For short-read structural-variant comparators (CCDG 17,795, 1KG 3202, ToMMo 48K CNV) see the companion Short-read SVs supertrack.
| Dataset | N samples | Cohort / disease | +Disease cases | Sequencing | SVs | Min | Median | Max | ||
|---|---|---|---|---|---|---|---|---|---|---|
| All merged | +— | +All long-read SV datasets merged on identical position+type+length, with per-database AC | +mixed | +mixed (PacBio HiFi, ONT) | +2,694,871 | +50 | +200 | +190,088,223 | +||
| CoLoRSdb | 1,427 | Consortium of Long-Read Sequencing, joint callset | +No | PacBio HiFi | 426,239 | 20 | 33 | 101,381 | ||
| Han 945 | 945 | Han Chinese, general population | +No | ONT (PromethION) | 111,288 | 0 | 254 | 99,743 | ||
| 1KG ONT 100 | 100 | -1000 Genomes, 5 superpopulations / 19 subpopulations | +1000 Genomes, 5 superpopulations / 19 subpop., high 37x seq. coverage | +No | ONT (R9.4.1) | 113,696 | 0 | 164 | 98,289 | |
| 1KG ONT Vienna | 1,019 | -1000 Genomes, globally diverse | +1000 Genomes, diverse, normal 17x seq. coverage | +No | ONT | 148,375 | 2 | 177 | 49,171 | |
| ToMMo Japanese | 333 (111 trios) | Japanese, general population | +No | ONT | 74,201 | 51 | 162 | 99,980 | ||
| AoU 1K | 1,027 | -All of Us, self-identified Black/African American | +All of Us, self-identified Black/African American, 8x cov.; biobank includes a variety of conditions (diabetes, hearing loss, etc.) | +Yes (mixed) | PacBio HiFi | 541,049 | 50 | 152 | 9,998 | |
| GA4K | 502 | Children's Mercy, pediatric rare disease probands + families | +Yes (probands) | PacBio HiFi | 115,554 | 50 | 186 | 809,711 | ||
| deCODE 3,622 | 3,622 | Icelandic general population | +No | ONT | 133,886 | 0 | 127 | 861,080 | ||
| HPRC v2 | 233 | HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies) | +No | PacBio HiFi (pangenome graph) | 1,483,114 | 50 | 280 | 97,718 | ||
| HGSVC2 | 32 | HGSVC2 haplotype-resolved assemblies (5 superpopulations) | +No | PacBio CLR + HiFi + Strand-seq | 111,746 | 50 | 168 | 57,207,414 | ||
| HGSVC3 | 65 | HGSVC3 diverse reference assemblies | +No | PacBio HiFi + ONT | 176,531 | 50 | 154 | 30,176,500 | ||
| Arab APR | +Arab UPR | 53 | -UAE-resident Arabs from 8 countries (Arab Pangenome Reference) | +UAE-resident Arabs from 8 countries (UAE Pangenome Reference) | +No | PacBio HiFi + ONT + Hi-C (pangenome graph) | 72,656 | 1 | 21 | 99,885 |
| CPC | 58 | Chinese Pangenome Consortium, 36 minority ethnic groups (HPRC-specific SVs removed) | +No | PacBio HiFi (pangenome graph) | 36,030 | 1 | 53 | 8,998,096 | ||
| Kim PD Brain | 100 | Parkinson's disease, ILBD, controls (post-mortem brain) | +Yes (PD + ILBD) | PacBio HiFi | 74,552 | 50 | 160 | 190,088,222 | ||
| SVatalog 101 | 101 | -Long-read WGS cohort for GWAS LD fine-mapping (SickKids) | +Cystic fibrosis (CF) patients from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT). Long-read WGS used for GWAS LD fine-mapping | +Yes (all CF) | long-read | 87,183 | 4 | 160 | 1,321,484 |
Note: there is likely some overlap in sample composition across these collections. For example, 1000 Genomes samples are also included in HPRC and CoLoRSdb.
-Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. -426,239 SVs (insertions, deletions, inversions) called with pbsv and +~426k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort.
--Structural variants from 945 Han Chinese individuals. 111,288 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.
-Structural variants from Oxford Nanopore long-read sequencing of 100 1000 Genomes samples (5 superpopulations, 19 subpopulations) released by the 1000 Genomes ONT Sequencing Consortium and described in -Gustafson et al. 2024. 113,696 SVs (insertions, deletions, duplications, +Gustafson et al. 2024. ~114k SVs (insertions, deletions, duplications, inversions) called with five callers and merged with Jasmine. This is a separate dataset from the Vienna 1KG-ONT release below; the 100 samples here do not overlap with the 1,019 samples in the Vienna release.
-Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). -161,332 SVs annotated with SVAN, classifying insertions and deletions by mechanism +~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. This is a separate dataset from the 1KG ONT 100 (Gustafson et al.) track above; the 1,019 samples here do not overlap with the 100 samples in that release.
-Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical -Megabank (ToMMo). 74,201 SVs (deletions and insertions) with trio-based Mendelian +Megabank (ToMMo). ~74k SVs (deletions and insertions) with trio-based Mendelian error rates and allele frequencies.
-Structural variants from 1,027 individuals from the All of Us (AoU) Research Program, -sequenced with PacBio HiFi long reads. 541,049 SVs (insertions and deletions) -with population-specific allele frequencies, gene annotations, and clinical -trait associations. +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.
-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. 115,554 +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.
-High-confidence structural variants from 3,622 Icelanders (deCODE genetics), -sequenced with Oxford Nanopore long reads. 133,886 SVs (deletions, insertions +sequenced with Oxford Nanopore long reads. ~134k SVs (deletions, insertions and combined insertion/deletion events). Site-only callset with annotated surrounding tandem-repeat regions.
-Structural variants derived from the Human Pangenome Reference Consortium release-2 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples). -1,483,114 SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with +~1.5M SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with vg deconstruct and decomposed with vcfwave (WFA2).
-Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2 -freeze 4, Ebert et al. 2021). 111,746 SVs (deletions, insertions and +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.
-Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 -(HGSVC3). 176,532 haplotype-resolved SVs (deletions, insertions and +(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.
-Structural variants from 100 post-mortem brain samples (Parkinson's disease, incidental Lewy body disease, and healthy controls) sequenced with PacBio -HiFi long reads. 74,552 high-confidence SVs (deletions, insertions, +HiFi long reads. ~75k high-confidence SVs (deletions, insertions, duplications, inversions) with per-cohort allele frequencies and case-control carrier-rate differentials, from Kim et al. 2026.
-Structural variants from 101 long-read whole-genome sequences released -alongside the GWAS SVatalog tool (Chirmade et al. 2026). 87,183 SVs +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.
Each subtrack has its own documentation page with details on how to download and intersect the underlying annotations.