+This track shows per-sample genotypes for 111,288 structural variants (SVs) +from 945 Han Chinese individuals, displayed as a VCF track. It is a companion +to the Han 945 SVs bigBed track, which +shows the same variants with summary statistics and filters. +
++The VCF format allows the genome browser to display a genotype matrix showing +which of the 945 individuals carry each structural variant. +
+ ++Each variant is shown with per-sample genotypes: 0/1 indicates the sample +carries the SV, 0/0 indicates it does not. The genotype coloring follows +standard VCF display conventions. +
++Samples are labeled Sample_001 through Sample_945, as the original data +release does not include individual sample identifiers. +
+ ++The original VCF from Gong et al. is a site-only file (no sample columns) +produced by merging per-sample SV calls with SURVIVOR v1.0.6. SURVIVOR +records which samples support each SV in the INFO/SUPP_VEC field — +a binary string of length 945, where each position represents one sample +and '1' indicates that sample's caller reported the SV. +
+
+To reconstruct per-sample genotypes, the SUPP_VEC was expanded into 945
+sample columns with a GT (genotype) FORMAT field. Samples with a '1' in
+SUPP_VEC were assigned genotype 0/1 (heterozygous carrier); samples with
+'0' were assigned 0/0 (homozygous reference). This is a simplification:
+the original per-sample callers may have reported homozygous alternate (1/1)
+genotypes for some individuals, but this information is not preserved in the
+SURVIVOR merge. The conversion was performed with the script
+lrSvHan945SuppVecToVcf.py.
+
+The source VCF was downloaded from the OMIX repository (accession OED00945268) +at the National Genomics Data Center (NGDC). +
+ ++Thanks to Gong et al. for making their structural variant calls publicly available. +
+ ++Gong J, Sun H, Wang K, Zhao Y, Huang Y, Chen Q, Qiao H, Gao Y, Zhao J, Ling Y et al. + +Long-read sequencing of 945 Han individuals identifies structural variants associated with +phenotypic diversity and disease susceptibility. +Nat Commun. 2025 Feb 10;16(1):1494. +PMID: 39929826; PMC: PMC11811171 +