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_002844635.1_USMARCv1.0.assembly.bb
type bigBed 6
html html/GCA_002844635.1_USMARCv1.0.assembly
searchIndex name
searchTrix ixIxx/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.gc5Base.bw
html html/GCA_002844635.1_USMARCv1.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_002844635.1_USMARCv1.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 7
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.simpleRepeat.bb
html html/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.windowMasker.bb
html html/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.allGaps.bb
html html/GCA_002844635.1_USMARCv1.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.augustus.bb
html html/GCA_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.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_002844635.1_USMARCv1.0.xenoRefGene.ix
html html/GCA_002844635.1_USMARCv1.0.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes version 103/Feb. 2021
group genes
priority 40
visibility pack
color 150,0,0
type bigBed 12 .
bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.ensGene.bb
searchIndex name
searchTrix ixIxx/GCA_002844635.1_USMARCv1.0.ensGene.ix
html html/GCA_002844635.1_USMARCv1.0.ensGene

##############################################################################
# susScr11 - Pig - Sus scrofa - taxId: 9823
##############################################################################
track chainNetSusScr11
compositeTrack on
shortLabel Pig Chain/Net
longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)), 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=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chainMinScore 3000
chainLinearGap medium
matrixHeader A, C, G, T
otherDb susScr11
html html/GCA_002844635.1_USMARCv1.0.chainNet

    track chainNetSusScr11Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetSusScr11
    spectrum on

        track chainSusScr11
        parent chainNetSusScr11Viewchain
        subGroups view=chain
        shortLabel Pig Chain
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainSusScr11.bb
        linkDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainSusScr11Link.bb
        priority 1

        track chainSynSusScr11
        parent chainNetSusScr11Viewchain
        subGroups view=chain
        shortLabel Pig synChain
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Syntenic Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainSynSusScr11.bb
        linkDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainSynSusScr11Link.bb
        priority 2

        track chainLiftOverSusScr11
        parent chainNetSusScr11Viewchain
        subGroups view=chain
        shortLabel Pig loChain
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Lift Over Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainLiftOverSusScr11.bb
        linkDataUrl bbi/GCA_002844635.1_USMARCv1.0.chainLiftOverSusScr11Link.bb
        priority 3

    track mafNetSusScr11Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetSusScr11

        track netSusScr11
        parent mafNetSusScr11Viewnet
        subGroups view=net
        shortLabel Pig net
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.susScr11.net.bb
        summary bbi/GCA_002844635.1_USMARCv1.0.susScr11.net.summary.bb
        speciesOrder susScr11
        priority 4

        track synNetSusScr11
        parent mafNetSusScr11Viewnet
        subGroups view=net
        shortLabel Pig synNet
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.susScr11.synNet.bb
        summary bbi/GCA_002844635.1_USMARCv1.0.susScr11.synNet.summary.bb
        speciesOrder susScr11
        priority 5

        track rbestNetSusScr11
        parent mafNetSusScr11Viewnet
        subGroups view=net
        shortLabel Pig rbestNet
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.susScr11.rbestNet.bb
        summary bbi/GCA_002844635.1_USMARCv1.0.susScr11.rbestNet.summary.bb
        speciesOrder susScr11
        priority 6

        track liftOverNetSusScr11
        parent mafNetSusScr11Viewnet
        subGroups view=net
        shortLabel Pig liftOverNet
        longLabel Pig (Feb. 2017 (Sscrofa11.1/susScr11)) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002844635.1_USMARCv1.0.susScr11.liftOverNet.bb
        summary bbi/GCA_002844635.1_USMARCv1.0.susScr11.liftOverNet.summary.bb
        speciesOrder susScr11
        priority 7