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_011100615.1_Macaca_fascicularis_6.0.assembly.bb
type bigBed 6
html html/GCA_011100615.1_Macaca_fascicularis_6.0.assembly
searchIndex name
searchTrix ixIxx/GCA_011100615.1_Macaca_fascicularis_6.0.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 dense
color 0,0,0
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.gap.bb
type bigBed 4
group map
html html/GCA_011100615.1_Macaca_fascicularis_6.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.gc5Base.bw
html html/GCA_011100615.1_Macaca_fascicularis_6.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_011100615.1_Macaca_fascicularis_6.0.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_011100615.1_Macaca_fascicularis_6.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.simpleRepeat.bb
html html/GCA_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.windowMasker.bb
html html/GCA_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.allGaps.bb
html html/GCA_011100615.1_Macaca_fascicularis_6.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.augustus.bb
html html/GCA_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.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_011100615.1_Macaca_fascicularis_6.0.xenoRefGene.ix
html html/GCA_011100615.1_Macaca_fascicularis_6.0.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2020_08
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.bb
searchTrix ixIxx/GCA_011100615.1_Macaca_fascicularis_6.0.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeperator " "
html html/GCA_011100615.1_Macaca_fascicularis_6.0.ensGene

track GCA_011100615.1_Macaca_fascicularis_6.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_011100615.1_Macaca_fascicularis_6.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=macFas5 s001=hg38 s002=mm39
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_011100615.1_Macaca_fascicularis_6.0.chainNet

    track GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility pack
    subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNet
    spectrum on

    track GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility pack
    subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNet
    spectrum on

    track GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility pack
    subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNet
    spectrum on

    track GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility pack
    subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNet
    spectrum on

        track chainMacFas5
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewchain off
        subGroups view=chain species=s000 chainType=c00
        shortLabel Crab-eating macaque/macFas5 Chain
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigChain macFas5
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainMacFas5.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainMacFas5Link.bb
        otherDb macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track chainSynMacFas5
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Crab-eating macaque/macFas5 synChain
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigChain macFas5
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynMacFas5.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynMacFas5Link.bb
        otherDb macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track chainRBestMacFas5
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Crab-eating macaque/macFas5 rbChain
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigChain macFas5
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestMacFas5.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestMacFas5Link.bb
        otherDb macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track chainLiftOverMacFas5
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Crab-eating macaque/macFas5 loChain
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigChain macFas5
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverMacFas5.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverMacFas5Link.bb
        otherDb macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track chainHg38
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainHg38.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainHg38Link.bb
        otherDb hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track chainSynHg38
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynHg38.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynHg38Link.bb
        otherDb hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track chainRBestHg38
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestHg38.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track chainLiftOverHg38
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverHg38.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track chainMm39
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel Mouse/mm39 Chain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainMm39.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainMm39Link.bb
        otherDb mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

        track chainSynMm39
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel Mouse/mm39 synChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynMm39.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainSynMm39Link.bb
        otherDb mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

        track chainRBestMm39
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel Mouse/mm39 rbChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestMm39.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainRBestMm39Link.bb
        otherDb mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

        track chainLiftOverMm39
        subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel Mouse/mm39 loChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverMm39.bb
        linkDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.chainLiftOverMm39Link.bb
        otherDb mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

    track GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
    shortLabel Nets
    view align
    visibility dense
    subTrack GCA_011100615.1_Macaca_fascicularis_6.0ChainNet

        track netMacFas5
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s000 chainType=c04
        shortLabel Crab-eating macaque/macFas5 mafNet
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.net.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.net.summary.bb
        speciesOrder macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track synNetMacFas5
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s000 chainType=c05
        shortLabel Crab-eating macaque/macFas5 synNet
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.synNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.synNet.summary.bb
        speciesOrder macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track rbestNetMacFas5
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s000 chainType=c06
        shortLabel Crab-eating macaque/macFas5 rbestNet
        longLabel Crab-eating macaque/macFas5/macFas5 (Jun. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.rbestNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.macFas5.rbestNet.summary.bb
        speciesOrder macFas5
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 4.960

        track netHg38
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s001 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.net.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track synNetHg38
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s001 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.synNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track rbestNetHg38
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s001 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.rbestNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 14.879

        track netMm39
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s002 chainType=c04
        shortLabel Mouse/mm39 mafNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.net.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.net.summary.bb
        speciesOrder mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

        track synNetMm39
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s002 chainType=c05
        shortLabel Mouse/mm39 synNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.synNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.synNet.summary.bb
        speciesOrder mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585

        track rbestNetMm39
        parent GCA_011100615.1_Macaca_fascicularis_6.0MafNetViewnet
        subGroups view=align species=s002 chainType=c06
        shortLabel Mouse/mm39 rbestNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.rbestNet.bb
        summary bbi/GCA_011100615.1_Macaca_fascicularis_6.0.mm39.rbestNet.summary.bb
        speciesOrder mm39
        html html/GCA_011100615.1_Macaca_fascicularis_6.0.chainNet
        priority 68.585