Enrichment analyses of primate CNV hotspots. (a) Chimpanzee and rhesus macaque CNV coordinates were converted to human reference build hg18 coordinates using the Galaxy Liftover tool. HC and HR CNVs are human CNVs that overlap one or more chimpanzee or macaque CNV(s), respectively, when using a 50% overlap criteria. For human CNVs that overlap both chimpanzee and macaque CNVs (HCR), critera were employed that required at least a 20% overlap between CNVs from any two species and a minimum of 50% overlap for overlapping CNVs from all three species. (b) We generated 1,000 random permutated CNV datasets containing CNVs of similar size distribution to the 12,146 human CNVs identified in Park et al.  and Conrad et al. . The CNVs in each permuted human dataset were then assessed for their overlap with known chimpanzee and rhesus macaque CNVs. The x-axis represents the number of human permuted CNVs that overlap with chimpanzee CNVs (red distribution) or macaque CNVs (blue distribution) during these permutation iterations. The green distribution represents human CNVs that overlap with both chimpanzee and rhesus macaque (HCR) CNVs during these same permutation iterations. The y-axis represents the frequency of the permutated human CNVs that fall into each category. The dotted vertical lines indicate the actual number of overlaps with either chimpanzee CNVs (1,387), rhesus macaque CNVs (467) or both (170). (c) Based on the expectation of overlap with 1,000 random sets of intervals depicted in (b), the fold enrichment of human CNVs that overlap with chimpanzee (HC) or rhesus macaque (HR) CNVs is plotted, as is the fold enrichment of human CNVs that overlap with both chimpanzee and macaque CNVs (HCR). Error bars represent 1 standard deviation from the mean fold enrichment.