Description

This track shows structural variants (SVs) from the third phase of the Human Genome Structural Variation Consortium (HGSVC3). The callset comes from 65 diverse individuals across five continental groups, each sequenced with PacBio HiFi (~47x), Oxford Nanopore ultra-long reads (~56x) and complemented with Strand-seq, optical mapping, Hi-C and Iso-Seq for haplotype-resolved assembly. SVs were discovered from the de novo assemblies with PAV v2.4.0.1 and cross-validated by ten additional orthogonal callers.

The track merges the two final SV annotation tables from the HGSVC3 v1.0 release on GRCh38: 176,232 insertions/deletions and 300 inversions, for a total of 176,532 SVs. Each row is a site-level variant with the list of carrier haplotypes and additional structural annotations.

Display Conventions and Configuration

Items are colored by SV type:

• Deletions (DEL) - red
• Insertions (INS) - blue
• Inversions (INV) - orange

Insertions are placed at the insertion site with a width of 1 bp; deletions and inversions span the affected reference interval. Filters are available for SV type, SV length, carrier-haplotype count, distinct sample count, whether the site falls in a Tandem Repeat Finder region and the fraction of the variant overlapping segmental duplications.

The detail page shows, where available:

• Allele / Sample Count: number of carrier haplotypes (out of the 2*65 = 130 phased haplotypes plus unphased "un" entries) and the number of distinct samples carrying the variant.
• Reference / Contig Homology: microhomology length (5',3') at the breakpoints in the reference and in the assembly contig (insertions and deletions only).
• Inner Inversion Region: for inversions, the coordinate range of the inner inverted sequence, distinct from the outer breakpoint interval.
• Transposable Element: when the inserted or deleted sequence was classified as a known TE family.
• Segmental Duplication Overlap: fraction of the variant interval overlapping UCSC segmental duplications in the reference.
• Carrier Haplotypes: full list of haplotype IDs (e.g. HG00096-h1, HG00096-h2, HG00514-un) carrying the variant.

Methods

HGSVC3 produced haplotype-resolved de novo assemblies for 65 samples spanning five continental groups. Assemblies were built from PacBio HiFi and Oxford Nanopore reads, phased with Strand-seq and further validated with Hi-C and optical mapping. Structural variants were called by aligning each haplotype back to the reference with PAV v2.4.0.1; calls were then cross-referenced with ten independent callers. The final annotation tables (this track's input) include merge statistics (MERGE_RO, MERGE_OFFSET, MERGE_SZRO, MERGE_OFFSZ, MERGE_MATCH) that describe how well each per-sample call matched the merged consensus site.

Two tables were merged for display here: variants_GRCh38_sv_insdel_HGSVC2024v1.0.tsv.gz (DEL + INS, 176,232 records) and variants_GRCh38_sv_inv_HGSVC2024v1.0.tsv.gz (INV, 300 records). Type-specific columns (HOM_REF/HOM_TIG/TE for insdel; RGN_REF_INNER for inversions) are shown as empty on the detail page when they do not apply.

Data Access

The data can be explored interactively in table format with the Table Browser or the Data Integrator, and accessed programmatically through our API, track=hgsvc3Sv.

The bigBed is available from our download server as hgsvc3.bb. Example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/hgsvc3.bb -chrom=chr21 -start=0 -end=100000000 stdout.

The original annotation tables are available from the HGSVC3 release on the IGSR FTP site.

Credits

Thanks to the Human Genome Structural Variation Consortium (HGSVC) and all participating sequencing and analysis centers for making the HGSVC3 annotation tables publicly available.

References

Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D et al. Complex genetic variation in nearly complete human genomes. Nature. 2025 Aug;644(8076):430-441. PMID: 40702183; PMC: PMC12350169