CNVRs that overlap with large SDs are present in multiple individuals. Overlapping calls from all individuals were merged into CNVRs and analyzed separately based on their intersection with SDs >10 kb. The number of individuals with CNV calls within each CNVR was counted (A). In total, we identified 1477 unique CNVRs that overlapped with SDs (blue) and 28,375 CNVRs that did not overlap with SDs (red). The graph shows the frequencies of CNVR presence across all samples. The length (B) and copy number (C) distributions of CNVs that overlap with genes differ significantly between the two data sets (KS test, P < 2.2 × 10−16). In the histograms shown in C, the bin with −10 values corresponds to events with absolute deletion; to ensure that all data were log2-transformable, these values were converted to a value of 0.001.
