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