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/GCF_012559485.2_MFA1912RKSv2.assembly.bb
type bigBed 6
html html/GCF_012559485.2_MFA1912RKSv2.assembly
searchIndex name
searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.gc5Base.bw
html html/GCF_012559485.2_MFA1912RKSv2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_012559485.2_MFA1912RKSv2.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.rmsk.bb
xrefDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_012559485.2_MFA1912RKSv2.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.simpleRepeat.bb
html html/GCF_012559485.2_MFA1912RKSv2.simpleRepeat

track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq gene predictions from NCBI
group genes
visibility pack
type bigBed
dragAndDrop subTracks
allButtonPair on
dataVersion NCBI Macaca fascicularis Annotation Release 102 (2021-12-09)
html html/GCF_012559485.2_MFA1912RKSv2.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        altColor 120,12,12
        shortLabel RefSeq All
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeq.bb
        longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
        idXref ncbiRefSeqLink mrnaAcc name
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 1

        track ncbiRefSeqCurated
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Curated
        longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqCurated.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 2

        track ncbiRefSeqPredicted
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Predicted
        longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqPredicted.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 3

        track ncbiRefSeqOther
        color 32,32,32
        parent refSeqComposite on
        shortLabel RefSeq Other
        longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
        priority 4
        searchIndex name
        searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.ncbiRefSeqOther.bb
        type bigBed 12 +
        labelFields name
        skipEmptyFields on
        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"

        track ncbiRefSeqPsl
        priority 5
        parent refSeqComposite off
        shortLabel RefSeq Alignments
        longLabel RefSeq Alignments of RNAs
        type bigPsl
        searchIndex name
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.bigPsl.bb
        indelDoubleInsert on
        indelQueryInsert on
        showDiffBasesAllScales .
        showDiffBasesMaxZoom 10000.0
        showCdsMaxZoom 10000.0
        showCdsAllScales .
        baseColorDefault diffCodons
        pslSequence no
        baseColorUseSequence lfExtra
        baseColorUseCds table given
        color 0,0,0

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/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.windowMasker.bb
html html/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.allGaps.bb
html html/GCF_012559485.2_MFA1912RKSv2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.augustus.bb
html html/GCF_012559485.2_MFA1912RKSv2.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/GCF_012559485.2_MFA1912RKSv2.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_012559485.2_MFA1912RKSv2.xenoRefGene.ix
html html/GCF_012559485.2_MFA1912RKSv2.xenoRefGene

track GCF_012559485.2_MFA1912RKSv2ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_012559485.2_MFA1912RKSv2
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=hg38 s001=GCF_002880755.1
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/GCF_012559485.2_MFA1912RKSv2.chainNet

    track GCF_012559485.2_MFA1912RKSv2ChainNetViewchain
    shortLabel Chains
    view chain
    visibility pack
    subTrack GCF_012559485.2_MFA1912RKSv2ChainNet
    spectrum on

    track GCF_012559485.2_MFA1912RKSv2ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility pack
    subTrack GCF_012559485.2_MFA1912RKSv2ChainNet
    spectrum on

    track GCF_012559485.2_MFA1912RKSv2ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility pack
    subTrack GCF_012559485.2_MFA1912RKSv2ChainNet
    spectrum on

    track GCF_012559485.2_MFA1912RKSv2ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility pack
    subTrack GCF_012559485.2_MFA1912RKSv2ChainNet
    spectrum on

        track chainHg38
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewchain off
        subGroups view=chain species=s000 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainHg38.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainHg38Link.bb
        otherDb hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track chainSynHg38
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainSynHg38.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainSynHg38Link.bb
        otherDb hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track chainRBestHg38
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainRBestHg38.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track chainLiftOverHg38
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainLiftOverHg38.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track chainGCF_002880755.1
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel chimpanzee Chain
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigChain GCF_002880755.1
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainGCF_002880755.1.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainGCF_002880755.1Link.bb
        otherDb GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

        track chainSynGCF_002880755.1
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel chimpanzee synChain
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigChain GCF_002880755.1
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainSynGCF_002880755.1.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainSynGCF_002880755.1Link.bb
        otherDb GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

        track chainRBestGCF_002880755.1
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel chimpanzee rbChain
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigChain GCF_002880755.1
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainRBestGCF_002880755.1.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainRBestGCF_002880755.1Link.bb
        otherDb GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

        track chainLiftOverGCF_002880755.1
        subTrack GCF_012559485.2_MFA1912RKSv2ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel chimpanzee loChain
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigChain GCF_002880755.1
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainLiftOverGCF_002880755.1.bb
        linkDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.chainLiftOverGCF_002880755.1Link.bb
        otherDb GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

    track GCF_012559485.2_MFA1912RKSv2MafNetViewnet
    shortLabel Nets
    view align
    visibility dense
    subTrack GCF_012559485.2_MFA1912RKSv2ChainNet

        track netHg38
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s000 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.hg38.net.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track synNetHg38
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s000 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.hg38.synNet.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track rbestNetHg38
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s000 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.hg38.rbestNet.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 12.960

        track netGCF_002880755.1
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s001 chainType=c04
        shortLabel chimpanzee mafNet
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.net.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.net.summary.bb
        speciesOrder GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

        track synNetGCF_002880755.1
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s001 chainType=c05
        shortLabel chimpanzee synNet
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.synNet.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.synNet.summary.bb
        speciesOrder GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175

        track rbestNetGCF_002880755.1
        parent GCF_012559485.2_MFA1912RKSv2MafNetViewnet
        subGroups view=align species=s001 chainType=c06
        shortLabel chimpanzee rbestNet
        longLabel chimpanzee/GCF_002880755.1_Clint_PTRv2 (2018-01-19) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.rbestNet.bb
        summary bbi/GCF_012559485.2_MFA1912RKSv2.GCF_002880755.1.rbestNet.summary.bb
        speciesOrder GCF_002880755.1
        html html/GCF_012559485.2_MFA1912RKSv2.chainNet
        priority 13.175