8efbcad3f2816dec50b5671a4445d2e6943f7f91
max
  Mon Apr 13 07:57:41 2026 -0700
Use light gray for monomorphic strVar loci (het=0), distinct from no-data gray, refs #36652

Add a separate color for loci where heterozygosity is exactly 0 (single allele
observed) across all four strVar subtracks: light gray (200,200,200). This
distinguishes them from the existing medium gray (128,128,128) used when no
allele frequency data is available. Previously het=0 was lumped into the
dark blue "nearly monomorphic" bin. Also expand the itemRgb field description
in all four .as files to list the full color scheme.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/scripts/tommoStr/tommoStr.as src/hg/makeDb/scripts/tommoStr/tommoStr.as
index 5c6c0cb6673..d830df08982 100644
--- src/hg/makeDb/scripts/tommoStr/tommoStr.as
+++ src/hg/makeDb/scripts/tommoStr/tommoStr.as
@@ -1,21 +1,21 @@
 table tommoStr
 "ToMMo 61KJPN Short Tandem Repeat allele counts from Expansion Hunter"
     (
     string chrom;        "Chromosome"
     uint chromStart;     "Start position"
     uint chromEnd;       "End position"
     string name;         "Repeat motif x copy count"
     uint score;          "Score (0-1000)"
     char[1] strand;      "Strand"
     uint thickStart;     "Thick start (same as chromStart)"
     uint thickEnd;       "Thick end (same as chromEnd)"
-    uint reserved;       "Item color RGB|by motif size: mono=red, di=blue, tri=green, tetra=orange, penta=purple, hexa=steelblue, >6=gray"
+    uint reserved;       "Item color RGB|by heterozygosity: light gray (het=0), dark blue (<0.1), medium blue (0.1-0.3), light purple (0.3-0.5), salmon (0.5-0.7), dark red (>=0.7), medium gray (no data)"
     string motif;        "Repeat unit motif"
     uint period;         "Length of repeat unit in bp"
     uint numCopies;      "Number of repeat copies in reference"
     float mean;          "Mean repeat count|Mean repeat copy number across all samples"
     float median;        "Median repeat count|Median repeat copy number across all samples"
     uint numAlleles;     "Number of alleles called|Total number of alleles (AN)"
     float het;           "Expected heterozygosity|1 - sum(p_i^2) computed from allele counts"
     lstring alleleHist;  "Allele count histogram|Space-separated pairs of copies=count (e.g. 3=100 4=5000 5=200)"
     )