9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 lrnassar Mon Jun 29 14:21:07 2026 -0700 lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released). diff --git src/hg/makeDb/trackDb/human/lrSv1kgOnt.html src/hg/makeDb/trackDb/human/lrSv1kgOnt.html index fa8be24c6ae..1f0600eecfd 100644 --- src/hg/makeDb/trackDb/human/lrSv1kgOnt.html +++ src/hg/makeDb/trackDb/human/lrSv1kgOnt.html @@ -1,118 +1,118 @@ <h2>Description</h2> <p> 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. </p> <p> 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 full release is native to the T2T-CHM13 assembly (hs1) and contains 161,332 annotated SVs (75,324 insertions, 66,192 deletions, and 19,816 complex rearrangements). For GRCh38 (hg38), coordinates were converted using liftOver and 148,375 records mapped successfully (73,298 insertions, 58,637 deletions, and 16,440 complex rearrangements). </p> <p> The 1,019 samples sequenced here are distinct from those in the <a href="hgTrackUi?g=gustafsonSv">1KG ONT 100</a> 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. </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV class: <ul> <li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li> <li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li> <li><span style="color: rgb(230,140,0);">Complex (CPX)</span> - orange</li> </ul> </p> <p> 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. </p> <p> The detail page for each item shows SVAN annotation fields including: <ul> <li><b>Insertion/Deletion Type</b>: 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</li> <li><b>Transposon Family</b>: Alu, L1, SVA, HERVK, or LTR5_Hs</li> <li><b>Percent Resolved</b>: fraction of inserted sequence resolved by assembly</li> <li><b>TSD Length</b>: target site duplication length</li> <li><b>Poly-A Length</b>: poly-A tail length</li> <li><b>Conformation</b>: structural conformation of the insertion (e.g. FOR+POLYA, Hexamer+Alu-like+VNTR+SINE-R+POLYA)</li> <li><b>Source Coordinates</b>: genomic location of the source element (for transductions)</li> </ul> </p> <h2>Methods</h2> <p> 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 <a href="https://github.com/REPBIO-LAB/svan" target="_blank"> SVAN</a> 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. </p> <p> The SVAN-annotated unphased VCF (<tt>final-vcf.unphased.SVAN_1.3.vcf.gz</tt>) was downloaded from <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/release/v1.1/svan-annotation/" target="_blank"> the IGSR 1KG_ONT_VIENNA v1.1 SVAN-annotation directory</a>; allele counts were added from the companion shapeit5-phased-callset (<tt>shapeit5-phased-callset_final-vcf.phased.vcf.gz</tt>) in the same release tree. </p> <p> The step-by-step build commands (download, liftOver, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> -makeDb/scripts/lrSv</a>. +makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSv.ra" target="_blank">trackDb/human/lrSv.ra</a>. </p> <h2>Data Access</h2> <p> Source data is available from the <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/" target="_blank">1000 Genomes ONT Vienna</a> data collection at IGSR. </p> <h2>Credits</h2> <p> Thanks to the 1000 Genomes ONT Vienna consortium for making their structural variant calls and SVAN annotations publicly available. </p> <h2>References</h2> <p> Schloissnig S, Pani S, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M <em>et al</em>. <a href="https://doi.org/10.1038/s41586-025-09290-7" target="_blank"> Structural variation in 1,019 diverse humans based on long-read sequencing</a>. <em>Nature</em>. 2025 Aug;644(8076):442-452. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702182" target="_blank">40702182</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350158/" target="_blank">PMC12350158</a> </p>