Primate CNV hotspots are more likely to be complex in nature. (a) Depiction of a typical primate CNV hotspot region, which is complex in nature, based on the presence of multiple overlapping CNVs with different breakpoints. Multiple members of a single gene family are present in this genomic region and may be contributing to some of the different CNV formations. CNVs were defined as complex based on whether they reciprocally overlapped other CNVs by less than 50% . (b) The ratio of complex and non-complex CNVs in primate CNV hotspot and non-hotspot regions. Note the greater number of complex CNVs among HCR CNVs. (c) Enrichment analyses for the 1000 Genomes Project hotspots overlapping HCR CNVs. We iterated 1,000 intervals that mimic the size distribution of 55 human CNV hotspot regions , and constructed the expected overlap distribution of these intervals. Blue bars show the expected distribution and the dotted line marks the observed overlap. Here, we are showing that the observed overlap is much higher than expected by chance independent of the size of the intervals (P < 0.001, Kolmogorov-Smirnov test).