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/clinPred.html src/hg/makeDb/trackDb/human/clinPred.html
index c24f8529d37..a49c91e1b46 100644
--- src/hg/makeDb/trackDb/human/clinPred.html
+++ src/hg/makeDb/trackDb/human/clinPred.html
@@ -18,31 +18,31 @@
 classifier.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 There are four subtracks in this collection, one for each possible alternate
 nucleotide. At every exome position covered by ClinPred, three of the four
 subtracks show a score (one per non-reference base) and the fourth, corresponding
 to the reference base, is set to 0. Synonymous alternates, those that do
 not change the encoded amino acid, are also set to 0, since ClinPred only
 scores missense variants. Positions with no exome coverage are shown as gaps.
 </p>
 
 <p>
-When using this track, zoom in until you can see every basepair at the top of
+When using this track, zoom in until you can see every base at the top of
 the display. Otherwise, several nucleotides fall under each pixel and no score
 will be shown on the mouseover tooltip.
 </p>
 
 <p><b>Track colors</b></p>
 
 <p>
 Each subtrack is colored by score using the threshold recommended by the
 ClinPred authors:
 </p>
 
 <table style="text-align: left;">
   <thead>
     <tr>
       <th>Range</th>
@@ -63,49 +63,49 @@
 
 <h2>Data Access</h2>
 
 <p>
 ClinPred scores are available at the
 <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred
 website</a>, which provides pre-computed scores for all possible human missense
 variants.
 </p>
 
 <p>
 The ClinPred data on the UCSC Genome Browser can be explored interactively with
 the <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated download
 and analysis, the data are stored in bigWig files and can be downloaded from
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/" target="_blank">our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/" target="_blank">our
 download server</a>. The files are named <tt>a.bw, c.bw, g.bw, t.bw</tt>.
 Individual regions can be obtained using <tt>bigWigToBedGraph</tt>, which can
 be compiled from source or downloaded as a precompiled binary; instructions
-are <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
+are <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
 For example:
 <br>&nbsp;<br>
-<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/a.bw stdout</tt>
+<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/a.bw stdout</tt>
 </p>
 
 <h2>Methods</h2>
 
 <p>
 Data were downloaded from the
 <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred
 website</a> on May 5, 2026, and converted into four per-alternate-base bigWig
 files using a custom script. As with all other tracks, a full log of the
 commands used for the conversion is available in our
-<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/" target="_blank">source repository</a>, for
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/" target="_blank">source repository</a> for
 <a href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt" target="_blank">hg19</a> and
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/clinPred.txt" target="_blank">hg38</a>.
 </p>
 
 <h2>Data Use</h2>
 
 <p>
 ClinPred scores are freely available for non-commercial applications. For
 commercial use, please see the licensing information on the
 <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred
 website</a>.
 </p>
 
 <h2>Credits</h2>