dc1e0e76dbe49861bd0ebe8db64e27f587737794 max Mon Mar 30 15:40:03 2026 -0700 adding two more phased variants tracks, refs #37306 diff --git src/hg/makeDb/trackDb/human/lrSv1kgOnt.html src/hg/makeDb/trackDb/human/lrSv1kgOnt.html new file mode 100644 index 00000000000..b678593dd8c --- /dev/null +++ src/hg/makeDb/trackDb/human/lrSv1kgOnt.html @@ -0,0 +1,97 @@ +

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 +