a6aaa3139f34f741d82d14c803bedef875620530 gperez2 Tue Apr 23 11:05:31 2024 -0700 Removing hg19 gnomadExomesTest track that was used for QA testing, refs #32916 diff --git src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra index 81cc8a4..10ae796 100644 --- src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra +++ src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra @@ -1,986 +1,955 @@ track gnomadSuper superTrack on shortLabel gnomAD longLabel Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint group varRep html gnomad pennantIcon Updated red ../goldenPath/newsarch.html#032624 "Updated Mar. 26, 2024" track gnomadCoverage compositeTrack on parent gnomadSuper shortLabel gnomAD Coverage longLabel Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage group varRep dataVersion Release 2.0.2 visibility dense subGroup1 view Views gAvg=GenomesAverage eAvg=ExomesAverage gRDepth=GenomesReadDepth eRDepth=ExomesReadDepth type bigWig html gnomadCoverage track gnomadGenomesAvgCoverage parent gnomadCoverage on shortLabel Genome Avg Cover longLabel Genome Aggregation Database (gnomAD) Average Genome Sample Coverage view gAvg aggregate none showSubtrackColorOnUi on type bigWig 0 100 maxHeightPixels 100:50:8 viewLimits 0:50 chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX visibility dense html gnomad track gnomadGenomesMeanCoverage shortLabel Mean Coverage longLabel gnomAD Mean Genome Sample Coverage parent gnomadGenomesAvgCoverage on color 255,0,0 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.mean.bw subGroups view=gAvg track gnomadGenomesMedianCoverage shortLabel Median Coverage longLabel gnomAD Median Genome Sample Coverage parent gnomadGenomesAvgCoverage off color 0,0,255 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.median.bw subGroups view=gAvg track gnomadGenomesReadDepthPct parent gnomadCoverage shortLabel Genome Coverage % longLabel Genome Aggregation Database (gnomAD) Percentage of Genome Samples with at least nX Coverage view gRDepth aggregate none showSubtrackColorOnUi on type bigWig 0 1 maxHeightPixels 100:16:8 viewLimits 0:1 chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX visibility hide html gnomad track gnomadGenomes1XPercentage shortLabel Sample % > 1X longLabel gnomAD Percentage of Genome Samples with at least 1X Coverage parent gnomadGenomesReadDepthPct off color 255,0,0 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth1.bw priority 1 subGroups view=gRDepth track gnomadGenomes5XPercentage shortLabel Sample % > 5X longLabel gnomAD Percentage of Genome Samples with at least 5X Coverage parent gnomadGenomesReadDepthPct off color 225,0,30 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth5.bw priority 2 subGroups view=gRDepth track gnomadGenomes10XPercentage shortLabel Sample % > 10X longLabel gnomAD Percentage of Genome Samples with at least 10X Coverage parent gnomadGenomesReadDepthPct on color 195,0,60 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth10.bw priority 3 subGroups view=gRDepth track gnomadGenomes15XPercentage shortLabel Sample % > 15X longLabel gnomAD Percentage of Genome Samples with at least 15X Coverage parent gnomadGenomesReadDepthPct off color 165,0,90 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth15.bw priority 4 subGroups view=gRDepth track gnomadGenomes20XPercentage shortLabel Sample % > 20X longLabel gnomAD Percentage of Genome Samples with at least 20X Coverage parent gnomadGenomesReadDepthPct on color 135,0,120 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth20.bw priority 5 subGroups view=gRDepth track gnomadGenomes25XPercentage shortLabel Sample % > 25X longLabel gnomAD Percentage of Genome Samples with at least 25X Coverage parent gnomadGenomesReadDepthPct off color 105,0,150 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth25.bw priority 6 subGroups view=gRDepth track gnomadGenomes30XPercentage shortLabel Sample % > 30X longLabel gnomAD Percentage of Genome Samples with at least 30X Coverage parent gnomadGenomesReadDepthPct on color 75,0,180 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth30.bw priority 7 subGroups view=gRDepth track gnomadGenomes50XPercentage shortLabel Sample % > 50X longLabel gnomAD Percentage of Genome Samples with at least 50X Coverage parent gnomadGenomesReadDepthPct off color 45,0,210 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth50.bw priority 8 subGroups view=gRDepth track gnomadGenomes100XPercentage shortLabel Sample % > 100X longLabel gnomAD Percentage of Genome Samples with at least 100X Coverage parent gnomadGenomesReadDepthPct off color 15,0,240 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.genomes.coverage.depth100.bw priority 9 subGroups view=gRDepth track gnomadExomesAvgCoverage parent gnomadCoverage shortLabel Exome Avg Cover longLabel Genome Aggregation Database (gnomAD) Average Exome Sample Coverage view eAvg aggregate none showSubtrackColorOnUi on type bigWig 0 100 maxHeightPixels 100:50:8 viewLimits 0:50 chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY visibility full html gnomad track gnomadExomesMeanCoverage shortLabel Mean Coverage longLabel gnomAD Mean Exome Sample Coverage parent gnomadExomesAvgCoverage on color 255,0,0 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.mean.bw subGroups view=eAvg track gnomadExomesMedianCoverage shortLabel Median Coverage longLabel gnomAD Median Exome Sample Coverage parent gnomadExomesAvgCoverage off color 0,0,255 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.median.bw subGroups view=eAvg track gnomadExomesReadDepthPct parent gnomadCoverage shortLabel Exome Coverage % longLabel Genome Aggregation Database (gnomAD) Percentage of Exome Samples with at least nX Coverage view eRDepth aggregate none showSubtrackColorOnUi on type bigWig 0 1 maxHeightPixels 100:16:8 viewLimits 0:1 chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX visibility hide html gnomad track gnomadExomes1XPercentage shortLabel Sample % > 1X longLabel gnomAD Percentage of Exome Samples with at least 1X Coverage parent gnomadExomesReadDepthPct off color 255,0,0 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth1.bw priority 1 subGroups view=eRDepth track gnomadExomes5XPercentage shortLabel Sample % > 5X longLabel gnomAD Percentage of Exome Samples with at least 5X Coverage parent gnomadExomesReadDepthPct off color 225,0,30 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth5.bw priority 2 subGroups view=eRDepth track gnomadExomes10XPercentage shortLabel Sample % > 10X longLabel gnomAD Percentage of Exome Samples with at least 10X Coverage parent gnomadExomesReadDepthPct on color 195,0,60 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth10.bw priority 3 subGroups view=eRDepth track gnomadExomes15XPercentage shortLabel Sample % > 15X longLabel gnomAD Percentage of Exome Samples with at least 15X Coverage parent gnomadExomesReadDepthPct off color 165,0,90 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth15.bw priority 4 subGroups view=eRDepth track gnomadExomes20XPercentage shortLabel Sample % > 20X longLabel gnomAD Percentage of Exome Samples with at least 20X Coverage parent gnomadExomesReadDepthPct on color 135,0,120 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth20.bw priority 5 subGroups view=eRDepth track gnomadExomes25XPercentage shortLabel Sample % > 25X longLabel gnomAD Percentage of Exome Samples with at least 25X Coverage parent gnomadExomesReadDepthPct off color 105,0,150 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth25.bw priority 6 subGroups view=eRDepth track gnomadExomes30XPercentage shortLabel Sample % > 30X longLabel gnomAD Percentage of Exome Samples with at least 30X Coverage parent gnomadExomesReadDepthPct on color 75,0,180 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth30.bw priority 7 subGroups view=eRDepth track gnomadExomes50XPercentage shortLabel Sample % > 50X longLabel gnomAD Percentage of Exome Samples with at least 50X Coverage parent gnomadExomesReadDepthPct off color 45,0,210 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth50.bw priority 8 subGroups view=eRDepth track gnomadExomes100XPercentage shortLabel Sample % > 100X longLabel gnomAD Percentage of Exome Samples with at least 100X Coverage parent gnomadExomesReadDepthPct off color 15,0,240 bigDataUrl /gbdb/hg19/gnomAD/coverage/gnomad.exomes.coverage.depth100.bw priority 9 subGroups view=eRDepth track gnomadStructuralVariants parent gnomadSuper shortLabel gnomAD Structural Variants longLabel Genome Aggregation Database (gnomAD) - Structural Variants compositeTrack on visibility dense group varRep type bigBed 9 + dataVersion Release 2.1 html gnomadSv noParentConfig on track gnomadSvFull parent gnomadStructuralVariants on bigDataUrl /gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.sites.bb shortLabel gnomAD All SV's longLabel gnomAD Structural Variants All type bigBed 9 + itemRgb on visibility dense url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r2_1 urlLabel gnomAD Structural Variant Browser filterLabel.svtype Type of Variation filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV filter.svlen 50:199840172 filterByRange.svlen on filterLabel.svlen Filter by Variant Size mouseOverField _mouseOver searchIndex name showCfg on track gnomadSvNonneuro parent gnomadStructuralVariants off bigDataUrl /gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.nonneuro.sites.bb shortLabel gnomAD Non-Neuro SV's longLabel gnomAD Structural Variants Non-neuro Only type bigBed 9 + itemRgb on url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r2_1 urlLabel gnomAD Structural Variant Browser filterLabel.svtype Type of Variation filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV filter.svlen 50:199840172 filterByRange.svlen on filterLabel.svlen Filter by Variant Size mouseOverField _mouseOver searchIndex name track gnomadSvControls parent gnomadStructuralVariants off bigDataUrl /gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.controls_only.sites.bb shortLabel gnomAD Control Only SV's longLabel gnomAD Structural Variants Controls Only type bigBed 9 + itemRgb on url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r2_1 urlLabel gnomAD Structural Variant Browser filterLabel.svtype Type of Variation filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV filter.svlen 50:199840172 filterByRange.svlen on filterLabel.svlen Filter by Variant Size mouseOverField _mouseOver searchIndex name track gnomadPLI parent gnomadSuper shortLabel gnomAD Constraint Metrics longLabel Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics (pLI and Z-scores) compositeTrack On group varRep type bigBed 12 labelFields name,geneName visibility pack dataVersion Release 2.1.1 (March 6, 2019) track pliByGene shortLabel gnomAD Gene LoF Constraint longLabel gnomAD Predicted Loss of Function Constraint Metrics By Gene (pLI) v2.1.1 type bigBed 12 + mouseOverField _mouseOver itemRgb on searchIndex name,geneName bigDataUrl /gbdb/hg19/gnomAD/pLI/pliByGene.bb url https://gnomad.broadinstitute.org/gene/$$?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 gnomadPLI on priority 1 track missenseByGene shortLabel gnomAD Gene Missense Constraint longLabel gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores) v2.1.1 type bigBed 12 + mouseOverField _mouseOver itemRgb on searchIndex name,geneName bigDataUrl /gbdb/hg19/gnomAD/missense/missenseByGene.bb url https://gnomad.broadinstitute.org/gene/$$?dataset=gnomad_r2_1 urlLabel View this Gene on the gnomAD browser labelFields name,geneName filter._zscore -10:10 filterLabel._zscore Show only items between this Z-score range filterByRange._zscore on parent gnomadPLI off priority 2 track pliByTranscript shortLabel gnomAD Transcript LoF Constraint longLabel gnomAD Predicted Loss of Function Constraint Metrics By Transcript (pLI) v2.1.1 type bigBed 12 + mouseOverField _mouseOver itemRgb on searchIndex name,geneName bigDataUrl /gbdb/hg19/gnomAD/pLI/pliByTranscript.bb url https://gnomad.broadinstitute.org/transcript/$$?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 gnomadPLI off priority 2 track missenseByTranscript shortLabel gnomAD Transcript Missense Constraint longLabel gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1 type bigBed 12 + mouseOverField _mouseOver itemRgb on searchIndex name,geneName bigDataUrl /gbdb/hg19/gnomAD/missense/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 -10:10 filterLabel._zscore Show only items between this Z-score range filterByRange._zscore on parent gnomadPLI off priority 2 track gnomadMissense parent gnomadPLI off shortLabel gnomAD Regional Missense Constraint (ExAc Dataset) longLabel gnomAD Predicted Regional Missense Constraint Metrics (O/E scores from ExAc Dataset) v2.1.1 bigDataUrl /gbdb/hg19/gnomAD/missense/missenseConstrained.bb itemRgb on labelFields name,geneName defaultLabelFields geneName group varRep type bigBed 12 + filter.obs_exp 0:5 filterLabel.obs_exp Show only items between this O/E range filterByRange.obs_exp on priority 3 mouseOverField _mouseOver track gnomadPext shortLabel gnomAD pext longLabel gnomAD Proportion Expression Across Transcript Scores (pext) parent gnomadSuper compositeTrack on type bigWig 0 1 maxHeightPixels 100:16:8 viewLimits 0:1 visibility full html gnomadPext dataVersion Release 2.1.1 (March 6, 2019) track gnomADPextmean_proportion bigDataUrl /gbdb/hg19/gnomAD/pext/mean_proportion.bw shortLabel Mean Proportion longLabel gnomAD pext Mean Proportion parent gnomadPext on color 66,139,202 visibility full priority 1 track gnomADPextAdipose_Subcutaneous bigDataUrl /gbdb/hg19/gnomAD/pext/Adipose_Subcutaneous.bw parent gnomadPext off shortLabel Adipose-Subcut longLabel gnomAD pext Adipose-Subcutaneous color 255,102,0 visibility hide track gnomADPextAdipose_Visceral_Omentum_ bigDataUrl /gbdb/hg19/gnomAD/pext/Adipose_Visceral_Omentum_.bw shortLabel Adipose-Visceral (Omentum) longLabel gnomAD pext Adipose-Visceral (Omentum) parent gnomadPext off color 255,170,0 visibility hide track gnomADPextAdrenalGland bigDataUrl /gbdb/hg19/gnomAD/pext/AdrenalGland.bw shortLabel Adrenal Gland longLabel gnomAD pext Adrenal Gland parent gnomadPext off color 51,221,51 visibility hide track gnomADPextArtery_Aorta bigDataUrl /gbdb/hg19/gnomAD/pext/Artery_Aorta.bw shortLabel Artery-Aorta longLabel gnomAD pext Artery-Aorta parent gnomadPext off color 255,85,85 visibility hide track gnomADPextArtery_Coronary bigDataUrl /gbdb/hg19/gnomAD/pext/Artery_Coronary.bw shortLabel Artery-Coronary longLabel gnomAD pext Artery-Coronary parent gnomadPext off color 255,170,153 visibility hide track gnomADPextArtery_Tibial bigDataUrl /gbdb/hg19/gnomAD/pext/Artery_Tibial.bw shortLabel Artery-Tibial longLabel gnomAD pext Artery-Tibial parent gnomadPext off color 255,0,0 visibility hide track gnomADPextBladder bigDataUrl /gbdb/hg19/gnomAD/pext/Bladder.bw shortLabel Bladder longLabel gnomAD pext Bladder parent gnomadPext off color 170,0,0 visibility hide track gnomADPextBrain_Amygdala bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Amygdala.bw shortLabel Brain-Amygdala longLabel gnomAD pext Brain-Amygdala parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Anteriorcingulatecortex_BA24_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Anteriorcingulatecortex_BA24_.bw shortLabel Brain-Anterior Cingulate Cortex (BA24) longLabel gnomAD pext Brain-Anterior Cingulate Cortex (BA24) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Caudate_basalganglia_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Caudate_basalganglia_.bw shortLabel Brain-Caudate (basal ganglia) longLabel gnomAD pext Brain-Caudate (basal ganglia) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_CerebellarHemisphere bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_CerebellarHemisphere.bw shortLabel Brain-Cerebellar Hemisphere longLabel gnomAD pext Brain-Cerebellar Hemisphere parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Cerebellum bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Cerebellum.bw shortLabel Brain-Cerebellum longLabel gnomAD pext Brain-Cerebellum parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Cortex bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Cortex.bw shortLabel Brain-Cortex longLabel gnomAD pext Brain-Cortex parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_FrontalCortex_BA9_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_FrontalCortex_BA9_.bw shortLabel Brain-Frontal Cortex (BA9) longLabel gnomAD pext Brain-Frontal Cortex (BA9) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Hippocampus bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Hippocampus.bw shortLabel Brain-Hippocampus longLabel gnomAD pext Brain-Hippocampus parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Hypothalamus bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Hypothalamus.bw shortLabel Brain-Hypothalamus longLabel gnomAD pext Brain-Hypothalamus parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Nucleusaccumbens_basalganglia_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Nucleusaccumbens_basalganglia_.bw shortLabel Brain-Nucleus Accumbens (basal ganglia) longLabel gnomAD pext Brain-Nucleus Accumbens (basal ganglia) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Putamen_basalganglia_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Putamen_basalganglia_.bw shortLabel Brain-Putamen (basal ganglia) longLabel gnomAD pext Brain-Putamen (basal ganglia) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Spinalcord_cervicalc_1_ bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Spinalcord_cervicalc_1_.bw shortLabel Brain-Spinal Cord (cervicalc 1) longLabel gnomAD pext Brain-Spinal Cord (cervicalc 1) parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBrain_Substantianigra bigDataUrl /gbdb/hg19/gnomAD/pext/Brain_Substantianigra.bw shortLabel Brain-Substantia Nigra longLabel gnomAD pext Brain-Substantia Nigra parent gnomadPext off color 238,238,0 visibility hide track gnomADPextBreast_MammaryTissue bigDataUrl /gbdb/hg19/gnomAD/pext/Breast_MammaryTissue.bw shortLabel Breast-Mammary Tissue longLabel gnomAD pext Breast-Mammary Tissue parent gnomadPext off color 51,204,204 visibility hide track gnomADPextCells_EBV_transformedlymphocytes bigDataUrl /gbdb/hg19/gnomAD/pext/Cells_EBV_transformedlymphocytes.bw shortLabel Cells-EBV-transformed Lymphocytes longLabel gnomAD pext Cells-EBV-transformed Lymphocytes parent gnomadPext off color 204,102,255 visibility hide track gnomADPextCells_Transformedfibroblasts bigDataUrl /gbdb/hg19/gnomAD/pext/Cells_Transformedfibroblasts.bw shortLabel Cells-Transformed Fibroblasts longLabel gnomAD pext Cells-Transformed Fibroblasts parent gnomadPext off color 170,238,255 visibility hide track gnomADPextCervix_Ectocervix bigDataUrl /gbdb/hg19/gnomAD/pext/Cervix_Ectocervix.bw shortLabel Cervix-Ectocervix longLabel gnomAD pext Cervix-Ectocervix parent gnomadPext off color 255,204,204 visibility hide track gnomADPextCervix_Endocervix bigDataUrl /gbdb/hg19/gnomAD/pext/Cervix_Endocervix.bw shortLabel Cervix-Endocervix longLabel gnomAD pext Cervix-Endocervix parent gnomadPext off color 204,170,221 visibility hide track gnomADPextColon_Sigmoid bigDataUrl /gbdb/hg19/gnomAD/pext/Colon_Sigmoid.bw shortLabel Colon-Sigmoid longLabel gnomAD pext Colon-Sigmoid parent gnomadPext off color 238,187,119 visibility hide track gnomADPextColon_Transverse bigDataUrl /gbdb/hg19/gnomAD/pext/Colon_Transverse.bw shortLabel Colon-Transverse longLabel gnomAD pext Colon-Transverse parent gnomadPext off color 204,153,85 visibility hide track gnomADPextEsophagus_GastroesophagealJunction bigDataUrl /gbdb/hg19/gnomAD/pext/Esophagus_GastroesophagealJunction.bw shortLabel Esophagus-Gastroesophageal Junction longLabel gnomAD pext Esophagus-Gastroesophageal Junction parent gnomadPext off color 139,115,85 visibility hide track gnomADPextEsophagus_Mucosa bigDataUrl /gbdb/hg19/gnomAD/pext/Esophagus_Mucosa.bw shortLabel Esophagus-Mucosa longLabel gnomAD pext Esophagus-Mucosa parent gnomadPext off color 85,34,0 visibility hide track gnomADPextEsophagus_Muscularis bigDataUrl /gbdb/hg19/gnomAD/pext/Esophagus_Muscularis.bw shortLabel Esophagus-Muscularis longLabel gnomAD pext Esophagus-Muscularis parent gnomadPext off color 187,153,136 visibility hide track gnomADPextFallopianTube bigDataUrl /gbdb/hg19/gnomAD/pext/FallopianTube.bw shortLabel Fallopian Tube longLabel gnomAD pext Fallopian Tube parent gnomadPext off color 255,204,204 visibility hide track gnomADPextHeart_AtrialAppendage bigDataUrl /gbdb/hg19/gnomAD/pext/Heart_AtrialAppendage.bw shortLabel Heart-Atrial Appendage longLabel gnomAD pext Heart-Atrial Appendage parent gnomadPext off color 153,0,255 visibility hide track gnomADPextHeart_LeftVentricle bigDataUrl /gbdb/hg19/gnomAD/pext/Heart_LeftVentricle.bw shortLabel Heart-Left Ventricle longLabel gnomAD pext Heart-Left Ventricle parent gnomadPext off color 102,0,153 visibility hide track gnomADPextKidney_Cortex bigDataUrl /gbdb/hg19/gnomAD/pext/Kidney_Cortex.bw shortLabel Kidney-Cortex longLabel gnomAD pext Kidney-Cortex parent gnomadPext off color 34,255,221 visibility hide track gnomADPextLiver bigDataUrl /gbdb/hg19/gnomAD/pext/Liver.bw shortLabel Liver longLabel gnomAD pext Liver parent gnomadPext off color 170,187,102 visibility hide track gnomADPextLung bigDataUrl /gbdb/hg19/gnomAD/pext/Lung.bw shortLabel Lung longLabel gnomAD pext Lung parent gnomadPext off color 153,255,0 visibility hide track gnomADPextMinorSalivaryGland bigDataUrl /gbdb/hg19/gnomAD/pext/MinorSalivaryGland.bw shortLabel Minor Salivary Gland longLabel gnomAD pext Minor Salivary Gland parent gnomadPext off color 153,187,136 visibility hide track gnomADPextMuscle_Skeletal bigDataUrl /gbdb/hg19/gnomAD/pext/Muscle_Skeletal.bw shortLabel Muscle-Skeletal longLabel gnomAD pext Muscle-Skeletal parent gnomadPext off color 170,170,255 visibility hide track gnomADPextNerve_Tibial bigDataUrl /gbdb/hg19/gnomAD/pext/Nerve_Tibial.bw shortLabel Nerve-Tibial longLabel gnomAD pext Nerve-Tibial parent gnomadPext off color 255,215,0 visibility hide track gnomADPextOvary bigDataUrl /gbdb/hg19/gnomAD/pext/Ovary.bw shortLabel Ovary longLabel gnomAD pext Ovary parent gnomadPext off color 255,170,255 visibility hide track gnomADPextPancreas bigDataUrl /gbdb/hg19/gnomAD/pext/Pancreas.bw shortLabel Pancreas longLabel gnomAD pext Pancreas parent gnomadPext off color 153,85,34 visibility hide track gnomADPextPituitary bigDataUrl /gbdb/hg19/gnomAD/pext/Pituitary.bw shortLabel Pituitary longLabel gnomAD pext Pituitary parent gnomadPext off color 170,255,153 visibility hide track gnomADPextProstate bigDataUrl /gbdb/hg19/gnomAD/pext/Prostate.bw shortLabel Prostate longLabel gnomAD pext Prostate parent gnomadPext off color 221,221,221 visibility hide track gnomADPextSkin_NotSunExposed_Suprapubic_ bigDataUrl /gbdb/hg19/gnomAD/pext/Skin_NotSunExposed_Suprapubic_.bw shortLabel Skin-Not Sun Exposed (Suprapubic) longLabel gnomAD pext Skin-Not Sun Exposed (Suprapubic) parent gnomadPext off color 0,0,255 visibility hide track gnomADPextSkin_SunExposed_Lowerleg_ bigDataUrl /gbdb/hg19/gnomAD/pext/Skin_SunExposed_Lowerleg_.bw shortLabel Skin-Sun Exposed (Lowerleg) longLabel gnomAD pext Skin-Sun Exposed (Lowerleg) parent gnomadPext off color 119,119,255 visibility hide track gnomADPextSmallIntestine_TerminalIleum bigDataUrl /gbdb/hg19/gnomAD/pext/SmallIntestine_TerminalIleum.bw shortLabel Small Intestine-Terminal Ileum longLabel gnomAD pext Small Intestine-Terminal Ileum parent gnomadPext off color 85,85,34 visibility hide track gnomADPextSpleen bigDataUrl /gbdb/hg19/gnomAD/pext/Spleen.bw shortLabel Spleen longLabel gnomAD pext Spleen parent gnomadPext off color 119,136,85 visibility hide track gnomADPextStomach bigDataUrl /gbdb/hg19/gnomAD/pext/Stomach.bw shortLabel Stomach longLabel gnomAD pext Stomach parent gnomadPext off color 255,221,153 visibility hide track gnomADPextTestis bigDataUrl /gbdb/hg19/gnomAD/pext/Testis.bw shortLabel Testis longLabel gnomAD pext Testis parent gnomadPext off color 170,170,170 visibility hide track gnomADPextThyroid bigDataUrl /gbdb/hg19/gnomAD/pext/Thyroid.bw shortLabel Thyroid longLabel gnomAD pext Thyroid parent gnomadPext off color 0,102,0 visibility hide track gnomADPextUterus bigDataUrl /gbdb/hg19/gnomAD/pext/Uterus.bw shortLabel Uterus longLabel gnomAD pext Uterus parent gnomadPext off color 255,102,255 visibility hide track gnomADPextVagina bigDataUrl /gbdb/hg19/gnomAD/pext/Vagina.bw shortLabel Vagina longLabel gnomAD pext Vagina parent gnomadPext off color 255,85,153 visibility hide track gnomADPextWholeBlood bigDataUrl /gbdb/hg19/gnomAD/pext/WholeBlood.bw shortLabel Whole Blood longLabel gnomAD pext Whole Blood parent gnomadPext off color 255,0,187 visibility hide track gnomadGenomes shortLabel gnomAD Genomes Variants longLabel Genome Aggregation Database (gnomAD) Genome Variants v2.1.1 itemRgb on type bigBed 9 + bigDataUrl /gbdb/hg19/gnomAD/variants/v2.1.1.genomes.bb parent gnomadSuper visibility squish dataVersion Release 2.1.1 labelFields _displayName,rsId defaultLabelFields _displayName sepFields AC_afr filterValues.annot pLoF,missense,synonymous,other filterType.annot multiple filterValues.FILTER PASS,InbreedingCoeff,RF,AC0 filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter maxItems 50000 mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN) url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r2_1&ignore=$<rsId> urlLabel View this variant at gnomAD detailsStaticTable Population Frequencies|/gbdb/hg19/gnomAD/variants/v2.1.1.genomes.popTable.txt html gnomadExomesGenomes track gnomadExomes shortLabel gnomAD Exomes Variants longLabel Genome Aggregation Database (gnomAD) Exome Variants v2.1.1 itemRgb on type bigBed 9 + bigDataUrl /gbdb/hg19/gnomAD/variants/v2.1.1.exomes.bb parent gnomadSuper visibility squish dataVersion Release 2.1.1 labelFields rsId,_displayName defaultLabelFields _displayName skipFields _displayName skipEmptyFields on filterValues.AC_non_cancer Non-Cancer filterValuesDefault.AC_non_cancer Non-Cancer filterType.AC_non_cancer single filterValues.annot pLoF,missense,synonymous,other filterValues.FILTER PASS,InbreedingCoeff,RF,AC0 filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter maxItems 50000 mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN) url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r2_1&ignore=$<rsId> urlLabel View this variant at gnomAD detailsStaticTable Population Frequencies|/gbdb/hg19/gnomAD/variants/v2.1.1.exomes.popTable.txt html gnomadExomesGenomes pennantIcon Updated red ../goldenPath/newsarch.html#032624 "Updated Mar. 26, 2024" - track gnomadExomesTest - shortLabel TEST gnomAD Exomes Variants - longLabel TEST Genome Aggregation Database (gnomAD) Exome Variants v2.1.1 - itemRgb on - type bigBed 9 + - bigDataUrl /gbdb/hg19/gnomAD/variants/v2.1.1.exomes.test.bb - parent gnomadSuper - visibility squish - dataVersion Release 2.1.1 - labelFields rsId,_displayName - defaultLabelFields _displayName - skipFields _displayName - skipEmptyFields on - filterValues.AC_non_cancer Non-Cancer - filterValuesDefault.AC_non_cancer Non-Cancer - filterType.AC_non_cancer single - filterValues.annot pLoF,missense,synonymous,other - filterValues.FILTER PASS,InbreedingCoeff,RF,AC0 - filterType.FILTER multipleListAnd - filterValuesDefault.FILTER PASS - filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation - filterType.variation_type multipleListOr - filter.AF 0.0 - filterLabel.AF Minor Allele Frequency Filter - maxItems 50000 - mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN) - url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r2_1&ignore=$<rsId> - urlLabel View this variant at gnomAD - detailsStaticTable Population Frequencies|/gbdb/hg19/gnomAD/variants/v2.1.1.exomes.popTable.txt - html gnomadExomesGenomes - searchTable pliByTranscript searchType bigBed searchDescription gnomAD Loss of Function Metrics by Transcript searchTable pliByGene searchType bigBed searchDescription gnomAD Loss of Function Metrics by Gene searchTable gnomadSvFull searchType bigBed searchDescription gnomAD Structural Variants - All structural variants searchTable gnomadSvNonneuro searchType bigBed searchDescription gnomAD Structural Variants - Non-neuro structural variants searchTable gnomadSvControls searchType bigBed searchDescription gnomAD Structural Variants - Control structural variants