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_054883265.1_H9_T2T.hap2.assembly.bb
type bigBed 6
html html/GCA_054883265.1_H9_T2T.hap2.assembly
searchIndex name
searchTrix ixIxx/GCA_054883265.1_H9_T2T.hap2.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 hide
color 0,0,0
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.gap.bb
type bigBed 4
group map
html html/GCA_054883265.1_H9_T2T.hap2.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.gc5Base.bw
html html/GCA_054883265.1_H9_T2T.hap2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_054883265.1_H9_T2T.hap2.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.rmsk.bb
xrefDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_054883265.1_H9_T2T.hap2.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.simpleRepeat.bb
html html/GCA_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.windowMasker.bb
html html/GCA_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.allGaps.bb
html html/GCA_054883265.1_H9_T2T.hap2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.augustus.bb
html html/GCA_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.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_054883265.1_H9_T2T.hap2.xenoRefGene.ix
html html/GCA_054883265.1_H9_T2T.hap2.xenoRefGene

track GCA_054883265.1_H9_T2T.hap2ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_054883265.1_H9_T2T.hap2
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=hs1 s001=GCA_054883195.1 s002=hg38
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_054883265.1_H9_T2T.hap2.chainNet

    track GCA_054883265.1_H9_T2T.hap2ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_054883265.1_H9_T2T.hap2ChainNet
    spectrum on

        track chainHs1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Human/hs1 Chain
        longLabel Human/hs1/hs1 (Jan. 2022) Chained Alignments
        type bigChain hs1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainHs1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainHs1Link.bb
        otherDb hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track chainGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel human Chain
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigChain GCA_054883195.1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainGCA_054883195.1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainGCA_054883195.1Link.bb
        otherDb GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track chainHg38
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainHg38.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainHg38Link.bb
        otherDb hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

    track GCA_054883265.1_H9_T2T.hap2ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_054883265.1_H9_T2T.hap2ChainNet
    spectrum on

        track chainSynHs1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Human/hs1 synChain
        longLabel Human/hs1/hs1 (Jan. 2022) Chained Alignments
        type bigChain hs1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynHs1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynHs1Link.bb
        otherDb hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track chainSynGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel human synChain
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigChain GCA_054883195.1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynGCA_054883195.1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynGCA_054883195.1Link.bb
        otherDb GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track chainSynHg38
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38_H9_T2T.hap1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynHg38.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainSynHg38Link.bb
        otherDb hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

    track GCA_054883265.1_H9_T2T.hap2ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_054883265.1_H9_T2T.hap2ChainNet
    spectrum on

        track chainRBestHs1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Human/hs1 rbChain
        longLabel Human/hs1/hs1_H9_T2T.hap1 (Jan. 2022) Chained Alignments
        type bigChain hs1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestHs1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestHs1Link.bb
        otherDb hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track chainRBestGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel human rbChain
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigChain GCA_054883195.1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestGCA_054883195.1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestGCA_054883195.1Link.bb
        otherDb GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track chainRBestHg38
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38_H9_T2T.hap1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestHg38.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

    track GCA_054883265.1_H9_T2T.hap2ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_054883265.1_H9_T2T.hap2ChainNet
    spectrum on

        track chainLiftOverHs1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Human/hs1 loChain
        longLabel Human/hs1/hs1_H9_T2T.hap1 (Jan. 2022) Chained Alignments
        type bigChain hs1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverHs1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverHs1Link.bb
        otherDb hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track chainLiftOverGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel human loChain
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigChain GCA_054883195.1
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverGCA_054883195.1.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverGCA_054883195.1Link.bb
        otherDb GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track chainLiftOverHg38
        parent GCA_054883265.1_H9_T2T.hap2ChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38_H9_T2T.hap1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverHg38.bb
        linkDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

    track GCA_054883265.1_H9_T2T.hap2MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_054883265.1_H9_T2T.hap2ChainNet

        track netHs1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Human/hs1 mafNet
        longLabel Human/hs1/hs1 (Jan. 2022) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hs1.net.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hs1.net.summary.bb
        speciesOrder hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track synNetHs1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Human/hs1 synNet
        longLabel Human/hs1/hs1 (Jan. 2022) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hs1.synNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hs1.synNet.summary.bb
        speciesOrder hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track rbestNetHs1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Human/hs1 rbestNet
        longLabel Human/hs1/hs1 (Jan. 2022) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hs1.rbestNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hs1.rbestNet.summary.bb
        speciesOrder hs1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.339

        track netGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel human mafNet
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.net.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.net.summary.bb
        speciesOrder GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track synNetGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel human synNet
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.synNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.synNet.summary.bb
        speciesOrder GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track rbestNetGCA_054883195.1
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel human rbestNet
        longLabel human/GCA_054883195.1_H9_T2T.hap1 (2026-01-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.rbestNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.GCA_054883195.1.rbestNet.summary.bb
        speciesOrder GCA_054883195.1
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.351

        track netHg38
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s002 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hg38.net.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

        track synNetHg38
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s002 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hg38.synNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954

        track rbestNetHg38
        parent GCA_054883265.1_H9_T2T.hap2MafNetViewnet off
        subGroups view=align species=s002 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_054883265.1_H9_T2T.hap2.hg38.rbestNet.bb
        summary bbi/GCA_054883265.1_H9_T2T.hap2.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCA_054883265.1_H9_T2T.hap2.chainNet
        priority 4.954