Figure 4

Allele frequency properties of the Exon Pilot SNP variants. (a) The allele frequency spectra (AFS) for each of the seven population panels sequenced in this study, projected to 100 chromosomes, using chimpanzee as a polarizing out-group. The expected AFS for a constant population undergoing neutral evolution, θ/x, corresponds to a straight line of slope -1 on this graph (shown here for the average value of the Watterson's θ nucleotide diversity parameter over the seven populations). Individuals with low coverage or high HapMap discordance (section 9, 'Allele sharing among populations', in Additional file 1) have not been used in this analysis. (b) Comparison of the site frequency spectra obtained from silent and missense sites in the Exon Pilot, as well as intergenic regions from the HapMap resequencing of ENCODE regions, within CEU population samples. The frequency spectra are normalized to 1, and S indicates the total number of segregating sites in each AFS. Individuals with low coverage or high HapMap discordance (section 9 in Additional file 1) have not been used in this analysis. (c) Allele frequency spectrum considering all 697 Exon Pilot samples. The inset shows the AFS at low alternative allele counts, and the fraction of known variant sites (defined as the fraction of SNPs from our study that were also present in dbSNP version 129).