We tested for biases of certain mutation processes or functional locations for CNVs with high VST values. We noted that VNTR are significantly enriched in both tails of the VST distribution (Supplementary Fig. 1.11), whereas CNVs formed by NAHR seem to be uniformly distributed across the spectrum of VST. The enrichment of VNTR in the low end of the VST distribution is expected given the recurrent mutation at these loci, but the enrichment at the highest decile of population differentiation suggests that among all CNVs, VNTR may be enriched for functional impact. The most differentiated CNV between CEU and YRI previously identified9 encompasses the CCL3L1 gene, and remains the most differentiated exonic CNV here. However, we identified 21 more highly differentiated loci, all of which are intronic or intergenic, suggesting a role in gene regulation might underpin any recent positive selection.
