hub GCA_040894015.1 genome assembly
shortLabel Tungara frog (aEngPut4 paternal hap 2024)
longLabel Tungara frog (aEngPut4 paternal hap 2024)/Engystomops pustulosus/GCA_040894015.1_aEngPut4.paternal genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_040894015.1_aEngPut4.paternal.description.html

genome GCA_040894015.1
taxId 76066
groups groups.txt
description Tungara frog (aEngPut4 paternal hap 2024)
twoBitPath GCA_040894015.1.2bit
twoBitBptUrl GCA_040894015.1.2bit.bpt
chromSizes GCA_040894015.1.chrom.sizes.txt
chromAliasBb GCA_040894015.1.chromAlias.bb
chromAuthority ucsc
organism aEngPut4.paternal Jul. 2024
defaultPos CM082094.1:101338699-101348699
scientificName Engystomops pustulosus
htmlPath html/GCA_040894015.1_aEngPut4.paternal.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/040/894/015/GCA_040894015.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/040/894/015/GCA_040894015.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/040/894/015/GCA_040894015.1
liftOver.xenTro10 liftOver/GCA_040894015.1ToXenTro10.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_040894015.1_aEngPut4.paternal.assembly.bb
type bigBed 6
html html/GCA_040894015.1_aEngPut4.paternal.assembly
searchIndex name
searchTrix ixIxx/GCA_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.gc5Base.bw
html html/GCA_040894015.1_aEngPut4.paternal.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_040894015.1_aEngPut4.paternal.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.rmsk.bb
xrefDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_040894015.1_aEngPut4.paternal.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.rModel.bb
xrefDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_040894015.1_aEngPut4.paternal.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.simpleRepeat.bb
html html/GCA_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.windowMasker.bb
html html/GCA_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.allGaps.bb
html html/GCA_040894015.1_aEngPut4.paternal.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.augustus.bb
html html/GCA_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.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_040894015.1_aEngPut4.paternal.xenoRefGene.ix
html html/GCA_040894015.1_aEngPut4.paternal.xenoRefGene

##############################################################################
# xenTro10 - X. tropicalis - Xenopus tropicalis - taxId: 8364
##############################################################################
track chainNetXenTro10
compositeTrack on
shortLabel X. tropicalis Chain/Net
longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)), 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 5000
chainLinearGap loose
matrixHeader A, C, G, T
otherDb xenTro10
html html/GCA_040894015.1_aEngPut4.paternal.chainNet

    track chainNetXenTro10Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetXenTro10
    spectrum on

        track chainXenTro10
        parent chainNetXenTro10Viewchain
        subGroups view=chain
        shortLabel X. tropicalis Chain
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainXenTro10.bb
        linkDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainXenTro10Link.bb
        priority 1

        track chainSynXenTro10
        parent chainNetXenTro10Viewchain
        subGroups view=chain
        shortLabel X. tropicalis synChain
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Syntenic Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainSynXenTro10.bb
        linkDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainSynXenTro10Link.bb
        priority 2

        track chainRBestXenTro10
        parent chainNetXenTro10Viewchain
        subGroups view=chain
        shortLabel X. tropicalis rbChain
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Reciprocal Best Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainRBestXenTro10.bb
        linkDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainRBestXenTro10Link.bb
        priority 3

        track chainLiftOverXenTro10
        parent chainNetXenTro10Viewchain
        subGroups view=chain
        shortLabel X. tropicalis loChain
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Lift Over Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainLiftOverXenTro10.bb
        linkDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.chainLiftOverXenTro10Link.bb
        priority 4

    track mafNetXenTro10Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetXenTro10

        track netXenTro10
        parent mafNetXenTro10Viewnet
        subGroups view=net
        shortLabel X. tropicalis net
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.net.bb
        summary bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.net.summary.bb
        speciesOrder xenTro10
        priority 5

        track synNetXenTro10
        parent mafNetXenTro10Viewnet
        subGroups view=net
        shortLabel X. tropicalis synNet
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.synNet.bb
        summary bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.synNet.summary.bb
        speciesOrder xenTro10
        priority 6

        track rbestNetXenTro10
        parent mafNetXenTro10Viewnet
        subGroups view=net
        shortLabel X. tropicalis rbestNet
        longLabel X. tropicalis (Nov. 2019 (UCB_Xtro_10.0/xenTro10)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.rbestNet.bb
        summary bbi/GCA_040894015.1_aEngPut4.paternal.xenTro10.rbestNet.summary.bb
        speciesOrder xenTro10
        priority 7