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_018400075.1_ASM1840007v1.assembly.bb
type bigBed 6
html html/GCA_018400075.1_ASM1840007v1.assembly
searchIndex name
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_018400075.1_ASM1840007v1.gap.bb
type bigBed 4
group map
html html/GCA_018400075.1_ASM1840007v1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.gc5Base.bw
html html/GCA_018400075.1_ASM1840007v1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_018400075.1_ASM1840007v1.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_018400075.1_ASM1840007v1.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.simpleRepeat.bb
html html/GCA_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.windowMasker.bb
html html/GCA_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.allGaps.bb
html html/GCA_018400075.1_ASM1840007v1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.augustus.bb
html html/GCA_018400075.1_ASM1840007v1.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_018400075.1_ASM1840007v1.xenoRefGene.bb
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_018400075.1_ASM1840007v1.xenoRefGene.ix
html html/GCA_018400075.1_ASM1840007v1.xenoRefGene

track GCA_018400075.1_ASM1840007v1ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: GCA_018400075.1_ASM1840007v1
subGroup1 view Views chain=Chains net=Nets
subGroup2 species Species s000=danRer10 s001=danRer11
subGroup3 clade Clade c00=human
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=clade dimensionY=species
sortOrder species=+ view=+ clade=+
configurable on
html html/GCA_018400075.1_ASM1840007v1.chainNet

    track GCA_018400075.1_ASM1840007v1ChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack GCA_018400075.1_ASM1840007v1ChainNet
    spectrum on

        track chainDanRer10
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel danRer10 Chain
        longLabel danRer10 (Sep. 2014) Chained Alignments
        type bigChain danRer10
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainDanRer10.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainDanRer10Link.bb
        otherDb danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 1

        track chainSynDanRer10
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel danRer10 synChain
        longLabel danRer10 (Sep. 2014) Syntenic Chained Alignments
        type bigChain danRer10
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainSynDanRer10.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainSynDanRer10Link.bb
        otherDb danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 2

        track chainRBestDanRer10
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel danRer10 rbChain
        longLabel danRer10 (Sep. 2014) Reciprocal Best Chained Alignments
        type bigChain danRer10
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainRBestDanRer10.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainRBestDanRer10Link.bb
        otherDb danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 3

        track chainLiftOverDanRer10
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel danRer10 loChain
        longLabel danRer10 (Sep. 2014) Lift Over Chained Alignments
        type bigChain danRer10
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainLiftOverDanRer10.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainLiftOverDanRer10Link.bb
        otherDb danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 4

        track chainDanRer11
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel danRer11 Chain
        longLabel danRer11 (May 2017) Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainDanRer11.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainDanRer11Link.bb
        otherDb danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 5

        track chainSynDanRer11
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel danRer11 synChain
        longLabel danRer11 (May 2017) Syntenic Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainSynDanRer11.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainSynDanRer11Link.bb
        otherDb danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 6

        track chainRBestDanRer11
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel danRer11 rbChain
        longLabel danRer11 (May 2017) Reciprocal Best Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainRBestDanRer11.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainRBestDanRer11Link.bb
        otherDb danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 7

        track chainLiftOverDanRer11
        subTrack GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel danRer11 loChain
        longLabel danRer11 (May 2017) Lift Over Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainLiftOverDanRer11.bb
        linkDataUrl bbi/GCA_018400075.1_ASM1840007v1.chainLiftOverDanRer11Link.bb
        otherDb danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 8

    track GCA_018400075.1_ASM1840007v1MafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack GCA_018400075.1_ASM1840007v1ChainNet

        track synNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel danRer10 synNet
        longLabel danRer10 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer10.synNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer10.synNet.summary.bb
        speciesOrder danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 1

        track rbestNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel danRer10 rbestNet
        longLabel danRer10 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer10.rbestNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer10.rbestNet.summary.bb
        speciesOrder danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 2

        track liftOverNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel danRer10 liftOverNet
        longLabel danRer10 (some date) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer10.liftOverNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer10.liftOverNet.summary.bb
        speciesOrder danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 3

        track synNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel danRer11 synNet
        longLabel danRer11 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer11.synNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer11.synNet.summary.bb
        speciesOrder danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 4

        track rbestNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel danRer11 rbestNet
        longLabel danRer11 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer11.rbestNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer11.rbestNet.summary.bb
        speciesOrder danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 5

        track liftOverNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel danRer11 liftOverNet
        longLabel danRer11 (some date) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer11.liftOverNet.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer11.liftOverNet.summary.bb
        speciesOrder danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 6