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 &mdash; 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>&mdash;</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>&gt;40x PacBio CLR + &gt;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