This track shows structural variants (SVs) from an integrated long-read callset spanning 1,218 individuals of the 1000 Genomes Project. Structural variants are genomic rearrangements larger than about 50 bp, such as deletions and insertions; because they alter large stretches of DNA at once, they can affect gene dosage and regulation more strongly than single-nucleotide changes, and long reads resolve them far better than short-read data.
Rather than coming from a single sequencing run, the calls are drawn together -from several 1000 Genomes long-read efforts that use different technologies: -HiFi and genome-assembly-based calls from the Human Pangenome Reference -Consortium (HPRC year 2), assembly-based -calls from the Human Genome Structural -Variation Consortium (HGSVC3), and Oxford Nanopore calls from the -Vienna 1000 Genomes ONT release, together -with Oxford Nanopore sequencing from the University of Washington 1000 Genomes -ONT effort (see 1KG ONT UW). Sequencing -of the 1000 Genomes collection is ongoing, so the number of individuals and -variants in this track is expected to grow over time. +from several 1000 Genomes long-read efforts that use different technologies. +The 1,218 individuals combine:
+-This track is preliminary and unpublished; its sample composition and variant -counts will be updated as more long-read data becomes available. -
--The current release contains more than 580,000 SVs on GRCh38 (about 391,000 -insertions and 196,000 deletions), each annotated with an overall allele -frequency and allele frequencies for the five 1000 Genomes superpopulations -(African, Admixed American, East Asian, European, South Asian). This is a -preliminary, unpublished callset; the counts and sample composition will be -updated as more data is added. +The current release contains more than 580,000 SVs on GRCh38 (391,410 +insertions and 196,369 deletions) and more than 610,000 SVs on T2T-CHM13 +(376,117 insertions and 238,405 deletions), each annotated with an overall +allele frequency and allele frequencies for the five 1000 Genomes +superpopulations (African, Admixed American, East Asian, European, South +Asian).
Items are colored by SV type, matching the other subtracks of the container:
| Deletion (DEL) | |
| Insertion (INS) |
Insertions are drawn at the insertion site with a width of 1 bp, and the length of inserted sequence is reported as the insertion length; deletions span the affected reference interval. The mouseover shows the variant name, SV type, reference and insertion lengths, allele count and per-population allele frequencies. Filters are available for SV type, SV length, insertion length, allele count, and overall and per-population allele frequency.
-Per-sample long-read SV calls from the contributing 1000 Genomes efforts -(HiFi and assembly-based calls from HPRC year 2 and HGSVC3, and Oxford -Nanopore calls from the Vienna and University of Washington releases) were -combined across the 1,218 individuals and merged into a single site-level -callset with Truvari v5.2.0. Overall and per-superpopulation allele -frequencies (EUR, AMR, EAS, AFR, SAS) were then added with bcftools -fill-tags. Only deletions and insertions are reported in the current release. -The callset is provided on both GRCh38/hg38 and T2T-CHM13/hs1 from the -respective native assemblies. +Lin et al. built the callset in two tiers. A baseline set of euchromatic SVs +was established from 293 near-T2T haplotype-resolved assemblies generated by +HGSVC and HPRC, and this was expanded with an additional 445 low-pass Oxford +Nanopore genomes (Schloissnig et al. 2025) and 480 roughly 30x Oxford Nanopore +genomes sequenced by the 1000 Genomes Long Read Sequencing Consortium (383 new +plus 97 from Gustafson et al. 2024), for 1,218 genomes of diverse ancestry. +Structural variants were discovered with ten long-read callers, and a +machine-learning tool, BoostSV, ranked and selected the best allele to +represent each SV across the different platforms and coverages, producing a +single nonredundant callset. The final callset contains 614,522 SVs (376,117 +insertions and 238,405 deletions) on T2T-CHM13 and 587,779 SVs (391,410 +insertions and 196,369 deletions) on GRCh38. See Lin et al. for full details.
-The data was provided by the laboratories of Evan Eichler and Danny Miller -(University of Washington) and is preliminary and unpublished; a manuscript -is in preparation. The step-by-step build commands (format conversion and -bigBed build) are recorded in the UCSC makeDoc for this track container: +The insertion/deletion callset VCFs (GRCh38 and T2T-CHM13 native), already +annotated with overall and per-superpopulation allele frequencies (EUR, AMR, +EAS, AFR, SAS), were provided by the laboratories of Evan Eichler and Danny +Miller (University of Washington). At UCSC the deletion and insertion records +were converted to bigBed; no re-merging or re-annotation was performed. The +step-by-step build commands (format conversion and bigBed build) are recorded +in the UCSC makeDoc for this track container: doc/hg38/lrSv.txt. The conversion script and autoSql schema live in makeDb/scripts/lrSv, and the track configuration is in trackDb/human/lrSv.ra.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=lrSv1kLin.
For automated download and analysis, the annotation is stored in bigBed files that can be downloaded from our download server: http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/lin1218.bb (GRCh38/hg38, native) and http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/lin1218.bb (T2T-CHM13/hs1, native). Individual regions or the whole annotation can be obtained with the bigBedToBed utility, which can be compiled from source or downloaded as a precompiled binary from our utilities page. The tool can also extract features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/lin1218.bb -chrom=chr21 -start=0 -end=100000000 stdout.
+-This is a preliminary, unpublished callset provided by the authors; the -underlying per-sample sequencing data is not yet publicly released. +Thanks to Jiadong Lin for providing the merged callset and the dataset +overview, and to Evan Eichler, Danny Miller and colleagues at the University of +Washington, together with the contributing 1000 Genomes long-read consortia +(HPRC, HGSVC and the 1000 Genomes ONT sequencing groups), for generating and +sharing this callset.
-+Lin J, et al. A high-resolution human pangenome structural variant +resource for improved disease association. Submitted. +
++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 +
++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 +
-Thanks to Evan Eichler, Danny Miller and colleagues at the University of -Washington, and to the contributing 1000 Genomes long-read consortia (HPRC, -HGSVC and the 1000 Genomes ONT sequencing groups), for generating and sharing -this callset. +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