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/svatalogSnv.html src/hg/makeDb/trackDb/human/svatalogSnv.html
index 20340d84bef..66c77d986fd 100644
--- src/hg/makeDb/trackDb/human/svatalogSnv.html
+++ src/hg/makeDb/trackDb/human/svatalogSnv.html
@@ -1,46 +1,46 @@
 <h2>Description</h2>
 <p>
 This track shows small-variant (single-nucleotide variant and short-indel)
 allele frequencies from 101 samples released as part of the
 <a href="https://svatalog.research.sickkids.ca/" target="_blank">GWAS
 SVatalog</a> tool (Chirmade et al. 2026). The same 101-sample cohort
 underlies the structural-variant sibling track
 <a href="hgTrackUi?g=chirmade101Sv">SVatalog 101 SVs</a> in the Long-read
 SV collection; this track provides the companion small-variant allele
 frequencies that SVatalog uses to compute linkage disequilibrium between
 SNPs and SVs.
 </p>
 <p>
-The callset contains approximately 8.8 million sites across the autosomes
+The callset contains about 8.8 million sites across the autosomes
 and chromosome X. Each site reports the alternate allele frequency in the
 101 samples, the gnomAD v3.1 non-Finnish European allele frequency (when
 annotated in the source release), and a dbSNP rsID when one was available.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 The track uses the standard VCF display. Variants appear as colored marks
 along the genome; clicking an item opens the detail page with per-site
 INFO fields: AF, AC, AN, the gnomAD v3.1 NFE allele frequency
 (<tt>GNOMAD_NFE_AF</tt>) and the dbSNP rsID (<tt>RSID</tt>).
 </p>
 <p>
 Note on AC/AN: the source allele-frequency release only ships AF. For this
-track AC and AN are synthesized by assuming the full 2x101 = 202-allele
-denominator (AN=202, AC=round(AF x 202)); these are therefore
-approximations at sites where some samples had missing genotypes.
+track we synthesize AC and AN by assuming the full 2x101 = 202-allele
+denominator (AN=202, AC=round(AF x 202)), so the values are approximate
+at sites where some samples had missing genotypes.
 </p>
 
 <h2>Methods</h2>
 <p>
 Small variants were called from 10X Genomics linked-read (paired-end
 short-read) whole-genome sequencing of the 101 SVatalog samples with
 <a href="https://gatk.broadinstitute.org/" target="_blank">GATK
 HaplotypeCaller v4.0.0.0</a> using default parameters. Calls were phased
 across the cohort with
 <a href="https://odelaneau.github.io/shapeit4/" target="_blank">SHAPEIT
 v4.2.0</a>, and per-site alternate allele frequencies were computed on
 the resulting joint callset. Structural variants, released as a separate
 lrSv subtrack, were called from long-read data and merged with these
 SNPs for the LD analyses reported by GWAS SVatalog.
 </p>