Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans.

Even after controlling for mutational composition with these models, a significant trend persists for nonsynonymous variants.

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Indeed, we find highly significant differences in the SFS at CpGs (see S1 text for details), consistent with this expectation: i.e., fewer rare variants in heterochromatin, where methylation levels are high.

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Looking more broadly across the primates, we observed a clear trend of cSFS across substituted species ( Fig 2C ): the more closely related the substituted species, the greater the skew towards high frequency variants.

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