9711cb56111546aeed1be4b2c0ba1738080c848c
lrnassar
  Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510

Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.

diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html
index 861cd0f6d0a..6ea8c2a8586 100644
--- src/hg/makeDb/trackDb/human/revel.html
+++ src/hg/makeDb/trackDb/human/revel.html
@@ -73,31 +73,31 @@
 field, some transcripts have been agreed-on as more relevant for a disease, e.g.
 because only certain transcripts may be expressed in the relevant tissue. So
 the choice of the most relevant transcript, and as such the REVEL score, may be
 a question of manual curation standards rather than a result of the variant itself.
 </p>
 <p>
 Note further that these thresholds represent the recommended score
 cutoffs for genes with no Variant Curation Expert Panel (VCEP) rules.
 For genes with published VCEP rules, the VCEP might
 select different thresholds, which are adjusted for the frequency of the
 relevant disorders. These are available in the ClinGen Criteria
 Specification.</p>
 </ul>
 
 <p>
-When using this track, zoom in until you can see every basepair at the
+When using this track, zoom in until you can see every base at the
 top of the display. Otherwise, there are several nucleotides per pixel under 
 your mouse cursor and no score will be shown on the mouseover tooltip.
 </p>
 
 <p><b>Track colors</b></p>
 <p>
 This track is colored according to Table 2 in Pejaver et al. The colors represent the recommended
 ClinGen score cutoffs.
 
 <table style="text-align: left;">
   <thead>
     <tr>
       <th>Range</th>
       <th>Classification</th>
     </tr>
@@ -162,31 +162,31 @@
 binary for your system. Instructions for downloading source code and binaries can be found
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
 The tools can also be used to obtain features confined to given range, e.g.
 <br>&nbsp;
 <br>
 <tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/revel/a.bw stdout</tt>
 <br>
 
 <h2>Methods</h2>
 
 <p>
 Data were converted from the files provided on
 <a href="https://sites.google.com/site/revelgenomics/downloads?authuser=0" 
 target = "_blank">the REVEL Downloads website</a>. As with all other tracks,
 a full log of all commands used for the conversion is available in our 
-<a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/">source repository</a>, for <a target=_blank href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt">hg19</a> and <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/revel.txt">hg38</a>. The release used for each assembly is shown on the track description page.
+<a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/">source repository</a> for <a target=_blank href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt">hg19</a> and <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/revel.txt">hg38</a>. The release used for each assembly is shown on the track description page.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to the REVEL development team for providing precomputed data and fixing duplicated values in the hg38 files.
 </p>
 
 <h2>References</h2>
 <p>
 Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, 
 Musolf A, Li Q, Holzinger E, Karyadi D, et al.
 <a href="https://doi.org/10.1016/j.ajhg.2016.08.016" target = _blank">
 REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants</a>
 <em>Am J Hum Genet</em>. 2016 Oct 6;99(4):877-885.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27666373" target="_blank">27666373</a>;