hub GCA_009819655.1 genome assembly
shortLabel blackcap (primary hap 2019 genbank)
longLabel blackcap (primary hap 2019 genbank)/Sylvia atricapilla/GCA_009819655.1_bSylAtr1.pri genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_009819655.1_bSylAtr1.pri.description.html

genome GCA_009819655.1
taxId 48155
groups groups.txt
description blackcap (primary hap 2019 genbank)
twoBitPath GCA_009819655.1.2bit
twoBitBptUrl GCA_009819655.1.2bit.bpt
chromSizes GCA_009819655.1.chrom.sizes.txt
chromAliasBb GCA_009819655.1.chromAlias.bb
chromAuthority ucsc
organism bSylAtr1.pri Dec. 2019
defaultPos CM020465.1:51064810-51074810
scientificName Sylvia atricapilla
htmlPath html/GCA_009819655.1_bSylAtr1.pri.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/819/655/GCA_009819655.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/819/655/GCA_009819655.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/819/655/GCA_009819655.1
liftOver.taeGut1 liftOver/GCA_009819655.1ToTaeGut1.over.chain.gz
liftOver.taeGut2 liftOver/GCA_009819655.1ToTaeGut2.over.chain.gz

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_009819655.1_bSylAtr1.pri.assembly.bb
type bigBed 6
html html/GCA_009819655.1_bSylAtr1.pri.assembly
searchIndex name
searchTrix ixIxx/GCA_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.gc5Base.bw
html html/GCA_009819655.1_bSylAtr1.pri.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_009819655.1_bSylAtr1.pri.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_009819655.1_bSylAtr1.pri.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rModel.bb
xrefDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_009819655.1_bSylAtr1.pri.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.simpleRepeat.bb
html html/GCA_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.windowMasker.bb
html html/GCA_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.allGaps.bb
html html/GCA_009819655.1_bSylAtr1.pri.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.augustus.bb
html html/GCA_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.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_009819655.1_bSylAtr1.pri.xenoRefGene.ix
html html/GCA_009819655.1_bSylAtr1.pri.xenoRefGene

track GCA_009819655.1_bSylAtr1.priChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_009819655.1_bSylAtr1.pri
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=taeGut1 s001=taeGut2
subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=chainType dimensionY=species
sortOrder species=+ view=+ chainType=+
configurable on
html html/GCA_009819655.1_bSylAtr1.pri.chainNet

    track GCA_009819655.1_bSylAtr1.priChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_009819655.1_bSylAtr1.priChainNet
    spectrum on

    track GCA_009819655.1_bSylAtr1.priChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_009819655.1_bSylAtr1.priChainNet
    spectrum on

    track GCA_009819655.1_bSylAtr1.priChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_009819655.1_bSylAtr1.priChainNet
    spectrum on

    track GCA_009819655.1_bSylAtr1.priChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_009819655.1_bSylAtr1.priChainNet
    spectrum on

        track chainTaeGut1
        parent GCA_009819655.1_bSylAtr1.priChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Zebra finch/taeGut1 Chain
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track chainSynTaeGut1
        parent GCA_009819655.1_bSylAtr1.priChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Zebra finch/taeGut1 synChain
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track chainRBestTaeGut1
        parent GCA_009819655.1_bSylAtr1.priChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Zebra finch/taeGut1 rbChain
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigChain taeGut1
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut1.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut1Link.bb
        otherDb taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track chainTaeGut2
        parent GCA_009819655.1_bSylAtr1.priChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Zebra finch/taeGut2 Chain
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

        track chainSynTaeGut2
        parent GCA_009819655.1_bSylAtr1.priChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Zebra finch/taeGut2 synChain
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainSynTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

        track chainRBestTaeGut2
        parent GCA_009819655.1_bSylAtr1.priChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Zebra finch/taeGut2 rbChain
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigChain taeGut2
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut2.bb
        linkDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.chainRBestTaeGut2Link.bb
        otherDb taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

    track GCA_009819655.1_bSylAtr1.priMafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_009819655.1_bSylAtr1.priChainNet

        track netTaeGut1
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Zebra finch/taeGut1 mafNet
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.net.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.net.summary.bb
        speciesOrder taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track synNetTaeGut1
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Zebra finch/taeGut1 synNet
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.synNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.synNet.summary.bb
        speciesOrder taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track rbestNetTaeGut1
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Zebra finch/taeGut1 rbestNet
        longLabel Zebra finch/taeGut1/taeGut1 (Jul. 2008) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.rbestNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut1.rbestNet.summary.bb
        speciesOrder taeGut1
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 10.410

        track netTaeGut2
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Zebra finch/taeGut2 mafNet
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.net.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.net.summary.bb
        speciesOrder taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

        track synNetTaeGut2
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Zebra finch/taeGut2 synNet
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.synNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.synNet.summary.bb
        speciesOrder taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

        track rbestNetTaeGut2
        parent GCA_009819655.1_bSylAtr1.priMafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Zebra finch/taeGut2 rbestNet
        longLabel Zebra finch/taeGut2/taeGut2 (Feb. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.rbestNet.bb
        summary bbi/GCA_009819655.1_bSylAtr1.pri.taeGut2.rbestNet.summary.bb
        speciesOrder taeGut2
        html html/GCA_009819655.1_bSylAtr1.pri.chainNet
        priority 11.627

track HLTOGAannotvGalGal6v1
bigDataUrl bbi/HLTOGAannotVsGalGal6v1.bb
shortLabel TOGA vs. galGal6
longLabel TOGA annotations using chicken/galGal6 as reference
group genes
visibility pack
itemRgb on
type bigBed 12
searchIndex name
searchTrix  ixIxx/HLTOGAannotVsGalGal6v1.ix
html html/TOGAannotation