d4262bca1e7f48775cd45562ff7e8a77dae739b1 gperez2 Wed Apr 24 11:41:11 2024 -0700 Combining the two abSplice.ra and html files for hg38 and hg19, refs #33251 diff --git src/hg/makeDb/trackDb/human/hg38/trackDb.ra src/hg/makeDb/trackDb/human/hg38/trackDb.ra index aef4974..4b24ecc 100644 --- src/hg/makeDb/trackDb/human/hg38/trackDb.ra +++ src/hg/makeDb/trackDb/human/hg38/trackDb.ra @@ -1,907 +1,905 @@ 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 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 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=$$ urlLabel COSMIC ID: searchIndex name,cosmLabel tableBrowser off mouseOverField _mouseOver html cosmicRegions noScoreFilter on pennantIcon snowflake.png ../goldenPath/newsarch.html#091523 "COSMIC data is now updated on the COSMIC track (not COSMIC Regions). See news archive for details." searchTable cosmicRegions searchPriority 2.07207 searchType bigBed searchDescription COSMIC Regions track cosmicMuts shortLabel COSMIC longLabel Catalogue of Somatic Mutations in Cancer V98 type bigBed 6 + 3 bigDataUrl /gbdb/hg38/cosmic/cosmic.bb group phenDis url https://cancer.sanger.ac.uk/cosmic/search?q=$$ urlLabel Genomic Mutation ID: noScoreFilter on dataVersion COSMIC v98 track vistaEnhancersBb shortLabel VISTA Enhancers longLabel VISTA Enhancers group regulation url https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&organism_id=1&experiment_id=$<experimentId> type bigBed 9 + 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 fishClones override origAssembly hg18 pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18" 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 track stsMap override 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 ctgPos2 shortLabel GRC Contigs longLabel Genome Reference Consortium Contigs group map visibility hide type ctgPos url https://www.ncbi.nlm.nih.gov/nuccore/$$ chromosomes chr1,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chrX,chrY searchTable ctgPos2 searchMethod prefix shortCircuit 1 termRegex [GK][LI][028][0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,contig from %s where contig like '%s%%' searchPriority 5 track scaffolds shortLabel Scaffolds longLabel GRCh38 Defined Scaffold Identifiers group map visibility hide color 0,0,0 type bed 4 . searchTable scaffolds searchMethod prefix searchType bed shortCircuit 1 termRegex [1-9HMXY][0-9A-Z_]* searchPriority 18 track analysisGap shortLabel Analysis Gap longLabel Extra Gap Locations in Analysis Set Sequence on chr5, 14, 19, 21, 22, Y group x visibility hide type bed 4 . chromosomes chr14,chr19,chr21,chr22,chr5,chrY track hg38ContigDiff shortLabel Hg19 Diff longLabel Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19) visibility hide group map type bed 9 . scoreFilterByRange on itemRgb on color 0,0,0 urlLabel Genbank accession: url https://www.ncbi.nlm.nih.gov/nuccore/$$ 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.soe.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.soe.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 beta,public include knownGene.alpha.ra alpha include knownGeneArchive.ra alpha include trackDb.100way.ra include trackDb.145way.ra alpha include trackDb.241wayT.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:$varType; Affected genes:$genes 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:$varType; Affected genes:$genes 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=$$;class=Sequence searchIndex name mouseOver ID:$name; Position; $chrom:${chromStart}-${chromEnd}; Type:$variant_sub_type; Frequency:$Frequency searchTable dgvGold searchType bigBed searchDescription DGV Gold Variants searchTable dgvMerged searchMethod exact searchType bigBed searchDescription DGV Merged Variants searchTable dgvSupporting searchMethod exact searchType bigBed searchDescription DGV Supporting Variants track gtexTranscExpr override bigDataUrl /gbdb/hg38/gtex/gtexTranscExpr.bb # ENCODE tracks include trackDb.gencode.ra include wgEncodeReg.ra include encode3.ra include hic.ra include gnomad.ra include platinumGenomes.ra track epdNew compositeTrack on shortLabel EPDnew Promoters longLabel Promoters from EPDnew html ../../epdNewPromoter type bigBed 8 group expression visibility hide urlLabel EPDnew link: bedNameLabel Promoter ID exonArrows on track epdNewPromoter shortLabel EPDnew v6 longLabel Promoters from EPDnew human version 006 parent epdNew on bigDataUrl /gbdb/$D/bbi/epdNewHuman006.$D.bb dataVersion EPDNew Human Version 006 (May 2018) url https://epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=$$ 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 include spliceAi.ra track genotypeArrays shortLabel Array Probesets longLabel Microarray Probesets type bigBed 4 visibility hide group varRep compositeTrack on pennantIcon Updated red hgTrackUi?db=hg38&g=genotypeArrays "New Affy CytoScan HD track" 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 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 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 abSplice.ra - include ../../trackDb.mgc-orfeome.ra