAAAACCTTTAAAACCTCAGCAGAAGCGTCGACAAAAGAGTCGTGCAAGTAC
106069 A G ACCCGATAAGGAAAGTGAGGAGATGGCTTGGTACGTACGACACGGCGGAAGAAGCTCATCAGGCTTATTCGTCCGCGTACAGTTCTCTGCAAGCGGAGAA[A/G]GAAGCGATGGTCTCTGGTGCATCTTCCAACTGTTCGGTTCCTTCCCCTTCGTCTGTTCTTGAAAGGAGCGGCCAAGATAGGCCGA
106069 T C ACACGGCGGAAGAAGCTCATCAGGCTTATTCGTCCGCGTACAGTTCTCTGCAAGCGGAGAAAGAAGCGATGGTCTCTGGTGCATCTTCCAACTGTTCGGT[T/C]CCTTCCCCTTCGTCTGTTCTTGAAAGGAGCGGCCAAGATAGGCCGAAGACTGACGATATGCTGCAGGAGGGTACGTTGATCGCGG
106069 C T CGGAAGAAGCTCATCAGGCTTATTCGTCCGCGTACAGTTCTCTGCAAGCGGAGAAAGAAGCGATGGTCTCTGGTGCATCTTCCAACTGTTCGGTTCCTTC[C/T]CCTTCGTCTGTTCTTGAAAGGAGCGGCCAAGATAGGCCGAAGACTGACGATATGCTGCAGGAGGGTACGTTGATCGCGGATATATT
106069 A G CGTACAGTTCTCTGCAAGCGGAGAAAGAAGCGATGGTCTCTGGTGCATCTTCCAACTGTTCGGTTCCTTCCCCTTCGTCTGTTCTTGAAAGGAGCGGCCA[A/G]GATAGGCCGAAGACTGACGATATGCTGCAGGAGGGTACGTTGATCGCGGATATATTCGAGGAAGATCCGTTATCGATGCACAAGG
106069 CT C AAAGCGAGGCGTATTTGGTGGGTAACTTGGATGATGATTATTTTGGGCTGGATGATTTGCCGATGTGGGAGCAGCAGTTTGATTGCTCTGATGATTTTTC[CT/C]TTCTTTGATCATTGTTGATTGGGTCTCTGGTTTTGGAATTTATATGTTGTAATGAAGATGTTAATGCTGCTCCGTTATTGTTTTAAGT
106071 G A GCTTCTCTGATTACATCGTCACTTATGCCCTTAACAACAATCTCTTTTGGTTGCTTGCGAAAATATACAAAAGAACTTTTACTATTATCTTTTTCTGATG[G/A]AGATACGTATTTGTTCAAGTACAACTTGAGAAGTTTGAAGCGTTCTTCTTCACGAGGGAGAGGGAACTCGATGACCTCGTCAATGCGGTC
106071 G A CGATGACCTCGTCAATGCGGTCGGTTATTGCCGCATCAAGGTCAGCAGGACGGTTTGTTGCAAGGACGAGAACAATGTCTCGTGATTGGTCACCAGTACG[G/A]AAGAGGAGGGCGTTAAGAGCACTTCTTTGTGCTTCACTCATATGTTTGCTGTTTCGTTGGCACAAAAATGCATCCGCCTCATCAAT
106071 C T TGTCTCGTGATTGGTCACCAGTACGGAAGAGGAGGGCGTTAAGAGCACTTCTTTGTGCTTCACTCATATGTTTGCTGTTTCGTTGGCACAAAAATGCATC[C/T]GCCTCATCAATGAAAAGCAACAGTCCTTTCTTTGATTTTTTAGCCCAGTCAAATATCTGATGAATCTTGGTAACAGCTTGTGAACCCAA
106071 A G TCTGATGAATCTTGGTAACAGCTTGTGAACCCAAAGGTGCAACATCACCTCCAGTCATCATTGCATAATCCAAGCCCGATTTTCGAGCCATCTCTCTAGC[A/G]ACTAATGTTTTTCCAGTACCTGGCGGTCCATAGAAAAGCATGTTACGAAAAGGTGCTTCATGAGATTTTGTGTTTTCTGTGGCTCGAGC
106071 C G AGATTTTGTGTTTTCTGTGGCTCGAGCAAGTTGCTCAATTCTTTTATGCAACGAGGGATGAAGAATAACATTGTCGAAACTGGTTCCACTTTCCAATGAT[C/G]CTGAACTAGAAGTTGACATCCTTTTGGTCAACTTAGTGGCAATTCCCGACCAGGGAAATCTGGCTATAGATGATTCTCGTATCAGTGA
106071 C T ACTTAGTGGCAATTCCCGACCAGGGAAATCTGGCTATAGATGATTCTCGTATCAGTGATGGTTGACCTAATAATCTGTTGACATAGCCCCACATTACTCT[C/T]GCACCTTCCCTAGTAGTGTAAACACCAGCAGCTAGAGCAGTAACTCCACCTACAGCCATTACCATTTTGCTTCTGTCAGTAAGCAACAT
106075 A T GAGGATTTGGCTTTGTTCAGTATATTGATCCAGAAGATGCAGCAGACGCCAAGTATGAAATGGATAGAAGGGTTTTCCTTGGCAGGGAGTTGACTGTTGT[A/T]TTTGCTGAAGAGAACAGGAAGAAGCCTTCTGAAATGAGAGCTAGGGAGAGGCTCAGGAGTCGATCTTATGACTATAGGTCGCCAC
106075 CT C TTCACCTCGTGATGATAGAAGGCATCGAGGAAGGTCGTATTCCCGTTCTCCCTATTACTGAAGTGGATACTCGATGTTGCCATGCTTTCTTTTTCCTACC[CT/C]TTTTTTTAACGGTTGCAGTGGTCATATTGTGTACTTAAATATTGTGCACTGCTTCAGAGTAGGTTTTCTAGTTTTGGATATTAGAACCA
106075 A T TTTTTCCTACCCTTTTTTTAACGGTTGCAGTGGTCATATTGTGTACTTAAATATTGTGCACTGCTTCAGAGTAGGTTTTCTAGTTTTGGATATTAGAACC[A/T]TTTTGAAATTCTGTTATTATTGCCGGCTTCAATGCTTGTTTCAAAAGTTCTCCGAAGTTGGTATCTTCTTTGATTTGGTAGAA
106075 T A TTCCTACCCTTTTTTTAACGGTTGCAGTGGTCATATTGTGTACTTAAATATTGTGCACTGCTTCAGAGTAGGTTTTCTAGTTTTGGATATTAGAACCATT[T/A]TGAAATTCTGTTATTATTGCCGGCTTCAATGCTTGTTTCAAAAGTTCTCCGAAGTTGGTATCTTCTTTGATTTGGTAGAA
106075 T G CGGTTGCAGTGGTCATATTGTGTACTTAAATATTGTGCACTGCTTCAGAGTAGGTTTTCTAGTTTTGGATATTAGAACCATTTTGAAATTCTGTTATTAT[T/G]GCCGGCTTCAATGCTTGTTTCAAAAGTTCTCCGAAGTTGGTATCTTCTTTGATTTGGTAGAA
106077 GA G ATGCATTTCTGCTGTAGGGGTAGGACTTGGGCAATCACTTTGGAAAATCTGGTTCTTACCAATATTAGTAGCAGCAGCAGCATTAGGAATATTATTTTGA[GA/G]AAATAACTGAAACAAAGCCTGGGCCGCCCCAGTGACCATTTAAGGTGTTTGTAGCTGGTGCTGGTGGAGGTGCATTAACTATAGA
106077 G A ACAGATTGTCCCCCAGGAGGCATGCCACCGAGCCACTGATTACTAGGGACAATAGGTAGGGGAGGTACAGGATTGTTAGAACTCCAATTACCATATGTAG[G/A]AGTGATTGGTACAGTAGTATTCTGAATTTGAATCTGAGGTCGAATTTGTCCAATTAACGTGTTAGCATCAGGCAATGGATTTGGCG
106105 G A CAAACAAGATCGGTACATCCAGCATCGACACCACCTGCACCATCTGGGACGTCGAGAAAGAGGTATTAGAAACTCAACTGATCGCGCACGACAAGGAAGT[G/A]TACGACATCGCGTGGGGCGGCGCGGGGAGTTTCGCGTCCGTCTCGGCCGACGGATCTGTACGGATGTTCGATTTGAGGGATAAG
106105 C T GGGATCCTAGGTACATCGGGGCTATAACGATGGACAGTAACAAGGTGGTGGTGTTGGATATTAGGGTTCCGCCGCTGCCGGTGGCGGAGCTGGTGAGGCA[C/T]AGGGGGAGCGTGAACGCGATCGCGTGGGCCCCGCAGAGTGGAAGGCACCTGTGCTCGGGCGGCGATGACGGGCAGGCTTTG
106105 T C ACGGGCAGGCTTTGATTTGGGAAGTGGATAACGGGTCGGGCGTGGTGGGTGGGGATGGGGTGGATCCGGTTCTGGCGTATTCTGCTGGGTGGGAGATTAA[T/C]CAGCTTCAGTGGTCTGTAGGGCAGCCCGATTGGATTGGGATTGCCTTTGCTAATAAGGTGCAGCTGCTTAGGGTTTGAACACT
106105 T C TGGGAAGTGGATAACGGGTCGGGCGTGGTGGGTGGGGATGGGGTGGATCCGGTTCTGGCGTATTCTGCTGGGTGGGAGATTAATCAGCTTCAGTGGTCTG[T/C]AGGGCAGCCCGATTGGATTGGGATTGCCTTTGCTAATAAGGTGCAGCTGCTTAGGGTTTGAACACTTGGGTTGGGTTGAACCA
106107 CA C GCGATAGCTGCACATGCATCACGAGGGTCCTTGAAGCTAGCAACCATATTAACAACGGTCTGACTAGACAAAAACTCAAAGACCCCATCACTAGCCACCA[CA/C]AAAAAACAAGCAATCATCTGTGATCTTCACCTCCTTCACCTCAGGAACGGCTACCACCCCAATCCCTTCTGCCATTAGATCCCCGAC
106107 C T TTAACAACGGTCTGACTAGACAAAAACTCAAAGACCCCATCACTAGCCACCACAAAAAACAAGCAATCATCTGTGATCTTCACCTCCTTCACCTCAGGAA[C/T]GGCTACCACCCCAATCCCTTCTGCCATTAGATCCCCGACGCTTCTAGTAAATGCCGTGCCTGGGTATAATGCATGCTCCACCCACAATC
106107 T C CATCTGTGATCTTCACCTCCTTCACCTCAGGAACGGCTACCACCCCAATCCCTTCTGCCATTAGATCCCCGACGCTTCTAGTAAATGCCGTGCCTGGGTA[T/C]AATGCATGCTCCACCCACAATCTAGGTGGATCACCTTCCTCATCCTCCTCTTCATCCCCCCAACTTTGTACCTCAGGATCTTTCAACCCCT
106107 TC T TGCCATTAGATCCCCGACGCTTCTAGTAAATGCCGTGCCTGGGTATAATGCATGCTCCACCCACAATCTAGGTGGATCACCTTCCTCATCCTCCTCTTCA[TC/T]CCCCCCAACTTTGTACCTCAGGATCTTTCAACCCCTCCACCTGATCCGCACTTAACACCCTCGCTCCGCACTTCTTAACCCTCTCGCACT
106109 A G TAATGGTGGATCCGAAAATCCACCACCAGATATCCTGTCAAATACAAATTTATTTCCCGCTTCAGTGTAATGAACTCCATCCCAGTTAACACGAGTAGCT[A/G]GATTTTTGCATGAGCTTCCAACAAGATGTTCTGTACCATTTACACTAACTTTTGCCCCACAACCAATGTGAACATTGTAGTTGTACTTGC
106109 C T TAAGCTTATGGTTAAAGAGTTTAGCCACATCATTGAACACAACACCACATCCATGTTTATCCTTCTCCGATACAAACTTAAGATCACGTTCAAGTACATA[C/T]GGTAAGCATCCAAATGGACCCGTGTTGTGTATCCAAAAGTGTCGCCCACCCTCTCCGTACACACTCTCTATGGTTATTTTGAACTTGTGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106109 T C CGTCTAGAGAGATTGGGCTGTAGCCGGTCTGAAAGAGAGTCGTGTTTTGACGCCTGATGGTTGATCCAGCTGTTGCGAAATTAGCTCCATGGCTGAAGTT[T/C]GTCCCCAGAGAGTCCAAGTATGCACTCAGGAAAGGCAAATTCAAACTGCTTGCAATGAAGTCGATGATGAGGCGGCCATCAGAGT
106113 T C TTTTTCAGGAATCCAACCGTTCGCTTCCAAATCTTTGATGAAATCGGGTACTACTGGAGGCTCAGTTAGATCTACCACGGCTGGGATTGGGCAGAGAATG[T/C]GCCTTCCATTTCCATATCCTAGCGCCTTCACCATGCCAGCTGGGGAAGCAAGTTCAGGCACCAAAACCCTGATCCTGGTCGGATCCT
106113 A G AGGCACCAAAACCCTGATCCTGGTCGGATCCTCTGGGCAAATCTGAGCAGAAAGCCCGGATTCATGCAGCAGCTGAGCATCCTCTCCAAGCGCTGCAAGC[A/G]CAAATGAATCGTCAACATCGTCATTTGGCAAGGGCTGTGACTGTGCTCGACCCCAACTATTCATCTCATCATCAACAAGTGCATCTG
106123 A G AGTGTCCATGAGACATTATCAACGGAGCATGGATCCTGCTTCACATATCGATGATTAAAAGTGCATCCACTTTGAAGATCGACTCTATGATTCTCCTTCA[A/G]ATGTGATAAAAGAGACTGGATGTCTCCATTAAATGGACAGTCTGATCCAGGATGAGGGCAATCATAAGGTCTAAAGTTACATTTTTCT
106123 A G GCGGAAACATAGAATTTAAGCACACTGGACACTCTAAAAGACCATCTATTTCACTGTTTGGAGGAATTGTTGGATTTTTCAAATTTGATGCTTTAGAGTG[A/G]TGAACCTTCTGATTTGTACTGCCATTCAAGTCACTTGAGTTGCCAAGATACGAGGATGTATCATCCATGTTCTTTGAAATAGTATAAGA
106123 T A CATCCATGTTCTTTGAAATAGTATAAGAAGATGTAATGTTTTGTTTATTTCCAAGCTTAATATTCTTCATGCCTGTGCGGATTCAAGCGTCTAAATCTCT[T/A]CTTCTATACCGTTCGGTAATCGAATCTTTATAAACGCAGTTTTCTCCTTTAGCTTTATTTTGTTCCGCAGAACATTCCAGTAGGCCAACAGT
106127 A G CTGCTTCTTCATCTGGGTACGGAATAACGGCAGCATCAGCTATTTCCTTATTTGATTGAAGTATTTGCTCCAGTTCAGCTGGAGGAACCTGATAACCTTT[A/G]TACTTAATCAACTCTTTTAGCCTATCGACAATAAAAGGAAGCCACTGTTATCAAAGTAGCATAAATCACCAGTTTTTAGCCAACCATCTG
106129 G C ATCATCCCAGCTAAAATTGAAAGTGAAAATGCCAGGAGCAGACTGGAGCTCAGGAATAGTAGTAGTTTTGGTAGAAAAGGGTGATGTTTGAACATCAGTA[G/C]TGACCATAAGATTAATAGAACTCATGCATACAAGTGTCCCATCTTTAGTTAATTGAACAGGACAATCAATAATATCTGCACCATCGT
106129 T C TCATCCCAGCTAAAATTGAAAGTGAAAATGCCAGGAGCAGACTGGAGCTCAGGAATAGTAGTAGTTTTGGTAGAAAAGGGTGATGTTTGAACATCAGTAG[T/C]GACCATAAGATTAATAGAACTCATGCATACAAGTGTCCCATCTTTAGTTAATTGAACAGGACAATCAATAATATCTGCACCATCGTC
106137 T C GCAGGAACTTCACTTCCATTGGCGCTAAGCACAATCGTTTACTTCATCAATCACCGGTATGATGGCACTCAACTGTGGCAACTGCAAAGTGTAACTGGAC[T/C]CCACGAGCTTGTTTGGATCTCAAACTTCGTCTCCTTTTTATTTCTCTACCCATCCACTTTCAACTTATTAGAAGTAGCTGCAGTTGATAA
106137 T C TCAACTGTGGCAACTGCAAAGTGTAACTGGACTCCACGAGCTTGTTTGGATCTCAAACTTCGTCTCCTTTTTATTTCTCTACCCATCCACTTTCAACTTA[T/C]TAGAAGTAGCTGCAGTTGATAAGCCCAAAATGCATTTATGGGAAACTGGAATAATGAGAATCACTAGACATCCACAGTTGGTAGGGCAA
106137 T C ACGAGCTTGTTTGGATCTCAAACTTCGTCTCCTTTTTATTTCTCTACCCATCCACTTTCAACTTATTAGAAGTAGCTGCAGTTGATAAGCCCAAAATGCA[T/C]TTATGGGAAACTGGAATAATGAGAATCACTAGACATCCACAGTTGGTAGGGCAAGTAATGTGGTGTCTGGCTCACACCTTATGGATTGG
106137 A G CTCAAACTTCGTCTCCTTTTTATTTCTCTACCCATCCACTTTCAACTTATTAGAAGTAGCTGCAGTTGATAAGCCCAAAATGCATTTATGGGAAACTGGA[A/G]TAATGAGAATCACTAGACATCCACAGTTGGTAGGGCAAGTAATGTGGTGTCTGGCTCACACCTTATGGATTGGAAATTCGGTGGCAGT
106137 A C CAGGCACGGCGAAGCCTTTGATGCAGTAAAATCAAGAACAAGCGTGTTTCCTTTCGCAGCAATACTAGATGGACGGCAGAAGCTTCCCAAGGATTACTAC[A/C]AGGAATTCATCAGATTGCCTTACTTTATTATTACTGCTTTGACGGTCGGTGCCTATTTTGCTCATCCGTTGATGCAGTCTTCTAGCTT
106139 T G TCGCCAAACTGAGGACCATGCCATTTTGCTTCGGGCATCATAGAGTACGGACCAGCTCCCATTCTCATATAACCGAACGGGCTTTGCATGTCTGTACGCA[T/G]TGGTGGCATATAAGGAGGAATGCCAAAAGGTGAAACAGGACCCATTGCTGCATTATAAGGCATCATCCCTGGGTGACCATACATGT
106141 CA C CCTTCTGGTAAAAATGCCTTCCATAGCCAGTCTGTTCTTTCTATTGATACTAATGGGGCATTCACCAACCTCAACTCTGAATCTGTTCTTTCTTCTCCAC[CA/C]AAAAAAAGGTTGGATCAAGATCATTCCAGCTAATTTCACCTTCTCCCAACTACTTTCTTCTGCATACATTTTTGCTACATGATGTGCGATA
106141 C CA CATCTCAGCACATCAACTCCGTCGACGTACGGTGCAGGCCATTTGTGTTCGGGCGATCGACGATACTCAACAGAAACAAGAACAGCGTTGAACCTCTTCG[C/CA]AAATCTCCTACAAACAATATCATAAGCGCGGGAAGCAGCAGAAAGAAACGCAAAACCGCCTCCATGAAAAAACACGACAACCGG
106141 G GA TCAACAGAAACAAGAACAGCGTTGAACCTCTTCGCAAATCTCCTACAAACAATATCATAAGCGCGGGAAGCAGCAGAAAGAAACGCAAAACCGCCTCCAT[G/GA]AAAAAACACGACAACCGGAATCTTCGCAGCAGCAGCTTCAGAATCCAGGGGAACGAAAATCCGAAACCATAGATCTCTAGCAGG
106141 C T CTTCAGAATCCAGGGGAACGAAAATCCGAAACCATAGATCTCTAGCAGGGTCCACGACGACGTCGAACGTACGCACGCCACGCACCGGATTAGGGTTTGC[C/T]GAAGTTTTGGGGTCGAGGAAGGACATAAGGCGGCGGTTGACAGTGCCGTCACGACGGCGGGAGAAATCTGTGGCGGCGGACA
106143 T C CAAATGCTTTCTGCAGCTTTTCACTTGGCAAAATACCAAATAAGCGCTGAAACAGTTTGTCGCTTCCTCCTTCTGCAAGCACCTTTGTTCCTTGTGCAAG[T/C]CTGCCTATTGATACATCGTATAAATTTGGACTGGTTCTGAGATGCTGCCATACGTTACCAGCAGTCTCATTGGCCTTTCTTGTACCATCTT
106143 AT A GCAAGTCTGCCTATTGATACATCGTATAAATTTGGACTGGTTCTGAGATGCTGCCATACGTTACCAGCAGTCTCATTGGCCTTTCTTGTACCATCTTCCA[AT/A]TTTTTTTTCACATCTCCCCAGCAATTTAATAACTGTATCCACCGGACCTTTATCTTTGGATGATCCATGATAACTAGGCTCAATCTGCAC
106143 CT C GAATCCCGGTAGCCGGCATGACTGCAGCGTTGGAGCCGGGCTGCTGATGAGGAAGTGGCGATCCCATGACCCACTTTACGTGCTTTTTCTGCTCCATTTC[CT/C]TTCTTTTAATCCTTGTTAATTGCTGAGGAACTACTTCAATTTGAGAATCTGAATCAATAAGTAGCGGCAAAAGCGGGAAAAAAGAT
106143 T C CGGTAGCCGGCATGACTGCAGCGTTGGAGCCGGGCTGCTGATGAGGAAGTGGCGATCCCATGACCCACTTTACGTGCTTTTTCTGCTCCATTTCCTTCTT[T/C]TAATCCTTGTTAATTGCTGAGGAACTACTTCAATTTGAGAATCTGAATCAATAAGTAGCGGCAAAAGCGGGAAAAAAGATGGGATTG
106155 C T CTAGGTTTCCATCTCCAGTTTTCATAGTCTTTATCAGGTCTTCCATTACCTTGGCAGTTTTGTGACTGTGTTAATATTGGGCATGTGTAGTTTGTATACA[C/T]AGGCCCCGAACCATCATGTATCCACTTTCCATGGTACAGATCACACTTCCTTGTATCAGACTTTCCATATTCTTTTGCAGCATTTTCTCCAG
106155 T A AGGTCTTCCATTACCTTGGCAGTTTTGTGACTGTGTTAATATTGGGCATGTGTAGTTTGTATACACAGGCCCCGAACCATCATGTATCCACTTTCCATGG[T/A]ACAGATCACACTTCCTTGTATCAGACTTTCCATATTCTTTTGCAGCATTTTCTCCAGGAACAATTTTC
106157 G A TTTCGTTCTATTGCAGAATTTTTCCTTCGAAGTACACGATGGGGTTTCCAATTCCTTAAAGGTAAAGGAGTATTTTGTAAACTTGGATTCTGACAAGCTT[G/A]TCCTCGCCTTTATCCCCGCTTCCACTTCCTCCTTCGCTTTTGTCAACGCAATCGAAGTGGTTTCTGCACCTGATGACCTTTTCGGAGACAA
106157 G A TTTTTCCTTCGAAGTACACGATGGGGTTTCCAATTCCTTAAAGGTAAAGGAGTATTTTGTAAACTTGGATTCTGACAAGCTTGTCCTCGCCTTTATCCCC[G/A]CTTCCACTTCCTCCTTCGCTTTTGTCAACGCAATCGAAGTGGTTTCTGCACCTGATGACCTTTTCGGAGACAAAGCGCGGCTGGTAAGA
106157 T C TCCCCGCTTCCACTTCCTCCTTCGCTTTTGTCAACGCAATCGAAGTGGTTTCTGCACCTGATGACCTTTTCGGAGACAAAGCGCGGCTGGTAAGAAATGA[T/C]ATAGTTGAGAGCTTTTACGGGTTAAACAAACAAGCACTGCAAAGTTTCTATAGAGTTAACGTTGGTGGCGCTAAAGTCACGCCTTTTA
106157 T C TTCTGCACCTGATGACCTTTTCGGAGACAAAGCGCGGCTGGTAAGAAATGATATAGTTGAGAGCTTTTACGGGTTAAACAAACAAGCACTGCAAAGTTTC[T/C]ATAGAGTTAACGTTGGTGGCGCTAAAGTCACGCCTTTTAACGATACGTTTTGGAGAAACTGGGTTCCTGATAGTTTTATAACATCCA
106157 A G TTTGTGACATTGCAAGTTTAGTTCTCAATGAACTTTACCTAGACATGTACATCAACGGGCATCTTGCATACAAAGATTTTGATATATCCGATGCTGTAGG[A/G]TACTTGGCATCTCCTTATTATATCGACTTCATTGTTGATGCTGGTAAATCTGGTTTTTTGACCGTCATTGTTGGACCTTCTAAGTTAACTG
106167 C T TCTCGAGGAGGTCAAAGACCTTTGTCACAGTTGTCATCTCGGAGTACAAGAAGACTTGCTGATTCAACGTTCGAGGATCAGCAATAGTGCGAGCCACGAA[C/T]TTCCCAACATCCCGATTATCTGTGAACGCTGACGGCATATTGCCGTCTCCAGGGATACGTATGTTCAGACCGCTGTGTGCATAGTCG
106169 A G GTAGCTACTCAAATCCGAGGCATTCTTCGCATAAAACCAGGAATTGTTGTCTTAAGACTTGGTTGATATCAATCCCGACACCAACGCTTCAGCTCCAAGC[A/G]AGCACTTTTCTCGCTGTTACCGCGACCCAAAGAAAAGGGATGTTGTAAGAAGCAGAACTCCAACCGAAGGAAACATAAGAGACTCTT
106171 C T AAGCGTCAGCGCCGCTGGAATGTAACTAGTACTAAAGCTTCTGATTCACAAACATCCAATTTAACAGTTGATACACCAAAAGCTGCTCTCCAGCCTACGC[C/T]CAGAAAACCATTTAATAGGTCCAGTTCTTCAGTTAGCGGAGATGCCACACCAAAAGAAAGAATAGTTCCACCATCGTTAAAGCCAGCT
106171 C T TCACAAACATCCAATTTAACAGTTGATACACCAAAAGCTGCTCTCCAGCCTACGCCCAGAAAACCATTTAATAGGTCCAGTTCTTCAGTTAGCGGAGATG[C/T]CACACCAAAAGAAAGAATAGTTCCACCATCGTTAAAGCCAGCTACTACTTCTTTGAGGATTGACCGCTTTCTGCGCCCTTTTACTCTGA
106171 C T CTACTTCTTTGAGGATTGACCGCTTTCTGCGCCCTTTTACTCTGAAGGCCGTCCAGGAATTGCTTGCAAAAACCGGAACTGTGTCTGATTTCTGGATGGA[C/T]CAGATCAAGACTCATTGCTATGTCACTTACTCGTCAGTAGAACAAGCTGTAGCCACGAGGGATGCCCTCTACAACCTACAATGGCCAA
106179 T C ACAAGAACCAACACACTAGAGTGACCGTGCTAGAGATAGTGAAGCGCTCCCCTCAGCAAACACAGTTGGAATGGTAAGGCAGAGCATCCAGACAGTAGCA[T/C]AGCGAGTCGCGTATTCATCAAGCGGCTTCAGAAGTTACTGCTATTGCAGTCCTCTGCGGTGGCCAAATGAACCCAACCATGACAA
106185 A C GATGCCCCCACATAAACTACACTTCCTGAAACAAATCAAAGCACCCAGTACCAAACTTAACAGGCTGACCAAGACACACGCTAGCAGAAGGGGTCTCAAT[A/C]AGGTCCCTCTCCCCAAGCAAAGCAGCATTCACAATGAACTTAGTAGCAGTCTCAAATGTCATTTTACTGAAAGGCGAGGTGTTTGTA
106185 AT A AGAAGAATACGCTGTTGATTCGTCAAGACAAAATGAGCCTCAAAATTTAACCCCTTTGTATCCACATAAATTAAACTTTTGACCTTTTTGCGGGAGGTTG[AT/A]TTTTTTTGTTGCTTTGCTTTTACTTTTGCTCTTGCTCTTATCGCTGGTTTTACTTTTTCCTTCCCTTTTGGTTTTCTTTTTCGCTGATGAAG
106191 C T CCGAGCTAAATATCTTCCGGTCCACAAGATGTTGCAGTTCGAAAGGATCCGCAAATACTCCAATTGGGAGTCTTTCAATTAATATAATGTTGCATGTGTT[C/T]TCATGATACCAAACTGAATCATCCGAATACATATTTAGAATAACAGTGGAGACTAAATGACGATGTGAGCCTTCACCAATTAAATCTCG
106191 T C TTATTCGTCTCTTTGCAGAAGTCAATAGACTTGATACTGCTATGTACGAAATCATGAAATTCTGAATCGATTAGTTTATCATGGTTATTGAAATATGAGG[T/C]CGATATATACTCTTGGTTGCATGGCAAGCATCCTTCAACGAATGTATTGTTTTCCATGAAGTTAGCATTGCAAGTTTTGGCCTTAGTCCG
106191 G A ATCCTTCAACGAATGTATTGTTTTCCATGAAGTTAGCATTGCAAGTTTTGGCCTTAGTCCGCCAGGAAGCGTGGAGCAGCAGAGCAGGACAACGGGAGCA[G/A]AGGCGTAGAGCGAGTAGACGCTGAATTAGTGGCGGTGACCGGCTCTAGGGTTGTGTAGCGCAGTAGTTTGCTGGAGAATTGCAG
106191 A G GCGAGTAGACGCTGAATTAGTGGCGGTGACCGGCTCTAGGGTTGTGTAGCGCAGTAGTTTGCTGGAGAATTGCAGTTACGTTGACAGCGAGGCATTTGAA[A/G]TTGTCGTGACTCGCGATGTAGTTCAGCTTGGTTTTTCCCCTGTTGAGAAAGGGGAAACTGGTTGCTCCAGCAG
106195 G A TTAACCTATACTCGATATCAGCCAAGTCATTGATTAAATTTACTCGAACATTTGATGGCATCATGATCTTGAACACAAACATAGTTACCTCCCTGACAAT[G/A]TCTATTAGTGCCAGCCCTTTCCTCGTTTTTGTCTCAGATATATATCTCAGGCTATCTGTGAAAGGTTCATTAAGAAGCCATTTCGCTATCT
106195 C A TTAAATTTACTCGAACATTTGATGGCATCATGATCTTGAACACAAACATAGTTACCTCCCTGACAATGTCTATTAGTGCCAGCCCTTTCCTCGTTTTTGT[C/A]TCAGATATATATCTCAGGCTATCTGTGAAAGGTTCATTAAGAAGCCATTTCGCTATCTGCTCAATGTCTTTTGGTAAGGGGTTTCCAGTAC
106195 C G CATTAAGAAGCCATTTCGCTATCTGCTCAATGTCTTTTGGTAAGGGGTTTCCAGTACAAAGGTAGACTGCTTCTTCTGTTATATGCTGAGAAGCCATATG[C/G]GTTGACTGCAATATGTTAAGAGCTTTCCTCATGTCACCATTGCTTAGCCTTACTAGCGCTTCCAGGCCATTTTGTGACACATCCAATCCT
106195 A T TCTGCTCAATGTCTTTTGGTAAGGGGTTTCCAGTACAAAGGTAGACTGCTTCTTCTGTTATATGCTGAGAAGCCATATGCGTTGACTGCAATATGTTAAG[A/T]GCTTTCCTCATGTCACCATTGCTTAGCCTTACTAGCGCTTCCAGGCCATTTTGTGACACATCCAATCCTTCAGAATTTATCACATATTGT
106195 A G CGTTGACTGCAATATGTTAAGAGCTTTCCTCATGTCACCATTGCTTAGCCTTACTAGCGCTTCCAGGCCATTTTGTGACACATCCAATCCTTCAGAATTT[A/G]TCACATATTGTAAACGCTCTGTGATATTTCTAGTGTCTAGTGGAGCAAACCGGAACCGAGTGCATCTTGATTGTAATGCTGGAATGATT
106195 T C ATATGTTAAGAGCTTTCCTCATGTCACCATTGCTTAGCCTTACTAGCGCTTCCAGGCCATTTTGTGACACATCCAATCCTTCAGAATTTATCACATATTG[T/C]AAACGCTCTGTGATATTTCTAGTGTCTAGTGGAGCAAACCGGAACCGAGTGCATCTTGATTGTAATGCTGGAATGATTTTGTTGACATTG
106195 G A CTAGCGCTTCCAGGCCATTTTGTGACACATCCAATCCTTCAGAATTTATCACATATTGTAAACGCTCTGTGATATTTCTAGTGTCTAGTGGAGCAAACCG[G/A]AACCGAGTGCATCTTGATTGTAATGCTGGAATGATTTTGTTGACATTGTTACAGATAAGCGCAAACCTTGTGCTCTTTGTATATTTTTCA
106195 G T TCATCAAGTAAAACCAATTTTACTGAAGTAGGTGTGCCAAAGGAGAGGCTTCGAGCACTCGCAAAATCCTGAATTTGTTGCCGAACAACATCAATTCCTC[G/T]ATCATCCGAAGCATTCAACTCCAAAATCATGTTATGATACTGATTACCATACAATTTTCTTGCCAATGCTAATATAGTCGAAGTCTTCC
106195 C T GCCGAACAACATCAATTCCTCGATCATCCGAAGCATTCAACTCCAAAATCATGTTATGATACTGATTACCATACAATTTTCTTGCCAATGCTAATATAGT[C/T]GAAGTCTTCCCAGTTCCTGGAGGCCCATATAGAAGCAGATGTGGCAGCCTATTTTCATTAGTCAACCTGTCAATTGTGTCGACGATGTCG
106195 A G CCTGTCAATTGTGTCGACGATGTCGCGATGTGCGGCAACATCGACCAGAGACTTCGGTCGGTACTTCTCGACCCAAGGAGCCGAAATTCCATCGGGTGCT[A/G]TAGCGACAGACTTTCCCTTGTTCAGAATCGGTGAATGGGAGGCGTCGATTTCCATAGGCGAGCAAACCTCCGTCATTTTGCAATCT
106195 G A CAATTGTGTCGACGATGTCGCGATGTGCGGCAACATCGACCAGAGACTTCGGTCGGTACTTCTCGACCCAAGGAGCCGAAATTCCATCGGGTGCTATAGC[G/A]ACAGACTTTCCCTTGTTCAGAATCGGTGAATGGGAGGCGTCGATTTCCATAGGCGAGCAAACCTCCGTCATTTTGCAATCTTAGGG
106195 C T CGACCCAAGGAGCCGAAATTCCATCGGGTGCTATAGCGACAGACTTTCCCTTGTTCAGAATCGGTGAATGGGAGGCGTCGATTTCCATAGGCGAGCAAAC[C/T]TCCGTCATTTTGCAATCTTAGGGTTTTGGTGGTGTAGGCGCCAAAATAAAATTATTGTAAGCCAGTAGGCCAACAGT
106199 C T CAAATAAGGATCATGCTTGTTGGGAAAGGCCTGAAGACATGGATACACCAAGAACCGTTCTTAAAATTGATCGCAGCAACCCAGGATCTGACGTGGCAGC[C/T]GAGACCGCTGCAGCTTTAGCTTCTGCTTCTCTTGTTTTCAGAAATTCGGACCGTTCATATTCTAGAATCTTGCTCAATAGAGCCATCA
106203 A G CCCTCTCCATCATTGCCAAGTGCTCCAAGTTTTCATGAGTCTGAAATAATGCTTCTCCCGAACAGAGCTCCACAAGAATACATCCAATGCTCCAAATGTC[A/G]CAGGGATAACTCCATCCAAGCCCTAATATGACCTCAGGTGCACGGTAGTGCCTGGTGGAGACAATGTAATTATGATCTTTATTGCCAT
106203 G A TCCATCCAAGCCCTAATATGACCTCAGGTGCACGGTAGTGCCTGGTGGAGACAATGTAATTATGATCTTTATTGCCATAGGTGGAGCTACCAAAATCAAT[G/A]ACTTTTATTGCACTTGATTTGGGTAGCCTCCTGAATGAGGCATCTTTAAAAGACCGAGATGAACCCTTGTAATCAGGTATCTCTATGA
106203 A G CAATCATGGCCGCATCTCTATATTTCTTAATGCCTCGAACAATTTTAATTGCCACCATTTCCTTTCTCTCCCTATCCCAGCATTCCAATACCTGTCCAAA[A/G]GTACCTTCACCCATTTTGCCATGAATTCGATCTTGGACTTTTGAGAAACAACGTCCCAACCCAATCGCGCTCGCTTCCTCGGCCTTCGATCC
106211 A G ACAACCCAAAGGGAAACTGCTCAAAAAAATTGCTAGACTACAAGCTTCATAATTTCCAGAGTATGCACATAGCACAGACCACCACCAAACATAAGCGACA[A/G]GGTCAGGGTCATAGGGACATCTCGTATTTATCTGCTACACATGGCGACATCCCATACATACAAACTTCAGGCATTAAAGGTTCAAGA
106211 A G GGAAACTGCTCAAAAAAATTGCTAGACTACAAGCTTCATAATTTCCAGAGTATGCACATAGCACAGACCACCACCAAACATAAGCGACAAGGTCAGGGTC[A/G]TAGGGACATCTCGTATTTATCTGCTACACATGGCGACATCCCATACATACAAACTTCAGGCATTAAAGGTTCAAGAGTACAGTAGCT
106211 G GA TCAAAGATCAAAAGAAAAACGAGGTTGTAAGGCAGTGGTACCAACAAGACAAACCACACAGAAACCATTGAATACCCAAAAATAAGAAAGACCCATTCCA[G/GA]CTGAGATCGAAACGTGAAATCAATCCTGGAAGTGGGAGTTTATGCTTACCATGTGGCCTCTGCATCAGTGATGGTCCCCCTTCAA
106213 T A GCTGTTGAGCAGTCTGAACTTGAGCAGAAGTGCCTTTGATATCAACTGTGATTTCATCGCGCGAGCTGCCACTTTCCTGAACAGTAAGGATTGCTCCACT[T/A]GTTCTACGAATGTAAGCTATGTTTGCTCCACCAACACCAATTATATCCTCTGCATATGATAGTGGAATCTGCATTGTTTGTGTCATTTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106213 A G GATTGAGCTTTATCATAAAGCTCCCATGGTGCTTTATCTTCATTCCCATTGAACCTGTCGCCACTCCAAGGTGATTTATCACTAAGCACGTTTTGCTGAG[A/G]CAGAGGCAAATGTTCCTGCGCTTGAGCAGACGGTAATGGAGCGTGTGGTGCATTTGGACTTTGCTCAAACAGCGGCACTACGCTATGA
106213 A G TTATCATAAAGCTCCCATGGTGCTTTATCTTCATTCCCATTGAACCTGTCGCCACTCCAAGGTGATTTATCACTAAGCACGTTTTGCTGAGACAGAGGCA[A/G]ATGTTCCTGCGCTTGAGCAGACGGTAATGGAGCGTGTGGTGCATTTGGACTTTGCTCAAACAGCGGCACTACGCTATGATCGACCAAA
106213 T C CATAAAGCTCCCATGGTGCTTTATCTTCATTCCCATTGAACCTGTCGCCACTCCAAGGTGATTTATCACTAAGCACGTTTTGCTGAGACAGAGGCAAATG[T/C]TCCTGCGCTTGAGCAGACGGTAATGGAGCGTGTGGTGCATTTGGACTTTGCTCAAACAGCGGCACTACGCTATGATCGACCAAAAAC
106213 T C GACTTTGCTCAAACAGCGGCACTACGCTATGATCGACCAAAAACTTACGGAGATGTCCAACAACAGCTTCAAGTGCCTTGAAAACTTTTGAATATTCACC[T/C]TGAATATCCACTATTCTTTCTTCAGCCGTTACATACGGCAAATCATCTCCAGTAAGGACTCTAATTGTGGCACCAGTTATCTCTTGAATT
106213 T C GGCACTAATAACCGAACAGGTGCGGGAGAGGATGATTGCTGAGCTGTGACATCAGCACCGATTTCAAAAACACGATTAAACACTCTAAGTACAGCATTCA[T/C]GGCAGGAGAGATTTCTGCTTCAAGATCCTCTTTACCAAAAATCAAAACCACGCGATCAGTAGTCCCAGCGATTCCGTCGAGAATCC
106215 GA G TCTCGACGAGTTGCCGTCGTGGGGATCGCGTGGAGTTGATTGCTTCGAAAAATTGGAGCAGATTGGTGAAGGAACTTATGGTCAGGTTTATATGGCAAAA[GA/G]AAATAAAGACTGGAGAAGTCGTGGCATTGAAGAAAATTAGAATGGACAATGAGAGAGAAGGGTTTCCTATAACCGCCATACGT
106215 C CAGT CGTGAAATAAAAATCCTCAAGAAACTGCACCATGACAATGTAATCCAGCTGAAAGAAATTGTAACTTCTCCAGGCCCCGAAAGAGATGAACAAGGGAGGC[C/CAGT]AGATGGAAACAAATACAAGGGGAGCATTTATATGGTATTTGAATATATGGATCATGATTTAACGGGACTTTCAGATAGACCTG
106215 A G AAATACCATGGTATAACAATTTCAAGCCACCCAGGCCCTTGAAAAGACGCGTTAGAGAAGTTTTTAAACATTTTGACCGCCATGCATTGGAGTTGCTCGA[A/G]AGGATGCTCACCCTTGATCCATCTCAGAGAATCTCTGCAAAAGATGCTCTAGATGCGGAGTATTTCTGGAATGATCCCTTGCCATGTG
106215 T C ACAATTTCAAGCCACCCAGGCCCTTGAAAAGACGCGTTAGAGAAGTTTTTAAACATTTTGACCGCCATGCATTGGAGTTGCTCGAAAGGATGCTCACCCT[T/C]GATCCATCTCAGAGAATCTCTGCAAAAGATGCTCTAGATGCGGAGTATTTCTGGAATGATCCCTTGCCATGTGATCCTAAAAGCTTGC
106221 A AG GTTCGAGTTCACCTGAAAATTGACCATTCACATCGCTGCCATCATGCATCTGCCCAAGACACATATCAGGCTGCTGATGATGATGCTGCATTTCGTGATC[A/AG]TTTTTAAAACCATAAGGGTGAAGCAAGCAACCGCCAGTCATGGCCATTGGCGGTACGCCATCAGTGGCACTGCACAAATGTGGAGG
106221 A G ATTCACATCGCTGCCATCATGCATCTGCCCAAGACACATATCAGGCTGCTGATGATGATGCTGCATTTCGTGATCATTTTTAAAACCATAAGGGTGAAGC[A/G]AGCAACCGCCAGTCATGGCCATTGGCGGTACGCCATCAGTGGCACTGCACAAATGTGGAGGGCGGTTCCCGGTGACAGATGGAGC
106221 T C ACATCCTTCCATAACGGGAAGGGCCAGGAGGCGGCTTCCTACGGCGCTCGTTGTGTCCAGCCAGGCGTCTGCGGCAGCTTCTTTTTCCTTGATCAAATTC[T/C]TGCAACTGATGGAACCTGCTGCACTGCTGACAGAACCTCTGTTCAATTCCAGCGACCACAACTTTTGGTGATTTTGAATGAACTCCGC
106221 A G AATAGGCTTTAGCTCCAGTCAAATCCACTTTGCATCCTTCAACCTGGCATCTAGGTATGCTTATTTGTTGCTGAGCAGAGTTGATATTAGTGGACGAAGA[A/G]GCTAAAGATTTTCCCTTTTTGGGAGCAGCAGCAATTGTATTGCCAGTAGTACTTGCAGTACTAGTAGTGGAATCTTCAAAGTAAATTT
106225 CA C TAATGTGCAGGCAACCAACGTTGGAACACAGGCTAATGTGCAGATGGGACAAACAATGCAGTCTGATCCTTTTGCATCACAAGCAGCAAGACCTCAGGTG[CA/C]AAAAAGGGAAATTTGAACCCAAATCAACTGTATGGGCTGACACATTGAGTCGAGGTTTAGTAAATCTTGACATATCTGGAGCCAA
106225 A G TTGCACCACCTCCAAATCCCATGATGGGCCCCAACAACGTGGGCATGGGAGGCATGGGCCCCATGGGTCCAATGGGCATGGGAATGAGAGGCCCACCAGG[A/G]ATGGGCATGGGTGGATATGGTGGGAATATGAACCAGGCCCCCATGGGCATGAACATGGGAATGATGGGCCAGCATGGGCCCA
106225 A G CATGGGTCCAATGGGCATGGGAATGAGAGGCCCACCAGGAATGGGCATGGGTGGATATGGTGGGAATATGAACCAGGCCCCCATGGGCATGAACATGGGA[A/G]TGATGGGCCAGCATGGGCCCATGCAACCTCCAAATCAAGGCATGCAACAAGGGGGTGGTGGTGGATTTAATCCTATGATGGG
106227 T C ATCGAGAAGCTTATCGATATCATCACCACAGCTACTACTCCCAACCCTTGCCTCCTCCATCTTCTCAATCTCCTTCATCCACAACCCAGCATGAATCCTC[T/C]GCTTTCTGATTCTATACTCATCCCCTTCCTTCTTATTACTCTTCCCAGTATCTTTATTGACTTCAGAAGCACTTAGTTTCCTTTTCGATGAGCC
106227 GT G ATCCACAACCCAGCATGAATCCTCTGCTTTCTGATTCTATACTCATCCCCTTCCTTCTTATTACTCTTCCCAGTATCTTTATTGACTTCAGAAGCACTTA[GT/G]TTTCCTTTTCGATGAGCCTTTTCTCTCGTTCCATCGCTCGTCCATTTCGGCCACAAAAGCTTTCGTGTCAGGATCGAGATCGGCAGGTGGT
106229 G A GATGCGTTTGTTTGGAGGAAATGCGAAATACGTGTTAGGGTTTGACGGAATCGAGGTCAGTAAAGAAGGTATTTTTAATTTCTGAGGGGGCAGAGAGGCA[G/A]AAAAGAATCTGCGGGCGAGCATCGAAGAGTACAGTGGATTAGCTTAACGCTTTGGTGATTCTAGTGCACTCCATCGCCATTTCTC
106231 T C CACTGTTGGCCTACTGGCTCTCCCTCTCCCTCCCTGGATTAAAATACGAAATCCCAACATATCGAAGAAATCGGCCAAACAGAATGACCGC[T/C]ATCATCAATGAAAACTCCCCACACATTCGCCTGATGTGCAGTTTCAATGGACGAATAATTCCCAGGCCTCATGACAATCAACTCAGATACGTAGGTG
106231 C G CCCTCTCCCTCCCTGGATTAAAATACGAAATCCCAACATATCGAAGAAATCGGCCAAACAGAATGACCGCTATCATCAATGAAAACTCCCCACACATTCG[C/G]CTGATGTGCAGTTTCAATGGACGAATAATTCCCAGGCCTCATGACAATCAACTCAGATACGTAGGTGGGGATACGCGCATGGTCACC
106231 T A CGGTTACATCCGATGAAGACGTTGAGAATATGATCGAAGAGTATGATCGTCTCCTTGCAGATTGTCATACTCCAAGCACTACTAGAACCCCAAGACTGCG[T/A]ATGTTCCTTTTCAACTCAGAGAATGATGGTAACAACAGCAGCAACGGCGGATTTGGATCCATTCTGAGTGGAACTGCATCAAAACAC
106231 A G GCGGATTTGGATCCATTCTGAGTGGAACTGCATCAAAACACGAAAGCTGGTTCCTAGATGCACTGAATGGGCGCTCGCTTGAAAGGGGTAGGTCTGAAGC[A/G]TCTTCTGTTGTATCAGAGATGCCTGATTATTTATCAGGCCTAGACGCAAGCTATGATGAACAAGGGAAGTTGAAGAACAACCTAA
106231 A G CTTGAAAGGGGTAGGTCTGAAGCATCTTCTGTTGTATCAGAGATGCCTGATTATTTATCAGGCCTAGACGCAAGCTATGATGAACAAGGGAAGTTGAAGA[A/G]CAACCTAACACCCTCTGATATTGGATCACCACATTATGGATCTACATCCTCAGCAGTGTCTGTACCCGTTGAGAACAGACCATCTGA
106231 T C TGCCTGATTATTTATCAGGCCTAGACGCAAGCTATGATGAACAAGGGAAGTTGAAGAACAACCTAACACCCTCTGATATTGGATCACCACATTATGGATC[T/C]ACATCCTCAGCAGTGTCTGTACCCGTTGAGAACAGACCATCTGAGCTAGAAGCGAACCCGAGCCCGACTTCCAACGTGAACCCGATT
106231 A C TATGATGAACAAGGGAAGTTGAAGAACAACCTAACACCCTCTGATATTGGATCACCACATTATGGATCTACATCCTCAGCAGTGTCTGTACCCGTTGAGA[A/C]CAGACCATCTGAGCTAGAAGCGAACCCGAGCCCGACTTCCAACGTGAACCCGATTTGGCAGTATGTGAACGAACAGGCGCCCGTTT
106231 A G ACCACATTATGGATCTACATCCTCAGCAGTGTCTGTACCCGTTGAGAACAGACCATCTGAGCTAGAAGCGAACCCGAGCCCGACTTCCAACGTGAACCCG[A/G]TTTGGCAGTATGTGAACGAACAGGCGCCCGTTTATTACATGCCAGGCCAGGGTCCGGTTCAGGTTCAAATGCCAATGCAATATGCA
106231 G A CAGTGTCTGTACCCGTTGAGAACAGACCATCTGAGCTAGAAGCGAACCCGAGCCCGACTTCCAACGTGAACCCGATTTGGCAGTATGTGAACGAACAGGC[G/A]CCCGTTTATTACATGCCAGGCCAGGGTCCGGTTCAGGTTCAAATGCCAATGCAATATGCACAACCTCAGATGCATGCCGGGTACA
106231 C T GGCAGTATGTGAACGAACAGGCGCCCGTTTATTACATGCCAGGCCAGGGTCCGGTTCAGGTTCAAATGCCAATGCAATATGCACAACCTCAGATGCATGC[C/T]GGGTACAGGCCCGTATACGTTGGTGGGCCCTATGATTATGCCATGGGGCCCAATATGATGGGACATGCTGTGGTAGCACCAGAGG
106245 T C AAAGAGAGCATTATCATTTGTGAACCCATTATCATACCTTGGTGGTAACACTAACCCATCAAATTTAGAGCCAGCTCCACGTACACTGCATACAGAAAGT[T/C]ACAGTTACCAATACCAGCCATACCGACCAAATGACGCACTTCAAGGCCGTCTATTGTCTGGGACAGCATCATCCACCCGTCCATCTGT
106247 A T TGCTGCTTCTATGCTTGGTTTTGGAGGCAGGTAGTGACTGGCCGGAGGGATGCACGTCTCTTCTCCTAGTCCGGAACGTTCTAGAATGCGCTTCTGGAAG[A/T]CGACCGAGCTTTCGTTGAAGAACGGAAACTGGCTTATGTGTTCGATGTGGCAGGCGAGCGGGACCCGTAATGCAGGCGGGGGCT
106247 T C CGACCGAGCTTTCGTTGAAGAACGGAAACTGGCTTATGTGTTCGATGTGGCAGGCGAGCGGGACCCGTAATGCAGGCGGGGGCTTGCAGCATGCGTAGTC[T/C]ATGAGGTAGATGGGTTTTGGAAGGTATAGGTAGTAGATTGTTGCGAGTGTGATGAGTGTGAATGAAACATACATGAGTGTGAT
106253 T C CAGTCAAGATAAGCCCAGCTGTTCCCATGGATCGAATTTGCCTTCTTAGCTGTGGAGTAGCTGCAGGCTATGGTGCAGCCTGGAAAGTTGCTGACATATC[T/C]AAGGGGTCAACTGTAGTTATATTTGGTCTTGGGACAGTTGGTCTTTCAGTTGCACAAGCTGCCAAGCACAGAGGAGCATCCATGAT
106255 G A AATAATCCAGATGCCCCCTATTCAAATTATCAGGTATCCATCCAAGTTTCCCATTTTTAGTTGTGATATCCATAACAATTATCACAAGCACCGAGCTAAG[G/A]TAATTACCGAGTGCAGTAGTGGTCAATGACAACGCTGAGCATGTGCTCCTCATAGCATCCGGTGCCTGATCATAAAAGAACTCCAACG
106255 G A GATGCCCCCTATTCAAATTATCAGGTATCCATCCAAGTTTCCCATTTTTAGTTGTGATATCCATAACAATTATCACAAGCACCGAGCTAAGGTAATTACC[G/A]AGTGCAGTAGTGGTCAATGACAACGCTGAGCATGTGCTCCTCATAGCATCCGGTGCCTGATCATAAAAGAACTCCAACGTTCCTATATT
106255 C T AATCTCAGATGCACCCACTATGAAGTACTGGGGCACTTGCCAAAATATCGACATAGGAACAAATCCTTTGGAGTCATAAAGATTGTCCCTGGCAACAATA[C/T]GGAGTCTAACTACTTCTACAATGCCCGCTGCTAACATAGCGAAAATTGAGATGACGAGACCTATGCCGATTCGTGTTAGCTGTGTGA
106255 C A ACTGGGGCACTTGCCAAAATATCGACATAGGAACAAATCCTTTGGAGTCATAAAGATTGTCCCTGGCAACAATACGGAGTCTAACTACTTCTACAATGCC[C/A]GCTGCTAACATAGCGAAAATTGAGATGACGAGACCTATGCCGATTCGTGTTAGCTGTGTGAATCCACGCTCGTGTCCTGTAAATTTT
106255 A G CAAATCCTTTGGAGTCATAAAGATTGTCCCTGGCAACAATACGGAGTCTAACTACTTCTACAATGCCCGCTGCTAACATAGCGAAAATTGAGATGACGAG[A/G]CCTATGCCGATTCGTGTTAGCTGTGTGAATCCACGCTCGTGTCCTGTAAATTTTCTAGCGATGGGTACGATGAGGCGATCGTATACT
106255 T A ATCCTTTGGAGTCATAAAGATTGTCCCTGGCAACAATACGGAGTCTAACTACTTCTACAATGCCCGCTGCTAACATAGCGAAAATTGAGATGACGAGACC[T/A]ATGCCGATTCGTGTTAGCTGTGTGAATCCACGCTCGTGTCCTGTAAATTTTCTAGCGATGGGTACGATGAGGCGATCGTATACTGGA
106255 G A TGGAGTCATAAAGATTGTCCCTGGCAACAATACGGAGTCTAACTACTTCTACAATGCCCGCTGCTAACATAGCGAAAATTGAGATGACGAGACCTATGCC[G/A]ATTCGTGTTAGCTGTGTGAATCCACGCTCGTGTCCTGTAAATTTTCTAGCGATGGGTACGATGAGGCGATCGTATACTGGAACGAG
106257 G A TTTTCCATGAAGCATATCTGAATGGGTCATTTACAAAGGTGGAGCTAAAATCGCGACTGTTTGAATTTTCGATGAACAATTTGATGACAATGATCGCTGG[G/A]AAGAAACCCTACATTTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGG
106257 T A TATCTGAATGGGTCATTTACAAAGGTGGAGCTAAAATCGCGACTGTTTGAATTTTCGATGAACAATTTGATGACAATGATCGCTGGGAAGAAACCCTACA[T/A]TTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATT
106257 T C TCATTTACAAAGGTGGAGCTAAAATCGCGACTGTTTGAATTTTCGATGAACAATTTGATGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAG[T/C]AAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGA
106257 A G CATTTACAAAGGTGGAGCTAAAATCGCGACTGTTTGAATTTTCGATGAACAATTTGATGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAGT[A/G]AAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGAT
106257 A G AATCGCGACTGTTTGAATTTTCGATGAACAATTTGATGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGT[A/G]GAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAA
106257 C G AACAATTTGATGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATG[C/G]ATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATA
106257 C G ATTTGATGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATC[C/G]AATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAG
106257 C T TGACAATGATCGCTGGGAAGAAACCCTACATTTCAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATAT[C/T]GGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCT
106257 T C CAAAAGAAGTAAAGAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGA[T/C]TTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACG
106257 A G GAAGTTTCAGGAAATAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATA[A/G]TGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGA
106257 A G TAGTAGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAA[A/G]CAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAA
106257 C G AGAAGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAG[C/G]TCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCAT
106257 G C AGAAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTC[G/C]ATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGAT
106257 T A AAACATTCAAGGTAGCAGATGCATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGA[T/A]GATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTG
106257 G A CATCCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCT[G/A]CAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGA
106257 A G CCAATATCGGAGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCA[A/G]AAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAA
106257 G A AGATTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATT[G/A]ATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGA
106257 G C TTTCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGAT[G/C]AGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAA
106257 G A TCTTGCCATTACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGA[G/A]CACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACT
106257 G T ACTAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAAC[G/T]TAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCA
106257 A G TAGGATGGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGT[A/G]AAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAA
106257 T TGAA GGATGGATTTGCAAGGAATAATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGC[T/TGAA]GAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106257 C G ATGAAGAAGTCAAAACAGCTCGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAA[C/G]CATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTG
106257 G T CGATGATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTG[G/T]CCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACA
106257 T G GATTATAGAGATAACCTTCTGCAAAAAATAATTGATGAGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCA[T/G]GCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACAACAT
106257 T G AGCACAGAAACGTAAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGT[T/G]ATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACAACATCAAACGCTTTAGAATGGGCAATGTCACAATTGCTAAA
106257 G A AAAAGCTGAGGAAGAAGAAGGCAAAACCATGATTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTC[G/A]CTCTAGATTTGCTATCAGCAGGCACAGATACAACATCAAACGCTTTAGAATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAA
106257 A C TTGGAAACTTGCTGGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATAC[A/C]ACATCAAACGCTTTAGAATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACT
106257 T A GGCCATGCAGAAAACTGACCCTGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACAACATCAAACGCT[T/A]TAGAATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAA
106257 T C TGAGAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACAACATCAAACGCTTTAGAATGGGCAATGTCACAA[T/C]TGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGAT
106257 C T GAACTATTCCGATCAAGTTATCAAAGCACTCGCTCTAGATTTGCTATCAGCAGGCACAGATACAACATCAAACGCTTTAGAATGGGCAATGTCACAATTG[C/T]TAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGATCTA
106257 T C TGCTATCAGCAGGCACAGATACAACATCAAACGCTTTAGAATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGAT[T/C]GATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGATCTATCCAAGCTTCCATACCTAGAACGTGTGATAAAAGAGACGTA
106257 G A CATCAAACGCTTTAGAATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAACG[G/A]TTAATAGAAGAATCTGATCTATCCAAGCTTCCATACCTAGAACGTGTGATAAAAGAGACGTATAGACTTTATCCTGGAGGCCCACT
106257 T C AATGGGCAATGTCACAATTGCTAAACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATC[T/C]GATCTATCCAAGCTTCCATACCTAGAACGTGTGATAAAAGAGACGTATAGACTTTATCCTGGAGGCCCACTACTGGTTCCACATGA
106257 A G ACAATCCGGAAAAACTGAAGAAAGCACAGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGATCTATCCAAGCTTCCATACCT[A/G]GAACGTGTGATAAAAGAGACGTATAGACTTTATCCTGGAGGCCCACTACTGGTTCCACATGAGAATTCGGAAGACTGTGTGGTAG
106257 T C CACAGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGATCTATCCAAGCTTCCATACCTAGAACGTGTGATAAAAGAGACGTA[T/C]AGACTTTATCCTGGAGGCCCACTACTGGTTCCACATGAGAATTCGGAAGACTGTGTGGTAGCAGGATACGATATACCTAAAGGAAC
106257 A G AGATGGAGATTGATGAACTTGTAAAGAATGAACGGTTAATAGAAGAATCTGATCTATCCAAGCTTCCATACCTAGAACGTGTGATAAAAGAGACGTATAG[A/G]CTTTATCCTGGAGGCCCACTACTGGTTCCACATGAGAATTCGGAAGACTGTGTGGTAGCAGGATACGATATACCTAAAGGAACGA
106259 T TA CATGCATTTTTACTTGGTTCATACAATCAATCCTGCTTTAATAACAATACAATGTAAACCTACATTGACACAAATACATACGTGTGATAGTGCTCAAATA[T/TA]AAAAAATACTTCTCCTCCAGAAATTAGCCCTTAATTTCCGATTCACCTAGGCAAAAACTGCCTCAGCAAGAACGTGCCTCTGCTTCTTAA
106259 G A CAACAATCTTATTTGGGGTGATCATCTCCATTCCATCTCCCATCAATAGGGAACCTTTAACGTTGACAATGCTCACCTCGTTTGTAGAAGTATAGGCTTT[G/A]TATAGGCGTCCGGCCGTGGTGTGTATTATAAGGAAATAACCGTTTGGGTGATACAATATGCCGTTTAGACTTATTATGTCTTTGTACCA
106259 C A CAACTGCCACATCGTCGGCCATTGCTGGTTCGTCGGCTGGCCCTCTCAACCAAGTCAAGAAAATCCTTTCCCAAGAATCCAACCGATATGCGCCAATCCC[C/A]GAGTGCTGGGCTCCAAACGAATCCCCATATACAACCAGTAAACGATCCCGTGCCCGATCCACAAGAACCCCAACTGACCCGTTACCG
106259 C T CTGGTTCGTCGGCTGGCCCTCTCAACCAAGTCAAGAAAATCCTTTCCCAAGAATCCAACCGATATGCGCCAATCCCCGAGTGCTGGGCTCCAAACGAATC[C/T]CCATATACAACCAGTAAACGATCCCGTGCCCGATCCACAAGAACCCCAACTGACCCGTTACCGGCGACATCAGGATCCCGGATGACG
106259 T C CGGCGACATCAGGATCCCGGATGACGACCCTCTCCTCAACTTCACCGTCCCTGATCTCGACAACTGTGCCGCAGTCGAGGGTTGAGGCCAGGAAGCGCTT[T/C]CCCACTGGGTCCCACTTGGTACATTCGCGAAAGTAGCCCTCGCCTCTGTAAGTGACGGACGATGTTGAGGTTTCAAAGTATGCCGA
106259 T A TTCACCGTCCCTGATCTCGACAACTGTGCCGCAGTCGAGGGTTGAGGCCAGGAAGCGCTTTCCCACTGGGTCCCACTTGGTACATTCGCGAAAGTAGCCC[T/A]CGCCTCTGTAAGTGACGGACGATGTTGAGGTTTCAAAGTATGCCGAGAGGAGAAAGGCGATTGGAACGGCGGAGAGGAGGGCTA
106259 G A CCCACTTGGTACATTCGCGAAAGTAGCCCTCGCCTCTGTAAGTGACGGACGATGTTGAGGTTTCAAAGTATGCCGAGAGGAGAAAGGCGATTGGAACGGC[G/A]GAGAGGAGGGCTAGTAAAGCGTATGAGCGGCGACCGAGGAGGACGCAGCAAGTCATTGTTGCTGGGTTTTGGATTTCCAGTAG
106263 A G GTTGACATCCAAATCACTCCATCGAGGAGTTAATCCATTTTTGACATGGTTTGCCGACTCCTCGTCTAGCTTAGGAAGTTTCCTGCTATCTTCATCTATG[A/G]TCGGACCACGGTCAACAAAAAAAGGTCCTATCTCTGCTCTAACTTCTTCGGGCATTTTAGACAGCCTTCTTGTAACTTTGTTCATCATCAC
106263 CA C CTCCATCGAGGAGTTAATCCATTTTTGACATGGTTTGCCGACTCCTCGTCTAGCTTAGGAAGTTTCCTGCTATCTTCATCTATGATCGGACCACGGTCAA[CA/C]AAAAAAAGGTCCTATCTCTGCTCTAACTTCTTCGGGCATTTTAGACAGCCTTCTTGTAACTTTGTTCATCATCACCCAAACACTTGTGGC
106269 AT A TATTAACACACGTCATGCCGACTTCAAACGTGGAAGAAAAGATGATACAAAATTGGAAATCAGAAGTGTAAATTCTAAACTTGATAAGCCAAGCTTAACT[AT/A]TTTTTTAGTATACTACCGAGTAAGAAGTTTATAGGACGGCATGTCTTCTATACGCTGAATGTCTTCCAGGAGCAGTTCTCTTTCGAT
106269 A G ATGCTCAGGTCAGCAAAAATCAAGATTCAACCAAATTCCAAACGAGGACAGGAAATATTGTTTGGGGTTTGGTATTTATGAACAGAACCCGCCTTTGTCT[A/G]GGATTTATTTTATCGATTCAAGATGGCGGACTCTTATTCATTTTATTTTTATTTTGTTTTTATTTTTATTTTT
106277 A G AGACAGCAATTTCAGAGACGCAGAGCGTGCGGTTCTAGTGATTGCTCTGATATCTTCCTTTCCCGTCCACACTCTTGGCATGGAATCTGAATCACGACTA[A/G]ACAATGTAGTGAACCTGTCCTTCATCCGAATCAAAACCCTTCCAGATTCTTCTGCAGCCTTAGATTCAACAACACTTCTAGCGTAATCT
106277 T C GTCATTTTCTCTACTGTTACATTGTCTAGATCAAATGCAGAAAGTGCAGAAGACAGATTGAATGTAGCTGACTTGGTCTCTCTTTGGAGAAGACTCCTTA[T/C]AGCTGGCCATGTATTATCGCTGGCTTCATCTAGAAGTGCTCCTACTGGCTCTAAAAGTGCTTTATCCAGTTGTTTCTCGTAAAGAGAAG
106277 A C GAAGACTCCTTATAGCTGGCCATGTATTATCGCTGGCTTCATCTAGAAGTGCTCCTACTGGCTCTAAAAGTGCTTTATCCAGTTGTTTCTCGTAAAGAGA[A/C]GTCAATTCCAACAGCTTTGCAGCACGAACTGAAGCAATATGTGCATCAACGTCACGGCGAAGCTTATCACGTGCTTTTGATGTGTCCCA
106277 C T GCTCCTACTGGCTCTAAAAGTGCTTTATCCAGTTGTTTCTCGTAAAGAGAAGTCAATTCCAACAGCTTTGCAGCACGAACTGAAGCAATATGTGCATCAA[C/T]GTCACGGCGAAGCTTATCACGTGCTTTTGATGTGTCCCAGTTTGCTTGTAGGATAACTGCATCTTTGATTCCTTCATCAAATTTTGAAA
106277 G A CTCCTACTGGCTCTAAAAGTGCTTTATCCAGTTGTTTCTCGTAAAGAGAAGTCAATTCCAACAGCTTTGCAGCACGAACTGAAGCAATATGTGCATCAAC[G/A]TCACGGCGAAGCTTATCACGTGCTTTTGATGTGTCCCAGTTTGCTTGTAGGATAACTGCATCTTTGATTCCTTCATCAAATTTTGAAATG
106277 A T AGTCAATTCCAACAGCTTTGCAGCACGAACTGAAGCAATATGTGCATCAACGTCACGGCGAAGCTTATCACGTGCTTTTGATGTGTCCCAGTTTGCTTGT[A/T]GGATAACTGCATCTTTGATTCCTTCATCAAATTTTGAAATGAAATTTTGACTGCAATCACGAGTAGCATCGGCAAACCGTGCACCACTT
106277 G T CGTGCACCACTTTCTAAGGCCTTAGCCAGTGCTTCCTTAAACTCATCTAAGGATTTAGATCTTAAATGGCCTGTCATGGACTGGTAAGCAGGATGCACCA[G/T]CTGTAGAAGTTTCGATTCCAGCTGCTGTCTCTTTGCATTTCTGACTTCTTCCTCAAAATAAGCAGCTTCCATGTCATATTCTGATAAGCC
106279 GA G ACAAAGGATGATGATAGAAACCGACTCACCATATTGTGACATTAGGAACACTCATGCTGGTATGCAGTTTGTTAAAACGGTTTGGCCTTCGAAGAAGAAA[GA/G]AAAAATACGATCAAGGTTCAACCGTTAAAGGTCGAAATGAACCTTGTTCTGTTAGACAAGTCCTTGAGGTGGTGGCAGGATGTAA
106287 CT C GTGGCGGCTGCGGCCATTAAAGCTTGTAAGCCTAACTCAGCTTTGACTGTAAAGGAAGTGCAGGAGGATGTTTTTAGGATTGTGGAAAGCGGGATGTTTT[CT/C]TTCTTGCATGCCTGTTGCTGTTGATACCAGAGATGGCATCAGGCTGGTTTTTCAGGTTGAGCCTAATCAAGAATTTCAAGGCTTG
106287 G GT TGTAAAGGAAGTGCAGGAGGATGTTTTTAGGATTGTGGAAAGCGGGATGTTTTCTTCTTGCATGCCTGTTGCTGTTGATACCAGAGATGGCATCAGGCTG[G/GT]TTTTTCAGGTTGAGCCTAATCAAGAATTTCAAGGCTTGGTTTGTGAAGGGGCAAGTGTTCTTCCTGCCAAATTTCTTGAGAATGCA
106287 C T AAGCTGAGGTTAATAACATTACACTGCGATTTCTTGATAGAAAAACTGGTGAGCCTACTGTTGGGAAGACGAGGCCAGAGACCATACTTAGACAGCTGAC[C/T]ACAAAAAAAGGACAGGTTTATAGTATGTTGCAAGGAAAAAGGGACGTGGAGACAATTCTAACTATGGGAATTATGGAGGACGTTT
106287 T C TGCGATTTCTTGATAGAAAAACTGGTGAGCCTACTGTTGGGAAGACGAGGCCAGAGACCATACTTAGACAGCTGACCACAAAAAAAGGACAGGTTTATAG[T/C]ATGTTGCAAGGAAAAAGGGACGTGGAGACAATTCTAACTATGGGAATTATGGAGGACGTTTCAATTATTCCACAACCTGCTGGAG
106287 C T AGACAATTCTAACTATGGGAATTATGGAGGACGTTTCAATTATTCCACAACCTGCTGGAGATACTGGCAAGGTGGATCTTGTAATGAATCTTGTTGAACG[C/T]CCTAGTGGTGGTTTTTCTGCTGGAGGTGGTATTTCTAGTGGGATAACAAGTGGCCCTCTGTCTGGACTTATTGGGAGCTTTGCATAT
106289 T C ATGGTGGGAATTTTAATGGGAAGAAGAAGGGAAATGGCAACAACAACAACAACAATGATAAGAAGGATAATAATAACAATAATTTGGTTGATAAGAGGTT[T/C]AAAACATTGCCTGCATCGGAAGCTTTGCCCAGAAATGAAGCTGTTGGTGGATATATTTTTGTTTGCAACAATGATACTATGCAGGA
106289 T A ACTTCTTGATATTTTCGCGGAAATTGACGCATGAGAAATATTTGTGAAGAAGACATGTAGGGATGAATGAGTAATAAAAGTAATATTGTAATGTTGCAAC[T/A]TTTTCAACGAGCATGGTGCGACTCGTCTATACTTGTGTAGAGCTATATATGAGCAAGTAATAGCTATTTATAGAGGGGGTGTTGGAT
106291 AT A TTCAATTGTGAATGTGATGGTACGTTTTAACTTATTGAGTATTCAATGCTTTTCTGGATCTCGTCTTGTTAGTAGTATGGAAATCGGAGTTGTGCTTGGT[AT/A]TTTTTTTATGGTCATCTGGTACTCGTTACCACTCATGTAAAGGTGAACTGCTCACCTTGTTCACGCTGGCGATGGTCCTGCTGTTTAGT
106291 A G CTGTTTGAATCATTTTGCTGAGCGGTTTGCTTATTGGATCTAGTCTGGTCTGCTTGGTGTTTTCCCTTTCTGGTCTGTCCGATATGTATTTTCCCATGTA[A/G]TTGATGACTCTGCTGTTCTTTGGTGAATAAGAGGTCCATGACTGATTTCAGTTCGGTACAGTGGTTTTGCCCTGTTCAACTTTGGTCTTGG
106293 C A CCTTATATAAATCTGGTCGCCGATCTCTGAATATTCCCCAACCGTGCCTCTGAGATTTCAGTTTATTCAGATCAAATTCAGCAACTAGTATTTCTTCATC[C/A]TTTTCATTAGCAAGAGCAACTATTTCACCTTTAGGACCAGCAATGAAGGAATTTCCGTAGAACGTTATCGCACTGTCACCATGTTCAGTAG
106293 G A GCCTCTGAGATTTCAGTTTATTCAGATCAAATTCAGCAACTAGTATTTCTTCATCCTTTTCATTAGCAAGAGCAACTATTTCACCTTTAGGACCAGCAAT[G/A]AAGGAATTTCCGTAGAACGTTATCGCACTGTCACCATGTTCAGTAGTAATTATCTCCTTCCCAATTCGATTTGAAGCAACAACAGGAACC
106293 A T TTTCTTCATCCTTTTCATTAGCAAGAGCAACTATTTCACCTTTAGGACCAGCAATGAAGGAATTTCCGTAGAACGTTATCGCACTGTCACCATGTTCAGT[A/T]GTAATTATCTCCTTCCCAATTCGATTTGAAGCAACAACAGGAACCAAGTTAGCCCCAGCATGTCCTTGCATTACCCGCTTCCAGTGCTCC
106293 G A CAACAACAGGAACCAAGTTAGCCCCAGCATGTCCTTGCATTACCCGCTTCCAGTGCTCCCTTGAGTCAAGTCCATCATCTTGGGGTTCAGATCCAATAGC[G/A]GTTGGATATAACAGTATTTCTGCACCTTGAAGAACCATCGCTCTTGCGGCCTCAGGGAACCACTGATCCCAGCAAATGGCAATTCCAA
106293 C T AGTGCTCCCTTGAGTCAAGTCCATCATCTTGGGGTTCAGATCCAATAGCGGTTGGATATAACAGTATTTCTGCACCTTGAAGAACCATCGCTCTTGCGGC[C/T]TCAGGGAACCACTGATCCCAGCAAATGGCAATTCCAATTTTAGCGAACTTGGTAGCAAAAACTTTAAAACCTGTGTCGCCCGGGTTGA
106293 G A GAAGAACCATCGCTCTTGCGGCCTCAGGGAACCACTGATCCCAGCAAATGGCAATTCCAATTTTAGCGAACTTGGTAGCAAAAACTTTAAAACCTGTGTC[G/A]CCCGGGTTGAAATAGAACTTTTCTTGATATCCTGGTCCATCCGGTATATGTGATTTCCTATACAGTCCAAGGTCAGTTCCATCGGCAT
106293 G A AGCAAAAACTTTAAAACCTGTGTCGCCCGGGTTGAAATAGAACTTTTCTTGATATCCTGGTCCATCCGGTATATGTGATTTCCTATACAGTCCAAGGTCA[G/A]TTCCATCGGCATCAATGATGGCTACAGAATTGTAATGAGCATTGTTGGCCTCTTCAAAGAAACTTACAGGTATCACAACACCCAACTCT
106293 T C GTCCAAGGTCAGTTCCATCGGCATCAATGATGGCTACAGAATTGTAATGAGCATTGTTGGCCTCTTCAAAGAAACTTACAGGTATCACAACACCCAACTC[T/C]TTTGCAAGATTCTGCATTCTAGAAACTGTGGGGTGGCCTTTGTAAGGCTTGGCTCGCTGGAAAAAATCCTCTCTTTGAGCTTGACAAA
106293 C T TGGGGTGGCCTTTGTAAGGCTTGGCTCGCTGGAAAAAATCCTCTCTTTGAGCTTGACAAAAGTAATAGCCTTCAAACAGTTCTTGAATGAGAATGATATT[C/T]GCACCCTTTTGGTGGGCAGCTCTAACCAACCTTTCAGCAGTATCAACATTCTGAGAAATGGAATCAGAGCAAGCAAACTGGAGAGCA
106297 C G TGGAATGAAAGAGCCGATAAAGCTAGCTGGAATTCAGGAGGCAGCAACAGTGGCTGGAGCAAGCAAGATGATACTAACAAGGCTACTGGAAATGAAGGTG[C/G]TGGTGGAAGTTGGGGTAGCGAACCAAAAGATTCTGACAACGGTGGTGGCAGTGGATCTGGTTGGAACGTAGAGAGGACTTCT
106297 G A GAAATGAAGGTGCTGGTGGAAGTTGGGGTAGCGAACCAAAAGATTCTGACAACGGTGGTGGCAGTGGATCTGGTTGGAACGTAGAGAGGACTTCTAACAA[G/A]GAGAAGGCTACGACTGGTTGGGGTGATGCAGAGCCCAGTACGAAGAACGATGATGCTGGATGGGGCAGCGGATCAGCTAAC
106297 G C AAGGTGCTGGTGGAAGTTGGGGTAGCGAACCAAAAGATTCTGACAACGGTGGTGGCAGTGGATCTGGTTGGAACGTAGAGAGGACTTCTAACAAGGAGAA[G/C]GCTACGACTGGTTGGGGTGATGCAGAGCCCAGTACGAAGAACGATGATGCTGGATGGGGCAGCGGATCAGCTAACTTGGGA
106297 C G ACAACGGTGGTGGCAGTGGATCTGGTTGGAACGTAGAGAGGACTTCTAACAAGGAGAAGGCTACGACTGGTTGGGGTGATGCAGAGCCCAGTACGAAGAA[C/G]GATGATGCTGGATGGGGCAGCGGATCAGCTAACTTGGGAAGCAAAGGAGGGTGGTAGGGCACATATATAATCCTGTATTCTG
106297 T C GGTGATGCAGAGCCCAGTACGAAGAACGATGATGCTGGATGGGGCAGCGGATCAGCTAACTTGGGAAGCAAAGGAGGGTGGTAGGGCACATATATAATCC[T/C]GTATTCTGTACTTGTATCTAGTGGCGACTTTGCAATGGTTTTTGGGGGATGGAAGCTTTGTCAACTCCATGATGTCATAAAGAG
106297 G T AGGAGGGTGGTAGGGCACATATATAATCCTGTATTCTGTACTTGTATCTAGTGGCGACTTTGCAATGGTTTTTGGGGGATGGAAGCTTTGTCAACTCCAT[G/T]ATGTCATAAAGAGCAGCCAGTAGCTGCTTTTTGCTGGGACATCCTATTAGTTGCTTGTTTTTGGTGTTCTGTTGGTATATCGGCCTCT
106307 T C GTGAAAGATGCTAATGTTTTCTCCCTTGTAACCTTTCTTCTTTGAAACCCCATGTCAATGGTTGTTGCTCTTAAGCTTTTCCATCTTGTGCTCCTTCATA[T/C]GATCCACAGTCATTAACCAATATCGATACGATCACATATGTACGCAACTCCGTATTTGCGAGAAGATGACGATAGCGCCACTTTATTGCCT
106309 A T TATCCGTTCCGTACAGGAACGCTTTCAATTTCTTCTTCAACTCACCGAGCTCGTCTACTTTTGGTTCCTCCGCGTCCGCTACAGCGACAGCTGAATCGTC[A/T]CCAATATTCGCGTTTACCCTCTCTACTCCCCATTCGAATTCGTTTTCGGACGATTTTGCAACGAATAACGGTTTTGATTTTAGGTTCAGGG
106309 A G GTCACCAATATTCGCGTTTACCCTCTCTACTCCCCATTCGAATTCGTTTTCGGACGATTTTGCAACGAATAACGGTTTTGATTTTAGGTTCAGGGTCCTT[A/G]GTTGGGAAAGAGGCGGGATTTGAAGGTTTTTAAGCGCTTTAGGAGGGTGCAGGGTTGATTTAGGACTGGATTTTAGAGCGAAAGAAT
106313 T C TAGGAAGCAATAATGGAAATGGTGTATTCAATGGGGAGAATTCTAACACTGGCAAGAAGGATACTGCTACACAAAGTGGTGGAAAATCTAGTCCAACTAC[T/C]ACTGCTCCGGATGCTCAAAATGATCAGCTGGCAAAGGGGTCTTCAGATAGCCTTCCACCTTGTTCTACTTTATTTATTGCAAATTTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106319 G A GCACCGCCCAGAGCCTTGCCCGCCCCCCAATATCGTCCTTTCATGTCGGCGTTGCTGCCGCCGGCGTCTCCGGCCGAATTTACATCGGCGTCAACGTCGA[G/A]TTCCCGAAAGTACCCCTCCATCACTCCATCCACGCCGAACAGTTTCTGCTGACTAACGCCCTTCTCCACTCCGAGCCGCAGCTCCTCC
106319 C T CGCCCTTCTCCACTCCGAGCCGCAGCTCCTCCACCTCGCCGTCACCGCCGCTCCCTGCGGCCACTGCCGCCAGTTCATGCAGGAGCTCCGCAACGCCTCT[C/T]GCCTCCAGATCCAGATCCTCTCCGATCCAAACCCTACCTACAGCCCTCTTATCGAATTGCTTCCACGAGCCTTTACCCCATTGGATCTCC
106321 A G GAATGCTCCGGGCTGTCCATCAACAGACTCCACCTGATATTGCTCTCCAGTCACCTCCGTCTTACCCTCATAGATTGTGTCCAACTTGAATTTGTTCAAA[A/G]TCCTGCGTCCAAGAAGTAGTCCAGTACAGTAAGCGGCAGCATAGTTCGTCAGCCCGACCTTAACACCGTATCTCGGCAGCTCGTGAGC
106327 A C TCAACACGTCCTGCATCCCTGAGGCTATCGCCAGACTGTTGCTGAGGAACTCCGACGAGTTCTTCATCGCAGATCCGAACTTTTGCTTCAATTTCTCTTC[A/C]TCGGTAGTTCCTTCGAATCCGTCCACGCAGGACTCCTGATTCGTCATGGCCGCGCTCAGCCAAGTTCTGATGTCGTTTATTTTGGGAAC
106327 C T AATTTCTCTTCATCGGTAGTTCCTTCGAATCCGTCCACGCAGGACTCCTGATTCGTCATGGCCGCGCTCAGCCAAGTTCTGATGTCGTTTATTTTGGGAA[C/T]AGTGAGGATTTTCTCGTTCGGGTCAGTAGGGCTGACGGACGAGATGGACTCCTGAACGCGGTCGACGGCTTCCTGGAACATGTCGGC
106327 T C AATCCGTCCACGCAGGACTCCTGATTCGTCATGGCCGCGCTCAGCCAAGTTCTGATGTCGTTTATTTTGGGAACAGTGAGGATTTTCTCGTTCGGGTCAG[T/C]AGGGCTGACGGACGAGATGGACTCCTGAACGCGGTCGACGGCTTCCTGGAACATGTCGGCGCAGTCGGAGATGGCCCTCTTGAGG
106327 G A CGACGGCTTCCTGGAACATGTCGGCGCAGTCGGAGATGGCCCTCTTGAGGCGGCCGTCGTTGGTGGGGATGGAAACGGAGTCCGGGAAGGACGCGAGGGC[G/A]GAGAGGGCGTCGGACGCGACGCGGAGGGAGAGCTTGAAGAGCTGTTCCGGATCGGTGGTGGAGTTGGCGCCTTTGATGGA
106331 A C TTCAATTTGGGGTACCTGGCACAAATTTGAAAATGGTTATGGCACATTCAAATGGCCATGTTAGGGTCTTTGAACTGCTGGATCCATTGGAACTTAATAA[A/C]TGGCAACTTCAGGCAGCATTTCAGAATCTGGTAGATTCAGTTTCTAGTTTTGGAAAACCGTCATGTTTATCTGCATCCATTGCATGGA
106331 G A GGCCATGTTAGGGTCTTTGAACTGCTGGATCCATTGGAACTTAATAAATGGCAACTTCAGGCAGCATTTCAGAATCTGGTAGATTCAGTTTCTAGTTTTG[G/A]AAAACCGTCATGTTTATCTGCATCCATTGCATGGAATCCATGTAGAAATGAAGGCAAACCATCTAGTTTTGTCATTGGATATAATTCAG
106331 T C ATCCATGTAGAAATGAAGGCAAACCATCTAGTTTTGTCATTGGATATAATTCAGATATAGCTCAATACAACTCTCCCAAGATTTGGGTATTTGAAGAGGC[T/C]CATCAAAGGTGGATACCAGTGGCTGACCTCTGTTTACCTGAAGTTAATGATGCGAGGGTACATGCTTTAGCTTGGGCTCCTAACATTG
106333 A G CTCCAACAGCCAAAATTCCCAATCCAACCATGTATTTCAGAATTCTAGATTCAGAAGTAGTTTCACCATCCATATCCGATAACTTAACAACTACATTTTG[A/G]TCAAGCCCAGAAAAAATCTCAAGAACATCATGAACCTGCCCATCATGATTCCCAACATACTCGAGCTTCATCTTCTCCCTGGTAGCAAAC
106333 A G CCATGTATTTCAGAATTCTAGATTCAGAAGTAGTTTCACCATCCATATCCGATAACTTAACAACTACATTTTGATCAAGCCCAGAAAAAATCTCAAGAAC[A/G]TCATGAACCTGCCCATCATGATTCCCAACATACTCGAGCTTCATCTTCTCCCTGGTAGCAAACAACCTCGTGTACCCGAACTCACCGCCA
106333 G A CACCATCCATATCCGATAACTTAACAACTACATTTTGATCAAGCCCAGAAAAAATCTCAAGAACATCATGAACCTGCCCATCATGATTCCCAACATACTC[G/A]AGCTTCATCTTCTCCCTGGTAGCAAACAACCTCGTGTACCCGAACTCACCGCCACGGTACATGGACCTTTCAGGCTGAGGATATATCGG
106339 A G TTATATTGCATAACAAGGACAAATATTATTATTCCATCCTAAAGGAGTTTTCACCCTTTTATCGTACCCTTTGCCCTTGCAATTCTTTATACATATCACC[A/G]TCTGTACTGCTAATACTACTACTACTGTTACTGCTACAGCATAGAGATCTACATACATGATTGATAATACAGCATCATACCTACATACAAAA
106339 T C CTAATCCCAGCCTTCACCACAGTACCATGAGAGCATATGAGCCTGCTCATCATGAAAAAAGGTTGAACTACAAGGCCCGTCCTCATCGAGGAACTCATCG[T/C]CGTCCTCTTCGACTTTAACACGATGATAGAACAATGGAGGCGATAATGAAGAGATGACTTGATTGTCAACCTTAAACGAAATGAGAG
106339 A G TGTAAATAAGAGGAGGATGTGCATCTTCTTCAACGTGGTTGATCCGGTTTTCAGATGCTATTCTCTCTTCGTTAACGGAGGAGAAGCTTTCTTCTCCACT[A/G]CCTCCCACCTTTGCCTTTAAATTCATTACCTGATCAAGAAGCGAAGCTTTGTCCCTAACAAGGGCATCATAATCGCTGCGCAATGCATC
106339 T C TTTCGCTCTGGTTCGAGCTTGTTTTCTACTTCAAAGCTCTTTTCTAGTGCTTTTACTTGGTCTGAGTGTAGCCGTCTCTTTTTCTCTCCACGATGACCTG[T/C]GGCTTCTTCCGCTATGTCTTCGTCATCCTCAAGCCATTCAGAAGGACAGATAGGAACTAAAGAGTCGGAGCTGCTGAGCCTTTTCATCAG
106341 GA G TAATATCCAGTTTCGCCTAGAGTCACATTACACATTCTAACATTTCAAAAAAACATCTACGTACACAGAACTGAAAGATAAATAAACACCCTCCCTCAAG[GA/G]AAAAGTAAACTTGCCACCTATCTGATCAGTACTGGAAGGCGGATTAATCGCGACCCAAAGCAAAGAAATAGTAATCGCAATCAACCC
106341 CA C CAAGGAAAAGTAAACTTGCCACCTATCTGATCAGTACTGGAAGGCGGATTAATCGCGACCCAAAGCAAAGAAATAGTAATCGCAATCAACCCCGACCAAA[CA/C]AAAAACAATTGTCGGCGTCCTACCCCTCCTACCCATCAACCCTTTGGCGAACGGGTACAGATGTGCCAGCACCCAAAAGCTGAAA
106341 T C CGGCTGCCAAATGCGCGCTCGTGCCCCCAATCAGCCAAAACTGTTCGTTCCTCCACCATTCCTCCAGCTCGATGCCGGACCACTTGACTTCGAGTATGGC[T/C]AGCATGCATAGAGTAATTGTAATTATTAGGAGGTAGGTAAGGAATGCGACATTTAGGGTTTTGACAATGAACTGGCCGGAGAAGAG
106349 GA G TCAAAATGGACTCAGAGATGCTAAGGCAAGGAAGAAATTTGAATCGGCGATGCTAGAATTGAGATAACATCATCGGTGTCACAGAGGTCATACTTCCAAA[GA/G]AAATAATGAATGGCGCAGCAAAATCAAGCAACAACATCAAAGCAGCATTCTCACACTGCGTGCAGCAGGTAAGAAACTACGACT
106349 G C CCGAGAGAGGTTAAGAGTAGGTGTGGGGAGGAGATGAACGAAGCAGTGTTTGAAATTGCGTCCGTAGCGAACGCCCATTTAGAGAAAGCGCGAGCACTGT[G/C]GAACACGGTGCCTAAGGAAGCTGTACCGGTGCTGCTTCCTGCTGTGCCTGCTCAGGTTTTGCTGGATTCGATTAGGAGGTGCG
106349 G A GTAGGTGTGGGGAGGAGATGAACGAAGCAGTGTTTGAAATTGCGTCCGTAGCGAACGCCCATTTAGAGAAAGCGCGAGCACTGTGGAACACGGTGCCTAA[G/A]GAAGCTGTACCGGTGCTGCTTCCTGCTGTGCCTGCTCAGGTTTTGCTGGATTCGATTAGGAGGTGCGGTTTTGATGTTTTTGATT
106349 A G GGGAGGAGATGAACGAAGCAGTGTTTGAAATTGCGTCCGTAGCGAACGCCCATTTAGAGAAAGCGCGAGCACTGTGGAACACGGTGCCTAAGGAAGCTGT[A/G]CCGGTGCTGCTTCCTGCTGTGCCTGCTCAGGTTTTGCTGGATTCGATTAGGAGGTGCGGTTTTGATGTTTTTGATTCGAGGTTGA
106353 G A CTACCTTTTTTCTGCTTCTTCTCTCAAAAATTCATGGCGAACCCAATTATTACAATGAGATCCACTTCACTTCACAACACACCATCTGGATTTCCATCCT[G/A]TTCTTCATTTTACAACTGTCCGTCAAAGAAGAGAGCCATGATGGTTAGAGCAGCGCTGACCATGGAGCAACAGGAGAAGACTAAGGTCA
106375 T C ACGTCGCCTCTCTCACATCTGAATTCACCACCGATTTGCTCGAGATCGCTTACGGTGACGTCACTGACCTCAGTTCCTTGGTCGACGCATGCT[T/C]CGGTTGCCACGTCATATTTCATACCGCTGCTTTGGTTGAACCTTGGCTACCAGATCCTGCTAGATTCTTTTCTGTCAATGTTGGAGGGTTGAAAAA
106375 G T GCCACGTCATATTTCATACCGCTGCTTTGGTTGAACCTTGGCTACCAGATCCTGCTAGATTCTTTTCTGTCAATGTTGGAGGGTTGAAAAATGTATTAGA[G/T]GCTTATAAGAAGACGGAGTCAATCAAGCGGGTGATATACACATCGTCTTATTTCGCCCTTGGATGCACTGATGGATATATTGCTGATG
106375 G A ATACCGCTGCTTTGGTTGAACCTTGGCTACCAGATCCTGCTAGATTCTTTTCTGTCAATGTTGGAGGGTTGAAAAATGTATTAGAGGCTTATAAGAAGAC[G/A]GAGTCAATCAAGCGGGTGATATACACATCGTCTTATTTCGCCCTTGGATGCACTGATGGATATATTGCTGATGAAGAGCAGGTTCAT
106375 G A TGGTTGAACCTTGGCTACCAGATCCTGCTAGATTCTTTTCTGTCAATGTTGGAGGGTTGAAAAATGTATTAGAGGCTTATAAGAAGACGGAGTCAATCAA[G/A]CGGGTGATATACACATCGTCTTATTTCGCCCTTGGATGCACTGATGGATATATTGCTGATGAAGAGCAGGTTCATGAGGGTAAGAA
106375 C A GGTTGAACCTTGGCTACCAGATCCTGCTAGATTCTTTTCTGTCAATGTTGGAGGGTTGAAAAATGTATTAGAGGCTTATAAGAAGACGGAGTCAATCAAG[C/A]GGGTGATATACACATCGTCTTATTTCGCCCTTGGATGCACTGATGGATATATTGCTGATGAAGAGCAGGTTCATGAGGGTAAGAAA
106375 A G GCAGGTTCATGAGGGTAAGAAATACTGTACTGAATATGAAAAATCAAAAGCTTTTGCAGACACAATTGCAATGCAGGCTGCAAGTGAAGGCATACCTATC[A/G]TCCTTCTTTATCCAGGCGTCATTTATGGTCCTGGGAAAATAACAGCTGGAAATATTGTTGCAAGGATTCTGATTGAAAGATTCAGTG
106375 A G GCATACCTATCATCCTTCTTTATCCAGGCGTCATTTATGGTCCTGGGAAAATAACAGCTGGAAATATTGTTGCAAGGATTCTGATTGAAAGATTCAGTGG[A/G]CGACTCCCAGGTTATATTGGTAGCGGAAATGACAAGAGCTCATTTTGTCATGTTGATGATGTTGTGAATGGTCATATATTAGCCATGC
106375 G A ATGACAAGAGCTCATTTTGTCATGTTGATGATGTTGTGAATGGTCATATATTAGCCATGCACAATGGAAAACTGGGTGAAAGATATCTTCTTACTGGAGA[G/A]AATGCTTCCTTTAAGCATGTTTTTGATATCGCTGCTATCATCACAAATTCAAAGAGACCTTGGTTTCACATACCTCTATGGTCTGTAGA
106375 G A TCATGTTGATGATGTTGTGAATGGTCATATATTAGCCATGCACAATGGAAAACTGGGTGAAAGATATCTTCTTACTGGAGAGAATGCTTCCTTTAAGCAT[G/A]TTTTTGATATCGCTGCTATCATCACAAATTCAAAGAGACCTTGGTTTCACATACCTCTATGGTCTGTAGAGATATATGGCTGGATATTG
106375 C T ATGTTGTGAATGGTCATATATTAGCCATGCACAATGGAAAACTGGGTGAAAGATATCTTCTTACTGGAGAGAATGCTTCCTTTAAGCATGTTTTTGATAT[C/T]GCTGCTATCATCACAAATTCAAAGAGACCTTGGTTTCACATACCTCTATGGTCTGTAGAGATATATGGCTGGATATTGGTTTTCATTGC
106375 C T GTTGTGAATGGTCATATATTAGCCATGCACAATGGAAAACTGGGTGAAAGATATCTTCTTACTGGAGAGAATGCTTCCTTTAAGCATGTTTTTGATATCG[C/T]TGCTATCATCACAAATTCAAAGAGACCTTGGTTTCACATACCTCTATGGTCTGTAGAGATATATGGCTGGATATTGGTTTTCATTGCTC
106375 A C TGCTTCCTTTAAGCATGTTTTTGATATCGCTGCTATCATCACAAATTCAAAGAGACCTTGGTTTCACATACCTCTATGGTCTGTAGAGATATATGGCTGG[A/C]TATTGGTTTTCATTGCTCACATTACGGGGAAGCTTCCTCTAATTAGTTATCCGACTGTCAAGGTTTTAAGGCATCAATGGGCATATTCTT
106375 A G GGAAGGAACTAGGTTACAGCCCTAGAAGCTTGAATGAAGGATTAACAGAGATGCTTCAGTGGTTAAAGAGTTTAGGTTTCATCAAATACTAAGGAATAGC[A/G]CAAAAAAGGCAGTGCAAGGCTTGGATAATTAAGTTTTAAAGAGGTATGTACGGTCATGGTGTCAAGCCATTCCAAATGCAGGTTA
106375 A T GAATGAAGGATTAACAGAGATGCTTCAGTGGTTAAAGAGTTTAGGTTTCATCAAATACTAAGGAATAGCACAAAAAAGGCAGTGCAAGGCTTGGATAATT[A/T]AGTTTTAAAGAGGTATGTACGGTCATGGTGTCAAGCCATTCCAAATGCAGGTTAATCTTCTGTACAAATTAACATGTGTAGATTATG
106375 G T ACAGAGATGCTTCAGTGGTTAAAGAGTTTAGGTTTCATCAAATACTAAGGAATAGCACAAAAAAGGCAGTGCAAGGCTTGGATAATTAAGTTTTAAAGAG[G/T]TATGTACGGTCATGGTGTCAAGCCATTCCAAATGCAGGTTAATCTTCTGTACAAATTAACATGTGTAGATTATGTGATAATTTGTCT
106375 A T ATGCTTCAGTGGTTAAAGAGTTTAGGTTTCATCAAATACTAAGGAATAGCACAAAAAAGGCAGTGCAAGGCTTGGATAATTAAGTTTTAAAGAGGTATGT[A/T]CGGTCATGGTGTCAAGCCATTCCAAATGCAGGTTAATCTTCTGTACAAATTAACATGTGTAGATTATGTGATAATTTGTCTGTACTCA
106381 T C GTTGAAGTTTGTTGGTGAACTGACAAGAGTAGCTGCTCCAGGAGCTACAATAATAATAGTAACATGGTGCCATCGAAATTTATCCCCTGAAGAAGAAAGC[T/C]TAAAGCCTGAAGAGAAGAGCCTTTTGAACAAGATATGCAATGCTTATTTTTTGCCAGAGTGGTGTTCGGCCTCTGATTATGTTAAAA
106381 G A GCCATCGAAATTTATCCCCTGAAGAAGAAAGCTTAAAGCCTGAAGAGAAGAGCCTTTTGAACAAGATATGCAATGCTTATTTTTTGCCAGAGTGGTGTTC[G/A]GCCTCTGATTATGTTAAAATGGCCCAGTCTCTTGGGCTTGTGGACATAAAGACAGCAGATTGGTCAGATAATGTAGCACCATTTTGG
106381 A G TTTTGAACAAGATATGCAATGCTTATTTTTTGCCAGAGTGGTGTTCGGCCTCTGATTATGTTAAAATGGCCCAGTCTCTTGGGCTTGTGGACATAAAGAC[A/G]GCAGATTGGTCAGATAATGTAGCACCATTTTGGCCAGCTGTGATTCGATCTGCCTTGACATGGCGAGGGTTTACTTCTTTGTTGCGAA
106381 G A ATTAAAGGAGCGTTAGCAATGCCATTGATGATTGAGGGCTACAATAAAAAGCTGATCAAATTTGAAATCATCACATGCCGTAAACCGGTGTAAATGGTTC[G/A]AGCACACCAACTCTCTGTAATTGATGGATAATATGAGGGTTCTAATCTGTTTTAGTGTATTTATGTAATTAACTTACTTATTATGAAG
106387 A G AAAAATATCAGACAGTACACAAATCCAAAGCAGGAAGACCAAATCAGAACAATGCTACAAGGACCGAAACTTTTTTGTCAAAAGTTGCGAAATAAAGAGA[A/G]AAAAATGGGTTCCACCTTCTATTTTTAAGGCGCAATTCATCGAGGGTCCTACTCATTTATCTCATATTTGCACAATTTGACATAAATT
106403 C T TGCCTGATTTGCCAACTGCACCGATGCTATGGGCCTCGTCTAAATACGTAAATGCCTTATACTTCTTGCAAACAGCTATGATTTCAGGAAGCTTGCAAAG[C/T]TCGCCTTCCATACTGTAAATTCCTTCAATAATCACAATTATTTTCTTCCATGGTCTATGTGTACGAGGTTGACCCTCAGCAATTTGCTCTC
106407 T C TGACCGATGTTATTTCATCTAAGGGCACATCGATGATGGCCTGCTCAAGTCTGTAGCTGGGCAATGGAGGTAGGGAGCCCAATGCAATAGGGGACAAAGA[T/C]GAAGGAGGTTTTGGGATGGTATGGCGATGCCATTTTGGTTCAATGGTTGGATATTCGAGTCCTCTGGCGAACTCAGCAATGCAGT
106407 C G TGCTCAAGTCTGTAGCTGGGCAATGGAGGTAGGGAGCCCAATGCAATAGGGGACAAAGATGAAGGAGGTTTTGGGATGGTATGGCGATGCCATTTTGGTT[C/G]AATGGTTGGATATTCGAGTCCTCTGGCGAACTCAGCAATGCAGTTCAAGAACTGCGCTGAACCTAAGCCATCAAAAACAGCATG
106407 G A GTAGGGAGCCCAATGCAATAGGGGACAAAGATGAAGGAGGTTTTGGGATGGTATGGCGATGCCATTTTGGTTCAATGGTTGGATATTCGAGTCCTCTGGC[G/A]AACTCAGCAATGCAGTTCAAGAACTGCGCTGAACCTAAGCCATCAAAAACAGCATGCGAGCTTTCAAGCCCAATCACCAAGCCTT
106407 C G TTGGATATTCGAGTCCTCTGGCGAACTCAGCAATGCAGTTCAAGAACTGCGCTGAACCTAAGCCATCAAAAACAGCATGCGAGCTTTCAAGCCCAATCAC[C/G]AAGCCTTTACATGCAAATTGTGTGACCTGAATGAGAACGAGCACGTCTGAAGGATCGACTTCAGGACGTGGATCTGGAAGGAGTTG
106407 A G CGAGTCCTCTGGCGAACTCAGCAATGCAGTTCAAGAACTGCGCTGAACCTAAGCCATCAAAAACAGCATGCGAGCTTTCAAGCCCAATCACCAAGCCTTT[A/G]CATGCAAATTGTGTGACCTGAATGAGAACGAGCACGTCTGAAGGATCGACTTCAGGACGTGGATCTGGAAGGAGTTGTTCATAGG
106407 A G GTTCATAGGTTGGAACAAGAGGATGACTCAGATTATTGATATCCTCTAGTGTGCAATCTGCAGTGGCTTCGACAAACCAAGCTCCCTGAGAATTGCACTC[A/G]ACCTGAAGCTCTCCCTTTAAGGATTTCACTAGACGACCTGCTAATGGATAGTAGTGCACCAACGCCCTTGATAGTGCATCTTTTATAA
106411 A AT CATCCGCAGCGCAGGGCCCAACAACCAACCAGAAACTGACACATGGCAAATCCCCGAAAGCATCGAGCAATTTCCGACCGACATCAAGTTCAACACAGAC[A/AT]CCATGATTCTCTGCTGTCTTCCTGCTTTGAGACCGTTCCTGAAAAATCCAACGTTGGTAATGAAATGATGATAAACAAACCGACTG
106413 A T TATACAAAGTGGTTTTGGGCAATGGAATTCCTGTTGCGGTTAGGAGGGTTGGAGAAGGAGGAAGGAGCGGGCAGAAGTATAAGGAGTTTGCGAACGAGGT[A/T]CAGGCGATAGCCAGAGTGAGGCATAGGAATTTGGTGAGGCTGAGGGCTTATTACTGGGCACCTGATGAGAAGTTGCTTATAA
106413 G GT CAAAGTGGTTTTGGGCAATGGAATTCCTGTTGCGGTTAGGAGGGTTGGAGAAGGAGGAAGGAGCGGGCAGAAGTATAAGGAGTTTGCGAACGAGGTACAG[G/GT]CGATAGCCAGAGTGAGGCATAGGAATTTGGTGAGGCTGAGGGCTTATTACTGGGCACCTGATGAGAAGTTGCTTATAAGTG
106413 C CA TTTTGGGCAATGGAATTCCTGTTGCGGTTAGGAGGGTTGGAGAAGGAGGAAGGAGCGGGCAGAAGTATAAGGAGTTTGCGAACGAGGTACAGGCGATAGC[C/CA]AGAGTGAGGCATAGGAATTTGGTGAGGCTGAGGGCTTATTACTGGGCACCTGATGAGAAGTTGCTTATAAGTGACTTTATTT
106413 G T GTGAGGCTGAGGGCTTATTACTGGGCACCTGATGAGAAGTTGCTTATAAGTGACTTTATTTCTAATGGCAATCTTGCTTCTGCTCTTAAAGCCCGGCCAG[G/T]TCAACCTACCCTATCATGGTCATTACGGCTTAAAATAGCAAAAGGAACAGCCCGTGGGCTAGCCCACCTCCACGAATGCAGCCCAAG
106413 A G TGCTTATAAGTGACTTTATTTCTAATGGCAATCTTGCTTCTGCTCTTAAAGCCCGGCCAGGTCAACCTACCCTATCATGGTCATTACGGCTTAAAATAGC[A/G]AAAGGAACAGCCCGTGGGCTAGCCCACCTCCACGAATGCAGCCCAAGAAAATTCATCCACAGCGACATAAAACCGTCAAACATCCTCC
106413 T C AGTCGAGGCTTTTGTCAGAGATGGTGGACCCTGCTTTGCACGCAGAAATGAATGCAAAGAAGGAGATCGTTTCTGTGTTTCATATCGCACTTGCATGTAC[T/C]GAGACTGACCCAGAGGCAAGGCCCAGGATGAAGAATGTATCAGAGAATCTTGATAGAATTGGATCATGAACAAGCAGTAGTTGAG
106417 G A TAACAGCTTTGTGGAAATGTGGAACGGCATCTTTATCGAGATCTTTATGGGAACGCACAGGGTCCGATAAATCTGTAGACACAATCATTCCAGGGCCTTC[G/A]GTGCATGGACCACCAACTAGCGCAATGATTCGGGCACCAGTTCCTGGTAAACATGCTCCCAGTAATCCGGCTGCAACACTTAAAGC
106421 C T AACCTGCCTTCCGATCAGTGCGCATAGCAAAAGTTCAGTAAACCAGCTACTTTCATTAGTGGAGGTAAAAATGAAAGAAGTGATATCTAGGGAACCCACG[C/T]TTCTTGTTATGGTTGTTGGTGTTCCAAATGTGGGCAAGTCGGCTCTTATTAATTCTATTCACCAAATTGCTACTTCTCGATTCCCTGTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106423 T C CTGTTACATTTATGTATGAACCTGACATTCATATTAATGAAGAGTTGATGGAGACTTTATCTCTTGAAGAGAAACAAGCTTGGATGGATAGCAGTCCTAC[T/C]AAAGTATTTGACATCGATCAAAATGGACAGGTGGTTGTAGTAGACCCAGAAGCATACACATACGACGACGAAGTGCTGAAGAAAGC
106423 C T AAGAGAAACAAGCTTGGATGGATAGCAGTCCTACTAAAGTATTTGACATCGATCAAAATGGACAGGTGGTTGTAGTAGACCCAGAAGCATACACATACGA[C/T]GACGAAGTGCTGAAGAAAGCAGAAGCAATGGGCAAACCGGGGCTAGTCGAAATCACAGCTAAAGAAGACAGCTTCATCTTCACA
106427 A T CTGAAGTGGCAAGGCTCCGAGAACTGCATACCTTGAAAGGGCATGTAGAATCAGTAGTGAAGCTGAAGGGATTGGACATTAGCACAATTCAGCAGCATTA[A/T]TCCGTTTAAAACGTTTTTGACTTGTAGAAGTAATTTTAGAGATGATAGCTGTCTGCTTAAACAGTTACTGGAAGAGGTAAAAAAAT
106427 T A TGAAGTGGCAAGGCTCCGAGAACTGCATACCTTGAAAGGGCATGTAGAATCAGTAGTGAAGCTGAAGGGATTGGACATTAGCACAATTCAGCAGCATTAA[T/A]CCGTTTAAAACGTTTTTGACTTGTAGAAGTAATTTTAGAGATGATAGCTGTCTGCTTAAACAGTTACTGGAAGAGGTAAAAAAATG
106433 G A CGTCATCGTCTGTTGTTTGCACATTTAGTGGAAGATCGTGAAGTAGGTTCTCGAGGTTGCCGTTCTCCATGTACTCGTAGATCGCTATCCTTTGGTCTCC[G/A]GCTAGGCAGTACCCAGTTAAGGGCACTAGGTTTTGATGCCTTATTCGACCTAGCCTCTCGAGCTCCCTAGAGAGTTCTTGATCAGTCA
106433 T A GGTTCTCGAGGTTGCCGTTCTCCATGTACTCGTAGATCGCTATCCTTTGGTCTCCGGCTAGGCAGTACCCAGTTAAGGGCACTAGGTTTTGATGCCTTAT[T/A]CGACCTAGCCTCTCGAGCTCCCTAGAGAGTTCTTGATCAGTCAATGTCGAGCTATGTACCAAAACCTTCATCGCGACTTGTGTGTTGTT
106435 CT C GTAGCAGAGCTGTATCTACATGGTATCGATTACTCCTTGTGCATGTAACATGTAGAAGCAGATCGGTCATTCAATATCAATGTAACAATATGGCGTTTTA[CT/C]TTCTTTTGTGGCAGTTTTTCTGTCAATTCGGGTAGCACATCAAATAAATCAGCGACGAGCCCATAGTCTGCAACCTGAAATATGGGTG
106435 A T ATACTGCATTTGACGTTGTTGCCAATGAGAATGATGTAGACCTGACTGTCAGTACACAAGGATCACCTCCAGTATATCGCACAGTACAAAGAGCATTTCC[A/T]GCATAAATCGGCCTGGTAAAGGTTTTTGGTTCAGATATTGCAACGACATCAGTGATTGGTGAAACGTCAAGAAGAGCTGCAGCTCTT
106435 T C TAGACCTGACTGTCAGTACACAAGGATCACCTCCAGTATATCGCACAGTACAAAGAGCATTTCCAGCATAAATCGGCCTGGTAAAGGTTTTTGGTTCAGA[T/C]ATTGCAACGACATCAGTGATTGGTGAAACGTCAAGAAGAGCTGCAGCTCTTGGCACTACATTTTTTCCGAAGGAGCTAGAAGCAGCA
106435 A AT TTCCAGCATAAATCGGCCTGGTAAAGGTTTTTGGTTCAGATATTGCAACGACATCAGTGATTGGTGAAACGTCAAGAAGAGCTGCAGCTCTTGGCACTAC[A/AT]TTTTTTCCGAAGGAGCTAGAAGCAGCAACAACATGTGAGTAGCTACCCTTCTTTTGAACCAAACAAATAAGCTCTGCCCATGTCTCA
106435 T C GCAGCTCTTGGCACTACATTTTTTCCGAAGGAGCTAGAAGCAGCAACAACATGTGAGTAGCTACCCTTCTTTTGAACCAAACAAATAAGCTCTGCCCATG[T/C]CTCAGCTAATGGGTGCTTCAAGGTATCTGCATCAGCGACAAGCACCTGTGAGACTGAAGGGTGACACGATGCAGCATGCGCTGCTG
106443 T C TTGGCAGCAGCCTTCTCTTCTTCTCAAACCATTCCGGTTTTATAAGCGCCCTCAGTCCTAGTTTGTTGTAGAACACCCTTCTCACTGACCCCCCTTTTGC[T/C]TCTACCGCTTCTTTTGCCTTAGCTGAAACCCTAGACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCCTCAGCTAACAGCCTAA
106443 A T CCGGTTTTATAAGCGCCCTCAGTCCTAGTTTGTTGTAGAACACCCTTCTCACTGACCCCCCTTTTGCTTCTACCGCTTCTTTTGCCTTAGCTGAAACCCT[A/T]GACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCCTCAGCTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGC
106443 C T CTAGTTTGTTGTAGAACACCCTTCTCACTGACCCCCCTTTTGCTTCTACCGCTTCTTTTGCCTTAGCTGAAACCCTAGACACCTCAATATGAATTGGCCA[C/T]TGAATTAGCTCAGCACCCTCAGCTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTAT
106443 T C CCTTCTCACTGACCCCCCTTTTGCTTCTACCGCTTCTTTTGCCTTAGCTGAAACCCTAGACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCC[T/C]CAGCTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATA
106443 G C TCTCACTGACCCCCCTTTTGCTTCTACCGCTTCTTTTGCCTTAGCTGAAACCCTAGACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCCTCA[G/C]CTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGT
106443 A G ACTGACCCCCCTTTTGCTTCTACCGCTTCTTTTGCCTTAGCTGAAACCCTAGACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCCTCAGCTA[A/G]CAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCT
106443 A G AAACCCTAGACACCTCAATATGAATTGGCCACTGAATTAGCTCAGCACCCTCAGCTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGC[A/G]TCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCTGCATTGATGAGGTTTGCAACATTCCCAAGCTTGACAGTCTGA
106443 G T CTAACAGCCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCTGCATT[G/T]ATGAGGTTTGCAACATTCCCAAGCTTGACAGTCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCG
106443 T C CCTAACACCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCTGCATTGATGAGG[T/C]TTGCAACATTCCCAAGCTTGACAGTCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGTCTG
106443 C T CCGTCTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCTGCATTGATGAGGTTTGCAA[C/T]ATTCCCAAGCTTGACAGTCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGTCTGCCCACCT
106443 C T CTTTTATTTGTTTCCTTAATGCACCTGCATCCTTGAGAGTTTTCATTGTTATAAGCTCTGATGAGTCAATATGTCCTGCATTGATGAGGTTTGCAACATT[C/T]CCAAGCTTGACAGTCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGTCTGCCCACCTTCAA
106443 C T CATTGATGAGGTTTGCAACATTCCCAAGCTTGACAGTCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGT[C/T]TGCCCACCTTCAAACCCAAACTTCATCGTCCCTCTCGCCTTTTGACCTTTATGACCTCGTCCAGCAGTTTTCCCTTTGCCCGAACCAATAC
106443 C A TCTGAAAATTGAGTCTGAATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGTCTGCCCACCTTCAAACCCAAACTTCATCGTCCCTCT[C/A]GCCTTTTGACCTTTATGACCTCGTCCAGCAGTTTTCCCTTTGCCCGAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTG
106443 A C ATCTGTTCTTAAACCCTCTCTTAGGCAGTCTCCTTCTAAGCGGAGTCTGCCCACCTTCAAACCCAAACTTCATCGTCCCTCTCGCCTTTTGACCTTTATG[A/C]CCTCGTCCAGCAGTTTTCCCTTTGCCCGAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTGTTGTCTCTAAGATCATTC
106443 C T GTCTCCTTCTAAGCGGAGTCTGCCCACCTTCAAACCCAAACTTCATCGTCCCTCTCGCCTTTTGACCTTTATGACCTCGTCCAGCAGTTTTCCCTTTGCC[C/T]GAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTGTTGTCTCTAAGATCATTCAGTCGAAGAAGGCTTGTTGAAGGAGA
106443 A C CCTTTTGACCTTTATGACCTCGTCCAGCAGTTTTCCCTTTGCCCGAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTGTTGTCTCT[A/C]AGATCATTCAGTCGAAGAAGGCTTGTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTG
106443 T C CAGCAGTTTTCCCTTTGCCCGAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTGTTGTCTCTAAGATCATTCAGTCGAAGAAGGCT[T/C]GTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTT
106443 A T TCCCTTTGCCCGAACCAATACCCCTACCTAATCGCTTCTTCTTCTTTCTCGCTCCTTTGTTGTCTCTAAGATCATTCAGTCGAAGAAGGCTTGTTGAAGG[A/T]GAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTT
106443 T A CTCGCTCCTTTGTTGTCTCTAAGATCATTCAGTCGAAGAAGGCTTGTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTA[T/A]GGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTT
106443 C T CCTTTGTTGTCTCTAAGATCATTCAGTCGAAGAAGGCTTGTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTA[C/T]GGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATA
106443 A C TTCAGTCGAAGAAGGCTTGTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCG[A/C]TATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACAT
106443 G A AAGAAGGCTTGTTGAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTA[G/A]GGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGAT
106443 A G GAAGGAGAAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGA[A/G]AAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGATACATTGTCATTGA
106443 G A AAAATGACAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGAAAAGCTG[G/A]ATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGATACATTGTCATTGATTTTGGAG
106443 T C CAGTGAACTGTAATTGTTGTTGGATCCAAATGACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAA[T/C]GGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGATACATTGTCATTGATTTTGGAGTGGAGAA
106443 A G ACGCTATGGGTACGGTGGTAATTTGGGGTTTCGATATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAG[A/G]TTAGAGAGGAGAGACATGCGTCGATACATTGTCATTGATTTTGGAGTGGAGAAAACTTCCGATGGACAGGTTATTCCTTGCGTTT
106443 A G TATGTTAGGGTTTTTAGGGAAAAGCTGGATGGAATGGGATTGGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGATACATTGTC[A/G]TTGATTTTGGAGTGGAGAAAACTTCCGATGGACAGGTTATTCCTTGCGTTTATTATTGGTTCAGAGTTTAGAGACCTCAAATTCCT
106443 T G GGGTGGCTCTTAGGGTTTTGGATAGATTAGAGAGGAGAGACATGCGTCGATACATTGTCATTGATTTTGGAGTGGAGAAAACTTCCGATGGACAGGTTAT[T/G]CCTTGCGTTTATTATTGGTTCAGAGTTTAGAGACCTCAAATTCCTCTCCTTCGCTGCGATAGGAGGACCATTTTTCCCCGAGCTATC
106445 A C AGATTGCGGCAGCTGCAGGTAAAGGTGAGGGATTTGAAATGAAGATGGCCAGCATAGAAGCTGACCTGCATATCCTAAAAGTTCAGGAAGACATGATGGA[A/C]CACTACCCGAACGAGGAAGAGATAAAGAAGAAAGCACTGCCTCCTAGGGAACTAATAAACCTATGCCTAAAAAACAAGGACCG
106445 C T GGAACACTACCCGAACGAGGAAGAGATAAAGAAGAAAGCACTGCCTCCTAGGGAACTAATAAACCTATGCCTAAAAAACAAGGACCGAGCCCTATCTTTG[C/T]TGGCCTTTGAAATATTTGCATGGACAAACTCTTCCTTCAGGAAGGCCAACCGGCACCTTCTGGAAGCATGCTGGAAGAACGCGGT
106445 G T AGGATTTTCCTGAGGCTGGTAAGTTGATGATAACTGCGGTTTTTATGGGTAAAGAAGGGGTTGACGATATCGCTGAAGAGGACGATGTTGCTATGGATTC[G/T]ACGTGATGCTGCTGTTTTTTGTTTCTTTTTGTATGTATGGTTTGCAAATGAGTATTCGACCTGATGCTGATCCTTATTGCATCACTCG
106449 GT G CCGCATCGCCGTCGTCGGCGAATGGTATGATGTGGCGAAGGATAAGGCGACGGGTCGAACTCGTGAGGGGTAGTTTGGCAATTTTAGGCGATTGGTTTAG[GT/G]TTTTTTAGGAATTTGGAAGTGGAAATGAAAGAGATAGGAGAAGGGGAGACGAAGAGGATGCTCCGCATTGTTCCTTTTTAATG
106451 A G TCACAGTTCGTGCTGGTTCTTACTCTGATGAACTCGTCAAAACTGCGAAAACAATAGCAACACCAGGGAAAGGAATAATGGCAATGGATGAATCGAACGC[A/G]ACATGTGGAAAAAGGCTTGACTCAATTGGACTTGAGAACACAGAAGCAAACAGACAGGCATACAGGACCCTTCTTGTGTCTGCTC
106451 T C ACTATGTATCTGGTGCAATCCTTTTTGAGGAAACTCTTTACCAATCCACTGTTGATGGGAAGAAGATTGTCGATGTTCTTACTGGCCAGGGCATCGTGCC[T/C]GGCATTAAGGTCGACAAGGGTCTAGTGCCACTTACAGGCTCAAACGATGAATCATGGTGCCAAGGTTTGGATGGTCTTGCATCACGA
106451 C T GCATCGTGCCTGGCATTAAGGTCGACAAGGGTCTAGTGCCACTTACAGGCTCAAACGATGAATCATGGTGCCAAGGTTTGGATGGTCTTGCATCACGATG[C/T]GCTGCTTACTATCAACAAGGGGCACGCTTTGCCAAATGGCGTACAGTGGTGAGCATCCCCAATGGGCCATCAGCTTTGGCAGTGA
106451 A G CAGGCTCAAACGATGAATCATGGTGCCAAGGTTTGGATGGTCTTGCATCACGATGCGCTGCTTACTATCAACAAGGGGCACGCTTTGCCAAATGGCGTAC[A/G]GTGGTGAGCATCCCCAATGGGCCATCAGCTTTGGCAGTGAAGGAAGCAGCATGGGGTCTTGCACGATATGCTTCCATTGCTCAGG
106451 G C GGTGCCAAGGTTTGGATGGTCTTGCATCACGATGCGCTGCTTACTATCAACAAGGGGCACGCTTTGCCAAATGGCGTACAGTGGTGAGCATCCCCAATGG[G/C]CCATCAGCTTTGGCAGTGAAGGAAGCAGCATGGGGTCTTGCACGATATGCTTCCATTGCTCAGGACAATGGACTAGTTCCAATAG
106451 T C CTGCTTACTATCAACAAGGGGCACGCTTTGCCAAATGGCGTACAGTGGTGAGCATCCCCAATGGGCCATCAGCTTTGGCAGTGAAGGAAGCAGCATGGGG[T/C]CTTGCACGATATGCTTCCATTGCTCAGGACAATGGACTAGTTCCAATAGTTGAGCCAGAGATTTTGCTTGATGGAGAGCATGGAA
106451 T A TTGAGGTTGCACAGCAAGTGTGGGCTGAGGTCTTCTTCTATATGGCTCTAAACAGTGTCATGTTCGAAGGCATTTTACTAAAACCAAGCATGGTTACTCC[T/A]GGCGCTGAATGCAAAGAAAGGGCAACCCCAGAGAAAGTTGCTGAATACACTCTGAAACTTCTTCAAAGAAGAGTCCCACCTTCAGTT
106451 T A ACAGTGTCATGTTCGAAGGCATTTTACTAAAACCAAGCATGGTTACTCCTGGCGCTGAATGCAAAGAAAGGGCAACCCCAGAGAAAGTTGCTGAATACAC[T/A]CTGAAACTTCTTCAAAGAAGAGTCCCACCTTCAGTTCCAGGCATTATGTTCCTTTCTGGAGGGCAGTCCGAAGTCGAGGCAACACTA
106451 A T CGTTCTCCTACGCTAGGGCACTTCAGAACACTTGCTTGAAGACATGGGGAGGAAGACCAGAAAATGTGAAAGCTGCTCAAGACGCTCTCCTTACCAGAGC[A/T]AAGGCAAACTCTCTTGCCCAGCTTGGAAAGTACACAGGCGAAGGTGAATCTGAAGAATCCAAGGAAGGAATGTATGTCAAGAACT
106453 C T CGAGCTGTGCCTTCTTCTCATTGATCATTTCATCTCCTCCCTCGACAAGGACACTGTCAGCATTGCCATTGTTGCCATTGTTCTCGTTTGATTCCACTGC[C/T]GCCTTCCTCTTCTCCATGTGCTTCATGAACCACTCATCGAAGGCACGTTTCCTTTTCACGTACTCTTTGTAAGTTCCCTCGCACTTGTCTTTT
106453 T C TGATTTCTGAAACGGTGGAATCCATGGATTGCATGTCCACTATGTATCTTGTATGCAAATGACTAACAGCAGCCTTGGTTTTTTCCAAAGTTTCAGAACT[T/C]GCGTTCCTTTTCTTTTGCTTCTGCAATGATGCAACCTTCCGCTGATATTCCATTTTCATTATCTCCCCCGCCTTCACTTCTTCAAACAACTT
106463 GT G TCTCCTTTCGTTCCACAGAATATCAAATAGGAAGACACAAGGACTAGTATTTCTTTTCTCCTTTTAAATAACAGAGAGAAAGGGTGATATTTTCCGCCTT[GT/G]TTGTTTTGGAATCGAGCTGTATTGAATACACCGAAGTTTTCGAGAAGTGGGTTCTGATCAAAATTGCATCCTGTGATGGTTTTGAGTT
106463 C G CCGCCTTGTTGTTTTGGAATCGAGCTGTATTGAATACACCGAAGTTTTCGAGAAGTGGGTTCTGATCAAAATTGCATCCTGTGATGGTTTTGAGTTGATT[C/G]GAGAATTTATTACCATGAGTTCATACTGCTGCTTCAAGTCAGCAGGAAATTCTTCCTCAAATGCTGGCAAAGGAAAAAGCACCCAAAA
106463 G C AAGAATTTTGGACATATCCAGATAGGGCAATTTCAAAAGCATATGACAAAACTGACAAGGCAATTCTATCTCACAGTCCCGATCTTGGTAGAGGTGGGTC[G/C]ACAGCCGTTACTGCAATTCTCATAAATGGCACTAAATTATGGATAGCAAATGTTGGGGACTCGAGAGCAGTAGTAGAAAAAGGCGG
106467 G A GTGATGCAGCAGTGGGCTCATTAATGATGCGAAGAACTTCTAAACCAGCAATTCGCCCTGCATCCTTTGTTGCTGTCCTTTGCGAATCATTAAAATATGC[G/A]GGAACTGTAACAACAGCTTTGGTGACCTTGTCATTCAAAAACTTTGATGCGTCATCTACAAGTTTTCTTAGGACCTGAGCAGAAATCT
106473 A G GTTACAGAATTCATCCTTATCGACCTCATCTAAAACCAGTGGAAGTAATATAAATAGCTCCATGTCACCCTATTCTGTTTCTCGAGGGGCCAATACCAAC[A/G]CAGCGAACATGACCTCTTATGGTAATGGAGGAATCAATGAGTTCAGGTATCAGAATGGAGTGCAAACTGAGCTAGGATTGCGCAGTT
106473 A G CAAAGACTAAGGATCTTTGGTCTGATCTGGAGGATGAAAGGTCAAACCAGATATCCTTTTCAAATACTCAGCTTTCAATTTCAATCCCAATGGCATCTTC[A/G]GATTTCTCTTCTACTGCATCTGGATCTAATTATCTTTGAAGAAGTTCCATACTATTGTGTTATCCATGTACAATGAATCTGAGAGCTGTA
106475 TA T CACTGTTGGCCTACTGGGGACCATGAGTGAGAAATAAAAATATTAGCACGCATCATTTGGAAGAATAAAATAGAGAAAACAAATA[TA/T]AAAAAAAATGGGCAGATCCCCCTGCTGTGAAAAGGTTGGACTGAAGAAAGGGCCATGGACACCAGAAGAAGATCAGAAACTTCTTGCTTACATTCAAGA
106475 C T AAAAAATGGGCAGATCCCCCTGCTGTGAAAAGGTTGGACTGAAGAAAGGGCCATGGACACCAGAAGAAGATCAGAAACTTCTTGCTTACATTCAAGAAAA[C/T]GGCCATGGCAGTTGGCGCGCACTTCCCATGAATGCTGGGCTTCAAAGGTGTGGGAAAAGCTGCAGACTAAGATGGACAAACTAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106475 C T GTGGGAAAAGCTGCAGACTAAGATGGACAAACTATTTAAGGCCTGACATAAAGAGAGGCAAATTCAGTCATCAAGAGGAACAAACCATCATCCAGCTTCA[C/T]GCTCTCCTAGGCAACAGGTGGTCAGCAATTGCCGGTCATCTTCCAAAAAGAACAGACAACGAAATAAAGAACTACTGGAACACAC
106475 C A GGCTTCTCGGTTGGGTTGCAAACTACAGTGTTTAGTACAGATGAAGATTCATCAAGGAAAGAATTTGTTCATGAAGGTTTCACTGGAATGCTGTTGGAAG[C/A]TACTGACGGTTGCAAGGATTATTCATTGGAGAGAGGTGCTGCTGATTCAGACAATGCTGATGAACTTTATGGAAGTTGCATCGAGG
106479 C CA TGCTTGAATCCGCAGAAATGAGCAGGTTAAGCTACGAAATTTTCTCCATTCTCGAAAACAAATTCCTATTCGATTCCGTCTCCCAACCACAAACCCCGAT[C/CA]AAAAATTCTTCCCAGAGTGCCCCTAAAGCGCCTAACCACAAGCATTTCAACGCCGGCAGCGGTAAAGTCCGCATACTTTCGATTGACG
106479 G T ATGCTACGACCTAGTCAGCGGATCGCCATTCGTGTTCTCCAGATCGGACGCCGTCGAGTCCGACGCCTACGATTTCAGCATCAGCGACGTCTGCGCCGCC[G/T]CTTGCGCCCGACGGACCGTTGGTGTCGAGTCATTGGACGGACGGGCCAGAATCTCCGCTGTAGGCAGCGGAGCAGCGGTTGGAA
106479 G C CGGACGCCGTCGAGTCCGACGCCTACGATTTCAGCATCAGCGACGTCTGCGCCGCCGCTTGCGCCCGACGGACCGTTGGTGTCGAGTCATTGGACGGACG[G/C]GCCAGAATCTCCGCTGTAGGCAGCGGAGCAGCGGTTGGAAACCCTACGGCCACGGTCATCACCCACGTACTGAACAACAAAACG
106479 A G ACACGATAGATCAGGCTGTAGCCATGGCATTTGGGGACTGTATGGAGAGCAGTTACGTTCGTATTCAGGCTAGTGGATTTGTAAGTGATGAGAGTAAGGC[A/G]GGTGAAATGCTATTTCACCAAAATGTGGAATCAGTATTATTCAGAGGGAAGAAGGTGTCAGTTATGACGAATGGAGAGAAGATG
106489 C T TTAAAGACTTCCATGGCGGATCCATCCCTTCCGATCTTTCTCTACCCTCCGCACCCGGCGCCGCGGGGTCATCGACAGCATCTAACAGGCTGCTCCGGGG[C/T]ATGCCGAATCAGATCCGGTCTGACCGAAGTCGGCCCGGATCCGCCGGAACTGAACGTGGTCCACTGTTTCCATCCACGTCGGTGAG
106489 A C ATGAGCGCAAGCCATTGTTTGATGCCTCTCCATTTCCACAGAGGCGGCCGGTGTTGGATCCTGGTAGTGGAAGATCCGACCCCAAACCGCATCACCAGCA[A/C]CAGCAGAGTACTCAGGTTCGGCCGATGTCAAGCACAGGGCAAATGGGGCATACGGGCCACGCAGGGAATCCATGGGGGTTGAAG
106489 A C GTAGTGGAAGATCCGACCCCAAACCGCATCACCAGCAACAGCAGAGTACTCAGGTTCGGCCGATGTCAAGCACAGGGCAAATGGGGCATACGGGCCACGC[A/C]GGGAATCCATGGGGGTTGAAGAAAGAAGCGATGGTGATGGAGGATCTATCGAGGAGGTTTGAAACTGCCAGCGCTATTGATA
106489 T C TACGGAGGAGATTAAGGGTTTGGAAGTGGATGATGAGAAGTCCAAGTTTGATTTAATAATGACGAGCCAAGTGTTGAATTTGGAGAAGCTGGAACATAAG[T/C]CAACTGTTGATCCCAACCCCACACGTCTTGAGAATTCCTGCGATTCTATGAGTACCGTGAATATGCCTAGACCAAGATCTGCTAGT
106489 G A AAAAAGAAAGGAAATCTGTTTTTGGTGGTGCACGTCCACGAGAACTGGTCCTGAAGGAGCGTGGAATAGATGATATTACTACATTTTTAGATGCCTCCCT[G/A]CCCGCTAATAGGATCAAGAGTGAAGCACCCAAAGTGGAGAACAAGCAACAACAAAACAGACCAGCCCAACCAACCCACGAAAAAC
106491 G A TTTTTAGGGGAAAACATTACTACAAATCGATGGCAGAAATCAGTTCTCTAATCTCCCAACCGGACTTGGAACTTGGAAGACCATCCGTCCCGATTGAC[G/A]CTCGGAAGAATGTTTCAAACGAGCTCAACCTTCGGATGGAAAAAGTTTCAAAAATGACCGAGGATGACAACCTGCATGATTCTCTGAAT
106491 C T TTTTTAGGGGAAAACATTACTACAAATCGATGGCAGAAATCAGTTCTCTAATCTCCCAACCGGACTTGGAACTTGGAAGACCATCCGTCCCGATTGACG[C/T]TCGGAAGAATGTTTCAAACGAGCTCAACCTTCGGATGGAAAAAGTTTCAAAAATGACCGAGGATGACAACCTGCATGATTCTCTGAAT
106491 C T CCCGATTGACGCTCGGAAGAATGTTTCAAACGAGCTCAACCTTCGGATGGAAAAAGTTTCAAAAATGACCGAGGATGACAACCTGCATGATTCTCTGAAT[C/T]TGAACAATGCAAGCTCCGATGATCATCGATCATGCATTCAAAATGATGAAGCATTGATCGATTCTAACACCAGCAATGATCAATCAA
106491 G C CGGAAGAATGTTTCAAACGAGCTCAACCTTCGGATGGAAAAAGTTTCAAAAATGACCGAGGATGACAACCTGCATGATTCTCTGAATCTGAACAATGCAA[G/C]CTCCGATGATCATCGATCATGCATTCAAAATGATGAAGCATTGATCGATTCTAACACCAGCAATGATCAATCAAATGTCAATAGCTC
106491 C T AAGAATGTTTCAAACGAGCTCAACCTTCGGATGGAAAAAGTTTCAAAAATGACCGAGGATGACAACCTGCATGATTCTCTGAATCTGAACAATGCAAGCT[C/T]CGATGATCATCGATCATGCATTCAAAATGATGAAGCATTGATCGATTCTAACACCAGCAATGATCAATCAAATGTCAATAGCTCCCTT
106491 G A CATTCTGTCATCTCTGCTGGTCATTGTGAAAAGGAATCTGCTCCATTTTCCATTAATCCTGATTGCCCAGAAATTGAGAAAACCAGTATAGAACTTCAGA[G/A]CGCTCAAACTTGCTTTCCTCTTCAGGGCTTCCCAGGTCCACCTTGGGCTTATCCCTGGGCACTCCCAATGATCATTGCACCGCCTACTAG
106491 A G CTCAAACTTGCTTTCCTCTTCAGGGCTTCCCAGGTCCACCTTGGGCTTATCCCTGGGCACTCCCAATGATCATTGCACCGCCTACTAGTGTTCCATTTCC[A/G]TATCTTCCAATGCTTCCTGTATTTTCTAATATGCCAAACTTAGGCGATCAATTGAACAGTGATGAAGGTAAGGAAGAAAAGAAGACTTTC
106495 TA T TTGACTCAGGTGCTGCTGACTCATCTGTTGCTGAGTCATCTGCTGCTGACTCAACTGAGAACTAATTTGCTGCGAATTGAGTTGCTGAGGAGCCATCTGC[TA/T]AGTTGGTAAAAATTCTGACCAGGAATTTTTGGAGGGCCCATGGAAGCCATTGCATTTCTCTGCAGTTGTGGATTTAAACTGATTCGG
106497 T C CAATCTGGACCCACTCTTCACTTTCTCAACTGCATCCCTAACCGCTATGTGCACTTCTTTAGGGCTCAGCCCTAGGCTCTCTTTGGTTTCAGATATCGCC[T/C]TAGAGGCAGCAGTTATGGCAGCTGCCTCGTCCATGAAGCTCACCTTTTGGGACATCCATACTTCATTTGCAGCAGTGTCCGCTAGCAACA
106497 T C GGGACATCCATACTTCATTTGCAGCAGTGTCCGCTAGCAACAGCCAAAAATTCTCCTCTTTGTTGAAGGGGTAGTAAGGACAGTGAGGAAGGGCTGCAAC[T/C]AAACCATTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTT
106497 A G GACATCCATACTTCATTTGCAGCAGTGTCCGCTAGCAACAGCCAAAAATTCTCCTCTTTGTTGAAGGGGTAGTAAGGACAGTGAGGAAGGGCTGCAACTA[A/G]ACCATTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGA
106497 A G TCCATACTTCATTTGCAGCAGTGTCCGCTAGCAACAGCCAAAAATTCTCCTCTTTGTTGAAGGGGTAGTAAGGACAGTGAGGAAGGGCTGCAACTAAACC[A/G]TTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGATGTC
106497 T C CCTCTTTGTTGAAGGGGTAGTAAGGACAGTGAGGAAGGGCTGCAACTAAACCATTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCC[T/C]TCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGATGTCAACATCGATTGATGGAATCATGCCGAGGACAGATTCGATATCGTCTA
106497 G A GAGGAAGGGCTGCAACTAAACCATTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTC[G/A]ATCTTGATGTCAACATCGATTGATGGAATCATGCCGAGGACAGATTCGATATCGTCTACTTCGGATTGAGTGAAGCCGGCGGTTTGAA
106497 A G CAACTAAACCATTTTTGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGATGTC[A/G]ACATCGATTGATGGAATCATGCCGAGGACAGATTCGATATCGTCTACTTCGGATTGAGTGAAGCCGGCGGTTTGAATGAGAAGTTCAG
106497 A G TGCGCTTTAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGATGTCAACATCGATTGATGG[A/G]ATCATGCCGAGGACAGATTCGATATCGTCTACTTCGGATTGAGTGAAGCCGGCGGTTTGAATGAGAAGTTCAGCGCGCTCTTCTTTGC
106497 C T TAGGGTTACCCAAGCATACATTGAAACCACGTCTCCTTCTTGAATGCCTTCTTCCCCTTCAGTCTCGATCTTGATGTCAACATCGATTGATGGAATCATG[C/T]CGAGGACAGATTCGATATCGTCTACTTCGGATTGAGTGAAGCCGGCGGTTTGAATGAGAAGTTCAGCGCGCTCTTCTTTGCCCATTTCT
106497 A T CGATCTTGATGTCAACATCGATTGATGGAATCATGCCGAGGACAGATTCGATATCGTCTACTTCGGATTGAGTGAAGCCGGCGGTTTGAATGAGAAGTTC[A/T]GCGCGCTCTTCTTTGCCCATTTCTTCCAGTTCTTGTAGTGTCCTTACTTTCTTTCTTGTAATTTTCTTCACAGCTGTTTCACTAAAGTGT
106499 T A GAAAACCTCGTTACTTGGGCTAGGCCAATACTCCGAGATAAAGAACGACTAGACGAGCTAGCTGATCCACGACTCTCAAATAAATATCCAAAAGAAGACT[T/A]CATCCGTGTCTGCACGATAGCAGCCGCTTGCGTCGCACCTGAAGCGAGCCAAAGACCGACAATGTGCGAAGTGGTCCAGTCTCTGA
106499 T C CCGTCGACTAGACCAAACATAAGACAATCATCCACGACTTACGAATCAGATGCAACATCATCGGTGTTCTCTTCTGGACCGTTCTCAGGCTTGAGCTTGT[T/C]TGATCATGAAAATATTTCCAGAACAGCGGTTCTTTCTGAAGATTTACACGAGGGGAGATGATAGTTTGGATTGTAAATGGTATTTGTG
106507 A G ACTTAATGATGCTGTGTTTTCAAGTGTTATGGTTTCTGGTGGTTGTACAGCTGGCTCATCGCCAGCGCGTAGTGGTGATACACGCGATGCTTAGCACGGA[A/G]CTTTGCTATTGCTCGTCTGGTGGTGTTTTTCGCTTGGCTGTTATGCTACTGGATTCTATGGTGCTTCTCTCATTGCTATGCTTTGCAGA
106511 G A GTATTCACACCTTATATTTCAATCTTCAAGCATCCCAACACTGCGTCATCCACGTAATTCACAACTGAACAATAATCTTGCCAGTAGCATGCCCCTCCAT[G/A]CTCTTGGCCCATGCCTCCTTCACATTTTCCAACTTAAAACTCGAATCGATGATCGTCTTCAACTTCCCTTGCTCCATCAACTCCATCAAAAA
106511 A G ATGCCTCCTTCACATTTTCCAACTTAAAACTCGAATCGATGATCGTCTTCAACTTCCCTTGCTCCATCAACTCCATCAAAAACCTCAACTCCTCCACCTT[A/G]GGCACCAACATAAACACAACCAGCCTCTTCTTACTAAACACAACCTTCTTCCAAACAGCCAATGCCATACTCCTGAAGGTCGGATTTACAT
106511 T C CCCCATCGTCGCTCAAATTACTCTCCATCACCCTCCATTCAACACCGCTCGCACAGTGTATCACTGCATCGTATCTTTTACCCGAAGGACTCTTCAAGGA[T/C]GCGCCCTCCGAGGTCGTATAGTCGAGCACTTCGTGAGCACCAAGGGAGTCTAGGAGGTCTATGTTGCGGGCCCCACATGTGGCAGTG
106511 A G TGAGGATGTTCTTCGGTTGTTTTTCAGAAGCTTCATTGTGCCCGTTACTGAAGGTGGCTCCGGCTGCTTTGAGGGCTAGGATAGCAGTTAGGGCAGCTGT[A/G]GGGATGCCTGCGCCTTCCACAGGGGAGACAGCTGTGGGGCGGATGACGGTTAGGGCAGTTGATGCTGTTGTGAACTCTGCTAGT
106511 C T GCTTCATTGTGCCCGTTACTGAAGGTGGCTCCGGCTGCTTTGAGGGCTAGGATAGCAGTTAGGGCAGCTGTAGGGATGCCTGCGCCTTCCACAGGGGAGA[C/T]AGCTGTGGGGCGGATGACGGTTAGGGCAGTTGATGCTGTTGTGAACTCTGCTAGTCCTCCGCCTTTCGTGACATTAAGAATGGAA
106511 A G CTTCATTGTGCCCGTTACTGAAGGTGGCTCCGGCTGCTTTGAGGGCTAGGATAGCAGTTAGGGCAGCTGTAGGGATGCCTGCGCCTTCCACAGGGGAGAC[A/G]GCTGTGGGGCGGATGACGGTTAGGGCAGTTGATGCTGTTGTGAACTCTGCTAGTCCTCCGCCTTTCGTGACATTAAGAATGGAA
106511 C T ACTTCTCCAGCCACATCTATGGCTGGTATGTATGGAAATTTTGGAGGCATAAAAGGTCGTAGCATGCCTTTCTGAACCTTCCAGTCAAAAGGGTTTATAC[C/T]AGAGGCTTCCACTCTTAACAATATTTCATCCTTCTTCGCTGTTGGTATTGGTACCTCAACATGCTTTAAAGCATCAGCGCCACCACCATA
106513 C T CGGAAATGAGCACCCTATGGTTAGACATGAAGCTGCTGAGGCTCTCGGGTCAATTGCAGATAATGAAAGCATCGAACTTTTGGAAAAATTTGCAAATGAT[C/T]CGGAGCCGCTTGTTTCTGAAAGTTGTCAAGTTGCTCTAAGCATGCTCGAGTACGAAAGATCAGGCAAATCATTTGAGTATCTGTTTT
106515 G A TACAACCAATAACGTTGCCCAAGGACACGCTACACACGAGAACATAAAACAACATCTATATAATCTTCAATGTGAAACATAAATGTATGAACATATATAT[G/A]ATTAACGAGGTTAGGAACCAGGGGCATTCTGGAAAAGCTCAGGAAGATGAGCATTAGTAAGCTTGGTCCTCTTGGTGATTTCCTTCT
106515 T C GCCCATGTATCTCAGCCATGGCCCGTCTCTTGGCAGTGTTGGTGGCGGGTCTCATGTTGCACCTCTGGAGGTCCTTCTCTATGTCAACCATATCTCTAGG[T/C]AGCTCTATGCTTCTGAACAGTTGTTTCAGGTCGTCATCCACTTTTATCCCCACTTTCGGATCATTTGGGTACACTATATCTTCTTGCGAG
106515 T C GTTGGTGGCGGGTCTCATGTTGCACCTCTGGAGGTCCTTCTCTATGTCAACCATATCTCTAGGTAGCTCTATGCTTCTGAACAGTTGTTTCAGGTCGTCA[T/C]CCACTTTTATCCCCACTTTCGGATCATTTGGGTACACTATATCTTCTTGCGAGTCCATGTTCGACAGCAACCACACATGCCCTGAACTTT
106515 C T TCCCCACTTTCGGATCATTTGGGTACACTATATCTTCTTGCGAGTCCATGTTCGACAGCAACCACACATGCCCTGAACTTTTTAAGGCCTGTAAGTCCTC[C/T]AGAACATTAGTATAAGAATCCTTCACATCAACTACAGGAAGACCTTCTGGGTGTTTCCTTATTAAAGAAAGAAGGTTATCTTTTCCCTTC
106519 G C TGCAGACCAAATTTTGAGCTTCTTTCCTTCCATTTCGAATTGACAAGCGAGTCATGGAAGCCACTACATTAATCTCGCACTTCCCCTCTCTTCGTACCCG[G/C]TTTCGATCCAAACTTAACCCGTTTCCAGTTCTGTACGCCTCCCCCTCTTCTTCGTCTGTCACGCGACGGTTGCTATCGGTGAAAGCCAATT
106519 G A ACCAAATTTTGAGCTTCTTTCCTTCCATTTCGAATTGACAAGCGAGTCATGGAAGCCACTACATTAATCTCGCACTTCCCCTCTCTTCGTACCCGGTTTC[G/A]ATCCAAACTTAACCCGTTTCCAGTTCTGTACGCCTCCCCCTCTTCTTCGTCTGTCACGCGACGGTTGCTATCGGTGAAAGCCAATTCCTCT
106519 C A TACATTAATCTCGCACTTCCCCTCTCTTCGTACCCGGTTTCGATCCAAACTTAACCCGTTTCCAGTTCTGTACGCCTCCCCCTCTTCTTCGTCTGTCACG[C/A]GACGGTTGCTATCGGTGAAAGCCAATTCCTCTTCCGGTGGGACCCACCACCAACAACGGAAAACTCTGTCAGAAGTATGGGACCCACTGT
106519 C A TTAACCCGTTTCCAGTTCTGTACGCCTCCCCCTCTTCTTCGTCTGTCACGCGACGGTTGCTATCGGTGAAAGCCAATTCCTCTTCCGGTGGGACCCACCA[C/A]CAACAACGGAAAACTCTGTCAGAAGTATGGGACCCACTGTGTGGCAAAGGCATCACGACGGCTCCCGTTTGGATGCCGAGTTTCGAG
106519 G A GTTTCGAGGAGTTGGATAGTGGAAATATGCTCTTGAAGCAGCGGATCGTCTTTCTTGGATCTCAGGTAGATCAAATAACAGCTGATCTAATCATTAGCCA[G/A]CTATTACTTTTAGACGCAGAAGACCAAAAGAAGGATATCAAAATGTTCATAAATTCTCCTGGTGGTTCAGTGACAGCAGGAATGGG
106519 T C TGTTCATAAATTCTCCTGGTGGTTCAGTGACAGCAGGAATGGGAATATATGATGCAATGAAGTTATGTAAGGCTGATGTATCAACTGTTTGCTTTGGTCT[T/C]GCGGCATCAATGGGTGCCTTTTTGCTTGCTGCTGGTTCAAAAGGAAAGAGATACTGTATGCCAAATGCAAGAGTCATGATTCATCAG
106519 T C CAGCCGGAGGCAAAACAACAGATATGGGACTGCAAATAAGAGAAATGATGTACCATAAGGTGAAGATGAACAAAATACTTTCAAGAATCACCGGGAAACC[T/C]GAGCACCAGATTGAAATAGACACGGATCGTGACAATTTCATGAATCCGTGGGAAGCAAAAGAATATGGTTTGGTGGATGCAGTT
106519 G A GAGTTTGGGGTTATTGGAAAATTGAAGGCAGCAAAAAGGCCAAAAAGAACTTGCCCTCGGAGAGTAAAGCCTCACCCAATGGGCTCGATGACAAAGAGAA[G/A]AACAGCTCTGAAGAAACAAAAGAGGCACAAACTCCTGTGTAGTTTGATCAAAAAGCATAATCACTGTATCTGATTATAGCTTTCG
106519 A AC GAACAGCTCTGAAGAAACAAAAGAGGCACAAACTCCTGTGTAGTTTGATCAAAAAGCATAATCACTGTATCTGATTATAGCTTTCGGTCATTACTATCTG[A/AC]AGTATTTTGATTGTGCTAGATTCATTCAGATTTTTAAGTCTCTGAAGATGTAGTTGAAGCGAACCTTCTATGGCTTGCAATGTAATTA
106521 CT C AGCTGCCATAGCCTCGACATACTATAAAGACCTTGGAATAGAAGAACCTGATATTTTTGTTTCAGATGGAGCCAAATGTGATATCTCACGTCTTCAGCTT[CT/C]TTTTTGGTTCGAACGTGACTGTAGCCGTACAAGATCCATCTTACCCAGCATATGTGGATTCCAGTGTCATTGTAGGCCAAACTAGCGG
106521 C T CATATGTGGATTCCAGTGTCATTGTAGGCCAAACTAGCGGATTCCAGAAAGATATTGAAAAATATGGAAAAATCGAGTACATGAGATGTTCTCCTGAAAA[C/T]GATTTCTTCCCTGATCTATCAACTACTAAAAGAGCAGATGTAATCTTCTTTTGTTCACCAAACAATCCAACTGGCGCAGCTGCCTCTAG
106521 C T TTTCTTCCCTGATCTATCAACTACTAAAAGAGCAGATGTAATCTTCTTTTGTTCACCAAACAATCCAACTGGCGCAGCTGCCTCTAGAGAGCAGCTGTCC[C/T]GTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCTATGTACATATCGGATGACAGTCCGCGTTCCA
106521 A T TAATCTTCTTTTGTTCACCAAACAATCCAACTGGCGCAGCTGCCTCTAGAGAGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCAT[A/T]GTATATGATTCAGCGTATTCTATGTACATATCGGATGACAGTCCGCGTTCCATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGA
106521 A T GTTCACCAAACAATCCAACTGGCGCAGCTGCCTCTAGAGAGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTC[A/T]GCGTATTCTATGTACATATCGGATGACAGTCCGCGTTCCATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCT
106521 A G CAATCCAACTGGCGCAGCTGCCTCTAGAGAGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCT[A/G]TGTACATATCGGATGACAGTCCGCGTTCCATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATT
106521 C T CAACTGGCGCAGCTGCCTCTAGAGAGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCTATGTA[C/T]ATATCGGATGACAGTCCGCGTTCCATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTG
106521 G A CTAGAGAGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCTATGTACATATCGGATGACAGTCC[G/A]CGTTCCATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGAC
106521 C T AGCAGCTGTCCCGTCTTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCTATGTACATATCGGATGACAGTCCGCGTTC[C/T]ATATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGACTTGGAT
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106521 T G TTGTTAAGTTTGCTAAGGAAAATGGATCCATCATAGTATATGATTCAGCGTATTCTATGTACATATCGGATGACAGTCCGCGTTCCATATTTGAAATTCC[T/G]GGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGACTTGGATGGACAGTGGTTCCAA
106521 A G TATTTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGACTTGGATGGACAGTGGTTCC[A/G]AAAGAGTTGCTCTTTTCTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTC
106521 A G TTGAAATTCCTGGTGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGACTTGGATGGACAGTGGTTCCAAA[A/G]GAGTTGCTCTTTTCTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCA
106521 T G TGCAAAAGAGGTTGCAGTAGAGACGGCTTCCTTCTCTAAATTTGCTGGTTTCACGGGTGTTCGACTTGGATGGACAGTGGTTCCAAAAGAGTTGCTCTTT[T/G]CTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCAGGCTGGTGGTTT
106521 C T AATTTGCTGGTTTCACGGGTGTTCGACTTGGATGGACAGTGGTTCCAAAAGAGTTGCTCTTTTCTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCAT[C/T]GTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCCCGAGGGTCAAAAGGCCATGCGTTC
106521 C T TTCGACTTGGATGGACAGTGGTTCCAAAAGAGTTGCTCTTTTCTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGG[C/T]GCTTCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCCCGAGGGTCAAAAGGCCATGCGTTCTGTTGTTGATTACTACAAAGA
106521 T C GACTTGGATGGACAGTGGTTCCAAAAGAGTTGCTCTTTTCTGATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGC[T/C]TCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCCCGAGGGTCAAAAGGCCATGCGTTCTGTTGTTGATTACTACAAAGAGAA
106521 C T ATGGATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCC[C/T]GAGGGTCAAAAGGCCATGCGTTCTGTTGTTGATTACTACAAAGAGAATACCAGAATTCTTGTTGAAACGTTCACTTCACTTGGATTCAAT
106521 G A GATTTCCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCCCGA[G/A]GGTCAAAAGGCCATGCGTTCTGTTGTTGATTACTACAAAGAGAATACCAGAATTCTTGTTGAAACGTTCACTTCACTTGGATTCAATGTC
106521 A T CCTGTTGCCAGAGATTTCAACCGCATCGTCTGCACCTGCTTCAATGGCGCTTCTAATATTTCTCAGGCTGGTGGTTTTGCTTGTCTTTCTCCCGAGGGTC[A/T]AAAGGCCATGCGTTCTGTTGTTGATTACTACAAAGAGAATACCAGAATTCTTGTTGAAACGTTCACTTCACTTGGATTCAATGTCCACGG
106541 A G ACCAAACGGAACCCTCCATGACAAACTCCACCCGTTCTTAACCTCATCATCACCGCCCCTCCCATGGCCCCGCCGCATGTCAATCCTCTTCCAGATCGCA[A/G]CGGCCATCGACTACCTCCACAACGGCAGCGATCTACAGATCATTCACGGCGACATCACTGCCTCCAACGTCCTTCTCGACTCCAACCTC
106543 T C TGAACTCTTTGAATCTTCCTGTGATGAATAAATAGTAGTTTTCTAGAAAGTCATTCGTGCCGATGCTCACAAGGTACACGGCTTCGTTCACTATGTACTT[T/C]GCCTTTGCTCTTCCTACGTATCTTCTGAGTTTTCTTTGATACTCCTTGAAGTTTTCTACTTCTTTCCACAGAGGAATTACCCTAAGAACGTC
106543 G C CCCGGGTCGAGGTAAGCGGGCACGGTAGGACTCAACCCGAAAGCCTCGGAAATGAAGTCAGGGGCCAGGCGGCCATTGCAGAACCTCCCCGTGGGCTTAC[G/C]TCCGATGAAATCTCTGCCGTAGGGTTCGAAGTTGCTCTTCAGTACAGTGCATATTTGGTTGTTGTTGCCGGTGTCGACGGTGGA
106545 C T GTTCACTTTCTCCACGCCATTTTGAAGCCAACGTAGCAGAAGATACATTAAAGAAAGTTGTTCCGCATTCAGTAGCAACTGCTTTAGCCAGAAGTGTTTT[C/T]CCGGTACCAGGTGGCCCAAACATAAGAACGCCCTTCCATGGTCTCCGAATCCCCTGGAAATATTCAGGCATCCATAGAGGAAGAACA
106545 C A TTTCCAATACATCTCTTTCAAGCATTGCTGCTAAATCTGCATCTGGTCCTTCATATTGCCCCTTCCTTGGTCTGCCATCATCCGTGTCACCACTCTGCGC[C/A]TCTGCTTTGTTAGAGCCTGATTTCCCTTTCTTTCCTCCAACCACAGATGCCGTTGATGATCGAACACTAGAACTTCCTTTACTTGCAGATTT
106551 G A AGGCAACTGCAAGCGAGGCGATTCGTGCGACATGTCGCACGGCGTGTTTGAATGCTGGCTCCATCCGGCTAGGTACCGGACCCAGCCTTGCAAGGACGGC[G/A]TAGCGTGTAGAAGAAGGGTCTGCTTCTTCGCGCATACTCCGGATCAGTTGAGGGTTCTGCCGACGAGTCCGAAGACCGTGTTGG
106551 A G GAAAGTGGAAGGGCTTTGAGGATGAAGTTGTACGAGAGGCTGAGCAAGGAGAACTGCGCTGTCGAGAAGAAGGATTCCGATGCAGATCCGGTGTGGTTTA[A/G]CTGAAAAAAGCAGAAACCGGTGGTGGTTTTTGTATATAGTGTGGGGATTTTGGAGGTAAGGTAATAGAAGGTACGATGGAGA
106553 C T ACTAAATTTCAAACAAACCATGCAGCGACGTAGACCAACATAAGCAAGCTAAAACCAACGTATAACACATCATACATTATTTACTTAGCATAGCATAAAT[C/T]ACAACCAGCTCAACCCACCAAAATAATCAGTAATCATCAAAGCCACCATCATCATAAGCCAAATCATCCTCAACCCTCTCAGCCACGTT
106573 A G GTGCATCTTAAACTATGCCTTTTGTAGCAATTAAGTGAGCAGTAGCGTGTGTTGCAACGTGGACATGTGTACTGTGAAAATTGCTTCTCGCATACACGGC[A/G]GATCAATTTGTATTCTGACGAAAATGAATTTGAAGAAGAGGGCTCGGATGTTGTCACCTCTTTATGCATGGTTTTTAGTTTGAATGAT
106573 A G AAATTGCTTCTCGCATACACGGCAGATCAATTTGTATTCTGACGAAAATGAATTTGAAGAAGAGGGCTCGGATGTTGTCACCTCTTTATGCATGGTTTTT[A/G]GTTTGAATGATTATGGGATTTGAACTGCCTCTAAGCCGGACTAAAGGACCAGCCTGACTTAATTTGGGCCAACTTAATTCACGTGGAC
106577 TTC T TGATCATTTCTATAGTCAACCACCAGAACTTCAAAGTCCCAAAGCGAAAACCCTAAACCTGAAATCTTAACATTCACTTTTTCCCTGGAAATCATTTGTT[TTC/T]TCTTTTATTTACTCTGCAATGGCCTCTTCTCCTCTTTCAAGCAGTGGCCTTACATTCAAACTACATCCTCTAGTAATTGTCAACATCTCAG
106577 T C TGGTATTCAACCGGAAGTGATGCACAGGAATCTGACATGCAAATACACAAAGGGTTGATGGATATTAATGAAAGTCCAGTTTATGTCATTCTGAATCCAA[T/C]AGTCAATCCTGCTCGGAAGGATTTACCAGTCACAATTTATGAAAGTGAACTGCATGTTATTGATGGAAATCCGCAACTTATATTTGTG
106577 G A AGTGATGCACAGGAATCTGACATGCAAATACACAAAGGGTTGATGGATATTAATGAAAGTCCAGTTTATGTCATTCTGAATCCAATAGTCAATCCTGCTC[G/A]GAAGGATTTACCAGTCACAATTTATGAAAGTGAACTGCATGTTATTGATGGAAATCCGCAACTTATATTTGTGAAGTCAAAGTACACA
106577 G A GGTTGATGGATATTAATGAAAGTCCAGTTTATGTCATTCTGAATCCAATAGTCAATCCTGCTCGGAAGGATTTACCAGTCACAATTTATGAAAGTGAACT[G/A]CATGTTATTGATGGAAATCCGCAACTTATATTTGTGAAGTCAAAGTACACAATTGAGACTGTGGAGGCTGAACGAATTTCTGTGGATC
106577 T C TGGATATTAATGAAAGTCCAGTTTATGTCATTCTGAATCCAATAGTCAATCCTGCTCGGAAGGATTTACCAGTCACAATTTATGAAAGTGAACTGCATGT[T/C]ATTGATGGAAATCCGCAACTTATATTTGTGAAGTCAAAGTACACAATTGAGACTGTGGAGGCTGAACGAATTTCTGTGGATCATGTTG
106577 C T AACGAATTTCTGTGGATCATGTTGCACATCTCAAACCTTCTGATGGTAGCTCAGCTGCTACCCAATTGGCTGCACATCTCACTGGAATACATAGTGCAAT[C/T]AAAATGCTTAACAGCAGAATCAGGGTTGTGCATCAGTATCTCCTTAGCATGAAGAAAGGTGAAATGCCACTTGATAATTCACTGCTTA
106577 A G GAATTTCTGTGGATCATGTTGCACATCTCAAACCTTCTGATGGTAGCTCAGCTGCTACCCAATTGGCTGCACATCTCACTGGAATACATAGTGCAATCAA[A/G]ATGCTTAACAGCAGAATCAGGGTTGTGCATCAGTATCTCCTTAGCATGAAGAAAGGTGAAATGCCACTTGATAATTCACTGCTTAGGC
106577 C T ATCATGTTGCACATCTCAAACCTTCTGATGGTAGCTCAGCTGCTACCCAATTGGCTGCACATCTCACTGGAATACATAGTGCAATCAAAATGCTTAACAG[C/T]AGAATCAGGGTTGTGCATCAGTATCTCCTTAGCATGAAGAAAGGTGAAATGCCACTTGATAATTCACTGCTTAGGCAGGTTTCAAGCC
106577 A C TCATGTTGCACATCTCAAACCTTCTGATGGTAGCTCAGCTGCTACCCAATTGGCTGCACATCTCACTGGAATACATAGTGCAATCAAAATGCTTAACAGC[A/C]GAATCAGGGTTGTGCATCAGTATCTCCTTAGCATGAAGAAAGGTGAAATGCCACTTGATAATTCACTGCTTAGGCAGGTTTCAAGCCT
106577 T C CTCAAACCTTCTGATGGTAGCTCAGCTGCTACCCAATTGGCTGCACATCTCACTGGAATACATAGTGCAATCAAAATGCTTAACAGCAGAATCAGGGTTG[T/C]GCATCAGTATCTCCTTAGCATGAAGAAAGGTGAAATGCCACTTGATAATTCACTGCTTAGGCAGGTTTCAAGCCTTTTGAAGAGATTG
106585 GT G TAAGTGAGCAGTAACTCCGATTAGGTAGTTCTTGGAGATAGTGGTGTTTTCTCTGTGTAGAGGGTGTATGTACTGGTGTTTGGATGCCTTCTTGCTGTCT[GT/G]TTTTTTTGGTCCTTTATGTTATGCGGCATTGTTGTCTTGTTCATGGAGACCTTTTTGTTCTTGTTTGGATTGTGCTTGTTTGGGTTACT
106589 G A CTTGAATACATCATCGTAGGTTAAAGGCCCATTGTTGCTTCTCACCTTATCAGAAACCGCGCGTACTACTGAGTCAATAAGAATAGTATCCTTCTGTGCA[G/A]ATCCAGACCTCAAAACCAACGAATCTTCCTCTGCGACTAATGGTACTGATGGAAATGATCTCTTCAACTCTAAACTGATAAGAGCCTGT
106589 A T TTGAATACATCATCGTAGGTTAAAGGCCCATTGTTGCTTCTCACCTTATCAGAAACCGCGCGTACTACTGAGTCAATAAGAATAGTATCCTTCTGTGCAG[A/T]TCCAGACCTCAAAACCAACGAATCTTCCTCTGCGACTAATGGTACTGATGGAAATGATCTCTTCAACTCTAAACTGATAAGAGCCTGTA
106589 C T TTAAAGGCCCATTGTTGCTTCTCACCTTATCAGAAACCGCGCGTACTACTGAGTCAATAAGAATAGTATCCTTCTGTGCAGATCCAGACCTCAAAACCAA[C/T]GAATCTTCCTCTGCGACTAATGGTACTGATGGAAATGATCTCTTCAACTCTAAACTGATAAGAGCCTGTACACCAAAATCAGCTACAGT
106589 T C ATCTCTTCAACTCTAAACTGATAAGAGCCTGTACACCAAAATCAGCTACAGTAACCGGAGTCTGGTCATCCTTCTCAATAATCCGATCATCATTGGAGAC[T/C]AATGTCCGTTTGACGTCCGCACAAAGACGGCAAGCTCTCTCGACTACATCGACAGCTTCTACCGCTTCTTTATAAAATCTGGCCTTCTCC
106589 C T AATCAGCTACAGTAACCGGAGTCTGGTCATCCTTCTCAATAATCCGATCATCATTGGAGACTAATGTCCGTTTGACGTCCGCACAAAGACGGCAAGCTCT[C/T]TCGACTACATCGACAGCTTCTACCGCTTCTTTATAAAATCTGGCCTTCTCCGACAAGAACGGAAGGCTCGATCTGATAACGAAGGAAA
106595 T C AGTAAAAATGAGAGCAAGCTTTTCAATGGCTGCTGCGAGTAGAAGCGCAATTCCCAAATGTTATCTGAGAACTCGAATCAGATGTTTTTCATCGTCGTCT[T/C]TATCTTCTCCTTCAGTTTCTTCTTATGATTCAATTGATCATGTTTCTTTCATCAGTAATGTTGCAGCAACGAAGCCTCCTGACCATTTGTC
106595 A G CATCCCTTCTAAGATGGCCAACGGCTCCTTTTGGAATGGAAATGCCAGTTGTTGAAGTGCGTAAGCATGGAGTTTGGTATTTGGCTAAAAGTGTAGACCA[A/G]TATATTCATAGATTGCTTGTCGAAGGAGACGTAAACGAACAAAATGCTGAAAATTTATGGGAAGCCGCATCTGACATTAGCTACAA
106595 C T ATGGAGTTTGGTATTTGGCTAAAAGTGTAGACCAATATATTCATAGATTGCTTGTCGAAGGAGACGTAAACGAACAAAATGCTGAAAATTTATGGGAAGC[C/T]GCATCTGACATTAGCTACAAATTCTATAAAAAGGGCGATTTTGTTGAATCTGGTATCCCTGATCTCGATGCCTATCTTTTGAGAAAGG
106595 G T TGGAGAGGAAAGTAGCACGCCACTTTGAGAAAGGCGACCAAGTATCTGCATTGGTAACTGGAGAATTCTACACACGAAATCATTTCCCTGGATTTGGCCG[G/T]CCCTTTGTGTTCAATGCCGAGGTTTTGCTGAAGGTTGGACGAAAGCCCGAAGCTAAAGATGCCGCTCGAGGTGCTTTAAAATCGCC
106595 T A TACAGAGAGTGAATTAGATTTGTGATGTGTTGTTTTCCTTTTCAAAGCTTGTTAACGGATGAATACTAGGTCAATGTCATGTTTTCATCCACATGCTCAA[T/A]TTTCCGGTTGTTCATGAGAGGGATATTTTGTCCCAGGCTATGCTTCCAATAATTATGCTTCTTTTTGTCT
106597 TC T GATGAACACAACCCTGCAGGGTACTACAATGGAGAAAACACTAAAAATGTGAGGGACTGGAAGGAGGTTTTTGATTTTATTGTGGCTGAACCCATGTATT[TC/T]CCCCCGTTACCAGCGAGCCCGGAGAGAGCGGAGTGTACGAGATCATGAATAGGTGGCCGGAGTACCCTCTTGGATTTAGAGAGG
106599 G A AGTGCAGAAATCAAGTGTCTGAAGGCTGTTTTCAAAGTACTCTTCTACTAACTCGAAAAGCTCAGGGCTTTTCCAAATGTCTTTCTTGTATTCCAGTATC[G/A]TCTTGACTACTTCTTGATTGTTGTCCAAAAGACAACCCGTGACTTGTCTAAGCACATCGAAAGAGATCGAACTACCGCCTGAGCTTGTG
106599 C T AATGTCTTTCTTGTATTCCAGTATCGTCTTGACTACTTCTTGATTGTTGTCCAAAAGACAACCCGTGACTTGTCTAAGCACATCGAAAGAGATCGAACTA[C/T]CGCCTGAGCTTGTGAGAATTGAAATTGCACCTAAAGTGCGCTGTTGAAGAGCTGAATCGAAATTCTGGAAATTAGGGTCTTGTAAGCA
106599 A G AGACAACCCGTGACTTGTCTAAGCACATCGAAAGAGATCGAACTACCGCCTGAGCTTGTGAGAATTGAAATTGCACCTAAAGTGCGCTGTTGAAGAGCTG[A/G]ATCGAAATTCTGGAAATTAGGGTCTTGTAAGCAGTCTGATTCGTATGATTTTAAATCTATTTGACTGGTGCTGCTGCTCACGCCAGC
106599 A G TGTCTAAGCACATCGAAAGAGATCGAACTACCGCCTGAGCTTGTGAGAATTGAAATTGCACCTAAAGTGCGCTGTTGAAGAGCTGAATCGAAATTCTGGA[A/G]ATTAGGGTCTTGTAAGCAGTCTGATTCGTATGATTTTAAATCTATTTGACTGGTGCTGCTGCTCACGCCAGCGCCATGGCTGGTGCT
106607 T C CAAGAGAAATGTTAGAGGAGCAAGAAGATGTCCGTGGTCGCCTATTCACTATTCAGGATGTATTGGCAAGTACAGTTCGGGCCTGGTTGCAGGATAAGAG[T/C]CTCCGGGTGACTCACAATTTAGGTATATTTGGTGGCTGTGGCCTTGTGCTGTCCATAATTACAGGCCTATTCGGGATCAACGTAGA
106609 T C GTGGTGCTGCTGGAGCCACGTCTCTCTGCTTCGTTTACCCTCTCGACTTCGCCCGTACCCGTCTTGCTGCTGATGTTGGCAAGGGCAGTGGCCGTGAATT[T/C]CAGGGTCTCGCAGACTGTCTCGTCAAGATCGCCAAGTCCGACGGACCTATCGGACTCTACCGTGGTTTCTTCGTCTCCGTCCAGGGT
CTCTCTGTACATCAATCAGCTGATACAAATCCCCTCTCCTTTGCTTTTCAAGCGGCAGGTTGGACCT
106611 A CCAACCGCTTCCATATAGTTCTGATGGTTGGATTTAATAATGAAGCAATAAATAACATGTATAATCATGGAGATCAATATTGGAACATTCAGCGAGAACC[A/AGCTCTCTGTACATCAATCAGCTGATACAAATCCCCTCTCCTTTGCTTTTCAAGCGGCAGGTTGGACCT]GCTCTCTGTACATCAATCAGC
106619 C G CAACCGAAGAAGAGAGAGGCTAAAACTTGCTCTACTCAATTTTAACATAACTGAGGTCAACTACTGGCAACAACTGTTACCACATGCAGAATCTAGTAAT[C/G]TGCGCTTAGATTACGCTAAAAGCAACTTGACTTGGGAAGATCTGTATCCTGAATGGATAGACGAGGAGCAAGAATCAGAAGTTCCT
106623 A T CTCCCAGCTTTTTCACGAAGAGCGTTGAAGAAGTTGTTTCTGTCTCTGGACATGCCATTAGCTTTTGGTTTTACAGGGTTGGAACTATTAACAGGAGCGG[A/T]ATTTGGCACTGTGGACTTCTTTTCATTGAGTCCTCCATTTGGTTTCTTTTCAACTTTTCCGTCTTTGGCAGTAGGAGATGTGACCATGTT
106623 C CT ACTATGAGCTTGCTTGGCTGAGGAGTTGTCTTAAGCGCATCAGGATTGGCGGCAGGTGGATGAATGGACTTTGCAGAAACAGCTTCCCCATTTCTGTTTC[C/CT]TTTAGTTTTGACTTTTCAACCAAAGTTTTAGGCCCTTGAGGTGTCACTGGTATGAGCTTGTTATACATTAATGCCAGTTCCTTGCGTT
106623 T C TGTCTTAAGCGCATCAGGATTGGCGGCAGGTGGATGAATGGACTTTGCAGAAACAGCTTCCCCATTTCTGTTTCCTTTAGTTTTGACTTTTCAACCAAAG[T/C]TTTAGGCCCTTGAGGTGTCACTGGTATGAGCTTGTTATACATTAATGCCAGTTCCTTGCGTTTTTCATTCTCATTTGACACCAGGGGTG
106629 A AG CGCAACAAAATCGTTCACTCATTCACGTAAGCTCTAATTTTATAACTGTTTCTGTGCCTCTTACAATGGCTTTTTTCTACTCGGTCATCGGTGATGTAAT[A/AG]AAGGATAGATGATTAAATGACTAGAGAAATAAATCACCATCTATTGCTAGGAGGTTTGACTTTGTAAATTCGAACGATCCAGTTTGAGG
106629 TC T GTTTGTACATAAGGCAGTTCAGCATTTTAGGTGCTGCTCCCTTGTCTACACGATATTCTCCATTAACAAGATAATCAGGTTCCTTTATTACAGGGAAGAC[TC/T]CCACCCCCAATTCTCACCATCCACAAAAATTTGTTGATATCATCTGAAGAATAACCCGTAACACCTCCAAAAACAACAAGGACATAATC
106629 A G CATTAACAAGATAATCAGGTTCCTTTATTACAGGGAAGACTCCACCCCCAATTCTCACCATCCACAAAAATTTGTTGATATCATCTGAAGAATAACCCGT[A/G]ACACCTCCAAAAACAACAAGGACATAATCAACATCAAGCGAACGCATAATCTCGTATGCTTCATCTTCATATGATGACATGGCACGTCC
106631 GA G CCTCTTTTTCTATTGATGATTTGCTATCTGGTTGCTGGTTTTCTCTATCGACATCTTAGATCTCCGTCTTAGTTTGCAATTAATAATTTTAAATATTTGA[GA/G]AAAAAAAATCTCTTTCCCGTGTTATGGATCAGTGGAACTCTTCAGGTCACATTATAGAGCATGATTTGATGGATCCCGTTGCTGTACGGA
106633 G T TTTATACAAGTTCGTCTCCAACCTGGGCACTGCAACAGCCTGAAGTGGCGTACTCTTGTAAGTCACTAACCCCGGAGCCTCGCTCATGTCCACTTCATTT[G/T]CCTTCATCCCTTCAGGAAGCTTCCATTCAAAATGATGTAGCAAATGGCCCAACATCGATGCAATCAACAAAATGCCTAGTTGTGCACCA
106633 T C TTAGCAAAGTCTGTTTCATCCATGATGCGATCTACTCCTACCACTCTATCAAGCTCTTCTTGTACCTTAAGTTGTATTCTCGGGTTTTTTACTATCTCTG[T/C]CATAGCCCACTCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCG
106633 C T CTGTTTCATCCATGATGCGATCTACTCCTACCACTCTATCAAGCTCTTCTTGTACCTTAAGTTGTATTCTCGGGTTTTTTACTATCTCTGTCATAGCCCA[C/T]TCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTG
106633 C T CTACCACTCTATCAAGCTCTTCTTGTACCTTAAGTTGTATTCTCGGGTTTTTTACTATCTCTGTCATAGCCCACTCGACAGTGATAACTGTTGTGTCCAT[C/T]CCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAG
106633 A C CTTAAGTTGTATTCTCGGGTTTTTTACTATCTCTGTCATAGCCCACTCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGA[A/C]CGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTTGTTACGG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106633 A G TTCTCGGGTTTTTTACTATCTCTGTCATAGCCCACTCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGT[A/G]TCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTTGTTACGGGCAAGTGTGTG
106633 C T TCATAGCCCACTCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTC[C/T]TGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTTGTTACGGGCAAGTGTGTGTTCGTTCATTATGTCTCTAGTGAG
106633 G C CCCACTCGACAGTGATAACTGTTGTGTCCATCCCAGCTGTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAG[G/C]GTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTTGTTACGGGCAAGTGTGTGTTCGTTCATTATGTCTCTAGTGAGCTGAT
106633 T A GTTATCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCAT[T/A]TTTGTTACGGGCAAGTGTGTGTTCGTTCATTATGTCTCTAGTGAGCTGATCTCTTCGAGCGGAGTGCTTTCCAAATGCTACTTCGTCC
106633 G A TCATATCCCAAAGAAGAACGATGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTT[G/A]TTACGGGCAAGTGTGTGTTCGTTCATTATGTCTCTAGTGAGCTGATCTCTTCGAGCGGAGTGCTTTCCAAATGCTACTTCGTCCAAAG
106633 G A TGATGGTATCTTCGCTAAGATCGTACTTTTCCTGAAGGGTGAGCAATGCATCGACAAAGTGTTGTTTGGCACCATTTTTGTTACGGGCAAGTGTGTGTTC[G/A]TTCATTATGTCTCTAGTGAGCTGATCTCTTCGAGCGGAGTGCTTTCCAAATGCTACTTCGTCCAAAGGGAACATCCATTCAAGCCAGC
106633 T C CAAAGTGTTGTTTGGCACCATTTTTGTTACGGGCAAGTGTGTGTTCGTTCATTATGTCTCTAGTGAGCTGATCTCTTCGAGCGGAGTGCTTTCCAAATGC[T/C]ACTTCGTCCAAAGGGAACATCCATTCAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTAT
106633 C A CGGAGTGCTTTCCAAATGCTACTTCGTCCAAAGGGAACATCCATTCAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTC[C/A]ACGCCTATTGCTTTAAACTCCAAACCTTGATCGTCCATTACGTCATCTGAGTTCATGAATCTCTTTCCGAATGCTAGTCTTGTTATGTTG
106633 C T CTACTTCGTCCAAAGGGAACATCCATTCAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAA[C/T]TCCAAACCTTGATCGTCCATTACGTCATCTGAGTTCATGAATCTCTTTCCGAATGCTAGTCTTGTTATGTTGTTAAACGCAACGCTTGAAA
106633 G A GGAACATCCATTCAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAACTCCAAACCTTGATC[G/A]TCCATTACGTCATCTGAGTTCATGAATCTCTTTCCGAATGCTAGTCTTGTTATGTTGTTAAACGCAACGCTTGAAAGGTGATTTCGAAGA
106633 G T ATTCAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAACTCCAAACCTTGATCGTCCATTAC[G/T]TCATCTGAGTTCATGAATCTCTTTCCGAATGCTAGTCTTGTTATGTTGTTAAACGCAACGCTTGAAAGGTGATTTCGAAGAACCAAGCTG
106633 A C CAAGCCAGCTTACGTATTCACCTAGTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAACTCCAAACCTTGATCGTCCATTACGTC[A/C]TCTGAGTTCATGAATCTCTTTCCGAATGCTAGTCTTGTTATGTTGTTAAACGCAACGCTTGAAAGGTGATTTCGAAGAACCAAGCTGCTT
106633 G A GTGAGATAGATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAACTCCAAACCTTGATCGTCCATTACGTCATCTGAGTTCATGAATCTCTTTCC[G/A]AATGCTAGTCTTGTTATGTTGTTAAACGCAACGCTTGAAAGGTGATTTCGAAGAACCAAGCTGCTTCCATTGATCGTACCTTGTGGAGTA
106633 G A GATGCGCCAAATTTCATTCCTTCCACGCCTATTGCTTTAAACTCCAAACCTTGATCGTCCATTACGTCATCTGAGTTCATGAATCTCTTTCCGAATGCTA[G/A]TCTTGTTATGTTGTTAAACGCAACGCTTGAAAGGTGATTTCGAAGAACCAAGCTGCTTCCATTGATCGTACCTTGTGGAGTAGAACA
106635 A G ATGCCTTGAGCAAGCTCCCAGGATAAAAATCCAAAAACTAACGCGATTGCAGCTCCAATATTGGCTTTCAATGGTGTCAGTTGAACTTGTAAACTTCCAA[A/G]CTTAAACATTCTAGTTTCCACGTCTGGCTTTTCATCAGTTTCATTGACTACTCCACTAGATAGCACCTCACCGGCCTTGATCATTGCCTT
106635 TTC T CATTGCCTTGGCAATTTTTTGGAGCTCTCCCTCACCATATAATCCCATGGACGAAAACCTCCTTCCAGCTTTTATTAGACGTTTGCCAAATGCTGATTTT[TTC/T]TCTTTTTCCTTTTAAAGAACTTAGCAGGGAGGGCAACTGTTGGACGATGGCATTTGAACTTGAGGTGTCAGCTTTCTCCCAAGCACGA
106635 TG T TCGGATTCCGCAAGAGCAAAAGTGATGGAGAGAACTGGGTTTCTTTTGGGAAAGGATTTCGTAAGAAAGGGGCGAAGGGATTGTAACGGATATATAGGGG[TG/T]GGTTTGGATAGCAAAATTATGGAGGGGAAGCAAGGAGAATAGCGTAGCCATTTTAAGTGGACTGGCGTGGCCTGGAGAAGA
106637 A G TACAATATGGAAGGCATGCAAATTTTTGGACATTGGGAATGAGAAATGGTTGAGAAAATCGCTTGAAGGTGTTGACGAATTTGCATATGAAGTGATAAGG[A/G]CCAGAAAGAAGGAACTAAAAATTGAAGGCAGTAAAAGAAGGTCGGATCTTTTGACGGTGTTTATGAAACTAAAGGATGAAGAAG
106643 G GT AGATCCACCGCACGTTGAACAAGTGGTCTGTAATAAAAAGGGGCCCCTTTGCATGGAAGACATCCCTGAACCTCTACAATTTTTACATGTTTCAGGTCTA[G/GT]TCCTGGTGGAGCACCATTCCCACCACAAGCTGCACAAGGCACGGCCGTCTGAAAATTCAAGGTTTTAGTGCATCCTTGTACTGCTTC
106645 A G CAAAACCACCTTCCTATCAAAACGTAACATTAGCAGGAATTGGAACGGGTGCTCTGCAAAGCCTAATTCTTAGCCCAGTGGAACTAATAAAAATAAGGCT[A/G]CAACTGCAAACCTCAAACAAAAACCAACACCAACAAAAAGAAGGTCCACTCCAAATAGCCAAAAAGATCATCAAAACCCAAGGGAT
106645 A AACCAAC CGTAACATTAGCAGGAATTGGAACGGGTGCTCTGCAAAGCCTAATTCTTAGCCCAGTGGAACTAATAAAAATAAGGCTACAACTGCAAACCTCAAACAAA[A/AACCAAC]ACCAACACCAACAAAAAGAAGGTCCACTCCAAATAGCCAAAAAGATCATCAAAACCCAAGGGATAAGAGGCATCTACCGT
106645 G T TAATAAAAATAAGGCTACAACTGCAAACCTCAAACAAAAACCAACACCAACAAAAAGAAGGTCCACTCCAAATAGCCAAAAAGATCATCAAAACCCAAGG[G/T]ATAAGAGGCATCTACCGTGGCCTAGCGATCACTACCCTCCGTGACGCCCCAGCTCATGGTGTTTATTTCTTGAGTTATGAGTATGCC
106645 G A GGCCTAGCGATCACTACCCTCCGTGACGCCCCAGCTCATGGTGTTTATTTCTTGAGTTATGAGTATGCCCGTGAAAAGTTGCACCCTGGCTGTAGAGAAA[G/A]TGGGCAAGAAAGTCTAAGAACCATGCTTTTAGCAGGGGGTTTGGCTGGAGTTGCTAGCTGGGTCTGTTGCTACCCTTTGGATGTGG
106645 A G CTCATGGTGTTTATTTCTTGAGTTATGAGTATGCCCGTGAAAAGTTGCACCCTGGCTGTAGAGAAAGTGGGCAAGAAAGTCTAAGAACCATGCTTTTAGC[A/G]GGGGGTTTGGCTGGAGTTGCTAGCTGGGTCTGTTGCTACCCTTTGGATGTGGTCAAGTCCAGGCTTCAGGCCCAGACTGGCAACGA
106645 C T GTAAAAGCGCCAGAGAGGAAGGGTACTCTGTGTTCTGGAAAGGTTTGGGTACTGCTGTTACCAGAGCTTTTGTTGTCAATGGCGCTATTTTCACTGCTTA[C/T]GAACTGGCGTTGAGGTTCTTGGTCAGTAACGGCAATGGTGATGGTGCTCGAAGAATCATGCTCGATGAAAATTGAAGATGGGTATA
106645 G C CCAGAGAGGAAGGGTACTCTGTGTTCTGGAAAGGTTTGGGTACTGCTGTTACCAGAGCTTTTGTTGTCAATGGCGCTATTTTCACTGCTTACGAACTGGC[G/C]TTGAGGTTCTTGGTCAGTAACGGCAATGGTGATGGTGCTCGAAGAATCATGCTCGATGAAAATTGAAGATGGGTATATGAAAATGT
106653 T C AAACTTATGGGGAGGTTGAAATGTTTGCCAAACAGATGATGGAGCAGTTGATGCAGTGGGTTCATCAACAGCCGATAGAGAATATTTATGTTGCTATTGG[T/C]GGCATCATTATTAGTTCGATTATCTTGATTTTCTTTAGTAATTTGACACGCTCAAAATCAAACAAAATAGTGCTTGCAGGCTTAAGTG
106653 A G ACTTGGAGTGCCTGGAGAGACATTCGCCTTCAATCAATGCGTCAACAAAGTGTCGATTGCTGAATTATCATGTGTAACCAATGAAATATCTCAAGTTGAG[A/G]AATTCATCCGTGAGCATGTGTAAGCCTAGAATTCTCCGAGGGATACATCTTTACAGAATTGTAAGAGAATTCAGAGATTGTCTAATTT
106655 A T AATTCCATTTAAGCCTTCAAATTACAAGTAACAAAACCATAACACGCAGTCCTAAATATTGACAACTGTGCACCCTAATA[A/T]GCTCCCGCAACACCTAGTCATCGAAGCAGCCTGCCTCCAGCCCCCATTAGCTGCCAGCACATTGACGTCAGACAACCGCACCATTCCCCGATTCATACCC
106655 A G CCATTTAAGCCTTCAAATTACAAGTAACAAAACCATAACACGCAGTCCTAAATATTGACAACTGTGCACCCTAATAAGCTCCCGCAACACCTAGTCATCG[A/G]AGCAGCCTGCCTCCAGCCCCCATTAGCTGCCAGCACATTGACGTCAGACAACCGCACCATTCCCCGATTCATACCCAAACTAATCACTC
106655 G GC ATTACAAGTAACAAAACCATAACACGCAGTCCTAAATATTGACAACTGTGCACCCTAATAAGCTCCCGCAACACCTAGTCATCGAAGCAGCCTGCCTCCA[G/GC]CCCCCATTAGCTGCCAGCACATTGACGTCAGACAACCGCACCATTCCCCGATTCATACCCAAACTAATCACTCCTCCAATGACATAAA
106655 A C ACATTCCGAACGCTGCCCGACCCATAAATTGCAAAGCCGGTGTTCCGGAATCTACCAGAATGTTCCCCATCGGTTGCTTCTGTATCATTCCTCCGTTGAA[A/C]ACATATGGCTCCCCATTCACAACAGCCGTCGGGCCGTCCAACCATTCGTAATCCACCACTTTCCACCCACCGCTCTCTTGCAGAATCTG
106655 A G CCCGACCCATAAATTGCAAAGCCGGTGTTCCGGAATCTACCAGAATGTTCCCCATCGGTTGCTTCTGTATCATTCCTCCGTTGAAAACATATGGCTCCCC[A/G]TTCACAACAGCCGTCGGGCCGTCCAACCATTCGTAATCCACCACTTTCCACCCACCGCTCTCTTGCAGAATCTGGACCGTTGATAAACC
106655 A T CCTCCCACAACTACGCCAGAACACGACCACGCGTGTTTAAGACACAAATCCGGAAGCGGGGACCATGTGTCGGTGTCGGGGTCGTACGTCTCCGCTTTCA[A/T]TGTCTGTCTCCTTTGGCTTGTGAAACCCCCTGCAACAACGATGCTTTTATCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCG
106655 T C CAACTACGCCAGAACACGACCACGCGTGTTTAAGACACAAATCCGGAAGCGGGGACCATGTGTCGGTGTCGGGGTCGTACGTCTCCGCTTTCAATGTCTG[T/C]CTCCTTTGGCTTGTGAAACCCCCTGCAACAACGATGCTTTTATCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCGTAAGCAT
106655 C G ACGCGTGTTTAAGACACAAATCCGGAAGCGGGGACCATGTGTCGGTGTCGGGGTCGTACGTCTCCGCTTTCAATGTCTGTCTCCTTTGGCTTGTGAAACC[C/G]CCTGCAACAACGATGCTTTTATCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGAC
106655 C T AGACACAAATCCGGAAGCGGGGACCATGTGTCGGTGTCGGGGTCGTACGTCTCCGCTTTCAATGTCTGTCTCCTTTGGCTTGTGAAACCCCCTGCAACAA[C/T]GATGCTTTTATCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGACGCCAGTGGCA
106655 A G CCGGAAGCGGGGACCATGTGTCGGTGTCGGGGTCGTACGTCTCCGCTTTCAATGTCTGTCTCCTTTGGCTTGTGAAACCCCCTGCAACAACGATGCTTTT[A/G]TCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGACGCCAGTGGCAAGATCGAAAG
106655 G A GGCTTGTGAAACCCCCTGCAACAACGATGCTTTTATCGTTCAGAGCACAGCAGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGAC[G/A]CCAGTGGCAAGATCGAAAGACCAAACCTCTTTGGTCACGAAGACGCCCTCGTGCTCCCCGGTTTGAGGGTCGACCTGGTCGCTGT
106655 G A GAGCACAGCAGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGACGCCAGTGGCAAGATCGAAAGACCAAACCTCTTTGGTCACGAA[G/A]ACGCCCTCGTGCTCCCCGGTTTGAGGGTCGACCTGGTCGCTGTCCCCACCAAACACGTAGAGCTTTCCGGAAACGGAGGCAGCT
106655 G A AGGCGAACATGACACGAGGCGTAAGCATGTCGGCTTTGCGGGTCCAGACGCCAGTGGCAAGATCGAAAGACCAAACCTCTTTGGTCACGAAGACGCCCTC[G/A]TGCTCCCCGGTTTGAGGGTCGACCTGGTCGCTGTCCCCACCAAACACGTAGAGCTTTCCGGAAACGGAGGCAGCTCCAAACCTC
106655 C T AAAGACCAAACCTCTTTGGTCACGAAGACGCCCTCGTGCTCCCCGGTTTGAGGGTCGACCTGGTCGCTGTCCCCACCAAACACGTAGAGCTTTCCGGAAA[C/T]GGAGGCAGCTCCAAACCTCGATAGACGGCGGATTAATGAGGGCATTTTGGGCAATGTGAACCATTTGTCTCTTGAAGGGTCGTAAA
106655 G A CTTCAGTCGACTTGAGCTCATGGCGAACTTTGAAAAGTTGTGTGCTGCGGAGGGCAAGTTTCCAAGTTCTGCAGACAAGTTGGAGTTTTGGGTGGTCGAC[G/A]AAAGGCACTCGGGCAAGGCACTGGAGAGCTACTGCATCTGGGAGACCTTCCAGAATGCTACATGTCATACTTGTTGCCATATTATA
106655 G T ACTTTGAAAAGTTGTGTGCTGCGGAGGGCAAGTTTCCAAGTTCTGCAGACAAGTTGGAGTTTTGGGTGGTCGACGAAAGGCACTCGGGCAAGGCACTGGA[G/T]AGCTACTGCATCTGGGAGACCTTCCAGAATGCTACATGTCATACTTGTTGCCATATTATAAATTATAGCCTGAGTTTTCCCTGATTT
106655 A G GTGGTCGACGAAAGGCACTCGGGCAAGGCACTGGAGAGCTACTGCATCTGGGAGACCTTCCAGAATGCTACATGTCATACTTGTTGCCATATTATAAATT[A/G]TAGCCTGAGTTTTCCCTGATTTCAGTCGCCAAAATTACATTGCATAAACTATTTAAGTCTTTCATTCAACAATTAGCATACTTGGGTA
106661 GT G AATGGAGTGCATAAGGTCTTTGCTGCTCCAAGATCACCTTTAGTCCGTGCTTTCACATCCTTCTCCACTTCCTCTTCATCGCACCAAGGAGCCAAAATCA[GT/G]TTTTTTATCATTGAGTGCAGTCACAAATTCATCCCAGGTACTAATGATCTTTACACATGCATCCCTTTTTTCCTTGGCTGCATTAAACAG
106665 AG A AAGAAGTTCGCGGACCGATCAGTAAAATTTCGGGAATGAATGGTAGAGTGGGTAAGTTCAGAAACGGAGAACAGAGAGGGAGAGTAAGATTTAAACTGTT[AG/A]GGGGGTAGGATTGAAAAAAAGGTAAGGAGAAGATGAATGGTGATTTATTTGGTTATGATGAAAGCAAGAAAGGTAATAATT
106665 G A GAGAGGGAGAGTAAGATTTAAACTGTTAGGGGGTAGGATTGAAAAAAAGGTAAGGAGAAGATGAATGGTGATTTATTTGGTTATGATGAAAGCAAGAAAG[G/A]TAATAATTTTTGAAGCTAGTTAGTTTGAAGTTTTTTCAAGGCAGCTTTCTGAATAATATCAGCATTGGAGTAAACTGAAGATTAG
106665 C T ATGAATGGTGATTTATTTGGTTATGATGAAAGCAAGAAAGGTAATAATTTTTGAAGCTAGTTAGTTTGAAGTTTTTTCAAGGCAGCTTTCTGAATAATAT[C/T]AGCATTGGAGTAAACTGAAGATTAGCTCCAAACCATACTGACAAACTGTATTTTAGGTTCGATGGATATGCATTTTAGGTATTACAGAT
106671 T G CCTCTCCAGTTGATCGTCACTCAAGCCTATACAGGGAACACCATCTAATATAGCAATTGTCGCTGGGGTTGCACCATTCTCCCGCACAATAGCCTCAACC[T/G]CCTTGGCAGTTTCAAGATTCTGTGGATAGGGCATACCATGTGAAATAATCGTTGATTCTAAAGCAACGACTGCATAGCCACGGGACAG
106671 C T CAATAGCCTCAACCTCCTTGGCAGTTTCAAGATTCTGTGGATAGGGCATACCATGTGAAATAATCGTTGATTCTAAAGCAACGACTGCATAGCCACGGGA[C/T]AGGGCTTCCTCGACGTCCTTGGAGACCTGAAACATGAGTGTAGTTACCACAGTTGCTCCGCAATCGATGATGCGGCCGATAATTTCC
106675 T C GGGCGACCAAGAATGTGGTCGACATGAGCTTTAGGATGGTGACGGCTTCCTCGGTCTTTCTGGCGGAGATGAGGCCGAGGGAGTTGACGTCCTGGTTGTG[T/C]TGCTCAGCGCTCTGCACGTGGTTTGTCACGGGATTCGCGAGAAACTGAAGCTCAGAGCAGTACGAGGCCATGGCGATCTCCGCA
106675 G A AGACGCCGATGGGGGTGCCTTGGAAGTTTCCACCGTGCACGGCTTTGTTCCTTGACACGTCGATCAATGGGTTGTCGTTCACGGAGTTTATTTCACGTTC[G/A]ATCGATTTAGTGGCTGCTCTAATGACCTCGATCTGTGGGCCGAGCCACTGTGGGGACGTTCGGAGGGCGTATCTGTCCTGCTTTGG
106675 A G GCACATTAGTTTCATAGAGGACGATGGAGGCCAAGCCGGATCCGACGGCTGTGCCATTGACCAGAGCGAGACCTTCTTTAGGTTGAAGCTGGAAGAATCC[A/G]GAAGTGATGCCGGCAAGCTGGAAGGCTTCTGGAGCGGTGAGGAGAGTGTTGTCGGAAGTGACTGATTTGGAGTTAGGGCGGC
106675 G A AAGCCGGATCCGACGGCTGTGCCATTGACCAGAGCGAGACCTTCTTTAGGTTGAAGCTGGAAGAATCCAGAAGTGATGCCGGCAAGCTGGAAGGCTTCTG[G/A]AGCGGTGAGGAGAGTGTTGTCGGAAGTGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGG
106675 G A CGGATCCGACGGCTGTGCCATTGACCAGAGCGAGACCTTCTTTAGGTTGAAGCTGGAAGAATCCAGAAGTGATGCCGGCAAGCTGGAAGGCTTCTGGAGC[G/A]GTGAGGAGAGTGTTGTCGGAAGTGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGGACCA
106675 G A GGAGAGTGTTGTCGGAAGTGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGGACCAGATCACCTGAGGCAGTGATTGT[G/A]CCACGAAGAGGTAGACAGGGGGTGATGTTTGCGTTTAGTAAACGGGTTATGGATTCTAGGATCTCGAAACGGATACCAGAAT
106675 A G GAGTGTTGTCGGAAGTGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGGACCAGATCACCTGAGGCAGTGATTGTGCC[A/G]CGAAGAGGTAGACAGGGGGTGATGTTTGCGTTTAGTAAACGGGTTATGGATTCTAGGATCTCGAAACGGATACCAGAATATCC
106675 A G AAGTGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGGACCAGATCACCTGAGGCAGTGATTGTGCCACGAAGAGGTAG[A/G]CAGGGGGTGATGTTTGCGTTTAGTAAACGGGTTATGGATTCTAGGATCTCGAAACGGATACCAGAATATCCCTGGAGGAGGG
106675 G A TGACTGATTTGGAGTTAGGGCGGCCAGTGAGTAGGGCAGCGATGTAGGACAGTGGGACCAGATCACCTGAGGCAGTGATTGTGCCACGAAGAGGTAGACA[G/A]GGGGTGATGTTTGCGTTTAGTAAACGGGTTATGGATTCTAGGATCTCGAAACGGATACCAGAATATCCCTGGAGGAGGGTGTT
106675 A G GTGGGACCAGATCACCTGAGGCAGTGATTGTGCCACGAAGAGGTAGACAGGGGGTGATGTTTGCGTTTAGTAAACGGGTTATGGATTCTAGGATCTCGAA[A/G]CGGATACCAGAATATCCCTGGAGGAGGGTGTTGACTCTGACTAGCATGGCGGCACGGCTCGTGGTTGATGGTAGGGAGTTCCC
106677 A G GATTTGTTGGGTTCCTAAGCTGCACATGTGCCGGGCGCATTGATGTTGGTAAGGGGGATATTGTTTGGAGGGCATTATCTGTTTTGGGATAGGTATCACA[A/G]TATGTTATCTATATACAGCAACTTGGGATCGGTATTACAGTATGTTATCTATATACAGCCACTTGATAATGCTCAATCCCGTTATTTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106679 T A GACTCACCTGTTTTTTCAAGATTCTGGGTGTCTTTAACTGGACTATCCCCTTGGCTGTTGAAAGAAGCTCTGTGTCTTGCCATGATAATTTGCTTATGTA[T/A]TTAACACGTCCAGTACTGGGTAATCAGAGTTTGGTTTGCTATTAAATTTTGTTCACTGCTGATCCATGGTGATGCTCACGCGCACGTTAT
106679 A C TGGTACTGTGCTTTGCGTATGGTCTCCATTTCGTAAAGCTGTATACAGCCAATCCACTGCTATGTCCTTGAGTTCACTGTTCACGAAGGATTTTCAACGG[A/C]TAGTCATGCTCCAGTATGTACTTGCTGAGCTTTCTAGCTAGGCTGAATTGTTTTGGAACTCAAGATGTAATTTAATAAAGTTATGTAATT
106681 GA G AGGGTTTTGGTTGCAATGCTCTCGGTGGTCTCCATGGCGCTGTCTATCATGTCACCAGCTTGGAAGATGATGGATGTGGTACACTTCGCGAGGCTTGTAA[GA/G]AAAAAACAACCACTATGGATAGTCTTTGATGTCTCAGGCACCATTAACCTCTCGACCCACCTTAGAGTTTCATCTTTCAAAACCATC
106681 A G CAAAACCATCGATGGCCGAGGACGGAGAATCAAGCTAACGGGCAAAGGCATTCAGCTCAGAGAATGTCAGCATGTCATTATATGCAACCTCATACTTGAA[A/G]GTGGTCGTGGACATGATGTCGATGCAATTCAAATCAAACCAAATTCAAGACATATATGGATCGATCGCTGTAGCTTATCAGATTTC
106681 T C CCATCGATGGCCGAGGACGGAGAATCAAGCTAACGGGCAAAGGCATTCAGCTCAGAGAATGTCAGCATGTCATTATATGCAACCTCATACTTGAAAGTGG[T/C]CGTGGACATGATGTCGATGCAATTCAAATCAAACCAAATTCAAGACATATATGGATCGATCGCTGTAGCTTATCAGATTTCAGCGA
106681 C T GACGGAGAATCAAGCTAACGGGCAAAGGCATTCAGCTCAGAGAATGTCAGCATGTCATTATATGCAACCTCATACTTGAAAGTGGTCGTGGACATGATGT[C/T]GATGCAATTCAAATCAAACCAAATTCAAGACATATATGGATCGATCGCTGTAGCTTATCAGATTTCAGCGATGGGTTGATCGACAT
106681 C T ATTCCATTGCCTCCAGATTATTCCGCGGATGTGGCAGGCTTTACTACTTCCTGATATGCCACATTATCACCTTTTCTTGTTCATTTTGTTATAAAACTTA[C/T]ATTCTAGTTGCTCTGCTGCTTTGTTAAGGTTGTATGTGTGTATGTGCTTTAATTTCTCCTTAAAAAACGAACGTACACTTGCTAATTAATAA
106681 T C TGCTCTGCTGCTTTGTTAAGGTTGTATGTGTGTATGTGCTTTAATTTCTCCTTAAAAAACGAACGTACACTTGCTAATTAATAAGGAACGCCGTAAGTCG[T/C]CATATGTTACAGTTCAAATGCAGTAATAAAAAGTACAGGAATTTAATCAAAAAAAAAAAAACGG
106695 T C CCGGTTTTGGATAAGATCGACAGAGAGTTGCTGAACCGGACTGAGAATGGGTTTGCTCCGGGCATGTGGTCCTTGACGGGTGATGATTCGGCATTTTCAG[T/C]GGGGAAAGGGGTTTACAGGTTCAGGGAGTTGATGGAGAAATTGATGGGGAAAGAGTTTAGGAATGGGAGTTGCTCTGATTTGA
106697 C CA ACTTTTCGTCAAATCTGAATCCCCATTTCTTTACCCTCCAAAATCTCGTCTGCCTTATCGTGCTGTCTCCCGTGCGTTCCTCCTTGTGCCCTGCTATCTA[C/CA]AAAAAACCCTTCACTGCTATGCGTGGTGACCATTCCAGGATTTATCTTACTCCACCGTATCGCCCTTGCAGACTGGTTTTCGTGACTGTCA
106705 C CT ATTTCCGGTTTTTCCTCTCCCATCTCTCCCATTCTCCCTTTAGCCGTCCTCTCTCCTCTATCAAACCGCTCCCTTCCCATCTCACCCTCTCGATCCCCA[C/CT]TTTTTTTCTTCTGAAATCACAAATAAAACTCCAAAACCAACTTCTAACCACCATCTAATTTCAGTTCTTCTCAGATTTAATCCCACTTCAACATC
106705 AAC A TCCTCTTTCATCCAACAAATAAACATATTTAATACTCCTTCAACCCCTACACCGTACTTCCAATTATGATCCCTGCTTTTTAGATTTGATGCAGCAAAAA[AAC/A]ACCATTAAAAACTGCATGCTTCCACCACCTTTTCAATACAGTAGAAAAGGATTTACAAAATCTCATATATAGCAGCATTGCAAATAGAA
106707 T C GTATTCAGAGGCGAAGAACAGCTGTTGATGAACTTAACATGCGCAGTATTTTTGAAGAAAACGATGTTGTGTGTGCCGAGGTTCGTGGATTTCAACATGA[T/C]GGGACTTTACAGCTACAAGCAAGAAGTCAGAAGTACGGAAAGTTGAAAAGAGGGCTAATGCTGACTGTACCATCCTATCTAGTAA
106707 T A TTGTGTGTGCCGAGGTTCGTGGATTTCAACATGATGGGACTTTACAGCTACAAGCAAGAAGTCAGAAGTACGGAAAGTTGAAAAGAGGGCTAATGCTGAC[T/A]GTACCATCCTATCTAGTAAAACGCCGAAAACAACACTTTCACCATCTAGAAAACTACAATGTGGATATGATACTTGGCTGCAATGG
106707 C T TTCAACATGATGGGACTTTACAGCTACAAGCAAGAAGTCAGAAGTACGGAAAGTTGAAAAGAGGGCTAATGCTGACTGTACCATCCTATCTAGTAAAACG[C/T]CGAAAACAACACTTTCACCATCTAGAAAACTACAATGTGGATATGATACTTGGCTGCAATGGTTTCATATGGGTTGGCGAACACAC
106707 T C GGCTAATGCTGACTGTACCATCCTATCTAGTAAAACGCCGAAAACAACACTTTCACCATCTAGAAAACTACAATGTGGATATGATACTTGGCTGCAATGG[T/C]TTCATATGGGTTGGCGAACACACAGAATTGATGGAAGACGATATGATGGCCGAGGTCGAGGATGAGGATAATGAAAAAGAGCAGC
106707 C T ATCTAGAAAACTACAATGTGGATATGATACTTGGCTGCAATGGTTTCATATGGGTTGGCGAACACACAGAATTGATGGAAGACGATATGATGGCCGAGGT[C/T]GAGGATGAGGATAATGAAAAAGAGCAGCATGCAACTCCACTTGAAACTAGACAGAATATATGCAGAATCGCTAATGCGATTCGCT
106707 C T GGCTGCAATGGTTTCATATGGGTTGGCGAACACACAGAATTGATGGAAGACGATATGATGGCCGAGGTCGAGGATGAGGATAATGAAAAAGAGCAGCATG[C/T]AACTCCACTTGAAACTAGACAGAATATATGCAGAATCGCTAATGCGATTCGCTTGCTCTCTGCTTTAGGCTTTACTTTATCGGTTG
106707 A G GCTGCAATGGTTTCATATGGGTTGGCGAACACACAGAATTGATGGAAGACGATATGATGGCCGAGGTCGAGGATGAGGATAATGAAAAAGAGCAGCATGC[A/G]ACTCCACTTGAAACTAGACAGAATATATGCAGAATCGCTAATGCGATTCGCTTGCTCTCTGCTTTAGGCTTTACTTTATCGGTTGA
106707 G A AGAGCAGCATGCAACTCCACTTGAAACTAGACAGAATATATGCAGAATCGCTAATGCGATTCGCTTGCTCTCTGCTTTAGGCTTTACTTTATCGGTTGAA[G/A]TGGTTTGCGAGACAGTGGAGGCAAGTTTGGCGTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTG
106707 C T CAGAATATATGCAGAATCGCTAATGCGATTCGCTTGCTCTCTGCTTTAGGCTTTACTTTATCGGTTGAAGTGGTTTGCGAGACAGTGGAGGCAAGTTTGG[C/T]GTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTTCGAAGA
106707 T G TAGGCTTTACTTTATCGGTTGAAGTGGTTTGCGAGACAGTGGAGGCAAGTTTGGCGTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGT[T/G]CAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTTCGAAGAGAAGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATGCAT
106707 G A GCGAGACAGTGGAGGCAAGTTTGGCGTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAA[G/A]CTTTCGAAGAGAAGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTT
106707 C T ACAGTGGAGGCAAGTTTGGCGTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTT[C/T]GAAGAGAAGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCT
106707 A G AGGCAAGTTTGGCGTCTAATGTTGCAATTAAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTTCGAAGAG[A/G]AGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCTTCTATGG
106707 T A AAAGACATGCTTGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTTCGAAGAGAAGAAGCTGATATCGAAACGGAGATGAGA[T/A]AAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCTTCTATGGTGAATCGATTGCCAGATCTATGTATTAGA
106707 C T TGGAGCCGAGTTTTGTGTTCAGGCAGCTGAGCGCCAAGTGCAGAGGAAGCTTTCGAAGAGAAGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATG[C/T]ATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCTTCTATGGTGAATCGATTGCCAGATCTATGTATTAGAAACTAGAGACTG
106707 C T TTCGAAGAGAAGAAGCTGATATCGAAACGGAGATGAGATAAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCTTCTATGGTGAAT[C/T]GATTGCCAGATCTATGTATTAGAAACTAGAGACTGACTGATTAGTTGATGTGTTAGACAATGTGTTATGCAACTCGTTTAGTTCCCTG
106707 AACTAGAG A AAACGGAGATGAGATAAGGTTGATGCATTGCGACCGTGTTAGCGTTTGATTGACCTTTGTATCTTCTATGGTGAATCGATTGCCAGATCTATGTATTAGA[AACTAGAG/A]ACTAGAGACTGACTGATTAGTTGATGTGTTAGACAATGTGTTATGCAACTCGTTTAGTTCCCTGTAGATTAGGTGGCTGG
106707 T C CCAGATCTATGTATTAGAAACTAGAGACTGACTGATTAGTTGATGTGTTAGACAATGTGTTATGCAACTCGTTTAGTTCCCTGTAGATTAGGTGGCTGGT[T/C]CCCAGTTTACAGTTATATTTTGGTCACTGTTACAATAGATTACTAGTGTTGTGGTTTTTGAATGATATTTCAGTTGATAAAAAAAAAA
106707 C G GATCTATGTATTAGAAACTAGAGACTGACTGATTAGTTGATGTGTTAGACAATGTGTTATGCAACTCGTTTAGTTCCCTGTAGATTAGGTGGCTGGTTCC[C/G]AGTTTACAGTTATATTTTGGTCACTGTTACAATAGATTACTAGTGTTGTGGTTTTTGAATGATATTTCAGTTGATAAAAAAAAAA
106709 A C CCTTAACGACGGCCCTATCATCCATCTCTGATCCCGACCTCGCCTTCGATATTTTCAGATGGTCGTCTCTTTCGACCCCTTCCTTCCGCCACACTCCTCA[A/C]ACCTACCATTCCATCCTCCACATCCTCATCCGCTCCCGTCGCTTCGCTGATGCCGAGCTGCTTTTACATGAAGTTTTGTCAGGTGCTGTGC
106709 G A CTTCGCGGAGGCATTTGTTTGCTACTGCCTTTGATTTATATAAGAAAATGACTGCTGCGGCTAATGGCGGTGATGCTGAGTGTCGCCCTGATTTGAATAC[G/A]TATTCTTACCTTTTGACCATGCTGCTGCGCAGGTTTGGGAAGCCGCCAGTATGTTATGTGCACATGCACGCAGTAAGATCACTGGTC
106709 T C CGGCTAATGGCGGTGATGCTGAGTGTCGCCCTGATTTGAATACGTATTCTTACCTTTTGACCATGCTGCTGCGCAGGTTTGGGAAGCCGCCAGTATGTTA[T/C]GTGCACATGCACGCAGTAAGATCACTGGTCAAACAAATGAAAATCAACGGCGTGATACCAGATATATACGTACTAAACCTAATAATC
106709 C T GGGCAATGGATAGAAGGATGCATTCAAGTTTGCTTGGTGGGTTGCATTGGATTAACCAGCCTCATAGTTGATGATGTTTAGTTTGTGTTATGTCGGGAGG[C/T]AGTATGTTGCAAGCCAATTTTAATGCATATAGGAGACAAAATGTTGTGAGATCTTACTTGCACATAAAGGTAAAAATCATGATACCT
106715 G A TACTAAGCAGTGGACATGCATGGGAAATTCAAAGGAAGATCATAGCTCCTGAGTTTTTCATGCTTAAGGTTAAGGGAATGATAGATTTAATGGAAGAGTC[G/A]GCACATATATTGTTGAAGTCATGGGACGAGAAAATTGAATCTGGAAAAGGGATCACGGACATAAAAATAGATGAAGACATTCATA
106717 T TA ACAATGAACCTTACGAACAATGATTTAGCAAAGGACCATCTAAGATATCTAGTAGGAGGTCGATCAAACGTTAAAAACGAACTGCTTTGCCGATTCATCT[T/TA]CCCTGAAAGGCCAGGTGCTCTAATGAAATTTTTGGATGCCTTCAGTCCACGTTGGAATATCAGTTTATTCCACTATCGTGCTCAGGG
106721 AT A TTCAGGAATCAAATTCAATCCACCATTGGAAGCAGCTTTATAAACACCATACAACAATTTCAGATCAAAATCATACAGAAACAACCTCGTCCCAGGCTTA[AT/A]TTTTTTCCACTAGATCTAGCTTATTTCTAGGCATGGCGAAAACTGTGTGCCTGTAACACTCGGCCTTCGTCTTTTTATTGCACATGAAT
106721 T C GGCATGGCGAAAACTGTGTGCCTGTAACACTCGGCCTTCGTCTTTTTATTGCACATGAATATGAAGCCGCTACTTTTCTCTTTCTTTCTCTCTTCCCTCG[T/C]AGTTTCGCTGCTTTTTTCTGGTTTGTTGATTTTCTTTGTAGGGGCTAAGTTTTTGCAAGAGGTAGATGGTGATTTGTTTTCGCCTTTTTTGG
106721 G GT TTTATTGCACATGAATATGAAGCCGCTACTTTTCTCTTTCTTTCTCTCTTCCCTCGTAGTTTCGCTGCTTTTTTCTGGTTTGTTGATTTTCTTTGTAGGG[G/GT]CTAAGTTTTTGCAAGAGGTAGATGGTGATTTGTTTTCGCCTTTTTTGGACCTTGTCATTGTAGAATTGAAGAAAAGCCCTAACCCTACAAA
106723 A G GCTGAGGGTTCTTTCAATACGAAACGCCAGAGGACAATTAGAGCACTGGCGACGCCTTTGAGACGAATACATGGAAAAGCGACCGCCAAACTGAAGGAGA[A/G]GAGGAAAAAGAAACAGGCACAAACAACTGAAGGAGAAGTATCAGACAAAACTGAAACACTGCGTCAGCGCTTGAAGCTCTGCT
106723 A G GGACAATTAGAGCACTGGCGACGCCTTTGAGACGAATACATGGAAAAGCGACCGCCAAACTGAAGGAGAAGAGGAAAAAGAAACAGGCACAAACAACTGA[A/G]GGAGAAGTATCAGACAAAACTGAAACACTGCGTCAGCGCTTGAAGCTCTGCTTTCTTGGACGCAGGCCCCGCCACAAGAGGCA
106727 CA C TTTTCTTGCAAATACAACAAAGACCACACAGATCAGCAAAAGCAAAAGAAACACAAAAAAGATTCAACTACATTAACAACAGCTACAGCAGCAGCTGCAA[CA/C]AAACAAAAGCTGCAAAACCTCTTCTTCACTGCCTGAAGTTTCAAAGAGAAGAGCATCTACTAGCGAGTCCCACATCACGAAATCTA
106727 A G CAAGCACAAATTCTTCTGTTGGGAGTTCATTTAGAGTGATGCACTTGAGAAGACTTTCCGGTTGCTATGAGTGCCGGATGGTGATCGATCCCATAAGCGG[A/G]GTATTAAGAGATGGTTCGGGTTTCAGGGATGCTGTTAGCAGTTGTGACGAGTGTGGTGAGATTTTTCTTAAGCCTGAGAGCTTAGA
106727 A G AACAAACCCCAACCCCGAAGATCGACCGCATTCTCAAAATCCATAATGCAAAATCAACAATCTCGAACTTCGAGCTCTACCGGAGCTCCATAAAAGCGAA[A/G]GCAACCGACCTTCCAAAGAAGCATCCAAGGTGCATTGCGGATGGCAACGAGCTCCTTAGGTTTTACTGCACAACCTTCACGTGCAAC
106727 G A CAAAGAAGCATCCAAGGTGCATTGCGGATGGCAACGAGCTCCTTAGGTTTTACTGCACAACCTTCACGTGCAACCTCGGATTCAATGGGCGTACGTCTTT[G/A]TGCTGCGATTTCTCACGTTGTAAGGCATGCAGCATTGTGAAGGATGGTGTAAAAGCGGAGAACGATGAAGTTGGTATGGTTAGGA
106727 T A GGTTTTACTGCACAACCTTCACGTGCAACCTCGGATTCAATGGGCGTACGTCTTTGTGCTGCGATTTCTCACGTTGTAAGGCATGCAGCATTGTGAAGGA[T/A]GGTGTAAAAGCGGAGAACGATGAAGTTGGTATGGTTAGGACGTGGGGGATGAGCGGGAAGGCGCATGATAGCATTGGAAGTTTG
106727 G C GGCGATGTTGGTGTGTAGGGTCATCGCGGGGAGGGTGAAGAGAGGGATGGAGGGTGGATTGGGTGGTGGTAAGTGGGATTCGATCTCCAGGAATGAGGAG[G/C]TTTCTTGCTTGGATTTTGACGAGCTGTTCGTGGTTGATGGGAGGGCTGTTCTTCCTTGTTTTGTCGTGGTTTATCAGGATTTTT
106739 A G CGGAAGAAGAATCACTAGCAGTAACCGACATATCATAAACTTCGTGATCAGCATAAACAGCATCTCTCAGTCTACCCCAACACTGCACTTTGTTGAATTC[A/G]GGCAGGCTGGAGTGGAAGTATACGTACACCAGTGCCTCTTCTAGCTCCGGGTACGTCTTGAACAAGCTTTTATCCCCATGCACAAATG
106739 A G ACTTTGTTGAATTCAGGCAGGCTGGAGTGGAAGTATACGTACACCAGTGCCTCTTCTAGCTCCGGGTACGTCTTGAACAAGCTTTTATCCCCATGCACAA[A/G]TGCCTTTAGTTACTACAGGGAGCTCCTTGCAGAAGATGTAGTAGCGGAGCTTGGCAATGAGATCAAGAAGGAAGTGTCCGCCGCTT
106739 GT G AATTCAGGCAGGCTGGAGTGGAAGTATACGTACACCAGTGCCTCTTCTAGCTCCGGGTACGTCTTGAACAAGCTTTTATCCCCATGCACAAATGCCTTTA[GT/G]TTACTACAGGGAGCTCCTTGCAGAAGATGTAGTAGCGGAGCTTGGCAATGAGATCAAGAAGGAAGTGTCCGCCGCTTATATGGCA
106739 A G TAGCTCCGGGTACGTCTTGAACAAGCTTTTATCCCCATGCACAAATGCCTTTAGTTACTACAGGGAGCTCCTTGCAGAAGATGTAGTAGCGGAGCTTGGC[A/G]ATGAGATCAAGAAGGAAGTGTCCGCCGCTTATATGGCAGTGTACATGAAGGGACATCTTTCCTTTCAACTTCATCCATTCAGCGACC
106739 T C ACCAGCCCTGTAGCTGAGCTCGATTGATGGTGTTGGAGATGGCCAAAGTGAGTTTGGACGTTATGTCGCTGTGTGTTAGCGTGTAGGTTCTTGGAAGTTT[T/C]CCTGGGTTTTTCTTTGCTTGATCGTCGTCTCCTCCCACGAACAACACCTTTAGCTTCGATGATTCGAATATGGCTGGTCCAAACAACC
106739 C T GACTGTTCTTCTTCGTAGGCTGTTTCCTGATGATGTCCAGGAGATGGCTTCTCTTTGACAGAGAAGATGGCTGCTGCAAGAAAAGTGCAGCTGAGGAACA[C/T]ATCTCTCTCTGTTATTTGATGGCAGATTAATCAAAATTTGGAGGATAGATTTGTGTGAGAGCAGAAAGCAACAAAGAGACTTGGTTT
106739 G A GAGGAACACATCTCTCTCTGTTATTTGATGGCAGATTAATCAAAATTTGGAGGATAGATTTGTGTGAGAGCAGAAAGCAACAAAGAGACTTGGTTTGTTT[G/A]TCAAGAAGTTGGAAAGTTCAGGGCTAACTGATGACTTGTCAATGGAAACACGGCTCTTATTTTGAAATAAGGAAACAAAAATCCAG
106745 G C TGCGTAACCAACCGAATGGTGATAGATGTTCCAATATAATCGATATTTGTGATCCTTGTTTGGCCTTAGAAACAGTGCAAATACTTGCAATGTACCAAGG[G/C]TGAAGAGGGTAATTCCAATATTTCGATGTGTGGTGTAAGTGATTCCCTTGGACTTGTTACCGAGATTAAGTCCAGTAGCCCAACCAG
106745 G A CAACCGAATGGTGATAGATGTTCCAATATAATCGATATTTGTGATCCTTGTTTGGCCTTAGAAACAGTGCAAATACTTGCAATGTACCAAGGGTGAAGAG[G/A]GTAATTCCAATATTTCGATGTGTGGTGTAAGTGATTCCCTTGGACTTGTTACCGAGATTAAGTCCAGTAGCCCAACCAGCAACACCG
106745 A G GATAGATGTTCCAATATAATCGATATTTGTGATCCTTGTTTGGCCTTAGAAACAGTGCAAATACTTGCAATGTACCAAGGGTGAAGAGGGTAATTCCAAT[A/G]TTTCGATGTGTGGTGTAAGTGATTCCCTTGGACTTGTTACCGAGATTAAGTCCAGTAGCCCAACCAGCAACACCGAGAGCGTATCCT
106745 A G TGTTCCAATATAATCGATATTTGTGATCCTTGTTTGGCCTTAGAAACAGTGCAAATACTTGCAATGTACCAAGGGTGAAGAGGGTAATTCCAATATTTCG[A/G]TGTGTGGTGTAAGTGATTCCCTTGGACTTGTTACCGAGATTAAGTCCAGTAGCCCAACCAGCAACACCGAGAGCGTATCCTATTATTT
106745 C T CGCTGCTAATTCCCTTAACCAAATCCAAGCTCCCTTTCGCCATCAAATTCTCCGGCGCAAATTCGTGCTTCTTCACGTCGCCATTTACCGCAATTGGACC[C/T]ACTTGCCACACCTGATTCACTTTCTTCACACCTTTACCAACGACCAACTTCCCAAATATTTTCATCTTCCCATCTGCATATTCAGCTGCCAA
106745 T C CGTCGCCATTTACCGCAATTGGACCCACTTGCCACACCTGATTCACTTTCTTCACACCTTTACCAACGACCAACTTCCCAAATATTTTCATCTTCCCATC[T/C]GCATATTCAGCTGCCAAACCCGAAACGGGATAACTTATAGGACCCTCCGTCACCGGTCCGTACGCTGTAATGTTGTAGGTTTTCACTACCA
106745 T C CATCTGCATATTCAGCTGCCAAACCCGAAACGGGATAACTTATAGGACCCTCCGTCACCGGTCCGTACGCTGTAATGTTGTAGGTTTTCACTACCATTTT[T/C]CCATTGGGGTCTTTGTAGGCGATTAGGGTTTGAGAACCCTCCATGCCAGTTTTGGTAGGGTTCAGAGCCCAAGAGATCCAGCCGTTAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106745 G C CCATTGGGGTCTTTGTAGGCGATTAGGGTTTGAGAACCCTCCATGCCAGTTTTGGTAGGGTTCAGAGCCCAAGAGATCCAGCCGTTAGGGGTCGGAGGCG[G/C]GGCCACGAAGGCGATGTCTAAATCTGACGTGGCGGAGGAATAGGTGTAGTGGAGAGAGGCGCCGAGGGTGGGGAGGTCGTTA
106747 G T TTTGACCTTCCTTATGCAAGCAAACCATCTTCTCTAGCTCCAACCACCCTCCAGTGAAATCCCCTCCAAACTGATTTTTGAGCTCTGCCACAGCCCATTT[G/T]GCCACCCCTTCCTTCTTTGCTTTCATTAGTTTATCAATGAAAATCTTCACAACTCCAAGGTCTGGAACTTTCTCCTTCTCCAACGCATTACTG
106747 C T CCTTAACGACCTCCTTAACCCCACTTACTTCTCCTGCCATTCTACCCATAATCCTCACGTTGTATGCTGGAACATCCAACTTAACCCCTTTCTTCTTCAT[C/T]GCCTTCCATAACTTCTCCGCATCCACCAGCTTCTTCTCCTTGTACAATGAATCAAGAATCGTTGTGTAAGCCACAGTCGTGATATTCACCCCT
106747 T C ATGCTGGAACATCCAACTTAACCCCTTTCTTCTTCATCGCCTTCCATAACTTCTCCGCATCCACCAGCTTCTTCTCCTTGTACAATGAATCAAGAATCGT[T/C]GTGTAAGCCACAGTCGTGATATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACAGAGA
106747 T C ACCCCTTTCTTCTTCATCGCCTTCCATAACTTCTCCGCATCCACCAGCTTCTTCTCCTTGTACAATGAATCAAGAATCGTTGTGTAAGCCACAGTCGTGA[T/C]ATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACAGAGATTTAATCAGCACACCATAAG
106747 CA C CACCAGCTTCTTCTCCTTGTACAATGAATCAAGAATCGTTGTGTAAGCCACAGTCGTGATATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAA[CA/C]AATAAGCTGCTTTTTTAGATTTGCACAGAGATTTAATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGC
106747 G A TCAAGAATCGTTGTGTAAGCCACAGTCGTGATATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACA[G/A]AGATTTAATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGG
106747 T C GAATCGTTGTGTAAGCCACAGTCGTGATATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACAGAGA[T/C]TTAATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGA
106747 A G TCGTTGTGTAAGCCACAGTCGTGATATTCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACAGAGATTT[A/G]ATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGAGTC
106747 C T TCACCCCTTTCTCCTCCATCTTCTCCAACAGCTTCAAACAATAAGCTGCTTTTTTAGATTTGCACAGAGATTTAATCAGCACACCATAAGAAACCTCATC[C/T]GGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGAGTCTGGGATGGAGGTTGAGGCTGGAGAGG
106747 G A ACAGAGATTTAATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGAGTCT[G/A]GGATGGAGGTTGAGGCTGGAGAGGAAGGCGTTGAGGGAGAGGGAGGAGGGAGTGGGGATCTCAGATACGGTTTTTAAGGCGT
106747 G A ATTTAATCAGCACACCATAAGAAACCTCATCCGGAGTAACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGAGTCTGGGATG[G/A]AGGTTGAGGCTGGAGAGGAAGGCGTTGAGGGAGAGGGAGGAGGGAGTGGGGATCTCAGATACGGTTTTTAAGGCGTGATCAA
106747 A T ACCAAATACTTAGGAAAGAGCGTTTGGAAGTAGCTGGGGACTTCACGGAAGAGTCTGGGATGGAGGTTGAGGCTGGAGAGGAAGGCGTTGAGGGAGAGGG[A/T]GGAGGGAGTGGGGATCTCAGATACGGTTTTTAAGGCGTGATCAACCATGCCGGAAACGGCGTATGAGTTGATGATCGGAAC
106747 G A CAGATACGGTTTTTAAGGCGTGATCAACCATGCCGGAAACGGCGTATGAGTTGATGATCGGAACCAAACGGGATTCAATTTGGGAAGATGGTAGCGGGTT[G/A]TTAGCAGGGTTTGAGGATTTGAAGGGCTCGAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGG
106747 A G ATACGGTTTTTAAGGCGTGATCAACCATGCCGGAAACGGCGTATGAGTTGATGATCGGAACCAAACGGGATTCAATTTGGGAAGATGGTAGCGGGTTGTT[A/G]GCAGGGTTTGAGGATTTGAAGGGCTCGAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGGTGT
106747 A G GCGTGATCAACCATGCCGGAAACGGCGTATGAGTTGATGATCGGAACCAAACGGGATTCAATTTGGGAAGATGGTAGCGGGTTGTTAGCAGGGTTTGAGG[A/G]TTTGAAGGGCTCGAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGGTGTTGTATTCGACGGTG
106747 A G CAATTTGGGAAGATGGTAGCGGGTTGTTAGCAGGGTTTGAGGATTTGAAGGGCTCGAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCG[A/G]CGGAGGGTGTTGTATTCGACGGTGGGAGGGAATGTGGAGGTGGAGAGGAGGCGGCGGAGGTGCTGTACGAGTTGGTGCCG
106747 G T TTGAGGATTTGAAGGGCTCGAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGGTGTTGTATTCGACGGTGGGAGGGAATGT[G/T]GAGGTGGAGAGGAGGCGGCGGAGGTGCTGTACGAGTTGGTGCCGGTCAGGGAACTTGCGGCGGGAGGCGGAATAAAGAG
106747 C T GAGAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGGTGTTGTATTCGACGGTGGGAGGGAATGTGGAGGTGGAGAGGAGGCGG[C/T]GGAGGTGCTGTACGAGTTGGTGCCGGTCAGGGAACTTGCGGCGGGAGGCGGAATAAAGAGACATGTTAGTCAACCGTAAG
106747 G A GAAGGGATTCGATCTGTGAGAAATTTTGGGCACGGGAGAGGCGACGGAGGGTGTTGTATTCGACGGTGGGAGGGAATGTGGAGGTGGAGAGGAGGCGGCG[G/A]AGGTGCTGTACGAGTTGGTGCCGGTCAGGGAACTTGCGGCGGGAGGCGGAATAAAGAGACATGTTAGTCAACCGTAAGTT
106747 T C TTGGGCACGGGAGAGGCGACGGAGGGTGTTGTATTCGACGGTGGGAGGGAATGTGGAGGTGGAGAGGAGGCGGCGGAGGTGCTGTACGAGTTGGTGCCGG[T/C]CAGGGAACTTGCGGCGGGAGGCGGAATAAAGAGACATGTTAGTCAACCGTAAGTTGTTTGTTTCCAGTAGGCCAAC
106749 C T GAAGATTAGCGATGAGGTGGCATCCTGATAAGAATCCGACCCATAAATCTGAAGCTGAGGCCAAATTCAAGCAGATCTCTGAAGCGTATGACGTTTTGAG[C/T]GATCCCCAAAAGAGAGCAATTTATGATCAATATGGAGAAGAAGGTCTCAAGGGCATGCCGCCTCCTGGCTCTCAAAGTGCAAACT
106749 T C AGTTTTTCGATAGCGGTCCATTTGGGTACGAGTCCACGGGGAGGACCAAGACCACTAGATTTCATACAGATGGTGGTGGGACCTATGCAGAGGGCCCCAG[T/C]TCTTCTAATGGAGGACAGTCACGGAAACCACCACCAGTCGAAAGTAAGCTACCATGTTCACTTGAAGAACTTTACACTGGTTCAAC
106757 G A ACTTATGAAAGGAAATGATGAAAAATCACATAGCAGTACACTGAAAAATTTCGACTTAAAGGATTCGATGATCATCATCGGCGCCTTCGTCGAAAACTCC[G/A]GATGATCCAACACGGAAATCTAGTTGTTTCTGATGCTTTAATCTTCTCCGCTCGTCAAATTCTTCCCATCCCTCTATCTGACGCAGAAC
106757 A AT TGATAAAGATTTAAGAGAAGACAAACTTTCCCAGCAAATCTTATCAACTGAAATATCATTTCCACTTAACAACAGTTTATTTAACTGTTTCAGAGCACAA[A/AT]TTTTTTCAGACACTTCCTGCAGAGAATTGTGGCTGAGGTCCAATACTCTCACAGATGGTCCGCAAGTCCAGACTACCTCGGGCACGGT
106757 A G GGTGAGAGGTTGAAGTTGAGACTTGAGGTCTTTAATGGTTGAATCAGGTGAAGCTGAGATTGGAAACTTTTGACCACTGAATTGAACGTTTACTTTGATT[A/G]TAGACGACGAAGTTTCAGCCGTTGTTCCGACATTAATATCATCCCCTTCCATTTTCCGGAATAATTACCGATCTTAATTTGTTCCAGTA
106757 T C GTGAGAGGTTGAAGTTGAGACTTGAGGTCTTTAATGGTTGAATCAGGTGAAGCTGAGATTGGAAACTTTTGACCACTGAATTGAACGTTTACTTTGATTA[T/C]AGACGACGAAGTTTCAGCCGTTGTTCCGACATTAATATCATCCCCTTCCATTTTCCGGAATAATTACCGATCTTAATTTGTTCCAGTAG
106763 C G TTCGCATATGAGCAAATCCAGTTTCCTTCAAGAATTCAAGCTTTAGGTACTCAGCCATATCATAGTTTTTAATGATTCGAAATAGGGTAGTGATAATGTC[C/G]GTAGGAGAGTAGCCTAAATCATAAAGCTCTTTCAGGCCAGCACATGCATCATCGAAGTTACCACTAAGTACATTTCGTATTATATTCTT
106763 A G TAGTAGAATTTGAATAGATTTCCATTGTTCTCCTTAGGGCTTGTTGTGCTGCGGAAGTCATACTGTCAGCTTCATCAAGAATTATAATCTTGTGCCGACC[A/G]GGGGGCAGAGTAACTTTCTTCTGGGCAAACATCTTAATCTTGTTCCTCACAACATCAATTCCTCTGTCATCAGAAGCATTTAGCTCGAG
106763 A G ACTTTTGTCGGACGGTATTTCTCGACCCATGGAATTTCGTAGTACGTTGTCGTGGACGAAGATGAGATGTTTTTAGATGAAGGACTGGCAGCAGCCATTG[A/G]TGCAATTTGATTGCTTGATACAGAGATTGTTTGGGAAGAAATGCTAAGTGAAACCCTTGGAGGGAAGAAC
106769 C T GAATCTCTAAAGGACATACCACCAAATTGTCTTCAGGAGATTACAGCAACCAGTTCAAACCCTACCGAGACATCGCCAGACAGTGCACTTGGTACCGCCT[C/T]TGAAACTAAAGAAACCGAGTCAAGCGAAGAACCTGAACCCAGCGCTGTAGAACCACAAACCACTGCAAAGTGTTCGATTGTAGATG
106769 C T TTAACTTCTTCAAGAGCAAGTCAATGAAGTGAGAACGGTCTCATTCCGTCACATGTACATGCCTAACCCTCATATCATCGGTTATACGGTTTATTGTTAT[C/T]AAAAGTTGAAAATGTTGTTGCCTTTTGTGAACATGCATTAAATTATCGGGAAACAGTGCAGTTTATATTGTGTATTTTGTGTCGCTTGGC
106769 T G GCCTTTTGTGAACATGCATTAAATTATCGGGAAACAGTGCAGTTTATATTGTGTATTTTGTGTCGCTTGGCTGATTATGTTTGCTGATTTGCTGCATACC[T/G]CGCCTAACATGTAGTACCCACTTGTTAGGTGCGACACTGTTACATGTACAAGTAGCTCAATTCTTTCGATGTGTTAAACTGGAGGAAAT
106779 G T GAATGGAGGTGCGTCGGTTCAAGTTCGTCACGGTTCCAGCCGAGGTTGTGCAGAAGAAGCGTAAGCCAGAGGTTCTTTCACCCCTCACCGTTACTGGCCT[G/T]GAAGGCGGTAGGGTTACAGGTTCATTAAATAAAAGCGACAAGCGTCCGAGGTACGGGGTGACGTCCGTCTGCGGGAGAAGGAG
106779 C A TGGAAGGCGGTAGGGTTACAGGTTCATTAAATAAAAGCGACAAGCGTCCGAGGTACGGGGTGACGTCCGTCTGCGGGAGAAGGAGGGACATGGAAGATGC[C/A]GTCTCGATTCAACCTAATTTCTTCGAGAGTAAAAAAGAAGAACAAAACAGAAGGCATCATTTTTTGGCAGTGTTCGACGGGCA
106779 G A GACCAGACGAGTTAGAGAGGATTCAAGCAGCAGGAGGAAGAGTCATATATTGGGACGGTGCTCGAGTTCTGGGAGTTCTTGCCATGTCTCGGGCCATAGG[G/A]GATAGCTACTTGAAGCCATATGTAACGGCAGAGCCAGAAATAACAGTAACAAGAAGATCGGAGGACGACGAATGCCTGATAAT
106779 A G AATCGCAAGCGATGGATTATGGGATGTGGTGACAAATCAGATGGCTTGCGATATTGTTCGAATGTGCCTACGAGGCAGCACACTAGGTAATGGAGTGTTA[A/G]CGGACGAGGCTTCGGATAAAGCGTGTTTGGATGCATCGGTCCTCCTGACGAAATTGGCTTTGGCAAGGCAAAGTACGGATAACG
106781 G T AATCTGAGGAAGCAGAGGCTAGAGCAAGAGAACTTGAAAAACAGGTTGCTGCTCTTGGAGAAGGAGTGTCTTTAGAAGCCCGTCTTCTTAGCAGGAAGGA[G/T]GCAGCTTTGCGACAAAGAGAGGCTGCTCTTAAGGCTGCTTCACAAAACAAGGATGGGAGAAATGAAGAAATGACAGCTCTTAG
106781 T A TTGAACTAAACAAAGAAGAAGTAGAAGACGTATTTTTCAAACAAGCATGGCTGTCATATTTTTGGAGACGAGCTAAAAATCATGACATAGAGGATGACAT[T/A]GCTGAGGATCGGTTACAATTTTGGACTAGCCACATTGGGAAGTCACCCACTTCTCACGATGCTGTAGATGTTGAGAGAGGATTACT
106781 A G ATTGCTGAGGATCGGTTACAATTTTGGACTAGCCACATTGGGAAGTCACCCACTTCTCACGATGCTGTAGATGTTGAGAGAGGATTACTAGAACTAAAGA[A/G]GCTTGGAATCGAACAGCAGCTCTGGGAAACATGTCGTAGAGAAATCGAGCTAGTCTCTCCTACCAATCCAGAATAAATACACGAAC
106781 C T GATTACTAGAACTAAAGAAGCTTGGAATCGAACAGCAGCTCTGGGAAACATGTCGTAGAGAAATCGAGCTAGTCTCTCCTACCAATCCAGAATAAATACA[C/T]GAACAAACCCTACAGTAATCGCGTCCGAGTTCAGAATACAAACCCTCTTGCTACTGCATCAACTTCTGAACATGCTGCGCAAGTTTG
106785 G C CACCCATCAAAAGCCCAATTCCAAACCCTAACTCAACACATTTCATCACGCGCTGCCAACTCCAGTACAATCGCAAGCCTGTCCTTGCGGGTCCCACTCC[G/C]CGCATTGTCGTCATCACCTCCGGGAAAGGTGGCGTCGGAAAGACAACCACCACCGCCAACCTCGGTCTCTCACTCTCCCGCCTCGGCT
106785 CT C TTGCTTTTGAGCAGGCGGCTTGGAGGCTGGTGGAGAGGGATAGTATGAAGGCGGTGGCAATGGAGGAGGAACCTAGAAAGAAAGGGTGGTTCTCCTTCTC[CT/C]TTTTTTGGTGGTTAGATTGTTTTTGTGCATTGGTTTTGTGTTGGTAGTAATTTTGGAAGTTTCTTTGGAGTTACAGTCTTGTTGT
106785 T C CTGGTGGAGAGGGATAGTATGAAGGCGGTGGCAATGGAGGAGGAACCTAGAAAGAAAGGGTGGTTCTCCTTCTCCTTTTTTGGTGGTTAGATTGTTTTTG[T/C]GCATTGGTTTTGTGTTGGTAGTAATTTTGGAAGTTTCTTTGGAGTTACAGTCTTGTTGTAGTGTTTTTGTATATGTGCATTGGTTCTC
106785 C CT TTTTGTGCATTGGTTTTGTGTTGGTAGTAATTTTGGAAGTTTCTTTGGAGTTACAGTCTTGTTGTAGTGTTTTTGTATATGTGCATTGGTTCTCCTTCTC[C/CT]TTTTTAGGTGGTTAGACTGTTTTTGTTATAGTGGAATTGGTGATAAGTTGATTATTATTGTATTTGTTTCATGCTGTTTAAAAAAAAAAAA
106785 G GT GGTTTTGTGTTGGTAGTAATTTTGGAAGTTTCTTTGGAGTTACAGTCTTGTTGTAGTGTTTTTGTATATGTGCATTGGTTCTCCTTCTCCTTTTTAGGTG[G/GT]TTAGACTGTTTTTGTTATAGTGGAATTGGTGATAAGTTGATTATTATTGTATTTGTTTCATGCTGTTTAAAAAAAAAAAAAAA
106789 T A TTTGCAGTGTGTGGAGATGAGCTCTGGAAGTGTTGCAACAACATCAGGCAATATGCAAGTTGCAACTGGAAGATACCATACCCTCATAATTCATGACACG[T/A]CCGTGTACTCTTGTGGCTCTAGTTATTGTGGTGTGCTTGGGCATGGTCAAGATACAACTCAGTGTGTATCATTTACACGTATCAGCT
106789 C T CTGCCGGTGCTAGTTACACTTTTGCTGTAACAAATGATGGAACAGTTCATTCTTTCGGTTCATGCACCAACTTCTGCCTTGGTCATGCTGACCAAACCGA[C/T]GAACTTACCCCCCGTGCTATCCAGTCATTCAACAGAAATAATATTCATGTAGTGCGGGTATCTGCTGGAGATGAGCATGCAGTAGCAC
106789 C G GTGCAAGGAAGAGGAAGACGTTCGTTTTGACGGATTCAGGCTCAGTGTTTGCTTTTGGGTGGATGGGTTTTGGAAGTTTGGGGTTTCCAGATCGTGGTCT[C/G]TCCGACAAAGTGATGAAACCACGAATTCTTCAAAAATCTAAGGTCACATTATGTATCTCAGATCAGCACAGGTCTGTACCACACTG
106797 T A GCCAACAGTGAATTTAATTCAGCTTCTCCAATGGTTTCGAGGCCTCCTTCAGAGCGTGATGATGGGCAAATGAATAAGAGAGGATCAGG[T/A]TTGCTGATTGTGGATTATGGCCATGATGAAGCTGCCATGTCACCTGAAGCTGAGGAGGGAGAGATATGTTTTAGCGGTGATGGCGTGGCAGATATG
106797 T C AAGGGGCAGCTTCAGGATCTGATCATCTGCTGACACCAAACAATCAATCAGAACCTCCACAACCTTCTGTTATGCATGATCAAACAATGTCTGAAGCTGA[T/C]GTTGCAAATGAGACTGCCAGTGCTGATCCTGAAATAGCTCAAAATGAAGTATGTGATGTAGTTACAGAGGGAGCTCAAAATCATGAT
106797 C G CTGGGTATAATGCTTTTGCCCAACAAAAGAGAAGAGAAGCAGAAGAAAAGAAGTCAGGTGAAAGGAGATCCGATAAAAGATCATGATATTCCTATTGATC[C/G]TATTATATATTGTCGAGGAGTGATTTAATTACCACACTTGATATGTTTACGTCTTCATATGTTTATGTCCAAGCCATGATTTTGATTC
106797 T C GCTTTTGCCCAACAAAAGAGAAGAGAAGCAGAAGAAAAGAAGTCAGGTGAAAGGAGATCCGATAAAAGATCATGATATTCCTATTGATCCTATTATATAT[T/C]GTCGAGGAGTGATTTAATTACCACACTTGATATGTTTACGTCTTCATATGTTTATGTCCAAGCCATGATTTTGATTCTAACCAGATGA
106803 GT G GTTTGTATTGTCGCATGCCACTTTCTACTAGCATATGTAATTCTATGTCAGAGACTCCTGATTGCAAAGCCGATCTGAGTTCACCAACGTGCTTCTTTTG[GT/G]TCTTCTATCCAATGTGTGTACTCCATCTCAAAGGCAGCAATTCCTGAATTAACAGATCCGGGTAATCCACCGAGGCTTGAATCTCTGCC
106819 T A GGATTATCACAGTCCTGAGCGATGTTATACAGTTTGCGGTCCAGCGATTAAGGGTATTGGTAATGATGAGCGTTACAATGTGAGGTCCAACTCTGGTGTA[T/A]CCGTTGTGCAGGAAACAAACAAGCGGCCTGGTTCAGGAAAATAAACCAAAAGGAGTTGTTAATTGCGGCTGCAAGAGATAGAGGA
106819 G GA GGTCCAGCGATTAAGGGTATTGGTAATGATGAGCGTTACAATGTGAGGTCCAACTCTGGTGTATCCGTTGTGCAGGAAACAAACAAGCGGCCTGGTTCAG[G/GA]AAAATAAACCAAAAGGAGTTGTTAATTGCGGCTGCAAGAGATAGAGGAGGTTGCCATCGTGACTCTATACTCTCTCTTGCATCT
106819 G A CTAAATCAAAGGATATTGATATCTAGTGGAAGAGACGGTGCTATCAAAGTATGGAAGTAGGAAGCTTGTCTATATTGCCAATCCGTGCTTTCACTTTCTC[G/A]TGTACATAATCTCACATAACTTGTTCAATGCTATTAAAGTGGAACAATCTCTATTTGTCAACTGTTCTAACTAGGAAGTGGATATAAGG
106827 C T GAATACCGCTTGCTCACTTACCCCGTTTCTCTCTGAGTTTTGTGATATGATATTCCTCCTATTGAAGTTGTCGACTTCTCTTATCAACTCATCCTTAGTG[C/T]TGTTGCATGATGTAATTACCAGTATGCCTCCAGGAGCCACTAAATTTGTTACTGATTCCCAGTACATTATCTTCTTGAGAGGGCCTTCTGG
106827 T C TGATATTCCTCCTATTGAAGTTGTCGACTTCTCTTATCAACTCATCCTTAGTGCTGTTGCATGATGTAATTACCAGTATGCCTCCAGGAGCCACTAAATT[T/C]GTTACTGATTCCCAGTACATTATCTTCTTGAGAGGGCCTTCTGGGTGCAACCCAATAGCATCTAACGTGCCTTTGTCCATTACCAGTTGAA
106827 C G CAGACGCAGCGCGAAAATTCGCAGCAGAGAGGGCATCGGAAGCATCTACGTGCCTCTGTTCATCATCAAGAGTACTTCCATACTCGCTTTTTATAGACCA[C/G]GAGTCCGCCGCCACTGATCTGTCGTCATCGGACACGAGATCGGAGGAGGCAACGGCAACTTGCTGGCGTTGCAGAACATGATCAG
106827 C A TGTTCATCATCAAGAGTACTTCCATACTCGCTTTTTATAGACCACGAGTCCGCCGCCACTGATCTGTCGTCATCGGACACGAGATCGGAGGAGGCAACGG[C/A]AACTTGCTGGCGTTGCAGAACATGATCAGAATCTTCAGGCAGTGGCCATTTAATTCCTACCATTACAACTGGTGGTTATTACCGATTG
106829 A T CGGAAAACCAACCTCAGTCACTGTCTCTAAAGTCCCCGATCTCGGAGCGATTTTAAATCATGGTGTCCTCACAGCTTGAAATTGACGGCAACACGTTGGC[A/T]GCTCTCGCCTTAAAGCGGTTCAATGTGTCGCACATGTTCGGAGTGGTCGGAATCCCCGTAACATCCCTCGCCACGCGCGCCGTCGCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106829 C T TCGCCTTAAAGCGGTTCAATGTGTCGCACATGTTCGGAGTGGTCGGAATCCCCGTAACATCCCTCGCCACGCGCGCCGTCGCGCTGGGTATCCGATTCAT[C/T]GCCTTCCACAACGAACAGGCGGCTGGGTACGCTGCATCGGCTTACGGATACCTGACGAAGTCGGCTGGCGTTTTCTTGACCGTGTC
106829 G A GATGCGTGCACGGGATTGCTGGTCTGGCCAACGCGCAGGCCAACGCTTGGCCTGCTGTTATGATCTCTGGCAGCTGCGATCAGGCTGATTTTGGGAAGGG[G/A]GATTTTCAGGAGTTAGATCAAATTGCTGCAGTGAAGCCCTTTGTGAAATTTTCGGCAAAAGCCACCGACATTTCTCAAATTCCACA
106829 C T CTGGCAGCTGCGATCAGGCTGATTTTGGGAAGGGGGATTTTCAGGAGTTAGATCAAATTGCTGCAGTGAAGCCCTTTGTGAAATTTTCGGCAAAAGCCAC[C/T]GACATTTCTCAAATTCCACAATTGGTTCTTGAAGTTATAAACACTGCCATATCTGGCCGTCCTGGTGGTTGCTATCTTGACATTCCAT
106829 T C TTCCACAATTGGTTCTTGAAGTTATAAACACTGCCATATCTGGCCGTCCTGGTGGTTGCTATCTTGACATTCCATCTGATGTCCTACGCCAGAAAATATC[T/C]GAATCACATGCTTCTGAAATTCTAAAAGAGGCGCACTACCCTGAAATACATGACCTTCAAATTTCAGGAACCCAGGATATCCAAATGGC
106829 A T TCTGGCCGTCCTGGTGGTTGCTATCTTGACATTCCATCTGATGTCCTACGCCAGAAAATATCTGAATCACATGCTTCTGAAATTCTAAAAGAGGCGCACT[A/T]CCCTGAAATACATGACCTTCAAATTTCAGGAACCCAGGATATCCAAATGGCTGTTTCTTTGCTTAGAAATGCAGAGAGGCCTTTAATTG
106829 T C GCCGTCCTGGTGGTTGCTATCTTGACATTCCATCTGATGTCCTACGCCAGAAAATATCTGAATCACATGCTTCTGAAATTCTAAAAGAGGCGCACTACCC[T/C]GAAATACATGACCTTCAAATTTCAGGAACCCAGGATATCCAAATGGCTGTTTCTTTGCTTAGAAATGCAGAGAGGCCTTTAATTGTATT
106829 G A AGGATATCCAAATGGCTGTTTCTTTGCTTAGAAATGCAGAGAGGCCTTTAATTGTATTTGGAAAAGGTGCCGCATTTTCACGGGCAGAAAGTTCTTTGAA[G/A]AAGTTAATTGATATCACCGGTATACCTTTTCTTCCAACTCCAATGGGAAAAGGATTGGTGCCTGACAGTCATGAACTTTCGGCAACAG
106829 C T TTTCTTTGCTTAGAAATGCAGAGAGGCCTTTAATTGTATTTGGAAAAGGTGCCGCATTTTCACGGGCAGAAAGTTCTTTGAAGAAGTTAATTGATATCAC[C/T]GGTATACCTTTTCTTCCAACTCCAATGGGAAAAGGATTGGTGCCTGACAGTCATGAACTTTCGGCAACAGCTGCTCGGTCTTTAGCCA
106829 C T GTGCCGCATTTTCACGGGCAGAAAGTTCTTTGAAGAAGTTAATTGATATCACCGGTATACCTTTTCTTCCAACTCCAATGGGAAAAGGATTGGTGCCTGA[C/T]AGTCATGAACTTTCGGCAACAGCTGCTCGGTCTTTAGCCATTGGTAAAACTGACGTTGCTTTAATCGTAGGTGCTCGACTTAATTGGC
106829 T C CACGGGCAGAAAGTTCTTTGAAGAAGTTAATTGATATCACCGGTATACCTTTTCTTCCAACTCCAATGGGAAAAGGATTGGTGCCTGACAGTCATGAACT[T/C]TCGGCAACAGCTGCTCGGTCTTTAGCCATTGGTAAAACTGACGTTGCTTTAATCGTAGGTGCTCGACTTAATTGGCTTCTTCATTTCGG
106829 T G CTCCAATGGGAAAAGGATTGGTGCCTGACAGTCATGAACTTTCGGCAACAGCTGCTCGGTCTTTAGCCATTGGTAAAACTGACGTTGCTTTAATCGTAGG[T/G]GCTCGACTTAATTGGCTTCTTCATTTCGGTGAGCCTCCGAAATGGTCAAAAGATGTCAAATTCATACTAATTGATATTTCAAAAGAGG
106829 C T ACAGTCATGAACTTTCGGCAACAGCTGCTCGGTCTTTAGCCATTGGTAAAACTGACGTTGCTTTAATCGTAGGTGCTCGACTTAATTGGCTTCTTCATTT[C/T]GGTGAGCCTCCGAAATGGTCAAAAGATGTCAAATTCATACTAATTGATATTTCAAAAGAGGAAATCGAGCTTCGAAAACCTCATCTAGG
106829 G A TTTCGGCAACAGCTGCTCGGTCTTTAGCCATTGGTAAAACTGACGTTGCTTTAATCGTAGGTGCTCGACTTAATTGGCTTCTTCATTTCGGTGAGCCTCC[G/A]AAATGGTCAAAAGATGTCAAATTCATACTAATTGATATTTCAAAAGAGGAAATCGAGCTTCGAAAACCTCATCTAGGTTTAGTTGGTGA
106829 A G AACTGACGTTGCTTTAATCGTAGGTGCTCGACTTAATTGGCTTCTTCATTTCGGTGAGCCTCCGAAATGGTCAAAAGATGTCAAATTCATACTAATTGAT[A/G]TTTCAAAAGAGGAAATCGAGCTTCGAAAACCTCATCTAGGTTTAGTTGGTGATGCAAAAATGATTCTTGATTTGATCAATGCTGAAATC
106829 A G TCCGAAATGGTCAAAAGATGTCAAATTCATACTAATTGATATTTCAAAAGAGGAAATCGAGCTTCGAAAACCTCATCTAGGTTTAGTTGGTGATGCAAAA[A/G]TGATTCTTGATTTGATCAATGCTGAAATCAAAGATAATCCGTTCTCTTTTGGGAAATCCCATCCTTGGGTGGAGATGATTTCAAAAAA
106835 A G GCGCAGTGAGCCCTGCAAGCTTTTTAAACAGAACGAGTGCTATGCTTAGTGGAATGGAGGTAAGTGCAAGGAGCGTCTTACCCTTGAAGAGCAGTGGGGC[A/G]GTGAGGTTCAGGTGGGGGATAAGGTTACCAGAGAAAAATGTGAGTGGTTTCAACATGTCTTTAAAGAAGCTGCCTATGCTGGTT
106835 A G GAAGAGCAGTGGGGCAGTGAGGTTCAGGTGGGGGATAAGGTTACCAGAGAAAAATGTGAGTGGTTTCAACATGTCTTTAAAGAAGCTGCCTATGCTGGTT[A/G]TGAACAAAATCTCAATTGAACACATACCAATTGCTAATAAAGTGAAGATGGATGAGACCCGCAAGGGGTTTGAAATGGTTGAGG
106835 A G TGCTGGTTATGAACAAAATCTCAATTGAACACATACCAATTGCTAATAAAGTGAAGATGGATGAGACCCGCAAGGGGTTTGAAATGGTTGAGGCTTGCGC[A/G]GAAGTGAAAAGGCAGCTGGAGGCCATGAAGGCGGAGAGTTGTGAGATGAAGAAGGCTGTTCAAGAGATCAGAGCAATGGCTTG
106837 A G GCTACAAGCACTGCTTATGCAAGATTGCAAGACAATGAAACAAACTAAGGGCAAACAACATGCAGCAGAAAATTATTATACATACAACCATGATCTGCAG[A/G]CCTAAGTTCACATCTAAGTGAGAATGATGTAATCATGATAACAGACTTTCTATTATCTGCTTGAGGGCTGTGTATGACCCCACTACC
106837 T C CCACTACCGCTGACGTTACTCCAACTGCTATAATTACAGTGCACAATGTAATCTCAAACCAAGTTACCCTACTCTTGACTATGCTTAGAAAGCAAAGGCA[T/C]GGTAGAATCAAAGCTACAAGCATGGTGAGCAAAGATCCAATCAAAGCCATCACCAAACCGAAGAAAGGTACAGAAATAGCGACTAAC
106837 T A TTGCGATGACTCCTCCAGCTGATAAGTAACTAAGGATACTGAGATCGCGAACCCATGTTGTTGGAAGAACAACAATGGTTGTTACGATCGCGAATAACAA[T/A]TGTGGTTCCATATGCAATCCACCCATGTGTAGTTTAGCATTTGGAAACAGTGATGATAGATTGTCGCTCTCAAGTATGATATACTCCA
106837 T C CCCATGTTGTTGGAAGAACAACAATGGTTGTTACGATCGCGAATAACAATTGTGGTTCCATATGCAATCCACCCATGTGTAGTTTAGCATTTGGAAACAG[T/C]GATGATAGATTGTCGCTCTCAAGTATGATATACTCCACGCAACCAGCATACAACTCCATGTATAAGATAATCGAAACCAGCAAGCGG
106845 T C AGTTTTGGAGTCCCGTCGAGCCCATATTGACTGTCGGGGTTGATCCCGACCAGCTTTGATAATATGGACCATTTTTATTGTTGGTAACATCATTGAAGCC[T/C]CAGGTGCGAACGACATTCAGGCCCGCGTTTGCAATATCCTTGAATGCATTATTCATGTTGGTGGTTGAGAGACCGGTTAGGCCAACCC
106851 A G ATGAAACAAAGATATGTTGGGCACTGCAATATTGGAACAGATATAAAGCAGGCTAGCTTTCTCGGGCAACAAGGAGAATTTGTGGCTAGCGGGAGTGATG[A/G]TGGAAGATGGTTTATATGGGAGAAAACTACAGGGCGACTCATAAAAATGTTGACTGGGGATGAAGCTGTTGTAAACTGCATCCA
106853 CA C TATATTCCCTACTACACATACTAACAGGACAGGCCATCATGAAGAGAGGAATAAAAAAGGCAACCTTCTGCATGGCACGCTCCTATATGCTACACTAAAA[CA/C]AAAAAAGAGGCAGACAGCCTCATCGGGAGCCCTTTGGAAGAATCAAAACGGAGTCGACGCAGAGTCCGCCCTTAGTATGAGTGC
106853 G A TCAAAACGGAGTCGACGCAGAGTCCGCCCTTAGTATGAGTGCAATCAATCTGGGTCATGGAGAACTTGACCTTGGTGGATGCGTTCGACCTGTGCACCAT[G/A]AAATCGCCCACGTTGTAGCGGTTCCAGAATCCAGGTTGACCCAACCGGCACTCGGAGGTCGAGTGCTGACCGTCGGATGTCCAGA
106853 A G TGAAATCGCCCACGTTGTAGCGGTTCCAGAATCCAGGTTGACCCAACCGGCACTCGGAGGTCGAGTGCTGACCGTCGGATGTCCAGAGTTGGAACTTAAC[A/G]GGCTTTTCATCCCAGCCGTGCACGTGATCCAGTTTGCACACGCGTCTTCCTAACCGCTTGCAGGGTCGGCCCAGCTGCAGCCGGA
106853 C A GTCGGCCCAGCTGCAGCCGGAAGTACAGGCTGTATGTGCCGGGCGGGAAGATGAAGTCCACTTCTCCTCGTACTTCTACCCACCAAATTTGCTGTAGGTA[C/A]GCCACACTTTGGAATCTAGACTCGTCAGTCAAAATGTGATTCCAGTATCTTCGGTCATCAATACCGGTAATCACCAACGCCTTGTAC
106853 AT A CTTATTCATCCAAAACGCCTTATTTCCATCATCAAAAACATTCCACTGACACAGCTGCGCATAAGTTTCCTTCTTGCTCTCAAACTTCTCACTACTCTTT[AT/A]TTTTTTCAACCAAATACTCATAGTTTGAGGGCAGCTTCGATTTCCAGACGAAGTCAGATGTAGCCGCAGTGCCAAATGCCCTGTTCACTG
106855 A T CAGTGATGTTGGAGAAAGAGAAGTTCATACTGTCTGCTGCTCTTACTATTTTGGATTGGACATTCTCCTCGGAGAGCAATGAGGATGCAGGTTCGACCAC[A/T]GCGAGTTGCAAGGAGCATGTTGTGCTTGCATTGTATGCTCCACAAAATGAAAAGAACTTGCTATTACGTGGGGTACCAGCTCAAAT
106855 T G TGCTGCTCTTACTATTTTGGATTGGACATTCTCCTCGGAGAGCAATGAGGATGCAGGTTCGACCACAGCGAGTTGCAAGGAGCATGTTGTGCTTGCATTG[T/G]ATGCTCCACAAAATGAAAAGAACTTGCTATTACGTGGGGTACCAGCTCAAATCCAATTTACAGTAAGGCACCTGTAGCTGATGTCAA
106855 G C AGAGCAATGAGGATGCAGGTTCGACCACAGCGAGTTGCAAGGAGCATGTTGTGCTTGCATTGTATGCTCCACAAAATGAAAAGAACTTGCTATTACGTGG[G/C]GTACCAGCTCAAATCCAATTTACAGTAAGGCACCTGTAGCTGATGTCAACCGCCCAGATGATGCTATTGAACTTAGAAACATTTCT
106855 A T AGCGTAATAGAGCGAAGACAGCGGAAAAAAGAACCTCTTCCTATTGCTGCTGCTATGTGCGCAATTCCAATTTCCAGTCAGGCACCTGCAGGTGATCTAG[A/T]CCAGCCAGATGATGTTGCTGATCAGAGAAACATTTCTGATTCGGGCAAAAGCTCTTCTGAGTACCACAATACAGCAGAAAATGCAG
106855 C A TATACGGAGCACCATACATCGGTACAAGTAGTCTGCATTTGAAGAACGGTACAAAGTCCGAAATGCAAATTCAAGAAGGCACACTGAGTGAAAAGGCACC[C/A]AATCCTGGTTGGGTTGCACCACCATCTCATCCTCATCTGCCCAATAGATTTCAACCAAAGGCTGCAC
106863 T C GAGCAACTATCACAATTCAAGAGTCGAAAGGTGTTCCTGGAGAGATGACTGTTGAGATTAATGGGACTGCTACACAGGTTCAAATTGCTCAGCAGTTAAT[T/C]CAGAATTACATGGCCCAAGCTGGCGCATCAGCAGGGCAAAACACAACGCCTCCGGACGCTGACCCGTATAGTACATCTTATCCTTC
106863 C T ACTGTTGAGATTAATGGGACTGCTACACAGGTTCAAATTGCTCAGCAGTTAATTCAGAATTACATGGCCCAAGCTGGCGCATCAGCAGGGCAAAACACAA[C/T]GCCTCCGGACGCTGACCCGTATAGTACATCTTATCCTTCATATGCGTCATCGGGGTATCCATCATCAGCATATCCGTCATCTGCATAT
106863 G A AGTTAATTCAGAATTACATGGCCCAAGCTGGCGCATCAGCAGGGCAAAACACAACGCCTCCGGACGCTGACCCGTATAGTACATCTTATCCTTCATATGC[G/A]TCATCGGGGTATCCATCATCAGCATATCCGTCATCTGCATATGGATCAGCTCCTCCAGACCCATATGGTGCGCCTGCTGCCTCTGCTC
106867 T C AGAATGTACTGCCTAAGTGGACTTCTTTGTGCAGTAATTCTGTTGCTGCTCGAGTTCAGCTTACTGGTTGCTATGCTTTGTATCAGGTCCAAGGATTCCC[T/C]CAAGTCTCAGGTACCCAAATGCTATTCAAAACATGCGGCTCTGGAAGTGCAGGAGATGAATTTGAACAGAAAAGGGATACGGCATTT
106867 C A TGTACGTCATGGCACAGTGTGAAAGCGATTTGTCTGCCACTGATTGTGGTCAATGTGTGTCTCAGGCTGTGCAGAAATCTGAAGTGGAATGTGGTGGAGC[C/A]AGCTCAGGACAAGTCTATCTTGATAAATGTTATATTAGCTATAATTATTATCCTAATGGCGTGCCTCACGGGGGCGGTGGAGGTGG
106867 GAGT G GGACAAGTCTATCTTGATAAATGTTATATTAGCTATAATTATTATCCTAATGGCGTGCCTCACGGGGGCGGTGGAGGTGGTCTAGGAGGTGGTGGCTTAG[GAGT/G]AGTAGGAGGAGGAGGAGGACAAACAGGTAAAACAGTGGCCATCGTCGTAGGAGGGGCAGCTGGTGTAGGGTTTCTTGTCA
106867 GA G TCTTTTTGATTGAAAATTGGAATAGTGTGGGATTTCTTGGCTCTTTCCTTCGCCATGTGCTTCTCATCAGTTCAAGATTCTTGTAAGTGGAAGAATGAAG[GA/G]AAAAAAAGTATTTTATTTCCTCAGTTAAGAGAAATTCCCTTATGCCTTAGTTTAATGTACATCTATCTTTTGTAGAGTAGAAAACAGAA
106867 A G CTTTCCTTCGCCATGTGCTTCTCATCAGTTCAAGATTCTTGTAAGTGGAAGAATGAAGGAAAAAAAGTATTTTATTTCCTCAGTTAAGAGAAATTCCCTT[A/G]TGCCTTAGTTTAATGTACATCTATCTTTTGTAGAGTAGAAAACAGAAAGCACAATGGTATTCAATGAATTCTTTTACAAAAAAAAAAAA
106869 C G ACCGACACGATATATCTCAGAATGTTAACATGATCCAAAATCTAAGATAACATAGTAGCAAA[C/G]ACAAAGTTGACATCAGAAACTTAATCGACTTAACAAAACCAACACATCATTTCGAAGAATATGCTAAGTTACAAGGCTATATTCCACAGAAGAGGGAAAA
106869 C T ACCGACACGATATATCTCAGAATGTTAACATGATCCAAAATCTAAGATAACATAGTAGCAAACA[C/T]AAAGTTGACATCAGAAACTTAATCGACTTAACAAAACCAACACATCATTTCGAAGAATATGCTAAGTTACAAGGCTATATTCCACAGAAGAGGGAAAAAA
106869 GA G CAAACACAAAGTTGACATCAGAAACTTAATCGACTTAACAAAACCAACACATCATTTCGAAGAATATGCTAAGTTACAAGGCTATATTCCACAGAAGAGG[GA/G]AAAAAAAATTGGAAGCTAAGAGATGCCTAGTCAAGCTTCAACCATTGGTTCAGGCCCAGATGAGTCTGTAAGGGTAGGACTCAAG
106869 T C ATCGACTTAACAAAACCAACACATCATTTCGAAGAATATGCTAAGTTACAAGGCTATATTCCACAGAAGAGGGAAAAAAAATTGGAAGCTAAGAGATGCC[T/C]AGTCAAGCTTCAACCATTGGTTCAGGCCCAGATGAGTCTGTAAGGGTAGGACTCAAGTTGCTGCTACTAGACTGCCTCACAGAGTT
106869 C T GAAAAAAAATTGGAAGCTAAGAGATGCCTAGTCAAGCTTCAACCATTGGTTCAGGCCCAGATGAGTCTGTAAGGGTAGGACTCAAGTTGCTGCTACTAGA[C/T]TGCCTCACAGAGTTGAAGAGTTTATCTTTAATTACCTGTGACATGAGACCATGGACCTGCTCTACTGTTATCTTTGAGCTATCACGG
106869 CT C AAGAGTTTATCTTTAATTACCTGTGACATGAGACCATGGACCTGCTCTACTGTTATCTTTGAGCTATCACGGGTTATCTTTGCCAACGGTGATTCCTCCT[CT/C]TTTTTTCCGTTGTGATGGTGTTATGAAAGAGCCAAAACGTGTATGAGTTAACTGATTCTCTGCCTGCTCCAACTTCTCAGCCAAATCAG
106869 G A ACATGAGACCATGGACCTGCTCTACTGTTATCTTTGAGCTATCACGGGTTATCTTTGCCAACGGTGATTCCTCCTCTTTTTTCCGTTGTGATGGTGTTAT[G/A]AAAGAGCCAAAACGTGTATGAGTTAACTGATTCTCTGCCTGCTCCAACTTCTCAGCCAAATCAGATATCTGTCCTGCAACATACTCCCGG
106869 C T AAGCGAAAGCGTCCATAACAATAATCGCATTCCCTTCCGTTTTTCCTTGCATCAGACCCATAATTTCGATATTACCACCCGATCGGGCGTGCACGACCAT[C/T]TTCAGCAAAGCGAGGGCGGAGATTTTGACGCGTTTGAAAAAATTCGGATCTTGTGTCCATGGCTTTTCATTGTTTATCTTCGTCTGCAA
106869 A G TTTTTCCTTGCATCAGACCCATAATTTCGATATTACCACCCGATCGGGCGTGCACGACCATCTTCAGCAAAGCGAGGGCGGAGATTTTGACGCGTTTGAA[A/G]AAATTCGGATCTTGTGTCCATGGCTTTTCATTGTTTATCTTCGTCTGCAACACCGGATCATAGTAGTAGATTAAATCGGAAGAGGACG
106871 TA T TCTTTTGCAGCCAAACCAATATACTGTGGGCCCATAAAAATGAGCAAAGAAATGTTGATGTTGACTTACAAGTTCTGGCTTGAGATTGCCATAACACTAA[TA/T]AAAATTAAGATGAAAATTTGGATATGAGTTTATCGACATGAATGATTATATCATCGATGTGAGGCCGGACTGCAGGCTGGGACTGT
106871 T C CTCTTCTCTTACAAGTGCCAATTGTTCCTCGCTTTGAATTATAACTTTCTTCATAGCGTATGTTCCATCATCTGAAACGTGAGAAGGATTCTTGATTTTA[T/C]TTCCAGCTAAACCGCCATTAGAAGTAGAGCTATCAGAAATGATTTCTTTAACAAGATAAACGAATGCGAAACCTCCTTCGCCTAATTGTTT
106879 A AT CTGCCTACTTGCTGTTCATTATCAGCTGAATCAGATGCCATCTACAACTCTGATTCCAGCCTTGCGGTCCCATTCATCAGGAGATGGAGCATCATCCATT[A/AT]TTTTTCTTGACCACGCCAAAGAATCTTGTCAATGACTCCGAACTCCTGAGCTCTCATGGAGTCCATATAAAATGGCCTTCGCATCACTT
106879 AT A TTGAAGAGAGCTTCGACAAAAACGGATCTTTAGGGTTTAACGGCGGCATCGGAATTGTCGCGGCCGATTTTGCTCGCATACAGTTCAAAATTGGCGATTT[AT/A]TTCTTTGAAAAATTTGATGAAGAGGATGAAGCTGGGAATTTTGGGGATAGGGATTGAATACTAAAGCTAGTTAACGCCATTTTTTG
106883 AT A GGTGGATCAGTCTCGAGGTCGGTTGCTGATTGTTTATGGCGATGCGCTTTGGTCGCAATACTCGGCCGTAGGGGCGTATCGGTTGGATTCCTGGGAGAGG[AT/A]TTTTTTTGACACGGTTGAGTGGACCAGATGACGAACCATCGTTTGCTGATGACGTAGCACTCGACCCTGAAGGCAATGCATACG
106883 C CTAAATGAAACTGTTAAGGACGGTAAAGTTTATGTCAATCATCTTTTTGGGTGGGGAATTGAGAAGCAGACTCATGTTCTTGCTGAGGCTATGTTTGCATCTGTGAACT[C/CTAAATGAA]GAGTTGGGTTTTGTGAAAGCTGTTCTAACGGTTATACCTCCGTTTAGACAGGAATATTGTCTTCTTTTGTATCATGAGTTG
106883 G T GTTAAGGACGGTAAAGTTTATGTCAATCATCTTTTTGGGTGGGGAATTGAGAAGCAGACTCATGTTCTTGCTGAGGCTATGTTTGCATCTGTGAACTCGA[G/T]TTGGGTTTTGTGAAAGCTGTTCTAACGGTTATACCTCCGTTTAGACAGGAATATTGTCTTCTTTTGTATCATGAGTTGTAATGACTAAT
106883 G A TTTATGTCAATCATCTTTTTGGGTGGGGAATTGAGAAGCAGACTCATGTTCTTGCTGAGGCTATGTTTGCATCTGTGAACTCGAGTTGGGTTTTGTGAAA[G/A]CTGTTCTAACGGTTATACCTCCGTTTAGACAGGAATATTGTCTTCTTTTGTATCATGAGTTGTAATGACTAATGAGTGATATTTGCTAT
106885 A G CAAGTCACCACCACCTTTCTCCTAAGCAATCAATGGCGGCCACCTCCTACAACCGCCGCCTTATCAACAAAGCGCCGCCGCCCACACCGATCGCCACGGC[A/G]AAAGGCATCCGCAACGCTGCCTTTAATGACGAAATCCTATCCCGGTACCTGGAATCTTCCCTCAGAATCCCAAGCCTCACTCTTCCCA
106885 A T CGGCAAAAGGCATCCGCAACGCTGCCTTTAATGACGAAATCCTATCCCGGTACCTGGAATCTTCCCTCAGAATCCCAAGCCTCACTCTTCCCATAAAAAA[A/T]TCTATATCTCCAGCTGAAATTAGATTCGAAAGCCTGATTAGTGGCGATTACGATGGGCTCATGGAGAGATTTATGGAGAGTGGAGTG
106885 T C TGGAGAGATTTATGGAGAGTGGAGTGTTTGGGATAGAGGGAGATGAGAGCGCTGAGATCGGAAGAGAGTTGTTTCAGGAGAAAGAAGAAGACGTTTCGAG[T/C]TTGGGTAGAGAAGGAGTCAGATTAGAAGCTTATCGGGTTCAGATCTTTAGGGAAAAGGTAAAAAAGTTACAGAGAAACTTGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106885 T G GATTTATGGAGAGTGGAGTGTTTGGGATAGAGGGAGATGAGAGCGCTGAGATCGGAAGAGAGTTGTTTCAGGAGAAAGAAGAAGACGTTTCGAGTTTGGG[T/G]AGAGAAGGAGTCAGATTAGAAGCTTATCGGGTTCAGATCTTTAGGGAAAAGGTAAAAAAGTTACAGAGAAACTTGAAATTGT
106885 G A TCGGGTTCAGATCTTTAGGGAAAAGGTAAAAAAGTTACAGAGAAACTTGAAATTGTTGCTGAATCCATTTCCAAACTACTTTCTCAACATGTTGGAAATA[G/A]AACCCTGGGGAAGAGTTTTCACAAGATGCAGCTATCTATAATATATAGGAGGAATGGAGAGCCAATAATTTTCTCAGATCCTCATGC
106885 A G CTTTCTTTCTTGAGTTCATGTACACTTTCACGGATCTAAACTGCATATCTAATCATAGTTTTCCAGAACCTGACTCGATCGGTGCAACTGATCTTAGTTT[A/G]TCCAGAACTCTTTCAGTAATGGATCAGCTATCAATCATGCTCATTCTCATATTCTTCTATTATTTACTGAGCTAAATTCATTCATATACGTTG
106885 A G CAGAACTCTTTCAGTAATGGATCAGCTATCAATCATGCTCATTCTCATATTCTTCTATTATTTACTGAGCTAAATTCATTCATATACGTTGTGCGAGCCC[A/G]TCAAAATTTCATAAGCACGACAGGCACATGCCATGCGGATTGGTTTGTGTTTCTTCTCAAGTTGACATTGAGACATGATTGTGGAGTAAT
106885 A G ATCAGCTATCAATCATGCTCATTCTCATATTCTTCTATTATTTACTGAGCTAAATTCATTCATATACGTTGTGCGAGCCCATCAAAATTTCATAAGCACG[A/G]CAGGCACATGCCATGCGGATTGGTTTGTGTTTCTTCTCAAGTTGACATTGAGACATGATTGTGGAGTAATATTTTTTCAGTTTTGCAACCA
106885 A G AAATTCATTCATATACGTTGTGCGAGCCCATCAAAATTTCATAAGCACGACAGGCACATGCCATGCGGATTGGTTTGTGTTTCTTCTCAAGTTGACATTG[A/G]GACATGATTGTGGAGTAATATTTTTTCAGTTTTGCAACCACTTTTTGATTGCTGCAAAGCTCAAGAGCTGTATACATGGATGAATATAC
106885 A T TTCATAAGCACGACAGGCACATGCCATGCGGATTGGTTTGTGTTTCTTCTCAAGTTGACATTGAGACATGATTGTGGAGTAATATTTTTTCAGTTTTGCA[A/T]CCACTTTTTGATTGCTGCAAAGCTCAAGAGCTGTATACATGGATGAATATACGTCAAGTTCGATCATACGGAGGATTGGATTTGAGGA
106885 C A CCATGCGGATTGGTTTGTGTTTCTTCTCAAGTTGACATTGAGACATGATTGTGGAGTAATATTTTTTCAGTTTTGCAACCACTTTTTGATTGCTGCAAAG[C/A]TCAAGAGCTGTATACATGGATGAATATACGTCAAGTTCGATCATACGGAGGATTGGATTTGAGGAGTGTGATATTGAGATAAGAAACT
106885 C T TGTGTTTCTTCTCAAGTTGACATTGAGACATGATTGTGGAGTAATATTTTTTCAGTTTTGCAACCACTTTTTGATTGCTGCAAAGCTCAAGAGCTGTATA[C/T]ATGGATGAATATACGTCAAGTTCGATCATACGGAGGATTGGATTTGAGGAGTGTGATATTGAGATAAGAAACTGGTTTGAGTTTGTTTT
106895 G A AAGTATATATACCAGAAATTAATTGGAGTCTCATGATACTTTGCATTGCTGTTATTGCTGGATTCAAAAATCAAGTTCAGATTGGAAATGCTTACGGAAC[G/A]GCAGTGATGATAGTAATGCTAGTGACGACACTACTAATGATCCCAATAATGCTACTTGTTTGGCGCACCCATTGGACCTTGGTGTCTG
106895 T C GATCTCAGCTGCGTTCCTCTTGGTCATGTACACATGGCACTATGGCACGAAGAAGCGGTACGAGTTCGAGCTCCACAGTCGGGTATCCATGGCCTGGATC[T/C]TGAGCCTCGGACCAAGCCTTGGCCTAGTCCGCGTCCCAGGTGTCGGTCTCGTGTACACTGAGCTCGCCAACGGCGTTCCCCACATC
106895 A T CGTTCCTCTTGGTCATGTACACATGGCACTATGGCACGAAGAAGCGGTACGAGTTCGAGCTCCACAGTCGGGTATCCATGGCCTGGATCTTGAGCCTCGG[A/T]CCAAGCCTTGGCCTAGTCCGCGTCCCAGGTGTCGGTCTCGTGTACACTGAGCTCGCCAACGGCGTTCCCCACATCTTTTCCCACCTC
106895 C T ACAGTCGGGTATCCATGGCCTGGATCTTGAGCCTCGGACCAAGCCTTGGCCTAGTCCGCGTCCCAGGTGTCGGTCTCGTGTACACTGAGCTCGCCAACGG[C/T]GTTCCCCACATCTTTTCCCACCTCGTTACCAACCTCCCTGCCATCCACTCTATTGTCGTCTTCGTCTGCGTCAAGTACCTTCCCGTTCC
106895 T C TCCGCGTCCCAGGTGTCGGTCTCGTGTACACTGAGCTCGCCAACGGCGTTCCCCACATCTTTTCCCACCTCGTTACCAACCTCCCTGCCATCCACTCTAT[T/C]GTCGTCTTCGTCTGCGTCAAGTACCTTCCCGTTCCCACTGTGCCGGTTGAAGAGCGGACGCTCGTTAAAAGGATCGGGCCTAGAACGTT
106895 C T TCGATAGCCTTTTAGATTTCATCACCATGGAGTCCTTCCTTGGGAAGATGTCGGGTTCGGAATACAGCTTTGAATCGTTGGATTTGGAGGTTGATGAAGG[C/T]GAGCTTAGCGACAATGAGGTGATCAGTAGGAGGAGGAGTTACACGGCGAGGAGAAAAGGCGGTGAGGATGAAGAGGTGGAGTT
106895 A G AGATTTCATCACCATGGAGTCCTTCCTTGGGAAGATGTCGGGTTCGGAATACAGCTTTGAATCGTTGGATTTGGAGGTTGATGAAGGCGAGCTTAGCGAC[A/G]ATGAGGTGATCAGTAGGAGGAGGAGTTACACGGCGAGGAGAAAAGGCGGTGAGGATGAAGAGGTGGAGTTCCTGAACAAGTCA
106895 G C TCCTTCCTTGGGAAGATGTCGGGTTCGGAATACAGCTTTGAATCGTTGGATTTGGAGGTTGATGAAGGCGAGCTTAGCGACAATGAGGTGATCAGTAGGA[G/C]GAGGAGTTACACGGCGAGGAGAAAAGGCGGTGAGGATGAAGAGGTGGAGTTCCTGAACAAGTCAAAGGAGGCGGGTGTGGTG
106895 C T AATACAGCTTTGAATCGTTGGATTTGGAGGTTGATGAAGGCGAGCTTAGCGACAATGAGGTGATCAGTAGGAGGAGGAGTTACACGGCGAGGAGAAAAGG[C/T]GGTGAGGATGAAGAGGTGGAGTTCCTGAACAAGTCAAAGGAGGCGGGTGTGGTGCATATATTGGGGAACACGGACATCCGA
106895 A G AAGGCGAGCTTAGCGACAATGAGGTGATCAGTAGGAGGAGGAGTTACACGGCGAGGAGAAAAGGCGGTGAGGATGAAGAGGTGGAGTTCCTGAACAAGTC[A/G]AAGGAGGCGGGTGTGGTGCATATATTGGGGAACACGGACATCCGAGCGCAAAAGGGGTCGAGTTTATTGAAGAAGATTGC
106895 G A CGGCGAGGAGAAAAGGCGGTGAGGATGAAGAGGTGGAGTTCCTGAACAAGTCAAAGGAGGCGGGTGTGGTGCATATATTGGGGAACACGGACATCCGAGC[G/A]CAAAAGGGGTCGAGTTTATTGAAGAAGATTGCAATAGACTATGTGTATGCTTTGCTCAGGAAGATGTGCAGGGAAAATAGCG
106897 GC G GCATGGTTGGGTCGCCTCGCTCTCGAGCCTCGTTGAACATAGCCTGAGCTCTTTCGAGGGAGTCATCCACCGTGTCTTCTATGTAATAACCTTTGCCTCC[GC/G]CCTCCCCAAATGCTGTCTTTCTTCTCTCCATCGGTAGCTCGTGTTATAGGCAACCTTGTGTCAGCGAACTCCAACTCGGATAAAGGAG
106897 G T CGGTTGGATCTATTGATACTGGGATGCTGTGCTCGACAGTTTGGTTGCTTTGTTCGTCTATGGTATTGGATTTTGCACGTTCATCGACATTACCTTCCTT[G/T]GAGTTATGGGGATGAACGGCTGAGTCCGCAGACTTGGATGAAACATGTGCTACCAGAGGACGGCAGGTGATGGGAAGATTGAGAAT
106899 C T ACCTGGATGCTGCCATTATAAGAGCTTCTTTACTGACATCAAGATCACCAGAAATCTGAACCATTTCATCATCTTCAGAAGCTACTTTCGGAAGATGCTC[C/T]TTCGAAAGGATACGAATATTAGCCCGTGTGGCCCTCCTCATCTCTGATATTATGCTCCCGGCTTTACCGATAAGGCAACCAATTCGGGA
106899 G A TCATCTCTGATATTATGCTCCCGGCTTTACCGATAAGGCAACCAATTCGGGATGTTGGAACAAGCAGTCGCGTCATATACAATTCACCCGCCTCTTTGTC[G/A]GTTCTTTCACTGCACTTCGGCTGCAAGCGAACAGCAGCATCTATGCATTTTGAGATGGGATCTTCAAGATGCTCATTTGCAGAAATTGT
106903 A G TTCCAAATATTCAGAATTTCAACCGATGGTGCTGTTCCTATTATACCAGGATGAGTTAAGCCGGGAAACCGTACACCTGGTATATGAGGAGAATATGCAT[A/G]TATTCCTTCAAAATACCAAATAGCTTTGGTTGCAGATGGAAAATGATCAGTTAAAAATCCACCACCATTTTCTCTGTCAAAAGTTCCAG
106905 G A TCTCCTCGAGTATCACCTCATCCCTTTCTGGTTCATTAGATGTTCTGGTGCGGGTAATCCTAGCAATTTGAGGATTGCCATCAAACCGTTTCCTCCCATC[G/A]GTCGGCATGCCTACATATCTGTAAGAGTATGTGAAACGGAGAACTTCCTGGACCTGCTGAGCCGTAACAGAAGACAGAATCAGGTTAA
106905 T C CATCCCTTTCTGGTTCATTAGATGTTCTGGTGCGGGTAATCCTAGCAATTTGAGGATTGCCATCAAACCGTTTCCTCCCATCGGTCGGCATGCCTACATA[T/C]CTGTAAGAGTATGTGAAACGGAGAACTTCCTGGACCTGCTGAGCCGTAACAGAAGACAGAATCAGGTTAACCATGACCTTGCGGAGT
106905 C T ATGACACTGTCACTGAGCCGGTAGCACCGTCAATGGATTGCGGATAGTTACCGGCCAACACAGTTTCGACCGTCGCTTCAAGTGGTGTGATGGTCAGCAT[C/T]AGATCCCGAACAACCACAGTTACTAGTCCAGCCAAGCACTGCGAAAATGCAACGCTTATGTCTTCTATGCTCTTAACTTCTGAAAAC
106905 A G TGAGCCGGTAGCACCGTCAATGGATTGCGGATAGTTACCGGCCAACACAGTTTCGACCGTCGCTTCAAGTGGTGTGATGGTCAGCATCAGATCCCGAACA[A/G]CCACAGTTACTAGTCCAGCCAAGCACTGCGAAAATGCAACGCTTATGTCTTCTATGCTCTTAACTTCTGAAAACGTGCCTCCCTTGC
106905 C T GATAGTTACCGGCCAACACAGTTTCGACCGTCGCTTCAAGTGGTGTGATGGTCAGCATCAGATCCCGAACAACCACAGTTACTAGTCCAGCCAAGCACTG[C/T]GAAAATGCAACGCTTATGTCTTCTATGCTCTTAACTTCTGAAAACGTGCCTCCCTTGCTAGCGTCTGCTATTGCCCTTAGAATTGATG
106905 A G CGAAAATGCAACGCTTATGTCTTCTATGCTCTTAACTTCTGAAAACGTGCCTCCCTTGCTAGCGTCTGCTATTGCCCTTAGAATTGATGGATCGTGATCC[A/G]AGCCAAAACCAAAAGTGTAAACAGGCACGTCACTGATGGGAAGCAAAGAAGCGTCAGCTCCATCGCAGTAACCGTCTGACATAAGCA
106907 G A CACCCACTTCAACCTGTTCATCGTGCTATCGCATTCAAACTCGATCAATCCATGCCCTGTTATAAGCCCAAAGCAACGTTGATCTTCATCAGCACCTCTC[G/A]CCCCTCTTTCATCCACTCCATGAACAACGCTCTTTTTCTTCTTCGAAAGAGCTCCACCTATGTGCTTGCTTTTGATCTTCACCATCACCTGA
106907 C G CCACTCCATGAACAACGCTCTTTTTCTTCTTCGAAAGAGCTCCACCTATGTGCTTGCTTTTGATCTTCACCATCACCTGAGACCTCCTATTGATATAAAC[C/G]GACACTCTTTTCCAGTGCAGGCTTCCTTTCCTCGATCTATGCAAGAGCTCGCCTTCCTTGCAACAAACATCCAAACCTCTCCCATTGCCTTT
106907 C T ACCTCCTATTGATATAAACCGACACTCTTTTCCAGTGCAGGCTTCCTTTCCTCGATCTATGCAAGAGCTCGCCTTCCTTGCAACAAACATCCAAACCTCT[C/T]CCATTGCCTTTGTCATAAGGTATCACTGCAGCAGCATTGCTCCTCGCCTCCCTTTGCAGTCTCATCTTCATAGTCGCAGCACCCCTCAACG
106907 T A TCGCCTCCCTTTGCAGTCTCATCTTCATAGTCGCAGCACCCCTCAACGCGGTCGCTGCAGCTGCAGTGAGCGTCATCAGATCTCCAGGCGTTTTTATATC[T/A]ACAGCGGATCGAACAGCAGAAGCAACACGTTCCCGATCGGCTCCGGTTTGTTCGGCTATCTCTATGCAGTGGGATGCCAGAAGCCCA
106907 C G CAGCACCCCTCAACGCGGTCGCTGCAGCTGCAGTGAGCGTCATCAGATCTCCAGGCGTTTTTATATCTACAGCGGATCGAACAGCAGAAGCAACACGTTC[C/G]CGATCGGCTCCGGTTTGTTCGGCTATCTCTATGCAGTGGGATGCCAGAAGCCCAGTAGCAGAAGCAAGCGCTTCCATCATCGTCGG
106907 G T CCCTCAACGCGGTCGCTGCAGCTGCAGTGAGCGTCATCAGATCTCCAGGCGTTTTTATATCTACAGCGGATCGAACAGCAGAAGCAACACGTTCCCGATC[G/T]GCTCCGGTTTGTTCGGCTATCTCTATGCAGTGGGATGCCAGAAGCCCAGTAGCAGAAGCAAGCGCTTCCATCATCGTCGGCTTATA
106907 A C TTATATCTACAGCGGATCGAACAGCAGAAGCAACACGTTCCCGATCGGCTCCGGTTTGTTCGGCTATCTCTATGCAGTGGGATGCCAGAAGCCCAGTAGC[A/C]GAAGCAAGCGCTTCCATCATCGTCGGCTTATAAGCCGTAATTTGGTCTCTGGAAGTTCTTATGCTTGCAGCTACAGAAGCAACGGCA
106915 A G TCAGTCCTCAAGCTTCGTACAAAGTAGCTGTACTAGGAGCAGCTGGTGGAATAGGTCAGCCCCTCTCCCTCCTAATCAAAATGTCTCCCCTTGTCTCTGC[A/G]TTACACCTGTACGATATCGCAAATGTCAAAGGAGTGGCAGCTGACCTCAGCCATTGCAATACTCCTTCGAAAGTCTTTGATTTCACTGG
106915 T C CCCTTGTCTCTGCATTACACCTGTACGATATCGCAAATGTCAAAGGAGTGGCAGCTGACCTCAGCCATTGCAATACTCCTTCGAAAGTCTTTGATTTCAC[T/C]GGGCCTTCCGAGCTAGCCAATTGCTTAAAAGGAGTTGATGTTGTAGTCATTCCAGCTGGTGTTCCAAGAAAGCCGGGCATGACCCGTG
106915 G A AAGGAGTTGATGTTGTAGTCATTCCAGCTGGTGTTCCAAGAAAGCCGGGCATGACCCGTGATGACTTATTCAATATCAATGCCAGTATAGTCAAATCGTT[G/A]GTTGAAGCGGTTGCCGAGAATGCCCCTGATGCCTTTATCCAGATCATCAGCAACCCAGTCAATTCCACTGTCCCTATTGCTGCAGAG
106915 C T TATTCAATATCAATGCCAGTATAGTCAAATCGTTGGTTGAAGCGGTTGCCGAGAATGCCCCTGATGCCTTTATCCAGATCATCAGCAACCCAGTCAATTC[C/T]ACTGTCCCTATTGCTGCAGAGGTTCTTAAACAGAAGGGCGTTTACGACCCTAAGAAGCTTTTTGGTGTCACCACGCTTGATGTCGTGA
106915 C T ATATCAATGCCAGTATAGTCAAATCGTTGGTTGAAGCGGTTGCCGAGAATGCCCCTGATGCCTTTATCCAGATCATCAGCAACCCAGTCAATTCCACTGT[C/T]CCTATTGCTGCAGAGGTTCTTAAACAGAAGGGCGTTTACGACCCTAAGAAGCTTTTTGGTGTCACCACGCTTGATGTCGTGAGGGCCA
106915 G A AGCGGTTGCCGAGAATGCCCCTGATGCCTTTATCCAGATCATCAGCAACCCAGTCAATTCCACTGTCCCTATTGCTGCAGAGGTTCTTAAACAGAAGGGC[G/A]TTTACGACCCTAAGAAGCTTTTTGGTGTCACCACGCTTGATGTCGTGAGGGCCAACACCTTTGTGGCTGAGAAAAAGAATCTGAATC
106915 T C ATGCCTTTATCCAGATCATCAGCAACCCAGTCAATTCCACTGTCCCTATTGCTGCAGAGGTTCTTAAACAGAAGGGCGTTTACGACCCTAAGAAGCTTTT[T/C]GGTGTCACCACGCTTGATGTCGTGAGGGCCAACACCTTTGTGGCTGAGAAAAAGAATCTGAATCTTATTGACGTGGATGTCCCTGTCA
106915 C T TCCAGATCATCAGCAACCCAGTCAATTCCACTGTCCCTATTGCTGCAGAGGTTCTTAAACAGAAGGGCGTTTACGACCCTAAGAAGCTTTTTGGTGTCAC[C/T]ACGCTTGATGTCGTGAGGGCCAACACCTTTGTGGCTGAGAAAAAGAATCTGAATCTTATTGACGTGGATGTCCCTGTCATTGGTGGA
106915 G A CTGTGAGGATTCAGAATGCTGGGACTGAGGTTGTGGAAGCGAAAGCCGGAGCTGGCTCTGCAACTCTTTCTATGGCTTATGCTGCTGCCAGATTTGTGGA[G/A]TCTTCTCTCAGAGCGCTGGATGGAGATAGCGATGTGTATGAATGTGCTTATGTTCAGTCTGATTTGACTGATTTGCCCTTCTTTGCT
106915 T C CTATGGCTTATGCTGCTGCCAGATTTGTGGAGTCTTCTCTCAGAGCGCTGGATGGAGATAGCGATGTGTATGAATGTGCTTATGTTCAGTCTGATTTGAC[T/C]GATTTGCCCTTCTTTGCTTCTAGAGTTAAACTGGGTAAGAAGGGCGTTGAAGCTGTAATTGGTAAAGATCTTCAAGGGATTACTGAC
106915 A C TGGAAGCTTTGAAGGCAGAACTGAAGGGAAGCATTGAGAAGGGTGTTGGGTTTGTTCAGAAGCAGGCAGTAGCTTCTGCAAACTAAGTTGATAAGTTTTT[A/C]TCTACTCCTGTATTTTGATAGCTATACATGAATAAAGTTGGACTTTGCCGGTTCTGCAGTGTAGAAGATAACATATCATTATTTACT
106915 C G GTTTGTTCAGAAGCAGGCAGTAGCTTCTGCAAACTAAGTTGATAAGTTTTTATCTACTCCTGTATTTTGATAGCTATACATGAATAAAGTTGGACTTTGC[C/G]GGTTCTGCAGTGTAGAAGATAACATATCATTATTTACTCTACTAGATAGAGGCATAAAGCTGCGAAGGAAATGTATCAGTTAGTAGAG
106917 T C ACCTAAACCAAAAAGGCTACTATATCTCGCACCAGGAACCAATCCTAGGCGTGGAAGGCCAAGTATTCCGAACTTCATTGCACCATATTTGTACAATACC[T/C]TGATCTCATCTACGTACTTGTCAATAAGACTAGCAATGAACCGTTTATTCTCTGTGGCATTTCGAGCTCCTTTAGTGTCACGGTAGTGT
106917 A G CTACGTACTTGTCAATAAGACTAGCAATGAACCGTTTATTCTCTGTGGCATTTCGAGCTCCTTTAGTGTCACGGTAGTGTGAGAACAAATCATTGCTACC[A/G]GCACTGATGAGAATTAAAGATTTTTTGATCAGTTCTGCCGTATATCCCTTGCCCACTTCTTTTTCCAGCACACGGATAGCAGTCACAAA
106927 T C GATCAAATACAGATACAACATTACAACTAGGCAGCAGGAGAGGGAAGGACGGAGCAAGTCTTGGATCCAAAATCCGGATTCTCTGACATCAAATATTCTG[T/C]AACTGCGAGAAAGAAATCCGAATAACGGAGTCGTCAAGAGCGGTCACATGCTTGCAAACAAGGGCCTCGGTCGCCTGCTCCTCAT
106927 G A CTTCCTGCATTTCTATTAGTGCATGGTCAGGTTTGTTCCGAAGTATTTTGATTCTTACAATGTTCCCGTAGAGAGAACACAAATTGAAGATCTTGTCTAC[G/A]TCAATTCTCTCTGGATCCAAATTAGATATAAGAATAGTGCATGCGGTATTTGTACCGGTAATGCCAGGAGGTAGAGCTCCACCAAAAGC
106931 A G CAAATTAGAAACCTTGAGGAAGAAAGGAAAAAAGTCCAAGTCTTTGAACGCGATCTTCCTTTTTGCAAATTTCTTCTCAACGAGGCTATTAGAGGAATGA[A/G]GATCGAACTCGAGAAATGGAGAAGAAAAAATGTTAATGCGTTGGAAGAATCCATGCCTGCAAAAAGCAGCAAATCAGAAGAGGAA
106931 A G GGTTATACGCCAGAAGAGAATCAAGCGCTAGAAGTGAAGTAAATAAAGTAAATAACGGCGTCATGTTAATGGGAGGATTACTGGTCAAGAACCAACAAGT[A/G]TTTAGTAAAATGCAGCAAACTGAATCACCTCAAGGACCATTTCAGTTGACCTCTTCTTCTCGTGTAATGACTTCTGTTACTAACAGC
106931 T C ACGCCAGAAGAGAATCAAGCGCTAGAAGTGAAGTAAATAAAGTAAATAACGGCGTCATGTTAATGGGAGGATTACTGGTCAAGAACCAACAAGTATTTAG[T/C]AAAATGCAGCAAACTGAATCACCTCAAGGACCATTTCAGTTGACCTCTTCTTCTCGTGTAATGACTTCTGTTACTAACAGCGATAGC
106931 T A CGGCGTCATGTTAATGGGAGGATTACTGGTCAAGAACCAACAAGTATTTAGTAAAATGCAGCAAACTGAATCACCTCAAGGACCATTTCAGTTGACCTCT[T/A]CTTCTCGTGTAATGACTTCTGTTACTAACAGCGATAGCTGTGACGACGATCGAAAGTCTGAAAGTTGTAGCTGGAATTGACTTTTTAC
106931 A G AAATGCAGCAAACTGAATCACCTCAAGGACCATTTCAGTTGACCTCTTCTTCTCGTGTAATGACTTCTGTTACTAACAGCGATAGCTGTGACGACGATCG[A/G]AAGTCTGAAAGTTGTAGCTGGAATTGACTTTTTACATTTTAAGCTGAACTTGTAAGCATTCATAGACTTAGGTGAGTTCGAAATTGGT
106933 A G GATGAGCTTCAAATGGAGGATTGTAAGAACAACCAGGTGGGTCCACTTCAACTGCAGGAATGGATGATTTAGGCATCTTCCTCGCTTGCACATTTGCTTC[A/G]TCTTCATTATTCCACAAGTCAAACACATCAGATTTCTTCTCTTCTTTGATTGTTTTCTGTGATTCTACATCCATATCTGATTTGGATTTTT
106933 G T TTGCAGCACACTCTCATGATACAGAACTTTCTCTCTATGTTTTTCTATCTTGCGCTTAATAGGTATATCAGTTGATTTGTCAATGAAGAAGAGTGAATCC[G/T]TTAGGATCTCATTCAGATTATTGGCTCCAGCAAGCGTATCTTTGGTCGTTTTCTCGACAAATGCATCAAAATCGTCGGTTTTGATATTTGC
106933 T A GCAGCACACTCTCATGATACAGAACTTTCTCTCTATGTTTTTCTATCTTGCGCTTAATAGGTATATCAGTTGATTTGTCAATGAAGAAGAGTGAATCCGT[T/A]AGGATCTCATTCAGATTATTGGCTCCAGCAAGCGTATCTTTGGTCGTTTTCTCGACAAATGCATCAAAATCGTCGGTTTTGATATTTGCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
106933 A G CAGCACACTCTCATGATACAGAACTTTCTCTCTATGTTTTTCTATCTTGCGCTTAATAGGTATATCAGTTGATTTGTCAATGAAGAAGAGTGAATCCGTT[A/G]GGATCTCATTCAGATTATTGGCTCCAGCAAGCGTATCTTTGGTCGTTTTCTCGACAAATGCATCAAAATCGTCGGTTTTGATATTTGCTC
106937 GA G TTTGGAGGCAGTGGAAGACTTTGAACAGGGAGCACTAATAAAAACGGAGACTAAAGCTAGGAAAAATGGCAATGTGGGAAGTGGGAAAGGTGGAAAAGGG[GA/G]AAAAAATGGTGGACGGTAAGAAATGGGGGAGATGAATGATGAAGATGCAAAAGGAAGAAAGGACGCGGAAGGGACGTT
106937 G A AGGGAGCACTAATAAAAACGGAGACTAAAGCTAGGAAAAATGGCAATGTGGGAAGTGGGAAAGGTGGAAAAGGGGAAAAAATGGTGGACGGTAAGAAATG[G/A]GGGAGATGAATGATGAAGATGCAAAAGGAAGAAAGGACGCGGAAGGGACGTTGCCAATTTTAAGATCTACATTTTGCTCAG
106937 C A TGGGAAAGGTGGAAAAGGGGAAAAAATGGTGGACGGTAAGAAATGGGGGAGATGAATGATGAAGATGCAAAAGGAAGAAAGGACGCGGAAGGGACGTTGC[C/A]AATTTTAAGATCTACATTTTGCTCAGAAGTTTTGGGATTGATTTTGATTTCCAGTAGGCCAA
106941 CT C GATCACGGATTATCTCATGCTGGACAACTTCACCATACTTGGAAAAGAAATTCTTGAGATCGTCTTCGGTTACATCAGCTGGTATCCCACCAACAAAGAT[CT/C]TTTTTTGTCTTAAAATCTTTATTGCTTTGAGCAGCACCCTTTGGAATGGTTCTTTTAATTTCAACTGTTTTCCCGTTGATAACGTGAGTG
106943 G GA TGATTCACCTGGGCTGGCTATGGCACGTGCATTTGGAGATTTCTGCATCAAGGATTTTGGATTGATTTCGGTTCCTGAAATATCCTACAGGCGCCTCAGT[G/GA]AAAAAGATGAGTTCATTGTGTTGGCTACAGATGGGATATGGGATGTACTTTCAAATGAGGAAGTAGTGGAAATTGTTGCATCATCA
106943 G C ATTGATTTCGGTTCCTGAAATATCCTACAGGCGCCTCAGTGAAAAAGATGAGTTCATTGTGTTGGCTACAGATGGGATATGGGATGTACTTTCAAATGAG[G/C]AAGTAGTGGAAATTGTTGCATCATCATCAAGTCGATCATCATCAGCTCCCACTCTTGTTGAGGCAGCAGTGCATGCATGGCGGCATA
106943 C T TGAGTTCATTGTGTTGGCTACAGATGGGATATGGGATGTACTTTCAAATGAGGAAGTAGTGGAAATTGTTGCATCATCATCAAGTCGATCATCATCAGCT[C/T]CCACTCTTGTTGAGGCAGCAGTGCATGCATGGCGGCATAAGTATCCTACCTCCAAAGTCGACGACTGTGCTGCAGTGTGTCTCTACC
106951 T TG TTGAATCTCATGTTAATACTAAGCGCCAATTCAGTGGATTTTTGGATGTTTACAAGAAAACTTTGAACAGCGATGGTTTTGTAGGCCTTTATAGAGGATT[T/TG]GGGGTTTCCATAATGGGCATCACATTGTATCGAGGTCTCTATTTTGGCATTTATGACACATTGAAGCCAGTCGTTCTAGTTGGACCAT
106951 T C ATGACACATTGAAGCCAGTCGTTCTAGTTGGACCATTTGAGGGTAACTTCATAGCCAGTTTTGCCTTGGGTTGGAGTGTGACGACGGCATCGAGCATCTG[T/C]GTATACCCTTTCGACACACTGCGTAGAAGAATGATGTTGACTTCAGGAGAGTCTTCTAAGTACCGAAACGCGATACAGGCTTTGAAA
106953 A G CGCTCCCATTCACAAGAATTGGGCTCCTAGGCTTTGATGGCATGTTCAAAGAATATTTCATCCAACTATCACCTCCACTGTTCGGGCAATATTGCAAAGC[A/G]GCAAGCTCTGTAAGAACAATAACAGATCCAGTAGGAGACACCAAAACAGTGCCGTGGCGAGACCATGCAGATCCGAGCTGAGGCAG
106953 T A TATCACCTCCACTGTTCGGGCAATATTGCAAAGCAGCAAGCTCTGTAAGAACAATAACAGATCCAGTAGGAGACACCAAAACAGTGCCGTGGCGAGACCA[T/A]GCAGATCCGAGCTGAGGCAGCAGCTTAAACTTCTTGGTAACCGGGTTGCATACAATCAAAGACTTCGGGTTCTTCAAATTAGGGTT
106955 A G AGGACATCCTAGAAACGCTAGCCCGTTGCAGCAGCGCCGGCAAAAAGATATCCCCATTGTCGGATCCAGATCAGAATCTAGACCCGTTCCTCCCGCCCGA[A/G]TCCATCACCATCCCTTTTTCTTCCGCCCACGACCTCCCTTCCGCCTTATCTTACGACCGGGACGACTCCGCCAAAGAATCCACCAACC
106955 T C CCCCATTGTCGGATCCAGATCAGAATCTAGACCCGTTCCTCCCGCCCGAATCCATCACCATCCCTTTTTCTTCCGCCCACGACCTCCCTTCCGCCTTATC[T/C]TACGACCGGGACGACTCCGCCAAAGAATCCACCAACCCCAAATCCCACCATCCCAACAACAACAACAACAATCACAACCACGGTAACAAT
106955 A G ATCTAGACCCGTTCCTCCCGCCCGAATCCATCACCATCCCTTTTTCTTCCGCCCACGACCTCCCTTCCGCCTTATCTTACGACCGGGACGACTCCGCCAA[A/G]GAATCCACCAACCCCAAATCCCACCATCCCAACAACAACAACAACAATCACAACCACGGTAACAATCCAAACCCTAGCCCTAACCTCTTC
106955 C A ATCCATCACCATCCCTTTTTCTTCCGCCCACGACCTCCCTTCCGCCTTATCTTACGACCGGGACGACTCCGCCAAAGAATCCACCAACCCCAAATCCCAC[C/A]ATCCCAACAACAACAACAACAATCACAACCACGGTAACAATCCAAACCCTAGCCCTAACCTCTTCAGATCCGCTTCGCAGCGGTACGCCA
106955 CAAT C CTTCCGCCCACGACCTCCCTTCCGCCTTATCTTACGACCGGGACGACTCCGCCAAAGAATCCACCAACCCCAAATCCCACCATCCCAACAACAACAACAA[CAAT/C]AATCACAACCACGGTAACAATCCAAACCCTAGCCCTAACCTCTTCAGATCCGCTTCGCAGCGGTACGCCAAAACCAGCGGTCCAA
106955 A C CGGTAACAATCCAAACCCTAGCCCTAACCTCTTCAGATCCGCTTCGCAGCGGTACGCCAAAACCAGCGGTCCAATCCTCGGGTTACCCAACCGGATCAAG[A/C]ACGTCACGTGCTCCTCCAGAAATTTCAGATCCTCTACCACAACCACCCATTCCAGGATCTTCCCGAGGAAGAAGAAGCCCGGATCCG
106955 C G CCGCTTCGCAGCGGTACGCCAAAACCAGCGGTCCAATCCTCGGGTTACCCAACCGGATCAAGAACGTCACGTGCTCCTCCAGAAATTTCAGATCCTCTAC[C/G]ACAACCACCCATTCCAGGATCTTCCCGAGGAAGAAGAAGCCCGGATCCGTCCCGATCGGGCCGCCGTCCTCGCCCAAGGTATCCTG
106955 C T AGAACGACGAGGGCGATGACGTGGCGAGAGGGAATGTTCCAGAAAGGAATATTCCGGCGGCGGCGGCGCCGCCGCAAGGGCTGGGAGGGATGACGAGGTT[C/T]GCGTCGGGGAGGAGGTCGGCGAGCTGGGGGAGCGACGTGGAGGCGGGACACGTGGCGGTAGATCTGAGGAGGAGATCG
106955 G T CAGAAAGGAATATTCCGGCGGCGGCGGCGCCGCCGCAAGGGCTGGGAGGGATGACGAGGTTCGCGTCGGGGAGGAGGTCGGCGAGCTGGGGGAGCGACGT[G/T]GAGGCGGGACACGTGGCGGTAGATCTGAGGAGGAGATCGGTGGATGGGTGTGGGGCGCTGTAGTTATTGTGGGTTGTTC
106955 C T GGCGAGCTGGGGGAGCGACGTGGAGGCGGGACACGTGGCGGTAGATCTGAGGAGGAGATCGGTGGATGGGTGTGGGGCGCTGTAGTTATTGTGGGTTGTT[C/T]GGTAATTGAATGCTACGCTGTGTTTTTTTGGTGGTTTGCTGGTGTTTTGATTTTTGTTGATTACGAGAGTGGTTTGTAATAATC
106955 G T AATCGCGTGGTGTGTACAGATAGGAAACGCAGGACTGCTTGTCTTTTTTCGCTCTGGTTTGGTTGATTAGTGGTTAGTTGGTTGTTAGAGCAGGACAAAT[G/T]GCTGTCATTAGGGCTTAATATCTTGTCCTTGCATTGCATTAAAAATATATTAAGTGCTATGGTCTTCAGCTCTGGTAGACTGGTACTG
106957 T C CGCAGCAGCTGGAATACTACAAAGAGTACCAATCCAAGCTTGCACAAGTCGCGGGGAGCAAAAAGGCATCGACCATCATCTCTGGTGCACTTTACTTAGT[T/C]AGTTCAGGCAGCAGTGACTTCATTCAGAATTACTACATCAACCCTTACCTTTACAAAGTTTATACACCTGATGAATTTTCTTCCTTTCT
106957 T C ATGATCTTAAAATTGCCATCTTCGACATCTACACCCCTTTTTATGATATCGTGGTCAATCCATCCAAAAATGGATTTGCGGAGGCAAGGAAAGGGTGCTG[T/C]GGGACTGGAGTCGTTGAGACTGCTGTACTGTGCAATCCAAAATCAGTTGGAACATGCTCGAATGCAAGTAGTTACGTGTTTTGGGAT
106957 C G AACTTAGTTACATGATTTAACTTACCTACGTAATATACAGGCTATATATTTATTGCTTATGGTTATCTTTCCAAGTGAGTGAATGTGTTGTATTCTTATT[C/G]TACCTTGTCTGTGTGCATCATTTGTAGATTCTGAATGAAACATTGTTGTAATAAAACTATCTTTTTAATTAGAAAAAAAAAAAAAACGGT
106967 T TC GCCGAAAAGATCCAATGTAGTCCGTTTATCCTCGACCATCAAACTTGGCAAACTAGCACGATCCTCGCAAGGCAGTAATCCAAGCCCTAGCCTACCATGA[T/TC]TAAGTTCAAACCCTGACTGTTCGCAGCTCCATGATTGGTCCAAGCGTCAAAATGCGAGGATGATGATGAAGAAGAAGACGATGATG
106967 C T CGCAGTCGCAGACAGATGTGGCTGAGGTTGCTGAGGTGCACTGAACTGCTGAGGCGGCAGCATGTGATTCGTGGATAAGCAGAGTGACGTGGGTTCAAGT[C/T]GATTCAGAGATCCGATGAGATCAGTGTAATTTGTGCTTTGAGATGAAGCTGAAGCTGTAGCAGAGGAGAACAAACTCGCAAATA
106969 GA G TCCCATTTTCAACCGCTGGGTGATAATCTCCCCGACCCGCTCCAACCGGCCTTTTGATTTCAAATCCCAAAACCCAAAACACTGTAGCCCCAAAAAACCC[GA/G]AAAAATCATGCCCGTTTTGCATTGGGCATGAGTCCGAATGCGCGCCGGAGATATTCCGCTTCCCAGCAGGATCCGATGATTGGAAA
106969 AG A GGTGAAGGAGTGATGGCAGGTTTCGGGTTTCATGATGTGGTAATTGAGTGCCCTCGGCATGACGTTGGGTTGATGGACTTGGATGATGAGGAGATTGGGG[AG/A]GGTGATTTTGGCATATAAAAAGAGGGTACTATTGCTAAAGCAGATTGAACCCGTTAAGTATGTACAGGTATTTAAAAATCATG
106969 G A ATCTCATTTTTTCTCCATTGTTCCATTCGCTGCTTCATTTCCTTTCGAGGTTTGGATTGTCACCAAGGAGCATTCACCATATTTTCATGATATAGAGGAG[G/A]AAAAGGCTGTTGAGCTTGGTGGTATGTTAAAGAAAATGCTGCTCAAGTTAAAGAAACAGCTAAACGATCCACCATTCAACTTCATGGTT
106969 C T TAGAGGAGGAAAAGGCTGTTGAGCTTGGTGGTATGTTAAAGAAAATGCTGCTCAAGTTAAAGAAACAGCTAAACGATCCACCATTCAACTTCATGGTTCA[C/T]ACCGCCCCGTTTGAATTGCAAAGCAATTTATTGGCCTGCACTCATTGGTTTCTTCAAATCATACCTCAACTGAGCGTTGTAGGCGGT
106987 T C CCTTGCATGGGATTGCTAACTCTATTTTGGTCCGCATGTTAAGATAGATTGTGTCTTGAAACATAATATTCCTTGATAGTTTCATATTCAGGTTGCATGT[T/C]GCCCTCTTGCATGGGGATGCTAACGTTAGTCCGGTCCGCCTGTTCTGTCGTGACCACGTTAATAGCATCTTGTGGAACTGGTTGTGTTG
106993 C T TTTCATTTCCAACTAGGGGAAAGACGGTACATGTTCCAAATAGCTATGATCGCCCACATAGTTGGTCGGATGCAAGATCACAGCCCATTGATGTTTATGG[C/T]AGTAACCGTGGTCTGAGTCGGAGGTATTCAGGGTTGTCTCCGACGTTGCTGTCTGATTCACCAACTCCATCTCCACCTGTGTATGGAA
106993 T C CACCATCTCCTAGGAGTACAAGGATGGAGCACTCTTCGCATGAGTCTCGGTCATTAGATGTTGGGATGTTTAAGAAGCTAGAAGCTGTGAAACTAGGAGA[T/C]GTCTATTCTAATCTGCATATGCATATGGCTCAGAAGGGACTTAAGGATGGTAGGGATGATTCAGGAAGGTTTTCTGGTGCATATTC
106993 G A ATCTGCATATGCATATGGCTCAGAAGGGACTTAAGGATGGTAGGGATGATTCAGGAAGGTTTTCTGGTGCATATTCTAGTACTGGGTCCCCTAGATTGGG[G/A]TTCTCCAGAAGCTCAAGCAGGGTGTCAGTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATG
106993 G A GAAGGGACTTAAGGATGGTAGGGATGATTCAGGAAGGTTTTCTGGTGCATATTCTAGTACTGGGTCCCCTAGATTGGGGTTCTCCAGAAGCTCAAGCAGG[G/A]TGTCAGTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATGCCAGAAATATCCTACACCCAG
106993 T C TTGGGGTTCTCCAGAAGCTCAAGCAGGGTGTCAGTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATGCCAGAAA[T/C]ATCCTACACCCAGTCTAGGAAAGCATATGGAAAGGAAGCAGTGGACTCTTTTCAGTCCAATAGTTCATCACACAAGTCACAGGAAGC
106993 T G GTTCTCCAGAAGCTCAAGCAGGGTGTCAGTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATGCCAGAAATATCC[T/G]ACACCCAGTCTAGGAAAGCATATGGAAAGGAAGCAGTGGACTCTTTTCAGTCCAATAGTTCATCACACAAGTCACAGGAAGCAGCAG
106993 C T TCTCCAGAAGCTCAAGCAGGGTGTCAGTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATGCCAGAAATATCCTA[C/T]ACCCAGTCTAGGAAAGCATATGGAAAGGAAGCAGTGGACTCTTTTCAGTCCAATAGTTCATCACACAAGTCACAGGAAGCAGCAGTC
106993 A T GTCCAGGATGATCTTGACGATGACATTGAATTTCCTTTTGCAGTAGATGATTTTGATATGCCAGAAATATCCTACACCCAGTCTAGGAAAGCATATGGAA[A/T]GGAAGCAGTGGACTCTTTTCAGTCCAATAGTTCATCACACAAGTCACAGGAAGCAGCAGTCGGCGCTCTTGTACATATGTTACGAAC
106993 A C CATCACACAAGTCACAGGAAGCAGCAGTCGGCGCTCTTGTACATATGTTACGAACGGCACCTCCTCTGCGCCAAGATCAGTCATTCTCATCTCTACATTC[A/C]AGGTCTGATGTAAATAGTGAAGCGGCCAGTTCCAGCTATTTCATGTCCAGGAAGACATCTGATGCACTGCAGGAACTTAAAACGTAC
106997 A T ATAGGCAGTCAGCTGCACGGTCAAAAGAAAGGAAGATGCGGTATATTGGCGAGCTTGAACGGAAGGTACAAACTCTGCAAGCAGAATCAACAACTTTGTC[A/T]GCTCAGTTGGCTATGTTGCAGAGAGATACGACAGGCCTGTCTGCTGATAATAGTGAGTTGAAGATGCGGGTTCAGACCATGGAG
106997 A G TGATAATAGTGAGTTGAAGATGCGGGTTCAGACCATGGAGCAACAAGTTCACCTCCAAGATGCAATAAACGATGCACTAAGAGAGGAGGTTCAGCGACTG[A/G]AGCTAGCAACTGGTCAGATGATGCAAAATGGACCGATGTTGAATTTTGGACAATCTTCGTTTGGTGCAAATCAGCAATTCCATAA
106997 GT G AATGAGTAGGCGAACTCTCTCCCCTCAGAATCTACGAGAGAATAACACCACCACTTCTCTTTGAATTGAATTTGTAGTACTACTACTGAGCCTTTGCCTT[GT/G]TTATTTTTCAAGTATCTATGTATAGTTTAATGGTGTAGTAAACTTGTAATGGCATAATTTGCAAGGGTGGCTTTGTCGTAGTTACTGTA
106997 A G CCTCAGAATCTACGAGAGAATAACACCACCACTTCTCTTTGAATTGAATTTGTAGTACTACTACTGAGCCTTTGCCTTGTTATTTTTCAAGTATCTATGT[A/G]TAGTTTAATGGTGTAGTAAACTTGTAATGGCATAATTTGCAAGGGTGGCTTTGTCGTAGTTACTGTAAGTTAATATTTTATAGCAAGCTT
107003 A C ACTTCCAGAACACGTGAAAGGTAGGTGGTAACTCGCATGCATGCAGTTGTTGGTCTGTGATCAGTAGCGATCCCATCGTCAGAAGATCTGTAGTCCGAAG[A/C]CTTCTGCTCTGTTGACAGCAATCTTTCTACCTCAGCCATCACAGTGTCGATACACTGGAGAAGACCTTTATGAGCAGCTGTCTCTAC
107003 G GA ATTTGTTTCTGAAGTTCAGCGCGCAGTTGTTCCATCTTTGATTGGTATAGCTGCCTAAGAGATGCCTGCTCATGTTCAGGGTAATCATCCTTATGGGAAA[G/GA]AACAAAGATTCTGTGAGGCCTTCAACATCTAAATCACCACAGCCTACGGATCGTAGCTCTTTAGAAAGATCTTGTGTCTTCTCATAAG
107009 A G GTTCCACATTCCTTGATTTTCCAGCGATACTAAAATTGCAGACCATCCGTTTGGATAAACCTGAACCGTGTGTCTAGTCACAGCATCTACTAGGTTGTAC[A/G]TCTGCCTCATGCTTCCTGACCATCTTCCACCGCCATATCCAACAACCCAGAAATCGTATCCATCAAGATGCCATGATTGCATGCTATTCT
107009 A G CATTTATCATTGGTGCTGAATTAGCAAAGAAAAGTTTTCTTGTTATTGGAACTGTTCCATAATGGTATGATCCTTGGGGATTTGGCCTCGCTGCATTTGC[A/G]GTTAGATTCCATCTAATGGTAGTGGCTTGACTCATTGATCCTTCTATTGTACTTGCAGGACCAACCGGAACCTGACCCGAAACCCGGAT
107009 C T GTTATTGGAACTGTTCCATAATGGTATGATCCTTGGGGATTTGGCCTCGCTGCATTTGCAGTTAGATTCCATCTAATGGTAGTGGCTTGACTCATTGATC[C/T]TTCTATTGTACTTGCAGGACCAACCGGAACCTGACCCGAAACCCGGATATTTGAATTGCTATAATGTAGAACACCAGTTGCAACCAAAC
107009 G A ATCCTTCTATTGTACTTGCAGGACCAACCGGAACCTGACCCGAAACCCGGATATTTGAATTGCTATAATGTAGAACACCAGTTGCAACCAAACTCTTTTC[G/A]GTGAATTGGGAGGATGCAACAATGTAATAATCTTTAGATGGTTGATCGAGAGTCACCAGAACAGACATTGACTGACCTACGTGTAGA
107009 T C TTCGGTGAATTGGGAGGATGCAACAATGTAATAATCTTTAGATGGTTGATCGAGAGTCACCAGAACAGACATTGACTGACCTACGTGTAGATCAAGCGAG[T/C]TGTACAAGTTCTGAATTGTGTGTGATCCTTCGACTTCCACAAGCTTTAGTTTGTGGTTTTGAATCTTGAAATTTACTGATACAGATAG
107009 A G TTGACTGACCTACGTGTAGATCAAGCGAGTTGTACAAGTTCTGAATTGTGTGTGATCCTTCGACTTCCACAAGCTTTAGTTTGTGGTTTTGAATCTTGAA[A/G]TTTACTGATACAGATAGACCAATGTTTGATACCCGGAACATGTAAGTTTTCCCTTGGTCTCCAGTAAAAGAAGCAGATTGAGTAACCCC
107009 C T TCGACTTCCACAAGCTTTAGTTTGTGGTTTTGAATCTTGAAATTTACTGATACAGATAGACCAATGTTTGATACCCGGAACATGTAAGTTTTCCCTTGGT[C/T]TCCAGTAAAAGAAGCAGATTGAGTAACCCCATTTATGAGAAGCCCATCAGGAAACCCAAGTCCTTTCCCTGCATCTAAACTTTGCCTCAA
107009 T A ATTGAGTAACCCCATTTATGAGAAGCCCATCAGGAAACCCAAGTCCTTTCCCTGCATCTAAACTTTGCCTCAATGCCTTATGTCCAGCTTTAAACCAATC[T/A]CCAACAAGAAGGCTAAAATCCCCATCGGGAGGGCTATAAGGAATGGGAATGGGCGCTCTCTTCCGCACAATCAGAGCACCAAACCCAC
107011 T C AGGTAGAGTTGAAGTCAAGATTAATGGCGCATCAATTCAACAACGTTCTAAGAATGATAGCTGGAAAACGATTCTCAAATGACGAAAATAGCCCCGACTC[T/C]GATGAAAAGGCAGCCTTCCACAAATGGATAGAAGACTTTTTTGAAATTCTCTGCGGTCGCTCCAACATCGCTGACTTCCTACCATCC
107011 CA C AAGAATGGAACAAAAAGGTACACTACATGTCCAGCTTCCGCGACCAGTTCTTCAAAAAGCTTATCGACAACGTCAAAAACAACCCTACCATTGACGAGTA[CA/C]AAAAAAACAATGGTCGCCAACATGCTTTCCCTTCAAAGCGCCGACCCCAAGTACTACACGGATGAAACCATCATAGGCTTCGCACT
107011 G A TGCTGAACAATCCGGAGAAGCTAGAGAAGCTAACAGCGGAGATCGATGAGAAAGTCGGAAAGGCCCGAATGGTAGAGGAGTCAGACGTGCAAAACCTCCC[G/A]TATCTGGTAAGGGTGGTGAATGAGACCCTGAGGCTGAAGCCGGCTGCGCCAATTCCGGTGCCGCACGAGGCATCCGAGGACT
107011 C G CGCACGAGGCATCCGAGGACTGCAAGGTGGGAGGATATGAGATCGAAAAGGGGACGATGTTGTTGGTGAACGCTTACAGGATACACAGAGACCCGGACAT[C/G]TGGGTTGAGCCAGAGAGGTTCGAGCCGGAGAGGTATGAGGAAGGGGAGTACGATGCAGGGAAAACGTTGATATTTGGGATG
107011 A G TTTGAGTGGAAGAGGGTCGGGGAAGGGTTAGAGGATATGACTGAAAGTACTGCTCTGGCTATGGGCAAAGAGGTTCCGCTTGAAGCCATGTATAGACCTA[A/G]GGAGATGATGATGGGTGTTTTAGGGCAACTCTAAATGAGCCATCTTTTGGAAGTTTGGACAATAATGTTGCAGAGCAAGTTACT
107011 AT A AGGGCAACTCTAAATGAGCCATCTTTTGGAAGTTTGGACAATAATGTTGCAGAGCAAGTTACTTGTAATAATACAAAGATATCTATGTTTTTACTTTGTT[AT/A]TTTTTATTAAATTTGTTTTCTTGTTTGTGCCGTGCGTACGCATATATACCACAAAATAAGAGAACGTGGTCTCGTTAATGAATATTGTA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107011 G GT TTTGGACAATAATGTTGCAGAGCAAGTTACTTGTAATAATACAAAGATATCTATGTTTTTACTTTGTTATTTTTATTAAATTTGTTTTCTTGTTTGTGCC[G/GT]TGCGTACGCATATATACCACAAAATAAGAGAACGTGGTCTCGTTAATGAATATTGTAACCATTTGAATATGTCTATTTGAATGTATGCAT
107013 T A CACAATGAACGAGAAACCTGGAGGGCGTGACAATGGCCCCAACTTCACTTTTCCACTTCCTAAAACTCCAAATTTATTTTCTGAACCACCACCTACGCCA[T/A]CTATGCCTACTTCACTGCAAGCTGCTAGCAAAGCACAGAAAGAAAAGCAAGGTCACGAGGACATTGTACCCTTGTTCAATTTCGGATC
107015 G A CTTCTGCCGCCACCTTTTTTCTATACCCGTTTCTTCTAGACTCCATTGTTACAGGTAAAGGTGCTGCAAGCCCATGCCTAACTCTAGGGCTTTCATCGCT[G/A]TCGCTCGACTGGCTAGAAAATCCTGTGTTTCTCAATTGGGTTTCTTCTTCTGATGTTCTCTCACTTGTACAGGCAAAGATACTGTCTTTGT
107015 G A CTGCCGCCACCTTTTTTCTATACCCGTTTCTTCTAGACTCCATTGTTACAGGTAAAGGTGCTGCAAGCCCATGCCTAACTCTAGGGCTTTCATCGCTGTC[G/A]CTCGACTGGCTAGAAAATCCTGTGTTTCTCAATTGGGTTTCTTCTTCTGATGTTCTCTCACTTGTACAGGCAAAGATACTGTCTTTGTTAC
107015 G A TAATCATCACATCAGAGCTCTGAATACAATCGAGCTTAAACATCAACTCCTCCACTTCCTTGAAAACGGCACGAGGATTCCTCACGCTTCTATCCCCCAA[G/A]CAATCCCTCAAACCCGCAACATTCGACTTAATCACAGCAAGCTCTTTGAGGTCACGTAGTGTGCGCGACCGCCTCACAAGAAAACTACG
107015 C A CGGCACGAGGATTCCTCACGCTTCTATCCCCCAAGCAATCCCTCAAACCCGCAACATTCGACTTAATCACAGCAAGCTCTTTGAGGTCACGTAGTGTGCG[C/A]GACCGCCTCACAAGAAAACTACGGAAATGACGCTGTATGGTAGCAGCAGCTAAATGTCTGACAGAACTCCTCTTAGGAGGCGAATG
107015 TG T AAGGAGATAGGCATGATTGTCGTTATTAGGGCGATGCAAGTTGCTGCTGGGGTTAGTGGGTTTAGAATAAACTGGTGAGTGGGGTTTCTGAGTTTGGGTT[TG/T]GGGGTTGGGAAAGGAGAAGGGAAGTTAGGGTTTGGAGGAGCTGGTGCTGCTGCTGATTTGAATCAGTTTGGGGATGTTGTGG
107017 G T TGAATTTCAGTATCCCTCTCAGCAATCAAGTTCCGAGCAAGTCGCAATTCAGACTGCACTTGATTCATCTCGGCGGATAGAGCTCGCAACTCCTGATCCC[G/T]AGCAGCTAGAAGATGAGCAAGATCAACTTGAGGGGTACTGCCATCATCAGATCGTTGGTACTTGCTCAGGCTTTCCTGTAAACGAAG
107017 G A TCGGGTTGACCATTCAAAGAATTGTACTGACGAATACATCCAATATACACACTCATAAAACTTCCAGCACAAATGACTTCTGCAAACATCAATATCCTCA[G/A]AAATGTGGAGAGAGAGAGTATAGGGAGATGTGGCTGCCACACTACAAAGAGAAGCATTAAAGCAGTTCCATAAGCAACAGTAGCAA
107019 C G CACCGACCGTATTCACTGGAACTGAATATTACTTCGTTCGCACGACCGTCGCTCTCTTCCTCTGGCTTGGTGCCATCCATTTCGTCGTGGTCCTCGTCCT[C/G]ACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGT
107019 G T GAACTGAATATTACTTCGTTCGCACGACCGTCGCTCTCTTCCTCTGGCTTGGTGCCATCCATTTCGTCGTGGTCCTCGTCCTCACGGCGCTTCTCTTCCT[G/T]CCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTA
107019 T C ACGACCGTCGCTCTCTTCCTCTGGCTTGGTGCCATCCATTTCGTCGTGGTCCTCGTCCTCACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGG[T/C]GTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGC
107019 C G CGCTCTCTTCCTCTGGCTTGGTGCCATCCATTTCGTCGTGGTCCTCGTCCTCACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGC[C/G]TGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGA
107019 T C CTTCCTCTGGCTTGGTGCCATCCATTTCGTCGTGGTCCTCGTCCTCACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTA[T/C]TGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTC
107019 T C TCGTCGTGGTCCTCGTCCTCACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAA[T/C]GATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACAT
107019 A G GTGGTCCTCGTCCTCACGGCGCTTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATA[A/G]GAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGG
107019 A G TTCTCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTT[A/G]GCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTA
107019 G A TCTTCCTGCCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGC[G/A]AGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTATGT
107019 T C CCCACTCCCTTCGCCATCACGGTGTTTGGCCTGCTATTGCTCTTTATGGTGATCCCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTA[T/C]TTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTATGTGTTCGGCT
107019 A G CCTCTGAATGATAAGAGTAAATTGGGAAGAAAGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAA[A/G]GGCATTTGATCCAAACAAAGCTTATGTGTTCGGCTATGAGCCACATTCAGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACT
107019 C T AGTTAGCGAGGTTTATTTGTAAATATGCGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTATGTGTT[C/T]GGCTATGAGCCACATTCAGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCT
107019 A G CGGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTATGTGTTCGGCTATGAGCCACATTCAGTGCTACC[A/G]ATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCC
107019 A G GGTTGGATATTTTCCAATCACTTTACACGTTGAAGACATAAAGGCATTTGATCCAAACAAAGCTTATGTGTTCGGCTATGAGCCACATTCAGTGCTACCA[A/G]TTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCCA
107019 C G ACATAAAGGCATTTGATCCAAACAAAGCTTATGTGTTCGGCTATGAGCCACATTCAGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATT[C/G]ATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGG
107019 G A CTATGAGCCACATTCAGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCT[G/A]TCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAA
107019 T G ATTCAGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACAC[T/G]CCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAAGGGATACAGCT
107019 T C AGTGCTACCAATTGCTGTGTGCGCTCTTGCTGACCTCACTGGATTCATGCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCCA[T/C]TCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAAGGGATACAGCTGTAT
107019 A G GCCTCTGCCAAAGATCAAAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGG[A/G]AGAATTTCTACTCTTACTTGGAAAAGGGATACAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATCATGATT
107019 C T AAGTTCTAGCAAGCAGTGCTGTCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTA[C/T]TTGGAAAAGGGATACAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATCATGATTCTGAGGTTGCCTTCCTTA
107019 G C CAAGCAGTGCTGTCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAA[G/C]GGATACAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATCATGATTCTGAGGTTGCCTTCCTTAAATCAAGAA
107019 A G AGTGCTGTCTTCTACACTCCATTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAAGGGAT[A/G]CAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATCATGATTCTGAGGTTGCCTTCCTTAAATCAAGAAAAGG
107019 A G TTCTTGAGGCAAATTTGGACATGGTGTGGCTTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAAGGGATACAGCTGTATAATTGTGCCTG[A/G]TGGTGTTCGGGAAATTCTACATATGGATCATGATTCTGAGGTTGCCTTCCTTAAATCAAGAAAAGGTTTTGTGCGAATAGCCATAGA
107019 A C TTGGCTCCGGCATCAAGGAAGAATTTCTACTCTTACTTGGAAAAGGGATACAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATC[A/C]TGATTCTGAGGTTGCCTTCCTTAAATCAAGAAAAGGTTTTGTGCGAATAGCCATAGAAAAGGGCGTGCCTCTTGTTCCTGTCTTTAGT
107019 C T AGAATTTCTACTCTTACTTGGAAAAGGGATACAGCTGTATAATTGTGCCTGATGGTGTTCGGGAAATTCTACATATGGATCATGATTCTGAGGTTGCCTT[C/T]CTTAAATCAAGAAAAGGTTTTGTGCGAATAGCCATAGAAAAGGGCGTGCCTCTTGTTCCTGTCTTTAGTTTTGGACAGAGTTATGTTTA
107019 T C GCATGCTCAGTTTGTTTCGGCATTAGAAGATCTGTTTGAGAAATATAAAGCCAGAGCTGGGTATCCTCGCCTCAAACTGAGAATCCTCTGATTGTATATG[T/C]GATATCAGCTGCGTTGGACATTTAGTGTATTGCCTTCAGGCCTGAAAGAGGTGCTACTAATTATATCATCCTCATTTCCCAAATGGTAC
107019 A AT GCTGCGTTGGACATTTAGTGTATTGCCTTCAGGCCTGAAAGAGGTGCTACTAATTATATCATCCTCATTTCCCAAATGGTACATATGTCAATCCAGATCC[A/AT]TGATATTTAAATGGTACAGGAGATGTAATTGTTATTCGAAACACATGAAGTGGAGTATATAAATCTACAGTACAATGTACATTAATAG
107023 T TC TGCTTCTTCTTCCACCACTGCCTCCAACTCTAGTTATAGCTGCAGCAACTCCTGTAATCATGGTTTCTCCCTTCTCAACCCCTGCATTCCAAAATCCCAA[T/TC]CGGATCTCCCCATCCACCTCACCGACCATACCCGACCCGTTCCGGACACTCAACTCGTGATGCGACCAAACGGCACCAGCACTGCCTCTT
107025 CA C TTCACAACACAAAGAGAATTAGGCGAAGACTGGCGATATGAAAGGGATACTAGAAGGGGAAATGCTGGAAATAAGAAAGAGGAATATGGTGATAAGCAGA[CA/C]AAAAAAATACGAGAGCAAACCAGATCTGAAAGATCGACCCCTGTGAGAAAGCATGAAAGCTGAAATACAGGGAACCAGGAA
107029 A AT,AC CTCTCCTCACCCGACCACTTCACAAAAATATACGCATTCGGGGACTCCTTCACGGACACTGGCAACACCCGGTCCACCACCGGCCCACAATCGTTCACGT[A/AT,AC]GTTTCCAACCCGCCGTACGGCACCACCTTCTTCCACCGCTCCACCAACCGCTACTCCGACGGCCGTCTCGTCGTCGACTTCCTCG
107029 C T ACTGGCAACACCCGGTCCACCACCGGCCCACAATCGTTCACGTAGTTTCCAACCCGCCGTACGGCACCACCTTCTTCCACCGCTCCACCAACCGCTACTC[C/T]GACGGCCGTCTCGTCGTCGACTTCCTCGCCTCCAGACTCTCCCTTCCCTTTCTGCCCCCGTACCATGCCACAGATTCCAACTTCACCCAC
107029 G A CTTCCACCGCTCCACCAACCGCTACTCCGACGGCCGTCTCGTCGTCGACTTCCTCGCCTCCAGACTCTCCCTTCCCTTTCTGCCCCCGTACCATGCCACA[G/A]ATTCCAACTTCACCCACGGGGTCAATTTCGCCGTTGCAGGCTCGACCGCGATCGAGTACGACTTCTTCGTTAAGAACAACATAACGCTG
107029 T C TACTCCGACGGCCGTCTCGTCGTCGACTTCCTCGCCTCCAGACTCTCCCTTCCCTTTCTGCCCCCGTACCATGCCACAGATTCCAACTTCACCCACGGGG[T/C]CAATTTCGCCGTTGCAGGCTCGACCGCGATCGAGTACGACTTCTTCGTTAAGAACAACATAACGCTGGATATCACGCCGCAATCGTTGA
107029 A G ACGGGGTCAATTTCGCCGTTGCAGGCTCGACCGCGATCGAGTACGACTTCTTCGTTAAGAACAACATAACGCTGGATATCACGCCGCAATCGTTGAGTAC[A/G]CAGCTTAAGTGGTTCGACGAGCATTTGGAGAGGGAAGGATGCGGAAGGAAGGGGTCGTGCGGTGAAGTGTTTAGAGATGCTTTG
107029 C T AGCTTAAGTGGTTCGACGAGCATTTGGAGAGGGAAGGATGCGGAAGGAAGGGGTCGTGCGGTGAAGTGTTTAGAGATGCTTTGTTCTGGGTTGGGGAGAT[C/T]GGGGTGAATGACTATGCGTACAGTACTATCGCTTCCTCTGTCAGTGCTGATGAGATCAGAGAACTTGCTGTCGGAAAAGTCGA
107029 T C GAGATTTGAATTTCGACCCGATGAACACATGTGGGTCGCCTGATGTGCTGAAAGCTTGTGACAGACCGGAGAAGTTTGTGAATTGGGATGGGGTTCATTT[T/C]ACCGAGGCGATGTATAAGAACGTCGCTGATATGTTTTTCGGTGGAGCCTTCATGAAACCCTCTTTTGGTGCGTTGTTTTGAAATTAA
107029 T C TGTGAATTGGGATGGGGTTCATTTTACCGAGGCGATGTATAAGAACGTCGCTGATATGTTTTTCGGTGGAGCCTTCATGAAACCCTCTTTTGGTGCGTTG[T/C]TTTGAAATTAAGCTGAGCTTTGAGCATTTGATGTAAGAGTGATGAGAAATGGAATGCTTGCTTTGTATGTAGTAGTTTGGCCACTGC
107029 A G ATATGTTTTTCGGTGGAGCCTTCATGAAACCCTCTTTTGGTGCGTTGTTTTGAAATTAAGCTGAGCTTTGAGCATTTGATGTAAGAGTGATGAGAAATGG[A/G]ATGCTTGCTTTGTATGTAGTAGTTTGGCCACTGCTATCTTTATAAAATCTTCTAATGTAGCATGATTTACTCTTGATTGTATATCCAGAT
107041 G A TTCCTCATCGATCCCCATCATCCTCGAAATCCAAAACCCAAACAGAAACCCAGAACCATGCAACAACAGTACAGGCAAAACCACCTGGAATCCAGAACTC[G/A]CAATTGTCGTCGCGTTCTGTGCAATGGCGCCACCTCCCAATATCGAGACGCTAGTGACGGCTATTAATGGCATCATAGGGGACACGA
107045 T C ACCGCCTACTCTGACCATTGTTAAGTTAAGGAAGTAGAATGGTGCTTGTTGTGCTTTTCCTTGGATCATTTTGGTGTATTGTATCGGTGTTGTGTTTTTG[T/C]ACATGGTCGGATCGTCTCCAAGGACTAGGTTGCCTGTCGAGTTATATGGTCTCGATGGCATGCAATATGAAAAGACTCCTCCAAATTGT
107045 G A CACGAACCCATCGACAAACACATCACCAAAATAAACTCTTTCGAGAGCAAGTTCGCCTCGAGTGTAGGACCCATCACCGTATCTGAGTGCGTAGTTGCAA[G/A]CATTACTGCCTGTACCCAACCACAACCACCCGAGCCGTAAGACAAGAAAGCAGAGCAGGGAGTGGAGTTGCACGGAATCGACTTG
107045 A AC ACATCACCAAAATAAACTCTTTCGAGAGCAAGTTCGCCTCGAGTGTAGGACCCATCACCGTATCTGAGTGCGTAGTTGCAAGCATTACTGCCTGTACCCA[A/AC]CCACAACCACCCGAGCCGTAAGACAAGAAAGCAGAGCAGGGAGTGGAGTTGCACGGAATCGACTTGTAAGTGCTCGATATTTTAG
107049 C G TGCAGAAAGCTACACAAAATTTCACCATTTGACTTAAGAGGCTTAGCATATACAGCCAGCTTTCTTTGAAATAAACAACTGATTGCTATAAATTAACCTT[C/G]AAGTTTCGTTGGCATTGCAACTATACCATCTTCCAACATCAGCAGAGTGTTTTTACTTAGGCATTCAGTTTTGATTTAAAATACACTGCT
107049 T C CCATTTGACTTAAGAGGCTTAGCATATACAGCCAGCTTTCTTTGAAATAAACAACTGATTGCTATAAATTAACCTTCAAGTTTCGTTGGCATTGCAACTA[T/C]ACCATCTTCCAACATCAGCAGAGTGTTTTTACTTAGGCATTCAGTTTTGATTTAAAATACACTGCTCTTTTTGCTACACGCAAAAGACACA
107049 A C CTTTCTTTGAAATAAACAACTGATTGCTATAAATTAACCTTCAAGTTTCGTTGGCATTGCAACTATACCATCTTCCAACATCAGCAGAGTGTTTTTACTT[A/C]GGCATTCAGTTTTGATTTAAAATACACTGCTCTTTTTGCTACACGCAAAAGACACAAAAACTGATGGATATATGCATGCAGAAAAAGGTA
107049 T C ACTGATTGCTATAAATTAACCTTCAAGTTTCGTTGGCATTGCAACTATACCATCTTCCAACATCAGCAGAGTGTTTTTACTTAGGCATTCAGTTTTGATT[T/C]AAAATACACTGCTCTTTTTGCTACACGCAAAAGACACAAAAACTGATGGATATATGCATGCAGAAAAAGGTATTAAGCTGGAACTGGTTC
107049 CT C ATTAACCTTCAAGTTTCGTTGGCATTGCAACTATACCATCTTCCAACATCAGCAGAGTGTTTTTACTTAGGCATTCAGTTTTGATTTAAAATACACTGCT[CT/C]TTTTTGCTACACGCAAAAGACACAAAAACTGATGGATATATGCATGCAGAAAAAGGTATTAAGCTGGAACTGGTTCAGTCATAGCTGT
107049 T C TGTTTTTACTTAGGCATTCAGTTTTGATTTAAAATACACTGCTCTTTTTGCTACACGCAAAAGACACAAAAACTGATGGATATATGCATGCAGAAAAAGG[T/C]ATTAAGCTGGAACTGGTTCAGTCATAGCTGTGGATGATGTACTAAGAAGCGGTGTTTTCTGAAAATCATTTCTTAGTTGACCACATGCT
107049 T C TTTTACTTAGGCATTCAGTTTTGATTTAAAATACACTGCTCTTTTTGCTACACGCAAAAGACACAAAAACTGATGGATATATGCATGCAGAAAAAGGTAT[T/C]AAGCTGGAACTGGTTCAGTCATAGCTGTGGATGATGTACTAAGAAGCGGTGTTTTCTGAAAATCATTTCTTAGTTGACCACATGCTGCA
107049 A G CTGGAACTGGTTCAGTCATAGCTGTGGATGATGTACTAAGAAGCGGTGTTTTCTGAAAATCATTTCTTAGTTGACCACATGCTGCACTTGCATCAAGGCC[A/G]CGTGTTTGTCGCACTGAGACAGTTATCTTACGAGATTCCAAGGCTTCCACGAAAGCTAGCACAGTTTTCTTGTAAGGCCTTCGATACT
107049 T C GCACTGAGACAGTTATCTTACGAGATTCCAAGGCTTCCACGAAAGCTAGCACAGTTTTCTTGTAAGGCCTTCGATACTCAGATCCTTCTATCGGATTGTA[T/C]GGTATCAAATTTACATGATAACCACGACCATTGTCATGGAGTAACTCCGCGAGTTCTATCGCATGTTCTTTTCCATCGTTAATCCCAGCT
107049 A T TAGTTTCTCGGAGTTTCTGGTTAGGGGCATGTAGACTGATTGCTAAGGTAGACTGGAGTTTATGTGATGCCAGCATCATAATTGTGTTGGGTACACCCAC[A/T]GTAGATATTGTCATCATTCTTTGTCCAATTTTGATATCCTTGTTTAAGCACGTATGTGCTTCAAGAACTGATTTTAGGTTCAACATTGG
107049 T A CTCGGAGTTTCTGGTTAGGGGCATGTAGACTGATTGCTAAGGTAGACTGGAGTTTATGTGATGCCAGCATCATAATTGTGTTGGGTACACCCACAGTAGA[T/A]ATTGTCATCATTCTTTGTCCAATTTTGATATCCTTGTTTAAGCACGTATGTGCTTCAAGAACTGATTTTAGGTTCAACATTGGTTCACC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107049 T C TTAGGGGCATGTAGACTGATTGCTAAGGTAGACTGGAGTTTATGTGATGCCAGCATCATAATTGTGTTGGGTACACCCACAGTAGATATTGTCATCATTC[T/C]TTGTCCAATTTTGATATCCTTGTTTAAGCACGTATGTGCTTCAAGAACTGATTTTAGGTTCAACATTGGTTCACCCATTCCCATAAAAA
107049 C T CACGTATGTGCTTCAAGAACTGATTTTAGGTTCAACATTGGTTCACCCATTCCCATAAAAACAACATTGGTCACCCTATCTTTGAAGAGTTCCTCTATGA[C/T]TAGTACCTGTTCGATAATTTCATGCCGCTTGAGGTTCCGAGAAAAACCACCTTTTCCTGTAGCACAAAATGAGCAACGTAAGGGGCATC
107049 T C ATAATTTCATGCCGCTTGAGGTTCCGAGAAAAACCACCTTTTCCTGTAGCACAAAATGAGCAACGTAAGGGGCATCCAACCTGAGAGGACACACAGGCAG[T/C]GAGTCTAGAACCTTTATCATCTTCAACGGGTATACCTACAGTTTCAATCAATCTGTCATCCTCTAACTTTAAGAGTACCTTAATAGTC
107049 G A AGGCAGTGAGTCTAGAACCTTTATCATCTTCAACGGGTATACCTACAGTTTCAATCAATCTGTCATCCTCTAACTTTAAGAGTACCTTAATAGTCCCATC[G/A]GCTGCATGAACAGCCTTGTGCACAGGCGACCTTCCAACTCTCCATCCTTCTTCTTTAAGGCTAGTTCTAAACGCCTGAGGCAAGTGACTG
107053 G A CTTGCATTCCGGAAGAGTAATGAAACGCTTTCTCGTCATGATATCTCCCCCACTCTTCTGGAACCTTCTTCGTCTCCTCCACAAACCTCTTCATCGAGTA[G/A]TACTTAACTAACCTCGCACACAGAACATCGAACCTGGAATCCGTTATCAACAGTGGTGCAGTATGCGATTTGCTGCAGGTTAAATGATC
107053 G C CACAAACCTCTTCATCGAGTAGTACTTAACTAACCTCGCACACAGAACATCGAACCTGGAATCCGTTATCAACAGTGGTGCAGTATGCGATTTGCTGCAG[G/C]TTAAATGATCGAGAAAGTGTATTGGCTGACATATGTACATTACCATGGCGACGCTGGCGCCGTACGGATGACAGAAGCACCCTTCTC
107053 C T CGCATAGATGCAGTATGTTACTGTTTACGAAGGAGAGTGTGGTTTTGGACCCCACGTACGGAGAATACCCTTGTATCCTTGCGTTGTTCAACCTAATCAC[C/T]GCTTCGTGGCTGTCGATGAACTGACCGTACTCCGTTTTTAGAAGGATTCCGCTGTTGCCGACAACCGCGCAGGAGCTGTAAAGCGGG
107055 T A TTTTCACTGATTGAAGAGGCTAGTGATTTGAGATTCGTGTATGCATTCGGCTATGATGAGGTACCAGAGACTAGGCCCAGATTTTCTACCACAGCCGAAC[T/A]CCGACCAGATATACAACGCTGACCTCTTACAAATGGGGTCCGGATCGGGATCGGGATCCGGATCTGCAACCCAAACCGAAGTAACA
107055 G GA GAGGTCGCGATGTTCTAGAACTTCATCAGCTGAGGATTCGTGTTCCAATCCTAGGCGGAATACGAAGATCCAAAAACGAGCTGCGGCTATAGTCGGCGCT[G/GA]AAAAAATTGCAGCCGTCGCTGCGTCTGAGATGCCACCGCCGGCGAACTTAAGAGCTTGTGTGCAATCGAATGTAACCATTCATC
107055 A G AACCACAGCCAGAGCATGATAGCTCGGGCACAGGATCCGGCTCCATGGCAGTGGAGAAAGTTAAGCTGGAGTGGCCGAGGATATACGTAACGCTTTCCAG[A/G]AAGGAGAAGGAAGATGACTTCTTTGCCCTTAAAGGCACCAAGCTGCCCCATAGGCCCAAGAAGAGAGCTAAGAATATCGACAA
107055 G GAATGAAGAAGATTTAACGAGAGGACGGTATGAAGTTAGGGAGAAGAAATGTGCAAAAAAGAAACAACGACTTGGATTGAAGGGCTTGGAGAGCATGGACAGCGATTCG[G/GAATGAAGA]AATGAATGTGAATTATCTAATCGGTTTTTATTATGGAATGGAAAGAAGCAAAACTCGTCAATTTGGAGTGGAGGG
107055 C G GGTATGAAGTTAGGGAGAAGAAATGTGCAAAAAAGAAACAACGACTTGGATTGAAGGGCTTGGAGAGCATGGACAGCGATTCGGAATGAATGTGAATTAT[C/G]TAATCGGTTTTTATTATGGAATGGAAAGAAGCAAAACTCGTCAATTTGGAGTGGAGGGAGAAGCAAAATTTGATGCCTTCTATT
107055 T C ATTTGGAGTGGAGGGAGAAGCAAAATTTGATGCCTTCTATTGTGCATAAAATGGTTGATTTATTTTCGAATAAATTTGGAAAGAATGCAAATAGAAAATG[T/C]GAGGATGACTATGATTTCAACTAGTATCTTCGTCTGTGTTCTGGCTGTTTGTTTATTTTTATTATTCTGAACAGTGGGT
107065 C T TTCCAACCTCTTTTGCAACAGCTTGAGCTGTTCTCCAATTATCGCCAGTAACCATAATTGGTATCACACCCATCTTCTTTAGTCCTTCAATTACAACAAC[C/T]GCCTCCCTCTTTAATGGGTCTGCTACACCCAGTACTCCGATAAAATTGCCATCATATGCCACAAGTATTCCAGTCTTGGCATTATTTTCCAG
107065 CT C TTGATGAAGCACTGAACTCCTCTTCCAGGCAATGAAGTGAAGTCTGATGCTTCCATAAGCCACGTAGATAATAAATCCTCTTTTTTACAATTCATGGAAT[CT/C]TTTTACTTTCCCGAAAAAATGATAATGGTATGCATAATCAACTATAGCTTTTCCAAGAGGATGCTCACTACTAGCCTCTGCAGACGCCA
107065 C T CCCCCAAATCTATTTCAGAAAATACTTTTGCAATTGTAACAGACGCCTTTCCCTGAGTAAGAGTACCTGTCTTATCAAATATTACGTGCTGAATACTCTG[C/T]GCTCTTTCAAGAGCATCTCCTCCTTTAATCAACACACCATGGTTAGCTCCAACACCAGTCGCCACCATGACTGCAGTTGGTGTTGCCAAG
107065 A C CTCCTCCTTTAATCAACACACCATGGTTAGCTCCAACACCAGTCGCCACCATGACTGCAGTTGGTGTTGCCAAGCCAAGAGCACATGGACATGCAATAAC[A/C]ACCACCGATATTGAAAACATGAGTGAAAATACAAAACAACTACCATTATCGGAAAGCCAGGTAGATGGGTATGCTCCTACTGAACCA
107069 T A AAATCGTAGTGTACAGTGGAAAGTCGAAGAACTCTCCAAATTGTAATGTGACGAGCACAAAGAAGAAGATAGGATCGTTCAAAGTAGAAGTGGGGCCTGA[T/A]TGGAGCGAGGGGAAGCCACAGTTGATTCATAACGGGTGGATTCGGATAGGGAAGAATCAGCTGGAGTTGCATTTGAGGGTGAA
107069 G A TGTACAGTGGAAAGTCGAAGAACTCTCCAAATTGTAATGTGACGAGCACAAAGAAGAAGATAGGATCGTTCAAAGTAGAAGTGGGGCCTGATTGGAGCGA[G/A]GGGAAGCCACAGTTGATTCATAACGGGTGGATTCGGATAGGGAAGAATCAGCTGGAGTTGCATTTGAGGGTGAAGCTTGATTT
107069 G A GGAGCGAGGGGAAGCCACAGTTGATTCATAACGGGTGGATTCGGATAGGGAAGAATCAGCTGGAGTTGCATTTGAGGGTGAAGCTTGATTTGGATCCTAG[G/A]TATGTGTTTCAGTTTGAAGATGAGACTGCATCCAGCCCTCAGATAGTTCAACTTCAAGGGAGCATTAGGCAACCTATATTTAGTT
107069 A G TGTTCATGGCAACCCCATTTGTGCCGTCCACAACCCACAACATAGTGTCCAAGTCGAACCCAGGCTCATGGCTGATAGTCCGGCCTGACCACGCCGGCCC[A/G]ACAGACAGCTGGTATCCATGGGGCCGCCTGGAGGCCTGGCGCGAGTCTGGTACCCACGACTCCCTCTATCTGCGCCTCTTCCTTCTT
107069 T C CCAAGTCGAACCCAGGCTCATGGCTGATAGTCCGGCCTGACCACGCCGGCCCAACAGACAGCTGGTATCCATGGGGCCGCCTGGAGGCCTGGCGCGAGTC[T/C]GGTACCCACGACTCCCTCTATCTGCGCCTCTTCCTTCTTCCCCAGGGTCAGGAGTCCGGTGTTCTGGTGTCTCAAGTAGTGATAGG
107069 A G TGGCTGATAGTCCGGCCTGACCACGCCGGCCCAACAGACAGCTGGTATCCATGGGGCCGCCTGGAGGCCTGGCGCGAGTCTGGTACCCACGACTCCCTCT[A/G]TCTGCGCCTCTTCCTTCTTCCCCAGGGTCAGGAGTCCGGTGTTCTGGTGTCTCAAGTAGTGATAGGAGTCGACAAAGGAGGTGAT
107071 T TA TAAACGTACCACATTCTTCCTCAATAGCTTTCTCTCTCCATTCCCACCTCTTCGTCTCCAGCGATTCCAGTTCCACCCCTAACTGGTAACGGTAATTCAC[T/TA]AATTTTCAAATCCACCCTCTTCTATCAAGCTCCAAAAACAAAACCATGGGTGTCAAAGGATTCGTTGAAGGAGGCATCGCTTCAATCGTC
107071 C T GCTTTCTCTCTCCATTCCCACCTCTTCGTCTCCAGCGATTCCAGTTCCACCCCTAACTGGTAACGGTAATTCACTAATTTTCAAATCCACCCTCTTCTAT[C/T]AAGCTCCAAAAACAAAACCATGGGTGTCAAAGGATTCGTTGAAGGAGGCATCGCTTCAATCGTCGCAGGCTGCTCCACTCATCCATTGGA
107071 CA C ATTCCCACCTCTTCGTCTCCAGCGATTCCAGTTCCACCCCTAACTGGTAACGGTAATTCACTAATTTTCAAATCCACCCTCTTCTATCAAGCTCCAAAAA[CA/C]AAAACCATGGGTGTCAAAGGATTCGTTGAAGGAGGCATCGCTTCAATCGTCGCAGGCTGCTCCACTCATCCATTGGACCTAATCAAAG
107071 T G TTCAAATCCACCCTCTTCTATCAAGCTCCAAAAACAAAACCATGGGTGTCAAAGGATTCGTTGAAGGAGGCATCGCTTCAATCGTCGCAGGCTGCTCCAC[T/G]CATCCATTGGACCTAATCAAAGTTCGCATGCAGCTCCATGGCGAATCCAATCAGGTCCCCAACCTCGCCTTCCCCAATTCCAACATGT
107071 G A ACCCTCTTCTATCAAGCTCCAAAAACAAAACCATGGGTGTCAAAGGATTCGTTGAAGGAGGCATCGCTTCAATCGTCGCAGGCTGCTCCACTCATCCATT[G/A]GACCTAATCAAAGTTCGCATGCAGCTCCATGGCGAATCCAATCAGGTCCCCAACCTCGCCTTCCCCAATTCCAACATGTCCGTCCCGA
107071 A G GGATTCGTTGAAGGAGGCATCGCTTCAATCGTCGCAGGCTGCTCCACTCATCCATTGGACCTAATCAAAGTTCGCATGCAGCTCCATGGCGAATCCAATC[A/G]GGTCCCCAACCTCGCCTTCCCCAATTCCAACATGTCCGTCCCGATACACATGAACCGACCTGTCCGCACGGGGCCCGTCTCCATCGC
107071 A G AGTTCGCATGCAGCTCCATGGCGAATCCAATCAGGTCCCCAACCTCGCCTTCCCCAATTCCAACATGTCCGTCCCGATACACATGAACCGACCTGTCCGC[A/G]CGGGGCCCGTCTCCATCGCCGTCCAGATCGTAAAAACCGACGGCGCCGCCGCCCTCTTTTCCGGCGTCTCCGCCACCGTTCTGCGTCA
107071 A C CCCGCATGGGCCTGTACGAGATCCTCAAAACCAAATGGTCCGACCCAACCACCAAATCCCTCCCCCTCAACCGTAAAATCGCGGCAGGCCTGCTCGCGGG[A/C]GGCGTCGGAGCCGCGGTCGGTAATCCAGCCGACGTGGCGATGGTGCGGATGCAGGCGGATGGCCGCCTCCCCGCGGCCGAACG
107071 T C TCCCCCTCAACCGTAAAATCGCGGCAGGCCTGCTCGCGGGAGGCGTCGGAGCCGCGGTCGGTAATCCAGCCGACGTGGCGATGGTGCGGATGCAGGCGGA[T/C]GGCCGCCTCCCCGCGGCCGAACGTAGGAACTACAAAAGCGTGGTGGATGCGATAACCAAGATGTGCAAAACGGAAGGGGTGA
107071 T C CAGGCCTGCTCGCGGGAGGCGTCGGAGCCGCGGTCGGTAATCCAGCCGACGTGGCGATGGTGCGGATGCAGGCGGATGGCCGCCTCCCCGCGGCCGAACG[T/C]AGGAACTACAAAAGCGTGGTGGATGCGATAACCAAGATGTGCAAAACGGAAGGGGTGAAATCGCTGTGGAGGGGGTCGGG
107071 AG A GGCGGATGGCCGCCTCCCCGCGGCCGAACGTAGGAACTACAAAAGCGTGGTGGATGCGATAACCAAGATGTGCAAAACGGAAGGGGTGAAATCGCTGTGG[AG/A]GGGGGTCGGGGCTGACGATCAACCGGGCGATGATTGTGACGGCTAGTCAGCTGGCGACTTACGATGAGGTGAAGGAAGGA
107071 C T TGAACATGAAGCCTGGGGATTACGACGGAGCTTTGGATTGCGCCTTTAAGACGGTGAGGAAGGAGGGGTTCATGGCCCTTTACAAAGGGTTTGTTCCTAC[C/T]GTGATGAGGCAGGGACCCTTCACCGTTGTGTTGTTTGTTACGCTTGAGCAGGTTAGGAAGTTGTTGAAGGATTTTTGATTTGGTTT
107071 A C GGGATTACGACGGAGCTTTGGATTGCGCCTTTAAGACGGTGAGGAAGGAGGGGTTCATGGCCCTTTACAAAGGGTTTGTTCCTACCGTGATGAGGCAGGG[A/C]CCCTTCACCGTTGTGTTGTTTGTTACGCTTGAGCAGGTTAGGAAGTTGTTGAAGGATTTTTGATTTGGTTTTTTTGGATTTTGAAT
107071 T C TTTGGATTGCGCCTTTAAGACGGTGAGGAAGGAGGGGTTCATGGCCCTTTACAAAGGGTTTGTTCCTACCGTGATGAGGCAGGGACCCTTCACCGTTGTG[T/C]TGTTTGTTACGCTTGAGCAGGTTAGGAAGTTGTTGAAGGATTTTTGATTTGGTTTTTTTGGATTTTGAATTTTGTTGATGATGATGG
107071 T C GGGGTTCATGGCCCTTTACAAAGGGTTTGTTCCTACCGTGATGAGGCAGGGACCCTTCACCGTTGTGTTGTTTGTTACGCTTGAGCAGGTTAGGAAGTTG[T/C]TGAAGGATTTTTGATTTGGTTTTTTTGGATTTTGAATTTTGTTGATGATGATGGCGAAAAACTTTAGGCGTTGCTAGAAGTTGTTCGA
107071 T C GGAAGTTGTTGAAGGATTTTTGATTTGGTTTTTTTGGATTTTGAATTTTGTTGATGATGATGGCGAAAAACTTTAGGCGTTGCTAGAAGTTGTTCGATTA[T/C]TGTGAGCATAATTATTATTCGTTAATGCCTAATGGCGATTAAATTTGTATTTTCATGGATACTTCAATATATTATATTGTATTAAATT
107071 C T TGATTTGGTTTTTTTGGATTTTGAATTTTGTTGATGATGATGGCGAAAAACTTTAGGCGTTGCTAGAAGTTGTTCGATTATTGTGAGCATAATTATTATT[C/T]GTTAATGCCTAATGGCGATTAAATTTGTATTTTCATGGATACTTCAATATATTATATTGTATTAAATT
107073 C T ACATTGACTATGTTGGTTCATGGGGACCAGCTATCATAGGTCATGCTGATGATAAGGTAAATGCAGCCCTAATTGAAGCTCTAAAGAAAGGCACAAGCTT[C/T]GGCGCGCCATGCTACCTTGAAAATGTGCTAGCCTCAATGGTGATATCTGCCGTACCAAGCATCGAAATGGTCCGGTTCGTCAACTCC
107073 C T ACGGCACCGAGGCTGTCAAGTCCCTTTTCGCATCCCACAGGGGAGAGATCGCCGCTGTTATCCTTGAGCCTGTTGTCGGGAACGCCGGCTTCATAAAACC[C/T]GATCCGGAATTCATGGCCGCCCTACGCCAACTAACCATGGAGGACGGTGCCCTTTTGATATTCGACGAGGTCATGACCGGGTTCCG
107073 T C TCATGACCGGGTTCCGTTTATCCTACGGAGGGGCCCAAGAGCTGTTTGGGATCACCCCGGATATGACCACCCTAGGGAAGGTCATAGGTGGAGGGCTCCC[T/C]GTTGGGGCATATGGGGGTAGAAGGGACATTATGGAAATGGTGGCCCCGGCAGGGCCAGTATACCAAGCTGGCACATTGAGTGG
107073 G A GGCAGGGCCAGTATACCAAGCTGGCACATTGAGTGGGAACCCGCTTGCGATGACGGCTGGCATTCATACATTGAAGAGGCTGCAAGAGGAGGGTACATAC[G/A]ACTATCTGGATAAGGTAACGGGAGATTTGGTAGGTGGGCTTTTGGAGGCTGGGAAGCAGGCTGGGCATGAGATGTGTGGGGG
107085 A AT AAGTGATTTTTCACATTGCCCCCTTATGCCGGGGCTACCTGATGATGTTTCCAAATTTTGCCTTGCTCTTGTTCCTAGAAAATACATACCTGTTATGGGT[A/AT]TGTTTGTAAAAAGTGGAGGTTGTTTATTAAAAGCAAGGAGTTCAATATTGTAAGGAAAGAAGCTGGTAAGCTAGAGGAATGGCTGTA
107085 A G AACTTGCCAGTATGGCCACCCCACGATTCGACTTCGCCTGCACAGAACTAAATGGCCTGATTTACGTGATCGGGGGCTACAGCTCCACCGGTGACAGTCT[A/G]TCCAGTGTCGAAGAGTATGACCCACAAACAAACAAATGGGCCCCCGCTCCGAGCCTCCACCGCCCGCGCTGGGGCTGCTTCGCTTG
107087 T A CAGTTATGACATCAATAACTTCTTATGCATTGGGAATACTCATGATCTCAAAATCTCCATGGTATTTGTTGCCTTTAGCGTGGGCATGGACCGGCACAGC[T/A]GTTACAGGGTTTTTTGTGGTCGGCCATGACTGTGCTCATAAATCATTTTCGAGAAACAAGCTGGTGGAAGACATTGTTGGAACTCTTG
107093 G A GGGCAACCCTCGTACTTGTCCTTGTCGTCTGAAGGACTGTGGTCAAGTATTCATGAATTTGCAAAATTTAAGTATCAGTTTGAATTACCAGAAGATGCAA[G/A]ATTGCAAGTGAAAAAGATCTCCGTTCTGCGAAATCTATGCCTAAAGGTTGGCATCTCGATTGCATCACGTAAATATGATCTCGATTCC
107093 A G GTCCTTGTCGTCTGAAGGACTGTGGTCAAGTATTCATGAATTTGCAAAATTTAAGTATCAGTTTGAATTACCAGAAGATGCAAGATTGCAAGTGAAAAAG[A/G]TCTCCGTTCTGCGAAATCTATGCCTAAAGGTTGGCATCTCGATTGCATCACGTAAATATGATCTCGATTCCACGTCGCCATTCCAACT
107093 C T TGGTTTTATATCATGCGGGCGATCTACCAGGTGCCATCCTACAGCAGCACAAAGAACTTATCATTAACGAGCGTTGCCTTGGTCTTGATCACCCTGATAC[C/T]GCTCACAGTTATGGAAATATGGCCTTGTTCTATCATGGTCTTACGCAAACAGAACTTGCTTTACGCTATATGTCTCGAACCATATTGCT
107095 CA C ACCACCGGATAGTTGGCTAAGTTCAGTGCCAAGGCATCTCGTGGATAGCCAACTGTCGGCGATGAAATCAAACGAAGAACACCCAACCAAAAACAGATTG[CA/C]AAAAAAATGGACCAACAGCTAAGCTGCAAGACATTCCGTCCCCAAACACTTGACAACCAGAAGACGCCCCTAAAATCAGATCTAA
107111 G C TTGTAGTCAACCTTGGCGACCATGGTCATTATTTGAGCAATGGTAGGTTCAAGAATGCAGACCACCAAGCGGTTGTGAACTCTAACTACAGCCGACTGTC[G/C]ATTGCCACGTTTCAGAATCCAGCACCAGAGGCGACTGTGTATCCTTTGGCAATTAGGGAAGGAGAGAAACCGATTTTGGAGGAGCC
107115 G A CTTGGCAATGCAGTGGTTCATTATACCAACGTATAACTAGTACAAATTGCTGAATAATTAGAATGGACAACAATAAATTGGCAAACATGCTGCTTCACTT[G/A]GAGAACAGCCCAAATGTAGCATAGAATCCAACCTTAACAGATAACAAAACTCAAATGTAGTATAGAATCCAACCTTAATAGATAACAG
107115 A T AGAATGGACAACAATAAATTGGCAAACATGCTGCTTCACTTGGAGAACAGCCCAAATGTAGCATAGAATCCAACCTTAACAGATAACAAAACTCAAATGT[A/T]GTATAGAATCCAACCTTAATAGATAACAGAACTCTAAAGTAGCAATCCACATATCTCAGACTGACATACAGTTTACCCAATAAAACTC
107115 C G CAGCCCAAATGTAGCATAGAATCCAACCTTAACAGATAACAAAACTCAAATGTAGTATAGAATCCAACCTTAATAGATAACAGAACTCTAAAGTAGCAAT[C/G]CACATATCTCAGACTGACATACAGTTTACCCAATAAAACTCAGCTGAATAAGCAGTTGAAAGATTAAAATAAAAATCTGGTTCAGTTT
107115 A C TAACAAAACTCAAATGTAGTATAGAATCCAACCTTAATAGATAACAGAACTCTAAAGTAGCAATCCACATATCTCAGACTGACATACAGTTTACCCAATA[A/C]AACTCAGCTGAATAAGCAGTTGAAAGATTAAAATAAAAATCTGGTTCAGTTTCAAAGAAACGAAATAGCAACTTTTAATGTCTACGAC
107115 T TA AACCTTAATAGATAACAGAACTCTAAAGTAGCAATCCACATATCTCAGACTGACATACAGTTTACCCAATAAAACTCAGCTGAATAAGCAGTTGAAAGAT[T/TA]AAAATAAAAATCTGGTTCAGTTTCAAAGAAACGAAATAGCAACTTTTAATGTCTACGACTGAGTCTTTTCCCCTTCCTCTTGTTTCTCT
107115 G GT TCCTCTTGCCCTTCTTCTCAGCCTTCTCCACTTTCTCTTCCTTCTGAATATCGGGATTATCCAATTCAATAGAAGCCGAAAGACGCATCTTAAGCTTAGG[G/GT]TCTTCAACTGCTGAGTACGGGAAGGCCTCGACATGTAAACCCTTTCGTTTTTGCACTCGTAGGTCCAGTGACCGGACTGGAAGCATTTC
107115 C T TTAAGCTTAGGGTCTTCAACTGCTGAGTACGGGAAGGCCTCGACATGTAAACCCTTTCGTTTTTGCACTCGTAGGTCCAGTGACCGGACTGGAAGCATTT[C/T]TGGCACTGAGATGACTGGTTTCCGGTAGACGAGGACATGGAAATCTGCTTATGATCTTTTCTTTCTCCTAGTTTCACAGCCTTCTCTG
107115 A G TCTCTGTGCTCATGAGGTACATCTGCCTCTTGGCTTCTTTCCGCTCCTGCCATCTGCTTGGGCCCTCTTCCTTTTGACCATAGGCGTTCACGTTTCGGGC[A/G]GCAGCTGTGGCTGCTCTCTCTGCCTGTGCACGGCTTAGCCCTTTGGCGGCCGACAGTGCCGCTGCTTTTATTCGATCAGCTGCTGCCTG
107115 A G GTGCCGCTGCTTTTATTCGATCAGCTGCTGCCTGGGTTTTCTCTTCGTTCTTCCCTGACATTTCTTATTTATCGTGAACCAATTAGCTCAGTAAGGTGGA[A/G]ATCGACAGTCTGCACTTCGAGATCGACAGGCGGCGGCTGGAACGAACAAGATTACGTTAGAGCGAGATGCGGATTTGAGAGTGGAAA
107115 AGGCGGCGGCGGCAGTAGGC
A TGCCTGGGTTTTCTCTTCGTTCTTCCCTGACATTTCTTATTTATCGTGAACCAATTAGCTCAGTAAGGTGGAAATCGACAGTCTGCACTTCGAGATCGAC[A/AGGCGGCGGCGGCAGTAGGC]GGCGGCGGCTGGAACGAACAAGATTACGTTAGAGCGAGATGCGGATTTGAGAGTGGAAATCAGGAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107117 AG A TCTGATAGCTCCTCACCTTGAGAAGGCTCAATCTGGACAGGAGACTCTAGTTCCTTGCGTGGAGAAGACTCAACCTATACAAAATGCTTCTCGTCCTAAA[AG/A]GGAAAACGCATCTGCGCCTCATAGCTGCAAGTCCAGTGAGCCAAAGAGTATAATAATGTTTGTTCTGGAAATCCCAACGCTCCGGA
107121 G A TCTTCATTATCTTCAGAAATGCCACTTTAAAAGCATTACATCCTTCCAGAAACTTAGTAATGGCTGAATCGGTTTTCTCTTCATATTCATCATCGTCATC[G/A]TTAAGATCGTAATTTCTATACTCTTCGTCACTAGAATCTTGTTCTTCCTCCTCAAAGTGTCCTTTTTCTTCAATTTCCTCATCTTCATCTTCTT
107123 A G CAGTTGATAACAACACATCCTGTGATCAAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGAC[A/G]GCAAGATGGCCCTTCATCGTGTTTCTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACC
107123 A T TTGATAACAACACATCCTGTGATCAAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGC[A/T]AGATGGCCCTTCATCGTGTTTCTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATG
107123 C T ACACATCCTGTGATCAAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCC[C/T]TTCATCGTGTTTCTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACC
107123 C T CCTGTGATCAAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCCCTTCAT[C/T]GTGTTTCTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCC
107123 T C ATCAAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCCCTTCATCGTGTT[T/C]CTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCCTCAACC
107123 G T AAGCCAATTTGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCCCTTCATCGTGTTTCT[G/T]TCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCCTCAACCGCC
107123 T C TGTTCAGTGTACTGTCCCCTCTGCTGAACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCCCTTCATCGTGTTTCTGTCAGGCTC[T/C]ATGTTCTGCTTGCTAAGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCCTCAACCGCCTAGACTACA
107123 T A ACATGGATCAGTCAAGCAACAGGGGAAGCACCGCGACAGCAAGATGGCCCTTCATCGTGTTTCTGTCAGGCTCTATGTTCTGCTTGCTAAGCAGCACATC[T/A]TGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCCTCAACCGCCTAGACTACACCGGCATCGCCGTCATGATAGTCACC
107123 CCTT C AGCAGCACATCTTGCCACCTGCTGTGCTGCCACAACCATGACCTGAACCTCTTCCTCAACCGCCTAGACTACACCGGCATCGCCGTCATGATAGTCACCT[CCTT/C]CTTCTTCCCTCCCATCTACTACATCTTCCAGTGCCAGCCCGTCTACCAAACCGCCTACCTTGCCACCATATCCGCTTTCGGCCTCTTA
107123 T C CTAGAAGGAATATAACCTTGGCCTATGAAGGCCTGATGGCTGGATCTTACTTGGTTGGGACCCTATTCTATGTTAGTAGAGTGCCCGAGCGCTGGAGGCC[T/C]GGCTGGTTCGACCTGACAGGAAATAGCCATCAGATTTTTCATGTGTTGGTCATGTGTGGTGCGCTAGCACATTACGCAGCAGGGCT
107123 C T GTGGTGCGCTAGCACATTACGCAGCAGGGCTCGTTTTTCTGGAGTTCAGGGATGCTGTTGGATGCAGTAGCTGATGATGGGCAAACTCTTAAGAATCTTG[C/T]ACCACTACAATACTATTGTTTCTTTAGACAGATTTGTATTTATTTATCTGTATAGGTTTGTGATTCTTCTGAAAAGTTCGTGCAAGCAA
107125 G A CTCCATATTTTCATCTATATGCACATATAATACATCACATCGCATATCATAAAAATACCAGCTGGGAGAAGGGCTTAA[G/A]GCACAGCTTAAAACACATCTAATGTTACATACATCACCAGACCTATCCACAGTCCTTGACCATAACAGTTCACCTGCACGGACCCAACGGGGCGCCACAC
107125 C T TATATGCACATATAATACATCACATCGCATATCATAAAAATACCAGCTGGGAGAAGGGCTTAAGGCACAGCTTAAAACACATCTAATGTTACATACATCA[C/T]CAGACCTATCCACAGTCCTTGACCATAACAGTTCACCTGCACGGACCCAACGGGGCGCCACACAAACAGTCGTTACTGGCGAAAGAC
107125 T C GCACAGTGAGATTGGTAAGCCTGCCGAAATTACCAGGAATGGTGCCAGTGAGCTGATTCCCGACAAGGTCAAGATGTCGCAAAAACGGCAAGGACATTCC[T/C]ACACATTCTGGAATCGTACCTGTAATCTGCTTCCAATCTGCAAGAATAAGCGAAGAAAGGCGCGACAGCTGACACACTGCCGGAG
107125 T G CAGTCCATTTGTTGCAGCAATTAGGACCAGTCCAAGATTTGAAGACACCAATGTAAGGGTCGTTGAGAGCGGCACGAAAACTGAGAAGGGCAGAGCGGTC[T/G]GTCGGGTGGCAAACTGGAACAGCACAAGTGTTGGCTGCTAAAGAGACGAGGAAGAAGATGGTTAGTAATGGAGACATTTATCA
107127 T A ATACTTTGTGCGTATGTGGCTATAATCACAGACATATATGAAAGTTATCACACAGTACCTTTTTCAGATATTTTTCAATAATATCAAACAAAATGGGAGA[T/A]GCAACTGTAGTATACACGCCTGCCGTAAAAGTTAGAGTAGCTCCTGCAACCATTTTCCAATTACTATTCAGGAAAGAGACCATTTTGCT
107127 G C ATCACACAGTACCTTTTTCAGATATTTTTCAATAATATCAAACAAAATGGGAGATGCAACTGTAGTATACACGCCTGCCGTAAAAGTTAGAGTAGCTCCT[G/C]CAACCATTTTCCAATTACTATTCAGGAAAGAGACCATTTTGCTCAGCTTCTTCTCATCTGGGGCTGCAATCACTTTAACTCCAATCGCTT
107127 C T TCACAAACATAAGTAAGGGAATCAACTACACCTCCATGGGTAATATAAATTTTTGTCAAACGGGTAGATGCATTGATTTCTATTGTTGAGTTTTCTTGTA[C/T]TGTACCTCCACTGGTGCCCCATGGTTCGGTTGTGATAGGTATCACCTGTTGATGTTCAGTATCTGCGAAGAAAAGACGGGAAAGTAGA
107127 T C AGAGATGTCACAACAATATTGCCATTAAATGAGCCATAGGTTCCTTTCATCGAAGTGAGGAACTCATTATTGCCAAAAGTAACCTCAGAACGTAGGCTGC[T/C]TGTACCTCCCCATGTGCCTGAAGATTGAGATATTCCATTGGTCTCACAAATAAACTCGATGGAAATAATTACAGCTGCATGAGCAATG
107127 T C GAACGTAGGCTGCTTGTACCTCCCCATGTGCCTGAAGATTGAGATATTCCATTGGTCTCACAAATAAACTCGATGGAAATAATTACAGCTGCATGAGCAA[T/C]GTTAATACTTCTCAAATGAGTAGTGGTGTCAAATTTTCCAGGATAATCTTGTCTATATTCCATAGTCAGACCCCAGGGCGATACCTTG
107137 C T TTACATCGCTGCACAACGAGATCCAACCTGATGGATTAGTTCCGGTTCTTTATGTCAAACTTTCACTACCTCATTCACAAATCCTAAATGCACATTAACT[C/T]GTGAGACCAGAAAAAACATGTTCATACAAAGCTTCCCAAACCTTAGACGCTGGACTTGAAATGGTTCTTTTTCCTCTTTTTCTGCAGACAG
107137 T A AATGGTTCTTTTTCCTCTTTTTCTGCAGACAGTGGATCGTGCAAAGGATGGAAACTTGAACGAAAAGAGAGGACACTTAGAAGAAGCGTTTTCTGAAACC[T/A]CTGGTCGTTGCTTGATAAGAGCGCATGAGAAGGCCGATACCAATTCCAATACCAACACACATTCCTAAACCTATTCCAACTCCAACTC
107137 G A TTCTTCAACTGGTTTCATAATATTTTGAGAAACCAATCCATTTTCCTTTCTCTCGGCACAACTCTCATCGTCTTCCAGTATGGAATTTAAACCTCCACAA[G/A]CCTTCTTACTTCTAGGACTCAACTGCATGGTCTGCGTCAAAATCAAAGGTGCCCCGCCATAACACCCAGCTATGTAAACCTCCACAGTTGG
107137 C T CAACTGGTTTCATAATATTTTGAGAAACCAATCCATTTTCCTTTCTCTCGGCACAACTCTCATCGTCTTCCAGTATGGAATTTAAACCTCCACAAGCCTT[C/T]TTACTTCTAGGACTCAACTGCATGGTCTGCGTCAAAATCAAAGGTGCCCCGCCATAACACCCAGCTATGTAAACCTCCACAGTTGGATTCA
107137 T C TCTCGGCACAACTCTCATCGTCTTCCAGTATGGAATTTAAACCTCCACAAGCCTTCTTACTTCTAGGACTCAACTGCATGGTCTGCGTCAAAATCAAAGG[T/C]GCCCCGCCATAACACCCAGCTATGTAAACCTCCACAGTTGGATTCAAACAAATCCCTTTCATCAAACCCGACCCGTTGATTCCCGCTCCC
107137 G A CACAACTCTCATCGTCTTCCAGTATGGAATTTAAACCTCCACAAGCCTTCTTACTTCTAGGACTCAACTGCATGGTCTGCGTCAAAATCAAAGGTGCCCC[G/A]CCATAACACCCAGCTATGTAAACCTCCACAGTTGGATTCAAACAAATCCCTTTCATCAAACCCGACCCGTTGATTCCCGCTCCCAGATAC
107137 T C AACCTCCACAAGCCTTCTTACTTCTAGGACTCAACTGCATGGTCTGCGTCAAAATCAAAGGTGCCCCGCCATAACACCCAGCTATGTAAACCTCCACAGT[T/C]GGATTCAAACAAATCCCTTTCATCAAACCCGACCCGTTGATTCCCGCTCCCAGATACATGTCCATGGTCCAACCTGATGATTTCTTTTGG
107137 A G TCAAACAAATCCCTTTCATCAAACCCGACCCGTTGATTCCCGCTCCCAGATACATGTCCATGGTCCAACCTGATGATTTCTTTTGGTCCTCATTGGACCC[A/G]TAAACGGTCCCGTTGCTCCATGCTGGCTCAATCTTCTCCAAAGTTCCGCAAAGAATCAATGTCTTGCTGGTATCATCGTATACCTCAAAG
107137 C T TCCCTTTCATCAAACCCGACCCGTTGATTCCCGCTCCCAGATACATGTCCATGGTCCAACCTGATGATTTCTTTTGGTCCTCATTGGACCCATAAACGGT[C/T]CCGTTGCTCCATGCTGGCTCAATCTTCTCCAAAGTTCCGCAAAGAATCAATGTCTTGCTGGTATCATCGTATACCTCAAAGTCTGACGCA
107137 T G TTTGTAGGGAAACGTTGGTCGGACGGCGGAGATGGGTAAGAGTGAGGGATGGCGGGGCGTGGGTGGTTGAGCAGGGGTTGATTCTGATGTAGAAGAGACG[T/G]ATCTCCAAGAATGAGGAGGAGGACATGTTTTGAGTGTATCAGCAACAAATCATCGATGAGTCAAGACTTGAATTAAAACTAG
107147 T C TAGCTTGGTTTGCAGTTCTAGTTGGGATGGCGAGTCAACTTACCAGCCTAGGAATTGTCACATGGATGTCTGGTTCTGTTGCAAAATTTCTACAGTCTTT[T/C]TCTTTGAGTTGGCCTGCTGCATTTGGCGTTCTTCAAGCATCGTATTTTTTCATTCATTATTTATTCGCAAGTCAAACAGGGCATGTTGGG
107147 T C TAGTTGGGATGGCGAGTCAACTTACCAGCCTAGGAATTGTCACATGGATGTCTGGTTCTGTTGCAAAATTTCTACAGTCTTTTTCTTTGAGTTGGCCTGC[T/C]GCATTTGGCGTTCTTCAAGCATCGTATTTTTTCATTCATTATTTATTCGCAAGTCAAACAGGGCATGTTGGGGCATTGTATTCTGCATTT
107151 C T CTTCTGTCAGATGGGGTTCAAGTACAGCTCAAGGGCCGAGGTCAGAGATGGAAGATGATGTTGTTATGATACTTGACGGGATTGATGGATTTGCCTTCGC[C/T]GCTGTTTTTGATGGTCATGCTGGCTTCTCTTCTGTTGAATTTCTCAGGGACAAGCTGTATGAAGAGTGCGTGGCTGCATTGCAAGG
107151 GT G TGTCAGATGGGGTTCAAGTACAGCTCAAGGGCCGAGGTCAGAGATGGAAGATGATGTTGTTATGATACTTGACGGGATTGATGGATTTGCCTTCGCCGCT[GT/G]TTTTTGATGGTCATGCTGGCTTCTCTTCTGTTGAATTTCTCAGGGACAAGCTGTATGAAGAGTGCGTGGCTGCATTGCAAGGTGG
107151 C T TTGAATTTCTCAGGGACAAGCTGTATGAAGAGTGCGTGGCTGCATTGCAAGGTGGTTCATTGCTGACTAGTAATAACTTTAATGCTATTAAAGATGGAAT[C/T]GCAAAAGCTTTCCAAGCAGCTGATGTTAAACTTTCATCTTGGCTTGAACAGGTAGGAAGAGACGTTGACTCTGGTGCGACAGCTACA
107151 A T ATGCTATTAAAGATGGAATCGCAAAAGCTTTCCAAGCAGCTGATGTTAAACTTTCATCTTGGCTTGAACAGGTAGGAAGAGACGTTGACTCTGGTGCGAC[A/T]GCTACAGCCATGTTCCTGGGAAAGGATGTATTGATAATATCACATGTTGGTGACTCAAGTGTGGTCATATCAAGAAATGGGAAAGC
107151 A G CTTGGCTTGAACAGGTAGGAAGAGACGTTGACTCTGGTGCGACAGCTACAGCCATGTTCCTGGGAAAGGATGTATTGATAATATCACATGTTGGTGACTC[A/G]AGTGTGGTCATATCAAGAAATGGGAAAGCTGAAACCTTAACAGGTCCACATAGGCCATACGGCAACAACAAAGTTTCTCTTGAAG
107151 T TA CGATTCAAGACAAAGAAGAATGAAATGCTTAGAAAAGGAGTTGAAGAGGGGAGATGGACAGAAAAGTTTGTGTCCAGAATACAATTCAAAGGTGACTTGG[T/TA]ACATCCTCCCCTGATGTCCTTCAACTTGAATTGGGATCTGATGTGGAATTTGTATTGCTTGCATCTGATGGTTTATGGGACTATC
107153 C G CGCCGCCACGACCTCTGCCACCTCCTCTGCCACCATCACGGCCACCCCTTCTCCCTCCTGATCTTCCACCTCGGCCTCCACTGAACCCACCATCTCCACT[C/G]TCAGGCCTTGGTCTTGCCTCATCCACTGATAAATAGCATCCATCCAGCTCTGATCCATTCAACTCCAAAGCTTTATTGATACTCTCTCTGTC
107153 C T ATCAACAACTTCCCCGGCCTTATTAAAAAACTCAGATATCTCCTCTCTTCCAGCATTAAAAGATAAATTTCCTACAAAGATAGTGTTTGATTTGGGGTCG[C/T]CTTGGGAAGGAGTTATTGGCTCTGATTTCCCAGATTTTGCAGGTGTTGCTGATAGTGCAGCATCCTTCATCTCAATGTCAGTGTCCTTCT
107155 T C GGACCTTGTTGTTAATCCCATTTGATGTAGGCAATGGAGCGTAAGACCTACCAGTGAGTTTTGAAGGCGAAGGAACAGGCTCAGACAATTTTCCTTCAAA[T/C]ACTGAAGTCACCACTCGCCAATACTCAGATTCTTCCTGCTCTGTCAGATCTATTATCTGTATGAAGGTCGGCAACATCCGCTGGAATT
107155 A G CAGATTCTTCCTGCTCTGTCAGATCTATTATCTGTATGAAGGTCGGCAACATCCGCTGGAATTGGTCTTGCTTGTGAAATATTTTATCCCGGCATAGCGT[A/G]TATTTTTCAAGACATGTACACCAATCACCATGCCCTGCAGCAAACCACCATTGGTCGGAGACCTTTTTATAGAGTCTAGCATAAGCTTC
107155 A G AGGTCGGCAACATCCGCTGGAATTGGTCTTGCTTGTGAAATATTTTATCCCGGCATAGCGTATATTTTTCAAGACATGTACACCAATCACCATGCCCTGC[A/G]GCAAACCACCATTGGTCGGAGACCTTTTTATAGAGTCTAGCATAAGCTTCCCAGCGCTTTTCCTGAAAAGAATGTCTTCTCTCAGCTAC
107155 C T TAATGGAACTCTGTTCCAAATCATCGTGAATATAATCCTCGCTTTCCATGCAGTTCGTATGGCAGGATGGCGAAGGTGAACATGCCACGGAATCATACAC[C/T]GGGCTTCTAATTTCCACATTATTTTCTTTGTACAACCAATGAGCTGCGAGTCCAAACTCAGCATATTCATGCATCCGCTGTGAGCGAA
107155 G A ATGGAACTCTGTTCCAAATCATCGTGAATATAATCCTCGCTTTCCATGCAGTTCGTATGGCAGGATGGCGAAGGTGAACATGCCACGGAATCATACACCG[G/A]GCTTCTAATTTCCACATTATTTTCTTTGTACAACCAATGAGCTGCGAGTCCAAACTCAGCATATTCATGCATCCGCTGTGAGCGAATC
107155 C T AATCATACACCGGGCTTCTAATTTCCACATTATTTTCTTTGTACAACCAATGAGCTGCGAGTCCAAACTCAGCATATTCATGCATCCGCTGTGAGCGAAT[C/T]TGCACTTCTATAGGTGCACCATCAGGGCCTTTCACAGCAGTATGAAGAGACTGATATCCACTAGGCTTCGGATTGATGATATAGTCATC
107167 C T GGGCTGGCTTCATAGGAACGCACACTGTGCTTCAGCTTCTCAAAGAAGACTTCCATGTCACCATCATCGACAATCTCGATAACTCGGTTCCAGATGCAGT[C/T]GATCGTGTTCGTGATCTTGCTGGCCCTGAGCTTTCTAAGAATCTGAAGTTTTGCATTGGAGATTTGAGGAATAAGAGCGATCTTGACA
107167 C T TGGCTTCATAGGAACGCACACTGTGCTTCAGCTTCTCAAAGAAGACTTCCATGTCACCATCATCGACAATCTCGATAACTCGGTTCCAGATGCAGTCGAT[C/T]GTGTTCGTGATCTTGCTGGCCCTGAGCTTTCTAAGAATCTGAAGTTTTGCATTGGAGATTTGAGGAATAAGAGCGATCTTGACAAGCT
107167 A G TGTGATCCATTTTGCTGGGTTGAAAGCTGTGGGAGAAAGCGTAGCTAAACCTCTCAGATACTTTGATAATAACTTGATTGGCACTTTGAATTTGTATGAA[A/G]CCATGACTAAATATGGTTGCAAAAAGATGGTGTTTTCCTCTTCTGCAACTGTGTATGGCCAACCAGAAAAAATCCCATGTGTGGAGG
107167 G C TTGAAATGGTTGCTGCATTTGAAAAGGCCGCTGGCAAAAAAATACCAATCAAGTTGTGTCCGAGGAGGCCAGGTGATGCAACTTCTGTTTATGCTTCTAC[G/C]GACAAAGCTCTCAAAGAACTTGGCTGGAAAGCAAAGTATGGAATAGAGGAGATGTGCAGAGATCAATGGAAATGGGCAAGCAAA
107167 AT A AGCAAAAATCCATTTGGTTACAAGTCCAAACCTTGAAAGCAACCAGTTACTGAAACTTTAAGTTTCATTTTAGTTCAAATAAGTGTGCATATGCAAATTA[AT/A]TTACCTTTTCATTGCTAAGAACTCGCTATTTAACTTGTAACCGACTTAAATGTTTCATTAAGTCGAGCAACGTAATGATGTTTT
107171 AT A CTAGCGATCATAAAGACAACACATCTGTTTCACACACAGTCGCATGCGGCATTGAAAAGTTGATGATGAAAGACGCGACAACCGATGACCTTCTTACGGG[AT/A]TTTTTTTCTATAATTTGCACAATCTGTCCTGTTTATCTAGAACTTGCGAAGAAGGTTTTAGGTGTGCTGGAATTCAATCCAAAATGC
107171
GTAGGTATGGCAGCCATAAC G GAATCCTAGCATTGACTGGACAGGAAAGCAGCTTTTAGGCAATCTTGCCTCCGAGGGAGGATCACAGCTGAGCCTCTCCACTTCTGCTTCCACTTGATAT[GTAGGTATGGCAGCCATAAC/G]TAGGTATGGCAGCCATAACTAGATCTTCCTGGTGAAACAATTTTGACTTATTCTCACGGTTACAAAAG
107171 T C CGGTTACAAAAGGTAGTTTCTACTTCAATGGCAGAACACGTCTGAAATCAATATAAGAAAGCAGTAAAACTCAGAGTTCCTATTTTGTATTTGTAGTGCA[T/C]TGGAGTTCCTACTGGTGTATTTGCAGTAAAGAATTTGAAGTATAACCTTTTATTGTTATAGTACTGTAGTGGTCTATTATTGAACTTTAT
107171 G T CAGAGTTCCTATTTTGTATTTGTAGTGCATTGGAGTTCCTACTGGTGTATTTGCAGTAAAGAATTTGAAGTATAACCTTTTATTGTTATAGTACTGTAGT[G/T]GTCTATTATTGAACTTTATACTGCTATACCGAATGATGTAATATTGTTGAGTGATGCTCATAAAATAGTCTATTTTAGAAGAAAAAAAAA
107175 G A AGCAACAAAGCTCGATGATTTGTACTGCTGCTCATAATTTTAACTAAACTCTCTACTAAACAACAATAAACAACAGTGGATCCTGCACCTGATGTTGAAA[G/A]TTCAGGCCAATCCCTGTTCTGCTGTTAAAATTTCGGCCGAAGGGTCAACATAACTACGCCCAAATTGCAAGAGTGGACATCAACCCTA
107175 C T GCACCTGATGTTGAAAGTTCAGGCCAATCCCTGTTCTGCTGTTAAAATTTCGGCCGAAGGGTCAACATAACTACGCCCAAATTGCAAGAGTGGACATCAA[C/T]CCTAATCCAAGCAGCAGCCCTACATATGCCCATAACTGTAGCCTCATGTTATTCTGCAGTCTCGGACTCATAAAATCTGCAGCTAAAA
107175 G T ATCCACCGAGTCCAATTCCTTCGAAGAACTGGTGGAAGCTCAAAGCACCCAACAATGGCCTAACTGTGGAGGAGCTTGTTGATGTGCCTAGTGATATGCC[G/T]ATTATTACTGAATGTACCACTATTCCCAGTTCTAATACTTGAGATATAACTCTCCTTCTAATGGTCTCGGCTTCTTCACCTTCTTCTCCA
107175 T G AATGGCCTAACTGTGGAGGAGCTTGTTGATGTGCCTAGTGATATGCCGATTATTACTGAATGTACCACTATTCCCAGTTCTAATACTTGAGATATAACTC[T/G]CCTTCTAATGGTCTCGGCTTCTTCACCTTCTTCTCCAAATCCAGCAAGCCGATGAGCATGCACACTCCCACTCTCAACAACCGCCATGTC
107175 A G TGGTCTCGGCTTCTTCACCTTCTTCTCCAAATCCAGCAAGCCGATGAGCATGCACACTCCCACTCTCAACAACCGCCATGTCATCAACGTCATCGTCAAC[A/G]GGTAAAGCCTTGCTAATCCTACCCCTCCTATAGAACCCCATGGCGAACCCATCCACCATCATCGTCATCACCGCCGATACCATGGCCAC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107175 T G AGTGGGTATGTTCTTACCGACTATTGGAGCAGCTACTCCGACTGCTGCGGCCGTGAGGATCGCGGCTATGGCGGCTAGTTTGAGAGGCAGGGTTTGTGAA[T/G]TGTGGCTGTCGTTTGGGTTTGTGTTGCATTCGCAGGAGGAGAGGGAGAGAAGAGGGTAGGAAAGGAGGGAAAGGATAAATAT
107175 G C TGTTCTTACCGACTATTGGAGCAGCTACTCCGACTGCTGCGGCCGTGAGGATCGCGGCTATGGCGGCTAGTTTGAGAGGCAGGGTTTGTGAATTGTGGCT[G/C]TCGTTTGGGTTTGTGTTGCATTCGCAGGAGGAGAGGGAGAGAAGAGGGTAGGAAAGGAGGGAAAGGATAAATATGTTTTGATT
107175 G A ACCGACTATTGGAGCAGCTACTCCGACTGCTGCGGCCGTGAGGATCGCGGCTATGGCGGCTAGTTTGAGAGGCAGGGTTTGTGAATTGTGGCTGTCGTTT[G/A]GGTTTGTGTTGCATTCGCAGGAGGAGAGGGAGAGAAGAGGGTAGGAAAGGAGGGAAAGGATAAATATGTTTTGATTCCCAGTA
107179 A G TGCCGGTACATCATCCAAGGAAGCAAGGCTTACAGAACCAATCGAATCTAAAGCTGTTTTAAACAATTGAGAACCTCTACGCTTTTCAGGTTGGTCAGGA[A/G]ACACAATGCAGGACCTGATTCCTTTTGTCTCATTTAATTTTCGCACGACAGCTAGAGCAAGTTGAATATTGGCATCTATGAACTCATC
107179 A G TGATTCCTTTTGTCTCATTTAATTTTCGCACGACAGCTAGAGCAAGTTGAATATTGGCATCTATGAACTCATCTGAAGATCCCTTGTACGTAGAAATGTC[A/G]CTCGGCAAGGGCGGGAAGTCGATTTCAAGTCGAGTTTTTCCTTCGTCGAGTGCAAATTCCAAACATTTGGTAGCATCGGAAACAAGAA
107179 T C GAAACACCAGACCTCGGATCAGGACCAGAAGAAGTGGGACCATCTACGTTCACTGCATGCCGTGGTTTCATGTGGGCATATGAGTTGGTAGCAGCAGTAG[T/C]AGTGGAAGAAGAAGAAGATATAGAACAAGATAATGGAGAGGGTAAAGAAGAAGGGTATAGATGGAACTGAGGTGGAGGAATA
107179 G C ACCAGACCTCGGATCAGGACCAGAAGAAGTGGGACCATCTACGTTCACTGCATGCCGTGGTTTCATGTGGGCATATGAGTTGGTAGCAGCAGTAGTAGTG[G/C]AAGAAGAAGAAGATATAGAACAAGATAATGGAGAGGGTAAAGAAGAAGGGTATAGATGGAACTGAGGTGGAGGAATAAGGGA
107179 G A GCATATGAGTTGGTAGCAGCAGTAGTAGTGGAAGAAGAAGAAGATATAGAACAAGATAATGGAGAGGGTAAAGAAGAAGGGTATAGATGGAACTGAGGTG[G/A]AGGAATAAGGGATGTAGATTGAAATAGAGTATAGAAGGGAATGGGAGAGTAAAGAATTTGAAGCCATGGAAAAGAAAATTT
107179 GA G GTAGTAGTGGAAGAAGAAGAAGATATAGAACAAGATAATGGAGAGGGTAAAGAAGAAGGGTATAGATGGAACTGAGGTGGAGGAATAAGGGATGTAGATT[GA/G]AAATAGAGTATAGAAGGGAATGGGAGAGTAAAGAATTTGAAGCCATGGAAAAGAAAATTTAAGAGTGAGAAAAAGAGGA
107181 G A CGATTCCTCATGGCTCCTTTCCAAATCAAATCTCCATCGCTCCCGCACCGCTCCTGCCATCTCCGTCATCCTGTCCGCCTTCTCCCCTTCCTCCTCCGCC[G/A]CCTCTTCCCCACTTTCCCGTCCCTCCATTGTCCGCACTTCCGTCCTCCTCCTCTTCCTCTACCTTTCCCTCGGCGTCGCCATCTACACCTTCTT
107181 A AC CTTCTTCAGAAACAATTTCTCCGCTCTCGCTACCCACCCTGTAATTGACGCCCTATACTTCTGTATCGTCACCATGTGCACCATCGGCTACGGCGACATC[A/AC]CCCCGCCACTCCGTTTGCTAAACTCTTCTCCATCATGTTCGTACTCTTCGGTTTCGGATTTATCGACATACTTCTCTCATCCATGGTCACA
107181 T C TTCTCCGCTCTCGCTACCCACCCTGTAATTGACGCCCTATACTTCTGTATCGTCACCATGTGCACCATCGGCTACGGCGACATCACCCCGCCACTCCGTT[T/C]GCTAAACTCTTCTCCATCATGTTCGTACTCTTCGGTTTCGGATTTATCGACATACTTCTCTCATCCATGGTCACATACGTTCTCGACCTTCA
107187 T C TCTCTGTATTGCTGCTTCTTCACTCTCAGAGTTAAGCTCCCTCACATCATTTTTTACTTCTTCAAATACTTCCTCAAGTTTTCTTGTTTCTTCTCTTTCA[T/C]TCTCCAACTCCAACTTCAAATCTAAAATTCTCTTCTGATTCTGCTCATATTCCACATCAGAGGAGTCAGCAACATATTTGGCCCATTTCAGCTTT
107189 CA C AAATTAACCAGATATCTTTCAGCCCGAGCTCATATTTTCTTGCTGCTGCTGATGATAGTGGCGAGGTTAAGATTATTGATACCCGTCAAAATTGTTTGTA[CA/C]AAAACATTGAGGGCAGTCCATACAAGTATTTGTAGTACCGTGCAGTTCATTCCTTGGAAGCCATGGTCAGCCATTACTGGTGGGCTT
107191 C T CAGATATGCTCCCTGTACGTTTCTTCTACCCAACGTGACTGACACTTCTCATTTATTTCCACACTATCATCTTCATAAAATGGAACTCGAACAAACGCTC[C/T]ATGCCGCGTCGAACTACAGACCGCGACATCCCCATGCGCACAGGCGTTTATACACACTGATACTTCATACGGTCTCGCAAACAAAACCTC
107191 GAA G AACCTACTCGGATGCTATATGCATGCATACAGACTCACGGACCTACTCCTTCCTTGTGTGAACATGGACCGGACGTGTACGTATATATATGATCTGAAGT[GAA/G]AAAAAAAATAAAGAAAGAAGAAGTGTTGAATTGGTTTTAGATTATCAAAGCCATTGCAAGGTTTCGGTCCTCTTTCATTTCTATCC
107195 T C ATTTTGCTGGATGCACCGGATATGGTCATGATGAAGGTGGAGGGCGTGAAGCACTAGACAATCTTTTTGCTGAAATAGTTGGAGCTGAATCTGCAATTGT[T/C]CGCTCACAGTTTTTCTCTGGAACACATGCCATCACGTGTGCTCTGTTTGCTTTCTTAAGGCCTGGGGATGAGCTTCTAGCAGTTGCT
107195 C T AGTCCCACTTGCAGAAGATGGTGGTCTGAACTGGGATTGTCTTTCTATTGCAGTTGGGCATAAAACAAAATGTGCCCTCATACAAAGGTCATGTGGCTAT[C/T]CATGGCGTCGAAGTTTGAGTATTGAAGATATCCAAAGAGCAATACAGATGATCAAGAGGCAAAAACCAGACTGCATGGTTATGGTG
107195 G A AGTGCAGGCAGTGCAACTAGGAAGTAGAGCAGGACTTATTTCATTTTGCGAGGCAGTACAGAGATGCAGTCCAGTTGGTTCCTTTATTAAGCCAGTTGCT[G/A]GTTTTACTCCAGGTTATGCATCAGAGGTTATATTTGCGGACGGGACATTTATTAATGGAAGTACAAGCGAAATGTCTTGTGATGGA
107197 A G ATCCATTCCCCATAACACTGGAAACTTCAACAACCTCGCCTTCCCTCATCTCGCAAATCAAATCCGCGGTCGATCCCGCAATCCTCTTCAATAAAAACTC[A/G]AAGACTCCCACACTCCTCGCCGTTTCAGGCGGTGAAGCTATAGCTAAAAAAGAGGGCTTTTGGGAGGACGGGATACGGACCTGGACA
107197 TA T TCATCTCGCAAATCAAATCCGCGGTCGATCCCGCAATCCTCTTCAATAAAAACTCAAAGACTCCCACACTCCTCGCCGTTTCAGGCGGTGAAGCTATAGC[TA/T]AAAAAAGAGGGCTTTTGGGAGGACGGGATACGGACCTGGACATATTGGCCGGCAGCGGTGAAATTACCAGGAAGCGGGGAGGCG
107197 A G CAAAGACTCCCACACTCCTCGCCGTTTCAGGCGGTGAAGCTATAGCTAAAAAAGAGGGCTTTTGGGAGGACGGGATACGGACCTGGACATATTGGCCGGC[A/G]GCGGTGAAATTACCAGGAAGCGGGGAGGCGGATACGTCGACGGTGACGTGAAACAGAGAGCAGTCGGCGGATGCGGGTTGG
107197 A AG GACGCGAAAGGTGGTTGCGCAGGTGGAGATGGGGAAAGGAGTGGCGAATCATTGGAATGGAGTGAAGGGGAAAAGCATGATTTGTAGAGGAGAGAAGAGC[A/AG]GGGGACGCGTAAGGGGAGATGACTGTGGCCATGTGTCGGAAGTATTGGAATCGTTATCGGCCTTAGGTCCAAAGGCGGT
107201 C T GCCGATTGTGGCTGGCGAGGGTCCATTTGGGTTGGTGGTGTGTCCTTCGCGTGAGTTGGCTAACCAAACTTTTCAAGTGGTGGAGGAGTTTTTGGCGGAG[C/T]TAAGGAAGAGCGGATATCCAGAGATAAGGGCAATGTTGTGTATTGGTGGAGTGGAGATGAAAAACCAATTGGATATGATTAAGA
107201 C T TAGGCTTTGAAGATGACATCCGGGAAGTTTTCGACCACTTCAAATCCCAGCGCCAAACCTTGCTCTTCTCCGCCACCATGCCCAAGAAGATCCAAAATTT[C/T]GCGCGCAACGCTCTCGTGCAGCCCGTCACTGTCAATGTTGGCCGTGCAGGTGCGGCCAACCTCGACGTAATCCAAGAAGTTGAGTAC
107201 G A AAACCTTGCTCTTCTCCGCCACCATGCCCAAGAAGATCCAAAATTTCGCGCGCAACGCTCTCGTGCAGCCCGTCACTGTCAATGTTGGCCGTGCAGGTGC[G/A]GCCAACCTCGACGTAATCCAAGAAGTTGAGTACGTCAAACAAGAAGCCAAAATCGTTTACCTGCTCGAATGCCTCCAGAAGACCCCT
107201 TC T GCCGTGCAGGTGCGGCCAACCTCGACGTAATCCAAGAAGTTGAGTACGTCAAACAAGAAGCCAAAATCGTTTACCTGCTCGAATGCCTCCAGAAGACCCC[TC/T]CCCCCCGTCCTCATCTTCTGCGAGAACAAATCAGACGTTGACGACATCCACGAGTACCTCCTCCTGAAAGGGGTGGAGGCCGTTG
107201 C T TGAAAGGGGTGGAGGCCGTTGCCATCCACGGTGGGAAGGACCAGGAGGAGCGGGAGCACGCCATCTCATCCTTCAAAGCAGGCCTCAAAGATGTGCTTGT[C/T]GCCACTGATGTCGCCTCCAAAGGGCTCGACTTCCCTGACATCCAGCACGTCATCAACTACGACATGCCTGCTGAAATAGAGAAC
107203 GA G TCTTGCCAAGAGCTAAGATGACCAATGCTGATTTGGGGAGAATTATCAACAGTGAAGAGGTTCAAAGTGTAGTGAGACCAATCAACAAGGAGGTAAAGAG[GA/G]AAAAAATTAAAGAAGAATCCTTTGAAGAATTTGAATGTTCTATTGAGGTTGAACCCGTATGCTAAGACTGCAAGAAGGATGGC
107209 T A CACTCGTCCGAGATTTAGATTACAATCCCAAGATGCAGCACGAACTTGTAACTGCTGAGGATGAATCTGGATTGCGCTTGTGGGATCTTAGAATGCCTAA[T/A]TCTCCTGTTAATGAATTTCCTGGGCATGCACATTGGACATGGGCTGTTCGATACAACCCTGAGCACGATCGGCTGATATTGAGTGCC
107209 A G CAACACGATTTGTCGATCCATTGCTAAGCTCATACGATGACTACGAAGATAGTGTTTATGGTATTGCGTGGAGCTCCAGGGACCCAACATTATTTGCATC[A/G]CTGTCATATGATGGACGGGTAGTAGTAGAGTCGATCAAGCATCATCTCCACAAAAGGTGAAACCTAACCATATTATATATCGATCCA
107209 G GA TCACTGTCATATGATGGACGGGTAGTAGTAGAGTCGATCAAGCATCATCTCCACAAAAGGTGAAACCTAACCATATTATATATCGATCCATTCACTAAAA[G/GA]AAAACGAAGGCTTCAAACCGATGTTTATGCTCCATTAAAATAGTTAAAGTGTATTTGCATTGATTTTGTTCATGATTCTGTTTCTCTA
107213 G T AGCACTCTTCCCTAAAGTAGCTGCCAAAACCAATATTTTCTCTTTCCTCCAAATACAAAACTGCTTTCCATGAAACTGCTTTCTCATCACATTTATCCAT[G/T]GTTAACCATGAGTTGCACTAAGATAAGCATTAGGAGTAGAATACATAGGCTTCCAAGCAGAAGCAGTGAGCAAACAAAGATCCTTCCATC
107213 T C TAAAGCCCGAGCGGCTGAGCTTTTCACGCCACATTCCAACTTTGTCCTCCCCGGTTCTGGCTGGCCCACCTACTGCTAGCACGTTTCGTATTTCACGAGA[T/C]AGGAGCTGCTGTTCAACAATGTGTCGGTCGTTATTGTCTTCGCCATAGCTTGCTCCTAGAGAGTCGAATAGTGCTGAATAATAGTGGA
107213 C T TTTCACGAGATAGGAGCTGCTGTTCAACAATGTGTCGGTCGTTATTGTCTTCGCCATAGCTTGCTCCTAGAGAGTCGAATAGTGCTGAATAATAGTGGAT[C/T]GCTTCTACAAATCGGTTTAGAAATGATCCCGTTTGAGTTAGGTCTTGCTCTACCATTGTTATCACCTTCGGATTTATCCTTTGCAGAAG
107213 A G CTTCTACAAATCGGTTTAGAAATGATCCCGTTTGAGTTAGGTCTTGCTCTACCATTGTTATCACCTTCGGATTTATCCTTTGCAGAAGCTTGAGTGTACT[A/G]CTATCAGACCCAGTAACATCATACAAAGAATGATGCAACCAATGCACAGCTACAGCTTCCCTTCTTCTAATCCCTAATCTCTCCGCATCTA
107213 A T CTTCCCTTCTTCTAATCCCTAATCTCTCCGCATCTAAATTCCCAATCTTTCCATTAATAGCAACATACTCAAAACTCAACCCTAAGGTCTCTGCGAAATC[A/T]GTCAATCTCTTCCCTGTGGCCTCTAGAGCCTCCGGTGAGTTCCCCAGACCTGTCAGTCTCACTTTGGGCGGGCCGCCGGGCCTTGAAGCG
107225 A G TGGAACACCTCCCACCGAGAGAAGGATCAACCATTCTAGATAAGTTGTCTATGTCATGAAGTTGAGATCGGGCCCATCTCACTAGATGTTGCTCAGCTCG[A/G]GGAAGTGAACTGTCAAAAGGTTTGCGGGATGTAAGTAGCTCTAACATGACTACTCCAAAGCTATAAACATCACTCTTCTCACTATAT
107225 C A GCTTGGTTCGAACTCCTGGTGAACAATAGAAGGCTGGCATCCCTCATGGAGATACTCTAGTGCTTTTGCAGCTCCTAGGACAACTTGGAGACGAGCAATC[C/A]ATGATAGTTTCTTCTTAAGGTCGTCTTCATAATAGAGTAAATCATGTAAGGTCTTTTTACTGAAATAGTTATAGACGAGTAGCCTCTG
107225 CT C ACTCTAGTGCTTTTGCAGCTCCTAGGACAACTTGGAGACGAGCAATCCATGATAGTTTCTTCTTAAGGTCGTCTTCATAATAGAGTAAATCATGTAAGGT[CT/C]TTTTTACTGAAATAGTTATAGACGAGTAGCCTCTGTCCATGCTCTGCAGAATAACCTACTAGCTCGACAATATTAGGATGTCGAAGTT
107225 T C GCAGGCGCTGGATGAGGTGGTGGAGGTGGCGGCGGAGGTGGGATCATAAAATCTTCAGACACAGCCCTATTAAGAACATGTTCGTTCTTCTTTTCTGTTT[T/C]TCGCATTGGAACTCCTGCCCCGTTCATATTGATTTCAACTTGGTTTCGGTCCTCAGAAGCATTCCGAACTCTCTTGCCGTTGGTGTCT
107227 A C AATCTTGCAGCCTTTTAATGTCGCGAGGGATGGGGCTTTGCCATTTATGGTCCCACCATGCAGAAGGGAGTAGTGGAGTGAATGCACATTGTTGCCTTTG[A/C]TGTCGACAGCTTAATGGGCCTGCAAACCGGTTCCAGGCATGGCCCCATCCAACTTGGTTTGATAGGCCTTCCGACAATAGGTTGCTC
107227 A G TGCAAACCGGTTCCAGGCATGGCCCCATCCAACTTGGTTTGATAGGCCTTCCGACAATAGGTTGCTCTGAAAGCTGCTCAAGAATGTGAAGTTGGAGTCC[A/G]TCGAATTTGTACCATGTCGATTGGTTGCAGCAAGTGCAGCAATAAGTTGGGCGTATGTTGTCCCTACTCGACGATGGGCTCCAGAA
107227 A AACCT AGAATCCGGGCTTCCAAGAAGATTTGATGCCGCTTCCTTCATTCCTGGATGTATATTCTTCAAGAAAAACTGAATGGCAACTGCATCATTTGTACCTTGG[A/AACCT]ACCAGATGATTGGTTGCTTCCAGTACCTCCAATCACTGCATAGAACATTTGTTCTTGTTCGAGCTTCAAAATTATCGATCCTAGCA
107235 T C CAGGCTCTCCAATCAGATTTCGGTGGCAGAAAGCTCCTAAAACGCTCTGAAATTGAACAGAAGAATATGCAGAAGCTCCGCGAAATCGAACAACAACATT[T/C]AAAGCTCTACCAAAACCCTAACACGTCCCAATCAGTAAACCATACCAATTCGCAATCCCAAAACTCTGATCCTAACACGTCATCCTCC
107235 G A GCAGAAAGCTCCTAAAACGCTCTGAAATTGAACAGAAGAATATGCAGAAGCTCCGCGAAATCGAACAACAACATTTAAAGCTCTACCAAAACCCTAACAC[G/A]TCCCAATCAGTAAACCATACCAATTCGCAATCCCAAAACTCTGATCCTAACACGTCATCCTCCCTCCCTCCTGCTCTGCAACCCAAACC
107235 A G TCCTAAAACGCTCTGAAATTGAACAGAAGAATATGCAGAAGCTCCGCGAAATCGAACAACAACATTTAAAGCTCTACCAAAACCCTAACACGTCCCAATC[A/G]GTAAACCATACCAATTCGCAATCCCAAAACTCTGATCCTAACACGTCATCCTCCCTCCCTCCTGCTCTGCAACCCAAACCCAAAACCGT
107235 C T AACAACAACATTTAAAGCTCTACCAAAACCCTAACACGTCCCAATCAGTAAACCATACCAATTCGCAATCCCAAAACTCTGATCCTAACACGTCATCCTC[C/T]CTCCCTCCTGCTCTGCAACCCAAACCCAAAACCGTCGAAACCCTAACCGAAGAGCAGCGAATTGAAAACCTCGATCTTCCAAAACAAGA
107235 A T TAACACGTCCCAATCAGTAAACCATACCAATTCGCAATCCCAAAACTCTGATCCTAACACGTCATCCTCCCTCCCTCCTGCTCTGCAACCCAAACCCAAA[A/T]CCGTCGAAACCCTAACCGAAGAGCAGCGAATTGAAAACCTCGATCTTCCAAAACAAGAAGTAGTTCGCCGGTTACGCTTCCTAAAGCAA
107235 A G CGTCATCCTCCCTCCCTCCTGCTCTGCAACCCAAACCCAAAACCGTCGAAACCCTAACCGAAGAGCAGCGAATTGAAAACCTCGATCTTCCAAAACAAGA[A/G]GTAGTTCGCCGGTTACGCTTCCTAAAGCAACCCATCACGCTTTTCGGTGAAGACGATGCTGCGAGGTTGGAGCGGTTGAAAACGACA
107235 C CA GGAGCGGTTGAAAACGACAATGAAATCTGGCGTTCTGGAAATTGATAGCGACATGACTGAAGGGCAGACCAACGATTTCTTAAGAGATATATACTTGCTG[C/CA]AAAAAAGGCAGAAGAGTGGCATGAACGATAGGAAGAAGGAAAAGAAGGGAAATGAAGGAGATGGGGAGGAGAAGGATGTG
107235 A G TTGATAGCGACATGACTGAAGGGCAGACCAACGATTTCTTAAGAGATATATACTTGCTGCAAAAAAGGCAGAAGAGTGGCATGAACGATAGGAAGAAGGA[A/G]AAGAAGGGAAATGAAGGAGATGGGGAGGAGAAGGATGTGAACGAGAAGGAGGATAAGGATGCGAAGAAGATGGCGGCTGA
107235 A G ATAGGAAGAAGGAAAAGAAGGGAAATGAAGGAGATGGGGAGGAGAAGGATGTGAACGAGAAGGAGGATAAGGATGCGAAGAAGATGGCGGCTGAATTTGA[A/G]GAGTTGTGTGATGAAGATAAGATTTTGGTGTTTTTTAAGAGGTTGCTGAATGAGTGGGGCAAGGAGTTGGAGGAGATGCC
107235 T C GGGAGGAGAAGGATGTGAACGAGAAGGAGGATAAGGATGCGAAGAAGATGGCGGCTGAATTTGAAGAGTTGTGTGATGAAGATAAGATTTTGGTGTTTTT[T/C]AAGAGGTTGCTGAATGAGTGGGGCAAGGAGTTGGAGGAGATGCCAGAGACAGAAAAGAGGACTGCTGCAGGGAAGTCAATG
107235 A G GAGGATAAGGATGCGAAGAAGATGGCGGCTGAATTTGAAGAGTTGTGTGATGAAGATAAGATTTTGGTGTTTTTTAAGAGGTTGCTGAATGAGTGGGGCA[A/G]GGAGTTGGAGGAGATGCCAGAGACAGAAAAGAGGACTGCTGCAGGGAAGTCAATGGTTGCAAAATATAAGCAGTGTGAGCGG
107235 A T TTTTGGTGTTTTTTAAGAGGTTGCTGAATGAGTGGGGCAAGGAGTTGGAGGAGATGCCAGAGACAGAAAAGAGGACTGCTGCAGGGAAGTCAATGGTTGC[A/T]AAATATAAGCAGTGTGAGCGGTATTTGCATCCATTGTTCAAGTTCTGTAGGAAGAAGGTTTTGCCCGATGACATCCGTCAAGGT
107235 A G TGGTGTTTTTTAAGAGGTTGCTGAATGAGTGGGGCAAGGAGTTGGAGGAGATGCCAGAGACAGAAAAGAGGACTGCTGCAGGGAAGTCAATGGTTGCAAA[A/G]TATAAGCAGTGTGAGCGGTATTTGCATCCATTGTTCAAGTTCTGTAGGAAGAAGGTTTTGCCCGATGACATCCGTCAAGGTTTA
107235 T C GACAGAAAAGAGGACTGCTGCAGGGAAGTCAATGGTTGCAAAATATAAGCAGTGTGAGCGGTATTTGCATCCATTGTTCAAGTTCTGTAGGAAGAAGGTT[T/C]TGCCCGATGACATCCGTCAAGGTTTAATGTACATGGTACGCCGCTGCATGATTCGTGACTACCTTGCAGCAATGGACCAATACATC
107235 G A CAGAAAAGAGGACTGCTGCAGGGAAGTCAATGGTTGCAAAATATAAGCAGTGTGAGCGGTATTTGCATCCATTGTTCAAGTTCTGTAGGAAGAAGGTTTT[G/A]CCCGATGACATCCGTCAAGGTTTAATGTACATGGTACGCCGCTGCATGATTCGTGACTACCTTGCAGCAATGGACCAATACATCAA
107235 C T ATATAAGCAGTGTGAGCGGTATTTGCATCCATTGTTCAAGTTCTGTAGGAAGAAGGTTTTGCCCGATGACATCCGTCAAGGTTTAATGTACATGGTACGC[C/T]GCTGCATGATTCGTGACTACCTTGCAGCAATGGACCAATACATCAAAATGGCCATAGGCAACGCACCATGGCCTATAGGAGTTACTA
107235 A T ATCCATTGTTCAAGTTCTGTAGGAAGAAGGTTTTGCCCGATGACATCCGTCAAGGTTTAATGTACATGGTACGCCGCTGCATGATTCGTGACTACCTTGC[A/T]GCAATGGACCAATACATCAAAATGGCCATAGGCAACGCACCATGGCCTATAGGAGTTACTATGGTTGGTATTCACGAGCGTTCTGCT
107235 C T TCAAGTTCTGTAGGAAGAAGGTTTTGCCCGATGACATCCGTCAAGGTTTAATGTACATGGTACGCCGCTGCATGATTCGTGACTACCTTGCAGCAATGGA[C/T]CAATACATCAAAATGGCCATAGGCAACGCACCATGGCCTATAGGAGTTACTATGGTTGGTATTCACGAGCGTTCTGCTCGTGAGAAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107235 C T CTAGCAGTGTGGCTCACATCATGAATGATGAGACTACTCGCAAGTATCTACAATCCGTGAAGAGGCTTATGACGTTTTGTCAAAGAAGGTACCCTGCACT[C/T]CCATCCAAGTCGGTTGAGTTCAACAGTTTGGCGAATGGAAGTGATCTGAGTGCGCTACTTAATGAAGAGAATGTGAAGGAGAAGAG
107235 G A TGACGTTTTGTCAAAGAAGGTACCCTGCACTCCCATCCAAGTCGGTTGAGTTCAACAGTTTGGCGAATGGAAGTGATCTGAGTGCGCTACTTAATGAAGA[G/A]AATGTGAAGGAGAAGAGTTCCGGGGATAGACTTCGCTTGGAGTAACAATGAGTTTAACTGGGGTCGTGTAAAGAGTATGGCAAAT
107235 C T ACCCTGCACTCCCATCCAAGTCGGTTGAGTTCAACAGTTTGGCGAATGGAAGTGATCTGAGTGCGCTACTTAATGAAGAGAATGTGAAGGAGAAGAGTTC[C/T]GGGGATAGACTTCGCTTGGAGTAACAATGAGTTTAACTGGGGTCGTGTAAAGAGTATGGCAAATCGAAAATCTGCACATCACTGG
107239 C T CATCCTATAAAAGGTCATCATGAGCGAATCCACCATCAATGTAAAAACCGCCGACAGCATGGCGACAAACGTCGTGAACGGGAACTTCGACCACGGCGCC[C/T]CCGGTAGGCACGGGGAGTTCAGATTATCGAACGAGTCAGGAAGCACATGCATGTACCCGGTGGCAAGGATGACGCCTGACGCGA
107239 T C TATAAAAGGTCATCATGAGCGAATCCACCATCAATGTAAAAACCGCCGACAGCATGGCGACAAACGTCGTGAACGGGAACTTCGACCACGGCGCCCCCGG[T/C]AGGCACGGGGAGTTCAGATTATCGAACGAGTCAGGAAGCACATGCATGTACCCGGTGGCAAGGATGACGCCTGACGCGAATGC
107245 G A TAGCTGAGCTTCAGGAGTTCTGCTCAAGGGACGGCTCTTTAACCATTAAAGAGATATTCGGTGTCACAGATGAGGATGCGGATTCCCTTCGAATCAACAC[G/A]CTTTCCGAAGCTGGTGATTTTGAGTCCCTTGAAAACATGGTCGATGATGAACCTGACTTGGAAGAGCCAGCTGATGATACTTCAGA
107249 G A TTGGCCTACTGGAAAATTCATTCCAAAAACCGCACTCTACCATGAGCAACGACACGCTGGACAAGCTAGTC[G/A]TCTTCCTCGCCAAGCGCGACGGCATCGATAAACTCGTCAAAACCTTCCAGTACGTCTCCAAACTAGCCCATCACACCTGCCCCTCCACCCGACCCGATTT
107249 G A TACCATGAGCAACGACACGCTGGACAAGCTAGTCGTCTTCCTCGCCAAGCGCGACGGCATCGATAAACTCGTCAAAACCTTCCAGTACGTCTCCAAACTA[G/A]CCCATCACACCTGCCCCTCCACCCGACCCGATTTAGCCGATCGGGCCAAAAAATGGGAAGTTGGATCTGGACTCAGCCGAAAGGCC
107249 A G CAACGACACGCTGGACAAGCTAGTCGTCTTCCTCGCCAAGCGCGACGGCATCGATAAACTCGTCAAAACCTTCCAGTACGTCTCCAAACTAGCCCATCAC[A/G]CCTGCCCCTCCACCCGACCCGATTTAGCCGATCGGGCCAAAAAATGGGAAGTTGGATCTGGACTCAGCCGAAAGGCCTTCCGAACG
107249 C T CCGATTTAGCCGATCGGGCCAAAAAATGGGAAGTTGGATCTGGACTCAGCCGAAAGGCCTTCCGAACGGGACGGTTCCTCACCGGCTTCAACGCCCTCCG[C/T]CGCTCACCCGGCCCGACTCCCACGCATCGGTTCCTAGCAGTGTTCGCCAACGCAGGGGAGATGGTCTACTTCTTCTTCGATCATTT
107249 C T CCGGCCCGACTCCCACGCATCGGTTCCTAGCAGTGTTCGCCAACGCAGGGGAGATGGTCTACTTCTTCTTCGATCATTTTTTGTGGCTGTCCAGACTCGG[C/T]GTCATGGACGAGAAGCTTGCAAGGAGAATGAGCTTTATATCGGCGTTTGGAGAGTCGGTCGGGTATCTGTTTTTTATTATATTGGAT
107249 A G TGTGGCTGTCCAGACTCGGCGTCATGGACGAGAAGCTTGCAAGGAGAATGAGCTTTATATCGGCGTTTGGAGAGTCGGTCGGGTATCTGTTTTTTATTAT[A/G]TTGGATTTTATTGCGATAAGGAAAGGCTTGGAGGAGAAGGTTGACGATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAG
107249 A G ATGGACGAGAAGCTTGCAAGGAGAATGAGCTTTATATCGGCGTTTGGAGAGTCGGTCGGGTATCTGTTTTTTATTATATTGGATTTTATTGCGATAAGGA[A/G]AGGCTTGGAGGAGAAGGTTGACGATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCATCAGGCTGATGGCTGTGG
107249 C G ACGAGAAGCTTGCAAGGAGAATGAGCTTTATATCGGCGTTTGGAGAGTCGGTCGGGTATCTGTTTTTTATTATATTGGATTTTATTGCGATAAGGAAAGG[C/G]TTGGAGGAGAAGGTTGACGATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCATCAGGCTGATGGCTGTGGCGGC
107249 C T GAATGAGCTTTATATCGGCGTTTGGAGAGTCGGTCGGGTATCTGTTTTTTATTATATTGGATTTTATTGCGATAAGGAAAGGCTTGGAGGAGAAGGTTGA[C/T]GATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCATCAGGCTGATGGCTGTGGCGGCTAATATAGCGGATTTGGTT
107249 C G TTTTTATTATATTGGATTTTATTGCGATAAGGAAAGGCTTGGAGGAGAAGGTTGACGATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCAT[C/G]AGGCTGATGGCTGTGGCGGCTAATATAGCGGATTTGGTTATTGCTGTTGCGGATATTGAACCGAACCCGTTTTGTTGTCATCCGG
107249 T C TGGATTTTATTGCGATAAGGAAAGGCTTGGAGGAGAAGGTTGACGATGATGAGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCATCAGGCTGATGGC[T/C]GTGGCGGCTAATATAGCGGATTTGGTTATTGCTGTTGCGGATATTGAACCGAACCCGTTTTGTTGTCATCCGGTCACCTTGGGG
107249 G A AGAAGAGGAGGGTTGAGATCAGGGGAGACAGGGTCATCAGGCTGATGGCTGTGGCGGCTAATATAGCGGATTTGGTTATTGCTGTTGCGGATATTGAACC[G/A]AACCCGTTTTGTTGTCATCCGGTCACCTTGGGGGTTAGCGGTCTTGTGTCGGCCTGGGCTGGCTGGTACAGGAACTGGCCATTG
107249 C G ACAGGGTCATCAGGCTGATGGCTGTGGCGGCTAATATAGCGGATTTGGTTATTGCTGTTGCGGATATTGAACCGAACCCGTTTTGTTGTCATCCGGTCAC[C/G]TTGGGGGTTAGCGGTCTTGTGTCGGCCTGGGCTGGCTGGTACAGGAACTGGCCATTGTAGACTTGTAAAATTACACTGTATGAGAC
107249 T C ATATAGCGGATTTGGTTATTGCTGTTGCGGATATTGAACCGAACCCGTTTTGTTGTCATCCGGTCACCTTGGGGGTTAGCGGTCTTGTGTCGGCCTGGGC[T/C]GGCTGGTACAGGAACTGGCCATTGTAGACTTGTAAAATTACACTGTATGAGACTAATTTCTATACTGGAGCCAATTAGTAGACATCT
107249 T C GCTGGCTGGTACAGGAACTGGCCATTGTAGACTTGTAAAATTACACTGTATGAGACTAATTTCTATACTGGAGCCAATTAGTAGACATCTTCTTAGCCAT[T/C]TTGTGTTTCCACATTCAATGATCTAAGGTTATGAAATTAAGGACTATGCTACGTCAAAAAATGGAAGTATTAATTTAACAGTAGAACAA
107249 A G TGGCCATTGTAGACTTGTAAAATTACACTGTATGAGACTAATTTCTATACTGGAGCCAATTAGTAGACATCTTCTTAGCCATTTTGTGTTTCCACATTCA[A/G]TGATCTAAGGTTATGAAATTAAGGACTATGCTACGTCAAAAAATGGAAGTATTAATTTAACAGTAGAACAACTGGGGTCGGACAAGAA
107249 C T AGACTAATTTCTATACTGGAGCCAATTAGTAGACATCTTCTTAGCCATTTTGTGTTTCCACATTCAATGATCTAAGGTTATGAAATTAAGGACTATGCTA[C/T]GTCAAAAAATGGAAGTATTAATTTAACAGTAGAACAACTGGGGTCGGACAAGAAAATATGGGAAAATCCAATGGTGTTCAAAATAGAA
107249 A G GAAGGCAAAGAAACTGATATAGCATGAAGCAGAGAGATAAGGATGCTGCCTTCTGGAGTTGGAAGATGAATATTCCTAGGGTTTGGACTTACTATGTTTC[A/G]CCTTGAAATCTTTGTTACCAATTCAGTTAAATATTTTGAGTGGGAATACATGCAAGGAGATGAAGTATTTTTCTAAAGGAAACCAG
107253 C G ACATGACCAGAGAAAAACAGACGACAACAAAAACATCACAAGTGGCGGGTCGACCTCGCTAGATGTTCCATATTTTGGCAACTCAATTAAGCAAAAGCTT[C/G]CGGCTACCACTTTGCTGCAATATTGGCCTTTGCAATATCAGTCTTATTATGATAGGTCAAAGGATCCTTGTCCTTCACTGATAGCATA
107253 C T ATAGGTCAAAGGATCCTTGTCCTTCACTGATAGCATATAAAAGCTTTTTGTACATGATCTCCTTGGTCGAGTAGGGAGGTAGTTTGAGGTAATTAGCACA[C/T]GTCATGACACTAGGCAAGTCATCATCAGCTGATTCAGAAACCCCAGCTGCATTTGTTGCAGTGTTTGTAGCAGTCGATGAGTGCTTTC
107253 C T GCTTTCTCACGATAGTCAGTTTTGGATTTAAAGCAGCTAGACCACCAGGGGGAAGGCGAGGTGCACCAGTGACAAACTGGCAAAACGCATGCTGTTGCTC[C/T]GGTGTGAATTCTCCCATTATTTCAAGCAAATTGACAATTGCCGGGCTTTTAGCAGTATATCCATGGTCAAACTTTATGTGGTCAGCT
107253 A T TGACCAATGAGTTTTCTTCTGTTTCTTTAAGGATATACTCAGGGTGTCCAGGAAGAGTAAAGTCAAAACACAAATCTTCTACAGGAACACCACGAAACCG[A/T]AGATCATCAATTGCTCTTTCATTGCTTCCACTTCCTGCCTCTAAAGACTTCTTTCGGCAAACAAGAATTTGCATTTCTTGCAAAATTTTC
107253 A G CCTCTAAAGACTTCTTTCGGCAAACAAGAATTTGCATTTCTTGCAAAATTTTCCCAAACTCGGCATCAAATGAAAGAATATCATATAAGTCAAGCTCTTG[A/G]CCAAGAATAAGTTTATAGAATGGTGCAGAAAGTGGTAGATCCAACAGGCGTCCATCTTGCAGAGCTTTTGCCATCACACGACCCAATA
107257 A G TTCAGAAAAAAAGATCAAGCTCCTGCTTTACAAACCTAGTTAGGAATATGTTTGGATGGTGTCCTCTTTCCATTGTGAACTGCTGCTACAATGGAGATCA[A/G]CATGCTTCTGAACAAGCGAGCGAGGATGGCATGTTTTATTGTAATTTATGCGAAGTTGAGGTCTTAAAATACAGTAAGCATTGCAGA
107257 C T CTGAACAAGCGAGCGAGGATGGCATGTTTTATTGTAATTTATGCGAAGTTGAGGTCTTAAAATACAGTAAGCATTGCAGAGTTTGTGACAAATGTGTAGA[C/T]AGCTTTGATCACCACTGCAGGTGGTTGAACAACTGCATTGGAAAAAGAAATTATGGACGATTTTTCATCCTTATGATTTCTGCAATTC
107257 T C ACAACTGCATTGGAAAAAGAAATTATGGACGATTTTTCATCCTTATGATTTCTGCAATTCTCATGCTTATTTTGCAATGGTCAATCGGGATCCTCGTGCT[T/C]ATTCTTTGCTTCTTGGAGCGAAAGCGTTTCTCCATAGAAATCAGTGCAAAACTAGGAAGCAGCTTCTCGTTGATGCCTTACATTATTGTA
107257 T C GCATTGGAAAAAGAAATTATGGACGATTTTTCATCCTTATGATTTCTGCAATTCTCATGCTTATTTTGCAATGGTCAATCGGGATCCTCGTGCTTATTCT[T/C]TGCTTCTTGGAGCGAAAGCGTTTCTCCATAGAAATCAGTGCAAAACTAGGAAGCAGCTTCTCGTTGATGCCTTACATTATTGTAGTTGTT
107257 A G TAGGTCAGCAAAGTCCTCAGATGTCATCAGTCAGCTCATTCACTGCCATTAGCAGTGCAAGCTCTTTCAATCAGTTCCGCCGTGATGCATGGTGTACTCC[A/G]CCAAGGCTGTTCCTTGAGGATCAGTTTGACGTAGTTCCCCCAGAAGTAGGCAACACATCCCTGAAGTTCCAACAGAAAA
107263 A G TATACAAACATGAGAGGGGGTTATGGTGAGCGTGAGTTATGGAACTGGCGTGTGAGTAGGAAGGTTTAATTTATGGGTAGGAGTAGTTTTGAATGGAAAG[A/G]AGCTAGTGGAGTTGATAGTTAAATTGGTGTTGATGGGGCATGTTGAGCGAGAGTTTCATTTGAAACTGTGGGAACTACTATTGA
107269 A G GGCCTACGAAGAGAGAGGCATAAACAAAGATTTGGCTAAGTACAAGATCATATTCTGCCATGGGTTCGGTGGTTCAAGAAAAGACATGCTTCGCCCTTCC[A/G]ATGCGATTGTGAACGAGTTGGGCATTCACATGGTTGGTTATGACCGTGCTGGGTATGGTGAAAGCGACCCAAACCCGAACAGGTC
107269 C T ATTTGGCTAAGTACAAGATCATATTCTGCCATGGGTTCGGTGGTTCAAGAAAAGACATGCTTCGCCCTTCCAATGCGATTGTGAACGAGTTGGGCATTCA[C/T]ATGGTTGGTTATGACCGTGCTGGGTATGGTGAAAGCGACCCAAACCCGAACAGGTCGCCCAAAAGCGAAGCCCGTGATATCGAAG
107269 C T CCGTGATATCGAAGAACTTGCTGATGCACTGAATCTTGGTTCCAGGTTCTACTTGATAGGGTTTTCTTTAGGTGGCCATGCTGTTTGGGGAAGCATAAAG[C/T]ATATCCCTGGAAGGCTTGCTGGAGTTGCACTGCTGTCACCAGTAGTGAACTATCGATGGCCAGGATTTCCAAAAAATCTATCAAGCA
107269 GA G ATGGTTACCCACCTCAACCGTAGTTAAAGGCACAATTCATTTGCCAAACCGATTAGATGCTCAACTTCGAGACAAAGCTTTGTCTTCTGGAATATATCAA[GA/G]AAAAAAGGAAGCTGGCTACACAACAAGGGATTCATGAGTCATACATGAGAGACATGATGGTGATGTTTGGAAAATGGGAGTTTGA
107273 T C CTAAAGGGGCTAATATGGGTGGTGTTGGTGGGAAGCAGGAGTCGATGAGGCAGGAGATATATAGAGTTGGTATGCATGGCGACGACACCGATGACGACGA[T/C]GATGATAGTGATGACGATGATGATAGTGGTGATGGTAGTGATGATGATAGTGAGGAGACCGAGGAGGAGCGTGATGATGTG
107273 C T TGGGTGGTGTTGGTGGGAAGCAGGAGTCGATGAGGCAGGAGATATATAGAGTTGGTATGCATGGCGACGACACCGATGACGACGATGATGATAGTGATGA[C/T]GATGATGATAGTGGTGATGGTAGTGATGATGATAGTGAGGAGACCGAGGAGGAGCGTGATGATGTGGTGAGGAACGATTGG
107275 G GC TAGCTTTACTTACAGAGGATTACAAACATAAACGTATTAAATATAGCATTGTTCTTCTATCCCCAAGTACGTATCAGCCATTGATTTCCACATCACCACT[G/GC]CTTTATTAAATGGGACATATGGAAACACGGAATTTGAGAACAGAGGAACTGATCTGATATACTTGCTATCAAGTAGGCTTCCAAACAG
107275 G A TCAAGCAACCTTTCTTCAGCTTGGGCAGCTGGTACAGCCAGGCCTCCTGAAGTCTTTCGAGCACGTTGGCCGAGCTTATGTCCTCGAGCAAACTCTCCTC[G/A]CAGCAGTTTTTCAAGTCAGCAATGTCGTACTTGTTTGCTGCACCTAGAAGGGCCAGTCTGTGCTTCCAGAAGTCTTCCTGCTTGATGT
107275 C T CGATGGTGGAGGAGGACTTCTCCAGGAGGTCGTGGAGGAACATGCTCTCGAAGACTGGGGAGGAGGATGAGAGGATAGCCCTGTGGGCTCGGAGGGTGCC[C/T]GTGGACGTATTGATGGTTACGTCCGCGTGGATGCTCTCTGTTAACATGCGGGAGACAGAGCGGAGTGTGTGTTGCCCCGAGG
107275 AG A CTGTGGGCTCGGAGGGTGCCCGTGGACGTATTGATGGTTACGTCCGCGTGGATGCTCTCTGTTAACATGCGGGAGACAGAGCGGAGTGTGTGTTGCCCCG[AG/A]GGGGGAGGTCAGGGCTCCTTCGTTTGTCCATATTGATGCGGGGTCCCCACCATTTAATGGAGATACTTTAAGGTCAAGAAACT
107277 CT C TCTTGGCGGCAAAAGCATCTTGAGTCTCACGAGAGATCTTGTTTTCTGCTGCGACATTTTCGGAGGTGATACCCATAGGAATCAAGCAATCCGCAGCCTC[CT/C]TTGTTGCCAAGGACGGCCTCGGAGAACTTGGTGGGCAGTGCATTGGGACCGTAGCCGAGCGTCATGCTCTCAACACCAGCGCCGA
107279 A G GTGCTACAATTAGTAAGATGCTATCCCCGTAAGAACTAGCATGGCTAAGTACTTCTTGTACTGATTTACCATGAGCTCCATGCTCAACATCAGACTGCGG[A/G]AGAGAAATCCCACCATTATGGCCAGCTTTGTTTTCTGCACCAACTCCATGCTCACCAACAGCTCCAGAATCGTTCATCTTCGTCCCTTC
107279 C T ACTGATTTACCATGAGCTCCATGCTCAACATCAGACTGCGGAAGAGAAATCCCACCATTATGGCCAGCTTTGTTTTCTGCACCAACTCCATGCTCACCAA[C/T]AGCTCCAGAATCGTTCATCTTCGTCCCTTCCTTTTTAGCAACAACAAAATTAATAACACAATCAGCTAGCATGGTAAGCAAATAGCCACC
107279 A G AATCCTCGAAAGTTTCATTAGAATCACTCAAAAAATGCATCATAGCCGTTCCCAAAAACACGCCGCCAGCAAACTGCGTCCCAAGCACCAAAAACGCTTC[A/G]TTCCACTTAAAGAAATACGGAGATACGCCCCCAATGAACGTGCCTAAGAACACAAGAATCAAACAGTATATTTTAACTAAGATCAACG
107293 A G CTGATTTGGGATTTCCTGCACCTAGCTCATTGCTTGTTCGTACACTTGCTGCGGCATTGAATCCTACAGAGATCATGAATACCCAACCAGAGATTGTCAT[A/G]CAAACAGAAAGAGAGTCGAGTGCGAGCTCTGGATTTTCCAACAACCCAGCAATCAAAACCAAAATCTGAAAATACCACGTCTCCAAAC
107293 G C TTTCCACTGCACTGCCCATTCCCAGCATGAGTCCATAAGCAAAAACTTGGATTCCAGTGTTCCCAAGAGAAGCAGCAGCAAGCTCAAGATTACCCAAATG[G/C]CCGGAGTAAATCTGGGTGGACATAGACATCAGATAATTGACCATATAAACGATTACAGCAGGGGCAGCCAGATGAAACAGCAATTT
107293 G C CCACTGCACTGCCCATTCCCAGCATGAGTCCATAAGCAAAAACTTGGATTCCAGTGTTCCCAAGAGAAGCAGCAGCAAGCTCAAGATTACCCAAATGGCC[G/C]GAGTAAATCTGGGTGGACATAGACATCAGATAATTGACCATATAAACGATTACAGCAGGGGCAGCCAGATGAAACAGCAATTTCGC
107295 T A ACCAAGCCTTCAGTTGTTTCAGCTAATCCAATGAATTATAATAATGCTTATGAATCTAAATGGTCCAATTTTCCAACTCCTTTTACCAATGAGAAAATCA[T/A]TTCAGTTACCAAACAGAATGATTCAACAGTGACTGGTGGTTTTGCATTTGGATATCCCAAATCTACACGAGTTGTTCCCTTAGATTCTACT
107295 G C ACAGTGACTGGTGGTTTTGCATTTGGATATCCCAAATCTACACGAGTTGTTCCCTTAGATTCTACTTACACACCTGCTGAGGGTGGTAGGTCAAATGAAG[G/C]TCCTAAAATTTCATTTCAGCAAATCAATCAGTATCCACCTCAACGCGGTAATGATTTGGGCAGGCCAAAGACTGTCCATATGAATGTT
107295 A G ACTGTGGGACCCAGTTTTCCGTCCGTTCCAAAGGAAGATCTTGTTCAAGGCACGGAATATGGAAAACAATGGCCGCGTACACATTTCCAGCATGAACGTC[A/G]TGAAGAATATAAACGGCTCAACCAGAGAAATAATTTGGACAGCGTACTCGTTAAAGACATGACTGTATTGGATGGAACAGTTATGC
107295 G T TCCAGCATGAACGTCATGAAGAATATAAACGGCTCAACCAGAGAAATAATTTGGACAGCGTACTCGTTAAAGACATGACTGTATTGGATGGAACAGTTAT[G/T]CTTCCTTCAACTCCTTTCATTAAAACATGGAGGATGCGCAACAACGGCACTGCCTACTGGCCCTATGGGACCCAACTAGTGTGGGTC
107297 A G TTTTTCCAGGTGATCAACCACGGTGTGCCGCTTGAGGTATTGGAAGAGCTTCAAGTTTTGATGAAGGAATTCTTCGAACTGACAATGGAGGAAAAGACGA[A/G]GGTGAGGCGAGACGAGGATAACCCGCTTGGTTATTATGAAGGCGAGAACACGAAGAATGTGAGAGATTGGAAGGAGGTCTTCG
107297 T C GAGACGAGGATAACCCGCTTGGTTATTATGAAGGCGAGAACACGAAGAATGTGAGAGATTGGAAGGAGGTCTTCGATTTCATGGTGAATGAACCTGCTCA[T/C]GTTCCGCTTACCAGCGAGCCTGGGGAAACTAGGGTTTATGAGATTCAGAATCAGTGGCCAGAATTTTCGGTCAGATTCAGGGAG
107307 A G GGAACACGACCTCCTTCATCATCAGATCAAAGAAATCAGGCGGGATCGCTTCCTTGCCTTCAGTGAGTCCAGCGACCCCCGCAATTCTTCCTACACCTAA[A/G]TTTTCTCCTTCTAGAGAAGGGTTGGTTGACATGGCGAAGGAAGAGTGGGGAGTGGATGGATATGGATCAATGAAGGGATTGATTAG
107307 G A ATTTGAGCAAGTTTGAAATGGTGCATCAGAGCTTTGGAGAAGATCAAGGCGCAACATCGGCTTATCTTTTGGAGAACAAAGTTGATAATCAAGAGGCAAG[G/A]ATTGCGAAGTTGGAAGAGGAGAATTTGACGTTGAAGGAGAGAATGTTTTTGATGGAGAGGGAGATGAGGGAGATGAGTGAGAG
107307 T G GGAGAATTTGACGTTGAAGGAGAGAATGTTTTTGATGGAGAGGGAGATGAGGGAGATGAGTGAGAGGTTAGTTAGACTTGAAACTATCAGTAACAATAAT[T/G]GTAATGGTGACAATGACAATGATGTTGGTGGCATTGATATCGAGGATAATGAGCAAGAACATAGTTATAATAGCAACATGCATT
107307 GTGACAA G TTGACGTTGAAGGAGAGAATGTTTTTGATGGAGAGGGAGATGAGGGAGATGAGTGAGAGGTTAGTTAGACTTGAAACTATCAGTAACAATAATTGTAATG[GTGACAA/G]TGACAATGACAATGATGTTGGTGGCATTGATATCGAGGATAATGAGCAAGAACATAGTTATAATAGCAACATGCATTTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107307 C G GAGCAAGAACATAGTTATAATAGCAACATGCATTTGAATGTTGATGAATCATGGGATAATGCTGCCGTTTGCTTGGAGGAGAAGAGTGGAGGCCATGATG[C/G]AGATGAGATAGGGGACAATTAGATGGGAGTGGAAGGAAGGTAAACATATTTCTAATTCATGTTATCAATCACAAACTGTGTTCAA
107307 GA G AATGTTGATGAATCATGGGATAATGCTGCCGTTTGCTTGGAGGAGAAGAGTGGAGGCCATGATGCAGATGAGATAGGGGACAATTAGATGGGAGTGGAAG[GA/G]AAGGTAAACATATTTCTAATTCATGTTATCAATCACAAACTGTGTTCAAAAATGTGAAACCCTGTGCTATCTTTTAAACTGAATA
107307 A G ATAATGCTGCCGTTTGCTTGGAGGAGAAGAGTGGAGGCCATGATGCAGATGAGATAGGGGACAATTAGATGGGAGTGGAAGGAAGGTAAACATATTTCTA[A/G]TTCATGTTATCAATCACAAACTGTGTTCAAAAATGTGAAACCCTGTGCTATCTTTTAAACTGAATACTTGGATTTTGTTGGGATTT
107309 A G TATGGTGCAAGTGAAGGTTACCCATCACAGAATGGCATTATAATGGATGCTCAGGCAGCCTTGGATCATCTTACTAAGAGAGTCGATATAGATGCTTCAA[A/G]AATAGTTGTTTTTGGAAGATCTTTGGGAGGAGCAGTGGGGGCAGTCCTTGCAAAAAATAATCCAGATAAGGTTTCTGCATTGATAT
107309 G T ACATTATTGCTCAGATCAAACAGCCAATTTTGTTCTTGTCCGGTTTGCTAGATGAGCTGGTGCCTCCTTCTCACATGCAAGTGTTGTACAACGAAGCACG[G/T]GAACATAATGACAAATGTATATCTGTTGATTTTCCTACTGGTATGCACATGGATACATGGATATCTGGTGGCGATCGTTACTGGAGAA
107311 C T CTTGTCCTTGTCCTTCTTGTCCTTCTTATCCTTCTTGTCATGGTCCTCGTCCTCGCCGTCATCATCCTTCTTTTTCTTGTCCTTCTTTTTCTTGTCCTTC[C/T]CATCATGCTCGTCGTCGTCGTCTTCATCCTTCTTCTTGTCTTTCTTCTTCTTGTCTTTCTTCTCCTCTCCCTCGGACTCTTTACCCTTGTCTTTGTCT
107311 T C TCCCTCGGACTCTTTACCCTTGTCTTTGTCTTTCTTATCTTTCTTGTCTTTCTTTTCCTTCTTCTCGTCGCCGGTATCCTCGTCGTCCTTGGACTTGGAC[T/C]TCTTCTCCTTCTTCTCCTTCTTGTGCTCGCCCTCGCTTTCACCTCCAGATACTTCCTTGTCTTTCTTGCCCATGGTCACGAAGTATCAGAAAATT
107311 T C TTTCCTTCTTCTCGTCGCCGGTATCCTCGTCGTCCTTGGACTTGGACTTCTTCTCCTTCTTCTCCTTCTTGTGCTCGCCCTCGCTTTCACCTCCAGATAC[T/C]TCCTTGTCTTTCTTGCCCATGGTCACGAAGTATCAGAAAATTCGAGGAGAGAGGGTGAAGAAAAGGGGGTGTTTTTCAAGCAAACGATCG
107313 C T GGTTATGGTGCGTACAACTCTTATATCTCGACTGCAACTCGCTATGGGGCTCTTGGTGCTCCTACACTATACGACCTTCCCTCCCAAGCTTACGACCGAT[C/T]GGGAGGGTATTATGGTCCTCCTCGTGTGGTGAGCAAGAAAATATTTGTTGGAAGACTTCCACAAGAGGCAACTGTTGGAGATCTGCG
107313 A G TGCAACTCGCTATGGGGCTCTTGGTGCTCCTACACTATACGACCTTCCCTCCCAAGCTTACGACCGATCGGGAGGGTATTATGGTCCTCCTCGTGTGGTG[A/G]GCAAGAAAATATTTGTTGGAAGACTTCCACAAGAGGCAACTGTTGGAGATCTGCGTCAATATTTTGGCAAATTTGGCCGCATCCAAG
107313 AT A ACGATTATGGTTATGGAGCAGGTGGCAGCAGAAGCAGCAGGCCTTCCAGAATGGACTGGAGGTACAGGCCTTACTAAATTGAGGACTGTCATGCCTATTT[AT/A]TTTTCTTGATAGGGGTGTCAAGTTATTAATCTGTATCTTACAAAGCTATCTTGTATTTCTATTATGATATACCTGAAATTGTGCTTG
107327 T A ATCATGTTAGCACGTGCTGGGGAGCTCCAGGTGGAAATAGCAATGGAGAAACAACTGTGAATGACACTGATAATGCATGGACTGGTTCATCCTCTAAATC[T/A]GCTGAAAATGTTCCTGTCTTAAGAGAATCAACCACACCTAAGTTTCCTGGCTCCGAAACAAAAGATACTAAAATGTGTAAAGGTGG
107327 CA C AATGACACTGATAATGCATGGACTGGTTCATCCTCTAAATCTGCTGAAAATGTTCCTGTCTTAAGAGAATCAACCACACCTAAGTTTCCTGGCTCCGAAA[CA/C]AAAAGATACTAAAATGTGTAAAGGTGGATTTTTTGAAGATTTCAAAGTGGACGATGTTGATCTAACATTTGAGAATTATGAAGAGTT
107327 T C TCGATACTAAGGAAACGGCATGCCAGGGAGAATTTGTGGGTGAGGCATCAGCGAGAAATGTGAAGTCAATGCAGCGAGAATGCAGCAATGGCGTGTCTGC[T/C]GATTCCATGAACAAGGCAGAGCTTAGTGTATCATCTTTGCCAGCAAGGCCAGCTCGGTCAAGTATATCTCTTACATTTTCAGGAA
107327 A G TTGTGGGTGAGGCATCAGCGAGAAATGTGAAGTCAATGCAGCGAGAATGCAGCAATGGCGTGTCTGCTGATTCCATGAACAAGGCAGAGCTTAGTGTATC[A/G]TCTTTGCCAGCAAGGCCAGCTCGGTCAAGTATATCTCTTACATTTTCAGGAATGACCGGAGAAAGTAGCGCTGGTGAGTTTACCG
107333 C T TGATAGAGGCACAAAGCCGGAGTCACGACCTGGGCCAGTGACAGTCAATTTGTTGATCGACGAAAGAAAAGTCAGGGTAGAGCAAATATCCAAGGAGGAA[C/T]CCACATCTGTACCAAAGCAACCACCAAGAGCTGAAGTCACCAAACCGGATGTGAAACCATCTTTCACTTCAAGAACCGATACACA
107333 A G GAGGAACCCACATCTGTACCAAAGCAACCACCAAGAGCTGAAGTCACCAAACCGGATGTGAAACCATCTTTCACTTCAAGAACCGATACACACTCACCGA[A/G]ACAAACCCAAAACCACTCTTCTGAAAACGTTCCTGCTCCCACACTAAAAAAACACCAACTAAAAGCCCATCCGAGTCAGCCCACCCA
107333 T C CGAAACAGGATACCATTCTAATGGGTATGGATATCAGCACTATTATGATCCGTGGCCTCCTTATGGTCTTCCTTACGATCACGACGATGGTCGATACGGG[T/C]ACAATGGGTATGCCTACAATGCCCAACCCGGTAACACTTGGCCTCAAAATGGGCTTTGAATGTATTCTAGGTGATTTGGTTACATTTG
107333 T C TGCCTACAATGCCCAACCCGGTAACACTTGGCCTCAAAATGGGCTTTGAATGTATTCTAGGTGATTTGGTTACATTTGGATGAGGATTCGAGGTTATTAG[T/C]ATAAACCTTTGTTTTATCTAGACAGTCTTGAGTGATTATGTTCTTTTTAATGCTTGGTTATAAGGTTTTTACTACACCAAAAGATGAAG
107335 T C AACCCACCACCCGAACCAGCACCTGCAAATCCACCACCTGAACCAAAGGCACCAAAACCGCCGCTTCCGCCTGAAGCAACAGCAGCAAATCCTCCCACTT[T/C]CACTGCAGCAGAGGCAAACCCACCACCTGCTGCAGCAGGTACAGTTGCCCCAAACCCGCTATTAATAACATTACTAGTGCTTGATGA
107335 CTCT C TCGGTGGAGTCGAAGACATTGTTGAACCAAGGCCGATCCCACTCAGAGATCCTAAGTTGAATCCACTTGTAGTGTCTGAAGCCTCTTCTTCCATTCCATC[CTCT/C]TCTTCTTGATCTGATAAATTAGCATCTGAAGATTTTCCTTTGTCGTCAGTGCTTGGCATTGTGGTGGATGATGATGCCACTGGTTG
107343 T C ACATTTATCAGACTGAAACTCTTCACCAAAGTAATTCACAATTAATTTAGCACGGCATGTTGCTGTATTCATACCATACCGAAAGCACTCAGAGAGCATT[T/C]TATATGCTTGATTTGTTTGTTCTTCACTCCTTTTGTTAGGAAGAAGTGTCGGAATGCTTGACAAATTGGCATATAGTGTACAATCAGATA
107345 C T TCTTCATCTTTCCCTCACTGTCTAATCAATATCTAATCCATTCTCCATCCATTTCGCCAAAATTCCCTCCCTCCGCTTCCACGACCAACGCTCGCTGTAG[C/T]TTCTCCGTATCAGCCGCCTCTTCTTCAGTAATAAGCGAGGAGGATAAGAGAACCATGCTCGAGGGATATGGACTCAATCCGGATGAGTAT
107345 A G ACCATGCTCGAGGGATATGGACTCAATCCGGATGAGTATATATCCGATCAAACTACGAGGCCACCTAGGAGGAGCAGGGAAGAGCAAATGAAGATGAGGA[A/G]GATGATGAAGAAAGGGAAAAATGGGAAGGGGGGATCAATGCAGGAAGAGCAGATGGCTGTGGTGGAAGGAAAAAAGACGC
107345 GA G AGGAGCAGGGAAGAGCAAATGAAGATGAGGAAGATGATGAAGAAAGGGAAAAATGGGAAGGGGGGATCAATGCAGGAAGAGCAGATGGCTGTGGTGGAAG[GA/G]AAAAAAGACGCCACGTACTACCCACAAATTATTAAAGGTTCTAGGAGGAAAAGCACGGAGAAAAAAGTTACTATCGCCTA
107345 GA G GGGGGATCAATGCAGGAAGAGCAGATGGCTGTGGTGGAAGGAAAAAAGACGCCACGTACTACCCACAAATTATTAAAGGTTCTAGGAGGAAAAGCACGGA[GA/G]AAAAAAGTTACTATCGCCTAAAAGCATGGATGTTCGCCCAATGATGGAAGTTGTACGAGGAGCTGCCTTTGATATTTTGCAGG
107353 T G TATGATCGTCAGTGGTGGTATCATCAGACTTGTCCATTTCACTATATAAAGATCTGCAAACTCATCATCCACATCTTCTCCTCCACACTTAGTAGTCAAT[T/G]TGAACGATATCTCTATCCCAGCTATGACTTTCAGTAAGCCTCGTAGAACAGCGGCTAAGTGTGCACTAGTCCCTCCTATAAGCCAGAACT
107353 T C ATCTTCTAAGCATATCTTCGACCACTTTATTTCGAGTATGGCCAACATGCATACAGTCAGCGTTATCGCTAATAGATACACCAGGAAAGTGGTTGACAAA[T/C]ACTCCACTATAAACTTCCCGGTAAACAGTGAAAACGCTGGCAAAAAGCAGTACACGATCAGAAAAAACGATGTGAACGGATAGATTC
107353 C T GCATACAGTCAGCGTTATCGCTAATAGATACACCAGGAAAGTGGTTGACAAATACTCCACTATAAACTTCCCGGTAAACAGTGAAAACGCTGGCAAAAAG[C/T]AGTACACGATCAGAAAAAACGATGTGAACGGATAGATTCCCACGTTGAGGTAGGCGATTCTCTGAAGAAGCTTCATTTTCGGGCTT
107357 A G ACTGTTGGCCTACTGGCTCTCCTGTTTCCGGTTTTTCTCATTTAAGACTTCCCTAGCAGCAGTCTAGATAGCTCCATCAATTCTTTGCAATGTCTCAG[A/G]TTAATAACAGGAATGCTTCTGCTGGAAAAAGGGCCCGAACTGATGGTGGTCGTAGAGAAGATGACTGGACATGTCCAAGCTGTGGAAATG
107357 C T GAGGACCTCCACTCTCTCCTTACAATATGAGGTATCCAAGTGGTTCTGCTTATCCTTTTGACTATGGAAACCGCTCCTATGATTATGGAAGCCGCTCTTT[C/T]GGGAGCCCATATGGACCAATGCACGTACCTGGACCTCCATACTCAAGCGGATCTATGATGGGAACAGGTGGTATGTATGGCATGTCTC
107357 C T GTGCTATGGCTCCGAGACCAGGAGCTTATCCCGAGGAGAGCTCCCACAAGAAGGCTGCTGGTGCAGGGCGTGAAGATGACTGGACATGTCCTACCTGTGG[C/T]AACCTCAACTTTGCATTCAGAAATGTTTGTAACATGCGGAAATGCGACACACCAAGACCTGGAAGTCAGGGTTCTAACAATTCCA
107359 T G CCCTAATAGAAAATGGGGAGAGAAAGGTAAGAAAATATAAACATAAAAGCAAACAATTTTGATTTCAACATGTACATGTTAATTAGTGATTTGAACGCGC[T/G]CCTGGCGCATCCCTCATGCTTATATTTAAACTGTTCCTCATAGTTCTTCGTCCAATTCCAATGTTCCCCTTTTGCATCATTGCAACAAA
107359 AT A TGTAATTGCACCACTGTTGTCTGTGTCCATTGCTGTGAACATTTCTCTTAATCCAGCAATTTCCTCTTCAGAAAGGCTTTCGGCTATCACTCTTAAGGCC[AT/A]TTTTTTTCAACTTATTCATTGCCGAAAATTGTTTCAGACGGGAGAGGACTGCTGGATCCAATGCTCGGTCAGGAGCAACTCCATTTTCA
107363 T TC GCGCTGATGAGCCACATCTCGCAGATGAACGGCGGAGATGGGTCGGAGTACGAAGCGCTGCACGCGGCGATCCACCGTAGACGGATGAACTGGATCCCCG[T/TC]CTCCAGATGCAGAAATTCTGCTCGATTGCCGATGTCGTCGTCGAATTGAAGAGAGTTGAGTTCAATCACAGTGTGAATGTCGG
107363 C T TCGTCGTCGAATTGAAGAGAGTTGAGTTCAATCACAGTGTGAATGTCGGTAACGGAATCGATGTTAGATCGGAGCGATCTGCTGTTAGCTATAAGAAGTC[C/T]GAAGATGGAAGCGCTGATTCTTCTGGCGGCGCTGATGATCTGAAAGTCCACTGCATTTCCGATTCAGGTTCTCAAGAAGAAGAAGT
107363 A G TTTCGTGCGACCCCAATGGCATCTATAAGGGCTCTCTCACCCTCCCACTTAAAGAAGGGTCATTGATAGTCATGCGTGGAAACAGCGCTGACAATGCAAG[A/G]CATGTCGTCTGCCCATCAAAGACAAGAAGAGTGACCATCTCATTCGTCCGGGTCAGGCCTGCCATCAGCCAACCCGACCCGTCAGT
107363 T C CGTGCGACCCCAATGGCATCTATAAGGGCTCTCTCACCCTCCCACTTAAAGAAGGGTCATTGATAGTCATGCGTGGAAACAGCGCTGACAATGCAAGACA[T/C]GTCGTCTGCCCATCAAAGACAAGAAGAGTGACCATCTCATTCGTCCGGGTCAGGCCTGCCATCAGCCAACCCGACCCGTCAGTAAC
107363 A C ATAAGGGCTCTCTCACCCTCCCACTTAAAGAAGGGTCATTGATAGTCATGCGTGGAAACAGCGCTGACAATGCAAGACATGTCGTCTGCCCATCAAAGAC[A/C]AGAAGAGTGACCATCTCATTCGTCCGGGTCAGGCCTGCCATCAGCCAACCCGACCCGTCAGTAACCCCTATGCATACCACTACAAGC
107363 A C TCTGCCCATCAAAGACAAGAAGAGTGACCATCTCATTCGTCCGGGTCAGGCCTGCCATCAGCCAACCCGACCCGTCAGTAACCCCTATGCATACCACTAC[A/C]AGCATGACACTATGGCAACCCCTACCACAGGTGCAGAACATACCTATGACCGAACCAGTGATCACTTATGCCAGCTCACAGG
107363 A G CAAAGACAAGAAGAGTGACCATCTCATTCGTCCGGGTCAGGCCTGCCATCAGCCAACCCGACCCGTCAGTAACCCCTATGCATACCACTACAAGCATGAC[A/G]CTATGGCAACCCCTACCACAGGTGCAGAACATACCTATGACCGAACCAGTGATCACTTATGCCAGCTCACAGG
107369 G A CGTTTACTGATCCTCATGTGTTGCCGGCTTCTCATGTCAGCTACTCGGATGGACTGAAGATCAAAGCGTATATCAAAGCAAATACTTCGGCCACTGCATC[G/A]ATCGCCTTCAAAGGTACAGTAACAGGATCATCAGTGGCGGCTCCGATACTAGCATATTTCTCATCTCGAGGACCAAACCAAGCAGAC
107369 C T ATTTCTCATCTCGAGGACCAAACCAAGCAGACCGGAACATTCTAAAGCCAGACATCATCGGGCCAGGAGTCAACATCCTGGCTGCATGGCCATTCGACAT[C/T]GGGACCCCGGGAACCAAATACAACCTAATCTCAGGAACTTCAATGGCAACCCCACATCTAAGTGGCATTGCAGCCTTATTAAAAGG
107369 G C TCTCATCTCGAGGACCAAACCAAGCAGACCGGAACATTCTAAAGCCAGACATCATCGGGCCAGGAGTCAACATCCTGGCTGCATGGCCATTCGACATCGG[G/C]ACCCCGGGAACCAAATACAACCTAATCTCAGGAACTTCAATGGCAACCCCACATCTAAGTGGCATTGCAGCCTTATTAAAAGGTGC
107369 A C GGAACATTCTAAAGCCAGACATCATCGGGCCAGGAGTCAACATCCTGGCTGCATGGCCATTCGACATCGGGACCCCGGGAACCAAATACAACCTAATCTC[A/C]GGAACTTCAATGGCAACCCCACATCTAAGTGGCATTGCAGCCTTATTAAAAGGTGCACATCCTAACTGGTCTCCTGCTGCAATCAAA
107369 G A CTGATCCCGGACTCGTTTATGACCTTGATCAGACTGATTATGTTTCGTATCTTTGTGGCATGAAGTATACTGATAGGCAGGTAAGTGTAGTTGTGCGTAA[G/A]ACAGTGAAGTGTTCCGACTATAGTCCGGTGTCGGGTGCCGACCTGAACTACCCATCTTTTATGGTATTCATGAACGATGATAGCCGG
107369 G A TCAGACTGATTATGTTTCGTATCTTTGTGGCATGAAGTATACTGATAGGCAGGTAAGTGTAGTTGTGCGTAAGACAGTGAAGTGTTCCGACTATAGTCCG[G/A]TGTCGGGTGCCGACCTGAACTACCCATCTTTTATGGTATTCATGAACGATGATAGCCGGACTGTTAAAAGAACAGCTACGAACGTTG
107369 G A GCTAGTTCCAGTTATACGGTTGAGGTGGTTGAACCTGAAGGGGTGACGGTTACGGTTGAGCCAAAGATACTGAGTTTTGAAGCCCTTAATGAGAAGGTTG[G/A]TTTTACTGTTACTTTCAGTGTAACGGGGAGTTTACGTGAAGGGTACTCGGAAGGGTATTTGTACTGGAAATCAGCTAATCATAGG
107369 G A TCATAGGGTTAAAAGTCCGATTATGGTGTCAATTGGGGGAAGTAGCTTACAGTCCATGTAGGATTGTAGATGTTTGTAAGTTCACAGTTTGTTTTGTTTC[G/A]GTAACAGTTCTTCCATGTTTGACAGATATGTCCTAATAAAATTTGATTTCTCCTGAAAAAAAAAAAAAAAAGG
107377 T C GTAATTCATGCCTGCTTTCTTTTTTTGGAGTTCTACATAGCAACCCAACTACTTGGACATGAGGTGGGCATTTTTTGGTAAGATGGTCCAATATGGTCTG[T/C]TTGATCACCTCCAACAGTGACTTGCGCTGGTCATCATTATCCTTATCAGCGGTCTGTATCATATAATCCAAAGCCATCATAAATCCCGGC
107389 T C TTTCAAGTTGAGGTTGCGGACTGGCATAGCAGTCTGAAATGGATTGAATTGAAACTTAACAGCATCCTCATGGCTTTCTCTGTAGTCACGTTGGTTAGTC[T/C]TTGAATTTTGATTTAGTACAATCGGCACTGCAGTGGGGATCTCAGGGTTAGAGTTGAAATTATGATTCCCGGTTGATACATTACAGTT
107389 A G CTCATCGGATCCCAGATCATCGTAATTTGAGTTATAATTGTAATTTTGAACTGAACCAATCGGCACTGCCATATGAATCTCACGTCTCTCTTTCTTCATG[A/G]GCTCGAATTCTTCATCTTCATCCTCATCCTCCATAATTGACGCAATCGGTTCTGCAACATGAACATTAAACTTTGATTTCTTCTTCAACTCG
107399 C T TGGAAGCTGTTTTTACACGTTGGCCGCATGTTATTGTACAGTTTGAAGATTTCCAGAGTAAGTGGGCATTTAAATTGCTGCAGCGCTACAGGAATACATA[C/T]CGAATGTTTAATGATGACGTGCAGGGAACTGCTGGAGTTGCAATAGCTGGTCTTCTAGGAGCTGTACGGGCACAAGGAAAACCAAT
107399 C T ACGAATTAGGTCGGCAGGGGCTAAGAGAAGGAGCTTCTCTGGTTGAAGTTGTTAAGAAAGTAAATCCCGATGTTCTTCTTGGATTATCTGCAGTTGGAGG[C/T]CTGTTTTCTAAAGAGGTTTTAGAAGCTCTTAAACACTCTTCCTCGGCTAGACCTGCGATTTTTGCGATGTCTAATCCAACAAAGAATG
107399 T A AGAAAGTAAATCCCGATGTTCTTCTTGGATTATCTGCAGTTGGAGGCCTGTTTTCTAAAGAGGTTTTAGAAGCTCTTAAACACTCTTCCTCGGCTAGACC[T/A]GCGATTTTTGCGATGTCTAATCCAACAAAGAATGCGGAATGCACACCTGAAGATGCCTTCTCCATTTTGGGAGAACATATTATATTTGC
107401 G A ACTGATCAACACAGCGAACATACTGAGCAAGAGGGACAGCAGGACCACGTAAAGGAAATATGCAGTTGCACAATGTTTCATTGTTCCTTAAAGTAGCACC[G/A]TCCCATTCTTTCTTTGGATTTTTCAAAGCAGCATCTGCTCTTCTTGCTTCTTGGTGGCACTGGAAATGTATGATGTTGAAATGGCTGA
107401 A G AACCTTCTATGATGGGTTGGGCTACCACTATTCGCTCACCTCCGTCTGAAGCTAACTCTTGACGCATACCAAGTCCTTGAAGCAACTGTTGTCGTTTTTT[A/G]AGAGCCCTACGTCGCATTTCATCCTTGGTAGCATCCCTCAGCTTATGAATCTGCTCTCCCAAAAATCCATCACCGTTACTATCAGCTAAA
107403 G C GCCGGACATGGAACCAGGCCTTGCGCAGCTCGGAGCTGTTCCAAGCCCGGCACGAGCTCAGGTGCACCGAGGACTTCCTCTGCGCCCTGGCCTTCGACCC[G/C]GAGAACGTATGGCAACTCTACGATCCCCGAAGGGACAAATGGTTCACGCTCCCCAAAATGCCCTCCCAGATCCGCCACCTGGCTC
107403 A C ATGACGGCATCTTCGCAACTGCTGACGTCTGGGCTTTCGACCTCCGCACCTCCCTCTGGTCCCAACGGGCATCCATGCTCGTCCCCCGGGCCATGTTCGC[A/C]TGCTGCACCGTCAACAACAGAATTGTCGTCGCCGGCGGCTTCACCAGCTTCAGGAAGTCCATATCCAAGGCCGAGGTCTACGACCCG
107403 A G AGAAGGTGGTGCTTTCGGCTTCCGAGTTCAAGAGCAGGATAGGGTTCGGGATGATCGGGCTGAAGGACGAGATTTATATGATTGGGGGAGTTATTGGGCC[A/G]GGCCCGGCGAATCAGTCCATTAAGCAGTTGTGTGACGTGGATGTGTTGCCTGTTGGGGCCGGTGGAGGGAAATGGCCAGTGT
107403 T A CAGGCCCGGCGAATCAGTCCATTAAGCAGTTGTGTGACGTGGATGTGTTGCCTGTTGGGGCCGGTGGAGGGAAATGGCCAGTGTGGAGGCAGGCTGCGCC[T/A]ATGTCCAGGTGTTGTGGCAGTATCTTTGGTTGCGCTGTGGTTAACATTTAGCAGTTGTGTTTTTTGTTGTTGATTATGTTTTGTGA
107407 GA G TCAAATGCTCACTAAACATAACGCAAACGTCTCCTTGCTCTCCTTCAAACATCTTCTGAAACCCCTCGAACCTCAGTATCTGGAGCTCGCAAGTAAGCCT[GA/G]AAAAAAACACAGACCAGCAAAAACACTCCACTCCTGTACACCCATGAAGCCAGCGTACCAGCCATGATGAGCGGCCGGATGTCTGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107407 G A TTAGAAAGGCGGGGAAAAGGATGTAGGCGAGGAAGCGGAAGGCGCGGTTGACTTCACGAGTGTAGGTGCGGCGGATGGAGGTGGAGTCGCTGAGGAGGGC[G/A]TCGTCGAGAAGGAGGATTTGGTTGAGCTTGTGCTCGCGGAAGAAGGAGGAAAGGGTCAGGAAGGCTATGACCGCGAGGC
107407 A G CTTCACGAGTGTAGGTGCGGCGGATGGAGGTGGAGTCGCTGAGGAGGGCGTCGTCGAGAAGGAGGATTTGGTTGAGCTTGTGCTCGCGGAAGAAGGAGGA[A/G]AGGGTCAGGAAGGCTATGACCGCGAGGCCCGATTCGAGGACTTGGGCCAGGAAGTTGAGGGAGAGGGAACCGCATGTTGG
107407 T G GCTTGTGCTCGCGGAAGAAGGAGGAAAGGGTCAGGAAGGCTATGACCGCGAGGCCCGATTCGAGGACTTGGGCCAGGAAGTTGAGGGAGAGGGAACCGCA[T/G]GTTGGAGTGGAGAAGAAGGAGGCCGATGTCAGGGAGGGGATGATGATCGTGAAGGTGAGGAAGGTTATGTAGGAGACTG
107413 G T CCAATGGCCAGCAAATAATCAGGCCATTGGAGAATCCTATCAAGCCAACTGGACATATTCAAATACTTTATGGGAACCTTGCACCAGATGGTTCTGTGGC[G/T]AAAATAACCGGCAAAGAAGGGCTCTACTTTTCAGGTCCTGCACTTGTTTTCGATGGTGAAGAGGCTATGCTTGATGCACTTGCGAAG
107413 C T GAGGTGAAGGGCCCAAAGGAGGACCAGGCATGCCTGAAATGTTGACGCCAACTAGTGCGATAATGGGTGCAGGTCTTGGGAAGGAATGTGCCTTACTGAC[C/T]GACGGAAGATTTTCTGGAGGATCACATGGATATGTAGTTGGACATATATGCCCTGAAGCCCAGGAAGGCGGACCCATTGGCCT
107431 G T GCATTCAATGCTGTCAAAAAACAAAGAACGCTCGAAGAAGCTTCCGAAACAGTTACAGCTGCTTTAGCTCAAGCAGGACTCTAGTTATTACTGCCACAGC[G/T]ATCCCTCTAAATTGGTTACAAAAGTTAAATCATTCTTCATGATGATTGCTCCCTTTTTGTGCAATTGTGATCAGGCCAACAGCTGAAAT
107431 T C GAACGCTCGAAGAAGCTTCCGAAACAGTTACAGCTGCTTTAGCTCAAGCAGGACTCTAGTTATTACTGCCACAGCGATCCCTCTAAATTGGTTACAAAAG[T/C]TAAATCATTCTTCATGATGATTGCTCCCTTTTTGTGCAATTGTGATCAGGCCAACAGCTGAAATTTCAAATCGCTTACAAAATTGCTGT
107433 C T TTGAAATAATCAAGAAGGCAATTCACAAACTTTCTCTGCGCCACAAGGAACACATTAGCGCATATGGTGAAGGCAATGAACGGAGATTAACTGGAAAACA[C/T]GAGACTGCAAGCATTGATCAATTCTCTTGGGGTGTGGCAAATCGTGGATGCTCAATCCGTGTGGGACGTGACACTGAAAAAGAAG
107441 A T TCCCCTGAACCGATCGCCCGGGAAGTGCAAACAGACGTAGTTTAAATAAATCATGCTTTACACAAACATCCAATCTACTGGACTCATATCTTAAGAGTGC[A/T]TTTCTGTAATCAGCACACTGTATAACCAGAATTGTTTTTACCCTACTGTTCTCCAGGAAGCATAGTATCCTCAGGTAGATCGCAGTATG
107441 G A TTGATCGGCATGGCATACTGAAGACAATATCCTCCTCAATACCGTATGGATTTCCATTCGTGTAAACCCCTGTAGAAAACCAATCGCCTTCTGGAGTGGG[G/A]GTAACAAGAGATCTTATCGCATCTACAATTGAAACAGCAGTTGATGCAGCCGAAGATCTTCCCCACTTCTTAATGAGCACGCCACCAC
107441 G A AAGATCTTCCCCACTTCTTAATGAGCACGCCACCACGCGTCTGAACTTTCTGAGTGAACTCTTCTTCTAACCATTTGATGTCAGTTATGACCTCCTTCAC[G/A]GGTTTTCCATCAATTTTTGCATTTAGAAAGTCTGGAACCTGAGTGGTCGAATGATTTCCCCAGATGGTCATGTTTGACACTTTATCATAG
107441 A G TGAACTCTTCTTCTAACCATTTGATGTCAGTTATGACCTCCTTCACGGGTTTTCCATCAATTTTTGCATTTAGAAAGTCTGGAACCTGAGTGGTCGAATG[A/G]TTTCCCCAGATGGTCATGTTTGACACTTTATCATAGAAAACACCCGCTTTGAGAGCTAGCTGACATTTGGCTCTGTTCTCATCTAACCTTG
107441 A T TCATGTTTGACACTTTATCATAGAAAACACCCGCTTTGAGAGCTAGCTGACATTTGGCTCTGTTCTCATCTAACCTTGTCAAGGCATGGAAGTTTCGGGC[A/T]GGTATATTAGGTGCATTTTTCAGACAAATAAGTGCATTTGTATTACACGGGTTCCCTACAACCATGACTTTGACATTTGGGGATGCCAC
107441 A T GAAGGGCCCATTCTGCATCCTGAAAGACTTCATATGGATCAATGCCTATGCTCACTGCCCTTAGTAAAGGGAACAAGGAGTCCTCCAGTTCCATAGCCAC[A/T]CCTTCAAGAGCTTGAAATGATCTTTCAGAACCGAGTAATTTAAGAGCAATAGGTTGGTCCTGTCCAAATACTTCACCAGATGCTAGTT
107441 T C CCTGAAAGACTTCATATGGATCAATGCCTATGCTCACTGCCCTTAGTAAAGGGAACAAGGAGTCCTCCAGTTCCATAGCCACACCTTCAAGAGCTTGAAA[T/C]GATCTTTCAGAACCGAGTAATTTAAGAGCAATAGGTTGGTCCTGTCCAAATACTTCACCAGATGCTAGTTTGAAGAGTAGATGATTCG
107443 A G AAGCAACTCGATGAATGCTGATATTGCGAAGAACAGCGTGGCACCCTTGCGAAGACCATTTTCAGACTTGTCAAATGCGGCCTTTGTAATGAATCTCAAG[A/G]CGGAGGTAAAAACACCCGATGCAGCCAAACCAGCGAAGAAGGACTGAAGAAATTCTGGGCACATCAAAGAAAGGTCACCAACCAT
107443 G A GCAACTCGATGAATGCTGATATTGCGAAGAACAGCGTGGCACCCTTGCGAAGACCATTTTCAGACTTGTCAAATGCGGCCTTTGTAATGAATCTCAAGAC[G/A]GAGGTAAAAACACCCGATGCAGCCAAACCAGCGAAGAAGGACTGAAGAAATTCTGGGCACATCAAAGAAAGGTCACCAACCATCC
107443 C T TAATGAATCTCAAGACGGAGGTAAAAACACCCGATGCAGCCAAACCAGCGAAGAAGGACTGAAGAAATTCTGGGCACATCAAAGAAAGGTCACCAACCAT[C/T]CCACCTTGAGCTAAAGCATCAGCAATTCCGAATAATGCGCTTGTTATACAAACTCCGAGGAATGGTCCGATGCCTCCTCTACCCGA
107443 T C ACACCCGATGCAGCCAAACCAGCGAAGAAGGACTGAAGAAATTCTGGGCACATCAAAGAAAGGTCACCAACCATCCCACCTTGAGCTAAAGCATCAGCAA[T/C]TCCGAATAATGCGCTTGTTATACAAACTCCGAGGAATGGTCCGATGCCTCCTCTACCCGAAGTAGCTACGTCTATAACGATGAGCA
107443 G A CCAAACCAGCGAAGAAGGACTGAAGAAATTCTGGGCACATCAAAGAAAGGTCACCAACCATCCCACCTTGAGCTAAAGCATCAGCAATTCCGAATAATGC[G/A]CTTGTTATACAAACTCCGAGGAATGGTCCGATGCCTCCTCTACCCGAAGTAGCTACGTCTATAACGATGAGCAAGAGCGAACTAAG
107443 A T CAATTCCGAATAATGCGCTTGTTATACAAACTCCGAGGAATGGTCCGATGCCTCCTCTACCCGAAGTAGCTACGTCTATAACGATGAGCAAGAGCGAACT[A/T]AGGAAGAAAAGAGAGAACCCAGCCAGATTTCGAACTCTTGTGTTAACCTTTGCTTCGTAGTATAGGAATATGGCGGTAGTCCCAAAC
107447 A T TAAATCCGAGGTGCATCTGTTTGATTTTGATGCGGAAGGAGACGAGCTGAACACACCGTTTGCTGTGTTGAAAGGGCACCAGGAATGTGAAGGGTATGGC[A/T]TGGATTGGAGTGAATTGAAGGAAGGTTGGATTTTGAGTGGTGGCTATGATTCTAAGATTTGCCTGTGGGATGTTGGTGTTGATG
107449 C T TATACTTCTTTCTGTCACTTTTTAACACATTTTGTTTTCCGCTTGTGCATTTGCACGAGCTGAGAAAGCCGAGTATCATATTCTCGATATATCAATGTTA[C/T]GAGTGATAAGAAACCATGTCTTTAAAACAATGAGTTTTAATGCAATATAATAATAATGACAATAAAAAGGTTCATTTGAACATTTTTCTTA
107453 AT A ACTGTTGGCCTACTGGAAGTATCCCCGCTTCAAAAACGATGCTTCCAATCAACTCTAGCTTCCCTTTCTTCTTTCTGCCCTAACCGAACTTAGCTTTG[AT/A]TTCAAAAAGGAGCACAGTTCTGAATGAGGAAAGAAGAAAGGGTTCGCAATAAAGAATCTGCTACTGTCGGAGCAGATGTTCGCAGCTTT
107453 T A AAATTCTTGATGTTGGAAATTGCAGAGGAACCATGATTGGTCTTGAAGCAATGAATTTCATCACCATTGCTTCTCCACACCTTGGTTCTAGAGGGAACAA[T/A]CAGGTTCCGTTTCTCTTTGGTGTCACTGCAATCGAAAGGGTTGCTTTCCACGTTATCCATTGGCTTTTCGGAAGAACAGGCAAACACC
107453 G A CTGCAATCGAAAGGGTTGCTTTCCACGTTATCCATTGGCTTTTCGGAAGAACAGGCAAACACCTTTTCCTTAGTGATAACGATAAGGGCGAACCTCCTTT[G/A]CTGTTGCGAATGATCAATGATGAGAGTGACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCC
107453 G T CCACGTTATCCATTGGCTTTTCGGAAGAACAGGCAAACACCTTTTCCTTAGTGATAACGATAAGGGCGAACCTCCTTTGCTGTTGCGAATGATCAATGAT[G/T]AGAGTGACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTG
107453 G T ACGTTATCCATTGGCTTTTCGGAAGAACAGGCAAACACCTTTTCCTTAGTGATAACGATAAGGGCGAACCTCCTTTGCTGTTGCGAATGATCAATGATGA[G/T]AGTGACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGA
107453 T C TTATCCATTGGCTTTTCGGAAGAACAGGCAAACACCTTTTCCTTAGTGATAACGATAAGGGCGAACCTCCTTTGCTGTTGCGAATGATCAATGATGAGAG[T/C]GACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGAGGA
107453 G A GAACAGGCAAACACCTTTTCCTTAGTGATAACGATAAGGGCGAACCTCCTTTGCTGTTGCGAATGATCAATGATGAGAGTGACCTTCGTTTCATGTCTGC[G/A]CTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGAGGACGTCTTCAATCAGACGCAAA
107453 G A GTGATAACGATAAGGGCGAACCTCCTTTGCTGTTGCGAATGATCAATGATGAGAGTGACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGT[G/A]GCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGAGGACGTCTTCAATCAGACGCAAATCAGAACTACCCGTGTGGGAGGA
107453 G A ATGATGAGAGTGACCTTCGTTTCATGTCTGCGCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGAGGAC[G/A]TCTTCAATCAGACGCAAATCAGAACTACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTC
107453 G A GCTAAATGCATTCCGACGCCGAGTGGCTTATTCGAACGTCCGCCATGACCATATTGTTGGTTGGAGGACGTCTTCAATCAGACGCAAATCAGAACTACCC[G/A]TGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATC
107453 G A CGAACGTCCGCCATGACCATATTGTTGGTTGGAGGACGTCTTCAATCAGACGCAAATCAGAACTACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCC[G/A]CATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCAATGTTTCGGTTGTAGACGGAAAATGCGATA
107453 C T TCCGCCATGACCATATTGTTGGTTGGAGGACGTCTTCAATCAGACGCAAATCAGAACTACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATAT[C/T]GTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCAATGTTTCGGTTGTAGACGGAAAATGCGATATGTTGGA
107453 G A CAATCAGACGCAAATCAGAACTACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTC[G/A]GAGGACTCGATCAATGTTTCGGTTGTAGACGGAAAATGCGATATGTTGGAAGAAAAAATAGTGACCGCTCTCACACGTTTTTCATG
107453 A T TCAGAACTACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCA[A/T]TGTTTCGGTTGTAGACGGAAAATGCGATATGTTGGAAGAAAAAATAGTGACCGCTCTCACACGTTTTTCATGGGAGAGGGTGGAT
107453 G A TACCCGTGTGGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCAATGTTTC[G/A]GTTGTAGACGGAAAATGCGATATGTTGGAAGAAAAAATAGTGACCGCTCTCACACGTTTTTCATGGGAGAGGGTGGATGTCAGCT
107453 C T GGGAGGAACCCCAGTGCGAGAGATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCAATGTTTCGGTTGTAGA[C/T]GGAAAATGCGATATGTTGGAAGAAAAAATAGTGACCGCTCTCACACGTTTTTCATGGGAGAGGGTGGATGTCAGCTTTCGCAACA
107453 GA G ATATCCGCATATCGTATATCAGGAACTGTCAAAAGGCTGTGTTGATTCGGAGGACTCGATCAATGTTTCGGTTGTAGACGGAAAATGCGATATGTTGGAA[GA/G]AAAAAATAGTGACCGCTCTCACACGTTTTTCATGGGAGAGGGTGGATGTCAGCTTTCGCAACAGTCGACAGAGATTCGATGCACA
107459 GA G GTTTTGTTAATTTTGAAAATCCCGATGATGCTGTCCGAGCAGTTCAGGAACTTAACGGGAAGAAATTTGGTGACAAAGAATGGTTTGTTGGAAAAGCTCA[GA/G]AAAAAATCCGAGAGGTTGATGGAATTAAAAGTGAAATTTGATCAGGGTGCTAAACAAGCTATTGAGAAATTTCAAGGAGTCAATT
107459 GT G TTTGAGGAGTGTGCATTAGTTTGGTGCATTGGATTAGCTTGCTAGAAGCTTTATTTTCTAAACATGCCCATTTTCTAGTCTTCCTTTTTGCTTGCTGTTA[GT/G]TTTTTATGTTAAGATTCCTTTAAGTACATAATCAGGATGTTTGGTTGGTTGAATTTTTGTGCTGAATCAATTGCTGGATTAATTGTTTTTT
107469 G T GGTAGAGAAACCACCGTGCCGAAACTGACGTACACCACTGAATGGGGCTTCTGCTGCTCCAGCCATCCGATGCAGCCGAATCGATCTACTGGTTTAGTCT[G/T]GACCGGATTCAGAAGGCTGAGAGGTCCAACTGGGTAGTACTTTTTGAACCTGGACCCGAAATCGGAATCCAGATCCGGATCCAGC
107469 A C TAGAGAAACCACCGTGCCGAAACTGACGTACACCACTGAATGGGGCTTCTGCTGCTCCAGCCATCCGATGCAGCCGAATCGATCTACTGGTTTAGTCTGG[A/C]CCGGATTCAGAAGGCTGAGAGGTCCAACTGGGTAGTACTTTTTGAACCTGGACCCGAAATCGGAATCCAGATCCGGATCCAGCCCT
107469 A G AAACCACCGTGCCGAAACTGACGTACACCACTGAATGGGGCTTCTGCTGCTCCAGCCATCCGATGCAGCCGAATCGATCTACTGGTTTAGTCTGGACCGG[A/G]TTCAGAAGGCTGAGAGGTCCAACTGGGTAGTACTTTTTGAACCTGGACCCGAAATCGGAATCCAGATCCGGATCCAGCCCTTGGAA
107469 G A ATCCGATGCAGCCGAATCGATCTACTGGTTTAGTCTGGACCGGATTCAGAAGGCTGAGAGGTCCAACTGGGTAGTACTTTTTGAACCTGGACCCGAAATC[G/A]GAATCCAGATCCGGATCCAGCCCTTGGAAAGTGTTGCCCACGACCGCATCGGCGTCAGGGAGCGCGAGGGCCATGTCGTGGAGA
107469 T C GAGAAGCTTGGGGAAGCCTTGACTCAAATCGCCGACCACAACGCCGTCGGGGAGATCTTTTACTCTGAGACCCGATAACCCGGTAATGAACCCAAGGTCG[T/C]CTTCGTCGCTGAGGTTTTTCTGGCGGAGCAGGTCTTTGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGAT
107469 T G CACAACGCCGTCGGGGAGATCTTTTACTCTGAGACCCGATAACCCGGTAATGAACCCAAGGTCGTCTTCGTCGCTGAGGTTTTTCTGGCGGAGCAGGTCT[T/G]TGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGCGATTGCGCCGCC
107469 G T CCGATAACCCGGTAATGAACCCAAGGTCGTCTTCGTCGCTGAGGTTTTTCTGGCGGAGCAGGTCTTTGTGGATATGAGCGGACAAACTGCACGGGCCTCC[G/T]GTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGCGATTGCGCCGCCAAAGGATAGGAACGCGTCACCGATCAGGCATGTGA
107469 A T ACCCAAGGTCGTCTTCGTCGCTGAGGTTTTTCTGGCGGAGCAGGTCTTTGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCA[A/T]GGAACGGCTAATTTATTGGCGATTGCGCCGCCAAAGGATAGGAACGCGTCACCGATCAGGCATGTGACGCCGATTCCGCCACTGG
107469 A C CGTCGCTGAGGTTTTTCTGGCGGAGCAGGTCTTTGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTT[A/C]TTGGCGATTGCGCCGCCAAAGGATAGGAACGCGTCACCGATCAGGCATGTGACGCCGATTCCGCCACTGGCGGTTACAGAGGCA
107469 G A TGAGGTTTTTCTGGCGGAGCAGGTCTTTGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGC[G/A]ATTGCGCCGCCAAAGGATAGGAACGCGTCACCGATCAGGCATGTGACGCCGATTCCGCCACTGGCGGTTACAGAGGCATCGAGG
107469 G A TGTGGATATGAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGCGATTGCGCCGCCAAAGGATAGGAACGC[G/A]TCACCGATCAGGCATGTGACGCCGATTCCGCCACTGGCGGTTACAGAGGCATCGAGGGCGTCGGTGAAGTTGGTGGGAACTTT
107469 C T GAGCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGCGATTGCGCCGCCAAAGGATAGGAACGCGTCACCGAT[C/T]AGGCATGTGACGCCGATTCCGCCACTGGCGGTTACAGAGGCATCGAGGGCGTCGGTGAAGTTGGTGGGAACTTTGGACATGAA
107469 G A GCGGACAAACTGCACGGGCCTCCGGTCCATACAGCGATCCAAGGAACGGCTAATTTATTGGCGATTGCGCCGCCAAAGGATAGGAACGCGTCACCGATCA[G/A]GCATGTGACGCCGATTCCGCCACTGGCGGTTACAGAGGCATCGAGGGCGTCGGTGAAGTTGGTGGGAACTTTGGACATGAAGC
107469 T G AGGCATCGAGGGCGTCGGTGAAGTTGGTGGGAACTTTGGACATGAAGCGGCCCACTTCCAGATGCGGCGGCTCGTGGACCGCCACGTGTCCGGGTGGGGT[T/G]CCATCGGAGACGGAGAAGATTTTGATTCGGGGGACTGGAGGGAGGGAGGAAGCGGAGCGGGCGGAGGTAAAGAAAGAGAA
107469 A G GTCCGGGTGGGGTTCCATCGGAGACGGAGAAGATTTTGATTCGGGGGACTGGAGGGAGGGAGGAAGCGGAGCGGGCGGAGGTAAAGAAAGAGAAGATGGC[A/G]CTGTTGTCGTCGGTCGTGGAAACGAGGGCCGAGGCGAGGGAATAAAGAGGAGCGGCGTGGGTGCCAAAGGGGAAGGCG
107469 T C GGTGGGGTTCCATCGGAGACGGAGAAGATTTTGATTCGGGGGACTGGAGGGAGGGAGGAAGCGGAGCGGGCGGAGGTAAAGAAAGAGAAGATGGCACTGT[T/C]GTCGTCGGTCGTGGAAACGAGGGCCGAGGCGAGGGAATAAAGAGGAGCGGCGTGGGTGCCAAAGGGGAAGGCGAGAAA
107469 G A GTGGGGTTCCATCGGAGACGGAGAAGATTTTGATTCGGGGGACTGGAGGGAGGGAGGAAGCGGAGCGGGCGGAGGTAAAGAAAGAGAAGATGGCACTGTT[G/A]TCGTCGGTCGTGGAAACGAGGGCCGAGGCGAGGGAATAAAGAGGAGCGGCGTGGGTGCCAAAGGGGAAGGCGAGAAAT
107469 T C CCATCGGAGACGGAGAAGATTTTGATTCGGGGGACTGGAGGGAGGGAGGAAGCGGAGCGGGCGGAGGTAAAGAAAGAGAAGATGGCACTGTTGTCGTCGG[T/C]CGTGGAAACGAGGGCCGAGGCGAGGGAATAAAGAGGAGCGGCGTGGGTGCCAAAGGGGAAGGCGAGAAATGCGACATG
107477 A G TTCTAATATGCAAACCTACAAATTCATTACCCTATACAACAAATCCGTATACCTTCACCTTAAATACTCAATAACACATATATTTTTCCTTAGCCACTGC[A/G]TAATATGGAGACCGCTCCAAGTTTGTTTCACGTATAAAAATCTTCATCAATTGTCACCTGCATTATTGCTTTTGCGTTTGCTTTTAAGAACA
107477 G A GCTTCAGTTGTAATCCTGTTTCTTGCACTAGCCTTGCCTTATCGTCTTCTGTAGGGTAAGGCCATTTTGAGTGAGCCTGCCACCAAGCTTTTAGAAGAGA[G/A]GTTGTATCTCCAGGTAATTTTCCAGCTCTTCTTTTCCGTAATATCTCTTCCCTGATATCAACCAGCTTCTCTTTGTATCCCTGTTTAAGTTC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107477 G A ATATCTCTTCCCTGATATCAACCAGCTTCTCTTTGTATCCCTGTTTAAGTTCATGTTTCAATTCTTGTCTAACCCGCTCCATTAGTGAGCGTTCACTTTC[G/A]GTAGGAAGACCAAATCCCATGCCCATACTATCGGTTCCATCCATAGTCGTATCATAAAAGTTGTTATCACCATCAGCTTGATCATCTTCATC
107477 G A TCCATAGTCGTATCATAAAAGTTGTTATCACCATCAGCTTGATCATCTTCATCATCTGACATAGTTGCTCCTGTACCTTCACCGGGTGAAACACCAGTTA[G/A]GCTTTGTAAAGCTTGTTCGAGCTCCCAACAGGCCATGACTGCTTCCATTGCATGAACCCGTACGTGCTGCTGTAGTTGTTCTTTGAACGA
107477 T C CGTTCTGCCACGTGCCCTCCTCGTGCTGAAGATGGCGGCTCATATCCTCCTCCTCTTGATCCTCCATGTGAGTGGACTGAGGCGCCGCCCACGTGGACGA[T/C]GATGCTGCCGACGTCGTGGAATCGAGGTGGTGCAGGAAGTTGTGCTGCTGTATGTACATGTCTTGTACGCCTCCTATTTGGTTTGAG
107477 A T GTGCAGGAAGTTGTGCTGCTGTATGTACATGTCTTGTACGCCTCCTATTTGGTTTGAGCCGGGGTAATTTGACATTAGTGGTTCTAATTAATTTATTTTA[A/T]TTTTCTTTTTTCGGGAAAGAATGGAAAGAGAAGAAGATGACGATGATATTGATGATGAGGGGTTTGTTGTTTTCCAGTAGGCCAACAG
107477 A G CTGTATGTACATGTCTTGTACGCCTCCTATTTGGTTTGAGCCGGGGTAATTTGACATTAGTGGTTCTAATTAATTTATTTTAATTTTCTTTTTTCGGGAA[A/G]GAATGGAAAGAGAAGAAGATGACGATGATATTGATGATGAGGGGTTTGTTGTTTTCCAGTAGGCCAACAG
107479 A G ACATTCTCTTTCTAACAGGAAATGGTTTGCTAGTTTCTCCTAATTTCCTAAAACTACCAGGTAATTTCCCACTATCATCAACTCGTAATTTTATTTCAGG[A/G]CTATGGTAGCAAGGCTCAAGAATATCATATATGTTCAGACCATCAATTTCCACATCAACTCGGTCCAAAATTTCCTGGCATTTATCATTCTC
107481 T C ACTCTCGCTTCTCCTACCTTTCCATAATATCCGTACTAGGTGTGCTCGTCATCCTGACCATGCTAGCTCCTTCTCTGTCCTCCCCGCGCTTTCGCCCTTT[T/C]AGGGCGTCCCTCTTCCTAGCCATGGGCTTCTCCGGGATCGTGCCTGCTGTCCATGCTTTGGTCCTACATTGGGGTCATAGGGCCTGCCAG
107481 A G TCCAGGATACCTGAGAGGTGGAAGCCTGGCGCCTTTGATTTTGTAGGACACAGCCATCAGATTTTTCATGTGTTTGTGTTGGTTGGGGCGTTGACCCATT[A/G]TGTTGCTACTAAGGTTTTGCTTGATTGGAGGGATGGCGGGGTGTTGTGCCCTACTTGATTGATTGAAGAGCTGTTATGTATTTTTTT
107481 A AG GGTTGGGGCGTTGACCCATTATGTTGCTACTAAGGTTTTGCTTGATTGGAGGGATGGCGGGGTGTTGTGCCCTACTTGATTGATTGAAGAGCTGTTATGT[A/AG]TTTTTTTCTGGGAAGATGTAGGACTAAAAGTACGTGTATAAGAGGGACTGGAGAGTTTTGTATGGTATTTTGTTGTATTGCTTGCG
107481 G A TTGTGCCCTACTTGATTGATTGAAGAGCTGTTATGTATTTTTTTCTGGGAAGATGTAGGACTAAAAGTACGTGTATAAGAGGGACTGGAGAGTTTTGTAT[G/A]GTATTTTGTTGTATTGCTTGCGTTTGGTGGTTTGATTGGTCAGAGTTGAGTGTATTTGTTTTAGAAGAGAAACAATGTTGTACTGGAT
107483 G C TTAACAGGCCTCCACCTTTACCTCAATTCTCTACGCGAAAAAGCATCTCCCGAACTTGCTTCGGGCTCCCACATTGTGGGTAACGTGTTGGTGCATGAAA[G/C]TGCAGTGATTGGAGAAGGGTGTCTGATCGGGCCAGATGTCGCAATAGGGCCGGGCTGTGTGGTTGGATCGGGTGTCAGATTGTCTA
107483 G A GAGAAGGGTGTCTGATCGGGCCAGATGTCGCAATAGGGCCGGGCTGTGTGGTTGGATCGGGTGTCAGATTGTCTAGGTGCACCCTCATGAGAGGGGTTCG[G/A]ATTAAGAATTATGCTTGTGTTTCTAGAAGCATTGTTGGCTGGCATTCTACTGTTGGAAAGTGGGCTAGGGTTGATAATATAACTG
107489 G C CCTCTTTCTCGACAGAAATCGATAAATAAAAATAATATTCAGATAACTAGAGAAAATAAAGATTAATGGAAGCAAAACTAGGTTTTACCGTTCGACCCTC[G/C]TTGGGTTTCTCAAATTTTAACAGTAGAAGAATCGGCAATGGCTTCAGATCTCGTACAATTTCAATGGCGTCTACTATTGGATCCTCTGC
107489 T C CTCCCCGTGAGGTGCATGTCCAAGTTACTCACTCAATGCCACCTCAAAAGATTGAACTTTTCAAGAATTTAGAGAGCTGGGCAGAGAACAATATTTTGAC[T/C]TTTCTAAAGCCTGTAGAAAAATGCTGGCAACCTCAGGATTTCTTACCTGATATGTCATCTGATGGATATGATGTTCAAATTAAAGAGC
107489 AT A TGCTGGCAACCTCAGGATTTCTTACCTGATATGTCATCTGATGGATATGATGTTCAAATTAAAGAGCTAAGAGAGCGAGCTAAAGAGTTACCAGATGATT[AT/A]TTTTGTTTGTCTAGTGGGAGATATGATAACTGAAGAGGCTTTGCCTACTTATCAGACTATGCTCAACACACTTGATGGTGTTAGGGA
107489 C T CTTTGCCTACTTATCAGACTATGCTCAACACACTTGATGGTGTTAGGGATGAAACAGGTGCAAGCCCAACTTCATGGGGAGTATGGACTAGAGCTTGGAC[C/T]GCTGAAGAGAATAGACATGGCGACCTTCTCAATAGGTATCTGTATTTATCCGGGAGAGTCGATATGAGACAGATTGAGAAGACTAT
107489 A G ATGAAACAGGTGCAAGCCCAACTTCATGGGGAGTATGGACTAGAGCTTGGACCGCTGAAGAGAATAGACATGGCGACCTTCTCAATAGGTATCTGTATTT[A/G]TCCGGGAGAGTCGATATGAGACAGATTGAGAAGACTATACAATACTTAATTGGCTCAGGCATGGACCCAAGAACAGAGAACAACC
107491 G A GCAGCACCAGCTGCACCACCGTGCCGTACTTCAATGGGTACACCTTCGTTGCCTGCACCGGATACCACAAACTCCGATCAATGTTCTTTGCGGTGTAATC[G/A]AACTCCACCGGCGGCGTGGCTGGGAAGTCCGTAGTGTAAACCCCAGGCAGTCCGAGCTGGTAAGCATGAAGCACCGATACAGTTGA
107503 C A CTGCCACTGAATTCTTATTGAGCGTGATAGAACTGATGTCCAATATCTTCTCCACTCGAGCTCCATCGATGCCCAATGGCCT[C/A]AGGTCGACTAAAACCAAGTGATTATCGCTGCCACCAGAAACCAACTGATAACCCAATTCCACCAGTCTTGATGCAAGCGCTTTGGAGTTAGATATGACCT
107503 C T TGTCCAATATCTTCTCCACTCGAGCTCCATCGATGCCCAATGGCCTCAGGTCGACTAAAACCAAGTGATTATCGCTGCCACCAGAAACCAACTGATAACC[C/T]AATTCCACCAGTCTTGATGCAAGCGCTTTGGAGTTAGATATGACCTGCTTCTGATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTAA
107503 C T CTCCATCGATGCCCAATGGCCTCAGGTCGACTAAAACCAAGTGATTATCGCTGCCACCAGAAACCAACTGATAACCCAATTCCACCAGTCTTGATGCAAG[C/T]GCTTTGGAGTTAGATATGACCTGCTTCTGATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTAAACACACAGCAAGGGCACCAATA
107503 A G AACTGATAACCCAATTCCACCAGTCTTGATGCAAGCGCTTTGGAGTTAGATATGACCTGCTTCTGATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTA[A/G]ACACACAGCAAGGGCACCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTCTAAATC
107503 C T CCCAATTCCACCAGTCTTGATGCAAGCGCTTTGGAGTTAGATATGACCTGCTTCTGATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTAAACACACAG[C/T]AAGGGCACCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTCTAAATCAACACCAAGA
107503 A G CCACCAGTCTTGATGCAAGCGCTTTGGAGTTAGATATGACCTGCTTCTGATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTAAACACACAGCAAGGGC[A/G]CCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTCTAAATCAACACCAAGAACTGGA
107503 A G GATAAGCTTTAAATTCAGGTGATTGGGCATGTTGTAAACACACAGCAAGGGCACCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGC[A/G]TTATTTATAGCAGTTTCTAAATCAACACCAAGAACTGGATCTTTCCTGTAAAAGATCATACCACCTCTAGGTCCCCGCAATGACTTG
107503 T C GTGATTGGGCATGTTGTAAACACACAGCAAGGGCACCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTC[T/C]AAATCAACACCAAGAACTGGATCTTTCCTGTAAAAGATCATACCACCTCTAGGTCCCCGCAATGACTTGTGAGTAGTTGTGGTGACC
107503 T C CAGCAAGGGCACCAATAGTATGATTATGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTCTAAATCAACACCAAGAACTGGATC[T/C]TTCCTGTAAAAGATCATACCACCTCTAGGTCCCCGCAATGACTTGTGAGTAGTTGTGGTGACCACATCACAATATTCAAAGGGATCA
107503 T G TGAGGACCACCCTGTAAACCAGGGAAAACAGCATTATTTATAGCAGTTTCTAAATCAACACCAAGAACTGGATCTTTCCTGTAAAAGATCATACCACCTC[T/G]AGGTCCCCGCAATGACTTGTGAGTAGTTGTGGTGACCACATCACAATATTCAAAGGGATCAGCAACAACAGAAGCAGCTACGAGCCC
107503 T C TAGACAGTTAAATTGCCTCTGCTTTTCTTTATTGATAAGTTCATGAAGTTCAGGATCAGCGTCTTTCAGTGGAAGGTCCACAAACTTATAGGAGTTCTCT[T/C]CATTTTCCAGGTCGTTGACAGAAGACGGTGGTTTTTGAGTAGACACGCTGCATTTGACATTAGAAAGCTTGCATCTTCTAGAAAGGCTA
107503 C T GAAGTTCAGGATCAGCGTCTTTCAGTGGAAGGTCCACAAACTTATAGGAGTTCTCTTCATTTTCCAGGTCGTTGACAGAAGACGGTGGTTTTTGAGTAGA[C/T]ACGCTGCATTTGACATTAGAAAGCTTGCATCTTCTAGAAAGGCTAACTTGATTAACATTTGCATAATCACTGTTTTTATAAAAATTTGG
107511 C G ATTCGCAAGAACAAGAAAAAAACAGAGCATGGATTGAGAATGCTTATATGAGTTAATAATATTCTACATCTACAGGTGTACCGGGTACGCTGCCATCGTC[C/G]GATGAATCGAGGCTGCTACTGCTAAATGGAGGTGGAATGTAAGGAGGAGATGCACATCTTAACAATGCCCAGTTAACTCTGCTGAA
107511 G T GTAGCCCTGCAATTAGTTCTTTAGTAGAGTTGGATATGGGTGGATCTTTAGGGAACTCGAGGGCTCGAGCGACAATGTTGGCCAATGTAAGTTCGTTATC[G/T]GATCCTTTGAATGGGGTAACACCGTAAAGAAGCTCGTACATGAATATGCCTAGTGTCCACCAATCCACTGCGCTTCCATGCCCTTCC
107511 T C ACTCGAGGGCTCGAGCGACAATGTTGGCCAATGTAAGTTCGTTATCGGATCCTTTGAATGGGGTAACACCGTAAAGAAGCTCGTACATGAATATGCCTAG[T/C]GTCCACCAATCCACTGCGCTTCCATGCCCTTCCCCTGAAACAATCTCAGGAGCCAAATATTCATGAGTGCCAACAAACGACATAGAT
107521 C A TCCACTCAGTTTCACTAAAGTAATCAGGGACCATGTGCCACTTTGCTTCTTGAACTCTCCAGCCAAAATTCTCACGTGAAATAAATGCATCTAGAAATCC[C/A]AGGTCCATAAATGCTTGGTGCGAATAATAGCCATCTGACGTGACAAGAATGACCGGCAGGCATCTCTCATTGATTCCAAGGGATATCA
107521 A G TCTCATTGATTCCAAGGGATATCACTCTCCATATAAAACTATCATGATACATTGCACCAGGCACCAAAGAATCATCATCAGTTGTTGCCCTACGAAGAAC[A/G]TCGATGTTGTTTATTACCAGCTTTGGCTGAAAGAAACCAACTTCTGCTGCCTCAGACAAAACCTCCATCAATAAAATAGGCCAATCAGT
107523 A G TCTCCGCCACATTCACGATCACGAATAACTGCGCCTACACGGTCTGGCCAGGCATCCTCTCCGGCGCCGGCACCTCCCCGCTCTCCACCACCGGCTTCGC[A/G]CTACCCACCGGCGCCAGCCAGTCCCTCACCGTCCCCGCAGGCTGGTCCGGCCGGCTCTGGGGCCGCACCCTCTGCTCCACCGACTCA
107523 G T CACGATCACGAATAACTGCGCCTACACGGTCTGGCCAGGCATCCTCTCCGGCGCCGGCACCTCCCCGCTCTCCACCACCGGCTTCGCACTACCCACCGGC[G/T]CCAGCCAGTCCCTCACCGTCCCCGCAGGCTGGTCCGGCCGGCTCTGGGGCCGCACCCTCTGCTCCACCGACTCATCCGGCCGATTCA
107523 C T ATAACTGCGCCTACACGGTCTGGCCAGGCATCCTCTCCGGCGCCGGCACCTCCCCGCTCTCCACCACCGGCTTCGCACTACCCACCGGCGCCAGCCAGTC[C/T]CTCACCGTCCCCGCAGGCTGGTCCGGCCGGCTCTGGGGCCGCACCCTCTGCTCCACCGACTCATCCGGCCGATTCACCTGCCTCACG
107523 A C CGGTCTGGCCAGGCATCCTCTCCGGCGCCGGCACCTCCCCGCTCTCCACCACCGGCTTCGCACTACCCACCGGCGCCAGCCAGTCCCTCACCGTCCCCGC[A/C]GGCTGGTCCGGCCGGCTCTGGGGCCGCACCCTCTGCTCCACCGACTCATCCGGCCGATTCACCTGCCTCACGGGCGACTGCGGCTC
107523 C T CTCCTCCCGCCACGCTGGCGGAGTTCACCTTGAACGGAGCCAACGATCTGGATTTTTACGACGTTAGCCTCGTGGATGGGTACAATTTGCCTATGCTGAT[C/T]GTGCCTTCCGGAGGGCAGAGCGGTAATTGCAGCTCCACCGGTTGTTTGGTTGATTTGAACGGGATCTGCCCGTCCGATCTGAAGGT
107523 G A TGGCGGAGTTCACCTTGAACGGAGCCAACGATCTGGATTTTTACGACGTTAGCCTCGTGGATGGGTACAATTTGCCTATGCTGATCGTGCCTTCCGGAGG[G/A]CAGAGCGGTAATTGCAGCTCCACCGGTTGTTTGGTTGATTTGAACGGGATCTGCCCGTCCGATCTGAAGGTGGTGGAGTCCAACG
107523 G A TGCTGATCGTGCCTTCCGGAGGGCAGAGCGGTAATTGCAGCTCCACCGGTTGTTTGGTTGATTTGAACGGGATCTGCCCGTCCGATCTGAAGGTGGTGGA[G/A]TCCAACGGCGATGGCGTGGCTTGTAAAAGCGCCTGCGAGGCCTTTGGTTCGCCGGAGTACTGCTGCAGCGGCCAGTACGCGAAT
107523 T C ACGCGTTTGACGACGGTACGAGCACTTTCACCTGTGGCAGAGCCGATTACGCCATCACTTTTTGTCCGAGCACCACCAGCCAAAGAGCGGAGACGCGACA[T/C]AACAATCCACAGGCGGTAACGCCGTTGGTGAATTATACGATGGTTATATTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGT
107523 C T CGTTTGACGACGGTACGAGCACTTTCACCTGTGGCAGAGCCGATTACGCCATCACTTTTTGTCCGAGCACCACCAGCCAAAGAGCGGAGACGCGACATAA[C/T]AATCCACAGGCGGTAACGCCGTTGGTGAATTATACGATGGTTATATTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGTTGG
107523 T G TGGCAGAGCCGATTACGCCATCACTTTTTGTCCGAGCACCACCAGCCAAAGAGCGGAGACGCGACATAACAATCCACAGGCGGTAACGCCGTTGGTGAAT[T/G]ATACGATGGTTATATTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAGC
107523 A C ACGCCATCACTTTTTGTCCGAGCACCACCAGCCAAAGAGCGGAGACGCGACATAACAATCCACAGGCGGTAACGCCGTTGGTGAATTATACGATGGTTAT[A/C]TTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAGCGGTAGTGCTGATGT
107523 G A TCACTTTTTGTCCGAGCACCACCAGCCAAAGAGCGGAGACGCGACATAACAATCCACAGGCGGTAACGCCGTTGGTGAATTATACGATGGTTATATTCGG[G/A]GCAAGCGACATCTACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAGCGGTAGTGCTGATGTGGATGG
107523 C T ACGCCGTTGGTGAATTATACGATGGTTATATTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAG[C/T]GGTAGTGCTGATGTGGATGGTATATATGGTTGGGTCCCACTAACATGGGATAAGGGATGGCAGCTAATTCATTTTTTGTCGTTTAG
107523 A G CGTTGGTGAATTATACGATGGTTATATTCGGGGCAAGCGACATCTACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAGCGGT[A/G]GTGCTGATGTGGATGGTATATATGGTTGGGTCCCACTAACATGGGATAAGGGATGGCAGCTAATTCATTTTTTGTCGTTTAGTGGG
107523 G C TACAGCAGTGGTTTGAAGTTGGATTTTAGCACGGGAAAATTCGGGATTTTAGCGGTAGTGCTGATGTGGATGGTATATATGGTTGGGTCCCACTAACATG[G/C]GATAAGGGATGGCAGCTAATTCATTTTTTGTCGTTTAGTGGGCCGCATGAATCGGTGCGACAGGATAAGTGAAGCCAGAGCTGGG
107525 CG C CATAAAGCGTTCCACCTTGGGTCAATATATGTCCATTGGCTAATACAGCTTCACAGTCCTCGTCTTCTTCCCATTCACACTTTAACCATCCAAAAGCAGG[CG/C]GAGGGCTCTCTACTTTGCTCGAAGTAAGAGCAGTATTTCTTTTTGATAATTTGAAGGGAGAATCGTTTTGAAGGAGAATTTGACACCA
107527 A AGC AACTAGCGAAGGACCCGTCTGTAAATAATTTGATTGAAGGGTATGATGATTATTCAAGAACCATTTGGCCTAGAAAAAGAAGGCTTTCAGAAAGAGAGGC[A/AGC]ATTTGGGTTGAAGACATCGGTTGGATTAGGAGCGTATCTTGGTATTATGGGCTCACGTAGGGATGTAGTCACCGCTGTCTGGA
107527 T G GGCAGACTAGTGCATTTTCACAACCAGGCGGGCCTAATCCAACAAATGAAAAAGAAGCATGGTGGATTGCGCGGTGGTCTAACGCTTGTCCTATGTGCGG[T/G]GGGACATGGGTTCGAGTTGTATGACTAGTATGGCAGTTGTTTATATCGCTAACAGAATTTATCCTACCACTTTGGGCTTCATTATAT
107527 AT A TTCATTATATATTTCATCACAAAGCTTGTACATAAAATGGAGAATTTCCTTGCTTTCTGGGCAAAAGATGCGACTTTTTAAACTGTTGAAATGCATGGTC[AT/A]TTATTTCAGCACTCAAGAATGCCGTGATCCATGGAAATTCATTTTGGTCTCCTATTTAAGGTCATGTAATGTAAATTTATGTGTTAGTAA
107529 C T GCCACCCAAAACTTCATTCCTTGGTAGCATTTCTGTCGCAGGTAGAGTTTTGAACCTCTTATCAGCAGCACAATTGCTGCTGTTGCTATTACTGTTGTTA[C/T]CACTGTTACTGCTACTGTTGTTATTGTTTTTGTTCACTTTGTTAATCCCATTGCCATAGTTGTTCACGTCTTTGACAACATTCATATTCCCG
107529 GT G GCATTTCTGTCGCAGGTAGAGTTTTGAACCTCTTATCAGCAGCACAATTGCTGCTGTTGCTATTACTGTTGTTACCACTGTTACTGCTACTGTTGTTATT[GT/G]TTTTTGTTCACTTTGTTAATCCCATTGCCATAGTTGTTCACGTCTTTGACAACATTCATATTCCCGTATTTGCTAATTGAACTATTCATGTT
107529 A C ACCCTAACTTTTCCCATGATTTTTCTTCTCCCATATTTTTAGAATAGTCGATTTTGTTCATAAGATCCCTTTTTGTTCTTGTAAGTTCAGCTAATTTTGA[A/C]GTCATGCACAGCCACTTCCGATCTTCGGTGACGTTTGATTGACCACGAAACTTATCTTCTTGTCGCCACAGGTTATCCATATCAAGCAAGGA
107535 TA T GTGGATTGTACATCCGTTCAACAATAAAGGTAAAACCTCTGATGATAAGAATTAAGACATGATTTTCATTCGAACTGAATAGCTAGGGACAAAACTTGAA[TA/T]AAAAAAGAACACTATACACAGCTACCAAACTCACTCGTTTTCTCCCCTCTATTCAAATATATATCAAAATATATTATGTTTCGTTTTCC
107535 G A CAATTCTATTAGCAATTTCTAGGGTGTGGTGCTCCGATGATAAGTCTAAACAATCAAGGAGACACTCAGGGGTAAACTGATCTGCCGTTATGTAGCGATA[G/A]ATGATTTCACCTAAACAAGATTTTCCGTTCTTAGGCAAAGTTTCCAAATATGCATCCGGGGTTTCCATTTCAGCAAGCACCCCACTAT
107537 C T GTCATTATTCCTCGAAGACTCTCTATTTGATGAGAATGAGTAATGTATGACTGAGGGACGATTGGCAATGCATCTGTCAATGGTATAATTCCTTCTTCCT[C/T]CTCTGCTGCAGTTGGATTGGCGCTTCGACGAGGATCAAGAAAACGTTTATCAAGGGCCAAAACCTGGTCGCTTATAGTTCCAATGAGT
107537 A AT TGACACTGTGTCTATAAGATATGCAATAAGCCAAGCTTCTTCCGGAGTAGCGGATCCAATCTCTCCAGAAGCTTTAGGAGAAACAGTTGCAACGAAAATT[A/AT]GTTTTTTGAAATGTATTTGTACATTACATCTTGATCTGCTACAACCTTTGCTTGGGTATGAACAATCTCATTCAATTTCCTAGTTGTGA
107543 C A TTTAGTATCTTCTGGAGATCAATGGCATTGCACACTTGTTCTTCCTGTCATTATAAATCCTCACTATAATTGCTGCTGATTCCTCGATTGCTTTCCCCGT[C/A]ACTTCAATAACAGGCCAAAGAGGATTCTGCCCAAAAATCTTATTGGCGTGCTCGAGCTCATCCTTGACATGATCCATTTCAGAATAATTAC
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107543 C T TCCTCACTATAATTGCTGCTGATTCCTCGATTGCTTTCCCCGTCACTTCAATAACAGGCCAAAGAGGATTCTGCCCAAAAATCTTATTGGCGTGCTCGAG[C/T]TCATCCTTGACATGATCCATTTCAGAATAATTACTCCTTGCACCCCGTTCCATCCCCAATGCCTTTGCCCTTGCCTTCCTAATTGTCTGGA
107543 G T TCAATAACAGGCCAAAGAGGATTCTGCCCAAAAATCTTATTGGCGTGCTCGAGCTCATCCTTGACATGATCCATTTCAGAATAATTACTCCTTGCACCCC[G/T]TTCCATCCCCAATGCCTTTGCCCTTGCCTTCCTAATTGTCTGGAGCACCCCTGCATTAATAGTCAATCCAAAGATCTTCTCCTGGTCAAC
107543 G C GCACCCCGTTCCATCCCCAATGCCTTTGCCCTTGCCTTCCTAATTGTCTGGAGCACCCCTGCATTAATAGTCAATCCAAAGATCTTCTCCTGGTCAACCT[G/C]AAACAGCATCTTGGGTAAGTCAACCCCCATGACTATAGGCACGTTCGCGACCTTGTACCCCTTCTGAGCTAAATATATAGACAGAGGAG
107543 C T ATAGGCACGTTCGCGACCTTGTACCCCTTCTGAGCTAAATATATAGACAGAGGAGTCTTCCCACTTCTCGAAACTCCAACAAGTATGATTGTCGCACGAG[C/T]TAGGTTATTGGGCTGGGCTCCATCATCTTGCTTAATGGTGAAGTCAATGGCCTCTATGCGTTTGAAGTAGGCCTCGCTCAGTGGGGT
107543 G A AGTATGATTGTCGCACGAGCTAGGTTATTGGGCTGGGCTCCATCATCTTGCTTAATGGTGAAGTCAATGGCCTCTATGCGTTTGAAGTAGGCCTCGCTCA[G/A]TGGGGTCTGGTGCTTGCCACGTGGAATGCCGGATGGAGCCACTCCTAGGTGGGCTGCAATGGCTTCTGTGGTGGGGCTGAGTATG
107543 A C CCTTTTTAGCAGTTTGGGCCATGGATGGGTCTACTAGGGTGTATAGTAGGAGGGCCTGTGCTTTTGCTGCTTGCTGTATTATCTCCATCAGCCTCTCTGT[A/C]GTTTCTACCCCAGAAAAGAGATGAGTATTGACAGGACATCCACGATCGACGAGACAATGTTCAAACTGCCCTAACGCAGCGTTAACG
107543 A C TCGCCTTGCCATCTCTCGCCTCGGCCAAGCACCCTTCATCGTCATCGTCCGATGTGGAAGGTGGAGACTCATCCACCAAAGACGTGCTCGACGATTTGGA[A/C]GACGTAGGCGAGGGGGTGGAGCTGTTGGTTTTATTTCTGAGGGCGGGCCAGTCCAGCCTTCTGCCCGATCGGACGGAGCGGGCTC
107543 A G CACCAAAGACGTGCTCGACGATTTGGAAGACGTAGGCGAGGGGGTGGAGCTGTTGGTTTTATTTCTGAGGGCGGGCCAGTCCAGCCTTCTGCCCGATCGG[A/G]CGGAGCGGGCTCGCGACCACCGGTTCAGTTGATGGCTCGGTTTGTTCGTCGGTTTAGGGCTTTCAGGGTTTCGTTCGCAGGAGA
107545 C CA GAGGGATTTGTTCGATTCGAGGGTGGGGAAAACGACATGGCCGTATGGATCTGGGGTGTGGAGCAAGAAGGAATTTGTGCTGCCCGAGATTTCGGATGAT[C/CA]ATATTGTGAGCTTGTTTGAAGGAAATTCCAACTTATTTTGGGCTGAGAGGCTGGGTATGGATCATTTGGATGGAATGAACGAT
TTTCGAAAGACAGCCTTAATATCTCGAAATCGATGAAAATCGTGCGATCGAAACC
107549 T GAAAATGAACCCCTAAACTAGCAAACTTGCATCCTTTGCAAGATAAGTTTTTTAGTTCTCTGTCAGGGGCTCAAATCATACAGCTCCAGCGGTGAATTAA[TCTGCAAATTTTCGAAAGACAGCCTTAATATCTCGAAATCGATGAAAATCGTGCGATCGAAACC/T]CTGCAAATTTTCGAAAGACAGCCTT
107551 T C CAGGGTGTATTTTAGCAGAACTTTTGGCTGGAAAACCTATAATGCCCGGACGAACTGAGGTTGAGCAACTGCATAAGATCTTTAAGCTATGTGGTTCCCC[T/C]ACAGAAGAGTATTGGAAGAAATCAAAGCTGCCACATGCAACAATATTTAAGCCTCAACAGCCATACAAGCGTTGCATGGTAGAGAT
107551 A T GGTGTATTTTAGCAGAACTTTTGGCTGGAAAACCTATAATGCCCGGACGAACTGAGGTTGAGCAACTGCATAAGATCTTTAAGCTATGTGGTTCCCCTAC[A/T]GAAGAGTATTGGAAGAAATCAAAGCTGCCACATGCAACAATATTTAAGCCTCAACAGCCATACAAGCGTTGCATGGTAGAGATGTTT
107551 C G TTCCACAGTACCCTCCTAGCAAAGAAATGGATGCCAAACTAAGGGATGAGGAGGCTAGAAGACTTAAAGCCGGTGGGAAAGCAGACGGTGATGGCACAAA[C/G]AAGACACGCACAAGAGGAAGAACTCGGAAACAAATTACTGTCCCCGAAGCCAATGCAGAGATTCAGGCAAATCTCGATAGGCG
107551 T C ACCCGCTTGGAGATTCGAACCACATGGACCCGATATTCGACCCTCCCGACCCATCTTCGTTTTCTACTGTGTTACCCTACCAGAAAGGGCAGTCTGCTTC[T/C]ACTTGGTCGGGTCCATTGTTTGACCCGGCAGCTGTAGGTCTTACAAGGCGTAGAAAGAAAGATAAGAACAGCTCTCGTGTCAGATAG
107553 T C TAATGATTTGACCATCATAAAGAAAAGTTTAACAAATATTCTAAAAGAACTAAGAAGAACAATAATACAGACTTGTTTAGTGACTATGAGCTTGGAGGAA[T/C]ATACAACATTAAATGCCAAATATCATGTGGATATATATGACTATGATGTACATGTAAGATAAATGGAAACTTGCACATTTATCCTAAG
107553 G A AGAAGCCCACAATATCCTGATACCTTGATGGTTGTAAAGAAAAATTCTCCAGGAGAAAGCTGGAGAAATCTAACTCCTTGAGTACTAACAGGTGCTTCCA[G/A]GATCTTAATCAAGTCTTTTGAGAAGACAAAGCAGCTTATAATAGCTGCCCCCACTGCTAGAACAGACACAAATATTCTATCTCGTAGT
107553 G A GAAGCCCACAATATCCTGATACCTTGATGGTTGTAAAGAAAAATTCTCCAGGAGAAAGCTGGAGAAATCTAACTCCTTGAGTACTAACAGGTGCTTCCAG[G/A]ATCTTAATCAAGTCTTTTGAGAAGACAAAGCAGCTTATAATAGCTGCCCCCACTGCTAGAACAGACACAAATATTCTATCTCGTAGTT
107553 T C TTCCTCTAAGTGATCAAATATGCTCATTTCTTTGTCATCAGGAAGTAGCTCTTGGCTAGGATAAAGAAAGCTATAGAGAGAACTCTTTGTTTCTTCTTGC[T/C]GAAAATTTGCTGATGTTTTTTCCAGGTTAGCACCAGGCCTGTCTTCAAGGGCAGCACCAACGCCGCTTAGTTGCTCCTGCTTATCTGCCT
107557 C T ATATCAAAGTTAAACAAGCTCAATCCCATTACCCTTCTTAACCCACTGGCTATCTCCGTCACAAAACCTACAGGCGGCATTTCCGCCTCCACCAAACCCT[C/T]GTTCCACGCAATCTCCTTCCTGTTCTTCTCCGTCAAATTCGAAACCTGCGAGAAGGTCATAGACTCTTCACAATCTCCGACCATCTCCTCC
107557 A G GCGGCATTTCCGCCTCCACCAAACCCTCGTTCCACGCAATCTCCTTCCTGTTCTTCTCCGTCAAATTCGAAACCTGCGAGAAGGTCATAGACTCTTCACA[A/G]TCTCCGACCATCTCCTCCTCCGACACATCCGGCAAACTCTTCCTCCTCACGCACTTCACCAAATCCCCCACCACGAAAATCTTAAAGATG
107557 C T TATGCGACTTCGCGCTGCCGTCGGCGACCAAGGGCTTCGCGATGACGGGAAACCGAAGCGCGTCGAAGTGGAGCAGCGCGTTCGCGTCGTAGACGACTAC[C/T]TGGCTGGGGATGCCGAAGGTTTCGGGTCGGGTTTTGGGCATCTCGAGCTCGGAGACGGCCTGGAGCATGGAGATTCGGTTGTG
107557 T C TCGGGTCGGGTTTTGGGCATCTCGAGCTCGGAGACGGCCTGGAGCATGGAGATTCGGTTGTGGAGGCGCTTGATGGAGATGGGTTTGTCGACGATAGGGA[T/C]TCTAGGGTTTTGAAGGGAGAACTGGTGGAGGTTGAATTCCCAATCTTCGCCGTATAGTTTCTGGATCACGCAGTCGAATGGCCC
107559 T C GAATTGAGCAGCTTTGCCCATTCCCATATAATCTTGTTCAGAGAGAGCTAAAGAGATATCCAAATGCTGAAATTGTTTGGTGTCAAGAGGAACCAATGAA[T/C]ATGGGTGCATATAGCTACATAAATCCTCGCTTATCCACTGCTATGAAATCAGTAGATAGAGGAACTATAGAGGACATAAAATACGTA
107559 A G GTCAAGAGGAACCAATGAATATGGGTGCATATAGCTACATAAATCCTCGCTTATCCACTGCTATGAAATCAGTAGATAGAGGAACTATAGAGGACATAAA[A/G]TACGTAGGAAGAGCTCCATCTGCTGCCACTGCTACTGGATTTTATGGCGTGCATGTGCAAGAGCAAACTGAGCTTGTCAAGAAAGC
107569 AT A CGTTTAATTTAACTGTAATTCCAGCAATTTCTGTCTCCGTCCAAACAGTCCCTAAATGTTGCGTTAGCCACCATGATTCCGTCGCGACTTGTTTTGTCCA[AT/A]TTTTTTAATTACGACAAACAGCCGACAGCCTTCTGACCGGTTACATCTGCTACACCGCTACATTCTGTTTCAACAACTCCACCAGACTCT
107569 CT C CTGTCTACCCTGAAAACACTTTCGTCCATCTATCAGTAATACCATCGGTCCACTCTGTTTTACTTCGTTCCCTTCTGATTTCACGCATCATGCCACTTTC[CT/C]TTCCTTCACAATTGTTCACATGCAACTCAATAAACCCGTACCCATACACTTCCGTCCTCGCGCCGCCATCCGCTCCTCCTGGAGTCCATCTG
107569 GC G AATTGTTCACATGCAACTCAATAAACCCGTACCCATACACTTCCGTCCTCGCGCCGCCATCCGCTCCTCCTGGAGTCCATCTGACGTCACCCCTTCAAGC[GC/G]CCTTAACCCCCTTGACCTTCGACAGAAGCCACACCTCGCCATCTCCCTCCAGTCGCTCCCAGTTCCGTCTCGAATGCAGCGACATCGA
107571 C CG TTGGCCTACTGGAAAAAAACCATTCTTCTGTATTCGCTCTCCTCTCTCGTGTACTCGAAGGGAAAAGGCTCTTCTGTTTCTGCTAA[C/CG]GCATTCAACCGCTCTCATTTACATACATTGTTTGCTATACTCACTGCTCTAACAATTTTTTTGCTGCAGGATTTTTATTCATTATTTACCTGTTCTTACT
107571 T C ACGCTAGACGCGCCCGACATGATGGACGACTACTACCTAAACCTTCTCGACTGGGGAAGCAGGAATGTGCTCTCCGTGGCCCTCGCCAACAGCGTGTACC[T/C]GTGGAACGCGTCTGAAGGCTACACATCCGAGCTGGTGACCGTGCACGAGGATCTAGGCCCGGTCACGAGCGTCAGTTGGGCACC
107575 C T CGGAGGATACCGGGATTGAAGTTGTATTTGATGAGTCGACCATGTCTGTGCCCGTGTGTTCATGCACGGGCAAGCAGCAGCCTTGTTATAAATGGGGCAA[C/T]GGTGGATGGCAATCGGCATGCTGTACCACTACTCTGTCCATGTACCCGCTGCCCATTATGCCCAATAAGAGGCATGCACGAATAAA
107575 A G GTGTTCATGCACGGGCAAGCAGCAGCCTTGTTATAAATGGGGCAACGGTGGATGGCAATCGGCATGCTGTACCACTACTCTGTCCATGTACCCGCTGCCC[A/G]TTATGCCCAATAAGAGGCATGCACGAATAAATGGTAGAAAAATGAGTGGTAGTGTGTTTAGTAAGCTGCTTAGTCGGCTGGCTGC
107575 T C GATGGCAATCGGCATGCTGTACCACTACTCTGTCCATGTACCCGCTGCCCATTATGCCCAATAAGAGGCATGCACGAATAAATGGTAGAAAAATGAGTGG[T/C]AGTGTGTTTAGTAAGCTGCTTAGTCGGCTGGCTGCAGAGGGTCATGATCTTCGAATGCCGGTAGATTTGAAAGATCATTGGTCTAA
107575 C CTG CATGTATACGTAGATGTAAAGTAAATTATGCTTGATATTTGTGTTGGGCATATCTAATCTCATGTAAGGAAACATGTTATAGTTTTGTAACTCGTGGTGT[C/CTG]TAGTGCTTGCTTTGACAATGTAATAGTAATCATCAGTTATTTTATGTTCGTGTATTGTTTGATGATAAAAAAAAGGCCACATGT
107581 GT G TTTTTCTACACAAGTTCCCTTTTTAGCTAACCATAAACTATATTTCGTGCAAAAAATCTATACATATCTAATTTTGACCAATAAACCCTGTCCAAACTAA[GT/G]TTTTTTTACTTGTGGATCATTCAAAGAATCTTGTTTGAGCTACTTTTAACCTCAAACTGTGTCCTGGTATCTTAATTTAGTGCTGTAAGTAA
107581 G GCTA TCCTTCTATGCAAAATATGAGATTGACTTTCACTCCCGATGGCACTGCTGTCTACAAACCAGTTACATCACCATCAGCTTCTCCTGCTATTGCTGCTGGT[G/GCTA]CTACTACTACTACTAATACTACGAGTTCACCGTCTCCTAATCCTCAGCCTCAGCCTCAGCCTTTAGGTGTTAGTGGGCCCACAGCCG
107581 G A GAGTTCACCGTCTCCTAATCCTCAGCCTCAGCCTCAGCCTTTAGGTGTTAGTGGGCCCACAGCCGAAGTAGCTGGGCCCACTGGAGGTAGTGGTGGACCC[G/A]CAGTAGGAGGAAATGGACCTGCTCCTATAATATTGACACCAGCTCCGCATGGGCTTGACATGAACACGAGCGACCCTTTGAGAAA
107581 G T CAAAAATCATGTCATTTTCTCAAAATGGGCCTCGTGCAATTTGCATCCTTTCAGCAAATGGTGCCATTTCACATGTTACTCTTCGTCAAGCTGCAACGTC[G/T]GGTGGAACTGTAACTTATGAGGGTCGGTTTGAAATATTATCACTTTCTGGCTCGTTCCTGTTATCTGAAAATGGGGGCCAGCGCAGCAG
107581 G A GTGCCATTTCACATGTTACTCTTCGTCAAGCTGCAACGTCGGGTGGAACTGTAACTTATGAGGGTCGGTTTGAAATATTATCACTTTCTGGCTCGTTCCT[G/A]TTATCTGAAAATGGGGGCCAGCGCAGCAGGACAGGTGGCCTCAGTGTATCACTGGCATATCCTGATGGCCGAGTTTTAGGCGGTGG
107583 C CG TACGTTTGGTGGATCAAGCTCGGATACGGGAGGCTTTTCTGCATCAGTTGCAGTAATTAAGCCTCCTTATGGCCGGACTTACTTTGGGATGCCTTCTGGA[C/CG]GTTCTGTGATGGCCGTCTAATCGTAGATTTCATGGCAAACGGTTTAGACTTGCCATATCTGAATCCTTATCTTAATTCGATTGGAGC
107583 G A AAATGATCTTACTGCATGTTTGTACAACAATATGAGTATCGTTGAAGTTAAATCTATCATTCCGGATATCGTTGAAAAAATTCAACAAGCAATACAGGGT[G/A]TACATAGAGAAGGTGGGCGGTATTTTTGGATACAGAGTACTACACCCATAGGTTGCCTACCAAAAGTATTGAAACGTGTGCCGAAAC
107583 A T ATGATCTTACTGCATGTTTGTACAACAATATGAGTATCGTTGAAGTTAAATCTATCATTCCGGATATCGTTGAAAAAATTCAACAAGCAATACAGGGTGT[A/T]CATAGAGAAGGTGGGCGGTATTTTTGGATACAGAGTACTACACCCATAGGTTGCCTACCAAAAGTATTGAAACGTGTGCCGAAACTA
107583 T C CGTTGAAAAAATTCAACAAGCAATACAGGGTGTACATAGAGAAGGTGGGCGGTATTTTTGGATACAGAGTACTACACCCATAGGTTGCCTACCAAAAGTA[T/C]TGAAACGTGTGCCGAAACTAGCAACCCCGAAAGATGCTTTTGGTTGTGGAGTTCTTCTTAACGATGTTGCACAAATTTTTAATAAAC
107583 G C TTCAACAAGCAATACAGGGTGTACATAGAGAAGGTGGGCGGTATTTTTGGATACAGAGTACTACACCCATAGGTTGCCTACCAAAAGTATTGAAACGTGT[G/C]CCGAAACTAGCAACCCCGAAAGATGCTTTTGGTTGTGGAGTTCTTCTTAACGATGTTGCACAAATTTTTAATAAACAACTGAAAAGC
107583 G A ACAGAGTACTACACCCATAGGTTGCCTACCAAAAGTATTGAAACGTGTGCCGAAACTAGCAACCCCGAAAGATGCTTTTGGTTGTGGAGTTCTTCTTAAC[G/A]ATGTTGCACAAATTTTTAATAAACAACTGAAAAGCGCAATAAATCAACTTAGGAAAAATATAAGTGATGCGCATTTGATGTATGTTGA
107583 A G CTACACCCATAGGTTGCCTACCAAAAGTATTGAAACGTGTGCCGAAACTAGCAACCCCGAAAGATGCTTTTGGTTGTGGAGTTCTTCTTAACGATGTTGC[A/G]CAAATTTTTAATAAACAACTGAAAAGCGCAATAAATCAACTTAGGAAAAATATAAGTGATGCGCATTTGATGTATGTTGATGTTTACT
107583 G A AACTAGCAACCCCGAAAGATGCTTTTGGTTGTGGAGTTCTTCTTAACGATGTTGCACAAATTTTTAATAAACAACTGAAAAGCGCAATAAATCAACTTAG[G/A]AAAAATATAAGTGATGCGCATTTGATGTATGTTGATGTTTACTCTGCCAAGTATGGCCTGATCAGTGAAGCTCAAAAGCACGGATTCG
107583 G A TTTTTAATAAACAACTGAAAAGCGCAATAAATCAACTTAGGAAAAATATAAGTGATGCGCATTTGATGTATGTTGATGTTTACTCTGCCAAGTATGGCCT[G/A]ATCAGTGAAGCTCAAAAGCACGGATTCGAGAACACGCTAATTGCTTGCTGCGGTCATGGTGGTGAGTATAACGTAGACGTTGATTGC
107583 T C AACTGAAAAGCGCAATAAATCAACTTAGGAAAAATATAAGTGATGCGCATTTGATGTATGTTGATGTTTACTCTGCCAAGTATGGCCTGATCAGTGAAGC[T/C]CAAAAGCACGGATTCGAGAACACGCTAATTGCTTGCTGCGGTCATGGTGGTGAGTATAACGTAGACGTTGATTGCGGGGTAGTAGA
107583 T C ATGCGCATTTGATGTATGTTGATGTTTACTCTGCCAAGTATGGCCTGATCAGTGAAGCTCAAAAGCACGGATTCGAGAACACGCTAATTGCTTGCTGCGG[T/C]CATGGTGGTGAGTATAACGTAGACGTTGATTGCGGGGTAGTAGAATATGTAAATGGAACGGAGCATATTGTTGGCAATTCATGCAG
107583 G A AAAAGCACGGATTCGAGAACACGCTAATTGCTTGCTGCGGTCATGGTGGTGAGTATAACGTAGACGTTGATTGCGGGGTAGTAGAATATGTAAATGGAAC[G/A]GAGCATATTGTTGGCAATTCATGCAGTAATCCATCAAGTAGGATCATTTGGGATGGAGTCCATTACACAGAAGCAGCGAACAAGT
107583 C G AGAACACGCTAATTGCTTGCTGCGGTCATGGTGGTGAGTATAACGTAGACGTTGATTGCGGGGTAGTAGAATATGTAAATGGAACGGAGCATATTGTTGG[C/G]AATTCATGCAGTAATCCATCAAGTAGGATCATTTGGGATGGAGTCCATTACACAGAAGCAGCGAACAAGTTCATATTTGAGTGGT
107595 T C TGCATGATTTAAGTATATACTTCTTAAGCTCCTGAATGCATTGATGACCAGCGTATCTCCCCAAATTAAGTGCACTGATAACCCCAAAAACATCTCCTTC[T/C]TTGTCATCATTCTTCTCACTGACAACCCCATCATCGTTATCTTGGTCATCTAACTTAATAACGGAGCCAACAGTGGTCTGCTGCAAAATCA
107595 A T CTTAAGCTCCTGAATGCATTGATGACCAGCGTATCTCCCCAAATTAAGTGCACTGATAACCCCAAAAACATCTCCTTCTTTGTCATCATTCTTCTCACTG[A/T]CAACCCCATCATCGTTATCTTGGTCATCTAACTTAATAACGGAGCCAACAGTGGTCTGCTGCAAAATCAAATCCACAAACCCACTCACATC
107595 C A AATATGTATTCATCAACATCTTCACACTACCAAAATCATCAGGTTTCGGGTCGAAAAACGCAAAATCCGCTTGCACGGTCATTTCTTCACCGTACATAAG[C/A]ACCTCCTCATCTTCGTCTACTTCCTCATCATAATCCTCGGACGACGAAGATGTGGGACTACTATTTGGTTCGGGCAGAGTTTCGGTTTTG
107595 C T AGCACCTCCTCATCTTCGTCTACTTCCTCATCATAATCCTCGGACGACGAAGATGTGGGACTACTATTTGGTTCGGGCAGAGTTTCGGTTTTGGGTTTAT[C/T]TTGGAGTTTGGATTTCAGTCCTGTAGAAGTTCTCGTGTTCGAAAGATGGCGAGAAAAAGAAGATGTTAAAGCAGGTAACCGGCGATG
107597 C A GCAAACACGTTCACAGCATCACGTACAATCATAATGCTGGCGGATCTAAACATATTGGCTTCTACTATGACTGCACAATAAATTACTTGAACCATATCAA[C/A]GGGAAATCACCAATTCAAACATTTGTATTTCCTAAACTTGTCAGCCTGGCCAGTACTCATTCTTGACTTCTCGGCCTGTTCAGACTTCTC
107597 AC A CAAACCTATTTTGTCGATATTCTTGTAAATGTCAAACCAGTATGTGTATTTTACTGGATATAATACTCTTAATCCTGAAAGAATTGGACTGTGTAGAACC[AC/A]CCCCTCTTAAATTAGGCAACCGCGATGCAAGATCTACTGTGGGCCCACTTCCAACAGATTGTCCATATAAAATAACATCCTCCTCAGAA
107599 A G CTAGAGTTTGCATATGTTCTGGAAACTGCCGGTTGTAAAACTCGATTTGGCCGACTGCGTTGAAGGCCTCGCCTATGCCTAGGATTATGAGTTGAGGTGA[A/G]AGCCAAAATGCAGACATGGGTGAAATTCCACCATGGGCTAGGGCCGAGGTTCTTCTCTTTTCTTCTACTAAGCCTGCTACGACCATG
107599 C A CTGCTACGACCATGGATAAGGCCAAGATTACCAGCCCGGCGCCTTGTCTTTGTAGAAGAGTTATGCCGCCTTCGAGTTTGGTGAACCTTCGCATAAAAGG[C/A]ACAAGTAAAAGGTCGTAGACGGGGATGAATATGGTTAGAGCAATTAGAGATAAGGTGCCGAGCGTGGCGGGTGGGACTTCGAAA
107599 A G ATATGGTTAGAGCAATTAGAGATAAGGTGCCGAGCGTGGCGGGTGGGACTTCGAAATGGGGGCCCATGTGGCGGTCCATCACTAAGCCCTGTAGGACTGC[A/G]AAAGTGAACTGTTGCGATAAGGCTACGAAGCCCACAATGCCTGATGCCCATATGGGTACTATTCGGAGCAGGCATTTTACTTCT
107599 G T TGGCGGTCCATCACTAAGCCCTGTAGGACTGCAAAAGTGAACTGTTGCGATAAGGCTACGAAGCCCACAATGCCTGATGCCCATATGGGTACTATTCGGA[G/T]CAGGCATTTTACTTCTTCAACTTGTTGGACCGTGCATAGCCTCCAATGTTTAGCAATTGTTCCATCTTCTTTTAGTTCTCCTTCGCGTT
107599 CT C ACTAAGCCCTGTAGGACTGCAAAAGTGAACTGTTGCGATAAGGCTACGAAGCCCACAATGCCTGATGCCCATATGGGTACTATTCGGAGCAGGCATTTTA[CT/C]TTCTTCAACTTGTTGGACCGTGCATAGCCTCCAATGTTTAGCAATTGTTCCATCTTCTTTTAGTTCTCCTTCGCGTTTGATTGCAGCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107603 AGAC A ATAATTTTAAAGAGGCAATTATCTCAGCGTCCGAAGATAAATTATTCAAAGATATTTACGACACATCCGTTTACCATGCCATTCATTGATTGAAGAGGTT[AGAC/A]GACGACGACGACGATAAACTCTACTTACATAGCGAAGCAAACTTAATTAAGCCCAAACGAAGTAATTACAAGCAGCACGCCTGG
107603 A T TTATCTCAGCGTCCGAAGATAAATTATTCAAAGATATTTACGACACATCCGTTTACCATGCCATTCATTGATTGAAGAGGTTAGACGACGACGACGATAA[A/T]CTCTACTTACATAGCGAAGCAAACTTAATTAAGCCCAAACGAAGTAATTACAAGCAGCACGCCTGGTTGCAACCCAATTACCGCACCC
107603 A G AGGTTAGACGACGACGACGATAAACTCTACTTACATAGCGAAGCAAACTTAATTAAGCCCAAACGAAGTAATTACAAGCAGCACGCCTGGTTGCAACCCA[A/G]TTACCGCACCCATAATAACTCCTACCATGCAGAGTTCCTCTGTAGCTTCTAAGCCCACAGTAGCAGTAGGCGGTGCAGTTCTCGATG
107603 C T AGAGTTCCTCTGTAGCTTCTAAGCCCACAGTAGCAGTAGGCGGTGCAGTTCTCGATGTATGCATGGAAATGGACAGGCGACATCAACGGAGATGGAGAGG[C/T]GGCGTTCACGGAATGGATGTCTATCAGTTGCGGAGGTGGGCCCCATATGAGGGAGTTGGTTATGGAGAAGCGGGTCCCGCGCC
107603 G A ATGCATGGAAATGGACAGGCGACATCAACGGAGATGGAGAGGCGGCGTTCACGGAATGGATGTCTATCAGTTGCGGAGGTGGGCCCCATATGAGGGAGTT[G/A]GTTATGGAGAAGCGGGTCCCGCGCCGCATCAGGTCTGTCAGAAGTCGGGCCGTGTTACGAGCGTCATCCAGCCCACAGTGTG
107603 T C AAGATGTTGATGATGCGAAGGTCGTACATAAGTCTGAAAAGAAGATTCTATTTTCCCAGTAGCACCATTAACAACAACAGATGGAAACTCGATAATTTCT[T/C]GAGGTTGAGGATTCTTTTCTTTGTCGCAAGTTGCTTCAAAATCTATAACTACGAAATAATGGAAATCCTGAAACTGAAACTCATGTGG
107603 T C ATGGAAATCCTGAAACTGAAACTCATGTGGACTACTATGATAAGACATCTTGAATGGAGCACACTGAAATCTAGTATCAGCCGGATACGAACATTCTCTA[T/C]TCATAGGGTAATAATGATTTCTGAAGTTACTCCAGTGACCTTGTTGAATAAATTGATTTTGTCCACCAGGATAAAAATTATGCCATAA
107605 C T CTTGGGGCACATCGTTGGGTGTCTACCCTACAAAGGAGATGCGAATGCTTGGCCATTCTGATGTCGACTTCGTTCCCTGCTGCTGACTCGACTGTAACAC[C/T]AGCTGGCAGAAGGAGCATGCTGAAGTTATCTCAAAGGATGATGGACAATTTCTGTTCTGGAGTGTGCATGTCTTCATCACGTAAGTG
107605 T C TCCCTGCTGCTGACTCGACTGTAACACCAGCTGGCAGAAGGAGCATGCTGAAGTTATCTCAAAGGATGATGGACAATTTCTGTTCTGGAGTGTGCATGTC[T/C]TCATCACGTAAGTGGAATCAGCTTACTGTGGGAAGCATTGGAAAAGATGTAAGGGTTATGACTAGGCAGAACCTGGACGACCCTG
107605 T G GCACGTCGTGATGAACGGTGGAGATTCAGCGTGCGTCGCACTGCTCCCTTCAGGATTTTCCATCCTACCGGATGGAACTGAGCAACAGGACGTAGGCGGC[T/G]CGCTCCTGACTGTCGGATTCCAGATCCTGGTCAACACCTTGCCAACTGCCAAATTGACCGTCGAGTCCGTTGAAACCGTCAGCAGT
107605 C T GAGATTCAGCGTGCGTCGCACTGCTCCCTTCAGGATTTTCCATCCTACCGGATGGAACTGAGCAACAGGACGTAGGCGGCTCGCTCCTGACTGTCGGATT[C/T]CAGATCCTGGTCAACACCTTGCCAACTGCCAAATTGACCGTCGAGTCCGTTGAAACCGTCAGCAGTCTCATATCCTGCACCGTTCAG
107605 A G CTGTCGGATTCCAGATCCTGGTCAACACCTTGCCAACTGCCAAATTGACCGTCGAGTCCGTTGAAACCGTCAGCAGTCTCATATCCTGCACCGTTCAGAA[A/G]ATCAAGGTTGCTCTGCATGTCGAATGAAGGAAGACGAGTAAAAAATAATAATTAAGGTAGTAGGCAAAAATATTTACATCGGGTTGA
107605 TA T CCAAATTGACCGTCGAGTCCGTTGAAACCGTCAGCAGTCTCATATCCTGCACCGTTCAGAAAATCAAGGTTGCTCTGCATGTCGAATGAAGGAAGACGAG[TA/T]AAAAAATAATAATTAAGGTAGTAGGCAAAAATATTTACATCGGGTTGAGTCAAGAACGAACCCTGCAAATTGGGGATCAAACCCA
107605 C T ATATCCTGCACCGTTCAGAAAATCAAGGTTGCTCTGCATGTCGAATGAAGGAAGACGAGTAAAAAATAATAATTAAGGTAGTAGGCAAAAATATTTACAT[C/T]GGGTTGAGTCAAGAACGAACCCTGCAAATTGGGGATCAAACCCATTGCTAATTGGTAAGTAATCACATCATCATCATCATCATTGTC
107605 A T AAAATCAAGGTTGCTCTGCATGTCGAATGAAGGAAGACGAGTAAAAAATAATAATTAAGGTAGTAGGCAAAAATATTTACATCGGGTTGAGTCAAGAACG[A/T]ACCCTGCAAATTGGGGATCAAACCCATTGCTAATTGGTAAGTAATCACATCATCATCATCATCATTGTCATCGTTACTTAACAAGGA
107605 A ACAT ATAATAATTAAGGTAGTAGGCAAAAATATTTACATCGGGTTGAGTCAAGAACGAACCCTGCAAATTGGGGATCAAACCCATTGCTAATTGGTAAGTAATC[A/ACAT]CATCATCATCATCATCATTGTCATCGTTACTTAACAAGGAGCAATGGTGGTGGTTCGGGTGGTGGTTCGGGTATTGACTCGAGT
107609 GC G GGGCGGATTCACCCTAAATATCGACAGAACCGCCGAGGGCACAGTCCAAATCCCATCCCCACAAATCAACCCGGAAGCCATAGCCCCAGCAAAATCGTCG[GC/G]CCCCCTTCCTATTAACCTTCTCCCAAACAAACAAAATGACTGTGCCAACAAACATATCAACCGCAAAGTACGCCCCAATGTAAAAA
107609 G T GGGCTGGAGCGAGGATGTAGCTGGCCAAGATGAGGTACCACGGTACTTGTGGGAAGATGCTGGGGATGGTGGCCGTGGAGATGGCTGCTAGGGCGATGTA[G/T]GAGGAGACCGCTACGTAGGTTGGAATACTGTCTTTGTTGAATGTCTTTTTTCGGAGTTCTTCTTCAGCGAGGAGCTTTGTGCTT
107613 T C ACTTACGAGTGCTTGGTAGTTTGGATCCACGCGGTGAGTCCATTGCTTAGTCGGTCTCCTTCTTCATCGAGATTGTATCGCGATTCGCTATCTTAGCCTT[T/C]CAGATTGCCAAAGTTCTGTACTTTTATACTGGGTTGCTACTGTGCCCTCGTATGTGACTGTTTATCGGTAAATTGAGGGTTTCTACTTGC
107615 A G CCCTGACCGACTTCACCCAGACGGGTATGTCTGACCCATGCTGCTCCACCAGGTCGTGGAATGGGGTCTTGCCTGTTAGGAGCTCGAGCAGAAGGACCCC[A/G]AAGCTGTAGATGTCCGACTGTGGGGAGAAGGGTGTGCTCCGACCATGGTGCGAGGAACGTGATTCCGGGGCTCGGTAGAAGAG
107615 G A TAGGTTGCCATGTACGTGGTTTGACTGGTGGAGGTAGAGGAGCCCAGTTGCTACGTCTTCCGCAATTTTCAGGCACGACGTCCAGTGTAATGGCTTGCCT[G/A]TTCCCGATGGCCGTGAACCATGGATCAAAGAGAATAGGCTTCCGTTAGGAAAATAATCATATACAAGCAACCTTTCTTCTTTAGCTT
107617 C T TTGGAATAACAGCAAACCAAGGGTTCTACTTGCTGGGACTAGACAATACATCCCCTACTTTTGCCTCCGCAATTCAAAATTCCGTCCCTGCCATAACATT[C/T]CTCATGGCTGCAATCTTAAGAATAGAAAAAGTGAGACTAAACAGAAGGGACGGCATAGGCAAACTAGTGGGCACACTACTATGTGTT
107623 T C TGACCCTAACAGCAGCTGTAAACGCACAGCAGAACTGCGCACAAACGAGCTTCAAAAACAACAAAGTGTACTCTTTATGCAATTCGCTCCCGAAGCTAGG[T/C]GCCTCCATCCACTGGACCTACCACCCGTCCAACGGCACGGCGGACATCGCGTACCGGGCCCCACAGTCGGCGACGGGCTGGGTGG
107623 G A AGCAGAACTGCGCACAAACGAGCTTCAAAAACAACAAAGTGTACTCTTTATGCAATTCGCTCCCGAAGCTAGGTGCCTCCATCCACTGGACCTACCACCC[G/A]TCCAACGGCACGGCGGACATCGCGTACCGGGCCCCACAGTCGGCGACGGGCTGGGTGGCCTGGGCCCTCAACACGCAATCCGCCT
107623 G A CCAACGGCACGGCGGACATCGCGTACCGGGCCCCACAGTCGGCGACGGGCTGGGTGGCCTGGGCCCTCAACACGCAATCCGCCTCCAGCATGATTGGGTC[G/A]CAAGCCCTAATCGCCTTCCCGGCCGGCAACGGGGCCCTCACCGTTTACACCGTTTCTCTCATCAGCTACGCTCCCACCATTGAAA
107623 T G CGGGCTGGGTGGCCTGGGCCCTCAACACGCAATCCGCCTCCAGCATGATTGGGTCGCAAGCCCTAATCGCCTTCCCGGCCGGCAACGGGGCCCTCACCGT[T/G]TACACCGTTTCTCTCATCAGCTACGCTCCCACCATTGAAAACGACACCCTCAGCTTTCCCGTTTACAGCCGGGAAGCCGAGTACGG
107623 T G GCCCTCAACACGCAATCCGCCTCCAGCATGATTGGGTCGCAAGCCCTAATCGCCTTCCCGGCCGGCAACGGGGCCCTCACCGTTTACACCGTTTCTCTCA[T/G]CAGCTACGCTCCCACCATTGAAAACGACACCCTCAGCTTTCCCGTTTACAGCCGGGAAGCCGAGTACGGGAGCGGGGTTATGACTAT
107623 G A AGCCGAGTACGGGAGCGGGGTTATGACTATTTATGCCAGTATCGGTGTGCCTAAGAACGGAACTAGGGTCAATCAGGTTTGGCAAGCGGGTACGAGTTTT[G/A]CTAAAGGGCTGCCATCGGGCCATGCGATTACCGGTGATAATATTCTGAGTATGGGTACTTTGGATCTGCTTTCTGGTGTTGCTGC
107623 C A GCCGAGTACGGGAGCGGGGTTATGACTATTTATGCCAGTATCGGTGTGCCTAAGAACGGAACTAGGGTCAATCAGGTTTGGCAAGCGGGTACGAGTTTTG[C/A]TAAAGGGCTGCCATCGGGCCATGCGATTACCGGTGATAATATTCTGAGTATGGGTACTTTGGATCTGCTTTCTGGTGTTGCTGCT
107623 G A GGTTATGACTATTTATGCCAGTATCGGTGTGCCTAAGAACGGAACTAGGGTCAATCAGGTTTGGCAAGCGGGTACGAGTTTTGCTAAAGGGCTGCCATCG[G/A]GCCATGCGATTACCGGTGATAATATTCTGAGTATGGGTACTTTGGATCTGCTTTCTGGTGTTGCTGCTCAGGCCGGCGGCAATTCT
107627 C T TGTCACACCAAATTGCGATAGCATTTGGGATTTTCAAAGCTGAATCTTGATGGTCTACAAGGCTTTTTATAAATTGTTTGCAGTCAAGTAGCTTTGCTGC[C/T]GAGCTTATTGCCGACTTCTGAAGTCCCTCAGGATTGTATTTATGCATTGTGTTTGGGTTGAGCAGATTGTCATATAGAAGTCTCAAGTC
107627 G A AGCCATCATCACATGTTTTACCACCCAACCCTCGGAGACAGTAATCGAGCAGCTCAGGTGATGCAACCGCTTTACAGGTCGCTCCTTTAAGCGCTTTCCA[G/A]CTTACCCACCTATTTACACCAACAGCTTTGAGCACTTTCACCATCGAGTCCTCTGCCTTCTCGATATCACATTTCCCCCAGGTGCATAAT
107627 A G TTTCACCATCGAGTCCTCTGCCTTCTCGATATCACATTTCCCCCAGGTGCATAATACACCAGCACAATCAGTCTTATTGCCTACTTCAGTTTTACCTGAC[A/G]GTGGCAACACTTGATGGGATTCGTGAAGAATATTAGTATGAGATTCATGAAGAAGATTAGTGAGGTAGACAAAAAGATCTCTAATGGTT
107629 C T CCTTCTGCATCGCCATCGGCTTCCTCGCCCACAGACTGCAGTTCTGAAACACCACCGCTGCGTTCCCAAATATGAAATCAACCGATCCGTACACGTCGCA[C/T]TCCCTGTAGAACTGCCTTTGAGAGTGCACGTACAGCGTGTCCTGATACCCTATTATGTTGCAGCGGTACACCACGGATCGGTCTGCGC
107629 A C TCCTCGCCCACAGACTGCAGTTCTGAAACACCACCGCTGCGTTCCCAAATATGAAATCAACCGATCCGTACACGTCGCACTCCCTGTAGAACTGCCTTTG[A/C]GAGTGCACGTACAGCGTGTCCTGATACCCTATTATGTTGCAGCGGTACACCACGGATCGGTCTGCGCCGACCCTTAGCGCCACTGCTT
107629 A G AGTGCACGTACAGCGTGTCCTGATACCCTATTATGTTGCAGCGGTACACCACGGATCGGTCTGCGCCGACCCTTAGCGCCACTGCTTGGTGCTTCGCCGG[A/G]CCTGCGTAGTTCTCTATCGTCATGTCCCTCATTATGAACCCTGCTCCCGTTGACGCAAATGTGGCGGTGTGAAACGTGGTGTAGTTT
107629 T G CGCTTCTGGAGCCCGTAACGATGGTCTTTCCTTTCCCATCGCCGATGAACATGAGATTGGTCTTTTTTCGAGCGACCTTGATGTTTTCTTCGTATTTGCC[T/G]GCCTTCACGTAGATGATGATTCTTCTATTGCTGTTTTCTGGTGCATGCTTTACTGCATCCGAGATCGTCTTGTAAGTTCCAGTCCCGTCCT
107629 T C GCTTTACTGCATCCGAGATCGTCTTGTAAGTTCCAGTCCCGTCCTTTGATACGGTTATATCAGCTTGCATCCCGGCAATTCCCGGCATTTGAAGCAACCT[T/C]CTGTCGCTGTTTTTCACCCATTTGGGAAACTGCAGCAGCTTTCTTTTGTTTTGAATCGGGATTCCGGCGAAATCTTTGTTTTTGGCGCTG
107629 C T TTCCAGTCCCGTCCTTTGATACGGTTATATCAGCTTGCATCCCGGCAATTCCCGGCATTTGAAGCAACCTTCTGTCGCTGTTTTTCACCCATTTGGGAAA[C/T]TGCAGCAGCTTTCTTTTGTTTTGAATCGGGATTCCGGCGAAATCTTTGTTTTTGGCGCTGATTGCGAAGATCGCGAGAGAATTGCTGAT
107629 CT C CTTTGATACGGTTATATCAGCTTGCATCCCGGCAATTCCCGGCATTTGAAGCAACCTTCTGTCGCTGTTTTTCACCCATTTGGGAAACTGCAGCAGCTTT[CT/C]TTTTGTTTTGAATCGGGATTCCGGCGAAATCTTTGTTTTTGGCGCTGATTGCGAAGATCGCGAGAGAATTGCTGATGAGTTCGGAGAG
107629 G T TTGCGAAGATCGCGAGAGAATTGCTGATGAGTTCGGAGAGGTCTTTCAAGTACCCCACCATCTGCTGCCGGACGTAGTTGTCGGCGACGCCGAACAGACC[G/T]TCGGAGCACGTGTCCTGGTTGGTAAGCGCGGCGCTGAGCCAGGTCAGCACGTCTTCGTCGGACGCGAAGCCTTTGGCGGCGGGG
107633 G A CCACTCACAGCTATCTGATTCGCGATCTTCGCCACCTGCCCACTCCCTGCCTGGCCCATGTACCTAACCCTACCCAGTACGTCAAACAGCGGCGATAGCC[G/A]TTCTACCACAGATCCGTCCCCACCTGCGAAGATCGCCAGATTCCCATCTCTGGCGCCTAGATCTCCACCCGACACCGGAGCATCCACC
107643 G A CAGTTTACGAGCAACTAAAAGGCTTGCTGTGTTCCAATGCGGATGGGGACCGGCTCTCTGTAGGTGCTAATATGATAGCTGCATCTGTCGCTGGTGCTGC[G/A]ACAACTATTGTAACCAACCCACTTTGGGTCGTAAAGACAAGATTCCAAACACAAGGTATGAGAGCTTCTGCGATACCTTATCGAGG
107643 G A CTATTGTAACCAACCCACTTTGGGTCGTAAAGACAAGATTCCAAACACAAGGTATGAGAGCTTCTGCGATACCTTATCGAGGCACAGTGTCAGCATTAAT[G/A]AGAATAGCTCATGAAGAAGGCATCAGAGGACTATACAGCGGTCTTGTGCCTGCACTTGCTGGGATAAGTCATGTTGCTATTCAGTTT
107645 GA G CAAATCTTTAGATGATTGGGCAGAAAAGAACATCTTGGTGCTTCTAAAAGACGTTGAAAAAAACTGGCAGCCCCAAGATTTTCTTCCGGAAGCTTCAAAA[GA/G]AAGAACTCTATGATGAGGTGAAGGAGTTACAAGAGCGCTGTAAAGAAATTCCTGATGATTATTTTGTTTGTTTAGTAGGGGATAT
107645 C T TTTAGATGATTGGGCAGAAAAGAACATCTTGGTGCTTCTAAAAGACGTTGAAAAAAACTGGCAGCCCCAAGATTTTCTTCCGGAAGCTTCAAAAGAAGAA[C/T]TCTATGATGAGGTGAAGGAGTTACAAGAGCGCTGTAAAGAAATTCCTGATGATTATTTTGTTTGTTTAGTAGGGGATATGATCACTG
107645 C T GTACGATGGCTGCGACGATAATCTTTTTGAGCACTATTCTAGTGTTGCTCAAAGGCTGGGAGTTTATACTGCCAAAGACTATGCAAACATTTTGGAACAT[C/T]TGGTCGGGAGATGGAAGCTGAGTGAAATCACAGGACTGTCCAGCGATGGAAATGAAGCTCAGGATTTTGTTTGTAATTTGACTCCTA
107647 A C TTAAACAAATCGATGTCTCCCGCCAACACAAATTGAATTCTTGCAAAGCGATGGATATCACGTCATGTGGGTGCTAACAAGAAGGCGGTAAGAGGGACGG[A/C]ATCCAATGTGTATAGAGTTTCAGATCCATCTGTCATTGCTCGGGGAGGAATAGCCGGATCCAGGCCCTGAATGAGAAAGGGACCT
107647 G A GCGATGGATATCACGTCATGTGGGTGCTAACAAGAAGGCGGTAAGAGGGACGGAATCCAATGTGTATAGAGTTTCAGATCCATCTGTCATTGCTCGGGGA[G/A]GAATAGCCGGATCCAGGCCCTGAATGAGAAAGGGACCTTCTGACAAATGGATGGTCTAATAGTTGAGAGGCGGATGGTCTCTCG
107647 G A GATATCACGTCATGTGGGTGCTAACAAGAAGGCGGTAAGAGGGACGGAATCCAATGTGTATAGAGTTTCAGATCCATCTGTCATTGCTCGGGGAGGAATA[G/A]CCGGATCCAGGCCCTGAATGAGAAAGGGACCTTCTGACAAATGGATGGTCTAATAGTTGAGAGGCGGATGGTCTCTCGGCTGGG
107647 A G TCATGTGGGTGCTAACAAGAAGGCGGTAAGAGGGACGGAATCCAATGTGTATAGAGTTTCAGATCCATCTGTCATTGCTCGGGGAGGAATAGCCGGATCC[A/G]GGCCCTGAATGAGAAAGGGACCTTCTGACAAATGGATGGTCTAATAGTTGAGAGGCGGATGGTCTCTCGGCTGGGCTTGCTTCT
107647 A G TCTCTCGAGATGCTGCTGGGGATAGGCGGTTTTTCCCCTTTACCAACCATGAAGAATACATGTTGCCATTCCATGTTGTTGTAGGGGACCTGACGAGTCA[A/G]CATCTCTAAAACAGTGCAGCCGAGGCTCCATATATCAGCTGCTGGCCCATATGTTGTTTTTGGGTTAGCAACCTCTGGAGCCATCCAA
107647 T C ATATGTTCGCACATTTTATGTCTCTATGAACTATATTGCGTTCATGAAGATAGTTTAAACCCTTTAATATCTGCCTGGTGTATGCCGATACTTGACTGTT[T/C]TGAAGGCGATACTTTCGGTACAATGACGCTAGAGAACCTTGAGTTACAAGTTCAAGGAAAATAAATAGCTTTGCCTCTTCCTTATCGGTT
107655 TA T TGATGAGTGGAGCGAAGTTGCCACTCGTGTCAATCAGGATTCTAGGATCATTCGATCTGATTCACAGTGTAGGAATAGGCTGGACACTTTGAAGAAGAAA[TA/T]ACAAAAAAGAGAAGGCAAGGATGGTGGAGGATCCTAATTATAAAAGTGACTGGATTTATTTTGAAAAGATGGATTCCTTGATATC
107655 AT A ATCTGATTCACAGTGTAGGAATAGGCTGGACACTTTGAAGAAGAAATACAAAAAAGAGAAGGCAAGGATGGTGGAGGATCCTAATTATAAAAGTGACTGG[AT/A]TTTATTTTGAAAAGATGGATTCCTTGATATCAAGTGCATTGGCAATTCCTGCGCCAACAAAAGAAATGTTAGTGCCGGTGTAAG
107655 TTG T TCACAGTGTAGGAATAGGCTGGACACTTTGAAGAAGAAATACAAAAAAGAGAAGGCAAGGATGGTGGAGGATCCTAATTATAAAAGTGACTGGATTTATT[TTG/T]TGAAAAGATGGATTCCTTGATATCAAGTGCATTGGCAATTCCTGCGCCAACAAAAGAAATGTTAGTGCCGGTGTAAGTGTTAA
107655 T TA GTGGAGGATCCTAATTATAAAAGTGACTGGATTTATTTTGAAAAGATGGATTCCTTGATATCAAGTGCATTGGCAATTCCTGCGCCAACAAAAGAAATGT[T/TA]AGTGCCGGTGTAAGTGTTAATACGAGCATGAACTCAGGGTCGCCTTTGAGATTGGGATGTGGAGTGGATGCAGGAGAGTATGTTT
107657 A G ATTGCAGTATTGGTGTTGAATTGAGGGTTTCTTCTGAGCGTCTTGTTCTTCTTGATACTCAGCCTATGTTCAGCCCTTCTGTTTTAATAGATATGATGAG[A/G]CCTGATGGTTCATCCGCAGTATCTGTTTTGAATGGGGAGGCTCTATCAGCTGATCTTGCACATGAATTGCTGGGAATCCAGCTTGCGAT
107657 A G CCTATGTTCAGCCCTTCTGTTTTAATAGATATGATGAGACCTGATGGTTCATCCGCAGTATCTGTTTTGAATGGGGAGGCTCTATCAGCTGATCTTGCAC[A/G]TGAATTGCTGGGAATCCAGCTTGCGATGTTCTTAGCATCTGTTTGCAATGTATTGCTGGTAACATCGGAGGGATTACGCGACTTTAAC
107657 G A TGAATGGGGAGGCTCTATCAGCTGATCTTGCACATGAATTGCTGGGAATCCAGCTTGCGATGTTCTTAGCATCTGTTTGCAATGTATTGCTGGTAACATC[G/A]GAGGGATTACGCGACTTTAACATGTGGAAATTGATGCTAACGGTGGACTTGTTAAAACATGGAATACCAGATCCGTCGATGTTGTAC
107657 A G AGAATGCTGATGGCTCAGATTTAACTGCGCCAGATTTGTTTATGCTTCCTGTAAACAGTGATCAATCGCCTCTTTTTGGAAGTTATAATGCCATGTTAGC[A/G]CAACTCCGTGACCATGTACTGTCAATGGATGGGCGATCTTTTGCTACGAATGTTACGGAGAGAGATTGGTTGCGAAACTCTGCAAAAA
107657 TC T GCAAATAAAAAAATCTCCAGTGATTTTAGATTATAGCAGAACTCTCCGAAAATCAGGGTTGTTTAGGAGGTGAGTTTTACATTTTATGGATGAAATTGTA[TC/T]CCACTGGTAATCAACCAAGTGTAATGAGAGCTGCGTTGTATTCATGAATCTAAGTTTTATATTATGATAGATAAGGAAGCAGCCATG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107659 G A ATCATCTGTAACAGCTTTTATCCTAGCATCCATATCCTGAGATGTTTCTTGATTTGGAATGCCAATTGAATTACATTCAGGCTCAGTTATTTCAGGTACC[G/A]TCTCTTTTTGACAATCTATCTCAGGTACCATCTCTTTTTGAAGCTTTATTTCTGTATCATCGGAAATTGAAGGTTCAATAGTAGAAATATTG
107665 G A CCGAAATATTTGGATCAGCCCAAAATGAAAAGGATACAATGTTCATTCCCAAGTTAGAAGAGACTCAAAGAAAGAAGAGGTGTGAATCCTGGACCAAAGC[G/A]GTATCAAAAACTTTTGATCTTGCAGACTTGTCCCTTTAGGCTTGAAACACTCTTTATGCCTTCACCTTCTCTTCTTTCGTTTTTAAAAA
107669 C A AATACCTGCCGAAGTTGATCTTCAGTGATATTAAAATGTAAATTTCCAATATAAATTTTTCTAGCAGCTTCAACTGCTGCAAGGCTTGATCCACCAGTGG[C/A]AGTCGATTGAACAAGATTCTTTTCAGCTTCTGAAGGTTTGACCATCACTGGTTGACCCAAAAGTAACTGACCACTCATAGCTATAGCCA
107669 A G AGATTCTTTTCAGCTTCTGAAGGTTTGACCATCACTGGTTGACCCAAAAGTAACTGACCACTCATAGCTATAGCCATGGGAACAGACATTGCATCGTAGA[A/G]CTCAATGTACCCAACACCTTTTGATCTTCTTGAATTTCGATCTGTGATCAAGCGTACATCTCTAGCCTTTCCTGCTTTTGAGAAAAACTC
107679 AG A ACCAAAACAAAGAAACAACCTGCAAGAAGGTATCTATCTATGTACACCAAAGAAGAGGCTATTGATGCATGGTATGCGGAGGAGGTACAGAATAAGGAGG[AG/A]GGGGGAGGAGGAGGAGGCATGACATAAGGGACATGACCATGATGGCCAGGCGGAAGCATAACGGGCATACCCATAGCAGA
107679 A G TACACCAAAGAAGAGGCTATTGATGCATGGTATGCGGAGGAGGTACAGAATAAGGAGGAGGGGGAGGAGGAGGAGGCATGACATAAGGGACATGACCATG[A/G]TGGCCAGGCGGAAGCATAACGGGCATACCCATAGCAGAGGCAGCATGCCCTTGAACAGGGTGCCCTACAGGATGACCGTAT
107679 G A GCTTCACCTCAGCCGCACTCTTCGTTGCGACTCTGCTGGCAATCTCGCTGTAGTAGAAATCGTCGTTTTCATCTCCATTGTTAAACTCGAGCTCCGCGAC[G/A]GCGTTTTCAAACAACTTCTCTTCGTCCCAGGTCCAGTTGATCGGTTGCGGCTCCATGGATGACGACGACGAAGCTGTCATGACAAGCA
107679 C T AGTAGAAATCGTCGTTTTCATCTCCATTGTTAAACTCGAGCTCCGCGACGGCGTTTTCAAACAACTTCTCTTCGTCCCAGGTCCAGTTGATCGGTTGCGG[C/T]TCCATGGATGACGACGACGAAGCTGTCATGACAAGCAAGTCCTAACCCCGCGCCGGAAAGGAGGGGAAGCGCAGGACTATGTATGG
107679 A T AAGGAGGGGAAGCGCAGGACTATGTATGGCGCAGGTTAGAGAAAAGATTTTTATTGATGCTGATTTGATTTTGATTCTACTGTGGGGGCAGAAGTGGCGG[A/T]AATTATAGGAAAATCTTGCTCCTTGTGCCTTACAAACAAAGATGTGGGCTATTTAATCATTTGAAATCACATCACATTTTCTATCAA
107681 G T CTCCCGCTTCAACTACTCCCACGTCCTCTCCAGCGCCATCGCCCAAACCTCTCCCCTCTCCTGCTCACGGCTAAACCCCCTAATCGGATCTTTCTCTGCA[G/T]CCGGGTCTAAAAAGCTCATCGTCGTCGGTGGAGCTCGCTTCATCGGTGGCCTGGTCGACATCGAAGACCACAAACGGCTCGTGGTCGA
107681 C T TAATCGGATCTTTCTCTGCAGCCGGGTCTAAAAAGCTCATCGTCGTCGGTGGAGCTCGCTTCATCGGTGGCCTGGTCGACATCGAAGACCACAAACGGCT[C/T]GTGGTCGAGATCTACGATTTCGCCTCCGATACTTGGGATCTAGGCCCACCTCTCCCCGACGATTTCAGATCCGGCAACTCCTCCCAA
107681 A T AAAGCTCATCGTCGTCGGTGGAGCTCGCTTCATCGGTGGCCTGGTCGACATCGAAGACCACAAACGGCTCGTGGTCGAGATCTACGATTTCGCCTCCGAT[A/T]CTTGGGATCTAGGCCCACCTCTCCCCGACGATTTCAGATCCGGCAACTCCTCCCAATGGCTCTGCTCATGCCTGCTTAACAACCAGC
107681 T TG AACGAGGATCACTGCAGAGGGTATCCGTGTTGTGTTTGTGAAATTGGGGAAGAAGATGATGGTGGTGTGGGGTGTAGGTGGAGGATGGTGCCGAGTTTGG[T/TG]GGGGTGGTTAGTAGGTTCCATAAGGTGGTCGGATTTTGCTCTCATGTGGGGCTGGAGGACGTTCTCAGTGACGGTGATGTTT
107681 T C ATTGGGGAAGAAGATGATGGTGGTGTGGGGTGTAGGTGGAGGATGGTGCCGAGTTTGGTGGGGTGGTTAGTAGGTTCCATAAGGTGGTCGGATTTTGCTC[T/C]CATGTGGGGCTGGAGGACGTTCTCAGTGACGGTGATGTTTAGTAGATCGTGCAAGAATATATGTTTAAAAGCCTGTGGGGTTG
107683 T A CCCGCTACTTCCACTCCCGCTGCTATCGCTCGAACTTGAACTGTCTTCATTTAAAGCTTCAGCTGCAGCATCGGGCTCTTCCCTTCCTGTCGATTCATCA[T/A]TTACATCCACATTTGCAAATTCATCGTCGCTCTCGTTCTGACTTGCAATATTTGTATCCACCCGTGTATATGGAGCTGAACCCTGTCTAGT
107685 T A ACATACGACAATATCACTACTAAAGAAAATATATTTCAATGACAGAAGCAATAAAAATTACTCATCTAGATACGTAGTAGCACGATCAAACTTTGCTTCT[T/A]CAAGGACTTCCAAGTGTAAGTAAGAACGGTCTTTTGATACTTGAAGATTATAGTTTTCCAGCCATAAACTTCAGCCTGGCTTTTCAAAG
107685 GA G CAAGTATACTTGCTTCACCTCAAACGACGTCCAAATGATTCCGTATTAAAACGCAGCCGATGCTGTCTTGTCGATCACTCGAGAATAGGAGTGACCAGCG[GA/G]ACTCATTTGCAAAAAAGGCCTTCAAATTACTCGCAAGTAAATCCGCAAGAGCATCATTTGACTCCGCCGTAAACGCCGCCTTGTGC
107685 A G CCCCACGTTCACTATAACCCCATCCCTCCCCAGCGCATCCATCACATCTCCGTTCACCACGCGACGTGTCTCCTCGCTCAGCGAGCAGCACAGCACCAGC[A/G]CATCGCTCCATCTCGCAAGATCTTTCACATTCGAAAAAAAGGGGTAACGAACCGAAGATTTCTTCGCTCTCGAAGTGTAAGCTACTTC
107685 T C GCTCTCGAAGTGTAAGCTACTTCGCACTTGAAAGCTTCCAGCCTTTCGGCGATTCGAGATCCGATCTTTCCAAGCCCTACGATCCCGATTCTCTTCCCGC[T/C]TACACTGAATCCGAGGCGGAAATCGTTTTTCCAGGAGCCGGCTCTGACGAATCGGTCTCCGGAGGAGATACCTCGTAGGACGTCGAT
107685 A T TCGAAGTGTAAGCTACTTCGCACTTGAAAGCTTCCAGCCTTTCGGCGATTCGAGATCCGATCTTTCCAAGCCCTACGATCCCGATTCTCTTCCCGCTTAC[A/T]CTGAATCCGAGGCGGAAATCGTTTTTCCAGGAGCCGGCTCTGACGAATCGGTCTCCGGAGGAGATACCTCGTAGGACGTCGATTAAG
107685 A G TGGCGACTTTGATGCCTTTGCTTTTGCATTCGAGCAAGTCGATGTGGTCCACGCCGGCGCTGGTGGTGGCGATGAAGCGGAGGTGAGGGAGGAGGGAGAG[A/G]AAGTGGGAGTCGACGCGGATGGAGGTGGAGACTATGACGGCGCGGGTGGAGGTGGAGTGGTTGGATATGAAGAGAGGGAT
107685 T A GACTTTGATGCCTTTGCTTTTGCATTCGAGCAAGTCGATGTGGTCCACGCCGGCGCTGGTGGTGGCGATGAAGCGGAGGTGAGGGAGGAGGGAGAGAAAG[T/A]GGGAGTCGACGCGGATGGAGGTGGAGACTATGACGGCGCGGGTGGAGGTGGAGTGGTTGGATATGAAGAGAGGGATGTCG
107685 C T TCGATGTGGTCCACGCCGGCGCTGGTGGTGGCGATGAAGCGGAGGTGAGGGAGGAGGGAGAGAAAGTGGGAGTCGACGCGGATGGAGGTGGAGACTATGA[C/T]GGCGCGGGTGGAGGTGGAGTGGTTGGATATGAAGAGAGGGATGTCGGTGGAGGGGAAGGAGGGGATGATGTTGAAGCC
107685 A G GGATGGAGGTGGAGACTATGACGGCGCGGGTGGAGGTGGAGTGGTTGGATATGAAGAGAGGGATGTCGGTGGAGGGGAAGGAGGGGATGATGTTGAAGCC[A/G]CGGGTGGAGAGTTTGGTCACGAGTTTGGTCGGAGTGTGTCGGATGAGGAGGACGGGTGGGAGAGGGGTGGAGGCAGAC
107687 C A GGTGGGTAACTGGGTACCGGGTAAGCTCCTGGAACTGGGGGAAACCCAGGTCTAAAACCATGCATGTTTGGGTCCCAAGCAGGTGCAGCAACGTTAGCAC[C/A]GTATACTGGTGTGGTGGCAACTGGATTCGGTATGGGTGGAATTTGAGGCACTGTTAGAAGAGACCCTTCAGGTATTGTATAGTC
107687 T A ACCCAGGTCTAAAACCATGCATGTTTGGGTCCCAAGCAGGTGCAGCAACGTTAGCACCGTATACTGGTGTGGTGGCAACTGGATTCGGTATGGGTGGAAT[T/A]TGAGGCACTGTTAGAAGAGACCCTTCAGGTATTGTATAGTCTCTGCTCTTGTCTGTGTTTGCCTTCACAATTAGATCGGTGTGACG
107687 AT A CTGTTAGAAGAGACCCTTCAGGTATTGTATAGTCTCTGCTCTTGTCTGTGTTTGCCTTCACAATTAGATCGGTGTGACGGGAGTAGGCCAGATGAAGCTT[AT/A]TTGTACCCACCGTCGTAGATGCAGTGTCCCTCCAGAGCTGCTTTAGCAGTTGCTGCAGTGGTAACATCAGGATATTGAATTAAAGCC
107687 AC A GAGACCCTTCAGGTATTGTATAGTCTCTGCTCTTGTCTGTGTTTGCCTTCACAATTAGATCGGTGTGACGGGAGTAGGCCAGATGAAGCTTATTGTACCC[AC/A]CCGTCGTAGATGCAGTGTCCCTCCAGAGCTGCTTTAGCAGTTGCTGCAGTGGTAACATCAGGATATTGAATTAAAGCCTGCATCCCG
107687 A C TGTTGAAGACATCGTGAGAAGACTAGGTTGAGATGTAGGGCAGCTCTTTACCTCAATTTATCTGTTGGAATTATAAAGGGCTAGGGTTTGGGATTTTTTA[A/C]GGGGGATGGAAATTTGAGGTTAGAAAAGGGAGAAAAGGGACACGAATCGAAATATCCAGTAGGCCAACAG
107691 A G ATATTAAACCAGATAACTTTCTGATGGGTTTAGGGCGTAAAGCAAATCAGGTTTACATAATAGATTATGGACTTGGGAAGAAATATAGAGATCTTCAAAC[A/G]CATAAGCACATACCATACAGGGAGAACAAAAATCTTACTGGGACTGCACGCTATGCAAGTGTAAATACGCATCTTGGAGTAGAGCA
107691 C T GGAGAGATGATTTAGAATCACTTGGTTATGTGCTCATGTATTTCCTAAGGGGGAGCTTACCATGGCAAGGATTAAAAGCGGGCACCAAGAAGCAGAAGTA[C/T]GATAGAATTAGCGAAAAGAAAATGCTTACTCCTGTTGAGGCTTTATGCAAATCATATCCATCTGAATTTGTGTCTTATTTCCATTAC
107691 T C GAGATGATTTAGAATCACTTGGTTATGTGCTCATGTATTTCCTAAGGGGGAGCTTACCATGGCAAGGATTAAAAGCGGGCACCAAGAAGCAGAAGTACGA[T/C]AGAATTAGCGAAAAGAAAATGCTTACTCCTGTTGAGGCTTTATGCAAATCATATCCATCTGAATTTGTGTCTTATTTCCATTACTGTC
107691 C T GTACGATAGAATTAGCGAAAAGAAAATGCTTACTCCTGTTGAGGCTTTATGCAAATCATATCCATCTGAATTTGTGTCTTATTTCCATTACTGTCGATCA[C/T]TGCGGTTTGAGGATAAGCCAGATTACTCTTATTTGAAAAGGCTTTTCCGCGACCTCTTCATTCGGGAAGGTTATCAGTTCGATTACGTG
107691 G A CTGAATTTGTGTCTTATTTCCATTACTGTCGATCACTGCGGTTTGAGGATAAGCCAGATTACTCTTATTTGAAAAGGCTTTTCCGCGACCTCTTCATTCG[G/A]GAAGGTTATCAGTTCGATTACGTGTTTGATTGGACAGTCTTGAAGTATCCTCAAATTGGTTCAAGTGGTAAAGCACGGCCATCCAGTGG
107691 T C ACCTCTTCATTCGGGAAGGTTATCAGTTCGATTACGTGTTTGATTGGACAGTCTTGAAGTATCCTCAAATTGGTTCAAGTGGTAAAGCACGGCCATCCAG[T/C]GGTAGACCAAGCGGAGAAGTCGGACAATCTCAAGAAAGAACAAAAGCAAGCCAAGAAATACGAGATAAATTCTCGGGTGCAGTTG
107697 T C GTGGAGGCCATTCAGCTGTTTTGACGGAGGCATGCTCTTTGAAGGAGCTATGCGAGTTTAAGCTTGCAGAAATTGTTGATGTTTCCAATTCTCTATTAGT[T/C]GAGGATGTGGCATCCAGAGCTGGTGCTGATGCTTTGGCACGCCTCTGTGGAAGGTTGAGGGCGCATATGACTGAACAAGGCAACCA
107703 C CA GAGTGAACTTGAATATGAGCATTCATAAACCCACTCAAAAATAGAACCATCACAATATGGGTATGAAAAAAAAATGCAGTATGCTCATCCAGACCCAAAC[C/CA]ATTAAACATCCTCTTCTGCCTATCTGGATGAACATACATATGAACAATCAAAAACCCAGAAATCCATTTGAACATGAACCAAAGATC
107705 CA C TCATACTCAGCCCCTTCCTGAGCGTTGCTATGCTCTATCTGTGCGGTATCCTCTGATGGTTGTTGGCACTGCTGACAGAAATATAATTATCTACAATCTG[CA/C]AAAAACCCTCAGAATGAATTCAAGAGAATTGTTTCACCTCTAAAGTATCAGACAAGATGTGTTGCTGCATTTCCAGATCAGCAAGGAT
107717 C T GGATCTAATGGCATTTCGCTCTATTTTCGATTCCGGCGCTTTAATATCAGAGTTTGAATCATCTGGAATCAGTACCCGTTTCATCCCAGTCATTTGGAAA[C/T]ATGTAATCCAACACCCAAACTGCCAGCTCGATGACGTATCCTCCCTGCCCGCGGCTGCTTATCTGCTTATTCGATCCAAGTTTAGACCAA
107717 A G CATTAAAAAACTATCAAAACAGCAGTCAACAGAAGATTTTTATCGAGTATATCATGCTGGATGGTGTCAATGATCAGGAGCTTCACGCGCACCAGCTTGG[A/G]AAATTACTTGAAAATTTTGATGTGGTTATAAATTTGATACCTTTTAATCCTATTGATTCCACTACAAGATGTTTCGAAACCAGCTCAGA
107719 T A CAGGATTGCCTGATGATTTAGCATTAAGATGCTTAGCAAAGATATCTCATGGATATCATGGATTGCTACAATGTGTATCCAAGAAGTGGAGACAAGCGAT[T/A]AGAAGCACAGAGTATGCAAATCTGAAATCTTACGAGGGTTGGTGTGGAAATTGGATTTTCGCATTTACAAATCCATCGATTAACTAT
107719 A C CTGATGATTTAGCATTAAGATGCTTAGCAAAGATATCTCATGGATATCATGGATTGCTACAATGTGTATCCAAGAAGTGGAGACAAGCGATTAGAAGCAC[A/C]GAGTATGCAAATCTGAAATCTTACGAGGGTTGGTGTGGAAATTGGATTTTCGCATTTACAAATCCATCGATTAACTATCATTGTATG
107719 A C GCTTCTAGTTATCGGAGGGCGTCTATCTTCGCCAAATAAACCAGCAAGTTTTGCCATAAACGATGTTGTGATGTTTGACCCTTTTAAACAGAAATGGAGT[A/C]ATGTGAGCGCTTTGAGAGTTGCAAGGTCAAATTTTGCTTGTGATGTGATTAATAACAAAGTTTATGTAGCTGGAGGAACTACGGGGA
107719 T C GTCGACAGTGATATATTACCATTTTCAAAACTCTGGCTCGATAACACTACTGTTATAGATGGTTCTTTATACACCATACTCGATGATGACAGCGTTAAAG[T/C]TTTCGATGCAAGTACAAGAGACTGGATCACAATCGGCATGTTACCTTCAGTTGTTCTTCAAGGTCACGCTCGCTATTTGAAACCATTTG
107719 C T AGACTGGATCACAATCGGCATGTTACCTTCAGTTGTTCTTCAAGGTCACGCTCGCTATTTGAAACCATTTGCATACAGCGTCGTGGGTTACAAGAATTTC[C/T]TGTATGTTTTAGGAGGAAGTGTTCTGAAATATGATTCTGATGCACACGGATATGATGTCGTTGAATTGAGCAGCGTGAGGTTTTGTGA
107719 C T ACGCTCGCTATTTGAAACCATTTGCATACAGCGTCGTGGGTTACAAGAATTTCCTGTATGTTTTAGGAGGAAGTGTTCTGAAATATGATTCTGATGCACA[C/T]GGATATGATGTCGTTGAATTGAGCAGCGTGAGGTTTTGTGATCCGACAATTATACCCCTGCAGTGGCATGAGGCTAGATCCATGCCT
107719 T C AGTGGCATGAGGCTAGATCCATGCCTGCACCGGCGAGTTATTTGGTCGGCTGTGCTTTGGTGGAGGGCTGAGATGTCATTTTACTTTCCTTGTATCACAC[T/C]GTGCTTTAATTTGTTTTATGATTCTTTCATGTATTCTTAGTTTGGTATTGATTGCCTGTAAACCTATTGTTTATTCGTTGTTGAATGGTT
107727 A G TCAGGGGGAGAGTAATTCTCACAAACAACAAATGCCTCAATACTTGAATTACGGCTGCTCTTTGGTTTTGCAAAAGTGACATGTGAGAAGAATATTTTTA[A/G]CTGGCAATAAAGGAGACTTGTGTCTTTACCCCGGAATATTTTAGCTATAAATTTGCCACCCACTCTAAGCACATGAGTAACAATAGTA
107727 G A AATTCTCACAAACAACAAATGCCTCAATACTTGAATTACGGCTGCTCTTTGGTTTTGCAAAAGTGACATGTGAGAAGAATATTTTTAACTGGCAATAAAG[G/A]AGACTTGTGTCTTTACCCCGGAATATTTTAGCTATAAATTTGCCACCCACTCTAAGCACATGAGTAACAATAGTAAGTGCAGCCAAAAT
107727 T C GGAGACTTGTGTCTTTACCCCGGAATATTTTAGCTATAAATTTGCCACCCACTCTAAGCACATGAGTAACAATAGTAAGTGCAGCCAAAATAAGTTGCGA[T/C]TGAACAAATTCGTCCATATCGTGTAGTCCAGTAACATCAGGGGCACCATCACAGACAACCAAGTCAGCTTTGCATCCATCAAAATGTC
107727 G T CAACTACCTGGGGCAGCACAAAGATCAATTACACGCTTTACTCCTTGAAAAATATTAAATTCCTCGTCAATTTGAAGAAGCTTGAAAGCACTCCTTGCTC[G/T]CCATCCTTCTTCTTTTGCTTTGCGATAGTATATATCCCTCTTGTCTTTAGAAGCTTTTCCCATATATATTCTATTCGTTTAGACAGTACAAA
107727 T C AAAGATCAATTACACGCTTTACTCCTTGAAAAATATTAAATTCCTCGTCAATTTGAAGAAGCTTGAAAGCACTCCTTGCTCGCCATCCTTCTTCTTTTGC[T/C]TTGCGATAGTATATATCCCTCTTGTCTTTAGAAGCTTTTCCCATATATATTCTATTCGTTTAGACAGTACAAAGCTTTTCCTTATTTTTACGT
107729 A T CCATCAACTTTTTTGAACGTTTCATCCAAACCAATTTCGAATTCTTCATTTCTAGATCCACCACTCTGAAAATAATCTGCCATATGATTTCCTAAAGATA[A/T]TCCACTTATGACTGCAGCTTCGATGCTCGACCCAAGAAGCCAATCACCACAGATTCCTGCCCGTCCCTTTGGATCAAAAATACATGGAACT
107729 C T AATTCTGTTACTCTGTTGAAGAATTGAATCTGCTAAAGGCCTCATTCCCATCCTCCCTATATATCTTTTAGTAGTATAAGGTAAGGGATTAAACTGACCA[C/T]CAACATCAAGTTCTCCCAACTGACCTTTCCATTCAAGAATTATACCTTCGTCCAACCATTTTGTAACAAATTTCTCAAACCTTGAATCATCA
107729 A G TACCTTCGTCCAACCATTTTGTAACAAATTTCTCAAACCTTGAATCATCAACAGTAAAGAATTGAGCAGCGTGATCAAACAACAACTCTTGGGAATTGAA[A/G]TCAATTTTTCTTGTCCCCAATCTCCCTCCTAACCCATGCATCCCCGTATCAAAGACAGTAGAGCGAATATTGCGCTCCTCGAGAGTCAG
107729 G T TCCCTCCTAACCCATGCATCCCCGTATCAAAGACAGTAGAGCGAATATTGCGCTCCTCGAGAGTCAGCGCGCAGATAAGACCCGATATTCCGCCGCCAAT[G/T]ATTGCGACAGTGGGATCCACAGGGAGGGGAGTGTCGAAATTGACCTGCTCTTGAGAGAAGCTCTTCTTTATCGCGGACTTCCTAGA
107735 T C AAGACATGCATTCGGTGGGCCTTCAGGTTCTCAACAACGGTTTCTGGGTACCTGTTAAGCCTGTGTCTAATGCCCTTGTCATCAACATTGGAGATACACT[T/C]GAGGTATTTACAAATGGAAGGTACAAGAGCGTTGAGCACAGAGCAGTGACCAACAGAGGAAAGCACCGGCTTTCTATAGTGACATT
107735 A G GAGGTATTTACAAATGGAAGGTACAAGAGCGTTGAGCACAGAGCAGTGACCAACAGAGGAAAGCACCGGCTTTCTATAGTGACATTCTATGCCCCAAGCT[A/G]TGATGTTGAGCTTGGCCCTGTGCCTGAGCTTGTCAGCAAGCTGCACCCTTCTGTTTACAGAAGGTATAAACATGCTGACTACAATA
107735 A G GTGGAAGCATCCAATTAGCAACTGCAAATATAATTATATATCAAATGAAATCTTTGGAGTCATGCTAATCATGCATCTAAAGTTAAGAATATTCATATGC[A/G]GAAACAATAATTAGAATGATAATATAGCTACTGTCTGTTATGTAATTGTTTAAGCCATGATTGGTGAAATTGTAACCGTGTACGTAGAT
107737 GA G AATAGCCATAGTAACTGGCTCGAGCAGAGGAATCGGTTTCCAAATCGCTCGGCAACTCTCCCTTCATGGACTCTTCGTCGTCATTGCTTCTAGAAACCCC[GA/G]ACAAATGTCAAGAAGCATTCGACAAAATCATACAAGAAAAAAGCACAAGTAATTTAGCATGGCATCAGCTCGATATCTCGGACTTA
107737 C T CTATGTTGCCACTGATGAGGGCTTCCAAGCATGGTGCTCGTATACTGAATGTGACATCAAGACTTGGCAGGATCAATGGAAGGCGCAACAGATTAGGAGA[C/T]GCTGCCCTAAGAGACCAGCTTTTGAAAGACGAGTGCCTTTCTGAAGAATTAATAGATGGTATGGTCATGAAATTTATCGAACAAAC
107737 G C ATCAAGACTTGGCAGGATCAATGGAAGGCGCAACAGATTAGGAGACGCTGCCCTAAGAGACCAGCTTTTGAAAGACGAGTGCCTTTCTGAAGAATTAATA[G/C]ATGGTATGGTCATGAAATTTATCGAACAAACTAAAGAAAAGCAGTCGGTTTTGAAAGAATGGCCGCAAGTTTTCACTGATTACTCG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107737 TA T ACAGATTAGGAGACGCTGCCCTAAGAGACCAGCTTTTGAAAGACGAGTGCCTTTCTGAAGAATTAATAGATGGTATGGTCATGAAATTTATCGAACAAAC[TA/T]AAAGAAAAGCAGTCGGTTTTGAAAGAATGGCCGCAAGTTTTCACTGATTACTCGGTTTCAAAACTGGCAGTGAACGCTTACACGC
107737 AG A TTTCCGGCAAGTTCTTTGCGGAGAGGCGTGAAATAAGTTTTTGAGGGAGGTTTGATTACAAGTTTTGTGTATGCTTGTAGGCTATGAAACTGCTATAGTT[AG/A]GGGGGACTGAAATGTAGGAATTTATCGTAGTTAAAGCAGACTCAACGTGCACATTGATATAAAATAAAATGTAACTTTATGTTTGT
107737 A AT GGCGTGAAATAAGTTTTTGAGGGAGGTTTGATTACAAGTTTTGTGTATGCTTGTAGGCTATGAAACTGCTATAGTTAGGGGGACTGAAATGTAGGAATTT[A/AT]TCGTAGTTAAAGCAGACTCAACGTGCACATTGATATAAAATAAAATGTAACTTTATGTTTGTCCCTTCATTGTGGGTTTAGAATGAT
107741 G A ACGACACTACATTTGCAAAAGAAAAACGTAAATAAATAAACATATACATATGCTATAACTAGGTAGCTTTGGTGGGTTCATCAGTGGCAGGGACAACATC[G/A]TCATCGTCGTGGTAGATGTTCTCAGCCATCTGCCAAATCTGAAGGATGTTGTCCTCGGCCACACTTGCAATAACCCAATCTTCGCAG
107741 A G AGGATGTTGTCCTCGGCCACACTTGCAATAACCCAATCTTCGCAGGGGTTGAATGAAAAGTCTGATATTTTGCTGGTGTGCCCTCCGTGTATGAATAGTA[A/G]CTCTGGCGGTCCGTCCTCTGCATCCTCGGGGGTTTGTTCATCGTCGATCCTGCTAAGATCCCAGACCATAAGCCGTCTACCAAGGCA
107741 C T CCTCCTCCTTGTGGGCATCAAAGGTATGAAGGGGTTTAGTTATCTTTCGGAGATCGAATAGGTTGACTGTCTTATCAGTTGAACCTGTTGCAACGACCCA[C/T]TCGTTAAAAGGATTGAATGCCAAGCAATTGACCTCACTTTCATGAGCAACAACGGACTGAACTGGCCTATTGGCGTTAGGCGATCTA
107741 C A GGCCTATTGGCGTTAGGCGATCTAAGATCCCATATTAGCAACTGCTGATCATCACCAACAGAGCCAAACAAATATTCATGCCTCAGATGCCATGCAACAT[C/A]CTCAACTACGCCTTCGTGTACCTTAAATATTTGAAGAGCATCAATGGATTTGTTTTTGGGAGTTGAGTTTATATCCCACAAGCATATTT
107741 A T AATTGTGTCCTCGCAATCGCAAATCAGGATTACAGGCACCATCTAAAGGAGCCTTAGATGGATGCTTGCTATAATCAAATACATAAACCTCTGCACTAAC[A/T]GTCTTTGTTGCAATTATAAAAGGATTCTGAGGCATATATCGAGCCCGGTTGACTTCTCCTTCGTGATTTATCTGCTGAATGATTTGCAC
107741 C T CAAATACATAAACCTCTGCACTAACAGTCTTTGTTGCAATTATAAAAGGATTCTGAGGCATATATCGAGCCCGGTTGACTTCTCCTTCGTGATTTATCTG[C/T]TGAATGATTTGCACCTTTCCAGAAGCCGATCCAAAACCACCGATATCGCCTCTCTCGTCATCATACATCCTCGCGTCATCCTCCGCGTCA
107743 T C TTCAACATATTCACCAGCCCGATCGGCGCAAACATCACATCTTTACTCACATGCCTAACCGGCGAAACGACAAAGAGTTCAAAGTGGACAGGATCGAGCG[T/C]GATATCAAAATCATCATCAAGCTTCAACAGCTGTAGCTTTCCCCCTCGATGCGAGTAGACTGCAAAGAGATCGAGATCACTAGCATC
107743 C T ACATCACATCTTTACTCACATGCCTAACCGGCGAAACGACAAAGAGTTCAAAGTGGACAGGATCGAGCGTGATATCAAAATCATCATCAAGCTTCAACAG[C/T]TGTAGCTTTCCCCCTCGATGCGAGTAGACTGCAAAGAGATCGAGATCACTAGCATCAATTGATGTTTTGAAGTAAGTCCACTCGATG
107743 C T TACTCACATGCCTAACCGGCGAAACGACAAAGAGTTCAAAGTGGACAGGATCGAGCGTGATATCAAAATCATCATCAAGCTTCAACAGCTGTAGCTTTCC[C/T]CCTCGATGCGAGTAGACTGCAAAGAGATCGAGATCACTAGCATCAATTGATGTTTTGAAGTAAGTCCACTCGATGTCCCCAGGCCTC
107743 T G AAGTGGACAGGATCGAGCGTGATATCAAAATCATCATCAAGCTTCAACAGCTGTAGCTTTCCCCCTCGATGCGAGTAGACTGCAAAGAGATCGAGATCAC[T/G]AGCATCAATTGATGTTTTGAAGTAAGTCCACTCGATGTCCCCAGGCCTCGCTTTCGCGGTTACGGTCCGAGAGTGCTCTTTGAACGG
107743 G C TTCCCCCTCGATGCGAGTAGACTGCAAAGAGATCGAGATCACTAGCATCAATTGATGTTTTGAAGTAAGTCCACTCGATGTCCCCAGGCCTCGCTTTCGC[G/C]GTTACGGTCCGAGAGTGCTCTTTGAACGGGACATTTTTGTGTAGCTTGGGGCTCCAGCCCCCTCCTTGGCAATTGAACCCTCCAAGA
107743 G T CTCGATGCGAGTAGACTGCAAAGAGATCGAGATCACTAGCATCAATTGATGTTTTGAAGTAAGTCCACTCGATGTCCCCAGGCCTCGCTTTCGCGGTTAC[G/T]GTCCGAGAGTGCTCTTTGAACGGGACATTTTTGTGTAGCTTGGGGCTCCAGCCCCCTCCTTGGCAATTGAACCCTCCAAGAACTCCG
107743 C T TTCGCGGTTACGGTCCGAGAGTGCTCTTTGAACGGGACATTTTTGTGTAGCTTGGGGCTCCAGCCCCCTCCTTGGCAATTGAACCCTCCAAGAACTCCGG[C/T]AAACTTGTTCACGTTCCAAATTTTGAGCATGGTCTTCCCATCATGCAAGGGGTCGAGGAAGAAGCAGTCCTTGGTTGGAAGGGCATA
107743 A G TCGCGGTTACGGTCCGAGAGTGCTCTTTGAACGGGACATTTTTGTGTAGCTTGGGGCTCCAGCCCCCTCCTTGGCAATTGAACCCTCCAAGAACTCCGGC[A/G]AACTTGTTCACGTTCCAAATTTTGAGCATGGTCTTCCCATCATGCAAGGGGTCGAGGAAGAAGCAGTCCTTGGTTGGAAGGGCATA
107743 C G CGGTCCGAGAGTGCTCTTTGAACGGGACATTTTTGTGTAGCTTGGGGCTCCAGCCCCCTCCTTGGCAATTGAACCCTCCAAGAACTCCGGCAAACTTGTT[C/G]ACGTTCCAAATTTTGAGCATGGTCTTCCCATCATGCAAGGGGTCGAGGAAGAAGCAGTCCTTGGTTGGAAGGGCATACCCTTGGCA
107743 G C CCATCCATAAGCTGTTGAAGGAGCAGTGTACCATGTGGACTCCTTGAAGCCAGAACGGCTCTCCGTCTGGGTCCACTGTCCAGAAGTCATCACCGACGCG[G/C]CCTAGAGCGATGTTCTCTGTGCCGAGGTACATGAAATCGTTGCAGTGCTCCATGCTGGCGATCACTCCGTTTCCTTTGAAGTGTTTC
107747 CAT C TTGTATATAATTCATTATGGCTCAGTCGTAGATAATACCAGCATATAAACCATCTTTCTCACCGTAAGATACTTTACACAATCACATATATATCAAATTA[CAT/C]ATATATAAACTTTCCTGGCGAAGAGAAATATGTTGATCTCTCCCTAGCCTTAAAATATCTCATCAAAGTTTCACCATCTTAATACATCAT
107747 A G TCTTTCTCACCGTAAGATACTTTACACAATCACATATATATCAAATTACATATATAAACTTTCCTGGCGAAGAGAAATATGTTGATCTCTCCCTAGCCTT[A/G]AAATATCTCATCAAAGTTTCACCATCTTAATACATCATAAGTTAGCTGTCCTCAATTTCGTTTCATGATCATGAAAAAAGCCAGCATCAAG
107747 A G TCAAATTACATATATAAACTTTCCTGGCGAAGAGAAATATGTTGATCTCTCCCTAGCCTTAAAATATCTCATCAAAGTTTCACCATCTTAATACATCATA[A/G]GTTAGCTGTCCTCAATTTCGTTTCATGATCATGAAAAAAGCCAGCATCAAGAAAATGCAAGTGTTACTACATAAAACCATCACCTAACAT
107747 T C ACATATATAAACTTTCCTGGCGAAGAGAAATATGTTGATCTCTCCCTAGCCTTAAAATATCTCATCAAAGTTTCACCATCTTAATACATCATAAGTTAGC[T/C]GTCCTCAATTTCGTTTCATGATCATGAAAAAAGCCAGCATCAAGAAAATGCAAGTGTTACTACATAAAACCATCACCTAACATCTTCACAC
107747 T C TATCTCATCAAAGTTTCACCATCTTAATACATCATAAGTTAGCTGTCCTCAATTTCGTTTCATGATCATGAAAAAAGCCAGCATCAAGAAAATGCAAGTG[T/C]TACTACATAAAACCATCACCTAACATCTTCACACTCTGCCGATTTTAAGTCCATTCATGGGCTGATTAAGCGCGTTCTGGTCTCCGATTTT
107747 C T TTCACACTCTGCCGATTTTAAGTCCATTCATGGGCTGATTAAGCGCGTTCTGGTCTCCGATTTTGTGCAATTCAGACTCAATCGTCTCTGCAATGATGGT[C/T]CCTTCTGGATCAGGCTCGGGCACACTGACATGGAATGATCCTTGCTTTGCAGGTGCGACGAATCGATACTTTAAGGTTTGTTGTTTCAT
107747 C T GTGCGACGAATCGATACTTTAAGGTTTGTTGTTTCATGTAGTTGTACAGTTGTTGGTGGAATGGATGGTCCAATGTGAAGCAGTCGTCCGAATCTGATGT[C/T]GAGTATCGTGATGAACCAGAGTTCGATCTTTTGCAGAAGTGGGGGAGGGCCGAATAGTCCATTATCCTCAACAATTCATCTCTACCG
107747 TG T GTTGTACAGTTGTTGGTGGAATGGATGGTCCAATGTGAAGCAGTCGTCCGAATCTGATGTCGAGTATCGTGATGAACCAGAGTTCGATCTTTTGCAGAAG[TG/T]GGGGGAGGGCCGAATAGTCCATTATCCTCAACAATTCATCTCTACCGTTGCCTTGAAGTACTTGCACTTTTTTCCTTGTTCTTTCTT
107749 T G AGACCTCACTTAACATGTTTGTGGGAATGGGGAGACCTGCTTGGAGAGAGGCTAGATCCACTATCCAAAAGCTTTTATCTGCTGATGAGCCAACTTTACG[T/G]GACAATGTTGATCTGAGGGAAAAGTCCCTTCATCCAATGAATCGTGTACAGATGCTTCTACCAATAGTGATAGGAGATTACACGGA
107749 G A GGGTCATTTTTCGCGGACCGGATAATCCTATTCTACCGAACTGGTTTCACCTTCCAGTTGCTTATCACGGAAGGGCGTCTTCTATAGTTGTCTCTGGAAC[G/A]GATATTGTTCGTCCAAGAGGCCAGAGTCATCCAAAAGGGGGGTCTTCACCACAATTTGGGCCCACTCAGAAATTAGATTTTGAGCTTG
107749 T G GGGGAAAGGCTACAATGTCGGTTTTGGAGCATGCACCGGGAGAATTTTGCCAAGCCTTCCTTGATTGCTGATGGCATAACGCTTTATTGTAGGTTCAGAT[T/G]TGTAAGGAATAAAATATAATGAAGATTGTAGTACATTTTAAATTGAAGGCTGAACTAGAACATGTAAAAACATCATTTTGTACAACT
107753 G A GCTCTACCGATGAAGTGCTAGTCAACGAAGGGAGGTTATCATCCACAAATAATGTACCTTTTGTCGGTGTTTCTAAAGCGCAGATCTATCTAGCATTCCA[G/A]CTCAATTTTTCAGCTCCTATCACGAAGCAAAATCTTTTGTTTGCCTTTGGAGCATCGATTCCTGTCAAGAATCACTTGAAGGAGCATAG
107767 G A AACTCTCACTTCGTTCCCCTTTCTACAATTGGTGTTTCGCCTTCAATTTTTTCCGCATAGGAGATGGCGGTGGAAACAGAAGGCGCTTCCGCCGCCGCCA[G/A]CATCGCGCTATCTGATGTAAATATCAATTGGGAGCGGTTGGACAAAACAAGGTTCCATGTGATTGGAGCTATTCTCTTCACTGCCCAA
107775 T A CATGTATGCCTAACTGGGGCGAGAGGTTCATGTTCGTGATGGCGAGCTTTTGCATCACGTCTATCCAGCATGTGCAGTTCACACTGAATCATTTCAGCGG[T/A]GACGTGTATGTAGGGCAGCCGAAAGGGAATGACTGGTTCGAGAAACAGACAGCAGGAACGGTTGATATCTCATGCTCAACATGGA
107787 G GA CATTGGTAACATCATCGCCGCTAATCAAACCTTAACAGATTCTTCCTCAGTTACCCACATTCTTTCACTCCTAACATCAAATCTGTCAACCCCTGCTGAA[G/GA]AATAAAAAAAGTGTTTGTTTCAGATATGGAAGATCACGAGAAGCGATGTTTGCCCAAAGAGGGTCTGTTTTATAAATTGGAGAAAGTT
107787 A G CATGGGTTTTGAAGTAGACACTTCCAGCCCATTGTATAAGAGCTTTCGTCTTAAGGGGTTAGGTCATTCATATAATCAAGGAGAGAAGGTTGACAGTTCC[A/G]AATTTGAGACAGACCCTGGCTCACGTACAAATTCAAACAATTGCGGTACTAATCTAAAAAGTGTGTACCGATGTAAAAAATGTCGAC
107791 A G CTTCCGGCCTGGCCCACACCTTCTCGTCGTGGGTAATCCCCCACATGTTCACCATCGCCGTCGTGCCCGCCGGCACCACCATCCCATTGCTCAGCTTAAC[A/G]TCGTCTGTTGACAGCCTGGCCCACGACAGCAGTGGGCCGGGCGGGTGGACTCTCAGCGTTTCCTTTATCACAGCCTGCAAATACGGC
107801 C T CAAAGCAATATCATGGAATCGTGCGCCGTAGACAGGCTCGTGCTAAAGCAGAGATGGCAAATAAACTCATCAGAGTTAGGAAGCCATACCTCCACGAGTC[C/T]AGACATCGCCACGCTATGCGCCGTGAAAGAGGAAGCGGAGGTCGTTTCCTAAACACCAAAAAGGAAAGCATCAAGCAAAACCCA
107801 T C CTAAAGCAGAGATGGCAAATAAACTCATCAGAGTTAGGAAGCCATACCTCCACGAGTCCAGACATCGCCACGCTATGCGCCGTGAAAGAGGAAGCGGAGG[T/C]CGTTTCCTAAACACCAAAAAGGAAAGCATCAAGCAAAACCCATCGAGAGACGAAAACACCCACAACGCACAGTTCACCAAATCAC
107801 G A CCACGCTATGCGCCGTGAAAGAGGAAGCGGAGGTCGTTTCCTAAACACCAAAAAGGAAAGCATCAAGCAAAACCCATCGAGAGACGAAAACACCCACAAC[G/A]CACAGTTCACCAAATCACCAAACTCCGTCCTCCACCATACCAACAGCGGAAACCTCTACTCCGGTAGGACCTCAGGATCTGAAAT
107801 G A AAAACCCATCGAGAGACGAAAACACCCACAACGCACAGTTCACCAAATCACCAAACTCCGTCCTCCACCATACCAACAGCGGAAACCTCTACTCCGGTAG[G/A]ACCTCAGGATCTGAAATCTCCACCATCTATTCTCGAGACGACTCCGAGCACTTCAACTTCGGCGACCACCTCCATCCGTCCATCTACA
107801 G T CTCCACCATACCAACAGCGGAAACCTCTACTCCGGTAGGACCTCAGGATCTGAAATCTCCACCATCTATTCTCGAGACGACTCCGAGCACTTCAACTTCG[G/T]CGACCACCTCCATCCGTCCATCTACATGATGGGCGGAGGAGGGGAGCTTCTCAAAGTTTGACGGTGTTCATTAGCTTGGGGATTCGG
107801 T C TCGAGACGACTCCGAGCACTTCAACTTCGGCGACCACCTCCATCCGTCCATCTACATGATGGGCGGAGGAGGGGAGCTTCTCAAAGTTTGACGGTGTTCA[T/C]TAGCTTGGGGATTCGGGTCACCTGTCCCCAAGGTTTTAGACAACCAGAGAAAAGGAAATGGTTCTTTCTGGCTGTTTGAAGGCAAA
107801 T C GAGCACTTCAACTTCGGCGACCACCTCCATCCGTCCATCTACATGATGGGCGGAGGAGGGGAGCTTCTCAAAGTTTGACGGTGTTCATTAGCTTGGGGAT[T/C]CGGGTCACCTGTCCCCAAGGTTTTAGACAACCAGAGAAAAGGAAATGGTTCTTTCTGGCTGTTTGAAGGCAAATCATTCTTGGCTTA
107801 G A CTTGGGGATTCGGGTCACCTGTCCCCAAGGTTTTAGACAACCAGAGAAAAGGAAATGGTTCTTTCTGGCTGTTTGAAGGCAAATCATTCTTGGCTTATCC[G/A]CATTCCGGGCTTTTCGTCTTTTCGATCCCTCCCCTTTAGGGCTTCTTATAAGATGAAGGTTCTTTCTGTGGAAAAAAACGACTTAAATA
107801 G A TCGGGTCACCTGTCCCCAAGGTTTTAGACAACCAGAGAAAAGGAAATGGTTCTTTCTGGCTGTTTGAAGGCAAATCATTCTTGGCTTATCCGCATTCCGG[G/A]CTTTTCGTCTTTTCGATCCCTCCCCTTTAGGGCTTCTTATAAGATGAAGGTTCTTTCTGTGGAAAAAAACGACTTAAATATTTATAGCT
107801 AC A GCAAATCATTCTTGGCTTATCCGCATTCCGGGCTTTTCGTCTTTTCGATCCCTCCCCTTTAGGGCTTCTTATAAGATGAAGGTTCTTTCTGTGGAAAAAA[AC/A]CGACTTAAATATTTATAGCTTGTTATTTGTATTGTGTGTCGGAAACTTAACTTGTGTGTGCAGTGTCTGAAGGCGCTGCCTATTTGCTTT
107803 C A TAATGATCAATGGGGACTCTACATTATTTTCTATCCGAAGCTCGCCGACGCCCATTTCAAGCTCTAACCCTCGTTAGATCATTCTTTTCTTATTCGTCTT[C/A]TCATCCGTCTGGGAATCTTCAGTCTTTCAGGTTTTCCTTCGGTGCGCCCTCGAGAAAGCTCATTAATTCCTCTTCTGCCTGTAAGGAGTTC
107803 T C TACATTATTTTCTATCCGAAGCTCGCCGACGCCCATTTCAAGCTCTAACCCTCGTTAGATCATTCTTTTCTTATTCGTCTTCTCATCCGTCTGGGAATCT[T/C]CAGTCTTTCAGGTTTTCCTTCGGTGCGCCCTCGAGAAAGCTCATTAATTCCTCTTCTGCCTGTAAGGAGTTCTGTACTTTAGAATCACGACC
107803 G A TCATTAATTCCTCTTCTGCCTGTAAGGAGTTCTGTACTTTAGAATCACGACCAAGTGAAAGCCAGATTCCAACTGAGCTGCTGAAAAAGCAGACAAACTT[G/A]AAACCTGATCGGACTGTAGGGCAATGTCAAGACCTTGTAACAAATGTAACTAATTTTGAAAATGAAGACAAAGGTCTTATCGTCTTGG
107803 A G AAGACAAAGGTCTTATCGTCTTGGCTGGTGATGTTTTTGATGTGCCAATCAGGAAGGACATAGTACACCGAGTTGTGAGGTGGCAACTTGCCAAGCGACA[A/G]CAGGGAACACATTCAACTAAAAGAATAAGTGAAGTTAGTGGCACTGGTAAAAAACCATACAATCAGAAGGGTACTGGAAGAGCA
107803 T C CAACTAAAAGAATAAGTGAAGTTAGTGGCACTGGTAAAAAACCATACAATCAGAAGGGTACTGGAAGAGCAAGGCATGGGACACTGCGGGGTCCACAGTT[T/C]AGAGGTGGTGCTATTGTGCATGGGCCTAAGCCACGCAGTCATGCATTCAAACTTAATAAGAAGGTCCGACGTCTTGGACTGAAG
107803 C T AAAAACCATACAATCAGAAGGGTACTGGAAGAGCAAGGCATGGGACACTGCGGGGTCCACAGTTTAGAGGTGGTGCTATTGTGCATGGGCCTAAGCCACG[C/T]AGTCATGCATTCAAACTTAATAAGAAGGTCCGACGTCTTGGACTGAAGATCGCTTTATCAGCTCGAGCAGCAGACGGAAAACTTC
107803 C G CTATTGTGCATGGGCCTAAGCCACGCAGTCATGCATTCAAACTTAATAAGAAGGTCCGACGTCTTGGACTGAAGATCGCTTTATCAGCTCGAGCAGCAGA[C/G]GGAAAACTTCTGGTATTTGAGGACCTCGAGCTTCCTAACCACAAGACAAAGAACATTGTGAAGTATGTTTCACAAATGGAGAACAC
107803 T A GACGTCTTGGACTGAAGATCGCTTTATCAGCTCGAGCAGCAGACGGAAAACTTCTGGTATTTGAGGACCTCGAGCTTCCTAACCACAAGACAAAGAACAT[T/A]GTGAAGTATGTTTCACAAATGGAGAACACAAAGAAGGTTCTGTTGGTGGATGGCGGCCTTATAAACGACAATCTCAAATTTGCCAC
107803 C T TGCCATCAATTGGTCTGAATGTGTATAGCATCCTTCAACATGATACGCTTGTAATGACACGCGATGCTATTGATAAGATTGTCACTCGAATGCATACTCC[C/T]ATCAATCGCTGATCAAGTGCATGGCATGGCATTTCAACGTTGCATTAATTTCACGACTTATTTGAGTTAAACAGAACCCAACCAAACGA
107803 T TA ATTGATAAGATTGTCACTCGAATGCATACTCCCATCAATCGCTGATCAAGTGCATGGCATGGCATTTCAACGTTGCATTAATTTCACGACTTATTTGAGT[T/TA]AAACAGAACCCAACCAAACGAGGATGCCAATGCCCAAAGTAACCGGATTTGCTACCTGAGCTCTGGCATTTGTGTATGCGCAGTTGA
107803 C T AATTTCACGACTTATTTGAGTTAAACAGAACCCAACCAAACGAGGATGCCAATGCCCAAAGTAACCGGATTTGCTACCTGAGCTCTGGCATTTGTGTATG[C/T]GCAGTTGAGTTTTCAAGAAAGACACAATATTCACATATCATTTACTGTATTTAGGCCATGTATCTGAAAACCGTGGTGGAGCTTTGAG
107803 T A AGTAACCGGATTTGCTACCTGAGCTCTGGCATTTGTGTATGCGCAGTTGAGTTTTCAAGAAAGACACAATATTCACATATCATTTACTGTATTTAGGCCA[T/A]GTATCTGAAAACCGTGGTGGAGCTTTGAGTGTTCATTTTGATTCTTTTTAATCCTAGATAAATATTTGCTGGGAACTTTTTTGTCTCAGC
107807 C T ACGCTTTCTTCTTCCACTCTCTCCTCTCTATACCTAGATTTTCCCAGTCCTGCATCTCAACTCGCTTGTGCTTCTTTCTAAGCCCTTCACTTTCCAGATC[C/T]AATACTTCTAGATCCACACCTCTCACTTCCAACTGCGAGTCACGCGATGTCCCCTTCTGCCTCACTCCTATTTTCTCCTTTGTGCGTCTGGCAT
107807 A G CGCTTTCTTCTTCCACTCTCTCCTCTCTATACCTAGATTTTCCCAGTCCTGCATCTCAACTCGCTTGTGCTTCTTTCTAAGCCCTTCACTTTCCAGATCC[A/G]ATACTTCTAGATCCACACCTCTCACTTCCAACTGCGAGTCACGCGATGTCCCCTTCTGCCTCACTCCTATTTTCTCCTTTGTGCGTCTGGCATG
107807 G A TCACTTTCCAGATCCAATACTTCTAGATCCACACCTCTCACTTCCAACTGCGAGTCACGCGATGTCCCCTTCTGCCTCACTCCTATTTTCTCCTTTGTGC[G/A]TCTGGCATGTCTTCTCGCGACTCCGCCGCTACCACTTATAAAGCCCTAAATCTGTCGTTTTGATCTTCTCTCAATCCACGGTTTTTGCGAGC
107807 C T TTTGACTATGTTTGTTAGCATGTTGTTGGTGATTCAATTTCCCTTTTGTATGAATTAGTTTGTTGGGTGGAGTTTATGCCGTTATATTGACTTGTGATGT[C/T]GTTTTGTCTGTTGTGTTTCCGAGAATTGGCGATTTAATTTTTTGGGTTGCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107807 AT A TTTCCCTTTTGTATGAATTAGTTTGTTGGGTGGAGTTTATGCCGTTATATTGACTTGTGATGTCGTTTTGTCTGTTGTGTTTCCGAGAATTGGCGATTTA[AT/A]TTTTTTGGGTTGCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCAC
107807 T C TGTGATGTCGTTTTGTCTGTTGTGTTTCCGAGAATTGGCGATTTAATTTTTTGGGTTGCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCT[T/C]AGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCA
107807 A G GTGATGTCGTTTTGTCTGTTGTGTTTCCGAGAATTGGCGATTTAATTTTTTGGGTTGCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCTT[A/G]GTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAA
107807 A G TAATTTTTTGGGTTGCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATA[A/G]AATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGA
107807 C A GCCTTGCCTGAGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTA[C/A]GGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGT
107807 A G AGGTTTGGAATGTGTGTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTG[A/G]TGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAG
107807 A G GTGTGTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTG[A/G]TGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGC
107807 A G GTTGGTTGGCGTTTGTCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGT[A/G]TTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGCATCA
107807 G A TCTTAGTACTATCGTTTTCAGCTACCATCCACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTC[G/A]TGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGCATCATGTGAGTCCCAACGA
107807 G A ACCATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGC[G/A]ATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGCATCATGTGAGTCCCAACGACAAAATACACGCTTCTTTGCCTGCTCATGG
107807 C A ATCCACGACGATAAAATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGAT[C/A]CGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGCATCATGTGAGTCCCAACGACAAAATACACGCTTCTTTGCCTGCTCATGGAAT
107807 C T AATTTCTATGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTC[C/T]TGTTCTTGGTTAGTTTAAACGTGCATCATGTGAGTCCCAACGACAAAATACACGCTTCTTTGCCTGCTCATGGAATCAAATTTTAATTGAA
107807 G T TGCTACGGTGGTTTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTT[G/T]GTTAGTTTAAACGTGCATCATGTGAGTCCCAACGACAAAATACACGCTTCTTTGCCTGCTCATGGAATCAAATTTTAATTGAAAGGTGTG
107807 C A TTGATGCTTGTCTGATGTATTCTTGCAACATTCGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAA[C/A]GTGCATCATGTGAGTCCCAACGACAAAATACACGCTTCTTTGCCTGCTCATGGAATCAAATTTTAATTGAAAGGTGTGTAAACATGAGAT
107807 A T CGTGCGCCTACTACCTGCATCATTTTATAGCGATCCGATTTGGAGCTCCTGTTCTTGGTTAGTTTAAACGTGCATCATGTGAGTCCCAACGACAAAATAC[A/T]CGCTTCTTTGCCTGCTCATGGAATCAAATTTTAATTGAAAGGTGTGTAAACATGAGATGAATTACTTGACCCGAGGACCTAGACCAAAT
107821 A G GACCCTTCAGGGCTGGATCCACCATCTTGTCCAGTGCATCGATATCGTGTAGCTGTGGAGTTGCCCATCTCACCAATGATTGCTCAGACCATGATCTTGC[A/G]CTATCAAAGGGCTTCCGTCCAGTTAAAAGCTCAAGCATGACGACACCAAAGCTGTAAACGTCACTCTTTATTGTGTACTGATCAGACA
107821 T C TGGGTAAGGCAGAAGAGTTTATTTTCTTTACAGCGAGAATCTTCCCATCGTTGAACTGAGCTCTAAAGACACGTCCAATGGAACCTTGTCCGATGAGGTT[T/C]TCTGCACTGAAACTATCAGTGGCAACTTGAAGATCTGCTACTGAGTATACAGTTGCTTTTACTGCAGGAGCTTTTTTTG
107827 A G CTGCGCAACAACAACCAGCGTACCCTAACAAAGATGAACTGGAAACCGTGCTGAAGATCATCGAATCATTCCCGCCAATCGTCTTCGCTGGTGAGGCCAG[A/G]AAGTTGGAGGAGAAATTGGGCGATGCGGCGATGGGAAACGCGTTTTTGCTGCAGGGCGGTGATTGCGCCGAGAGCTTTAAGGAG
107827 A G CAAAATTGATAGAGATTTTGAACCCACATAATAAGCCTGGGAGAATAACAATAATTACAAGGATGGGGGCAGATAATATGAGAGTGAAGCTACCTCATCT[A/G]ATAAGAGCGGTACGTGGAGCAGGCCAGATTGTTACATGGGTTAGCGATCCTATGCATGGTAACACCATCAAGGCACCGTGTGGCC
107827 T C CACCGTGTGGCCTCAAAACTCGACCTTTTGATGCTATTCGGGCTGAATTGAGGGCATTCTTCGATGTGCATGAGGAGGAAGGCAGCCACCCAGGTGGTGT[T/C]CACCTAGAGATGACAGGTCAAAATGTGACGGAGTGCGTTGGAGGGACCAAAACGGTCACTTTTGATGACTTGAACAGTCGCTACC
107829 C T GTGGAAAAGTCTCATTGTTTAACATGATGACATTCAAGGTAATGACAACTTTCATGCCTCCCCCTCCTGCAGCGACCTTCTTAGCATTTCATCCTCAGGA[C/T]AATAATATTATTGCCATTGGGATGGACGATTCCTCCATTCAAATATATAACGTCAGAGTTGATGAGGTTAAAACCAAGCTCAAAGGTCA
107829 A G CGATGGATCAGTCAATGTTATCGAACCATCTGATGCGGATCTCAAATGGGGGCCGCCGCCTCCTTCACAGCCCCAAACACAAGAAAACGGAGGAACATCC[A/G]CCCTCCCTTCGATTTCATCGAACCCTTCTCTTAGTAGTCAAGCTTCCGAGCCTCCTCCAAGGTGACGGATGTCACGAGAAGTAATAT
107833 G A CATTACGATCACTTCTGATGAGGTTCAGTTCATCAGGGATCGTAGAATCATAGAGCCTTATGCCTGGGTTCTCCGCATAACACACGTAGTAACATGCTAC[G/A]CAAGCGTTTGGCAACGCCATAGCAATCCTTGTCATGAGATAGCCAACAAAGAAGGCAAGAAGTGAAACCGTAGCCGTATAATGCTTA
107833 T G CAAAGAAAGACCCTAAGCTCGCACTCCCTAAGTTGTAGGACATGGCCCTTTGAAAGCAAAACCGTGTACTGGACTGCATGCCTCTCAAGTAATACAAAGA[T/G]ATCACTCTACTAACAGTTAAATTTATGACATTCCTCATGACTTCAACCGTCCATGCCAAACTCAGAATCAGCCCCAAAATGGTCAATG
107833 A G AGTTGTAGGACATGGCCCTTTGAAAGCAAAACCGTGTACTGGACTGCATGCCTCTCAAGTAATACAAAGATATCACTCTACTAACAGTTAAATTTATGAC[A/G]TTCCTCATGACTTCAACCGTCCATGCCAAACTCAGAATCAGCCCCAAAATGGTCAATGGAGGGTAGTAAAAGTTCTGTGCACCGATCA
107833 A T TAACAGTTAAATTTATGACATTCCTCATGACTTCAACCGTCCATGCCAAACTCAGAATCAGCCCCAAAATGGTCAATGGAGGGTAGTAAAAGTTCTGTGC[A/T]CCGATCACAGCAAAGCACCAAACCGTAATGTACAAAAACCCGACCCCCATGACTAGGTAAGCGGGTCCGTTCAAGTCGCGGAACTTC
107839 C T TATCTGAAAATGAGGTTATAACCCAAATCTGGGTATTGCTTCTGGGAGGCCTTTGTCTAGCAGGCTTACTAGATGTGTGGGCAGGTCATGATTTCCCTAC[C/T]ATCTTCTACCTAGCTCTTGGTGGATCATTACTTTCTTATATATATTCTGCTCCACCCCTGAAGCTTAAACAAAATGGGTGGATTGGAAA
107841 G A TGAAACCACGTCCACTATCCCTATCATAGTGTCTACCCCCTCTCCCACGATAAGGAGGCATGCTCTTCGAATTGTAGGGAGGTGACTTGCTCCTCTTCCT[G/A]GCCCACCGATCTCTAGCAAATGGAGGCAGCTCTCGCCTATCATATCCTTCCCTTCTTGTAGGAGAAGCAGTTCGCCATTCATCGTCCGA
107843 ATATAATAAG A CCTCATCACTGAAAAAATAACATAAAAGCTGCACAAAGCCTTCAACCAAAATATGAATATTGACATCTTCGTTGTTACGATATGCACCCATCCACAGTGT[ATATAATAAG/A]TATAATAAGTAAAGGGAGGGATCTGAATTGTTTGCTAGTGACGGAATGTTCTTACAACTTGGTCGATTCTTCTGCGGCA
107843 A G GAACTCGTTTCTGCATATCTATTCGACGATTTCTTTCCGCGATGTACTGGACTGTATGCTTTACTAGAAGATAGACCCCATAAGCTGTGAATCCCATAGA[A/G]GCATATTTGTACCACCTCGCCCATTTTCCAAGGTTAGCAATTAAATCATCAATATTCTTCGGAGTTACATAAAATGGCCCTTTATGGGGT
107843 T C TATGGGGTTTCTGAATTCGAACTGTTCCAATATCATCTTTTATAGCCTCGCCAACCACGGTCAAAGAAGTACCAGTAGGAAGTACTTTTTCAGTCCTCTT[T/C]ACTCCAAGCATCTTTAAACCTTGAAGGTAATCCAATGTTCCACGGACAAGAGATCTCCCTGATTCCTCAAATACTTCACTTGCAACAGTT
107843 G C CCTCGCCAACCACGGTCAAAGAAGTACCAGTAGGAAGTACTTTTTCAGTCCTCTTTACTCCAAGCATCTTTAAACCTTGAAGGTAATCCAATGTTCCACG[G/C]ACAAGAGATCTCCCTGATTCCTCAAATACTTCACTTGCAACAGTTAGCACCATTCCTGAAGCACTTCGTGCCCCCAAAACATATACCCG
107849 A G AGCTTGGGCATGTGCTAAACGATCCTAGCACTCTCAGGCAGACACTAGAAGCTGCAAGGAATCCTGAGATCATGAGGGAGATGATGCGTAACACTGACAG[A/G]GCAATGAGCAATATTGAATCTTCTCCAGAAGGCTTCAACATGCTTAGGCGAATGTATGAAACCGTTCAGGAACCGTTTCTGAATG
107849 T C CTGTTCCGAATGCCAATCCACTGCCTAATCCATGGGGAAATGCTGCGGGTACACCGACAAGCAACGCTAGGTCTACTGCTGCCAATTCAGAAACAGTGGC[T/C]CCTGGAATTGCTGGGTTAGGCGGGCTTGGGTTACCAGGGTTGGGTAGTATGGCTGGTGGCATACCGGACCCTAGCATGCTTAATC
107849 G A CTGCCTAATCCATGGGGAAATGCTGCGGGTACACCGACAAGCAACGCTAGGTCTACTGCTGCCAATTCAGAAACAGTGGCTCCTGGAATTGCTGGGTTAG[G/A]CGGGCTTGGGTTACCAGGGTTGGGTAGTATGGCTGGTGGCATACCGGACCCTAGCATGCTTAATCAGGTTATGCAAAACCCGGCC
107849 A C CGTCTAATTTGCCTCCAGAAGAATTATATGCTACACAGCTAACACAGCTCCGAGAAATGGGTTTCTTTGATACCCAAGAAAACATCCGTGCTCTTAGCGC[A/C]ACTGCTGGAAACGTTAGTGCTGCAGTTGAAAGGTTGTTGGGCAATCTCGGTCAATAAGATAGATAACTCAGAGAAAAAAAAAAACTA
107855 G GACGAGC CACGTTCGATTTCGGAACTTTCAGAGAACCCATGGCGGCACATAACCCGTGGTTAGGATTAGGGTTAGGGTTCGAGATCGAAGATGATAACGAGGACGAG[G/GACGAGC]ACGAGCACGAGCACGAGCACGAGCGCGGTGCTAACATCAGCCGTGAGCCGCAGCAAGATACTGGTCTTCGTATTGCA
107855 T C ATCCAACCCTGAATCCGGAGACTGATTTCCGGTCCTGTTGGGGCTTGGAAGAGGATTTGGAATGGGAAGAAGTGGATGGATGCATCGACGAGAGGGACTT[T/C]TTGAGCACGATGGTCGGCCAATATCAAGACGAAGAAAGTGATGAAGAAGAGGAAGCCAGGAACTGGGAAATCCTATTATCCAT
107857 A T CAGTGTTCCAGAGTTGTCTTTGTCCGCAACCTTAAAGATCTCAGATACATCATCCATGACTTTTCTTTGGCTTATCGTGGCACAGTCTCCAAGTGCATAC[A/T]CTCCGTCACATCCATGCACTCTGAGCCATTCATCAGTTGCTAAGACACGTCTATTCCCCTGACCAATCTGCTTCATTAGATCCAACATGAC
107857 A G ATGACTTTAAATCCTGTTTTGACATCAATACCATCTCTTCGAAATTTTTCTAGAGCAAATTGTGTGATCCTTTTGTCAAACATGGTCAAAATATTTTCTG[A/G]TGCTTCAATAACTGAGATCTTTACTAAGTCTCGAACTGTGGGATAGAGCTTAGCTAAATCTTCAGATACAAAATCATGCAGCTCTGCAGC
107859 A G GAGTTGTCAATGCCTCCACCTCATCAAAGAAAAGTATGCAGGGTGAGCATGTTCTTGCACGGGAAAATATTGTCCTAATTGCTAGCTCACTCTCTCCAAC[A/G]TATTTATTTAGAATTTCAGCAGCCTTGATATGAATGAAATTGGCGCCTGATTCATTTGCAACAGCTTCGGCAATTAATGTTTTTCCACA
107859 A G CTTTCCTTAATGATTTCAGACCACCTACATCATCCCAGGTGGTCTTAGGGACCAATGAAAAACCTTCCCTGGTGGAAGATGGTTGGGTCATTTTAACAGC[A/G]TCCTCAAAATCAGACATGGAAATGCAAAGATTATCCATTTCATCTTGAGACCATGGTGGCTTCCACCAATGATCAATAATTTTCCCTTT
107859 G A AACTCCTAATGCAATTTCTCGGGTAAATCTTCCAGGTCTTCTCAACGCTTGATCAATAACATCAGGCCTATTTGTTGCTCCAATTACCAGAACATGTTTA[G/A]GTTTTGTTTCACAATTTTCACCTTCTGAATTGTGGTCATTTGATTGAGTTGGCTGATAAGATTCATCCATGCAAGTCATAAGTTGTGTAAC
107859 G T GGTCTTCTCAACGCTTGATCAATAACATCAGGCCTATTTGTTGCTCCAATTACCAGAACATGTTTAGGTTTTGTTTCACAATTTTCACCTTCTGAATTGT[G/T]GTCATTTGATTGAGTTGGCTGATAAGATTCATCCATGCAAGTCATAAGTTGTGTAACTATCCTTCTTTCCATTTCTCTTTGCGAGTTTTCCC
107861 C A AATTCGAAAATGGGCAATACAGATCCATACGATACCGCTTTCACTATTAAGCAGGTATACA[C/A]CAAATTAGCAACAGTGAACATTCTCTTAGTAAGTACATGAATTTTGATATCATATCAATTACACCATGGAAATGGCAGGCAATAAAACGTCCCCGTCGAC
107861 T C AATTCGAAAATGGGCAATACAGATCCATACGATACCGCTTTCACTATTAAGCAGGTATACACCAAATTAGCAACAG[T/C]GAACATTCTCTTAGTAAGTACATGAATTTTGATATCATATCAATTACACCATGGAAATGGCAGGCAATAAAACGTCCCCGTCGACCTCTTTGTCTTTGCA
107861 C T AATTCGAAAATGGGCAATACAGATCCATACGATACCGCTTTCACTATTAAGCAGGTATACACCAAATTAGCAACAGTGAACATTCTCTTAGTAAGTA[C/T]ATGAATTTTGATATCATATCAATTACACCATGGAAATGGCAGGCAATAAAACGTCCCCGTCGACCTCTTTGTCTTTGCATTTCTTCAGAAAC
107861 C A CTTTCACTATTAAGCAGGTATACACCAAATTAGCAACAGTGAACATTCTCTTAGTAAGTACATGAATTTTGATATCATATCAATTACACCATGGAAATGG[C/A]AGGCAATAAAACGTCCCCGTCGACCTCTTTGTCTTTGCATTTCTTCAGAAACATTAGTTGCCTGCGCAGGTGTAGAACCTCCTCCTGAAG
107861 A G TCGACCTCTTTGTCTTTGCATTTCTTCAGAAACATTAGTTGCCTGCGCAGGTGTAGAACCTCCTCCTGAAGTACATCGGGAAGATTCTGAAATGAAACTA[A/G]AGCACGAATTTCATCAAGCAGCTTCTTATTGCTGATATCGAACCAAGAGTTGGTAAACAAGGCTAGTGAAAGAATAGTTAATACGTCA
107861 G A ATGAAACTAAAGCACGAATTTCATCAAGCAGCTTCTTATTGCTGATATCGAACCAAGAGTTGGTAAACAAGGCTAGTGAAAGAATAGTTAATACGTCACC[G/A]TGTCCCGGGTGAGCTATAGCACAGGAAGAAGAAGAACCTGCATTGCAACCATGTGATTTTGATGGCGATGTGGGTACCAACATATC
107861 T TC AAACTAAAGCACGAATTTCATCAAGCAGCTTCTTATTGCTGATATCGAACCAAGAGTTGGTAAACAAGGCTAGTGAAAGAATAGTTAATACGTCACCGTG[T/TC]CCCGGGTGAGCTATAGCACAGGAAGAAGAAGAACCTGCATTGCAACCATGTGATTTTGATGGCGATGTGGGTACCAACATATCAA
107863 T A TGTGTTATGGCTGGTGCCTGGATTAGTGTTAGCTGGTGTTGGAGAGGCATGGCATTTTCCGGGGTTTCTGGAATTTTATTATAGGGAGATCCCTGAATCC[T/A]TAAGTAGTCTGTCTACTGGAATGATAGCGTTGGTGGCTGCGTGTGGGTTTTTTGCTAGTGCTTCTCTGATTGAATTGGTTCGCAATG
107863 G A GGCTGCGTGTGGGTTTTTTGCTAGTGCTTCTCTGATTGAATTGGTTCGCAATGTGACTCCTTGGTTGAAGAATGATTTGAACGAGTCTAGACTGGATTGT[G/A]TTTATTGGATGGTTTATGCAGTTGGAGTATTGAATTTGGTCTACTTTCTGGTCTGCGCTAAGTTTTATAAAAAGAGACTTGTATGAAT
107867 T C TCTTCTTTTGCCAACTCTGGCATGTAGGCAGAGTCTCCAATTACAATTATCAACCTAATGGCCAGGCGCCTGTATCAAGCACTGATAGAGGGATCCCACC[T/C]CAGCTACAACATGATGGCAACGTCTTTGAGTATTGTCCCCCTCGGAGATTGGCTTCCGATGAACTACATCTAATTGTCGAGGAGTATA
107867 T A ATGGCAACGTCTTTGAGTATTGTCCCCCTCGGAGATTGGCTTCCGATGAACTACATCTAATTGTCGAGGAGTATAGACTTGCTGCAAGAAATGCCATTGA[T/A]GCTGGTTTTGATGGAGTAGAAATACATGGTGCACACGGATATCTGATCGAGCAGTTCATGAAAGACAGCGTGAACGACCGAACAGA
107867 T C CCGATGAACTACATCTAATTGTCGAGGAGTATAGACTTGCTGCAAGAAATGCCATTGATGCTGGTTTTGATGGAGTAGAAATACATGGTGCACACGGATA[T/C]CTGATCGAGCAGTTCATGAAAGACAGCGTGAACGACCGAACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACT
107867 G A ATGAACTACATCTAATTGTCGAGGAGTATAGACTTGCTGCAAGAAATGCCATTGATGCTGGTTTTGATGGAGTAGAAATACATGGTGCACACGGATATCT[G/A]ATCGAGCAGTTCATGAAAGACAGCGTGAACGACCGAACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACTTGA
107867 C T AGTATAGACTTGCTGCAAGAAATGCCATTGATGCTGGTTTTGATGGAGTAGAAATACATGGTGCACACGGATATCTGATCGAGCAGTTCATGAAAGACAG[C/T]GTGAACGACCGAACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATCTGCTGTGGCAGACGA
107867 G A GCTGGTTTTGATGGAGTAGAAATACATGGTGCACACGGATATCTGATCGAGCAGTTCATGAAAGACAGCGTGAACGACCGAACAGACGACTACGGTGGAA[G/A]CCTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATCTGCTGTGGCAGACGAAGTTGGGCCTGACCAGGTTGGGATCCGACTA
107867 T C ATCTGATCGAGCAGTTCATGAAAGACAGCGTGAACGACCGAACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATC[T/C]GCTGTGGCAGACGAAGTTGGGCCTGACCAGGTTGGGATCCGACTATCACCATATGCAAACGAGGTTGAAGCCTACGACTCGGACC
107867 A G GTGAACGACCGAACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATCTGCTGTGGCAGACGAAGTTGGGCCTGACC[A/G]GGTTGGGATCCGACTATCACCATATGCAAACGAGGTTGAAGCCTACGACTCGGACCCGGAAGGGCTTGGAATCTATGTAGTGGAG
107867 C A AACAGACGACTACGGTGGAAGCCTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATCTGCTGTGGCAGACGAAGTTGGGCCTGACCAGGTTGGGATC[C/A]GACTATCACCATATGCAAACGAGGTTGAAGCCTACGACTCGGACCCGGAAGGGCTTGGAATCTATGTAGTGGAGCGACTAAATGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107867 A C CTTCTCAACCGCTGTCGCTTCCCACTTGAAATCGTATCTGCTGTGGCAGACGAAGTTGGGCCTGACCAGGTTGGGATCCGACTATCACCATATGCAAACG[A/C]GGTTGAAGCCTACGACTCGGACCCGGAAGGGCTTGGAATCTATGTAGTGGAGCGACTAAATGAACTGAACATATTGTACGTGCACA
107867 A G CAGACGAAGTTGGGCCTGACCAGGTTGGGATCCGACTATCACCATATGCAAACGAGGTTGAAGCCTACGACTCGGACCCGGAAGGGCTTGGAATCTATGT[A/G]GTGGAGCGACTAAATGAACTGAACATATTGTACGTGCACATGATAGAACCGAGGATGCATGTCGTGGATGGAAGAATGAAAATC
107867 A G ACACGTTCATTGCGGCAGGTGGGTATGATAAGAAGGATGGAGATAGGGTGGTGGACGAAGGGTATACGGATTTGGTTGCGTTTGGAAGGTTGTTCTTGGC[A/G]AACCCGGATTTGCCTAAGAGGTTTGAGGCGGGTGCGGAGTTGAATAGGTATAACAGGTTGACCTTTTATACTCCGGATCCGGTT
107867 G A TCATTGCGGCAGGTGGGTATGATAAGAAGGATGGAGATAGGGTGGTGGACGAAGGGTATACGGATTTGGTTGCGTTTGGAAGGTTGTTCTTGGCAAACCC[G/A]GATTTGCCTAAGAGGTTTGAGGCGGGTGCGGAGTTGAATAGGTATAACAGGTTGACCTTTTATACTCCGGATCCGGTTGTCGGG
107867 C G ATACGGATTTGGTTGCGTTTGGAAGGTTGTTCTTGGCAAACCCGGATTTGCCTAAGAGGTTTGAGGCGGGTGCGGAGTTGAATAGGTATAACAGGTTGAC[C/G]TTTTATACTCCGGATCCGGTTGTCGGGTATACGGATTACCCGTTCATGGAGGAGAGTACTTCTGCTGTTTCCGCCTGAGCATATAT
107867 CATAT C AATAGGTATAACAGGTTGACCTTTTATACTCCGGATCCGGTTGTCGGGTATACGGATTACCCGTTCATGGAGGAGAGTACTTCTGCTGTTTCCGCCTGAG[CATAT/C]ATATATACTTGGATGTTGTGGCATCTGGAAGATGAATTGTAGCTGGGGAATTGTAAGAATTGTGAAAGAGTGTGTATTGCTTT
107867 A G TTATACTCCGGATCCGGTTGTCGGGTATACGGATTACCCGTTCATGGAGGAGAGTACTTCTGCTGTTTCCGCCTGAGCATATATACTTGGATGTTGTGGC[A/G]TCTGGAAGATGAATTGTAGCTGGGGAATTGTAAGAATTGTGAAAGAGTGTGTATTGCTTTTGTAATGTGTCATGTTTCATGTTGTTG
107867 GA G TCATGGAGGAGAGTACTTCTGCTGTTTCCGCCTGAGCATATATACTTGGATGTTGTGGCATCTGGAAGATGAATTGTAGCTGGGGAATTGTAAGAATTGT[GA/G]AAAGAGTGTGTATTGCTTTTGTAATGTGTCATGTTTCATGTTGTTGCTATGGAAGTTTTAAATGCCTTTTCAACTATCATCTGGTCA
107867 T C GGAGAGTACTTCTGCTGTTTCCGCCTGAGCATATATACTTGGATGTTGTGGCATCTGGAAGATGAATTGTAGCTGGGGAATTGTAAGAATTGTGAAAGAG[T/C]GTGTATTGCTTTTGTAATGTGTCATGTTTCATGTTGTTGCTATGGAAGTTTTAAATGCCTTTTCAACTATCATCTGGTCATCAAAGAG
107867 T C ATCTGGAAGATGAATTGTAGCTGGGGAATTGTAAGAATTGTGAAAGAGTGTGTATTGCTTTTGTAATGTGTCATGTTTCATGTTGTTGCTATGGAAGTTT[T/C]AAATGCCTTTTCAACTATCATCTGGTCATCAAAGAGATGGTAAGTTTGTTAAGATAACTTTGTTCGCTAACATAAACCCGTTTTGGGTC
107871 A G GAAACTAAAAGACTTGTTACGGCGAGACATGATGACACGTGTTACGGGTACGACCGATATCATATGCCTTTCACAAATAACTCTGGAAGCAGGAGGTACA[A/G]CAGAGCGTTCTGCTATGATTTCTGAAGAAAATCTGTTCAGTAAATACGAATCTGCAAAATAGGCAGGCATGCACTGGTAAGCTTGC
107871 T C TCAACCCACGTGAAGCACACATTACACACTGCAGTTTGCCCGTTCCATTGCACATATTGCATATTGTGTCTGAACCATCTCTATGAGCTATCAATCCTCT[T/C]CCATGACATACGAGACATTGCGTCATTTGATTTGGCTTATAAAATCCAGGTTTCTGACCAGGATTACAAGTAGGACAGGGTATCTCTCCA
107871 G C AACCTGAGCATTTTTCTTTAGCTTCAGAATGAGGTATAGTCACCCTTATCTCTTTTTCAGGAACAAATAGTTGAGGAAATTCAGACCGAAGATCAATTTC[G/C]CATAATCCAGGTTCTTGTCCATTATCTTTTCCATCAAAATTTCCACCTTCATATGGCTCGGTTTCTTTCACAACTTCTCTTTCCTCTACGAA
107871 C A ATATGGCTCGGTTTCTTTCACAACTTCTCTTTCCTCTACGAAAGTTTCTAAAGTTCCAACATATACGTTGCAATCCTCAATTGCAGAAATACTCCATTTT[C/A]TAGCAGGTTGACTCGCCCAACAACAACGATGACCGACATGATCAATAAGTAGTTGACGTACTTCAACAGCATCTAATGCTGGCCTCACAT
107871 A G GTTGACTCGCCCAACAACAACGATGACCGACATGATCAATAAGTAGTTGACGTACTTCAACAGCATCTAATGCTGGCCTCACATGCTGATTTGGAGAAAA[A/G]CCACCATATAAATCACCACCATATCCTCCTTGATGTACAATAGCTTGATCTTGATAACGGTCAGATTGAACAGAAGGAGCGAGCAGG
107871 T C CAGGCCAGAATGAATGGACGGTGGATAGTAATTAGGAGGATTATGATCAGAGAAAACAGAAGCAGATCTGACTTCGTCAACGCTGACACCGTCGCCTCCT[T/C]TTGATGGAGTGTTGAATGACATCATCCTTCCGATGTACTGATAAGATTTTAACGAATCGTTATTGTCGCTAGCTTCATCTCCTCGCT
107871 A G TGGATAGTAATTAGGAGGATTATGATCAGAGAAAACAGAAGCAGATCTGACTTCGTCAACGCTGACACCGTCGCCTCCTTTTGATGGAGTGTTGAATGAC[A/G]TCATCCTTCCGATGTACTGATAAGATTTTAACGAATCGTTATTGTCGCTAGCTTCATCTCCTCGCTTCACGTCTGATAGTAGAGCTTG
107875 T C GACCACCAGAGCCCAAGCTGACCCATCCACTCTGCATCACCATGGCGCGAGACAGCCCACTCTCCACGTCGACCGCGATCCTCACCCTCCCCAACTTCAC[T/C]CTACCCACATTGACCCCACACGCGTGGGTCGTCCTTCGACCCATGTACACGGTCGCTATGAGGCTGACTTTCTTCAGCGTTTGGACGA
107875 C G TTTTGGTCGAGCGTGAAGATGAGGGGTGGGGGTAGGGAGGTGGGGTCGGGAGTGTCGGTGAGGGAGGTGACCGGACTCGGGGAGGAGGAGGAGGAGGGAA[C/G]GGCTATAAGGAGAGGGGTAGTTTGGGGATTTGACGTGGGATGGTCTTGGATATGAAGAGTGGCGAAGCATTGGATGGG
107875 A G GAGCGTGAAGATGAGGGGTGGGGGTAGGGAGGTGGGGTCGGGAGTGTCGGTGAGGGAGGTGACCGGACTCGGGGAGGAGGAGGAGGAGGGAACGGCTATA[A/G]GGAGAGGGGTAGTTTGGGGATTTGACGTGGGATGGTCTTGGATATGAAGAGTGGCGAAGCATTGGATGGGTGAAGGG
107877 C T AAGGGCTCGGATATGAAAGGCCAAGCATAAAAATTCCTGTGTCTGTTATGATGCCGATAGCCCGTCTGGTAGAGTTGACATACAAGATGTTTGCCAAGTA[C/T]GGTATGCGTGTACCTCAGCTGACTCCGTCGAGAATTAGGCTTCTTACATGCAACAGAACTTTCAGTTGTACCAAAGCTAGAGTTCAG
107877 T C CTGTGTCTGTTATGATGCCGATAGCCCGTCTGGTAGAGTTGACATACAAGATGTTTGCCAAGTACGGTATGCGTGTACCTCAGCTGACTCCGTCGAGAAT[T/C]AGGCTTCTTACATGCAACAGAACTTTCAGTTGTACCAAAGCTAGAGTTCAGATTGATTACGAACCCCTTATAACACTTAAGGAAGGTA
107877 TA T CCGTCGAGAATTAGGCTTCTTACATGCAACAGAACTTTCAGTTGTACCAAAGCTAGAGTTCAGATTGATTACGAACCCCTTATAACACTTAAGGAAGGTA[TA/T]AAAAAGGACCCTTGATTCTTATCCTAATCTGAGAGCTGTACCACGGAGTGGGGTGTCTAAGGCTTCTGCAATACTTGGAACCGGTA
107877 C A TTGAATATACATTCATTACAGCAACTTCAAAGCTTCTCTCGTTAGCTGCACTGTTCTTGTTCGTTCATGGAATATTGCCTACCAAAATACTGGGTGTCAA[C/A]TTAGAGAAGATTCCAGCGTCATGTTTTCAACTATCCGAAGATAATTCACAATGCATTGCTCGCTCTGTGACATCTTTGTGGAATT
107879 A G GGTGTGATGTGTTTCTAGTGCAGCCAACGTGTCCACCAGCAAATGAAAATCTCATGGAACTCTTAGTGATGATTGATGCATGTCGACGAGCGTCTGCTAA[A/G]AATATCACTGCAGTTATACCTTATTTTGGATATGCTAGAGCTGATAGAAAGACTCAAGGGCGTGAGTCAATCGCAGCCAAACTTGTT
107879 A G GAACTCTTAGTGATGATTGATGCATGTCGACGAGCGTCTGCTAAAAATATCACTGCAGTTATACCTTATTTTGGATATGCTAGAGCTGATAGAAAGACTC[A/G]AGGGCGTGAGTCAATCGCAGCCAAACTTGTTGCTAATTTGATAACAGAAGCAGGTGCACATCGTGTACTTGCTTGCGACCTTCACTC
107881 G C GCCATCGAATTGTTGAATGGACCTCCGATCTCACCAATGCCTCACCCACCAGCACAGTCATCACGCTCATGGGCGTCATCACTGCCGACCCAACCACCGT[G/C]GAGCACATCACCAAAACCAAATTCGAGTCCTACATCAAAGGCAACAACTCAATCTCCATACTGCACGATTTCCTAGGCGATGGGATAT
107883 T C CCGGAACGTCTCTTTCACTATGGCCTGTAGGTACGGAAGGTTCCGGATGTCTGCTTCCGAGACTAGCCGATCACGGCCAACCACCTCGTCCAGCTCCCGT[T/C]GTGCTCGTTTCATCGTATCCGGATGTTGGATCATCTCGGACAAGGCCCATTCAACCGTGCTCGACGATGTATCCGTCCCAGCTGTGA
107885 C T AAAACGTCACCGCCACCTGGACGGGCCCCCGCCCATGCACCTACCTTGGTTTTGCCTGCGACACCCCTCCCGGTCTGAAGGCCACTCCCAAAATCGCCTC[C/T]GTCGACTTCAACCAGTTCATGCTTTGCGCACCCACCATCTCCGGCTTCATTGATCAGCTCCCCGACATCGCAATCTTCCACGCTAACTC
107885 A T CCAATTCCTTCTCCGGATCCGTACCCAATTTGAAAAACCTAACCTACCTCTACGAACTTGATCTCAGTAACAACAAGCTCTCCGGTCCCTTTCCTTCCTC[A/T]CTCCTTCCATTAAATCAATTGATCTTCCTCGATGTACGATTTAACCAGTTTTCCGGATCCGTACCCGCTATTATTTTCAAGTCGGGTTTGGA
107885 T C ACAAGCTCTCCGGTCCCTTTCCTTCCTCACTCCTTCCATTAAATCAATTGATCTTCCTCGATGTACGATTTAACCAGTTTTCCGGATCCGTACCCGCTAT[T/C]ATTTTCAAGTCGGGTTTGGATGTACTATTCCTCAACAATAACGGGTTTTCACAACCATTGCCTTCCGATCTCGGATCCGTATCCTACTTAAC
107885 G A CCGGTCCCTTTCCTTCCTCACTCCTTCCATTAAATCAATTGATCTTCCTCGATGTACGATTTAACCAGTTTTCCGGATCCGTACCCGCTATTATTTTCAA[G/A]TCGGGTTTGGATGTACTATTCCTCAACAATAACGGGTTTTCACAACCATTGCCTTCCGATCTCGGATCCGTATCCTACTTAACTCTCGCGAA
107885 T C CTTCCTCACTCCTTCCATTAAATCAATTGATCTTCCTCGATGTACGATTTAACCAGTTTTCCGGATCCGTACCCGCTATTATTTTCAAGTCGGGTTTGGA[T/C]GTACTATTCCTCAACAATAACGGGTTTTCACAACCATTGCCTTCCGATCTCGGATCCGTATCCTACTTAACTCTCGCGAATAACGGGTTTAC
107897 C A TCCAGGAAGAACTTGCAAAACGTGATAAAACAGAGAAGGAGCGTATGCAGCAAATAACAAGCCTTGTCACAAATTATATGAACAAGGATTTTCCTACTGT[C/A]CTTGAGAAAACAGTAAAGAAGGAGATTCCTACGGTAGGTTCAATCCTAACTCGAGCAGTCACTCCTGTCATTGAAAAATGCATTGC
107897 G A CAAGACAGATTCAGGCACAATTCCAAACCACTGGAAAACAAGCTCTTCAGGAAACTTTGAAATCGAGCTTGGAGTCATCTGTGATTCCAGCATTTGAGCA[G/A]TCTTGCAAGGCAATGTTTGATCAAGTAGATGCAACCTTCCATAAAGGGTTGAGTGAACACACTGCTGCTGCTCAACAGCAATTTGAC
107897 A C CATTTGAGCAGTCTTGCAAGGCAATGTTTGATCAAGTAGATGCAACCTTCCATAAAGGGTTGAGTGAACACACTGCTGCTGCTCAACAGCAATTTGACTC[A/C]ACACATTCTGGTTTGGCGATTACTTTAAGGGATGCAATCAACTCTGCCTCTTCAGTCACTAAAAATCTCAGTAATGAATTGGTAGATG
107901 T C GAGTGGACGATGGGGTTTTGCTCAAATGGAAGGCTAATTTTGGATCTACGCTTGATAGATGTGTGATTCTTGGTGCATCCTCATGCTCCACCATGATAAA[T/C]AAATCAGAGAGTTGTTCTAGTCTAAACGATTCAAGTTCATTGGAGTTATGCGGAGCCGACGATAGTGGAAATATTCCAGAATCGTTC
107907 C T GCAACTTTTCCTGAAGTCCAGTAGGACCAAAAACAATACCAGGTGTATAAACCCCGCCTTTGGGCAAATTACTCCTCTGCCCCAAAACGATCAACGCGCA[C/T]TGCACCAAAATGATGGGTGTAGTCAAGTACCCTATCTCCGGCCCTGAAACCCTAGTCACAACCTCCATATCAAATTCCTCTGTGTTACC
107907 C G GCCCAGTTTTACTCCAAAATGGGCGGGTTTGATGGAGGCCCAAAAGGTTTTTCTTTTCTCGATTTGATCTTCGGTTTCTTGGACGCCTGGAAGTCCGTGA[C/G]GGTTTTCAGTTAAGGCTGCAAAGGTTCTGCGGACAACGATGGAGTCGGCCGAGGGGAGTTTTATAGCCCAAAATCCGAGTGATTTT
107907 G C TGATGGAGGCCCAAAAGGTTTTTCTTTTCTCGATTTGATCTTCGGTTTCTTGGACGCCTGGAAGTCCGTGACGGTTTTCAGTTAAGGCTGCAAAGGTTCT[G/C]CGGACAACGATGGAGTCGGCCGAGGGGAGTTTTATAGCCCAAAATCCGAGTGATTTTTGATGTTCGACCAGCGATGCTTTAGAAGG
107907 C T TTCTTTTCTCGATTTGATCTTCGGTTTCTTGGACGCCTGGAAGTCCGTGACGGTTTTCAGTTAAGGCTGCAAAGGTTCTGCGGACAACGATGGAGTCGGC[C/T]GAGGGGAGTTTTATAGCCCAAAATCCGAGTGATTTTTGATGTTCGACCAGCGATGCTTTAGAAGGTGGTGGACCTGGAATCTGTGG
107907 T C GGGCGAGGTTGGAGAGGGAGGACTGATCGTGGACGTCGCACTGGATGGAGTGGATGTCGAAGTCAGCGGTGATCTGGGGATTTTGAGAGCGGGCCCAGGC[T/C]AGGGTTTGAGAGAGTTTGGTGGAGCTGCGACCGGCGATGGCTAGGGTTTTGAGAGGTGAGTTTGGGGTGAAGAGGTGTTTG
107907 T C GATTTTGAGAGCGGGCCCAGGCTAGGGTTTGAGAGAGTTTGGTGGAGCTGCGACCGGCGATGGCTAGGGTTTTGAGAGGTGAGTTTGGGGTGAAGAGGTG[T/C]TTGATGGCTTCGGCGACGACGTATTTTCCAGTGAATCCTGTTACGCCCAGGATTACTGCATCGAATTCGCGCGGAGGAGAATG
107907 C T GCCCAGGCTAGGGTTTGAGAGAGTTTGGTGGAGCTGCGACCGGCGATGGCTAGGGTTTTGAGAGGTGAGTTTGGGGTGAAGAGGTGTTTGATGGCTTCGG[C/T]GACGACGTATTTTCCAGTGAATCCTGTTACGCCCAGGATTACTGCATCGAATTCGCGCGGAGGAGAATGCATTTTTGTGCGGTT
107907 A G GGAGCTGCGACCGGCGATGGCTAGGGTTTTGAGAGGTGAGTTTGGGGTGAAGAGGTGTTTGATGGCTTCGGCGACGACGTATTTTCCAGTGAATCCTGTT[A/G]CGCCCAGGATTACTGCATCGAATTCGCGCGGAGGAGAATGCATTTTTGTGCGGTTTTTTTCTCAAATTCCAGTAGGCCAA
107913 C A TTTACACATGAAATCTACCACCCGTAGTACATAGCTCTTTAGATACAATCAAAGCCGTGAATTTTGACGTTACAAGACATGAATACAAACAATATCCTTA[C/A]TTAATCAACCCGGTTCAACAAAAACTCAAATCTCTGCGCAATTTCCTCAGGCACCGACACCAAAACGGTGAACCCGTGCACGTCCCCAA
107913 T C TACACATGAAATCTACCACCCGTAGTACATAGCTCTTTAGATACAATCAAAGCCGTGAATTTTGACGTTACAAGACATGAATACAAACAATATCCTTACT[T/C]AATCAACCCGGTTCAACAAAAACTCAAATCTCTGCGCAATTTCCTCAGGCACCGACACCAAAACGGTGAACCCGTGCACGTCCCCAACA
107913 C T CAAACAATATCCTTACTTAATCAACCCGGTTCAACAAAAACTCAAATCTCTGCGCAATTTCCTCAGGCACCGACACCAAAACGGTGAACCCGTGCACGTC[C/T]CCAACAACGGGCAAAAAAAGACAGTAAATCTCACTGGCCACCGGCCCCATGTGAACGGCCTTCCCCTCACCAAAGTCGAGGTCCTCCA
107913 CA C TTACTTAATCAACCCGGTTCAACAAAAACTCAAATCTCTGCGCAATTTCCTCAGGCACCGACACCAAAACGGTGAACCCGTGCACGTCCCCAACAACGGG[CA/C]AAAAAAAGACAGTAAATCTCACTGGCCACCGGCCCCATGTGAACGGCCTTCCCCTCACCAAAGTCGAGGTCCTCCAACCCCAACTT
107913 T C CGACCACATCCCTAACGTACCCATCGTTCACTTCCTCCTTCGCCTTCTGCACCACTTCAACCCCATGCCGTGCGTTTGACCCGATCAGTTTCTCGACAGA[T/C]GACTCGGCGCACCCGAGCACGAAGCCGTTCCCATAATACCCTTTCGGTAGCTCAGGACTCAGCTTCTTGCGCACGTTTACAGAGAACAA
107913 T G ACAGATGACTCGGCGCACCCGAGCACGAAGCCGTTCCCATAATACCCTTTCGGTAGCTCAGGACTCAGCTTCTTGCGCACGTTTACAGAGAACAAGAGCC[T/G]CACTTTAAGAGTCATCGAGGCAACCAATGATCTGACCCACGCGCGCCACACGTGGGAAGCCAGCACCTCGAACGAGCTACACTTGA
107913 C A TTTGAGCCCAAGCGCTCAGGAACTGTGCCGTGCCTACTCCGTCGCATATACAGTGGTTGATCGACGTTATCAGTATCATGCCTCTGCAAGTGAGGTGGAT[C/A]ACCTGAACAACAAGAGGAGGAACGGCCAGAAAGGAAGGAGTTTGAAGAGGATAGAGAAGCTTCCTCCAGGACCTGTTGGGTCTTC
107913 T C GAGAAGCTTCCTCCAGGACCTGTTGGGTCTTCCAGAACCTTCTAGAAACTCATCAGCAGACAAATTGACGAACCCCTCAGCAAAGACTGCTCCTTTTCCA[T/C]TGCAGTCGACTTCAATTTTATCTTCCTTGCCAGCTCTCAACCTTCCAGCCAATGGGTAGTAATCAACCAAAATTCGAGAAAGGGAAAG
107913 T G TGGGTCTTCCAGAACCTTCTAGAAACTCATCAGCAGACAAATTGACGAACCCCTCAGCAAAGACTGCTCCTTTTCCATTGCAGTCGACTTCAATTTTATC[T/G]TCCTTGCCAGCTCTCAACCTTCCAGCCAATGGGTAGTAATCAACCAAAATTCGAGAAAGGGAAAGCTTCAGACTTTCTACGCAAGTCGA
107913 T G TATCGGATCGGAAATCTTAAAAATGGCTGGTCGTCTAAGTTCGATAGGTACATAATGTGGTTCGGCGTCTCTGAGATTGGTGCTACGAGGACTGCTTCTC[T/G]CGGGTAGTTGCAGTCTGGGATTTCTACGGAATTAAACATGGGTTTGTTCGAGAGTTGATTCATGGTAGCTTGAGAAAATGT
107921 T C GAAGAATCGAGAGCAGTGGTGAAGCGACAGTAGTCGAGTATTCCGGTCCATGACCCGCTGTTGATGCACAGGCCTGTGGCTTTGACCATAGCTTCTCTGA[T/C]GTTGGATGAACTGAGTTTGGTTTGGTAACCTTCAATTTTCAAATTCTTTCCCATGTAAGATGACGGTTTGGCCACCATGGATCCACC
107921 G A TCCAATTTTCAACATTGAACTCTAAACCGGAGGAAGATGTGTCTATTATCACCCTCGCATCAAATCGAGCACACACTGACAGTAGTTCTGTAATCTCCTC[G/A]TTGCTATAAAGCGAACCAGTTGGGTTGATAGTAGGACCTGATATGTACACCCATGGCTTGGTTACTTTATTGATAACGTTTTCAAGTGT
107923 T A AACTGTTGCTTTAAAGCAGATATTTTATCGGATATATCAACCGAATCATCGGTCATCATTGCATCTGCTTGTTCTGCTTCTTCAAATAAAGGTCCATTTG[T/A]GATTTCAGATGCGTTGTTTACATTTGTGCAGTTAGTAATTTTCTCCGAGTTATCTGGAAGACCATTGCAGTCGGGTTCTTGGGTTGGTCC
107923 C G ATTTTATCGGATATATCAACCGAATCATCGGTCATCATTGCATCTGCTTGTTCTGCTTCTTCAAATAAAGGTCCATTTGTGATTTCAGATGCGTTGTTTA[C/G]ATTTGTGCAGTTAGTAATTTTCTCCGAGTTATCTGGAAGACCATTGCAGTCGGGTTCTTGGGTTGGTCCTCCTGGCTTTGAAGAGTCTGC
107923 T C CATTTGTGCAGTTAGTAATTTTCTCCGAGTTATCTGGAAGACCATTGCAGTCGGGTTCTTGGGTTGGTCCTCCTGGCTTTGAAGAGTCTGCATTTTGCTG[T/C]TCTTGCTCTAATGGGGAACATGATTTTTCTTCGCCAGCTGATCCTGCTTGCTCATGCTCTGTGTTTTTCTTAGCCCGCTTCAATGCTTCAT
107923 A G ATTTTTCTTCGCCAGCTGATCCTGCTTGCTCATGCTCTGTGTTTTTCTTAGCCCGCTTCAATGCTTCATAACTCTGAGATAGATTAACCGCTGGTTGGAC[A/G]TTGCGTAGTCGGGCACTTGATCTGGTTACAGATGCAAGTTGCATGACTGGCGTTGACAAACGAGACAGCCCCCCTATATCATCTGATAC
107923 G A CTTGCTCATGCTCTGTGTTTTTCTTAGCCCGCTTCAATGCTTCATAACTCTGAGATAGATTAACCGCTGGTTGGACATTGCGTAGTCGGGCACTTGATCT[G/A]GTTACAGATGCAAGTTGCATGACTGGCGTTGACAAACGAGACAGCCCCCCTATATCATCTGATACTTGTACCGGGCCTCCCTGTTCTGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107923 A T GACAAACGAGACAGCCCCCCTATATCATCTGATACTTGTACCGGGCCTCCCTGTTCTGCAATTTTGTCACAAAAGGCAACCAAAGCAGGATCCATCTGTG[A/T]TAACATGCCTTGAATCACATCACGAAGCTCATGAGCTCTGCTAACAATCCTAGAGCCATTGTAATCATCTCCATTGTACGCCTTTGCAT
107923 A G TCAAAATCTTGTAGAAAAGATGCACGTGTAAGATACTGCCCACAATCCACACGCTGCAACAGAGTCGCCATATCCATTGGGTTCTGCACAATGGAACGGT[A/G]ATTTGGTGCATCCTCGTCTGAGACTGGATAGTGGAACACGCTGAACCGTTTATCATACAATATCCGGTTGCATACATCCCGAAGACA
107923 A T TTGGTTTGTTCTTCCAAACGAATAGAGAAGGCAAGATCAACCAATTTCTCAACAAATTCAGACCTGTCCTCTCTGGTTGGCTTATCAACTAAATACACAC[A/T]CTGTGGTGCAAATACAGATGTGGAATCTTCTTCCAGCTCGCTCAATAACACTGATGACGTTCCCAGTAATAATACCGGAAGATCAGATG
107923 C T GATCAACCAATTTCTCAACAAATTCAGACCTGTCCTCTCTGGTTGGCTTATCAACTAAATACACACACTGTGGTGCAAATACAGATGTGGAATCTTCTTC[C/T]AGCTCGCTCAATAACACTGATGACGTTCCCAGTAATAATACCGGAAGATCAGATGGCAATTCTGCTAAGAGAGTCATCAAGACAGCCT
107925 A G CTTCAAGATCTGTATTTAGTAATGGCAGGGAAGCTATGTCTACATACTCAATTAGCAGCCCACATACAGACTCCTTAGACAACTGAATTGCCAAGTCCAA[A/G]AGACCGCGGTTCGATGAAGCTTTATGAAGTGACCCGCAAATTGCAGCTACTTTTACAATACGCCTCATTTCTCTTCTATTTATCACAAT
107925 G A CTCAATTAGCAGCCCACATACAGACTCCTTAGACAACTGAATTGCCAAGTCCAAAAGACCGCGGTTCGATGAAGCTTTATGAAGTGACCCGCAAATTGCA[G/A]CTACTTTTACAATACGCCTCATTTCTCTTCTATTTATCACAATTTCACTGAAGTTCTCATCCTTGTATCCATTAACATTCCCAAACACGG
107925 A G ATTTTCTTTATGTTCATTCACATTCTCAACCACACTATTGACCTTCCTCCTCTTCCTTCCACCACTTGTTCCCACATTCTCTCTGTAAATACCAGAACAG[A/G]CTAGCATAGGATTCATCTCATGGTTATGTTCATTATCAACCTCCATTAAATGCAGCATTCCATCTGCCAACAGCCTTGTTATAATCTTTGCTG
107925 A G GTACTATAGCTAATTGTGTATTCAGTGATTCGTTCGTCATGTCAAAATTCTCTGTGTATATGCAAAGGAGAATGGTTAAGTGTCCAGAAATAATCTGTTT[A/G]TTTGTTTCATACCAACTACCTACCTTGAAATGGAAATCATGTAAGACACTGAGTCTAAGGAACAGAGGACATAGAACAAGCAAAGCCG
107927 CT C CTCACTGAACCTAGACAAGCAGGTGATGGTCACCACCACTCACTCAGTAGCCATTCTTGAATCCTCCTACCCTCCTTCTGCCGGCAAGTTCAAAAAAACC[CT/C]TTCCTCCCGTACATCTGCCCTATTTTGAACTTCCACTCAAAAACCGGATCCCCTTTCCTAATCAACGCGTACCCCTTCTTCGCCTTCAAA
107927 TC T CACTGAACCTAGACAAGCAGGTGATGGTCACCACCACTCACTCAGTAGCCATTCTTGAATCCTCCTACCCTCCTTCTGCCGGCAAGTTCAAAAAAACCCT[TC/T]CCTCCCGTACATCTGCCCTATTTTGAACTTCCACTCAAAAACCGGATCCCCTTTCCTAATCAACGCGTACCCCTTCTTCGCCTTCAAATC
107927 C T ACCCCTTCTTCGCCTTCAAATCGGACCCCAAACAGGTCCCGCTCAACTACGTCCTCTTCGAACCCAACGACGGGGTCCAAGACGGCAATCTGAAGTACGA[C/T]AACATGCTTTACGCCCAGATCGACGCGATTTACTCCGCCATAAAGTCAGCAAACGGAGGAGCTGGAGGGAATATTGAGGTCCGGGT
107929 C T GCCCATCCTTCGCTCAGCACGTGGACCCATTCCAGATCGACACGCTTCAGCCTCACGCGTGGAAGTGCCTGCCCGGCAGTCAAAGCCTCCTTGACGCGGG[C/T]ATCGCGGGCAAGGCCTGCTGGAATGACGAGGTTCCGGAGAGAACCACCGTCCGGCTCGATTAGGGAGCAGGCAATACGATGGTG
107929 A G GCTCAGCACGTGGACCCATTCCAGATCGACACGCTTCAGCCTCACGCGTGGAAGTGCCTGCCCGGCAGTCAAAGCCTCCTTGACGCGGGCATCGCGGGCA[A/G]GGCCTGCTGGAATGACGAGGTTCCGGAGAGAACCACCGTCCGGCTCGATTAGGGAGCAGGCAATACGATGGTGAGTGGAGCAT
107933 C T GGTCGAAATACGGATTCGAACCTTCCCTAAAGGGCATGACGATTCATCAAACACCGATAAAGTTAACACAGTGCATAAGTCGTAAACGGGCCATGTGTAT[C/T]GCTCATTCCATAATGGGTCATGGCTGTTGAATACGGTTCGTGTCCTGGCCCACTTGGGCCCATATTTAGCGACCACGTAGGAGTTGG
107935 G GA TTTACAAGAACTGGTATAGGTCAAAGAAGAAAGCATTTACCAAGTACTCCAAGAAATACGAAACCGAAGAGGGCAAAAAGGACATTCATGCACAGCTTGA[G/GA]AAAATGAAGAAGTATGCAACCATTGTTCGTGTTTTGGCACATACACAGATCCGGAAAATGAAGGGCTTAAAGCAGAAGAAAGC
107935 C G TTTTTTGAGAAGCAAATCCCGGTTGATGCCATATTCCAGAAAGACGAGATGATTGACGTCATTGGAGTTACTAAAGGGAAGGGATACGAAGGAGTAGTGA[C/G]TAGGTGGGGTGTGACTCGTCTTCCTAGAAAAACCCACAGAGGTCTTAGGAAGGTGGCTTGTATTGGTGCTTGGCACCCTGCAAGA
107935 CT C CCAAATTTGGCCATGGCCGTTTTCAGACTACTGAGGAGAAGCGCAGGTTCTATGGAAGGCTCAAGGCTTAAATTGTTTGCCCAGAAGCTTATGGGACTTC[CT/C]TTTTTGGTTCATAATCTGATTGTTCCCTTTTGTTTACCTAGTTTTGGAAAAACTGTTGTTTTTGGTAATTTGATTTTGTTCGTGGATGA
107939 GT G CTGTTGGCCTACTGGCTTTTCTCCAAACCCTAAAAGCTTCCTCCCAAATCATAATTTTAAAATTAGGTCGAGTAGTTCCACTTCTGCTAAATGAACCCGT[GT/G]TTTTTTTACACGTGTTCTAATAGGCAACCTCACCCTTTCTCTCCCCGTCAACTCCCGTCCCGCCGTCGCCGGAGTCCACCCTTCCTCCTCT
107939 A C ATAATTTTAAAATTAGGTCGAGTAGTTCCACTTCTGCTAAATGAACCCGTGTTTTTTTACACGTGTTCTAATAGGCAACCTCACCCTTTCTCTCCCCGTC[A/C]ACTCCCGTCCCGCCGTCGCCGGAGTCCACCCTTCCTCCTCTCCCTGCTTCTGTGTCATCCGCTTCAACAACCAGAAGTTCACCTGCCCCGT
107939 T C GGGTCGGGATTGGTAGTGGGAGGAAGGAGGACGGGAAGTTGCATCTGACCGTGAGGAGCGAGCCGGATCCGAGGTTTGTTTTCGAATTTGACGGCGAGCC[T/C]GAGTGCAGTCCTCAGATAATCGCGGTTAATGGGCGGATTCGCCAGCCTGCTTTCAGCTGCAAGTTCGACTGTAACCATCGCGG
107939 A G CGCCAGGCACCGACCGGGTCAGCAGCTCGAACCCAGGCTCATGGATCATTTTCCGGCGGGACGAAAACAAAGTGTTGAAACCATGGGGCTGCCTGCAAGC[A/G]TGGCGCGAGCGCGGAGGCTACCATGATGCTCTCGGATACAAGTTCGAGCTCATGCCCGAAGCCAGCAACCTCGATAACAGCGG
107939 T A TGCAAGCATGGCGCGAGCGCGGAGGCTACCATGATGCTCTCGGATACAAGTTCGAGCTCATGCCCGAAGCCAGCAACCTCGATAACAGCGGGGGAAGGGT[T/A]CCGCTAGCCGAGTCAAGGATCGACATAAGAAATGGTGGTGATTTTATTATCGATTTAACGGGTAATGCGACGTTGGGTAAGAAT
107939 T A CTCTCGGATACAAGTTCGAGCTCATGCCCGAAGCCAGCAACCTCGATAACAGCGGGGGAAGGGTTCCGCTAGCCGAGTCAAGGATCGACATAAGAAATGG[T/A]GGTGATTTTATTATCGATTTAACGGGTAATGCGACGTTGGGTAAGAATTTAACACCTGGGTGTAGCCCTAGAGGGAGCGGGGAC
107939 C T ACATAAGAAATGGTGGTGATTTTATTATCGATTTAACGGGTAATGCGACGTTGGGTAAGAATTTAACACCTGGGTGTAGCCCTAGAGGGAGCGGGGACTT[C/T]GGGTATGCGATGTACCCATTTTGCTATAGAGGGTTTGTGATGAGCTCGAAGGTGGAAGGCGAAGGGAGATGCAGTAAGCCAAGA
107939 G T CGTTGGGTAAGAATTTAACACCTGGGTGTAGCCCTAGAGGGAGCGGGGACTTCGGGTATGCGATGTACCCATTTTGCTATAGAGGGTTTGTGATGAGCTC[G/T]AAGGTGGAAGGCGAAGGGAGATGCAGTAAGCCAAGAATTGAGGTAGGTGGGCAACATGTTGGGTGCATGGAGGATGCGGCTG
107939 A G TTGGGTAAGAATTTAACACCTGGGTGTAGCCCTAGAGGGAGCGGGGACTTCGGGTATGCGATGTACCCATTTTGCTATAGAGGGTTTGTGATGAGCTCGA[A/G]GGTGGAAGGCGAAGGGAGATGCAGTAAGCCAAGAATTGAGGTAGGTGGGCAACATGTTGGGTGCATGGAGGATGCGGCTGCT
107939 G C TGGGTAAGAATTTAACACCTGGGTGTAGCCCTAGAGGGAGCGGGGACTTCGGGTATGCGATGTACCCATTTTGCTATAGAGGGTTTGTGATGAGCTCGAA[G/C]GTGGAAGGCGAAGGGAGATGCAGTAAGCCAAGAATTGAGGTAGGTGGGCAACATGTTGGGTGCATGGAGGATGCGGCTGCTT
107939 G A TCGGGTATGCGATGTACCCATTTTGCTATAGAGGGTTTGTGATGAGCTCGAAGGTGGAAGGCGAAGGGAGATGCAGTAAGCCAAGAATTGAGGTAGGTGG[G/A]CAACATGTTGGGTGCATGGAGGATGCGGCTGCTTTCATGGCCCTTTCCGCTGCCATAGATTTGAGTATGGATGCTTGCAGGCTT
107941 G GC AATGCCCACAAAAAACATGCACCATACCGAAGCCATATCTTAAAAAGTAATTGTAAAATACCTGCTTGGAAAGGAAAGGTTCATCACATACAAATCGAGA[G/GC]CCCATCTCACCAACCAAGAGAGCAGCCTCTGCCCTATATACATCCATACCTTCTACATAAGGCAATCCAAAGTCAGAGCCAACCAC
107941 C T ACCAACCATCGTCCCTGACCCTCTCCGGTAGAGGGGATAAACCCAAAGATCCAGAGAAGACTGGAGAGAGTTCCATAAAAATTTCTTCAACGACAAGAAA[C/T]CGGTGGCGCAGCAAGGCAGCAAAGTGCCTCAAATCGCATAAGCGAATAACCACCGAAGAAGCACCTGAACACTCAACCGACACTG
107943 T G CTTACCAAATCATTTATCATCTATATTTTCTTGAGTTACTTCTGTCCCCACATCAGCAGCAGAAGACACTGCTTCTGCAGCTTGGCTCTGACTCGTTTGC[T/G]CAGCTTGGCTTTGACTCGTTTGCGCAGCTTGACTTTGACTCGTTTGGGCATTATGACTTTGACTCGTTTGTACAGCTTGACTTTGGCTTAC
107943 A G GAGTTACTTCTGTCCCCACATCAGCAGCAGAAGACACTGCTTCTGCAGCTTGGCTCTGACTCGTTTGCTCAGCTTGGCTTTGACTCGTTTGCGCAGCTTG[A/G]CTTTGACTCGTTTGGGCATTATGACTTTGACTCGTTTGTACAGCTTGACTTTGGCTTACCTGTGCAGCATGACCTTGGCTTACAGGTGC
107943 TTTGGCTTACCTGTGCAGCATGACC
T TGGCTCTGACTCGTTTGCTCAGCTTGGCTTTGACTCGTTTGCGCAGCTTGACTTTGACTCGTTTGGGCATTATGACTTTGACTCGTTTGTACAGCTTGAC[T/TTTGGCTTACCTGTGCAGCATGACC]TTGGCTTACCTGTGCAGCATGACCTTGGCTTACAGGTGCAGCTTGACTTTGATTCATTTGGGTATT
107943 T C TGGGAATCATTCGCAAGACCCAAGACAACAAGAATTGACCTTGGAAGAGTAGCACGTATATTCATCTGACTAGCATGCTCAATTAGTTGTGGCTTCAGAG[T/C]TGGATTTCGATTCAACGCATTCTCCAACTGTGTAGCTGGCAGCTGTAATAAAACACCAAAAGATTGAGGTACTGTCTGGATAACACA
107943 A G TCAATGCCTTTGCCAAAACCTGTTGAGTAAATATGTGCCGCTGCTCAAAGCAAACAGTGCAAGCCTCCATAACCTTTTTAAGAGGCACTCCTTCTTTTTC[A/G]GGATCAATAACATGGATAGCAATCAAAACTTCAGCAGGAGTAAGGGAACTACTAGTTTGAGGTGAACCCTGCAACAAGCGATTAACTG
107943 T G AGGCACTCCTTCTTTTTCAGGATCAATAACATGGATAGCAATCAAAACTTCAGCAGGAGTAAGGGAACTACTAGTTTGAGGTGAACCCTGCAACAAGCGA[T/G]TAACTGCAGCTTGAAATTTATCCTGAGGAAGATTGACAAGCTGGGGGAAAACAGCAAGAACCTCTTCCTTTGAAAGGAATGACAAT
107947 T C AAGCTTCTACTGCCATGTTTGCAGCACTAGATGAGCTTTTCGAGAAATGTCGTATTCGCCCTAAAGACGTAGGCATATTGGTTGTGAACTGTAGTTTGTT[T/C]AACCCAACTCCGTCGCTCTCTGCCATGATTGTGAACCATTACAAAATGAGAGGAAATATTTTGAGTTATAATCTTGGTGGCATGGGAT
107947 T C TAAAGACGTAGGCATATTGGTTGTGAACTGTAGTTTGTTTAACCCAACTCCGTCGCTCTCTGCCATGATTGTGAACCATTACAAAATGAGAGGAAATATT[T/C]TGAGTTATAATCTTGGTGGCATGGGATGCAGTGCTGGGATCATTTCTCTTGATTTGGCTAGTGATATCCTTCAGGCAAATCCTAACAA
107947 A C CTAGGGCAAAGTATCAATTGGAGCACATTGTTAGGACTCATAAGGGCGGTGATGATCGAAGCTTCAGGAGCGTTTACCAGGAAGAAGACGACCAGCGAAT[A/C]AAAGGTCTATCAATAAGCAGGGACCTTCTGGAAGTCGGCGGACAAGCCTTAAAAGCAAACATAACAACCCTAGGCCCACTGGTG
107947 C T TGGAGCACATTGTTAGGACTCATAAGGGCGGTGATGATCGAAGCTTCAGGAGCGTTTACCAGGAAGAAGACGACCAGCGAATAAAAGGTCTATCAATAAG[C/T]AGGGACCTTCTGGAAGTCGGCGGACAAGCCTTAAAAGCAAACATAACAACCCTAGGCCCACTGGTGCTCCCATTCTCCGAGCAAC
107949 AG A ACGTCAAAGTCCAGCAGCTCGCTCCCCACTGCGCTCGACGACGACTGGTTATGACTCCCGTGGCTGTCTTCTTCTATCATGGCTTGCTGCTGCTCCTCGT[AG/A]GGGTCGGGGTGAGGGGAAGCGGTTGAGAGACGTACTCTTCGTATAGCTCGTGAATGGCATCATCGACCATTTTTATGTGATTTGAA
107951 T C CTTTTGGGTATCTTGCACCTGAATATGCTGTAACGGGTCGAGTAACAACCAAAGCGGACGTGTTCAGCTTTGGAGTGATACTAATGGAGCTCATAACGGG[T/C]CGCAAAGCCCTAGACGAAACCCAGCCTGAAGAAAGCGTGCATCTAGTCACATGGTTCCGCCGCATGCAACTGAACAACAGCAGCG
107965 T TA TTAACCCCTCGTCCGATTTTGGAATTTGTATGGTTTGAGGGCAATTAATTAATGTGGTTGCAGTTGAGATATAAAAATATTGACCACTGGACGACCAAAA[T/TA]AAAATAAAAATGATGCCCTTGGTATTCTTTCTGTAGCAGTGGTGTCCTTCGGTTTATGTTAACAGGTCAATTCTCTTGTCTTTACGTTG
107967 G A GTTTCTGAAAAAAGGATGATCAAGAGCTTCTCTTGCTGTGAGGCGTTCTGATGGTTCAAACTGTAGAAGTCCGTACAATAGATCGGCTAATTTATTTCCC[G/A]TGTGATGATCCACGTGTCTTAATATCATTTCCTTTAGACGGTCAAGCTTCCTTACAGCCCTAATGCTTTCGCTTGATACAGCACCTTCTG
107967 A G CTCCTTACTACTTTAATGGCTACATATTCACGTGCTTCACGATCCCAACATTCTAATACTCGACCAAACGTACCTTCACCAATCTTGCTAAGTATTTTAT[A/G]TCTAGGAGTGAGATTCTCTCCAAGTTCAAAACAAAATGCCCATCTCGATCGTCTTCGCGAACTGGTGGCGACAATCCTCGTCTTTCAACCT
107973 G A GAGGTGGTGCAGCATGAAAACAGACAATGACAACAGCCACATTGTCTCCACTTTTCCTTTTAAGGGCTTCGTTGACGAGCTCTTTGCAGCAAAGTTGGGG[G/A]TCGTTGTGCTCTTGTAGTTTTCTACGTGCAAAGTCTATGGCGTTTTGGCTTCGGAACACGTCCCATAAGCCGTCGCATCCTATGATTA
107975 AC A GTCCATAACGATATCTGCGGTCCTCGTATGGAAATCCCCAGTCAAAACATCAACTTCAACTTCGGCGAACGCAGCTCCATACGTAAAATACGAAAATGGC[AC/A]CCCCTTTCCCAACATTCCAATCAAAGCCAATATCAGGTGTTGCATAAAATCCATGAGCTGACAGATCTATTCTTTCCAAGAAACATG
107975 A G TATCTGCGGTCCTCGTATGGAAATCCCCAGTCAAAACATCAACTTCAACTTCGGCGAACGCAGCTCCATACGTAAAATACGAAAATGGCACCCCTTTCCC[A/G]ACATTCCAATCAAAGCCAATATCAGGTGTTGCATAAAATCCATGAGCTGACAGATCTATTCTTTCCAAGAAACATGCACGCACTAGCT
107977 T TC CCCATAATCTGCATCTCTTGAGCGAGGCCTATGATCGTCCTCCTGCATCCTTGACTTGCTTCGAGCCCTTGAAGATTGCCCCCTCTCATCATAGTCATCC[T/TC]CCCATCATAATCGCGTTCTCTAGCCTTATAGCCCCGATACCCATCTTTCTCTTCTCTGTACCTTTCTTTATCCCAATCTTGCTCTTGAACTT
107987 A C CAACCAGATCCGAGTGAAACCCCTGCTCCACGATCCTCCCGTCCTTCACCACCGCTATATTATCCACGTTCCTTATCGTGGACAGCCTATGCGCCACGAT[A/C]ACGGTCGTTCTTCCCCTCATCAACCTCTCCAGGGCCTCCTGCAGCACGCACTCCGACTCCGCGTCCAGCGCGCTCGTCGCCTCGTCCAG
107987 T C TACCATAGGATTAGGGCTTCGGACGCGTACAGGGAGAGTTGGGAGACCCCGAAAAGGAGGCCTGAGGTTTGGCTTTTGCGCAGGCTGCGCTTTCGAGGGA[T/C]GCGGAGCTCGTTGCAGAAAAGGGAGATTATTTTGTCCTGCGCGTTGAAGGCTGCCACGGTTCGAATGTTGCTTACGCCTTCTCC
107991 G A CCCGCGGCTCTAACCTTTATCTTCGACCGCCGGCAATAGCTACTCGCCTAGGCTGCTGCTGCTGAGCATTTGATAGCTGAGATTCCACTTGCCCAATGTC[G/A]AGCTTGGAGAAGCCTTTGACTCTTGAGAATTACACAAGCTCAATATTCAATTCAAGTTATTGCAGATCAAGGGCAGATGAAAGGGAA
107991 A C AATAGCTACTCGCCTAGGCTGCTGCTGCTGAGCATTTGATAGCTGAGATTCCACTTGCCCAATGTCGAGCTTGGAGAAGCCTTTGACTCTTGAGAATTAC[A/C]CAAGCTCAATATTCAATTCAAGTTATTGCAGATCAAGGGCAGATGAAAGGGAAATGAGCAGCTTGTTGAACGAAGGAAGACAGTGC
107991 GT G TTGGTAGGGGTAGAAGAGTCTCTGATATTTCTGACTCATGGCAAACTCGTCATCACTGTACTTCTGGATACAGCAAAGAGACAAGAGACCTAGAAACTAA[GT/G]TTTTTTAAGGGAATGCCAAATTTTGTAAAGATAGTTGAAGTTGGGCCAAGAGATGGATTACAGAATGAAAAGAGTACTATACCTA
107991 C T GGGTATCAGTGTGATCGATGCATCAGTGGCTGGTCTAGGTGGTTGCCCTTATGCAAAGGGCGCTTCTGGAAATGTCGCTACAGAAGATGTTGTTTACATG[C/T]TGCAAGGCCTCGGCATCAAAACTGATGTCGACCTCCGTAAGCTCATTGCTGCTGGAGAGTTTATTTGCAAGCATTTGGGGCGCCAA
107993 T TA GCTGTAAGGAACGAATGTTGTATTAAAAAATTGAACAACAATATGCAACATTATTCAAACGGATTGAAACTGATATTTCGATTCAACATAACTTTCAGCC[T/TA]CCCATAAAAATGAACCAAAAGCAACTGCTTCCAAAATCAACATGGTAAGTCCGGAGTAACTTATACTAACCACTTCATCATTTGAGGT
107993 A G TTTTCCATCATCTTCTTCCAAACTTTCGCCATCTGGTGAAATCTGAACCATCGATTCCATATCCCAAAAAGGATTTGGATTTGGATTATCGACGATTCTA[A/G]GATCGTTGATTTTTGGTGGTAACGTATTCATGCTTCTTTCGAGTTGGTATCTTTCATCCACTCTTTTGAGGAAATATCCATACATTATTGAT
107993 G GT GGTTAGGCCATGAGTCAATATCCATCGTAGGATGTGGTGGCCTTGAAATTGATGGGATCATTGCGATGTTGTTTTCTACAAATTTATGTACGATGAAACA[G/GT]TAGATTATTTCTTCAATTGTTTTCTGCCTTTCTTTGTTCTTCACTTCTGCAATTCTCCTATATAGGAGAAGATCTTGGGCCCCAGGTGG
107993 A G ATTGCGTTCTGATTGAAGATTCTCAAGCTGTTGATCAATGGCTGCTGGTAATAAATGAGGATGTGTGTGCAATATCTGATAAAGTAATTGCCCTGTTGGC[A/G]ATTCTAACCCAAGAGGAGCAATTTGTGTTCTTCCATCACCTGAATTTTCCGTTGCTCTAGCTTTTAAGCACCCTCCTCGCCCAGTTTCT
107995 T A ATCTTCCAGAGAGAGATAGAAGGTGCAGTCTGGAAGTATGCGAATACTTTGGAAACAAATCCAAAAGATTCTCGGACACAAGCGCAGATTTCATGCGTAT[T/A]ATCTACAGCAAATCGGGTCTCGGTGATGAAACATATGGGCCTCCATTTGTGTTCCAAACAGACTTCGAAGCGAAACTGACGAATGC
107995 TC T TGATGAAACATATGGGCCTCCATTTGTGTTCCAAACAGACTTCGAAGCGAAACTGACGAATGCGGTGGTAGAAGCTGAAGAGACGATGTTCACTGCCGTT[TC/T]CCTTCCGTTCTTTCAAAAACATCTACCCATACCTCTAAGATTACACACCTAATCGTGGTATGTAGCATGTTTTCGCCTTCACCTTCCT
107995 T C TATGGCAGCACAGCTTTTGAGATGGGAGATTGGTTATGTGCTTATTGTTGCTACTGAAAATACTAGCTTGAACTGGTACTTTGGAGACAACCGCCATATG[T/C]TGGTCACGAACTGTATATTCCGGGTCGGGTCAGCTGCAGCACTGATAACCAACGACCCACGTGCACGACACCTTGCAAGAATGGAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
107995 G A TTGTTGCTACTGAAAATACTAGCTTGAACTGGTACTTTGGAGACAACCGCCATATGTTGGTCACGAACTGTATATTCCGGGTCGGGTCAGCTGCAGCACT[G/A]ATAACCAACGACCCACGTGCACGACACCTTGCAAGAATGGAGTTGGTCAGCACACTAAGGACCCATCATGGTGCGGATGATGCAGC
107995 G A TCCGGGTCGGGTCAGCTGCAGCACTGATAACCAACGACCCACGTGCACGACACCTTGCAAGAATGGAGTTGGTCAGCACACTAAGGACCCATCATGGTGC[G/A]GATGATGCAGCATACAACGCCGCCACCCAGCAAGAGGATGAAGAGGGAAACTTAGGAGTTGCCCTTACACAAGACCTAGTCCGA
107995 A C CAGCTGCAGCACTGATAACCAACGACCCACGTGCACGACACCTTGCAAGAATGGAGTTGGTCAGCACACTAAGGACCCATCATGGTGCGGATGATGCAGC[A/C]TACAACGCCGCCACCCAGCAAGAGGATGAAGAGGGAAACTTAGGAGTTGCCCTTACACAAGACCTAGTCCGAGTGGCCGGAGCA
108011 C T GATGTTAGGAAATTGATATGGACTCCTTATAAAGAACAGTGATGTTATTGACTAGAGTCTACCAAAATGTAAATCTGTTACACAGTTTACCACCCCTAAC[C/T]GAACTTGACTATGTAGTCCTATATGTAATTCTGGTTGTCGCATTGGTGAATGTTTATTAATTCGAGTAGAGGTCTTTT
108011 C T AAATTGATATGGACTCCTTATAAAGAACAGTGATGTTATTGACTAGAGTCTACCAAAATGTAAATCTGTTACACAGTTTACCACCCCTAACCGAACTTGA[C/T]TATGTAGTCCTATATGTAATTCTGGTTGTCGCATTGGTGAATGTTTATTAATTCGAGTAGAGGTCTTTT
108019 TG T TGTTCCAGCGGCGAAGCATCCATTATCTTGATTGAATGATAGGTGAAGGAGGGAGGGAGGCGGTGACGTGATGGATTGGAGTCCGGTTTCGTGTTGGGGT[TG/T]GGGGTTGGAGTTGGGATTGGGGTTGAGGGTCGGGGTCGGAAACGGATTTGGAATTGGAATCGGAATCAGAGTCGGGAACG
108025 C T CACGGCACGATGATCCATGGTTGATGGTGGTGGAGCCTCATGCCTATGGTAGTAATCGTACGGTGGTGGTGCTGCTGCTGCAGATAGAACAGAAGAAACA[C/T]AGTTATCCATGTGTCTTGTAAACGGACCCATGTCCTGAGCTCGGCTCATACGTGGAGGCGGTGACTCTCTTCTTTGCCTCAGGGG
108025 A G ACTTTTCCTCTGGCAGGGGTAAGCAATCATCGAACACTTTGAAACGAACCTGAGCTGGATACGCTGAGTTGAATGCTTTAGGTTCAATATCATAACCCCC[A/G]GGAGTAGCAGCTTTGAAAATTCCATACATCAACTTGAGATCCACATCAAATAAAAACAGTCTCATACCCGGATATATTTTTGTAACCA
108027 C T TCGCCATGCCGAATGAAAACCTCACAATAGCTGCCAAAAACCCATCCTTTGCAGCGCAGTGGGTGCAGTCCAACGTTGCAGCTTACTATCCAGGCACTCG[C/T]ATCCAGACCATCGCCGTTGGAAACGAGGTTTTCGTCGATCCGAAGAACCTGACTAATTATTTGGTTCCAGCAATGCAGAACGTTCAC
108027 C T CCATGCCGAATGAAAACCTCACAATAGCTGCCAAAAACCCATCCTTTGCAGCGCAGTGGGTGCAGTCCAACGTTGCAGCTTACTATCCAGGCACTCGCAT[C/T]CAGACCATCGCCGTTGGAAACGAGGTTTTCGTCGATCCGAAGAACCTGACTAATTATTTGGTTCCAGCAATGCAGAACGTTCACAAC
108027 A G TTCCAGCAATGCAGAACGTTCACAACGCGCTTGCGAAGCTAAACCTCGATAAGTTCGTGAAAGTTTCTTCGCCGATTGCTCTCACCGCGTTGCAGAGTTC[A/G]TATCCTTCGTCCTCGGGTTGTTTTCGCGAAGATTTGGGCGAAACAGTCATGAAACCGATGCTGCAACTGCTTAGACAAAGCGGATCG
108027 G A CAATGAGAATATGAAGCCAGGACCTACTTCGGAGAGAAATTATGGATTGTTCTATCCTAATGAGGAGAAAGTTTATGATATTCAGCTGAGTATCAAAGGC[G/A]GCAGTGGTGGAAATTCTGGCTTGAGGTGGCAAGAGCGAAGAGGAAGGGGAAGCGATGGATCACCGCAAAACAAAGGAAGCAGT
108027 G A GAGAATATGAAGCCAGGACCTACTTCGGAGAGAAATTATGGATTGTTCTATCCTAATGAGGAGAAAGTTTATGATATTCAGCTGAGTATCAAAGGCGGCA[G/A]TGGTGGAAATTCTGGCTTGAGGTGGCAAGAGCGAAGAGGAAGGGGAAGCGATGGATCACCGCAAAACAAAGGAAGCAGTGGAG
108027 C T ATCCTAATGAGGAGAAAGTTTATGATATTCAGCTGAGTATCAAAGGCGGCAGTGGTGGAAATTCTGGCTTGAGGTGGCAAGAGCGAAGAGGAAGGGGAAG[C/T]GATGGATCACCGCAAAACAAAGGAAGCAGTGGAGGATCTGGAAGTGGGAGAGTTGTGAAGAGTTCAACGGGAGAGACATGG
108027 G A GCAGTGGTGGAAATTCTGGCTTGAGGTGGCAAGAGCGAAGAGGAAGGGGAAGCGATGGATCACCGCAAAACAAAGGAAGCAGTGGAGGATCTGGAAGTGG[G/A]AGAGTTGTGAAGAGTTCAACGGGAGAGACATGGTGTGTTGCAATGCAGAGGTGGGGAAGGAGAAGCTACAAGCAGCGTTG
108027 A G GGTGGCAAGAGCGAAGAGGAAGGGGAAGCGATGGATCACCGCAAAACAAAGGAAGCAGTGGAGGATCTGGAAGTGGGAGAGTTGTGAAGAGTTCAACGGG[A/G]GAGACATGGTGTGTTGCAATGCAGAGGTGGGGAAGGAGAAGCTACAAGCAGCGTTGAATTACGCCTGTGGAGAAGGAGG
108027 C CA GGAAGGGGAAGCGATGGATCACCGCAAAACAAAGGAAGCAGTGGAGGATCTGGAAGTGGGAGAGTTGTGAAGAGTTCAACGGGAGAGACATGGTGTGTTG[C/CA]AATGCAGAGGTGGGGAAGGAGAAGCTACAAGCAGCGTTGAATTACGCCTGTGGAGAAGGAGGAGCAGATTGTAAAAAGA
108027 G A AGTGGAGGATCTGGAAGTGGGAGAGTTGTGAAGAGTTCAACGGGAGAGACATGGTGTGTTGCAATGCAGAGGTGGGGAAGGAGAAGCTACAAGCAGCGTT[G/A]AATTACGCCTGTGGAGAAGGAGGAGCAGATTGTAAAAAGATACAACCGGGTGCAGATTGCTATGATCCAGATACAGTAGAG
108027 A G GTGAAGAGTTCAACGGGAGAGACATGGTGTGTTGCAATGCAGAGGTGGGGAAGGAGAAGCTACAAGCAGCGTTGAATTACGCCTGTGGAGAAGGAGGAGC[A/G]GATTGTAAAAAGATACAACCGGGTGCAGATTGCTATGATCCAGATACAGTAGAGGCCCATGCCAGTTATGCGTTTAATAGTTA
108027 C T CCCATGCCAGTTATGCGTTTAATAGTTACTATCAGAAGAAAGGAAGGGTTTCTGGTACTTGTTCGTTTCAGGGCGCTGCCTATGTTGTTTCCCAAGCTCC[C/T]AAAGTAGGTAAATGCGATCTTCCAACAAGGGTTTGATGAATCCAGCACACAGCAGAAGAAAGTGATCACATGCTTGCCAATTATTTTT
108029 A AC GTTACCGCAGATGGTAAAAGAAGTGCTCAATTTGAGCACACTCTTCTGGTGACTGAAACAGGAGTTGATGTTTTGACAGCAAGGTTGCCGTCATCCCCCG[A/AC]GTTTTCCCTTGGTTGAAGTCTTAGGAAGTTTTTGGCTGTTCATATTTTTGAGTCAAATAGATGATTTATTCTATTGTTCTTACTATTG
108029 CT C AGATGGTAAAAGAAGTGCTCAATTTGAGCACACTCTTCTGGTGACTGAAACAGGAGTTGATGTTTTGACAGCAAGGTTGCCGTCATCCCCCGAGTTTTCC[CT/C]TTGGTTGAAGTCTTAGGAAGTTTTTGGCTGTTCATATTTTTGAGTCAAATAGATGATTTATTCTATTGTTCTTACTATTGTATAATCTA
108031 TA T TATATAACTTAGCATACATTACTACTTAAATTGAATCTACGAAGCAAATATGTCACAGCTCATAAATATTACAAAGATACGGCCGCCTAATTTTTCCAAA[TA/T]AAAATATGAAAACTTAGGGATTTACAGGCTTTCCTAATAATTTGGGGAAGGGATCTTGTTTGCTGAGGACAACTACTTTGTTCTTGTGA
108031 C A CCTGCAGTTTCTCTGGATTCTTTCCCAAATTTGCCAACTCTTTATCTGCTAGCTCAGCAAGCACACGTATCTCACGCGTCATACAGTATATAGCATCTAA[C/A]GCCCATGCGGTCTCCCAATTCCTAAACTCTTGCAAAAATGCACTTGCAGATTTCTCAAACGACACATAAGCCTCTGCGTACCGACCAACA
108031 G C CGTACCGACCAACACGACAACACTGAATCGCTTTCAAAAGAGGCCCAAGGATCTCCGTTAGTTCCTGATCGTAGTTCGATAAATGACGATTAACGGCGTC[G/C]GAGGCAACGGCTACTGCGTCAGCGACACCGGTGATGAACGGAGAGTTGGAACTGACAGAAAGTAAGGAAGAAAGGGTACCAGCG
108031 T A GACAACACTGAATCGCTTTCAAAAGAGGCCCAAGGATCTCCGTTAGTTCCTGATCGTAGTTCGATAAATGACGATTAACGGCGTCGGAGGCAACGGCTAC[T/A]GCGTCAGCGACACCGGTGATGAACGGAGAGTTGGAACTGACAGAAAGTAAGGAAGAAAGGGTACCAGCGTCTTGGTCGGAGATG
108031 T G AGGCAACGGCTACTGCGTCAGCGACACCGGTGATGAACGGAGAGTTGGAACTGACAGAAAGTAAGGAAGAAAGGGTACCAGCGTCTTGGTCGGAGATGGA[T/G]GTGGCGAATCGAGAGAGGAAGTCAGCGATGCGACGATGAGATTCGCCTACGCTCAGATACGACATTAGCCTGCGGCTAATTT
108035 TA T AAATTGAAGGATCCCAAGGGAAGTCTGCTTACACGGTTATTTATAAAGCTGGTGAGTGCATGCAAGAACTTCTAAAATCATGGAAAGAATTTGAAACAAC[TA/T]AAAAAGGGTAAAAATGATGAAGCTTCTGAAAACTACCCAGTTCTGGAAATTCGGATACCTGCAGAATATGTTACTTCTAGCAACCG
108035 T C GTAAAAATGATGAAGCTTCTGAAAACTACCCAGTTCTGGAAATTCGGATACCTGCAGAATATGTTACTTCTAGCAACCGTCAGGTAAGAGGTGCTCAGCT[T/C]TGGGGAACTGATATATACACTAATGATTCAGATCTCTTTGCTGTTCTTATGCACACTGGTTATTGTCGTCCAACTTCGTCCCCACCGGC
108035 G A GTCTTACCTATATCTCTGCTTTGGAGCCAACTCTTGCTCCCGTTTCCGTGGAACGCACCATGACCACAAGATCTGCAGCAACAAATGCTTTGCGGCAACA[G/A]AGATTTGTCCGAGAAGTCTCTATACAGTACAATCTTTGCTGTGAGCCCTGGCTGAAGTACAGCATTAGCGTGGTTGCTGATAAAGGAT
108047 GA G AAGACTCGGCACATAGCAAGTTAGATACAGACCGTTAATAACAACAGATTACTAGTGCATTGCTATTCAATGTTCCACATTTAACAGCGGTTGG[GA/G]AAAAAAGGGTACTGGTTCTTCTTGAACAATCTTTCATTTAAAGCAGGCATTGCCGTTAGAGCACACGTTTAGCATGCTCAATGGTTACTGCTT
108047 T C TTCTTGACACCCTTCGACCTCCCTTGCGGGGAGGACTAGGAGAATCTGAGTAAGAAGAAGTTGACCTTCCACGTCGTGGTGGACCTCGTCCTCTGCGAGG[T/C]GAAATTGATCTAGAAGGGGAACGGCCAGGCCTACGAATGGGAGAGCGGCTACGACGACGTGGTGGAGGTGATCGCCTTGGCGG
108047 A G TTGACACCCTTCGACCTCCCTTGCGGGGAGGACTAGGAGAATCTGAGTAAGAAGAAGTTGACCTTCCACGTCGTGGTGGACCTCGTCCTCTGCGAGGTGA[A/G]ATTGATCTAGAAGGGGAACGGCCAGGCCTACGAATGGGAGAGCGGCTACGACGACGTGGTGGAGGTGATCGCCTTGGCGGGCT
108047 A G GAAATTGATCTAGAAGGGGAACGGCCAGGCCTACGAATGGGAGAGCGGCTACGACGACGTGGTGGAGGTGATCGCCTTGGCGGGCTTCTTGCTCGTCTCA[A/G]AGGGGGTGATCGTCGCCTAGGTGGTAAAGGCGAACGCTTCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAG
108047 C T TACGAATGGGAGAGCGGCTACGACGACGTGGTGGAGGTGATCGCCTTGGCGGGCTTCTTGCTCGTCTCAAAGGGGGTGATCGTCGCCTAGGTGGTAAAGG[C/T]GAACGCTTCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAA
108047 T A AGCGGCTACGACGACGTGGTGGAGGTGATCGCCTTGGCGGGCTTCTTGCTCGTCTCAAAGGGGGTGATCGTCGCCTAGGTGGTAAAGGCGAACGCTTCCT[T/A]ACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAACGCCTTCTGATA
108047 C T AAGGGGGTGATCGTCGCCTAGGTGGTAAAGGCGAACGCTTCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCT[C/T]GGAGGGGAGGGAGAACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGA
108047 G A GTGATCGTCGCCTAGGTGGTAAAGGCGAACGCTTCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGG[G/A]GAGGGAGAACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGT
108047 A G AAGGCGAACGCTTCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAACGCCTTCTGAT[A/G]GGAGAAGCTCCTCTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAG
108047 T C TCCTTACAGGACTTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAACGCCTTCTGATAGGAGAAGCTCC[T/C]CTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACG
108047 C G TTCCACGACCCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGG[C/G]GGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAG
108047 G A CCCTTCTTGGTGAACCCCGTGCAGGTGACCTAAGCCTTCTCGGAGGGGAGGGAGAACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGGCGGTGTATC[G/A]CCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGT
108047 AGGG A TCGGAGGGGAGGGAGAACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCG[AGGG/A]GGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGG
108047 A G AACGCCTTCTGATAGGAGAAGCTCCTCTTCTACGAGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATC[A/G]GGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACG
108047 T C AGGCGGTGTATCGCCACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGA[T/C]GCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTG
108047 G A ACGACGGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCC[G/A]GTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGAT
108047 T A GGCGTGGAGGAGGAGAATTGGGTCGACGGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTT[T/A]CGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGT
108047 A T GGCGAGGGGGAGGAGAATCAGGTCGACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACG[A/T]CGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGT
108047 A T ACGGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTT[A/T]GTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATC
108047 T C GGCGCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAG[T/C]ACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTC
108047 C T GCGGAGGAGAGTCTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTAC[C/T]GGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAG
108047 T C CTGGTCTGCGATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGG[T/C]CTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAGAGGGGCATCTCG
108047 C T GATGCGGAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATG[C/T]GGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGC
108047 C T GAGGAGAATCCGGTTTTCGGCGGGGAGGAGAATCTGGTCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGA[C/T]GACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGC
108047 T C TCGACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTA[T/C]TAACGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTG
108047 A G ACGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTA[A/G]CGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCA
108047 C T CGACGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAA[C/T]GCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAAT
108047 C T CGTATAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGC[C/T]AACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTA
108047 T G TAGGCGACTTTGATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAAC[T/G]TTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATT
108047 A T ATCTCTTTAGTACCGGTGGTGATGGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAG[A/T]GGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCCGCACTA
108047 C G GGTCTACGATGCGGTGACGACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAG[C/G]AGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCCGCACTATGTTCCCATCAATTTGTCCCCCAT
108047 G C ACTCCCTTAATCGTGCAGGACCGTCCTTATCATTATTAACGCCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGG[G/C]GGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCCGCACTATGTTCCCATCAATTTGTCCCCCATTCATGTACAGAAGAGCCTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108047 G A CCAACTTTATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCC[G/A]CACTATGTTCCCATCAATTTGTCCCCCATTCATGTACAGAAGAGCCTTTTCAGCATCTGATCGTTTCTTGAACTCAACATATCCATATCC
108047 G A TATCTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCCGCACTAT[G/A]TTCCCATCAATTTGTCCCCCATTCATGTACAGAAGAGCCTTTTCAGCATCTGATCGTTTCTTGAACTCAACATATCCATATCCTCGAGG
108047 C T CTCTTAGAGGGGCATCTCGTTTAGATGCAGCAGCAACTGCCTTTGGTGGGGGAGATACCCTCTGCTTTGGTGCCAATGTAAATTTTGCCCGCACTATGTT[C/T]CCATCAATTTGTCCCCCATTCATGTACAGAAGAGCCTTTTCAGCATCTGATCGTTTCTTGAACTCAACATATCCATATCCTCGAGGAAG
108051 AC A TGGTACAGGCCAAGAAAATGGAACGTGTGTGTGATCGGATCCCATGATCTGTACGAACACCCTCACATAAATGATCTTGCGTACATGCCTGCAATAAAAA[AC/A]CTGGACGGTTGGGATTCAACCTTTTAGTTGGAGGATTTTTCAGCCCAAAAAGATGTGCTGAAGCTATCCCTCTTGATGCCTGGGTG
108051 G A TGAAGGGGCCGATGTTTATTTGGGTGGGAGGGTAGGGAGCGACTCTCATTTGGGGGAGATTTATAGGAAGGCCGTCCCTTGTAAGGACCTGGTGCCTGTT[G/A]TTGTGAATATTTTGGTTGAGAGGTTTGGGGGTGTGCTTAGGGTCAGGGAGGAGAACGATGAGGAATGAGTCTCTCTTGTGTTTT
108053 C T CTCAATGGTTCGGTGGAGCCGAGCACTGTGGTCAAGCACGTGCTCAAGGCCAGCACTTCAGATAACATGAAGGACTACTATTCTATCGGGACCTACAACC[C/T]TGCACTGAACACATGGCTTCCGGATGAAGAAGGGCTAGACGTCGGAGTTGGTTTGAGGTACGACTGGGGGAGATTCTACGCTTCA
108053 A G CGGTCCTGGAAGAACAGTTGAGGTCCGTGTAGGTCAAGCTGTGCAGTTGGACATAGAGGCCGAATTCGAAATTGATAAAGAGGCGTTAGAGACTATGAAC[A/G]GTACAGATGTAACGTATGAATGCGACAGGAGCGGTGGTGCAGCACAGAGGGGGTCGCTTGGTCCGTTTGGGTTGATTGTGCTG
108053 A C CGTTCAAGGTGAGAGTGTTGGTCGATCACTCGATAGTTGAGAGTTTTGCTCAAGGAGGAAGGGCGAGTGCAACGTCTAGAGTGTACCCTACGGAGGCTAT[A/C]TACGACGAAGCTCGGGTATTTCTGTTCAATAATGCGACGGGAACGGCTGTTACGGCAACTAGAATGAAAGTTTGGCAAATGAAA
108053 G A GGCAAATGAAATCCACTTCATTTAGCAACTTCTTGGATTTTCGAAGTGTGTAAGCTTTGAGTAAACATCGTAGTTTTGGATAGTAGCTGATAGGTGAATC[G/A]CTTGTTATGTAAATATAAAGCAAGAAAGTTGCAGTCTGTAACAAGGTTATGTATTTCGGAATTTTTCTTCTTTTATGTCA
108063 A G GGGTGTCCCCCGCTGGGTGGAGACAAAACTTTGATGCCCGCATCCCTTGTGCTGACATTCTTATGCCTTCCCCATTAGCAAAACTATCTTCAAAACGGAC[A/G]TCTTTATGGCCCTTTAGTATATTGGCCAGCTGTTTGCGAACTATTCCTTCATCTTTTCTAATTGTTCTCCCACGAAAGAATAAAAGTGTG
108065 G A TGGCCCCCCAGACCTTGGCCTCTGCGATCGCACTTTCTCGATCGATGAGGGAACGGGCGTCGTCTCTTGGAGATATTTGACGTGGCGAGTCGTTGGCGGC[G/A]GCACGTGGGCTGTTGTCGTATTCGCCACCTAGGCTTCGGCGCTCGTCTTTGGATCTGCTGCTTTTGGAGTTTGGGTCGTAGTTTTG
108067 TA T TCCTAAAGATATTTTGTTCTCCACAATTGAATCTATCGACAACCACTTCTGATTTCAGTGCGATTACATTATTCATTCTTTAGTTCCACCTTCAGACTCT[TA/T]AAAAAGATTTTTGATATCCACCTCGAATCCTTCTTCAACCTGAGAAGTAATCGTCAAATCTAAAATATGTTCTGAAAATTGAACTGAGTTT
108067 CCTGCAA C TGAATGTACTGATCCCAATCATCATCTCCGGTTAAATAAATATCTAAACTGTTTGAAGCAGCATCCCATGGACGATTTGTGTAGTTCATGCTTTCTCTTT[CCTGCAA/C]CTGCAAAGTGGAAAGCTTGGACGCCGACTCTTTTGCTTGAGCTAGCAGTTTCGAAATGGGTGAAGTGGTTAACGCATCAACCA
108069 C CG TGCATGGCTGTCGAGTCATGAGAGGAATTTGAAGCCTTTTATCGATTTGTACTATTCTATGGGTTGGATTTCTCTTGTCTGCCATTCAGAGTTTCTTACT[C/CG]TTTTTTTACCTGAAAAAGCAACATCTCTGGCCATTGGGGTGTTAAATGAGCTTGTTAAGGAAGTAAAGTTTAGTCCACTGCCTATTGTG
108069 A G GAAGCACAACGGGCCGAATACTGGGAGACGCTGTACTCCTCGGTTAATGTTGGTCCAATACTCATATTTTGTTCAGAAGATGATGAACTTGCTCCATACC[A/G]AATCGTTTCAAATTTTGCCAGTCGTTTAAAAGAACTTGGTGGTGATGTTAGTCTAGTAAAATGGGCAAGCTCCCCTCATGTAGGCCA
108069 A T AGTAACTTCAAACGAGAGCTTAAAAAGAGTAGCAAGCAGTCCAAGCGACCATTTCTTCATACCAAGCTCAGCCGAGTACCAAGAAACCAAAGAAGGAGGT[A/T]CGCTTATGAACGAGCAAAGGGATGGATCGTTTCATGTGCACAGTCCACCAAAATTGAATGCCAGTGGGGTTTTAGGTAAATTGCT
108069 G A AGCTCAGCCGAGTACCAAGAAACCAAAGAAGGAGGTACGCTTATGAACGAGCAAAGGGATGGATCGTTTCATGTGCACAGTCCACCAAAATTGAATGCCA[G/A]TGGGGTTTTAGGTAAATTGCTGTTCGACGTATGTGTTCCTAAAGACGTAGAAGACTGGGATCTTAAGGAAGCTGGTTCATCTGCG
108071 C T ACGTTGGTGACATAGACTTCAATATTTCATTGACCGCCTTCGTTAATTTATTGCCAACGGCAGAATTGTTTGAAGCAAGATTACTGGGATTGGAATTAGT[C/T]GGAAGTTCGGGTCCATTTACTTGCCTAGGATTATGAGCAACCATCTTGGAAGTATCTGGATAAACAACTGTTGAAGTTGGGCCAACTA
108073 C T TTAATGTCACTCCTCGATATGCTCGACTTCGAGCTTCAGGAGCAAATGGCTCGGCTAGAGGACCAATTATTGGGTGGCAAAACATTGAACTCATTAGCGA[C/T]AGACCGCTTGAAACAATGTTGAAGGAATTCAAACAATTGAAAGCAGAATATCCTGATAGAATACTTATCGCTTCGATAATGGAAGAA
108073 C T TTGAAATAAATTTTTCATGCCCACATGGCATGCCAGAGAGAAGAATGGGTGCTGCTGTTGGCCAAGACTGTGCATTATTAGAGGAGGTTTGTGGATGGGT[C/T]AATGAAAAAGCCACTGTCCCTGTTTGGGCAAAGATGACTCCAAATATTACGGATATTACTCAACCAGCGAGGGTGTCTTTGGAATC
108073 G A GTGCATTATTAGAGGAGGTTTGTGGATGGGTCAATGAAAAAGCCACTGTCCCTGTTTGGGCAAAGATGACTCCAAATATTACGGATATTACTCAACCAGC[G/A]AGGGTGTCTTTGGAATCTGGATGTGAAGGAGTTGCTGCCATCAACACTATCATGAGTGTAATGGGTATCAATCTTAACTCATTACGT
108073 G T CTGGATGTGAAGGAGTTGCTGCCATCAACACTATCATGAGTGTAATGGGTATCAATCTTAACTCATTACGTCCTGAGCCTTGTGTTGAAGGGTACTCGAC[G/T]CCTGGTGGTTATCTGCAAAAGCTGTACATCCAATTGCGCTTGCAAAAGTAATGCAGATTGCAAAAATGATCAGAGAAGATTTTGGCG
108073 A AT GGAGTTGCTGCCATCAACACTATCATGAGTGTAATGGGTATCAATCTTAACTCATTACGTCCTGAGCCTTGTGTTGAAGGGTACTCGACGCCTGGTGGTT[A/AT]TCTGCAAAAGCTGTACATCCAATTGCGCTTGCAAAAGTAATGCAGATTGCAAAAATGATCAGAGAAGATTTTGGCGATAGAGATAT
108073 C T CAAAAGCTGTACATCCAATTGCGCTTGCAAAAGTAATGCAGATTGCAAAAATGATCAGAGAAGATTTTGGCGATAGAGATATATCACTTTCTGGGATTGG[C/T]GGTGTTGAAACCGGTGCTGATGCTGCTGAGTTTCTTCTTCTTGGTGCAAATTCAGTTCAGGTTTGCACGGGTGTCATGATGCATGGA
108073 C G ATCCAATTGCGCTTGCAAAAGTAATGCAGATTGCAAAAATGATCAGAGAAGATTTTGGCGATAGAGATATATCACTTTCTGGGATTGGCGGTGTTGAAAC[C/G]GGTGCTGATGCTGCTGAGTTTCTTCTTCTTGGTGCAAATTCAGTTCAGGTTTGCACGGGTGTCATGATGCATGGATATGGTCTGGTC
108079 C A TACCATCAAAAAATTGTCACTTCAGCTTCTCCCTCACCCTGAAAAACATTATAAAATCCAGTAGTAATCACGGCGGTTTCCCTCCAATTCGTGGCGGCGG[C/A]GGCGGCGGCGGCAGCGGTGGAGGAGATGATGATGATCACGAAGAAGAAGAGTTTGGTCCTATACTGAAATTTGATGAGGTTATGAA
108079 T C GAGTATTCCTTGCTGTTTCATCAAATACCCGATATCAGATCATCAATGGACTAGAACAGATAGTCGAATCATCACCTCTGGCCAAAAGAATACCACCTAT[T/C]GCCATGGCTTTTACAGTTGGTATTCGCTTTGCCAATAACACTTATGGTGGCATGCAGTTTGTGGACTGGGCTCGCCTGAGTGGTGTTC
108079 T A ATACCCGATATCAGATCATCAATGGACTAGAACAGATAGTCGAATCATCACCTCTGGCCAAAAGAATACCACCTATTGCCATGGCTTTTACAGTTGGTAT[T/A]CGCTTTGCCAATAACACTTATGGTGGCATGCAGTTTGTGGACTGGGCTCGCCTGAGTGGTGTTCAATGAATGCATACGCATTCCCTTT
108085 G C TCCCGCGCCGCCCCTCCGGCATGTCCGTCCTCGTCACCGGAGCTGCGGGCTTCGTCGGATCCCACGTGTCCCTCGCTCTCAAGAAGCGCGGCGACGGCGT[G/C]GTCGGCGTGGACAACTTCAACTCCTACTACGACCCTTCCCTCAAAAAGGCCAGGAAAACCCTCCTCTCATCCCACGGCATCTTCGTC
108085 C G TCAACTCCTACTACGACCCTTCCCTCAAAAAGGCCAGGAAAACCCTCCTCTCATCCCACGGCATCTTCGTCATAGAAGCCGACATCAACGACGCCAAGCT[C/G]CTGGCCAAGCTCTTCGACGTCAATCAGTTCACCCACGTGATGCATCTAGCCGCCCAAGCCGGCGTCCGCTACGCCATCGAAAACCCAT
108085 G A CCCACGTGATGCATCTAGCCGCCCAAGCCGGCGTCCGCTACGCCATCGAAAACCCATCCTCCTACGTCCACTCCAACATCGCCGGCCTAGTGACCCTACT[G/A]GAAGCCTGCAAATCAGCGGATCCGCAACCCGCTATCGTTTGGGCGTCCTCCTCGTCCGTCTACGGGTTAAACGACAAGGTCCCCTTC
108085 C G ACATCGCCGGCCTAGTGACCCTACTGGAAGCCTGCAAATCAGCGGATCCGCAACCCGCTATCGTTTGGGCGTCCTCCTCGTCCGTCTACGGGTTAAACGA[C/G]AAGGTCCCCTTCTCGGAGGAGGACCGTACGGACCAACCTGCTTCGCTCTACGCAGCGACGAAGAAAGCCGGGGAGGAGATCACCC
108085 G C TGACCCTACTGGAAGCCTGCAAATCAGCGGATCCGCAACCCGCTATCGTTTGGGCGTCCTCCTCGTCCGTCTACGGGTTAAACGACAAGGTCCCCTTCTC[G/C]GAGGAGGACCGTACGGACCAACCTGCTTCGCTCTACGCAGCGACGAAGAAAGCCGGGGAGGAGATCACCCACACTTACAATCACA
108085 T C CAGCGGATCCGCAACCCGCTATCGTTTGGGCGTCCTCCTCGTCCGTCTACGGGTTAAACGACAAGGTCCCCTTCTCGGAGGAGGACCGTACGGACCAACC[T/C]GCTTCGCTCTACGCAGCGACGAAGAAAGCCGGGGAGGAGATCACCCACACTTACAATCACATCTACGGGTTATCAATCACCGGTCT
108085 G A CGCTGGACACGGCGGAGAAGAGCACGGGCAGCGGGGGGAAGAAGAAAGGAACGGCGCAGTACAGGATATTCAACTTGGGCAACACTTCGCCTGTGACCGT[G/A]CCGAAGTTGGTGTCGATACTGGAGAAGTACCTGAAGGTGAAGGCGAAGAAGAACGTGGTGGAGATGCCTGGAAACGGAGA
108085 G C TGGACACGGCGGAGAAGAGCACGGGCAGCGGGGGGAAGAAGAAAGGAACGGCGCAGTACAGGATATTCAACTTGGGCAACACTTCGCCTGTGACCGTGCC[G/C]AAGTTGGTGTCGATACTGGAGAAGTACCTGAAGGTGAAGGCGAAGAAGAACGTGGTGGAGATGCCTGGAAACGGAGACGT
108087 T TA GAAACTCGTTTTTCACGTCACAAGATCTTTAGACGAAAATCCACACTATGTACAAAATTGCAACAATCTGAACAAAACAAGCAAACGTGAACGTACAAAG[T/TA]AAAAAGAAGAGAAAAGGACTTATCGTTTTTTGACCATTTCATCTGCCATCAGAGCTAGTGAATGAATCGGCAAACCCAGCTGGTCT
108087 G A AAGCAATATTAATCCTTCTTTTCCAAGTCAAAGGCTCTAAACCATACTCTTTCCAATGAAAAAGATGTCTACTTAAAGCACCCATTGACATGTACTCGTA[G/A]ACTAATAGTTTCTCATTGCCTTCAGCAGAAAACCCCAACAAAGAAACTAAATTTCGGTGTCTAACTTTTGAAAGAACCGCAATTTCAGCT
108095 A G TCAGTTTGTAGTAACAATCATAAATAACAAGATTACATTATAAACAGAATGATTCACAAATGGACTACGTTTACGTGAAAGTTCACTCAAACTTCCTTCT[A/G]ATCAACTCCATCACAATCTCATTCCAAGTATCAACAGGTCCAGGCATGCACCAATGCAAGCAATCCTGCGGAGGCGGCTTACCATCCGC
108095 T C ATTACATTATAAACAGAATGATTCACAAATGGACTACGTTTACGTGAAAGTTCACTCAAACTTCCTTCTAATCAACTCCATCACAATCTCATTCCAAGTA[T/C]CAACAGGTCCAGGCATGCACCAATGCAAGCAATCCTGCGGAGGCGGCTTACCATCCGCCCCCTCTTAGTAACCTTATTCGGGTCAAGAC
108095 A AT TTTGGGAGCGAAGTGGAAAGGATCAGGGGTTTGGTGGACAAGCCATGAGGACCAGATGCGGACTATCGTGGTTGAGGTGGACTGGAAGTACCATCTCTGC[A/AT]TTTTTCGACTTCCTCGGTTCTTTGGTGCTTCTTCCTGCCATAGAATGCAAATCAATGATTCATACTGATTCCTGGAGACAGAATC
108095 G A AAAGGATCAGGGGTTTGGTGGACAAGCCATGAGGACCAGATGCGGACTATCGTGGTTGAGGTGGACTGGAAGTACCATCTCTGCATTTTTCGACTTCCTC[G/A]GTTCTTTGGTGCTTCTTCCTGCCATAGAATGCAAATCAATGATTCATACTGATTCCTGGAGACAGAATCTCCAACAAAAGCAATCGT
108095 TC T GACTTCCTCGGTTCTTTGGTGCTTCTTCCTGCCATAGAATGCAAATCAATGATTCATACTGATTCCTGGAGACAGAATCTCCAACAAAAGCAATCGTCTT[TC/T]CCCCTCATCATCTCCAAAAATTTCCTCGGATTGAACCGTGGAAGGTCGCATTGATCAGGCTTCCATCTATAGTTCTCGTACTCTTTGTCT
108097 A G CCGAACAATGGGAGAAAATTGCAGATGTTATTGAAGAAAAGAACCATATCCCTTTCTTTGATGTCGCATACCAGGGATTTGCTAGTGGAAGCCTGGACGA[A/G]GATGCATCATCGGTGAGAAATTTTGTTGCACGAGGTATGGAAGTTCTGGTTGCACAGTCTTACAGCAAAAACTTAGGGTTGTATGC
108097 G A AGAAAATTGCAGATGTTATTGAAGAAAAGAACCATATCCCTTTCTTTGATGTCGCATACCAGGGATTTGCTAGTGGAAGCCTGGACGAAGATGCATCATC[G/A]GTGAGAAATTTTGTTGCACGAGGTATGGAAGTTCTGGTTGCACAGTCTTACAGCAAAAACTTAGGGTTGTATGCCGAAAGAGTTGG
108097 G A CACAGTCTTACAGCAAAAACTTAGGGTTGTATGCCGAAAGAGTTGGAGCCATCAATGTTGTTTGTGCATCTTCAGATGCCGCGACAAGGGTGAAGAGCCA[G/A]TTGAAACGACTTGCACGCCCAATGTATTCAAACCCTCCAGTTCATGGTGCTAAAATTGTTGCTAATGTCGTTGGCGATCCTACTCTT
108097 G A ATCTTCAGATGCCGCGACAAGGGTGAAGAGCCAGTTGAAACGACTTGCACGCCCAATGTATTCAAACCCTCCAGTTCATGGTGCTAAAATTGTTGCTAAT[G/A]TCGTTGGCGATCCTACTCTTTTCAATGAGTGGAAGCAAGAGATGGAATTAATGGCAGGCCGCATAAAGAATGTAAGGCGAAGATTG
108097 C T ATATGACAAACAAATGGCATGTGTATATGACGAAGGATGGTAGAATATCTTTAGCTGGACTTTCTTTGGCAAAATGTGATTACCTTGCCGATGCCATTAT[C/T]GACTCCTACCACAACGTGAGCTAGGGAAAACATCGGCATTCCAATTTATTTCTTGTTCTACAGCATGGTGAGCTTGGAACATTTTGAT
108097 C T GGCATGTGTATATGACGAAGGATGGTAGAATATCTTTAGCTGGACTTTCTTTGGCAAAATGTGATTACCTTGCCGATGCCATTATCGACTCCTACCACAA[C/T]GTGAGCTAGGGAAAACATCGGCATTCCAATTTATTTCTTGTTCTACAGCATGGTGAGCTTGGAACATTTTGATCTTGTTCCATAAATTG
108099 T C TGTTGAGGAAAGGGAAGGTGAATGCGATATATGATCCTAGAGTGTCGCCTATTGGGAATGTAAACCTTAGAAGGCAGCTAGGGTTGATTGCGGTGAATTG[T/C]GTTAAGTCTAGTGATGAGAGAAGGCCTTCCATGGAGGAGGTTGTAGCGCATCTTAAGATTGTTTTGCGTATGTTGGTTTCTAGTT
108103 C G TCGGTATGCAACCAAAAACCATAGCCAAATATACTTACGCTTTAAAAAGCGGACAATGCTACTTAAACCGATGGAAGTTTCGATCAAAAAATGCGACTAG[C/G]ACAAATTGGAGGATTTCAGGGAGCAAAAATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTGACGCATATTTTGACAGAA
108103 G A AACCAAAAACCATAGCCAAATATACTTACGCTTTAAAAAGCGGACAATGCTACTTAAACCGATGGAAGTTTCGATCAAAAAATGCGACTAGCACAAATTG[G/A]AGGATTTCAGGGAGCAAAAATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTGACGCATATTTTGACAGAATGTGTTCCGG
108103 T C GACAATGCTACTTAAACCGATGGAAGTTTCGATCAAAAAATGCGACTAGCACAAATTGGAGGATTTCAGGGAGCAAAAATGTCATTTTGCGGTCGATCCT[T/C]CGAATTTTGTGTTAACTGACGCATATTTTGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAGTCTTCTTTGTTTTTC
108103 A T ATGGAAGTTTCGATCAAAAAATGCGACTAGCACAAATTGGAGGATTTCAGGGAGCAAAAATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTG[A/T]CGCATATTTTGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAGTCTTCTTTGTTTTTCAACAAGCTCCGGCGCGAA
108103 G A GGAAGTTTCGATCAAAAAATGCGACTAGCACAAATTGGAGGATTTCAGGGAGCAAAAATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTGAC[G/A]CATATTTTGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAGTCTTCTTTGTTTTTCAACAAGCTCCGGCGCGAAAC
108103 T C AAAATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTGACGCATATTTTGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAG[T/C]CTTCTTTGTTTTTCAACAAGCTCCGGCGCGAAACCCAATCACCTTCTTCCCTACGTCATAAACAACATTAAACCTTCTCTGCTGCGTATTC
108103 T C AATGTCATTTTGCGGTCGATCCTTCGAATTTTGTGTTAACTGACGCATATTTTGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAGTC[T/C]TCTTTGTTTTTCAACAAGCTCCGGCGCGAAACCCAATCACCTTCTTCCCTACGTCATAAACAACATTAAACCTTCTCTGCTGCGTATTCCC
108103 C T TGACAGAATGTGTTCCGGTTGATTTAGCATTTCCGTTAAAAGGCAGTCTTCTTTGTTTTTCAACAAGCTCCGGCGCGAAACCCAATCACCTTCTTCCCTA[C/T]GTCATAAACAACATTAAACCTTCTCTGCTGCGTATTCCCTATGATCATAACATCGCTGTCATCCCCGGTAGGCGCAAACGCCAAGCAAGC
108103 A T CCTGAAACAGCAACCCCACCTTTGGTACTGTCACTGTTCCATATTTACTCAAGTCGTAGCATGTGTCCAGTATCGATGCAGCAGGGGCGGTTGGGTACTT[A/T]GACATTAGCTTCCGGAACGCTGCACGTAATGCACTGTATGCTGTTGGGGCAATGCGAGTGATCACCGTGCCTGAGTCGATTATCACA
108103 T A TAGGCGAAATCGCGAGCTTCTGCCCACCAACACTAACCCCAACCATCTTTAGAAAGTAAAACGTCGACAGACTCGGCTGACTAAGCATCGGCGTGTACTG[T/A]ACTTTGGACACCGAACCCCTTCCAAACGTTAGGTACCCACTTTGGCCCAAGCCCGGAGGCAAACAGTACGAAAACACCCCACCGAA
108103 G A TGGTGTATGTGGACGATTTTGTAGGGTCAAAGAGTGAGTCCTTTTGTTGGTAGCAAGCTGACACACAGGGCTGACACTGGATCCATGTAACGTCGGACCC[G/A]GTGTCGAAGACAACGGATTGGGCCACTTTTGGGGTGCCCATGGAGAGGGTGACTATGTAGTTGCCTGTGCCTAAAGCGATGCCTC
108103 T C GCTGACACACAGGGCTGACACTGGATCCATGTAACGTCGGACCCGGTGTCGAAGACAACGGATTGGGCCACTTTTGGGGTGCCCATGGAGAGGGTGACTA[T/C]GTAGTTGCCTGTGCCTAAAGCGATGCCTCGCTGGGCCGGGATTGTGGATGCAGGTATCGGGTTCTTTTTGTGGTGGTTGTGGTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108105 G A ATCAAAATCCCCAAAATGTCCATCTCTCTTAATACAAAATCTGCTCTCAAATTTAACAGGGAACTCAAATTCGAAATCGAAGAAGAAGAATCCAACAGCA[G/A]CAGTATTGATTCTAAGGAAGATGAAGAGGATAGGTGGTCGAAAATGCTCCCAGATCTCTTGAGAGAGATTATAAAAAAGCTTGAGAC
108105 T A CCTTTTATTTGTATCTTTCTTTGACTAAATCGTTTGTGGAAAAAGGTAAGTTTCTGTTGGCAGCTAAAAGAATCAGAAATGGCGGCCATGTTGAGTATAT[T/A]ATCTCTCTGGATGCTGATGATATCTCCCAAAGAAGTAATGCGTACTTGGGAAAATTAAGAGCCGATTTCCTGGGCACAAAGTTCAGAA
108107 G GA AAAATGCTGGGTGGCAAGCACTACCCCTAGTACAGAATTTTGCATGCCAACTTCTATTGAGATGGTGCGAGCCGAAGAGACATCAATTCCTATAATCCTT[G/GA]AAAAAACATATCCAAAGAAAAAACCAGAAGCATGTAGAGAACAAACAGCAACCACTACTTGAAACCCTGATGCTAATATGGCTGA
108107 A G CCACTACTTGAAACCCTGATGCTAATATGGCTGAGGCAGTCTGTGCAATAGCACTACCACATAAAATGGCAACTGTGGCCACTGCAATGAATGGCATCAC[A/G]GGAGAAACAAGCTCAACCAAGTTATTGCAATATTGGTTTAATGCAGCACCTACTATTACAGGGGCAAGCACGACCTGGACAGTTGA
108107 T C TCACAGGAGAAACAAGCTCAACCAAGTTATTGCAATATTGGTTTAATGCAGCACCTACTATTACAGGGGCAAGCACGACCTGGACAGTTGACATAAAAAG[T/C]CCAACTGGATCTACAGCAACGAACTGTCCAGCAAGTTTGGATGTCAGAAAAGGCGTCATTACCGCGGAAGCAAAGGTGCTTGCTG
108107 A T AAGTGTAGTTGAGAATTTATGGTGAAATCGAAGAGTTTGGGCTTGGTTGAGTTTTGATTTGGGTCTTGATGGAGCAGGGAAGGAGGTTTTGATTTGAAAA[A/T]TTGGGGCTTTGAGCCGGCGGTAGACGGAGTTGGATGTGGCAGGCGGCTGAGATAGTCTGATTATTTTCATTTTGGACTCTCCCAG
108111 G GT TCACTATATATGAGAATTTGAGCTCGTTCCCAGAGTTATTTTTGCCATTAAATGATCTGCTACATGCCGCACAAAAAAGAATTTTACCAGGCTTGTTACA[G/GT]CAGAAGTGAATGATGTTATTGATTTGATCAAGAAAAAAGCTGATGAACATCATATGCTGAGGATACCACTTCAAATGCGAAAACAAA
108111 C A AACAGGAGCATGCTTTTAAGTCCGGTCAGTTGGGTAAAGGACCTAGATGTGGAAAACGAAGGCGATAATCAACGCCTGCATGTTAGTTTTTTGTAGTGTT[C/A]TATGCAGTAACAGTTGAGAAATTTTAGCTTGCTTTGATTTTGTGGACTTTTCTTCCATTTTTGAAAGTTGATTATGATATTCAGCCTAG
108115 A T TGTCGGTGGGGTATACCGGGAGTGTTGAGCAGAGGTGGGCTCAATTTGAAAAGGCTTTGAAGACCGTGGAGAAGGCCTAGTAATATTGATGAGAATTGAA[A/T]TAGGGATTGTGGGCTTAGTTAATTCTTACATAAGTTGGTTTTGCTTCATGTAGTAACTAGAGTATAATCATATGCCGTATCGCCTA
108117 AT A TCGATTAGTCGACGACTAGTCGCGACTAATCGAGCGCCGTAATAAAAGTGATGCCAATATATATACCACTGTTCATCAAAGAATGATATTTTGATGTTTT[AT/A]TTTTGTTTCAAAATGGATGATATATTTGAAATTGTACAATTGATGTCAATTTAAAATTGCACCAAAAAGTAAAATGTATTATAGTCATT
108119 G C GGTGCACTTCCAGATGCTACATGTGAGGAACTCTCTGCATTTAATGATGAATGTGCTATTTGTAGAGGACCAATGTCCAGGGCTAAAAAACTGTCTTGCA[G/C]CCATCTTTTCCACCTTGCATGTCTGAGATCATGGTTGGATCAAGGTGCAACTGATGTTTACTCATGTCCCACATGTCGAAGACCACTA
108119 T G GTCCCACATGTCGAAGACCACTATTTGTACCAAATTCACTGAACCACAGAAACTTGGTGCCGGCACATGGATCTAGTAACAATTCTGTACCTGATCAACC[T/G]AATACTGGAATAGAGCAACAGAGGGCACTGGAACATGCAATGCCTGCTGGTATATATCCAGATCAGCAGTCAAGTGCATCTGATGAT
108119 G A GGCACTGGAACATGCAATGCCTGCTGGTATATATCCAGATCAGCAGTCAAGTGCATCTGATGATGCTGTGTGGAGAGGTGTAGGATTTGACTCAAGCTGG[G/A]CACCACCTTGGCCAACTCCCGTAACCGATATAGCAGGAACATCAAACTCGATTAGATCAGTTGGATTCAGTGGGGTTCGAATGAT
108127 A G TTCTAGTTCTTCTACTTCGTCTACTAAATCCAACGAAGAAGATGAAGAAGCGGAGGAAGATGATAAGTTTTCTAGATCTGATGCATTTGGAATGCGATCT[A/G]AATTTGATAGAACAGAATCTATGCACAGACAGGCTCCTAGTGAAATCGGATCTTCAATGAGGAAAACGGGTCGGTTTGATAGGGCT
108127 T G ATACAGTCTTGATGCTGGCAACGTTGGTGGTGTAACTAGTCTTGGTTCAACTATGGAAAAGCTCTTGGCTTGGGAGAAGAAGCTTTATGAGGAGGTCAAG[T/G]CAAGAGAAGGAGTCAAGATAGAGCATGAGAAGAAGCTATCAACATTACAGAGCCTCGAATATAAAGGAAAAGATGACGTAAAGA
108127 T C GTGAATCCACATCTGATCTTCACCGATTCGCCACCCGCGACCTCGAAGCAGCCGTATCCTCCTGGCACTCGAACTTCAACCGTCTCATCAAATACCAACG[T/C]GAGTACGTCCGTTCCATCTACGGCTGGCTCAAGCTCACCCTCATCCAAGTCAACAACGTCGACGACATCAACCAAAACGAGCACTCAT
108129 A G AGATCTCGATTAACTTCACTAGCTCACTTGGATCCATCTTGTCACTTACCTTGATGCCAAGTGGATTGGCAACACCTCTAAGGAACTCAACATGAGCTCC[A/G]TCAAGCTGGCGAGTTCGCTCACCAACCCAAAGCATGTGCGCAGAGCAATCATAGAAGAGTCCTGAGGTGGAATCCTCACGAGTAAGG
108137 T C CATGTAATATTTCCTTGGTTTTTTTGTGCCATCTCTTCAAGTGCCTTGGCGCTGTACACATAACCATTTGGCAATACTAGAGGTGGATTCTCGCTATCCA[T/C]GAGCTCTTTAGTTATGTAGCAAACTAACTTTGAATGGTGCTGTTTTGAGTAAGGTAGTTTGGATGCTAATTTACGGAAACCTTCTTGTGA
108137 A G CAACAAAGTCCTGTATGTTATTGCTTTCAGCAAGCTTAGCAGCAGAATCGAAGTATGACATGCGCAACATGTAGTCAACAAGTATTCTTTTTAACCTGGT[A/G]TTGCTCCACTCGTCCAAATTATCTGCATTTGCACTGTCCAAGTGGTCAAGTCTGGCTCGGCATCTTTGTACCTGCAGAGTCTCCATTTT
108137 A G TGCTGCTATCTTCTAGCTTTCGCTTCAATCCTTGCAAATTAGAAACGAGGCCCTCCAGATGTGAGACAGCATACTCGCTTGACATCATAATGACATCGCC[A/G]TCGCCATCGTTAGTACTACTGCTACTCTTCGTTGGTCGTGCGACGGAGTTAACAACGGCCGATACTTCTTTTTCTGCGATGCGGTTGTC
108137 G A TGCTATCTTCTAGCTTTCGCTTCAATCCTTGCAAATTAGAAACGAGGCCCTCCAGATGTGAGACAGCATACTCGCTTGACATCATAATGACATCGCCATC[G/A]CCATCGTTAGTACTACTGCTACTCTTCGTTGGTCGTGCGACGGAGTTAACAACGGCCGATACTTCTTTTTCTGCGATGCGGTTGTCAGT
108143 A G GCCCACTTTCAACCATCAAATCCATGAGAGATGATTCGAAAACCCGATCCTTGAAGGCAGATGTCCATATTGATCTGACAGCCAAAGCAACTCCATATCC[A/G]GCTAAGTCAGCAAGTTGAAATGGACCCATTGGCATGCCAAAGTTTTTTATGACAGTGTCAATTCTGAACAGATCAACACCCAGATGTA
108145 G C TTTTCAGATGGATGCAACATGATATTGGGATATTGATGCTTGTAGTTGTAAATTAATTCGCAGGCCATCGGAAGGACAGATTCTTGAAGCTCTTCATGTC[G/C]ATCCTGCATCTTCTTTCTTGTCGATCGAACATGATAAGGTTTCAAAATCGTTAAAACCACCAGTAAGTACTGGCACTTCATCATCAGCG
108145 GCAGGAGCAGAAC G CTCGCTGAAGCAAGGAGGTTAAGGCGTTATAGTCGCAGCCCCAGCACAAGTCGCTCTCCGCCAAGAAGGTACAGACGCAGAAGCCGTAGCAGAACCAGGA[GCAGGAGCAGAAC/G]CAGGAGCAGAACCAGGAGCAGAAGCTCACGCAGATATAGTTCACGTTCAAGTTCACGCTCTCGCTCTCCCA
108145 A C TCGCTCTCCGCCAAGAAGGTACAGACGCAGAAGCCGTAGCAGAACCAGGAGCAGGAGCAGAACCAGGAGCAGAAGCTCACGCAGATATAGTTCACGTTCA[A/C]GTTCACGCTCTCGCTCTCCCAGGTACAGGAGTCGGTCAAGACGTTGAAGTTTGATTAGTTT
108163 A G CCCAGACCCATGAAAGGTGCCTTCGTCTTGCTTCCTCTTTGTCGTCTCTTGGTCTCTCTCATGGCGATGTGGTATCGGTGATGGCACCAAACATCCCGGC[A/G]ATGTACGAGATGCACTTCGGAGTCCCCATGTGTGGAGCCATCCTGAACACTATAAACCTCCGCCTCGACGCTCGCACAATCTCGGTCC
108163 C A CGGTGATGGCACCAAACATCCCGGCAATGTACGAGATGCACTTCGGAGTCCCCATGTGTGGAGCCATCCTGAACACTATAAACCTCCGCCTCGACGCTCG[C/A]ACAATCTCGGTCCTTCTCCAGCACAGCAAAGCCAAGTTATTAATACTCGACGCCCATTCCCACTCCCTCGCCCTCTCTGCAATAAAAC
108163 T C GCACTTCGGAGTCCCCATGTGTGGAGCCATCCTGAACACTATAAACCTCCGCCTCGACGCTCGCACAATCTCGGTCCTTCTCCAGCACAGCAAAGCCAAG[T/C]TATTAATACTCGACGCCCATTCCCACTCCCTCGCCCTCTCTGCAATAAAACTCTTCCCACCCACCCATCCTTCTCCCAAACTCATCATAA
108163 A C GAGTCCCCATGTGTGGAGCCATCCTGAACACTATAAACCTCCGCCTCGACGCTCGCACAATCTCGGTCCTTCTCCAGCACAGCAAAGCCAAGTTATTAAT[A/C]CTCGACGCCCATTCCCACTCCCTCGCCCTCTCTGCAATAAAACTCTTCCCACCCACCCATCCTTCTCCCAAACTCATCATAATAGAAGAC
108163 C T CATTCCCACTCCCTCGCCCTCTCTGCAATAAAACTCTTCCCACCCACCCATCCTTCTCCCAAACTCATCATAATAGAAGACCACCACGAACCCTCCGCCA[C/T]TTCACATTCCCTACCCACCTACGAAAGCATGATCCAATCCGGGGACCCGAACTTTCAGTGGATCCGCCCTAAATCGTCGTGGTCGCCCAT
108163 T C CCCTACCCACCTACGAAAGCATGATCCAATCCGGGGACCCGAACTTTCAGTGGATCCGCCCTAAATCGTCGTGGTCGCCCATGGTCCTGAACTACACCTC[T/C]GGCACCACCTCCTCCCCTAAAGGCGTCGTCCACTGCCATCGCGCCCTCTTCCTCATGACCACGGACTCCATCCTCGACTGGCCCCTTCC
108163 A G CTGGCACCACCTCCTCCCCTAAAGGCGTCGTCCACTGCCATCGCGCCCTCTTCCTCATGACCACGGACTCCATCCTCGACTGGCCCCTTCCGAAAAACCC[A/G]ACCTACCTATGGACCCTCCCCATGTTCCATGCCAACGGGTGGAGCTTCCCCTGGGGTGTCTGCGCCATGGGCGGCACTAACATCTGCC
108163 A G ACCCAACCTACCTATGGACCCTCCCCATGTTCCATGCCAACGGGTGGAGCTTCCCCTGGGGTGTCTGCGCCATGGGCGGCACTAACATCTGCCTCCGCAA[A/G]TTCGACGCCTCCACCATCTATGCCACGCTCCTGCATCACAACGTCACCCACATGTGCGGCGCACCCGTCGTCCTCAACATGCTCGCCA
108163 C T ACATCTGCCTCCGCAAATTCGACGCCTCCACCATCTATGCCACGCTCCTGCATCACAACGTCACCCACATGTGCGGCGCACCCGTCGTCCTCAACATGCT[C/T]GCCAACGCCCCCAACCCCACCTTACCCGCCCATCCCGTCCACATTCTTACAGCTGGCGCCCCACCCCCAGCGCCCGTGCTGCACCGTAC
108163 T C ACAACGTCACCCACATGTGCGGCGCACCCGTCGTCCTCAACATGCTCGCCAACGCCCCCAACCCCACCTTACCCGCCCATCCCGTCCACATTCTTACAGC[T/C]GGCGCCCCACCCCCAGCGCCCGTGCTGCACCGTACGGAGTCGCTGGGCTTCGTCGTAAGCCATGGGTACGGCCTCACGGAGACTGGT
108163 A G CCAACCCCACCTTACCCGCCCATCCCGTCCACATTCTTACAGCTGGCGCCCCACCCCCAGCGCCCGTGCTGCACCGTACGGAGTCGCTGGGCTTCGTCGT[A/G]AGCCATGGGTACGGCCTCACGGAGACTGGTGGGCTACCGATCTCGTGCGCTTGGAAGGGGAAGTGGGACCGGTTGCCTGGAGATG
108163 C A TAAGCCATGGGTACGGCCTCACGGAGACTGGTGGGCTACCGATCTCGTGCGCTTGGAAGGGGAAGTGGGACCGGTTGCCTGGAGATGCCAGAGCCCGGCT[C/A]AAGGCCCGGCAGGGGGTGAGACGGCTCGGCACGACGGATGTTGATGTTTTGGATTCGGATGGGAAGAGCGTTAAGAGGGAT
108163 T C GAGATGCCAGAGCCCGGCTCAAGGCCCGGCAGGGGGTGAGACGGCTCGGCACGACGGATGTTGATGTTTTGGATTCGGATGGGAAGAGCGTTAAGAGGGA[T/C]GGGGCGAGCATGGGGGAGATAGTGTTGAGAGGTGGGTGTGTAATGCTTGGGTATTTGAACGACGAGGAAGGGACGAGGAA
108163 TG T ATAGTGTTGAGAGGTGGGTGTGTAATGCTTGGGTATTTGAACGACGAGGAAGGGACGAGGAAGGCGATAAGGCCGGACGGGTGGTTTTATACCGGGGATG[TG/T]GGGGGTGATGCACCCGGATGGATACATTGAGATTAGGGATAGGTCGAAGGATGTGATCATAAGTGGAGGGGAGAATTTGA
108163 T A TTGGGTATTTGAACGACGAGGAAGGGACGAGGAAGGCGATAAGGCCGGACGGGTGGTTTTATACCGGGGATGTGGGGGTGATGCACCCGGATGGATACAT[T/A]GAGATTAGGGATAGGTCGAAGGATGTGATCATAAGTGGAGGGGAGAATTTGAGTAGCGTGGAGGTGGAGTCGATTTTGTAC
108163 G A TTAGGGATAGGTCGAAGGATGTGATCATAAGTGGAGGGGAGAATTTGAGTAGCGTGGAGGTGGAGTCGATTTTGTACGGGCATCCGGATGTGAATGAGGC[G/A]GCGGTCGTGGCACGTGCGGATGAGTTTTGGGGTGAGTCGCCATGCGCATTTGTTAGCTTGAAGGAGGGGAGGACGGTGAG
108165 G A AAACTCTATGCCAGGCAATTTGTTGGCTTCAAATGCACAACCTCGAGAATTTGATCTTCCACCATTACACACAACCGAATCAATGACTTCACAGTATAAC[G/A]CAGGAACACCTTCCATCAGCACGTCTCTTTCGGCGGCAGAGGTTAAACCAGAAGTTTTTTCAACTGCACAACCAAATCAACAAAATTTA
108165 A G ACTCTATGCCAGGCAATTTGTTGGCTTCAAATGCACAACCTCGAGAATTTGATCTTCCACCATTACACACAACCGAATCAATGACTTCACAGTATAACGC[A/G]GGAACACCTTCCATCAGCACGTCTCTTTCGGCGGCAGAGGTTAAACCAGAAGTTTTTTCAACTGCACAACCAAATCAACAAAATTTACC
108165 T C TGAAGTTTAATAGTATGCTACCACAGTACAAATCTGGAATTTCAGGAACTAATTTGACTCAGTCTTCTGCTCTCCCACCAGGGTATGGGGGTTTAACTGC[T/C]TCGGCTAATAACATTCCAGATAATTTCAACTCAAACCCGTCTACTGCTTTGGGTAATACAGCTGTTGGATTTGAGGATGCTTTGCGCTC
108165 T C TCCCACCAGGGTATGGGGGTTTAACTGCTTCGGCTAATAACATTCCAGATAATTTCAACTCAAACCCGTCTACTGCTTTGGGTAATACAGCTGTTGGATT[T/C]GAGGATGCTTTGCGCTCTCAGTACAAAGATGTTTCACATTATCTTCCAGTTCAACATAACGATAGCTCAGCGATGTGGTTACAAGGAG
108165 T C CAGAGCGCTCCTCCCACTTTCAGACAAGCTCCACAGCAGCATCCTTCACAACAGTATGCCCAAATGGGATACCTCAACATGTACCAATCGCAAGGGGGAG[T/C]CTCCCAAGAGCAGCAGCAGCAGCAAAACCCTAACCCTAACGAGAGCAACATGGGCGGCTCTCAGGGTCAGATGTGGCAGCATGGC
108165 GAGC G TCCTCCCACTTTCAGACAAGCTCCACAGCAGCATCCTTCACAACAGTATGCCCAAATGGGATACCTCAACATGTACCAATCGCAAGGGGGAGTCTCCCAA[GAGC/G]AGCAGCAGCAGCAGCAAAACCCTAACCCTAACGAGAGCAACATGGGCGGCTCTCAGGGTCAGATGTGGCAGCATGGCTACTG
108169 A G ATATTTTAGGCTACCCAATGAATCCTAATGAAAAGGAGTGTACATACTATTTAAAAACCGGACTGTGCAAATTTGGCAGCACTTGTAAATTCAATCATCC[A/G]CAACCAACCAATGGGATGATCGCATTGCGTGGAGATTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAA
108169 A C GAGTGTACATACTATTTAAAAACCGGACTGTGCAAATTTGGCAGCACTTGTAAATTCAATCATCCACAACCAACCAATGGGATGATCGCATTGCGTGGAG[A/C]TTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAATTTTGCCCCAGTAATACTGCCCCAAGGAATGGTTC
108169 T A GTAAATTCAATCATCCACAACCAACCAATGGGATGATCGCATTGCGTGGAGATTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCC[T/A]TCAAATTTTGCCCCAGTAATACTGCCCCAAGGAATGGTTCAAGTTCCTAGCTGGAACTCTTTTTCTTTAGGATCGACATCGTCTATACAG
108169 T C CCAACCAATGGGATGATCGCATTGCGTGGAGATTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAATTTTGCCCCAGTAA[T/C]ACTGCCCCAAGGAATGGTTCAAGTTCCTAGCTGGAACTCTTTTTCTTTAGGATCGACATCGTCTATACAGAACCAACAAATGTCACAAC
108169 C T ATGGGATGATCGCATTGCGTGGAGATTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAATTTTGCCCCAGTAATACTGCC[C/T]CAAGGAATGGTTCAAGTTCCTAGCTGGAACTCTTTTTCTTTAGGATCGACATCGTCTATACAGAACCAACAAATGTCACAACAAAGTGA
108169 A G GGATGATCGCATTGCGTGGAGATTCTGCTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAATTTTGCCCCAGTAATACTGCCCCA[A/G]GGAATGGTTCAAGTTCCTAGCTGGAACTCTTTTTCTTTAGGATCGACATCGTCTATACAGAACCAACAAATGTCACAACAAAGTGATAC
108169 C T CTCAATTTGCAAATCTTCCCATGTCAAGAGCTTGGCCTTCTCCTTCAAATTTTGCCCCAGTAATACTGCCCCAAGGAATGGTTCAAGTTCCTAGCTGGAA[C/T]TCTTTTTCTTTAGGATCGACATCGTCTATACAGAACCAACAAATGTCACAACAAAGTGATACTAATGCATTTCCTGAAAGACCCGATGAG
108169 C T CGACATCGTCTATACAGAACCAACAAATGTCACAACAAAGTGATACTAATGCATTTCCTGAAAGACCCGATGAGCCCGTGTGCCAGTTTTACATGAAGAC[C/T]GGAGACTGCAAATTTGGTGCTTCCTGTAGATTTCATCATCCTAAAGAAAGATATTTTTCGCCTCCTACTTGTCTTTTGACTCCTCTTGG
108169 C G TTTGGTGCTTCCTGTAGATTTCATCATCCTAAAGAAAGATATTTTTCGCCTCCTACTTGTCTTTTGACTCCTCTTGGTCTTCCACTTCGCCCTGGAGAGC[C/G]TGTGTGCATATTTTATTCGCGGTATGGCATTTGCAAATTCGGGCCAAGTTGCAAATTCAACCATCCAACGGAGAATGCGATTGACGTTTC
108169 C T ATTTTTCGCCTCCTACTTGTCTTTTGACTCCTCTTGGTCTTCCACTTCGCCCTGGAGAGCCTGTGTGCATATTTTATTCGCGGTATGGCATTTGCAAATT[C/T]GGGCCAAGTTGCAAATTCAACCATCCAACGGAGAATGCGATTGACGTTTCACCAATACATCTATTATCATCTTCTACCCCACCACCATATG
108169 G A TCGCCCTGGAGAGCCTGTGTGCATATTTTATTCGCGGTATGGCATTTGCAAATTCGGGCCAAGTTGCAAATTCAACCATCCAACGGAGAATGCGATTGAC[G/A]TTTCACCAATACATCTATTATCATCTTCTACCCCACCACCATATGCATTATCATCGGAAGGTTCTAGAAGATTATCGTCGCCCGATTCA
108169 T C TGACGTTTCACCAATACATCTATTATCATCTTCTACCCCACCACCATATGCATTATCATCGGAAGGTTCTAGAAGATTATCGTCGCCCGATTCAGAACAA[T/C]TAGCAGCTAACGATAACAAGGTAGATGAACATCCAACCATCTAAGGGCACATTCTTGTGTATTCATGTAAATATCAGAGTGCAGCATCG
108169 A G CCAATACATCTATTATCATCTTCTACCCCACCACCATATGCATTATCATCGGAAGGTTCTAGAAGATTATCGTCGCCCGATTCAGAACAATTAGCAGCTA[A/G]CGATAACAAGGTAGATGAACATCCAACCATCTAAGGGCACATTCTTGTGTATTCATGTAAATATCAGAGTGCAGCATCGGCGACATTTG
108169 TTG T TCATCGGAAGGTTCTAGAAGATTATCGTCGCCCGATTCAGAACAATTAGCAGCTAACGATAACAAGGTAGATGAACATCCAACCATCTAAGGGCACATTC[TTG/T]TGTGTATTCATGTAAATATCAGAGTGCAGCATCGGCGACATTTGATGTATAATAAATAAGATATATGACAAATAAAACGCAACAG
108169 C T CCCGATTCAGAACAATTAGCAGCTAACGATAACAAGGTAGATGAACATCCAACCATCTAAGGGCACATTCTTGTGTATTCATGTAAATATCAGAGTGCAG[C/T]ATCGGCGACATTTGATGTATAATAAATAAGATATATGACAAATAAAACGCAACAGATTGGTTGATGATGTGTAAGCTAAAGTTGTTC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108169 C T GATTCAGAACAATTAGCAGCTAACGATAACAAGGTAGATGAACATCCAACCATCTAAGGGCACATTCTTGTGTATTCATGTAAATATCAGAGTGCAGCAT[C/T]GGCGACATTTGATGTATAATAAATAAGATATATGACAAATAAAACGCAACAGATTGGTTGATGATGTGTAAGCTAAAGTTGTTCAAG
108169 G A AATAAATAAGATATATGACAAATAAAACGCAACAGATTGGTTGATGATGTGTAAGCTAAAGTTGTTCAAGTTGTATGTACAACGTTGATAGTGCGATTTA[G/A]GCTATGACAGCAATGTAAACTGAGCTAGACCTTGAAATAAATGCTTGTATGATTGGTTGTGAAAACCAGTGATTTAAGAAGATTGTT
108177 C T ACTTCGACTTACTGTTAGCCCGACATACTCCAACCGTCTACTTTTACCGGTCCAACAACGCACCGCGTTTTTTCTCAGTCGAACCGCTTAAAATTGCGCT[C/T]GGGAAGGCATTGGTTCCGTTCTATCCGCTGGCCGGTCGGCTTGGAGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGAT
108177 C T TTACTGTTAGCCCGACATACTCCAACCGTCTACTTTTACCGGTCCAACAACGCACCGCGTTTTTTCTCAGTCGAACCGCTTAAAATTGCGCTCGGGAAGG[C/T]ATTGGTTCCGTTCTATCCGCTGGCCGGTCGGCTTGGAGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGATGGTGTGTT
108177 G A CTCCAACCGTCTACTTTTACCGGTCCAACAACGCACCGCGTTTTTTCTCAGTCGAACCGCTTAAAATTGCGCTCGGGAAGGCATTGGTTCCGTTCTATCC[G/A]CTGGCCGGTCGGCTTGGAGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCA
108177 G A TACCGGTCCAACAACGCACCGCGTTTTTTCTCAGTCGAACCGCTTAAAATTGCGCTCGGGAAGGCATTGGTTCCGTTCTATCCGCTGGCCGGTCGGCTTG[G/A]AGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGAAAATCGATG
108177 T C CGCTTAAAATTGCGCTCGGGAAGGCATTGGTTCCGTTCTATCCGCTGGCCGGTCGGCTTGGAGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGG[T/C]GATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGAAAATCGATGATTTTGGTGATTTTCAGCCGTCCGATGAGATGAGGAGTA
108177 A T TATCCGCTGGCCGGTCGGCTTGGAGTGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGA[A/T]AATCGATGATTTTGGTGATTTTCAGCCGTCCGATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGG
108177 G A TGGACCAGACCGGTCGGCTTGAGATCAAATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGAAAATCGATGATTTTGGTGATTTTCA[G/A]CCGTCCGATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAG
108177 T C CAAATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGAAAATCGATGATTTTGGTGATTTTCAGCCGTCCGATGAGATGAGGAGTATG[T/C]TGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGGTGTATGCCTAGGCACAG
108177 G A AATGCAGCGGTGATGGTGTGTTATTTTTGGTTGCACGGTCAGATATGAAAATCGATGATTTTGGTGATTTTCAGCCGTCCGATGAGATGAGGAGTATGTT[G/A]GTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGGTGTATGCCTAGGCACAGC
108177 G A AAATCGATGATTTTGGTGATTTTCAGCCGTCCGATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTT[G/A]ACGTTCTTCAAGTGTGGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACA
108177 TG T GTGATTTTCAGCCGTCCGATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTG[TG/T]GGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACAT
108177 T C TTCAGCCGTCCGATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGG[T/C]GTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGT
108177 C T ATGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGGTGTATGCCTAGG[C/T]ACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAAC
108177 A G TGAGATGAGGAGTATGTTGGTGCCTAACGTGGAGAATGCTGATGTTCCTTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGGTGTATGCCTAGGC[A/G]CAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAACA
108177 A G TTTGGTTATGTTTCAGTTGACGTTCTTCAAGTGTGGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTT[A/G]TTAACACATGGTCAGACATTGCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACC
108177 T C CGTTCTTCAAGTGTGGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACAT[T/C]GCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCA
108177 C T TCTTCAAGTGTGGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGC[C/T]CGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAG
108177 G A TTCAAGTGTGGGGGTGTATGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCC[G/A]TGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCG
108177 G C TGCCTAGGCACAGCTGTCCACCACACCGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAACATAT[G/C]TGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATT
108177 G A CGCTGCAGATGGTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACC[G/A]TCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTT
108177 T C GTCTTGCTGCCCTACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGC[T/C]CGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCG
108177 A G ACACTTTATTAACACATGGTCAGACATTGCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCC[A/G]ACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGT
108177 G C CATGGTCAGACATTGCCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAA[G/C]CACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATT
108177 C T CCCGTGGCATCACCAACATATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTC[C/T]CCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACG
108177 G A TATGTGTTCCACCTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCAC[G/A]AGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCC
108177 C A CTTCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAA[C/A]ATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTA
108177 T C TCTTTGGACCGCACCGTCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACA[T/C]ACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATC
108177 G A TCTTGAAAGCTCGTTCTACCCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGC[G/A]CATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTT
108177 T A CCCCAACATTCTTTTCAAGCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAA[T/A]ATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAG
108177 C A GCACAGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTG[C/A]AGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGC
108177 C T AGCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGA[C/T]GGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTC
108177 G A GCGAGTACTCCCCTAAACCATTAGCCACGAGCACCACCAACATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGAC[G/A]GATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCT
108177 G A ATACCTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTA[G/A]GGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCGACCTGACCAAGAAAGTTGTCTTACAATCACCGCTGACG
108177 T C CTTTCGTGTCTGCGCATCTTAAATTGTCCAAATATCAAATTTTGAAACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGC[T/C]GTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCGACCTGACCAAGAAAGTTGTCTTACAATCACCGCTGACGCACG
108177 C G ACTGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTT[C/G]GACCTGACCAAGAAAGTTGTCTTACAATCACCGCTGACGCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGC
108177 A T TGCAGACGGATGATTTAAGCGATCCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCG[A/T]CCTGACCAAGAAAGTTGTCTTACAATCACCGCTGACGCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGCCA
108177 C T CCCAAAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCGACCTGACCAAGAAAGTTGTCTTA[C/T]AATCACCGCTGACGCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGCCATATTCCGCACTTCTGCGGTTGCTA
108177 C G AAAGACCTTTATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCGACCTGACCAAGAAAGTTGTCTTACAAT[C/G]ACCGCTGACGCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGCCATATTCCGCACTTCTGCGGTTGCTAGCG
108177 C T TATCTACCTTTAGGGCTGTTGTGGCTCATGTTTGGAAGTCTGCTTGTAAAGCTCGCTCTCTTCGACCTGACCAAGAAAGTTGTCTTACAATCACCGCTGA[C/T]GCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGCCATATTCCGCACTTCTGCGGTTGCTAGCGCAGGTGACA
108177 A G GTCTTACAATCACCGCTGACGCACGTGCGCGAATGCAACCTCCTCTTCCTCCAGGGTTTCTCGGGAATGCCATATTCCGCACTTCTGCGGTTGCTAGCGC[A/G]GGTGACATTTTGTCGAACACACTTGAGTATGGTGCTAACAAGATAGCTGAAGCAACCAAAAAACTGGATAGTACCTACATCCGTTCC
108177 A G TGTCGAACACACTTGAGTATGGTGCTAACAAGATAGCTGAAGCAACCAAAAAACTGGATAGTACCTACATCCGTTCCCTAGCGGATTACTTGGAGACACT[A/G]AACAACATAACAGAATTGCAAACAGGGAAGTGGGTGATGCCGAAAAGCGATTTATGGGTGACAAGCTGGCTAGGGCTACCAATGT
108177 A G CCAAAAAACTGGATAGTACCTACATCCGTTCCCTAGCGGATTACTTGGAGACACTAAACAACATAACAGAATTGCAAACAGGGAAGTGGGTGATGCCGAA[A/G]AGCGATTTATGGGTGACAAGCTGGCTAGGGCTACCAATGTATGATGCAGATTTTGGATGGGGGAAACCCATATTCATGGGAAGA
108177 G A ATTACTTGGAGACACTAAACAACATAACAGAATTGCAAACAGGGAAGTGGGTGATGCCGAAAAGCGATTTATGGGTGACAAGCTGGCTAGGGCTACCAAT[G/A]TATGATGCAGATTTTGGATGGGGGAAACCCATATTCATGGGAAGAGTGAGTTTGAAGTTCAGTGGGGTTGTTTATGTGATGCAG
108177 T G GTTTAAGAGAGTCTTTTATGCAAAATTTCATGAGTTCGAACATACAGTTGGGTGAACTGTTGTTACTTGTTAGTAAGCTTTGATTTGAACATGTGTTGTA[T/G]TGTTTGATATTTTGTAAGTGTTGAATTTGAAATGAAGTTGAGTGGAAGATATTATCTGTAAAAAAAAAAAAAACGGC
108179 G A AATCCGAAATCGCCCTAAAAAGCTCAGGCAAATGCGACTTCAAACTCCCAAGCGACTTCTCCCTAACCTGCCTGCACAGCTTCTGATGCTCTTCAACCTC[G/A]GCATCCAGCCTCGTCTTCAAAGAATCAACCACAAACTTCCTCTCCGCCACCAAATCCTTGGCGTTCTCACCCCCTTCAACGCTGTTCTCC
108179 C T CGATCGGGATGAGGTTCAGCTTGAGCCAGCTGTTGAGGAACTGCACGTACTCTCTCTGATGGGTTATCAGTTTGTCAAAGTGGGTGTACCAATCACGGAC[C/T]ACGTCGTGTAGTTGGAGGGTGCGGCCATGGTGGTGCTCTGTTGTTTCGCGGATTGTGGTGGAGATGTCCAGGGATCGGATGTCCG
108185 GAAC G ATATAGTAGTACCCTTCTCTTTAGAGCAAGACTTTTGACGTCCTCTAAGAACAATTTGATTACATGTTATTCTGCGGGTACACAAAGCAATGAAACTAAA[GAAC/G]AACATGCAAGGAGCACAGACGATGAAAAAATAATATCCAATGCGAAGCATGAGAATGAGCAAATTGGAGGAAGCAGTATTCAG
108185 C A TGACCAAGCCACTAGAAAAATTATTTCTGCATATTCGATTGTTTACAATGATGCAATATATATAAATGAAAGAGCACGCAATGACACTGTGTTGCTTTCT[C/A]GGAGCATAACACGACTCGATGATCGGGCACGCCAGGATGTTGCTGTACTCGGATCGGGGATATTGAAGCTTGATGCTAGAGCAAGG
108185 A C CAATGACACTGTGTTGCTTTCTCGGAGCATAACACGACTCGATGATCGGGCACGCCAGGATGTTGCTGTACTCGGATCGGGGATATTGAAGCTTGATGCT[A/C]GAGCAAGGAAAGACACTGAGAAAATTGATCATGGAATGAAGAAAAAAGCTGCACGCTTGAACCATATAACTACAATAATAAAAGA
108185 GA G ATGATCGGGCACGCCAGGATGTTGCTGTACTCGGATCGGGGATATTGAAGCTTGATGCTAGAGCAAGGAAAGACACTGAGAAAATTGATCATGGAATGAA[GA/G]AAAAAAGCTGCACGCTTGAACCATATAACTACAATAATAAAAGACAGAGCTGTAACTAAACTGAAAAGAGTAGCAGACCAGCA
108185 G A AGCACTGGAGCGATGGTGCCTTGGAGGCCGACTTAAAGCGAGCTGACTTTGCTGTTAGGAGACGAGCTATGGAAGATGCATTCATGGCTTTAAAGTTTGT[G/A]AAGAACATTCTTGACACAATGGCAAGTAAATTGTACCAGCAGCCTCAGAAGCAAGGTTCTTTTACCGTAGACAGTACATTAGGATT
108185 T C GCAGTGTCTCTCTTTTGGCTGAATGCTCGAGTTCACCGGATGTTAACACGAGGCAAGCTCTAGCAAATGCACTGGCAGCAGCTCCATCCATGTGGATTCT[T/C]GGAAATGCGGGCATGGGAGCATTACAAAGATTAGCACAGGATACCAATCCTGCAATTGCAGCTGCAGCATCAAAAACAATTGAAGA
108191 G A CAACCCGACATAGTAATGGACAGCCTCACCATCCGGGGCCTAGGCCTGGTCCACCCCAAAAAGGTCTACTCCTTCTACAATGAACTTCACCAGTATTTAA[G/A]ATCATGTGGAGTGGATGGAGTGAAAGTGGATGTTCAGAACATTATAGAGACCCTTGGGTCAGGATTTGGAGGACGTGTGTCTTTGA
108191 C T CTCTGTTTCTTGGGGAGTTTATGCAGCCTGATTGGGATATGTTTCATAGCCTGCATCCTGCTGCAGAGTATCATGCAGCGGCTCGAGCTATTGGTGGTTG[C/T]CCCATCTATGTTAGTGACAAGCCAGGGCACCATAACTTTGACCTACTAAAGAAATTGGTCTTTCCAGACGGGTCAATTCTTCGAGCCC
108191 T C GTGGTTGCCCCATCTATGTTAGTGACAAGCCAGGGCACCATAACTTTGACCTACTAAAGAAATTGGTCTTTCCAGACGGGTCAATTCTTCGAGCCCAGCT[T/C]CCGGGCCGTCCGACCCGTGATAGCCTTTTCAACGACCCTGCTCGAGATGGCACCAGCCTGTTAAAAATATGGAATGTTAACAAATGC
108191 GA G TGCTCGAGATGGCACCAGCCTGTTAAAAATATGGAATGTTAACAAATGCACTGGGGTGGTAGGAGTATTCAACTGTCAAGGTGCCGGTTGGTGCAAAGTG[GA/G]AAAAAAAGACTCGCATTCATAATGCTGATCCCGGCACTTTAACTGGACATGTTCGTGCACAAGATGTGGATACCATTGCAGAAC
108191 A T CTGTCAAGGTGCCGGTTGGTGCAAAGTGGAAAAAAAGACTCGCATTCATAATGCTGATCCCGGCACTTTAACTGGACATGTTCGTGCACAAGATGTGGAT[A/T]CCATTGCAGAACTCGCTGGCGATAGCTGGAATGGACAAACAATTGTTTACTGCTATCGATCTGGTGCGCTCATTCGTTTGCCAAAG
108191 A T AGAGGTGAGAGCACTGTTGTTGCATTGAAGGTTAGAGGATGCGGTAAATTTGGAGCTTACGTATCCCAAAAGCCGAGTAAATGCACGCTAGACTCATCTG[A/T]AGTGGAATTCGACTATGATTCGGAGAATGGGTTACTGGGTTTGGATATTCCTGTGCCCGAGAAGGAGATGTATAGATGGAACTTG
108205 A G TTACGCCCATGCTTTCAGGTGAGAGAAGCTCCGGTGAAATGCAAGATGGGCTCAGCGGGCTTCTAGGGCTTGTGCTGAATTGCTGTGGTCGATAGAGCCC[A/G]TACCCTAAAAAGAAATACTCCATTGGGATCAACATGGCATACGGTTGCTCTTCTGTTACCATAGATCCACATGCTTGTACCTCAACC
108205 C T AAGATGGGCTCAGCGGGCTTCTAGGGCTTGTGCTGAATTGCTGTGGTCGATAGAGCCCATACCCTAAAAAGAAATACTCCATTGGGATCAACATGGCATA[C/T]GGTTGCTCTTCTGTTACCATAGATCCACATGCTTGTACCTCAACCAAGGCACTGTATCTTCTATCTAGTTTTGAAGTCATATGGATAG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108205 T G CGTCCAGAAAACTTCTGCAGGCTTGGACAAAATCAGATTCAGCGTACTGACCAATTCCCCGAACTTCCTTGCTAAAGTAGCGCTGAAGTAGACAATCCTT[T/G]ATTAAACCACACATGCCATAGTAATAGAGCAAATTAGACATGACTTTGTTGAACAACCACTCCTTCCAAGAAGGTGCTTTACACAACG
108205 G A AGAAGTCCAGAACATCAGCTATTTGATCTGCCAAGTCATCAACGGAAAGTACAGGAATATCGGAAGGAACTGGAGCAGCCCCTAACTCATGGCCAGGAGG[G/A]CTAATATGATATATGCAAAAGTTGTGAAGCAACAATGAAGCAGCTTCAGGCCAAAAGAATAATCCTTGGAAGCATGACGTATGAT
108205 G A ATGACGTATGATTTAGAGCTAAATCTGGATATGTAATAAGAGCAGGTTTCTCTTGATCTCCATATACAGAAACTGACACTAAGCCACAATTTGTATGCAC[G/A]AGATGTTCCTTTCCACCAAAAGAGACTCGATCCACGTCGACGGAGACGGAGCTACCCGATTCTCCCATCCTCACCGGACCCGAAAACC
108205 A G TGGATATGTAATAAGAGCAGGTTTCTCTTGATCTCCATATACAGAAACTGACACTAAGCCACAATTTGTATGCACGAGATGTTCCTTTCCACCAAAAGAG[A/G]CTCGATCCACGTCGACGGAGACGGAGCTACCCGATTCTCCCATCCTCACCGGACCCGAAAACCCGCTTTTTTCCTCCGGAAACTAAAA
108205 G T ACTAAGCCACAATTTGTATGCACGAGATGTTCCTTTCCACCAAAAGAGACTCGATCCACGTCGACGGAGACGGAGCTACCCGATTCTCCCATCCTCACCG[G/T]ACCCGAAAACCCGCTTTTTTCCTCCGGAAACTAAAATAAAAACAATCAAAGCTGTTTACTCTCCAGTAGGCCAACAGT
108209 A G ATAAAAAAGCTTCATAAATATAAGTGCTCCTACATGTAGCTACATAAATACTAAAATATAGAAGCAACTGCAAAATACATGTCAAATTTGGAATAACCCC[A/G]AGCGCAAATAAATATAAATTAGATCGGGAAACTCGAATGATGGTCGCCAGGCATGCATAACAGTTATTTGGTAACTTTGTAGGACTTT
108209 A T ATATAAGTGCTCCTACATGTAGCTACATAAATACTAAAATATAGAAGCAACTGCAAAATACATGTCAAATTTGGAATAACCCCAAGCGCAAATAAATATA[A/T]ATTAGATCGGGAAACTCGAATGATGGTCGCCAGGCATGCATAACAGTTATTTGGTAACTTTGTAGGACTTTACAACTTTCAACAACCC
108209 C T AAATACTAAAATATAGAAGCAACTGCAAAATACATGTCAAATTTGGAATAACCCCAAGCGCAAATAAATATAAATTAGATCGGGAAACTCGAATGATGGT[C/T]GCCAGGCATGCATAACAGTTATTTGGTAACTTTGTAGGACTTTACAACTTTCAACAACCCTTTTGCCACACTGTCAGTTTCAAAGTGA
108209 T TA GCAGTACTCTCTTGCAAGAACGTTAACTTTCCTCTGATCCATCCCAAGTTGGCAGATGTCAGCCTTCAGGAAGAAAACATCTGCACATTGCATGCATGGA[T/TA]AAAAAATTTGAGCAGCAGTCAAATCGTCTGTCTCCTTACGACCCATGATCTGGCTACACCTGACTATCCTAGCAAGTGTGTTTGCTTT
108209 G A TCTCCTCAGCACTTAATCCAGAATTTGCAGGTGAAGGCTGAGAAGAAGAGGCTTCTACTTCCACTGCCAGAGCTTCTGTCACGTCGGCAGATACAACTGC[G/A]GGAGTTGATTCTAAGAAGGGAGCTGAGTCGGCGGCGGGAGATAGATCGGCGGAAGGAGCTGAATCAGCGGGGGGAGCTGAGTT
108211 G A CAGCGTGTTCTGCTGCATTTCCAACAATAGGCAGTAATATGACACTGATGAAGCTAACAGATATGCCCCATGATTCTGATGCAGCCTCAATGGTGCCAAC[G/A]GTATACTCAGACAATACTGCTATTAGGACTGTCATCCCAACTAACCACGCAAATGCACTTCCATAACCTATAACAGGCCCTTCTTCAG
108211 C T AACCGATTAAGGAATACTTGACAACGTCTATCTTTCCTTGGTAAAGTGCAAATAGAGCTATGATAAGCTCCGTGGCATTGCCACATGTTGCATTCAATAG[C/T]CCACCAACAGTAGGACCAGTGAAATAGGAAATTTGCTCAGTAAGGAAGCTGACACGTTCAGCTAGTGGAGTTAGGCCTAGCAAGCTT
108211 G A GCGGCACAGCAGGGAACAAAACGAAGAGCTTGGTACCCAGAAATATCTCCTGCAGATTCCCAAGCACGTCCCTCAGAACCCCGCACCTCACCTTGGACAC[G/A]AGCGTCCGGTCCGACCTCTTACGGAGCGAAGTGGCGGACATGTTGTGCGCCGTGCGGCTGTGGTTGTGATGGTGGTGGCGCATT
108211 A C CGAAGAGCTTGGTACCCAGAAATATCTCCTGCAGATTCCCAAGCACGTCCCTCAGAACCCCGCACCTCACCTTGGACACGAGCGTCCGGTCCGACCTCTT[A/C]CGGAGCGAAGTGGCGGACATGTTGTGCGCCGTGCGGCTGTGGTTGTGATGGTGGTGGCGCATTTCCTTGGTCAACGGCACACCAC
108211 G A GATTCCCAAGCACGTCCCTCAGAACCCCGCACCTCACCTTGGACACGAGCGTCCGGTCCGACCTCTTACGGAGCGAAGTGGCGGACATGTTGTGCGCCGT[G/A]CGGCTGTGGTTGTGATGGTGGTGGCGCATTTCCTTGGTCAACGGCACACCACCACCGCCGCCGGATCCGCTTCCGTTCCCGTTATG
108217 T C AGGCTGTGGGAGAGCTTCGGCTCCAGGCTTATACTGAGATAACCAAGAACGTCGTAAATGACAATATATTTTCTCAATTTATGTACAAAACACTGCCTAG[T/C]GGCAATCATCTTTGGGCTTTCAAAAAGCAGTTTGCTATCCATTTGGCTCTTTCCTGTTTTATGTCCTACATGCTGCAAATTGGTGGGAG
108217 A G AGCAGAAAGTCGTGACCAATGTCGACAATGTTATTGATCGCATTAAAGCAATAGCTCCGCAAACTTTTGTCGAAGAGGAAGAGGACACCACTGATCCTCC[A/G]CAATCCGTTCAAAGAGGTGTGACTGATCTGATCGATGCTTCTCTGAGCCCTAGGAATTTGTGCATGATGGACCCAACTTGGCACCC
108219 T C TCTTTCCTGCTGCACCGTACACTGGAGCGAGACCTCCAGCAACTGGACCTGGGTTTGCACTCACAGTTTTTACAGCATCCTTCAAATCTCTCAGGAAGTC[T/C]TCGTATACTGGAACATGTTGAAGCGTCACACAAATATGTATGCTGTTGGGTCTTTGCAATGCATTCAAGTGCCAACCTTTTGATGACAT
108219 G A TGGGTCTTTGCAATGCATTCAAGTGCCAACCTTTTGATGACATGATATCATTAACCTCAAATATATCGATTGTGTTAGAGCCAAATGCAATAACTGTCAT[G/A]TCCGGTTTTCCAATAACGAACAGCTCAGAAATCTCTCCGATGCCTTTCTCTATCTTCTTAGATACTTCCATAATCTCTTTCGTGTTTTCCA
108225 A C GTTGGGCATACAAATTACAAGGTTTTCTTCGTTTTCCTGTTGTATGCTGTGATAGCCTGCATTTATTCACTGGTCCTTTTGTTGGGAAGTACTGCTGATG[A/C]TGTACACAAAGACCATGGTTCTTTCAAGATTACATACATTATTAGTGGACTGTTGCTTGTTCCCCTTACAATGGCCCTTAGCATACTTTTT
108225 T C AATCTATAATAACTTCACCTCGGTCCTTGGCCCAAATGTATTTTCTTGGATCTGCCCAACAACCAAACATATAGGCTCTGGTATAAGGTTTCGTACCTCA[T/C]ATGATCAAAGTCCAGTGCCTCAAGGCGATAAGTCAATCAATTAGCAATGTAAACATGCACATAATATATGGCAGTTGTTTATTTTGTACT
108227 T C TCTCCTCCATTCGGAAGGTGCTAATGGACAAGCTCGCATTGAAGGGTCCAACAAAGGAAGGTGCAGGGTACCTCCCTCATACTGCACAAGTGAAGGCCTG[T/C]ATCGCAGTTTGAGACGAGGAAAAGCATGTCCATATAGTGACGGTGAAGTCTGTACCAAAATATCAGAGAACCTTTTATCGTGCTTA
108229 C T AAAACACAGTCATTTCTCGAGCAGGATCGCCCCAGTTATGCCAACCACTAGGTATGATGATGTCTTCCATGTAAGTATATGCAAAAACTACACGGGAGAA[C/T]AGTCCCCAAGCTCTTCCAAGGTACAGTGCCCCAGATCCTGTCACTTTGCAGTTCACAAAAGAAAAGCCTGTGTCCTCTAGCATGCTCA
108229 G A ATATCCTTAATGCCACTGCTTGCTTTCCTACTGCTCCTGGTCCAGGCGCTGGTGTTGTATTCTTGAAAGTGATATTTCTTGCAAGGAAGTAAGGGGAATT[G/A]ACAGCAAAAGTAGCAGACCCGAAAGTGCCGAGGGGCAGCCCTTTAGGGCCTAGAGTTTGGGCAGTGTCCCCAAACTGTACGACTGT
108229 T C TTGATCCTGATCGCAACTCTAACCAAATTAACAAGAGGCAGAGAATCAATAGCATCTTGTATGGTTGTGAAATCTCCTTTGGAAGGATTCTTATCCACTG[T/C]CAAAGCAAAAGAAGGTATCACTTTGTTCTTTGCTCTACTGTAGACAGAGTGCTTTAGTCCACCTACAAATTTAACCCATTTCATGAAGT
108229 T C GTGTCGCCCTGGCCTTAGTCCCTTGGTATGGCTTAATGCTATGCCAAAGTTCAGAGCTATAAGTAACAAGATTGTGGTAGAGAACAAATGATTAGAGCCT[T/C]GCATAATTTGCATGTACAAATGTGATAGATAGAGAAAGTTTGATTTCTTTTGTGTAATTTTGTTTTTTAGGTGGGAAATAGAATGGAA
108229 A T CCTTGGTATGGCTTAATGCTATGCCAAAGTTCAGAGCTATAAGTAACAAGATTGTGGTAGAGAACAAATGATTAGAGCCTTGCATAATTTGCATGTACAA[A/T]TGTGATAGATAGAGAAAGTTTGATTTCTTTTGTGTAATTTTGTTTTTTAGGTGGGAAATAGAATGGAAGTTTAAGTGGACGTCTTTTA
108239 G A TCGAATACTGCCCCATTGCTCTTCCTACGTACAGTTTGCCCGTTCCCGTAACATTGCAGTTCACAAAGGCAAACCCTGATTGCTCGCACGGCGAATTTCT[G/A]GCTTGTGCTGCTATTGATCCGAATCTCTCTGCTATCGAGTGTAGCTCACATCCCTTGTACATGGATCTGCCATTGCCAAATATGAAATCA
108239 T C GCCCCATTGCTCTTCCTACGTACAGTTTGCCCGTTCCCGTAACATTGCAGTTCACAAAGGCAAACCCTGATTGCTCGCACGGCGAATTTCTGGCTTGTGC[T/C]GCTATTGATCCGAATCTCTCTGCTATCGAGTGTAGCTCACATCCCTTGTACATGGATCTGCCATTGCCAAATATGAAATCAATGGATCC
108239 G T CCCGTAACATTGCAGTTCACAAAGGCAAACCCTGATTGCTCGCACGGCGAATTTCTGGCTTGTGCTGCTATTGATCCGAATCTCTCTGCTATCGAGTGTA[G/T]CTCACATCCCTTGTACATGGATCTGCCATTGCCAAATATGAAATCAATGGATCCTTCGATGTAGCAATTTTTGAAGTAATGCCTTCCTG
108239 G T CCATCCTTCCATTCCAGGCATTGGTGCTGGTGCTGTATTCTGTTTTCATTTTCATATATATTACCAAAAATTAAGTTAGTACAAGTTCTACATTCACAAA[G/T]ATTCAACCACGTCTGGTTGTTTCATTTACGATAACAGAGCTTCTGCTGCCTGAGTTGCAAGAATCCGCACGCAGTCTCCGAGAGTTGAAC
108239 CACG C CCATTCCAGGCATTGGTGCTGGTGCTGTATTCTGTTTTCATTTTCATATATATTACCAAAAATTAAGTTAGTACAAGTTCTACATTCACAAAGATTCAAC[CACG/C]ACGTCTGGTTGTTTCATTTACGATAACAGAGCTTCTGCTGCCTGAGTTGCAAGAATCCGCACGCAGTCTCCGAGAGTTGAACTTGG
108239 T C CATTGGTGCTGGTGCTGTATTCTGTTTTCATTTTCATATATATTACCAAAAATTAAGTTAGTACAAGTTCTACATTCACAAAGATTCAACCACGTCTGGT[T/C]GTTTCATTTACGATAACAGAGCTTCTGCTGCCTGAGTTGCAAGAATCCGCACGCAGTCTCCGAGAGTTGAACTTGGAAGCAAGAAAGAA
108239 A G GCTGTATTCTGTTTTCATTTTCATATATATTACCAAAAATTAAGTTAGTACAAGTTCTACATTCACAAAGATTCAACCACGTCTGGTTGTTTCATTTACG[A/G]TAACAGAGCTTCTGCTGCCTGAGTTGCAAGAATCCGCACGCAGTCTCCGAGAGTTGAACTTGGAAGCAAGAAAGAACTTACCTTGAAGG
108239 G A TATATATTACCAAAAATTAAGTTAGTACAAGTTCTACATTCACAAAGATTCAACCACGTCTGGTTGTTTCATTTACGATAACAGAGCTTCTGCTGCCTGA[G/A]TTGCAAGAATCCGCACGCAGTCTCCGAGAGTTGAACTTGGAAGCAAGAAAGAACTTACCTTGAAGGTGATATTTCTAGCAGTAAAATG
108239 CCGCA C AAAAATTAAGTTAGTACAAGTTCTACATTCACAAAGATTCAACCACGTCTGGTTGTTTCATTTACGATAACAGAGCTTCTGCTGCCTGAGTTGCAAGAAT[CCGCA/C]CGCACGCAGTCTCCGAGAGTTGAACTTGGAAGCAAGAAAGAACTTACCTTGAAGGTGATATTTCTAGCAGTAAAATGAGAAGC
108239 T G TTCTACATTCACAAAGATTCAACCACGTCTGGTTGTTTCATTTACGATAACAGAGCTTCTGCTGCCTGAGTTGCAAGAATCCGCACGCAGTCTCCGAGAG[T/G]TGAACTTGGAAGCAAGAAAGAACTTACCTTGAAGGTGATATTTCTAGCAGTAAAATGAGAAGCAAAAACAGTTACAGATGCAGTGTT
108239 T C TAAAATGAGAAGCAAAAACAGTTACAGATGCAGTGTTATATGTTCTTAATTGTTGACCGTTAGGTCCTTTATCACTTGCTCTATCATGCCATTGAATAAC[T/C]GTCGAGTCCCATCCTGCTCCTTGGAATGTAATGTATGGTTTTGATGCCGGCACAGTTACTTTCTCTATGTAAAGTCCTGCTTTGATTTTG
108239 C T AAGCAAAAACAGTTACAGATGCAGTGTTATATGTTCTTAATTGTTGACCGTTAGGTCCTTTATCACTTGCTCTATCATGCCATTGAATAACTGTCGAGTC[C/T]CATCCTGCTCCTTGGAATGTAATGTATGGTTTTGATGCCGGCACAGTTACTTTCTCTATGTAAAGTCCTGCTTTGATTTTGAGGATGACA
108239 A G GCAAAAACAGTTACAGATGCAGTGTTATATGTTCTTAATTGTTGACCGTTAGGTCCTTTATCACTTGCTCTATCATGCCATTGAATAACTGTCGAGTCCC[A/G]TCCTGCTCCTTGGAATGTAATGTATGGTTTTGATGCCGGCACAGTTACTTTCTCTATGTAAAGTCCTGCTTTGATTTTGAGGATGACATA
108239 C A ATTGTTGACCGTTAGGTCCTTTATCACTTGCTCTATCATGCCATTGAATAACTGTCGAGTCCCATCCTGCTCCTTGGAATGTAATGTATGGTTTTGATGC[C/A]GGCACAGTTACTTTCTCTATGTAAAGTCCTGCTTTGATTTTGAGGATGACATATACAGAATTGTTATCAGGAATTGAATCTACGGCTTCT
108239 A C GGATGACATATACAGAATTGTTATCAGGAATTGAATCTACGGCTTCTTGCACTGATAAGAAATCTCCTGCTCCTCTTGCATCCACTACAATGGTACGTTG[A/C]GAGGTGGGTTCAAAATAGTTGTGGTGATGGTGCTTGTAAGTGGAATCGACTTTACAAGCATTCGAAACTTGGAATGAAAGAAGGAAG
108239 G A CATATACAGAATTGTTATCAGGAATTGAATCTACGGCTTCTTGCACTGATAAGAAATCTCCTGCTCCTCTTGCATCCACTACAATGGTACGTTGAGAGGT[G/A]GGTTCAAAATAGTTGTGGTGATGGTGCTTGTAAGTGGAATCGACTTTACAAGCATTCGAAACTTGGAATGAAAGAAGGAAGAAGAAT
108239 A G ACGGCTTCTTGCACTGATAAGAAATCTCCTGCTCCTCTTGCATCCACTACAATGGTACGTTGAGAGGTGGGTTCAAAATAGTTGTGGTGATGGTGCTTGT[A/G]AGTGGAATCGACTTTACAAGCATTCGAAACTTGGAATGAAAGAAGGAAGAAGAATAGAAGAAGTATTGATTTTATGAAGATTGCCA
108239 G A GCACTGATAAGAAATCTCCTGCTCCTCTTGCATCCACTACAATGGTACGTTGAGAGGTGGGTTCAAAATAGTTGTGGTGATGGTGCTTGTAAGTGGAATC[G/A]ACTTTACAAGCATTCGAAACTTGGAATGAAAGAAGGAAGAAGAATAGAAGAAGTATTGATTTTATGAAGATTGCCATTGCAATGTT
108239 C T CTCCTGCTCCTCTTGCATCCACTACAATGGTACGTTGAGAGGTGGGTTCAAAATAGTTGTGGTGATGGTGCTTGTAAGTGGAATCGACTTTACAAGCATT[C/T]GAAACTTGGAATGAAAGAAGGAAGAAGAATAGAAGAAGTATTGATTTTATGAAGATTGCCATTGCAATGTTAAATGGATGATGAAG
108243 T C TGAAGGATTCTGCAGTGAACGCTATCTGTTATGGTGCAAAGCTGATGATTCCTGGGTTGCTGAGGTTTGAGAATGGGATTGAGAACGGAGAGGAGGTTGT[T/C]ATGATGACCACAAAGGGGGAGGCTATAGCTTTGGGCATTGCAGAGATGACTACTGCTGTTATGGCTACCTGTGATCACGGAGTT
108251 C CT CCCTAATGCAAATCCATTTCCAAAGAAATTCCCAATGCAGCTCGATAAGAGACAATCCTCTTCTCTTACGCAACCGCCTCAACAGTCCGGATCGAAAATA[C/CT]TCCTATGATCCATCCAAGATCAAATAATAATAATAGTAACAGCAACAATTCAAGATACAGTAGACCGACTTCTCCTTCACCAGCACCT
108253 G A ACCTGGATTTTGATTATGGTGCTCTCAACCAGTTACAACATTTCTCCATTAACAATCTTGGTGACCCATTTATTGAGAGCAACTATGGTGTTCACTCTAG[G/A]CAATTTGAACTGGGAGTCTTAGATTGGTTTGCTCGGCTATGGGAACTGGAAAAGGATGAATATTGGGGTTACATTACTAACTGTGGTA
108253 G A ATCTTGCTTCTAGAGATGCAACTATCATGGGCAGTAGAAACGGCCATGCCCCCATATACCTCTGGTACACCTTAAACAGAAAAGGATACAAAGGATTCCA[G/A]AATGAAGTTCAAAAATGCCTGAAAAACGCACACTATCTTAAGGATCAACTAAGAGCGGCAGGCATTGGAGCCATGCTCAACGAACT
108257 T C GATCTGCTGGGTGATGTTGACATCGATGATCCTTCTCAGCTGGTTGCCGCAGTACAGAAACAGAAGGTGGCTGTCGTAGCTCCGGCTGTCAAGCCTGTCG[T/C]AAAATTACCTACGAAACCTGTTCCGCCATCTCAAGCTGTGAGAGATGCTAGGAGTGCTAACAATGCTCCAGCACGAGGTGGTGCCG
108257 A AT GGAAAATTTAGTTAACATCATCATATTAGTTGTTATTGTTACTAGTTAGTACAAGTTTAAGTTCTCTTGCTTTCCCTTTATTTACTGCTGGTTTTGTCTT[A/AT]TTTTTTTTGTTTGATTATGAAAACGTCAACTCCCCTCATTTTCGTATGTTCTCTCCGTTTAAATTCGGGTTATTTTTGTGTACTGAGCTGGAT
108257 C T TTGCTTTCCCTTTATTTACTGCTGGTTTTGTCTTATTTTTTTTGTTTGATTATGAAAACGTCAACTCCCCTCATTTTCGTATGTTCTCTCCGTTTAAATT[C/T]GGGTTATTTTTGTGTACTGAGCTGGATGGTGGAAAGAGTGTGTTATTCAGAGAAGAATTTTACTTTTATTCATATGTTTTATGTTCAAAAAAA
108263 C T GCTCCAACAGAAAAATGCATTCGACTGCTGAACGCTTTCACTGTTTCGCTACCACGAAGCACGATGATGAAATCCGTGAGCTCACCCCCGAACTGTGGCC[C/T]CCATCCTAAACCAGCTGATGCTATAGCTGATGGAGCAGACCATGATCCATCCAGTCTTTTAGAAACTACTAGACCAGTGCCAAGCTTG
108269 C T GCCATGCTTCCTTTCCTTCTTTAACTCTTCTGTTCTCCGAAAAATAGTGTTCCGCTCTTTTTGCCAACTTCACATCTAATTCGTCCTTAAAAGCTTCATA[C/T]GAGCGAAAATCAACATGGCAAAGGAGAGGTTCTGATATTTGATTATTACCTGAAGCAATTGATAGAATTTTTGCAGCCTGTTTGCATTCAG
108269 T C AGAAGGTCATCAAATTGAGCAGAACGCAGTACAATCCTGGCATCATTTGATGGTACAAAAGCTAATAAAATGCCTCTGTTGATGGTCATAGCTGAAACTG[T/C]TCCACCTTGATGATCTACATGCGCCCCTAACGGGCATATTCTGTATGGGGAAACTGCTACCCTAATTGCTTCATCTTGTTTTTCGTCTT
108269 G A AAAAGCTAATAAAATGCCTCTGTTGATGGTCATAGCTGAAACTGTTCCACCTTGATGATCTACATGCGCCCCTAACGGGCATATTCTGTATGGGGAAACT[G/A]CTACCCTAATTGCTTCATCTTGTTTTTCGTCTTCTCCATTTTCAACACTATTATTGTTTTCATTATATCTACTATTTCTCACTAGAAACCCT
108269 A T CTATTTCTCACTAGAAACCCTCGCATTCCAGCTGCCATTCTTTTCACTCGTTCCAGCTCGTCGGTAGACGGCCATGGCGAGGATGAAGGAATGGAGGCGC[A/T]AACACCGTTGCTCTTGAGACCCATCGGTTTATTATTTCTCAGTTATTTGTTATTCCAGTAGGCCAACA
108271 CA C TGTGCACAAGCACAAGTCTCCCCTCTTCTCTCAAACTTCCCCTCCTCCTCCTCCTCCTTTCCATAACCATAACCATTCCAGCCAACTGCATGGACATCAA[CA/C]AAAAACATCAGTATTGGTTCAAGCCCACCAGCTCCACCTGAACCCGAATCTGCACCCGCCCCGAGCCCCAAACCAGAACCCGTACCTGA
108271 G A GCATACCGGGATTGCCTAATCAGAGATCGTGGAAAGAGTGTTGGTCGTTTTATAGCAAGTGCAAATACTGTCCTTTTCTGCCTTTCATGCCTTGCGCGCC[G/A]CCACGACATGGATGGGATAAGGAGATGGAGAAGAAGGAGCTTGGTTCAAAATCGGGCCCTGTTACTTACAGTTATCTGCATAATCG
108275 A G GCATACAGACAATGGTCATGTGAACCGCACCACATCAGGCCATTACACTTGTCCAGAACCGGCTGCATTTTAACCTCGCCGTCTGTTTGGAATACCCAGG[A/G]TACACTGCCAGACACGTAATCAAGAAAATATATTTTCCCTTCGTAGCAACCAACTACGACATGAAGAGTGTCTCCAGTGATTGCAGC
108277 A G TAAAAAGAATTCATTCCCATCCCATTAGCATATTTCTTACTCCCTCGACAACCTTGCTTCGGGAAGCTGATAACCCATAATCATCGCCAAGGAGAATTCT[A/G]TAGACTTCCCATTCTCTGTCACCTATCACATTTCTACCGATCTCAGCCAAGAAAATACGAGCGTGCAGGGTTTTCAAGGCAAGAGTGAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108277 G T CATTTCTACCGATCTCAGCCAAGAAAATACGAGCGTGCAGGGTTTTCAAGGCAAGAGTGATATCGTGGAAAACAAGAGGTCGGCCCTTTCCTGATAGCTC[G/T]ACTGGGTTCGCAACCAAAAGCTCAGTGTCAGGCCCACGATTCACCACAGTAACACGGAGTGGACAAAGTAATTCCAGCTTCAAGCG
108277 T C TTGTGAGCTCCAGCTCACATAGTACTTGAGTCACATCATGCAAAAGGCCAATTCGGTCGTAACAACAAAACTTGAGCAGAAAAAGCTGAGATTTCCGCTC[T/C]AATAACATCATTTCCTGTTGCTTATAATAACAATTATATAACTCAGAAGCCGACGAAGCAGCAGGGCATGCTTCCAATAATCTATTCT
108277 C A GGTCGTAACAACAAAACTTGAGCAGAAAAAGCTGAGATTTCCGCTCTAATAACATCATTTCCTGTTGCTTATAATAACAATTATATAACTCAGAAGCCGA[C/A]GAAGCAGCAGGGCATGCTTCCAATAATCTATTCTTCAATAAATTCCATCTTATAGCTTTTCCTTGACTGCTTTCTACCCAAAACACACAA
108279 C T GAGGTGTCGATACTGCCTTCAGGAGTAATAACAATCTCAGGCCTTCCAAACAAGGCTTCCGTATGCTTCTCGATGATACTAAAAGCCTCTCTCGACCTTA[C/T]AGTTGCGTAGCTCTGAAGCGTTTCGGTGTCAAACGACATCACATAGGTACGCAGCTTACACGGCTTGATCTTATCGGCAAAGCCATCG
108279 G A TTGCGTAGCTCTGAAGCGTTTCGGTGTCAAACGACATCACATAGGTACGCAGCTTACACGGCTTGATCTTATCGGCAAAGCCATCGGCACCAAAGGAGGA[G/A]GAAGCTTCAGCTTCGGAAGCTTCCGGATGCATCGTTCCGACAAAAGGACGAGATTCGTCCGGCATGGACGGTTTAACAGCGGTGG
108279 C G CCTGACCTTGGCTTCCTCCCCATGGAAGGGTCTTCATTGACTTTTCGAGCTGGAACCTTTGGTCTACTCGTTTGAGAAAGTAACCGTACATTATGGAGGC[C/G]GCGTACACTTGCCCGACTCTGAGCTTGCTTATTGGAGCGATGACGGTTTTGTTATCGTCCAAGTGCTTCCCTAAAATGAGGGAAAGG
108279 G A ACTTTTCGAGCTGGAACCTTTGGTCTACTCGTTTGAGAAAGTAACCGTACATTATGGAGGCCGCGTACACTTGCCCGACTCTGAGCTTGCTTATTGGAGC[G/A]ATGACGGTTTTGTTATCGTCCAAGTGCTTCCCTAAAATGAGGGAAAGGTGGTTTTTTATCATTTCGTATGCTTCGGATGAGTGGAGG
108279 C T GTTGATCAACAGCAGCAGGAATGAGATGAGGATGACTGTAGAGTATCTGAGACAAAAATTGACCAACTGGTGATTCCAGTTGAAGTGGAGCAATAGGAGA[C/T]GAAGGATTTGAAGCATCGGAAGAATCTGAAGATGAAGTTGATTCTCCTCTGATTGAGAAAATTCTTCTTGATGTTGAGAGAGATA
108279 T C AAAAATTGACCAACTGGTGATTCCAGTTGAAGTGGAGCAATAGGAGACGAAGGATTTGAAGCATCGGAAGAATCTGAAGATGAAGTTGATTCTCCTCTGA[T/C]TGAGAAAATTCTTCTTGATGTTGAGAGAGATAAGCTTCTCTGTCTACGATTGGATAGTGAAAACGCACATCGGCCCTTCAAAAAGC
108279 T TA AGGAATCGATACCGGAGATCCAGATCTAAAATCTGAAAATTTGAGAGAAACTGAGGCAGACTGAAACATTGTTGCAGCATCCATTATTGAAATTAAGAAT[T/TA]GGACAAAAAAAATAGAGAATAGAAGAGCTTCGACAAAAATTGGGATTGGATTCGGGAGAGTGGTTATAAAATGAAGATAAAATA
108279 C CA ATCGATACCGGAGATCCAGATCTAAAATCTGAAAATTTGAGAGAAACTGAGGCAGACTGAAACATTGTTGCAGCATCCATTATTGAAATTAAGAATTGGA[C/CA]AAAAAAAATAGAGAATAGAAGAGCTTCGACAAAAATTGGGATTGGATTCGGGAGAGTGGTTATAAAATGAAGATAAAATAAATG
108279 T TA ATCTGAAAATTTGAGAGAAACTGAGGCAGACTGAAACATTGTTGCAGCATCCATTATTGAAATTAAGAATTGGACAAAAAAAATAGAGAATAGAAGAGCT[T/TA]CGACAAAAATTGGGATTGGATTCGGGAGAGTGGTTATAAAATGAAGATAAAATAAATGCAATGTAATTTTTTAGTTATAAACTGG
108279 G A GAAACATTGTTGCAGCATCCATTATTGAAATTAAGAATTGGACAAAAAAAATAGAGAATAGAAGAGCTTCGACAAAAATTGGGATTGGATTCGGGAGAGT[G/A]GTTATAAAATGAAGATAAAATAAATGCAATGTAATTTTTTAGTTATAAACTGGAAAATATCTAATTTCCAGTAGGCCAACAG
108281 A G TGATTGGATCGACGCAGTGGAAGCTATTGACGAAACCGAAGACATGGGTTTGCTTGGATTTTGATTTGGATCGAAATCAAAATTCTCCGCGTTGACTTCG[A/G]ATTGAACCACAGAATATCCACGAAGAGGAAGTGAATAACAAAATTACGGGTCAGGGATGATCGTAACTTGGAGAGGACCAAAAGC
108285 T C GGTTAAACAGCTTAATTGCACACTCACATATCAATCACTCAACCAAGCTCTCTCCTTATTTCACACAAGAACTAATCCTAAAACAATGATGATTTCATCA[T/C]CATCATTCGCAATCGGTGAACTTCCAAATGTTGGAAGCCCACAAGAATGTGAAAATAGGAAGAAAAAAACTAAAATAAAAACATTCCAT
108285 G GA ACACAAGAACTAATCCTAAAACAATGATGATTTCATCATCATCATTCGCAATCGGTGAACTTCCAAATGTTGGAAGCCCACAAGAATGTGAAAATAGGAA[G/GA]AAAAAAACTAAAATAAAAACATTCCATCAAACATGGCTATCCAAGGCCCCTTTCAGCAAATGCAGCCCTTCCAACGAAATGCTTCTT
108285 G A CATCATCATTCGCAATCGGTGAACTTCCAAATGTTGGAAGCCCACAAGAATGTGAAAATAGGAAGAAAAAAACTAAAATAAAAACATTCCATCAAACATG[G/A]CTATCCAAGGCCCCTTTCAGCAAATGCAGCCCTTCCAACGAAATGCTTCTTCGAACCCTCGATTTCGGTATCTCAATCTTCGGTGGTG
108285 G A CATAAGCTCTCTTCTAACTATAGTCACTGCACACTGACTGCTCATTACGTCCCATAGGCCGTCGCAGCCTATTATAAGGAATTCGTCTTCTTCTGTGAGG[G/A]TGGTTTCTTGAAGTTCGGGTTCGGAGCTTAGCGGGCAAAGGGAGCCCTTTGTGCCCTTCATATGCCAGTCGCCTAGGGCCCTTGCAAC
108285 G A AGGCTCCTGGAGTTGGAAAATTTGCTCTTTTCCCAAGATAACCAACAAGATCATCAATGCAAAGATGTTCATCTTCCATTTGAGCTTTTGGCCCGATTTC[G/A]GAACAGCTTCCAGACCGGAATACAGGAATGAACCCTGATGTCCCATCTTCTTGTGATTTCAAGCTCAAAGCCGAAGGATCCGATTCAA
108285 A G TCATCTGTTTCATGTCCTCCGGAGATTCTGGACTTTCGCACTCGGATGAAGTCCCATTTTTCTGCTTATTATCACTAGTCTTTGAATTGTTGATGTTGCT[A/G]TTGTTATACCTGCTCTCTGTATATAAATTTGCTTGTTAATTAGATAATTAATCAATGGAGGAGTATGAAATCTGAGAGGATACGCAAGAG
108289 G A GTCTTTAGGGAGTTCGGATATGGTATTTCGTGACGTCGGAGATGCTTGCGTTAAAGAGCCGTTTGTATCAGATTTGGATACCCACGCCGCTGAAGTCTCG[G/A]GTTGCCTGTTGTCAATGGTGCTTGTTAGATCTGAAAAATGTTGCATGGACTGACAAGAGATTGCCATCTCTAGGTATTTGAGTTTGG
108289 A T TTTTCATGAGTCGAGATCTGCAACTAACAGATTGGTCAGAGATGAAAGCGGCATCGGAAGTTGTGTTGCGTAGGGTATTTGCTTATATTTGCAACGTTAG[A/T]TACTCCACTTACCGCCCGCAGTAACTTTTGTGCTGTTGTCCATCAAGTTGCCCGCAGTATTCAGATGCCTGCGGGGATAGCTCAGTTG
108291 G A GCCCAACCATTTCTTTATGAGTGCAAATACTTTCTCATCGCTCAGCAGGCCTCTGTGATTTGCCTTTACTCCCACTCTACAAACTGCTTCAAATCCATCA[G/A]CCTTAGCGGATTCTGCTGGAACAGTTTCGTCCCCCTCTACATAAGTATACTCAGGAACTGTATGGCACACTTCTGACAGATCCCCAATAG
108291 C T CTCCCACTCTACAAACTGCTTCAAATCCATCAGCCTTAGCGGATTCTGCTGGAACAGTTTCGTCCCCCTCTACATAAGTATACTCAGGAACTGTATGGCA[C/T]ACTTCTGACAGATCCCCAATAGGCGAGGTTTCTGATCCGTAGCAGACATTAAAAGGAGTCTCAAGAGATGTGCCATAGATGTTATAAA
108291 G A CCCATTCATAAATCGAGTGATTGAAAGGTAGAGCGATTGACTTCCCATCATACTTCAGCTCATTATTTCTTAATGCTTCTTCAAACAATGCAGGACACCT[G/A]TCTGAATCATAAACTTCAAGCTCAACATCGTCCTTCTCTGATTGTTTGCGCCATATCTGAACCACTGGCTGTTGGCTCCACTTAAAATTTT
108291 A G GACACCTGTCTGAATCATAAACTTCAAGCTCAACATCGTCCTTCTCTGATTGTTTGCGCCATATCTGAACCACTGGCTGTTGGCTCCACTTAAAATTTTT[A/G]CATGGCAGAACCTCATAAATAGAAGGGCATTCAACCAACAGTTGATGCATTGTCCATTTTGATACAAAGAGGAAGCTTTCAAAACCATA
108291 A G GCATTGTCCATTTTGATACAAAGAGGAAGCTTTCAAAACCATAAACAAACTGCAATCCTGTCAATAGAGAATCGTTGGCACTTCCTGCTGCACCTTGGAA[A/G]GGGCATGCTATGCATATCCACTTGTTAACGTACTTTGCAAATACCTTAGGATGCAGTGAAAGGAAACATCGAACAATTAAACCGCCCA
108291 C CT ATGCATATCCACTTGTTAACGTACTTTGCAAATACCTTAGGATGCAGTGAAAGGAAACATCGAACAATTAAACCGCCCATAGAATGCGAGATTATGTCAA[C/CT]TTTTTTCCCTCCAGAAGCTTTGAAAGCAGTCTCCAATTTCAATTTCAGCCCATCCATTCTTTCGTCAATTCTGCAGCTTTGACGAAAAT
108295 T C GGCACATTCTTTGATCGGGTAAGTTACTGATATCAAGGATGATGTCCCTTGAAGGAAACCTATGAACAATTTCGCTTCGTCCTCTGAAACTAGAAGATAG[T/C]TGCCATGGATGATGAGCTGGTGATCGGTAAGTTGAATGCATGTTGTGGCGCAATTGTTGCTCTTTGAAAGTGTAGAGATTTGAGAGG
108305 A G CCCATATGATCACAAATACTAGACAAAACGCACTAACGATGGTGTACAGAGCAAACGTTCCTCCGCTGTTCCAAGTTAAAAGCAAATTGGCAGTCATCGT[A/G]ATCACCCAAGCAGTCAACCAATTGGCAAGAGTTGCAACACTACCAGCAAGACTCTTAATATTCACAGGAAGAATCTCTGACATTATA
108305 A G GCCATCTTGGAGACTCAGGGATGAAAAACAAACCAGGTATCAAGACTATGCATGGTAAGGATCCCATAACAGCTAGCACTCTCCACGGAAGAAACATGCC[A/G]AAAATATATGCAAGCATTATACCAATAGTGACAGAAAGCTGATTCACGGAACCAAGTCCTCCTCTCATGTTCTGAGGAGCTATCTC
108307 A G CGGATGGGATATGGGATGTGTTATCCAATGAAGAAGTGGTATCCATTATATCATCTGCCCCTGTTCGATCCCATGCTGCTCGTGCTTTAGTGGAAGCAGC[A/G]GTTAGATCGTGGAGGACTAGGTATCCTACCTCAAGAGTAGATGACTGTGCCGCAGTCTGTCTTTTCCTAAATTCCCCAGAAAATCTG
108307 A G CGGGTCCAACGTCACTGGACAGAGCAGCAACAGTCAGGTCTGACGGAGGAGGAGGTGATGAAATTGAAGGCGTGCCACGGGTTGATACCCTCATTTCTCT[A/G]CCTAGGTTTGTTCCCGATACAAAAATCAAAAAATAGACGTCATCTGTTTTCTATGTTGTTTTTTTGAAGTTGTTATTTTTAAGGGGG
108313 A G CTTGTCTGTGGAACGCTGCAGGACTGGCAGGACCAAGATAATACAACGATGGGTGCGCATCTTTTCTGAAAGCGGACATTTCAGTTACATTTAGAACATC[A/G]ATCATATTTAACAGAGATGTGGCATTTGTAAATGGCAGCATGTATTTGGACCACGATTTTGGCGATATAGATGGTGCTATTTCTGGA
108315 A G AAGAAAGACGACTATCTCCATTTTGGCCAGCTCTAAGCCTGCGCAGTTTCTGAGCCCTTGCCCAAAAGGCATGTAGTTGTCTATCCTTGCTGTACTCGAC[A/G]ATATCGTCAGCCATCTCCAAGGATCGAACTTCTGAGGGTTTTCGTACACATTAGAATCAAGATGAGCAGCCGCAAACACTGGAATCAC
108315 T A TGAGGGTTTTCGTACACATTAGAATCAAGATGAGCAGCCGCAAACACTGGAATCACCCCCCATCCTTCTGGAATATCATACCCTTTGAACTTAACATTGG[T/A]AACCGCTTTTCTCTGAACGAACTTGATAATGTTTCCGAGTCTAAGAGTCTCGCTCACGACACATTGGCTGAATTCCATATGCTTGTAGT
108315 A G TTCCTGCCTTTTTCTTTGCGATCCTTTCTTTCATCAGTTGCTCGATTGTTTTCAATATTGTGACCCTTGCCTGCATGGCTTTCTTATAAGCAGTTCCAGG[A/G]AAGTTAAGAGGAAGAGATATAACACCCTTCATAAAAGACATGTACAGAATCCTAAGCCTCTCTGTTTCAGGCTCTCCTGGATTCATGCTCA
108315 T A CGATCCTTTCTTTCATCAGTTGCTCGATTGTTTTCAATATTGTGACCCTTGCCTGCATGGCTTTCTTATAAGCAGTTCCAGGAAAGTTAAGAGGAAGAGA[T/A]ATAACACCCTTCATAAAAGACATGTACAGAATCCTAAGCCTCTCTGTTTCAGGCTCTCCTGGATTCATGCTCAATATATTCTTCACCATCA
108315 T G TGGCTTTCTTATAAGCAGTTCCAGGAAAGTTAAGAGGAAGAGATATAACACCCTTCATAAAAGACATGTACAGAATCCTAAGCCTCTCTGTTTCAGGCTC[T/G]CCTGGATTCATGCTCAATATATTCTTCACCATCAGATTAAATGTTATCTTAGAAGCCTCTTCTTTAGCAGGGAAGACAACACCCTCCTT
108315 C A TCTCTGTTTCAGGCTCTCCTGGATTCATGCTCAATATATTCTTCACCATCAGATTAAATGTTATCTTAGAAGCCTCTTCTTTAGCAGGGAAGACAACACC[C/A]TCCTTCCAGGTATTGAAGTTCTGCATAGTATACATCTCCGAATCACCAAGAAAATTGTTTCTAAGTTTAGCAATGCCCATGAAATTTACAG
108315 G A CTGGATTCATGCTCAATATATTCTTCACCATCAGATTAAATGTTATCTTAGAAGCCTCTTCTTTAGCAGGGAAGACAACACCCTCCTTCCAGGTATTGAA[G/A]TTCTGCATAGTATACATCTCCGAATCACCAAGAAAATTGTTTCTAAGTTTAGCAATGCCCATGAAATTTACAGTGAGAGACTTCATGTAT
108315 A G AGACAACACCCTCCTTCCAGGTATTGAAGTTCTGCATAGTATACATCTCCGAATCACCAAGAAAATTGTTTCTAAGTTTAGCAATGCCCATGAAATTTAC[A/G]GTGAGAGACTTCATGTATCTGTGCATTTCACCAGTGATTACAAGCATAGAAGTATTTCCTAAAATATCAGCTACACTCTTTGGAAAACA
108315 T C AGGTATTGAAGTTCTGCATAGTATACATCTCCGAATCACCAAGAAAATTGTTTCTAAGTTTAGCAATGCCCATGAAATTTACAGTGAGAGACTTCATGTA[T/C]CTGTGCATTTCACCAGTGATTACAAGCATAGAAGTATTTCCTAAAATATCAGCTACACTCTTTGGAAAACACGGCTCGAACAGCTTTCC
108329 T C CTGAGAATCCTGCAGCTTTCCAACAGCATATCCGAAATGAATCTCAAATAATGGCTCAGCTGTTTCAGAACGATCCTGCACTAGCACAAGCAATCCTTGG[T/C]GATAACCTCGATGATCTTCAGAAACTTCTGCGAGAACGCCATGAGCAGAAAGTGCAATTACGACGGAAACAAGAGGAAGAGCTAGC
108329 G A CAGGAACATCCAGTGCGACAAACAGAATTAGCAATGTGCCCGTCCAGGCTAAAAGTCCTGGTCCTCAACAAAATACTCCTCAGGGAACCGATTTTGAGGC[G/A]AAAGTAACAAAGTTGATTGAGTTGGGATTTGATAGAGCTGCAGTTATACAGGCTCTTAAACTATTCAATGGCAATGAAGAACAAGC
108333 A G CAACGCTGGCCAACTGCAGCCTCACCCTCAAATCCCTTGTCCTCTTCAGCAAACACCTGAACGACCTCCCCAAATGCTTCACCCACTCGGCTGGTAGACC[A/G]CCAGGCGACAACCACACGGAAAAGTGGGACTGGTCCCCTCTGGCAGCCACCTCCGCCCTGTAGAACCGAGCCAGCTCCAGCAGCATG
108333 G A ACAGGACAGGGGCCCACTCGCTCGGCTGGTTTAGGTCGTAGGCCTCAGCCACGATTAAGGCCTCCTGGAAGCGGGACTGATCGACGAGCGCACGGCGAGC[G/A]TTTGTCTCGGTCAGCTCCAGCCAGCTCAGGTCAGGGATCCGGATCTGCAGGGAGAGGAGGGAGGCGCGCGCGCATGCCCGGT
108341 CT C TCCGTCAAAATAGATGGGCAGCTCAGTTTCAAGTGCTCAAATCCTTCAGTCTGCATCACAGCTTTAAGATTTTCAGGCGAAGCTATAAAGTTAAGACAGG[CT/C]TTTTTTAAGTTGAAAACAATGGTGCTGCTCAGCCAAAGCTAAGGTAGTTGCCACAGTGTTAATGGAGACATCTTCACATAGTTTTGC
108341 C A ATGTTTCTAAGGCATTTCTTCTAAAAAATCTCTTGAAACCCCACATACTCCCGCGGTACTTCAGAGTATAGGGACCATCATGCAAAACCCTGCCAAAATG[C/A]GAATGAACCTTATGATTCCCTTTCCCACTCTGATCCAAAAGACTCAACTCGAATAAAGCTCTCACGTCACTTCCATCACTAACCAATGCT
108341 G A CGCGGTACTTCAGAGTATAGGGACCATCATGCAAAACCCTGCCAAAATGCGAATGAACCTTATGATTCCCTTTCCCACTCTGATCCAAAAGACTCAACTC[G/A]AATAAAGCTCTCACGTCACTTCCATCACTAACCAATGCTATAAATAGCGACACATAAGTCGAATTATCCTCCGCGCTTTTACCATCGGG
108345 A T CAGATAGCACAGTTGTGATTAGCCCTAAGGTTAGACTTCCAGTGGAAACAGCTTTGGAATGATTATGGAGACCATTGCATTCATAGTCTCTCGGCTCACT[A/T]GCAAGAGCACTGTAGCAAAGGTAAGTACAATACAGTGAAAGCACTGAAGCAGGAAGTAGGCTACCATTTATCTTTGGGTGTAGTGC
108349 G A ACACCTTCAGGTTCTACTCACAGCAGTGGAGGACATGGGCTGCCTGTTTCATACAGGCAGCATGGAGAAGGTACTCGAGGAAGAAGCTGGAAGAAAGCTT[G/A]CGCGAAGAGGAAAGTAGGCTGCAGCAGGCTTTGGTGAAGGAAAATGGCAATGCACCTAGTTTTGGAGCGGCTATATATGCTTCT
108357 A C AATCACCTCCCTTTGCAAACGATATGTCGAGCTTATTTTTGAAATGTAGATAATTTAGGAAAACCTCTACCCAGGCCAAGTGCAAAAACATCAGTTAAAA[A/C]TCCTCTCTTCTTGTCATGATAACACGAGGCTCTTCAGTCTGAAATTCTCACTTCCACTCCAAGGATATCCTTTACCTGCTCGTATGTGAC
108357 C A CAAACGATATGTCGAGCTTATTTTTGAAATGTAGATAATTTAGGAAAACCTCTACCCAGGCCAAGTGCAAAAACATCAGTTAAAAATCCTCTCTTCTTGT[C/A]ATGATAACACGAGGCTCTTCAGTCTGAAATTCTCACTTCCACTCCAAGGATATCCTTTACCTGCTCGTATGTGACAAATGCAAGTGCAA
108357 C T GGACAGTGATTCTTCCCCGAACCATGTCCATAGGGTAAGTTGCAGACATAGCAATAATCCCGGCACAAGCTCCAGCTCCAAGACGTAATACTGGGGAAAG[C/T]TGAGCATCATCATTGCCAGATTGTCGCCGATAAAGCCATAAAATTGCACTTGATGCCTGCTCATAACTGAAAAACTTGACAGCTGAA
108357 A T AGACTAACTATGGTGTTCACCGCCGATTCGCCAGTGCTCTTCCCCGCTACATCTTCAGATGCCATTAGAATCTAACTATTTCTAGTTTTAAGGGTCTAAA[A/T]TTTATTTCTAGATGTAATTTAGGTCAGGCACGGGATCGAAGAAGAAATGGGATCACTGAGCGAAAGGGTGACGGCGGAGAAATGGGG
108357 G A CCGATTCGCCAGTGCTCTTCCCCGCTACATCTTCAGATGCCATTAGAATCTAACTATTTCTAGTTTTAAGGGTCTAAAATTTATTTCTAGATGTAATTTA[G/A]GTCAGGCACGGGATCGAAGAAGAAATGGGATCACTGAGCGAAAGGGTGACGGCGGAGAAATGGGGAGGGATGAGAAATGAGCAAA
108363 C T GGCTCAGTTTAAGCAGAACCTGATGTGGCTTGAAGCTGTGTCCTAGAGGAGTAGACAACTTTAATGATAATCGCAACTTCTGTAAATGATTTGCCGACAA[C/T]GAAAGTGTGTTCTCCTTTGACAAATCCAATTTCTGCACAGATTCTTCACCACCATTATCACTGTTCAAAATTGCAATTTCTGCCTTGTCG
108363 T C TCTGCACAGATTCTTCACCACCATTATCACTGTTCAAAATTGCAATTTCTGCCTTGTCGATTGAAATGGTTCCCGTTAGAAGAGCAGATGTTATAGTCTG[T/C]CCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAGAGG
108363 A G ATTATCACTGTTCAAAATTGCAATTTCTGCCTTGTCGATTGAAATGGTTCCCGTTAGAAGAGCAGATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTT[A/G]CAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATG
108363 C T CTGCCTTGTCGATTGAAATGGTTCCCGTTAGAAGAGCAGATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAAT[C/T]TCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCA
108363 T C TTGAAATGGTTCCCGTTAGAAGAGCAGATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCAT[T/C]GTGTACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108363 A G CCGTTAGAAGAGCAGATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCC[A/G]GCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGT
108363 G A GAAGAGCAGATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATC[G/A]AGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGG
108363 A G ATGTTATAGTCTGTCCTCCAGTACTGTACGTGTTTACAAGTTCTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAG[A/G]GGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATG
108363 T C CTGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAA[T/C]TGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAG
108363 T G TGGATCTTGTAGGGAAATCTCGAAAACCATTGTGTACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAAT[T/G]GGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAG
108363 G A ACTTCCCAGCATCGAGTTTAAGAGGTACAATGTCCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTC[G/A]GTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGG
108363 T A CCAAGTAATGGATGTTATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTAC[T/A]GTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGG
108363 G A TATTTTCTTGGTCAAATTGGAGCACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATAC[G/A]GCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGAAGGAAAGAATGAG
108363 G A CACCTGATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTC[G/A]CCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGAAGGAAAGAATGAGCGGTATAGAAATCCTATTGTTT
108363 G A GATTCTCCAAAACAGGCGAGTTCTCGGTACCAGATGTGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTC[G/A]GCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGAAGGAAAGAATGAGCGGTATAGAAATCCTATTGTTTTCTAG
108363 G A TGAAAACTTTTACCAAATTTACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCAC[G/A]GTAGCTGGGAAGGAAAGAATGAGCGGTATAGAAATCCTATTGTTTTCTAGGAGAGATAATGAATCTAATTGATTGAACAAATCATT
108363 A G ACCAAATTTACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGA[A/G]GGAAAGAATGAGCGGTATAGAAATCCTATTGTTTTCTAGGAGAGATAATGAATCTAATTGATTGAACAAATCATTGCTGCCGCCAG
108363 T C ACTGTAAGTGGAGATACGGCAGAGCCAAAAACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGAAGGAAAGAA[T/C]GAGCGGTATAGAAATCCTATTGTTTTCTAGGAGAGATAATGAATCTAATTGATTGAACAAATCATTGCTGCCGCCAGGAATTCCAA
108363 G A ACTGTAGTCGCCTCGGCCTTTAGCTGGTCTTTAGTGGTTAATGAAAGCACGGTAGCTGGGAAGGAAAGAATGAGCGGTATAGAAATCCTATTGTTTTCTA[G/A]GAGAGATAATGAATCTAATTGATTGAACAAATCATTGCTGCCGCCAGGAATTCCAATGCTGAGAAAGAATTTGGCCAAGCCTACAA
108363 C T GAAAGCACGGTAGCTGGGAAGGAAAGAATGAGCGGTATAGAAATCCTATTGTTTTCTAGGAGAGATAATGAATCTAATTGATTGAACAAATCATTGCTGC[C/T]GCCAGGAATTCCAATGCTGAGAAAGAATTTGGCCAAGCCTACAATTTTGTCGTCTGGAATACTAAGCTTCTCGGAAACAACTTGAG
108367 A G GGTTCCGGGCAATCCTTCCCTTGTTTCTGGTCTCAAAAGCACACGCAAATCCGCTGCTTATTGTAGGATCAGCAGATGGAGATGTCCAAAGGCAGCAGTA[A/G]CAACTAATTCACGTATTCCGATGCGCAGCCTAGAAGTTAAAAACAGAACATCAGTTGAAGACATAAAAAGTCTCCGCCTAATCACAG
108367 A G TGAGCTGGGATGAGCACATCATGCTCATAGGCCACACGGTTAACTGCTTCGGTTCCCAAATTAAAGTCATAGGGAACACAGGCAGCAACTCAACAAGAGA[A/G]GCAAAACACGCTTCCGAACAAGGATTCGCCGTAGGCATGCATGCCGCCCTCCACATAAACCCGTACTACGGCAAAACTTCCTTAAA
108367 T C ACTGCTTCGGTTCCCAAATTAAAGTCATAGGGAACACAGGCAGCAACTCAACAAGAGAAGCAAAACACGCTTCCGAACAAGGATTCGCCGTAGGCATGCA[T/C]GCCGCCCTCCACATAAACCCGTACTACGGCAAAACTTCCTTAAATGGAATAGTGTCCCATTTCGAGTCCGTGCTCTCCATGGGTCCT
108367 GT G CGAGAGGGTCAAGGAGTACACTAGTAAAGGAATTGCTACATGGAGCGGAAACGACGACGAATGTTTTGATGCTAGGTGGGAATATGATGCCACTGGAGTT[GT/G]TTTCGGTTGCTAGTAATCTTATTCCTGGTTTGATGCACAGGCTCATGTACCAGGAAGGTGATTCGTCTTTGAATGTGAAGCTGA
108369 G A TTACTGGAAGACATACGTTGAAGAAGTTGATCAGGAAAGGGAAATGTGGTTGAACTCATTTTATAAAGCTCCACTTCGACTTCCTATGCCTGCTGAACTT[G/A]AGCATTGGTGGTCTAAATATCAAGGCCCAGAGTTTGTCCTCATCAACAAGGAACCTGAGCCTGATCCAGAAGACCCATCGAACCTCA
108369 A G AAAGCTCCACTTCGACTTCCTATGCCTGCTGAACTTGAGCATTGGTGGTCTAAATATCAAGGCCCAGAGTTTGTCCTCATCAACAAGGAACCTGAGCCTG[A/G]TCCAGAAGACCCATCGAACCTCATATACACTGAAGACCCGCTTATCATGCATGTCCCAACCGGAAGGCTAATCAATTACATCGAGGA
108369 C T ATCCAGAAGACCCATCGAACCTCATATACACTGAAGACCCGCTTATCATGCATGTCCCAACCGGAAGGCTAATCAATTACATCGAGGATGAGGAGCATGG[C/T]ATTCGCCTTTTTTGGCAGCCCGAACTGAAAGAAGGCGAAGAAATTGATGAAGCAAACATTGAATTTTTACCTCTTGGCTACGACGAA
108369 CT C AGACCCATCGAACCTCATATACACTGAAGACCCGCTTATCATGCATGTCCCAACCGGAAGGCTAATCAATTACATCGAGGATGAGGAGCATGGCATTCGC[CT/C]TTTTTTGGCAGCCCGAACTGAAAGAAGGCGAAGAAATTGATGAAGCAAACATTGAATTTTTACCTCTTGGCTACGACGAATTCTTC
108371 A AT GAGGGAGAGGGCTAGGTTTCCGATCAGGACACGCACGAATGAGCACGGATCCATACTTCGGTTGGGGAAATTTGAAATTGTGAGAATCAATTCTTTATGG[A/AT]TTTTGAGGAAGTAAAAAGGGGATTTTATATGAAGGGAGAAGGCATAGTGAAATTGAGAGGACTAATTGTCCAGTAGGCCAACA
108379 G A CAGCGACTGTGTTCTCAATGGCGAGAACGAATTTATAGTTAGACATGGCACAATGAAGGTGGTCGTACCAATGAAGGGTAGAACCGTGACTCGAGCATTC[G/A]GGGTACATAGATAGAGCCATGTCTAGACCACCTACGTTGTTCAGGCATTTTCCAAATGAGTGATGAGGGATTAAGGAGAGGAAG
108379 A G TCTAGGTCAATATAAACGCGAAGAGGATCGCCTTTTCTTCGCACAGCAGGCGGCATAACATTCTCAAACAGCAAAGCATCAGGCTTATCAGCAAGAATTG[A/G]TGACTTGGTCCACAAGCAAGCCAACCCACATCGACACTGATACAGATTATCCAAATTATCAGGAATCCAAGTCCACCCTTTTACCAG
108379 T C ATATAAACGCGAAGAGGATCGCCTTTTCTTCGCACAGCAGGCGGCATAACATTCTCAAACAGCAAAGCATCAGGCTTATCAGCAAGAATTGATGACTTGG[T/C]CCACAAGCAAGCCAACCCACATCGACACTGATACAGATTATCCAAATTATCAGGAATCCAAGTCCACCCTTTTACCAGAACACTAACA
108383 C CT TAAAATCTATATTACACATTCTCTGAACCGCATGTATTGTGGGCTCAGCCCATATTACACATTCTCTGGAAATACAACCGTTAC[C/CT]TTTTTTTCCATACAATGTACTGATGTAAACGTCCTTAACTACTGAGAAATAAAAGATACAAGCATTATTTTTCTACTCTGTTGTGATCTCTATTTTTGTA
108383 G GGT CCTACAGCTTAACAGCTTTTACCCTCTTCAACAGCGATTACCAGACCAGCTAATTTCAATCAATCAAGGCAGGAGGAAGATTATATTCTTTATCTCCTCA[G/GGT]TTTTTTTTATCTTCATCGGAGATTATACCCTTCCGTTCTTCCTTTTGGCCTCGATCTCGACTGTTTCTTGTCACCACAGCCTCGCCAGG
108391 T C CCAGTCTTCCCTCACGACCTAATTTTGAAGGGTTCGACGCCGACGAACTCGACGAGGAATTCGACGAACAGGAACCCTTACCATCCATTCCGCTTCCAAA[T/C]CCAACCACTTCCACCTCAACCCTAACCAACCCCGAGCCAAGCAATCTCAGCCCTCCGTCTCCCTCCTCAAACCCCTCCCCTCCATCCGA
108391 C T AAGGGTTCGACGCCGACGAACTCGACGAGGAATTCGACGAACAGGAACCCTTACCATCCATTCCGCTTCCAAATCCAACCACTTCCACCTCAACCCTAAC[C/T]AACCCCGAGCCAAGCAATCTCAGCCCTCCGTCTCCCTCCTCAAACCCCTCCCCTCCATCCGATCCCCTCTTCGATTTTTATGACTCCGAC
108391 A AC ACCAACCCCGAGCCAAGCAATCTCAGCCCTCCGTCTCCCTCCTCAAACCCCTCCCCTCCATCCGATCCCCTCTTCGATTTTTATGACTCCGACGAGTTCG[A/AC]GGGGATTCCCGTCCCGCCATCCCAGAACGAACAACCAATCTCTGTTGAACAGCCTCCTTCGTCTGATATGAACGGCACGATTTCAACA
108391 T C ATCCGATCCCCTCTTCGATTTTTATGACTCCGACGAGTTCGAGGGGATTCCCGTCCCGCCATCCCAGAACGAACAACCAATCTCTGTTGAACAGCCTCCT[T/C]CGTCTGATATGAACGGCACGATTTCAACACCGTCTGATCCGCCATCCGTCCGTAAGTACACCGTGGAAATTGTGTGCGTGAGTTTCTTG
108391 A G CTATGCCAGTGGGCGGAGGTTTTGCCAGGCTGTGTTGGCAACGATGGAGCTGAAATGTAGGCATGATTTGTTAGGGAAGGCTGTGGATTTGGTATTTAGA[A/G]AGAAGGATACTATAACATTCGAGGTGGTGATGAACGAGGAGAATATGGATCATGTGGTGATGGCTGTGGCAAGAAAGAAGCAG
108395 GAC G AATTACAAATCTGCATTGAATATATGGCATAAACAGGAATACAATGGTATCCAAATAACATGCTACACAGTAAACTTCTTTCACAGGGACTCCAATGAAA[GAC/G]ACACACCATGAAAGTACGAATTTCTACACAATAATAAACAATGATACATAGCAATGCCGCGGGAGTTGAATAATAAGAAAAGCTA
108395 TG T ATGATACATAGCAATGCCGCGGGAGTTGAATAATAAGAAAAGCTATAATTTGTACATTATAATATAAACCCAAATATGCAACCGATCTTTACAAAACTCA[TG/T]GGTTTATCAGCAGCAACTCGACACAATTACGAAGTCATATCTGAAAATGTAGCCTTATGAAGAAGGAGAACATGCTTCAAGCTTAGG
108395 A C AGCCCCAGATCTGCAGTTTTCTGCTCTTGGAACCGAACCATTTCTTCATCCATCAGCTTAACAATGGTTTCGTATTTTTGTTTAGCTTCTTCACTCTCTG[A/C]CTTCAACTCTCTGTACTCGAGTTCTGCTTCCCCAGCCTTTTCCGATCTTACCATCATCAGCTTGTCAAGAGCTATCTCTTTGAGCTTTGTTGC
108395 T C GTTTAGCTTCTTCACTCTCTGACTTCAACTCTCTGTACTCGAGTTCTGCTTCCCCAGCCTTTTCCGATCTTACCATCATCAGCTTGTCAAGAGCTATCTC[T/C]TTGAGCTTTGTTGCTTCAGTCAAATCGTACTGCTGTCGAAAAGCATTGGCTCTATCAACCATCGTGGCCTTAATTGATTGTACCGCTCTCAC
108395 A G CACATGCACCTAGTAGTTTAACTGCCTTTCCAAATTCTGATAGAGACTGCCCCAGCTCTCTGTGCCTCTTAACGAGTCGAAATGCCTGCTTTTGTGCCTC[A/G]GCTAAATGATCTTCAAGCTCGTAGATATAATGCTTCATTTTCTCATATTCAGGAGTTGACTCCTCAACGGGTTTTTCCTTACCCAATACAA
108395 C T GTTTTTCCTTACCCAATACAACATCACTAACCCTAGTCTGTACATCCTTAAATATTTGGAAGAAGTCAGCAGGTTTTTTCTTAAAAATTCCAGTTTCTTG[C/T]GCTCTTGCTCTTTCCATTATCTCTTCATCTTCCACCAGAAATATCCGTAAATCCTCGCTTCGCTTTAGTTCAGGGTGAGAAGCTATTCGATT
108397 C CG AGCTGAACGACACGCTGCTGGCGTGCTTCTTGATTTTGAGCATCGCGCTCAGATGTTGTAGGGTAATTTGTTAGCGGATGAGGATGATCGATGCCTCCAT[C/CG]TTTTTTATAGCAGGCATTGCATACGTCAAATTCGGGGCATTCTTCACAGCGCCATCCTTGACCAGCTTCAACATCTCGAAGGCACA
108397 G A CGGGGCATTCTTCACAGCGCCATCCTTGACCAGCTTCAACATCTCGAAGGCACACGTTGCATGTGGTTACAAATGCAGGAGCAGTTGGATTATGAAGGTG[G/A]TATAACATCATCATAGATGAATGTTTGGCACGTCTTAGTGTATCGTATTGGTAATGGTTTCCTTGACAGAGGCTCAAGAATGCCTGT
108405 T A CCTCACCAGTATTCGGGTTCCAGCCAAGGGATTCCAAAAAGGCTTTTTCTTCTTCATCAGGATCTAGAGCTTCAATTTCAGGTTCACCGTTGCAAGCAAC[T/A]TTGTTCCCATTCTCAGTTAGCATACAGTGTTTCATATCAGAATTTGATGCAGGCAGAACAGTCTTTTCCTGAATATTCAGCTCGTTTGAC
108405 A G ATCAGGATCTAGAGCTTCAATTTCAGGTTCACCGTTGCAAGCAACTTTGTTCCCATTCTCAGTTAGCATACAGTGTTTCATATCAGAATTTGATGCAGGC[A/G]GAACAGTCTTTTCCTGAATATTCAGCTCGTTTGACTTTTCTTCTGGATGTATTACACCATTTTTCAGCTTAGCTTGATCTCTTAGACAACT
108405 T A CAACTTTGTTCCCATTCTCAGTTAGCATACAGTGTTTCATATCAGAATTTGATGCAGGCAGAACAGTCTTTTCCTGAATATTCAGCTCGTTTGACTTTTC[T/A]TCTGGATGTATTACACCATTTTTCAGCTTAGCTTGATCTCTTAGACAACTGAAGAATTTTTTTCTATCTTGAGACTGAGATGAAGGGTTCT
108405 C T CTGGCAGTAGATATAGGATGAAGATTATTGGAAGAGGTTGCCACTCTGCCAGTGGCATTAGATTGGGTTGGCGCGCTTTTCGTATTATTAGAAAAGGTAC[C/T]TTCTCGATTTAGTACCTGAAGTTTTCCAGATAAAGAAGTCTTCAAAATATCCGGTTTGATAGGAGACGGCTTGATTTCTTGATTGGC
108407 A G TGCCTATCCACCACCGTCAACCCAAACCCCAAACTCGCAAGCGACAAAATCATCCCAGCCGTTCCTGTTAGCAGCAACGGCCTCCGTCCCACCCGATCCA[A/G]TAACACCGTCGCAACCAATATGAAAATCGTTTTCGTGAATCCGACCGCAACCGTAGCTCCGAGCAAAGCGTTCTCGGAGGTGATCCC
108407 C A CCACCACCGTCAACCCAAACCCCAAACTCGCAAGCGACAAAATCATCCCAGCCGTTCCTGTTAGCAGCAACGGCCTCCGTCCCACCCGATCCAATAACAC[C/A]GTCGCAACCAATATGAAAATCGTTTTCGTGAATCCGACCGCAACCGTAGCTCCGAGCAAAGCGTTCTCGGAGGTGATCCCCGCCTTT
108407 C T AAATCATCCCAGCCGTTCCTGTTAGCAGCAACGGCCTCCGTCCCACCCGATCCAATAACACCGTCGCAACCAATATGAAAATCGTTTTCGTGAATCCGAC[C/T]GCAACCGTAGCTCCGAGCAAAGCGTTCTCGGAGGTGATCCCCGCCTTTTTGAAGACACGCGGGCTGTACAGTACGACTGAGTCGATC
108407 A C CAGCCGTTCCTGTTAGCAGCAACGGCCTCCGTCCCACCCGATCCAATAACACCGTCGCAACCAATATGAAAATCGTTTTCGTGAATCCGACCGCAACCGT[A/C]GCTCCGAGCAAAGCGTTCTCGGAGGTGATCCCCGCCTTTTTGAAGACACGCGGGCTGTACAGTACGACTGAGTCGATCCCTGATGCC
108407 C CT CCAATATGAAAATCGTTTTCGTGAATCCGACCGCAACCGTAGCTCCGAGCAAAGCGTTCTCGGAGGTGATCCCCGCCTTTTTGAAGACACGCGGGCTGTA[C/CT]AGTACGACTGAGTCGATCCCTGATGCCTGCTGAAAAAAGTGCATGCCCACCGCAGTGATCAGTATTTTTAGCACTCCCGGGCTGG
108407 G A TTAGCACTCCCGGGCTGGGGTGCAGTAAGAGCTCCCTCCACACCCCATCCCCTTTGCGCCGCTTTGGTACATCGACCACATCTTCGTTGCACTCTACGGG[G/A]ATCTGCGCGGCTTCCTTGATCTCCGCCAGCCTAGCAGCGGCTTCCTCGGGGGAGTCCGACGTCCTGTCGAGCACCTTTTTGGCATCTG
108407 C CG TCCCCTTTGCGCCGCTTTGGTACATCGACCACATCTTCGTTGCACTCTACGGGGATCTGCGCGGCTTCCTTGATCTCCGCCAGCCTAGCAGCGGCTTCCT[C/CG]GGGGGAGTCCGACGTCCTGTCGAGCACCTTTTTGGCATCTGCTAGCCTCCCTTGCATCACCAGCCATCGTGGCGATTCCGGCATGCC
108407 T C CGAGGTTGATAAACACTTCGGGGAAGGAGGTGAGGAAGCCACGAGAGGAGGCGGGAGAGACCTCGGCGGTGTAAACGGGGGCGATCATGAGGGCGTACCC[T/C]ACGCCGATGCCGGCAACGAAGCGTCCAACCATGAGGAAGGCGTAGTTGGGGGACAGACCCATCATGATGGCACCCACGAA
108407 G A ACACTTCGGGGAAGGAGGTGAGGAAGCCACGAGAGGAGGCGGGAGAGACCTCGGCGGTGTAAACGGGGGCGATCATGAGGGCGTACCCTACGCCGATGCC[G/A]GCAACGAAGCGTCCAACCATGAGGAAGGCGTAGTTGGGGGACAGACCCATCATGATGGCACCCACGAAGAAGATGACCGC
108407 T A AGAGGAGGCGGGAGAGACCTCGGCGGTGTAAACGGGGGCGATCATGAGGGCGTACCCTACGCCGATGCCGGCAACGAAGCGTCCAACCATGAGGAAGGCG[T/A]AGTTGGGGGACAGACCCATCATGATGGCACCCACGAAGAAGATGACCGCGGCGAAGACGATGGTGTAGCGGCGCCCGATCC
108407 G T ACAGACCCATCATGATGGCACCCACGAAGAAGATGACCGCGGCGAAGACGATGGTGTAGCGGCGCCCGATCCAGTCGGATGTGCGCCCCGCCGCGAAGGA[G/T]CCGAGGAGGGAGTACAGGTTTAGGATTCCTAGTAGGACTTCGATTTGGGTGTCAGAGACATTTAGGTCGTCTTTGATGAACAG
108409 T C AAGGACCGGCCCTGATTGCAAGTCAAACAGAAAGCAGGTTGATTAGCATACACAACAATCAATGGCTGTATCAAACAACCACCACCATTATGTCCAGATT[T/C]TCCACCGGAATCAAACTTCCGAAACTTTTATCGGATGGTCCAGATCGACCAGGAGAGCACGGACGTCGAGAATGACTCTGACGGTG
108419 A T AGCTGCTTGGATATTGCTGGGAAGGCACAGAATTACTCCTTGTGTATGAATTTATGGCAAAGGGAAGCCTTGAGAACCACCTTTTCAGGAAATCTGCAGA[A/T]CCACTATCATGGAGCCTAAGGCTAAAGATTGCAATTGGAGCTGCTCGAGGTCTTGCATTTTTGCACTCATCAAAAAGACATATAATT
108419 T C CGCTGCAAGCCGCCCAACTCACATATAGATGTCTCGAGGCTGAGCATAGAAATAGACCTTCTATGAAAGAGGTTGTTGAAACTTTAGAAAAAATCGAAGC[T/C]GTGAAAAGTAGGTCGAGGCAGTCTAGAGAAAGCTCAAGCCAGAATTCAAGTCGAACTACTCCACAACGTTCGCCTCTTCATTCCAA
108421 C T GTGACATCAGTTCGATTCGAAGCTACAAAGACCTTCCGGAAGCTGCTAGAAGATACGTCGAGAGGATAGAAGAGCTCGTTGGCGTACCCATTCATTACAT[C/T]GGTGTCGGCCCAGGCCGTGATGCCCTAATTTATAAGTAGGCTTTAAGTTCAATCGCAATAATGTTTTTCAGAACTTCGAAAATTTTC
108421 A AT GAGGATAGAAGAGCTCGTTGGCGTACCCATTCATTACATCGGTGTCGGCCCAGGCCGTGATGCCCTAATTTATAAGTAGGCTTTAAGTTCAATCGCAATA[A/AT]TGTTTTTCAGAACTTCGAAAATTTTCAGTTGCGAAAATTCAGAAAATATCCAATTTGAGTTTACTGTTATACTAGAGATATATGAACA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108433 C T TAGAGAGCCTCAAACGACACCCAAAGCAAGGTGGAAAAAGTAGTACAGGAGTTGATCTTGTATTGAGCTGTGTAGATAATTACGAGGCTCGTATGGTTGT[C/T]AATCAGGCATGCAATGAGCTGAACCAGACATGGATGGAATCTGGTGTATCCGAAGATGCAGTTTCTGGACACATACAATTGCTAG
108433 A G CTCCTTTGGTTGTGGCATCTGGTGTAGACGAACGCACACTTAAGCGGGAAGGAGTATGTGCTGCATCTTTGCCCACTACCATGGGGGTTGTTGCTGGTCT[A/G]CTAGTTCAAAACACTCTTAAATATTTACTGAAGTTCGGACAAGTTTCTCCTTACCTGGGGTACAATTCTCTGAAAGATTTTTTTCCAAC
108433 T C CAAGTGCCGACAAGCTTCAAGATTCAACGAATACAGAAGAGACAAACATCATAGTCGATGATCTTGAAGATCTCCAGAGGCAGCTTGAAGCCTTAAATGC[T/C]GCTTAGTACACCATTTTCATTCTTATGGTGGAAGATCGGCGGATGTTCATGCGTTATGTAACATTGGATTTTCAAGAAGCATACTAA
108433 G A GAGACAAACATCATAGTCGATGATCTTGAAGATCTCCAGAGGCAGCTTGAAGCCTTAAATGCTGCTTAGTACACCATTTTCATTCTTATGGTGGAAGATC[G/A]GCGGATGTTCATGCGTTATGTAACATTGGATTTTCAAGAAGCATACTAAATTAGTTCAATTTTTACCAAACTAATAACTTATCAGAAAC
108437 G C CTATCAACGCGTCCAAGATTGTCTAGAATCACAGGTCGGTTGTCTTCGCAGGCGTCATTAGAGTGAACAAAATCGGCATGGGACTGGAGGAGGTAGCGGA[G/C]AGAGCGGACGCCGCAGCCGCACATTGCGTCCAGGACGCGGAAACTGGTTTCATGAGACGACAAGGTGGTGCGATGGAGGAAAG
108437 A G TATCAACGCGTCCAAGATTGTCTAGAATCACAGGTCGGTTGTCTTCGCAGGCGTCATTAGAGTGAACAAAATCGGCATGGGACTGGAGGAGGTAGCGGAG[A/G]GAGCGGACGCCGCAGCCGCACATTGCGTCCAGGACGCGGAAACTGGTTTCATGAGACGACAAGGTGGTGCGATGGAGGAAAG
108437 T A AAATCGGCATGGGACTGGAGGAGGTAGCGGAGAGAGCGGACGCCGCAGCCGCACATTGCGTCCAGGACGCGGAAACTGGTTTCATGAGACGACAAGGTGG[T/A]GCGATGGAGGAAAGCGGCGAGGACGGCAAGGTCGCGTGCGGTGGAAGATTCAGGGCGGAAGAAGGTGTCGCCGGTTGAG
108437 A G AGCCGCACATTGCGTCCAGGACGCGGAAACTGGTTTCATGAGACGACAAGGTGGTGCGATGGAGGAAAGCGGCGAGGACGGCAAGGTCGCGTGCGGTGGA[A/G]GATTCAGGGCGGAAGAAGGTGTCGCCGGTTGAGAAGGGGATGCCACGTTCTGAATGGGTGGTTTTTTTAGGATTTTGAGGG
108437 A G ACAAGGTGGTGCGATGGAGGAAAGCGGCGAGGACGGCAAGGTCGCGTGCGGTGGAAGATTCAGGGCGGAAGAAGGTGTCGCCGGTTGAGAAGGGGATGCC[A/G]CGTTCTGAATGGGTGGTTTTTTTAGGATTTTGAGGGCAGAGGAGAGATGAAGGCGATAGCATTCTTTTGGGGAGAGACAA
108445 TC T CATATAATCAACTTTGACAGCATCAAGTTTTGCTTGCAGCTTTACAATTGAACCTACACACTTCATCATAACGACTTGCCCTCAACGTTAAATTCTAATA[TC/T]CCCCCTCCATACGTACACTCCTGGAAGGCAACATCATCTATAGACAGCTTGTCCTCCGGATACTGACACGGACCCGCTACCCCTCCCTG
108445 AC A CTGGAAGGCAACATCATCTATAGACAGCTTGTCCTCCGGATACTGACACGGACCCGCTACCCCTCCCTGCCCAGCCAGCGCAGCACAAACTTCCGGGCTC[AC/A]CCCCACTCGAAACCCCCTCCACGTTCTCGCACATCCACTGCACCTTCTTCGCCTTCACCGCCGTGTGCACCGTCACATTCGACACAC
108445 AC A ATCATCTATAGACAGCTTGTCCTCCGGATACTGACACGGACCCGCTACCCCTCCCTGCCCAGCCAGCGCAGCACAAACTTCCGGGCTCACCCCACTCGAA[AC/A]CCCCCTCCACGTTCTCGCACATCCACTGCACCTTCTTCGCCTTCACCGCCGTGTGCACCGTCACATTCGACACACATATCCCCTTAAA
108445 A G ATGGCCCTGTCAGCCACTTCCCGGCTGGCACATACAGAATACCGCCTCCATCACCTGCATACTGTGACAGACTACTGACAGCGTCACTGAACGCCTTTGT[A/G]TTGGACGTCACACCATCCCCGATGCCTCCGAAGTCGGTTAAGGACGCGGAGTGGGCACGACAGTTTGTGGCTACGTATTTGAAGCC
108445 C G TCCCGGCTGGCACATACAGAATACCGCCTCCATCACCTGCATACTGTGACAGACTACTGACAGCGTCACTGAACGCCTTTGTATTGGACGTCACACCATC[C/G]CCGATGCCTCCGAAGTCGGTTAAGGACGCGGAGTGGGCACGACAGTTTGTGGCTACGTATTTGAAGCCCGAGATCGGAACGTCTTT
108445 T C GCTGGCACATACAGAATACCGCCTCCATCACCTGCATACTGTGACAGACTACTGACAGCGTCACTGAACGCCTTTGTATTGGACGTCACACCATCCCCGA[T/C]GCCTCCGAAGTCGGTTAAGGACGCGGAGTGGGCACGACAGTTTGTGGCTACGTATTTGAAGCCCGAGATCGGAACGTCTTTGTTCC
108445 T C AAGTCGGTTAAGGACGCGGAGTGGGCACGACAGTTTGTGGCTACGTATTTGAAGCCCGAGATCGGAACGTCTTTGTTCCTCGCCCTGATTGAATGGACGG[T/C]CGTGATCGACAGCGCCAGAACTAAAAATGTGAAGATTTTAATTAGCCCCAGCTCCATAGTCACGGATGATGAGAGTGCAGT
108445 C A TTAAGGACGCGGAGTGGGCACGACAGTTTGTGGCTACGTATTTGAAGCCCGAGATCGGAACGTCTTTGTTCCTCGCCCTGATTGAATGGACGGTCGTGAT[C/A]GACAGCGCCAGAACTAAAAATGTGAAGATTTTAATTAGCCCCAGCTCCATAGTCACGGATGATGAGAGTGCAGT
108459 TA T CCGAAGGTCGAAGGGATAAAAAGTCTTTCATTTACGGCTGATGGATCGGGTGCTGTATTTGATGTACCTGCCGATGACGTGAGCTTGTTTATTGATGGAC[TA/T]AAAAAAATCAAGTGATATGTCATTGGAAGTGATTGAGAAGTTACCTCCCTTGCAAGAAAGAGAGGAATCAAGAGGCAGAGGCGG
108461 GT G TTATATGCATACACCCCTGGTTCTTCTCAATTGGCCTCTTGCACTTAGGACAAGGTTTTGAATTAGCTAATATCCAATTCATATTCTCAGACTCTGCGCT[GT/G]TTTTTTAATATCCACTTGGCTACTGTTTCACAATCGACTGGTCTGTGAGCTTCTTCTGTACAATTCCAACAAAAGCTATATGAACAGTTG
108463 T C TAGGTGACTATGCTAGTGGAACAAACCACGTGCTCCCGACTTATGGGTATGCTAAAATGTACAGCGGCGTTTCACTGGATTCTTTCCTCAAGTACATCAC[T/C]GTCCAGTCTCTGACCGAAGAAGGGTTAAGGAAGCTAGGACCGTATGTTGCCACAATGGCAGAAGTCGAAGGCTTAGAGGCGCATAA
108463 C G AGGAAGCTAGGACCGTATGTTGCCACAATGGCAGAAGTCGAAGGCTTAGAGGCGCATAAACGAGCCGTTACTCTCAGGCTTGAATCCATGAAAGCAGCGG[C/G]TCGCTCCATGTAATATTTATTGTTTACAGTTAAAGGAAGTAGCCAAAGAAGGGGTAACGATTCAAGTCTATTGGATTGTTAAATTT
108463 A G AGGACCGTATGTTGCCACAATGGCAGAAGTCGAAGGCTTAGAGGCGCATAAACGAGCCGTTACTCTCAGGCTTGAATCCATGAAAGCAGCGGCTCGCTCC[A/G]TGTAATATTTATTGTTTACAGTTAAAGGAAGTAGCCAAAGAAGGGGTAACGATTCAAGTCTATTGGATTGTTAAATTTGCTACTCT
108469 T C CTTCTCCGACTGGGACAAACGACGTAGAGCCAGAGCCGCCGTCACTAGCAGCTCAGGCGATCAGGGCTTCATCTGCTCATCGAGATTCTTCAATCTCCTC[T/C]GCTTACTACGGGGACAGAACTGTTCCTTCACCCACCTCTGCTTCTTCTTCCAGTTTCAAGGAATCTACAAATCGGGATTCCAGGGCTG
108469 G A GTACGGATTCTGGGGTGTTCTTGCGAGAAAAGCTAAATCTCTTATTGATGATGATAATGCACCTTCAACATTTGAAAATGACAGCAGAAAGCCACATCAA[G/A]CATCAAAGTCTAGAGATGAGGCTCAACAATCTTATGAATCGTTTGATGGATACCGAAAACCTGAAAGTGTATCCTCTCATAGAAGTG
108469 A G ATGCACCTTCAACATTTGAAAATGACAGCAGAAAGCCACATCAAGCATCAAAGTCTAGAGATGAGGCTCAACAATCTTATGAATCGTTTGATGGATACCG[A/G]AAACCTGAAAGTGTATCCTCTCATAGAAGTGCAGATTCAATTTCATCTTCTCTCAATCACATCGGCGGTACAATCAAAAATAAATTTG
108469 A G AAAATGCTGAGGGAGAGTCATGACAAAAGAGGACCTGAAGATGATGATTTGATACGGCTGCAGCTAGAAACATTATTAGCGGAAAAAGGGAGGCTAGCAC[A/G]CGAGAACTCATTATATGCTAGGGAAAATCGATTCTTAAGAGAGATAGTAGAGTACCATCAGCTTACAATGCAGGATGTAGTATA
108469 C T AATAGAAGAAGTCACTGAAGTATTCTCCAACAGTCCTAGACAATTATTATCTCGAACCAGTTCCATTTCAAATTCATTTAACAACGTTGGTTCATCTACG[C/T]CAGTCGATGAAGTGTCTACAACTACAGCAGCTAATAACGCAAGTTCTTCAAGGGTGGTTGTGCATGAAGCTTGCGGTGTTATTCCTACA
108469 A AC GTTCATCTACGCCAGTCGATGAAGTGTCTACAACTACAGCAGCTAATAACGCAAGTTCTTCAAGGGTGGTTGTGCATGAAGCTTGCGGTGTTATTCCTAC[A/AC]CCCCCCTACAACTCGGATGAAGGGCAATGAAGATGGGAGTTTGAAACTGTAGAAATTGTGGTTTTGAATGTGGAGTTTTCTTGCCT
108471 T C GCTTGGCATTTCTCCGTTTTTGCTTGACGATCTAGCGTCAACTCCAACAGGCTTATCCATCATTGCATTCTGGCCATGAGGAAAGTTGGTAGTATCTTTG[T/C]CCAGCATTTCTACAGGATTCACATCATCTGAGACTCCATTTTTAACCTTCAATTTTCCTTTTCCCTTGCCACCGCCATCTTCATCACCAGTC
108475 AC A TTTTTAGGGCATCCGTACCACCTGGCATGCATCGATTTCGAGGCAACATTTGGGATTTTGATAACAGACCCAAAGTGTTGGAAGCACTCGGGTATCCACG[AC/A]CCCAATGAATGATAGAATTCCAGAAATCACTGAGGCTAGGAATATCGAACTTGGTCTTGGACTTCAACTATGCTTCTTGCACCCTTC
108475 A G CGAGGCAACATTTGGGATTTTGATAACAGACCCAAAGTGTTGGAAGCACTCGGGTATCCACGACCCAATGAATGATAGAATTCCAGAAATCACTGAGGCT[A/G]GGAATATCGAACTTGGTCTTGGACTTCAACTATGCTTCTTGCACCCTTCCAAGTACAAGTTTGAGCATCCACGATTTTGTTTAGAAA
108475 A G AAGCACTCGGGTATCCACGACCCAATGAATGATAGAATTCCAGAAATCACTGAGGCTAGGAATATCGAACTTGGTCTTGGACTTCAACTATGCTTCTTGC[A/G]CCCTTCCAAGTACAAGTTTGAGCATCCACGATTTTGTTTAGAAAGATTGGAATACATTGGCCAAAAGATTCAGGATCTTGTAATGGCG
108481 T C ACTTAAACCTTTCAATAGTCATACTCTCAGGTGGAGCGGTAGGCAGATTAGCACGCTGTAAGATTCTAAGTACACGGTCAACAATAGTGCCATCGATCCA[T/C]CCAAGCCTTTTCGACATATCAACAGCCATAACTGTACCAGCGGCAACAGCTTCTCCATGGAGCCATTGCCCGTACCCGATTCCGTTTT
108483 GT G ACCCCTGGTTGAACTTCTGAGCGTACTGAAGGTTGGCGTTCATGTCCCCATCCGTGGGCCAGCCGATCTCACCGATTATGATGGGCAGGTTGTCGAACCC[GT/G]TTTTTTTTAAGGGCCCAGACGAGGGTATCATGGTTGGCATCAAACACATTCTCATAGGTGGTGGAGCCGTCCGTGACGGGCGTGG
108483 A G GAAGGTTGGCGTTCATGTCCCCATCCGTGGGCCAGCCGATCTCACCGATTATGATGGGCAGGTTGTCGAACCCGTTTTTTTTAAGGGCCCAGACGAGGGT[A/G]TCATGGTTGGCATCAAACACATTCTCATAGGTGGTGGAGCCGTCCGTGACGGGCGTGGCAGAGCCATCGAAGAAAGCGTAATTGA
108483 T A ACGGCTTTCCGGATTCGGATTGGTAAACATCAGCGTTTTGAGGGCATGTGACTTTTACTTGGTTGGCGAGCCCGGCTTTGATGATGGCCGATTGGATGTT[T/A]TGGAGTGCGGGGAATGTCGTTTGAAGGAAGCTTCCGTTGAACGTTTTCAGGAATGGTTCGTTTCCAACTGCGACGTACCTGATATT
108483 C T TTTTCAGGAATGGTTCGTTTCCAACTGCGACGTACCTGATATTAACTCCATCACTAACATATCCAGACACATTCCTGGCCACCCAATTCTCCGCAGACTG[C/T]AGACTAGTAGCCAAACTTTGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGTCTTCTTTAGTGCAATGAGAGTTGCATCT
108483 G A TTCAGGAATGGTTCGTTTCCAACTGCGACGTACCTGATATTAACTCCATCACTAACATATCCAGACACATTCCTGGCCACCCAATTCTCCGCAGACTGCA[G/A]ACTAGTAGCCAAACTTTGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGTCTTCTTTAGTGCAATGAGAGTTGCATCTTC
108483 C A CAGACACATTCCTGGCCACCCAATTCTCCGCAGACTGCAGACTAGTAGCCAAACTTTGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGT[C/A]TTCTTTAGTGCAATGAGAGTTGCATCTTCAGCATCAAAAAGCTTCGCTTTTTTAATCCCATTCGCTTTAAGCATCTGTACTACTATATTTG
108483 G A CCACCCAATTCTCCGCAGACTGCAGACTAGTAGCCAAACTTTGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGTCTTCTTTAGTGCAAT[G/A]AGAGTTGCATCTTCAGCATCAAAAAGCTTCGCTTTTTTAATCCCATTCGCTTTAAGCATCTGTACTACTATATTTGGTGATAATGGATGA
108483 G A AGCCAAACTTTGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGTCTTCTTTAGTGCAATGAGAGTTGCATCTTCAGCATCAAAAAGCTTC[G/A]CTTTTTTAATCCCATTCGCTTTAAGCATCTGTACTACTATATTTGGTGATAATGGATGACTTGTTTGTGTACCCCAGTTAGCACCAATCCC
108483 T A TGCAGCAATTCATTTGGAATGCCAACCATTACCTCAATGTTAGTCTTCTTTAGTGCAATGAGAGTTGCATCTTCAGCATCAAAAAGCTTCGCTTTTTTAA[T/A]CCCATTCGCTTTAAGCATCTGTACTACTATATTTGGTGATAATGGATGACTTGTTTGTGTACCCCAGTTAGCACCAATCCCATTAACTGTT
108483 A G GTCTTCTTTAGTGCAATGAGAGTTGCATCTTCAGCATCAAAAAGCTTCGCTTTTTTAATCCCATTCGCTTTAAGCATCTGTACTACTATATTTGGTGATA[A/G]TGGATGACTTGTTTGTGTACCCCAGTTAGCACCAATCCCATTAACTGTTACTGTTGCTAATAACCAAGTAACCAAATACAACTTCATATAT
108483 T C TGAGAGTTGCATCTTCAGCATCAAAAAGCTTCGCTTTTTTAATCCCATTCGCTTTAAGCATCTGTACTACTATATTTGGTGATAATGGATGACTTGTTTG[T/C]GTACCCCAGTTAGCACCAATCCCATTAACTGTTACTGTTGCTAATAACCAAGTAACCAAATACAACTTCATATATAATTTCTTCATGGTAG
108483 A G GTACCCCAGTTAGCACCAATCCCATTAACTGTTACTGTTGCTAATAACCAAGTAACCAAATACAACTTCATATATAATTTCTTCATGGTAGAGTGATAAA[A/G]TTCCAATCTTAACCAAAATATCGAAAAGATGGACGTTTGCAATCTTGACGAAGAGCTAAAGAGTATTTGCTGCTAAAGTGTGATTTTGA
108483 C T AAGTAACCAAATACAACTTCATATATAATTTCTTCATGGTAGAGTGATAAAATTCCAATCTTAACCAAAATATCGAAAAGATGGACGTTTGCAATCTTGA[C/T]GAAGAGCTAAAGAGTATTTGCTGCTAAAGTGTGATTTTGATGGAAATCCAGTAGGCCAACAG
108485 A G AGCCTGACAGTCCAGCAATGGACAGCAGGCAAAAAGCTTTGGAACGGAAGCTTTCTAATTCAGATGGCTCTGTGTTCAATTTAGGTGGAGGACCAGGAAC[A/G]GTTGGGATAGCAATTACTCCATAATTTTGTAAAAGAGTAGTCAAGGCAGCACGGATTTCATCCCTAAAAGTCAAATAGCATCCTAG
108485 G C CAAGCCTTTGGAGAGAACGCATGACATAGGAAATACTTCCTAATGCTGGTGTGCTGGAAGATTGAAAGTCCGGTATTTTGCTGAGAACATTTCTTAGTGA[G/C]GGAACTTCATTGTGTATATAGTCACCAAGGTTCAGATATTTTACAATATTACATCCATAAATTTTTTCAGAGGAAATGGTTACTATTTG
108485 C T GCAGGTACACGGACACTACCTCCAGTATCGGTACCAAGAGAGAAGAGAACAAGGCCGGCAGCAACAGCCACTGCGGATCCGCTGGAAGAACCTCCTGGAA[C/T]TCTATCTGGTGCAACAGGGTTCATAGGTGTACCATAGTGATAGTTTTCTCCATTTATACTGTAGGCCATCTCATCCATAACAGTTT
108487 AT A AGGTTTTGGGGTGCATACTGCACAAAGGAGGATCTTCTTATTCTAATCTTACTTCCTTGATTGATGAGCTCGCTGCACTGACCAAGTAAAAGGAATGGTT[AT/A]TTTTTAGTTAATGTTTTTATTCTAGTTTATATTCATCTGCTGCTGTAACTTTCCAAATTGCCTTCGTTTGTGATCTATATTTGTTTTGGTT
108487 GT G CATACTGCACAAAGGAGGATCTTCTTATTCTAATCTTACTTCCTTGATTGATGAGCTCGCTGCACTGACCAAGTAAAAGGAATGGTTATTTTTAGTTAAT[GT/G]TTTTTATTCTAGTTTATATTCATCTGCTGCTGTAACTTTCCAAATTGCCTTCGTTTGTGATCTATATTTGTTTTGGTTTGAAAAAAAAAAA
108499 C T TTAATGTTTTCCACAATGTATAGGACGTTGTCTTCGTTGATTTCTCCTTTCTTCTCGGCATCCATTATGTGGTCAATGGCACACTTTAGGCCTGCGTTGT[C/T]GGTTGTCGTTGTGCTCGATAATTTCTTCCTCTCCTCAAGAAAGTAATCCTTGAACAACTGAATCCTCCTCTCCTTAACTTCCTTGCAAATCT
108499 T C ATCCATTATGTGGTCAATGGCACACTTTAGGCCTGCGTTGTCGGTTGTCGTTGTGCTCGATAATTTCTTCCTCTCCTCAAGAAAGTAATCCTTGAACAAC[T/C]GAATCCTCCTCTCCTTAACTTCCTTGCAAATCTTCAAGTAACCCCTCAAAAATGGTCTCAAAATAGGAATAAAATCACCATAATTGTACTC
108499 T A TCCTTAACTTCCTTGCAAATCTTCAAGTAACCCCTCAAAAATGGTCTCAAAATAGGAATAAAATCACCATAATTGTACTCAAAACTCTGCGCCAACCTAC[T/A]CCTCTCATTATTCAAAGCTTTCAGCTTCAAAAACAAGGGATCGTTTTCACTCTCAAATCTCCTATCAAACATAATCCTATACATGTTATTGT
108501 C G ATCTCCTCTTCATTTTCCCCTTTCCAGTTTCTCCGTTTGCAATCAGTCGACCAAAAAAACTTTAAACTCAAACCCTTAAATCCCAAATTC[C/G]GAGACCTAATTCTGTACGTGTTCTCAATTATTTGCACAAAATCACTCCTGATGATCCCAGATCCATCTGAAAAGGAAGCATCGCTCTCCTCTCCGACGGT
108501 T C AGAACTGCCCTTCGCTTCAGTCAGAACTCCTAAAGATAATAGCAGGGTGCGAAGAAGAGTGTGGAAGTGCCGCCAAAGCACGAAGTGTGTGGGCGCAGCT[T/C]TCTGATGGGGGAGACTCGAACGACAGGAGAGTCAGGCCTCGCACTTGATATAACAGACGCGGCGTTCGGTTTTAACCCTGGGA
108501 T C CGTTATGTGAGGACATATATACTTGATCTGTGCTGTACATCATCATTCAGTACTCTGGAAATTTATATAATGTTTGACATAAAAACTTAGTGATTTTGAT[T/C]AATTGCTTTTACTACTCGCTTGATTATAAAAGTTTGCATGCAATATTTCGATTCAAAAAAAAAAAAAGGCC
108503 G A CACGTGGGCACCGACGAGCGCAGTCGGAGATCATCAGTCTCCCCGATGACCTTAATTTTGACGTCAGCGACCTAGGTTTTGTGGACCCTACCGAAGAAAT[G/A]GAAGAGGAAGAAGATTTCCTATCAATGTATCTCGATATGGACAAAGTTAGCAAGGAGGGACAGAGTTCGCAAAACGAGGAGAGT
108503 T G CCGAAGAAATGGAAGAGGAAGAAGATTTCCTATCAATGTATCTCGATATGGACAAAGTTAGCAAGGAGGGACAGAGTTCGCAAAACGAGGAGAGTGGAAG[T/G]GTTGGAACGCAAAATTTGGGAAGTGGAGGTGTCGGATCGCAGAACGTAGAAAGTGGGGGAAATGCCTTGCAAAGTTCTAATG
108503 G A TCGATATGGACAAAGTTAGCAAGGAGGGACAGAGTTCGCAAAACGAGGAGAGTGGAAGTGTTGGAACGCAAAATTTGGGAAGTGGAGGTGTCGGATCGCA[G/A]AACGTAGAAAGTGGGGGAAATGCCTTGCAAAGTTCTAATGTGAGGGCTAGGCATCAGCATAGCCAGAGCATGGATGGCTCCA
108503 C T GAACGCAAAATTTGGGAAGTGGAGGTGTCGGATCGCAGAACGTAGAAAGTGGGGGAAATGCCTTGCAAAGTTCTAATGTGAGGGCTAGGCATCAGCATAG[C/T]CAGAGCATGGATGGCTCCAGTTCAATGAAGATGGAACAGCTTGTTGGGTCGAGTTCCGATGTTGGGTCGCTTGCGGAGGCCAA
108503 A G CACTTGTGGACCCAAAAAGGGCAAAAAGAATTTGGGCAAACAGACAATCAGCTGCACGATCGAAAGAAAGGAAAATGCGCTACATTGGTGAACTTGAGCG[A/G]AAAGTTCAGACACTGCAAACTGAAGCAACAACATTGTCAGCCCAGCTTACAATGTTACAGAGAGACACCACTGGATTAACTGCTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108503 T C ACATTGGTGAACTTGAGCGAAAAGTTCAGACACTGCAAACTGAAGCAACAACATTGTCAGCCCAGCTTACAATGTTACAGAGAGACACCACTGGATTAAC[T/C]GCTGAAAATAACGAACTCAAAATTCGGGTACAAACAATGGAGCAACAAGTTCACCCTCAAGATGCTTTAAATGAAGCATTACGCGA
108503 C T TCAGCCCAGCTTACAATGTTACAGAGAGACACCACTGGATTAACTGCTGAAAATAACGAACTCAAAATTCGGGTACAAACAATGGAGCAACAAGTTCACC[C/T]TCAAGATGCTTTAAATGAAGCATTACGCGATGAGGTTCATAGATTGAAAATGGCAACTGGGCAAATGATGGCAAATGGACCAGCCA
108503 G A ACCCTCAAGATGCTTTAAATGAAGCATTACGCGATGAGGTTCATAGATTGAAAATGGCAACTGGGCAAATGATGGCAAATGGACCAGCCATGAATTACGG[G/A]CAGCCATCTTTTGGACCTAACCAACAATTCTATCATAGTAACAGTAACAGCAATAACAATAACAGTCAGGCAACACAATCGCTTTTG
108503 GCAATAA G AAAATGGCAACTGGGCAAATGATGGCAAATGGACCAGCCATGAATTACGGGCAGCCATCTTTTGGACCTAACCAACAATTCTATCATAGTAACAGTAACA[GCAATAA/G]CAATAACAATAACAGTCAGGCAACACAATCGCTTTTGACAGCTAGACAATTACAACAACTGCAGATTCACCCTCACCAGTA
108503 T C CTGGATATGAGAATGAAAGGAACACTTGGTCCTCAAAATCAAAGGGAAATTAATGCAGATAGAAGCAATCATTCTATTAATTGATGATATATTTGGAGAT[T/C]GTCGGTTCCTTTTGGTGAGTTTTAACTTTCTATTTTTACATGATGTTAAATGATTTTCTAAAAGAGATTGACGTAGTTACTTCGCATAT
108507 CCTG C TCTTTCTGATTACCACTAGAAGGTCCTACGGTAGAAGATGCAGTTGTGTAAGTCCCTTGAAATGCTGGAGCTGAAGGAGATAGTTGAACACTGGATTGTG[CCTG/C]CTGCTGGTATGGACTCCAACCGGAAACTGGAACCATGCCTGGTGATATCATCATCGACCCATATGTTGGTTGCATATATTGAGC
108511 C G AAAATCCCAACAACTCATTTGTAATCATGTCTGCTAATCCAAAGCCATCAACGAACCACATAATAATCGTTGGCGGCGGTGTCATCGGCGCCTCCACCGC[C/G]TACTTTCTATCTAGAAAACTTGCCTCTTCTGTAGCCCCTACAAAAATCACACTAATCGAAAAGTCATCGATTGCTGCTGCGGCTTCGGG
108511 C T GCCCCTACAAAAATCACACTAATCGAAAAGTCATCGATTGCTGCTGCGGCTTCGGGGAAAGCCGGCGGCTTTCTGGCACTCGACTGGTGCGACTCTTCTT[C/T]GCTCTCATCTCTTGCGCGTGCCAGTTTTAGTCTCCATCGTGAACTGTCGCAGGCATTGGATGGTGAACGAAATTACGGATATCGTCC
108511 T C TCACACTAATCGAAAAGTCATCGATTGCTGCTGCGGCTTCGGGGAAAGCCGGCGGCTTTCTGGCACTCGACTGGTGCGACTCTTCTTCGCTCTCATCTCT[T/C]GCGCGTGCCAGTTTTAGTCTCCATCGTGAACTGTCGCAGGCATTGGATGGTGAACGAAATTACGGATATCGTCCTCTCACTACTCTGT
108511 T A CTCTGTCTCTTAGCCTTATGGGTAATAAGAATAACAGTGGGGGCAGATCAAAAGTTAGTGTTCCTGCTTGGATTGATGAATCTAGTGTGGGGAATTTGAA[T/A]ACGATTGGGACTGCTGAAACCACAGCTCAGGTTCATCCAAAGCTCTTCACCCAAACACTTATCGACGCTTGTACAAAAACTAATAAA
108511 G A GAATACGATTGGGACTGCTGAAACCACAGCTCAGGTTCATCCAAAGCTCTTCACCCAAACACTTATCGACGCTTGTACAAAAACTAATAAACTCAATCTC[G/A]TTTTCGGGGAAGTTAAAGAAGTGGTGATAGACGGTGGTAAGACCACCGGAGTAGTGGTGATGGAAAAAGGACATGAAGACAACAA
108511 T A TACGATTGGGACTGCTGAAACCACAGCTCAGGTTCATCCAAAGCTCTTCACCCAAACACTTATCGACGCTTGTACAAAAACTAATAAACTCAATCTCGTT[T/A]TCGGGGAAGTTAAAGAAGTGGTGATAGACGGTGGTAAGACCACCGGAGTAGTGGTGATGGAAAAAGGACATGAAGACAACAAGGT
108511 C T AAGCTCTTCACCCAAACACTTATCGACGCTTGTACAAAAACTAATAAACTCAATCTCGTTTTCGGGGAAGTTAAAGAAGTGGTGATAGACGGTGGTAAGA[C/T]CACCGGAGTAGTGGTGATGGAAAAAGGACATGAAGACAACAAGGTTTTGAATTGTGACATTGTGGTGCTTGCAGTGGGACCATGG
108511 T C GTACAAAAACTAATAAACTCAATCTCGTTTTCGGGGAAGTTAAAGAAGTGGTGATAGACGGTGGTAAGACCACCGGAGTAGTGGTGATGGAAAAAGGACA[T/C]GAAGACAACAAGGTTTTGAATTGTGACATTGTGGTGCTTGCAGTGGGACCATGGTCGAGCAGTATGCAGATTCTAAGCGAGATA
108511 C T AGTTAAAGAAGTGGTGATAGACGGTGGTAAGACCACCGGAGTAGTGGTGATGGAAAAAGGACATGAAGACAACAAGGTTTTGAATTGTGACATTGTGGTG[C/T]TTGCAGTGGGACCATGGTCGAGCAGTATGCAGATTCTAAGCGAGATATTCAGAATTAGTGGGACTAAAGCACATAGCATTGTGG
108511 T C AGCATTGTGGTGCGACCAAAAGAGATGGAGGCAATCACACCACATGCTCTGTTTCTCTCTTATCAAGATTCTCCTGGTGGCAAAATGCTTGATCCCGAAG[T/C]TTATCCTCGGCCTACAGGGGAAGTGTATATATGCGGGATGTCACAGGAGTTACAAGTACCGGAAAACCCCGAGGAGGTCACAGGG
108511 G A ATCAAGATTCTCCTGGTGGCAAAATGCTTGATCCCGAAGTTTATCCTCGGCCTACAGGGGAAGTGTATATATGCGGGATGTCACAGGAGTTACAAGTACC[G/A]GAAAACCCCGAGGAGGTCACAGGGGACCCAGCTTCAATACAAATGCTTCACAAAGTAGCAGGAAAAGTGTCGAGTCATTTGCAGA
108511 C G CTCCTGGTGGCAAAATGCTTGATCCCGAAGTTTATCCTCGGCCTACAGGGGAAGTGTATATATGCGGGATGTCACAGGAGTTACAAGTACCGGAAAACCC[C/G]GAGGAGGTCACAGGGGACCCAGCTTCAATACAAATGCTTCACAAAGTAGCAGGAAAAGTGTCGAGTCATTTGCAGAAGGAGAAA
108511 C T TGCTTCACAAAGTAGCAGGAAAAGTGTCGAGTCATTTGCAGAAGGAGAAAGGAGCTGAAGTGATAGCAGAGCAGGCATGCTTTCTGCCTTGCAGCGCTGA[C/T]GGTTTGCCTGTGATTGGCGAATTGCCAGGGGTAAAGGGCTGCTATGTAGCCACTGGACATAGCTGTTGGGGTATACTCAATGCT
108511 C A AGAAGGAGAAAGGAGCTGAAGTGATAGCAGAGCAGGCATGCTTTCTGCCTTGCAGCGCTGACGGTTTGCCTGTGATTGGCGAATTGCCAGGGGTAAAGGG[C/A]TGCTATGTAGCCACTGGACATAGCTGTTGGGGTATACTCAATGCTCCCGCAACTGGAGCTTCTTTAGCTGAACTCATTCTGGATG
108511 T C TGTTGGGGTATACTCAATGCTCCCGCAACTGGAGCTTCTTTAGCTGAACTCATTCTGGATGGGGAGTCTACTACTGTAGATTTAACGCCTTTCAGTCCTT[T/C]CAGATTTTTGACCGGTCGTACTAGGAAATAGCATTTGAACGCTTTGATAATGATGTGCATAGTATGACTATGAGGGTGCGATAATGTG
108511 A G TCCCGCAACTGGAGCTTCTTTAGCTGAACTCATTCTGGATGGGGAGTCTACTACTGTAGATTTAACGCCTTTCAGTCCTTTCAGATTTTTGACCGGTCGT[A/G]CTAGGAAATAGCATTTGAACGCTTTGATAATGATGTGCATAGTATGACTATGAGGGTGCGATAATGTGTGTGTTATGTGTTGTTTCTTA
108515 C T CCTTCCCAAGTGCAACCACAACCTTCTTAAGAATAGCTTCAACAGGCAAATGAGAATTTTCAACCGCCTTGCTAATTGCTGTCCATTTCTCACCATGCTT[C/T]GGCTCTGCATTAACGCACCTCTTTAAGACGTCCTTCTGCTCTTCCTCGCCACCATGCTGAAGCTCAAATTTGTAGTACAAAGCCCAAAAA
108515 T C AACCAATTCCTCGCCTTGTCCACTTTCCTATCGAGCCAGAACAATTTCGCAACAGCAGCAAAAACATAAGGATCGTGATCGCACCTCTTGATAGCATCAG[T/C]ACTCTTTGTTTTTCTATGTGGGCGTGGCGCCATCTCAATAGCAGCAGCCCACAATATACCACTAGTAGGGCATTCTTGTAATGCCTTTG
108523 T C AACACCCTCACAATGCTGTTCTCCTCACATGCACCTCCATCGAAAAAGGCTGTAGACCTTTCATGTGTGATACAAGCTACCGTCATTCAAATTGCCTCGA[T/C]CAATACAAAAAAGCCTTCACCAAAATCTCATGCCCTCTCTGTCGTGGCAGCGTCGATGGTTGGAGCGTGGACAAATCTGCACGTAGGT
108523 G A CAGCGTCGATGGTTGGAGCGTGGACAAATCTGCACGTAGGTACATGGATTCCAAAGTCCGGTCCTGTTCAAAAGAGTCATGCGGATTCAGTGGTACATAC[G/A]TAGAACTCAGAAAGCATGCAAGAAAAGAGCATCCGCTGGATAGGCCATCAACGGCTGATCCAGAGAGGCAGCAGGACTGGCAG
108523 C T AAAACGAGACGGCAGTTAGAGAGAGGAGGAGGAGGACGAGAGAAATACTGAGGAGGCGGATGACTATGAGGTTTCCAGATTATGAAAGCGATGATGCTAG[C/T]GAGGAAGCTGTTAGAGTAAGGCGACGGCTTATGCGGCTATCTCCTGTTGCTGAGAGTAATGACGAGGATGAAAATGATAGAT
108523 A G ACGATGATAGTGTTGATAGGGTAGAGGAAAGGCCAAGGCGAAGGCGTATGAGGTTGCCTGACGATGGAAGCGATGATTGCTAGTGATGTTTTGATCGATC[A/G]TGGTTTGCATTTCAAGTGATGTTCTTTGTAACTTTAATGCTGTAATGGTGAGATTTTCTGGGCTGCTTCTTTGATTGGATATAATT
108523 T A GAAAGGCCAAGGCGAAGGCGTATGAGGTTGCCTGACGATGGAAGCGATGATTGCTAGTGATGTTTTGATCGATCATGGTTTGCATTTCAAGTGATGTTCT[T/A]TGTAACTTTAATGCTGTAATGGTGAGATTTTCTGGGCTGCTTCTTTGATTGGATATAATTGCAGCTTTTAAACATTTGTTGTGCAAAT
108525 G A TAAAACATCACGATACAATAGCTAACAGGGATTAAACAGTTGAATAAAATTCAAAGTAGAATAACTAT[G/A]ACTAAGATAGTACCCTCCATCAGCTATCAGCAGGATTAGTCTTTGAAGCAGCAGCTGGGGAGGCAGAAGGAGCAGCAGCAGCGGTAGCATCGGTAGAATT
108525 C CAGT TCAAAGTAGAATAACTATGACTAAGATAGTACCCTCCATCAGCTATCAGCAGGATTAGTCTTTGAAGCAGCAGCTGGGGAGGCAGAAGGAGCAGCAGCAG[C/CAGT]GGTAGCATCGGTAGAATTGTAAGCAGCAGGAGCTTGAGGGTATCCATACCCATATCCGTAACCCGGCTGACTATAGTATCCA
108525 G C GGGATACGATTGCTGAGCATAGTAGTTAGCTGCTGGCGGTGGTAGCGGCTGCTGCTGCGGTGGTGGGGTCCACATTGGCGGCTGAGGTGGCGGTTGGTAG[G/C]TCTGTTGCGAGTATCCTCCTGATACTGCCTGATTCCTCATACGATTCTCGCCACTTATAACTTCATTAACCAACTGTTTTGCAGCT
108525 A G GCTGCGGTGGTGGGGTCCACATTGGCGGCTGAGGTGGCGGTTGGTAGGTCTGTTGCGAGTATCCTCCTGATACTGCCTGATTCCTCATACGATTCTCGCC[A/G]CTTATAACTTCATTAACCAACTGTTTTGCAGCTTCGATTTGCTCATTTGTGCCATCAATTTGCACTGTTCTCTCTAGTGATGTATCACC
108525 A T CCTCAGCAAGCACATCATTAATCAGTTGCTCTGCCCTGTTAACTTGTTCAGAACTGCCAGTAATATCCACGCTCCTTGTTTGTGAAAAAGGAATTGCATC[A/T]GCATCTCTTGTAATTTGTATTTTTGCTCCAGATTGTGCTTGAAGATATTTAATGGTCTCTCCACCTTTACCAATTAAGACACCAACCCTTC
108525 T C GCTTGAAGATATTTAATGGTCTCTCCACCTTTACCAATTAAGACACCAACCCTTCCATTTGGAATTTCTATTGTCTTGCTGGAACTTTGAGATCCATATG[T/C]TGACATGAAATACTGTGACTGTGCTGGTTGCCCTGTAGGATTTTGTGCATAATCATTGGAGTAAGCCGGATTGTCTCCATTTTCAGGTTT
108529 T C TCTAACCTTCAAAATGTAGCCAAAGCACAAAACACAACATCCATCTTTATCACCTACTAACAATTTTTGCTTGTGGATCCAACTTCTCCAAAACCTCCAA[T/C]GGCTTATCAGTCTCCTTCCTGATCCTCTTAATCTTTGCGCTCTCCAACCCTGTATGAGCAAACCCGTAGATCCTCAAAACTTGGTTATCCGC
108535 C G GTTCTAGAAGAACCACTCCGAAGCTGTATACGTCGCTCTTCTCGTTTACTTTCCACGTGTATGCATACTCAGGAGCAATATAGCCGTGCGTTCCAGCAAT[C/G]ACATGAGTTAACGAGTCTTTCCCTACCCCTGACTGCAATATCTTAGCAAGCCCGAAATCGGCAATCCTGGGCTTAAAGAACTCATCCAG
108535 T C CCATGATGCAAATACTCTAAACCTCTAGCGGCGCCTAAAGCTATTTCGTATCTCGTCTCCCAATCCAGACCAAGCTTCTCCCCAGCCGCTGTATGCAACC[T/C]GTCCCACAGGCTCCCATTAGGCAAATACTCGTACACCAACAAGCTCGAATCCTCACTTGTTATACTACAATATAGCTTCACCACATTCAC
108547 A G ATGTGGGTTGGGGACATAGTAGTAAAAATGACCCTAGTAATGTTTGGATTCACGAAAGAGTCAACCCAGTTAGCCCAAGTCTTCAGCCCAAGTCGATAAG[A/G]AACTGCAGCTTCTAGCTCCTCGTATCCATCCATCCCATTGCTAAAAGAACCCCACAGGGATTTGATTTTTGGATCGCTTGTCCACCAC
108549 A G AAATTAAAGAACTTATAGAAATAGCGAAGGAGTACGTGTTGGGGTTGAAAATTGAGGTCAAAAGGAAGGAACTGCCTAAAGAAGATGTAGTTAGGCAGCA[A/G]GAACTAGCTGCGTACTTCACGAATTGCAAGCTTCAGAAAGGTCATGCAAGGCTTGTTCTCACTAGCGCTATGAACATATGCTACA
108549 T G CGTTGTTTGCGGAGCCACTTTTGTTCCTATCTATCGTGGCCAGAAGGATGTCTCGTGCCCTTATTGTGGGGCGCACTTTGTTCCAACTTACGAGGGTCAG[T/G]TATGTGCTATTTGTGAGCTGGCCCTGGTCGGAGCTGATGCTTCTGGATTGCTATGCTCTCCTACGCAGAGGAGATAAGTTGCAGTTC
108549 C G TCCTATCTATCGTGGCCAGAAGGATGTCTCGTGCCCTTATTGTGGGGCGCACTTTGTTCCAACTTACGAGGGTCAGTTATGTGCTATTTGTGAGCTGGCC[C/G]TGGTCGGAGCTGATGCTTCTGGATTGCTATGCTCTCCTACGCAGAGGAGATAAGTTGCAGTTCCTTTGTTTTTCGTGTTTTATTGGGG
108551 A G TCATATAGCTTGCAAATTCGCATATAATATACATAAAACCAAGCATATAATTTCACTCCAACATACAGCTAGATACAAGTATATACCAAACATAGAAGAC[A/G]GAGTGATCACAGAAGAAACAGACATATCTAGCCAGTGTTCTGCATGCCTGCAGCAATGCCTTTCATTGTGAGAATCAATGTATCTTCTA
108551 T C AAACAGACATATCTAGCCAGTGTTCTGCATGCCTGCAGCAATGCCTTTCATTGTGAGAATCAATGTATCTTCTAGTCCAGGAGCATATTCGCTGGTAGGG[T/C]TAAGTTTAACCAATTCGGCTGCAGGTTTGCGAGACTCTATTACTTCCTTTGACAGGTGGGGCCTGAGATTCACGTGAAAATCAGGATC
108551 A G ACAGGTGGGGCCTGAGATTCACGTGAAAATCAGGATCTCTTATTCTCTTCAATGTGTATGCTTGGCATACGTTCAGAGTTGTTATGTATGAATCACGAAG[A/G]CGAAGTCTTTGCTTTAGGTAGGGGTCTCCCTCAAGCAAATCTCTATGTCCAGCAACTTGTAGAAGAAGACGCTTTGTTTCTCCGTAGT
108551 G A TTCAGAGTTGTTATGTATGAATCACGAAGACGAAGTCTTTGCTTTAGGTAGGGGTCTCCCTCAAGCAAATCTCTATGTCCAGCAACTTGTAGAAGAAGAC[G/A]CTTTGTTTCTCCGTAGTTTGCTCTTAGTCGCTCTCCGAGTTCCCATAGGTCTTTAGAAACTAAAAGTTTATCATACAATGCTGCAATAC
108551 T A CAACTTGTAGAAGAAGACGCTTTGTTTCTCCGTAGTTTGCTCTTAGTCGCTCTCCGAGTTCCCATAGGTCTTTAGAAACTAAAAGTTTATCATACAATGC[T/A]GCAATACCAGGGTCTCCCTTGGCAAAAACCATCTCAATCAAGTCTATGGTCACTCTGAAAAATGGCCATTGATTGTACATTTCCTGTAGG
108551 A C CATATTTGAATGCTGCACCAAAGCCAAGCCAAACAGGGAGATGAAACCTCGTTTGAGTCCATGCGAAAATCCACGGAATTGCACGTAATGTCTCTATGCC[A/C]CCACTCGGCTTTCTTTTAGATGGTCGGCTGCCAATGTTCATCCTACCATATTCTGTTTCAGGTGTAGCCAAACGGAAGTACTCAACAA
108551 G A TAATTGTATCAGGCGGCTGAGATAATATAGCAAGATGTGTGGGTCCACCTCCTCTTCCAACAGTACCTCCTCTACCATGAAACATGGTTAACTTGATGCC[G/A]TATTCTTTTGCCACTTTAACCAGCTCCTCCTGTGCTTTGTACAGTTGCCAAGCTGCGGAAAGCCTACCTGCGTCTTTACCCGAATCCGA
108551 G A CAACAGTACCTCCTCTACCATGAAACATGGTTAACTTGATGCCGTATTCTTTTGCCACTTTAACCAGCTCCTCCTGTGCTTTGTACAGTTGCCAAGCTGC[G/A]GAAAGCCTACCTGCGTCTTTACCCGAATCCGAGTATCCAATCATAACTTCTTGCATGCCATTAATTCTATTCTTGTACCATTCGATCGAGA
108551 G A GCCAAGCTGCGGAAAGCCTACCTGCGTCTTTACCCGAATCCGAGTATCCAATCATAACTTCTTGCATGCCATTAATTCTATTCTTGTACCATTCGATCGA[G/A]AACAATCTTGCTACAGCTGCAGGAGCAGTTTCAAGGTCGGCAAGCTTTTCAAATAGAGGCACGACCCTTAAAGGTTTCGTTACATGAC
108553 C A TCCCCTCGCGGGTACTGTTCAGATCTATGAACGACACGTGTTTTTGTGCTACAAGAACCCTCAGGTCTGGCCTTCTCATGTTGAGGCTTCCGAGTTCGAC[C/A]GGTTGCCTAGGCTGCTGACTGCTGCGCTTAAGGCTAAGAAGAATGAGATGGCAAAGAAGACTCGTTTGACTATATGCGAAGGAGAG
108553 A C GGGTACTGTTCAGATCTATGAACGACACGTGTTTTTGTGCTACAAGAACCCTCAGGTCTGGCCTTCTCATGTTGAGGCTTCCGAGTTCGACCGGTTGCCT[A/C]GGCTGCTGACTGCTGCGCTTAAGGCTAAGAAGAATGAGATGGCAAAGAAGACTCGTTTGACTATATGCGAAGGAGAGGATGGAAC
108553 T C TGTGCTACAAGAACCCTCAGGTCTGGCCTTCTCATGTTGAGGCTTCCGAGTTCGACCGGTTGCCTAGGCTGCTGACTGCTGCGCTTAAGGCTAAGAAGAA[T/C]GAGATGGCAAAGAAGACTCGTTTGACTATATGCGAAGGAGAGGATGGAACCGATTCATCAAATGGAGATGTATTAATTTTCCCTGA
108553 T C CTGAAATGGTTCAAGAAGCAACCAATGGCTGCTGCCAAGGAAACAATAAAAACATCAGCTGTTGCCAAAACGGTGCATCAGAAGCGAATATTGAGTCAAA[T/C]GACACAGAAATTGAAAACATAGTGGAGAGGGAAGGGAAGAAGGAAAGCAGCACGGGAAGCAGCAGGCGTAAGGTGTGTGGAA
108553 G A GCTGCTGCCAAGGAAACAATAAAAACATCAGCTGTTGCCAAAACGGTGCATCAGAAGCGAATATTGAGTCAAATGACACAGAAATTGAAAACATAGTGGA[G/A]AGGGAAGGGAAGAAGGAAAGCAGCACGGGAAGCAGCAGGCGTAAGGTGTGTGGAATGCCAACATGGTATGAAACTTGGGAGC
108553 CA C TGAGGACACTTATGCAGCTCTCGCTGTAATTACCGCTGTTGCCTCCATTGCTGTTGCTTATAGCTGCTACAGACAATCGCGTTAAGCAGTTCTTCATACA[CA/C]AAAAAATATGTTCAGCAGAACTGTTAGTAGGGTTATGTAGTTTGCTTACATTGCTTGACGACTAGGTACCGTCACTGTAACGCTCAGG
108555 C A CTGAAATTCAAAAGGACAAGAGCACTCCTCTTGTAAAGAAGGTTTTTGCTGCAGAGTATTCTCTCATTTGCAAAATATTTGATTACAAAAAGCCTTATAT[C/A]AGCTTCATGGATGGAGTTACTATGGGGTTTGGAATTGGATTATCTGGTCATGGTAGTTACAGGATTATTACGGAGAAATCTCTTCTTGC
108555 A G CGGAAAATGGAATTGGCTTATTTCCAGATGTTGGGTTTGCTTACATAGCTGCACGAAGCCCAGGAAATGGGGCAGTGGGAGCTTATCTTGGACTCACTGG[A/G]AAGAGGATATCTTCTCCTGCTGATGCATTGTATGCTGGTATTGGATCTCATTATGTACCATCTGGAAGCTTAGCAGCACTAAAGGA
108555 T C AATTGGCTTATTTCCAGATGTTGGGTTTGCTTACATAGCTGCACGAAGCCCAGGAAATGGGGCAGTGGGAGCTTATCTTGGACTCACTGGAAAGAGGATA[T/C]CTTCTCCTGCTGATGCATTGTATGCTGGTATTGGATCTCATTATGTACCATCTGGAAGCTTAGCAGCACTAAAGGAGTCGCTTCTCT
108555 C T GGGCAGTGGGAGCTTATCTTGGACTCACTGGAAAGAGGATATCTTCTCCTGCTGATGCATTGTATGCTGGTATTGGATCTCATTATGTACCATCTGGAAG[C/T]TTAGCAGCACTAAAGGAGTCGCTTCTCTCACTTACATTCTCTGACGACCCACATAAAGATGTGCTGTCACTTTTGGAAAAGTATGGGA
108555 T C GCTTTGGTGCCGATAAATCAGTGTCTGGAACAATGGATGAATTGAAAAGGCTTCAACAAAGCAATGATTCTAAAGTGGCAGAATGGGCTAGCGAAACTCT[T/C]CTTGGACTAGGGAAAGGGGCTCCTTTCTCTCTTTCTTTGACAAGGAAGCATTTTACAGAAGTTGCTTCTGCCTATGGAAAAGAGGA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108557 A AG GTACTGGTCTGGATCAATGCCAAGAGTCTGCGTCACAGATGCAGAGCAAGCAAAGCAAATTCTGTCAAACAAGTTTGGGTTTTATGGCAAGCCAAAACCA[A/AG]GGGGCATATACTGGGACTCATAGGACGTAAGAGTTTACTTATTGCTGAGGGCTCAGAGTGGGCGAGGCATCGGAGAGTTATCG
108557 G GA TGGTCTGGATCAATGCCAAGAGTCTGCGTCACAGATGCAGAGCAAGCAAAGCAAATTCTGTCAAACAAGTTTGGGTTTTATGGCAAGCCAAAACCAAGGG[G/GA]CATATACTGGGACTCATAGGACGTAAGAGTTTACTTATTGCTGAGGGCTCAGAGTGGGCGAGGCATCGGAGAGTTATCGGCCC
108557 G A ACCATGGACAAGCTCAAGTTATCGACGAAGGTGATGGCGCATTGCATAACATCAATGTTGAATACTTGGCATAACAAAGTGACAGAAGCACACGATGAAC[G/A]CAACTGGATTGAAGTTAACAAGGAATTTCAGGAATTAACAGCTGATATCATCTCCCATGCAGCTTTTGGTAGTAGTTTCGTGGAAG
108557 C G TTTGCTGGGCAAGAGACAACTTCACAGTTGCTGACATGGGCTATGTTCTTGTTAAGTACAAATCAAGATTGGCAGGATAAACTAAGACAAGAAGTCATCA[C/G]TGAATGCGGCACACAAATTCCCACAGCTGACAACTTAACCAAGTTCAAATTTATGACTATGGTTATTCTAGAAACACTGAGGCTGTA
108559 C T ATATTTGTTAATGTTGCTTTCGGTATAACATACACTCATACAGCACATACATAAAAAAGCTCGGGCATGTGTTATGATGCCATTATAAAAAGAGTCCTTC[C/T]GGATTGCAGACTGATAATCCATAACATCAACTTATTCCTCAAAATCCTCCAAATGAAATTTTGTGCTCTTTCATGATATTATTAACAAATT
108559 G A CATGTGTTATGATGCCATTATAAAAAGAGTCCTTCCGGATTGCAGACTGATAATCCATAACATCAACTTATTCCTCAAAATCCTCCAAATGAAATTTTGT[G/A]CTCTTTCATGATATTATTAACAAATTTATGTTATGCATTCACCCAGATTTTGTGACCTCGTGGATCGCATTAGCCAGATATTCTACATTTT
108559 A G ATGCCATTATAAAAAGAGTCCTTCCGGATTGCAGACTGATAATCCATAACATCAACTTATTCCTCAAAATCCTCCAAATGAAATTTTGTGCTCTTTCATG[A/G]TATTATTAACAAATTTATGTTATGCATTCACCCAGATTTTGTGACCTCGTGGATCGCATTAGCCAGATATTCTACATTTTTCGAAGTTACT
108559 G T TCTTGAATTGGCGTGATATCTCCCTCCATTGTTCTTCAGATGGATCTACACCAGTGGGATTATGGGCGCATGCATGGAGCAAGAAAAACGAGCCATTTGG[G/T]GCATTCTTGACATCTTCAATCAGTGCTGCAAAATCTAGACCCTTTGTTTCAGGATGATAATAGTGGAAGGTCTTCTGTGGCACATGTG
108569 TG T AAGTGAGTTTGGTTGCCGCTTTTAGCCCGGGAGTAATTAGCATGGGGCTTCAAGCTGGAAAATTTATAGGGAATATCGCAAAACTATGTGGCGGTGGAGG[TG/T]GGGGGAAGGCCAAATTTTGCTCAGGCTGGTGGCCGAAAACCCGAGAAGCTTCCAGAAGCTCTGGAAAATGCTAGAAGTGACCT
108571 T C CACTGCGTTCTTCAAGTTCTTCTTCACTGCGCTCTTCAGTTTCTTCTTCCAATCCAAATTGAACCAAGTTACTAGACAATTTCGAGATCCCTCTCCTAAA[T/C]TTGCCCCCGATTTCAACAAAATCATTTCGAATCCCATGAAAATTTGATGACGATTCACTGCTGACGGCAGGATCGGGATCGGGATCGGGT
108571 T C CTTCCAATCCAAATTGAACCAAGTTACTAGACAATTTCGAGATCCCTCTCCTAAATTTGCCCCCGATTTCAACAAAATCATTTCGAATCCCATGAAAATT[T/C]GATGACGATTCACTGCTGACGGCAGGATCGGGATCGGGATCGGGTGGTAAATTGGACGGAGGAGGAGCGAGGAAGGTAGCAAAGCC
108571 T C GAAGGTAGCAAAGCCCCTGAATTGGCGGGTTAATGTTTCAGTCAACTCGGAGAGGTCTTCCTTCACGCCCCGATTCGGGTCGCCGGAGGTTGAGGCGGCG[T/C]CTACATCTTCTTTTTCATTGCTGTCCGGATTATGACCAGAGAGAAGTGGGTTGGTAATAGAGCTAGGCAGCCATGACATTTCTCTT
108575 T C CATTTTTGCTTTCCTTCTTTCGGCAGCAAACAAATCCTTCAATAAAGGAACTGGAGGATTACTCTCACCAGGCTGAGGATGCCACTCAAGAAGAACATCA[T/C]TATTCTCAACAGCATCTCTAACGTGTTCATACATATTCATTGCAGTCCTAGAATGAAAATCTCCGCCAGCCTCAAAGGCATCTAACATG
108575 T C TCTCCGCCAGCCTCAAAGGCATCTAACATGCTCTTGCAATTCGACAGATGAGCTAAAATTCTTAGCTCCAGCTGTCCATAATCTGCAACGATGAGTGAGT[T/C]CCCTGGAGCGGCAACAAAAGCCTGCCGTATTTTGTAGCGATCCTTCTCGAGAGCAGGTTGATTCTGCAGATTTGGTCGCCTTGCTGAC
108575 G A CAAGGAATCAATAGCACAGACTTCACAGAGAGCTGCAATTGCATGACAAGCTTCCCTCCCATGTCTACCTTCTCCAAATGCTTGGTAAGCTGTTCCATAT[G/A]CAGATTTGTCTACATCATCCGAAATTGATTTAACACTTGAAATTTGTGTTTCTCCATCAGAATAATATTCATCATCGTCTTCACACAAAT
108581 GC G CACCGGATAGGACAGTTTATCCATCTATGGATCCGCAGCGGATGGGCGCGTTGGTCCAAAACGCACAGGAGGGGACCAGTTCCGATGGGGTACGTTCTAC[GC/G]CCCCAACCTTATGTGCCCAACCAGTATCAGTATTATCAACCACAGCCATCCCAGTATGGTGGTTACATGGGACCACCCCGCCTCA
108581 A AC CCAGTTCCGATGGGGTACGTTCTACGCCCCAACCTTATGTGCCCAACCAGTATCAGTATTATCAACCACAGCCATCCCAGTATGGTGGTTACATGGGACC[A/AC]CCCCGCCTCATGCTTATCAGCCACCTTATCCGTCACATCCGCCGCCACATCAACAAATGCTGCCTCAGCCACAGCCAACACAGCCAC
108585 A G ATCATCAGCCATGAACTGTGTTTACAAATACAACCCTGTTCTAAACACATGGCATCAAGTGACCTCCATGAACGTACCTCGGGCCTTCTCTAAGATAAGC[A/G]TTCTGAATGACAAGCTTTATGTTGTGGGCGGTGTTAGCAGAACAAGAGGTGGTTTGACACCTTTGCAGTCTGCAGAAGTGTATAATC
108585 T C TCGTACATGGGGAAGTTATGTGTCCCTCAGAGCTTGTATTCATGGCCATTCTTCGTGGATGTTGGAGGAGAGGTGTATGACCCAGAAATGGATGCATGGG[T/C]CGAGATGCCACCGGGCATGGGTGAGGGGTGGCCCGCTAAGCAAGCGGGTACGAAATTGAGTGTGGTGGTGAATGATGAGCTTT
108585 A G GGGCATGGGTGAGGGGTGGCCCGCTAAGCAAGCGGGTACGAAATTGAGTGTGGTGGTGAATGATGAGCTTTACGCTTTAGATCCTTCAAACTCCGTGCAT[A/G]CTAGTAAGATAAAGGTTTATAATCAGGAGGATGATACATGGAAGGTGGTTATCGATGAAGTGCCTTTACATGATTATACTGATGC
108585 C T CAAACTCCGTGCATACTAGTAAGATAAAGGTTTATAATCAGGAGGATGATACATGGAAGGTGGTTATCGATGAAGTGCCTTTACATGATTATACTGATGC[C/T]GAATCTCCTTATTTGCTTGCATGTTTGCATGGAAATCTGCATTTGGTAGTGAAGGATGCAAGTAATTTGACTTTGGTGTTAGAGACTG
108585 A G AGATAAAGGTTTATAATCAGGAGGATGATACATGGAAGGTGGTTATCGATGAAGTGCCTTTACATGATTATACTGATGCCGAATCTCCTTATTTGCTTGC[A/G]TGTTTGCATGGAAATCTGCATTTGGTAGTGAAGGATGCAAGTAATTTGACTTTGGTGTTAGAGACTGATGTAAAGAAAACTAATGCT
108585 T C ATTATACTGATGCCGAATCTCCTTATTTGCTTGCATGTTTGCATGGAAATCTGCATTTGGTAGTGAAGGATGCAAGTAATTTGACTTTGGTGTTAGAGAC[T/C]GATGTAAAGAAAACTAATGCTGGAGAGTCGAGTTCTGAGGTAGATGGAGAGGTTTGGAGAGCTGTAGCTAGTAAGAATTTTGATGG
108585 GA G ATGCCGAATCTCCTTATTTGCTTGCATGTTTGCATGGAAATCTGCATTTGGTAGTGAAGGATGCAAGTAATTTGACTTTGGTGTTAGAGACTGATGTAAA[GA/G]AAAACTAATGCTGGAGAGTCGAGTTCTGAGGTAGATGGAGAGGTTTGGAGAGCTGTAGCTAGTAAGAATTTTGATGGTGCAGAG
108585 T C GCTTGCATGTTTGCATGGAAATCTGCATTTGGTAGTGAAGGATGCAAGTAATTTGACTTTGGTGTTAGAGACTGATGTAAAGAAAACTAATGCTGGAGAG[T/C]CGAGTTCTGAGGTAGATGGAGAGGTTTGGAGAGCTGTAGCTAGTAAGAATTTTGATGGTGCAGAGTTGATAAGCTGTCAAGTTCT
108593 G A GCTCTATTATACCTTTGGTGATCATAGCCCTTAAAATTCTTGTGTCCAAATCATCTGGATCTCTAGCGGAGGTGTACACCACTTTGACTCCTTTGATACC[G/A]CTTCCGCCCGCTACGAGTTGTACGGCTAGCCTACCAAGCTTCTCCGCTAGGACTACATAAGGGGCTAGTTCGGATAGAACCTCAGCAGG
108593 C T TACCTTTGGTGATCATAGCCCTTAAAATTCTTGTGTCCAAATCATCTGGATCTCTAGCGGAGGTGTACACCACTTTGACTCCTTTGATACCGCTTCCGCC[C/T]GCTACGAGTTGTACGGCTAGCCTACCAAGCTTCTCCGCTAGGACTACATAAGGGGCTAGTTCGGATAGAACCTCAGCAGGAACCATGG
108593 A C CTCTAGCGGAGGTGTACACCACTTTGACTCCTTTGATACCGCTTCCGCCCGCTACGAGTTGTACGGCTAGCCTACCAAGCTTCTCCGCTAGGACTACATA[A/C]GGGGCTAGTTCGGATAGAACCTCAGCAGGAACCATGGGAGCATTTACGGCAGTTGCAGCAAGTTCGCCCTTTAAAGCCCCAACAACA
108593 A G CTACACCTTCCTGAGCCTCCACAGTGCTAGCTCCGAGATGGGGAGTCACGGTAACATTCTTGTGCTGCACCAACTTGCTGTCTTTTGCTGGTGGCTCCTT[A/G]GTAAATACATCAAGTGCAGCCTGTGCAACAGTTTCATTATCTAGAGCTCTGACTAGGGCATCCTCATCAATCACACCACCCCTTGCAAC
108593 C A ACAGTGCTAGCTCCGAGATGGGGAGTCACGGTAACATTCTTGTGCTGCACCAACTTGCTGTCTTTTGCTGGTGGCTCCTTAGTAAATACATCAAGTGCAG[C/A]CTGTGCAACAGTTTCATTATCTAGAGCTCTGACTAGGGCATCCTCATCAATCACACCACCCCTTGCAACATTGATGATACGCACTCCTT
108593 A C CACCAATGGCACGAGCTCTATCCGCTGGAGCATAGGGATCATGTGCGACCACATGCATTCCTAGACCTTTTGCACGCCTAGCAACTTCAGAACCAACCTT[A/C]CCAAATCCCATAACTGCTAGTGTCTTGTTTACTAAAGATACACCAACGTATTTGTTTCGCTCCCATTTCCCAGCCTTCATAGACGCGTC
108593 G A TCCCATGCTCAGCCGCTGCAATTGTATTTGCCGTCGGCGCGTTAACAACCAAACACCCAAACTCAGTCGCTGCCTGCAGATCCACGTTATCGATACCGAC[G/A]CCTGCCCTTCCAACAACCTTCAGCTTCCCCTTTGCCGCCTCAAACACCTCCCTTGTCACCTTCGTCCCGCTCCTCACTATCAATGCATCG
108593 T C ATTGTATTTGCCGTCGGCGCGTTAACAACCAAACACCCAAACTCAGTCGCTGCCTGCAGATCCACGTTATCGATACCGACGCCTGCCCTTCCAACAACCT[T/C]CAGCTTCCCCTTTGCCGCCTCAAACACCTCCCTTGTCACCTTCGTCCCGCTCCTCACTATCAATGCATCGCTCTCCGCCACCTTCCTACAA
108593 T A GGTTGTACGCACAATCCACGTTCGCAAACGAGCGAAGAAGTTTAATCCCTGATTCCGAGAGCTTCTCTGAGACAAGGACCGTAGGTTTGTCTGACGACTT[T/A]TCAGATTTGAGTTTCGGATCTTGAGCGACGGTTATGTTTGAAGCGACAGCAGCTGAGATTTTCAGGTTGAATTGAACTCTGGAGTTG
108595 CA C GCATACGCGACATCAGATTCTTGTTGCTCATGCCCTCACTTTTTTCCAATTTCAGGCATTTGACTGTGAATGATTTCATCACCGTGAAAGATTCGATGAA[CA/C]AAAAAAGATGAAGAACCTGTGGCCTCACCTGTATCGTGTGCTCCCAGTGCGAGCCTTGGAAGTGTAATTGACATTCTAGCATCGAAA
108601 A G GGAGGTACCCGTTCCCTTTACAAGGGGACAGAGATCACAGTTTCATCTACGAAGATGAAATGGGCTTCAGGTTAGTGGACGTTAATATTCAGGTCCATCA[A/G]CCAAATCATAGAGGCGAGCACGTGCCTTGGGTGTCCTTATCGAGCAAAGGCAACCACGGCAAACCTATTGTAGGGCACCCTATCCA
108601 C T AAGGGGACAGAGATCACAGTTTCATCTACGAAGATGAAATGGGCTTCAGGTTAGTGGACGTTAATATTCAGGTCCATCAACCAAATCATAGAGGCGAGCA[C/T]GTGCCTTGGGTGTCCTTATCGAGCAAAGGCAACCACGGCAAACCTATTGTAGGGCACCCTATCCAAGTCGAGGTATTGGAGGATG
108601 T C AGGTTAGTGGACGTTAATATTCAGGTCCATCAACCAAATCATAGAGGCGAGCACGTGCCTTGGGTGTCCTTATCGAGCAAAGGCAACCACGGCAAACCTA[T/C]TGTAGGGCACCCTATCCAAGTCGAGGTATTGGAGGATGCCTCTACCCTACTTGATTATGGTCATCTTGTGCCTGCTCGTGTGACCAA
108601 C T ACCAAAACAGGTAAGAAAAGCGCAGCAATAAAGAGAACTCGTTCTGATCAACAAAAGCCTTTGAAGACGAAAAACAGTTCTGTTAAAAGCGCAGGAAGGG[C/T]TGAACCTTCTAGAAGAGCAGGACGACTTCCTGTTATCACTTGTGTACCTGTGAAAGTGGTGTTTAGTAGGATACTGGAATCAGTC
108603 C T GGCGTAGACCCCTCCGAAGTACACATCCACGTAGACCGAATCAAGCCTTTGGACATTCCATCGACCGAACCCGAAGTTTCTGATTGGCTAATGCAAAGAT[C/T]CAAACTCAAAGATGAACTGCTTTTCAAATTCATTTCTCAAGGTTCTTTCCCAAATCAGTATGCAGAAGGCAACTTATCTACAGCAAAA
108607 G A AGAAAGTTTTGATTTTGATGAGTGATACTGGTGGTGGGCATCGAGCTTCTGCAGAGGCTATTAAGGCTGCTTTTAACCAGGAGTTTGGTGATGAATACCA[G/A]GTATTTGTGACTGATCTATGGACAGAACACACTCCTTGGCCATTTAACCAATTGCCAAGAAGTTACAATTTCTTGGTGAAACACGAG
108607 C T GAAGGGAGTTAGGGATGGATGAAGATTTGCCTGCTGTTTTATTGATGGGAGGCGGCGAAGGCATGGGGCCCATTGAAGCTACAGCACGGGCTCTTGGGGA[C/T]GTATTACATGATGAGTTGGGAGGACCGATGGGTCAAATTCTTATTATCTGTGGTCGCAATAAGAAACTTGCTAACAGACTGGGT
108607 T G CGATGATCCGTGGTCTTCCTATCATTCTCAATGATTACATTGCTGGCCAGGAAGTTGGCAATGTACCATATGTGGTTGAAAATGGATGCGGAAAGTACTC[T/G]AAATCTCCCAAGGAGATAGCAAGAATAGTCTTCGAATGGTTTGGTCCTAAGACGCATGAACTCCAAATAATGTCGCAAAATTGCTTG
108615 A G GTTTATTATGGTTAGGCCTTTTGCTATGAAGCCCGGTCCCATTGCAGCGACGGTTGCAGAGTTGTACGTAGTGTAACCATCAGCAACGTTCCTGCTCCCA[A/G]CAACGACAGATTTACCCTTGCCATCACCCATCAGCATGACATTTTTCTGCTTTTTGGGAATGTTAATGTTTTCTTTGTAGACTCCACTCT
108617 G T CACAGAGAACTCAAGGCGCGCAACCTTGAAAAATATTCATGAATTGCTAGTAAAGCTCGTGCTGCTTGTCGAGTTGTTAATATACGAAGCATTTGTTGCA[G/T]AGTTTGCTGCCGCAGTTTGTCAGCCTGACTGAGGAAAGTTTCCAGTGTACCAAGCTTTCCCATGGCCATTGCCATCTGGCCCATGTAA
108617 A G AGCATTTACAGCTCCTCTCAGCTCGTTGATCTTTCGATTTTGATCTTCTAGCCACCGCCCGTATTCAACATCAAAAGCCAAAGCACCATTACCACCAGTC[A/G]AATGAGCCTGATCACCTGCGTTTGATATAAAAATTCCCTGTTGCCGAGCTCGCTGAAGCTCCTGTTCAAGTTGAGTAAGCTTCATCCTAC
108627
ACCTGCATTTGTAAGAGGATCATA CACCTGGTACTGCTCCAACAGACCCATATGCTTTGGAATAACCATCCATGATGCTTGCATCACACTCTACATTGCCGTCCTCTGTTAGATTTGATCCACG[ACCTGCATTTGTAAGAGGATCAT/A]CCTGCATTTGTAAGAGGATCATCCTCTAAAATCTGAATGGCAGCTGAAACAGCATCTAAAACTGAAC
108627 G A GTACCTTAGGTTGATTACAAGTTCCAACTTTGAAGGCTGAAACAAGTGAGAGATTGAAGATACGAGAGAGAGAAAACCCACGCAATTTAGAGCGAAACGC[G/A]TACTACGATATGAGAGCTAGAGCTGTTGGACATCGTGTTTTGATTCTTTTGAATCAAGAAATCAGTTTACCAATT
108627 C T TAGGTTGATTACAAGTTCCAACTTTGAAGGCTGAAACAAGTGAGAGATTGAAGATACGAGAGAGAGAAAACCCACGCAATTTAGAGCGAAACGCGTACTA[C/T]GATATGAGAGCTAGAGCTGTTGGACATCGTGTTTTGATTCTTTTGAATCAAGAAATCAGTTTACCAATT
108629 C T CATTGCTTCCACCACTATGGTCACAATGCAGAATGTCATGTATCAATAAACTTATACATGATTTGCTTTGGTATCATTCAGATTGTTCTAAGTCAGATTC[C/T]AAATTTTCATGATATATCATGGCTTTCGATTGTTGCAGCAGTTATGTCTGTTACTTACTCTTTCATAGGCCTTGGGCTCTCTGCCGCGGCA
108629 C T GGTTTGTTTGGATATTCAGCATTTGGTAATGCTGCTCCTGGCAATTTTCTTACTGGGTTCGGGTTTTACGAGCCTTTTTGGTTGATTGACATTGCCAACA[C/T]CTGCATTGCTGTCCACCTTGTTGGTGCATATCAGGTTTTTGCCCAGCCGGTATTCCAGTGTGTTGAGAACGCATGCTCTAAGCGATGGC
108635 A G CAATCCCCTCACTAAGAACCCACTCTACCACCCTCTACCTTCCTTCTACATCGCCCCTTCCGACATCGTCATACGCCAAATCCTCTTCGACACCAGCAGC[A/G]CCCAGATCCAGCAGAACATCGCCTACCTACGGGCTGGCCCTCGAAAGATGATCCGGTTTGACCCGGCTCAGGTGAAGGCAGCCGTAGT
108635 C T CTGGCATACCAAAAACAGTGGATAATGATGTGGGCATCATAGACCGCTCTTTTGGGTTTCAAACAGCGGTCGAGATGGCTCAACAGGCAATAAGTGCAGC[C/T]CATGTGGAGGCAGAGAGCGCTGTGAATGGCATTGGACTAGTGAAGCTGATGGGCCGAAGCACAGGTCATATTGCTCTACATGCC
108635 A G CAGTTTTCTTAGACGTAGGCCCGTGGCTGAAATCGGAGCTCAAAACATGGTGGGAGAGGGAACACAAAGGAGAACTATTTACAGTGAAGTACATCGATCC[A/G]ACATACATGATAAGAGCAGTTCCTGCAAATGCAACTGATAATTTGTACTGCACTTTGTTGGCTCATTCGTCTATTCATGGAGCTATG
108635 C G CACTTTGTTGGCTCATTCGTCTATTCATGGAGCTATGGCGGGCTATACCGGGTTTGTGTCTGGTCCGATTAACGGAAATTATGCTTATATTCCAGTTGAG[C/G]AAGTCGCCGTTGCAAAGAATGTGGTGGATGTTGCTGATCATAAGTGGGCTTGGGTCCGATCCGTTACGAACCAACCTGATTTTGTTA
108635 A T GTGGGCTTGGGTCCGATCCGTTACGAACCAACCTGATTTTGTTAAGCAATTGTAAATTAGATTATAGAGCGGCAATGTTGAAGGAAAACAGCTTATTTGC[A/T]TCATTTTCAGCTTGTTAATTTGATGGTGACATCTGGATTTTGCTTAAATAAAAAGTTGTAGTGACCTAAAAAAAAAAAAAACGAAA
108641 C G TTGGTTCATTCAATTATAACAGCGGGAATAGATTCTTTCACAATAAGAACAATGGGTACAACCAACAGTCGGATAAGTTTCAAGTTAATCAGGGTTCAGC[C/G]GTCTCAATTCAGCCAACAACTACAGCTGAACCGGGCATGCAGCAGCAACAATCACAACCTCAACAAAATAATGCGACTCAAGCACCA
108641 C T AAGAGAAGGCGAAAGGAGTAAGCACGGACGATGCCGTGGGAAACCCGGACATAGTCCTGTTTGAAGAAAACGAAGACGAGGAGGAAGAGGAAGAAGAGAG[C/T]GATGAGGAAGAAGACCCGTCACAAGCCCACATGAGAGGAGGGATGAACATGGGGCACATGGGAATGGGAAGAGGAAACA
108643 T TG TCAATGCAATAGATAAGCAGAACTTTGAATCACCACCGTCCGTTGCCATACTGCCAGCTGGCACCGGCAATGACCTTGCACGAGTTCTAAGCTGGGGGGG[T/TG]GGCTCGGTGTTATGAAAAGCATGGTGGCTTATTAGCATTTCTTGAAAACATTGAGCATGCTGCGGTCTCTATACTTGATAGATGG
108643 T TA TAAGCAGAACTTTGAATCACCACCGTCCGTTGCCATACTGCCAGCTGGCACCGGCAATGACCTTGCACGAGTTCTAAGCTGGGGGGGTGGCTCGGTGTTA[T/TA]GAAAAGCATGGTGGCTTATTAGCATTTCTTGAAAACATTGAGCATGCTGCGGTCTCTATACTTGATAGATGGGAAGTACATATTAA
108645 G C CCCGTGGGGCTAATAGAAGCGATCTTGTTAGTTGTCCAGCATCGGTTTGTTGAGCCAGTCTGTTAACCTTTACGTTGCCATCAAATACAGCTTGACCTGA[G/C]GAGTGTGACACAATGCACTTATGGAGCTGGCGAGAAAAGCCTCTTGGGTAGTCCATTATTAGCCTACTGTGCAGGTCTTGTATCTGG
108649 G A CCCCAAACCCAGCAGTAGCGATAGTATCGCCTGCTTTGACTTTCCCATTCCTAACGGCCTCATCTAACGCTAAAGGAATTGATGCAGCACTTGTGTTTCC[G/A]TAGTTTGCTAGATTTGATATTACTTTCTCCGATGGAATTTCTAAACGGTTCGATACTGCATCTATTATCCTTTGGTTTGCCTGGTGAAGT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108649 C T CGGGTGGCAGTGATCAATCCTACAACAAACCCACTGCATGCAGCTGTGATGTCAAATGCTAAGGCACTTTTGCAGCCTAGATCGCCTTGGATCCGAGAAG[C/T]ACCACCAAAAAGATCATCCGGTGTGGAAGAGCAAAATATAACGAGGTCAACGTTCTCGGCCTCAACTTCAGCCATTTGAAGAGCAC
108651 T C CAGCACACTCCCCGCTTAAATCCACTGTAGCACCACTCAGCCCAACCACCACCACCTTCAAAAGTCCAAACGCCCCTGCAGCACTCTGAAACGCGTTACA[T/C]GCCACTTTAATCCCGTCCCCCTTATCCCTATCCACCCCCAATGCGATCTGACTATAAACCGCCCCCAAATTGAACAAAACTGCGCATTTC
108653 CA C TTCAATTTGCGGAGCGACCTGCAGCGGTCGCTCTTCCGATGAAGTGGTCTGTAGACAGCTGGAGATCTAAGAAGGCATTGCAGCTGCCGGAGTACCCGAA[CA/C]AAAAAAGAGTTGGACGAGGTTCTGAAGACGATAGCAAGCTTCCCTCCGATTGTGTTCGCAGGCGAAGCGCGGCATTTGGAAGA
108653 C T CAACTCTCAATCTTCTACGTGCATTTGCCACTGGTGGCTATGCTGCCATGCAGCGTGTCACTCAGTGGAACCTTGATTTCACTGAAAGCAGTGAACAAGG[C/T]GATAGATATAGAGAGCTGGCAAACAGAGTGGATGAGGCATTGGGATTCATGGCGGCTGCAGGGTTGACTACTGACCACCCAATCAT
108655 C T GAAGGTGCGATCGATCCTTGAGAAGATGATCGATTGGTGTAAGTTAACTCCTCAGAATCAGAGAAGTCTTCCATCATGCTTTCGAGCTGAACAAATAGAA[C/T]AATGCTGTCGAATAACATTTTCTCAAAATTTTCATCTTTTGCATGCACGTCCTTGTAGCCATACCTTGCAACACATCGAAACATACGAA
108655 A G GTGTACACGAACCCGATACCGGGGACCCGGACCAGGCCAAGGCTGGGGCCCAACCCGAGGATCCAAGCCATGGAGACACGCCCATGGAGTTCAAACTCAT[A/G]CCTCTTGACTGTGCCATAGTGCCAGACATACATTATGATTAGGAAGACCCCAGCAATCACGAGAGGGACCCACCCACCCTGGTC
108655 A G ACCTCTTGACTGTGCCATAGTGCCAGACATACATTATGATTAGGAAGACCCCAGCAATCACGAGAGGGACCCACCCACCCTGGTCCACCTTGAAGAGGAC[A/G]GCCGAGAAGTAGGTCAGCTCAGCCAGTAGAGAGAGGGTCGTGAAGGCCAGGACCAGGGCCCAGTGGGTTTTGAAGACTAGTAG
108655 AT A GCGTTTCCAATTTGACTTTGATTTTTAAACCCAGCGGTAACAGCTATACATAGCACCATAAGAATCCAATTTATATCAGGGCTATATATTTGTCCGAGGA[AT/A]TTTTTTTGATGTATGAACAACTTTAACCCTAGGAAAACATCCAAGTGCAAGAGCTTGTTTGATTATTGAAAATGTTGCAGATATAGTTG
108655 C T CGTTGCTATAATGAACATTGGCCAATATACACTGGCCGGAATAGATAGATAGAAAGCATCAACGGCATGCCCTTGGTTCTTCATAATGTAAGCTGCCTGG[C/T]CAATGTATGCCAAAAGAAGGCAGGGAAATACTACAAATGTAAATGCAATCTGAATAGCCAAGACAGGGAAGTGGCACAAATCAGC
108655 T C ATATGTAAACAGGGTTAAAAGCCTTGAGAACAGAGCTATCATATTTGCATATGTTGAGAACACCGATGGAGCCAATAGATAGGAACCAAATAAGAACTAT[T/C]GGAGCAAATAGCCAGCCAACTCTATCGGTTCCGTAATGTTGCACCAGTAGGCCAACAGTG
108657 T TG TAGCTGGGGATAGGTTGGGATGTTTTAATTTGTCGGTGAAAGGACATGCAGATTGCCTTCGGTTTCTCAGGTCTTTTAATGTACCACTTATGGTATTAGG[T/TG]GGGGTGGTTATACAATTCGGAATGTAGCGAGGTGTTGGTGCTATGAGACAGCAGTTGCTCTTGGAGTAGAGCCTGAAAACCAATT
108667 T C TGGAGGGGGAGAGGAAATATGCAGAGTTCTGGATGGGCACGCACCCCTCTGGACCTTCGTATGTCCTCCTTGAGAAGGAGAAGCCGAAGTTGAAGGAATT[T/C]ATTGAGAAGAATAGCTGTAGGGTTTTGGGGCAGAAGGTTTTCGATGAGTGGGGAGATGATCTTCCTTTCTTGTTTAAGGTTTTAT
108669 A G ATCTTCAGCCGTTTGGGAGAAACGGGAGCTGCTGAAATCATTAGAGCGGTCGAACATGACGGAGGAAGAGGTGGTGGTGCTGCGAAAGGAGTCGTCAAGG[A/G]TGGACCGGGCAAGGATGTTGTCAAGCTGACCGGGAACGGATCCGCCCGGCTCGATGGACGAGGCCGGGATCGAGTGCATGA
108669 T C TGTAAGAGGAGTTTGATTTTGAAATGTTATCAGCGTCCATGGAGATTATGTACTCTGTACATGTAGTGCGGCGATTTCTTTTTGCTGATAAAAGGAACTT[T/C]CCATTTTCGACCAGCACAGCAGGACTAAGGCAGAGGTAGAGATGATAAGTGAGTTTCGATTTATCTCTCTTGATAAAACACTGAATAG
108669 T C GGAATGACATGCTACTTGCGTAAGAGCTTAGCCTTTGTTGCAACTTTTAAAAAACAGAAGGCCTCGACAAAGATGACCAATTTTGACTTGACACTGAAGG[T/C]AAAGAGATTTTATCGCATGATTTCTCCTTTTTCTCTTTTTAAAAGCAGTAGAAATGGAAAGAAAATGAAAATAACGGATTTGAAAGGT
108671 T TA GGCCTACACGACCCCTTCCTAAAAGGTGCCATGAAACGTGGTGATTGGTACAGAACCAAAGATTTGGTGCTTAAAGGCGCAGATTGGATTGTTAATGAAG[T/TA]AAAAAATCCGGGCTTCGTGGACGTGGGGGTGCAGGTTTCCCCTCAGGCCTCAAATGGTCATTCATGCCCAAAGTCTCCGATGGCC
108671 C T TGGATTGTTAATGAAGTAAAAAATCCGGGCTTCGTGGACGTGGGGGTGCAGGTTTCCCCTCAGGCCTCAAATGGTCATTCATGCCCAAAGTCTCCGATGG[C/T]CGTCCTTCATATTTAGTCGTAAATGCCGATGAAAGTGAACCTGGAACATGCAAAGATCGTGAAATCATGCGTCATGATCCACACAA
108671 C T TAAATGCCGATGAAAGTGAACCTGGAACATGCAAAGATCGTGAAATCATGCGTCATGATCCACACAAACTTCTTGAAGGTTGCTTGATTGCAGGGGTCGC[C/T]ATGCGTGCCACAGCTGCTTATATTTATATTAGAGGCGAGTATGTGAATGAGCGTCTGAACCTTGAAAAAGCAAGGCAGGAGGCCTA
108671 T A GTGAACCTGGAACATGCAAAGATCGTGAAATCATGCGTCATGATCCACACAAACTTCTTGAAGGTTGCTTGATTGCAGGGGTCGCCATGCGTGCCACAGC[T/A]GCTTATATTTATATTAGAGGCGAGTATGTGAATGAGCGTCTGAACCTTGAAAAAGCAAGGCAGGAGGCCTACAAAGCTGGGTTGT
108671 T G ATGATCCACACAAACTTCTTGAAGGTTGCTTGATTGCAGGGGTCGCCATGCGTGCCACAGCTGCTTATATTTATATTAGAGGCGAGTATGTGAATGAGCG[T/G]CTGAACCTTGAAAAAGCAAGGCAGGAGGCCTACAAAGCTGGGTTGTTGGGTAAAAATGCTTGTGGGTCTGGGTATGACTTTGATG
108671 C A TCGCGAGCTTCGGCCGAAAAAACAACTCGGGCACGAAGCTATTCTGCATTTCGGGCCACGTGAACAAACCATGCACTGTAGAAGAGGAAATGAGCATCCC[C/A]TTACGAGAGTTGCTCGAAAGGCACTGTGGCGGCGTCCGTGGCGGCTGGGACAACCTGCTTGCGGTCATACCCGGAGGCTCCTCC
108671 AT A ATGGTGCTGGTTTTGTAATGTCTCTTTTATAAATTGGAATAAAATTTGTACAACTGTTATGTAACCTCTTTATACAGGAAAAAGAGCTCTTCTTTCTCAA[AT/A]TTTGAGGAGTGGGTGCTTTGATTATTAAGTTTATGTTATTTGTTTCGACCGTGTAAGCGGCATGGACCCTGGATATGGTTTTCTGTTTA
108673 C T TGTTAGCATGCAAATCGATATCAAAGAGGAAGCTGAGGACGAGTGTGGATGTAGAGGATGTTAGAAGAGAAGTGGCAATTATGAAACATTTGCCTAGTAA[C/T]GTGAATATTATAAGTTTGAGAGAAGCATGCGAGGATGAAAGCGGGGTGCATTTGGTAATGGAGTTGTGTGAAGGTGGAGAATT
108675 C T TCAGTTTCCACAGTTTTCTCGCATCCATCTTCCTTCGCTAATTTCAACAGCCAGTAATGATGCTATAAGTTTAATTTCGTGGCTTTGTTCCTGGGATCCG[C/T]GAAAGAGGCCCACTGCAGCAGAAGCCCTTCAACATCCTTTCTTTCAGCGCTGCTATTATATACCATCTTCATTGCTCCCAAGAGTATGTGA
108675 T C TCCGCGAAAGAGGCCCACTGCAGCAGAAGCCCTTCAACATCCTTTCTTTCAGCGCTGCTATTATATACCATCTTCATTGCTCCCAAGAGTATGTGAAGTG[T/C]CAAAAACGCCTCCGTCTGGAGGTAGTAGAGGTATGGAGCCACAAAAAAGCACTTCTAGACCCAATGGGAATTTTTTTAGTCCTAAGCT
108675 G GAGACTTTGCCAATGGGAATTTTTTTAGTCCTAAGCTTGCTAACACTATTTCATTTCCTTATGTTGACGAGTCCTTAAAAACAGGCGCACAAAGAAAGCTTGAATTGGAT[G/GAGACTTTGC]AGGGTTATGAAAGGAATGCCAAATACGTGCAAAACAAATATAAACAACTTTCATACCGATCATCACAAATCAATAATAA
108677 C CG GCGGCCCAGGAAGTGGTGGGGGCAGAGACGGCACAGGAGGCTGAAAAGGAGGCAGAGGAGGAGATCCGTAGCATGGAGTCGTAGGGTCGTGCTTCTGCTT[C/CG]TTCTCGGGAGGGACCAATTTGGAAGAGGCTTCTTCTGCGACTAAGGTGGAGAGAATGGAGGAGAGCATTTGAGCGGAGG
108677 T C CTGCTATCTTCCCAACAAGAAGAATAGCAGCTTCTGATTTATTTAAAGCAGTGTCTTCCTCGGAATGCTCTTCAAGAACGGACTGATAAGCGCTTATAAT[T/C]TTTTCGGGCATCCCTCCTACTGCTAATTTTAGTCTCAATGTTTGTGAATCTTTACGGGCAACTTTTATGAGGCTTGAATTTGAACTCTTCC
108681 G GA TGCACCGCCTCCTCCGCAGCCTGCAGATTTGCAAGGAGGAGGTAGCATCAACAACAGTGGTGGATCCCAACCATCTTCAGGGCTTATGGTAAACATGGGG[G/GA]AAAAAAGAAAAGAGGCAGGCCAAGGAAGTATGGGCCTGATGGTGCACCGGTGCATGTAGCGGGCCTGGGCTCACCTCAGTCA
108681 ATC A AGCATTCGTAAGCAGCGGCAACAACAATAATCATTCCGGAATGGTCAATATGCAGTGGAAATGATTCTGCTGTGCTGATTTCATTTCCCGCTTTGGGTGC[ATC/A]TCTGTGTATTGGTAGATTATGCAGTATTTTTCTTCTTTCCTTGATGTGTTAGTAGTAGCAACTATCCGAGAGTGCTTAGTTGATGTA
108683 GT G TTCTCTATCTCGGATTCCATGGTTTCGAACAATTGGTTGAAAGTCTGCACGAATTCAGGGACGACGAAGTGGCGACGGGTGGAGAGCATGTGGAAGATGA[GT/G]TTTTTTAAGATCGGAGTGGTTGGGCTCGCGGACGTCGAGGTAGGAGAGGGTGCGGTGGCCGCCGGAGAGGTCGGTGGAGGG
108685 C T AGTAATTCATTCCTTTAATCACATCTAAAGCCATTCTCAGCCGTCTCTTTTCATCTAGTTTAACATTGGGTCGATGCAACAGTCTGTACAAACTTCCTCT[C/T]GGAAGAAACTCTGTCAAAATTGATAAATTTGGAGGGCGAGTTACTGCTCCCATGAAAAGAACAACATTCGGATGCCTTAATCTCAACATT
108685 AT A ACTTCCTCTCGGAAGAAACTCTGTCAAAATTGATAAATTTGGAGGGCGAGTTACTGCTCCCATGAAAAGAACAACATTCGGATGCCTTAATCTCAACATT[AT/A]TTTTTACTTCGCATCTGAACTGTTCCAGTGCATCACCTGATAAACCTTGGTCCAGGAATTTTTTTACAGCCACCTCCGTGCCATTCCAA
108685 T C TCTCCACGGTAAACTTCACCATAGGAACCCAGGCCAATTCGCTCCCCAATCTGAAGAGCGTCCCATGGGATCTCCCATTCCGCAACACCATCCAACAATG[T/C]CTTTAACCTTTCGTTCATATTTTCTTCTTTGGTTGTATTACTTGCTTCAGGGCGTTCATTTTCAGAAGTGCATTGTGTTCCTACTAAATTA
108685 A G CAATGTCTTTAACCTTTCGTTCATATTTTCTTCTTTGGTTGTATTACTTGCTTCAGGGCGTTCATTTTCAGAAGTGCATTGTGTTCCTACTAAATTATTC[A/G]CAATTTCACTCTGGCATGGAGCAGATGGCAAATACCGATTTAACTGACATGCAACGGAAGGGCTTAAAATTATATCACGACATTGTAGAT
108693 G A CAGGGTTCAAGTGCAATAGCGCCGTTTGGAAAGCTTTGAAGACCGTCGATCCTACAAAGGAGAAGAATCCATGGATGGATGAGATCGATAGTTTTCCGAG[G/A]TCGATTCCTAGGGTGTCCGAGCTTTGAGTTTGTAGGTATGTCATAACTCTTATTGTGAATTGGAAGTGGTGATTGTTTTGATGGGA
108693 CT C TCCTAGGGTGTCCGAGCTTTGAGTTTGTAGGTATGTCATAACTCTTATTGTGAATTGGAAGTGGTGATTGTTTTGATGGGAGATGGTATGATTGTTTTTA[CT/C]TTGTATTGGTTCAAATTTATTGTTTGAATTGCGAAGAAGCTATTTGTTCTTGCCATTTCATAACCTGCATGCTGCATGTAGATGGAAC
108693 G A GTCCGAGCTTTGAGTTTGTAGGTATGTCATAACTCTTATTGTGAATTGGAAGTGGTGATTGTTTTGATGGGAGATGGTATGATTGTTTTTACTTGTATTG[G/A]TTCAAATTTATTGTTTGAATTGCGAAGAAGCTATTTGTTCTTGCCATTTCATAACCTGCATGCTGCATGTAGATGGAACTTTAGAAGCA
108697 C T TCCTAGAAGACTTATGTGCCTTGCTCCTCTGGTGCCCTACATTTCTAGGGCTCTGACTCCCACGTCTAGACAAAGAGCTCATACCAGAGCTCCTGTTAAC[C/T]CTTCTTCCAGACCTTCTTTCTCCGCTTCCCAGTGCAGCTTTAACCACGCTGTCAGGAACAGCTTCTCTGGCCTTCTGCACTTTGATGGCC
108697 C T GGATAGGGTTCCCTATCAGGTTTAGGGCTAGAATGGAGCTGTAGTTGGCTACAAGCTGCCCTAACGCTTTGGTGGTTGTTATTTTGTTGAAGCTTAGGTC[C/T]AGGACGGTCAGTTTCAGGAGGCGGTGCAGGCCTTCTATTGAGCTTATTTTGTTGCCAGAGAGATACAGTTCTTTTATTTGTCTGCAG
108697 T C TGGTTAGCTTGCATGACCTCTTCTGCTGTTTTTTTGCATCCATGCAATGAATGATTCTTTTTGGAAGATTCTCCAACCTCCTGTGTAGAAATTACCAAAT[T/C]ATCCTCTGTCTCATCCATGTCATCTCCATCATTATTTGCACAAGGCTCTGTTTCCTCTATGCTATTAACCCATGCATTGATTCTATCATAGGG
108697 C T GGCAACCCATTGATTACCAGATTCCATCGTTTTCTGCTTCCTCTTCTGAAGGTCTTGGGTTGGCTCAAGGGTATCAGAAGAGTAACCAGCTTGATGGTGA[C/T]GACATACTAATTTTGGGATCGAAGGTTTTGAAAAAGATGAAGAATTATGAAGATTACGATGACTCCATAGAAAAAGCTTCCACCACA
108705 GA G CCAAAGATTTCCACAAAAATTATAAACTGCTGGATATCCATCCAGAGCATCTACCTTTTAAATTCAGATTCCTAAATATCGTATTTACAAAGCAAAAAAA[GA/G]AAGAAAAGATTAATGATCCAAGCCACTTTTGCTCCACACTAAGCTGTTAAGGCCTTGACATAAGAAACGACGACAGTAATGTCATCG
108705 A G ATAAACTGCTGGATATCCATCCAGAGCATCTACCTTTTAAATTCAGATTCCTAAATATCGTATTTACAAAGCAAAAAAAGAAGAAAAGATTAATGATCCA[A/G]GCCACTTTTGCTCCACACTAAGCTGTTAAGGCCTTGACATAAGAAACGACGACAGTAATGTCATCGAGCTTGCCTCCATAGTATCGGT
108709 A G TCCGAAACGTTAAAAAGAGATGATTCTCGTATAGGAATATGAATGCTGAAGGTGTCATGAATTCGGTTCTACTGACTTCAGTAAGATACGAGTCCCTTAC[A/G]TCAAGAATTTGGAGATTCTCGTTTTCCTGTTTGACCAGGAGCTTCTCATTGAACTGCTCAATGAAATCAATCTTTTTGTTCCGATGTAA
108709 CT C TGACTTCAGTAAGATACGAGTCCCTTACATCAAGAATTTGGAGATTCTCGTTTTCCTGTTTGACCAGGAGCTTCTCATTGAACTGCTCAATGAAATCAAT[CT/C]TTTTTGTTCCGATGTAAATGATGATTGAAAGATTTTAGTATCGTTCCATCATCAATTGAGAGTATTTTTAATGGTACATAACTTGGTGC
108709 AT A CAGGAGCTTCTCATTGAACTGCTCAATGAAATCAATCTTTTTGTTCCGATGTAAATGATGATTGAAAGATTTTAGTATCGTTCCATCATCAATTGAGAGT[AT/A]TTTTTAATGGTACATAACTTGGTGCCCTGTGGTAAATTAGCAACATGATTCCTGGACTGATTTTGATCTCCTGCACATTCTTGTCAGAT
108709 A G GCTGAATATTACGGAACTTCTCAGGGGCGTTGGATGAAGAGCCGCGTGTCAACATGGGGAACCCTCCGATCTCCCGCCGCTGCAGTTTCTTCACCGAATT[A/G]ATGCACTCTCTCTTGATTTTCCTGGCGGATGAAACTGATGACGAGATGGTCAGATCTCTCCCGCGCTTTTTCGCCGTGACTCGTCGC
108713 CA C AATTCTCTTGTAGAAAATTACCTGTTTGGAAATATACTTCTTGATCTCATCCTCTGTAATATCAGAACCATTTGATCTAA[CA/C]AACAAATGCCACTGGGAGCTCTCCAGCCACTTCATCTTTCATGGAGACAACAGCGGCACCAGCAACCTCAGGATGTGCAATGAGCATAGCCTCAATCTCT
108713 G A CCTCAGGATGTGCAATGAGCATAGCCTCAATCTCTGCAGGAGCTACTTGAAATCCCTTGTATTTAATCAACTCTTTTAATCGATCTACGATGAAGATCTC[G/A]TCATCGTTGTCCACATATCCTATGTCTCCTGTATGCAACCATCCTTCTTTGTCTATTGTTCTTTCGGTCGCCTCCAGATCGTTCAGATATC
108713 G A GTGCAATGAGCATAGCCTCAATCTCTGCAGGAGCTACTTGAAATCCCTTGTATTTAATCAACTCTTTTAATCGATCTACGATGAAGATCTCGTCATCGTT[G/A]TCCACATATCCTATGTCTCCTGTATGCAACCATCCTTCTTTGTCTATTGTTCTTTCGGTCGCCTCCAGATCGTTCAGATATCCTTTCATGAT
108713 C G GAGTTCAGCGAATATATGTGAAAAAGCGGCAACACACACAAAAGCACATCATCGCTTCTAAAATACAAATTCGGATTCTCTCCATCCACCTGCTGAGCCA[C/G]GCTTGTAATCAAGCCTTCATGTGTCAACATAACTCCTTTCGGTAGCCCTGTAGTTCCAGACGAATAAGGAAGTGCCACCACATCATCA
108713 T C GACGAATAAGGAAGTGCCACCACATCATCAGGACTAATATCCACCTCCGGAAGATTCCTTTCGTCAGCGGAAGACAATTGCGAAAAAGGGATGCATGCAC[T/C]GTGTTCATCGACCGACTCATCGATAACCACGATCTTGACGTTGTTTTCCAAGTCTCTGATCTTGGGCACGTAGCAGGATTCTGTTAT
108717 A G ATTGCCCTCTAAAAGGGTCGTCTTCCTCAATGTCGACTGAACTACAGGTGGCAAGGCACGATGTGTTTCCATCTTGGATTGTGGTCTCTTTATCAGTGTC[A/G]TATGTTGCGTATTTGGACTTGAGGTCGTACACCTCGCGGAAGTAATCTTCTTCGTACGATAGTTTTGGTTCCACTGGGCTTTGTATGGG
108717 C T GGGCGAATTTGATACCGTCGGATTTGCGGGTGGCAAGGTATACGTCGGCGTAGGATCCGGATCCAATACGGGATTGGATGTTGTAGCGGCTAGTGATTTC[C/T]GTGCGGCCGTAGATGCTCCAGGCTCGGGTTTTAGGTTTGGATTGGGGAGCAGGTTCCATTAGTCTAGCGAGTGGCAATGGCCTT
108719 C T GCGCACACAATCTTGACCTCGTTCGGGTCGCATTTGTAGGTGACGCCTGAAATTGTTTTACCATTAGGACCTGGATCAGTGGTTGAAACCCATGGAAGAT[C/T]AGGATATGTTCCACTTCCACCAAACTTGACTTCGGATGCAATGCCTGGCTTTATGGTGGAAACAAGTGAAACTGAAGGCTGGTTTGT
108719 G GA ATCTCTATTCTCAAGAGAAGCAACATTTTTTGGTTGAAAATTAAATGCCCAAGAGGATCCTGTTTCCAATGTTGGCAGCTGACTGTGTGAGTATCCAAAA[G/GA]AAGCTGGGAGTTACTTAAGTTTAAATTCACTGCTTGCACATTCTGACACTCACTTTTATCAATAGGCATTAATTGCATCACAGGTGTG
108731 G A ATTTGGCACGGACTGAGAATAATGGATCTTCGGATGAGGCTAAAGGGAACTCTGCTATTCTGTCAATTCTTGGGGCGTTTACTGATACATCAGGCGAATC[G/A]AGTTGTTGGATGATGTTGGCAGTTGACCGACGATTTTTTGGAGTTTCAAACGGAAGGGAAGATCTTCGGTTTGGACGTGCTAGTCT
108731 C A CTGCTATTCTGTCAATTCTTGGGGCGTTTACTGATACATCAGGCGAATCGAGTTGTTGGATGATGTTGGCAGTTGACCGACGATTTTTTGGAGTTTCAAA[C/A]GGAAGGGAAGATCTTCGGTTTGGACGTGCTAGTCTGTCCATCGGAGTTTTTGATGACTGTGACGATCTGCGATTTGTTCCAGTATGTG
108731 T C GGGAAGATCTTCGGTTTGGACGTGCTAGTCTGTCCATCGGAGTTTTTGATGACTGTGACGATCTGCGATTTGTTCCAGTATGTGTGCCTTTTGCAGGCAA[T/C]ACAACATGCTTCTTAGGAGTGGTAAAAGCTTTGGAAGGAGTATAGCCTGTTCTGGTAACACTTTGTCTGATCTGACTGCTTCCTACCG
108731 A C AAGATCTTCGGTTTGGACGTGCTAGTCTGTCCATCGGAGTTTTTGATGACTGTGACGATCTGCGATTTGTTCCAGTATGTGTGCCTTTTGCAGGCAATAC[A/C]ACATGCTTCTTAGGAGTGGTAAAAGCTTTGGAAGGAGTATAGCCTGTTCTGGTAACACTTTGTCTGATCTGACTGCTTCCTACCGATTG
108731 T A ATGACTGTGACGATCTGCGATTTGTTCCAGTATGTGTGCCTTTTGCAGGCAATACAACATGCTTCTTAGGAGTGGTAAAAGCTTTGGAAGGAGTATAGCC[T/A]GTTCTGGTAACACTTTGTCTGATCTGACTGCTTCCTACCGATTGTTCTTTCATTCCCCGATTTGGATAATCTGGATATGTTTTGATACTT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108731 C T CTGGTAACACTTTGTCTGATCTGACTGCTTCCTACCGATTGTTCTTTCATTCCCCGATTTGGATAATCTGGATATGTTTTGATACTTCTTGTTGAACTTA[C/T]AGAATCATGCAAATTTGTGGGTCGATTTTGCTTCAAGATCCTCTCTCTTTCCAACGGAAATGAGTACCTTTTATCCCTGTCTTTGCACACAG
108733 T C CCAGACGTTTACGTGGACCACCGAGCCTTTAGGGATGTCGTAACCTCCGATTTTGGTGTTGGACGTGGCTTTGTGTGGGAGCATGAGGGGGGTTGGAGGG[T/C]GGAGGCGTAAGGCTTCTTTTACTACACATTGGAGGTAGGGTAGGTTGGCAAAGTCCGTTTCGTTCATTATGCGGTCTACTCCTAC
108733 T C ATAGATTCAACCATAGCAGTAACTTCATCCTCCCGAATCGGCCTCAACCCTTCCAGCCTCTTCGGTGAAAACAGCTCCAAATTACAAACCTTCCTAACCT[T/C]AACATAGTGCGGACCATAATCCGCCCAAATCAAATCTTTCCCTTCTCTACTAAACCGAGCCGCCGCCCTATTCCTTGGTCGGTCTGCAAG
108733 T C ATAGTGCGGACCATAATCCGCCCAAATCAAATCTTTCCCTTCTCTACTAAACCGAGCCGCCGCCCTATTCCTTGGTCGGTCTGCAAGAACCTGATCGTGC[T/C]CCTTCAAAACAGCCTTCGCCAGCTCAGAACTCGACACGACCACATTCAAAGTCGTTCCGAACCAAACCGACATGATTGGGCCGTACTTC
108735 T C TACTGGACCATCTCTCCGTCACGGTATCAGGCGAAAACGGCACGACGTTCTTCAACAACTTAGACTCCTCCTTCACCGGACTATCAACAACACCGCCATC[T/C]GCATCAACTTCACCCTTTACACATCTCAAAATGTCGAGGACTTCCTTGATACCGGGCCTCATCTCGCCATCCGACTGCAAGCACCTGAA
108735 C T CGGGCCTCATCTCGCCATCCGACTGCAAGCACCTGAACGCCAGCTCCGCCACCTGATTAACCATCCTCCTGACCTCCGGATCGGTCTCGTACCCCAGGTC[C/T]GGATCCACCAGCTCCCCTATCTTGGAGTTTTGAATCTTCGTGATCGCCATGTTCGCAAGGTTGATCTCGTGCCTGTGCCTGCTGATATC
108735 A G GCCTCATCTCGCCATCCGACTGCAAGCACCTGAACGCCAGCTCCGCCACCTGATTAACCATCCTCCTGACCTCCGGATCGGTCTCGTACCCCAGGTCCGG[A/G]TCCACCAGCTCCCCTATCTTGGAGTTTTGAATCTTCGTGATCGCCATGTTCGCAAGGTTGATCTCGTGCCTGTGCCTGCTGATATCGAC
108735 T G TCGGTCTCGTACCCCAGGTCCGGATCCACCAGCTCCCCTATCTTGGAGTTTTGAATCTTCGTGATCGCCATGTTCGCAAGGTTGATCTCGTGCCTGTGCC[T/G]GCTGATATCGACAGCGGGCATGGACGATATGAGCTCGATCAATACGACCCCGAAGCTGTACACATCGCTTTTGTCGGTGAGCTGGAA
108735 G A CGAAGCTGTACACATCGCTTTTGTCGGTGAGCTGGAAGCAGAGGTGGTACTCGGGGTCGACGTAGCCTGGGGTTCCCTGCGGGGCGGTGGAGACGTGGGT[G/A]GCATCGAGGGGGAAGAGCCGGGAGAGTCCGAAGTCGGCTACTTTGACCTGGAAGTTGTTGTCGACGAGGATGTTGGTGGTTT
108735 A G GGGTGGCATCGAGGGGGAAGAGCCGGGAGAGTCCGAAGTCGGCTACTTTGACCTGGAAGTTGTTGTCGACGAGGATGTTGGTGGTTTTGATGTCGCGGTG[A/G]ATGATCTGGGGCTCGACGGAGTGAAGGTAGAATAGGGCTTCGGCCGTCTGGATAAGGATGGACAGACGGGTGGGCCATGGG
108735 A G TCCGAAGTCGGCTACTTTGACCTGGAAGTTGTTGTCGACGAGGATGTTGGTGGTTTTGATGTCGCGGTGAATGATCTGGGGCTCGACGGAGTGAAGGTAG[A/G]ATAGGGCTTCGGCCGTCTGGATAAGGATGGACAGACGGGTGGGCCATGGGAGGCCGGGTATGGATGTGAGGGGCCCGTGGAG
108735 A G GGAAGTTGTTGTCGACGAGGATGTTGGTGGTTTTGATGTCGCGGTGAATGATCTGGGGCTCGACGGAGTGAAGGTAGAATAGGGCTTCGGCCGTCTGGAT[A/G]AGGATGGACAGACGGGTGGGCCATGGGAGGCCGGGTATGGATGTGAGGGGCCCGTGGAGGTGGTCCGCCAGGGTCCCGTTG
108735 G A GGATGTTGGTGGTTTTGATGTCGCGGTGAATGATCTGGGGCTCGACGGAGTGAAGGTAGAATAGGGCTTCGGCCGTCTGGATAAGGATGGACAGACGGGT[G/A]GGCCATGGGAGGCCGGGTATGGATGTGAGGGGCCCGTGGAGGTGGTCCGCCAGGGTCCCGTTGGGGATGTATTCGTAGACG
108735 T G TGGCGCAGGCGGGATAGAATCTCGACTTCATTCATGAATTGTTCCAGTCGGCGGTAGTTGTTTTCGTATAGACGTTTCACCGCTACTGTTCTTCCATCTC[T/G]GAGTTTACCTTTGTAGACGGTACCAAAGCCGCCATCGCCAACCTCTCTAGATTCATGAAATCCATGAGTCGCCTCTTCAAGCTCTTCAT
108735 T G CTGTTCTTCCATCTCTGAGTTTACCTTTGTAGACGGTACCAAAGCCGCCATCGCCAACCTCTCTAGATTCATGAAATCCATGAGTCGCCTCTTCAAGCTC[T/G]TCATAGGTGAATATATGAGTATTGTAATTATGTTCTCCTGTCTCAGGATCCATTTTAGAAGATAACATCGAAGAAGCAGTTTGTGAAAG
108739 C T ACACTTCTCCACCGCCGCCGCTGCTGCCGAGATGCCCACCCCTCCTCTTGATTCATCCACCGTCGTCAAGGGCGTCAAGCTCTCCGGCCGCCCTCTCTAC[C/T]TCGACATGCAATCGACCACCCCGATCGACCCGCGCGTCCTCGACGCCATGCTCCCCTTTTTCATGCACCGATTCGGCAACCCTCACTCC
108739 G C TCCCCTTTTTCATGCACCGATTCGGCAACCCTCACTCCCGCACCCACCTTTTCGGCTGGGAAGCCGAATCCGCCGTCGAAACCGCCCGTTCCCAAATCGC[G/C]GACCTGATCCACGCCAACCCCAAAGAGCTCTTCTTCACCTCCGGCGCGACTGAATCCAACAACATCTCGGTTAAAGGTCTTATGCACTT
108739 G A AGTGCGTGCTCGATTCCTGCAGGTACTTACAGCAGGAAGGGTTTGACGTCACCTACCTCCCAGTTAAAAAAGACGGATTGATTGATCTCGAGCTTCTCGA[G/A]AAATCAATCAGAAGCGATACTGGATTGGTATCCGTTATGATGGTGAACAACGAGATCGGTGTGGTTCAACCCATGGAAGACATCGG
108739 C T AGGTGGAGAAGTTGAGGGAGATGAGTCCGCTTTATGAGATGGTGAAAGAAGGCATTGATATCAAGAGCATTCAATGGTCGCAGCATTAATAGGTTGAGAG[C/T]GGAGGGTGGTTGAAGGTTCAACATGGCATATCAGGTTAGATATCTGAACTTTGATTTAGTGTTATGATGGTAATGATGATATGAA
108739 C T ATATGCATGCATATCTTGGTGCATGTTTGTTATGAAACACGATCTTGTAATCGTGTGTGTGCATGTATGTATCATACAGTTGATTTTGTAGTTCAATAAA[C/T]GAACAAGTTAGATTTGTTTGCTGATGAAAACTTGGAGCATTAGCTATTTGTATTATTATTCAAGGCTGAATT
108749 C CA CTCTATTTACCAGACATGGAAAGACGATATACGAGTCAAGTTGCGGCGGTTGACATTGCTACACGCCAAAAACACTTTGCCATTAACACACAACCTTCCA[C/CA]AAAAAACAAGACAGTGACCAGTTGAAAATCAGAGTAACCAGACTAACTCGGACAGAAAGAAAAGAGAGTTGCAGCCCCGAAATTC
108749 TA T GTTGAGCAGATCTGGAAGAAGCCCGATGAGAGTGAAGGCAACGTCAGAATCCACGATAATGGGTAAAATGAGGAGGAGTCTAGCTAGAGAGTGGAAAAGG[TA/T]AAAGAAGAGTGGAAGAAAAGCGAACTACTAAGGGGAGGAAAGATTTGGAAGAGGCGGCGGCTAACCCTAATCGTCCCCAT
108749 C CG ATGAGGAGGAGTCTAGCTAGAGAGTGGAAAAGGTAAAGAAGAGTGGAAGAAAAGCGAACTACTAAGGGGAGGAAAGATTTGGAAGAGGCGGCGGCTAACC[C/CG]TAATCGTCCCCATTAAAATGAAGACCAGACGCGCGTATTGATTATAACATGATAGGACATATATACATCCAGTAGGCCAA
108753 A G GATCGTAAGAACATTGAGCATCATGCCCTTCTCTGTGATAGCAGTTAGATTGCTGAATTGCCCTCATGCTAATCGCAGCAGTGAGAGTATAGACGACCCC[A/G]GTTCCATATAGCCCGACATGCTGGATAAAACCAACAACCCAGACGCTTGGCTCGCCTAAGTTGTACTTGACGGCATCGAGATAGGTT
108757 C T CTTCTCTTGACCTCAAAACTACCACCATCTTCTATTTAATTCACATTCTTTATTCCGTATCTCTGCAAATCTAATTTCTAACTGTATTTTATTCAATACT[C/T]TCCCCGCTAAGGCAATGGCGGCTGTTGCGGAACTAATACCGAGTCACTTGTGCGATCCACGATCCGTCCGGCTGTCTCCAGTTGCGTCTGGG
108757 C T CTTGACCTCAAAACTACCACCATCTTCTATTTAATTCACATTCTTTATTCCGTATCTCTGCAAATCTAATTTCTAACTGTATTTTATTCAATACTCTCCC[C/T]GCTAAGGCAATGGCGGCTGTTGCGGAACTAATACCGAGTCACTTGTGCGATCCACGATCCGTCCGGCTGTCTCCAGTTGCGTCTGGGCTTT
108757 G A TCTCCCCGCTAAGGCAATGGCGGCTGTTGCGGAACTAATACCGAGTCACTTGTGCGATCCACGATCCGTCCGGCTGTCTCCAGTTGCGTCTGGGCTTTCG[G/A]ATCAGAAGAACTCAGCTCGGATTTTGAGGAACCGTGAGAGTTTCGAGCTTCAAATTAGTAGATCATTTTTGAGTATTTCTAGGACGA
108757 G A ACTTGTGCGATCCACGATCCGTCCGGCTGTCTCCAGTTGCGTCTGGGCTTTCGGATCAGAAGAACTCAGCTCGGATTTTGAGGAACCGTGAGAGTTTCGA[G/A]CTTCAAATTAGTAGATCATTTTTGAGTATTTCTAGGACGACGCATCTAAAATTTCCTTTGAGGTCATGTACATGTATGGCTTTAGTTG
108757 T C CTCTTGTTCATGAAGGATTCTCTATGGCAGTAGCACGGTGGGTGGTTACAAATCTTCGGCCAAATGGATCAGCATCAACACCAGGGTTTTCATGGGGCTT[T/C]GATCTAAAAGGTATTGCAGAGATGTTCAAGTCTTACGAGGCTACAAATCTATGGAAAATCGTGGAGAATGTGCCCAGGGGTGTTCA
108757 T C AATGGATCAGCATCAACACCAGGGTTTTCATGGGGCTTTGATCTAAAAGGTATTGCAGAGATGTTCAAGTCTTACGAGGCTACAAATCTATGGAAAATCG[T/C]GGAGAATGTGCCCAGGGGTGTTCATGTAAATTTCTTGAAAGCAGAGAGAAGCTTGCATAGGTGGGCAGTTGAAGATATTGAAAGA
108759 C T TAAAAATGACAAAATGATCGGGGAAAATGATATTATCAACTCATGGCTGCTCTTCAACAGGTAATTTGTTTGACCACTGAAATTCTATTTCAAGATTTCT[C/T]GGAGGACCGCTCTTGCTTTGAGGTAGAAGCGCATATTCTCCGGCCACCGAACCTAGCATGACCACTCTGTCTATTTGAATGGTGACTTT
108759 T C GGGCATGCAGTCCAAGCTTGTCTTAAGAGAAATAATGATTCAAGTGCTGCTTCTTGAGTTGCTTCTGACCCAGTTTTGAGAGATGAAACAAGATGTGGTA[T/C]ACTTAATGTAGCAGGTTCGGATGCTCTTAATCGGGGAAAATTGCCTAGTAATGCATTTAGGGCTATTAGATATTCTTCATGTGTGCTT
108763 G A GCAAACCATGGACATGTTGTATTAGGAACTCCATCGCCAATTCTGTTTTATCCGATAAGCAGCAATGAGGTCCGATGTTTAGTTGATGTGCCAAGCCAGA[G/A]AGTGCCTTCAATATCTAGTGGGGAAATGGCAAATCATTTAAAGACTGTGGTAGCTCCTCAGGTGCCTGCTGAGCTGAAGGAAGCTT
108763 T C TTGCATTGTCTGATATTGTTGTGTTAAGAAATCTTCTCAAACCTCTGCGCGATCTTCACGATTCTTCGTCTTTGTGCAAATATTTAGAGTCCTTCTACAC[T/C]CTGCGTAAGCCAGTGGCGTCTACGATAAACACATTGGCCGGTGCATTGTATAAAGTATTTTGTGCCTCGCCTGATGAAGCAAGAAGTGA
108779 A G ATGCAGATTTCTGAATCCCAGATCCCCTACTGCTACTATATCTTGATGCGTAGTTAAGTGGTATCTTTCTTTCAGCTTCCTGAACATATACAATACCAAG[A/G]ACTAAAAGAATAAAGGACAATACAATGGTTGCAAGTCCAACATAGTTCCCATTTTGATATGCCTCAGCTACTGTTCTTCCAAATGATGCA
108779 C T AAAGAGATGTTCCATTTCCAAGTTTCAGGTCGGATATTCTCTCTCCAATATAAGTAGTGAACACTGCTCCCAGGGTCAATAATACTACTGACGATACTGC[C/T]CATTCAGTACTGAAATCATTGACATATGGTCGAAGATATACTACTTGCCCAATAGCCTGTACAACTGCAAATCCGACAGAAGCATATCT
108779 A G CCAATGAACCAATTCCAAGTCTCCCAATTCCACCACCAGAAAATGAATCTAAGGTACTCAACAGGCTATTTTGGTCCAAATTACCAGCAAAAGCTTCACG[A/G]TTTACTCCACCTAAAGGAACGTATACGCCTAGTCGAGACAGAGCTAAAAATCCTAAAAGCTTTAGGAATTTCCCTGGAAGAGGGCCTT
108779 C T AGCAAAAGCTTCACGATTTACTCCACCTAAAGGAACGTATACGCCTAGTCGAGACAGAGCTAAAAATCCTAAAAGCTTTAGGAATTTCCCTGGAAGAGGG[C/T]CTTTGAAGAAATCACCAAAATCGATGGAGCTATCCTCGATGGAAGCTGCAAGTCCTCTGGAAGATTTGTCCCTTTTGGTGCCTGATG
108779 TC T CTGGAAGATTTGTCCCTTTTGGTGCCTGATGAGCTTTCAAATGTTTGAGAAAAGAAATCTACAACATTTCCCCAGGCAGAGTTGAAACTCGAAGATTTCT[TC/T]CAAATTAAGACCCAAAGGATCAAAATCCTCTTGAGTAACACTTTTAGTTTTGGGACTGCCGCCGACCGACATAGCTGCTTTGCAGAA
108781 C T TTAGGCAAAGGCAATCCGGAAAGCATTTTTCAGAACAAGCTGTAAAGTTCTATGTAGCTGAAGTTCTTCTAGCAATGGAATACTTGCACATGCTTGGAAT[C/T]GTGTATCGTGACCTCAAACCCGAAAATGTGCTTGTCCGTGCTGATGGACACATAATGCTTTCTGATTTTGATCTCTCTCTCCGATGCTC
108783 CT C AGCATGCTGATCATCAAATCAAGAATCTGGTCTCTTGTTATGTTAGTATTTCTTGCGACTGAGGCAAGAAGATCCTCTTCTTCCAGTCCTTTACAGCCTT[CT/C]TTTTATTTTCTGCATCCTTTCGTCGAGTTTTTGCCCCATTATTGCCAGAATCCTGGACCTTGACAGTAGAGCTCTTCTGTAGGCGGTTCC
108783 T G GGTCTCTTGTTATGTTAGTATTTCTTGCGACTGAGGCAAGAAGATCCTCTTCTTCCAGTCCTTTACAGCCTTCTTTTATTTTCTGCATCCTTTCGTCGAG[T/G]TTTTGCCCCATTATTGCCAGAATCCTGGACCTTGACAGTAGAGCTCTTCTGTAGGCGGTTCCAGGAAGGTTTAAAGGAATGGAAGCCATC
108783 T C CTGATTTCTTCTGCATCTGGCATTCCAGGATCCAGATTCATCAGATGCTTCACCATCAGGTTAAATGCAAACTTCTTTCCTTCATCCTGTGCAGAGAAGG[T/C]AGAGTTCACCTTCCAAGCATCAAGAATATTAACAGCCTGAATACCAATATCTCTCAAAAAATAAGTTCTAAGCTTAACACTGCTCATGAA
108783 C T ATGCTTCACCATCAGGTTAAATGCAAACTTCTTTCCTTCATCCTGTGCAGAGAAGGTAGAGTTCACCTTCCAAGCATCAAGAATATTAACAGCCTGAATA[C/T]CAATATCTCTCAAAAAATAAGTTCTAAGCTTAACACTGCTCATGAAATTCACAGCAATGGATCTCATTTCTTTATGTATGTCCCCAGCCA
108783 C T CATCAGGTTAAATGCAAACTTCTTTCCTTCATCCTGTGCAGAGAAGGTAGAGTTCACCTTCCAAGCATCAAGAATATTAACAGCCTGAATACCAATATCT[C/T]TCAAAAAATAAGTTCTAAGCTTAACACTGCTCATGAAATTCACAGCAATGGATCTCATTTCTTTATGTATGTCCCCAGCCAAAGCAAGCA
108783 CA C TCAGGTTAAATGCAAACTTCTTTCCTTCATCCTGTGCAGAGAAGGTAGAGTTCACCTTCCAAGCATCAAGAATATTAACAGCCTGAATACCAATATCTCT[CA/C]AAAAAATAAGTTCTAAGCTTAACACTGCTCATGAAATTCACAGCAATGGATCTCATTTCTTTATGTATGTCCCCAGCCAAAGCAAGCAT
108783 C T CGGAAGAATGAGGCATCATGAACGGAATAGTGTCACCGATGAATGGCCAACCTCCAAGATTGCCGGGTGGAAGCGTTGACGGTGATTTGCTCTCCGTTTT[C/T]CCATTGCTTCTAAATCCAAGAAATATTAGTAGCGATATGATCAATGTAGACACTAATATTATCTCCATTGCCATTTCGCTTTTATTTC
108793 A G CATCAAGCCTGCCTAAGGTGGCTGGATGGAAAGATGTAGGGTAGGGGATTGCATGCTCCTGCCATGGCCATGCCCTGGCCTCCACAGTCAAAAGAGTGAC[A/G]TTCCAAAATTCAGGTATCTGCAGGAAGGAAGTCCCCCAAAGGGGAGGATCGGCAGCTGGATCCTGGGAGAGATCCCAAGCAGG
108793 A G AAAATTCAGGTATCTGCAGGAAGGAAGTCCCCCAAAGGGGAGGATCGGCAGCTGGATCCTGGGAGAGATCCCAAGCAGGCCTGGCAGAAATGAGGAAGAA[A/G]TCGTGGCCGGAATGAGCGTTCCAGATCTTAGCAGTGTGAGGGGAAGATTTGAGGTAGGAGTAGAGATCGAGGCCGTGGAGA
108793 A G CGGCAGCTGGATCCTGGGAGAGATCCCAAGCAGGCCTGGCAGAAATGAGGAAGAAATCGTGGCCGGAATGAGCGTTCCAGATCTTAGCAGTGTGAGGGGA[A/G]GATTTGAGGTAGGAGTAGAGATCGAGGCCGTGGAGATTGGAGTTGTTGTAGGAATCAGGGGAGTAAAGGAACGGGAGGGC
108795 CA C CTATCCCTTGCCTTTTCTTGGTGTTCTTTTCAATCTGGGCAAGCACCCCTGCAGCCTGAGCCCCACCCATCACAGAGATCTTAGCCGTTGGCCAAAGAAA[CA/C]AAAAAATTAGGACTGTAAGCACGTCCACACATCCCATAATTTCCAGCGCCAAAACTTCCACCCACAATTAATGTTATCTTAGGAACCT
108795 G A CTGCAGCCTGAGCCCCACCCATCACAGAGATCTTAGCCGTTGGCCAAAGAAACAAAAAATTAGGACTGTAAGCACGTCCACACATCCCATAATTTCCAGC[G/A]CCAAAACTTCCACCCACAATTAATGTTATCTTAGGAACCTTGGCACATGATACCGCCATAACCATTTTCGCCCCAGCTTTAGCAATACC
108795 T C ACAAAAAATTAGGACTGTAAGCACGTCCACACATCCCATAATTTCCAGCGCCAAAACTTCCACCCACAATTAATGTTATCTTAGGAACCTTGGCACATGA[T/C]ACCGCCATAACCATTTTCGCCCCAGCTTTAGCAATACCAGCTGCTTCCGATCGAGATCCTACCATGAAACCTGTGATATTTTGGAGAAA
108795 A G GTGGGTCCCTTTTCCAGCCATGTGTATATTCTTTACAATATTTCTTCCAATTGCCAGTCCATCAAGTTCATCACTTGCAAAATGATCCGAAACCCCTGAA[A/G]TTTTGCAATGCAAGGAAGCCCCACCCAAATCCTCCGCTGAGACGACTTCTCCTGTAGCAGCCTTCACAAGAGGAGGTCCAGCTAGAAAT
108795 G A CTCCAGCAGTGCATGATCCTAAAACAAGGGCAATTTGGGGAATGCCCTCAGATGACATTTTTGCTTGATTATAGAAAATTCTACCGAAATTATCACGGTC[G/A]GGAAAGACATCAGCTTGCCTTGGAAGGTTGGCACCTCCGCTATCTACTAAATATATGCAAGGCAGTTTACACTCCCAAGCAATTTCTT
108797 A C GAAGTCTGGATGCTCTTTTGTGTCTTACTCTTCATCTGTAATAATGTTAGGTGTTGTTCTTTCCTGTGTCGATGTCCCGTCTTCTTCTTCTTCTTCTTTG[A/C]TAAATGGATGTACCTGTAATGGCTCTTCTTCCTTTGCTTCTTCTTCGGAAGTTCTATGGGGAAGCGGCCCTTGAGGAACGCCAAAAAGAGT
108797 G A GTTCCCTGCCAAATATGTATGGGGCCAAGAAAGCCGGCCCATTCCTTGTCAGAATGAGTGAAGATAGATTTAAGCCATACAAGAAGACCTGCACCCTCAT[G/A]CTTCTTCTGCACTTGCAGATCAGCTAGTCTGAATCCCCAGTCTGAAACTTCAAGCATTGCTTCTTCCACAAATGGCTTTGCATTGCGT
108803 A AT AATCATCCAACTGCGACAAAATTGAACAATCAATGTATACATTAGGGCAAGCACACCACGAACAAAGATACACTGACAAGAAAAACAGAAAACACCGCCC[A/AT]TCACACACAGATGCATGCATATAAAACATAAAGTACTCATGTGGCTTCATTAAAACTCAGACTGCTGCCTTGGTCAGCTCATTCAC
108815 C T TGGGCTGAACTGTTCAATGTATGATAACCCGGCCACTTAACCCTACCAGCAAGCCCGGAACCAGGCCCAAAGTTCATAAACTCCGCATAATACAATGTAT[C/T]GAGTGCGAAATCCCCCTGCCATTCCAGCCACCCTTCGGGTCTTATCGCACTCCCCAAATTCGACTGCATGACGATGGTCCTTGAGAAC
108815 T C ATGGTCCTTGAGAACTCCTTCCATGGTCTTCCTAGGTACGTGTACGATTGGTTCACAGCATTCACGAGGTCCGAGTCGGCGGTTAGGTTGCAGAACTGAA[T/C]GGAGAAGCCGGTGTTCTGGTTCGGGTCCTTCCGGCCCTGGGCTGTAATGGTGTTCTTCTGGTTGGGGAGCGGGAGACGGGCTAGG
108815 C A GCGGGAGACGGGCTAGGATTTGGGAGTTTTGGATCACGGCGGCTGCGTTACCAAAGATGAAGTCGATGGTGCCCGTGATGATACACTCACGGTAGAACTG[C/A]CGGAGGGAGTGGGCATAGAGTGTGTCCTGGTAGCCTCTAAAGGCACACCGGTAGTACACTGAGAGGTCTGAGTCGGAGCGGA
108815 T A TATCTGCTGGATTTCGTTGATGGTGGATTGGATGGTGGATGTGAAGGCGGAGGAGATGCCCGTGGATGGTGACTTGGTGCATTCTGGTTGGATGGTGGAG[T/A]GCGAAGGGGAGGTGAGTAGGAGGAGGAGGAAGACAAGCAGGAGATGGCGCATTTTGGGTGTAGTTATTGGTTAATGAGATG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108815 A AG GGATGTGAAGGCGGAGGAGATGCCCGTGGATGGTGACTTGGTGCATTCTGGTTGGATGGTGGAGTGCGAAGGGGAGGTGAGTAGGAGGAGGAGGAAGACA[A/AG]GCAGGAGATGGCGCATTTTGGGTGTAGTTATTGGTTAATGAGATGAAGTGAATGCAGGCAGAGATCCAGTAGGCCAACA
108831 T TA ATGGAATGAGCTGCTGTTTAACCTTCTCTAACATTCATTCTCAAGCTCTTTTGTTTTATTTTTGATAGGTTTTTGTCCATAATTTTCGAGCATTCACAGC[T/TA]AAATGTGGTTTTCAGTCTTAGGATCAAAATGTTGATTTTGTCCACTAAAGTAAAAATGGGACATAAACTGCTACATAACAAATATTTGTTG
108833 T A AAGGGGGTTTCCTTCCTTTCTGTCCTCACTTAATTATAGGAGAAAAACTACTGGTTTTTGTTCAAGTTTGATAAATTAAGGATTTGGAAGAGATTTGAAA[T/A]TTTTCCGATGGGCAATTGTTGGGGTGCGAATTTGGCTGATTTCAGTTCAGGTACAAGCTCTAGAATCAGTCGCAAAGACGGAAAAGG
108833 C T GTTTCCTTCCTTTCTGTCCTCACTTAATTATAGGAGAAAAACTACTGGTTTTTGTTCAAGTTTGATAAATTAAGGATTTGGAAGAGATTTGAAATTTTTC[C/T]GATGGGCAATTGTTGGGGTGCGAATTTGGCTGATTTCAGTTCAGGTACAAGCTCTAGAATCAGTCGCAAAGACGGAAAAGGATCAGGT
108833 T A GTGCGAATTTGGCTGATTTCAGTTCAGGTACAAGCTCTAGAATCAGTCGCAAAGACGGAAAAGGATCAGGTGCTTATAGTAGCAAGGTCTCGTCATTATC[T/A]GTGCCGCCTACACCGAGAAGTGAAGGCGAGATTCTATTATCAACAAATTTAAAGAACTTCACATTTAATGAGCTGAAGAGCGCTAC
108833 C T ACGATAAAAGTCATGTTTCCACAAGAATCATGGGGACTTACGGTTATGCAGCGCCTGAATATCTTGCCACAGGTCACTTAACATCGAAGAGCGATGTTTA[C/T]AGCTTTGGAGTAGTACTTCTAGAGATGCTGTCGGGGCGACGAGCGATAGACAAAAATCGTCCACGTGGAGAACAAAATCTTGTGGA
108833 C A TTACGGTTATGCAGCGCCTGAATATCTTGCCACAGGTCACTTAACATCGAAGAGCGATGTTTACAGCTTTGGAGTAGTACTTCTAGAGATGCTGTCGGGG[C/A]GACGAGCGATAGACAAAAATCGTCCACGTGGAGAACAAAATCTTGTGGAATGGGCAAAGCCTTACCTCTCAAACAAGCGCAAGATT
108833 T C CCCAAAAGGCTGCTGCCTTAGCTGTTCAATGCCTATCTGCAGATGCCAAGTACAGACCCACCATGGCTGAAATTGTAAAGTCACTTGAGGAGCTACAGTA[T/C]CTTAAAGATTCTGGTCGTGCCCCTAAAACCGAAGAGAGGACTCGAAGGAGAAGCTTGGAGGACTATGGTGGTAGGCATGGTAACC
108833 G C GCCTTAGCTGTTCAATGCCTATCTGCAGATGCCAAGTACAGACCCACCATGGCTGAAATTGTAAAGTCACTTGAGGAGCTACAGTATCTTAAAGATTCTG[G/C]TCGTGCCCCTAAAACCGAAGAGAGGACTCGAAGGAGAAGCTTGGAGGACTATGGTGGTAGGCATGGTAACCGCACCCCTTTGGCC
108833 A G AAGTCACTTGAGGAGCTACAGTATCTTAAAGATTCTGGTCGTGCCCCTAAAACCGAAGAGAGGACTCGAAGGAGAAGCTTGGAGGACTATGGTGGTAGGC[A/G]TGGTAACCGCACCCCTTTGGCCTCTCCTCTATGTGTCTAGAACAAACATATGTGTATTTTTAATGTTAGGCTGTTGTCTTCTTTACT
108833 G T TCACTTGAGGAGCTACAGTATCTTAAAGATTCTGGTCGTGCCCCTAAAACCGAAGAGAGGACTCGAAGGAGAAGCTTGGAGGACTATGGTGGTAGGCATG[G/T]TAACCGCACCCCTTTGGCCTCTCCTCTATGTGTCTAGAACAAACATATGTGTATTTTTAATGTTAGGCTGTTGTCTTCTTTACTTCAT
108833 A C ATTCTGGTCGTGCCCCTAAAACCGAAGAGAGGACTCGAAGGAGAAGCTTGGAGGACTATGGTGGTAGGCATGGTAACCGCACCCCTTTGGCCTCTCCTCT[A/C]TGTGTCTAGAACAAACATATGTGTATTTTTAATGTTAGGCTGTTGTCTTCTTTACTTCATGTACATGTTTGTGAATTTATCTGAGTTC
108837 T G ACTACTAGTGCTACACCCGTCCGGTCTGAAAAAGATGGGAGAGATACACTTGGCTATTCGATTCTCATCCACCTCGTTAATAAACATGATGTACACTTAC[T/G]CTCGCCCTCTTCTTCCAAAAATGCATTACGTTCGCCCCTTAACTGTGATGCAACTTGACATGCTAAGGCATCAAGCAGTGCAAATCGTA
108843 T A CTCCCCTCCTCCTCGTCCTCCTCCGCATCCTGGCGCTGCACACTCCGATCTCGCGACTCCGTCGTTTTTCAACGCTCCTACAGCGGCAACCCCAACGATC[T/A]CCTCTCGCACGTCTCCAAGTTCTGCAAGTTCCACCACAGCAGCCTCGTCAAGCTCCTCGGTGTTTCCCTCAGTGGCGACAACCACATCTA
108843 A G TCTCCAAGTTCTGCAAGTTCCACCACAGCAGCCTCGTCAAGCTCCTCGGTGTTTCCCTCAGTGGCGACAACCACATCTACCTCGTCTACGAGTACGTCGC[A/G]GGCGCCAGCCTCCTTCACTGTTTACGTAACCCTAGAAACCCTAATTTCACCCCGCTCTCGAAGTGGATTTCGAGGATGCAGATCGCCA
108843 T C AGTTCCACCACAGCAGCCTCGTCAAGCTCCTCGGTGTTTCCCTCAGTGGCGACAACCACATCTACCTCGTCTACGAGTACGTCGCAGGCGCCAGCCTCCT[T/C]CACTGTTTACGTAACCCTAGAAACCCTAATTTCACCCCGCTCTCGAAGTGGATTTCGAGGATGCAGATCGCCACCGATTTAGCTGAGG
108843 G A CCCTCAGTGGCGACAACCACATCTACCTCGTCTACGAGTACGTCGCAGGCGCCAGCCTCCTTCACTGTTTACGTAACCCTAGAAACCCTAATTTCACCCC[G/A]CTCTCGAAGTGGATTTCGAGGATGCAGATCGCCACCGATTTAGCTGAGGGATTAAGCTACATCCACAGCCAGTGCGAAACCGTTCAT
108857 GC G TGTTGGCCTACTGGATTTCCTTCTCCATTCCCTTCTACGATGGCCGCCGCAGCTACCTGTTTCTTCTCAAAGTCCATTTCCACCATCTCAAATTCCC[GC/G]CCCGACCCCCAATCCCAATTTCACCTACTCGCCTCAAAACTCAAACCATAAATCTTGGTCAAACCCTAGATCTTCCATTCGCCATGGCTTATCC
108857 C T CCGCTGCTGCTGCCCTTCCTGCTGCTTCTGCGCTGGATGGAGCCGTGGTTGTGCCGGAGGAGGAGGGGATTGCGGTCACTGCCAGTGAAGGTGGTGACTG[C/T]AACGGTGTGGTTGTAGGTAGAGGTGTAGATAGCGAGGCTGAGGTTAAATATGATCCTGCGGTGTTTAGCTCTGATGAGAGCGT
108857 CT C CATTGAGAATGAGCTTCCATTGAAGGGCATATCGTGTACTGTCATTGCTCCTTATGACATGGATGCCCTCGAAAGAGCACTAAACGAAAACAAAGTATCT[CT/C]TTTTCTTCACGGAAACTCCAACTAATCCGTTTCTCAGATGCATTGATATCGAATTTGTTTCAGAGCTTTGCCACAAAAAGGGAGCTCT
108859 A G TATTATCGGTTTTGCCGTCTGACATAACCATGATAGCTGTGGTACGACCCTCTGGGTATCTGCGTGCCTCTACCACATACAAGGCCTGCTGCAAACCAGC[A/G]GGAATGTCTGTGCCACCAGCAGCAGTGAAACTGTTAACGATTGCTTCAATCTCAGGTTGAGCTTCTTCAGTCACCTGGCGTAGACGA
108859 G C ACGACCCTCTGGGTATCTGCGTGCCTCTACCACATACAAGGCCTGCTGCAAACCAGCAGGAATGTCTGTGCCACCAGCAGCAGTGAAACTGTTAACGATT[G/C]CTTCAATCTCAGGTTGAGCTTCTTCAGTCACCTGGCGTAGACGACAGTATCTTGCGGCAACATTGCAGAAGGCTACAATGGACAAA
108861 T C AAGTTTGATCTTAATTTTCCAATGTAGGTACCACTACTCTTGGACATGTCTTCTGCATCCAGTGAAATAAGATAATCTGTACAGGTAGCTCTCCGATTTT[T/C]TCTTGCTGCTAGGAGGAATTTTCCATCATCAGTCAATGCTTGGGATAGACCAAGATAAAGACGATATGTTTGAGTATTACGATCCCTCTT
108861 T C ATTTCAGGAACCTTAATAATCTCCTTCATAATTTCTCGCCAGCTTCTACAAACCCCAGCACAGGCAACGACGTCTTTACGAGGTGGCCACGCGGCTTCGC[T/C]CTCCTCGATCCTCATCAGAACATCCATCAATAGCTCAGTCGGCATATTCGCCCAGCTACTTTGCTTCAATGCATCGATCACCTCCAGCTT
108865 GA G CATTATCACGCATGGTTCCATACCTTACAGCCAAAGAGCCAGAACAGCGAGTAGAGCACATGCCTCCAATGGAAGCACCAGGCCCTGGATCAAGAGGAAA[GA/G]AAAAGTCCATAAGGCTTAAGATACTCATTAAGTTCAATCCATCCAATCCCTGGTTCCACAACTACATCCATGTCTTCAACATGCAA
108865 T C ACTCATTAAGTTCAATCCATCCAATCCCTGGTTCCACAACTACATCCATGTCTTCAACATGCAATGATTTGACTTTCTTCATCGAAGACATATCAATAGA[T/C]ACACCTCCATTTGGAGCCAAGATGTGGCCTTCGAGTGATGTCGCTCCACCATATGGAACTATTGGGACCTTATACTTACTGCAAGTTAAA
108867 C T CTGATGAAAATGAACCACCATGAGACAACCCAGACTGTAAAGTATCAGGTGTTAAGCTATCACTGGAAATTGAAGAAACCGCAATTGAAGTTTTGCCAAA[C/T]CTATTTCGGTTAAATGTCGTCTTAGGCAATGATTCATGAGAAAGGACCCCAGGGGCAGTGTATTCTTCATCTATTGCATTCATAGCTT
108867 T C GCAATTGAAGTTTTGCCAAACCTATTTCGGTTAAATGTCGTCTTAGGCAATGATTCATGAGAAAGGACCCCAGGGGCAGTGTATTCTTCATCTATTGCAT[T/C]CATAGCTTCCATCCGACTGCAATCAATCACAAGATCTAGAGGGACCTTACAAAACTGAGAACGAACAACTTTGGCACCCCCTGTTAGT
108867 A G ATAAGACAAGATCCACATGTTGCAGCTGCTGCTTAACTACGTCAATGCTTAAAATCTTGTCAAGCGATTCAGCATCAACCACGGCAACAGTCATATCTAA[A/G]TGTATGCCAACTTGTTCCAAATCAGCCACAAACTTATCCGGCCTTGCCAATCCAGAAGTCTCAATCAGCAAAGAATCAAAATTATGCTT
108867 G C ATCAACCACGGCAACAGTCATATCTAAATGTATGCCAACTTGTTCCAAATCAGCCACAAACTTATCCGGCCTTGCCAATCCAGAAGTCTCAATCAGCAAA[G/C]AATCAAAATTATGCTTGCTATCTACAATCCGTTGCAATGCTTCCCTAAATGGCCCTTTCACATCACAGCAACCGCATCCATGGGTCAGT
108871 GT G GAGGTATCCCGATATTGACGAAGAGTTGGTGGAGATGCTGCAGATTGGGATGATGTGCGTTGTTAGGGTGCCCGAAAGGAGGCCCAAGATGGCCGATGTT[GT/G]TTACTTTGCTCGAGGATGTTAGAAGGTTCGAAGTTTAGGTCATGAAGGTCATTGGTAGGATGTGCTATGTTTCTTTCACTGTTT
108881 G A GGGTGACACATGCACACGTGGTTGTAGATTTTGTGCTGTAAAGACAAGTCGAACGCCTGCTCCACCTGATTCAATGGAGCCCGAGAATACTGCAAGGGCA[G/A]TTGCTAGTTGGGGTGTTGACTATATTGTATTGACAAGTGTTGATCGTGATGACTTGCCTGATGGTGGAAGTGGCCACTTTGCTAAG
108885 C T CAAAGATCACATCTTTGTCGCTTCGCATGACTACGGAGCTTGTTTTCACGCAATGGAAGACGTAGCAATGGCGAAAGGAATCCCGGAATTTTTGAAGAAT[C/T]CGATCTTACTGCAGACTTTCGGCGTGGTTTCGCCGCACCCATGTCAGGAGGCGGAGCATGTGCTGATTCCGCCGTACATTTCGCCGG
108885 A T TCCCAAAAACATCAGTGGTCGGTTTTACAGCAGGAAGGTGAGAACGCAAATATGGAGAAATTACGGGAGCAATAAGAAATTTTACTTGAAGAGGAAGCGG[A/T]ACGACGGGTACCGGTCTGAGATAGGAAGATCGGTATTCTGTTTATGTCCGTTGGGGTGGGCCCCTTGGAGTCCGAGGCTGGTAG
108889 T TA CCACACTACTGAGTTTTCAAGGTATAACCTAGGACACATGAAAATTTCAGAACATTATTGACCAGTTTTTCAGAATATACTAATTTACCACACTACTGAG[T/TA]CCCCCCCTTGTTCATAGATGAAATACCCCCTTTCAACTTTATTACAAAACCAAAAACCCAGAGGAAGTCAAAACTCAAAACTGCTCAAA
108891 C CG,CA TATAAAAGATTACTCCCACTTTACTTTCCAAGGGATAAGCATGAAGAGGAGATAGCAATATCTAAACTGCCGGCTGATGTCGGAGATGAGAATGGTGAGA[C/CG,CA]ACAGTCGAAGAACGCAAAATTAGAATAAAACCTTTACCTGCTGTGTCAGCAGCTGCTAGCAATGCTCCAGACATGTTCAAAG
108893 T TA GGCTTAATTGCACGGATGATGGATTCTATGAGTCAAAAAGGGAATGGATGGGAAAAAGGCATTTCATTTCAGCTTATGAAGGCTCAGATCCTGGTTTTTT[T/TA]AAGATACTTCGACCTGCCATAGGGGAGGTATTGAGGGAAATGCCTACAGCTGAGCTAAAAACCAAGTACAGAAAAGTGTCTTCAA
108893 G GT TACAAATTACATCAGTGGGCAAATTGTCAATCTGTGACTGCGCCATGGTAATTATTGATATGATGACCATATGACTCTTATATCATTAATATTTTTTGGA[G/GT]AGAAGATATCAATGAAAGCTTCAGCTGACCTGGGTTGATACGATGGACAAATGTTGTGACTGGTTGTCCAAATTTATCATTTGATTTT
108895 CA C AAATAGAACATCCTTGCGGAACTGAACCCGAATCACATGGTTCGGATTTTTCATCTGCTGTGACACTTGCAATGAGTGATGATACACTAACCGGATTTAG[CA/C]AAAAAACAAGCTATTAAAAAATCTATATGCGAGGAGTTGATTGCGCAGGACATGGCTACATGCACAAACTTCTCCAAAGTTGATGA
108895 T C AAATACAAGAAATGAGGTCAACGGCAGCAATAGAATGGCATCAACTTCAAACAAAGCAAATCGTCCACCTCATAATCTACCCAAAGCACAGAATATCTGC[T/C]TTAGATCATCAGAAAAACCAAGTCCTCAGCCTGTTGCATCCAACAGTGGATGGACACAAGTGCAAAATGGAACAAGAAAGCAAGAT
108895 T C AATGTCATCCCGTTAATCAAAGTGAAGGCGGAACCAAACACCGATGATTCCCCTAACGCACTTCCTACAGCATATGCAAATCTGCAGAAGAATCAGTTAC[T/C]GTTCCAGTCCAATAAGTCCTCAGAAATCAACTTTTCAAGAACCCAACCGCAGCACAATTACCCTCAGTTCGAAACTCACTACTGGCAA
108895 A G CGGTGCCACTGCCAAGTGGAAAAGATCGATCCATCCCGTTAGTCCCTGTGTCATCGAAGGTGGTGGTGCAAATGCAAGACAAGAATTTTCTCAAGGGGTC[A/G]TGGATAATAATAATAGTTCTAGAGGGCAGCAGTCCAATAAAAGATTGTTTGTGTTTCCAGATTTGAATCTGAACTTCCAACCTCCTG
108899 A G AAAACTGCAGGGCGTGACCCATCGCCATACAGTATAGCAAAGCCAGATTTCCTAGCTGCCTGTACGACACCTGGATTCAGATCGAATGCAACGTAAGGCC[A/G]CCCAGCTTTCTCACCATCCAAGCCTGACGATAGTGGTGTAGATAAAAAATTGGCTAGCACCTGCCCCATTTGCTCAAACCCAAGAAT
108899 GA G AAGGTCATTCAGCAAAGGAGTTAGTGCCATTGAAAGCACGACTACGATAATTAGAAGTTTATTCAACTCAAGCGGCAATACTCCAAGCCTGTTTGCCAAA[GA/G]AAAACACCACAAATCCAAATTCTCCTCCTTGGGAAAGAAGAAAACCTATTCTAACACTTTCTTGAAGAGTTAGTCCGACACGTGGC
108899 T C AACACCACAAATCCAAATTCTCCTCCTTGGGAAAGAAGAAAACCTATTCTAACACTTTCTTGAAGAGTTAGTCCGACACGTGGCCCAATAGCAGTTATTA[T/C]CAGTGTTTTGATAGTAATTAAACCGGCTAAGAGGGCTAGCACATTTGGCCACTCTCTGAATAGTACCTGCATATCAATAGAGGTACCC
108899 G T CTAAGAGGGCTAGCACATTTGGCCACTCTCTGAATAGTACCTGCATATCAATAGAGGTACCCGTGGTTACAAAGAATAAACCAAGAAGTAGTCCTCTAAA[G/T]GGTCTTATATCAGCTTCGATCTGAGTTCGAAAATTTGTTTCTGCAAGAATTGCCCCAGCAATAAATGCCCCTAATGTATCACTGAAGC
108903 AG A AAGCTGGCCTCAAGGGCTCCTCTGGTTTTGGGACAGGAGATTTCAGCAGCCCCTTCGATATTTTTGAATCCTTATTTGATGGCATGAATGGAATGGGAGG[AG/A]GGGGGGCGGGCATCTCGCAACCGTCCAGTCCAAGGCGATGATGAGACCTACAACCTTATCCTAAAATTCCAAGAAGCAATCTTCG
108903 C T GGGGGCGGGCATCTCGCAACCGTCCAGTCCAAGGCGATGATGAGACCTACAACCTTATCCTAAAATTCCAAGAAGCAATCTTCGGCATTGAGAAAGAAAT[C/T]GAGATAACCCGTCTCGAACCCTGCTCCACATGCGATGGATCGGGCTCCAAACCCGGTACCCAGCCCACCAAATGCAACACATGCAA
108903 G A TCTCGCAACCGTCCAGTCCAAGGCGATGATGAGACCTACAACCTTATCCTAAAATTCCAAGAAGCAATCTTCGGCATTGAGAAAGAAATCGAGATAACCC[G/A]TCTCGAACCCTGCTCCACATGCGATGGATCGGGCTCCAAACCCGGTACCCAGCCCACCAAATGCAACACATGCAACGGGCAGGGCC
108903 A C GCAATGGAACGGGCGAGTCCTCCACCCCATGCAACACGTGCAGAGGAGACGGCAGAGTTCGTAAAGCCAAAAAGATAAGCCTTAAAGTTCCAGCTGGAGT[A/C]GACTCCGGAAGCAGGCTTAGGGTTAGGTCGGAAGGAAGTGCCGGAAGACGCGGTGGTGGGCCCGGAGATTTGTATGTTTTTAT
108903 T C ATCCCGTGCTGAAAAGAGACGGCACAAATATTTTGTGCACGTGTAAGGTGAGTTATACAGACGCAATATTGGGAACAAAGATTGAAGTTCCGACTGTGGA[T/C]GGGATGGTGGATTTGAAGATTCCGGCAGGTACACAGCCAGGGACGACGCTTGTGATGGCCAAGAAGGGAGTTCCATATCTAGGA
108903 A T TATGTTTTTTCTTCTTTTTATTTTATAGTGGTTTTGTGATTGTGTATTTCTGGAGATTGGTTAGCTAGCCAGTGGTACTTTACGTTAATGTTAGTTACAC[A/T]TTGCTAAAATGCTGGCTCGTACTTTGATCCGTGTATCATGTTTCTAAATAGAACTAGCGAATCGCCTGGTGAGTTCGTTATAAATTATTCAA
108903 C A TTTATTTTATAGTGGTTTTGTGATTGTGTATTTCTGGAGATTGGTTAGCTAGCCAGTGGTACTTTACGTTAATGTTAGTTACACATTGCTAAAATGCTGG[C/A]TCGTACTTTGATCCGTGTATCATGTTTCTAAATAGAACTAGCGAATCGCCTGGTGAGTTCGTTATAAATTATTCAATGCACGAAGTTAAC
108907 CT C TCCAGGAAATAATGGTGGCGATGGTCTAGTTGCTGCAAGACACCTTCACCATTTTGGATATAAACCATTTGCCTGTTATCCCAAAAGAACAGAAAAACCT[CT/C]TTTTTACTGGGTTGGTTACTCAGTTGGCATCACTAGCAATCCCATTCTTATCGGTTGAAGAAATGCCTCTGAGTTTATCAGATGACTT
108907 C T TTTTAAAAGGAATAGACCAAGGTGGCTTTGTCTGGTACACCAACTATGGAAGTCGAAAGGGTCGAGAATTGTTTGAGAATCCTCATGCATCACTCAATTT[C/T]CATTGGAATCAACTTAATCGTCAGGTGAGGGTAGAAGGAACTGTGGAAAAGGTTTCCGATGACGAATCTGAGAAATACTTTCACAG
108907 C A GAGAATTGTTTGAGAATCCTCATGCATCACTCAATTTCCATTGGAATCAACTTAATCGTCAGGTGAGGGTAGAAGGAACTGTGGAAAAGGTTTCCGATGA[C/A]GAATCTGAGAAATACTTTCACAGTCGTCCTCGTGGAAGCCAGCTTGGTGCAATTGTCAGCAAACAGAGTTCAGTTATTGCTGGAAG
108907 A G GCTTGGTGCAATTGTCAGCAAACAGAGTTCAGTTATTGCTGGAAGGCACGTGCTTCAGCAAGCATATAAGGAGTTGGAAGTAAAATATTCTGATGGAAGC[A/G]TAATTCCTAAACCAGACTTTTGGGGCGGATATAGACTCACTCCAACCCTCATTGAGTTTTGGCAAGGACAGACTTCTCGCCTACATG
108907 T G GAAGGCACGTGCTTCAGCAAGCATATAAGGAGTTGGAAGTAAAATATTCTGATGGAAGCATAATTCCTAAACCAGACTTTTGGGGCGGATATAGACTCAC[T/G]CCAACCCTCATTGAGTTTTGGCAAGGACAGACTTCTCGCCTACATGACCGGTTGCAATACAGTATCAAAGATAACAATGGAAGCCG
108907 T C CAGTATCAAAGATAACAATGGAAGCCGTGAATGGATCATAGAAAGACTGGCCCCATGACTTCGGCCTGCTCTCTCTTCCTTATAGCAAGTTAAAGGAGCT[T/C]TGCACTGTTGTTGTATGAAGAGGCAAAATCCTAATGCTAAATAGAGCCAAATACACATGAGGATGAAACTTTATATTATGTTTTATGC
108907 C G TCAAAGATAACAATGGAAGCCGTGAATGGATCATAGAAAGACTGGCCCCATGACTTCGGCCTGCTCTCTCTTCCTTATAGCAAGTTAAAGGAGCTTTGCA[C/G]TGTTGTTGTATGAAGAGGCAAAATCCTAATGCTAAATAGAGCCAAATACACATGAGGATGAAACTTTATATTATGTTTTATGCTACTT
108907 G A AAAGATAACAATGGAAGCCGTGAATGGATCATAGAAAGACTGGCCCCATGACTTCGGCCTGCTCTCTCTTCCTTATAGCAAGTTAAAGGAGCTTTGCACT[G/A]TTGTTGTATGAAGAGGCAAAATCCTAATGCTAAATAGAGCCAAATACACATGAGGATGAAACTTTATATTATGTTTTATGCTACTTTT
108907 A G ACTGTTGTTGTATGAAGAGGCAAAATCCTAATGCTAAATAGAGCCAAATACACATGAGGATGAAACTTTATATTATGTTTTATGCTACTTTTATGATAGA[A/G]TTGCATGTAATTTCAGCTTTTGCCAAAAACTGAGTCTAGACGGTTGTCTTCCGGGTCATACGTGTTTCGTTTTGTAAGACAAGGTATTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108911 C T AGATATCCAAAGGGCGTGGGTTGCTGATAACATCAACATGGGCCCAGCTAATTCAGCTAGACTTCTTCAAACGTGTTCTTGCAAGTGGTTTTCTGAAGCA[C/T]GCACAGGAGAATGAACTGCTTTATGAAATTTTTGACCTGACCCCAGATGAAAATGATTTTCTATCGTCAGCAGATAAGAGGATCAAC
108911 C T AGAGGATCAACCGATCATCAGAAGAAAAAGGGAGAACTGTAATGATGAACAAAAACCGTCAGATTGCTCAGCAACGGAAGAAAGGGCACCTTTTCACCAA[C/T]GACGATTAAATTATTGATTATTCTCATTCATCATATCTTTCAAATAAGCCTCAGAGTTGCTAGATGTTTGTATCCATAATAGTACCTT
108911 T C ACGATTAAATTATTGATTATTCTCATTCATCATATCTTTCAAATAAGCCTCAGAGTTGCTAGATGTTTGTATCCATAATAGTACCTTGTAATATTTGGAC[T/C]GATGTTACTGCATGACGTGGTTATCATTTTGGAAAATACATGAATTGTATAATTGACAGTTATAAAAGCGAGGAACATACGTGATTATGT
108921 T C TTTTTTTTGATTATTAATCATTTACTTGCAAAACATAGCTCGCAAGCTAATTAGGCATATAGCAACTCCCATCTGTTTGAACACAGTTCAGATATTTAAA[T/C]AAATAAACCACACAGGTAAAGCAGTATGGAGAGCTAACTGAATTAAATTACAAATTCAATAATAAATGGAATGCTATTTTATCCCCCTTA
108921 TA T TTTTTTTTGATTATTAATCATTTACTTGCAAAACATAGCTCGCAAGCTAATTAGGCATATAGCAACTCCCATCTGTTTGAACACAGTTCAGATATTTAAA[TA/T]AAATAAACCACACAGGTAAAGCAGTATGGAGAGCTAACTGAATTAAATTACAAATTCAATAATAAATGGAATGCTATTTTATCCCCCTTA
108921 TA T AGCAACTCCCATCTGTTTGAACACAGTTCAGATATTTAAATAAATAAACCACACAGGTAAAGCAGTATGGAGAGCTAACTGAATTAAATTACAAATTCAA[TA/T]AATAAATGGAATGCTATTTTATCCCCCTTATAATAAGAAACACTCCTTTTTGCCCCCAGTCCTTCCTGGCTCATAGGAGCATGCATATC
108921 T C GAAACACTCCTTTTTGCCCCCAGTCCTTCCTGGCTCATAGGAGCATGCATATCTACCACACAAATAAATGTTGCAATACAACCGATATGTTATCACTGGC[T/C]AGTAACTCGCCAAAGTTATATGTAAAACCACTTCTGTCTCAGTGGGTATATTCAAATTCAGGATCTAGATCAAGTTTTCTCTTCAGGTGA
108921 C T CCTTTTTGCCCCCAGTCCTTCCTGGCTCATAGGAGCATGCATATCTACCACACAAATAAATGTTGCAATACAACCGATATGTTATCACTGGCTAGTAACT[C/T]GCCAAAGTTATATGTAAAACCACTTCTGTCTCAGTGGGTATATTCAAATTCAGGATCTAGATCAAGTTTTCTCTTCAGGTGAGTCCTATC
108921 T C AGTGGGTATATTCAAATTCAGGATCTAGATCAAGTTTTCTCTTCAGGTGAGTCCTATCAGCACTAGTAAGTGTTGGCCTTGGAGGCGGTCTTGAGCCAAG[T/C]AAAGCCACGGTGTCTACAGACATTGGCATATCTCCACTTGGACCAGTAGTCATTGCAGACCTTCCAGTATTATTCACGGCATGGTCAT
108921 A G GGTGTAACCCTTCTCAGTTTTCTAGATGGCGATAAAACTAAAGGACCATCTCTTTGGCTAACAACATTTTCCAAAGAGCCCTTCTTATGTGGTCTTGGTA[A/G]CTTTTCTGGAATTGTAGGTAGTGGCTGGGAAGTAAAATACCTATGCTCAAGTGCCTGTTGTGCGGAGATTCTTGAATTAGGATCGTAC
108921 C T GTGCCTGTTGTGCGGAGATTCTTGAATTAGGATCGTACGTAAACATTTTCGATAGAAGATCTAAAGCATCATCGCTTGCTGTAGCAAATAAGGAGCGCAA[C/T]GAAGGAGCAGGAACATACTGATATTCTACGTAATCAGGAAGATATACCATGTTAGGCCATTGGGATTCTTTTGGTGTTCCGAACGCT
108921 A G GCCTGTTGTGCGGAGATTCTTGAATTAGGATCGTACGTAAACATTTTCGATAGAAGATCTAAAGCATCATCGCTTGCTGTAGCAAATAAGGAGCGCAACG[A/G]AGGAGCAGGAACATACTGATATTCTACGTAATCAGGAAGATATACCATGTTAGGCCATTGGGATTCTTTTGGTGTTCCGAACGCTG
108921 C T CAAATATGCACCCTGCAGCCCATACATCCACACCAGATCCGTACTGTTTACTGCCAAATAATAATTCAGGTGCTCTATACCAACGAGCAAAAACCTGATG[C/T]GTGAATTTGCGATCTGGGCTTCCAAAAATTCGTGCTAAACCAAAATCAGCAAGCTTAAGTTGGCCATCCGCAGCAATAAGCAAATTGT
108921 C T GGCTTCCAAAAATTCGTGCTAAACCAAAATCAGCAAGCTTAAGTTGGCCATCCGCAGCAATAAGCAAATTGTTCGGCTTCATATCTCTGTGCAGAACCCA[C/T]TTTTTGTGGCAAACAGCTAAGCCTTTCAACGTCATTTGCATGTATGATTTTATATCAGCTGGGGAAAGAAGAATGTTCCGGTCACGGA
108921 G A GCAAATTGTTCGGCTTCATATCTCTGTGCAGAACCCACTTTTTGTGGCAAACAGCTAAGCCTTTCAACGTCATTTGCATGTATGATTTTATATCAGCTGG[G/A]GAAAGAAGAATGTTCCGGTCACGGATAACAGCTTCCAAGTCAGTTTCCATGAATTCAAATACAAGATGCAAGTTACCCTTGTGAGGGA
108925 G T CTGTTGGCCTACTGGATATAAGTTTAAATTTTTTGTTTAGAAGATTTAAACCCTAAAGCAAAGGGGAA[G/T]TCTGAATCCCCATATCATATGTTTAGTTCTTAAGCTCAGATTCCTTGATTAGGTTCAGGATATTTCGTGTCAGGAGAAGTTGAAGACGTTGACTAGTCCT
108925 AAGC A AATGGGATTTCGAATGGAAGAAGTTTCCAATCTGAGTAGAAGTTCCCCATTAGGCAGCCAACAGATTGCTAACAATGCTATAGAGTATGGCTCATTTTCT[AAGC/A]AGCAGCCTACTTCAAACGATATACCTGCGAGCACTAGGGTTGGCTCTTTATCTTTCAACAACATTGAGAATTGGGGAGATTCAA
108925 C T CTGTGGCCATGGGAAAGCTTGGCACAATTGAAAATTTTCTCATTCAGGCTGATAAGCTGAGACAGCAGACCCTGCAGCAAATGCAACGCATACTAACAAC[C/T]CGTCAGTCTGCTCGTGCCTGGCTTGCTATCCATGACTACTTTTCTAGGCTTCGTGCCTTAAGCTCTCTATGGCTTGCTCGACCGAAGG
108925 C T TTCTAGGCTTCGTGCCTTAAGCTCTCTATGGCTTGCTCGACCGAAGGAATGATAGACTGGCTTACTATTTACATCTTGTGGTTCTTCATGTATGTTTTAC[C/T]ATATGCTCATGATTTATAATGCAATACTGTAATGTGTTTAGGGTTCTTAATTTGTCCCTAAGTTTATATATTTGTAAAAATGTAATAATTTA
108925 AG A TTTACCATATGCTCATGATTTATAATGCAATACTGTAATGTGTTTAGGGTTCTTAATTTGTCCCTAAGTTTATATATTTGTAAAAATGTAATAATTTAGG[AG/A]GGGAGTTTTCATGTTACTTTTATGTATGTAAGGGATATGAATTGTTCTAAAGTACGTGGTGTCCGCAGATATATCTGAGTTTGCAGAGG
108925 CT C ATTTATAATGCAATACTGTAATGTGTTTAGGGTTCTTAATTTGTCCCTAAGTTTATATATTTGTAAAAATGTAATAATTTAGGAGGGAGTTTTCATGTTA[CT/C]TTTTATGTATGTAAGGGATATGAATTGTTCTAAAGTACGTGGTGTCCGCAGATATATCTGAGTTTGCAGAGGTTTGTAATTCTTATTGA
108927 G C TTTTGAACAATAACTAAAGGAATCACATAAAAAAGTCATCAGCATGAGGCTTGGGTGAAGTGAGCAAAGCAGTGTACAGCCTAAGCTTCTCCTCCCCAAG[G/C]GACGAACATCTCGAAAGAGGTCTCCTCGGCCTAATAAAGCTCAAGGAAGTCAAAGTCTTTCTATGAGTATAACGTCTCCATGCAAG
108927 T A CCCACTGAAGTTGCCTGGGCCTAACATGCAGTAGCTTTTGACTCCATCACGCAGTTGTTGGCTACTCTGAAGGTGGCCCCGCACTACGAAGATCATCCTT[T/A]GCACTGGATCCCCTTCCCTAGTTATTATTTCACCCTTGGGGAAAATTAGAGATTTCACCCTGTCGCATATGTTCTCCAGGACAAGTTCA
108927 TC T GTTGCCTGGGCCTAACATGCAGTAGCTTTTGACTCCATCACGCAGTTGTTGGCTACTCTGAAGGTGGCCCCGCACTACGAAGATCATCCTTTGCACTGGA[TC/T]CCCCTTCCCTAGTTATTATTTCACCCTTGGGGAAAATTAGAGATTTCACCCTGTCGCATATGTTCTCCAGGACAAGTTCATCCATATG
108927 T C CGAAGATCATCCTTTGCACTGGATCCCCTTCCCTAGTTATTATTTCACCCTTGGGGAAAATTAGAGATTTCACCCTGTCGCATATGTTCTCCAGGACAAG[T/C]TCATCCATATGCTGAAACAAGGGCACCTGCCTTACAAGATCAAGGCACAAATGATACTTAATGTCCCTTCTCAGCCCCTCAGGCAAATT
108927 G C GCACCTGCCTTACAAGATCAAGGCACAAATGATACTTAATGTCCCTTCTCAGCCCCTCAGGCAAATTCCTAACCATCTCAACCTCATCCACACCTCTCAT[G/C]GCTGCCCACCTTTGCCTTTCATATTGCCTAACCCTCTGTCTGAACCCCTGAGGCACCTTCTTCTTCTTCATCCACCAGTCCATGCTTCTCAT
108927 A G TCTCAAGCCTGTTATTATTGGTAACAAGCTGAACCGTCCATTTGTAAGCTCCGTACTGGAACTTATCGCTTGTGGCTAAGCATATGTCTCTTCCTGATTG[A/G]TAATGAGCCCATGATATTCTAGAAGCATCCGTAATCGTCATTGACGTGCCATAGTAGATGGGCTTTACACATGCAGTAGTGTAACTAGG
108929 C A CACATCGATTTTTATCTTTGAAGCGATGCTTTCCTGGTTTCTGTATCGTCAAGATTTGTAGTATTTTGGTATGCTAAAAATATTGGGTTAAAGCTAGTGG[C/A]CTATTTTCCCCAATACTGTTCTATTTGTATGGAGTTGGAATCATTTTTATGGTGGTTTATTGATCCCAAAAACCAAATTGATGTACAATAT
108931 G C ACAACCCAATCTCCACACTTGTTCTTTCTGACACTACCCTTGCCTTTGGACGTGTGCTTGCAAGTGATCCTAATGGAAATTACAAAGGCTCACTCTCTCT[G/C]CCGCTGAAAGAAGGGTCACTCTTAGTTATGCGTGGAAACAGTGCTGACATGGCAAGGCACGTGGTGTGCCCTTCAGAGAGTCAGAGG
108931 T C CCTTTGGACGTGTGCTTGCAAGTGATCCTAATGGAAATTACAAAGGCTCACTCTCTCTGCCGCTGAAAGAAGGGTCACTCTTAGTTATGCGTGGAAACAG[T/C]GCTGACATGGCAAGGCACGTGGTGTGCCCTTCAGAGAGTCAGAGGGTGACCGTCACGTTCATCAGAGTGCGTCCTCCAGTGAGTCA
108935 G C ACATAATTTCATATGTCCCTTTAAATTTAAGCATTCCATCCTGGTGAATACCACTTTCGTGGGCAAAAGCATTTGCACCGACAACAGCTTTATGTGGTTG[G/C]ACATACAATCCAGTATATTCTGCCACCATCTTGCTAGCCATAGAAATGTGTTCTGTGTTGATTCCTGTGTATAGCTTTCCCATTTGCTCTG
108935 T A TTGCACCGACAACAGCTTTATGTGGTTGGACATACAATCCAGTATATTCTGCCACCATCTTGCTAGCCATAGAAATGTGTTCTGTGTTGATTCCTGTGTA[T/A]AGCTTTCCCATTTGCTCTGGTCGGCATTGTATGGTCATAACAACCTCTTCCAATGAAGCATTTCCAGCTCTTTCACCAATACCATTGATAG
108935 C T TGTATAGCTTTCCCATTTGCTCTGGTCGGCATTGTATGGTCATAACAACCTCTTCCAATGAAGCATTTCCAGCTCTTTCACCAATACCATTGATAGTGGA[C/T]TCTAGCTGCCTTGCTCCAGCACAGGCTCCTGATAATGTGTTGGCAGTTGCAAGGCCCAGATCATTTTGGCAATGTGTTGAAATGATCAC
108935 G A CTAGCTGCCTTGCTCCAGCACAGGCTCCTGATAATGTGTTGGCAGTTGCAAGGCCCAGATCATTTTGGCAATGTGTTGAAATGATCACATTATCTATCCC[G/A]CGTGTGTTGGCCTTTATATCAGCAATCAATTGACCAAATTCAGGAGGAAGCGTGTAGCCAACTGTGTCTGGTATATTCAGTGTTGTTG
108935 T C TGATCACATTATCTATCCCGCGTGTGTTGGCCTTTATATCAGCAATCAATTGACCAAATTCAGGAGGAAGCGTGTAGCCAACTGTGTCTGGTATATTCAG[T/C]GTTGTTGCTCCTGCTTTAATAACTTCCTCGAGAATATGATAGAGAAATTCTCTGTCCGACCTTCCTGCATCTTCAGGACTAAACTCAACA
108939 T C TTGATATATTCACAATCGCCTGATTGACAATGTTCACTAGCTGGAAAGTGACTTCTTTGCTTCTGTTCATTGATTCTGTGGCGGTTGCAGTGTCTACACA[T/C]GGCAAGATGTCGTCTAATGCTGTGTGCGAGTGAGGGTGGTGTACCCAATCGTCCATTGCTACACATGTGTCTGCCACAACGTTGTGGA
108939 T C GTTCACTAGCTGGAAAGTGACTTCTTTGCTTCTGTTCATTGATTCTGTGGCGGTTGCAGTGTCTACACATGGCAAGATGTCGTCTAATGCTGTGTGCGAG[T/C]GAGGGTGGTGTACCCAATCGTCCATTGCTACACATGTGTCTGCCACAACGTTGTGGAAAAGGAGAGCAATCCCACATAATAGCAATG
108943 A C CAGAAGTAGAACCAAAAAATTATCTATATTTTTAACAAATACAAGTAGTTCATCCATGTTACACCCACCTATCCGCAACTGCTTCTAGAGAATATGAAAT[A/C]TTTGGGAACAGCTAGCCTACTCACACTTGATGGATCGGTAAATGTGGCGAACGAACAAGAGAGAGGCTCTGAATCCGATCATGCCCAG
108943 G A TATGAAATATTTGGGAACAGCTAGCCTACTCACACTTGATGGATCGGTAAATGTGGCGAACGAACAAGAGAGAGGCTCTGAATCCGATCATGCCCAGCAT[G/A]AGGAAGAAGCCATAGCAGATGCAGGCCATGTACCCGAAAAAGAAAGATGTCTGCATGAAGCCTGACATGTCCGATCTAGCATGG
108943 GA G TGATGGATCGGTAAATGTGGCGAACGAACAAGAGAGAGGCTCTGAATCCGATCATGCCCAGCATGAGGAAGAAGCCATAGCAGATGCAGGCCATGTACCC[GA/G]AAAAAGAAAGATGTCTGCATGAAGCCTGACATGTCCGATCTAGCATGGTAGTAATATAAGCAGTATCCATATATGTATAGCCC
108947 C T ATATACTGATTGCGTGGAAAGCACAATTCCATACACATACGGTGACATGCTTGTAAAGAGTTGTGTGCATACATAACAAAGATGAACGAGTGGGAGACTA[C/T]ATTATTATACTTACATATGCGCTGAGAAGTTCGTCATTGTCAATCAACCTTTACACTCCAAATCACCAAAGGAGCAGTCTTCATCAAA
108947 C T ATTATACTTACATATGCGCTGAGAAGTTCGTCATTGTCAATCAACCTTTACACTCCAAATCACCAAAGGAGCAGTCTTCATCAAACCCTTGACACTTCTC[C/T]TCTCTGTCTAACCTGAGCAGAAAGTGGTTTCTTCATAACAACAGTGAACTCGAAAGCTTCAGCCATGTCAACACCATCTTCATCACTAGC
108947 G C GGAGCAGTCTTCATCAAACCCTTGACACTTCTCCTCTCTGTCTAACCTGAGCAGAAAGTGGTTTCTTCATAACAACAGTGAACTCGAAAGCTTCAGCCAT[G/C]TCAACACCATCTTCATCACTAGCCTTCCATTCAAACTCCCTCACCAAATTGGCTACAAAGAACTCCAAATGCAAAGTCGCTAACTCGTAC
108947 T C CACTTCTCCTCTCTGTCTAACCTGAGCAGAAAGTGGTTTCTTCATAACAACAGTGAACTCGAAAGCTTCAGCCATGTCAACACCATCTTCATCACTAGCC[T/C]TCCATTCAAACTCCCTCACCAAATTGGCTACAAAGAACTCCAAATGCAAAGTCGCTAACTCGTACCCCGGACAAATTCTTCTTCCAGCTC
108947 T C TTCCATTATCACCGCCTTCAAGTAATGCATCTTCTCCAGTTCTTCCTCTTCTATCTCCTCCTCATCTTTCACGACATGATAGATCTCATCCCTTAACTTA[T/C]TCTGAACACTTTGGTTTTTCACTAGCTCCGCCATGATCCACTCGAGTAACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACA
108947 T C CTTCTATCTCCTCCTCATCTTTCACGACATGATAGATCTCATCCCTTAACTTATTCTGAACACTTTGGTTTTTCACTAGCTCCGCCATGATCCACTCGAG[T/C]AACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTC
108947 T G CTCCTCCTCATCTTTCACGACATGATAGATCTCATCCCTTAACTTATTCTGAACACTTTGGTTTTTCACTAGCTCCGCCATGATCCACTCGAGTAACACG[T/G]ATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGG
108947 G A CTCCGCCATGATCCACTCGAGTAACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTT[G/A]CCTCGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATC
108947 T C CGCCATGATCCACTCGAGTAACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCC[T/C]CGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCA
108947 G A CTCGAGTAACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCA[G/A]CAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTC
108947 G A AGTAACACGTATGTTGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAG[G/A]GATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAAC
108947 T A TGTATCTGTACCTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGGGATTTCAAGGTCG[T/A]GAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCAT
108947 A G CTGCAGACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATC[A/G]ACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTAC
108947 G A ACAAGAACTCATGACACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATA[G/A]GAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATA
108947 T C ACAAGTGCACAATCTCCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCT[T/C]TCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTT
108947 C T CCCCTTCTTTGAGTTTCCTTGCCTCGTTATTCTCAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGG[C/T]AGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAA
108947 T C CAGCAGGGATTTCAAGGTCGTGAAGAGAATCAACATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCC[T/C]ACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGA
108947 C T CATAGGAATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAA[C/T]TTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACT
108947 A T AATGCCTTTTCCTTTCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGT[A/T]ACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCA
108947 T C TCTTTGATAAGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATA[T/C]TGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCC
108947 G A AGAGGCAGGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAAT[G/A]GTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACA
108947 T G GGAATATCTCACTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAA[T/G]CGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATA
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108947 G A CTTTGCCTTCTTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACA[G/A]CAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAA
108947 G A TTCTAACTCCTACAATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGAT[G/A]AAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAAT
108947 T C AATTTCATTCCACCTCTTACGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATG[T/C]CTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAATCGAAAAATTTCT
108947 C G CGGAATAACAACTTTGTAACTTGAGGCAATATTGCAAAATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCA[C/G]TCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAATCGAAAAATTTCTCTTACCAACACCACTTTAT
108947 A T AATGGTTGAATCGGGTGTACAGCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCAT[A/T]AGCAATCTAAACATCACAAATCGAAAAATTTCTCTTACCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGAT
108947 T C GCAAGAGGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAA[T/C]CGAAAAATTTCTCTTACCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGA
108947 A T GGATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAATCGAAA[A/T]ATTTCTCTTACCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGATTAACGC
108947 A T GATGAAGTATTGAATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAATCGAAAA[A/T]TTTCTCTTACCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGATTAACGCT
108947 A G ATGTCTTGGGCTTCTTTAATCACTCTCTCATCAACCTCATGCCCAAAACACATAATCATAAGCAATCTAAACATCACAAATCGAAAAATTTCTCTTACCA[A/G]CACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGATTAACGCTTGAACTGTGAAGG
108947 C T AAAAATTTCTCTTACCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGATTAACGCTTGAA[C/T]TGTGAAGGACTTTAGAAGTCATGTTGCGGCGTAAGGTGCGCCACAAAGGACCATAACTGGACGAGTTGATTTCGCAGGAGTTGCAACT
108947 A C CCAACACCACTTTATCCTTCTTAATCATCTCGATAAGTAGATCAAGACTTGATTTTCTGCCGAAATCGAAGTGATTAACGCTTGAACTGTGAAGGACTTT[A/C]GAAGTCATGTTGCGGCGTAAGGTGCGCCACAAAGGACCATAACTGGACGAGTTGATTTCGCAGGAGTTGCAACTCAAGGAAAGCAAA
108947 G A TGACGAGCTGTTCGAGTTCGAAGAGGGATTTTCTTCCGAGGACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTT[G/A]CGGTTGCGTTTGAAGAGGAGCAGTTTTGTGGAGAAGAGGACTGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACC
108947 G A CGAAGAGGGATTTTCTTCCGAGGACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAG[G/A]AGCAGTTTTGTGGAGAAGAGGACTGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGT
108947 C G AGAGGGATTTTCTTCCGAGGACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAGGAG[C/G]AGTTTTGTGGAGAAGAGGACTGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGTAGA
108947 T C GGGATTTTCTTCCGAGGACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAGGAGCAG[T/C]TTTGTGGAGAAGAGGACTGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGTAGATCA
108947 A G CCGAGGACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAGGAGCAGTTTTGTGGAGA[A/G]GAGGACTGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGTAGATCATTAAACAATTT
108947 C T ACGATGTTTTTGAAGATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAGGAGCAGTTTTGTGGAGAAGAGGA[C/T]TGTGATGAGGAGGAAGATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGTAGATCATTAAACAATTTAATTGCA
108947 A G ATGAAGGCGATTGCGTTGGGGCCGGGAGGCAAGGGGGGTTTGTTGCGGTTGCGTTTGAAGAGGAGCAGTTTTGTGGAGAAGAGGACTGTGATGAGGAGGA[A/G]GATGATTGTCAACGGTTCCATGGCACCGTTCACTGCGTGTTCAGTAGATCATTAAACAATTTAATTGCACAGAAGTT
108951 A G CTTTTGTTGATGCCAAATGCTGATCTTGTGATCGGTTGCCATCGGAAACTACCATCTGTTCATGACCCGCTATCACGCTTCTCTTAATTGGTGAGGCAAA[A/G]ACCAACGATGGCTGAAATGATGTGACTGCTTTTGGTTTTTGCTGTGGTCCATTGACACTTGATGCTTGTGGCTCTTGAGGTTCTTGGTA
108951 G C CATGCGACAAATTTTCTTTGTCACTTGATCCATTGATAGAGGTTGATTGCTGCTGCTGGTTTACATGATTGTCATAGCTATGATGAAAATCAGACACAGA[G/C]TGATTTTGCTGAATTTGTGCAGGCTGGTGTTTGTTCTGAATTGGATTTTGTGAACCATCGGGTAAAGCCTGCAGCTGCTGAAGCTGCC
108951 A G GCTGGTTTACATGATTGTCATAGCTATGATGAAAATCAGACACAGAGTGATTTTGCTGAATTTGTGCAGGCTGGTGTTTGTTCTGAATTGGATTTTGTGA[A/G]CCATCGGGTAAAGCCTGCAGCTGCTGAAGCTGCCAATGTTGGTGAGCTGAAATTGCCGAAACAGGCTGGAAATGACCAACAAACTG
108951 G A TTACATGATTGTCATAGCTATGATGAAAATCAGACACAGAGTGATTTTGCTGAATTTGTGCAGGCTGGTGTTTGTTCTGAATTGGATTTTGTGAACCATC[G/A]GGTAAAGCCTGCAGCTGCTGAAGCTGCCAATGTTGGTGAGCTGAAATTGCCGAAACAGGCTGGAAATGACCAACAAACTGAGGAAT
108953 G A AGTTGGTAACCACATTTCCATCACCGGGGTAGTGAGGGTCGGTCGATATTAGTGATACTAAATAGTCGGAAGGAGCGACATAGCCGAACCTTCCAGGATC[G/A]TTGGTGGAGGTGGGGCTGACGCTAGTTAGTCCTCCACATGAGAGGATGAAGGAGATTGCAAACATAGAAGCTTCCAGTGGTGGG
108955 CA C TATAGGCTTTCATCTGAGAGTTTTATGCATCAAAATCCACTTCGACAGCATAGTGCTCCTGTTTGCTTGTTTAAGCATCATACCCAAACTTTCCTGAAAA[CA/C]AAAAGCAAAGTATTTTACCCCCACTTCTACTGCATCTTTCATCTGATATTTCCTCACCCCACTTCAATTCATCAAGCAAACATGGCTTTAC
108955 GA G CATCGTGAACATGGTGGACATTGCGAAAGCCTTGGCTAGACCCCCTTCTTACACCACCAAATACTTCGGGTGTGAACTTGGTGCCCAATCCAAGTTTGAT[GA/G]AAAAAACTGGAACCTCGCTTGTTAATGGTTCGCATGATACCGCGAAGCTTGCTGGACTTCTGGAAAACTTCATCAAGAAGTATGTC
108955 T C CTGCTGATGATGCCAATGACGATGACGTTGAATGGCAGACCGATACATCGCTAGAAGCTGCAAAACAGCGTATTCAAGAACAGCTCAACTCTGTAACTGC[T/C]GAAATGGTCATGCTTTCCACCTTAGAAGCCGAGAAGGAGAAAACAGCCAAGGCTAAAAAAGAAGAATCTCTTGTAGCTCAAATCAA
108955 A G GCAAAACAGCGTATTCAAGAACAGCTCAACTCTGTAACTGCTGAAATGGTCATGCTTTCCACCTTAGAAGCCGAGAAGGAGAAAACAGCCAAGGCTAAAA[A/G]AGAAGAATCTCTTGTAGCTCAAATCAAGAAAAAGCTGACTGATGGTTCCACACCTAATGAGATACACTCATTTCTCAACTCAATAGA
108955 T A CCACCTTAGAAGCCGAGAAGGAGAAAACAGCCAAGGCTAAAAAAGAAGAATCTCTTGTAGCTCAAATCAAGAAAAAGCTGACTGATGGTTCCACACCTAA[T/A]GAGATACACTCATTTCTCAACTCAATAGAAGGAACGAGTGCTGAGCAGAACGTGGTCGCTTTATTTGAAGCGCTGTTTGATGGAG
108959 T C GCCTAATAATAGTTTGATATATCTTGCTCTTGCTGCATAGCCATGCCTAAACAAACCAGCACATATACATATAACTTTACAGCTCTTTGAAACAGGAACT[T/C]GACACCCAATGTGCAGTGCAGTGCAGTGCAAGCCGGCCCTGAGAGATGACCTTGATGTTCATGTGACACTGAAAATTGCCTAAGTAGC
108959 G T AGCCGGCCCTGAGAGATGACCTTGATGTTCATGTGACACTGAAAATTGCCTAAGTAGCCAGTTTGGCAAGGCTGCTCAGTTCCAATATTTTTACATCAAA[G/T]GTGCTGTCAAGCTTCACAATACCGTCGTTGCCGTCTATACCTATAAGCTTTCCGCTAAGTCCACGTTGGCCACCTCCAATTATCTTGAT
108959 G A GTTGGCCACCTCCAATTATCTTGATCCTGTCTGCCTTTTTCGGCCTCACGGGCTCCAACTCCCCCTGAAGAAAAGTCTCCACTTCTCTACCCAAAGCAAC[G/A]CGACATGACCCGTCCGTGTTGACCTCACTAATGACCCCGAGAAGAGGTTCTTCTCCCGTCCTCGATACATACACATATATGTCCGTCACT
108959 C T TACCAGGAAGATATGAATTGGAACTCGGTGTCATTGGTTGCATGCCAGGAGTTGATGGCAAATAAGGACTGGCAGCACTTCCATATAGTGGGCTGCCTTC[C/T]CTTGTTGCTCCAGATTCATTATTATTACCAGGAGTATTTGCCCAGCCGGAACCAGGTGTAGGTGCTTCATAAGGTCGAGCCGTAGG
108959 G A GAGTTGATGGCAAATAAGGACTGGCAGCACTTCCATATAGTGGGCTGCCTTCCCTTGTTGCTCCAGATTCATTATTATTACCAGGAGTATTTGCCCAGCC[G/A]GAACCAGGTGTAGGTGCTTCATAAGGTCGAGCCGTAGGCGTTGGCTGGCGCTGTGGGCTGGCTCCCCACGATCCAGGGTTTCCATC
108959 TC T CAGATTCATTATTATTACCAGGAGTATTTGCCCAGCCGGAACCAGGTGTAGGTGCTTCATAAGGTCGAGCCGTAGGCGTTGGCTGGCGCTGTGGGCTGGC[TC/T]CCCCACGATCCAGGGTTTCCATCTTCCCAACTATCTCTAGGGGGACTCATAGGCGCCCACGCTCTATTTACCATGGGAGTTCTCAT
108959 A G AACCAGGTGTAGGTGCTTCATAAGGTCGAGCCGTAGGCGTTGGCTGGCGCTGTGGGCTGGCTCCCCACGATCCAGGGTTTCCATCTTCCCAACTATCTCT[A/G]GGGGGACTCATAGGCGCCCACGCTCTATTTACCATGGGAGTTCTCATGCCATCATGTATAGGGGTAGCTCCAGGATCTCTCATGGG
108959 G A TCTTTCCAACTAAAGAATCATGTCCTCTTCCGCCCCTGAATCTTCCACCAAATTCTTGTGCAGGTCCTCTCGGTGGTCTAGCAGGAGAAGATAAATAATT[G/A]TTCTTTAATGCATTCATCCTTGTGTCAAAGGGGTTGAGACCGTTCTTCTCGCGGTTCCCACCAAGAAGCATACAAGATTCAGGTTTCAC
108959 C T AGGTTTCACACAAATAAAACCAGCATGTTCAAGATGATGGCGATCATGGATGAATATGACTCCCCTATAAATGTGGTGAATAACACCTCGTTTTTCCTTA[C/T]ATGGCCCCTCAAGAACCTTCACAATATCCTTGGCACATATACGATTTTTACCACGGTCTTGAGCATTACTTTGTCTCTCAATTTTGCTTTT
108971 G A CACAGTTGAATACAGCAGAAAATACAAATGCAGTAAACCAACAAAAGCAAATCGATAAACGCCCTCATTTCTTCAAAAATGTAGCGCTACACTGGGCCAT[G/A]ATCTTCGAAGCCCTGGTTATAGCATCTGTCATGTAGAAATTCTCCACAGCCGGTTTAAAATCCTGGTTTAGATCCACCGTCTCCTTCA
108971 C T TCGCCATGGTGACCTTGGTAAACTACAAATGCGTCTTTAGGTAGGTTTTCTAAGGGTATATCATCTGCACCCATTAAATATAAAAATTTAGCGTTAGGAA[C/T]GCATTCATTGGGGTTGGAAACAAGTCCTAGATCTAGAGAGGCAGCTTGAGCAGCGTTGTGGAGTAAGACATTGAAACCGTTCCAGTC
108971 G A GTATATCATCTGCACCCATTAAATATAAAAATTTAGCGTTAGGAACGCATTCATTGGGGTTGGAAACAAGTCCTAGATCTAGAGAGGCAGCTTGAGCAGC[G/A]TTGTGGAGTAAGACATTGAAACCGTTCCAGTCGGGAGTTGTGAAATTTCCTATTTTGGCGATTTTTTCGAGAGTGGAGATGACGGC
108971 C T GAGGCAGCTTGAGCAGCGTTGTGGAGTAAGACATTGAAACCGTTCCAGTCGGGAGTTGTGAAATTTCCTATTTTGGCGATTTTTTCGAGAGTGGAGATGA[C/T]GGCATTTTGATCATTTCGTGAGAAAAGGCCTGCTCCTACGATCAGGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGA
108971 G A CGGGAGTTGTGAAATTTCCTATTTTGGCGATTTTTTCGAGAGTGGAGATGACGGCATTTTGATCATTTCGTGAGAAAAGGCCTGCTCCTACGATCAGGGC[G/A]GGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATGTCGTCCTTCGGCGATTTCCAGGAGGATTTTCGGGCCTGCTCCAAGGT
108971 T C GAGTGGAGATGACGGCATTTTGATCATTTCGTGAGAAAAGGCCTGCTCCTACGATCAGGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATG[T/C]CGTCCTTCGGCGATTTCCAGGAGGATTTTCGGGCCTGCTCCAAGGTATTGATGGTCATAGTTTAAGTCGGCTGGTGGGCCTATG
108971 G C TGATCATTTCGTGAGAAAAGGCCTGCTCCTACGATCAGGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATGTCGTCCTTCGGCGATTTCCA[G/C]GAGGATTTTCGGGCCTGCTCCAAGGTATTGATGGTCATAGTTTAAGTCGGCTGGTGGGCCTATGTAGCCTACTTTTGCTTGATTTG
108971 A G ATTTCGTGAGAAAAGGCCTGCTCCTACGATCAGGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATGTCGTCCTTCGGCGATTTCCAGGAGG[A/G]TTTTCGGGCCTGCTCCAAGGTATTGATGGTCATAGTTTAAGTCGGCTGGTGGGCCTATGTAGCCTACTTTTGCTTGATTTGCTCGG
108971 T C CTACGATCAGGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATGTCGTCCTTCGGCGATTTCCAGGAGGATTTTCGGGCCTGCTCCAAGGTA[T/C]TGATGGTCATAGTTTAAGTCGGCTGGTGGGCCTATGTAGCCTACTTTTGCTTGATTTGCTCGGATGGTTTTTCGTATTCTTGCGTTC
108971 A G GGGCGGGGTTCTTGGCAGAAAGGATTGCAGAGTGGAAAGGATGTCGTCCTTCGGCGATTTCCAGGAGGATTTTCGGGCCTGCTCCAAGGTATTGATGGTC[A/G]TAGTTTAAGTCGGCTGGTGGGCCTATGTAGCCTACTTTTGCTTGATTTGCTCGGATGGTTTTTCGTATTCTTGCGTTCACCATTGG
108971 T G GGTGGGCCTATGTAGCCTACTTTTGCTTGATTTGCTCGGATGGTTTTTCGTATTCTTGCGTTCACCATTGGTGCTTCAACTCTAGGCTGGCTACCAACAA[T/G]AAGGAAAAGATCAGCCTTCTCAAGGCCAGAAATATGTGAATTCATAAGGTAACTTGAACGCAGATCAGCTTGAGGGTTTGGACCATTT
108973 C CT GGTACTTCACCTTTGAGTATGGCTTGTATCTGCTTTGCATTCTCTCTCAACTTATTAGCCATCTCTTGTTCTTTACTGTATAATTTGGTAGTTCCTATTT[C/CT]TTTTTCTCTGAATATGCATATGCATTTGTGCCTGCATCTGCATCAGCATCCACACCTGCAACAACATCCGCGCCTGCAACAGCAACTGCAT
108973 C CT ACCTTTGAGTATGGCTTGTATCTGCTTTGCATTCTCTCTCAACTTATTAGCCATCTCTTGTTCTTTACTGTATAATTTGGTAGTTCCTATTTCTTTTTCT[C/CT]TGAATATGCATATGCATTTGTGCCTGCATCTGCATCAGCATCCACACCTGCAACAACATCCGCGCCTGCAACAGCAACTGCATCCGCACCT
108973 T A CTGTATAATTTGGTAGTTCCTATTTCTTTTTCTCTGAATATGCATATGCATTTGTGCCTGCATCTGCATCAGCATCCACACCTGCAACAACATCCGCGCC[T/A]GCAACAGCAACTGCATCCGCACCTGCAACAGCATCAATGCCTGCACCTGCAACAGCACCAGTGTTTGCACCTGCAACAGCGTCAGCGTC
108973 GTCAGCGCCAGCACCCACATCAGCA
G CAGCAACTGCATCCGCACCTGCAACAGCATCAATGCCTGCACCTGCAACAGCACCAGTGTTTGCACCTGCAACAGCGTCAGCGTCAGCACCAGCATCTGC[G/GTCAGCGCCAGCACCCACATCAGCA]TCAGCGCCAGCACCCACATCAGCATCAGCGTCAGCGCCAGCACCTACATCAGCATCAGCGTC
108973 GT G TTTTCCACAACCTTCAGCAACAATCTTCCACCTTTGAATAGAAGGAAGCGCTTTGGCTAATTCATGATCTTGACTAGCCATTTCATTCAATAAAATCATT[GT/G]TTTCCTTTTTGTCCATTCTGGAGCAACTTGGGAACGAGTGCATCGGGATATTGATCTACCCGCCGCTTCCTTGAAGGACTTCTTCAATG
108973 A G AGGTTTCCTGCCTTTTCTTTGTTTGGCGTGCTTGTGATGCTCGTTCTCCTAATTTTCTGCTGCTCCTCCTCCTGGTTTCTTGCTTTATCCATGTTTGGTG[A/G]GCTTGAATTTTAGGCCTAGAGTCTTCTTCTTCCATTTCCCCTCAATAAAAATTTCAGTATGTCCTTCTAACTTTCTAAGTTTCAACCAAGAAC
108975 T C GAAGGCCGCTTTTCAGGGACAAAATCAAGGATAGGGATGAGAAATTCTGCCAACTCTGTGGCGTCTCGCTCGCTGAAGTCGTATTTTTCCATTAGGACTT[T/C]GTTTAGTGGCCAGAAACGAAGGCGGCGAATGTGTCTCAAGTCACCATATCTGTTAAAGAAGTCACGAGAGTATCGACCACCTAAGG
108975 G A TTTTCAGGGACAAAATCAAGGATAGGGATGAGAAATTCTGCCAACTCTGTGGCGTCTCGCTCGCTGAAGTCGTATTTTTCCATTAGGACTTTGTTTAGTG[G/A]CCAGAAACGAAGGCGGCGAATGTGTCTCAAGTCACCATATCTGTTAAAGAAGTCACGAGAGTATCGACCACCTAAGGCAATCTTCCG
108975 T C AGGGATGAGAAATTCTGCCAACTCTGTGGCGTCTCGCTCGCTGAAGTCGTATTTTTCCATTAGGACTTTGTTTAGTGGCCAGAAACGAAGGCGGCGAATG[T/C]GTCTCAAGTCACCATATCTGTTAAAGAAGTCACGAGAGTATCGACCACCTAAGGCAATCTTCCGAGGCATCATACCGAGAAGCTCCA
108975 A G TCTTTTTCTTCTGATTACGTGTCAAATCACCATTACTAGATGCCTGATTCACCTTAATAAGAGGGTCGCTTGACTTTACAGTTGGAATTATAGGGGGTGC[A/G]TTAGACAAACGAGGATCATTGCTTGGGTCTATGGTAGAAACAAGTAGGATATTTTCAGGTTTAAGATCTGTGTGGATTATGGAGAGTT
108975 T C TGTCAAATCACCATTACTAGATGCCTGATTCACCTTAATAAGAGGGTCGCTTGACTTTACAGTTGGAATTATAGGGGGTGCATTAGACAAACGAGGATCA[T/C]TGCTTGGGTCTATGGTAGAAACAAGTAGGATATTTTCAGGTTTAAGATCTGTGTGGATTATGGAGAGTTCACGATGAAGGTAGTCTA
108979 GT G CTCCTCTTCTCGCCTCCACCTGCGTCGGGACCCTAGAGTTCAGATCCGTCGCTGAACCTATCGGCCGGATCCAGCCGGCCATCTCCACTGCGCCTGGATC[GT/G]TTTTTTTACCTGGCTAACTGTACCGGGATCGATCACGAGTCACATACGGTACATTGCGAAACGGTTACCGATGGAAACAACATGGG
108981 A C AGGTTCATAAAAAACAACAGGAAATATATGTCAAAATGGTTTCGTAATGTAAGCTCACCAAACACAAAAGAGGATAAAAGTCTGGTATACAACGAAACCA[A/C]ACATCATACAAACATTCTATTCCAGCTTCCTGTGCAAAAAACGGATGCTTAACTTCGATCAAACGCAGCCTCTCATCAAAATAAACTG
108981 G A AAAAGAGGATAAAAGTCTGGTATACAACGAAACCAAACATCATACAAACATTCTATTCCAGCTTCCTGTGCAAAAAACGGATGCTTAACTTCGATCAAAC[G/A]CAGCCTCTCATCAAAATAAACTGTACCCTTTTCCTCCTTCGAACCAATCGGTAACATTTCAATTACCCTATTTTCTCATCAAACTAAAGC
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
108981 C T GGTGTCGTCACTGTCGAATTTTGCACCCCATGATGGTTCATCGAAGAATCCAACTCCAGATATTGTGGACTCGGCATCAAAATGGTCACTCTGAAATTCT[C/T]TAGCACGAGGTGAAAGATTATCATAACTGACTTGTTTTGACTGAAACTTAGGGGACGAACTATGTGAAGTAGCTGTCTTAGGACTAG
GGTAAGGATTTCTGATCCAACGGCAATGGCAGTGATGTTGACGGAGGGAACATGGGGGAGGACGT
108983 A ATGATCGAGGAGGAATGTGGGGTGGAGATTTTGATTTGACGGTCGAGATTAGAGGCCACGAGGGCAGAATGAATGAAACTAAGGGCGGACACGAGGATGG[AGGCGGCGTTGGGGAGGGTGGTAAGGATTTCTGATCCAACGGCAATGGCAGTGATGTTGACGGAGGGAACATGGGGGAGGACG
108983 C T CAACCCAGTTGGAAGCGGTTTTGTTCGATTGGCCAATGCCTAGAATCAGTTCGTTTGGGATAGAGATAGTGACTTCGATGCCGGTGTTTGCAAGAGCTGT[C/T]AGCATTGGGAGGGACGCGTCGTAGAGACGGATGTGTTTGATTTGTTGCTTTTTTTAGGAGGGCAACCACTTGTGTTGGTGATGGTG
108983 C T CTGTCAGCATTGGGAGGGACGCGTCGTAGAGACGGATGTGTTTGATTTGTTGCTTTTTTTAGGAGGGCAACCACTTGTGTTGGTGATGGTGGGGTGGAGA[C/T]GGCAGTTCCGATGTTTACGCCAATGAACGCATCATCAGCAGAAGCCAGAGCGAGTACATACATCAGCAGTAAAAGCAGCTTCATT
108983 T C GCATTGGGAGGGACGCGTCGTAGAGACGGATGTGTTTGATTTGTTGCTTTTTTTAGGAGGGCAACCACTTGTGTTGGTGATGGTGGGGTGGAGACGGCAG[T/C]TCCGATGTTTACGCCAATGAACGCATCATCAGCAGAAGCCAGAGCGAGTACATACATCAGCAGTAAAAGCAGCTTCATTGAAGA
108993 G A GTAGAGATTAGGCCTTCGTTAACACCAACTAGACCATACTCAAGAGCTTCAGACACTCGCCAAGACCGCGGTATGCTTTTGGTGAAAATATATGCTGCTA[G/A]TCCAGCATTGGTGTCATTAGCCATCCTTATAGCATCTTCTTCCATTTTAAAAGGTAAAAGAGGAGCAACAGGCCCAAACACCTCTTCC
108993 T C CATCATCAAAAACAATGCACGGTGCATTTCCACCAAGTTCCAAGGATATCTTTTTAACTGTATTTGCTGAACCAGCCATTAATTTCTTTCCAACAGCAGT[T/C]GAACCAGTAAACGTAATTTTCCTCACCTGTGTGCTCTCAAGTAGCATTTCCCCGATTTCGGGAGCATTTCCCATTACTACATTCAAAGCAC
108993 T G GTGTGCTCTCAAGTAGCATTTCCCCGATTTCGGGAGCATTTCCCATTACTACATTCAAAGCACCTGGAGGTATCCCAGCTTGAATGGAAAGTTGGGCCAT[T/G]GCTAATGCAGTCAGAGGTGTATATTCTGATGGCTTAACAACGACAGTGCAGCCACAAGCCAAGGCAGGACCCACCTTGCGTGCAAT
108993 CA C ATTGCTCCAACAACACCAACAGGCTGTTTCAGAACAAAGAGTTTACGATCAGCAAGTGTAGATGGAATGATGTCTCCATATACACGTTTTGCTTCTTCAG[CA/C]AAAAAATTCAATAAAGCTAGCACCATAGGTAACCTCGCCTAGAGCCTCCTTTAGGGGCTTTCCCTGCTCTAAAGTGATAAGTAATGC
108993 C T CTTGCTTCTTTGGTTTGCAGTAAGCTTGCTCCATGAGCTGAATGTAGAATATGCTGAAGATATTGCATCTGAAGTTTCATTCCTCCCCATCTTTGGTACG[C/T]TTGCAATAACATCTCCCGTGGCTGGATTTAGCACCTCAAACGTTTTCCCATCATGAGCATCACTCCATTTCCCCCCAATTAAACCTTTATT
108995 A T ACTGCAGATAACCATACGCTCGTCAGACATCCAATACATCAATAAGGAAATATATTTAACATACGCACTCAATAACGTTCCACATTAAAATATCACTCAG[A/T]GACTGAAATACGTACTGTAAAAGGCAAAATATTATTCAAATACAAACGGAACTTGTTAAAAGAAATAGCATACTTCTGACACATATTTA
108995 C T GTTTAAACCTCTCGGTCTTGGTTATCTTCTCTAACTGCTCATCCGCCCCTCCATACATATCCGAATCTGCATCCTTTTTGGGTCTGTACAAGGTTGACAA[C/T]GTAGGCTGAGCAGTGAATAAACCTTTATCATATATATTGTACTGATCATCAGCAGCAAATCCTGATTCCATTCCCTTGTCCTGATTAAAGA
108999 A T CCTCTTCGTACTCGGCCTCAGGTGCCTGATCACTTCCACCTTGAGACCCACCAGACCCACCACCACTCATATGCTGACCAATTTTAGAAACAGCCTTATT[A/T]GCAGCGTCGAGCTTCTCCTTTATCTTAGCAGCATCGTCTCCAGCCATGGCATTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCA
108999 G A CGTACTCGGCCTCAGGTGCCTGATCACTTCCACCTTGAGACCCACCAGACCCACCACCACTCATATGCTGACCAATTTTAGAAACAGCCTTATTAGCAGC[G/A]TCGAGCTTCTCCTTTATCTTAGCAGCATCGTCTCCAGCCATGGCATTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCACCTCA
108999 G A ACTCGGCCTCAGGTGCCTGATCACTTCCACCTTGAGACCCACCAGACCCACCACCACTCATATGCTGACCAATTTTAGAAACAGCCTTATTAGCAGCGTC[G/A]AGCTTCTCCTTTATCTTAGCAGCATCGTCTCCAGCCATGGCATTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCACCTCAGCT
108999 A G CAGACCCACCACCACTCATATGCTGACCAATTTTAGAAACAGCCTTATTAGCAGCGTCGAGCTTCTCCTTTATCTTAGCAGCATCGTCTCCAGCCATGGC[A/G]TTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCACCTCAGCTGGAATCTTGTCCCTGTACTCGCCCAAACTCTTCTCTATGCTGT
108999 G A CGAGCTTCTCCTTTATCTTAGCAGCATCGTCTCCAGCCATGGCATTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCACCTCAGCTGGAATCTT[G/A]TCCCTGTACTCGCCCAAACTCTTCTCTATGCTGTATATAGCGGTGTCTGCGGAGTTCCTTACATCGATGAGGTTCTTCCTCTCTTGGTCCT
108999 A G TGGCATTTCTCAATTCCTTAACGGCATTCTCTATCTCAGTCGCCACCTCAGCTGGAATCTTGTCCCTGTACTCGCCCAAACTCTTCTCTATGCTGTATAT[A/G]GCGGTGTCTGCGGAGTTCCTTACATCGATGAGGTTCTTCCTCTCTTGGTCCTTCTGGGCATGCAGTTCGGCTTCCTTCACCATTTTCTCTA
108999 C G CCTTCTGGGCATGCAGTTCGGCTTCCTTCACCATTTTCTCTATTTCATCCTCCGACAAACCGCCCGATGATCTGATTGTGATCTGCTGCTCTTTTCCAGT[C/G]GCTTTGTCCTTCGCGGATACAGTGACGATGCCATTCGCGTCGATGTCGAAAGTGACTTCGATTTGAGGAAGGCCTCGTGGCGCAGGTGG
108999 A G GAGGAAGGCCTCGTGGCGCAGGTGGGATTCCAACCAGCTCGAATTCTCCGAGTAGTTTGTTATCAGATGCCATCTCACGTTCTCCTTGGAGCACTCGGAC[A/G]CCCACTTGGGTTTGGTTATCGGCAGCAGTTGAAAATACCTGGCTTTTCTTTGTAGGAATGGTCGTGTTTCTGTTGATTAGTCGAGTG
108999 G T CCTTGGAGCACTCGGACACCCACTTGGGTTTGGTTATCGGCAGCAGTTGAAAATACCTGGCTTTTCTTTGTAGGAATGGTCGTGTTTCTGTTGATTAGTC[G/T]AGTGAAGATGCCACCAAGAGTTTCGATGCCAAGAGACAAAGGAGTGACATCCAACAAAAGCAATTCTTTGACATCCCCACGCAGTAT
108999 A T CTTCCCGAAAATCTCTGCGACAACTTCTTGAACTTTCGGCACTCTAGTCATGCCACCAACTAGAAGAACTTCATCGATTTCTTTTGTTGTTACATTAGCA[A/T]CTTTTAAGCAACTTTTGCATGGATTTCTAGTCCGCTCGATCAAGTTATTCACCAAAGCTTCGAACTTTGATCTGGTTAAGGTGATGGTCAG
108999 A G TTTCTAGTCCGCTCGATCAAGTTATTCACCAAAGCTTCGAACTTTGATCTGGTTAAGGTGATGGTCAGATGCTTTGCTCCTGTAGAATCAGCAGTGATGA[A/G]TGGCAAGTTTATTTCAGTTTGTGATGTTGACGAAAGTTCAATTTTGGCTTTCTCTGCTGCTTCACGGAGCCTTTGTAAAGCCAATCTGT
108999 T G AAACACCATTGGAGATCTCCAAGATAGAAACATCAAAGGTACCACCACCAAGATCAAAAACGGCAATAAGTCCTTCCTTATTGTTCATCCCATAAGAAAG[T/G]GCAGCAGCAGTTGGTTCATTAATGATCCTTTGCACATCAAGACCAGCAATTCTTCCTGCATCTTTTGTAGCTTGCCTTTGAGCATCATT
109003 A G ATTTCAGTATTAATAACATCATTAAACCACTCGGTATATTTACCAAGACGTGTAGACCTGAGAACTTCCAAATCACAGGAAGGCAACAAGTTTGGGACAC[A/G]TAGAGGTCCAGGATTCAGACTCGTTCTGTTTGATACTGACGATCCAGCCATTGCAGTGTACACAAGCATGACATCCTCAACTGTAGCT
109003 T C TCCAGCCATTGCAGTGTACACAAGCATGACATCCTCAACTGTAGCTGCAAGTGGAGAGATGACTTCAACTGTTCCACAATCACATAACGACCCTTCCATG[T/C]CTACACGACCATATGTTGTTTTCAGGCCAACCACACCACAGAGTGAAGATGGAATGCGAATTGAACCTCCACCATCTGTTCCTAGCGC
109003 A G AGCATAATCCAGATGCTACAAGTGCTGCTGGACCTGATGATGATCCTCCTGTGTATGCATCAACTGAGTGTGGATTTCTTGTTGTCCCATGGTTAATATT[A/G]TTTCCAGTTGTCCCCATGCCCAACTCATGCATATTGGCTTTTCCAATAAATATCACACCACAACTTCGCAGTCTGGAAACACAGACAGC
109005 GA G ACTTATAAGTTGCTCAATGTCGCCGTTTACTAACCTCCACTACAATTCCACTCTCCGGAAATTTAGAATCCTTTCTTGTGTAGCTTCACCGAAATCTGAA[GA/G]AAAAACAAACTCCGATTTCACAAACAATGTCGAGCAAAAGCAAGGAAATTGCTAGTATGGAAGCCAAATATTTAGTTGGCACTTATGC
109005 A G ACAAGTAAAGAGCACTATCGGTTACCATTTTCTCCTGTAATGCCAGGTGTAACATTCATAGAATACGGTAATATCGATAAGGCCAGGGAAGCTATTATAC[A/G]TGACAAAACCGCTGCAGTTTTTGTTGAACCTATTCAAGGTGAAGGTGGGATATATACTGCAACAAAAGAATTTCTGCAGGCTTTGAG
109005 G A AAGGTGGGATATATACTGCAACAAAAGAATTTCTGCAGGCTTTGAGGAGTGCTTGTGATGAAACCGGAGCTCTGTTAGTGTTTGATGAGGTTCAGTGCGG[G/A]CTGGGCCGAAGCGGAAATCTGTGGGCCTATGAAGCATTTGGTGTGCTTCCTGACATAATGACCCTGGCCAAACCGCTTGCCGGCG
109005 CT C GCATCAGCCATAAAATATGGAGACCATGGCAGCACTTTTGCAGGCAATCCTTTCGTCTGCAAAATAGCACTAAAAGCATTCGATAAAATTCAAAATCCAG[CT/C]TTTTTTGGCAGATGTTCGTAAAAAAGGGGAATATCTGAGGAAGATTTTGCGTGCGAAACTGGAAGGTGAGAGCCATGTGGTAGAA
109005 A T TAAAATATGGAGACCATGGCAGCACTTTTGCAGGCAATCCTTTCGTCTGCAAAATAGCACTAAAAGCATTCGATAAAATTCAAAATCCAGCTTTTTTGGC[A/T]GATGTTCGTAAAAAAGGGGAATATCTGAGGAAGATTTTGCGTGCGAAACTGGAAGGTGAGAGCCATGTGGTAGAAGTAAGAGGAG
109005 G A AAGGTGAGAGCCATGTGGTAGAAGTAAGAGGAGTTGGACTTATTGTAGGAATCGAGCTTGATGTACCTGCTTCGCCTTTAGTTGATGCATGTAGAGAATC[G/A]GGACTTCTGATTCTGACTGCCGGGAAAGGTAACGTGGTTAGGATAGTTCCGCCTTTGATTATATCCGAAGAGGAATTGGAGTTTG
109011 A G CACCAAACATAAATGGAACTTGGACAATGATGGATGGTGACGAGCAAGTCGCGTATCCTTTACGGCCAATCGTTGAACATGCAAAACCAACCTTACGGCA[A/G]ATAATGGCGCATTTTTCAGCACTCGCGGAGGCATACATTGAAATGAGAAATTCAGAGCAGGCTTATATGCCAAGGTATGGATTGCA
109021 G GA CTGTGTTTACCCAACAAGATTCAGGGTATTATGGAGTCTTAGAACATACAGTAACATTTGAATACGTTTGGTTCAAACTTTGTATCACATGGTACCAATG[G/GA]CACAAAACGAGAAAACAAAAATTACATAAAATGACATTTCGACTAGTTAAAAATAAGTGGGAAAATAATAATAATAAAGGGATTCA
109021 TA T CAGTAACATTTGAATACGTTTGGTTCAAACTTTGTATCACATGGTACCAATGGCACAAAACGAGAAAACAAAAATTACATAAAATGACATTTCGACTAGT[TA/T]AAAAATAAGTGGGAAAATAATAATAATAAAGGGATTCAAGTGTACAGCTGTGAAGAATCATATATCCCGATATTACTCATATTCCTC
109021 CA C CTTTATCCAATGAACAATCATGGTTCCATTTTGAGGGAACTCCTCCAAAATTTTGTAATATGTAAGCATGTTGTCCCACTTACACCTAAACTCATCATCC[CA/C]AAAAAAAATCTCTTACTATCTCAGCAGTAGCATCCTCGAATACAGTTCTACTGCGATAAATTACTGCACCCGCTGGAGGATCAAGACGC
109021 CG C CTGGATCTTTCCTACGAAAATTGGAAAGAATCTTGCCACAAACAGAGAAAGCCGACAGCGCGGTAAATGCGAACCAGAGCCTCCTCGCACCCAACCCAGG[CG/C]GGGACGGTCCAGAGGAACCTGAAACGGCTCCTCAATCCAAGAAAACCAAACCTGTCCATCTCGGGCGCCACGACCACCCGATAA
109021 G GA ACAGAGAAAGCCGACAGCGCGGTAAATGCGAACCAGAGCCTCCTCGCACCCAACCCAGGCGGGACGGTCCAGAGGAACCTGAAACGGCTCCTCAATCCAA[G/GA]AAAACCAAACCTGTCCATCTCGGGCGCCACGACCACCCGATAACCAACCCGATCATCACCGCCAACCATATCGGAACAGTTACC
109023 AT A TTTGGAAACAACTTTTTAACTTGCTCCACAAGATCTTCATGTTTAACTCCACCAGCAGCAGATATAACCATTCTGGGTGCCGTGTAGTGAGTTTCAATAT[AT/A]TTTTTTTAGGTGTGCTTTCGTTATCGTTTTGATATTCTTGGCTGGTCCAAGAATGGTTCTTCCAAGAGGAGTATACTGAAAAGCCGTGG
109025 A G CGTATGTTTTGATGGCTTGCCTGGTTGCTGCCGTCGGTGGCGCTATTTTCGGTTATGACATTGGAATTTCCGGCGGAGTCACATCAATGGATCCATTCCT[A/G]GAAAAATTCTTCCCAGTCGTGTACAAAAAGAAGAACAGCCCATCTAAGAACCACTATTGCAAGTACGACAACCAAGGACTATCTGCC
109025 GA G TCTCTCACTGGGTCTAGCAGCAGTGCCAGCACTCTTCATGACTGTAGGAGGACTATTCCTTCCGGAAACTCCGAACTCCTTAATAGAACAAGGATTCAAA[GA/G]AAAAAGGAAGGCAAGTGCTAGAAAAAATACGAGGCACTAAAGAAGTCGATGCAGAGTTCGAGGACATGCTAGAAGCAAGCGAG
109025 GA G AGTGCCAGCACTCTTCATGACTGTAGGAGGACTATTCCTTCCGGAAACTCCGAACTCCTTAATAGAACAAGGATTCAAAGAAAAAGGAAGGCAAGTGCTA[GA/G]AAAAAATACGAGGCACTAAAGAAGTCGATGCAGAGTTCGAGGACATGCTAGAAGCAAGCGAGCTCGCAAACTCCATAGAACAT
109027 AG A TTCAATCTCATCTGTATCCGCCTCCACCTCCACCTCCATAAGGCTGTTGTGGGCCGTACCCACCCATCCCCGGGGCATACCCTGTCATTCCTGGGCCTCG[AG/A]GGGGGGCGCATTGGGCCTTGCTGATTCAGGCCCATACCCATGGAAGGTTGATTGTTCATGCCCATCCCCATCATACCCGCTCGACCG
109027 A G TGGTGTTGACAACGCTGAAGAGCTCTTCTCTTTTCTCTTGTCCATTCTGTTTATCGCTTCAAAATCGACTCCTACGTTCGCTATTAATGGGTTTACTTTC[A/G]CTCCAGATATATTGAGATCGACCAAGCCTCGGTTCAAAGTGTCAGCCCAAACAGTAGATTTGGTCTCAAACTTACCCTTCGTTGGTTGGG
109027 T C CATGAGGTACCTGTTGTGGAAGAGGACCAGACGATGCAGGTTGTGGTGGTACATAACTAACATTTGGTGCATTGTACATATTTCCTTGATATCCATGTTG[T/C]TGCTGCAGTGATGGTTGTCGAAACGCCTGTTGCTGTGGTTGTTGAAATGATTGCTGTTGGTGAGATGACAGTTGTGGTTGTTGAAAT
109027
TGGTTGGTGAAACGACTGTTGTGGTTGCTGAAATGATTGC
T GAAATGATTGCTGCTGTTGGAATGACTGTTGTGGTTGTTGAAATGACTGAGGTTGTTGAAATGACTGTTGGAATGGCTGTTGTGGTTGCTGAAACGATTG[T/TGGTTGGTGAAACGACTGTTGTGGTTGCTGAAATGATTGC]GGTTGGTGAAACGACTGTTGTGGTTGAGGCATGGAGTAATCACTGG
109029 G A CACCATCTTGTGTCTGCGAAATAACCTTTGCCGTATAAGTACCTGCCGACCCTACGTTAGTTAAAGTTCTCGTATGTGTGACTGAAACCGTAGACCCTTC[G/A]CCTCCTGATCCGCTTGCAGTCGCAAATGGTACTGCAAAAGAAGGGTAGTTGAGAGCAGACAATGCATAGGTCTTCTTGCTATCGCATG
109029 G T TTGGTGGATCCACGTGTCCTGCTCCATAATCAAACGGCGTAGCTGCTCCGTTTGTGGCCACATCTATCAGCCCGTTGCCATTCGAGTAACTAGAGTAGGC[G/T]GTTGTCATCAATGCAGATTTGATTCCAGCAGGGGACCATTCTGGATGCACCGCTTTCAGAAGTGCAGCCAAACCGCTCACATGTGGG
109029 C T TCATCAATGCAGATTTGATTCCAGCAGGGGACCATTCTGGATGCACCGCTTTCAGAAGTGCAGCCAAACCGCTCACATGTGGGCATGACATTGAAGTTCC[C/T]GAAATTATGTTAAACTCCACTCTTCTGCTGTCAACTGCTAACCCGGTCGGACCCACCGCTCTGGTCCAACCAGCCAAAATGTTGACTC
109029 T C GCCAAACCGCTCACATGTGGGCATGACATTGAAGTTCCCGAAATTATGTTAAACTCCACTCTTCTGCTGTCAACTGCTAACCCGGTCGGACCCACCGCTC[T/C]GGTCCAACCAGCCAAAATGTTGACTCCTGGTGCTATCATATCAGGCTTCAGTATCTCTGGAGTAACCGCATTCGGCCCACGCGACGAA
109029 C A TCGGACCCACCGCTCTGGTCCAACCAGCCAAAATGTTGACTCCTGGTGCTATCATATCAGGCTTCAGTATCTCTGGAGTAACCGCATTCGGCCCACGCGA[C/A]GAAAATGCTGCAACCACCGGCGATGGCTGGATGTTCACCTTCGTCCCTCCAAAACTGATCGTAGCTGTTGGTTTGGTGGTGCTCAAT
109029 A T CACGCGACGAAAATGCTGCAACCACCGGCGATGGCTGGATGTTCACCTTCGTCCCTCCAAAACTGATCGTAGCTGTTGGTTTGGTGGTGCTCAATATATA[A/T]GATTTTATCATTTTTCCTGCAGACTCACCTACCAAAGTAGCAGGCAGAAGATGTGCATCTGCCACAAGTTCTTCCCCATTTGCAGCCG
109029 A T GCAGAAGATGTGCATCTGCCACAAGTTCTTCCCCATTTGCAGCCGTGTTCGCCAACACCATCCCTGCTCCACCTGCGTCTTTCACCACCAACCCCTTCTG[A/T]ACCCTGGCGCTCACCCCACGGTCGCAGAACACAATTTTTCCTGCGACTTTCTCCGGTATCAAAGTCCCAGCCATGCACAGATTACCATTA
109029 C T CAATTTTTCCTGCGACTTTCTCCGGTATCAAAGTCCCAGCCATGCACAGATTACCATTAGTCGCATTTGTCGCATTCCCAGCATACACGATCTCCAACTG[C/T]GAACTCGGCAGCTTCGCGTCCCCACTGTACAGCGAAACCCCTGAAAACTTCTTCCCATTACCCAACTCCACATCTGCAGGAAAGTCCCGG
109033 C T AGGAAATGAAAGCCAAAGAAGCTCAAAGTAGAGCAGTTGCTGAACATGGCGAACTGGCACTTATTACTGTTGATACCCCACAGGTTTCAACAACTGAGCG[C/T]ATATCATTAAGGCCTCCGATGTTGCAGGTAGTTAGGTTAGCCTCCTTTCAGCACACACCAACAATTCCCCCATTCATAGCTCTACCG
109033 A G TAGGTTAGCCTCCTTTCAGCACACACCAACAATTCCCCCATTCATAGCTCTACCGAAGCAATCCAAGATTGATGGAGATGATGCAGCTGGAAACAAGGAG[A/G]CACATGAAAGAAAAGTAAGCGAAGTCGCTGTTGCAGGTGGAGGGGTTTCTGTTGCACTCACTCGGTTCCCTCTTGAGCAGAAACGT
109033 T C ACGGAGTACTCTGGCTCATCGATAGGTATATGTGCGCACATGCTTTGGCTCTTAGCCACCCAGGCATTCGTTGCCGCTGTTTAGCTGCTTATGGAGATGC[T/C]GTCAGTGCTGTGAAATGGGCAAGCAGACTTGGTCGTGAGCACCATGATGACTTGGCTCAGTTCATGCTAGGGATGGGCTATGCGAC
109033 G A CTGGACATGGGCGTGAAGCGGCATTTGCAGCTGCAATTTTAGGTGATAATGCACTAATGGAAAAGGCGTGGCAAGATACCGGTATGCTTGCTGAAGCCGT[G/A]CTTCATGCGCATGCTCATGGTCGTCCAACATTGAGGAACCTAGCTCAAGCGTGGAACAAGATGCTACAAAAGGAGCTTGAACCAA
109033 G C AGGGAAGAAACCACCCATAGAGATTCTGCCTCCTGGCATGCCATCGCTTACAGCTCCTCCCATTGTGATCAAGAAATCAAATGCTGGTGCTACCCCTGCC[G/C]CAACTCTAACTCCACCTGAAAAGCCATTGATGCTTGAAGCAGCTGTACCTGCTACTGACCAAACCAGCTCAGCAGCTGACAAGGCAA
109033 C A CTCCACCTGAAAAGCCATTGATGCTTGAAGCAGCTGTACCTGCTACTGACCAAACCAGCTCAGCAGCTGACAAGGCAACATCGAGTCCTAACTCTGACGC[C/A]ACGGATAGTCAGAACCCTGATCAGGGAAATGGCACAAACACTGAGGGGGCTGATGGTGCAAAAGCTGAAGTGGCCGATGGTGCA
109033 C T CTGCTACTGACCAAACCAGCTCAGCAGCTGACAAGGCAACATCGAGTCCTAACTCTGACGCCACGGATAGTCAGAACCCTGATCAGGGAAATGGCACAAA[C/T]ACTGAGGGGGCTGATGGTGCAAAAGCTGAAGTGGCCGATGGTGCAAAAGCTGAGGCGGCAGTCAGTCAGGATACTGAGGTGGA
 Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
109033 TGATGGTGCAAAAGCTGAAGTGGCC
T AAACCAGCTCAGCAGCTGACAAGGCAACATCGAGTCCTAACTCTGACGCCACGGATAGTCAGAACCCTGATCAGGGAAATGGCACAAACACTGAGGGGGC[T/TGATGGTGCAAAAGCTGAAGTGGCC]GATGGTGCAAAAGCTGAAGTGGCCGATGGTGCAAAAGCTGAGGCGGCAGTCAGTCAGG
CGATGGTGCAAAAGCTGAAGTGGCCGATGGTGCAAAAGCTGAAGTGGCT
109033 C CAACATCGAGTCCTAACTCTGACGCCACGGATAGTCAGAACCCTGATCAGGGAAATGGCACAAACACTGAGGGGGCTGATGGTGCAAAAGCTGAAGTGGC[C/CGATGGTGCAAAAGCTGAAGTGGCCGATGGTGCAAAAGCTGAAGTGGCT]GATGGTGCAAAAGCTGAGGCGGCAGTCAGTCAGG
109033 T C TGGAGGGTGCTCCAAACGCTGGGGTTGAGGGTGCAACAAATGCGGAGCCACCAAGCAGTACAACTGCTGGGGATGATGCTGATGTTCTTCGTAGTACAAC[T/C]GATACGGCTAATGAGCCTAGAGAGGCTGTTTGAGCATCACTTTACATATCCTGATTTTCATTTTCAGTTTTGGTTATATTGATTGAC
109035 G A AGAATAAGAATGTTAATGCCATAGAATCATGCTTATCTTATTCCAGCCAATCTTGGCTTCTCTATGCCTGCAACCAGACAACATAAAATTACGTCTTCTA[G/A]GCAGAAACTGTTGTCATGGCAGGTTGCAGGCATGCCCAAGCCCCTTAACGGGGCCGGGCTACTCCAAAACTTGATTCAGACTGCTGCT
109035 T A TTCCAAAATGCGGTGGAACAGGGTGATACTGAGAAGAATTATGCATATAGACTGATGTAGGGCGACCTCTAATAAAACCAGGGCTATAAGGAGGCATGCT[T/A]TCAGGATGACCATATCTTATTGGAGAATGTGGTGATGCAACTGACCAAGGACCATGCATGTGTTGTGGCATGGGTCGAGGTTGG
109035 G GT TACTCTTCTTTCCTTTCTTCAACGCTTTTCAAGCCGCTGGATTTTGAAGAAGATTTTCCATCTGAACTACTACCGGTTTGTGAATTCCTTTGTGACCTTG[G/GT]TTTATAGCTACCTTGACAGCGGTGGTCGTTCGCTCCTGAGGCAAACTCACAGGAATGTCCACAAGTCGAATTGTTGGGAGTTTGTTAGA
109035 T A TTCCTTTCTTCAACGCTTTTCAAGCCGCTGGATTTTGAAGAAGATTTTCCATCTGAACTACTACCGGTTTGTGAATTCCTTTGTGACCTTGGTTTATAGC[T/A]ACCTTGACAGCGGTGGTCGTTCGCTCCTGAGGCAAACTCACAGGAATGTCCACAAGTCGAATTGTTGGGAGTTTGTTAGAATAGGATGT
109035 C T AGCCGCTGGATTTTGAAGAAGATTTTCCATCTGAACTACTACCGGTTTGTGAATTCCTTTGTGACCTTGGTTTATAGCTACCTTGACAGCGGTGGTCGTT[C/T]GCTCCTGAGGCAAACTCACAGGAATGTCCACAAGTCGAATTGTTGGGAGTTTGTTAGAATAGGATGTTTTGCTAAGAACAATTAAAGA
109035 G A AGAACAATTAAAGAGCCGGTCCCATCAGGAAGAATATTTTCAGGCATTGCAATCGACTGCAGAAAATAATGTTGAGCCAGACGATGTGCTGCTAACCTCA[G/A]GTATGATGTTGGCAGATCTTTAAATTCCAGTTGTTGGCGGTTTGGATCGCGGATGAATTTTAAAATGTCTTGCTCCATTCGCAGAAT
109035 C A AGGTATGATGTTGGCAGATCTTTAAATTCCAGTTGTTGGCGGTTTGGATCGCGGATGAATTTTAAAATGTCTTGCTCCATTCGCAGAATCGAAATTCTTT[C/A]CCTAGGTTTTTCCAGCGCCTCTCTAAGAAACTGATCCACCTGCTTGAACTCATCCTCTACAGCAGCATTTTCCGCTGTAGAAGCAGATG
109035 T G GGTTTTTCCAGCGCCTCTCTAAGAAACTGATCCACCTGCTTGAACTCATCCTCTACAGCAGCATTTTCCGCTGTAGAAGCAGATGTGGAAGACGGAGGTT[T/G]TACATCGGTTGGTTTCTCGGGCGATATTAACAATCGCTTCATGCTCTCGTCCAGATCTGCGGACTCCCATGAATCAGGAGCTGGGAC
109035 T C ATCCTCTACAGCAGCATTTTCCGCTGTAGAAGCAGATGTGGAAGACGGAGGTTTTACATCGGTTGGTTTCTCGGGCGATATTAACAATCGCTTCATGCTC[T/C]CGTCCAGATCTGCGGACTCCCATGAATCAGGAGCTGGGACATCAGCCATGGGATCTAGATGGCGAACGAGGCAAGTTAGGGTTTGA
109035 A AG GCTCTCGTCCAGATCTGCGGACTCCCATGAATCAGGAGCTGGGACATCAGCCATGGGATCTAGATGGCGAACGAGGCAAGTTAGGGTTTGAAGTACGGGA[A/AG]GGGGAAAGCATTGAAATAGCGAACGAGAATCCAAGACGATTAGGGTTTGGAATAATTTTGGGGGAAGAAGTGTGATTTTATC
109037 A G CATGGAAAGAAAAATTAAGGGAGAAAGCACCACACCCGCATCGTTTTGGAAGGTCTCAAATAGCAGAATACTCGAACGGCTGTGGTGGCTGCGGGTCTTC[A/G]TCAACGGCCATGGCTGTAGAGGCCGACGTTGTTGCTGCTGCAGGTTGGGCGGTGGAAGGCGATGTCATTGATGATGGAGCGTC
109037 G A TCATTGATGATGGAGCGTCGGTTAGTGCAAGAACCTCGGCTTCTTCAGGCTTTAAATCTTTGAGAAGGACAAAACCAGAAGGCGAAAGTTTAACCGGAAC[G/A]TATCGGCTATCTTCTAGAAAACGTATGTACTTCTCTTGTGCAGGGACAACTCTGGCTGGGTTTGTTAGGATTTCAAATGATGGCTCT
109037 T C GATGGAGCGTCGGTTAGTGCAAGAACCTCGGCTTCTTCAGGCTTTAAATCTTTGAGAAGGACAAAACCAGAAGGCGAAAGTTTAACCGGAACGTATCGGC[T/C]ATCTTCTAGAAAACGTATGTACTTCTCTTGTGCAGGGACAACTCTGGCTGGGTTTGTTAGGATTTCAAATGATGGCTCTGGCTCAG
109037 T C CAGTTGTCGATAAAACAGCAGTAGGTAATCTCACTGCTGATGTAGCAGTGGCTGTTGTAGTCGCTTTAGGGTACTCAAACAACGAAGGTTTGGCAGTTGA[T/C]AAGAACTCAAATTTTGGCATTTTAAGATCATAGTTGAGCCCAACAAAAGCGGTGGGAGAGAATGCAAGGCTTATGAAATACGTGAG
109037 A G CGTTAGTCTGGATCATAACCATTGCCATAGCTATGAGAGCTCCTTGACGAACAAAATCAACAACGTCTGATGTCAGAGGCTCCAACAAAGAAATTGCTTC[A/G]CTTAAACCAGTACCGGCACATGAAATTCCTACTGCTAATGCTGCACCGTATCTGACATGTGGGTTGTAAGATTCTGACAGAAGGGAA
109037 A G CGGCACATGAAATTCCTACTGCTAATGCTGCACCGTATCTGACATGTGGGTTGTAAGATTCTGACAGAAGGGAAACAATTCTAGGAGTCTGCTCAGGTTC[A/G]TTATAGAGAACGAACCCAAGTGCAAGGACAGCGGTCCTTCGCACATCATCGCTGACATCCGACACAGCAAAATGTAACAACTGGTG
109037 A G AATTCCTACTGCTAATGCTGCACCGTATCTGACATGTGGGTTGTAAGATTCTGACAGAAGGGAAACAATTCTAGGAGTCTGCTCAGGTTCATTATAGAGA[A/G]CGAACCCAAGTGCAAGGACAGCGGTCCTTCGCACATCATCGCTGACATCCGACACAGCAAAATGTAACAACTGGTGGATGGCCTTG
109039 C T GCAGAATTATGGTGCTTTTCTTGAGAAAGATGGAGCTGGATTCAGAGGGCAAGTTAAGTTGATTGGTGTGAAAGCTGGAGAAATAGACTTGTCCACTTCA[C/T]TTTGGACATACCAGGTAGGTTTAAAAGGGGAGCTTAAAAAACTTTATGCTATAGAAGAGCAAGAAAATGCAGAGTGGGCTGATAT
109039 T C GGCAAGCATGGGTAAATGGACATGGAATTGGACGATTTTGGTCTCTTGTTGCACCAAAAGATGGATGTCCTGAAACTTGTGATTATCGTGGTACTTATAA[T/C]GAGAACAAATGTGCAACAAACTGTGGGGTACCTACCCAAACCAGGTACCATATTCCCAGAGAATGGTTACAACCCTCAAACAACCTT
109039 T A GGACGATTTTGGTCTCTTGTTGCACCAAAAGATGGATGTCCTGAAACTTGTGATTATCGTGGTACTTATAATGAGAACAAATGTGCAACAAACTGTGGGG[T/A]ACCTACCCAAACCAGGTACCATATTCCCAGAGAATGGTTACAACCCTCAAACAACCTTCTTGTGCTGTTTGATGAAGAAGGGGGAAA
109039 G A CTTGTTGCACCAAAAGATGGATGTCCTGAAACTTGTGATTATCGTGGTACTTATAATGAGAACAAATGTGCAACAAACTGTGGGGTACCTACCCAAACCA[G/A]GTACCATATTCCCAGAGAATGGTTACAACCCTCAAACAACCTTCTTGTGCTGTTTGATGAAGAAGGGGGAAACCCTTCACAGATTTC
109039 T C AGTGTCTGAAACCCACTACCCGCCTCTGTCTGCTTGGTCCCTTGCCAATTTAGCCAATGGAAGCATATCAGTTGATAACAGTGCACCTGAACTACATTTG[T/C]GTTGTGATGATCACCAGAAGATATCTTCTGTAACTTTTGCAAGCTATGGAAACCCTAGTGGCAGCTGCCAACAGTTCTCTGTTGGGAA
109039 T C CTGAAACCCACTACCCGCCTCTGTCTGCTTGGTCCCTTGCCAATTTAGCCAATGGAAGCATATCAGTTGATAACAGTGCACCTGAACTACATTTGTGTTG[T/C]GATGATCACCAGAAGATATCTTCTGTAACTTTTGCAAGCTATGGAAACCCTAGTGGCAGCTGCCAACAGTTCTCTGTTGGGAAATGCG
109039 A C CTCTGTCTGCTTGGTCCCTTGCCAATTTAGCCAATGGAAGCATATCAGTTGATAACAGTGCACCTGAACTACATTTGTGTTGTGATGATCACCAGAAGAT[A/C]TCTTCTGTAACTTTTGCAAGCTATGGAAACCCTAGTGGCAGCTGCCAACAGTTCTCTGTTGGGAAATGCGATGCACAAGATTCACTGT
109039 CA C GCCAACAGTTCTCTGTTGGGAAATGCGATGCACAAGATTCACTGTCTGTAGTGTCAGAGGCATGCCAAGGGAGAAATAGTTGCACCATCAGCGTTTCAAA[CA/C]AAGAAGTTTGGGCAAGATCCATGTCACGGAACTGTGAAGACATTAGCCGTTCAAGCTGAATGCATCGACATGGATGTCAATTACG
109041 A G AAAAACATGTTCCCTCCATTAATGCAACAGGAGTCAAGTTTATTCTGTTTGTAACGTCACCCACTGCCCATATGCTGGGGACATTCGTTCTGGAGTACTC[A/G]TCAACCTTAACTGCACCAGTACGGTCAAGTTCAACACCAGCACCTTCTAAATTCAGCCTTTTTGTGTTTGGAATCCTTCCTGTGGCAAAT
109041 C T CTGTTTGTAACGTCACCCACTGCCCATATGCTGGGGACATTCGTTCTGGAGTACTCATCAACCTTAACTGCACCAGTACGGTCAAGTTCAACACCAGCAC[C/T]TTCTAAATTCAGCCTTTTTGTGTTTGGAATCCTTCCTGTGGCAAATAAAACCACATCAGCCATAAGTTCTTCCCCATTATCAGAAATAAC
109045 C G GATCTACCTCGCCATCACCCACAAGATCAAGAAGCCCGCACTTTGGCAAATGTGCCTCTACATCTGCGTCGGCGCCAACTCCCAGTCGTTCGCCAACACC[C/G]GCGCCCTCGTCACCTCCGTGAAGAACTTCCCGGAACACCGCGGCATGGTGCTCGGCCTCATCAAGGGCTTCGTCGGCCTCAGCGGC
109045 T C ATCAAGGGCTTCGTCGGCCTCAGCGGCGCCATCTACACCCAACTCTACCACGCCTTCTACGGCGACGACGCCAAGTCCCTCGTCCTTCTCGTAGCTTGGC[T/C]ACCTGCCGTCGTCTCCATCGTCTTCATTGGCACCATCAGAATCATCGAAGTTGTCAAGACGGACACCAAGGAACGTACAAAACCCTAC
109045 G A GTGCCATCGTAGTTGTTTTTCTTCTCTTTTTACCGCTTTTAGTAGTTATCAAAGAGGAAATCGGTTTAGCAAAAAAGGAACCTATGGTTGTCGCTTCTTC[G/A]AAAGAAGTGGTGTCCCTACCGACGATGAAGCGGTAAAGCAATTGGAGAGTGGATCTACGGCCACGGATGGTTCTAAAGTGAAAAGAA
109045 G GT AGTTGTTTTTCTTCTCTTTTTACCGCTTTTAGTAGTTATCAAAGAGGAAATCGGTTTAGCAAAAAAGGAACCTATGGTTGTCGCTTCTTCGAAAGAAGTG[G/GT]TGTCCCTACCGACGATGAAGCGGTAAAGCAATTGGAGAGTGGATCTACGGCCACGGATGGTTCTAAAGTGAAAAGAATGTTTAAAG
109045 T TC GTTGTTTTTCTTCTCTTTTTACCGCTTTTAGTAGTTATCAAAGAGGAAATCGGTTTAGCAAAAAAGGAACCTATGGTTGTCGCTTCTTCGAAAGAAGTGG[T/TC]GTCCCTACCGACGATGAAGCGGTAAAGCAATTGGAGAGTGGATCTACGGCCACGGATGGTTCTAAAGTGAAAAGAATGTTTAAAGC
109049 A G GCTGTTAAGTTGTTCTAGTGTGAAAATACCACCAGTGAAGCTGCTTTCTAATTCACTGCCTGTTCAGTTACATAGAAGAGATCATAGAGATTTCAATTAC[A/G]CAAAGCCTTCATCAAACACAGCTACCAAAATGGAGACTTCAGCTACAGAGTATCCTTCTTTGAGGAAAGTACAATCCATCAATATCGCT
109049 G A ACAAAGCCTTCATCAAACACAGCTACCAAAATGGAGACTTCAGCTACAGAGTATCCTTCTTTGAGGAAAGTACAATCCATCAATATCGCTCCTGGCACCA[G/A]TGCTACTAGTGCACAGGTGAAACCCAGAAATAGCAATGTGACAAACAATGAAGTGAAAACAATGAGAGAGCCGATACAGCTAATGC
109049 A G TGCACAGGTGAAACCCAGAAATAGCAATGTGACAAACAATGAAGTGAAAACAATGAGAGAGCCGATACAGCTAATGCAGCGACCACAATCCAGTAATGGC[A/G]TTAGACAGAATGCACCGCCTACATCATCTTCAAATTGGTACCCTAGAACCTCTTCCCCTTCTGCCATTGACATGATGAAGTTAGCC
109049 G A CACCGCCTACATCATCTTCAAATTGGTACCCTAGAACCTCTTCCCCTTCTGCCATTGACATGATGAAGTTAGCCAATGGTGGTCTAGGGCAACAGATGCA[G/A]AACCCAAGGTCAAATATGAAAACCCAACAGTTATATAATAATACCGGTAGAGCTGGATACTACAGTGATGCTATTAGATCTTCGCTTG
109049 G A TGCCTTCTTCATTAGGTTTGTTTAAGAAAACAATGCCATCATCTACAGTCGATTGGGGAAGCAGCAGCAGGAAGAATAATATGTTGTACTGCGACTACAC[G/A]AGCGTTGATTGGAGTTTGGACTCTACGCCATTAGGGCTACCGGCTTCGAGCTTGAAGGGCGAACGTTTATACGATAGTGCGGTGTA
109049 T C CATTAGGTTTGTTTAAGAAAACAATGCCATCATCTACAGTCGATTGGGGAAGCAGCAGCAGGAAGAATAATATGTTGTACTGCGACTACACGAGCGTTGA[T/C]TGGAGTTTGGACTCTACGCCATTAGGGCTACCGGCTTCGAGCTTGAAGGGCGAACGTTTATACGATAGTGCGGTGTACGTCTCGTA
109049 G T GTTGTACTGCGACTACACGAGCGTTGATTGGAGTTTGGACTCTACGCCATTAGGGCTACCGGCTTCGAGCTTGAAGGGCGAACGTTTATACGATAGTGCG[G/T]TGTACGTCTCGTATTTGAAAAATTCGAGATACGGAGAGAATGGAGGGTTGATGGCTGAGAATG
109051 A T TTTTTTTTTTAAAAAACTGCAATTGGCTTACATACATTGAAACTTGAAAGCATGTCAACATACATA[A/T]TCATAGTACAAGGACCGAACAAATTATTGATCCTAATAAATATCAGAACATGTAAAAGAATGTTTATTTCCAGAAGCATTAGCTATGGTAAGAGAATCAC
109051 A T TTGGTACATGAAGAACATTTCCCCATGAACCCATTGTAAGCGGAGAAGAGACGATCTTCTTAGATAGAGTTGCGATATCCTTTAGTGTTACTTCACTGGC[A/T]AGTTTAAGGAAATGCTCGATTGGTTTCCTCTGCCCATACGTCAATATTTGGCGCCCAATGTCTTCAGACACAACCATCCGTGATTCTAG
109051 TC T TGAAGGCAGAGAAAGACTGGATCTGTTGATACTCATTCAACACATTTTGATATAATCTGGAAAACATCCCTTTCCCTGGGCCTCCAGCAGAAAAGGAACC[TC/T]CCCCCACCCATGAGCATCTGAAGTACAGTAAGAATCATTGAATCTTTTTCGTTGTGCCAGCCACCAGGAACTTCAAAAGCAAGAGCA
109051 A G GGAGGTCAGAAAGAAGTGGTTCAGCAAGTGACACCAATTCCTCATGGTCTACACCATATGCTGCAAGTACCATTCTAGGGGCAGTGTAGTTTTCAGCAAC[A/G]AATTCCTCCAAGGTACTACTGTTCAACTTATTAACTGCAGACTCAGGAGCAATGAGGGGATTTGCCAATGCGCCAGAGTACCCAGC
109051 C T CAGTGTAGTTTTCAGCAACAAATTCCTCCAAGGTACTACTGTTCAACTTATTAACTGCAGACTCAGGAGCAATGAGGGGATTTGCCAATGCGCCAGAGTA[C/T]CCAGCTGAATGAAGTGCCTCCAATAGCAAACTTTGTGGATTTTTAGAAGCATCCTTTAGCTCGTCGTTTATTTTTTGCAGCTGCTCTTT
109051 T C CTTCAACCATTTCAGGCATGTGAGTTTTAAGAGCATCATAAGTGTAGCTCATTTGCTCACGAGAAGCAGAAGCGCTGGCATTGCCTCCAATAGCTTCGAT[T/C]TCACGAATTATGCGCAAATGACTTCTGTTGGTTGTGCTTTTGAATGCCATCTTCTCCAAGAGATGTGTGGTACCAAATGAAGAAGGTG
109051 C T TGGTTGTGCTTTTGAATGCCATCTTCTCCAAGAGATGTGTGGTACCAAATGAAGAAGGTGTTTCATACACAGAACCACTGTCTAAATAGAGACCAATCGA[C/T]GCAGCTGGGTATGGTGATGGTTCTGAAGCAATTTTCACTCCATTTGGAAGTGTGGTAACTTTAGTTTTGCTTGGCTCAACGGAATCCG
109051 G A TAAGCCAGCTTAACAAACCTCCGGATGACTGTTTAGCTACAGCGGTACTTGCTAATCTTGTGGCAGCGCCAACAACTCCTGTCTCACCAGCATTTCTCTT[G/A]AGAGATCTGAGATTAGAACCGGCGACCCTATACATGACTTGAGCAGATATATCAACCCTAGATCCGCTTTTTCTTTTTTCTCAGAAGAA
109051 C T ACAGCGGTACTTGCTAATCTTGTGGCAGCGCCAACAACTCCTGTCTCACCAGCATTTCTCTTGAGAGATCTGAGATTAGAACCGGCGACCCTATACATGA[C/T]TTGAGCAGATATATCAACCCTAGATCCGCTTTTTCTTTTTTCTCAGAAGAAATTGAGAATGGAAAT
109053 A G AGACTATAATACCATCTAGTTTTCTTTCACGCACCACCCTTAACCCCTCCATCCGCATCAAAGCCTCAAGCTTATGCCTATCAGTCCACTTATTAGGCAT[A/G]TCCTTCTCAAATCCCAAGTGCACAATGTTCTTCAAACCCGATTTTTCAATTAAATTTCTAGTCTCATTCGTGACCCCACCAGCTTCAACGAC
109053 G A TATGCCTATCAGTCCACTTATTAGGCATATCCTTCTCAAATCCCAAGTGCACAATGTTCTTCAAACCCGATTTTTCAATTAAATTTCTAGTCTCATTCGT[G/A]ACCCCACCAGCTTCAACGACAATCCAAGTCAACTCGCTTTTCACCAACATCAATCCATGCATCAACCCAGTCAAATGCATTGCCTGAAAAG
109053 G A ACCACGTGGCTGTGACGACCAACTGTATTGGTCAGATTGGTCGGGTTTTGCAGAGAGAAAACGTCCCCGTTGTCCCCAGTGCTGCTGGCAAGAAGGGCCG[G/A]CTGGTGATTAGACGAGGGAGAGAAGAGGAGGAAGAAGAGAAGGCGGGAGAAGCGGAAGCCGAGCAGGAGGCTGAAGAGGC
109055 A AC TTACTGGAAGGTTGCTGACTGCTTCCAGTTTTCGCCTTTTAGATTGATTGTTAATTGAATCGAATGTTTCATGACTTGTAGATGCGTATGATCCGACATC[A/AC]TGGAAGGTGCATTTGGTCCAATTTGCAATGGCGGGCAGTTTGAAGGTCCAGTCTGAAAAGCCTGAGATGTCATAGGGGGCGGCGGC
109055 AGGTGACTATTTTGAATAGGTGGCG
A TTGCAATGGCGGGCAGTTTGAAGGTCCAGTCTGAAAAGCCTGAGATGTCATAGGGGGCGGCGGCAAATAAGACTGCTGGTGACTATTTTGTATAGATGGC[A/AGGTGACTATTTTGAATAGGTGGCG]GGTGACTATTTTGAATAGGTGGCGGAGAATAAATACCAGCACTTGTAGCCACAGGAGGCC
109055 G A GGCAGGTGACTATTTTGAATAGGTGGCGGAGAATAAATACCAGCACTTGTAGCCACAGGAGGCCCGAATGCCTGATTATTAGGAGGAGGCACTTGTAAAG[G/A]CGGAATTTGTGAAGGAAGGCTGCCATGTGCTGGTGGCATTATCGCGATTCCAGGTCTATTTGGAGGCTGAAAAAGAGACTGAAC
109055 T G AGGAATAGAACTAGATGATGGCCTAGTATTTGCTGTTTGCATCATGTGTGGTGGAACCATACCAAGCATTATTTGTGCCTGAAATATAGCTTTCAGTAGC[T/G]GTGGACACTCTTGCAGCAGCTGCTGAGCAAGTGGCTTGTTTCGTACCACCAAAGTCTTTAATTCAGCCATTATTTCGTTTATCTGTTGT
109059 G A TGCCATTGGATGTGGTTTCCACATGCTGCTCAATGCTGGCTTGCACGATATTAATATTCTGGCACACTGCGTTGCGAGCTGCATTGACGCAATCATTGAT[G/A]CGTTCTCGCGTCTGATCAACGTAAGTAGTTGTTACAATGGTCATGTGCGCTCCAAGAGAATGACTTCACCACATCTGGTATGTGTTCT
109059 CT C TAAGGAAATGAATAACCAGGGTGAGTGTGATTGCCGCAAAGAATGGTAGGACTGAGAAGACGTGGGAGGATCCAGTTTGGGGTCCGTTGTAGAGGATTCT[CT/C]TTTGTTACCGTCGCAGTACCGCCCTCCGTGTGGCAAATGATGTGTGTTATCCCCTACGTGTGTGAGGTGGTTAGACCTAAGAGT
109063 G T AGTTGGTTAACCTTGTGGTGGTGGCGGGAGATCATGGAAAGGAAGCGAAAGATCTTGAAGAAATAGAGGAGAAAAAGAAGATGTATAAGCTTATTGAAGA[G/T]TATAAACTGGAGGGCCATATCCGTTGGATCTCTGCTCAGATGAACCGTGTTCGTAATGGCGAACTTTATCGCTGCATTGCCGACA
109063 T C ACACGAAGGGTGCTTTTGTTCAGCCTGCACTATACGAAGCGTTTGGGCTTACAGTTGTAGAAGCTATGACTTGTGGGCTTCCAATGTTTGCAACTGTATA[T/C]GGAGGCCCAGCTGAGATTATAGTTAACGGGGTTTCTGGATATCATATTGATCCTTACCAAGGCGACAAAGCTTCTGAACTCCTTGTG
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
109063 G A TATACGAAGCGTTTGGGCTTACAGTTGTAGAAGCTATGACTTGTGGGCTTCCAATGTTTGCAACTGTATATGGAGGCCCAGCTGAGATTATAGTTAACGG[G/A]GTTTCTGGATATCATATTGATCCTTACCAAGGCGACAAAGCTTCTGAACTCCTTGTGAACTTCTTTGAAAAATGCAACAAAGATCCTA
109063 T A GCTTCTGAACTCCTTGTGAACTTCTTTGAAAAATGCAACAAAGATCCTACTCACTGGGACAAAATTTCTCAAGCCGGGTTAAGAAGGATCGAGGAGAAGT[T/A]CACATGGAAGAAGTATTCTGAGAGGCTAATGACACTTTCTGGTGTCTACGGATTCTGGAAGTTTGTTTCGAACTTGGATCGTCGTGA
109063 A G GCAACAAAGATCCTACTCACTGGGACAAAATTTCTCAAGCCGGGTTAAGAAGGATCGAGGAGAAGTTCACATGGAAGAAGTATTCTGAGAGGCTAATGAC[A/G]CTTTCTGGTGTCTACGGATTCTGGAAGTTTGTTTCGAACTTGGATCGTCGTGAAACCAAGCGTTACCTAGAGATGTTTTATGCACT
109063 G GT CTGTTACCAGTGCGGTTAATGGCACTAACTAATGGGTATTGAGATGATGAGTGAATGAGAAGAATAAATGAGATTGTGGTGAAGGAACTTTTGTTCAAGT[G/GT]TTTCAGTTTTCATTGGTAATATGAAAGGGGAAGTGAGTTTTCTTTGTTGCTGTTTGTGTAACGTTGTAATGCATCATAAGGCTCAT
109063 AG A AACTAATGGGTATTGAGATGATGAGTGAATGAGAAGAATAAATGAGATTGTGGTGAAGGAACTTTTGTTCAAGTGTTTCAGTTTTCATTGGTAATATGAA[AG/A]GGGGAAGTGAGTTTTCTTTGTTGCTGTTTGTGTAACGTTGTAATGCATCATAAGGCTCATATGCCAAATTGTACTGTAAAAGACAT
109063 CT C GATGATGAGTGAATGAGAAGAATAAATGAGATTGTGGTGAAGGAACTTTTGTTCAAGTGTTTCAGTTTTCATTGGTAATATGAAAGGGGAAGTGAGTTTT[CT/C]TTTGTTGCTGTTTGTGTAACGTTGTAATGCATCATAAGGCTCATATGCCAAATTGTACTGTAAAAGACATTGCTTGTTGGTTATCAT
109067 A G TTTCCACCTGACAAGTATTTGGATGTAGTCACTAAATAATATATGACAAAGTTGCTTACCGACACAAAACTGCTGTCGGGCTTAATTCTAAGTACAATCA[A/G]ACCCAATAACATCTCTTAAATTCAAAATACAGACAAACAACACTTGGGCTAGTAACCAAAAAGAAAAAGAGTAAAACAGTGGACTGAA
109067 CA C ACCGACACAAAACTGCTGTCGGGCTTAATTCTAAGTACAATCAAACCCAATAACATCTCTTAAATTCAAAATACAGACAAACAACACTTGGGCTAGTAAC[CA/C]AAAAAGAAAAAGAGTAAAACAGTGGACTGAATATCAAAAGCAGTTGTGCAATATGCCAGGATGATGAAACGCAAGCAGATAACCA
109067 AAG A ACACAAAACTGCTGTCGGGCTTAATTCTAAGTACAATCAAACCCAATAACATCTCTTAAATTCAAAATACAGACAAACAACACTTGGGCTAGTAACCAAA[AAG/A]AGAAAAAGAGTAAAACAGTGGACTGAATATCAAAAGCAGTTGTGCAATATGCCAGGATGATGAAACGCAAGCAGATAACCAGGA
109067 GA G TTGGGCTAGTAACCAAAAAGAAAAAGAGTAAAACAGTGGACTGAATATCAAAAGCAGTTGTGCAATATGCCAGGATGATGAAACGCAAGCAGATAACCAG[GA/G]AAAAAGCTATGGGTTAAACAATTTGCGAAAAGGCCCATCTTTTCTGTCTTTTGCAGCCTCTGTCAGGGCAAGAAACCTCTTGAA
109067 CT C AGTTGTCCAGTAGAAGGCATGGTAACCACTGGTGCTACAGAAGGGTGCCTAATTCCTGAGCTGTGCTTGTTAAATTCCTCCATTATTCCTTGTTGGTCAG[CT/C]TTTTTTTAGACCCTTGAGGTCAAGTATTCTCTGGAATTCTGAAGGCGTGCCCTCAGGAAGAAGAGCACGATATGTATTTCCAACAGA
109067 T A ATATTAAGGTAAAACCGCGGACCAAGAGATGCTGCAAGCTTGTCAAGAAAAAACTGAAAGTAGGTCGGAGAAAGTAGGGTCCCAAACACTGGAATGCTAC[T/A]AGAAAGAATCAGACTTATGCCATTGACATACTCTGACTGGTCACCAACACTTTCAAGAGTAGCCCATGGCACGCGTGTCATAGCA
109067 T C TAGGTCGGAGAAAGTAGGGTCCCAAACACTGGAATGCTACTAGAAAGAATCAGACTTATGCCATTGACATACTCTGACTGGTCACCAACACTTTCAAGAG[T/C]AGCCCATGGCACGCGTGTCATAGCAATCATCTCAGCGTCAAATTTGGTTTCAAGACCATGTACCAATGTCAGCAATGCTTTAGTGAT
109067 C T GAATGCTACTAGAAAGAATCAGACTTATGCCATTGACATACTCTGACTGGTCACCAACACTTTCAAGAGTAGCCCATGGCACGCGTGTCATAGCAATCAT[C/T]TCAGCGTCAAATTTGGTTTCAAGACCATGTACCAATGTCAGCAATGCTTTAGTGATAACAGCTGAAAACTCATCCTGAACATCAGACA
109067 A G ACATACTCTGACTGGTCACCAACACTTTCAAGAGTAGCCCATGGCACGCGTGTCATAGCAATCATCTCAGCGTCAAATTTGGTTTCAAGACCATGTACCA[A/G]TGTCAGCAATGCTTTAGTGATAACAGCTGAAAACTCATCCTGAACATCAGACATATCTACCTTGTCTGCATATACAGAGTCTATGATCT
109067 G A TCTGACTGGTCACCAACACTTTCAAGAGTAGCCCATGGCACGCGTGTCATAGCAATCATCTCAGCGTCAAATTTGGTTTCAAGACCATGTACCAATGTCA[G/A]CAATGCTTTAGTGATAACAGCTGAAAACTCATCCTGAACATCAGACATATCTACCTTGTCTGCATATACAGAGTCTATGATCTTTGAAA
109071 A G GGGCATTAGAAACCATTAGCTATAAATAGCTAACATAATAATATACATAGACATGACTATAACAAATAATGAACTCTGTGTATTATAGGTTGGGTATGTT[A/G]TCATATGGGCTGTCAGATGTCTGTAGCAATGTAGTTGCATCGCCTTCGTATGCTTGAGGAGTGAATCCCTCAGAGGGAGGTTGCTGC
109071 A G AGATGGGCTGGGAAAGAATGCATCGAATTTGATACCAATGTGTGGTAGGAGAACCTGGAGCAGTTGTGAGCCACCTTTGGACAGAACTCCCATCAAATAG[A/G]ACATCAAACCAACAAGCTAACCCATGCATCCTTGTGCCAACTGTAGCTATAAAGTTCAGAGGAATATCAATCTCATACAGGTCTTC
109073 G A CGGCTTCGGAGTTTTGATGCGGGACTAGGAGAATTTGGAGTAGAATTTGGGTGGTTCGGTTAATCTGATTGAATTCTAGTGTTCTAATCGA[G/A]ATACGCATGAGAAGGATTGTAAATCTGGGGTTTTCACCAAATTCGAATCATTTTATCACCTGCCTCTTGATTTTTAGTCTTCATTACTCGCCTCAATT
109073 G A AGATACGCATGAGAAGGATTGTAAATCTGGGGTTTTCACCAAATTCGAATCATTTTATCACCTGCCTCTTGATTTTTAGTCTTCATTACTCGCCTCAATT[G/A]TCCACCCCCATTATTAATTCCAGAAGTCTTTGGAATATAGATTACCGATCGTCTAGATATGGAGAAAGACAGTAATTCTAATGGTTCTTA
109073 G A AGACGAAACCTTCTTCCTCTCCTTCTGCCGTTGTCATTGGCAGTGGTTTTGCTGGCCTTGCTGCTGCTCATGCTCTTCAGAATGCCTCTTTCAAGGTAAC[G/A]TTGTTAGAATCAAGAGATAGAATTGGTGGCCGAGCATATACCAACTACAAATTTGGTTTTCCTATTGATATGGGTGCAGCTTGGCTCCA
109073 C T ATTCTGTGTTGTTTGATCATGATCTTGAGAGCTATGCTCTTTTTGATACTGATGGCCGTCAAATTCCTCAAGATCTTGTAACCAAAGTTGGTGAGGTATT[C/T]GACATGATGTTGAAAGAGGCAGATAAATTGAGGCAGGAAATTAGTAAAGACATTTCAATAGCTAAGGCATTGACCTTGGTTAATGAGA
109073 G A TAACCAAAGTTGGTGAGGTATTCGACATGATGTTGAAAGAGGCAGATAAATTGAGGCAGGAAATTAGTAAAGACATTTCAATAGCTAAGGCATTGACCTT[G/A]GTTAATGAGAGGAGGCCCGATCTAAGGCAAGAGGGGTTGGCTCACAAAGTTCTACAGTGGTATTTATGTAGAATGGAAGGATGG
109073 C T AAGAGGGGTTGGCTCACAAAGTTCTACAGTGGTATTTATGTAGAATGGAAGGATGGTTTGCTGCTGATGCTGACACCATCTCTCTCAAATACTGGGATGA[C/T]GAAGTTCTCCTTCCTGGTGGGCATGGTCTCGTGGTTAACGGTTACCGCCCTGTAATCAACACTTTAGCTAAGGGTTTAGACATTCAA
109073 C T GGTATTTATGTAGAATGGAAGGATGGTTTGCTGCTGATGCTGACACCATCTCTCTCAAATACTGGGATGACGAAGTTCTCCTTCCTGGTGGGCATGGTCT[C/T]GTGGTTAACGGTTACCGCCCTGTAATCAACACTTTAGCTAAGGGTTTAGACATTCAACTTAATCACAGGGTTAAAAAGATAGTGAGA
109073 A C TAATCAACACTTTAGCTAAGGGTTTAGACATTCAACTTAATCACAGGGTTAAAAAGATAGTGAGAGGCAAATTAGGAGTAGAAGTACAAGTAGACAATGG[A/C]AAATCATTCGTTGCAGATGCAGCTGTTATAACAGTACCTCTAGGAGTTTTGAAGGCCAACTCCATAGACTTTGAGCCGAAGCTTCCA
109073 G A CAGCTGTTATAACAGTACCTCTAGGAGTTTTGAAGGCCAACTCCATAGACTTTGAGCCGAAGCTTCCACAATGGAAGCAGGAAGCAATACGGGACATAGC[G/A]GTTGGAACAGAGAACAAAATCGTTCTGCACTTTGATGAAGTCTTCTGGCCAAATGTGGAGTTCCTTGGGGTGGTTTCATCTTCTAC
109073 C T CCTTGGGGTGGTTTCATCTTCTACCTACAGCTGCAGCTACTTTCTTAATCTTCACAAGGCAACAGGTCATCCCGTGCTTGTTTATATGCCTGCAGGCACT[C/T]TAGCCCATGACATTGAAAAGATGTCTGATGAGGCTGCGGCTGACTTTGCTTTCGTTCAGTTGAAGCAGATTCTTCCTGATGCTTCTCATC
109073 A G CGGCTGACTTTGCTTTCGTTCAGTTGAAGCAGATTCTTCCTGATGCTTCTCATCCGATAAACCACCTAGTTTCGCGCTGGGGTTCGGATGCAGACTCGTT[A/G]GGATCATATAGTTACGACTCTGTAGAAAAGCCGCATTATCTGCACGAGTGGCTAAGGACTCCCGTAGACAACCTCTTCTTTGCAGGAG
109073 T C CTTTCGTTCAGTTGAAGCAGATTCTTCCTGATGCTTCTCATCCGATAAACCACCTAGTTTCGCGCTGGGGTTCGGATGCAGACTCGTTAGGATCATATAG[T/C]TACGACTCTGTAGAAAAGCCGCATTATCTGCACGAGTGGCTAAGGACTCCCGTAGACAACCTCTTCTTTGCAGGAGAAGCAACTAGTA
109073 A G AAGCAGATTCTTCCTGATGCTTCTCATCCGATAAACCACCTAGTTTCGCGCTGGGGTTCGGATGCAGACTCGTTAGGATCATATAGTTACGACTCTGTAG[A/G]AAAGCCGCATTATCTGCACGAGTGGCTAAGGACTCCCGTAGACAACCTCTTCTTTGCAGGAGAAGCAACTAGTATGGACTATACTGG
109073 A C AGCAGATTCTTCCTGATGCTTCTCATCCGATAAACCACCTAGTTTCGCGCTGGGGTTCGGATGCAGACTCGTTAGGATCATATAGTTACGACTCTGTAGA[A/C]AAGCCGCATTATCTGCACGAGTGGCTAAGGACTCCCGTAGACAACCTCTTCTTTGCAGGAGAAGCAACTAGTATGGACTATACTGGT
109079 G A CAGGACGATAAAGCAAGCGAATTGGTCCTCGAAACCAACAGTGAAACGGCTGCTTTGGATGATGCCGGGAAAGGGCAGATAGATTTGAATGCTGTTGTGT[G/A]TGAAGACCGTACTGCTGCTGAAGCTAGTGCCTCGTCCAAGACCAGCATGATTGATTTGGTGCATGTTGCAACTCTACCTTTGGAT
109081 A G TTATGATCCACCCCATTACGAAGAAACAGGTATATGGATGCCCGTATCAGTACCCCCATTATCAAAAAGTGATCACGAAGAGTGGAGCAAAGGATTTTCA[A/G]ACAACAGTTCATATTTAGCAAACAAGGATATTTTCGATGAAGAGAACACAGAAATGACAATGTGGGATGTGTTTTCTGAGATGCTTA
109081 G GT AAAATGGCTTGCTGATAGTGCAGCAGCTTCTTGCATGCTTTGCGGGTCTGGGTTTCACCCGATTATGTGCTCTAGGCACCACTGTAGGTTTTGCGGTGGA[G/GT]TTTTTTGTGGGCAGTGCACTAGAGGAAGAAGCCTGTTGCCACCTAAGTTTAGAGTCGAAGACCCGCAGCGTGTATGTGATGTTTG
109081 A T TGAACTTTCCATGGGGTCAATCTATGGAATATGAGATATACAAAGCGGCAAATATAATTCAAGGCTATACTAAGGTTGGTTCACTGAAACCCGAGAAAAC[A/T]ATTCCAGAGGCTGTGCTAAAACAAGCAAAGGGCCTTGCGATCCTTACTGTTGCAAAAGTTGGGTTGATGGTTACATATAATGTCGG
109081 C T GATATACAAAGCGGCAAATATAATTCAAGGCTATACTAAGGTTGGTTCACTGAAACCCGAGAAAACAATTCCAGAGGCTGTGCTAAAACAAGCAAAGGGC[C/T]TTGCGATCCTTACTGTTGCAAAAGTTGGGTTGATGGTTACATATAATGTCGGCACAGGCTTAGTAATTGCACGTAGAGAAGATGGT
109081 T A TGCAAAAGTTGGGTTGATGGTTACATATAATGTCGGCACAGGCTTAGTAATTGCACGTAGAGAAGATGGTTCGTGGTCCGCACCTTCTGCAATTTCCACC[T/A]TTGGTCTTGGATGGGGAGCTCAGGTTGGTGGAAACTTCACTGATTTCATAATCGTGCTGAGAAATACAGACGCTATAAAAACTTTTT
109081 A G GCACCTTCTGCAATTTCCACCTTTGGTCTTGGATGGGGAGCTCAGGTTGGTGGAAACTTCACTGATTTCATAATCGTGCTGAGAAATACAGACGCTATAA[A/G]AACTTTTTGTGGTAATGCGCATGTTTCTGTTGGAGCTGGTGTTGGTGCAGCTGCTGGCATAGTTGGACGAGCAGCTGAGGCTGATTT
109081 A G CTGCTGGCATAGTTGGACGAGCAGCTGAGGCTGATTTTCGTGCAGGTGATGGTGGATATGCTGCTTGTTATACTTACAGCTGCAGCAAGGGTGCATTTGT[A/G]GGTTGTGCACTCCAAGGAAGCATGGTTATGACCCGAGCTTCCGAGAACTGCAGATTTTATGGTTCTTCTTCCATTCAGGCCGTGGA
109081 T G TGCAGGTGATGGTGGATATGCTGCTTGTTATACTTACAGCTGCAGCAAGGGTGCATTTGTAGGTTGTGCACTCCAAGGAAGCATGGTTATGACCCGAGCT[T/G]CCGAGAACTGCAGATTTTATGGTTCTTCTTCCATTCAGGCCGTGGATATTCTTCTTGGATCGGTGCCAAGGCCGCCTGCTGCTGCCA
109081 G A GCAAGGGTGCATTTGTAGGTTGTGCACTCCAAGGAAGCATGGTTATGACCCGAGCTTCCGAGAACTGCAGATTTTATGGTTCTTCTTCCATTCAGGCCGT[G/A]GATATTCTTCTTGGATCGGTGCCAAGGCCGCCTGCTGCTGCCATTCTCTATCAAGCTTTATCTGATTTGTCACGGAAACTTAATAAAT
109081 A G CACTCCAAGGAAGCATGGTTATGACCCGAGCTTCCGAGAACTGCAGATTTTATGGTTCTTCTTCCATTCAGGCCGTGGATATTCTTCTTGGATCGGTGCC[A/G]AGGCCGCCTGCTGCTGCCATTCTCTATCAAGCTTTATCTGATTTGTCACGGAAACTTAATAAATGATCCTTTCAATGCCAACGCCAAGT
109081 T A TGGTTATGACCCGAGCTTCCGAGAACTGCAGATTTTATGGTTCTTCTTCCATTCAGGCCGTGGATATTCTTCTTGGATCGGTGCCAAGGCCGCCTGCTGC[T/A]GCCATTCTCTATCAAGCTTTATCTGATTTGTCACGGAAACTTAATAAATGATCCTTTCAATGCCAACGCCAAGTGATTGTGTATATAACA
109081 T C GCCGTGGATATTCTTCTTGGATCGGTGCCAAGGCCGCCTGCTGCTGCCATTCTCTATCAAGCTTTATCTGATTTGTCACGGAAACTTAATAAATGATCCT[T/C]TCAATGCCAACGCCAAGTGATTGTGTATATAACACCCATTCATTGAAGAAATCCTGATTTTATGATTTGTACATATGTTTGTTTGCAAAT
109085 T C GTGGTAGGGGATCCAAGTCCTGTTTCAAGACCCTATATATATACATTTTACCAAACAAGCACACATTTGTAGT[T/C]GAGACATGTACTACGCCTAGAACAGAATTAACTGACCTGAACAGCAGCAGTGTTACTGGGACCTGCAATATTCCTACTAGTGAGCGAAGGCCTCATGGTG
109085 A G ACTCATTCACCAAAGCAGTATAAACTGGAACCAAGTCAGGAGTAAATCCACTCATGACGGTCTGAGCCATTCCCTGACCCATGCTCTCGGCCTGCTGTGC[A/G]AACCCATTCATGGGAGCGGTACTGTAAGAAGAAGTCAGCTTCTCGCTAAGACCGCCGAAGATCTGCTCAGTGATAGCTTGGATAGA
109085 C A CATTCACCAAAGCAGTATAAACTGGAACCAAGTCAGGAGTAAATCCACTCATGACGGTCTGAGCCATTCCCTGACCCATGCTCTCGGCCTGCTGTGCAAA[C/A]CCATTCATGGGAGCGGTACTGTAAGAAGAAGTCAGCTTCTCGCTAAGACCGCCGAAGATCTGCTCAGTGATAGCTTGGATAGAGTG
109085 T C ACTGGAACCAAGTCAGGAGTAAATCCACTCATGACGGTCTGAGCCATTCCCTGACCCATGCTCTCGGCCTGCTGTGCAAACCCATTCATGGGAGCGGTAC[T/C]GTAAGAAGAAGTCAGCTTCTCGCTAAGACCGCCGAAGATCTGCTCAGTGATAGCTTGGATAGAGTGGCCAGGGTCGGAATCGACG
109085 G A TGACGGTCTGAGCCATTCCCTGACCCATGCTCTCGGCCTGCTGTGCAAACCCATTCATGGGAGCGGTACTGTAAGAAGAAGTCAGCTTCTCGCTAAGACC[G/A]CCGAAGATCTGCTCAGTGATAGCTTGGATAGAGTGGCCAGGGTCGGAATCGACGAACACGGCCTGATCAGAAACGAACACTTTGG
109085 A G GCTGTGCAAACCCATTCATGGGAGCGGTACTGTAAGAAGAAGTCAGCTTCTCGCTAAGACCGCCGAAGATCTGCTCAGTGATAGCTTGGATAGAGTGGCC[A/G]GGGTCGGAATCGACGAACACGGCCTGATCAGAAACGAACACTTTGGGGGAGGATGGGTCGGAGGCAACGACGTGGTTGTATTC
109085 A G AGATCTGCTCAGTGATAGCTTGGATAGAGTGGCCAGGGTCGGAATCGACGAACACGGCCTGATCAGAAACGAACACTTTGGGGGAGGATGGGTCGGAGGC[A/G]ACGACGTGGTTGTATTCGGACCCGGTAAGGCCGTCGATGTCAGGTCGACTGGATTTGAGCCATCCGAGCATGTGATCGAAGG
109085 G A ACACGGCCTGATCAGAAACGAACACTTTGGGGGAGGATGGGTCGGAGGCAACGACGTGGTTGTATTCGGACCCGGTAAGGCCGTCGATGTCAGGTCGACT[G/A]GATTTGAGCCATCCGAGCATGTGATCGAAGGAGCGATTCTCCATGACGACGACCACTAGGGTTTTGATGGGGCCGTTGATTTCG
109085 C T CATGTGATCGAAGGAGCGATTCTCCATGACGACGACCACTAGGGTTTTGATGGGGCCGTTGATTTCGTGCTTCTTCTTCTTTCTACCCCATTTTAAATTG[C/T]TGGTGGAAGAGTCCAAGCAGTGAGCGGATATTAGGAGATAGAGGAAGACAACGAAGAGGAGAAGGTGGCGGCGGTGACGGCCGA
109085 A G GATGGGGCCGTTGATTTCGTGCTTCTTCTTCTTTCTACCCCATTTTAAATTGCTGGTGGAAGAGTCCAAGCAGTGAGCGGATATTAGGAGATAGAGGAAG[A/G]CAACGAAGAGGAGAAGGTGGCGGCGGTGACGGCCGAAATTTTGGCGGTGAAAGTAGTCCATGGGCCCACCGCCTAACCGAGTGC
109089 T C TATTTTTTCATAAATTACTTCAGCACTATATGTTACCTTCCCAGCTAAAGCCATATGATTTGTGGAAGGTGGCTAACGTGAACATGCGACTCACTTGACA[T/C]TCATAACTTGCGTAATTGTAAAGCAGAAGACAAATATCATAATTTGAGGATGTTAGTCTTTGGCCATTATGCTCTTTCTTAACTTCCTGTC
109089 G A AATTACTTCAGCACTATATGTTACCTTCCCAGCTAAAGCCATATGATTTGTGGAAGGTGGCTAACGTGAACATGCGACTCACTTGACATTCATAACTTGC[G/A]TAATTGTAAAGCAGAAGACAAATATCATAATTTGAGGATGTTAGTCTTTGGCCATTATGCTCTTTCTTAACTTCCTGTCATGATTCAGCA
109089 A G CCTAATAGAAAAACTACAGGTATAATTAAAACTACGGGATAAAGGGACAAATGTGTAGCCATAACCCATCCGAACGCGGCTAAAGGAGTAATACCAGCAC[A/G]GGCTCCATATATGGTCAAGACAACCATCAGATTATCAACTGGTGATGTGGATGAACCAATGCAAGTGATTATTGACAATGGGTTCC
109089 T A ATAGAAAAACTACAGGTATAATTAAAACTACGGGATAAAGGGACAAATGTGTAGCCATAACCCATCCGAACGCGGCTAAAGGAGTAATACCAGCACAGGC[T/A]CCATATATGGTCAAGACAACCATCAGATTATCAACTGGTGATGTGGATGAACCAATGCAAGTGATTATTGACAATGGGTTCCATAA
109089 C T ATGGTCAAGACAACCATCAGATTATCAACTGGTGATGTGGATGAACCAATGCAAGTGATTATTGACAATGGGTTCCATAAATATACTAGCGATGCCAACT[C/T]TCCGGCACTTAAAATATCTGATGATTCATTCTCTTTTAATAAGTTCAACAGCTGCATATTCTGGCGACTAGTCGCTAAAAGCTTCTGTC
109089 A G AATATACTAGCGATGCCAACTCTCCGGCACTTAAAATATCTGATGATTCATTCTCTTTTAATAAGTTCAACAGCTGCATATTCTGGCGACTAGTCGCTAA[A/G]AGCTTCTGTCCAGTAGCATGAATGAGCATAGCAGCTATAAAATCTACAATCACAAAGATCAAACTGTATCTGCAAAAACTATAGTCTGG
109089 T C GCGACTAGTCGCTAAAAGCTTCTGTCCAGTAGCATGAATGAGCATAGCAGCTATAAAATCTACAATCACAAAGATCAAACTGTATCTGCAAAAACTATAG[T/C]CTGGTTGTCCTTCAAAATCACTCCTTACAGTCAAAGGTCCAAGAATGGACAACAAGAGAGGAGAGCCATGGTACATTGATCCAGAAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
109089 C T CATGAATGAGCATAGCAGCTATAAAATCTACAATCACAAAGATCAAACTGTATCTGCAAAAACTATAGTCTGGTTGTCCTTCAAAATCACTCCTTACAGT[C/T]AAAGGTCCAAGAATGGACAACAAGAGAGGAGAGCCATGGTACATTGATCCAGAATAAGGCGACATATTGGATTGCTTGAGCCAGTAA
109089 C T AACTATAGTCTGGTTGTCCTTCAAAATCACTCCTTACAGTCAAAGGTCCAAGAATGGACAACAAGAGAGGAGAGCCATGGTACATTGATCCAGAATAAGG[C/T]GACATATTGGATTGCTTGAGCCAGTAACCTTCAGCCAAACGGCGGAGACTAGTGACTGGAGTGGCGACTTCAGGCCGCGTGGCTA
109089 G T CTGGTTGTCCTTCAAAATCACTCCTTACAGTCAAAGGTCCAAGAATGGACAACAAGAGAGGAGAGCCATGGTACATTGATCCAGAATAAGGCGACATATT[G/T]GATTGCTTGAGCCAGTAACCTTCAGCCAAACGGCGGAGACTAGTGACTGGAGTGGCGACTTCAGGCCGCGTGGCTAGGCTGAGTT
109089 A T TTGGATTGCTTGAGCCAGTAACCTTCAGCCAAACGGCGGAGACTAGTGACTGGAGTGGCGACTTCAGGCCGCGTGGCTAGGCTGAGTTCGCCAGCGAAGA[A/T]TATGAGTAAAAGTCTAACGATTTATGGCGGCTGCCACTAGAATCCAATAATTTTGCAGACCTGCCATTGAGAGACTCAGTGAAAG
109089 AT A ACCTTCAGCCAAACGGCGGAGACTAGTGACTGGAGTGGCGACTTCAGGCCGCGTGGCTAGGCTGAGTTCGCCAGCGAAGAATATGAGTAAAAGTCTAACG[AT/A]TTTATGGCGGCTGCCACTAGAATCCAATAATTTTGCAGACCTGCCATTGAGAGACTCAGTGAAAGAGTGGTTTTAAGAGTTGCG
109091 T C TGACTGGTTGCTTCGCCCACACTGGCGAACTTATCTCCATCAAGATCATCCGCAACAAGATCACGGGGCACCCCGAGGGCTACGGCTTTATTGAATTCAC[T/C]TCTCATGCAGCTGCCGAACGCATCCTTCAATCTTACAACGGTATCCCCATGCCCGGGACGGAGCAGCCCTTCCGTCTCAACTGGGCC
109091 C T ACAAGATCACGGGGCACCCCGAGGGCTACGGCTTTATTGAATTCACTTCTCATGCAGCTGCCGAACGCATCCTTCAATCTTACAACGGTATCCCCATGCC[C/T]GGGACGGAGCAGCCCTTCCGTCTCAACTGGGCCTCATTTGGACTCGGCGAGAAGAGGGCTGATGCGGGTCCTGACCACTCTATATTT
109091 T C AGGGGTATGGGTTTGTGAAGTTTGGGGATGAGATGGAGAAGAATAGAGCAATGTCAGAGATGAATGGTGTTTATTGCTCGAGTAGGCCAATGAGGATAAG[T/C]GCTGCAACTGCAAAGAGACCGGGGGTTGGTGTTGGGTTGCAACCATATCCTGCTGCTGTTGTTAAAGCTACATATCCAGGATCA
109091 C G GGCTATGATCCCTACGGATATGCTGCTGTACAGGATCCATCTTTATATGCATACGGTGCTTATGCTGGATATGGTCAATACCCACAGCAGGTTGAAGCTG[C/G]GCAAGATATGAATGCAATGACCGGGGTAGTTTCAACTGTGGAAAATAAAGAAGAACTCTATGATCCACTAGCCATACCCAACGTGG
109091 T A AGTATACAAAGAGAAGGAAGCAAGAATCTCAGACTTTGCAGACTACGTAAATTCATAAATAATGCTGGTGAAATGAATATCTGATGCAGACAAGGGATGA[T/A]CTGAACTATGCACTTATGCTGGCATGGTTTTGATAAAAAATCGTGCCTTGCATGTATGCTAATGTACACTTATGTCTATGCCATTGA
109091 TA T TTTGCAGACTACGTAAATTCATAAATAATGCTGGTGAAATGAATATCTGATGCAGACAAGGGATGATCTGAACTATGCACTTATGCTGGCATGGTTTTGA[TA/T]AAAAAATCGTGCCTTGCATGTATGCTAATGTACACTTATGTCTATGCCATTGATCGCTCTGTGGCCAGTTAAATTTTCTATTTGTTCTT
109095 GA G CCTACATCACACGGAAAAGAACTCTAATTTCTGCCTGTTTATGCCCATGTTCGATGCTTTAGGGGGGACACTGAACAAGGAATCATGGCCATTACAGAAG[GA/G]AAATAAGCTCAGGGAAAGACCTGGTTCCTGATTTCGTGTTCCTGGCTCATGTAGTGGACGTTGCCTTCTCTTTGCATTCTCCGTTCA
109095 A G GCCATTGTGGCCTGGCGCTTTTGTTATCATGTTGTTCATGTGGGCATTTTCAAAGACTTTTCTTCTCTCATTCTACAATATTAGAGGCCGATTGCATCAA[A/G]CTTGGTTGGTCCCAAGATATGGATTTCAGTACTTCTTACCATTTGCTAAAAATGGAATCAACGATCAAATTGAGTTGGCTATTTTAAGGG
109095 T C TTACCAAATATCAAGCTGCCAAAAACTGCAAGACATGGATAGTGGGGAAGTGGCTGACACCAAGAGAGCAATGCTGGGCTCCACGCGGCACACATTTCCA[T/C]CAGTTTGTGGTGCCGCCTATCATCAGCTTCCGAAGAGATTGCACTTATGGAAAGCTCGCTGCAATGTGGTTGCCAAAAGACGTAC
109097 G GT ACCCAACAGCTTTCAGCCTTCTGATCCTCTTCTCACTCTAGCGGTTGATTGTGGACTAAAGGATGATCTTGTATTCGCCGACCCCAAAGCACCCCGTTTT[G/GT]TTTTTGGAGTGGAAAACTAAGGCCAGTTCCTTCAAAACCTACTGATTTACCTTTCTTTGACCTGATGAGCATTGGTGGTAAATTGAGG
109099 T C GGTGCTCAATTTGCTAATGATCTGGTCAGCATCATGGCTAATATGAGTTAGCCATTCTAAGCTATTCTTGTGCAGCGCATGCAACAACCCGTAAAGCTCA[T/C]CCAAGGGGAGGGAAGTAGTGGGCAAGTTGTATCTAGCAGGTGGCACGTGTGTTAGCAGATTCCCTGTAGCAGTGAGTGCTGCATCC
109103 CA C TCACACACGTCAAAACTTGTGTATATCTGCCCTCTTCATCACCTCAGTCAGTCACAAACGCTTGTTAAATTTTATCCAGTAAAAAGCAAAACAGAAGTTG[CA/C]AAAAAAAGGAGTCCGGCTTTTTCTAAATGGATCTCTGTGTGAAGCAACTATACTTCGAGGCCGTGAGATCCGGCGATATCGCCGCCT
109103 C T ATTAGACATCGATGAGAATTCAATGATGATAGTGAGGAGAAACGGCAAAACTTCGCTTCATATGGCTGCTAGAAATGGTTACCATGCAGTAGTCAAAACA[C/T]TGGTTGATAGGAATCCAGGAATAGTTTCTATAACAGATAAGAAGGGCCAGACTGCACTTCACATGGCTGTGAAAGGGAAAAGTAC
109103 G T GAATCCAGGAATAGTTTCTATAACAGATAAGAAGGGCCAGACTGCACTTCACATGGCTGTGAAAGGGAAAAGTACCGATGTAATTGAAGAACTCGTCAAT[G/T]CAGATCCCTCTATACTTAATATACATGACAGAATGGGAAATACCGCATTGCACTTAGCCACAAAAAAATGGAGACCACTGAACGTG
109103 T C ACAACCGTCAAGAAACTCCGCTGGACATAGCAGAAGAAGTCCCGTACGAGAAATCCCAATCAGATTTGATGGCAATCCTACGAGAATCAGGTGGAAGAAA[T/C]GCCAGAAACATCAACAAACTCGATGAAGAGTCAGTTCTAAGAAGAACCGTAAGTGACATAAAGCACGGAGTGCACGACCAACTCA
109103 G C GTCGAGTGGTAGTAAATCCTTTTCCTGGTCGCACTATTCTGCGTATTCTGAGGATGGTTACTCTGATCATGAGAAGAAACGGATATACGCGTTGTGATTT[G/C]GATAATTTTTAAGTTGATGTAAGTAGTGTGGAGGTGCAATGTTGCGTCTCTTTGTTGTATATATTTGTACTTGTTATGGCTGAAGTTTG
109105 T C GAAGCATCATCCGCATTAAGCCCGGTATTATTATTGCTAGGTCGACCCCAGCCATCGATGAAATCCGAAGAATCGCGATCACCGTCGAGCTCTTCTATGA[T/C]ACTGGAACCGCCACTGCTACCTCTTTCACCGGCGTAGCCACTGCTGCTTGGACTCGCCGGCGCTGCCACTGCCTCCTCGAATATCTCT
109111 C T TTTAAGAAATGGGAGGGTTACTCCAGAAAGCGTGATATTCAGCTTTGGCACTGTCCTCTTGGATCTTCTTAGCGGAAAACGTATCCCTCCAAGCCATGCT[C/T]TTGACATGATTCGAGGTAAAGACATTCTACGGTTGATGGATTCACACTTGGAGGGGAACTTTTCAACAGAAGAGGCAACGATACTGG
109111 C G ACGAAGCGGCTGGACTCGAGAAAAAGAGGCAAAACGGCGGGAAGGCTTAGAAAGGGAATTTTATATGTTATAGGAATGATTTTCTTCAGATTATCCTCTT[C/G]CAGTGAAAATTGTATTATAGAGGCGAAATGTCCTTTGATTGTTAGTCCTGCATTATTTGGTTTGTAATTTATCATACTAATTCTCATA
109113 T TA TGGAAGTTGCAGATCCTGATGCTGTCCATGCTGTCCGTAGTTTCATCAGGAAGCAACTTGCTCTTCAACTCAAGGATGATTTGCTTAGTACAGTCAAAAA[T/TA]ACAAGTGCTCTGGGCCCTATATTTTTGATCATCATAATATGTCCAGGCGTGCTCTGAAAAACGCGGCTCTAATCTACCTTGCATCATT
109117 C T CCATCGACTCGCGAAACCGGGCACCCACCGACGTGGCCTCCAGCTCCAATGCCAGCATCCGCAGCAGCACCAGCATGGATTTCGGGCTTGGGGCCCACCC[C/T]GACTCCCATTCCTTACCCAAGCACTCCCCTCTTTCTGCTTCCTACCCTCACAGCTTAGCAAGCAAAGACGGGTACGATACAGTCACC
109117 A G CAGCATCCGCAGCAGCACCAGCATGGATTTCGGGCTTGGGGCCCACCCCGACTCCCATTCCTTACCCAAGCACTCCCCTCTTTCTGCTTCCTACCCTCAC[A/G]GCTTAGCAAGCAAAGACGGGTACGATACAGTCACCCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCA
109117 A C TCGGGCTTGGGGCCCACCCCGACTCCCATTCCTTACCCAAGCACTCCCCTCTTTCTGCTTCCTACCCTCACAGCTTAGCAAGCAAAGACGGGTACGATAC[A/C]GTCACCCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACA
109117 C T GGCTTGGGGCCCACCCCGACTCCCATTCCTTACCCAAGCACTCCCCTCTTTCTGCTTCCTACCCTCACAGCTTAGCAAGCAAAGACGGGTACGATACAGT[C/T]ACCCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACAGAC
109117 C T CCTACCCTCACAGCTTAGCAAGCAAAGACGGGTACGATACAGTCACCCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCAC[C/T]GTGATCCACAACCCCGTTCCGACCCACAGACCTTTGCCTGCGAAGGTACCCCTGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGC
109117 C G TAGCAAGCAAAGACGGGTACGATACAGTCACCCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCC[C/G]GTTCCGACCCACAGACCTTTGCCTGCGAAGGTACCCCTGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGT
109117 G A CCCTACTGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACAGACCTTTGCCTGCGAAG[G/A]TACCCCTGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCC
109117 C T TGCCAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACAGACCTTTGCCTGCGAAGGTACCC[C/T]TGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCCGGCAAA
109117 C T CAGCAGCATCAGCAGCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACAGACCTTTGCCTGCGAAGGTACCCCTG[C/T]CTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCCGGCAAATAA
109117 T C GCCCTGTTCGCCCCGGGACCAACAAGCCCACCGTGATCCACAACCCCGTTCCGACCCACAGACCTTTGCCTGCGAAGGTACCCCTGCCTAGGGCTTCGGT[T/C]GTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCCGGCAAATAATCAGAATGTAAGGG
109117 C A GACCCACAGACCTTTGCCTGCGAAGGTACCCCTGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCC[C/A]CAAGGGCTCCGGCAAATAATCAGAATGTAAGGGGCGGTTGTCGGGTGATTGAGCCCGAGAAGCTGGTGTACACGAACCAGTCCA
109117 T G GACCTTTGCCTGCGAAGGTACCCCTGCCTAGGGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGC[T/G]CCGGCAAATAATCAGAATGTAAGGGGCGGTTGTCGGGTGATTGAGCCCGAGAAGCTGGTGTACACGAACCAGTCCATATTCTTT
109117 T G GGCTTCGGTTGTGTGGGACCAGGAAGCGGGTCGTTACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCCGGCAAATAATCAGAATGTAAGGGGCGGT[T/G]GTCGGGTGATTGAGCCCGAGAAGCTGGTGTACACGAACCAGTCCATATTCTTTGGTGGGCCGCTGTTGGGTGGAAGACGGGCC
109117 G T ACGTGTCGGTTACGAACCCGAATGCCCCAAGGGCTCCGGCAAATAATCAGAATGTAAGGGGCGGTTGTCGGGTGATTGAGCCCGAGAAGCTGGTGTACAC[G/T]AACCAGTCCATATTCTTTGGTGGGCCGCTGTTGGGTGGAAGACGGGCCGAAAACGAAAGAGATAGGAATGGCGGGCCTAGCGA
109117 C T AGAATGTAAGGGGCGGTTGTCGGGTGATTGAGCCCGAGAAGCTGGTGTACACGAACCAGTCCATATTCTTTGGTGGGCCGCTGTTGGGTGGAAGACGGGC[C/T]GAAAACGAAAGAGATAGGAATGGCGGGCCTAGCGACTCTTTTCCGGTCTTTATTCCTGGAGAGTATCAAAGAAACTAAGGTGTG
109117 A G GCCCGAGAAGCTGGTGTACACGAACCAGTCCATATTCTTTGGTGGGCCGCTGTTGGGTGGAAGACGGGCCGAAAACGAAAGAGATAGGAATGGCGGGCCT[A/G]GCGACTCTTTTCCGGTCTTTATTCCTGGAGAGTATCAAAGAAACTAAGGTGTGCACGGAAAAAGAACAGTGAGTGTGTTGCTAA
109119 T C TAGTTAAGTGGAGAAGAATGATTGATCAGAACAATATTTATAAAGCGCATTACTCCAACATGCATCAAGCTCCACTGCTGAATTTAGCTTCATACTCGCT[T/C]GGTTTCATAAAAGTGGCAGAAATTGCCCTTCCAGCAAACCATCTCAGATGCATTGCTCGCTGACAGCTTGATGCTGCCATCACATTATC
109119 C T CGCATTACTCCAACATGCATCAAGCTCCACTGCTGAATTTAGCTTCATACTCGCTTGGTTTCATAAAAGTGGCAGAAATTGCCCTTCCAGCAAACCATCT[C/T]AGATGCATTGCTCGCTGACAGCTTGATGCTGCCATCACATTATCAAACCTTAGAAATACATTGCCATTGCTGTATTTATCAACAAAAATA
109119 T C ATTTATCAACAAAAATATGCTTCACTGGACCAAATTTTGAACACTCCTCTTGCACATCATCCCTAATTTCCAAATCAAACTCTGGATCCGTCTCTGTTTT[T/C]GGGTCAAACATATTCTTTAATAGAAGGCATTCACTAGGCTCTCCAATAGTCACAGCTGCCGGCACAGTAGCAAGGGCTGGATTCAACAAT
109119 C T TCATCCCTAATTTCCAAATCAAACTCTGGATCCGTCTCTGTTTTTGGGTCAAACATATTCTTTAATAGAAGGCATTCACTAGGCTCTCCAATAGTCACAG[C/T]TGCCGGCACAGTAGCAAGGGCTGGATTCAACAATGTTGGCGCAGCAGGTATCATCATAGGCTGCCCATTTATAGGCAAAGGCAGGGAC
109123 A G GTGGCCTTTTTTTTTTTGCTGCAATCAAACTACGCCTAGATTCAAAATAACTTCTTAAAACCTAAATTTACACCATATATT[A/G]TACTTTTACATATTACATACATTGCAGTCTTGAAAAATGAACAGGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAAAATAGGATAAACGGT
109123 G A AACTTCTTAAAACCTAAATTTACACCATATATTATACTTTTACATATTACATACATTGCAGTCTTGAAAAATGAACAGGCCATGCAGAAAAATAGCCTGC[G/A]CAACTGACTCGAAGTGAAAATAGGATAAACGGTATAAGCAGGCACACGGGATTAAAATAATAGTCCAAGCGTATAGGAAAAAAAATT
109123 A T TTACACCATATATTATACTTTTACATATTACATACATTGCAGTCTTGAAAAATGAACAGGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAA[A/T]ATAGGATAAACGGTATAAGCAGGCACACGGGATTAAAATAATAGTCCAAGCGTATAGGAAAAAAAATTACCGTTCAAAATAATATGA
109123 A G CACCATATATTATACTTTTACATATTACATACATTGCAGTCTTGAAAAATGAACAGGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAAAAT[A/G]GGATAAACGGTATAAGCAGGCACACGGGATTAAAATAATAGTCCAAGCGTATAGGAAAAAAAATTACCGTTCAAAATAATATGAACA
109123 A G TACTTTTACATATTACATACATTGCAGTCTTGAAAAATGAACAGGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAAAATAGGATAAACGGT[A/G]TAAGCAGGCACACGGGATTAAAATAATAGTCCAAGCGTATAGGAAAAAAAATTACCGTTCAAAATAATATGAACAGAAAAATAGCA
109123 C CA AAAAATGAACAGGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAAAATAGGATAAACGGTATAAGCAGGCACACGGGATTAAAATAATAGTC[C/CA]AAGCGTATAGGAAAAAAAATTACCGTTCAAAATAATATGAACAGAAAAATAGCAAGACTAGTATAATAACACTACTAAACAGAC
109123 G GA GGCCATGCAGAAAAATAGCCTGCGCAACTGACTCGAAGTGAAAATAGGATAAACGGTATAAGCAGGCACACGGGATTAAAATAATAGTCCAAGCGTATAG[G/GA]AAAAAAAATTACCGTTCAAAATAATATGAACAGAAAAATAGCAAGACTAGTATAATAACACTACTAAACAGACGTGCTGTTTGG
109123 A T AATCGACAACACCAATTTTCTCGTGAGCAGGCTCGACACATTTTCTAAGAGCAAAATCAAGACCCCAGCCATGGACTAAGTCGTTCTGAATCATGTGCCA[A/T]ACGCATCGCCATGCATTTCGTGAGAAAACAGGCGCCATTATTTCCACAAATGCAGCACAGGGTGGCAAATGAGGATCAGAGCACCA
109129 AT A TTCCTTTTTAAGTCTCTTTAACCGCAAGATACTGAGAGTGCGAAGCAGCAAGGAGGGCTGCACCAATACCAGACCCATCATTCGCGTGCACGATTTCCAC[AT/A]TTTTTTTTGACATCTTTTCCAATCATCTCTTCAATAGTTGTTTCTAAGCATTTACTGAAAATTGTATAATGTTCATACAATCCACCATCC
109129 GT G GTTGTTTCTAAGCATTTACTGAAAATTGTATAATGTTCATACAATCCACCATCCATTGCCAGAACTGTCCTTCGATCAATGGCTGCGGTGTCTCTACCTT[GT/G]TTTTTTGAGAATGCCTACTATTCCAGCTGCAGCCAAGCGAGCTCCGCGTTTTGCCACTATGTCACATATATCTACTATGGCTTTTCTTGT
109129 AT A TGCAGCCAAGCGAGCTCCGCGTTTTGCCACTATGTCACATATATCTACTATGGCTTTTCTTGTTTTTAAAGAGGTATTGGTAATCCCGAATACGTCTTTC[AT/A]TTTTTTTGCTTACGACCTTTAGGTCGAGTGATGTGTCGTGATGCATTGCAGACATGTCCGGAGTTCGTAATGAGAATGGAACGCTAAG
109129 G A TCCCGAATACGTCTTTCATTTTTTTGCTTACGACCTTTAGGTCGAGTGATGTGTCGTGATGCATTGCAGACATGTCCGGAGTTCGTAATGAGAATGGAAC[G/A]CTAAGTTTTTGGGGGACATTATCACCGAAAAAGGCAGCTTCTTCAGCCAACTTCCATAAAACTCTTCTCACGATGTCTCCTAAATACAT
109129 C T ATTCTGTTACCGGGAGATGAGATGATCTGAAATTACCCCATTCCATGTTGATAACCATTTCGCCAGATTTTGGTACCGAACCATGCCATTTTGGAATAGC[C/T]TGTGCTCGTTCTACGTATGCTGCATTTGTACCAGTGCCTAATATCACGGCTATGACAACATCATTATCGTAGTATCTCCCACCAGCCAAT
109129 TA T GATTGAGACTTCCTCGGCTTCTTGTTTGACAACACGTCCTACTCTTCCTCCTAGTAGAATGCGCAAAACACGAAAGTTGGTTCCACCAAGATCCAATGCA[TA/T]AAAATAAACCTTCCTCGTCCCCAGTAGGAAGATTATCAACGTAGCTAATAAGCATCTTAAGCTTGCTGCCTCCATCAGAAGCAAGGCC
109129 G A CACAATCAGCGCTGCCACCGCCACTGTCGTCGCCGTCAGCGCCACCGTTACGCCCACCGCTACTTTCCCCATTAATAATAAAACGAATATCAAACAAGGA[G/A]AGAGTTAAATGGAATTGAGAATTGAGCTGGATCTCGGACAATGGACGTATTGAGCAAGTGATGCGTATTTGTGGATCAAAGGTCGT
109131 A T CACCAGAGAAATGCTTGATGGACCCAAGCAAGCTTTTGGAAGCACCAAAATGCCTTATCCTGTAAACTCCTGAACTCGCACTCTCCGGGATTCTCCACTC[A/T]ATGGTAGCATAACTCCTGGTACTAAACTTGGACGGCCTCGACCACTTGAATCTCAAGCAAAAATCATCGTCGTCATAAGCAGGAATCC
109131 G A CTGAACTCGCACTCTCCGGGATTCTCCACTCAATGGTAGCATAACTCCTGGTACTAAACTTGGACGGCCTCGACCACTTGAATCTCAAGCAAAAATCATC[G/A]TCGTCATAAGCAGGAATCCAAGTAGCCGTACCCTCTAATACTTCCACTAAAGCGAAAGTGCCTTGTGTGTGTAGATCGTTTCTTGGGC
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
109131 T C ACTCGCACTCTCCGGGATTCTCCACTCAATGGTAGCATAACTCCTGGTACTAAACTTGGACGGCCTCGACCACTTGAATCTCAAGCAAAAATCATCGTCG[T/C]CATAAGCAGGAATCCAAGTAGCCGTACCCTCTAATACTTCCACTAAAGCGAAAGTGCCTTGTGTGTGTAGATCGTTTCTTGGGCACGC
109131 C T AAAAATCATCGTCGTCATAAGCAGGAATCCAAGTAGCCGTACCCTCTAATACTTCCACTAAAGCGAAAGTGCCTTGTGTGTGTAGATCGTTTCTTGGGCA[C/T]GCGGACCTGAACTTCGCAGTCACAGTGTCCCCTCTTTTGAAGGAAGAGTTTCTAGGCAAATCGAGGACCATATCTCCAAATTTGACAC
109131 G T AATCATCGTCGTCATAAGCAGGAATCCAAGTAGCCGTACCCTCTAATACTTCCACTAAAGCGAAAGTGCCTTGTGTGTGTAGATCGTTTCTTGGGCACGC[G/T]GACCTGAACTTCGCAGTCACAGTGTCCCCTCTTTTGAAGGAAGAGTTTCTAGGCAAATCGAGGACCATATCTCCAAATTTGACACCTA
109131 A G TCTTGGGCACGCGGACCTGAACTTCGCAGTCACAGTGTCCCCTCTTTTGAAGGAAGAGTTTCTAGGCAAATCGAGGACCATATCTCCAAATTTGACACCT[A/G]AAGGAGTTGAGTCTGCAATTACTGGAGGAAGCAAACCGATCTGCTTGTTTAAGAGGTCTGGAGGTTGTGGCCCTGGTGCGACCTTT
109131 T C AAATTTGACACCTAAAGGAGTTGAGTCTGCAATTACTGGAGGAAGCAAACCGATCTGCTTGTTTAAGAGGTCTGGAGGTTGTGGCCCTGGTGCGACCTTT[T/C]GATGGCTGACAAGGGATAAGGCTAGCTTTTTGAACTCCTGAATGTAGGCACTTAACGTGTGCGGTCCGTACAGAGTTGATGCACCC
109131 G C TTGACACCTAAAGGAGTTGAGTCTGCAATTACTGGAGGAAGCAAACCGATCTGCTTGTTTAAGAGGTCTGGAGGTTGTGGCCCTGGTGCGACCTTTTGAT[G/C]GCTGACAAGGGATAAGGCTAGCTTTTTGAACTCCTGAATGTAGGCACTTAACGTGTGCGGTCCGTACAGAGTTGATGCACCCTCGT
109131 G C TCTCTCCAGTATCAAGTAAAATTGGCTTCGGATGATGACATGCATCTTGTTCTTTACCAGGGGTTTTCAAAACATCCCTTACCAATCTCCAGAATGGATT[G/C]CCCTTGTCATCTCCCTGTTCAAAATCAAAAGCTCCAGGACCGTCAGTAGTTCCTGCTGCAAAAGCAAATCCCATAGCAGCTGGACACGT
109131 T C TCATCTCCCTGTTCAAAATCAAAAGCTCCAGGACCGTCAGTAGTTCCTGCTGCAAAAGCAAATCCCATAGCAGCTGGACACGTGCTATATATTTTTTGAT[T/C]TCCGTCATATGATGTAACGGAAACTTCTAGTTTTGACATATTCAAATATGCATGACGATACTCGATTTTTCCAGCAATCAACTCCTTTGC
109131 T A CTAGTTTTGACATATTCAAATATGCATGACGATACTCGATTTTTCCAGCAATCAACTCCTTTGCTGTGTTAAAGAGTTGTACAGCCTTTTTGAACTGCAT[T/A]TCTCCAATTATGCGGGTACTTTCAAACTCGTCTGGATAACCAGGGCCACGTCCATAGCATAGTTCATTCTTCCCATTGCAAGTGCTGTGA
109139 A AG TGAAGCTTGGGCCTATGAAAATGCTTGCGCTGCAGGATTTCTTTAGTGGGGATGGAGAGGAAATGGATTTGAAGAAGGTGGCTTCTGCTGTAACTTTATG[A/AG]GTTTTTTTATGTAATTGTTGATGAGTTCGTATACAACTCGGCTTGCTTTGGCTAAAAGTGTAATCTGTTCTGCTTTCTTGATGTTTT
109139 G GT GAAGCTTGGGCCTATGAAAATGCTTGCGCTGCAGGATTTCTTTAGTGGGGATGGAGAGGAAATGGATTTGAAGAAGGTGGCTTCTGCTGTAACTTTATGA[G/GT]TTTTTTTATGTAATTGTTGATGAGTTCGTATACAACTCGGCTTGCTTTGGCTAAAAGTGTAATCTGTTCTGCTTTCTTGATGTTTTG
109139 T C TGAAAATGCTTGCGCTGCAGGATTTCTTTAGTGGGGATGGAGAGGAAATGGATTTGAAGAAGGTGGCTTCTGCTGTAACTTTATGAGTTTTTTTATGTAA[T/C]TGTTGATGAGTTCGTATACAACTCGGCTTGCTTTGGCTAAAAGTGTAATCTGTTCTGCTTTCTTGATGTTTTGAATAAATAATTATGTA
109147 A G CATTTGTGTTCACAAAAAGTGGAGCATAGCTTGCCATTTCAACAGCATCGCTGTTCTTTTCCAGTCCAATAAGAAATGCAGCTTCACCTAAAGCAGCTAA[A/G]AGGCTACCAGTGCCAGCATCATTTCCTGTAACGGCATATTCACTTACAAAAGCCTTTGGACCCTTACGTGATGTAGTGTCAAATTTATT
109147 T C TAAAAGGCTACCAGTGCCAGCATCATTTCCTGTAACGGCATATTCACTTACAAAAGCCTTTGGACCCTTACGTGATGTAGTGTCAAATTTATTAGCCATT[T/C]GGAACAATGTATTAGCACTGCTGTAGACATGAAAATCATACAGGTGAGCTGGATGATCTAATGCACGAGAAGATCCATCACAATTTGA
109147 C T GTTGGTTGGTAGTCAACTGAAGCCTCGAATTACTGTTTGATTCAGTAGCATCTAACTGAAATTCCATTTTTTTCCAGTCTGATACTTCCGAATTTGATGC[C/T]GATATAGCATGAGAAGCCAGAACTTGCAATCCATCAGAACTTGTAAGTGAAACCAATAGGTTCAGCGAGCCCGTCGACTTCACAAATAG
109147 C G TCCAGTCTGATACTTCCGAATTTGATGCCGATATAGCATGAGAAGCCAGAACTTGCAATCCATCAGAACTTGTAAGTGAAACCAATAGGTTCAGCGAGCC[C/G]GTCGACTTCACAAATAGTACCACTTTATAGCTTTTTCCCTTTTCAATGTTCATTCCCCAATATCCAGGGTTATATACACCCACACCACCG
109147 T A CAGTCTGATACTTCCGAATTTGATGCCGATATAGCATGAGAAGCCAGAACTTGCAATCCATCAGAACTTGTAAGTGAAACCAATAGGTTCAGCGAGCCCG[T/A]CGACTTCACAAATAGTACCACTTTATAGCTTTTTCCCTTTTCAATGTTCATTCCCCAATATCCAGGGTTATATACACCCACACCACCGA
109149 T C TGGGGTCAGGCGAACATTTTCATCTTTTCCTGGAGCACGTATGTTAGTCAACTCTTTTGTCCGAACAGGGTTTACATCAAGATCAGTATCACGGGAATGT[T/C]CTCCAACAATCATTCCATCATATGTCTCCATTCCAGGAGCCACAAAAAGAGTTCCACGGGGCTCCAAACTCGCCAGTGCGTGAGCAGT
109149 G A TTGTTTCGGATTCTGCATATAGACGATCGCCGATTTTTCCTCCAGTCAAATGAGTCCCATCACGACCAGCTAATGGAGAATCATTGACACCAAAAGTCAT[G/A]GAAATTGTTGGAGGATCCAACTCAACGGTAGGAAGAGCAGTCATGACCTCCACATTTGTTATTGTGTGACCAATTGATGGATTAGATA
109149 A G ACACCAAAAGTCATGGAAATTGTTGGAGGATCCAACTCAACGGTAGGAAGAGCAGTCATGACCTCCACATTTGTTATTGTGTGACCAATTGATGGATTAG[A/G]TAATCCGGTCATTGAGATAATATCACCAGCTCCTGCGCTGTCTATTACAATCACGCTTGTTCCTTTCTTTTTCATTAGCTTAGTTATCC
109155 AT A CCCGAATGGGGCTTGGTAAATCTACTTCGAAAGATGAACCACCAGAATTTGGTGCAGCAGCCGATGGTGATGCAGATCGTAATATGATCCTTGGTAAAAG[AT/A]TTTTTTGTTACTCCGTCGGATTCTGTTGCAATAATTGCTGCTAATGCTGTGGAAGCTATACCTTATTTTTCTTCTGGGCTGAAAGGA
109155 GA G AGTTTCTGTGGAAGACATTGTTCGCCAGCATTGGGCAACTTATGGTCGCCACTACTATACTCGATATGATTATGAGAATGTTGATGCTGGTGCTGCCAAA[GA/G]AACTAATGGCATATTTGATCAAACTACAATCCACTCTTCAAGAGGTTAACAAGATCATTCAAGGAATAAGGTCAGATGTCTCAACCG
109155 A G GCCAAAGAACTAATGGCATATTTGATCAAACTACAATCCACTCTTCAAGAGGTTAACAAGATCATTCAAGGAATAAGGTCAGATGTCTCAACCGTAGTTG[A/G]CGCAGATGAATTTGAGTACAAAGATCCCGTTGATGGTTCGATTTCTAAACACCAGGGTATTCGATATCTCTTCCAAGATGGTTCTAGA
109159 CT C TCAACTGTAGTTTCTCAAGCAGTCACTGCCAACAGAATAAAATTTTCAGAGTTCTACATAACCCTAACAACTAAAGCATGTATAATGTATATTACATTCA[CT/C]TTTTAACTTAAAAACCCGTGTTCTAATCACAAATATAAACAACTAAACAGCAACAGCCGGAGGCGAAGTTTCAGCCAATCCACTTTCAC
109161 A G AAGTACGTTATTCTATGACTCATATATCTGCAGTTTTCATGGTGGAGATTCGATCGTTCAAGGTGACAACCAAATCGTGTGCATCATCTAGAAGCTTCCA[A/G]ACATCCAAGTTTCCAGCCATACTGTTACACTCTCTAATGATCTCGTCCATGCTACTATAACTCTCAATTATCAACTTCCTCCTCTGCAGAA
109161 C T TGATTTTATTATTTTCGACACTATGTTCAGCTGTCTCCTTATACCGACCTCGTCCAGCCTGAAATTATGCCGAGCTTTCCTCATGAAGCTCACAAAACAC[C/T]AAAACGCTTCATCATCTTCTTCCATCACGGCTAAAATAGGAGACAAAAGGTCGCTCATTCCTTGACAGTAGCCGATCTCTTGGTCATATA
109165 A AT GCTTACAGTGAGAATTTACCCGTGATTTGTATCGTTGGCGGGCCCAATTCGAATGATTTTGGGAGTGGTCGGATTCTGCATCATACTATTGGACTGACGG[A/AT]TTTTTCGCAGGAGCTCAGGTGTTTTCAAGCTGTTACTTGCTTTCAGGCCGTGGTGAATAACTTGGAGGATGCACATGAGTTGATTG
109167 G A CATACCCGCCATGGATGCTCAAGACATTGAGTCCCGTCACCCCCTCATCGGCGCGCGCCCTCGAAGGAGAGCTTTAAGGTCTCTTTCGGTTCTTCTGGCC[G/A]CTGCTCTTTTGCTCGGTTTGGTTCTGTTTTATGCTAACGGGACTGGTTCGGGTACGGCCGTGGATCCGGTACGGGTTGATAACGAGT
109167 C T TAACCGAAAATACTGCAACTTACTTCTATGTTAGCAAAGGAATCGATGGCTCTTTACGCACTCACTTTTGCCAAGATGAAACAAGGTCATCAAAGGCTAA[C/T]GATATCGTTAAAAGGGTGGTAGGAGGCACTGTTCCAGTGCTTGACGGTGAAACCTTTGCAGTAAGAATATTGGTGGACCACTCGGTG
109167 A T CTCACTTTTGCCAAGATGAAACAAGGTCATCAAAGGCTAACGATATCGTTAAAAGGGTGGTAGGAGGCACTGTTCCAGTGCTTGACGGTGAAACCTTTGC[A/T]GTAAGAATATTGGTGGACCACTCGGTGATTGAAAGCTTTGCCATGGGAGGTAGGACGAGTGCGACTTCTAGAGCGTATCCAACCG
109167 G T GAGGCACTGTTCCAGTGCTTGACGGTGAAACCTTTGCAGTAAGAATATTGGTGGACCACTCGGTGATTGAAAGCTTTGCCATGGGAGGTAGGACGAGTGC[G/T]ACTTCTAGAGCGTATCCAACCGAGGCAATAAATTCCGCGGCTAGGGTCTTCCTCTTCAACAACGCAACCGGCGTAGATGTGATTG
109167 T C CCATGGGAGGTAGGACGAGTGCGACTTCTAGAGCGTATCCAACCGAGGCAATAAATTCCGCGGCTAGGGTCTTCCTCTTCAACAACGCAACCGGCGTAGA[T/C]GTGATTGCCGAATCTGTGAAAATTTGGCAAATGAACTCCACTTACAATGATTTTTATCATTTTTAAGTGTGCCATGAAGAGCTCTCT
109167 A G CGACTTCTAGAGCGTATCCAACCGAGGCAATAAATTCCGCGGCTAGGGTCTTCCTCTTCAACAACGCAACCGGCGTAGATGTGATTGCCGAATCTGTGAA[A/G]ATTTGGCAAATGAACTCCACTTACAATGATTTTTATCATTTTTAAGTGTGCCATGAAGAGCTCTCTTTATCTTTAAATGGTTCCACTG
109173
GAGCCTTTTTACCGAACAATTGA
G AACAGAAGGTCAAATTAATTTGTGAAAACCTAAGCACATTATCAGCTCATGCATCATCGTTGATTCCAAATTTACTGAATAATGAGGATATTGAGCTTGT[GAGCCTTTTTACCGAACAATTGA/G]AGCCTTTTTACCGAACAATTGAAGAAATTACCCCCTCCGAAGGAGGAGTGTCATATTCAGGGTGTT
109181 TC T ATTCCGCCATAATGCCTGGAATCATCTCTCCGGTCGGTGCTCCGACAGTCGAAATTCCACAGACTGATCTGAATCCAAACCCCAACCCTCAGATCCGAAC[TC/T]CCCCAAAACCCTAGGAACCGTATGTCCCCTAGCCCTAGAAAAACCGCATCGCCTTCGCCTTCTTCCGCGCTAAAGAAGCGTGGATCG
109181 T C GCAATGGATGAGTCCGCGCTAGACAACCCGGATCTTGGGCCGTTTCTGTTGAAATTGGCAAGAAATACGATTGCATCGGGCGAGAGTCCGATCAAGGCGC[T/C]TGATTATGCTATTCGAGCTTCCAGATCGTTCGAGAGGTTTGAGGGTATGAAGCTGGATCTTGCTATGAGTTTGCATGTTACCGCAG
109181 T C CATACATTTCTCTTGGTCGTTTCGATGAATCCATCTTTTCTTACCAGAAAGCACTGACTGTATTCAAATCAGCTAAAGGAGACAATCATCAATCAGTTGC[T/C]TTAGTCTATGTACGGTTAGCTGAACTTTATTACAAGACAGGCAAGCTTCGTGAATCAAAGTCGTATTGTGAGAATGCTTTAAGAATCTAT
109181 A G TAGCTGAACTTTATTACAAGACAGGCAAGCTTCGTGAATCAAAGTCGTATTGTGAGAATGCTTTAAGAATCTATGCAAAACCCGTTCCTGGAACTCCAGT[A/G]GAAGATATAGCTGGTGGTTTGATGGAGATATCTGGTATCTATGAGGCAATGGATGAACCTGAGGAAGCATTGAAATTATTACAGAA
109181 A G AAGATATAGCTGGTGGTTTGATGGAGATATCTGGTATCTATGAGGCAATGGATGAACCTGAGGAAGCATTGAAATTATTACAGAAAGCTTTGAAACTTCT[A/G]GAAGATGTGCCTGGACAATGGAGCACAGTTGCAGGGATTGAGGCGCAAATGGGAGTAATTTATTATATGGTAGGAAAGTATGTAG
109181 C T CTAGCGGCGAAAGAAAGTCAGCATTTTTTGGAGTTGTATTGAACCAATTGGGTCTGGCTTGTGTACAGTTGTTTAAGATTGATGAAGCTGCAGAATTGTT[C/T]GGGGAAGCAAGGGCAATATTGGAACAGGAATACGGGGCTTGTCATCAGGATACCCTTGGTGTGTACAATAATCTAGCTGCAACTTA
109181 G C CAATATTGGAACAGGAATACGGGGCTTGTCATCAGGATACCCTTGGTGTGTACAATAATCTAGCTGCAACTTATGATGCCATGGGAAGGGTAGAAGATGC[G/C]ATAGAGATAATGGAATTTGTAGTAAAACTCAGGGAGGAAAAACTGGGTTCTGCGAACCCCGAAGTGGACGAGGAAAGGAGAAG
109185 G A AGCTGCTACTTACTCCCAGACTCTCTGCAAGTCTAAGTATATATGACTGTATCGATCTACAGTTTGATGATACAGAATCTGGAAGCTCGGGTAGACACTC[G/A]GGCAGAGATTGACTACTTCTATCTGGAGAATTGTACAGTGAAAGTACAGCTCTGCAGAATATAAACCTAACAATCAAGCGGCGCAGG
109185 G A TATTTGATGTGCAAAGGGCGATTTCCCAATCAGCCAAGGCAGATGATATTATAGCATCACCATTGTTGTATGCATCATCATCGGTATCTAATGTAAGACC[G/A]ACTAGCTGGCAAAATGCTAGCAATGGAGCAGTTAGGAAAAATGTGAACTGACTTCCATTTGGTGTTTGATCTGAAGATGCTGATATC
109195 T C AAGTTTTTTTATTCCTGAACCCCACAACTTCATTCCTTGCACCAACGCTCAACTCATAACAGAAACTAACAAACGCACTCCCTTCTCCCTCTTCTCTATA[T/C]GTCTGACCCTAACTCAAAACTGGCAAGAAGTGCCAAGTCTCTGCTTCTGCTTCCCAGCCGCTCCACACTTCCTGTCAACAAATGCTTCGTG
109195 A G TGAAACGGCGGGAACCAGATGCTTACTGATAGCTCGAGGATTTGACGCTGCATCATCACTCTCACAACCCTCCTCTTCATCTTCCTCGTCCAAGCTTCCG[A/G]GCCTTGAAAATGGGTTCCTGTAATGGGGCTTATACGGCGACGAAACGTCTTCAGAATCAAGCAAAAACTGAGTTTCGTCTTCGTCTCC
109195 C T CCTCTTCAGAAAATGGGATAGAAGCCTGAGGCCAGTGAATCCACTCAAAATATGGGTCTTCCAAGTTTTCCGGTAAGCAAAGCCCATGGTCGATAGGGAT[C/T]AATTCCATCGTCGCCCTCCCGAACCTTCCATTTCCACCACTCTCGACTCTTTTCACAAGTAAATTACCAGCATGCCGATCGGTGTTAA
109195 G A CAAAATATGGGTCTTCCAAGTTTTCCGGTAAGCAAAGCCCATGGTCGATAGGGATCAATTCCATCGTCGCCCTCCCGAACCTTCCATTTCCACCACTCTC[G/A]ACTCTTTTCACAAGTAAATTACCAGCATGCCGATCGGTGTTAAATATGCGTATATCGAGTATACCGATCCTATGCACAGCAGATACAGA
109195 A G TTCCATTTCCACCACTCTCGACTCTTTTCACAAGTAAATTACCAGCATGCCGATCGGTGTTAAATATGCGTATATCGAGTATACCGATCCTATGCACAGC[A/G]GATACAGAATAGCTTGAAGTTCCATGATCGCTAGCGTCAAAGTCATGAGGTATGAATTGCTGAAATGAGGCGATCTTGCTAACAGGTT
109195 G A TATCGAGTATACCGATCCTATGCACAGCAGATACAGAATAGCTTGAAGTTCCATGATCGCTAGCGTCAAAGTCATGAGGTATGAATTGCTGAAATGAGGC[G/A]ATCTTGCTAACAGGTTGCGGGTTCTGTGAGTTCCTTTCATGCACATTGCTGTTCACATTGAAGATCGAGTGGGTCACCTTGACAAGC
109195 T G CTATAGCAACACTATCGCCTTTACTATTCCTAAAGTTATATGCTCCCCCTAGCCCACCGTTTACAGGTACAGGGTCCACACCGCTTTTTATAGCTTTGAC[T/G]ACGTCTTGAACAAGCTGTTTGGTACGGGTATCGGGTCCACAGCCTAAAATTTCGACTAATCCACTTTGATCTCTTTGCTGAAGATCTTTTG
109199 A G CTGGAGCTTTCAAGATAGGGGATACTGCCGGAACCATTGATAACATAGTTCACTGCAAGCTTTATAGACCTGGCTCGGTTGGATTTGTTTCGAAATCAGG[A/G]GGCATGTCCAATGAGATGTACAACACAATTGCCCGTGTAACTGATGGAATTTATGAAGGCATTGCAATTGGCGGGGATGTTTTTCC
109199 G C AGCAAAAAATCAAGCTTTAAAAGAAGCTGGAGCGGTTGTGCCAACCTCATTTGAAGCATTAGAAGCTTCAATTAAAGAGACATTTGATAAACTTGTTGAA[G/C]AAGGGAAGATTGACCCAGTACATGAAGTTACACCACCTCAGATCCCTGAGGATCTCAGCACTGCAATTAAAAGTGGAAAAGTCCGT
109199 T C ATGGTCCGTGTGTATCTGGTGCTCATAACTCTATAGTGACTGCAAGGGCTGGAAAGGATTTGGTTTCTAGTCTTGTTTCAGGGTTGCTAACTATTGGTCC[T/C]CGATTCGGTGGTGCAATTGATGATGCTGCTCGGTACTTTAAGGATGCCTATGATAGGGGCCTCACTCCTTATGAGTTTGTTGAGAGCA
109209 C T TTACAAGCACAGGTTCACTCTTCTGGTCTGCTCCTAAACGCTTTCCCAAAGCATTGGAATTCTCATCTAATGATCCTACACACCTTCAATTCATCTTGTC[C/T]GCATCTATACTGAGAGCCGAAACATTTGGAATCCATATACCTGAGTGGGCAAAAAACCCGACTAAGTTGGCAGGTGTTGTTGATGACGT
109209 T TA TGAGAGCCGAAACATTTGGAATCCATATACCTGAGTGGGCAAAAAACCCGACTAAGTTGGCAGGTGTTGTTGATGACGTAATAGTTCCTGATTTTGAACC[T/TA]AAAAAGATGCAAAGATTGTTACAGATGAGAAAGCAACTAGCATGTCTAGTTCATCTATTGATGATGCTGTTGTCATCAGCCAACTT
109209 T C TGACACAAGGATGGAAAATGAATCCAATTCTGTTTGAAAAGGATGATGATACAAACTATCACATGGACTTCATAGCAGGACTTGCCAACATGCGGGCGCG[T/C]AACTACAGTATCCCAGAAGTGGACAAACTGAAAGCAAAATTCATAGCAGGAAGGATCATCCCAGCTATCGCGACTACAACTGCCAT
109209 G A GCTCCCCATGATCTCCATAGCGGAACCAGTTCCACCCAAGAAGATCAAACATCAAAGCCTGTCTTGGACCTTATGGGATAGATGGTCCATTCATGGGGAC[G/A]TCACCGTAAAAGAGCTCCTGGACTGGTTCAACAACAAAGGTTTGAACGCTTATAGCGTTTCTTGCGGCACTTCTTTGCTTTACAACAC
109211 T G ATGCTTGCTTGCAAGTTGCGGTTGCAAATATGAACGGATGTTTGGGGAAGAAGGGAGGGTTCGCCGTGGATGTGGCTTGTTTCATGAGGTTTTCGGATGT[T/G]GATTTTTTCGGGAATTACCCGACTGTCAATCTTCAGTCTCTTTTGTCCTCGATTTCAACCTCAGGAAAGTCAAGCCACAAATGGGCC
109213 C G TCCTTGAAAGACTGGTGAGCAGATGCTCTAATCTAGAAACCCTAAAGCTCAATCATTCTCTGCCTCTTGACCGCTTAGCAAATCTTCTTCTTCTGGCTCC[C/G]AAATTGATTGAACTTGGAACGAGCCGGTTTGCAGGAGACAGTAGGCCTGATCTTTATGCTAAGCTTCAAGCTGCATTTGCAGCATGCA
109213 C T TGCATTCGATCCTCTACTTCTGCCGCCAAATGACCAATTCCGCGCTTCAATCTGTAGCCAAAAGCCTCCCAGACCTTGTCCGTTTCCGTCTTTGCATCAT[C/T]GACCCTCAGACTCCTGACCACCAAACCGGACAACCCTTGGACCTTGGCTTTAGTTCGATTGTTGCCCTATGCAAAAACCTAAGACGGCTG
109213 A G AAATTAGGGATTGCCCCTTCGGGGACAAGGCTTTGCTAGCAAACATGAAGAAGTTGGAGACAATGCGATCCCTTTGGATGTCTTCATGCAACCTGAGTTT[A/G]GGAGCGTGTAGGGCGCTCGCCAGAAAGATGCCGAGTCTTAACGTGGAGGTGATCGACGAGAAGAGAGGCAAATGTGGCGGGTT
109221 CAT C TTTCATCTTCCTTCTCTTAAACTTCATCTAATTTCATCAGTTTGAACCAACAGATTCTTTGCTTTCCATCCTCCCTCTCTTTCTTATCCTTTTAA[CAT/C]ATATATATATTACTGAATAATCGGTTAAACAGAAGACGAAGAAACCTTACAAATGGTAAGGCCATCTCAAGACGCAATTAATACCTTCATCAGCAT
Supplemental Table 1. Sequences flanking single nucleotide polymorphisms and insertion-deletion events in cDNA assemblies of garlic. Positions of polymorphisms are shown in brackets

Putative Allele
cDNA 1 2 Sequence
109221 A G AAAATGGGTGAATTGGGTAAACATGCCGGGGAGCCTTCTGATTCAGTGGACATTGATTTGGATGACGTGGGAATAAGATCTCTTCCAAGTAGAAGGCAAG[A/G]ATCTGTTGCTGTTAATCGTCGGGCTTCAGGTAAATCTGTACTAGAGAGGGGAGGTACATCAATAGCTGAAGAAGCTGAAGATGT
109221 A G GTCGGGCTTCAGGTAAATCTGTACTAGAGAGGGGAGGTACATCAATAGCTGAAGAAGCTGAAGATGTCGATCTACAGCCTCTAGTGAGAAATCGCTCTAG[A/G]CGGTCTGCATCAGCACATGGAGTTTATAGTCCTCCATTAAGTCCTCGTGATAATCAACATGATGATCATCAGTCAAATGGAGGAAC
109221 T C AGAGAGGGGAGGTACATCAATAGCTGAAGAAGCTGAAGATGTCGATCTACAGCCTCTAGTGAGAAATCGCTCTAGACGGTCTGCATCAGCACATGGAGTT[T/C]ATAGTCCTCCATTAAGTCCTCGTGATAATCAACATGATGATCATCAGTCAAATGGAGGAACCTTTCCTATGGAGTGGGGAGGCAT
109221 T C CTGAAGAAGCTGAAGATGTCGATCTACAGCCTCTAGTGAGAAATCGCTCTAGACGGTCTGCATCAGCACATGGAGTTTATAGTCCTCCATTAAGTCCTCG[T/C]GATAATCAACATGATGATCATCAGTCAAATGGAGGAACCTTTCCTATGGAGTGGGGAGGCATCTCTTCTGAAGAACATGATGAGGC
109221 A G GTGGAGTCCCTGATGGAGTTCCTTATAATTTTAGTTACCCACGTGTAAGTGAACGTGTTCCTCCTCGGCCCCCGTCTCCTTCGCTTACTGCACAACGCCT[A/G]TTGAGGGAACAGCAGGATGATGAGTATCTGGCAGCATTGCAAGCTGATAGAGAAAAGACTGAACGCCTTCGCTTAGAAGAAGCTGTT
109221 T C GACAAGCTGCAGTATCTTTTTGATTACATTGACATTGGGAGAGCTGTGAAGCCTGGAACATACAGACTGGTACGGCCTTACCCGAGGCGCACATTCAGTA[T/C]TGAGGAGTCTGCATCTACAATGAGCGACCTGGGTTTGATTAACAAGCAGGAAGCCTTATTCCTAGAGCTAATATAGTGTGCTCTGC
109221 C A TTGACATTGGGAGAGCTGTGAAGCCTGGAACATACAGACTGGTACGGCCTTACCCGAGGCGCACATTCAGTATTGAGGAGTCTGCATCTACAATGAGCGA[C/A]CTGGGTTTGATTAACAAGCAGGAAGCCTTATTCCTAGAGCTAATATAGTGTGCTCTGCTAGATTAATCCTGTTGGTATACGCTTTCC
109221 G C TTTGATTAACAAGCAGGAAGCCTTATTCCTAGAGCTAATATAGTGTGCTCTGCTAGATTAATCCTGTTGGTATACGCTTTCCTGATTGGTTGTGTGTTAT[G/C]TTTTGCTGTTTGAATTTATTTTGAATTATTAAAAGGTATTTTATAACTTTGTTTGGCTATGATGAAGGGTATCACTATGACGCCCTCAGTA
109221 C T TAACAAGCAGGAAGCCTTATTCCTAGAGCTAATATAGTGTGCTCTGCTAGATTAATCCTGTTGGTATACGCTTTCCTGATTGGTTGTGTGTTATGTTTTG[C/T]TGTTTGAATTTATTTTGAATTATTAAAAGGTATTTTATAACTTTGTTTGGCTATGATGAAGGGTATCACTATGACGCCCTCAGTAGCATC
109221 A G GACGCCCTCAGTAGCATCATCAATCATCTCTGCTGGAATCATGGGCTTGAAATGTGTATCTTAGCAGATTGTTTTAATTGTTCTAAAGAAAGATAAATAT[A/G]TGATACTTTGTCAGATGATTCTGATATTTGCTTTATACAGGAAATAGATTTAAGGGTGCTAAAAAAAAAAAAAAAAG
109225 T C CAAAATTATTTATAGAAAATTTTCTCCTACTTCAACCAGGAAGCAAATCTTACTGTGGATTTGGTGGTCTGCTATTAGCTGCCGAAACCCTGGAACCCCA[T/C]TCAAGCAACTCTTTGCTGGTATCATCCTTGTGCACGGTAACTTCGATGAAGCAAAAGCTGTCTTTCTTCTCCCCTGTAGCCTTCTTAATT
109225 G C TGTCTTTCTTCTCCCCTGTAGCCTTCTTAATTGCATCCACCAGCTCTTCCTCATTGAATACTTTAGTAGTCCAGCATTTTCCTTCGCCATTATGGATGGC[G/C]TCGACTAATCCAGTGTAATTCCAGTTCTTTATCACGTTGTATGGACCATCGTGGATTTCTACTTCTATCGTGTAGCCTCCATTGTTTATCAG
109225 C T TCCAGCATTTTCCTTCGCCATTATGGATGGCGTCGACTAATCCAGTGTAATTCCAGTTCTTTATCACGTTGTATGGACCATCGTGGATTTCTACTTCTAT[C/T]GTGTAGCCTCCATTGTTTATCAGGAATATAATGCAGTTTTGTCCATTCCTTATCATGGTAGATACATCTTGTGCAGTCACCTGAAAGCTCC
109225 A C ATCGGGCAATTTTAGCTTCTGGCAGTTGAACCAAGAATCACCAGTCTCAGCAATCACAGCAGTATCACCAGACAACATTTCTTGAATGTGTTTAAACAGT[A/C]CATTCACTCTCAATGGCTCTTTAGGACCTGCCTTTAATGGCTGCCCTTCGGGTACAAAAATCCGACTATAGTTCTCATGTGCAGTGGTA
109225 C T GGCTGCCCTTCGGGTACAAAAATCCGACTATAGTTCTCATGTGCAGTGGTATTCTTCTTTAGCTTCTTAGACAGCTCCTCCAGAAAGTCTTTCATTAGAA[C/T]GCAACCGAATGCAGGTCCATTAGCAACCATAACTCGATCAGGTTGGATAATGATTGCCTTCTCCTTTTTTAGTAGTAAGGAGTACCCTA
109225 A G TCCGACTATAGTTCTCATGTGCAGTGGTATTCTTCTTTAGCTTCTTAGACAGCTCCTCCAGAAAGTCTTTCATTAGAACGCAACCGAATGCAGGTCCATT[A/G]GCAACCATAACTCGATCAGGTTGGATAATGATTGCCTTCTCCTTTTTTAGTAGTAAGGAGTACCCTACGGAGCTGTAATCATTAAATATA
109225 T G TGCGCCCCAGTACGTGCCAATAAACCTTGGGTGGGTTTCAGGCACGAGGCCCTTAGCGGATGGCATTACTGCTACTGGATATCCGCATGCATCAGCCAGT[T/G]CGACGAAGGCTTTGCATGCTTTGGATACGCGGAGTTTGGGACCTCCTACCATTACGGGTTTTACAGCTTTGTTGAGAAAAGCAGCT
109225 A G GATATCCGCATGCATCAGCCAGTTCGACGAAGGCTTTGCATGCTTTGGATACGCGGAGTTTGGGACCTCCTACCATTACGGGTTTTACAGCTTTGTTGAG[A/G]AAAGCAGCTGTGGCTTCTACTGCAGCCTCAAGACCCATTTGGTTGCTTACTTTAGGGGCCAAGGAGAAAGGAACAGGCTCTGTACT
109225 G C CACCAACAATGCAGATCAAAGGCAGATTTTCGGAATAAGCACCGGCGATGGCGTTTATGACGCTCAACCCGCCGACGGTAAATGTGACGACGCATGCGCC[G/C]ACACCGTTGGCACGAGCGTAGCCATCTGCGGCGTATCCGGCGTTGAGCTCGTTACAGCAGCCAATGTTAGTGAGGCCGGGTTCG
109227 C G CCAAAATCCTAATTTCCCCGCTAAAATGCCCCCGCTTTCTTCAATTTTCATTCCAACTCTCCTGCTCTTTCAGCTCGCGTGCTCAATGGAAGACCCCGCT[C/G]CTCAGATTACCGAAAACCCACAAAACCAGGATGGAGCACTTTCTCTTCTTGAGCGACACGAAGCTCAGCTCAACCGACTCGAATCCCAG
109227 G A ATGGTGGCGGAAGAATTAGGGTTTTTACAGAGACCGCTGGGACGCTGTTTGGGACTGTCATTGCTTCGGGAAAGGTTCTTGCTTTCATGAAGCAGCGCTT[G/A]CTTTTTCTGACCGAGAGAGGTGCTGGCTCGCTTGATTTGAGGTCAATGATGGTGAAAGAGACGGAATGCGAAGGTCTGAACGGA
109227 A G TTTTCTGACCGAGAGAGGTGCTGGCTCGCTTGATTTGAGGTCAATGATGGTGAAAGAGACGGAATGCGAAGGTCTGAACGGATCCATCGCCCAGACCTAC[A/G]CTTTTGACCGATCCGAACCAACCAAAGCATACGGCTTCACCTCCTCCGGAGACCTCATCCACATAGTCCTGCTAGGCGAAGCAGG
109227 C T ATTTGAGGTCAATGATGGTGAAAGAGACGGAATGCGAAGGTCTGAACGGATCCATCGCCCAGACCTACACTTTTGACCGATCCGAACCAACCAAAGCATA[C/T]GGCTTCACCTCCTCCGGAGACCTCATCCACATAGTCCTGCTAGGCGAAGCAGGCAACCTCAAATGCCGGGTTCGCTCCATTCGAAA
109227 G A CAAATGCCGGGTTCGCTCCATTCGAAAATCCGAAATCAACCCCGAAACCGTTTCCATCAAATCCATCCGAGGCTACCTTCTCGCCGCAACAGTGCAAAAA[G/A]TGCACATCTACAACATACCTCCCAGTACCACGGTCGGGTTGGTGCTCCTCGACCTCTCTTCTTCTCAACCCTCCAAGAAATCATACCCG
109227 A AT CCATTCGAAAATCCGAAATCAACCCCGAAACCGTTTCCATCAAATCCATCCGAGGCTACCTTCTCGCCGCAACAGTGCAAAAAGTGCACATCTACAACAT[A/AT]CCTCCCAGTACCACGGTCGGGTTGGTGCTCCTCGACCTCTCTTCTTCTCAACCCTCCAAGAAATCATACCCGATAATAACATTGAAAC
109227 G T TTGGTGCTCCTCGACCTCTCTTCTTCTCAACCCTCCAAGAAATCATACCCGATAATAACATTGAAACAGCTAACATACCCGTACCCGCATTGAGAAAACC[G/T]AGCCCGCTAATTGCAACAGATGGTGAGAAGCTTGTGTTGTTGGGTTTGGGCGGTGGTTACGTTGGTATATTCCGATCGAGACTACCGG
109227 T C CAGCTAACATACCCGTACCCGCATTGAGAAAACCGAGCCCGCTAATTGCAACAGATGGTGAGAAGCTTGTGTTGTTGGGTTTGGGCGGTGGTTACGTTGG[T/C]ATATTCCGATCGAGACTACCGGTGTATAAGGCGGTGAGCAGCCACGTGTTTTGGAGCGTGCCGCTACTTCTGTTCCTTCTGTTTCTG
109227 TC T CAGCCACGTGTTTTGGAGCGTGCCGCTACTTCTGTTCCTTCTGTTTCTGATAGGGCTGTGGCAGTTTTACGTGAGGAAGAAGGATTCACTTGGATGGGCC[TC/T]CCGGACGAAGCGTTCAGTACGTCATCGTCATCGACCGCTGCTGCAGCAGCCGCTGCTGCGACCGAAAGAGTGTATGGTGATGTGG
109227 CG C GCCACGTGTTTTGGAGCGTGCCGCTACTTCTGTTCCTTCTGTTTCTGATAGGGCTGTGGCAGTTTTACGTGAGGAAGAAGGATTCACTTGGATGGGCCTC[CG/C]GGACGAAGCGTTCAGTACGTCATCGTCATCGACCGCTGCTGCAGCAGCCGCTGCTGCGACCGAAAGAGTGTATGGTGATGTGGG
109227 A T AAGCGTTCAGTACGTCATCGTCATCGACCGCTGCTGCAGCAGCCGCTGCTGCGACCGAAAGAGTGTATGGTGATGTGGGTGATGTACGAGAGATTAGAGG[A/T]GGGGGGCTGAGGGGCCCTCCGAGAAGGTATGTGTCCCCTCCGTCTACGTACCCTGCAGGCCCAGCGATACCGTTCCGATCAGCT
109227 C T TGTCCCCTCCGTCTACGTACCCTGCAGGCCCAGCGATACCGTTCCGATCAGCTGCTGCTGGAGCAGAGTTAAAGTACAGAGGGGGTGGTGGTGGTAGTAG[C/T]CTTGAAACTCCTCCTGGGTTTCCTCCGAGGAGAGATCAGCAGTTGTTTTCTAGTAATGCTCCTGCTGTTGACCAGCATATCGACTG
109227 T C TTGAAACTCCTCCTGGGTTTCCTCCGAGGAGAGATCAGCAGTTGTTTTCTAGTAATGCTCCTGCTGTTGACCAGCATATCGACTGATCTTTACTGCATAT[T/C]GTCAATGGAAATGGTTGGGTGGCTTAATTTTCTTGTAACACGGAAAGAGCCTGCTACATGCTCGAGTTATATTTTGGTATGTACCATGG
109227 A T CTAGTAATGCTCCTGCTGTTGACCAGCATATCGACTGATCTTTACTGCATATTGTCAATGGAAATGGTTGGGTGGCTTAATTTTCTTGTAACACGGAAAG[A/T]GCCTGCTACATGCTCGAGTTATATTTTGGTATGTACCATGGCTTAGACAAACTGTTCGTTGAGTTATTTGTCTATTAAGCTTCACTAAAC
109227GCTTAGACAAACTGTTCGTTGAGTTATTTGT
G TTACTGCATATTGTCAATGGAAATGGTTGGGTGGCTTAATTTTCTTGTAACACGGAAAGAGCCTGCTACATGCTCGAGTTATATTTTGGTATGTACCATG[G/GCTTAGACAAACTGTTCGTTGAGTTATTTGT]CTTAGACAAACTGTTCGTTGAGTTATTTGTCTATTAAGCTTCACTAAACATATGTAATAA
109227 C T ACACGGAAAGAGCCTGCTACATGCTCGAGTTATATTTTGGTATGTACCATGGCTTAGACAAACTGTTCGTTGAGTTATTTGTCTATTAAGCTTCACTAAA[C/T]ATATGTAATAATTTTATGAAAGCTGTTAGTAACGAATGTCCACATTCTAGTTTCCGGGAAGAAAAAATGTAGTTAATGTTGATAAATCC
109229 T C TTGATCGACCTGAAGAAGGGATCTATGCACTCCCTGGAATTTTAGCAGCAACTGTTGGCAGGAGCATTGAGGATGTGTATAGAGGAAGCGATAAGGGAGT[T/C]TTGGCGGATGTTGAATTGCTTAGACAGATAACGGAAGCTTCGCGAGGTGCGATTTCTGCGTTTGTTGATCGTACCACAAACAAAA
109229 CA C GAGGAAGCGATAAGGGAGTTTTGGCGGATGTTGAATTGCTTAGACAGATAACGGAAGCTTCGCGAGGTGCGATTTCTGCGTTTGTTGATCGTACCACAAA[CA/C]AAAAAAGGTCAGGTGGTCGATGTGGCCAACAAACTAAGCTCGATATTGGGGTTCGGGGTAGAAGAACCATGGATTCAGTACTT
109229 AT A CCAGTGGGAGAGGATACTGGGAAACTTCCGAAGAGAATTTGGAGAAGTTGAAACAGTTGTATTCGGAAGTGGAGGACAAGATTGAAGGAATTGATCGATG[AT/A]TTTTTATGCAAAATCATTATCAGTGTACACAATGACTGATCATATTTCCCAAACTGTTAATGTATTTGATGTAATATTCATATAGA
109233 T C TGAGCCTCTTGACAGCATCCACAGGGCATCCGCGCAGACGACTTTGAGCTCGAGCTTGACTTCCGGGCTCTCGTTTTCTCTTTCTTTCCTGTTGTGGTGG[T/C]GGTCGGTGAAGCTTCCTGAATTGTCGGAATGAAGGGCATTTCTTGATATGCCTTGTACTACGGAGTGGACGCTGGTGTGCTTTTTGTT
109233 TC T GGTGTGCTTTTTGTTGGGAGGTTTGGTGAAGTCGTCAAGTTGGACTTCGAACGATAGAAGAGAGACTAAAGGCCGGATGGCGTTTTCGATGGCGAACTCT[TC/T]CCTTTTGCGACTGGGTCGTAGGATGCCATTTTGGATATGAGTTTGGCTACACGGGTTTGGAGTTTCATAGGGGAGTCTGAGAGT
109237 G T TTATGTACCCTATGAAGGCAACTAGGAGAGGGATACTGTCCTTCATGAAGACCTCAGTCCTACGCTTGTCGTCGAAGGAGACTGCATCGGTCGTGGCATC[G/T]GACTTGTCATCGCAGGAGATTGGGAGGGTGCTGGCTTTGCTGGAGCGGGTTTGGGCATAGATCCCGATTATGGTTTTGCCGAGGA
109241 CA C TTTTTTTTTTTAAAAACTTAAATCTCATTAAAATTTATACAACACTTTGTCAATTAAAATCGTGCATGTTCACAAGTATATATATAACAACAAATTATA[CA/C]AAATGGAGATCAAGACACTCAAACAGGAAGAGCTGTTGGTTTAGCAGGAGCAACCCTATTCTCAACTGGAATCTCAACAAATTCTGAAAG
109241 A G AATCGTGCATGTTCACAAGTATATATATAACAACAAATTATACAAATGGAGATCAAGACACTCAAACAGGAAGAGCTGTTGGTTTAGCAGGAGCAACCCT[A/G]TTCTCAACTGGAATCTCAACAAATTCTGAAAGGATTGCTCGGAACTCATCGCCGGTCATTGTTTCTTTTTCAATTAGGACCTCTACAA
109241 G A TTCCGAAAGTGGTTACCATCTGTTTAGCAAGACCAGTAATTTGTATCAAATCACCAACAGCACCAGTTGTCACTTCAGAATCCCCAAATATAATTTCTTC[G/A]GCTGCTCTGCCACCAAGACCGCCAACAATTCTTGCAAATAACTGTTGCTTTGAGATCAGTGTAGGATCATCGGCTGGGATAAACCATGT
109241 G A TGCCACCAAGACCGCCAACAATTCTTGCAAATAACTGTTGCTTTGAGATCAGTGTAGGATCATCGGCTGGGATAAACCATGTGAGACCACGTGCTTGACC[G/A]CGGGGTATTAACGTAACTTTTTGTACTGCATCATGGCCCGGAGTTAAAGTTCCACAAATTGCATGCCCGACTTCGTGGTAGGCAACC
109241 C T GCTTTGAGATCAGTGTAGGATCATCGGCTGGGATAAACCATGTGAGACCACGTGCTTGACCGCGGGGTATTAACGTAACTTTTTGTACTGCATCATGGCC[C/T]GGAGTTAAAGTTCCACAAATTGCATGCCCGACTTCGTGGTAGGCAACCAAGCTTTTACTTTTACCATCTGTCATGACTGTACCTTCCA
109241 C T TCCCACCTCCAATCCCAGTCCCCCTCTGCCTCCCAACCGCATCTATCTCATCTACAAACACAATGCAGGGCGCGTTCTCCTTCGCCTTCTTGAACAGGTC[C/T]CTCACCCTGGAGGCTCCAACCCCTACAAACATTTCCACAAACTCCGACCCTGAAATTGAAAAGAAGGGCACACCTGCCTCACCTGCAATG
109241 G C TGAACAGGTCCCTCACCCTGGAGGCTCCAACCCCTACAAACATTTCCACAAACTCCGACCCTGAAATTGAAAAGAAGGGCACACCTGCCTCACCTGCAAT[G/C]GCCTTAGCCAGCAGGGTTTTCCCTGTGCCAGGTGGACCAATCAGAAGCACTCCTTTCGGAATACGGGCACCCACTGCAGTAAATCGT
109241 T C CTGCCTCACCTGCAATGGCCTTAGCCAGCAGGGTTTTCCCTGTGCCAGGTGGACCAATCAGAAGCACTCCTTTCGGAATACGGGCACCCACTGCAGTAAA[T/C]CGTTCAGGCTTCTTCAAAAACTCCACCACTTCCATGAAATCCTGTTTGGCTTCATCAACACCGGCTACATCGTCAAACGTGACACCTG
109241 T C GGAACTTGGCCTTGGACTGCCCGAACTGGAGCGGGAACCCACCACCTGGCCCACCCATTCCGCCTCCTGACCTTCTAGATAACAGAAACAGGCCTCCGAT[T/C]AGTAGTAAAGGGAAGGCCAGGTTTCCAATCAAGTTGAATAACACATTGCCTGAGTCTTCTTGTGCGTTGTGTGCTGCGAAGTCGAT
109241 A G ACAGGCCTCCGATTAGTAGTAAAGGGAAGGCCAGGTTTCCAATCAAGTTGAATAACACATTGCCTGAGTCTTCTTGTGCGTTGTGTGCTGCGAAGTCGAT[A/G]TTTTTCTCTCTGAGCTTTTGAAGGAGCTCTTGACTTAGACCTGGAAGCTGGACACGTACTCTTTGGATGCGGTTTCCAAGTTCAGGT
109247 GA G TATCCATTGATTGGTGGTGGATCTGTGAAATCTAATTCGAGCACTGAGACGGAATCAAGTCACTGCGAGATTGGTGAATTGGATCCAAGTAAGATTAAAG[GA/G]AAAAATAATTTTCTGCAAACATTCAACTGGCGATTCTTCAAAGACATCAAAAGCAGATTTCATGAAAAGAGATGGTGCGATCGGA
109247 T A AATTGGATCCAAGTAAGATTAAAGGAAAAATAATTTTCTGCAAACATTCAACTGGCGATTCTTCAAAGACATCAAAAGCAGATTTCATGAAAAGAGATGG[T/A]GCGATCGGAGCAATATTTGCAGTTGAAACAGAAACTGCCAATTTTGGATCTTTCGTCGACTTCCCAGTCACTATAGTCTCTCCAAAAG
109247 A G CGGTAACAGTGGAAAAACACAAACCAGCACCTGCAGTGGCGTCTTTTTCGTCAAGAGGCCCATGTTCTCAAACTGGTAACATACTGAAACCCGATATCGC[A/G]GCACCAGGGGTTAACATACTTGCATCATGGATTCCAACAAACGATTCATCAGAAGTCCCTGTAGGGCAAAAGCCTTCATCTTTCAGT
109247 T C GCTCAAAAAATTCAAGTTCGGACTTGATATCTAACCTGAATTACCCTTCTATATCCGTTTCTAAGTTTAATGGAAAAGAAAGAAGGGTGAATAGAATAGT[T/C]ACCAACGTTGGAGCTGAAGAAGAAACATCATATGTTGCAAGCATTAAATCTCCCGATGGTTTAGACGTGAAGGTGAACCCCGAAAAG
109247 G C ATGGAAAAGAAAGAAGGGTGAATAGAATAGTTACCAACGTTGGAGCTGAAGAAGAAACATCATATGTTGCAAGCATTAAATCTCCCGATGGTTTAGACGT[G/C]AAGGTGAACCCCGAAAAGCTCCGGTTTACCAAAAACATCAAGAGTTTGAGTTATGAAGTAACATTCTCCGGTTCAAGTTCTTCACT
109247 CA C TTACCAACGTTGGAGCTGAAGAAGAAACATCATATGTTGCAAGCATTAAATCTCCCGATGGTTTAGACGTGAAGGTGAACCCCGAAAAGCTCCGGTTTAC[CA/C]AAAAACATCAAGAGTTTGAGTTATGAAGTAACATTCTCCGGTTCAAGTTCTTCACTCAAAGGATCTGTGTTCGGGTCAATAACTTG
109247 T C CTCAAAGGATCTGTGTTCGGGTCAATAACTTGGTCGGATGGAGTACACAGAGTCAGAAGTCCGTTTTCCGTAGAAACTAATTAACTGGAATCGGTTTCCA[T/C]ATAGTTCGATAAGGAATGACATTGAAGTGTAATGCCTAACTGGCTATATATAGCAACAAAAATGTAAACTAGAAACGGCCGGTAAA
109249 T TC ACAGTTACTGTGCAAGAGCTTCCCTTTTTTGACACCGTTAAAGTCAACTGTGCTGATGCACAAGCTATTGCAGAGGCTGCACAGAAGCATGAGATGAATC[T/TC]AGAGTTGTAGATGCTAACACAATAACTGTAGCATTTGATGAGACAACAACTATTGAAGATGTGGATACACTGTTCAAAGTATTCGC
109249 C T ACGTATGCCATTTGAATCTCCACAAAACATTTTGCATTCCACATGGTGGAGGAGGTCCTGGTATGGGACCAATCGGTGTCAAGAAACACTTAGCTCCATT[C/T]TTACCATCGCATCCTGTGATTCCAACTGGAGGATTACCTCCTCCTGAGGAAGCACAACCGCTGGGTACAATAGCTGCAGCACCTTGG
109249 G A ATTTGAATCTCCACAAAACATTTTGCATTCCACATGGTGGAGGAGGTCCTGGTATGGGACCAATCGGTGTCAAGAAACACTTAGCTCCATTCTTACCATC[G/A]CATCCTGTGATTCCAACTGGAGGATTACCTCCTCCTGAGGAAGCACAACCGCTGGGTACAATAGCTGCAGCACCTTGGGGTTCTGCT