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).
| Dataset | N samples | Cohort / disease | Sequencing | SVs | Min | Median | Max |
|---|---|---|---|---|---|---|---|
| Han 945 | 945 | Han Chinese, general population | ONT (PromethION) | 111,288 | 0 | 254 | 99,743 |
| 1KG ONT | 1,019 | 1000 Genomes, globally diverse | ONT | 148,375 | 2 | 177 | 49,171 |
| ToMMo Japanese | 333 (111 trios) | Japanese, general population | ONT | 74,201 | 51 | 162 | 99,980 |
| AoU 1K | 1,027 | All of Us, self-identified Black/African American | PacBio HiFi | 541,049 | 50 | 152 | 9,998 |
| GA4K | 502 | Children's Mercy, pediatric rare disease probands + families | PacBio HiFi | 115,554 | 50 | 186 | 809,711 |
| deCODE 3,622 | 3,622 | Icelandic general population | ONT | 133,886 | 0 | 127 | 861,080 |
| HGSVC3 | 65 | HGSVC3 diverse reference assemblies | PacBio HiFi + ONT | 176,531 | 50 | 154 | 30,176,500 |
| Kim PD Brain | 100 | Parkinson's disease, ILBD, controls (post-mortem brain) | PacBio HiFi | 74,552 | 50 | 160 | 190,088,222 |
| SVatalog 101 | 101 | Long-read WGS cohort for GWAS LD fine-mapping (SickKids) | long-read | 87,183 | 4 | 160 | 1,321,484 |
Structural variants from 945 Han Chinese individuals. 111,288 SVs (deletions, insertions, duplications, inversions, translocations) merged with SURVIVOR. Includes allele frequencies and per-sample support.
Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). 161,332 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.
Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical Megabank (ToMMo). 74,201 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.
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 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 and combined insertion/deletion events). Site-only callset with annotated surrounding tandem-repeat regions.
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 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, 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 (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.
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
Kim K, Lin Z, Simmons SK, Parker J, Kearney M, Liao Z, Haywood N, Zhang J, Cline MP, Tuncali I et al. Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease. bioRxiv. 2026 Mar 23;. PMID: 41929179; PMC: PMC13041997
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