ac18a42f0dafb4febaaeaebcd53fe75df9b83234 max Mon May 11 08:29:14 2026 -0700 lrSv: add Coverage column, drop redundant Sequencing column, rename SVs to SV count Coverage values pulled from the per-subtrack methods sections and the underlying papers (Han 17x, deCODE 17x, GA4K 27x, HPRC 60x HiFi + 30x ONT, etc.). Sequencing technology is now folded into the Coverage cells. Also cross-links to the new HGSVC3 Mobile Insertions tracks. refs #36642 diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index ae8d30a51e9..ebf9c5bdf1f 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -7,213 +7,221 @@ 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>Sequencing</th> - <th>SVs</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>—</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>2,694,871</td> <td>50</td> <td>200</td> <td>190,088,223</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>PacBio HiFi</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>ONT (PromethION)</td> + <td>~17x ONT</td> <td>111,288</td> <td>0</td> <td>254</td> <td>99,743</td> </tr> <tr> <td><a href="hgTrackUi?g=gustafsonSv">1KG ONT 100</a></td> <td>100</td> - <td>1000 Genomes, 5 superpopulations / 19 subpop., high 37x seq. coverage</td> + <td>1000 Genomes, 5 superpopulations / 19 subpopulations</td> <td>No</td> - <td>ONT (R9.4.1)</td> + <td>~37x ONT (R9.4.1)</td> <td>113,696</td> <td>0</td> <td>164</td> <td>98,289</td> </tr> <tr> <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a></td> <td>1,019</td> - <td>1000 Genomes, diverse, normal 17x seq. coverage</td> + <td>1000 Genomes, diverse</td> <td>No</td> - <td>ONT</td> + <td>~17x ONT</td> <td>148,375</td> <td>2</td> <td>177</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>ONT</td> + <td>~22x ONT</td> <td>74,201</td> <td>51</td> <td>162</td> <td>99,980</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, 8x cov.; biobank includes a variety of conditions (diabetes, hearing loss, etc.)</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>PacBio HiFi</td> + <td>~8x HiFi</td> <td>541,049</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>PacBio HiFi</td> + <td>~27x HiFi</td> <td>115,554</td> <td>50</td> <td>186</td> <td>809,711</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>ONT</td> + <td>~17x ONT</td> <td>133,886</td> <td>0</td> <td>127</td> <td>861,080</td> </tr> <tr> <td><a href="hgTrackUi?g=hprc2Sv">HPRC v2</a></td> <td>233</td> <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td> <td>No</td> - <td>PacBio HiFi (pangenome graph)</td> + <td>~60x HiFi + ~30x ONT (pangenome graph)</td> <td>1,483,114</td> <td>50</td> <td>280</td> <td>97,718</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>PacBio CLR + HiFi + Strand-seq</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> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td> <td>65</td> <td>HGSVC3 diverse reference assemblies</td> <td>No</td> - <td>PacBio HiFi + ONT</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 UPR</a></td> <td>53</td> <td>UAE-resident Arabs from 8 countries (UAE Pangenome Reference)</td> <td>No</td> - <td>PacBio HiFi + ONT + Hi-C (pangenome graph)</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> </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>PacBio HiFi (pangenome graph)</td> + <td>~30x HiFi (pangenome graph)</td> <td>36,030</td> <td>1</td> <td>53</td> <td>8,998,096</td> </tr> <tr> <td><a href="hgTrackUi?g=kwanhoSv">Kim PD Brain</a></td> <td>100</td> <td>Parkinson's disease, ILBD, controls (post-mortem brain)</td> <td>Yes (PD + ILBD)</td> - <td>PacBio HiFi</td> + <td>~17x HiFi</td> <td>74,552</td> <td>50</td> <td>160</td> <td>190,088,222</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>long-read</td> + <td>~50x PacBio CLR (34, Sequel I) + ~76x HiFi (67, Sequel II)</td> <td>87,183</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