merged individual callsets to construct our unified release (Table 1), comprising 42,279 biallelic deletions, 6,025 biallelic duplications, 2,929 mCNVs (multi allelic copy-number variants), 786 inversions, 168 nuclear mitochondrial insertions (NUMTs), and 16,631 mobile element insertions (MEIs, including 12,748, 3,048 and 835 insertions of Alu, L1 and SVA (SINE-R, VNTR and Alu composite) elements, respectively).Table 1Phase 3 extended SV releaseSV classNo. sitesMedian size of SV sites (bp)Median kbp per individualMedian alleles per individualSite FDRBiallelic site breakpoint precision (bp)Genotype concordance (non-ref.)Sensitivity estimatesDeletion (biallelic)42,2792,4555,6152,7882%*–4%†15 (±50)** 0.7 (±9.5)††98%¶88%¶Duplication (biallelic)6,02535,890518171%*–4%†683 (±1,350)‡‡94%¶65%¶mCNV2,92919,46611,3463401%*–4%†–NANAInversion7861,697783717%§ (9%)‡||||32 (±47)||||96%§32%MEI16,6312976911,2184%‡0.95 (±5.93)98%||83# −96%★NUMT16815735.310%‡0.25 (±0.43)86.1%‡NAFDR estimates are based on intensity rank-sum testing8 using*Affymetrix SNP6 and†Omni 2.5 arrays,‡PCR, as well as§long-read||PCR-free (250 bp-read) and¶CG sequencing (CG-based estimates used reciprocal overlaps of 50% and 20% for deletions and duplications, respectively). Estimate by comparing MEIs to all#calls or all★PCR-validated calls from20 (estimates for individual MEI classes are in Supplementary Table 4). NA, no previous data available. Differences in deletion and duplication counts are driven by size-cutoffs and classification of common duplications as mCNVs27.**Ascertained using read-pairs or read-depth††Ascertained with split-reads23.‡‡Estimated for tandem duplications||||Estimated for inversions with paired-end support from both breakpoints.
