be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/trackDb/trackDb.ra src/hg/makeDb/trackDb/trackDb.ra index 1f2f19b..8eac2e2 100644 --- src/hg/makeDb/trackDb/trackDb.ra +++ src/hg/makeDb/trackDb/trackDb.ra @@ -1,3038 +1,3037 @@ # "$Id: trackDb.ra,v 1.643 2010/06/11 22:12:18 mary Exp $"; include trackDb.chainNet.ra include trackDb.chainNet.primates.ra include trackDb.chainNet.euarchontoglires.ra include trackDb.chainNet.laurasiatheria.ra include trackDb.chainNet.afrotheria.ra include trackDb.chainNet.mammal.ra include trackDb.chainNet.birds.ra include trackDb.chainNet.sarcopterygii.ra include trackDb.chainNet.fish.ra include trackDb.chainNet.insects.ra include trackDb.chainNet.other.ra include trackDb.chainNet.asmHub.ra include trackDb.encode3.ra include trackDb.transMap.ra include trackDb.nt.ra include trackDb.genbank.ra include trackDb.uniprot.ra # Root trackDb.ra file. Files from the organism subdirectory and the database sub-sub directory # will be layered on. Organism is something like 'human' and database is something # like 'hg18'. See the README file in this directory for a description of the format. # track stsMarker shortLabel STS Markers longLabel STS Markers on Genetic (blue), FISH (green) and RH (black) Maps group map visibility dense altColor 128,128,255, type bed 5 + track stsMap shortLabel STS Markers longLabel STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps group map visibility dense altColor 128,128,255, type bed 5 + track stsMapMouse shortLabel STS Markers longLabel STS Markers on Genetic Maps group map visibility dense altColor 128,128,255, type bed 5 + track fishClones shortLabel FISH Clones longLabel Clones Placed on Cytogenetic Map Using FISH group map visibility hide color 0,150,0, type bed 5 + track recombRate shortLabel Recomb Rate longLabel Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default) group map visibility hide exonArrows off type bed 4 + track ctgPos shortLabel Map Contigs longLabel Physical Map Contigs group map visibility hide color 150,0,0 type ctgPos track gold shortLabel Assembly longLabel Assembly from Fragments group map visibility hide color 150,100,30 altColor 230,170,40 type bed 3 + track gap shortLabel Gap longLabel Gap Locations group map visibility dense type bed 3 + track par shortLabel PAR longLabel Pseudoautosomal Regions group map visibility hide color 160,0,50 type bed 4 chromosomes chrX,chrY track clonePos shortLabel Coverage longLabel Clone Coverage/Fragment Position group map visibility hide altColor 180,180,180 type clonePos track bacEndPairs shortLabel BAC End Pairs longLabel BAC End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 80,80,80 exonArrows off track bacEndPairsBad shortLabel Incorrect BAC End Pairs longLabel Orphan, Short and Incorrectly Oriented BAC End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 90,90,90 exonArrows off track bacEndPairsLong shortLabel Long BAC End Pairs longLabel Long BAC End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 90,90,90 exonArrows off track traceClone shortLabel Clone Ends longLabel NCBI Trace Clones group map visibility hide type bed 6 + color 0,0,0 altColor 80,80,80 trackHandler bacEndPairs lfPslTable traceEnd exonArrows off searchTable traceClone searchType bed searchPriority 100 track traceCloneBad shortLabel Clone Ends Flagged longLabel Flagged NCBI Trace Clones (too long/short or orphan end) group map visibility hide type bed 6 + color 0,0,0 altColor 80,80,80 trackHandler bacEndPairsBad lfPslTable traceEndBad exonArrows off searchTable traceCloneBad searchType bed searchPriority 100 track fosEndPairs shortLabel Fosmid End Pairs longLabel Fosmid End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 90,90,90 exonArrows off track fosEndPairsBad shortLabel Bad Fosmid End Pairs longLabel Orphan, Short and Incorrectly Oriented Fosmid End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 90,90,90 exonArrows off track fosEndPairsLong shortLabel Long Fosmid End Pairs longLabel Long Fosmid End Pairs group map visibility hide type bed 6 + color 0,0,0 altColor 90,90,90 exonArrows off track gcPercent shortLabel GC Percent longLabel Percentage GC in 20,000-Base Windows group map visibility hide spectrum on type bed 4 + track celeraCoverage shortLabel WSSD Coverage longLabel Regions Assayed for SDD group map visibility hide type bed 4 . track celeraDupPositive shortLabel WSSD Duplication longLabel Sequence Identified as Duplicate by High-Depth Celera Reads group map visibility hide type bed 4 + track celeraOverlay shortLabel WSSD Overlay longLabel Celera WGS Assembly Overlay on Public Assembly group map visibility hide type bed 4 + track genomicDups shortLabel Duplications longLabel Duplications of >1000 Bases Sequence group map visibility hide type bed 6 + color 170,0,0 altColor 160,150,0 track dupes shortLabel Duplications longLabel Duplications of >98% Identity >1kb group map visibility dense type bed 6 . track altSeqLiftOverPsl shortLabel Alt Haplotypes longLabel Reference Assembly Alternate Haplotype Sequence Alignments group map type psl indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffBases baseColorUseSequence db color 0,0,100 visibility dense track fixSeqLiftOverPsl shortLabel Fix Patches longLabel Reference Assembly Fix Patch Sequence Alignments group map type psl indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffBases baseColorUseSequence db color 231,203,21 darkerLabels on priority 1 visibility pack track knownAlt shortLabel UCSC Alt Events longLabel Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes group genes visibility hide color 90,0,150 noScoreFilter . type bed 6 . track ccdsGene shortLabel CCDS longLabel Consensus CDS group genes visibility hide color 12,120,12 type genePred baseColorUseCds given baseColorDefault genomicCodons track crispr shortLabel CRISPR longLabel CRISPR/Cas9 Sp. Pyog. target sites group genes visibility hide type bed 3 superTrack on html crispr track crisprRanges shortLabel CRISPR Regions longLabel Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp) visibility dense color 110,110,110 type bed 3 parent crispr html crispr track crisprTargets shortLabel CRISPR Targets longLabel CRISPR/Cas9 -NGG Targets visibility dense type bigBed 9 + itemRgb on parent crispr mouseOverField _mouseOver scoreLabel MIT Guide Specificity Score # details page is not using a mysql table but a tab-sep file detailsTabUrls _offset=/gbdb/$db/crispr/crisprDetails.tab url http://crispor.org/crispor.py?org=$D&pos=$S:${&pam=NGG urlLabel Click here to show this guide on Crispor.org, with expression oligos, validation primers and more html crispr track crispors superTrack on shortLabel Crispr kMers longLabel WGE Crisprs from Ensembl release v89 and kMer locations group genes visibility hide type bed 3 html crispors track crisprEnsembl parent crispors shortLabel WGE Crisprs longLabel WGE Crisprs from Ensembl release v89 visibility squish type bigBed 9 + colorByStrand 0,0,128 128,0,0 priority 1 track crisprKmers parent crispors shortLabel kMer Crisprs longLabel kMer Crisprs 10K shoulders visibility squish type bigBed 9 . itemRgb on priority 2 include crisprAll.ra include crispr10K.ra # prospective testing of crispr 10K on hg38 # include nullModelCrispr10K.ra alpha track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility hide color 180,0,0 type genePred # NSCAN gene predictions from BrentLab # - local trackDb must specify $informant for use in html # - will need to override searchTable entry for non-chrom assemblies track nscanGene shortLabel N-SCAN longLabel N-SCAN Gene Predictions group genes visibility hide color 34,139,34 type genePred nscanPep baseColorUseCds given baseColorDefault genomicCodons informant BUG: INFORMANT DESCRIPTION NOT SET IN TRACK DB FILE searchTable nscanGene searchType genePred termRegex chr[0-9a-zA-Z_]+\.([0-9]+|pasa)((\.[0-9a-z]+)?\.[0-9a-z]+)? searchPriority 50 track rgdEst shortLabel RGD EST longLabel RGD EST group rna visibility hide spectrum on color 12,12,120 type psl est url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword= track rgdGene shortLabel RGD Genes longLabel Rat Genome Database Curated Genes group genes visibility dense color 12,12,120 type genePred url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword= track rgdSslp shortLabel RGD SSLP longLabel Rat Genome Database Simple Sequence Length Polymorphisms group varRep visibility hide color 12,12,120 type bed 4 . url http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword= track rgdQtl shortLabel RGD QTL longLabel $Organism Quantitative Trait Locus from RGD group phenDis visibility hide color 12,12,120 type bed 4 . url http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id= track rgdRatQtl shortLabel RGD Rat QTL longLabel $o_Organism Quantitative Trait Locus from RGD Coarsely Mapped to $Organism group phenDis visibility hide color 12,100,100 type bed 4 . otherDb rn4 url http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id= track pubs shortLabel Publications longLabel Publications: Sequences in Scientific Articles group pub visibility dense color 0,0,0 type bed 4 compositeTrack on nextExonText Next Match prevExonText Prev Match pubsArticleTable hgFixed.pubsArticle pubsSequenceTable hgFixed.pubsSequenceAnnot pubsPslTrack pubsBlatPsl pubsMarkerTable hgFixed.pubsMarkerAnnot noInherit on track pubsBlat shortLabel Sequences longLabel Sequences in Articles: PubmedCentral and Elsevier parent pubs on type bed 12 + visibility dense priority 2 configurable off configureByPopup off track pubsBlatPsl shortLabel Indiv. Seq. Matches longLabel Individual Sequence Matches of One Selected Article from Sequences Track parent pubs off type psl visibility hide priority 1 configurable off configureByPopup off color 0,115,70 track pubsMarkerBand shortLabel Bands longLabel Cytogenetic Bands in Publications parent pubs off visibility hide priority 3 type bed 5 track pubsMarkerSnp shortLabel SNPs longLabel SNPs in Publications parent pubs on visibility dense priority 3 type bed 5 track pubsMarkerGene shortLabel Genes longLabel Gene Symbols in Publications parent pubs off priority 3 visibility hide type bed 5 track pubsBingBlat shortLabel Web Sequences longLabel DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research group pub type bed 12 + visibility hide configurable off configureByPopup off nextExonText Next Match prevExonText Prev Match pubsArticleTable hgFixed.pubsBingArticle pubsSequenceTable hgFixed.pubsBingSequenceAnnot pubsPslTrack pubsBingBlatPsl pubsMarkerTable hgFixed.pubsBingMarkerAnnot track patSeq shortLabel Lens Patents longLabel Lens PatSeq Patent Document Sequences group phenDis visibility hide type bigBed 12 + itemRgb on compositeTrack on linkIdInName on mouseOverField mouseOver urlLabel Open Lens PatSeq Analyzer with this chromosomal range skipFields mouseOver,fprint sepFields claimGrantSeqIds exonNumbers off urls intDocIds="http://www.lens.org/lens/patent/$$" claimGrantSeqIds="http://www.lens.org/lens/patent/$$" claimSeqIds="http://www.lens.org/lens/patent/$$" grantSeqIds="http://www.lens.org/lens/patent/$$" appSeqIds="http://www.lens.org/lens/patent/$$" track patNonBulk shortLabel Non-bulk patents longLabel Patent Lens Non-bulk patents parent patSeq type bigBed 12 + visibility dense priority 1 track patBulk shortLabel Bulk patents longLabel Patent Lens Bulk patents parent patSeq type bigBed 12 + visibility hide priority 2 track genieAlt shortLabel AltGenie longLabel Genie Gene Predictions from Affymetrix group genes visibility dense color 125,0,150 type genePred genieAltPep track ensGene shortLabel Ensembl Genes longLabel Ensembl Genes group genes exonNumbers on visibility hide color 150,0,0 type genePred ensPep -pennantIcon Updated red ../goldenPath/newsarch.html#101520 "Updated to v101 Oct. 15, 2020" track ensEstGene shortLabel Ensembl EST Genes longLabel Ensembl EST Gene Predictions group genes visibility hide color 150,0,0 type genePred ensEstPep url http://www.ensembl.org/perl/geneview?db=estgene&transcript=$$ track sibGene shortLabel SIB Genes longLabel Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs group genes visibility hide color 195,90,0 type genePred url http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search_internal.pl?query_str=$$ urlLabel SIB link: track ECgene shortLabel ECgene Genes longLabel ECgene Gene Predictions with Alt-Splicing group genes visibility hide color 155,0,125 type genePred ECgenePep track ensEst shortLabel Ensembl ESTs longLabel $Organism ESTs From Ensembl group genes visibility hide color 175,20,125 type genePred ensEstPep track twinscan shortLabel Twinscan longLabel Twinscan Gene Predictions Using Mouse/Human Homology group genes visibility hide color 0,100,100 type genePred twinscanPep track contrastGene shortLabel CONTRAST longLabel CONTRAST Gene Predictions group genes visibility hide color 34,34,139 type coloredExon searchTable contractGene searchType bed termRegex CONTRAST\..+ searchPriority 50 track sgpGene shortLabel SGP Genes longLabel SGP Gene Predictions Using $Organism/Human Homology group genes visibility hide color 0,90,100 type genePred sgpPep track softberryGene shortLabel Fgenesh++ Genes longLabel Fgenesh++ Gene Predictions group genes visibility hide color 0,100,0 type genePred softberryPep track geneid shortLabel Geneid Genes longLabel Geneid Gene Predictions group genes visibility hide color 0,90,100 type genePred geneidPep track genscan shortLabel Genscan Genes longLabel Genscan Gene Predictions group genes visibility hide color 170,100,0 type genePred genscanPep track rnaGene shortLabel RNA Genes longLabel Non-coding RNA Genes (dark) and Pseudogenes (light) group genes visibility hide color 170,80,0 altColor 230,180,130 type bed 6 + track superfamily shortLabel Superfamily longLabel Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function group genes visibility hide color 150,0,0 type bed 4 + url http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/gene.cgi?genome= track exonWalk shortLabel ExonWalk longLabel ExonWalk Alt-Splicing Transcripts color 23,58,58 group genes visibility hide type genePred track exonWalk2 shortLabel ExonWalk2 longLabel ExonWalk Alt-Splicing Transcripts - take 2 color 23,58,58 group genes visibility hide type genePred track exonWalkRna shortLabel ExonWalkRna longLabel ExonWalk Alt-Splicing Transcripts mRNA Only, No Orthology color 23,58,58 group genes visibility hide type genePred track exonWalkRnaNoCds shortLabel ExonWalkRnaNoCds longLabel Exonwalk on RNA Only, No Orthology, No CDS Mapping color 23,58,58 group genes visibility hide type bed 12 track interPro shortLabel InterPro longLabel InterPro Domains group genes visibility hide color 12,12,120 type bed 4 track protBlat shortLabel Protein BLAT longLabel Protein Blatted Against Genome group genes visibility hide color 0,100,0 altColor 255,240,200 type psl protein track tigrGeneIndex shortLabel TIGR Gene Index longLabel Alignment of TIGR Gene Index TCs Against the $Organism Genome group rna visibility hide color 100,0,0 type genePred autoTranslate 0 url http://www.tigr.org/tigr-scripts/tgi/tc_report.pl?$$ track uniGene_2 shortLabel UniGene longLabel UniGene Alignments and SAGE Info group rna visibility hide spectrum on type bed 12 . track uniGene_3 shortLabel UniGene longLabel UniGene Alignments group rna visibility hide url https://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID= spectrum on type psl track uniGene shortLabel UniGene longLabel UniGene Alignments and SAGE Info group rna visibility hide type psl . track rnaCluster shortLabel Gene Bounds longLabel Gene Boundaries as Defined by RNA and Spliced EST Clusters group rna visibility hide color 200,0,50 type bed 12 . exonNumbers off track genieBounds shortLabel Clone Bounds longLabel Clone Boundaries from EST Mate Pairs group rna visibility hide color 178,34,34 type bed 9 . track altGraph shortLabel AltGraph longLabel AltGraph group rna visibility hide type psl . track sibTxGraph shortLabel SIB Alt-Splicing longLabel Alternative Splicing Graph from Swiss Institute of Bioinformatics group rna visibility hide type altGraphX url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?species=H.+sapiens&tromer=$$ urlLabel SIB link: idInUrlSql select name from sibTxGraph where id=%s track sibAltEvents shortLabel SIB Alt Events longLabel Alt-Splicing, Alternative Promoters, Alternative Poly-A etc from SIB group rna visibility hide type bed 6 . track cgapSage shortLabel CGAP SAGE longLabel CGAP Long SAGE group rna visibility hide type bed 8 + track miRNA shortLabel miRNA longLabel MicroRNAs from miRBase group genes visibility hide useScore 1 color 255,64,64 type bed 8 . url http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$ urlLabel miRBase: track allenBrainAli shortLabel Allen Brain longLabel Allen Brain Atlas Probes group regulation visibility hide color 50,0,100 type psl . track cpgIsland shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility hide color 0,100,0 altColor 128,228,128 type bed 4 + track cpgIslandSuper superTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation color 0,100,0 altColor 128,228,128 type bed 4 + html cpgIslandSuper track cpgIslandExt parent cpgIslandSuper pack shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) priority 1 html cpgIslandSuper track cpgIslandExtUnmasked parent cpgIslandSuper hide shortLabel Unmasked CpG longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) priority 2 html cpgIslandSuper track cpgIslandGgfAndyMasked shortLabel CpG Islands (AL) longLabel CpG Islands - Andy Law, Masked Sequence (Islands < 300 Bases are Light Green) group regulation visibility hide color 0,100,0 altColor 128,228,128 type bed 4 + track cpgIslandGgfAndy shortLabel CpG Islands (AL) longLabel CpG Islands - Andy Law (Islands < 300 Bases are Light Green) group regulation visibility hide color 0,100,0 altColor 128,228,128 type bed 4 + track firstEF shortLabel FirstEF longLabel FirstEF: First-Exon and Promoter Prediction group regulation visibility hide spectrum on type bed 6 . scoreMin 500 scoreMax 1000 url http://rulai.cshl.org/tools/FirstEF/Readme/README.html track eponine shortLabel Eponine TSS longLabel Eponine Predicted Transcription Start Sites group regulation visibility hide color 0,100,100 type bed 4 + track nibbImageProbes shortLabel NIBB Frog Images longLabel Xenopus Laevis In Situ mRNA Probes from NIBB group regulation visibility hide color 50,0,100 type psl xeno track esRegGeneToMotif shortLabel Reg. Module longLabel Eran Segal Regulatory Module group regulation visibility dense spectrum on noScoreFilter . type bed 6 + exonArrows off track oreganno shortLabel ORegAnno longLabel Regulatory elements from ORegAnno group regulation visibility hide color 102,102,0 type bed 4 + track rosetta shortLabel Rosetta longLabel Rosetta Experimental Confirmation of Chr22 Exons group regulation visibility hide chromosomes chr22, type bed 15 + track exoFish shortLabel Exofish Ecores longLabel Exofish Tetraodon/Human Evolutionarily Conserved Regions group compGeno visibility dense color 0,60,120 altColor 200,220,255 spectrum on type bed 5 . track blatFish shortLabel Tetraodon Blat longLabel Tetraodon nigroviridis Translated Blat Alignments group compGeno visibility dense color 0,60,120 altColor 200,220,255 spectrum on type psl xeno track blatFugu shortLabel Fugu Blat longLabel Takifugu rubripes Translated Blat Alignments group compGeno visibility hide color 0,60,120 altColor 200,220,255 spectrum on type psl xeno track blatFr1 shortLabel Fugu Blat longLabel $o_Organism ($o_date) Translated Blat Alignments group compGeno visibility hide color 0,60,120 altColor 200,220,255 spectrum on type psl xeno fr1 otherDb fr1 colorChromDefault off track blatCi1 shortLabel Squirt Blat longLabel Ciona intestinalis Translated Blat Alignments group compGeno visibility hide color 0,60,120 altColor 200,220,255 spectrum on type psl xeno track blatTetra shortLabel Tetra Blat longLabel Tetraodon nigroviridis Translated Blat Alignments group compGeno visibility dense color 0,60,120 altColor 200,220,255 spectrum on type psl xeno track mouseSyn shortLabel NCBI Synteny longLabel Corresponding Chromosome in Mouse (NCBI) group compGeno visibility hide color 120,70,30 altColor 0,0,0 type bed 4 + shortLabel Rat Synteny longLabel Human/Rat Synteny Using Blastz Single Coverage (100,000-base window) group compGeno visibility hide color 0,100,0 altColor 255,240,200 type bed 4 . track clinvarLift shortLabel ClinVar Lift longLabel Human ClinVar variants lifted to $Organism group compGeno visibility hide type bigBed 12 + bigDataUrl /gbdb/$D/bbi/clinvarLift.bb itemRgb on urls origPos="/cgi-bin/hgTracks?position=$$" rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" mouseOverField _mouseOver scoreLabel ClinVar Star-Rating (0-4) track syntenyRat shortLabel Rat Synteny longLabel $Organism/Rat Synteny Using Blastz Single Coverage (100k window) group compGeno visibility hide color 0,100,0 altColor 255,240,200 type bed 4 + # Affy Exon supertrack track affyAllExonSuper superTrack on shortLabel Affy Exon longLabel Affymetrix All Exon Microarrays group regulation track affyExonTissues shortLabel Affy Exon Tissues longLabel Affymetrix Exon Array 1.0: Normal Tissues superTrack affyAllExonSuper dense group regulation visibility full type expRatio expScale 3.0 expStep 0.5 expTable affyExonTissuesExps groupings affyExonTissuesGroups track affyAllExonProbes shortLabel Affy Exon Probes longLabel Affymetrix Exon Array 1.0: Probesets superTrack affyAllExonSuper dense group regulation visibility pack spectrum on useScore 1 exonArrows on type bed 6 . track refSeqFuncElems shortLabel RefSeq Func Elems longLabel NCBI RefSeq Functional Elements type bigBed 9 + noScoreFilter . itemRgb on bigDataUrl /gbdb/$D/ncbiRefSeq/refSeqFuncElems.bb group regulation urls geneIds=https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=$$ pubMedIds=https://www.ncbi.nlm.nih.gov/pubmed/$$ soTerm=http://www.sequenceontology.org/browser/obob.cgi?rm=term_list&release=current_svn&obo_query=$$ mouseOverField _mouseOver track snp148Common shortLabel Common SNPs(148) longLabel Simple Nucleotide Polymorphisms (dbSNP 148) Found in >= 1% of Samples group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp148Seq snpExceptionDesc snp148ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp148CodingDbSnp, track snp148Flagged shortLabel Flagged SNPs(148) longLabel Simple Nucleotide Polymorphisms (dbSNP 148) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp148Seq snpExceptionDesc snp148ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 codingAnnotations snp148CodingDbSnp, track snp148Mult shortLabel Mult. SNPs(148) longLabel Simple Nucleotide Polymorphisms (dbSNP 148) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp148Seq snpExceptionDesc snp148ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp148CodingDbSnp, track snp148 shortLabel All SNPs(148) longLabel Simple Nucleotide Polymorphisms (dbSNP 148) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp148CodingDbSnp, track snp147Common shortLabel Common SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp147CodingDbSnp, track snp147Flagged shortLabel Flagged SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene type bed 6 + trackHandler snp125 codingAnnotations snp147CodingDbSnp, track snp147Mult shortLabel Mult. SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp147Seq snpExceptionDesc snp147ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp147CodingDbSnp, track snp147 shortLabel All SNPs(147) longLabel Simple Nucleotide Polymorphisms (dbSNP 147) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 codingAnnotations snp147CodingDbSnp, track snp139Common shortLabel Common SNPs(139) longLabel Simple Nucleotide Polymorphisms (dbSNP 139) Found in >= 1% of Samples group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp139Seq snpExceptionDesc snp139ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp139CodingDbSnp, track snp139Mult shortLabel Mult. SNPs(139) longLabel Simple Nucleotide Polymorphisms (dbSNP 139) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp139Seq snpExceptionDesc snp139ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp139CodingDbSnp, track snp139 shortLabel All SNPs(139) longLabel Simple Nucleotide Polymorphisms (dbSNP 139) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp139CodingDbSnp, track snp138Common shortLabel Common SNPs(138) longLabel Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp138Seq snpExceptionDesc snp138ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp138CodingDbSnp, track snp138Mult shortLabel Mult. SNPs(138) longLabel Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp138Seq snpExceptionDesc snp138ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp138CodingDbSnp, track snp138 shortLabel All SNPs(138) longLabel Simple Nucleotide Polymorphisms (dbSNP 138) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp138CodingDbSnp, track snp137Common shortLabel Common SNPs(137) longLabel Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp137Seq snpExceptionDesc snp137ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp137CodingDbSnp, # Need to request new tag #codingAnnoLabel_snp137CodingDbSnp dbSNP track snp137Mult shortLabel Mult. SNPs(137) longLabel Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp137Seq snpExceptionDesc snp137ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp137CodingDbSnp, # Need to request new tag #codingAnnoLabel_snp137CodingDbSnp dbSNP track snp137 shortLabel All SNPs(137) longLabel Simple Nucleotide Polymorphisms (dbSNP 137) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + codingAnnotations snp137CodingDbSnp, # Need to request new tag #codingAnnoLabel_snp137CodingDbSnp dbSNP track snp135Common shortLabel Common SNPs(135) longLabel Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp135Seq snpExceptionDesc snp135ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp135Flagged shortLabel Flagged SNPs(135) longLabel Simple Nucleotide Polymorphisms (dbSNP 135) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp135Seq snpExceptionDesc snp135ExceptionDesc defaultGeneTracks knownGene type bed 6 + track snp135Mult shortLabel Mult. SNPs(135) longLabel Simple Nucleotide Polymorphisms (dbSNP 135) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp135Seq snpExceptionDesc snp135ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + track snp135 shortLabel All SNPs(135) longLabel Simple Nucleotide Polymorphisms (dbSNP 135) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp132Common shortLabel Common SNPs(132) longLabel Simple Nucleotide Polymorphisms (dbSNP 132) Found in >= 1% of Samples group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp132Seq snpExceptionDesc snp132ExceptionDesc defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp132Flagged shortLabel Flagged SNPs(132) longLabel Simple Nucleotide Polymorphisms (dbSNP 132) Flagged by dbSNP as Clinically Assoc group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp132Seq snpExceptionDesc snp132ExceptionDesc defaultGeneTracks knownGene type bed 6 + track snp132Mult shortLabel Mult. SNPs(132) longLabel Simple Nucleotide Polymorphisms (dbSNP 132) That Map to Multiple Genomic Loci group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: snpSeq snp132Seq snpExceptionDesc snp132ExceptionDesc defaultGeneTracks knownGene defaultMaxWeight 3 maxWindowToDraw 10000000 type bed 6 + track snp132 shortLabel All SNPs(132) longLabel Simple Nucleotide Polymorphisms (dbSNP 132) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp131 shortLabel SNPs (131) longLabel Simple Nucleotide Polymorphisms (dbSNP build 131) group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp130 shortLabel SNPs (130) longLabel Simple Nucleotide Polymorphisms (dbSNP build 130) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp129 shortLabel SNPs (129) longLabel Simple Nucleotide Polymorphisms (dbSNP build 129) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + track snp128 shortLabel SNPs (128) longLabel Simple Nucleotide Polymorphisms (dbSNP build 128) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: maxWindowToDraw 10000000 type bed 6 + track snp127 shortLabel SNPs (127) longLabel Simple Nucleotide Polymorphisms (dbSNP build 127) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: maxWindowToDraw 10000000 type bed 6 + track snp126 shortLabel SNPs (126) longLabel Simple Nucleotide Polymorphisms (dbSNP build 126) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: maxWindowToDraw 10000000 type bed 6 + track snp125 shortLabel SNPs longLabel Simple Nucleotide Polymorphisms (dbSNP build 125) group varRep visibility dense url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: maxWindowToDraw 10000000 type bed 6 + track snp shortLabel SNPs longLabel Simple Nucleotide Polymorphisms (SNPs) group varRep visibility dense type bed 6 + track snpMap shortLabel SNPs longLabel Simple Nucleotide Polymorphisms (SNPs) group varRep visibility hide type bed 4 . track genomicSuperDups shortLabel Segmental Dups longLabel Duplications of >1000 Bases of Non-RepeatMasked Sequence group varRep visibility hide type bed 6 + noScoreFilter . track rmsk shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility dense spectrum on type rmsk maxWindowToDraw 10000000 canPack off priority 1 track nestedRepeats shortLabel Interrupted Rpts longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID group varRep visibility hide useScore 1 type bed 12 + exonNumbers off track rmskUpdate shortLabel RM update longLabel Updated Repeating Elements by RepeatMasker group x visibility hide spectrum on type rmsk maxWindowToDraw 10000000 canPack off track nestedRepeatsUpdate shortLabel Update Intrptd Rpts longLabel Update Fragments of Interrupted Repeats Joined by RepeatMasker ID group x visibility hide useScore 1 type bed 12 + track rmskCensor shortLabel CENSOR Repeats longLabel Repeating Elements by CENSOR and Repbase 11.6 (Giri Institute) group varRep visibility hide spectrum on type rmsk canPack off track rmskRM327 shortLabel RepMask 3.2.7 longLabel Repeating Elements by RepeatMasker version 3.2.7 group varRep visibility hide spectrum on type rmsk canPack off track nestedRepeatsRM327 shortLabel Intr Rpts 3.2.7 longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID (RM version 3.2.7) group varRep visibility hide useScore 1 type bed 12 + include joinedRmskComposite.ra #include joinedRmsk.ra public track windowmasker shortLabel WindowMasker longLabel Genomic Intervals Masked by WindowMasker group varRep visibility hide type bed 3 track windowmaskerSdust shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility hide type bed 3 track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility hide type bed 4 + track microsat shortLabel Microsatellite longLabel Microsatellites - Di-nucleotide and Tri-nucleotide Repeats group varRep visibility hide type bed 4 track ancientR shortLabel Ancient Repeats longLabel Human/Mouse Ancient Repeats group x visibility hide spectrum on type bed 12 . track quality shortLabel Quality Scores longLabel $Organism Sequencing Quality Scores group map visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar windowingFunction Mean gridDefault OFF color 0,128,255 altColor 255,128,0 spanList 1,1024 type wig 0 100 # when quality is a bigWig file track qualityBw shortLabel Quality Scores longLabel $Organism Sequencing Quality Scores group map visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar windowingFunction Mean gridDefault OFF color 0,128,255 altColor 255,128,0 type bigWig 0 100 html quality track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 spanList 5 type wig 0 100 # when gc5Base is a bigWig file track gc5BaseBw shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility hide autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 type bigWig 0 100 html gc5Base track ensemblGeneScaffold shortLabel Ensembl Assembly longLabel Ensembl Gene Scaffold Assembly group map visibility hide color 0,0,0 useScore 1 type bed 6 + searchTable ensemblGeneScaffold searchMethod prefix searchType bed shortCircuit 1 termRegex GS_[0-9]+(\.[0-9]+)? searchPriority 18 track blatHg16KG shortLabel Human knownGene BLAT longLabel Human knownGene BLAT group compGeno visibility hide colorChromDefault off type psl protein track blastDm2FB shortLabel D. mel. Proteins (dm2) longLabel D. melanogaster Proteins (dm2) Mapped by Chained tBLASTn group genes visibility dense colorChromDefault off type psl protein pred dm2.blastFBPep01 blastRef dm2.blastFBRef01 url http://flybase.bio.indiana.edu/.bin/fbidq.html? track blastDm1FB shortLabel D. mel. Proteins longLabel D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn group genes visibility dense colorChromDefault off type psl protein pred dm1.blastFBPep00 blastRef dm1.blastFBRef00 url http://flybase.bio.indiana.edu/.bin/fbidq.html? track blastHg16KG shortLabel Human Proteins longLabel Human Proteins (hg16) Mapped by Chained tBLASTn group genes visibility hide colorChromDefault off type psl protein pred hg16.blastKGPep00 blastRef hg16.blastKGRef00 track chainDm1 release beta,public shortLabel D. mel. Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 133 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain dm1 otherDb dm1 track netDm1 release beta,public shortLabel D. mel. Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 134 visibility dense spectrum on type netAlign dm1 chainDm1 otherDb dm1 track chainDm1 release alpha shortLabel (dm1) D. mel. Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 133.91 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain dm1 otherDb dm1 track netDm1 release alpha shortLabel (dm1) D. mel. Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 133.92 visibility dense spectrum on type netAlign dm1 chainDm1 otherDb dm1 track chainDm2 shortLabel D. mel. Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 133.81 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain dm2 otherDb dm2 track netDm2 shortLabel D. mel. Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 133.82 visibility hide spectrum on type netAlign dm2 chainDm2 otherDb dm2 # release alpha: $o_db in shortLabel track chainDm3 shortLabel ($o_db) D. mel. Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 133.71 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 dm3 otherDb dm3 release alpha # release alpha: $o_db in shortLabel track netDm3 shortLabel ($o_db) D. mel. Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 133.72 visibility hide spectrum on type netAlign dm3 chainDm3 otherDb dm3 release alpha # release beta,public: no $o_db in shortLabel track chainDm3 shortLabel D. mel. Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 133.71 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 dm3 otherDb dm3 release beta,public # release beta,public: no $o_db in shortLabel track netDm3 shortLabel D. mel. Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 133.72 visibility hide spectrum on type netAlign dm3 chainDm3 otherDb dm3 release beta,public track chainOtoGar1Best shortLabel $o_Organism Best Chain longLabel $o_Organism ($o_date) Chained Alignments Recip Best group compGeno priority 274.1 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain otoGar1 otherDb otoGar1 track chainBorEut13 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 200 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain borEut13 otherDb borEut13 track chainHg16 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 250 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain hg16 otherDb hg16 track chainCi2 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments group compGeno priority 209 visibility hide color 100,50,0 altColor 255,240,200 spectrum on type chain ci2 otherDb ci2 track netCi2 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net group compGeno priority 209.1 visibility hide spectrum on type netAlign ci2 chainCi2 otherDb ci2 track blastHg17KG shortLabel Hg17 Proteins longLabel Hg17 Proteins Mapped by Chained tBLASTn group genes visibility pack colorChromDefault off type psl protein pred hg17.blastKGPep01 blastRef hg17.blastKGRef01 track blastHg18KG shortLabel Human Proteins longLabel Human Proteins Mapped by Chained tBLASTn group genes visibility pack colorChromDefault off type psl protein pred hg18.blastKGPep04 blastRef hg18.blastKGRef04 track BRout shortLabel BRout longLabel BRout group x spectrum on visibility hide type psl xeno track phastConsElements shortLabel Most Conserved longLabel PhastCons Conserved Elements group compGeno visibility hide exonArrows off showTopScorers 200 type bed 5 . track phastConsElementsPaper shortLabel Most Cons. (Std) longLabel PhastCons Conserved Elements, Standardized Across Species group compGeno visibility hide exonArrows off useScore 1 showTopScorers 200 type bed 5 . track encodeRegionsLiftOver shortLabel liftOver Regions longLabel liftOver ENCODE Region Orthologs (Freeze 3) group encode color 0,200,0 visibility hide type bed 4 . track encodeRegionsMercator shortLabel Mercator Regions longLabel Mercator ENCODE Region Orthologs (Freeze 3) group encode color 0,0,200 visibility hide type bed 4 . track encodeRegionsMercatorMerged shortLabel Mercator Regions longLabel Merged Mercator ENCODE Region Orthologs (Freeze 3) group encode color 0,0,200 visibility hide type bed 4 . track encodeRegionsConsensus shortLabel ENCODE Region Consensus longLabel Consensus Orthology of ENCODE Regions from LiftOver and Mercator (Freeze 3) group encode color 150,100,30 visibility hide type bed 4 . track phastConsTopPaper shortLabel phastCons HCE longLabel PhastCons Highly Conserved Elements (HCEs) group compGeno visibility hide color 0,100,0 type bed 5 . searchTable ctgPos searchMethod exact shortCircuit 1 termRegex (ctg|NT_|NG_|NC_)[0-9]+ query select chrom,chromStart,chromEnd,contig from %s where contig like '%s' searchPriority 5 searchTable cytoBand searchMethod exact searchType cytoBand shortCircuit 1 termRegex (x|y|[1-9][0-9]?)[pq]+[0-9]+(\.[0-9]+)? searchPriority 6 padding 500000 searchTable clonePos searchMethod exact searchType bed shortCircuit 1 termRegex [a-z]+_?[0-9]+\.[0-9]+ searchPriority 7 searchName clonePosNoVers searchTable clonePos searchMethod prefix shortCircuit 1 termRegex [a-z][a-z0-9]_?[0-9]+ query select chrom,chromStart,chromEnd,name from %s where name like '%s.%%' dontCheck [a-z][a-z0-9]_?[0-9]+\.[0-9]+ searchPriority 7 searchTable gold searchMethod exact searchType gold shortCircuit 1 termRegex [abuz].[0-9]+(\.[0-9]+)? searchPriority 8 searchTable par searchMethod exact searchType bed termRegex PAR[0-2]? searchPriority 8 searchName knownGeneAcc searchTable knownGene searchMethod exact searchType knownGene shortCircuit 1 semiShortCircuit 1 termRegex (uc[0-9]{3}[a-z]{3}(\.[0-9]+)?|N(M|R)_[0-9]{6}[0-9]*|[a-z][a-z0-9][0-9]{4}[0-9]*) searchPriority 9 searchName stsMapAliasMrnaAcc searchTable stsMap searchType bed xrefTable stsAlias xrefQuery select trueName,alias from %s where alias like '%s' searchBoth on termRegex [a-z][a-z0-9][0-9]+ dontCheck [^[:space:]]+ searchDescription Alias of STS Marker searchPriority 11 padding 100000 searchTable encodeRegions searchMethod prefix searchType bed shortCircuit 1 termRegex EN[rm][0-9]+(_[0-9]+)? searchPriority 11 searchTable encodeRegionsConsensus searchMethod prefix searchType bed shortCircuit 1 termRegex EN[rm][0-9]+(_[0-9]+)? searchPriority 11 searchName snpMapShort searchTable snpMap searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?) searchPriority 12.999 padding 250 searchName snpShort searchTable snp searchMethod exact searchType bed semiShortCircuit 1 termRegex (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?) searchPriority 12.998 padding 250 searchTable snp125 searchMethod exact searchType bed semiShortCircuit 1 termRegex ([0-9]+|rs[0-9]+) searchPriority 12.997 padding 250 searchTable snp126 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.996 padding 250 searchTable snp127 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.995 padding 250 searchTable snp128 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.994 padding 250 searchTable snp129 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.993 padding 250 searchTable snp130 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.992 padding 250 searchTable snp131 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.991 padding 250 searchTable snp132Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9901 padding 250 searchTable snp132Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9902 padding 250 searchTable snp132Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9903 padding 250 searchTable snp132 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9904 padding 250 searchTable snp135Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9891 padding 250 searchTable snp135Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9892 padding 250 searchTable snp135Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9893 padding 250 searchTable snp135 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9894 padding 250 searchTable snp137Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9885 padding 250 searchTable snp137Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9886 padding 250 searchTable snp137Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9887 padding 250 searchTable snp137 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9888 padding 250 searchTable snp138Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9875 padding 250 searchTable snp138Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9876 padding 250 searchTable snp138Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9877 padding 250 searchTable snp138 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9878 padding 250 searchTable snp147Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9846 padding 250 searchTable snp147Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9847 padding 250 searchTable snp147Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9848 padding 250 searchTable snp147 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.953 padding 250 searchTable snp148Common searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9843 padding 250 searchTable snp148Flagged searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9844 padding 250 searchTable snp148Mult searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9845 padding 250 searchTable snp148 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.952 padding 250 searchTable ensGene searchType genePred shortCircuit 1 termRegex ENS([A-Z]{3})?T[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensDotPrefix searchTable ensGene query select chrom,txStart,txEnd,name from %s where name like '%s.%%' shortCircuit 1 termRegex ENS([A-Z]{3})?T[0-9]+ dontCheck ENS([A-Z]{3})?T[0-9]+\.[0-9]+ searchPriority 50 searchName ensGeneGtpGene searchTable ensGene searchType genePred searchMethod prefix shortCircuit 1 xrefTable ensGtp xrefQuery select transcript,gene from %s where gene like '%s%%' termRegex ENS([A-Z]{3})?G[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensGeneGtpProtein searchTable ensGene searchType genePred searchMethod prefix shortCircuit 1 xrefTable ensGtp xrefQuery select transcript,protein from %s where protein like '%s%%' termRegex ENS([A-Z]{3})?P[0-9]+(\.[0-9]+)? searchTable ensEstGene searchType genePred shortCircuit 1 searchMethod prefix termRegex ENSESTT[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensEstGeneGtpGene searchTable ensEstGene searchType genePred searchMethod prefix shortCircuit 1 xrefTable ensEstGtp xrefQuery select transcript,gene from %s where gene like '%s%%' termRegex ENSESTG[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensEstGeneGtpProtein searchTable ensEstGene searchType genePred searchMethod prefix shortCircuit 1 xrefTable ensEstGtp xrefQuery select transcript,protein from %s where protein like '%s%%' termRegex ENSESTP[0-9]+(\.[0-9]+)? searchPriority 50 searchName ensGeneName searchTable ensGene searchType genePred searchMethod prefix xrefTable ensemblToGeneName xrefQuery select name,value from %s where value like '%%%s%%' searchPriority 50 searchTable knownGene searchType knownGene searchPriority 1 searchTable pseudoYaleEncode searchType genePred searchMethod exact searchPriority 4 searchTable pseudoHavana searchType genePred searchMethod exact searchPriority 4 searchTable pseudoGIS searchType genePred searchMethod exact searchPriority 4 searchTable superfamily searchType bed searchMethod fuzzy xrefTable sfDescription xrefQuery select name,description from %s where description like '%%%s%%' searchDescription Description of Superfamily Protein searchPriority 6 padding 100 searchTable fishClones searchMethod exact searchType bed termRegex (RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+ searchPriority 7 searchTable bacEndPairs searchMethod exact searchType bed termRegex ([[:alnum:]_ ]+|((RP|CT|GS|CH|TAM|MSMG)[[:alnum:]]+)?(-[[:alnum:]_]+)+) searchPriority 8 searchTable bacEndPairsBad searchMethod exact searchType bed termRegex ([[:alnum:]_ ]+|((RP|CT|GS|CH|TAM|MSMG)[[:alnum:]]+)?(-[[:alnum:]_]+)+) searchPriority 8 searchTable fosEndPairs searchMethod exact searchType bed termRegex ([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+) searchPriority 9 searchTable fosEndPairsBad searchMethod exact searchType bed termRegex ([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+) searchPriority 10 searchName stsMapAliasComprehensive searchTable stsMap searchType bed xrefTable stsAlias xrefQuery select trueName,alias from %s where alias like '%s' searchBoth on termRegex [^[:space:]]+ searchDescription Alias of STS Marker searchPriority 11 padding 100000 searchName snpMapLong searchTable snpMap searchMethod exact searchType bed semiShortCircuit 1 termRegex ([0-9]+|rs[0-9][0-9]?[0-9]?) dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?) searchPriority 16.999 padding 250 searchName snpLong searchTable snp searchMethod exact searchType bed semiShortCircuit 1 termRegex ([0-9]+|rs[0-9][0-9]?[0-9]?) dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?) searchPriority 16.998 padding 250 searchTable genieAlt searchType genePred termRegex A\.chr.*-.*\.[0-9]+ searchPriority 50 searchTable softberryGene searchType genePred termRegex C[A-Z0-9][A-Z0-9][0-9]+ searchPriority 50 searchTable acembly searchType genePred termRegex [^[:space:]]+ searchPriority 50 searchTable genscan searchType genePred termRegex [[:alnum:]_?]+(\.[0-9]+)* searchPriority 50 searchTable twinscan searchType genePred termRegex (chr)?.*\.[0-9]+\.[0-9]+\.[a-z] searchPriority 50 searchTable sgpGene searchType genePred termRegex chr[^_]+_((gl[0-9]+_)?(random_)?|([a-z0-9]+)_hap[0-9]_)?[0-9]+(\.[0-9]+)? searchPriority 50 searchTable geneid searchType genePred searchMethod prefix termRegex chr[^_]+_((gl[0-9]+_)?(random_)?|([a-z0-9]+)_hap[0-9]_)?[0-9]+(\.[0-9]+)? searchPriority 50 searchTable ECgene searchType genePred termRegex [[:alnum:]_]+\.[0-9]+ searchPriority 50 searchTable sangerGene searchType genePred searchPriority 50 searchTable vegaGene searchType genePred searchPriority 50 searchTable vegaPseudoGene searchType genePred searchPriority 50 searchTable vegaGene searchName vegaGene2 searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 50.1 searchTable vegaPseudoGene searchName vegaPseudoGene2 searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 50.1 searchTable slamRat searchType genePred termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+ searchPriority 50 searchTable slamMouse searchType genePred termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+ searchPriority 50 searchTable slamHuman searchType genePred termRegex [[:alnum:]_]+\.[0-9]+\.[0-9]+ searchPriority 50 searchTable rgdQtl searchType bed searchMethod fuzzy searchPriority 50 searchTable rgdRatQtl searchType bed searchMethod fuzzy searchPriority 50 searchTable rgdSslp searchType bed searchPriority 50 searchTable rgdEst searchType psl searchPriority 50 searchTable rgdGene searchType genePred searchPriority 50 searchTable NIAGene searchMethod prefix searchType psl searchPriority 50 searchTable rnaCluster searchMethod exact searchType bed termRegex chr[0-9a-z_]+[.][0-9]+ searchPriority 50 searchName oreg searchTable oreganno searchMethod exact query select chrom, chromStart, chromEnd, id from %s where id = '%s' termRegex OREG[0-9]+ padding 500 searchPriority 55 searchTable blastDm2FB searchMethod prefix searchType psl searchPriority 25 searchTable blastDm1FB searchMethod prefix searchType psl searchPriority 25 searchTable blastHg16KG searchMethod prefix searchType psl searchPriority 25 searchName blastHg16KGSprot searchTable blastHg16KG searchMethod prefix searchType psl xrefTable hg16.blastKGRef00 xrefQuery select acc,extra1 from %s where extra1 like '%s%%' searchPriority 25 searchName blastHg16KGGene searchTable blastHg16KG searchMethod prefix searchType psl xrefTable hg16.blastKGRef00 xrefQuery select acc,geneId from %s where geneId like '%s%%' searchName blastHg17KGSprot searchTable blastHg17KG searchMethod prefix searchType psl xrefTable hg17.blastKGRef01 xrefQuery select acc,extra1 from %s where extra1 like '%s%%' searchPriority 25 searchName blastHg17KGGene searchTable blastHg17KG searchMethod prefix searchType psl xrefTable hg17.blastKGRef01 xrefQuery select acc,geneId from %s where geneId like '%s%%' searchPriority 25 searchTable blastHg17KG searchMethod prefix searchType psl searchName blastHg18KGSprot searchTable blastHg18KG searchMethod prefix searchType psl xrefTable hg18.blastKGRef04 xrefQuery select acc,extra1 from %s where extra1 like '%s%%' searchPriority 25 searchName blastHg18KGGene searchTable blastHg18KG searchMethod prefix searchType psl xrefTable hg18.blastKGRef04 xrefQuery select acc,geneId from %s where geneId like '%s%%' searchPriority 25 searchTable blastHg18KG searchMethod prefix searchType psl semiShortCircuit 1 searchName blastDm2FBGene searchTable blastDm2FB searchMethod prefix searchType psl xrefTable dm2.blastFBRef01 xrefQuery select acc,geneId from %s where geneId like '%s%%' searchPriority 25 searchName blastDm1FBGene searchTable blastDm1FB searchMethod prefix searchType psl xrefTable dm1.blastFBRef00 xrefQuery select acc,geneId from %s where geneId like '%s%%' searchPriority 25 searchTable phastConsTopPaper searchType bed searchPriority 50 termRegex pc[a-z][a-z].[[:alnum:]]+ searchTable allenBrainAli searchMethod exact searchType psl searchPriority 5 shortCircuit 1 termRegex RP_.+ track encodeRegions2 shortLabel ENCODE Region Consensus (Freeze 2) longLabel Consensus Orthology of ENCODE Regions from liftOver and Mercator (Freeze 2) group encode color 200,0,0 visibility pack type bed 4 . searchName assemblyAcc searchTable gold searchMethod prefix query select chrom,chromStart,chromEnd,frag from %s where frag like '%s' xrefTable contigAcc xrefQuery select contig,acc from %s where acc like '%s%%' searchPriority 5 shortCircuit 1 termRegex [A-Z]{4}[0-9]{8,10}(\.[0-9]+)? searchTable eponine searchType bed searchMethod exact termRegex chr[0-9]+[.][0-9]+ searchPriority 50 searchTable ccdsGene searchType genePred searchPriority 1.1 track grcIncidentDb shortLabel GRC Incident longLabel GRC Incident Database group map visibility hide type bigBed 4 + url https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=$$ urlLabel GRC Incident: track tRNAs shortLabel tRNA Genes longLabel Transfer RNA Genes Identified with tRNAscan-SE group genes visibility hide color 0,20,150 type bed 6 + nextItemButton on noScoreFilter . searchName tRNA-name searchTable tRNAs searchType bed searchMethod fuzzy query select chrom,chromStart,chromEnd,name from %s where name like '%%%s%%' searchDescription tRNAscan-SE tRNA Name searchPriority 63 track refGenePfam shortLabel Pfam in RefSeq longLabel Pfam Domains in RefSeq Genes group genes type bed 12 color 20,0,250 url http://pfam.xfam.org/family/$$ track ucscGenePfam shortLabel Pfam in UCSC Gene longLabel Pfam Domains in UCSC Genes group genes type bed 12 color 20,0,250 url http://pfam.xfam.org/family/$$ track numtSeq2012 compositeTrack on shortLabel NumtS Sequence longLabel $Organism NumtS Mitochondrial Sequence group varRep visibility hide noInherit on type bed 3 . html numtSeq2012 track numtS parent numtSeq2012 shortLabel NumtS longLabel $Organism NumtS color 0,60,120 useScore 1 priority 1 type bed 6 . html numtSeq2012 track numtSAssembled parent numtSeq2012 shortLabel NumtS assembled longLabel $Organism NumtS Assembled color 0,60,120 priority 2 useScore 1 type bed 12 . html numtSeq2012 track numtSMitochondrion parent numtSeq2012 shortLabel NumtS on chrM longLabel $Organism NumtS on Mitochondrion useScore 1 color 0,60,120 priority 3 type bed 6 . html numtSeq2012 chromosomes chrM track bamAllNumtSSorted parent numtSeq2012 shortLabel NumtS SNPs longLabel $Organism NumtS on Mitochondrion SNPs priority 4 visibility pack configurable on type bam bamSkipPrintQualScore . chromosomes chrM pairEndsByName on showNames on noColorTag . bamColorMode strand bamGrayMode aliQual aliQualRange 0:255 baseColorDefault diffBases baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 100 maxWindowToDraw 1000000 track qPcrPrimers shortLabel qPCR Primers longLabel $Organism ($db) Whole Transcriptome qPCR Primers group expression type bedDetail 14 visibility hide noScoreFilter on itemRgb on searchTable qPcrPrimers searchMethod exact searchType bed searchTable refGenePfam searchMethod exact searchType bed searchTable ucscGenePfam searchMethod exact searchType bed track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bed 4 + track ucscToINSDC shortLabel INSDC longLabel Accession at INSDC - International Nucleotide Sequence Database Collaboration group map visibility hide url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel INSDC link: type bed 4 track ucscToRefSeq shortLabel RefSeq Acc longLabel RefSeq Accession group map visibility hide url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel RefSeq accession: type bed 4 searchTable ucscToRefSeq shortCircuit 1 termRegex ^[A-Za-z0-9_]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,name from %s where name like '%s%%' searchPriority 20 track spMut shortLabel UniProt Variants longLabel UniProt/SwissProt Amino Acid Substitutions group phenDis visibility hide type bigBed 12 + itemRgb on urls variationId="http://www.uniprot.org/uniprot/$$" uniProtId="http://www.uniprot.org/uniprot/$$" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" mouseOverField comments exonNumbers off noScoreFilter on track spUniprot shortLabel UniProt longLabel UniProt/SwissProt Annotations group genes visibility hide type bigBed 12 + itemRgb on exonNumbers off compositeTrack on track spAnnot shortLabel UniProt Annot. longLabel UniProt/SwissProt Protein Annotations parent spUniprot group genes visibility hide type bigBed 12 + itemRgb on urls uniProtId="http://www.uniprot.org/uniprot/$$#section_features" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" mouseOverField comments noScoreFilter on exonNumbers off track spStruct shortLabel UniProt Structure longLabel UniProt/SwissProt Protein Primary/Secondary Structure Annotations parent spUniprot group genes visibility hide type bigBed 12 + itemRgb on urls uniProtId="http://www.uniprot.org/uniprot/$$#section_features" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" mouseOverField comments noScoreFilter on exonNumbers off track ncbiRefOverlap shortLabel NCBI Overlaps longLabel NCBI Gene Annotations with Exon Overlaps group genes visibility hide priority 1 color 12,12,120 type genePred baseColorUseCds given baseColorDefault genomicCodons searchTable ucscToINSDC shortCircuit 1 termRegex ^[A-Za-z0-9_]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,name from %s where name like '%s%%' searchPriority 10 track animalQtl shortLabel $Organism QTL longLabel $Organism Quantitative Trait Loci from animalQTLdb group map visibility hide type bed 4 . color 255,123,89 # iframeUrl http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$p searchTable animalQtl searchType bed termRegex ^[a-zA-Z0-9]+([a-zA-Z0-9:/.-]+[a-zA-Z0-9:/.-_%]+)* searchMethod fuzzy searchPriority 50 track augustusGene shortLabel AUGUSTUS longLabel AUGUSTUS ab initio gene predictions v3.1 group genes visibility hide color 12,105,0 type genePred baseColorUseCds given baseColorDefault genomicCodons searchTable augustusGene searchType genePred shortCircuit 1 searchMethod fuzzy termRegex g[0-9]+(\.t[0-9]+)? searchPriority 50 track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bed 12 group map track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly track tantan shortLabel tantan Repeats longLabel Repeats by tantan group varRep visibility hide type bed 3 .