bb83f26ce1141e98f2f1db4534fef7dbd4384269
angie
  Wed Apr 30 11:15:55 2025 -0700
Added explanation of gray deletion box for delins variants (#33538)

diff --git src/hg/makeDb/trackDb/human/dbSnp155Composite.html src/hg/makeDb/trackDb/human/dbSnp155Composite.html
index 376e91bb1e2..4f3bc79cf78 100644
--- src/hg/makeDb/trackDb/human/dbSnp155Composite.html
+++ src/hg/makeDb/trackDb/human/dbSnp155Composite.html
@@ -75,30 +75,34 @@
 individuals have "TAAG" at the same location, then the variant is a deletion of a single
 A relative to the reference genome.
 However, which A was deleted?  There is no way to tell whether the first, second or third A
 was removed.
 Different variant mapping tools may place the deletion at different bases in the reference genome.
 To reduce errors in merging variant calls made with different left vs. right biases,
 dbSNP made a major change in its representation of deletion/insertion variants in build 152.
 Now, instead of assigning a single-base genomic location at one of the A's,
 dbSNP expands the coordinates to encompass the whole repetitive region,
 so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's.
 In the track display, there will be a half-height box covering the first two A's,
 followed by a full-height box covering the third A, to show a net loss of one base
 but an uncertain placement within the three A's.
 </p>
 <p>
+When a variant has both insertion and deletion alternate alleles, the full-height box for the
+deletion(s) is drawn in a lighter shade so that the insertion tickmark is still visible.
+</p>
+<p>
 Variants are colored according to functional effect on genes annotated by dbSNP:
 </p>
 
 <p><b><font color=red>Protein-altering variants and splice site variants are
 red</font></b>.
 <br><b><font color=green>Synonymous codon variants are
 green</font></b>.
 <br><b><font color=blue>
 Non-coding transcript or Untranslated Region (UTR) variants are
 blue</font></b>.
 </p>
 <p>
 On the track controls page, several variant properties can be included or excluded from
 the item labels:
 rs# identifier assigned by dbSNP,