971ae4b10f79d994d419c94d932e5b9163b72098
gperez2
  Tue Dec 2 10:39:58 2025 -0800
Updating the Display Conventions and Configuration section for gnomAD MPC, refs #36531

diff --git src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
index aa07dfe5e08..44881937e1a 100644
--- src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
+++ src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
@@ -1,39 +1,37 @@
 <h2>Description</h2>
 <p>
 The <b>${longLabel}</b> track shows a score that tries to identify missense-depleted
 regions using the patterns of rare missense variation in 125,748 gnomAD v2.1.1 exomes,
 compared to a null mutational model. Missense-depleted regions are enriched for ClinVar pathogenic
 variants, de novo missense variants in individuals with neurodevelopmental disorders (NDDs), and
 complex trait heritability. The score's publication suggests that regions
 with less than 20% of their expected missense variation achieve moderate
 support for pathogenicity according to ACMG criteria.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
-Transcripts with constraint predictions are highlighted. Observed and expected
-number of missense mutations are shown on mouse overs, as well as their
-Observed/expected ratio (OE), and the Chi-square and P-value of the ratio.
-Regions are colored using the viridis palette, with yellow for the lowest OE
-values and dark blue for the highest values.
+Transcripts with constraint predictions are colored with the viridis palette, where yellow
+indicates the lowest OE values and dark blue-purple indicates the highest.
 </p>
 
 <p><strong>OE Constraint Legend</strong><br>
-Yellow = strongest constraint, Purple = weakest</p>
-
+Yellow = strongest constraint<br>
+Purple = weakest constraint
+</p>
 <table>
   <thead>
   <tr>
     <th style="border-bottom: 2px solid #6678B1;">Color</th>
     <th style="border-bottom: 2px solid #6678B1;">OE Range</th>
   </tr>
   </thead>
     <tr>
         <th bgcolor="#FDE724"></th>
         <th align="left">OE = 0.0066884</th>
     </tr>
     
     <tr>
         <th bgcolor="#74D054"></th>
         <th align="left">OE = 0.36229 </th>
@@ -43,30 +41,35 @@
         <th bgcolor="#22898d"></th>
         <th align="left">OE = 0.66993</th>
     </tr>
     
     <tr>
         <th bgcolor="#39558B"></th>
         <th align="left">OE = 0.93385 </th>
     </tr>
     
     <tr>
         <th bgcolor="#440154"></th>
         <th align="left">OE = 2.2429</th>
     </tr>
 </table>
 
+<p>Mouseovers on an item show the observed and expected number of missense mutations, the
+observed/expected (OE) ratio, and the associated Chi-square statistic and P-value.
+</p>
+
+
 <H2>Methods</H2>
 <p>
 The study analyzed only canonical, coding transcripts as defined by GENCODE v19/Ensembl v74. Some
 were excluded: transcripts that had outlier counts of variants expected under neutrality (zero
 expected pLoF, missense, or synonymous variants; too many observed pLoF, missense, or synonymous
 variants compared to expectation; or too few observed synonymous variants compared to expectation).
 In total, the study analyzed 18,629 transcripts.
 </p>
 
 </p>125,748 gnomAD v2.1.1 exomes were used on hg19.
 Median coverage was calculated on a random subset of the gnomAD exomes.
 The set of sites with possible missense variants was described using a
 synthetic Hail Table (HT) containing all possible single nucleotide variants in the exome. 
 Ensembl VEP annotated this HT against GENCODE version 19, and filtered to
 variants with the consequence "missense_variant" in the canonical, coding