fe73446acf43f70e385dadbbb281634adf3cac9e
lrnassar
  Tue Apr 21 16:44:16 2026 -0700
NMD Escape QA tweaks: hide Gencode subtrack by default, bold rule numbers in mouseovers. refs #33737

- nmdEscGencode default visibility changed from on/dense to off/hide so
only the RefSeq Curated subtrack is on by default. Per Lou's request.
- RULE_DESCRIPTIONS mouseover strings wrap the rule number in <b>...</b>
so the rule shows bold in the tooltip. Both bigBeds rebuilt.

diff --git src/hg/makeDb/trackDb/human/hg38/nmd.ra src/hg/makeDb/trackDb/human/hg38/nmd.ra
index 7d89a5ede01..19fd1d30d2f 100644
--- src/hg/makeDb/trackDb/human/hg38/nmd.ra
+++ src/hg/makeDb/trackDb/human/hg38/nmd.ra
@@ -1,91 +1,91 @@
 track nmd
 shortLabel NMD Escape
 longLabel NMD Escape: Predicted regions where premature termination codons escape NMD
 group genes
 type bed 4
 visibility hide
 superTrack on
 pennantIcon New red ../goldenPath/newsarch.html#042226 "Released Apr. 22, 2026"
 
         track nmdEscGencode
         shortLabel NMD Escape Gencode
         longLabel NMD escape 50bp/100bp/intronless/400nt ruleset: Gencode transcripts
-        parent nmd on
+        parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdEscRegions.bb
-        visibility dense
+        visibility hide
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         # this could use a text file one day with the version
         dataVersion Gencode V49
         priority 1.5
 
         track nmdEscNcbiRefSeq
         shortLabel NMD Escape RefSeq
         longLabel NMD escape 50bp/100bp/intronless/400nt ruleset: NCBI RefSeq Curated transcripts
         parent nmd on
         bigDataUrl /gbdb/hg38/nmd/nmdEscNcbiRefSeq.bb
         visibility pack
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         # this could use a text file one day with the version
         dataVersion GCF_000001405.40-RS_2025_08
         priority 1.6
 
         track nmdDetectiveA
         shortLabel NMDetective-A
         longLabel NMDetective-A: Random forest prediction of NMD efficiency (Lindeboom 2016)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/NMDetectiveA.bw
         type bigWig
         visibility hide
         color 0,128,255
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 2
 
         track nmdDetectiveB
         shortLabel NMDetective-B
         longLabel NMDetective-B: Decision tree prediction of NMD efficiency (Lindeboom 2016)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/NMDetectiveB.bw
         type bigWig
         visibility hide
         color 0,128,255
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 3
 
         track nmdDetectiveA_ptc
         shortLabel NMDetective-A PTC
         longLabel NMDetective-A: Random forest NMD efficiency for first out-of-frame PTC
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDectA-ptc.bw
         type bigWig
         visibility hide
         color 0,153,102
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 4
 
         track nmdDetectiveB_ptc
         shortLabel NMDetective-B PTC
         longLabel NMDetective-B: Decision tree NMD efficiency for first out-of-frame PTC
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDectB-ptc.bw
         type bigWig
         visibility hide
         color 0,153,102
         autoScale off
         viewLimits -1:1
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 5