hub GCA_028533165.1 genome assembly
shortLabel golden lion tamarin (Coari 2023)
longLabel golden lion tamarin (Coari 2023)/Leontopithecus rosalia/GCA_028533165.1_Leontopithecus_rosalia_HiC genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_028533165.1_Leontopithecus_rosalia_HiC.description.html

genome GCA_028533165.1
taxId 30588
groups groups.txt
description golden lion tamarin (Coari 2023)
twoBitPath GCA_028533165.1.2bit
twoBitBptUrl GCA_028533165.1.2bit.bpt
chromSizes GCA_028533165.1.chrom.sizes.txt
chromAliasBb GCA_028533165.1.chromAlias.bb
chromAuthority ucsc
organism Leontopithecus_rosalia_HiC Feb. 2023
defaultPos CM052648.1:64698360-64708360
scientificName Leontopithecus rosalia
htmlPath html/GCA_028533165.1_Leontopithecus_rosalia_HiC.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1
liftOver.GCA_011100555.2 liftOver/GCA_028533165.1ToGCA_011100555.2.over.chain.gz

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_028533165.1_Leontopithecus_rosalia_HiC.assembly.bb
type bigBed 6
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.assembly
searchIndex name
searchTrix ixIxx/GCA_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.gc5Base.bw
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.gapOverlap.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.rmsk.bb
xrefDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.simpleRepeat.bb
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.windowMasker.bb
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.allGaps.bb
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.augustus.bb
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.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_028533165.1_Leontopithecus_rosalia_HiC.xenoRefGene.ix
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.xenoRefGene

##############################################################################
# GCA_011100555.2 - golden lion tamarin - Leontopithecus rosalia - taxId: 30588
##############################################################################
track chainNetGCA_011100555.2
compositeTrack on
shortLabel golden lion tamarin Chain/Net
longLabel golden lion tamarin (2023-02-09), 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=+
otherDb GCA_011100555.2
html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainNet

    track chainNetGCA_011100555.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_011100555.2
    spectrum on

        track chainGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel golden lion tamarin Chain
        longLabel golden lion tamarin (2023-02-09) Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainGCA_011100555.2.bb
        linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainGCA_011100555.2Link.bb
        priority 1

        track chainSynGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel golden lion tamarin synChain
        longLabel golden lion tamarin (2023-02-09) Syntenic Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainSynGCA_011100555.2.bb
        linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainSynGCA_011100555.2Link.bb
        priority 2

        track chainRBestGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel golden lion tamarin rbChain
        longLabel golden lion tamarin (2023-02-09) Reciprocal Best Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainRBestGCA_011100555.2.bb
        linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainRBestGCA_011100555.2Link.bb
        priority 3

        track chainLiftOverGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel golden lion tamarin loChain
        longLabel golden lion tamarin (2023-02-09) Lift Over Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainLiftOverGCA_011100555.2.bb
        linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainLiftOverGCA_011100555.2Link.bb
        priority 4

    track mafNetGCA_011100555.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_011100555.2

        track netGCA_011100555.2
        parent mafNetGCA_011100555.2Viewnet
        subGroups view=net
        shortLabel golden lion tamarin net
        longLabel golden lion tamarin (2023-02-09) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.net.bb
        summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.net.summary.bb
        speciesOrder GCA_011100555.2
        priority 5

        track synNetGCA_011100555.2
        parent mafNetGCA_011100555.2Viewnet
        subGroups view=net
        shortLabel golden lion tamarin synNet
        longLabel golden lion tamarin (2023-02-09) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.synNet.bb
        summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.synNet.summary.bb
        speciesOrder GCA_011100555.2
        priority 6

        track rbestNetGCA_011100555.2
        parent mafNetGCA_011100555.2Viewnet
        subGroups view=net
        shortLabel golden lion tamarin rbestNet
        longLabel golden lion tamarin (2023-02-09) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.rbestNet.bb
        summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.rbestNet.summary.bb
        speciesOrder GCA_011100555.2
        priority 7