hub GCA_000247795.2 genome assembly shortLabel zebu cattle (Nelore 2014 genbank) longLabel zebu cattle (Nelore 2014 genbank)/Bos indicus/GCA_000247795.2_Bos_indicus_1.0 genome assembly useOneFile on email genome-www@soe.ucsc.edu descriptionUrl html/GCA_000247795.2_Bos_indicus_1.0.description.html genome GCA_000247795.2 taxId 9915 groups groups.txt description zebu cattle (Nelore 2014 genbank) twoBitPath GCA_000247795.2.2bit twoBitBptUrl GCA_000247795.2.2bit.bpt chromSizes GCA_000247795.2.chrom.sizes.txt chromAliasBb GCA_000247795.2.chromAlias.bb chromAuthority ucsc organism Bos_indicus_1.0 Nov. 2014 defaultPos CM003021.1:53702830-53712830 scientificName Bos indicus htmlPath html/GCA_000247795.2_Bos_indicus_1.0.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/247/795/GCA_000247795.2 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/247/795/GCA_000247795.2 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/247/795/GCA_000247795.2 track assembly longLabel Assembly shortLabel Assembly visibility hide colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.assembly.bb type bigBed 6 html html/GCA_000247795.2_Bos_indicus_1.0.assembly searchIndex name searchTrix ixIxx/GCA_000247795.2_Bos_indicus_1.0.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track gap longLabel AGP gap shortLabel Gap (AGP defined) visibility hide color 0,0,0 bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.gap.bb type bigBed 4 group map html html/GCA_000247795.2_Bos_indicus_1.0.gap track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility dense 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_000247795.2_Bos_indicus_1.0.gc5Base.bw html html/GCA_000247795.2_Bos_indicus_1.0.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_000247795.2_Bos_indicus_1.0.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.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_000247795.2_Bos_indicus_1.0.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.rmsk.bb maxWindowToDraw 5000000 html html/GCA_000247795.2_Bos_indicus_1.0.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.simpleRepeat.bb html html/GCA_000247795.2_Bos_indicus_1.0.simpleRepeat track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility dense type bigBed 4 + html html/GCA_000247795.2_Bos_indicus_1.0.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_000247795.2_Bos_indicus_1.0.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_000247795.2_Bos_indicus_1.0.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.windowMasker.bb html html/GCA_000247795.2_Bos_indicus_1.0.windowMasker track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility hide type bigBed 3 bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.allGaps.bb html html/GCA_000247795.2_Bos_indicus_1.0.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_000247795.2_Bos_indicus_1.0.augustus.bb html html/GCA_000247795.2_Bos_indicus_1.0.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_000247795.2_Bos_indicus_1.0.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_000247795.2_Bos_indicus_1.0.xenoRefGene.ix html html/GCA_000247795.2_Bos_indicus_1.0.xenoRefGene track evaSnp8 shortLabel EVA SNP Release 8 longLabel Short Genetic Variants from European Variant Archive Release 8 type bigBed 9 + visibility dense group varRep itemRgb on bigDataUrl contrib/evaSnp8/evaSnp8.bb url https://www.ebi.ac.uk/eva/?variant&accessionID=$$ searchIndex name mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange filterValues.varClass SNV|SNV,deletion|Deletion,indel|Indel,insertion|Insertion,MNV|MNV,sequence_alteration|Sequence alteration filterLabel.varClass Variant class from EVA SO term filterLabel.ucscClass Functional effect per UCSC Variant Annotation filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant filterType.ucscClass multipleListOnlyOr filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants filterLabel.itemRgb General variant types by color grouping maxWindowCoverage 250000 maxItems 1000000 html contrib/evaSnp8/description