An integrated map of structural variation in 2,504 human genomes.

Phase 3 integrated SV callset.a, Novelty based on overlap of our SV set with DGV19 (upper panel, broken down by SV class), of collapsed CNVRs with earlier 1000 Genomes Project releases6,8 (middle panel) and of our SV set with refs 6, 8 (bottom panel). b, Size distribution of ascertained SVs (bin width is uniform in log-scale). DEL, biallelic deletion, DUP, biallelic duplication, INV, inversion, INS, non-reference insertion (including MEIs and NUMTs). c, Breakpoint precision of assembled deletions stratified by VAF (split-read caller Pindel23 shown separately). d, SV allele sharing across continental groups. e, LD properties of biallelic SV classes.PowerPoint slide

SV functional impact.a, Relative enrichment or depletion of genomic elements within breakpoint-resolved deletions binned by VAF. TF, transcription factor binding site; nc, noncoding. RVIS range from 0–100 (low < 20, medium 20–50, high ≥ 50). *no element intersected. b, Enrichment/depletion of genomic elements within different SV classes, compared with breakpoint-resolved deletions. c, Manhattan plot of DUSP22-eQTL. Inset, boxplots of association between copy-number genotype and expression. d, Manhattan plot of ZNF43-eQTL. e, Enrichment of SV-containing haplotypes at previously reported GWAS hits (error bars show s.e.m.).PowerPoint slide

SV complexity at different scales.a,PSG locus with clustered SVs. Population copy-number state histograms are shown for two example SVs. b, Schemes depicting assembled complex deletions. c, Smaller-scale complex deletions identified with Pindel23. Flanking sequences are shown for reference (REF) and alternate (ALT) alleles, further to insertions at the breakpoints. Proximal stretches matching the insertion are labelled in red (forward) and green (reverse complement). Blue, insertions lacking nearby matches. d, Alignment dot plots depicting inversions (inverted sequences are in red within each dot plot). Adjacent schemes depict allelic structures for REF and ALT. e, Inversion complexity summarized.PowerPoint slide