This track collection contains structural variant (SV) calls derived from long-read sequencing studies. Structural variants are genomic rearrangements larger than ~50 bp, including deletions, insertions, duplications, inversions, and translocations. Long-read sequencing technologies can span repetitive regions and resolve complex rearrangements that are difficult to detect with short-read methods.

Available Datasets

SV length statistics (min / median / max) are computed from the svLen field of each track, in base pairs. Some tracks include sites with svLen=0 (complex events where the reference and alternate alleles differ in sequence but not in length).

For short-read structural-variant comparators (CCDG 17,795, 1KG 3202, ToMMo 48K CNV) see the companion Short-read SVs supertrack.

Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) called from HGSVC3 long-read assemblies are released as a separate track collection; see the Mobile Insertions tracks. Those MEIs are the insertions identified in the 65 HGSVC3 samples relative to the reference, available on both GRCh38/hg38 and T2T-CHM13/hs1.

Note: there is likely some overlap in sample composition across these collections. For example, 1000 Genomes samples are also included in HPRC and CoLoRSdb.

CoLoRSdb SVs

Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. ~426k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort.

Han 945 SVs

Structural variants from 945 Han Chinese individuals. ~111k SVs (deletions, insertions, duplications, inversions, translocations) merged with SURVIVOR. Includes allele frequencies and per-sample support.

1KG ONT UW SVs

Structural variants from Oxford Nanopore long-read sequencing of 100 1000 Genomes samples (5 superpopulations, 19 subpopulations) from the University of Washington-led 1000 Genomes ONT sequencing effort, described in Gustafson et al. 2024. ~114k SVs (insertions, deletions, duplications, inversions) called with five callers and merged with Jasmine. This is mostly a separate dataset from the Vienna 1KG-ONT release described next (directly below); only two samples (HG03499 and HG03548) overlap.

1KG ONT Vienna SVs

Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). ~161k SVs annotated with SVAN, classifying insertions and deletions by mechanism of origin (mobile elements, VNTRs, processed pseudogenes, etc.). Original coordinates are on T2T-CHM13 (hs1); the hg38 version was created via liftOver. Two samples (HG03499 and HG03548) overlap with the 1KG ONT UW dataset.

ToMMo Japanese SVs

Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical Megabank (ToMMo). ~74k SVs (deletions and insertions) with trio-based Mendelian error rates and allele frequencies.

AoU 1K SVs

Structural variants from 1,027 individuals from the All of Us (AoU) Research Program, sequenced with PacBio HiFi long reads. AoU is a deeply phenotyped biobank that includes participants with a range of conditions (e.g. diabetes, hearing loss, hypertension), so the cohort is not disease-free. ~541k SVs (insertions and deletions) with population-specific allele frequencies, gene annotations, and clinical trait associations.

GA4K SVs

Structural variants from 502 probands and family members enrolled in the Genomic Answers for Kids (GA4K) pediatric rare-disease program at Children's Mercy Research Institute, sequenced with PacBio HiFi long reads. ~116k replicated SVs (deletions, insertions, duplications, inversions) called with pbsv and merged with JASMINE. The matched GA4K small-variant callset (SNVs and short indels) lives alongside other population allele-frequency resources as GA4K 552 PacBio LR in the Variant Frequencies track collection.

deCODE 3,622 SVs

High-confidence structural variants from 3,622 Icelanders (deCODE genetics), sequenced with Oxford Nanopore long reads. ~134k SVs (deletions, insertions and combined insertion/deletion events). Site-only callset with annotated surrounding tandem-repeat regions.

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 (CHM13 + diverse 1000 Genomes samples). About 550k SV-sized alleles (insertions and deletions) extracted from the graph with vg deconstruct.

HGSVC2 32 SVs

Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2 freeze 4, Ebert et al. 2021). ~112k SVs (deletions, insertions and inversions) called from phased de novo assemblies with PAV, with per-variant 1000 Genomes population allele frequencies (insertions and deletions) and rich structural/gene annotations. An earlier HGSVC release complementary to HGSVC3.

HGSVC3 65 SVs

Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 (HGSVC3). ~177k 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.

Arab APR 53 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). ~73k SVs on hg38 (deletions, insertions, complex and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track uses the native coordinates.

CPC 58 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. ~36k SVs on hg38 (deletions, insertions and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track is native.

SVatalog 101 SVs - Cystic Fibrosis

Structural variants from 101 long-read whole-genome sequences released alongside the GWAS SVatalog tool (Chirmade et al. 2026). The samples come from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT), a cystic-fibrosis (CF) patient cohort assembled to model patient-specific responses to CFTR modulator therapies (most participants are F508del homozygotes or F508del / minimal-function compound heterozygotes; a smaller number carry rare nonsense or missense CFTR mutations). ~87k SVs (deletions, insertions, duplications, inversions and complex events) annotated with gene overlaps, ClinGen / gnomAD constraint scores, OMIM / ClinVar / DGV / Decipher regional annotations.

NIH CARD 351 SVs

Structural variants from Oxford Nanopore long-read sequencing of post-mortem brain tissue (prefrontal cortex) from 351 individuals, generated by the NIH Center for Alzheimer's and Related Dementias (NIH CARD) Long-Read Initiative (Billingsley et al. 2024). These are population brain-tissue cohorts with no Alzheimer's disease cases. The cohort combines 205 European-ancestry samples (North American Brain Expression Consortium, NABEC) and 146 African / African-admixed samples (NIMH Human Brain Collection Core, HBCC). ~229k SVs (insertions, deletions, inversions) with per-cohort allele counts and allele frequencies.

Noyvert 888 SVs

Structural variants from Oxford Nanopore long-read sequencing of 888 individuals from the 1000 Genomes Project, spanning five ancestry groups (European, Admixed American, East Asian, South Asian, African; Noyvert et al. 2025). ~107k SVs (insertions, deletions, inversions, breakends and duplications) called with Sniffles2, with overall and per-superpopulation allele frequencies, Sniffles2 and Hardy-Weinberg quality metrics, and imputation accuracy. The panel was used to impute SVs into about 500,000 UK Biobank participants and test them for association with disease traits and protein levels; genome-wide significant UK Biobank associations are listed on each variant's details page.

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