f4d6633d6a724d7b682f9f49ed983e22a5e0975d
max
  Mon Apr 20 14:41:07 2026 -0700
updating a few lrSv subtracks, and moving the colorsDbSnv track under
the varFreqs track. refs #36642

diff --git src/hg/makeDb/trackDb/human/han945Sv.html src/hg/makeDb/trackDb/human/han945Sv.html
index 2cd2b28f29d..4bf2ac8d4db 100644
--- src/hg/makeDb/trackDb/human/han945Sv.html
+++ src/hg/makeDb/trackDb/human/han945Sv.html
@@ -1,64 +1,72 @@
 <h2>Description</h2>
 <p>
 This track shows structural variants (SVs) identified by long-read sequencing
 of 945 Han Chinese individuals. The dataset contains 111,288 SVs merged across
 samples using SURVIVOR, including 49,518 deletions, 42,300 insertions,
 13,503 duplications, 5,595 inversions, and 372 translocations.
 </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>
 <li><span style="color: rgb(140,0,200);">Translocations (TRA)</span> - purple</li>
 </ul>
 </p>
 <p>
 Filters are available for SV type, SV length, allele frequency, and number of
 supporting samples. For insertions, the item is placed at the insertion site
 with a width of 1 bp. For translocations, only the first breakpoint is shown;
 the second breakpoint chromosome and position are listed in the item details.
 </p>
 
 <h2>Methods</h2>
 <p>
 Long-read sequencing was performed on 945 Han Chinese individuals.
 Structural variants were called per sample and then merged across all samples using
 <a href="https://github.com/fritzsedlazeck/SURVIVOR" target="_blank">SURVIVOR</a>
 (v1.0.6). The merged VCF was converted to bigBed format for display.
 Allele frequencies and per-sample support information were extracted from the
 INFO fields of the merged VCF. The study identified two notable variants:
 an ancestral deletion in GSDMD associated with bone density and kidney injury
 risk, and a modern human-specific variant in WWP2 influencing height, body
 composition, and facial features.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The raw VCF data was obtained from the
-<a href="https://ngdc.cncb.ac.cn/omix/" target="_blank">OMIX</a> repository
-(accession OED00945268) at the National Genomics Data Center (NGDC),
+<a href="https://ngdc.cncb.ac.cn/omix/release/OMIX005649" target="_blank">OMIX</a>
+repository (accession OED00945268) at the National Genomics Data Center (NGDC),
 China National Center for Bioinformation.
 </p>
+<p>
+The source VCF also encodes phased per-sample genotypes: the <tt>sampleList</tt>
+field on the detail page is derived from the SURVIVOR <tt>SUPP_VEC</tt> bitmask
+and is an ordered list of the 1-based indices of the 945 samples carrying
+each SV. The full per-sample phased VCF can be browsed as a separate track in
+the <a href="hgTrackUi?g=han945SvVcf">SVs from 945 Han Chinese</a> entry of
+the <a href="hgTrackUi?g=phasedVars">Phased Variants</a> track collection.
+</p>
 
 <h2>Credits</h2>
 <p>
 Thanks to Gong et al. for making their structural variant calls publicly available.
 </p>
 
 <h2>References</h2>
 
 <p>
 Gong J, Sun H, Wang K, Zhao Y, Huang Y, Chen Q, Qiao H, Gao Y, Zhao J, Ling Y <em>et al</em>.
 <a href="https://doi.org/10.1038/s41467-025-56661-9" target="_blank">
 Long-read sequencing of 945 Han individuals identifies structural variants associated with
 phenotypic diversity and disease susceptibility</a>.
 <em>Nat Commun</em>. 2025 Feb 10;16(1):1494.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39929826" target="_blank">39929826</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811171/" target="_blank">PMC11811171</a>
 </p>