hub GCA_018400075.1 genome assembly
shortLabel zebrafish (T5D 2021)
longLabel zebrafish (T5D 2021)/Danio rerio/GCA_018400075.1_ASM1840007v1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_018400075.1_ASM1840007v1.description.html

genome GCA_018400075.1
taxId 7955
groups groups.txt
description zebrafish (T5D 2021)
twoBitPath GCA_018400075.1.2bit
twoBitBptUrl GCA_018400075.1.2bit.bpt
chromSizes GCA_018400075.1.chrom.sizes.txt
chromAliasBb GCA_018400075.1.chromAlias.bb
organism ASM1840007v1 May 2021
defaultPos CP068738.1:25519774-25529774
scientificName Danio rerio
htmlPath html/GCA_018400075.1_ASM1840007v1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/400/075/GCA_018400075.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/400/075/GCA_018400075.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/018/400/075/GCA_018400075.1
liftOver.danRer10 liftOver/GCA_018400075.1ToDanRer10.over.chain.gz
liftOver.danRer11 liftOver/GCA_018400075.1ToDanRer11.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_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 hide
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 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_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
xrefDataUrl bbi/GCA_018400075.1_ASM1840007v1.rmsk.align.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 dense
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 hide
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
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
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 alignments to target sequence: GCA_018400075.1_ASM1840007v1
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=danRer10 s001=danRer11
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_018400075.1_ASM1840007v1.chainNet

    track GCA_018400075.1_ASM1840007v1ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_018400075.1_ASM1840007v1ChainNet
    spectrum on

    track GCA_018400075.1_ASM1840007v1ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_018400075.1_ASM1840007v1ChainNet
    spectrum on

    track GCA_018400075.1_ASM1840007v1ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_018400075.1_ASM1840007v1ChainNet
    spectrum on

    track GCA_018400075.1_ASM1840007v1ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_018400075.1_ASM1840007v1ChainNet
    spectrum on

        track chainDanRer10
        parent GCA_018400075.1_ASM1840007v1ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Zebrafish/danRer10 Chain
        longLabel Zebrafish/danRer10/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 0.336

        track chainSynDanRer10
        parent GCA_018400075.1_ASM1840007v1ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Zebrafish/danRer10 synChain
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) 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 0.336

        track chainRBestDanRer10
        parent GCA_018400075.1_ASM1840007v1ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Zebrafish/danRer10 rbChain
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) 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 0.336

        track chainLiftOverDanRer10
        parent GCA_018400075.1_ASM1840007v1ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Zebrafish/danRer10 loChain
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) 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 0.336

        track chainDanRer11
        parent GCA_018400075.1_ASM1840007v1ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Zebrafish/danRer11 Chain
        longLabel Zebrafish/danRer11/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 0.508

        track chainSynDanRer11
        parent GCA_018400075.1_ASM1840007v1ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Zebrafish/danRer11 synChain
        longLabel Zebrafish/danRer11/danRer11 (May 2017) 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 0.508

        track chainRBestDanRer11
        parent GCA_018400075.1_ASM1840007v1ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Zebrafish/danRer11 rbChain
        longLabel Zebrafish/danRer11/danRer11 (May 2017) 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 0.508

        track chainLiftOverDanRer11
        parent GCA_018400075.1_ASM1840007v1ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Zebrafish/danRer11 loChain
        longLabel Zebrafish/danRer11/danRer11 (May 2017) 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 0.508

    track GCA_018400075.1_ASM1840007v1MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_018400075.1_ASM1840007v1ChainNet

        track netDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Zebrafish/danRer10 mafNet
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer10.net.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer10.net.summary.bb
        speciesOrder danRer10
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 0.336

        track synNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Zebrafish/danRer10 synNet
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) Chained Alignments
        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 0.336

        track rbestNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Zebrafish/danRer10 rbestNet
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) Chained Alignments
        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 0.336

        track liftOverNetDanRer10
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c07
        shortLabel Zebrafish/danRer10 liftOverNet
        longLabel Zebrafish/danRer10/danRer10 (Sep. 2014) Chained Alignments
        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 0.336

        track netDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Zebrafish/danRer11 mafNet
        longLabel Zebrafish/danRer11/danRer11 (May 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_018400075.1_ASM1840007v1.danRer11.net.bb
        summary bbi/GCA_018400075.1_ASM1840007v1.danRer11.net.summary.bb
        speciesOrder danRer11
        html html/GCA_018400075.1_ASM1840007v1.chainNet
        priority 0.508

        track synNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Zebrafish/danRer11 synNet
        longLabel Zebrafish/danRer11/danRer11 (May 2017) Chained Alignments
        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 0.508

        track rbestNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Zebrafish/danRer11 rbestNet
        longLabel Zebrafish/danRer11/danRer11 (May 2017) Chained Alignments
        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 0.508

        track liftOverNetDanRer11
        parent GCA_018400075.1_ASM1840007v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c07
        shortLabel Zebrafish/danRer11 liftOverNet
        longLabel Zebrafish/danRer11/danRer11 (May 2017) Chained Alignments
        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 0.508