Control CNVs were merged into CNVRs by comparing each CNV to all of its overlapping partners and merging those with 50% reciprocal overlap. These CNVRs were then analyzed in the context of sliding 300 kbp genomic windows to identify regions of high variability (Supplementary Figure 9, Supplementary Table 13). Regions of high SNP diversity were obtained from Kidd et al.44 and used to identify regions where the breakpoint variability is likely to result from general sequence variation (such as the HLA locus on 6p). To perform a gene-based search for highly variable loci, we first generated a merged RefSeq list that combined overlapping splice variants into a single, large gene definition. We then analyzed these loci in the context of overlapping gain and loss CNVs that either contained the entire gene, overlapped the transcript (gene breaking or exon hits), or were contained within an intron. Finally, we analyzed each gene in the context of the number of unique CNVRs that overlapped the gene space (exonic or intronic).
