c15a59c6ddc7428025519ec671af0a7d4649d7be
gperez2
Thu Oct 30 16:50:26 2025 -0700
Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
diff --git src/hg/makeDb/trackDb/human/hg38/trackDb.ra src/hg/makeDb/trackDb/human/hg38/trackDb.ra
index a6fcb707233..afb247db780 100644
--- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
+++ src/hg/makeDb/trackDb/human/hg38/trackDb.ra
@@ -1,917 +1,916 @@
include barCharts.ra
include hoffMap.ra
include cancerExpr.ra
include mane.ra
include gdcCancer.ra
include cortexVelmeshev.ra
include heartCellAtlas.ra
include kidneyStewart.ra
include muscleDeMicheli.ra
#include lungVieiraBraga.ra
include fetalGeneAtlas.ra
include bloodHao.ra
include lungTravaglini2020.ra
include skinSoleBoldo.ra
include liverMacParland.ra
include pancreasBaron.ra
include ileumWang.ra
include colonWang.ra
include rectumWang.ra
include placentaVentoTormo.ra
include singleCellMerged.ra
#include lungMadissoon.ra
#include spleenMadissoon.ra
include tabulaSapiens.ra
include toothKrivanek.ra
include hippocampusAyhan.ra
include brainDevRegions.ra
include t2t.ra alpha
include gtexEqtlHighConf.ra
include liftOver.ra
include exomeProbesets.ra
include chm13LiftOver.ra
include reMap.ra
include recombRate.ra
include fantom5.ra
include nuMtSeq.ra
include gnomad.pext.ra
include rnaMod.ra alpha
track miRnaAtlas
compositeTrack on
shortLabel miRNA Tissue Atlas
longLabel Tissue-Specific microRNA Expression from Two Individuals
type bigBarChart
group expression
maxLimit 52000
barChartLabel Tissue
configurable off
subGroup1 view View a_A=Sample1 b_B=Sample2
track miRnaAtlasSample1
type bigBarChart
visibility pack
parent miRnaAtlas
view a_A
configurable on
track miRnaAtlasSample1BarChart
url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$
url2Label miRBase v21 Precursor Accession:
parent miRnaAtlasSample1
visibility full
shortLabel Sample 1
longLabel miRNA Tissue Atlas microRna Expression
bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample1.bb
barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1Matrix.txt
barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample1.txt
barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin \
spleen stomach testis thyroid small_intestine bone gallbladder fascia bladder epididymis \
tunica_albuginea nerve_nervus_intercostalis arachnoid_mater brain
barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \
\#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #BD34D7 #CDA7FE #4C7CD7 #CBD79E #A6F6A1 \
\#A6CEA4 #FFD700 #86BF10 #EEEE00
group expression
maxLimit 52000
barChartLabel Tissue
barChartUnit Quantile_Normalized_Expression
html miRnaAtlas
configurable on
subGroups view=a_A
searchIndex name
track miRnaAtlasSample2
type bigBarChart
visibility pack
parent miRnaAtlas
view b_B
configurable on
track miRnaAtlasSample2BarChart
url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$
url2Label miRBase v21 Precursor Accession:
parent miRnaAtlasSample2
visibility full
shortLabel Sample 2
longLabel miRNA Tissue Atlas microRna Expression
bigDataUrl /gbdb/hg38/bbi/miRnaAtlasSample2.bb
barChartMatrixUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2Matrix.txt
barChartSampleUrl /gbdb/hgFixed/human/expMatrix/miRnaAtlasSample2.txt
barChartBars adipocyte artery colon dura_mater kidney liver lung muscle myocardium skin \
spleen stomach testis thyroid small_intestine_duodenum small_intestine_jejunum pancreas \
kidney_glandula_suprarenalis kidney_cortex_renalis kidney_medulla_renalis esophagus prostate \
bone_marrow vein lymph_node nerve_not_specified pleura brain_pituitary_gland spinal_cord \
brain_thalamus brain_white_matter brain_nucleus_caudatus brain_gray_matter \
brain_cerebral_cortex_temporal brain_cerebral_cortex_frontal \
brain_cerebral_cortex_occipital brain_cerebellum
barChartColors #F7A028 #F73528 #DEBE98 #86BF80 #CDB79E #CDB79E #9ACD32 #7A67AE #9745AC #1E90FF \
\#CDB79E #FFD39B #A6A6A6 #008B45 #CDB79E #CDB79E #CD9B1D \
\#CDB79E #CDB79E #CDB79E #AC8F69 #D9D9D9 #BD3487 \
\#FF00FF #EE82EE #F7E300 #73A585 #B4EEB4 #EEEE00 \
\#EEEE00 #EEEE00 #EEEE00 #EEEE00 \
\#EEEE00 #EEEE00 \
\#EEEE00 #EEEE00
group expression
maxLimit 52000
barChartLabel Tissue
barChartUnit Quantile_Norm_Expr
html miRnaAtlas
configurable on
subGroups view=b_B
searchIndex name
searchTable miRnaAtlasSample1BarChart
searchType bigBed
searchPriority 1
searchDescription miRNA Tissue Atlas Sample 1
searchMethod exact
semiShortCircuit 1
searchTable miRnaAtlasSample2BarChart
searchType bigBed
searchPriority 1
searchDescription miRNA Tissue Atlas Sample 2
searchMethod exact
semiShortCircuit 1
include unusualcons.ra
track cosmicRegions
shortLabel COSMIC Regions
longLabel Catalogue of Somatic Mutations in Cancer V82
type bigBed 8 +
bigDataUrl /gbdb/hg38/cosmic/cosMutHg38V82.bb
labelFields cosmLabel
group phenDis
color 200, 0, 0
url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$$
urlLabel COSMIC ID:
searchIndex name,cosmLabel
tableBrowser off
mouseOverField _mouseOver
html cosmicRegions
noScoreFilter on
pennantIcon snowflake.png ../goldenPath/newsarch.html#091523 "COSMIC data is now updated on the COSMIC track (not COSMIC Regions). See news archive for details."
searchTable cosmicRegions
searchPriority 2.07207
searchType bigBed
searchDescription COSMIC Regions
track cosmicMuts
shortLabel COSMIC
longLabel Catalogue of Somatic Mutations in Cancer V101
type bigBed 6 + 3
bigDataUrl /gbdb/hg38/cosmic/cosmic.bb
group phenDis
url https://cancer.sanger.ac.uk/cosmic/search?q=$$
urlLabel Genomic Mutation ID:
noScoreFilter on
dataVersion COSMIC v101
track vistaEnhancersBb
shortLabel VISTA Enhancers
longLabel VISTA Enhancers
group regulation
url https://enhancer.lbl.gov/vista/element?vistaId=$$
type bigBed 9 +
mouseOverField patternExpression
urlLabel View on the VISTA Enhancer Browser
bigDataUrl /gbdb/hg38/vistaEnhancers/vistaEnhancers.bb
itemRgb on
track coriellDelDup override
origAssembly hg19
pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"
track revel override
origAssembly hg19
pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"
include nonCodingRNAs.ra
#track wgRna override
#dataVersion miRBase Release 15.0 (April 2010) and snoRNABase Version 3
#pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"
track hgIkmc override
origAssembly hg19
pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"
track fosEndPairs override
origAssembly hg18
pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18"
track interactions override
directUrl hgGeneGraph?db=hg38&gene=%s
track par override
group x
visibility hide
track windowmaskerSdust override
group rep
priority 8
track nestedRepeats override
group rep
priority 2
track simpleRepeat override
group rep
priority 7
track rmskJoinedBaseline override
group rep
priority 4
visibility hide
searchName assemblyAcc
searchTable gold
searchMethod prefix
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 5
shortCircuit 1
termRegex [A-Z][A-Z0-9]+(\.[0-9]+)?
# Local declaration so that local gap.html is picked up.
track gap override
html gap
visibility hide
include rmskTracks.ra
track analysisGap
shortLabel Analysis Gap
longLabel Extra Gap Locations in Analysis Set Sequence on chr5, 14, 19, 21, 22, Y
group x
visibility hide
type bed 4 .
chromosomes chr14,chr19,chr21,chr22,chr5,chrY
track hg38ContigDiff
shortLabel Hg19 Diff
longLabel Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19)
visibility hide
group map
type bed 9 .
scoreFilterByRange on
itemRgb on
color 0,0,0
urlLabel Genbank accession:
url https://www.ncbi.nlm.nih.gov/nuccore/$$
track centromeres
shortLabel Centromeres
longLabel Centromere Locations
group map
visibility hide
type bed 4 .
chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY
color 255,0,0
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI accession record:
include ../chainNetPrimate.ra
include ../chainNetPlacental.ra
include ../chainNetVertebrate.ra
# a large composite with many chain/net experiments to other human assemblies
include chainNetHumanExperiment.ra alpha
track contigAlignmentSegments
shortLabel ContigSegments
longLabel Non-bridged Contig Segments Used in lastz/chain/net Alignment Pipeline
group x
visibility hide
type bed 4
track chainSelf override
longLabel $Organism Chained Self Alignments
group rep
priority 6
chainColor Normalized Score
matrixHeader A, C, G, T
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
type chain hg38
otherDb hg38
chainNormScoreAvailable yes
scoreFilter 20000
track multiz4way
shortLabel Cons 4-way
longLabel 4-Way Multiz Alignment & Conservation
group compGeno
visibility hide
color 0, 10, 100
altColor 0,90,10
type wigMaf 0.0 1.0
maxHeightPixels 100:40:11
# wiggle phastCons4way
# spanList 1
pairwiseHeight 12
yLineOnOff Off
# frames multiz4wayFrames
# irows on
autoScale Off
windowingFunction mean
summary multiz4waySummary
speciesCodonDefault hg38
speciesGroups mammal
sGroup_mammal rheMac3 mm10 canFam3
treeImage phylo/hg38_4way.gif
include defaultPriority.ra
track altSeqLiftOverBigPsl
#superTrack altSequence pack
visibility hide
shortLabel Big Alt Map
longLabel Big GRCh38 Alignments to the Alternate Sequences/Haplotypes
type bigPsl
bigDataUrl http://hgwdev.gi.ucsc.edu/~braney/altSeqLiftOverPsl.bb
html altSequence
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsMaxZoom 10000.0
showCdsAllScales .
baseColorDefault diffBases
baseColorUseSequence lfExtra
#baseColorUseSequence extFile seqNcbiAltSequence extNcbiAltSequence
release alpha
track altSequenceExp
superTrack on
shortLabel Exp Alt Map
longLabel GRCh38 Haplotype to Reference Sequence Mapping Correspondence
visibility hide
group x
track ncbiAltMappingsChain
superTrack altSequenceExp pack
shortLabel Alt Map Chain
longLabel Chain Mappings to the Alternate Sequences/Haplotypes
type chain hg38
spectrum on
html altSequence
track ncbiAltMappingsMaf
superTrack altSequenceExp pack
shortLabel Alt Map Maf
longLabel Maf Mappings to the Alternate Sequences/Haplotypes
type maf
html altSequence
include trackDb.4way.ra alpha
include trackDb.5way.ra alpha
include trackDb.7way.ra alpha
include trackDb.17way.ra alpha
include trackDb.20way.ra alpha
include trackDb.27way.ra alpha
include trackDb.30way.ra
include trackDb.10way.ra
include trackDb.mito204way.ra
track ucscRetroAli8
shortLabel Retroposed Genes 8.0
longLabel Retroposed Genes V8, Including Pseudogenes
group genes
type psl
color 20,0,250
visibility hide
ucscRetroInfo ucscRetroInfo8
baseColorDefault diffCodons
baseColorUseCds table ucscRetroCds8
baseColorUseSequence extFile ucscRetroSeq8 ucscRetroExtFile8
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsAllScales .
showCdsMaxZoom 10000.0
searchName ucscRetroInfoRefSeq8
searchTable ucscRetroAli8
searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
xrefTable hgFixed.refLink, ucscRetroInfo8
dontCheckXrefQueryFormat 1
xrefQuery select ucscRetroInfo8.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc
searchPriority 3.52
track mrnaBig
bigDataUrl http://hgwdev.gi.ucsc.edu/~braney/bigMrna.bb
shortLabel Big $Organism mRNAs
longLabel Big $Organism mRNAs from GenBank
group x
visibility hide
type bigPsl
baseColorUseCds given
#baseColorUseSequence genbank
baseColorUseSequence lfExtra
baseColorDefault diffCodons
#baseColorDefault diffBases
showDiffBasesAllScales .
indelDoubleInsert on
indelQueryInsert on
indelPolyA on
release alpha
searchName ucscRetroInfoMrna8
searchTable ucscRetroAli8
searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
searchPriority 3.55
searchName ucscRetroUniProt8
searchTable ucscRetroAli8
searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
dontCheckXrefQueryFormat 1
xrefTable kgXref, ucscRetroInfo8
xrefQuery select ucscRetroInfo8.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID
searchPriority 3.54
searchName ucscRetroKnownGene8
searchTable ucscRetroAli8
searchDescription Retroposed GenesV8, Including Pseudogenes - 2014-07-08
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
dontCheckXrefQueryFormat 1
xrefTable kgXref, ucscRetroInfo8
xrefQuery select ucscRetroInfo8.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID
searchPriority 3.53
track ucscRetroAli9
shortLabel RetroGenes V9
longLabel Retroposed Genes V9, Including Pseudogenes
group genes
type psl
color 20,0,250
visibility hide
ucscRetroInfo ucscRetroInfo9
baseColorDefault diffCodons
baseColorUseCds table ucscRetroCds9
baseColorUseSequence extFile ucscRetroSeq9 ucscRetroExtFile9
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsAllScales .
showCdsMaxZoom 10000.0
dataVersion Jan. 2015
exonNumbers off
searchName ucscRetroInfoRefSeq9
searchTable ucscRetroAli9
searchDescription Retroposed Genes V9, Including Pseudogenes
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
xrefTable hgFixed.refLink, ucscRetroInfo9
dontCheckXrefQueryFormat 1
xrefQuery select ucscRetroInfo9.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc
searchPriority 3.52
searchName ucscRetroInfoMrna9
searchTable ucscRetroAli9
searchDescription Retroposed Genes V9, Including Pseudogenes
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
searchPriority 3.55
searchName ucscRetroUniProt9
searchTable ucscRetroAli9
searchDescription Retroposed Genes V9, Including Pseudogenes
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
dontCheckXrefQueryFormat 1
xrefTable kgXref, ucscRetroInfo9
xrefQuery select ucscRetroInfo9.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID
searchPriority 3.54
searchName ucscRetroKnownGene9
searchTable ucscRetroAli9
searchDescription Retroposed Genes V9, Including Pseudogenes
query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
dontCheckXrefQueryFormat 1
xrefTable kgXref, ucscRetroInfo9
xrefQuery select ucscRetroInfo9.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID
searchPriority 3.53
track genomicSuperDups override
group rep
priority 5
track sibTxGraph override
url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?db=hg38&species=H.+sapiens&tromer=$$
track gtexGene override
pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19"
track ucscGenePfam override
shortLabel Pfam in GENCODE
longLabel Pfam Domains in GENCODE Genes
html gencodePfam
include trackDb.cloneEnd.ra
include hg38Patch11.ra alpha
-include knownGene.ra public
-include knownGene.alpha.ra alpha,beta
+include knownGene.ra
include knownGeneArchive.ra
include knownGene.nmd_deco.ra alpha
include trackDb.100way.ra
include trackDb.145way.ra alpha
include trackDb.241way.ra
include trackDb.447way.ra
# track multiz145way
# shortLabel 145way maf
# longLabel 145-way MAF track
# group compGeno
# visibility hide
# type maf
track microsat override
group rep
priority 3
searchTable sgpGene
searchType genePred
termRegex chr[0-9MUXYn]+[BGHIJKLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)?
searchPriority 50
searchTable geneid
searchType genePred
searchMethod prefix
termRegex chr[0-9MUXYn]+[BGHIJKLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)?
searchPriority 50
track gwasCatalog override
snpTable snp144
snpVersion 144
# override to use hg38 specific html page
track crispr override
html crispr
track ncbiRefSeqRefGene
compositeTrack on
shortLabel refGeneRefSeq
longLabel comparing gene tracks refGene with ncbiRefSeq
visibility hide
type bed 12
group x
track lostRefGene
subTrack ncbiRefSeqRefGene
shortLabel lostRefGene
longLabel refGene predictions 'lost' in NCBI RefSeq track
color 155,0,0
track exactRefGene
subTrack ncbiRefSeqRefGene
shortLabel exactRefGene
longLabel refGene predictions 'exact' in NCBI RefSeq track
color 0,155,0
track compatibleRefGene
subTrack ncbiRefSeqRefGene
shortLabel compatibleRefGene
longLabel refGene predictions 'compatible' in NCBI RefSeq track
color 0,0,255
track gtexBrain
release alpha
type barChart
maxLimit 370000
barChartUnit RPKM
barChartLabel Brain Regions
barChartMetric median
barChartBars \
brainAmygdala brainAnCinCortex brainCaudate brainCerebelHemi brainCerebellum brainCortex \
brainFrontCortex brainHippocampus brainHypothalamus brainNucAccumbens brainPutamen \
brainSpinalcord brainSubstanNigra
bedNameLabel Gene accession
shortLabel GTEx Brain
longLabel GTEx Brain Gene Expression in barChart track format
group expression
track dgvPlus override
group varRep
track dgvMerged override
parent dgvPlus on
type bigBed 9 +
bigDataUrl /gbdb/hg38/dgv/dgvMerged.bb
filter._size 1:9734324
filterByRange._size on
filterLabel._size Genomic size of variant
filterValues.varType complex,deletion,duplication,gain,gain+loss,insertion,inversion,loss,mobile element insertion,novel sequence insertion,sequence alteration,tandem duplication
dataVersion 2020-02-25
searchIndex name
mouseOver ID: $name
Position: $chrom:${chromStart}-${chromEnd}
Size: $_size
Type: $varType
track dgvSupporting override
parent dgvPlus
type bigBed 9 +
bigDataUrl /gbdb/hg38/dgv/dgvSupporting.bb
filter._size 1:9320633
filterByRange._size on
filterLabel._size Genomic size of variant
filterValues.varType complex,deletion,duplication,gain,gain+loss,insertion,inversion,loss,mobile element insertion,novel sequence insertion,sequence alteration,tandem duplication
dataVersion 2020-02-25
searchIndex name
mouseOver ID: $name
Position: $chrom:${chromStart}-${chromEnd}
Size: $_size
Type: $varType
track dgvGold
parent dgvPlus
shortLabel DGV Gold Standard
longLabel Database of Genomic Variants: Gold Standard Variants
bigDataUrl /gbdb/hg38/dgv/dgvGold.bb
type bigBed 12 +
url http://dgv.tcag.ca/gb2/gbrowse_details/dgv2_hg38?ref=$S;start=${;end=$};name=$$;class=Sequence
searchIndex name
mouseOver ID: $name
Position: $chrom:${chromStart}-${chromEnd}
CNV subtype: $variant_sub_type
Frequency: $Frequency
searchTable dgvGold
searchType bigBed
searchDescription DGV Gold Variants
searchTable dgvMerged
searchMethod exact
searchType bigBed
searchDescription DGV Merged Variants
searchTable dgvSupporting
searchMethod exact
searchType bigBed
searchDescription DGV Supporting Variants
track gtexTranscExpr override
bigDataUrl /gbdb/hg38/gtex/gtexTranscExpr.bb
# ENCODE tracks
include trackDb.gencode.ra
include wgEncodeReg.ra
include encode3.ra beta,public
include encode.cCREs.override.ra alpha
include hic.ra
include gnomad.ra
include platinumGenomes.ra
track epdNew
compositeTrack on
shortLabel EPDnew Promoters
longLabel Promoters from EPDnew
html ../../epdNewPromoter
type bigBed 8
group expression
visibility hide
urlLabel EPDnew link:
bedNameLabel Promoter ID
exonArrows on
track epdNewPromoter
shortLabel EPDnew v6
longLabel Promoters from EPDnew human version 006
parent epdNew on
bigDataUrl /gbdb/$D/bbi/epdNewHuman006.$D.bb
dataVersion EPDNew Human Version 006 (May 2018)
url https://epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=$$
color 50,50,200
priority 1
track epdNewPromoterNonCoding
shortLabel EPDnew NC v1
longLabel ncRNA promoters from EPDnewNC human version 001
parent epdNew on
bigDataUrl /gbdb/$D/bbi/epdNewHumanNc001.$D.bb
dataVersion EPDNewNC Human Version 001 (April 2019)
url https://epd.epfl.ch/cgi-bin/get_doc?db=hsNCEpdNew&format=genome&entry=$$
color 180,0,134
priority 2
track clinGenCnv override
filter.size 773:11309456
filterLimits.size 773:11309456
track covidHct
shortLabel Transcription response
longLabel High-confidence SARS-CoV-2 infection transcriptional response target genes
priority 100
type bigBed 8 +
color 150,20,20
mouseOver $_mouseOver : $name - CQV: $cqv - Rank: $rank
group varRep
bigDataUrl /gbdb/hg38/covidHct/covidHct.bb
release alpha
track orphadata override
urls ensemblID="https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" pmid="https://pubmed.ncbi.nlm.nih.gov/$$" orphaCode="http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$" omim="https://www.omim.org/entry/$$?search=$$&highlight=$$" hgnc="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$"
include dbSnpArchiveHg38.ra
include affyArchive.ra
include genePredArchive.ra
include tgpArchive.ra
track genotypeArrays
shortLabel Array Probesets
longLabel Microarray Probesets and OGM sites
type bigBed 4
visibility hide
group varRep
compositeTrack on
pennantIcon Updated red ../goldenPath/newsarch.html#072325 "Bionano DLE-1 released July 23, 2025"
track genetiSureCytoCghSnp
parent genotypeArrays on
shortLabel Agilent GenetiSure Cyto CGH+SNP
longLabel Agilent GenetiSure Cyto CGH+SNP 4x180K 085591 20200302
type bigBed 4
visibility pack
bigDataUrl /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bb
priority 1
track genetiSureCytoCgh4x180
parent genotypeArrays on
shortLabel Agilent GenetiSure Cyto CGH 4x180K
longLabel Agilent GenetiSure Cyto CGH 4x180K 085589 20200302
type bigBed 4
visibility pack
bigDataUrl /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bb
priority 2
track genetiSureCytoCghSnp8x60
parent genotypeArrays on
shortLabel Agilent GenetiSure Cyto CGH 8x60
longLabel Agilent GenetiSure Cyto CGH 8x60K 085590 20200302
type bigBed 4
visibility pack
bigDataUrl /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bb
priority 3
track epicV2illuminaMethylation
parent genotypeArrays on
shortLabel Illumina EPIC v2
longLabel Illumina EPIC v2 Methylation Array
type bigBed 12 +
bigDataUrl /gbdb/hg38/bbi/illumina/illuminaEPICv2.bb
visibility pack
colorByStrand 255,0,0 0,0,255
html genotypeArrays
priority 3.5
noScoreFilter on
mouseOver Probe ID: $IlluminaName
Address ID: $addressAID
Probe sequence in column: $alleleAProbeSeq
rsID: $sNPID
track snpArrayIllumina850k
parent genotypeArrays on
shortLabel Illumina 850k
longLabel Illumina 850k EPIC Methylation Array
type bigBed 6
bigDataUrl /gbdb/hg38/bbi/illumina/epic850K.bb
visibility pack
urls refGeneAccession="https://www.ncbi.nlm.nih.gov/nuccore/$$" rsID="https://www.ncbi.nlm.nih.gov/snp/?term=$$"
colorByStrand 255,0,0 0,0,255
html genotypeArrays
priority 5
noScoreFilter on
track snpArrayIllumina450k
parent genotypeArrays on
shortLabel Illumina 450k
longLabel Illumina 450k Methylation Array
type bigBed 6
bigDataUrl /gbdb/hg38/bbi/illumina/illumina450K.bb
visibility pack
urls refGeneAccession="https://www.ncbi.nlm.nih.gov/nuccore/$$" rsID="https://www.ncbi.nlm.nih.gov/snp/?term=$$"
colorByStrand 255,0,0 0,0,255
html genotypeArrays
priority 4
noScoreFilter on
track snpArrayCytoSnp850k
parent genotypeArrays on
shortLabel CytoSNP 850k
longLabel Illumina 850k CytoSNP Array
type bigBed 6 +
bigDataUrl /gbdb/hg38/bbi/cytoSnp/cytoSnp850k.bb
visibility pack
urls rsID="https://www.ncbi.nlm.nih.gov/snp/?term=$$"
colorByStrand 255,0,0 0,0,255
html genotypeArrays
priority 6
noScoreFilter on
track affyCytoScanHD
parent genotypeArrays on
shortLabel Affy CytoScan HD
longLabel Affymetrix Cytoscan HD GeneChip Array
type bigBed 12
bigDataUrl /gbdb/hg38/genotypeArrays/affyCytoScanHD.bb
visibility pack
html genotypeArrays
itemRgb on
priority 7
mouseOver Probe ID: $name
Size: $blockSizes
Strand: $strand
track bionano
parent genotypeArrays on
bigDataUrl /gbdb/hg38/bionano/hg38_CTTAAG_0kb_0labels.bb
shortLabel Bionano DLE-1
longLabel Bionano DLE-1 CTTAAG sites
type bigBed
searchTable snpArrayIllumina450k
searchMethod exact
searchType bigBed
termRegex cg[0-9]+
semiShortCircuit 1
searchPriority 55
searchTable snpArrayIllumina850k
searchMethod exact
searchType bigBed
termRegex cg[0-9]+
semiShortCircuit 1
searchPriority 55
include trackDb.470way.ra
track michaelMaf
release alpha
shortLabel Michae's Big MAF
longLabel Michael Alignment
bigDataUrl http://genome.senckenberg.de/data/hg38/bigMaf.bb
summary http://genome.senckenberg.de/data/hg38/bigMafSummary.bb
type bigMaf
speciesOrder panPan3 panTro6 gorGor6 ponAbe3 HLhylMol2 HLnomLeu4 HLpapAnu5 HLtheGel1 cerAty1 HLmanSph1 manLeu1 macNem1 HLmacFas6 HLmacFus1 rheMac10 HLcerMon1 HLcerNeg1 HLallNig1 HLeryPat1 chlSab2 HLpilTep2 colAng1 HLsemEnt1 HLtraFra1 nasLar1 HLpygNem1 HLrhiRox2 rhiBie1 HLpitPit1 HLpleDon1 HLateGeo1 HLaloPal1 HLsaiBol1 saiBol1 HLsapApe1 cebCap1 HLcebAlb1 aotNan1 HLsagImp1 HLcalJac4 HLcalPym1 tarSyr2 HLnycCou1 otoGar3 HLcheMed1 proCoq1 HLindInd1 HLlemCat1 HLproSim1 HLeulFul1 HLeulMon1 eulFla1 HLeulFla1 eulMac1 HLmicTav1 HLmicSpe31 micMur3 HLmirZaz1 HLmirCoq1 HLdauMad1 HLgalVar2 HLacoRus1 HLacoCah1 HLpsaObe1 HLmerUng1 HLrhoOpi1 HLratNor7 rn6 HLratRat7 mm39 mm10 HLmusSpi1 HLmusSpr1 HLmusCar1 HLmusPah1 HLmasCou1 HLapoSyl1 HLgraSur1 HLarvNil1 HLcriGri3 mesAur1 HLonyTor1 HLperNas1 HLperCri1 HLperEre1 HLperCal2 HLperLeu1 HLperManBai2 HLperPol1 HLneoLep1 HLsigHis1 HLondZib1 HLmyoGla2 HLellTal1 HLellLut1 HLarvAmp1 HLmicFor1 HLmicOec1 micOch1 HLmicArv1 HLmicAgr2 HLcriGam1 nanGal1 HLrhiPru1 jacJac1 HLallBul1 HLzapHud1 HLcasCan3 HLperLonPac1 HLdipSte1 dipOrd2 HLpedCap1 HLcteGun1 HLhysCri1 HLereDor1 HLcoePre1 HLdasPun1 HLhydHyd1 HLcavTsc1 cavPor3 cavApe1 HLdolPat1 chiLan1 HLdinBra1 HLmyoCoy1 HLcteSoc1 octDeg1 HLthrSwi1 HLpetTyp1 hetGla2 HLfukDam2 HLaplRuf1 HLsciVul1 HLsciCar1 HLxerIna1 HLmarFla1 HLmarHim1 HLmarMar1 HLmarVan1 HLmarMon1 HLmarMon2 HLspeDau1 HLuroPar1 speTri2 HLcynGun1 HLmusAve1 HLgraMur1 HLgliGli1 ochPri3 HLsylBac1 HLoryCunCun4 oryCun2 HLoryCun3 HLlepAme1 HLlepTim1 tupBel1 tupChi1 panHod1 HLoviCan1 HLhemHyl1 HLoviCan2 HLoviNivLyd1 HLoviAmm1 HLoviAri5 HLoviOri1 HLammLer1 HLoreAme1 HLcapSib1 HLcapIbe1 HLcapHir2 HLcapAeg1 HLconTau2 HLbeaHun1 HLdamLun1 HLoryGaz1 HLoryDam1 HLhipNig1 HLhipEqu1 HLredRed1 HLkobEll1 HLkobLecLec1 HLmadKir1 HLrapCam1 HLeudTho1 HLsaiTat1 HLantMar1 HLlitWal1 HLcepHar1 HLsylGri1 HLphiMax1 HLoreOre1 HLneoPyg1 HLnanGra1 HLproPrz1 HLneoMos1 HLaepMel1 HLbubBub2 HLsynCaf1 HLtraImb1 HLtraStr1 HLtraScr1 HLbosFro1 HLbosGau1 HLbosGru1 HLbosMut2 bosTau9 HLbosInd2 bisBis1 HLmosMos1 HLmosBer1 HLmosChr1 HLhydIne1 HLcapPyg1 HLalcAlc1 HLelaDav1 HLranTar1 HLranTarGra2 HLodoHem1 HLodoVir3 HLodoVir2 HLodoVir1 HLmunRee1 HLmunMun1 HLmunCri1 HLcerHanYar1 HLaxiPor1 HLprzAlb1 HLcerEla1 HLantAme1 HLokaJoh2 HLgirCam1 HLgirTip1 HLgirCam2 HLtraKan1 HLtraJav1 orcOrc1 HLhipAmp1 HLhipAmp3 HLphyCat2 phyCat1 HLkogBre1 HLplaMin1 HLzipCav1 HLmesBid1 HLlagObl1 HLgloMel1 HLpepEle1 HLsouChi1 HLturAdu2 HLturAdu1 HLturTru4 turTru2 HLturTru3 HLdelLeu2 HLmonMon1 HLneoAsi1 HLphoSin1 HLphoPho2 HLphoPho1 lipVex1 HLponBla1 HLlniGeo1 balAcu1 HLbalBon1 HLbalPhy1 HLmegNov1 HLbalMus1 HLbalEde1 HLescRob1 HLeubGla1 HLeubJap1 HLbalMys1 susScr11 HLcatWag1 HLcamFer3 HLcamDro2 HLcamBac1 HLlamGla1 HLlamGuaCac1 HLlamGlaCha1 HLvicPacHua3 HLvicVicMen1 vicPac2 HLtapTer1 HLtapInd1 HLtapInd2 HLrhiUni1 HLdicSum1 HLdicBic1 cerSim1 HLcerSimCot1 equPrz1 equCab3 HLequQuaBoe1 HLequAsi1 HLequAsiAsi2 HLursThi1 HLursAme1 HLursAme2 ursMar1 HLursArc1 HLailMel2 HLpotFla1 HLnasNar1 HLbasSum1 HLproLot1 HLeriBar1 HLhalGry1 HLphoVit1 neoSch1 lepWed1 HLmirLeo1 odoRosDiv1 HLodoRos1 HLcalUrs1 HLarcGaz2 HLzalCal1 HLeumJub1 HLailFul2 HLmusFur2 HLmusPut1 HLmusErm1 HLneoVis1 enhLutKen1 enhLutNer1 HLlutLut1 HLlonCan1 HLpteBra1 HLpteBra2 HLgulGul1 HLmarZib1 HLcroCro1 HLhyaHya1 HLparHer1 HLpanLeo1 HLpanOnc2 HLpanOnc1 HLpanPar1 panTig1 HLneoNeb1 HLfelNig1 felCat9 HLpumYag1 HLlynPar1 HLlynCan1 HLpriBen1 HLpumCon1 HLaciJub2 HLtaxTax1 HLmirAng2 HLvulVul1 HLvulLag1 HLlycPic2 HLlycPic3 canFam4 HLcanLupDin1 canFam5 HLmanJav1 HLmanJav2 HLmanPen2 manPen1 HLphaTri2 HLmanTri1 HLmelCap1 HLspiGra1 HLmunMug1 HLhelPar1 HLsurSur1 HLsurSur2 HLcryFer2 HLsacBil1 HLnatTum1 HLmyoMyo6 myoDav1 HLmyoLuc1 myoLuc2 myoBra1 HLmyoSep1 HLmurAurFea1 HLnycHum2 HLaeoCin1 HLlasBor1 eptFus1 HLantPal1 HLpipKuh2 HLpipPip1 HLpipPip2 HLminSch1 HLminNat1 HLmolMol2 HLtadBra2 HLtadBra1 HLmacCal1 HLlepYer1 HLgloSor2 HLanoCau1 HLartJam2 HLartJam1 HLstuHon1 HLcarPer3 HLcarPer2 HLtonSau1 HLphyDis3 HLdesRot2 HLmicHir1 ptePar1 HLmorBla1 HLnocLep2 HLnocLep1 HLeonSpe1 HLrouLes1 HLrouAeg4 HLrouMad1 HLrhiSed1 HLrhiTri1 HLrhiLuc1 HLrhiSin1 HLrhiAff1 HLaseSto1 HLcraTho1 HLmegLyr2 HLhipArm1 HLhipLar1 HLhipGal1 HLhipCyc1 HLrhiFer5 HLpteRuf1 HLpteGig1 HLpteVam2 HLptePse1 pteAle1 HLeidHel2 HLeidDup1 HLmacSob1 HLcynBra1 HLsolPar1 eriEur2 sorAra2 HLuroGra1 HLscaAqu1 HLtalOcc1 conCri1 echTel2 HLmicTal1 eleEdw1 oryAfe1 chrAsi1 HLhetBru1 HLproCap3 HLloxAfr4 HLeleMax1 HLhydGig1 triMan1 HLdugDug1 dasNov3 HLtolMat1 HLtamTet1 HLmyrTri1 HLchoHof3 HLchoDid2 HLchoDid1 HLphaGym1 HLtriVul1 HLpseOcc1 HLpseCor1 HLthyCyn1 HLantFla1 HLsarHar2 HLdidVir1 HLgraAgi1 monDom5 HLphaCin1 HLvomUrs1 macEug2 HLnotEug3 HLospRuf1 HLmacGig1 HLmacFul1 HLgymLea1 HLpseCup1 HLtacAcu1 HLornAna3
include topmed.ra alpha
include gerp.ra alpha
include crossTissueMaps.ra
include problematic.ra
# Brian's original experiment, April 2022
include hprcChain.ra alpha
include hprcCoverage97.ra alpha
# other HPRC experiments
include hprcChainNet.ra
# the hprcChainNet.ra replaces these two:
# include hprcChains.ra alpha
# include hprcNets.ra alpha
#include chainsHprc.ra alpha
include hprcCoverage.ra alpha
include trackDb.hprc90way.ra
include hprcArr.ra
include hprcVCF.ra
include hprcVCFTest.ra alpha
track ncbiRefSeq override
parent refSeqComposite off
include ../../trackDb.mgc-orfeome.ra
include assemblyTracks.ra
include primates11way.ra alpha
include pseudogenes.ra
include recount3.ra alpha
include long_read_transcripts.ra
include mavedb.ra
include vgpLiftOver.ra alpha
include psuVsUcscChains.ra alpha
include varFreqs.ra alpha
include LCR.ra alpha