hub GCA_018467165.1 genome assembly shortLabel human (HG01891.pat 2021) longLabel human (HG01891.pat 2021)/Homo sapiens/GCA_018467165.1_HG01891.alt.pat.f1_v2 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_018467165.1_HG01891.alt.pat.f1_v2.description.html genome GCA_018467165.1 taxId 9606 groups groups.txt description human (HG01891.pat 2021) twoBitPath GCA_018467165.1.2bit twoBitBptUrl GCA_018467165.1.2bit.bpt chromSizes GCA_018467165.1.chrom.sizes.txt chromAliasBb GCA_018467165.1.chromAlias.bb organism HG01891.alt.pat.f1_v2 May 2021 defaultPos JAGYVO010000001.1:37091872-37101872 scientificName Homo sapiens htmlPath html/GCA_018467165.1_HG01891.alt.pat.f1_v2.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/467/165/GCA_018467165.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/467/165/GCA_018467165.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/467/165/GCA_018467165.1 liftOver.hg38 liftOver/GCA_018467165.1ToHg38.over.chain.gz track assembly longLabel Assembly shortLabel Assembly visibility pack colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.assembly.bb type bigBed 6 html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.assembly searchIndex name searchTrix ixIxx/GCA_018467165.1_HG01891.alt.pat.f1_v2.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility full 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 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.gc5Base.bw html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.rmsk.bb xrefDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.rmsk.align.bb maxWindowToDraw 5000000 html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.simpleRepeat.bb html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.simpleRepeat track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility pack type bigBed 4 + html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.cpgIslands track cpgIslandExt parent cpgIslands off shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) type bigBed 4 + priority 1 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.cpgIslandExt.bb track cpgIslandExtUnmasked parent cpgIslands on shortLabel Unmasked CpG longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) type bigBed 4 + priority 2 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.windowMasker.bb html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.windowMasker track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility dense type bigBed 3 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.allGaps.bb html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.augustus.bb html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.augustus track xenoRefGene shortLabel RefSeq mRNAs longLabel RefSeq mRNAs mapped to this assembly group rna visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCA_018467165.1_HG01891.alt.pat.f1_v2.xenoRefGene.ix html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.xenoRefGene track ensGene shortLabel Ensembl genes longLabel Ensembl genes 2022_07 group genes priority 40 visibility pack color 150,0,0 itemRgb on type bigGenePred bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.ensGene.bb searchTrix ixIxx/GCA_018467165.1_HG01891.alt.pat.f1_v2.ensGene.ix searchIndex name labelFields name,name2 defaultLabelFields name2 baseColorUseCds given baseColorDefault genomicCodons labelSeperator " " html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.ensGene track ebiGene shortLabel Ensembl 2022_08 longLabel Ensembl genes version 2022_08 group genes visibility pack color 150,0,0 itemRgb on type bigGenePred bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.ebiGene.bb searchTrix ixIxx/GCA_018467165.1_HG01891.alt.pat.f1_v2.ebiGene.ix searchIndex name,name2 labelFields name,name2 defaultLabelFields name2 labelSeperator " " html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.ebiGene ############################################################################## # hg38 - Human - Homo sapiens - taxId: 9606 ############################################################################## track chainNetHg38 compositeTrack on shortLabel Human Chain/Net longLabel Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90 chainMinScore 5000 chainLinearGap medium matrixHeader A, C, G, T otherDb hg38 html html/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainNet track chainNetHg38Viewchain shortLabel Chain view chain visibility pack parent chainNetHg38 spectrum on track chainHg38 parent chainNetHg38Viewchain subGroups view=chain shortLabel Human Chain longLabel Human (Dec. 2013 (GRCh38/hg38)) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainHg38.bb linkDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainHg38Link.bb priority 1 track chainSynHg38 parent chainNetHg38Viewchain subGroups view=chain shortLabel Human synChain longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Chained Alignments type bigChain hg38 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainSynHg38.bb linkDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainSynHg38Link.bb priority 2 track chainRBestHg38 parent chainNetHg38Viewchain subGroups view=chain shortLabel Human rbChain longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Chained Alignments type bigChain hg38 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainRBestHg38.bb linkDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainRBestHg38Link.bb priority 3 track chainLiftOverHg38 parent chainNetHg38Viewchain subGroups view=chain shortLabel Human loChain longLabel Human (Dec. 2013 (GRCh38/hg38)) Lift Over Chained Alignments type bigChain hg38 bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainLiftOverHg38.bb linkDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.chainLiftOverHg38Link.bb priority 4 track mafNetHg38Viewnet shortLabel Net view net visibility full parent chainNetHg38 track netHg38 parent mafNetHg38Viewnet subGroups view=net shortLabel Human net longLabel Human (Dec. 2013 (GRCh38/hg38)) Net Alignment type bigMaf bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.net.bb summary bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.net.summary.bb speciesOrder hg38 priority 5 track synNetHg38 parent mafNetHg38Viewnet subGroups view=net shortLabel Human synNet longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.synNet.bb summary bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.synNet.summary.bb speciesOrder hg38 priority 6 track rbestNetHg38 parent mafNetHg38Viewnet subGroups view=net shortLabel Human rbestNet longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.rbestNet.bb summary bbi/GCA_018467165.1_HG01891.alt.pat.f1_v2.hg38.rbestNet.summary.bb speciesOrder hg38 priority 7