hub GCA_028535905.1 genome assembly shortLabel California scrub oak (Qber.S.LA.60 alternate hap 2023) longLabel California scrub oak (Qber.S.LA.60 alternate hap 2023)/Quercus berberidifolia/GCA_028535905.1_dhQueBerb1.0.hap2 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_028535905.1_dhQueBerb1.0.hap2.description.html genome GCA_028535905.1 taxId 1266315 groups groups.txt description California scrub oak (Qber.S.LA.60 alternate hap 2023) twoBitPath GCA_028535905.1.2bit twoBitBptUrl GCA_028535905.1.2bit.bpt chromSizes GCA_028535905.1.chrom.sizes.txt chromAliasBb GCA_028535905.1.chromAlias.bb organism dhQueBerb1.0.hap2 Feb. 2023 defaultPos JAPQVW010000001.1:32045347-32055347 scientificName Quercus berberidifolia htmlPath html/GCA_028535905.1_dhQueBerb1.0.hap2.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/535/905/GCA_028535905.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/535/905/GCA_028535905.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/535/905/GCA_028535905.1 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_028535905.1_dhQueBerb1.0.hap2.assembly.bb type bigBed 6 html html/GCA_028535905.1_dhQueBerb1.0.hap2.assembly searchIndex name searchTrix ixIxx/GCA_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.gc5Base.bw html html/GCA_028535905.1_dhQueBerb1.0.hap2.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_028535905.1_dhQueBerb1.0.hap2.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_028535905.1_dhQueBerb1.0.hap2.rmsk.bb maxWindowToDraw 5000000 html html/GCA_028535905.1_dhQueBerb1.0.hap2.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_028535905.1_dhQueBerb1.0.hap2.simpleRepeat.bb html html/GCA_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_028535905.1_dhQueBerb1.0.hap2.windowMasker.bb html html/GCA_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.allGaps.bb html html/GCA_028535905.1_dhQueBerb1.0.hap2.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_028535905.1_dhQueBerb1.0.hap2.augustus.bb html html/GCA_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.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_028535905.1_dhQueBerb1.0.hap2.xenoRefGene.ix html html/GCA_028535905.1_dhQueBerb1.0.hap2.xenoRefGene