2e0addd016cfcbf61485b90d8980a8d75be622c2
lrnassar
  Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258

After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv     133,886 -> 119,453 displayed
gustafsonSv  113,696 -> 113,159 displayed
chirmade101  87,183  -> 87,068  displayed
aou1k        541,049 -> 540,155 displayed
hprc2v21Sv   596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).

diff --git src/hg/makeDb/trackDb/human/gustafsonSv.html src/hg/makeDb/trackDb/human/gustafsonSv.html
index e31e5a7bc66..c2d21fdad24 100644
--- src/hg/makeDb/trackDb/human/gustafsonSv.html
+++ src/hg/makeDb/trackDb/human/gustafsonSv.html
@@ -1,27 +1,28 @@
 <h2>Description</h2>
 <p>
 This track shows structural variants (SVs) from Oxford Nanopore long-read
 whole-genome sequencing of 100 individuals in the 1000 Genomes Project,
 as released by the 1000 Genomes Project ONT Sequencing Consortium and
 described in Gustafson et al. 2024. The cohort spans all five 1000
 Genomes superpopulations and 19 subpopulations. Samples were sequenced
 with ONT R9.4.1 pores at ~37x coverage with median read N50 of ~54 kb.
 </p>
 <p>
-The track contains 113,696 SVs (63,177 insertions, 49,704 deletions,
-744 inversions, 71 duplications). Each variant was called by up to five
+The track contains 113,159 SVs (63,177 insertions, 49,700 deletions,
+211 inversions, 71 duplications; byte-identical duplicate records have been
+removed). Each variant was called by up to five
 independent methods (three alignment-based: Sniffles2, cuteSV, SVIM;
 and assembly-based hapdiff on Flye or Shasta/Hapdup assemblies) and then
 merged across callers and samples with Jasmine to produce a
 cross-sample consensus catalog.
 </p>
 <p>
 This 100-sample Gustafson cohort is distinct from the Vienna
 1000-Genomes-ONT release (<a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT SVs</a>),
 which uses different samples, pore chemistry and callers; the two
 releases share neither samples nor calls.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type: