Identified SNPs and small indels. Identified SNPs (A) and small indels (B). We used the RefSeq and GenBank gene sets (16,635 genes) to annotate the detected variants. We found 1,003,695 intron SNPs, 17,684 untranslated regions (UTRs), 801 splice-site SNPs, 8,719 synonymous SNPs, and 11,713 nonsynonymous substitutions. Among the identified indels, 104,389 were found in intron regions, 2,942 in exon regions, and 138 in splice-sites.