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.
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.
| Dataset | N samples | Cohort / disease | Disease cases | Coverage | SV count | 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) | 2,317,508 | 0 | 147 | 190,088,223 |
| CoLoRSdb | 1,427 | Consortium of Long-Read Sequencing, joint callset | No | mixed (HiFi) | 426,239 | 20 | 33 | 101,381 |
| Han 945 | 945 | Han Chinese, general population | No | ~17x ONT | 111,288 | 0 | 254 | 99,743 |
| 1KG ONT 100 | 100 | 1000 Genomes, 5 superpopulations / 19 subpopulations | No | ~37x ONT (R9.4.1) | 113,159 | 0 | 164 | 98,289 |
| 1KG ONT Vienna | 1,019 | 1000 Genomes, diverse | No | ~17x ONT | 148,375 | 2 | 177 | 49,171 |
| ToMMo Japanese | 333 (111 trios) | Japanese, general population | No | ~22x ONT | 74,201 | 51 | 162 | 99,980 |
| AoU 1K | 1,027 | All of Us, self-identified Black/African American; biobank includes a variety of conditions (diabetes, hearing loss, etc.) | Yes (mixed) | ~8x HiFi | 540,155 | 50 | 152 | 9,998 |
| GA4K | 502 | Children's Mercy, pediatric rare disease probands + families | Yes (probands) | ~27x HiFi | 115,554 | 50 | 186 | 809,711 |
| deCODE 3,622 | 3,622 | Icelandic general population | No | ~17x ONT | 119,453 | 0 | 127 | 861,080 |
| HPRC v2.1 | 233 | HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies) | No | ~60x HiFi + ~30x ONT (pangenome graph) | 549,649 | 50 | 276 | 1,064,897 |
| HGSVC2 | 32 | HGSVC2 haplotype-resolved assemblies (5 superpopulations) | No | >40x PacBio CLR + >20x HiFi (+ Strand-seq) | 111,746 | 50 | 168 | 57,207,414 |
| HGSVC3 | 65 | HGSVC3 diverse reference assemblies | No | ~47x HiFi + ~56x ONT | 176,531 | 50 | 154 | 30,176,500 |
| Arab APR | 53 | UAE-resident Arabs from 8 countries (Arab Pangenome Reference) | No | ~35x HiFi + ~54x 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 | ~30x HiFi (pangenome graph) | 36,030 | 1 | 53 | 8,998,096 |
| SVatalog 101 | 101 | 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) | ~50x PacBio CLR (34, Sequel I) + ~76x HiFi (67, Sequel II) | 87,068 | 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. ~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. ~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. ~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). ~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). ~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. 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. ~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. ~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-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples). About 596k SV-sized alleles (insertions and deletions) extracted from the graph with vg deconstruct.
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.
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.
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.
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.
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.
Each subtrack has its own documentation page with details on how to download -and intersect the underlying annotations. +and intersect the underlying annotations. The build process for all subtracks +is recorded in the UCSC makeDoc, +doc/hg38/lrSv.txt +(and doc/hs1/lrSv.txt +for T2T-CHM13); the conversion scripts are in +makeDb/scripts/lrSv, +and the track configuration is in +trackDb/human/lrSv.ra.
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
Schloissnig S, Pani S, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M et al. Structural variation in 1,019 diverse humans based on long-read sequencing. Nature. 2025 Aug;644(8076):442-452. PMID: 40702182; PMC: PMC12350158
Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S et al. Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- read sequencing technology. Commun Biol. 2022 Sep 20;5(1):991. PMID: 36127505; PMC: PMC9489684
Garimella KV, Li Q, Wertz J, Lee SK, Cunial F, Huang Y, Mostovoy Y, Lorig-Roach R, English A, Su H et al. Population-scale Long-read Sequencing in the All of Us Research Program. medRxiv. 2025 Oct 5;. PMID: 41256123; PMC: PMC12622093
Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B et al. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med. 2022 Jun;24(6):1336-1348. PMID: 35305867
Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA, Kristmundsdottir S, Mehringer S, Hardarson MT et al. Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits. Nat Genet. 2021 Jun;53(6):779-786. PMID: 33972781
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
Chirmade S, Wang Z, Mastromatteo S, Sanders E, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Lin F, Keenan K, Patel RV et al. GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations. Heredity (Edinb). 2026 Mar;135(3):199-210. PMID: 41203876; PMC: PMC13031531
Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W et al. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res. 2024 Nov 20;34(11):2061-2073. PMID: 39358015; PMC: PMC11610458
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021 Apr 2;372(6537). PMID: 33632895; PMC: PMC8026704
Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K et al. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell. 2022 Sep 1;185(18):3426-3440.e19. PMID: 36055201; PMC: PMC9439720