10db3769dd9edfa38ac8d900ca400fdfb514d9a7
gperez2
  Wed Jul 29 22:41:46 2026 -0700
An in-place update for gnomad v4.1 to v4.1.1 that swaps bigDataUrl, labels, dataVersion, detailsTabUrls, search descriptions, and removes the alpha-only gnomadVariantsV4.1.1 composite. Updates to gnomad.html, gnomadV4.1.html, and gnomadPLI.html regarding the addition of the gnomad v4.1.1 data, refs #37351

diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
index b5d2371fc8a..471c94b6989 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
+++ src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
@@ -1,221 +1,221 @@
 track gnomadPLI
 parent gnomadVariants 
 shortLabel gnomAD Constraint Metrics
 longLabel Genome Aggregation Database (gnomAD) Predicted Constraint Metrics (LOEUF, pLI, and Z-scores)
 compositeTrack On
 group varRep
 type bigBed 12
 labelFields name,geneName
-dataVersion Release v4.1.1 (March 2026), Release v4.1 (April 19, 2024), Release v4 (November 2023), Release 2.1.1 (March 6, 2019)
+dataVersion Release v4.1.1 (March 30, 2026), Release v4.1 (April 19, 2024), Release v4 (November 2023), Release 2.1.1 (March 6, 2019)
 subGroup1 view Views v2=constraintV2 v4=constraintV4 v4_1=constraintV4.1 v4_1_1=constraintV4.1.1
 html gnomadPLI.html
 visibility hide
 
     track constraintV2
     parent gnomadPLI off
     shortLabel Constraint V2
     longLabel gnomAD Constraint Metrics V2
     view v2
     visibility pack
     type bigBed 12 +
 
         track pliByGene
         shortLabel Gene LoF
         longLabel gnomAD Predicted Loss of Function Constraint Metrics By Gene (LOEUF and pLI) v2.1.1
         subGroups view=v2
         type bigBed 12 +
         itemRgb on
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByGene.bb
         url https://gnomad.broadinstitute.org/gene/$$?dataset=gnomad_r2_1
         urlLabel View this Gene on the gnomAD browser
         labelFields name,geneName
         defaultLabelFields geneName
         filter._pli 0:1
         filterLabel._pli Show only items between this pLI range
         filterByRange._pli on
         parent constraintV2 on
         priority 1
         mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
 
         track missenseByGene
         shortLabel Gene Missense
         longLabel gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores) v2.1.1
         subGroups view=v2
         type bigBed 12 +
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByGene.bb
         url https://gnomad.broadinstitute.org/gene/$$?dataset=gnomad_r2_1
         urlLabel View this Gene on the gnomAD browser
         labelFields name,geneName
         filter._zscore -19:11
         itemRgb on
         filterLabel._zscore Show only items between this Z-score range
         filterByRange._zscore on
         parent constraintV2 off
         priority 2
         mouseOver Z: $_zscore<br> $synonymous<br> $missense
 
         track pliByTranscript
         shortLabel Transcript LoF v2
         longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v2.1.1
         subGroups view=v2
         type bigBed 12 +
         itemRgb on
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._pli 0:1
         filterLabel._pli Show only items between this pLI range
         filterByRange._pli on
         parent constraintV2 off
         priority 2
         mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
 
         track missenseByTranscript
         shortLabel Transcript Missense v2
         longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1
         subGroups view=v2
         type bigBed 12 +
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r2_1
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._zscore -20:11
         filterLabel._zscore Show only items between this Z-score range
         filterByRange._zscore on
         parent constraintV2 off
         priority 2
         mouseOver Z: $_zscore<br> $synonymous<br> $missense
 
     track constraintV4
     parent gnomadPLI off
     shortLabel Constraint V4
     longLabel gnomAD Constraint Metrics V4
     view v4
     visibility hide
     type bigBed 12 +
     
         track pliByTranscriptV4
         shortLabel Transcript LoF v4
         longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4
         subGroups view=v4
         type bigBed 12 +
         itemRgb on
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._pli 0:1
         filterLabel._pli Show only items between this pLI range
         filterByRange._pli on
         parent constraintV4
         priority 2
         mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
 
         track missenseByTranscriptV4
         shortLabel Transcript Missense v4
         longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4
         subGroups view=v4
         type bigBed 12 +
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._zscore -20:11
         filterLabel._zscore Show only items between this Z-score range
         filterByRange._zscore on
         parent constraintV4
         priority 2
         mouseOver Z: $_zscore<br> $synonymous<br> $missense
 
     track constraintV4_1
     parent gnomadPLI off
     shortLabel Constraint V4.1
     longLabel gnomAD Constraint Metrics V4.1
     view v4_1
     visibility pack
     type bigBed 12 +
 
         track pliByTranscriptV4_1
         shortLabel Transcript LoF v4.1
         longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1
         subGroups view=v4_1
         type bigBed 12 +
         itemRgb on
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.1.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._pli 0:1
         filterLabel._pli Show only items between this pLI range
         filterByRange._pli on
         parent constraintV4_1
         priority 2
         mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF
 
         track missenseByTranscriptV4_1
         shortLabel Transcript Missense v4.1
         longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1
         subGroups view=v4_1
         type bigBed 12 +
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.1.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._zscore -20:11
         filterLabel._zscore Show only items between this Z-score range
         filterByRange._zscore on
         parent constraintV4_1
         priority 2
         mouseOver Z: $_zscore<br> $synonymous<br> $missense
 
     track constraintV4_1_1
     parent gnomadPLI off
     shortLabel Constraint V4.1.1
     longLabel gnomAD Constraint Metrics V4.1.1
     view v4_1_1
     visibility pack
     type bigBed 12 +
 
         track pliByTranscriptV4_1_1
         shortLabel Transcript LoF v4.1.1
         longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1.1
         subGroups view=v4_1_1
         type bigBed 12 +
         itemRgb on
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/pliByTranscript.v4.1.1.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._pli 0:1
         filterLabel._pli Show only items between this pLI range
         filterByRange._pli on
         parent constraintV4_1_1
         priority 1
         mouseOver LOEUF: $_loeuf<br> pLI: $_pli<br> $synonymous<br> $pLoF<br> Gene flags: $geneFlags<br> Constraint flags: $constraintFlags
 
         track missenseByTranscriptV4_1_1
         shortLabel Transcript Missense v4.1.1
         longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1.1
         subGroups view=v4_1_1
         type bigBed 12 +
         searchIndex name,geneName
         bigDataUrl /gbdb/hg38/gnomAD/pLI/missenseByTranscript.v4.1.1.bb
         url https://gnomad.broadinstitute.org/transcript/$$?dataset=gnomad_r4
         urlLabel View this Transcript on the gnomAD browser
         labelFields name,geneName
         filter._zscore -20:11
         filterLabel._zscore Show only items between this Z-score range
         filterByRange._zscore on
         parent constraintV4_1_1
         priority 1
         mouseOver Z: $_zscore<br> $synonymous<br> $missense<br> Gene flags: $geneFlags<br> Constraint flags: $constraintFlags