This track shows structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 1,019 individuals from the 1000 Genomes Project, representing 26 populations across 5 continental regions: Africa (275 samples), East Asia (192), South Asia (199), Europe (189), and Americas (164). Median sequencing coverage was 16.9x per sample with a median N50 read length of 20.3 kb.
SVs were discovered using the SAGA framework (SV Analysis by Graph Augmentation) and annotated with SVAN, which classifies insertions and deletions by their mechanism of origin. The dataset contains 161,332 annotated SVs, including 75,324 insertions, 66,192 deletions, and 19,816 complex rearrangements. The original coordinates are on the T2T-CHM13 assembly (hs1); for GRCh38 (hg38), coordinates were converted using liftOver (148,375 records mapped successfully).
The 1,019 samples sequenced here are distinct from those in the 1KG ONT 100 track (Gustafson et al. 2024); the two releases were produced by separate consortia (Vienna and the 1000 Genomes ONT Sequencing Consortium, respectively) and there is no sample overlap between the two.
Items are colored by SV class:
Filters are available for SV type, insertion/deletion type, transposon family, and SV length. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region.
The detail page for each item shows SVAN annotation fields including:
Schloissnig et al. 2025 generated intermediate-coverage Oxford Nanopore long-read sequencing of 1,019 samples from the 1000 Genomes Project on PromethION 48 instruments with R9.4.1 (FLO-PRO002) flow cells (SQK-LSK110 libraries, 24-h runs with flow-cell wash and reload). SVs were discovered with the SAGA framework (SV Analysis by Graph Augmentation), which combines linear-reference callers (Sniffles and DELLY, run against both GRCh38 and T2T-CHM13), graph-aware discovery with SVarp (local long-read assembly of SV-supporting graph-aligned reads) and graph-based joint genotyping with Giggles across a pangenome graph. Insertions and deletions were then annotated with SVAN v1.3, which classifies SVs by mechanism of origin. The release contains 161,332 SVAN-annotated SVs: 75,324 insertions, 66,192 deletions and 19,816 complex rearrangements. The original VCF is on T2T-CHM13 contig coordinates; for the hg38 version of this track, SVs were lifted with liftOver (148,375 of 161,332 records mapped), while the hs1 version uses the native coordinates.
The SVAN-annotated unphased VCF (final-vcf.unphased.SVAN_1.3.vcf.gz) was downloaded from the IGSR 1KG_ONT_VIENNA v1.1 SVAN-annotation directory; allele counts were added from the companion shapeit5-phased-callset (shapeit5-phased-callset_final-vcf.phased.vcf.gz) in the same release tree.
The step-by-step build commands (download, liftOver, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: doc/hg38/lrSv.txt. The conversion scripts and autoSql schemas live in makeDb/scripts/lrSv.
Source data is available from the 1000 Genomes ONT Vienna data collection at IGSR.
Thanks to the 1000 Genomes ONT Vienna consortium for making their structural variant calls and SVAN annotations publicly available.
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