Extended Data Fig. 7: Lenient SV catalog.

Similar to Fig. 5a but including SVs close to centromeres, telomeres, or within segmental duplications were removed. Number of SVs across samples. In the left panel, SVs were annotated with three SV catalogs (the gnomAD-SV database, a long-read-based SV catalog, and the HPRC v1.0 SV catalog). SVs are matched if they have at least 10% genomic overlap. The colors highlight the maximum frequency across these catalogs, the lighter blue showing ‘rare’ SVs (with an allele frequency below 1%) in the catalogs, or unmatched. SVs may be unmatched, either because they are novel or due to the difficulties in the database comparison. The right panel shows the number of rare SVs in protein-coding genes, grouped by their impact on the gene structure.