+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. +
++This track is preliminary and unpublished; its sample composition and variant +counts will be updated as more long-read data becomes available.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 This is a +preliminary, unpublished callset; the counts and sample composition will be +updated as more data is added. +
+ ++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. +
++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: + +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 accessed +programmatically through our API, +track=lrSv1kLin. +
+ ++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. +