Fig. 2

Annotation of the 32mSNPs. a Distribution of the SNPs along 20 chromosomes compared with the dbSNPs. The outermost circle represents the 20 soybean chromosomes. 0, 20, and 40 outside the circle represent 0 Mb, 20 Mb, and 40 Mb positions on the chromosome, respectively. The solid gray boxes and black bars indicate pericentromeric regions and centromeric repeats, respectively. The black, red, and blue curves of the inner circle showed the distribution of the SNP set identified in the 1.5 K accessions, soybean dbSNPs, and the subset of SNPs with minor allele frequency ≥ 0.25, respectively. b Percent of the SNPs in the 32mSNPs in genome features (intergenic and intragenic). c Percent of genic SNPs in the 32mSNPs (Intron, CDS, UTR). d Percent of synonymous (Syn), non-synonymous (Nonsyn) SNPs, and the SNPs in splicing sites, start codons, stop codons, and the SNPs causing premature in the 32mSNPs. e Percent of identity at the coordinate-matched SNPs for the accessions that have been genotyped by genome-resequencing and SoySNP50K. f A SNP report exemplified with two previously identified domestication genes. G encodes a stay-green gene controlling soybean dormancy and GmHs1-1 encodes calcineurin-like protein controlling hard-seededness. The SNP report contains 30 annotation categories for each identified SNP in the 32mSNPs. Reference and alternative alleles were highlighted in green and red, respectively