SV non-reference genotype concordance estimates ranged from ∼98% for biallelic deletions and MEI classes to ∼94% for biallelic duplications. 60% of SVs were novel with respect to the Database of Genomic Variants (DGV)19 (50% reciprocal overlap criterion, Fig. 1a), whereby 71% of SVs (50% reciprocal overlap) and 60% of collapsed copy-number variable regions (CNVRs, 1 bp overlap) were novel compared to previous 1000 Genomes Project releases6,8, reflecting methodological improvements and inclusion of additional populations. Novel SVs showed enrichment for rare sites, which we detected down to an autosomal allele count of ‘1’. And while variations in FDR estimates were evident with SV size and VAF (variant allele frequency), we consistently estimated the FDR at ≤5.4% when stratifying deletions and duplications by size and frequency, including for rare SVs with VAF < 0.1% (Extended Data Figs 1, 2). A comparison with deep-coverage Complete Genomics (CG) sequencing data indicated an overall sensitivity of 88% for deletions and 65% for duplications, with the false negatives driven largely by the relatively lowered sensitivity for ascertaining small SVs in Illumina sequencing data (Fig. 1b, Extended
