9bfd58221b1539193cb7f0a317b4e959c1c7e49a
max
  Thu May 21 01:00:45 2026 -0700
varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/varFreqsAll.html src/hg/makeDb/trackDb/human/varFreqsAll.html
index 849c9abd374..9a07af3d6b9 100644
--- src/hg/makeDb/trackDb/human/varFreqsAll.html
+++ src/hg/makeDb/trackDb/human/varFreqsAll.html
@@ -58,40 +58,40 @@
 This track supports extensive filtering via the track settings page. Click on the track
 title or use the &quot;Configure&quot; button to access filters:
 </p>
 
 <h3>Variant Type and Consequence</h3>
 <ul>
   <li><b>Variant Type</b>: Filter by SNV, Insertion, Deletion, or MNV.</li>
   <li><b>Consequence</b>: Filter by predicted consequence (Missense, Synonymous, Stop Gained,
       Frameshift, Splice Donor, Splice Acceptor, Intron, 3' UTR, 5' UTR, Non-coding,
       Intergenic, Other). The filter uses OR logic across the comma-separated consequence
       tokens on each variant: a variant tagged
       <code>stop_gained,frameshift</code> is selected by either the &quot;Stop Gained&quot;
       or the &quot;Frameshift&quot; filter. The &quot;Other&quot; bucket catches the less
       common <a href="http://www.sequenceontology.org/" target="_blank">Sequence Ontology</a>
       consequence terms emitted by <code>bcftools csq</code> that don't fit the named
-      buckets above &mdash; for example
+      buckets above. Examples include
       <code>splice_region</code> (variant near a splice site but outside the canonical
       donor/acceptor),
       <code>start_lost</code> / <code>stop_lost</code> (variant disrupts the start codon
       or replaces the stop codon with a coding amino acid),
       <code>stop_retained</code> (variant changes the stop codon but keeps it a stop),
       <code>inframe_insertion</code> / <code>inframe_deletion</code> (in-frame indel
-      adding or removing whole codons), and
+      that adds or removes whole codons), and
       <code>coding_sequence</code> (CDS variant where the precise impact is undetermined).
-      Including &quot;Other&quot; in the filter selection guarantees that no records are
+      If you include &quot;Other&quot; in the filter selection, no records will be
       hidden by the consequence filter.</li>
 </ul>
 
 <p><b>How to find protein-truncating variants:</b> Set the Consequence filter to include
 only &quot;Stop Gained&quot;, &quot;Frameshift&quot;, &quot;Splice Donor&quot;, and
 &quot;Splice Acceptor&quot;. These will appear as red items in the track display.</p>
 
 <h3>Frequency and Count Filters</h3>
 <ul>
   <li><b>Max Allele Frequency</b>: Filter by the maximum allele frequency observed across
       all databases. Useful for finding rare variants (e.g., set max to 0.01 for variants
       with AF &lt; 1% in all databases).</li>
   <li><b>Total Allele Count</b>: Filter by the sum of allele counts across all databases.
       Useful for excluding singletons (e.g., set minimum to 2 to remove AC=1 variants
       that may be sequencing errors).</li>
@@ -136,38 +136,37 @@
 <a href="https://www.ensembl.org/info/data/ftp/index.html" target="_blank">Ensembl</a>
 GRCh38 release 115 gene annotation (GFF3).
 </p>
 
 <p>
 The annotated VCF was converted to bigBed format using a custom Python script
 (<code>vcfToBigBed.py</code>) that reads frequency data from each source VCF in parallel,
 matches variants by position/ref/alt, and writes a BED file with consequence coloring,
 per-database allele counts and frequencies, and population breakdowns.
 The database configuration (which VCFs to include, field mappings, and population definitions)
 is stored in two TSV files
 (<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs/databases.tsv"
 target="_blank">databases.tsv</a> and
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs/populations.tsv"
 target="_blank">populations.tsv</a>)
-to make future updates easy.
+so that future updates only require editing these files.
 </p>
 
 <p>
-We provide documentation that indicates how all source files of the varFreqs track were
-converted in the
+The track's
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt"
-target="_blank">makeDoc file</a> of the track.
+target="_blank">makeDoc file</a> documents how each source VCF was converted.
 Scripts are available from
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs"
 target="_blank">Github</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The data 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 programmatic access, our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a>
 can be used; the track name is <em>varFreqsAll</em>.
 </p>
 <p>
 Because the merged callset includes data from multiple sources whose redistribution