Description

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).

Display Conventions and Configuration

Items are colored by SV class:

• Deletions (DEL) - red
• Insertions (INS) - blue
• Complex (COMPLEX) - orange

Filters are available for SV class, 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:

• Insertion/Deletion Type: solo (single mobile element), partnered (with transduction), orphan (transduction only), VNTR, PSD (processed pseudogene), NUMT (nuclear mitochondrial insertion), DUP (tandem duplication), DUP_INTERSPERSED, INV_DUP (inverted duplication), COMPLEX_DUP, or chimera
• Transposon Family: Alu, L1, SVA, HERVK, or LTR5_Hs
• Percent Resolved: fraction of inserted sequence resolved by assembly
• TSD Length: target site duplication length
• Poly-A Length: poly-A tail length
• Conformation: structural conformation of the insertion (e.g. FOR+POLYA, Hexamer+Alu-like+VNTR+SINE-R+POLYA)
• Source Coordinates: genomic location of the source element (for transductions)

Methods

Oxford Nanopore sequencing was performed on 1,019 samples from the 1000 Genomes Project. Base-calling was done with Guppy 6.2.1. SVs were discovered using the SAGA framework, which combines:

• Linear-reference tools: Sniffles and DELLY (applied to both GRCh38 and CHM13)
• Graph-aware discovery: SVarp, which searches for SV patterns from graph-aligned reads and performs local long-read assembly
• Graph-based genotyping: Giggles, for unified genotyping across a pangenome graph

Variants were annotated with SVAN (SV Annotator v1.3), which leverages allelic representations and genomic annotations to classify SVs by mechanism. SVAN annotated 96.0% of insertions, 32.2% of deletions, and 57.1% of complex sites.

The original SV coordinates are on the T2T-CHM13 assembly (hs1). For the GRCh38 (hg38) version of this track, coordinates were converted using liftOver; 148,375 of 161,332 records mapped successfully (~92%). The hs1 version contains all 161,332 records at their native coordinates.

Data Access

Source data is available from the 1000 Genomes ONT Vienna data collection at IGSR.

Credits

Thanks to the 1000 Genomes ONT Vienna consortium for making their structural variant calls and SVAN annotations publicly available.

References

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