7bdcd030cdf434c72f3f6a492ee8f84372c752c7
max
  Sat Jul 25 19:22:57 2026 -0700
noyvertSv: note the Boehringer/Vienna relationship and call-level overlap

The Noyvert panel is an independent reprocessing of the same ONT reads as the
1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with
the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and
the concordance both ways (about a third of this track's deletions and a fifth
of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions
match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888

diff --git src/hg/makeDb/trackDb/human/noyvertSv.html src/hg/makeDb/trackDb/human/noyvertSv.html
index 84225b9824b..597b64f7cd4 100644
--- src/hg/makeDb/trackDb/human/noyvertSv.html
+++ src/hg/makeDb/trackDb/human/noyvertSv.html
@@ -14,31 +14,38 @@
 Each variant is annotated with its overall allele frequency; allele
 frequencies across five superpopulations (African, Admixed American, East
 Asian, European, and South Asian); Hardy-Weinberg equilibrium p-values; and
 imputation accuracy metrics from internal leave-one-out validation and UK
 Biobank imputation. For SVs reaching genome-wide significance, the associated
 traits, p-values, and INFO scores are listed on the corresponding variant
 details page.
 </p>
 <p>
 This dataset is an independent reprocessing of the same Oxford Nanopore reads
 used for the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track
 (Schloissnig et al. 2025). The 888 samples in this dataset are a subset of the
 1,019 samples included in that track, with both datasets based on the same
 underlying sequencing data.
 However, the data-processing and SV-calling methods differ between the two
-tracks. The imputation reference panel, UK Biobank imputation results, and
+tracks, so the individual calls are only partially concordant. This track has
+about 38,000 deletions and the Vienna track about 58,000; at a 50%
+reciprocal-overlap threshold roughly 12,000 are shared. That is about a third
+of the deletions in this track and, conversely, about a fifth of the Vienna
+deletions; requiring at least 90% mutual overlap lowers these shares to roughly
+a quarter and a sixth, respectively. A similar fraction (about a quarter) of
+the insertions in this track have a size-matched Vienna insertion within
+100 bp. The imputation reference panel, UK Biobank imputation results, and
 SV-wide association study (SV-WAS) results described here are specific to this
 track.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type, matching the other subtracks of the container:
 </p>
 <table class="stdTbl">
   <tr><th style="background-color:#C80000;width:2em">&nbsp;</th>
       <td>Deletion (DEL)</td></tr>
   <tr><th style="background-color:#0000C8;width:2em">&nbsp;</th>
       <td>Insertion (INS)</td></tr>
   <tr><th style="background-color:#00A000;width:2em">&nbsp;</th>
       <td>Duplication (DUP)</td></tr>