6120d02a6aa7faf052299967d8bace2d2d706ad3
hiram
  Mon Dec 15 13:06:28 2025 -0800
one additional color code definition for paralogous annotations refs #35776

diff --git src/hg/makeDb/trackDb/TOGAv2.html src/hg/makeDb/trackDb/TOGAv2.html
index 995cce59d39..40a83b03d08 100644
--- src/hg/makeDb/trackDb/TOGAv2.html
+++ src/hg/makeDb/trackDb/TOGAv2.html
@@ -78,30 +78,35 @@
 <li><span style='display:inline-block; width:40px; height:15px; background-color:#828282;'>&nbsp;</span>
     <span style='color:#828282'>"missing"</span>: &lt;50% of the CDS is present
      in the query and the middle 80% of the CDS exhibits no inactivating
      mutation. There is currently no evidence for transcript loss; however, the uncertainty is higher
 as more than half of the CDS is missing. Note that Missing transcripts can also arise if no genome alignment
 chain spans the transcript.</li>
 <li><span style='display:inline-block; width:40px; height:15px; background-color:#FFA078;'>&nbsp;</span>
     <span style='color:#FFA078'>"uncertain loss"</span>: there is at least one
      inactivating mutation in the middle 80% of the CDS, but evidence is not
      strong enough to classify the transcript as lost. These transcripts may
      or may not encode a functional protein.</li>
 <li><span style='display:inline-block; width:40px; height:15px; background-color:#FF3232;'>&nbsp;</span>
     <span style='color:#FF3232'>"lost"</span>: typically several inactivating
      mutations are present, thus there is strong evidence that the transcript
      is unlikely to encode a functional protein.</li>
+<li><span style='display:inline-block; width:40px; height:15px; background-color:#9F8170;'>&nbsp;</span>
+    <span style='color:#9F8170'>"paralogous"</span>: Special category. Transcript is classified as paralogous
+by TOGA2’s machine learning classifier and these are only retained if the respective query locus does not have
+an orthologous projection. Transcripts in this color have enough inactivating mutations or missing sequence
+    such that there loss status is "missing" or "deleted".</li>
 </ul>
 </p>
 <p>
 Clicking on a transcript provides additional information about the orthology
 classification, inactivating mutations, the query's nucleotide/protein sequence, and protein/exon
 alignments.
 </p>
 
 <h2>Credits</h2>
 <p>
 This data was prepared by the <a href="https://www.senckenberg.de/en/research/institutes-overview/sf/ffm-dept-comparative-genomics/"
 target="_blank">Michael Hiller's Lab</a>
 </p>
 
 <h2>References</h2>