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/allofus.html src/hg/makeDb/trackDb/human/allofus.html
index 8ea4960da35..29d73657d5d 100644
--- src/hg/makeDb/trackDb/human/allofus.html
+++ src/hg/makeDb/trackDb/human/allofus.html
@@ -34,32 +34,32 @@
 
 <h2>Methods</h2>
 <p>
 Whole-genome sequencing was performed on the Illumina NovaSeq 6000 platform with PCR-free library
 preparation targeting 30x coverage. Reads were aligned to GRCh38 and variants were called using
 the Illumina DRAGEN (Dynamic Read Analysis for GENomics) pipeline, which performs mapping,
 alignment, sorting, duplicate marking, and variant calling (SNVs and indels) in a single
 hardware-accelerated workflow. Joint genotyping was performed across all samples. Quality control
 included sample-level filtering for contamination, sex discordance, and relatedness, and
 variant-level filtering using VQSR.
 Population-specific allele frequencies were determined using local ancestry inference at UCSC by the Ioannidis group.
 The ancestry breakdown into European, East Asian, African, Indigenous American, Oceanian,
 and South Asian components is part of a pending publication.
 </p>
 <p>
-At UCSC, we provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track.
-For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
+The conversion of all source files for the varFreqs track is documented in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track.
+For some tracks, python scripts were needed and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
 </p>
 
 <h2>Credits</h2>
 <p>
 The All of Us Research Program is supported by the National Institutes of Health. We thank the
 participants and the program for making frequency data available.
 The local ancestry inference was performed by Qudsi Aljabiri and Cole Shanks under
 Prof. Alexander Ioannidis, UC Santa Cruz.
 </p>
 
 <h2>References</h2>
 <p>
 All of Us Research Program Genomics Investigators.
 <a href="https://doi.org/10.1038/s41586-023-06957-x" target="_blank">
 Genomic data in the All of Us Research Program</a>.