Advances in Illumina sequencing towards longer read lengths (∼100 bp versus 36 bp)6 in conjunction with the population-level data allowed us to perform an in-depth investigation of SV complexity and clustering. We identified 3,163 regions where SVs seemed to cluster (>2 SVs mapping within 500 bp; Supplementary Table 11). To reduce redundancy caused by multiple overlapping calls per sample, we calculated distinct CNVRs per cluster by merging calls per sample and haplotype and then counting the distinct CNVRs produced across samples (average 6.4 ± 7.2 CNVRs per cluster). We identified 30 genomic regions with an excess of CNVRs (>4 s.d. or >36 CNVRs per cluster). This clustering effect was not correlated with segmental duplications (r = 0.02) and only partially explained by SNP diversity (r = 0.15; Extended Data Fig. 9). CNVR clusters showed enrichment near late-replicating origins (P = 0.013, permutation test) and at cytogenically defined ‘fragile’ sites (P = 0.0017; permutation test). Although the proportion of gene content in regions exhibiting excessive SV clustering was significantly reduced when compared to a null distribution (P < 0.000001, permutation test),
