Description

This track collection shows structural variants (SVs) from long-read sequencing, called natively against the T2T-CHM13 reference (hs1). It is the T2T-CHM13 companion to the GRCh38 Long-read SVs collection.

Only a subset of the long-read SV datasets have been released with native T2T-CHM13 coordinates, and those are the subtracks shown here. The remaining cohorts in the collection were released on GRCh38 only. For the full set of datasets, see the hg38 Long-read SVs track.

Available datasets (T2T-CHM13 native)

HGSVC3 and HPRC v2.1 are built directly from the consortia's T2T-CHM13 releases; CoLoRSdb, 1KG Lin merged, 1KG Vienna ONT, Arab APR, and CPC are built from callsets or pangenome graphs native to T2T-CHM13. Per-subtrack details, cohorts, and citations are on each subtrack's own description page.

CoLoRSdb SVs

Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. ~840k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort.

1KG Lin merged SVs

A merged long-read SV callset spanning 1,218 individuals of the 1000 Genomes Project (Lin et al.), combining 293 near-T2T haplotype-resolved assemblies (HPRC and HGSVC), 480 University of Washington Oxford Nanopore genomes, and 445 Vienna Oxford Nanopore genomes. Structural variants were discovered with ten long-read callers, and the BoostSV machine-learning tool selected the best allele to represent each SV across platforms and coverages. ~615k SVs (insertions and deletions) in native T2T-CHM13 coordinates.

1KG Vienna ONT SVs

Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT), called natively against T2T-CHM13. ~161k SVs annotated with SVAN, classifying insertions and deletions by mechanism of origin (mobile elements, VNTRs, processed pseudogenes, and others).

HPRC v2.1 SVs

Structural variants derived from the Human Pangenome Reference Consortium release-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies. ~541k SV-sized alleles (insertions and deletions) extracted from the T2T-CHM13 graph with vg deconstruct.

HGSVC3 SVs

Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 (HGSVC3), from the consortium's native T2T-CHM13 annotation tables. ~189k haplotype-resolved SVs (deletions, insertions and inversions) called with PAV and cross-validated with ten additional callers, with per-site carrier haplotype lists and structural annotations.

CPC SVs

Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. 2023). This track shows the CPC contribution to the joint CPC+HPRC graph with HPRC-specific SVs removed. ~46k SVs (deletions, insertions and mixed snarls) in native T2T-CHM13 coordinates.

Arab APR SVs

Structural variants from the Arab Pangenome Reference (APR), a haplotype-resolved pangenome graph built from 53 UAE-resident Arab individuals drawn from eight countries (PacBio HiFi + ultralong ONT + Hi-C; Nassir et al. 2025). ~103k SVs (deletions, insertions, complex and mixed snarls) in native T2T-CHM13 coordinates.

Display Conventions and Configuration

Items are colored by SV type:

• Deletions (DEL) - red
• Insertions (INS) - blue
• Duplications (DUP) - green
• Inversions (INV) - orange
• Complex and other multi-allele events - purple

Data Access

Each subtrack has its own documentation page with details on how to download and intersect the underlying annotations. The T2T-CHM13 build steps are recorded in the UCSC makeDoc, doc/hs1/lrSv.txt (with the shared pipeline in doc/hg38/lrSv.txt); the conversion scripts are in makeDb/scripts/lrSv, and the track configuration is in trackDb/human/lrSv.ra.

Contact

If you know of additional long-read structural-variant datasets on T2T-CHM13 that we could add, please contact us at genome@soe.ucsc.edu.