hub GCA_000003205.6 genome assembly
shortLabel cattle (Hereford 2015)
longLabel cattle (Hereford 2015)/Bos taurus/GCA_000003205.6_Btau_5.0.1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_000003205.6_Btau_5.0.1.description.html

genome GCA_000003205.6
taxId 9913
groups groups.txt
description cattle (Hereford 2015)
twoBitPath GCA_000003205.6.2bit
twoBitBptUrl GCA_000003205.6.2bit.bpt
chromSizes GCA_000003205.6.chrom.sizes.txt
chromAliasBb GCA_000003205.6.chromAlias.bb
chromAuthority ucsc
organism Btau_5.0.1 Nov. 2015
defaultPos CM000177.6:52990958-53000958
scientificName Bos taurus
htmlPath html/GCA_000003205.6_Btau_5.0.1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/003/205/GCA_000003205.6
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/003/205/GCA_000003205.6
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/003/205/GCA_000003205.6
liftOver.GCF_002263795.1 liftOver/GCA_000003205.6ToGCF_002263795.1.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_000003205.6_Btau_5.0.1.assembly.bb
type bigBed 6
html html/GCA_000003205.6_Btau_5.0.1.assembly
searchIndex name
searchTrix ixIxx/GCA_000003205.6_Btau_5.0.1.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 dense
color 0,0,0
bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.gap.bb
type bigBed 4
group map
html html/GCA_000003205.6_Btau_5.0.1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.gc5Base.bw
html html/GCA_000003205.6_Btau_5.0.1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_000003205.6_Btau_5.0.1.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.tandemDups.bb
    type bigBed 12

track repeatMasker
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility dense
type bigBed 6 +
colorByStrand 50,50,150 150,50,50
maxWindowToDraw 10000000
spectrum on
html html/GCA_000003205.6_Btau_5.0.1.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 6
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 7
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.simpleRepeat.bb
html html/GCA_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.windowMasker.bb
html html/GCA_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.allGaps.bb
html html/GCA_000003205.6_Btau_5.0.1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.augustus.bb
html html/GCA_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.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_000003205.6_Btau_5.0.1.xenoRefGene.ix
html html/GCA_000003205.6_Btau_5.0.1.xenoRefGene

##############################################################################
# GCF_002263795.1 - cattle - Bos taurus - taxId: 9913
##############################################################################
track chainNetGCF_002263795.1
compositeTrack on
shortLabel cattle Chain/Net
longLabel cattle (2015-11-19), 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=+
otherDb GCF_002263795.1
html html/GCA_000003205.6_Btau_5.0.1.chainNet

    track chainNetGCF_002263795.1Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_002263795.1
    spectrum on

        track chainGCF_002263795.1
        parent chainNetGCF_002263795.1Viewchain
        subGroups view=chain
        shortLabel cattle Chain
        longLabel cattle (2015-11-19) Chained Alignments
        type bigChain GCF_002263795.1
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainGCF_002263795.1.bb
        linkDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainGCF_002263795.1Link.bb
        priority 1

        track chainSynGCF_002263795.1
        parent chainNetGCF_002263795.1Viewchain
        subGroups view=chain
        shortLabel cattle synChain
        longLabel cattle (2015-11-19) Syntenic Chained Alignments
        type bigChain GCF_002263795.1
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainSynGCF_002263795.1.bb
        linkDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainSynGCF_002263795.1Link.bb
        priority 2

        track chainRBestGCF_002263795.1
        parent chainNetGCF_002263795.1Viewchain
        subGroups view=chain
        shortLabel cattle rbChain
        longLabel cattle (2015-11-19) Reciprocal Best Chained Alignments
        type bigChain GCF_002263795.1
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainRBestGCF_002263795.1.bb
        linkDataUrl bbi/GCA_000003205.6_Btau_5.0.1.chainRBestGCF_002263795.1Link.bb
        priority 3

    track mafNetGCF_002263795.1Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_002263795.1

        track netGCF_002263795.1
        parent mafNetGCF_002263795.1Viewnet
        subGroups view=net
        shortLabel cattle net
        longLabel cattle (2015-11-19) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.net.bb
        summary bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.net.summary.bb
        speciesOrder GCF_002263795.1
        priority 4

        track synNetGCF_002263795.1
        parent mafNetGCF_002263795.1Viewnet
        subGroups view=net
        shortLabel cattle synNet
        longLabel cattle (2015-11-19) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.synNet.bb
        summary bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.synNet.summary.bb
        speciesOrder GCF_002263795.1
        priority 5

        track rbestNetGCF_002263795.1
        parent mafNetGCF_002263795.1Viewnet
        subGroups view=net
        shortLabel cattle rbestNet
        longLabel cattle (2015-11-19) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.rbestNet.bb
        summary bbi/GCA_000003205.6_Btau_5.0.1.GCF_002263795.1.rbestNet.summary.bb
        speciesOrder GCF_002263795.1
        priority 6