fcb3dd044df301a3c0ea4588e1debf7068b00333 lrnassar Mon Jun 29 15:43:06 2026 -0700 lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields. diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index 9d69f9b1e9c..b817c9f36ab 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -1,496 +1,496 @@ <h2>Description</h2> <p> This track collection contains structural variant (SV) calls derived from long-read sequencing studies. Structural variants are genomic rearrangements larger than ~50 bp, including deletions, insertions, duplications, inversions, and translocations. Long-read sequencing technologies can span repetitive regions and resolve complex rearrangements that are difficult to detect with short-read methods. </p> <h3>Available Datasets</h3> <p> SV length statistics (min / median / max) are computed from the <tt>svLen</tt> field of each track, in base pairs. Some tracks include sites with <tt>svLen=0</tt> (complex events where the reference and alternate alleles differ in sequence but not in length). </p> <p> For short-read structural-variant comparators (CCDG 17,795, 1KG 3202, ToMMo 48K CNV) see the companion <a href="hgTrackUi?g=srSv">Short-read SVs</a> supertrack. </p> <p> Polymorphic <b>Mobile Element Insertions</b> (Alu, L1, SVA, HERVK, snRNA) called from HGSVC3 long-read assemblies are released as a separate track collection; see the <a href="hgTrackUi?g=mei">Mobile Insertions</a> tracks. Those MEIs are the insertions identified in the 65 HGSVC3 samples relative to the reference, available on both GRCh38/hg38 and T2T-CHM13/hs1. </p> <table class="stdTbl"> <tr> <th>Dataset</th> <th>N samples</th> <th>Cohort / disease</th> <th>Disease cases</th> <th>Coverage</th> <th>SV count</th> <th>Min</th> <th>Median</th> <th>Max</th> </tr> <tr> <td><a href="hgTrackUi?g=lrSvAll"><b>All merged</b></a></td> <td>—</td> <td>All long-read SV datasets merged on identical position+type+length, with per-database AC</td> <td>mixed</td> <td>mixed (PacBio HiFi, ONT)</td> <td>2,317,508</td> - <td>0</td> + <td>1</td> <td>147</td> - <td>190,088,223</td> + <td>57,207,413</td> </tr> <tr> <td><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb</a></td> <td>1,427</td> <td>Consortium of Long-Read Sequencing, joint callset</td> <td>No</td> <td>mixed (HiFi)</td> <td>426,239</td> <td>20</td> <td>33</td> <td>101,381</td> </tr> <tr> <td><a href="hgTrackUi?g=han945Sv">Han 945</a></td> <td>945</td> <td>Han Chinese, general population</td> <td>No</td> <td>~17x ONT</td> <td>111,288</td> - <td>0</td> + <td>1</td> <td>254</td> - <td>99,743</td> + <td>99,744</td> </tr> <tr> <td><a href="hgTrackUi?g=gustafsonSv">1KG ONT 100</a></td> <td>100</td> <td>1000 Genomes, 5 superpopulations / 19 subpopulations</td> <td>No</td> <td>~37x ONT (R9.4.1)</td> <td>113,159</td> - <td>0</td> - <td>164</td> - <td>98,289</td> + <td>1</td> + <td>167</td> + <td>98,290</td> </tr> <tr> <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a></td> <td>1,019</td> <td>1000 Genomes, diverse</td> <td>No</td> <td>~17x ONT</td> <td>148,375</td> <td>2</td> - <td>177</td> + <td>157</td> <td>49,171</td> </tr> <tr> <td><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese</a></td> <td>333 (111 trios)</td> <td>Japanese, general population</td> <td>No</td> <td>~22x ONT</td> <td>74,201</td> <td>51</td> - <td>162</td> - <td>99,980</td> + <td>158</td> + <td>99,985</td> </tr> <tr> <td><a href="hgTrackUi?g=aou1kSv">AoU 1K</a></td> <td>1,027</td> <td>All of Us, self-identified Black/African American; biobank includes a variety of conditions (diabetes, hearing loss, etc.)</td> <td>Yes (mixed)</td> <td>~8x HiFi</td> <td>540,155</td> <td>50</td> <td>152</td> <td>9,998</td> </tr> <tr> <td><a href="hgTrackUi?g=ga4kSv">GA4K</a></td> <td>502</td> <td>Children's Mercy, pediatric rare disease probands + families</td> <td>Yes (probands)</td> <td>~27x HiFi</td> <td>115,554</td> <td>50</td> <td>186</td> - <td>809,711</td> + <td>809,712</td> </tr> <tr> <td><a href="hgTrackUi?g=decodeSv">deCODE 3,622</a></td> <td>3,622</td> <td>Icelandic general population</td> <td>No</td> <td>~17x ONT</td> <td>119,453</td> - <td>0</td> - <td>127</td> - <td>861,080</td> + <td>1</td> + <td>154</td> + <td>861,081</td> </tr> <tr> <td><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1</a></td> <td>233</td> <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td> <td>No</td> <td>~60x HiFi + ~30x ONT (pangenome graph)</td> <td>549,649</td> <td>50</td> - <td>276</td> + <td>261</td> <td>1,064,897</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2</a></td> <td>32</td> <td>HGSVC2 haplotype-resolved assemblies (5 superpopulations)</td> <td>No</td> <td>>40x PacBio CLR + >20x HiFi (+ Strand-seq)</td> <td>111,746</td> <td>50</td> <td>168</td> - <td>57,207,414</td> + <td>57,207,413</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td> <td>65</td> <td>HGSVC3 diverse reference assemblies</td> <td>No</td> <td>~47x HiFi + ~56x ONT</td> <td>176,531</td> <td>50</td> <td>154</td> <td>30,176,500</td> </tr> <tr> <td><a href="hgTrackUi?g=aprSv">Arab APR</a></td> <td>53</td> <td>UAE-resident Arabs from 8 countries (Arab Pangenome Reference)</td> <td>No</td> <td>~35x HiFi + ~54x ONT (+ Hi-C, pangenome graph)</td> <td>72,656</td> <td>1</td> - <td>21</td> - <td>99,885</td> + <td>121</td> + <td>584,016</td> </tr> <tr> <td><a href="hgTrackUi?g=cpc1Sv">CPC</a></td> <td>58</td> <td>Chinese Pangenome Consortium, 36 minority ethnic groups (HPRC-specific SVs removed)</td> <td>No</td> <td>~30x HiFi (pangenome graph)</td> <td>36,030</td> - <td>1</td> - <td>53</td> + <td>50</td> + <td>134</td> <td>8,998,096</td> </tr> <tr> <td><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101</a></td> <td>101</td> <td>Cystic fibrosis (CF) patients from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT). Long-read WGS used for GWAS LD fine-mapping</td> <td>Yes (all CF)</td> <td>~50x PacBio CLR (34, Sequel I) + ~76x HiFi (67, Sequel II)</td> <td>87,068</td> <td>4</td> <td>160</td> <td>1,321,484</td> </tr> </table> <p> Note: there is likely some overlap in sample composition across these collections. For example, 1000 Genomes samples are also included in HPRC and CoLoRSdb. </p> <h3><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb SVs</a></h3> <p> Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. ~426k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort. </p> <h3><a href="hgTrackUi?g=han945Sv">Han 945 SVs</a></h3> <p> Structural variants from 945 Han Chinese individuals. ~111k SVs (deletions, insertions, duplications, inversions, translocations) merged with SURVIVOR. Includes allele frequencies and per-sample support. </p> <h3><a href="hgTrackUi?g=gustafsonSv">1KG ONT 100 SVs</a></h3> <p> Structural variants from Oxford Nanopore long-read sequencing of 100 1000 Genomes samples (5 superpopulations, 19 subpopulations) released by the 1000 Genomes ONT Sequencing Consortium and described in Gustafson et al. 2024. ~114k SVs (insertions, deletions, duplications, inversions) called with five callers and merged with Jasmine. This is a separate dataset from the Vienna 1KG-ONT release below; the 100 samples here do not overlap with the 1,019 samples in the Vienna release. </p> <h3><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna SVs</a></h3> <p> Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). ~161k SVs annotated with SVAN, classifying insertions and deletions by mechanism of origin (mobile elements, VNTRs, processed pseudogenes, etc.). Original coordinates are on T2T-CHM13 (hs1); the hg38 version was created via liftOver. This is a separate dataset from the 1KG ONT 100 (Gustafson et al.) track above; the 1,019 samples here do not overlap with the 100 samples in that release. </p> <h3><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese SVs</a></h3> <p> Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical Megabank (ToMMo). ~74k SVs (deletions and insertions) with trio-based Mendelian error rates and allele frequencies. </p> <h3><a href="hgTrackUi?g=aou1kSv">AoU 1K SVs</a></h3> <p> Structural variants from 1,027 individuals from the All of Us (AoU) Research Program, sequenced with PacBio HiFi long reads. AoU is a deeply phenotyped biobank that includes participants with a range of conditions (e.g. diabetes, hearing loss, hypertension), so the cohort is not disease-free. ~541k SVs (insertions and deletions) with population-specific allele frequencies, gene annotations, and clinical trait associations. </p> <h3><a href="hgTrackUi?g=ga4kSv">GA4K SVs</a></h3> <p> Structural variants from 502 probands and family members enrolled in the Genomic Answers for Kids (GA4K) pediatric rare-disease program at Children's Mercy Research Institute, sequenced with PacBio HiFi long reads. ~116k replicated SVs (deletions, insertions, duplications, inversions) called with pbsv and merged with JASMINE. The matched GA4K small-variant callset (SNVs and short indels) lives alongside other population allele-frequency resources as <a href="hgTrackUi?g=ga4kSnv">GA4K 552 PacBio LR</a> in the Variant Frequencies track collection. </p> <h3><a href="hgTrackUi?g=decodeSv">deCODE 3,622 SVs</a></h3> <p> High-confidence structural variants from 3,622 Icelanders (deCODE genetics), sequenced with Oxford Nanopore long reads. ~134k SVs (deletions, insertions and combined insertion/deletion events). Site-only callset with annotated surrounding tandem-repeat regions. </p> <h3><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1 SVs</a></h3> <p> Structural variants derived from the Human Pangenome Reference Consortium release-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples). About 596k SV-sized alleles (insertions and deletions) extracted from the graph with <tt>vg deconstruct</tt>. </p> <h3><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2 32 SVs</a></h3> <p> Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2 freeze 4, Ebert et al. 2021). ~112k SVs (deletions, insertions and inversions) called from phased de novo assemblies with PAV, with per-variant 1000 Genomes population allele frequencies (insertions and deletions) and rich structural/gene annotations. An earlier HGSVC release complementary to <a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a>. </p> <h3><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3 65 SVs</a></h3> <p> Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 (HGSVC3). ~177k haplotype-resolved SVs (deletions, insertions and inversions) called with PAV and cross-validated with ten additional callers, with per-site carrier haplotype lists and structural annotations. </p> <h3><a href="hgTrackUi?g=aprSv">Arab APR 53 SVs</a></h3> <p> Structural variants from the Arab Pangenome Reference (APR), a haplotype-resolved pangenome graph built from 53 UAE-resident Arab individuals drawn from eight countries (PacBio HiFi + ultralong ONT + Hi-C; Nassir et al. 2025). ~73k SVs on hg38 (deletions, insertions, complex and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track uses the native coordinates. </p> <h3><a href="hgTrackUi?g=cpc1Sv">CPC 58 SVs</a></h3> <p> Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. 2023). This track shows the CPC contribution to the joint CPC+HPRC graph with HPRC-specific SVs removed. ~36k SVs on hg38 (deletions, insertions and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track is native. </p> <h3><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101 SVs</a></h3> <p> Structural variants from 101 long-read whole-genome sequences released alongside the GWAS SVatalog tool (Chirmade et al. 2026). The samples come from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT), a cystic-fibrosis (CF) patient cohort assembled to model patient-specific responses to CFTR modulator therapies (most participants are F508del homozygotes or F508del / minimal-function compound heterozygotes; a smaller number carry rare nonsense or missense CFTR mutations). ~87k SVs (deletions, insertions, duplications, inversions and complex events) annotated with gene overlaps, ClinGen / gnomAD constraint scores, OMIM / ClinVar / DGV / Decipher regional annotations. </p> <h2>Data Access</h2> <p> Each subtrack has its own documentation page with details on how to download and intersect the underlying annotations. The build process for all subtracks is recorded in the UCSC makeDoc, <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank">doc/hg38/lrSv.txt</a> (and <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hs1/lrSv.txt" target="_blank">doc/hs1/lrSv.txt</a> for T2T-CHM13); the conversion scripts are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">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>References</h2> <p> Gong J, Sun H, Wang K, Zhao Y, Huang Y, Chen Q, Qiao H, Gao Y, Zhao J, Ling Y <em>et al</em>. <a href="https://doi.org/10.1038/s41467-025-56661-9" target="_blank"> Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility</a>. <em>Nat Commun</em>. 2025 Feb 10;16(1):1494. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39929826" target="_blank">39929826</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811171/" target="_blank">PMC11811171</a> </p> <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> <p> Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S <em>et al</em>. <a href="https://doi.org/10.1038/s42003-022-03953-1" target="_blank"> Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- read sequencing technology</a>. <em>Commun Biol</em>. 2022 Sep 20;5(1):991. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36127505" target="_blank">36127505</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9489684/" target="_blank">PMC9489684</a> </p> <p> Garimella KV, Li Q, Wertz J, Lee SK, Cunial F, Huang Y, Mostovoy Y, Lorig-Roach R, English A, Su H <em>et al</em>. <a href="https://doi.org/10.1101/2025.10.02.25336942" target="_blank"> Population-scale Long-read Sequencing in the All of Us Research Program</a>. <em>medRxiv</em>. 2025 Oct 5;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41256123" target="_blank">41256123</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12622093/" target="_blank">PMC12622093</a> </p> <p> Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S1098-3600(22)00653-0" target="_blank"> Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes</a>. <em>Genet Med</em>. 2022 Jun;24(6):1336-1348. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35305867" target="_blank">35305867</a> </p> <p> Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA, Kristmundsdottir S, Mehringer S, Hardarson MT <em>et al</em>. <a href="https://doi.org/10.1038/s41588-021-00865-4" target="_blank"> Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits</a>. <em>Nat Genet</em>. 2021 Jun;53(6):779-786. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33972781" target="_blank">33972781</a> </p> <p> Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D <em>et al</em>. <a href="https://doi.org/10.1038/s41586-025-09140-6" target="_blank"> Complex genetic variation in nearly complete human genomes</a>. <em>Nature</em>. 2025 Aug;644(8076):430-441. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank">40702183</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350169/" target="_blank">PMC12350169</a> </p> <p> Chirmade S, Wang Z, Mastromatteo S, Sanders E, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Lin F, Keenan K, Patel RV <em>et al</em>. <a href="https://doi.org/10.1038/s41437-025-00809-2" target="_blank"> GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations</a>. <em>Heredity (Edinb)</em>. 2026 Mar;135(3):199-210. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41203876" target="_blank">41203876</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031531/" target="_blank">PMC13031531</a> </p> <p> Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W <em>et al</em>. <a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=39358015" target="_blank"> High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation</a>. <em>Genome Res</em>. 2024 Nov 20;34(11):2061-2073. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39358015" target="_blank">39358015</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610458/" target="_blank">PMC11610458</a> </p> <p> Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R <em>et al</em>. <a href="https://www.science.org/doi/10.1126/science.abf7117" target="_blank"> Haplotype-resolved diverse human genomes and integrated analysis of structural variation</a>. <em>Science</em>. 2021 Apr 2;372(6537). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33632895" target="_blank">33632895</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026704/" target="_blank">PMC8026704</a> </p> <p> Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00991-6" target="_blank"> High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios</a>. <em>Cell</em>. 2022 Sep 1;185(18):3426-3440.e19. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank">36055201</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9439720/" target="_blank">PMC9439720</a> </p>