hub GCA_902686455.1 genome assembly shortLabel Eurasian red squirrel (v1.1 2019) longLabel Eurasian red squirrel (v1.1 2019)/Sciurus vulgaris/GCA_902686455.1_mSciVul1.1 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_902686455.1_mSciVul1.1.description.html genome GCA_902686455.1 taxId 55149 groups groups.txt description Eurasian red squirrel (v1.1 2019) twoBitPath GCA_902686455.1.2bit twoBitBptUrl GCA_902686455.1.2bit.bpt chromSizes GCA_902686455.1.chrom.sizes.txt chromAliasBb GCA_902686455.1.chromAlias.bb chromAuthority ucsc organism mSciVul1.1 Nov. 2019 defaultPos LR738611.1:71064765-71074765 scientificName Sciurus vulgaris htmlPath html/GCA_902686455.1_mSciVul1.1.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/902/686/455/GCA_902686455.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/902/686/455/GCA_902686455.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/902/686/455/GCA_902686455.1 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_902686455.1_mSciVul1.1.assembly.bb type bigBed 6 html html/GCA_902686455.1_mSciVul1.1.assembly searchIndex name searchTrix ixIxx/GCA_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.gc5Base.bw html html/GCA_902686455.1_mSciVul1.1.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_902686455.1_mSciVul1.1.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.gapOverlap.bb type bigBed 12 track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.rmsk.bb maxWindowToDraw 5000000 html html/GCA_902686455.1_mSciVul1.1.repeatMasker track repeatModeler shortLabel RepeatModeler longLabel RepeatModeler Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.rModel.bb xrefDataUrl bbi/GCA_902686455.1_mSciVul1.1.rModel.align.bb maxWindowToDraw 5000000 html html/GCA_902686455.1_mSciVul1.1.repeatModeler track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.simpleRepeat.bb html html/GCA_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.windowMasker.bb html html/GCA_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.allGaps.bb html html/GCA_902686455.1_mSciVul1.1.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.augustus.bb html html/GCA_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.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_902686455.1_mSciVul1.1.xenoRefGene.ix html html/GCA_902686455.1_mSciVul1.1.xenoRefGene track ensGene shortLabel Ensembl genes longLabel Ensembl genes 2020_01 group genes priority 40 visibility pack color 150,0,0 itemRgb on type bigGenePred bigDataUrl bbi/GCA_902686455.1_mSciVul1.1.ensGene.bb searchTrix ixIxx/GCA_902686455.1_mSciVul1.1.ensGene.ix searchIndex name labelFields name,name2 defaultLabelFields name2 baseColorUseCds given baseColorDefault genomicCodons labelSeperator " " html html/GCA_902686455.1_mSciVul1.1.ensGene track HLTOGAannotvHg38v1 bigDataUrl bbi/HLTOGAannotVsHg38v1.bb shortLabel TOGA vs. hg38 longLabel TOGA annotations using human/hg38 as reference group genes visibility pack itemRgb on type bigBed 12 searchIndex name searchTrix ixIxx/HLTOGAannotVsHg38v1.ix html html/TOGAannotation