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/viennaVntr/viennaVntr.as src/hg/makeDb/scripts/viennaVntr/viennaVntr.as
index e6ad052d4a6..a7863aa65b5 100644
--- src/hg/makeDb/scripts/viennaVntr/viennaVntr.as
+++ src/hg/makeDb/scripts/viennaVntr/viennaVntr.as
@@ -1,26 +1,26 @@
 table viennaVntr
 "1000 Genomes Vienna ONT VNTR allele statistics from VAMOS genotyping"
     (
     string chrom;          "Chromosome"
     uint chromStart;       "Start position"
     uint chromEnd;         "End position"
     string name;           "VNTR locus summary"
     uint score;            "Score (0-1000)|Number of unique VNTR alleles, capped at 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 average repeat unit length"
+    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)"
     uint numHaps;          "Haplotypes genotyped|Number of haplotypes where allele has been genotyped"
     float ruLenAvg;        "Avg motif length|Average length of the repeat unit in bp"
     uint numUniqueVntrs;   "Unique alleles|Number of unique VNTR alleles found at the site"
     uint maxRus;           "Max repeat units|Maximum repeat unit count observed"
     uint minRus;           "Min repeat units|Minimum repeat unit count observed"
     float medianRus;       "Median repeat units|Median repeat unit count across all haplotypes"
     float pct25Rus;        "25th pct repeat units|25th percentile of repeat unit counts"
     float pct75Rus;        "75th pct repeat units|75th percentile of repeat unit counts"
     uint uniqueNumRus;     "Unique repeat counts|Count of uniquely observed repeat unit numbers"
     uint maxBps;           "Max allele bp|Maximum allele length in base pairs"
     uint minBps;           "Min allele bp|Minimum allele length in base pairs"
     float medianBps;       "Median allele bp|Median allele length in base pairs"
     float het;             "Expected heterozygosity|1 - sum(p_i^2) computed from allele frequencies across 1,019 samples"
     )