Site frequency spectrum of derived variants.

(A) The site frequency spectra of 2,983,700 variants classified according to their mutational origin as defined by comparison to the outgroup. Variants are: SW (strong-to-weak; red line; 2,037,148 SNPs in total); WS (weak-to-strong; blue dashed line; 719,365 SNPs); SS (strong-to-strong; light grey; 117,806 SNPs); WW (weak-to-weak; dark grey; 109,381 SNPs). (B) The relative site frequency spectra of the four variants (variants and colours as in A). (C) Average frequencies of derived variants of different mutational classes. SW and WS mutations are classified as transitions (Ti, blue) or transversions (Tv, green), SS and WW as in A. (D) Average frequency of WS and SS variants that create CpG sites compared to those that create GpC sites. The blue dashed line represents the mean frequency of WS variants, the red line is the mean frequency of SW variants and the grey line is the mean frequency of SS variants. 95% confidence intervals generated from 200 bootstrap subsamples of all SNPs attributed to a particular class.