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/chirmade101Sv.html src/hg/makeDb/trackDb/human/chirmade101Sv.html
index 1ffe94e15a3..dc35b075c66 100644
--- src/hg/makeDb/trackDb/human/chirmade101Sv.html
+++ src/hg/makeDb/trackDb/human/chirmade101Sv.html
@@ -1,28 +1,29 @@
 <h2>Description</h2>
 <p>
 This track shows structural variants (SVs) identified by long-read
 whole-genome sequencing of 101 individuals, released together with the
 <a href="https://svatalog.research.sickkids.ca/" target="_blank">GWAS SVatalog</a>
 web tool described in Chirmade et al. 2026. GWAS SVatalog computes and
 visualizes linkage disequilibrium between these SVs and GWAS-associated
 SNPs so that investigators can assess whether a SNP association signal
 may be tagging an underlying SV.
 </p>
 <p>
-The table contains 87,183 SVs (42,435 deletions, 41,734 insertions,
-1,394 duplications, 912 inversions, 708 complex events). Each SV is
+The table contains 87,068 SVs (42,435 deletions, 41,619 insertions,
+1,394 duplications, 912 inversions, 708 complex events; byte-identical
+duplicate records have been removed). Each SV is
 annotated with gene overlaps, GC content, repeat context, ClinGen
 haploinsufficiency / triplosensitivity scores, gnomAD per-gene constraint
 metrics (pLI, LOEUF, missense O/E), OMIM phenotype associations, ClinVar
 variant IDs, and overlaps with DGV, Decipher and ClinGen regional
 annotations.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type:
 <ul>
 <li><span style="color: rgb(200,0,0);">Deletions (del)</span> - red</li>
 <li><span style="color: rgb(0,0,200);">Insertions (ins)</span> - blue</li>
 <li><span style="color: rgb(0,160,0);">Duplications (dup)</span> - green</li>
 <li><span style="color: rgb(230,140,0);">Inversions (inv)</span> - orange</li>