574399b4a7d8fc75c1745fa83564f547ddcb9e8c
chmalee
  Sat Jun 13 00:43:54 2026 -0700
gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

diff --git src/hg/makeDb/gnomad/missenseMetrics.v4.1.1.as src/hg/makeDb/gnomad/missenseMetrics.v4.1.1.as
new file mode 100644
index 00000000000..bef4993ac75
--- /dev/null
+++ src/hg/makeDb/gnomad/missenseMetrics.v4.1.1.as
@@ -0,0 +1,24 @@
+table missenseMetricsV4_1_1
+"bed12+8 for displaying gnomAD v4.1.1 missense constraint scores"
+    (
+    string chrom;      "Reference sequence chromosome or scaffold"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "ENST or ENSG Name"
+    uint   score;      "pLI score between 0-1000, or -1 for NA"
+    char[1] strand;    "strand of transcript"
+    uint thickStart;   "Start of where display is thick"
+    uint thickEnd;     "End of where display should be thick"
+    uint itemRgb;      "Color of item"
+    int blockCount;    "Number of exons"
+    int[blockCount] blockSizes;  "Size of each exon"
+    int[blockCount] chromStarts; "0-based start position of each exon"
+    string _mouseOver;  "Mouseover label"
+    float _zscore;      "Missense Z-score value for filters"
+    string geneName;    "Gene symbol"
+    string synonymous;  "Synonymous metrics"
+    string missense;    "Missense metrics"
+    string constraintFlags; "Constraint outlier flags (e.g. outlier_mis, no_exp_mis)"
+    string geneFlags;   "Gene quality flags (low_exome_coverage, low_exome_mapping_quality)"
+    string qualityMetrics; "Exome quality metrics: prop bp AN90, mean AS MQ, prop segdup, prop LCR"
+    )