aaa2d4e074608d3e07ecf7d7a7e35cfa96b0a06d
max
  Tue Apr 21 08:29:35 2026 -0700
tommoJpSv: fix broken jMorp download link

The previous dataset-specific URL (tommo-jsv1-20211208-af) returned an
error. Point to the general jMorp downloads page instead, where users
can find the current ToMMo SV callset.

refs #36258

diff --git src/hg/makeDb/trackDb/human/tommoJpSv.html src/hg/makeDb/trackDb/human/tommoJpSv.html
index bf20054adf7..10015b98804 100644
--- src/hg/makeDb/trackDb/human/tommoJpSv.html
+++ src/hg/makeDb/trackDb/human/tommoJpSv.html
@@ -1,81 +1,81 @@
 <h2>Description</h2>
 <p>
 This track shows structural variants (SVs) identified by Oxford Nanopore long-read
 sequencing of 333 Japanese individuals from the Tohoku Medical Megabank (ToMMo)
 project. The 333 individuals form 111 parent-offspring trios, enabling
 Mendelian consistency checks on the SV calls. Activated T lymphocytes were used
 as a source of high-molecular-weight DNA for nanopore sequencing at a median
 coverage of 22.2x with an N50 read length of 25.8 kb.
 </p>
 <p>
 The dataset contains 74,201 SVs (37,981 deletions and 36,220 insertions),
 merged across individuals using SURVIVOR v1.0.6. Over 95% of the SVs are
 concordant with Mendelian inheritance in the trio families.
 </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>
 </ul>
 </p>
 <p>
 Filters are available for SV type, SV length, and allele frequency.
 For insertions, the item is placed at the insertion site with a width of 1 bp;
 for deletions, the item spans the deleted region.
 </p>
 <p>
 The detail page for each item shows:
 <ul>
 <li><b>Allele Frequency</b>: fraction of alleles carrying this variant
 (based on 444 alleles from 222 unrelated parents)</li>
 <li><b>Allele Count / Allele Number</b>: number of variant alleles and
 total alleles genotyped</li>
 <li><b>Mendelian Error Rate</b>: fraction of trio families showing
 inheritance errors for this variant</li>
 <li><b>Families with Errors / Families Genotyped</b>: number of families
 with Mendelian errors and total families with complete genotype calls</li>
 </ul>
 </p>
 
 <h2>Methods</h2>
 <p>
 Oxford Nanopore sequencing was performed on genomic DNA extracted from activated
 T lymphocytes of 333 individuals (111 trios) from the Tohoku Medical Megabank
 (ToMMo) cohort. SV calling was performed with Sniffles on each sample, and
 calls were merged across individuals with SURVIVOR v1.0.6 using a maximum
 distance of 1 kbp. Allele frequencies were computed from 222 unrelated parents
 (excluding offspring to avoid double-counting). Mendelian error rates were
 calculated by checking transmission consistency within each trio family.
 </p>
 
 <h2>Data Access</h2>
 <p>
 Source data is available from the
-<a href="https://jmorp.megabank.tohoku.ac.jp/datasets/tommo-jsv1-20211208-af"
-   target="_blank">jMorp data portal</a> (ToMMo Japanese Multi Omics Reference Panel).
+<a href="https://jmorp.megabank.tohoku.ac.jp/downloads"
+   target="_blank">jMorp downloads page</a> (ToMMo Japanese Multi Omics Reference Panel).
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to the Tohoku Medical Megabank Organization for making their structural
 variant calls publicly available through the jMorp data portal.
 </p>
 
 <h2>References</h2>
 
 
 
 <p>
 Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N,
 Kuriyama S <em>et al</em>.
 <a href="https://doi.org/10.1038/s42003-022-03953-1" target="_blank">
 Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-
 read sequencing technology</a>.
 <em>Commun Biol</em>. 2022 Sep 20;5(1):991.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36127505" target="_blank">36127505</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9489684/" target="_blank">PMC9489684</a>
 </p>