b86eab362ce697c350764ffe438ccdba8829e0f3
gperez2
  Mon Jul 20 17:37:35 2026 -0700
Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843

diff --git src/hg/makeDb/trackDb/human/hg38/nmd.ra src/hg/makeDb/trackDb/human/hg38/nmd.ra
index 84f042f2885..829e93d4f0f 100644
--- src/hg/makeDb/trackDb/human/hg38/nmd.ra
+++ src/hg/makeDb/trackDb/human/hg38/nmd.ra
@@ -1,144 +1,144 @@
 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 nmdEscMane
         shortLabel NMD Escape MANE
         longLabel NMD escape predictions: MANE Select Plus Clinical transcripts
         parent nmd on
         bigDataUrl /gbdb/hg38/nmd/nmdEscMane.bb
         visibility pack
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         labelFields ncbiIds,name,transcripts
         defaultLabelFields ncbiIds
         labelSeparator " / "
         filterText.transcripts *
         filterType.transcripts wildcard
         filterLabel.transcripts Gencode accession (e.g. "*ENST00000269305*")
         filterText.ncbiIds *
         filterType.ncbiIds wildcard
         filterLabel.ncbiIds RefSeq accession (e.g. "*NM_000546*")
         dataVersion MANE 1.5
         priority 1.4
 
         track nmdEscGencode
         shortLabel NMD Escape Gencode
         longLabel NMD escape predictions: Gencode transcripts
         parent nmd on
         bigDataUrl /gbdb/hg38/nmd/nmdEscRegions.bb
         visibility dense
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         filterText.transcripts *
         filterType.transcripts wildcard
         filterLabel.transcripts Filter on transcript ID (e.g. "*ENST00000269305*")
         # 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 predictions: NCBI RefSeq Curated transcripts
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdEscNcbiRefSeq.bb
         visibility hide
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         filterText.transcripts *
         filterType.transcripts wildcard
         filterLabel.transcripts Filter on transcript ID (e.g. "NM_005228*")
         # this could use a text file one day with the version
         dataVersion GCF_000001405.40-RS_2025_08
         priority 1.6
 
         track nmdDetectiveAi
         shortLabel NMDetective-AI
         longLabel NMDetective-AI: Deep-learning NMD efficiency prediction per position (MANE Select only)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDetectAi.bw
         type bigWig
         visibility hide
         color 128,0,128
         autoScale off
         viewLimits -1.1:1.5
         maxHeightPixels 128:120:8
         html nmdDetectiveAi
         priority 1.7
 
         track nmdDetectiveAiBed
         shortLabel NMDetective-AI variants
         longLabel NMDetective-AI: Per-stop-gain predictions for every codon (MANE Select only)
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdDetectAi.bb
         type bigBed 9 +
         itemRgb on
         visibility hide
         mouseOverField mouseOver
         html nmdDetectiveAi
         priority 1.8
 
         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
+        viewLimits -0.3:1.5
         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
+        viewLimits -0.3:1.5
         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
+        viewLimits -0.3:1.5
         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
+        viewLimits -0.3:1.5
         maxHeightPixels 128:32:8
         html nmdDetective
         priority 5