062e08e4116be810b29621d9863e22bffdedcf50
gperez2
  Sun Aug 2 23:45:08 2026 -0700
Updating gnomad.html's Constraint Metrics bullet to say per-gene is only available for v2.1.1, and gnomadPLI.html's flags-section field count, Transcripts Included version list, shading description (pLI to LOEUF), and missense track color description. refs #37351

diff --git src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
index a8c56be6841..4f82aff201b 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
+++ src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
@@ -14,38 +14,40 @@
   <li>Observed and expected variant counts per transcript/gene
   <li>Observed/Expected  ratio (O/E)
   <li>Z-scores of the observed counts compared to expected
   <li>Probability of loss of function intolerance (pLI), for predicted loss-of-function (pLoF) variation only
 </ul>
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 There are two &quot;groups&quot; of tracks in this set, and four gnomAD versions (v2.1.1, v4.0, v4.1, and v4.1.1):
 <ol>
   <li><b>Gene/Transcript LoF Constraint tracks</b>: Predicted constraint metrics at the whole gene
     level or whole transcript level for three different types of variation: missense, synonymous,
     and predicted loss of function. The Gene Constraint track displays metrics for a canonical 
     transcript per gene defined as the longest isoform. The Transcript Constraint track displays 
-    metrics for all transcript isoforms. Items on both tracks are shaded according to the pLI score,
-    with outlier items shaded in grey.
+    metrics for all transcript isoforms. Items on both tracks are shaded according to the LOEUF score
+    (the upper bound of the O/E confidence interval, see Methods below) with outlier items shaded in
+    grey.
   <br><img src="../images/gnomAD_LOEUFkey.png"  width='33%'alt="LOEUF score legend"><br>
     Please note there is no gene-level track available for v4.0, v4.1, or v4.1.1.
   <li><b>Gene/Transcript Missense Constraint tracks</b>: The missense constraint tracks are built
     similarly to the LoF constraint tracks, however the items displayed are based on 
     <a href="https://gnomad.broadinstitute.org/help/constraint" target="_blank">missense Z scores</a>.
-    All items are colored black, and individual Z scores can be seen on mouseover. 
+    Items are colored red when the missense Z-score exceeds 3.09, and black otherwise; individual Z
+    scores can be seen on mouseover. 
 </ol>
 All tracks follow the general configuration settings for bigBed tracks. Mouseover on the 
 Gene/Transcript Constraint tracks shows the <b>pLI score</b> and the loss of function 
 observed/expected upper bound fraction <b>(LOEUF)</b>, while mouseover on the Regional
 Constraint track shows only the missense <b>O/E ratio</b>. Clicking on items in any track brings
 up a table of constraint metrics.
 </p>
 
 <p>
 Clicking the grey box to the left of the track, or right-clicking and choosing the Configure option,
 brings up the interface for filtering items based on their pLI score, or labeling the items
 based on their Ensembl identifier and/or Gene Name.
 </p>
 
 <H2>Methods</H2>
@@ -114,75 +116,76 @@
 <ul>
   <li>null: heterozygous or homozygous protein truncating variation is completely tolerated
   <li>recessive: heterozygous variants are tolerated but homozygous variants are not
   <li>haploinsufficient: heterozygous variants are not tolerated
 </ul>
 An expectation-maximization algorithm was then used to assign a probability of belonging in each
 class to each gene or transcript. pLI is the probability of belonging in the haploinsufficient class.
 </p>
 
 <p>
 Please see Samocha et al., 2014 and Lek et al., 2016 for further discussion of these metrics.
 </p>
 
 <h3>Constraint and Gene Quality Flags (v4.1.1)</h3>
 <p>
-Starting with v4.1.1, the Transcript LoF and Transcript Missense tracks carry two additional flag
+Starting with v4.1.1, the Transcript LoF and Transcript Missense tracks carry three additional
 fields, shown on the item details page:
 <ul>
   <li><b>Constraint flags</b>: <code>outlier_lof</code>, <code>outlier_mis</code>, and
   <code>outlier_syn</code> mark transcripts whose raw z-score for that class of variation is a
   statistical outlier (outside gnomAD's default -5.0 to 5.0 range) and should be interpreted with
   caution. <code>no_exp_lof</code>, <code>no_exp_mis</code>, and <code>no_exp_syn</code> mark
   transcripts with a missing or zero expected variant count for that class, so constraint metrics
   are not calculated for it.
   <li><b>Gene flags</b>: <code>low_exome_coverage</code> and <code>low_exome_mapping_quality</code>
   mark transcripts overlapping regions of low exome sequencing coverage or low mapping quality.
   Constraint metrics for flagged transcripts should be treated with caution.
+  <li><b>Exome quality metrics</b>: <code>prop bp AN90</code> (proportion of transcript bases with
+  allele number at or above 90% of the maximum) and <code>mean AS MQ</code> (mean allele-specific
+  mapping quality) are the coverage and mapping-quality statistics underlying the gene flags above.
+  <code>prop segdup</code> and <code>prop LCR</code> report the proportion of the transcript
+  overlapping segmental duplications or low-complexity regions. Not available for all transcripts.
 </ul>
-The underlying per-transcript coverage and mapping statistics used to derive these flags
-(proportion of bases with allele number at or above 90% of the maximum, mean allele-specific
-mapping quality, and proportion of the transcript overlapping segmental duplications or
-low-complexity regions) are also shown on the item details page.
 </p>
 
 <h3>Transcripts Included</h3>
 <p>
 For version 2.1.1 only, the GENCODE transcripts were filtered according to the following criteria:
 <ul>
   <li>Must have methionine at start of coding sequence
   <li>Must have stop codon at end of coding sequence
   <li>Must be divisible by 3
   <li>Must have at least one observed variant when removing exons with median depth &lt; 1
   <li>Must have reasonable number of missense and synonymous variants as determined by a Z-score cutoff
 </ul>
 </p>
 <p>
 For version v2.1.1, the gnomAD gene/transcript data is based on hg19. In order to map transcripts and genes to the hg38 genome the following steps were taken:
 <ul>
 <li><b>Transcript track:</b> The gnomAD ENST identifiers were attempted to be matched to all GENCODE versions
 between V20 and V44, giving coordinate priorities to the most recent models. In total 74550/80950 
 transcripts were mapped.</li>
 <li><b>Genes track:</b> The gnomAD file ENSG identifiers were attempted to be matched to all GENCODE versions
 between V20 and V44, giving coordinate priorities to the most recent models. This mapped 19221/19704
 genes. The remainder of the genes were attempted to be mapped using the same strategy, but matching
 on gene symbols instead of ENSG identifiers. In total 19567/19704 genes were mapped.</li>
 </ul>
 </p>
 
 <p>
-For version v4.0 and v4.1, the gnomAD transcript data is based on hg38. In order to map the
+For version v4.0, v4.1, and v4.1.1, the gnomAD transcript data is based on hg38. In order to map the
 transcripts to hg38, the transcript version numbers in the gnomAD download file were joined with
 GENCODE V39 and NCBI RefSeq coordinates available at UCSC.
 </p>
 
 <h3>UCSC Track Methods</h3>
 <h4>Version based on gnomAD v2.1.1</h4>
 <h5>Gene and Transcript Constraint tracks</h5>
 <p>
 Per gene and per transcript data were downloaded from the gnomAD Google Storage bucket:
 <pre>
 gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz
 gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz
 </pre>
 These data were then joined to the Gencode set of genes/transcripts available at the UCSC
 Genome Browser (see previous section) and then transformed into a bigBed 12+5. For the full list of commands used to