Using annotations from dbSNP release 125 we identified 17,427 polymorphic non-synonymous SNPs in release 21 and 15,976 polymorphic synonymous SNPs. Of these, 15,583 non-synonymous and 14,324 synonymous SNPs were autosomal and could have ancestral allele status unambiguously assigned by parsimony through comparison to the chimpanzee and macaque genomes. We used the phased haplotypes for analysis in which missing data had been imputed. FST was calculated using the method of Weir and Cockerham59.
