1a2f5a5b07855da8d191c0b9358c945d6abe9f74 braney Mon Sep 28 15:17:28 2026 -0700 trackDb: fix the netThaSir1 chain table and drop missing hg18 pgSnp prediction tables, refs #37424 The hg38 netThaSir1 stanza was copied from netAnoCar1 and kept its type line, so hgc looked for chainAnoCar1 and every click failed. It now names thaSir1 and chainThaSir1. The hg18 pgKb1Comb, pgNb1, pgMd8, pgTk1 and pgAbtSolid tracks named SIFT and PolyPhen tables that exist only on hgwdev and were never released. The details page warned on every click on beta and the RR. The two settings are removed. diff --git src/hg/makeDb/trackDb/human/hg18/trackDb.ra src/hg/makeDb/trackDb/human/hg18/trackDb.ra index 1fab9101854..c0c17ee88f6 100644 --- src/hg/makeDb/trackDb/human/hg18/trackDb.ra +++ src/hg/makeDb/trackDb/human/hg18/trackDb.ra @@ -1,3844 +1,3823 @@ # "$Id: trackDb.ra,v 1.491 2010/06/11 00:03:54 ann Exp $"; include trackDb.chainNet.ra include trackDb.encode.ra include trackDb.wgEncode.ra include trackDb.pipeline.ra track clonePos override longLabel Clone Coverage track knownGene bigGeneDataUrl /gbdb/hg18/knownGene.bb priority 1 shortLabel UCSC Genes longLabel UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) group genes visibility pack color 12,12,120 type genePred knownGenePep knownGeneMrna idXref kgAlias kgID alias hgGene on hgsid on directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s baseColorUseCds given baseColorDefault genomicCodons defaultLinkedTables kgXref intronGap 12 track altLocations type bed 4 group map color 32,32,190 shortLabel Alt Haplotypes longLabel Alternate Haplotypes to Reference Sequence Correspondence url ../cgi-bin/hgTracks?db=$D&position=$$ urlLabel Corresponding position: track phyloPCons28way shortLabel 28-Way Base Cons compositeTrack on longLabel Basewise Conservation by PhyloP for 28-Species Multiz Align. spanList 1 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno priority 4 visibility hide altColor 70,130,70 color 0,90,20 type wig 0.0 2.87 viewLimits .2:1.6 track phyloP28wayPlacMammal parent phyloPCons28way shortLabel Mammal Cons longLabel Placental Mammal Basewise Conservation by PhyloP priority 1 track phyloP28way parent phyloPCons28way shortLabel Vertebrate Cons longLabel Vertebrate Basewise Conservation by PhyloP priority 2 track phastConsHq release alpha shortLabel 28-Way HQ compositeTrack on longLabel PhastCons Conservation: Species with high-quality assemblies spanList 1 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno visibility hide color 0, 10, 100 altColor 0,90,10 type wig 0.0 1.0 track phastCons28wayHq release alpha parent phastConsHq shortLabel Vertebrate longLabel Vertebrate HQ PhastCons Conservation (18 species) priority 2 track phastCons28wayHqPlacMammal release alpha parent phastConsHq shortLabel Plac Mammal longLabel Placental Mammal HQ PhastCons Conservation (8 species) priority 1 track multiz28way shortLabel 28-Way Cons longLabel Vertebrate Multiz Alignment & PhastCons Conservation (28 Species) irows on summary multiz28waySummary frames multiz28wayFrames wiggle phastCons28wayPlacMammal Mammal Placental_Mammal phastCons28way Vertebrate Vertebrate spanList 1 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno priority 5 visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 speciesCodonDefault hg18 speciesGroups Primate Placental_Mammal Vertebrate sGroup_Primate panTro2 rheMac2 otoGar1 sGroup_Placental_Mammal tupBel1 mm8 rn4 cavPor2 oryCun1 sorAra1 eriEur1 canFam2 felCat3 equCab1 bosTau3 dasNov1 loxAfr1 echTel1 sGroup_Vertebrate monDom4 ornAna1 anoCar1 galGal3 xenTro2 danRer4 tetNig1 fr2 gasAcu1 oryLat1 speciesDefaultOff panTro2 rn4 otoGar1 felCat3 loxAfr1 bosTau3 echTel1 danRer4 fr2 tetNig1 oryLat1 tupBel1 cavPor2 oryCun1 sorAra1 eriEur1 itemFirstCharCase noChange treeImage phylo/hg18_28way.gif track mostConserved28way compositeTrack on shortLabel 28-Way Most Cons longLabel PhastCons Conserved Elements, 28-way Vertebrate Multiz Alignment group compGeno priority 6 visibility hide exonArrows off showTopScorers 200 type bed 5 . track phastConsElements28wayPlacMammal parent mostConserved28way shortLabel Mammal longLabel PhastCons Placental Mammal Conserved Elements, 28-way Multiz Alignment color 100,50,170 priority 1 track phastConsElements28way parent mostConserved28way shortLabel Vertebrate longLabel PhastCons Vertebrate Conserved Elements, 28-way Multiz Alignment color 170,100,50 priority 2 track multiz17way shortLabel 17-Way Cons longLabel Vertebrate Multiz Alignment & Conservation (17 Species) group compGeno priority 2 visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 wiggle phastCons17way spanList 1 pairwiseHeight 12 yLineOnOff Off frames multiz17wayFrames irows on autoScale Off windowingFunction mean summary multiz17waySummary speciesGroups mammal vertebrate sGroup_mammal panTro1 rheMac2 mm8 rn4 oryCun1 canFam2 bosTau2 dasNov1 loxAfr1 echTel1 monDom4 sGroup_vertebrate galGal2 xenTro1 danRer3 tetNig1 fr1 speciesDefaultOff panTro1 rheMac2 bosTau2 echTel1 danRer3 fr1 treeImage phylo/hg17_17way.gif speciesCodonDefault hg18 track phastConsElements17way shortLabel 17-Way Most Cons longLabel PhastCons Conserved Elements, 17-way Vertebrate Multiz Alignment group compGeno priority 3 visibility hide exonArrows off showTopScorers 200 type bed 5 . track multiz6waySyn shortLabel Syn Conservation longLabel Vertebrate Multiz Alignment & Conservation (6 Species) using Syntenic Alignments group compGeno visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 #wiggle phastCons6way pairwiseHeight 12 spanList 1 yLineOnOff Off frames multiz6wayFrames irows on autoScale Off windowingFunction mean summary multiz6waySummary speciesGroups mammal sGroup_mammal panTro2 rheMac2 mm8 rn4 canFam2 #speciesDefaultOff #treeImage phylo/syn_6way.jpg speciesCodonDefault hg18 track rdmr shortLabel R-DMR longLabel Reprogrammed Differentially Methylated Regions group phenDis visibility hide color 0,20,150 type bed 4 track consIndelsHgMmCanFam shortLabel Cons Indels MmCf longLabel Indel-based Conservation for human hg18, mouse mm8 and dog canFam2 group compGeno priority 7 visibility hide useScore 1 color 0, 60, 120 type bed 5 . track stsMap override visibility hide #track fakeChromGraph #shortLabel Fake ChromGraph #longLabel Fake Nested Sine Wave ChromGraph Data #group phenDis #priority 151 #visibility hide #color 50,0, 175 #type chromGraph #maxHeightPixels 100:32:8 #maxGapToFill 20000 #linesAt 50,100,150 #minMax 0,200 #track fakeChromGraph2 #shortLabel Fake ChromGraph2 #longLabel Fake Nested Sine Wave ChromGraph Data 2 #group phenDis #priority 152 #visibility hide #color 30,70,75 #type chromGraph #maxHeightPixels 100:32:8 #maxGapToFill 20000 #minMax 0,200 #track fakeHomozygousity1 #shortLabel Fake Homozygousity #longLabel Fake Homozygousity Data #group phenDis #priority 153 #visibility hide #color 30,70,75 #type chromGraph #maxHeightPixels 100:32:8 #maxGapToFill 10000 #minMax 0,1 #track fakeHomozygousity2 #shortLabel Fake Homozygousity2 #longLabel Fake Homozygousity Data #group phenDis #priority 154 #visibility hide #color 30,70,75 #type chromGraph #maxHeightPixels 100:32:8 #maxGapToFill 10000 #minMax 0,1 track haplotypePos shortLabel $Organism hapPos longLabel $Organism Haplotype Position group varRep visibility hide type psl . track hapmapSnps override longLabel HapMap SNPs (rel27, merged Phase II + Phase III genotypes) dataVersion rel27 hapmapPhase III track hapmapSnpsPhaseII compositeTrack on shortLabel HapMap SNPs Old longLabel Outdated HapMap SNPs (rel22, Phase II genotypes) group varRep visibility hide type bed 6 + exonArrows off track hapmapSnpsCEUPhaseII parent hapmapSnpsPhaseII shortLabel HM r22 SNPs CEU longLabel Outdated HapMap SNPs from the CEU Population (Northern and Western European Ancestry in Utah, US - CEPH) priority 2 track hapmapSnpsCHBPhaseII parent hapmapSnpsPhaseII shortLabel HM r22 SNPs CHB longLabel Outdated HapMap SNPs from the CHB Population (Han Chinese in Beijing, China) priority 3 track hapmapSnpsJPTPhaseII parent hapmapSnpsPhaseII shortLabel HM r22 SNPs JPT longLabel Outdated HapMap SNPs from the JPT Population (Japanese in Tokyo, Japan) priority 6 track hapmapSnpsYRIPhaseII parent hapmapSnpsPhaseII shortLabel HM r22 SNPs YRI longLabel Outdated HapMap SNPs from the YRI Population (Yoruba in Ibadan, Nigeria) priority 11 track hapmapAllelesChimpPhaseII parent hapmapSnpsPhaseII shortLabel Chimp Alleles longLabel Outdated HapMap SNPs Orthologous Alleles from Chimp (panTro2) priority 100 track hapmapAllelesMacaquePhaseII parent hapmapSnpsPhaseII shortLabel Macaque Alleles longLabel Outdated HapMap SNPs Orthologous Alleles from Macaque (rheMac2) priority 101 track hapmapLd compositeTrack on shortLabel HapMap LD Unph. longLabel HapMap Linkage Disequilibrium - Phase II - from unphased genotypes group varRep visibility hide canPack off chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX dataVersion HapMap release 22 type ld2 track hapmapLdYri parent hapmapLd shortLabel Unphased YRI longLabel Linkage Disequilibrium for the Yoruba (YRI) from unphased genotypes priority 1 track hapmapLdCeu parent hapmapLd shortLabel Unphased CEU longLabel Linkage Disequilibrium for the CEPH (CEU) from unphased genotypes priority 2 track hapmapLdChbJpt parent hapmapLd shortLabel Unph JPT+CHB longLabel LD for the Han Chinese + Japanese from Tokyo (JPT+CHB) from unphased genotypes priority 5 track hapmapRecombRateBW shortLabel Hapmap Recomb BW longLabel BigWig - Hapmap Recombination Rate (phase II, release 22) - BigWig group varRep visibility hide type bigWig 0 90.6690141023 #viewLimits 0 90 -- ignored for bigWig! autoScale Off maxHeightPixels 128:32:11 track hapmapRecombRate shortLabel Hapmap Recomb longLabel Hapmap Recombination Rate (phase II, release 22) group varRep visibility hide type bedGraph 4 minLimit 0 maxLimit 90.6690141023 autoScale Off maxHeightPixels 128:32:11 track tajdSnp override longLabel Tajima's D SNPs (from Human May 2004 assembly) track tajdSnpAd override longLabel SNPs from African Descent used for Tajima's D (from Human May 2004 assembly) track tajdSnpEd override longLabel SNPs from European Descent used for Tajima's D (from Human May 2004 assembly) track tajdSnpXd override longLabel SNPs from Chinese Descent used for Tajima's D (from Human May 2004 assembly) track tajD override longLabel Tajima's D (from Human May 2004 assembly) track tajdAd override longLabel Tajima's D from African Descent (from Human May 2004 assembly) track tajdEd override longLabel Tajima's D from European Descent (from Human May 2004 assembly) track tajdXd override longLabel Tajima's D from Chinese Descent (from Human May 2004 assembly) track ucscRetroAli1 shortLabel Retroposed Genes longLabel Retroposed GenesV1, Including Pseudogenes - November 2010 group genes type psl color 20,0,250 visibility hide nextItemButton on ucscRetroInfo ucscRetroInfo1 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds baseColorUseSequence extFile ucscRetroSeq ucscRetroExtFile indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 searchName ucscRetroInfoRefSeq1 searchTable ucscRetroAli1 searchDescription Retroposed GenesV1, Including Pseudogenes - November 2010 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo1 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo1.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna1 searchTable ucscRetroAli1 searchDescription Retroposed GenesV1, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt1 searchTable ucscRetroAli1 searchDescription Retroposed GenesV1, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo1 xrefQuery select ucscRetroInfo1.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene1 searchTable ucscRetroAli1 searchDescription Retroposed GenesV1, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo1 xrefQuery select ucscRetroInfo1.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track knownGeneOld3 shortLabel Old UCSC Genes longLabel Previous Version of UCSC Genes group genes visibility hide color 82,82,160 type genePred hgsid on oldToNew kg3ToKg4 baseColorUseCds given baseColorDefault genomicCodons -# Overrides for track pgSnp: - track pgKb1Comb override - pgSiftPredTab pgKb1Sift - pgPolyphenPredTab pgPolyKb1 - - track pgNb1 override - pgSiftPredTab pgNb1Sift - pgPolyphenPredTab pgPolyNb1 - - track pgMd8 override - pgSiftPredTab pgMd8Sift - pgPolyphenPredTab pgPolyMd8 - - track pgTk1 override - pgSiftPredTab pgTk1Sift - pgPolyphenPredTab pgPolyTk1 - - track pgAbtSolid override - pgSiftPredTab pgAbtSift - pgPolyphenPredTab pgPolyAbt - track pgPop compositeTrack on shortLabel Pop Vars longLabel Population Genome Variants group varRep visibility hide color 0,153,0 type bed 4 + track pgPopYRI parent pgPop shortLabel YRI variants longLabel YRI variants from the 1000 genomes low coverage data group varRep priority 1 track pgPopCEU parent pgPop shortLabel CEU variants longLabel CEU variants from the 1000 genomes low coverage data group varRep priority 2 track pgPopJPTCHB parent pgPop shortLabel JPTCHB variants longLabel JPT and CHB variants from the 1000 genomes low coverage data group varRep priority 3 track augustus #replaces record augustus in parent dir missing/extra color compositeTrack on shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility hide type genePred cdsDrawDefault genomic\ codons baseColorUseCds given baseColorDefault genomicCodons track augustusHints parent augustus shortLabel Augustus Hints longLabel Augustus Gene Predictions Using Hints priority 1 color 139,0,0 track augustusXRA parent augustus shortLabel Augustus De Novo longLabel Augustus De Novo Gene Predictions priority 2 color 180,0,0 track augustusAbinitio parent augustus shortLabel Augustus Ab Initio longLabel Augustus Ab Initio Gene Predictions priority 3 color 255,0,0 searchTable augustusHints searchType genePred termRegex g[0-9]+\.t[0-9]+ searchPriority 50 searchTable augustusXRA searchType genePred termRegex g[0-9]+\.t[0-9]+ searchPriority 50 searchTable augustusAbinitio searchType genePred termRegex g[0-9]+\.t[0-9]+ searchPriority 50 track nscan compositeTrack on shortLabel N-SCAN longLabel N-SCAN Gene Predictions group genes visibility hide type genePred baseColorUseCds given baseColorDefault genomicCodons track nscanPasaGene parent nscan shortLabel N-SCAN PASA-EST longLabel N-SCAN PASA-EST Gene Predictions color 34,139,34 priority 1 track nscanGene #replaces record nscanGene in parent dir missing/extra group,visibility,type,baseColorUseCds,baseColorDefault,informant parent nscan shortLabel N-SCAN longLabel N-SCAN Gene Predictions color 84,119,34 priority 2 searchTable nscanGene searchType genePred termRegex (chr)?.*\.[0-9]+\.[0-9]+\.[a-z]+ searchPriority 50 searchTable nscanPasaGene searchType genePred termRegex (chr)?.*\.[0-9a-z]+\.[0-9]+\.[a-z]+ searchPriority 50 track phastConsElements override longLabel PhastCons Conserved Elements, Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish track gap override visibility hide track exaptedRepeats shortLabel Exapted Repeats longLabel Repeats Exapted as Conserved Non-Exonic Elements group varRep visibility hide color 255, 127, 0 type bed 4 + searchTable exaptedRepeats searchMethod exact searchType bed searchPriority 11 termRegex exap[0-9]+ track chainTetNig1 override matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 matrixHeader A, C, G, T track chainEchTel1 override shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 251.1 visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 type chain echTel1 otherDb echTel1 track netEchTel1 override shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 251.2 visibility hide spectrum on type netAlign echTel1 chainEchTel1 otherDb echTel1 track chainDasNov1 override shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 255.1 visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 type chain dasNov1 otherDb dasNov1 track netDasNov1 override shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 255.2 visibility hide spectrum on type netAlign dasNov1 chainDasNov1 otherDb dasNov1 track netEquCab1 override shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno visibility hide spectrum on type netAlign equCab1 chainEquCab1 otherDb equCab1 track chainOrnAna0 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 256.5 visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 matrixHeader A, C, G, T type chain ornAna0 otherDb ornAna0 track chainOryCun1 override shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 259.5 visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 matrixHeader A, C, G, T type chain oryCun1 otherDb oryCun1 track netOryCun1 override shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 259.6 visibility hide spectrum on type netAlign oryCun1 chainOryCun1 otherDb oryCun1 track chainPonAbe0 shortLabel chainPonAbe0 longLabel chainPonAbe0 group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain ponAbe0 otherDb ponAbe0 track netHomIni13 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 301 visibility hide spectrum on type netAlign homIni13 chainHomIni13 otherDb homIni13 track chainHomNea0 shortLabel Neandertal Chain longLabel Neandertal Chain group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain homNea0 otherDb homNea0 track chainHomIni13 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 300 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain homIni13 otherDb homIni13 track chainMapHomIni14 shortLabel $o_Organism Map longLabel $o_Organism ($o_date) Mapping Chain group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain homIni14 otherDb homIni14 track chainMapHomIni13 shortLabel $o_Organism Map longLabel $o_Organism ($o_date) Mapping Chain group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain homIni13 otherDb homIni13 track cnp compositeTrack on shortLabel Structural Var longLabel Structural Variation group varRep visibility hide type bed 4 + track delConrad2 parent cnp shortLabel Conrad Dels longLabel Deletions from Genotype Analysis (Conrad) noInherit on type bed 8 . priority 1 track delHinds2 parent cnp shortLabel Hinds Dels longLabel Deletions from Haploid Hybridization Analysis (Hinds) noInherit on type bed 4 + priority 2 track cnpIafrate2 parent cnp shortLabel Iafrate CNPs longLabel Copy Number Polymorphisms from BAC Microarray Analysis (Iafrate) noInherit on type bed 4 + priority 3 track cnpLocke parent cnp shortLabel Locke CNPs longLabel Copy Number Polymorphisms from BAC Microarray Analysis (Locke) noInherit on type bed 4 + priority 4 track delMccarroll parent cnp shortLabel McCarroll Dels longLabel Deletions from Genotype Analysis (McCarroll) noInherit on type bed 4 . priority 5 track cnpRedon parent cnp shortLabel Redon CNPs longLabel Copy Number Polymorphisms from SNP and BAC microarrays (Redon) noInherit on type bed 6 . priority 6 track cnpSebat2 parent cnp shortLabel Sebat CNPs longLabel Copy Number Polymorphisms from ROMA (Sebat) noInherit on type bed 4 + priority 7 track cnpSharp2 parent cnp shortLabel Sharp CNPs longLabel Copy Number Polymorphisms from BAC Microarray Analysis (Sharp) noInherit on type bed 4 + priority 8 track cnpTuzun parent cnp shortLabel Tuzun Fosmids longLabel Structural Variation identified by Fosmids (Tuzun) noInherit on type bed 4 . priority 9 track chainSelf override longLabel $Organism Chained Self Alignments chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrM,chrX,chrY,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22 chainColor Normalized Score chainNormScoreAvailable yes 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 hg18 otherDb hg18 group varRep track netSelf shortLabel Self Net longLabel $Organism Chained Self Alignment Net group varRep priority 401 visibility hide spectrum on type netAlign hg18 chainSelf otherDb hg18 track chainSelf2K shortLabel Self 2K Chain longLabel $Organism Chained Self Alignments, chainMinScore=2,000 group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrM,chrX,chrY,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22 color 100,50,0 altColor 255,240,200 chainColor Normalized Score chainNormScoreAvailable yes spectrum on 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 hg18 otherDb hg18 track monDom4PileUp shortLabel monDom4 Pile Ups longLabel Pile Ups of Opossum chains to Hg18 group x visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Maximum color 0,0,0 altColor 128,128,128 viewLimits 0:4000 spanList 1 type wig 0 10310 track evofold override mafTrack multiz17way origAssembly hg17 track evofoldV2 shortLabel EvoFold v.2 longLabel EvoFold v.2 Predictions of RNA Secondary Structure group genes visibility hide color 20,90,0 type bed 6 + mafTrack multiz44way track ncRna shortLabel Ensembl Noncoding longLabel Ensembl Noncoding Genes group genes color 150,0,0 visibility hide type bed 8 + urlLabel Ensembl Non-Coding Gene: url https://www.ensembl.org/Homo_sapiens/geneview?gene=$$ track polyA release alpha compositeTrack on shortLabel Poly(A) longLabel Poly(A) Sites, Both Reported and Predicted group rna visibility hide noInherit on type bed 3 . track polyaDb release alpha parent polyA shortLabel PolyA_DB longLabel Reported Poly(A) Sites from PolyA_DB color 51,153,51 priority 1 type bed 4 . track polyaPredict release alpha parent polyA shortLabel Poly(A) SVM longLabel Predicted Poly(A) Sites Using an SVM color 102,0,153 priority 2 type bed 8 . track polyA release beta,public compositeTrack on shortLabel Poly(A) longLabel Poly(A) Sites, Both Reported and Predicted group rna visibility hide type bed 8 . track polyaDb release beta,public parent polyA shortLabel PolyA_DB longLabel Reported Poly(A) Sites from PolyA_DB color 51,153,51 priority 1 track polyaPredict release beta,public parent polyA shortLabel Poly(A) SVM longLabel Predicted Poly(A) Sites Using an SVM color 102,0,153 priority 2 track fantomCageGraphTop compositeTrack on shortLabel Fantom 4 CAGE longLabel Fantom and Riken 4 CAGE group rna visibility hide minLimit 0 maxLimit 1000 type bed 3 autoScale Off noInherit on subGroup1 view Views SIG=Clusters BED=Reads #dragAndDrop subtracks allButtonPair on track fantomCageGraphTopViewSIG shortLabel Clusters view SIG visibility full parent fantomCageGraphTop viewLimits 0.0:1.0 minLimit 0 maxLimit 1 autoScale Off windowingFunction mean maxHeightPixels 128:32:16 track FantomCageForwardPowerLawGraph parent fantomCageGraphTopViewSIG shortLabel Fantom 4 + CAGE longLabel Forward Fantom/Riken 4 CAGE subGroups view=SIG priority 2 minLimit 0 maxLimit 1000 type bedGraph 4 configurable on color 43,51,109 track FantomCageReversePowerLawGraph parent fantomCageGraphTopViewSIG shortLabel Fantom 4 - CAGE longLabel Reverse Fantom/Riken 4 CAGE subGroups view=SIG priority 3 minLimit 0 maxLimit 1000 type bedGraph 4 configurable on color 43,51,109 track fantomCageGraphTopViewBED shortLabel Reads view BED visibility squish parent fantomCageGraphTop track FantomCageBedForward parent fantomCageGraphTopViewBED shortLabel Fantom (+) CAGE longLabel Fantom/Riken CAGE Reads Forward subGroups view=BED priority 7 configurable on useScore 1 bedFilter on exonArrows off type bed 12 . track FantomCageBedReverse parent fantomCageGraphTopViewBED shortLabel Fantom (-) CAGE longLabel Fantom/Riken CAGE Reads Reverse subGroups view=BED priority 8 configurable on useScore 1 exonArrows off bedFilter on type bed 12 . track tfbsConsSites shortLabel TFBS Conserved longLabel HMR Conserved Transcription Factor Binding Sites group regulation visibility hide type bed 6 + scoreMin 685 scoreMax 1000 spectrum on urlLabel Transfac matrix link: url http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/getTF.cgi?AC=$$ track genotypeArrays shortLabel Agilent Array longLabel Agilent Microarray Probesets compositeTrack on group varRep visibility hide noScoreFilter . type bed 6 . track agilentCgh1x1m parent genotypeArrays shortLabel Ag CGH 1x1m longLabel Agilent SurePrint G3 Human CGH Microarray 1x1M AMADID 021529 color 0,128,0 priority 1 track agilentHrd1x1m parent genotypeArrays shortLabel Ag HRD 1x1m longLabel Agilent SurePrint G3 Human High-Resolution Microarray 1x1M AMADID 023642 color 255,128,0 priority 2 track agilentCgh2x400k parent genotypeArrays shortLabel Ag CGH 2x400k longLabel Agilent SurePrint G3 Human CGH Microarray 2x400K AMADID 021850 color 0,128,0 priority 3 track agilentCgh4x180k parent genotypeArrays shortLabel Ag CGH 4x180k longLabel Agilent SurePrint G3 Human CGH Microarray 4x180K AMADID 022060 color 255,128,0 priority 4 track agilentCgh8x60k parent genotypeArrays shortLabel Ag CGH 8x60k longLabel Agilent SurePrint G3 Human CGH Microarray 8x60K AMADID 021924 color 0,128,0 priority 5 track agilentCgh244a parent genotypeArrays shortLabel Ag CGH 1x244k longLabel Agilent SurePrint HD Human CGH Microarray 1x244K AMADID 014693 color 255,128,0 priority 6 track agilentCgh105a parent genotypeArrays shortLabel Ag CGH 2x105k longLabel Agilent SurePrint HD Human CGH Microarray 2x105K AMADID 014698 color 0,128,0 priority 7 track agilentCgh44k parent genotypeArrays shortLabel Ag CGH 4x44k longLabel Agilent SurePrint HD Human CGH Microarray 4x44K AMADID 014950 color 255,128,0 priority 8 track targetScanS shortLabel TS miRNA sites longLabel TargetScan miRNA Regulatory Sites group regulation visibility hide color 0,96,0 scoreFilterMax 100 type bed 6 . urlLabel TargetScan link: url https://www.targetscan.org/cgi-bin/targetscan/vert_40/view_gene.cgi?gs=$P&taxid=9606&members=$p&showcnc=1 # Uppsala University, Sweden ChIP-chip supertrack track uppsalaChipSuper superTrack on shortLabel Uppsala ChIP longLabel Uppsala University ChIP-chip group regulation track uppsalaChipSignal superTrack uppsalaChipSuper dense compositeTrack on shortLabel UU ChIP Signal longLabel Uppsala University ChIP-chip Signal group regulation visibility hide type wig -1.9 4.23 spanList 1 maxHeightPixels 128:16:16 windowingFunction maximum viewLimits .5:1.5 autoScale off origAssembly hg16 track uppsalaChipH3acSignal parent uppsalaChipSignal shortLabel UU H3ac Signal longLabel Uppsala University ChIP-chip Signal (H3ac) color 150,50,50 priority 1 track uppsalaChipUsf1Signal parent uppsalaChipSignal shortLabel UU Usf1 Signal longLabel Uppsala University ChIP-chip Signal (Usf1) color 50,50,150 priority 2 track uppsalaChipUsf2Signal parent uppsalaChipSignal shortLabel UU Usf2 Signal longLabel Uppsala University ChIP-chip Signal (Usf2) color 50,150,50 priority 3 track uppsalaChipSites superTrack uppsalaChipSuper dense compositeTrack on shortLabel UU ChIP Sites longLabel Uppsala University ChIP-chip Sites group regulation type bed 3 track uppsalaChipH3acSites parent uppsalaChipSites shortLabel UU H3ac Sites longLabel Uppsala University ChIP-chip Sites (H3ac) color 150,50,50 priority 1 track uppsalaChipUsf1Sites parent uppsalaChipSites shortLabel UU Usf1 Sites longLabel Uppsala University ChIP-chip Sites (Usf1) color 50,50,150 priority 2 track uppsalaChipUsf2Sites parent uppsalaChipSites shortLabel UU Usf2 Sites longLabel Uppsala University ChIP-chip Sites (Usf2) color 50,150,50 priority 3 # AFFY TRANSCRIPTOME SUPERTRACK track affyTxnPhase3Super superTrack on shortLabel Affy Txn longLabel Affy Transcriptome Phase 3 group expression track affyTxnPhase3FragsL superTrack affyTxnPhase3Super dense compositeTrack on shortLabel Affy Tx lRNA Reg longLabel Affymetrix Transcriptome Phase 3 Long RNA Fragments group expression origAssembly hg17 type bed 3 . track affyTxnPhase3FragsHDF parent affyTxnPhase3FragsL shortLabel HDF lRNA longLabel Affymetrix HDF Long RNA (Cytosolic) Fragments priority 1 track affyTxnPhase3FragsHeLaCyto parent affyTxnPhase3FragsL shortLabel HeLa Cyto lRNA longLabel Affymetrix HeLa Long RNA (Cytosolic) Fragments priority 2 track affyTxnPhase3FragsHeLaNuclear parent affyTxnPhase3FragsL shortLabel HeLa Nucl lRNA longLabel Affymetrix HeLa Long RNA (Nuclear) Fragments priority 3 track affyTxnPhase3FragsHepG2Cyto parent affyTxnPhase3FragsL shortLabel HepG2 Cyto lRNA longLabel Affymetrix HepG2 Long RNA (Cytosolic) Fragments priority 4 track affyTxnPhase3FragsHepG2Nuclear parent affyTxnPhase3FragsL shortLabel HepG2 Nucl lRNA longLabel Affymetrix HepG2 Long RNA (Nuclear) Fragments priority 5 track affyTxnPhase3FragsJurkat parent affyTxnPhase3FragsL shortLabel Jurkat lRNA longLabel Affymetrix Jurkat Long RNA (Cytosolic) Fragments priority 6 track affyTxnPhase3FragsNCCIT parent affyTxnPhase3FragsL shortLabel NCCIT lRNA longLabel Affymetrix NCCIT Long RNA (Cytosolic) Fragments priority 7 track affyTxnPhase3FragsPC3 parent affyTxnPhase3FragsL shortLabel PC3 lRNA longLabel Affymetrix PC3 Long RNA (Cytosolic) Fragments priority 8 track affyTxnPhase3FragsSK_N_AS parent affyTxnPhase3FragsL shortLabel SK-N-AS lRNA longLabel Affymetrix SK-N-AS Long RNA (Cytosolic) Fragments priority 9 track affyTxnPhase3FragsU87MG parent affyTxnPhase3FragsL shortLabel U87MG lRNA longLabel Affymetrix U87MG Long RNA (Cytosolic) Fragments priority 10 track affyTxnPhase3L superTrack affyTxnPhase3Super dense compositeTrack on shortLabel Affy Tx lRNA Sig longLabel Affymetrix Transcriptome Phase 3 Long RNA Signal group expression viewLimits 0:150 autoScale Off origAssembly hg17 maxHeightPixels 100:30:10 canPack off type wig 0 1000 track affyTxnPhase3HDF shortLabel HDF lRNA parent affyTxnPhase3L longLabel Affymetrix HDF Long RNA (Cytosolic) Signal priority 1 track affyTxnPhase3HeLaCyto shortLabel HeLa Cyto lRNA parent affyTxnPhase3L longLabel Affymetrix HeLa Long RNA (Cytosolic) Signal priority 2 track affyTxnPhase3HeLaNuclear shortLabel HeLa Nucl lRNA parent affyTxnPhase3L longLabel Affymetrix HeLa Long RNA (Nuclear) Signal priority 3 track affyTxnPhase3HepG2Cyto shortLabel HepG2 Cyto lRNA parent affyTxnPhase3L longLabel Affymetrix HepG2 Long RNA (Cytosolic) Signal priority 4 track affyTxnPhase3HepG2Nuclear shortLabel HepG2 Nucl lRNA parent affyTxnPhase3L longLabel Affymetrix HepG2 Long RNA (Nuclear) Signal priority 5 track affyTxnPhase3Jurkat shortLabel Jurkat lRNA parent affyTxnPhase3L longLabel Affymetrix Jurkat Long RNA (Cytosolic) Signal priority 6 track affyTxnPhase3NCCIT shortLabel NCCIT lRNA parent affyTxnPhase3L longLabel Affymetrix NCCIT Long RNA (Cytosolic) Signal priority 7 track affyTxnPhase3PC3 shortLabel PC3 lRNA parent affyTxnPhase3L longLabel Affymetrix PC3 Long RNA (Cytosolic) Signal priority 8 track affyTxnPhase3SK_N_AS shortLabel SK-N-AS lRNA parent affyTxnPhase3L longLabel Affymetrix SK-N-AS Long RNA (Cytosolic) Signal priority 9 track affyTxnPhase3U87MG shortLabel U87MG lRNA parent affyTxnPhase3L longLabel Affymetrix U87MG Long RNA (Cytosolic) Signal priority 10 track affyTxnPhase3FragsS superTrack affyTxnPhase3Super dense compositeTrack on shortLabel Affy Tx sRNA Reg longLabel Affymetrix Transcriptome Phase 3 Short RNA Fragments group expression origAssembly hg17 type bed 3 . track affyTxnPhase3FragsHeLaTopStrand parent affyTxnPhase3FragsS shortLabel HeLa + sRNA longLabel Affymetrix HeLa Plus Strand Short RNA (Whole Cell) Fragments priority 1 track affyTxnPhase3FragsHeLaBottomStrand parent affyTxnPhase3FragsS shortLabel HeLa - sRNA longLabel Affymetrix HeLa Minus Strand Short RNA (Whole Cell) Fragments priority 2 track affyTxnPhase3FragsHepG2TopStrand parent affyTxnPhase3FragsS shortLabel HepG2 + sRNA longLabel Affymetrix HepG2 Plus Strand Short RNA (Whole Cell) Fragments priority 3 track affyTxnPhase3FragsHepG2BottomStrand parent affyTxnPhase3FragsS shortLabel HepG2 - sRNA longLabel Affymetrix HepG2 Minus Strand Short RNA (Whole Cell) Fragments priority 4 track affyTxnPhase3S compositeTrack on superTrack affyTxnPhase3Super dense shortLabel Affy Tx sRNA Sig longLabel Affymetrix Transcriptome Phase 3 Short RNA Signal group expression viewLimits 0:150 autoScale Off origAssembly hg17 maxHeightPixels 100:30:10 canPack off type wig 0 1000 track affyTxnPhase3HeLaTopStrand shortLabel HeLa + sRNA parent affyTxnPhase3S longLabel Affymetrix Hela Plus Strand Short RNA (Whole Cell) Signal priority 1 track affyTxnPhase3HeLaBottomStrand shortLabel HeLa - sRNA parent affyTxnPhase3S longLabel Affymetrix Hela Minus Strand Short RNA (Whole Cell) Signal priority 2 track affyTxnPhase3HepG2TopStrand shortLabel HepG2 + sRNA parent affyTxnPhase3S longLabel Affymetrix HepG2 Plus Strand Short RNA (Whole Cell) Signal priority 3 track affyTxnPhase3HepG2BottomStrand shortLabel HepG2 - sRNA parent affyTxnPhase3S longLabel Affymetrix HepG2 Minus Strand Short RNA (Whole Cell) Signal priority 4 track ceuBcellComposite compositeTrack on shortLabel B-Cell Transcriptome longLabel B-Cell Transcriptome (RNA-Seq) group expression visibility hide noInherit on autoScale on html ceuBcellRNASeq type bed 3 track ceuBcellRNASeqBW parent ceuBcellComposite shortLabel B-Cell Coverage longLabel B-Cell RNA-Seq Coverage priority 1 type bigWig 0 716249 configurable on autoScale on html ceuBcellRNASeq maxHeightPixels 200:100:20 track ceuBcellRNASeq parent ceuBcellComposite shortLabel B-Cell Junctions longLabel B-Cell RNA-Seq Junctions configurable on html ceuBcellRNASeq priority 2 type bed 12 track stanfordNRSFSites shortLabel Stanf NRSF Sites longLabel Stanford Neuron-Restrictive Silencer Factor (NRSF/REST) ChIP-seq Sites group regulation chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY,chrM visibility hide type bed 3 . origAssembly hg17 dataVersion March 2007 track stanfordNRSFOverlaps compositeTrack on shortLabel Stanf NRSF Counts longLabel Stanford Neuron-Restrictive Silencer Factor (NRSF/REST) ChIP-seq Counts group regulation chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY,chrM type wig 1 915 viewLimits 1:26 spanList 1 origAssembly hg17 dataVersion March 2007 track stanfordNRSFEnrichedOverlaps parent stanfordNRSFOverlaps shortLabel Stanf NRSF longLabel Stanford NRSF/REST Enriched Counts priority 1 color 0,128,0 track stanfordNRSFControlOverlaps parent stanfordNRSFOverlaps shortLabel Stanf Control longLabel Stanford NRSF/REST Control Counts priority 2 color 0,128,0 track stanfordNRSF compositeTrack on shortLabel Stanf NRSF Tags longLabel Stanford Neuron-Restrictive Silencer Factor (NRSF/REST) ChIP-seq Tags group regulation itemRgb on chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY,chrM type bed 9 . origAssembly hg17 dataVersion March 2007 track stanfordNRSFEnriched parent stanfordNRSF shortLabel Stanf NRSF longLabel Stanford NRSF/REST Enriched Tags priority 1 color 0,128,0 track stanfordNRSFControl parent stanfordNRSF shortLabel Stanf Control longLabel Stanford NRSF/REST Control Tags priority 2 color 0,128,0 track uc16 override longLabel Ultraconserved Elements (200 bp 100% ID in Rat/Mouse/Human) track ux16 override longLabel Extended Ultraconserved Elements (Until 5 Bases Below 85%) color 200,0,0 track hars shortLabel Human Accelerated longLabel Human Accelerated Regions group compGeno visibility hide exonArrows off color 0,0,150 type bed 6 . searchTable hars searchMethod exact searchType bed searchPriority 10 termRegex har[0-9]+ track snp130BadApples compositeTrack on shortLabel Bad Apples (130) longLabel SNPs from dbSNP that overlap regions masked by 1000 Genomes pilot group varRep type bed 6 + exonArrows off url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: track snp130BadApplesDepth parent snp130BadApples shortLabel Depth longLabel SNPs that overlap 1000 Genomes pilot high-read-depth masked regions color 180,0,0 track snp130BadApplesMapQ parent snp130BadApples shortLabel Mapping Qual longLabel SNPs that overlap 1000 Genomes pilot low-mapping-quality masked regions color 224,108,108 track snp130BadApplesUncov parent snp130BadApples shortLabel No Coverage longLabel SNPs that overlap 1000 Genomes pilot no-read-coverage regions color 150,150,150 track snp130BadApplesUnion parent snp130BadApples shortLabel Union longLabel SNPs that overlap union of 1000 Genomes pilot masked regions track snp130 override chimpOrangMacOrthoTable snp130OrthoPt2Pa2Rm2 chimpDb panTro2 orangDb ponAbe2 macaqueDb rheMac2 hapmapPhase III codingAnnotations snp130CodingDbSnp, codingAnnoLabel_snp130CodingDbSnp dbSNP configureByPopup off tableBrowser noGenome priority 2 track snp129 override visibility hide chimpOrangMacOrthoTable snp129OrthoPt2Pa2Rm2 chimpDb panTro2 orangDb ponAbe2 macaqueDb rheMac2 hapmapPhase III tableBrowser noGenome configureByPopup off track snp128 override visibility hide chimpMacaqueOrthoTable snp128OrthoPanTro2RheMac2 chimpDb panTro2 macaqueDb rheMac2 tableBrowser noGenome configureByPopup off track snp127 override visibility hide snpSeq snp127Seq tableBrowser noGenome configureByPopup off track snp126 override visibility hide chimpMacaqueOrthoTable snp126orthoPanTro2RheMac2 chimpDb panTro2 macaqueDb rheMac2 tableBrowser noGenome configureByPopup off track divMKAR shortLabel Recent Selection NC longLabel Recent selection in non-coding regions compositeTrack on group varRep visibility hide yLineOnOff Off subGroup1 specRec Species_reckoned_with ch=chimp or=orangutan type wig track divChimpRpd parent divMKAR shortLabel log2 r_pd longLabel log2 (r_pd) divergence from chimp subGroups specRec=ch color 200,100,0 altColor 0,0,250 priority 1 track divChimpFet parent divMKAR shortLabel -log10 p-value longLabel -log10 (p-value) divergence from chimp subGroups specRec=ch priority 2 track divChimpFdr parent divMKAR shortLabel -log10 FDR longLabel -log10 (FDR) divergence from chimp subGroups specRec=ch noInherit on type wig yLineOnOff On yLineMark 1.0 maxHeightPixels 128:64:11 color 25,150,25 priority 3 track divChimpRpd129 parent divMKAR shortLabel dbSNP129 log2 r_pd longLabel dbSNP129 log2 (r_pd) divergence from chimp subGroups specRec=ch color 200,100,0 altColor 0,0,250 priority 7 track divChimpFet129 parent divMKAR shortLabel dbSNP129 -log10 p-value longLabel dbSNP129 -log10 (p-value) divergence from chimp subGroups specRec=ch priority 8 track divChimpFdr129 parent divMKAR shortLabel dbSNP129 -log10 FDR longLabel dbSNP129 -log10 (FDR) divergence from chimp subGroups specRec=ch noInherit on type wig yLineOnOff On yLineMark 1.0 maxHeightPixels 128:64:11 color 25,150,25 priority 9 track divChimpRpdPg8 parent divMKAR shortLabel pgSnp8 log2 r_pd longLabel 8 Personal Genomes log2 (r_pd) divergence from chimp subGroups specRec=ch color 200,100,0 altColor 0,0,250 priority 10 track divChimpFetPg8 parent divMKAR shortLabel pgSnp8 -log10 p-value longLabel 8 Personal Genomes -log10 (p-value) divergence from chimp subGroups specRec=ch priority 11 track divChimpFdrPg8 parent divMKAR shortLabel pgSnp8 -log10 FDR longLabel 8 Personal Genomes -log10 (FDR) divergence from chimp subGroups specRec=ch noInherit on type wig yLineOnOff On yLineMark 1.0 maxHeightPixels 128:64:11 color 25,150,25 priority 12 track divChimpRpdPg8plus parent divMKAR shortLabel pg8+ log2 r_pd longLabel 8+ Personal Genomes log2 (r_pd) divergence from chimp subGroups specRec=ch color 200,100,0 altColor 0,0,250 priority 13 track divChimpFetPg8plus parent divMKAR shortLabel pg8+ -log10 p-value longLabel 8+ Personal Genomes -log10 (p-value) divergence from chimp subGroups specRec=ch priority 14 track divChimpFdrPg8plus parent divMKAR shortLabel pg8+ -log10 FDR longLabel 8+ Personal Genomes -log10 (FDR) divergence from chimp subGroups specRec=ch noInherit on type wig yLineOnOff On yLineMark 1.0 maxHeightPixels 128:64:11 color 25,150,25 priority 15 track divOrangRpdPg8plus parent divMKAR shortLabel pg8+ log2 r_pd longLabel 8+ Personal Genomes log2 (r_pd) divergence from orangutan subGroups specRec=or color 200,100,0 altColor 0,0,250 priority 16 track divOrangFetPg8plus parent divMKAR shortLabel pg8+ -log10 p-value longLabel 8+ Personal Genomes -log10 (p-value) divergence from orangutan subGroups specRec=or priority 17 track divOrangFdrPg8plus parent divMKAR shortLabel pg8+ -log10 FDR longLabel 8+ Personal Genomes -log10 (FDR) divergence from orangutan subGroups specRec=or noInherit on type wig yLineOnOff On yLineMark 1.0 maxHeightPixels 128:64:11 color 25,150,25 priority 18 track vsigMaf shortLabel VSIG MAF longLabel VSIG MAF (built with atoms) group x visibility hide color 0, 10, 100 altColor 1,128,0 type wigMaf 0.0 1.0 irows on speciesOrder mm8 rn4 canFam2 track chainMm8WM shortLabel Mm8 Chain WM longLabel $o_Organism ($o_date) Chained Alignments - Window Masker masked group x visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 matrixHeader A, C, G, T type chain mm8 otherDb mm8 track netMm8WM shortLabel Mm8 Net WM longLabel $o_Organism ($o_date) Alignment Net - Window Masker masked group x visibility hide spectrum on type netAlign mm8 chainMm8WM otherDb mm8 track chainOrnAna1Pre shortLabel ornAna1Pre Chain longLabel $o_Organism ($o_db pre-release) Chained Alignments group compGeno priority 185.2 visibility hide color 100,50,0 altColor 255,240,200 spectrum on matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 matrixHeader A, C, G, T type chain ornAna1 otherDb ornAna1 track netOrnAna1Pre shortLabel ornAna1Pre Net longLabel $o_Organism ($o_db pre-release) Alignment Net group compGeno priority 185.3 visibility hide spectrum on type netAlign ornAna1 chainOrnAna1Pre otherDb ornAna1 track atomHomIni20_1 shortLabel atomHomIni20_1 longLabel atomHomIni20_1 (ponAbe2=green,homIni20=blue,homPan20=brick,panTro2=dk blue,hg18=dk green) group x visibility hide type bed 6 track chainHomPan20 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 300 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain homPan20 otherDb homPan20 track atom13480779 shortLabel atom13480779 longLabel atom13480779 (canFam2=orange,mm8=green,rn4=blue,rheMac2=brick,panTro2=dk blue,hg18=dk green) group x visibility hide type bed 6 track atom97565 shortLabel atom97565 longLabel atom97565 (canFam2=orange,mm8=green,rn4=blue,rheMac2=brick,panTro2=dk blue,hg18=dk green) group x visibility hide type bed 6 track atom992 shortLabel atom992 longLabel atom992 (canFam2=orange,mm8=green,rn4=blue,rheMac2=brick,panTro2=dk blue,hg18=dk green) group x visibility hide type bed 6 track reTraceStacks shortLabel Trace Stacks longLabel Re-sequencing trace pileups group x visibility hide type wig 1 7960 viewLimits 1:500 autoScale off track multizMetazoan shortLabel Metazoan Maf longLabel Metazoan Multiz Alignment (4 species: hg18, ce3, dm2, ci2) group x visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 #wiggle phastCons6way pairwiseHeight 12 spanList 1 yLineOnOff Off # frames multizFrames # irows on autoScale Off windowingFunction mean summary multizMetazoanSummary speciesOrder ci2 dm2 ce3 # speciesGroups # sGroup_mammal panTro2 rheMac2 mm8 rn4 canFam2 # speciesDefaultOff # treeImage phylo/syn_6way.jpg # speciesCodonDefault hg18 track jkTestChipData shortLabel Factor/Source longLabel Test of Unified Factor/Source Type Display group x visibility hide type factorSource sourceTable jkTestChipExps track jkTestYaleData shortLabel Yale Unified TF longLabel Test of Unified Yale Factor/Source Type Display group x visibility hide type factorSource sourceTable jkTestYaleExps track jkgInputRefSeq shortLabel RefSeq Input longLabel JKG Input RefSeq Alignments Take 11 group jkX visibility hide color 0,0,100 type psl . track jkgRefSeqUnusual shortLabel RefSeq Unusual longLabel JKG Unusual conditions in RefSeq Alignments Take 11 group jkX visibility hide color 150,75,0 type bed 4 + track jkgInputMrna shortLabel mRNA Input longLabel JKG Input mRNA Alignments (Snapshot of DB Feb 21 2007) Take 11 group jkX visibility hide color 50,50,50 type psl . track jkgAntibodyBed shortLabel Antibody Frags longLabel JKG Antibody fragments filtered out of mRNA Take 11 group jkX visibility hide color 150,0,0 type bed 12 . track jkgRefSeqBed shortLabel RefSeq BED longLabel JKG RefSeq merged at short breaks, broken at long non-intron break Take 11 group jkX visibility hide color 0,0,100 type bed 12 . track jkgMrnaBed shortLabel mRNA BED longLabel JKG mRNA merged at short breaks, broken at long non-intron break Take 11 group jkX visibility hide color 50,50,50 type bed 12 . track jkgNativeGraph shortLabel Native Graph longLabel JKG Transcription Graph for mRNA and RefSeq Take 11 group jkX visibility hide type altGraphX track jkgOrthoExons shortLabel Ortho Exon longLabel JKG Exons Supported by Orthologous Mouse Transcription Graph Take 11 group jkX visibility hide color 100,60,0 type bed 6 . track jkgOrthoIntrons shortLabel Ortho Intron longLabel JKG Introns Supported by Orthologous Mouse Transcription Graph Take 11 group jkX visibility hide color 125,110,60 type bed 6 . track jkgEstExons shortLabel EST Exon longLabel JKG Exons supported by at least 2 ESTs Take 11 group jkX visibility hide color 0,60,100 type bed 6 . track jkgEstIntrons shortLabel EST Intron longLabel JKG Introns supported by at least 2 ESTs Take 11 group jkX visibility hide color 60,110,125 type bed 6 . track jkgTxWalkPrelim shortLabel txWalkPrelim longLabel JKG txWalk Transcripts Preliminary Take 11 group jkX visibility hide color 90,100,180 type bed 12 . track jkgTxWalk shortLabel txWalk longLabel JKG txWalk Transcripts Take 11 group jkX visibility hide color 30,0,80 type bed 12 . track jkgAltSplice shortLabel AltSplice longLabel JKG Alternative Splicing Events in txWalk Take 11 group jkX visibility hide color 90,0,150 type bed 6 . track jkgTxCdsPick shortLabel txCdsPick longLabel JKG CDS Mappings of txWalk Transcripts Take 11 group jkX visibility hide color 0,70,40 type genePred cdsEvidence jkgTxCdsEvidence txInfo jkgTxInfo track jkgTxCdsRepick shortLabel txCdsRepick longLabel JKG CDS Re-Mappings of txWalk Transcripts Take 11 group jkX visibility hide color 70,0,140 type genePred cdsEvidence jkgTxCdsEvidence txInfo jkgTxInfo track jkgUcscGenes shortLabel txUcscGenes longLabel JKG UCSC Known Genes After Weeding Take 11 group jkX visibility hide color 70,0,220 type genePred cdsEvidence jkgTxCdsEvidence txInfo jkgTxInfo track jkgNoncoding shortLabel Noncoding Genes longLabel JKG Noncoding Genes Take 11 group jkX visibility hide color 100,0,160 type bed 12 . ########## Take 10 track jkgInputRefSeq2 shortLabel RefSeq Input longLabel JKG Input RefSeq Alignments (Snapshot of DB March 6 2007) Take 10 group jkX2 visibility hide color 0,0,100 type psl . track jkgRefSeqUnusual2 shortLabel RefSeq Unusual longLabel JKG Unusual conditions in RefSeq Alignments Take 10 group jkX2 visibility hide color 150,75,0 type bed 4 + track jkgInputMrna2 shortLabel mRNA Input longLabel JKG Input mRNA Alignments (Snapshot of DB March 6 2007) Take 10 group jkX2 visibility hide color 50,50,50 type psl . track jkgAntibodyBed2 shortLabel Antibody Frags longLabel JKG Antibody fragments filtered out of mRNA Take 10 group jkX2 visibility hide color 150,0,0 type bed 12 . track jkgRefSeqBed2 shortLabel RefSeq BED longLabel JKG RefSeq merged at short breaks, broken at long non-intron break Take 10 group jkX2 visibility hide color 0,0,100 type bed 12 . track jkgMrnaBed2 shortLabel mRNA BED longLabel JKG mRNA merged at short breaks, broken at long non-intron break Take 10 group jkX2 visibility hide color 50,50,50 type bed 12 . track jkgNativeGraph2 shortLabel Native Graph longLabel JKG Transcription Graph for mRNA and RefSeq Take 10 group jkX2 visibility hide type altGraphX track jkgOrthoExons2 shortLabel Ortho Exon longLabel JKG Exons Supported by Orthologous Mouse Transcription Graph Take 10 group jkX2 visibility hide color 100,60,0 type bed 6 . track jkgOrthoIntrons2 shortLabel Ortho Intron longLabel JKG Introns Supported by Orthologous Mouse Transcription Graph Take 10 group jkX2 visibility hide color 125,110,60 type bed 6 . track jkgEstExons2 shortLabel EST Exon longLabel JKG Exons supported by at least 2 ESTs Take 10 group jkX2 visibility hide color 0,60,100 type bed 6 . track jkgEstIntrons2 shortLabel EST Intron longLabel JKG Introns supported by at least 2 ESTs Take 10 group jkX2 visibility hide color 60,110,125 type bed 6 . track jkgTxWalk2 shortLabel txWalk longLabel JKG txWalk Transcripts Take 10 group jkX2 visibility hide color 30,0,80 type bed 12 . track jkgAltSplice2 shortLabel AltSplice longLabel JKG Alternative Splicing Events in txWalk Take 10 group jkX2 visibility hide color 90,0,150 type bed 6 . track jkgTxCdsPick2 shortLabel txCdsPick longLabel JKG CDS Mappings of txWalk Transcripts Take 10 group jkX2 visibility hide color 0,70,40 type genePred cdsEvidence jkgTxCdsEvidence2 txInfo jkgTxInfo2 track jkgTxCdsRepick2 shortLabel txCdsRepick longLabel JKG CDS Re-Mappings of txWalk Transcripts Take 10 group jkX2 visibility hide color 70,0,140 type genePred cdsEvidence jkgTxCdsEvidence2 txInfo jkgTxInfo2 track jkgUcscGenes2 shortLabel txUcscGenes longLabel JKG UCSC Known Genes After Weeding Take 10 group jkX2 visibility hide color 70,0,220 type genePred cdsEvidence jkgTxCdsEvidence2 txInfo jkgTxInfo2 track omicia compositeTrack on shortLabel Omicia OMIM longLabel Omicia OMIM mapping, Early Access R1 visibility hide group phenDis exonArrows off type bed 6 . chromosomes chr22 track omiciaAuto parent omicia shortLabel Omicia OMIM longLabel Omicia OMIM mapping, Early Access R1, April 2007 priority 1 track omiciaHand parent omicia shortLabel Omicia OMIM Hand-Curation longLabel Omicia OMIM Hand-Curation, Early Access R1, May 2007 priority 2 track mammothMaf shortLabel PSU Mammoth longLabel PSU Mammoth PCR Products group x visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 pairwiseHeight 12 spanList 1 yLineOnOff Off frames mammothMafFrames irows on autoScale Off windowingFunction mean summary multizPrimateSummary #speciesDefaultOff speciesCodonDefault hg18 speciesOrder loxAfr1 African_eleph_F African_eleph_R Indian_eleph_F Indian_eleph_R mammoth_M4_F mammoth_M4_R mammoth_M25_F mammoth_M25_R searchName rnaGene searchTable rnaGene searchType bed searchPriority 50 padding 250 searchName affy6SV searchTable snpArrayAffy6SV searchMethod exact searchType bed termRegex (CN_[0-9]+) searchPriority 12 padding 250 searchName affy6 searchTable snpArrayAffy6 searchMethod exact searchType bed termRegex (SNP_A-[0-9]+) searchPriority 12 padding 250 searchName affy5 searchTable snpArrayAffy5 searchMethod exact searchType bed termRegex (SNP_A-[0-9]+) searchPriority 12 padding 250 searchName affy250Nsp searchTable snpArrayAffy250Nsp searchMethod exact searchType bed termRegex (SNP_A-[0-9]+) searchPriority 12 padding 250 searchName affy250Sty searchTable snpArrayAffy250Sty searchMethod exact searchType bed termRegex (SNP_A-[0-9]+) searchPriority 12 padding 250 searchName illumina300 searchTable snpArrayIllumina300 searchMethod exact searchType bed termRegex (rs[0-9]{3}[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName illumina550 searchTable snpArrayIllumina550 searchMethod exact searchType bed termRegex (rs[0-9]{3}[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName illumina650 searchTable snpArrayIllumina650 searchMethod exact searchType bed termRegex (rs[0-9]{3}[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName snpArrayIlluminaHuman660W_Quad searchTable snpArrayIlluminaHuman660W_Quad searchType bed searchMethod exact termRegex ((rs|MitoA|MitoC|MitoG|MitoT|cnvi|pgxUn|hCV|[0-9])[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName illumina1M searchTable snpArrayIllumina1M searchType bed searchMethod exact termRegex ((rs|SNP|GA|cnvi|[0-9])[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName snpArrayIlluminaHumanOmni1_Quad searchTable snpArrayIlluminaHumanOmni1_Quad searchType bed searchMethod exact termRegex ((rs|SNP|GA|JK_SNP|LE_SNP|LW_SNP|HPA#_|MNS_S|ABO_SNP|DI_SNP|FY_SNP|MitoA|MitoC|MitoG|MitoT|cnvi|pgxUn|hCV|VG|VGXS|[0-9])[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchName snpArrayIlluminaHumanCytoSNP_12 searchTable snpArrayIlluminaHumanCytoSNP_12 searchType bed searchMethod exact termRegex ((rs|cnvi)[0-9]+) searchPriority 14 padding 250 semiShortCircuit 1 searchTable consIndelsHgMmCanFam searchType bed searchMethod exact shortCircuit 1 termRegex IGS.+ searchPriority 50 track vegaGeneComposite compositeTrack on shortLabel Vega Genes longLabel Vega Annotations group genes visibility hide 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,chr6_cox_hap1,chr6_qbl_hap2 type genePred vegaPep urlLabel Vega Transcript: url http://vega.sanger.ac.uk/Homo_sapiens/transview?transcript=$$ track vegaGene #replaces record vegaGene in parent dir missing/extra release,group,visibility,chromosomes,type,url parent vegaGeneComposite shortLabel Vega Protein Genes longLabel Vega Protein-Coding Annotations priority 1 color 0,50,225 html vegaGeneComposite track vegaPseudoGene #replaces record vegaPseudoGene in parent dir missing/extra release,group,visibility,chromosomes,type,url parent vegaGeneComposite shortLabel Vega Pseudogenes longLabel Vega Annotated Pseudogenes and Immunoglobulin Segments priority 2 color 30,130,210 html vegaGeneComposite track multizPrimate shortLabel Primate Multiz longLabel Primate Multiz group x visibility hide color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 maxHeightPixels 100:40:11 wiggle phastConsPrimate pairwiseHeight 12 spanList 1 yLineOnOff Off frames multizPrimateFrames # irows on autoScale Off windowingFunction mean summary multizPrimateSummary speciesGroups mammal sGroup_mammal panTro2 ponAbe2 rheMac2 calJac1 otoGar1 tupBel1 mm9 rn4 canFam2 #speciesDefaultOff treeImage phylo/hg18_multizPrimate.gif speciesCodonDefault hg18 track mammalPsg shortLabel Pos Sel Genes longLabel Positively Selected Genes (6 species) group genes visibility hide itemRgb on type bed 12 . track mafHomPan20 shortLabel HomPan20 Alignment longLabel HomPan20 Alignment group x visibility hide type wigMaf 0.0 1.0 #speciesTree ((echTel1,loxAfr1)afrothere,(dasNov1,((bosTau2, canFam2)laurasia,((oryCun1,(rn4,mm8)rodent)glire,(rheMac2,(panTro2,hg18)ape)primate)euArc)borEut13)nonAfro)eutherian; #speciesTarget human summary mafHomPan20Summary speciesOrder homPan20 panTro2 homIni20 ponAbe2 # speciesOrder mouse/human chimp/human hg17 panTro1 rheMac1 oryCun1 rn3 mm6 bosTau1 canFam1 dasNov1 tenrec loxAfr1 # speciesOrder euArc primate ape hg18 panTro2 rheMac2 rn4 mm8 rodent oryCun1 glire bosTau2 canFam2 laurasia dasNov1 nonAfro echTel1 loxAfr1 afrothere eutherian speciesCodonDefault hg18 track uwNucOcc superTrack on shortLabel Nucleosome Occupancy longLabel UW Predicted Nucleosome Occupancy group regulation track uwNucOccA375 superTrack uwNucOcc full shortLabel Nucl Occ: A375 longLabel UW Predicted Nucleosome Occupancy - A375 group regulation priority 300 visibility hide spanList 1 type wig -10 10 track uwNucOccDennis superTrack uwNucOcc full shortLabel Nucl Occ: Dennis longLabel UW Predicted Nucleosome Occupancy - Dennis group regulation priority 300 visibility hide spanList 1 type wig -10 10 track uwNucOccMec superTrack uwNucOcc full shortLabel Nucl Occ: MEC longLabel UW Predicted Nucleosome Occupancy - MEC group regulation priority 300 visibility hide spanList 1 type wig -10 10 track zhaoLabNucleosome compositeTrack on shortLabel Zhao Nucleosome longLabel Zhao lab Nucleosome measurements group x visibility hide type bed 3 subGroup1 view Views PK=Sites SIG=Density subGroup2 FAC Factor H3=Histone-H3 NUC=Nucleosome POL2S=Pol-II_Serine-5 POL2U=Pol-II_Unphosphorylate subGroup3 ACT Activation ACTV=Active REST=Resting subGroup4 STRAND Strand DBL=Double FWD=Forward RWD=Reverse dimensions dimensionX=ACT dimensionY=FAC dimensionZ=STRAND dimensionZchecked DBL,FWD,RWD sortOrder FAC=+ ACT=+ STRAND=+ view=+ dragAndDrop subTracks chromosomes chr1 track zhaoLabNucleosomeViewPK shortLabel Sites view PK visibility pack parent zhaoLabNucleosome track zhaoLabActivatedNucleosomeFwd parent zhaoLabNucleosomeViewPK shortLabel ActiveNucleosome longLabel Activated nucleosome forward strand subGroups FAC=NUC STRAND=FWD ACT=ACTV view=PK exonArrows off type bed 12 itemRgb on priority 1 noInherit on track zhaoLabActivatedNucleosomeRev parent zhaoLabNucleosomeViewPK shortLabel ActiveNucleosome longLabel Activated nucleosome reverse strand subGroups FAC=NUC STRAND=RWD ACT=ACTV view=PK exonArrows off type bed 12 itemRgb on priority 2 noInherit on track zhaoLabRestingNucleosomeFwd parent zhaoLabNucleosomeViewPK shortLabel RestingNucleosome longLabel Resting nucleosome forward strand subGroups FAC=NUC STRAND=FWD ACT=REST view=PK exonArrows off type bed 12 itemRgb on priority 3 noInherit on track zhaoLabRestingNucleosomeRev parent zhaoLabNucleosomeViewPK shortLabel RestingNucleosome longLabel Resting nucleosome reverse strand subGroups FAC=NUC STRAND=RWD ACT=REST view=PK exonArrows off type bed 12 itemRgb on priority 4 noInherit on track zhaoLabRestingH3Fwd parent zhaoLabNucleosomeViewPK shortLabel RestingHistoneH3 longLabel Resting histone H3 forward strand subGroups FAC=H3 STRAND=FWD ACT=REST view=PK exonArrows off type bed 12 itemRgb on priority 5 noInherit on track zhaoLabRestingH3Rev parent zhaoLabNucleosomeViewPK shortLabel RestingNucleosome longLabel Resting histone H3 reverse strand subGroups FAC=H3 STRAND=RWD ACT=REST view=PK exonArrows off type bed 12 itemRgb on priority 6 noInherit on track zhaoLabActiveUnphosPolII parent zhaoLabNucleosomeViewPK shortLabel Active Unphosphor PolII longLabel Activated Unphosphorylated Pol II subGroups FAC=POL2U STRAND=DBL ACT=ACTV view=PK exonArrows off type bed 9 itemRgb on priority 21 noInherit on track zhaoLabRestingUnphosPolII parent zhaoLabNucleosomeViewPK shortLabel Resting Unphosphor PolII longLabel Resting Unphosphorylated Pol II subGroups FAC=POL2U STRAND=DBL ACT=REST view=PK exonArrows off type bed 9 itemRgb on priority 22 noInherit on track zhaoLabActiveSer5PhosPolII parent zhaoLabNucleosomeViewPK shortLabel Active Ser5 PolII longLabel Activated Ser5 Phosphorylated Pol II subGroups FAC=POL2S STRAND=DBL ACT=ACTV view=PK exonArrows off type bed 9 itemRgb on priority 23 noInherit on track zhaoLabNucleosomeViewSIG shortLabel Density view SIG visibility full parent zhaoLabNucleosome viewLimits 0:10520 viewLimitsMax 0:10520 track zhaoLabActivatedNucleosomeFwdWig parent zhaoLabNucleosomeViewSIG shortLabel ActiveNucleosome longLabel Density graph, activated nucleosome forward strand subGroups FAC=NUC STRAND=FWD ACT=ACTV view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 11 noInherit on track zhaoLabActivatedNucleosomeRevWig parent zhaoLabNucleosomeViewSIG shortLabel ActiveNucleosome longLabel Density graph, activated nucleosome reverse strand subGroups FAC=NUC STRAND=RWD ACT=ACTV view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 12 noInherit on track zhaoLabRestingNucleosomeFwdWig parent zhaoLabNucleosomeViewSIG shortLabel RestingNucleosome longLabel Density graph, resting nucleosome forward strand subGroups FAC=NUC STRAND=FWD ACT=REST view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 13 noInherit on track zhaoLabRestingNucleosomeRevWig parent zhaoLabNucleosomeViewSIG shortLabel RestingNucleosome longLabel Density graph, resting nucleosome reverse strand subGroups FAC=NUC STRAND=RWD ACT=REST view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 14 noInherit on track zhaoLabRestingH3FwdWig parent zhaoLabNucleosomeViewSIG shortLabel RestingHistoneH3 longLabel Density graph, resting histone H3 forward strand subGroups FAC=H3 STRAND=FWD ACT=REST view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 15 noInherit on track zhaoLabRestingH3RevWig parent zhaoLabNucleosomeViewSIG shortLabel RestingNucleosome longLabel Density graph, resting histone H3 reverse strand subGroups FAC=H3 STRAND=RWD ACT=REST view=SIG type wig 0 10520 viewLimits 0:10520 spanList 1 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 16 noInherit on track zhaoLabActiveUnphosPolIIBedGraph parent zhaoLabNucleosomeViewSIG shortLabel density Active Unphosphor PolII longLabel Density graph, activated Unphosphorylated Pol II subGroups FAC=POL2U STRAND=DBL ACT=ACTV view=SIG type bedGraph 4 viewLimits 0:10520 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 31 noInherit on track zhaoLabRestingUnphosPolIIBedGraph parent zhaoLabNucleosomeViewSIG shortLabel density Resting Unphosphor PolII longLabel Density graph, resting Unphosphorylated Pol II subGroups FAC=POL2U STRAND=DBL ACT=REST view=SIG type bedGraph 4 viewLimits 0:10520 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 32 noInherit on track zhaoLabActiveSer5PhosPolIIBedGraph parent zhaoLabNucleosomeViewSIG shortLabel density Active Ser5 PolII longLabel Density graph, activated Ser5 Phosphorylated Pol II subGroups FAC=POL2S STRAND=DBL ACT=ACTV view=SIG type bedGraph 4 viewLimits 0:10520 minLimit 0 maxLimit 10520 autoScale On maxHeightPixels 128:40:11 configurable on priority 33 noInherit on track barskiChIPseq compositeTrack on shortLabel Barski ChIP-seq longLabel Barski et al. 2007 Chromatin Methylation ChIP-Seq group regulation subGroup1 view View SIG=Signal subGroup2 AB Target H3K04=H3K4 H3K09=H3K9 H3K27=H3K27 H3K36=H3K36 H3K79=H3K79 H3R2=H3R2 H4K20=H4K20 H4R3=H4R3 H2BK5=H2BK5 H2AZ=H2AZ PolII=PolII CTCF=CTCF subGroup3 METH Methylation m1=me1 m2=me2 m3=me3 NA=N/A dimensions dimensionX=METH dimensionY=AB sortOrder AB=+ METH=+ view=+ dragAndDrop subTracks #settingsByView SIG:viewLimits=.2:1.6,viewLimits=0:319 visibility hide type bed 3 track barskiChIPseqViewSIG shortLabel Signal view SIG parent barskiChIPseq viewLimitsMax 0:319 track barskiChIPseqH3K4me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K04 METH=m1 shortLabel Barski H3K4me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K4me1) type wig 1 121 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 1 track barskiChIPseqH3K4me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K04 METH=m2 shortLabel Barski H3K4me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K4me2) type wig 1 57 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 2 track barskiChIPseqH3K4me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K04 METH=m3 shortLabel Barski H3K4me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K4me3) type wig 1 153 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 3 track barskiChIPseqH3K9me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K09 METH=m1 shortLabel Barski H3K9me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K9me1) type wig 1 78 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 4 track barskiChIPseqH3K9me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K09 METH=m2 shortLabel Barski H3K9me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K9me2) type wig 1 99 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 5 track barskiChIPseqH3K9me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K09 METH=m3 shortLabel Barski H3K9me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K9me3) type wig 1 114 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 6 track barskiChIPseqH3K27me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K27 METH=m1 shortLabel Barski H3K27me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K27me1) type wig 1 106 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 7 track barskiChIPseqH3K27me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K27 METH=m2 shortLabel Barski H3K27me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K27me2) type wig 1 119 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 8 track barskiChIPseqH3K27me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K27 METH=m3 shortLabel Barski H3K27me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K27me3) type wig 1 86 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 9 track barskiChIPseqH3K36me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K36 METH=m1 shortLabel Barski H3K36me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K36me1) type wig 1 99 noInherit on configurable on priority 10 track barskiChIPseqH3K36me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K36 METH=m3 shortLabel Barski H3K36me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K36me3) type wig 1 132 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 11 track barskiChIPseqH3K79me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K79 METH=m1 shortLabel Barski H3K79me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K79me1) type wig 1 89 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 12 track barskiChIPseqH3K79me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K79 METH=m2 shortLabel Barski H3K79me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K79me2) type wig 1 115 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 13 track barskiChIPseqH3K79me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3K79 METH=m3 shortLabel Barski H3K79me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3K79me3) type wig 1 179 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 14 track barskiChIPseqH3R2me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3R2 METH=m1 shortLabel Barski H3R2me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3R2me1) type wig 1 101 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 15 track barskiChIPseqH3R2me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H3R2 METH=m2 shortLabel Barski H3R2me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H3R2me2) type wig 1 102 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 16 track barskiChIPseqH4K20me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H4K20 METH=m1 shortLabel Barski H4K20me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H4K20me1) type wig 1 154 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 17 track barskiChIPseqH4K20me3 parent barskiChIPseqViewSIG subGroups view=SIG AB=H4K20 METH=m3 shortLabel Barski H4K20me3 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H4K20me3) type wig 1 196 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 18 track barskiChIPseqH4R3me2 parent barskiChIPseqViewSIG subGroups view=SIG AB=H4R3 METH=m1 shortLabel Barski H4R3me2 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H4R3me2) type wig 1 156 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 19 track barskiChIPseqH2BK5me1 parent barskiChIPseqViewSIG subGroups view=SIG AB=H2BK5 METH=m1 shortLabel Barski H2BK5me1 longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H2BK5me1) type wig 1 122 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 20 track barskiChIPseqH2AZ parent barskiChIPseqViewSIG subGroups view=SIG AB=H2AZ METH=NA shortLabel Barski H2AZ longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. H2AZ) type wig 1 65 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 21 track barskiChIPseqPolII parent barskiChIPseqViewSIG subGroups view=SIG AB=PolII METH=NA shortLabel Barski PolII longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. PolII) type wig 1 319 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 22 track barskiChIPseqCTCF parent barskiChIPseqViewSIG subGroups view=SIG AB=CTCF METH=NA shortLabel Barski CTCF longLabel Barski et al. 2007 Chromatin Methylation (ChIP-Seq ab. CTCF) type wig 1 152 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 #viewLimits .2:1.6 noInherit on configurable on priority 23 track jkPilotK562Enhancer shortLabel CHMM Enhancer Peaks longLabel Peaks of Chromia HMM for Enhancers on K562 Cells Using ENCODE Broad Histone Marks type bigWig 0 7.5 maxHeightPixels 100:50:11 group regulation color 0,60,120 track jkPilotK562EnhancerAll shortLabel CHMM Enhancer All longLabel Chromia HMM for Enhancers on K562 Cells Using ENCODE Broad Histone Marks type bigWig 0 7.5 maxHeightPixels 100:50:11 group regulation color 0,60,120 track jkPilotK562EnhancerMerge shortLabel CHMM Enhancer K562 longLabel Merged Chromia HMM Pilot Run for Enhancers on K562 Cells Using ENCODE Broad Histone Marks type bed 5 group regulation useScore 1 color 0,60,120 track jkPilotK562Promoter shortLabel CHMM Promoter Peaks longLabel Peaks of Chromia HMM for Promoters on K562 Cells Using ENCODE Broad Histone Marks type bigWig 0 25 maxHeightPixels 100:50:11 group regulation track jkPilotK562PromoterAll shortLabel CHMM Promoter All longLabel Chromia HMM for Promoters on K562 Cells Using ENCODE Broad Histone Marks type bigWig 0 25 maxHeightPixels 100:50:11 group regulation track jkPilotK562PromoterMerge shortLabel CHMM Promoter K562 longLabel Merged Chromia HMM Pilot Run for Promoters on K562 Cells Using ENCODE Broad Histone Marks type bed 5 group regulation useScore 1 track cons44way compositeTrack on shortLabel Conservation longLabel Vertebrate Multiz Alignment & Conservation (44 Species) subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements subGroup2 clade Clade primate=Primate mammal=Mammal vert=Vertebrate dragAndDrop subTracks dimensions dimensionX=clade visibility full type bed 4 group compGeno priority 1 configureByPopup off track cons44wayViewalign shortLabel Multiz Alignments view align visibility pack viewUi on parent cons44way track multiz44way parent cons44wayViewalign on shortLabel Multiz Align longLabel Multiz Alignments of 44 Vertebrates subGroups view=align clade=vert noInherit on irows on summary multiz44waySummary frames multiz44wayFrames group compGeno color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 speciesCodonDefault hg18 speciesGroups Primate Placental_Mammal Vertebrate sGroup_Primate panTro2 gorGor1 ponAbe2 rheMac2 calJac1 tarSyr1 micMur1 otoGar1 sGroup_Placental_Mammal tupBel1 mm9 rn4 dipOrd1 cavPor3 speTri1 oryCun1 ochPri2 vicPac1 turTru1 bosTau4 equCab2 felCat3 canFam2 myoLuc1 pteVam1 eriEur1 sorAra1 loxAfr2 proCap1 echTel1 dasNov2 choHof1 sGroup_Vertebrate monDom4 ornAna1 galGal3 taeGut1 anoCar1 xenTro2 tetNig1 fr2 gasAcu1 oryLat2 danRer5 petMar1 speciesDefaultOff panTro2 gorGor1 ponAbe2 calJac1 otoGar1 equCab2 tarSyr1 micMur1 tupBel1 rn4 dipOrd1 cavPor3 speTri1 oryCun1 ochPri2 sorAra1 eriEur1 felCat3 pteVam1 myoLuc1 turTru1 bosTau4 vicPac1 choHof1 echTel1 dasNov2 taeGut1 proCap1 danRer5 tetNig1 fr2 oryLat2 petMar1 itemFirstCharCase noChange treeImage phylo/hg18_44way.gif priority 100 track cons44wayViewphyloP shortLabel Basewise Conservation (phyloP) view phyloP visibility full parent cons44way viewLimits -0.5:3.0 viewLimitsMax -15.41:7.13 configureByPopup on # PhyloP conservation track phyloP44wayPrimate parent cons44wayViewphyloP off subGroups view=phyloP clade=primate shortLabel Primate Cons longLabel Primate Basewise Conservation by PhyloP noInherit on configurable on type wig -8.17 .99 maxHeightPixels 100:50:11 autoScale off spanList 1 color 10,10,70 altColor 70,10,10 priority 1 track phyloP44wayPlacMammal parent cons44wayViewphyloP on subGroups view=phyloP clade=mammal shortLabel Mammal Cons longLabel Placental Mammal Basewise Conservation by PhyloP noInherit on configurable on type wig -14.42 3.46 maxHeightPixels 100:50:11 spanList 1 color 25,25,95 altColor 95,25,25 priority 3 track phyloP44wayAll parent cons44wayViewphyloP off subGroups view=phyloP clade=vert shortLabel Vertebrate Cons longLabel Vertebrate Basewise Conservation by PhyloP noInherit on configurable on type wig -15.41 7.13 maxHeightPixels 100:50:11 spanList 1 windowingFunction mean color 40,40,120 altColor 120,40,40 priority 4 # PhyloP V2 conservation (chrX-specific tree) #track phyloP44wayPrimates_v2 #parent cons44wayViewphyloP off #subGroups view=phyloP clade=primate #shortLabel Primate Cons2 #longLabel Primate Basewise Conservation by PhyloP V2 #noInherit on #visibility hide #configurable on #type wig -7.87 .69 #maxHeightPixels 100:50:11 #autoScale off #spanList 1 #windowingFunction mean #color 10,10,70 #altColor 70,10,10 #priority 5 #track phyloP44wayPlacental_v2 #parent cons44wayViewphyloP on #subGroups view=phyloP clade=mammal #shortLabel Mammal Cons2 #longLabel Placental Mammal Basewise Conservation by PhyloP V2 #noInherit on #configurable on #type wig -14.12 3.15 #maxHeightPixels 100:50:11 #autoScale off #spanList 1 #windowingFunction mean #color 25,25,95 #altColor 95,25,25 #priority 6 #track phyloP44way_v2 #parent cons44wayViewphyloP off #subGroups view=phyloP clade=vert #shortLabel Vertebrate Cons2 #longLabel Vertebrate Basewise Conservation by PhyloP V2 #noInherit on #configurable on #type wig -15.11 6.83 #maxHeightPixels 100:50:11 #autoScale off #spanList 1 #windowingFunction mean #color 40,40,120 #altColor 120,40,40 #priority 8 track cons44wayViewphastcons shortLabel Element Conservation (phastCons) view phastcons visibility hide parent cons44way # phastCons conservation track phastCons44wayPrimates parent cons44wayViewphastcons off subGroups view=phastcons clade=primate shortLabel Primate Cons longLabel Primate Conservation by PhastCons noInherit on configurable on type wig 0 1 maxHeightPixels 100:40:11 autoScale off spanList 1 windowingFunction mean color 10,70,10 altColor 70,10,10 priority 10 track phastCons44wayPlacental parent cons44wayViewphastcons on subGroups view=phastcons clade=mammal shortLabel Mammal Cons longLabel Placental Mammal Conservation by PhastCons noInherit on configurable on type wig 0 1 maxHeightPixels 100:40:11 autoScale off spanList 1 windowingFunction mean color 25,95,25 altColor 95,25,25 priority 12 track phastCons44way parent cons44wayViewphastcons off subGroups view=phastcons clade=vert shortLabel Vertebrate Cons longLabel Vertebrate Conservation by PhastCons noInherit on configurable on type wig 0 1 maxHeightPixels 100:40:11 autoScale off spanList 1 windowingFunction mean color 40,120,40 altColor 120,40,40 priority 13 track cons44wayViewelements shortLabel Conserved Elements view elements visibility hide parent cons44way # Conserved Elements (Most Conserved) track phastConsElements44wayPrimates parent cons44wayViewelements off subGroups view=elements clade=primate shortLabel Primate El longLabel Primate Conserved Elements noInherit on type bed 5 . color 170,50,100 priority 20 track phastConsElements44wayPlacental parent cons44wayViewelements on subGroups view=elements clade=mammal shortLabel Mammal El longLabel Placental Mammal Conserved Elements noInherit on type bed 5 . color 100,50,170 priority 22 track phastConsElements44way parent cons44wayViewelements off subGroups view=elements clade=vert shortLabel Vertebrate El longLabel Vertebrate Conserved Elements noInherit on color 170,100,50 type bed 5 . priority 23 # PhyloP lineage-specific conservation track phyloPConsLs44way shortLabel Clade Cons compositeTrack on longLabel Clade-specific Relative Conservation by PhyloP (44 Species) #altColor 70,130,70 #color 0,90,20 type wig -10 4 spanList 1 maxHeightPixels 100:32:16 autoScale off windowingFunction mean group compGeno track phyloP44wayPrimatesLs_v2 parent phyloPConsLs44way shortLabel Primates V2 longLabel Primates V2 type wig -9.28 3.91 maxHeightPixels 100:32:16 noInherit on autoScale off windowingFunction mean spanList 1 viewLimits -3:3 color 10,10,70 altColor 70,10,10 priority 1 track phyloP44wayGliresLs_v2 parent phyloPConsLs44way shortLabel Glires V2 longLabel Glires (Rodent, Rabbit and Pika) V2 type wig -6.99 5.95 maxHeightPixels 100:32:16 noInherit on viewLimits -3:3 spanList 1 windowingFunction mean color 25,25,95 altColor 95,25,25 priority 2 track phyloP44wayPrimateLs parent phyloPConsLs44way shortLabel Primates longLabel Primates type wig -9.28 3.91 maxHeightPixels 100:32:16 noInherit on autoScale off windowingFunction mean spanList 1 viewLimits -3:3 color 10,10,70 altColor 70,10,10 priority 3 track phyloP44wayGlireLs parent phyloPConsLs44way shortLabel Glires longLabel Glires (Rodent, Rabbit and Pika) type wig -6.99 5.95 maxHeightPixels 100:32:16 noInherit on viewLimits -3:3 spanList 1 windowingFunction mean color 25,25,95 altColor 95,25,25 priority 4 track ensembl31wayGerp compositeTrack on shortLabel GERP Conserved longLabel GERP Conservation for Ensembl PECAN Alignments (31 Mammal Species) subGroup1 view Views scores=Basewise_Conservation elements=Conserved_Elements #settingsByView elements:pValueFilter=0.0,pValueFilterLimits=0:100,scoreFilter=0,scoreFilterLimits=0:99,minScore=0,maxScore=99 scores:viewLimits=1:20,viewLimitsMax=-1:473622.75,autoScale=off,maxHeightPixels=100:32:16,windowingFunction=mean useScore 1 type bed 4 group compGeno track ensembl31wayGerpViewscores shortLabel Basewise Conservation view scores visibility full parent ensembl31wayGerp track ensembl31wayGerpViewelements shortLabel Conserved Elements view elements visibility dense parent ensembl31wayGerp #track ensembl31wayGerpScores #parent ensembl31wayGerp on #subGroups view=scores #shortLabel GERP Scores #longLabel GERP Conservation for 31-Mammal Ensembl PECAN Alignments #noInherit on #type wig -14.42 3.46 #maxHeightPixels 100:50:11 #viewLimits -.3:2 #autoScale off #spanList 1 #windowingFunction mean #color 0, 10, 100 #altColor 0,90,10 #type wig 0.0 1.0 track ensembl31wayGerpElements parent ensembl31wayGerpViewelements on subGroups view=elements shortLabel GERP Elements longLabel GERP Conserved Elements for 31-Mammal Ensembl PECAN Alignments noInherit on color 170,100,50 type broadPeak useScore 1 pValueFilter 0.0 pValueFilterLimits 0:100 scoreFilter 0 scoreFilterLimits 0:99 minScore 0 maxScore 99 track fantom4CageGraphTop compositeTrack on shortLabel Fantom 4 Promoter longLabel Fantom and Riken 4 CAGE Promoters group rna visibility hide minLimit 0 maxLimit 500 type bed 3 autoScale on noInherit on subGroup1 view Views SIG=Clusters BED=Reads #dragAndDrop subtracks allButtonPair on track fantom4CageGraphTopViewSIG shortLabel Clusters view SIG visibility full parent fantom4CageGraphTop viewLimits 0.0:50.0 minLimit 0 maxLimit 50 autoScale Off windowingFunction mean maxHeightPixels 128:32:16 track Fantom4CageLevel1Forward parent fantom4CageGraphTopViewSIG shortLabel Level 1 Forward longLabel Level 1 Forward Fantom/Riken 4 CAGE subGroups view=SIG priority 2 minLimit 0 maxLimit 1 type bedGraph 4 configurable on color 30,25,110 track Fantom4CageLevel1Reverse parent fantom4CageGraphTopViewSIG shortLabel Level 1 Reverse longLabel Level 1 Reverse Fantom/Riken 4 CAGE subGroups view=SIG priority 3 minLimit 0 maxLimit 1 type bedGraph 4 configurable on color 170,35,45 track Fantom4CageLevel2Forward parent fantom4CageGraphTopViewSIG shortLabel Level 2 Forward longLabel Level 2 Forward Fantom/Riken 4 CAGE subGroups view=SIG priority 4 minLimit 0 maxLimit 10 type bedGraph 4 configurable on color 50,50,170 track Fantom4CageLevel2Reverse parent fantom4CageGraphTopViewSIG shortLabel Level 2 Reverse longLabel Level 2 Reverse Fantom/Riken 4 CAGE subGroups view=SIG priority 5 minLimit 0 maxLimit 10 type bedGraph 4 configurable on color 170,40,70 track Fantom4CageLevel3Forward parent fantom4CageGraphTopViewSIG shortLabel Level 3 Forward longLabel Level 3 Forward Fantom/Riken 4 CAGE subGroups view=SIG priority 6 minLimit 0 maxLimit 50 type bedGraph 4 configurable on color 75,75,225 track Fantom4CageLevel3Reverse parent fantom4CageGraphTopViewSIG shortLabel Level 3 Reverse longLabel Level 3 Reverse Fantom/Riken 4 CAGE subGroups view=SIG priority 7 minLimit 0 maxLimit 50 type bedGraph 4 configurable on color 225,75,130 track fantom4CageGraphTopViewBED shortLabel Reads view BED visibility squish parent fantom4CageGraphTop track FantomCageReadForward parent fantom4CageGraphTopViewBED shortLabel Fantom (+) CAGE longLabel Fantom/Riken CAGE Reads Forward subGroups view=BED priority 8 configurable on useScore 1 bedFilter on exonArrows off type bed 12 . track FantomCageReadReverse parent fantom4CageGraphTopViewBED shortLabel Fantom (-) CAGE longLabel Fantom/Riken CAGE Reads Reverse subGroups view=BED priority 9 configurable on useScore 1 exonArrows off bedFilter on type bed 12 . track HInvGeneMrnaBed shortLabel H-Inv(7.0) longLabel H-Invitational(7.0) Genes mRNA Alignments group rna visibility hide color 0,100,100 html ../HInvGeneMrna url http://www.jbirc.jbic.or.jp/hinv/soup/pub_Detail.pl?acc_id=$$ type bed 6 track brTestPlus extTable brTestMinus shortLabel multiWig Test #1 longLabel Test of multiwig using bigWigs and two tables group x visibility hide type bigWig -120 120 autoScale Off maxHeightPixels 128:32:11 track hg18ContigDiff shortLabel Hg19 Diff longLabel Contigs dropped or changed from NCBI build 36(hg18) to 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/$$ track evoCpg shortLabel Evo Cpg longLabel Weizmann Evolutionary CpG Islands visibility hide group compGeno priority 8 type bed 9 . noScoreFilter . itemRgb on color 0,0,0 track testChainHg19Overlap500 shortLabel hg19 liftOver 500 longLabel hg19 liftOver Chains 500 base overlap 5,000 base chunk size group map visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain hg19 otherDb hg19 track haplotypeLocations shortLabel HapsLocate longLabel Haplotype locations on reference sequence (on chroms: 4, 5, 6, 17) visibility hide type bed 4 group map color 0,0,0 chromosomes chr4,chr5,chr6,chr17 track cactusMaf shortLabel cactusMaf longLabel cactusMaf group x visibility hide type wigMaf #speciesOrder panTro20 panTro21 panTro22 panTro23 panTro24 panTro25 panTro26 panTro27 ponAbe20 ponAbe21 ponAbe22 ponAbe23 ponAbe24 ponAbe25 ponAbe26 ponAbe27 ponAbe28 rheMac20 rheMac21 rheMac22 rheMac23 rheMac24 rheMac25 rheMac26 frames multizPrimateFrames # speciesOrder hg180 hg181 panTro20 panTro21 panTro22 panTro23 ponAbe20 ponAbe21 rheMac20 rheMac21 rheMac22 rheMac23 #speciesOrder hg180 hg181 panTro2 panTro20 panTro21 panTro22 panTro23 ponAbe2 ponAbe20 ponAbe21 rheMac2 rheMac20 rheMac21 rheMac22 rheMac23 speciesOrder hg181 hg182 panTro20 panTro21 panTro22 panTro23 ponAbe20 ponAbe21 ponAbe22 rheMac20 rheMac21 rheMac22 track cactusBed shortLabel cactusBed longLabel cactusBed group x visibility hide type bed 12 track microattrLoci shortLabel Microattribution longLabel Loci involved in microattribution reviews group varRep visibility hide type bedDetail 14 itemRgb on url https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&sendto=t&extrafeatpresent=1&list_uids=$$ track microCuratedVars shortLabel Curated variants longLabel Curated variants from loci involved in microattribution group varRep visibility hide type bedDetail 6 color 128,0,128 track sibGene override url http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search_internal.pl?db=hg18&query_str=$$ urlLabel SIB link: track sibTxGraph override url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?db=hg18&species=H.+sapiens&tromer=$$ include defaultPriority.ra track phastBias override group compGeno priority 9 track ecoresTetNig1 override group compGeno priority 630.3