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
@@ -34,175 +34,175 @@
   <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>&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>2,317,508</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>&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>
+  <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>