3dd0329ee0e804f5841a9998c4e7f024d3276921
lrnassar
  Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261

Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.

Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.

Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.

diff --git src/hg/makeDb/trackDb/human/alphaGenome.html src/hg/makeDb/trackDb/human/alphaGenome.html
index eba79ecd514..9242a48f2d5 100644
--- src/hg/makeDb/trackDb/human/alphaGenome.html
+++ src/hg/makeDb/trackDb/human/alphaGenome.html
@@ -16,34 +16,33 @@
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Because there are three possible substitutions at each position, the scores are split across
 four separate graphs, one for each alternate allele. The graph labelled "Mutation: A" shows the
 score for changing the reference base to an A, and so on. At any given position only three of
 the four graphs carry a real prediction; the fourth is the one matching the reference base,
 where no substitution exists, and it is shown as zero.
 </p>
 <p>
 The source data gives two numbers per variant, a raw model score and a PHRED-scaled version of
 it. This track displays the PHRED-scaled score, which is easier to compare across variants: it
 is a rank in which 10 corresponds to the top 10 percent of the most impactful substitutions in
 the genome, 20 to the top 1 percent, and 30 to the top 0.1 percent. Higher values therefore
-indicate a variant predicted to be more damaging. Any score above 20 can be considered high, and
-the authors recommend treating 50 as the top of the useful range. Most positions score low, with
-a genome-wide median near 1.6, so the default view is scaled to 0 to 30 rather than to the
-observed maximum of about 89. Scores above the top of the range are drawn clipped at the top of
+indicate a variant predicted to be more damaging. Most substitutions score low, with a
+genome-wide median near 2.9, so the default view is scaled to 0 to 30 rather than to the observed
+maximum of about 89. Scores above the top of the range are drawn clipped at the top of
 the graph; the range can be changed on the track configuration page.
 </p>
 <p>
 Individual scores are only shown when the view is zoomed in far enough. At wider zoom levels the
 graph shows the range of scores in each screen pixel rather than a single value.
 </p>
 
 <h2>Methods</h2>
 <p>
 The AVI score comes from a machine learning model that combines several kinds of evidence about
 a variant: AlphaGenome regulatory predictions, AlphaMissense pathogenicity scores for changes
 that fall in coding sequence, measures of evolutionary sequence conservation, and further
 functional annotations. Google DeepMind precomputed the score for all single-base substitutions
 in GRCh38 and released it as a tab-separated, tabix-indexed table of chromosome, position,
 reference allele, alternate allele, raw score and PHRED score. The method is described in the