hub GCA_001949185.1 genome assembly
shortLabel R.varieornatus (YOKOZUNA-1 2016 tardigrades)
longLabel R.varieornatus (YOKOZUNA-1 2016 tardigrades)/Ramazzottius varieornatus/GCA_001949185.1_Rvar_4.0 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_001949185.1_Rvar_4.0.description.html

genome GCA_001949185.1
taxId 947166
groups groups.txt
description R.varieornatus (YOKOZUNA-1 2016 tardigrades)
twoBitPath GCA_001949185.1.2bit
twoBitBptUrl GCA_001949185.1.2bit.bpt
chromSizes GCA_001949185.1.chrom.sizes.txt
chromAliasBb GCA_001949185.1.chromAlias.bb
organism Rvar_4.0 Nov. 2016
defaultPos BDGG01000001.1:3111028-3121028
scientificName Ramazzottius varieornatus
htmlPath html/GCA_001949185.1_Rvar_4.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/949/185/GCA_001949185.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/949/185/GCA_001949185.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/949/185/GCA_001949185.1
liftOver.GCA_002082055.1 liftOver/GCA_001949185.1ToGCA_002082055.1.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_001949185.1_Rvar_4.0.assembly.bb
type bigBed 6
html html/GCA_001949185.1_Rvar_4.0.assembly
searchIndex name
searchTrix ixIxx/GCA_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.gc5Base.bw
html html/GCA_001949185.1_Rvar_4.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_001949185.1_Rvar_4.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_001949185.1_Rvar_4.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.simpleRepeat.bb
html html/GCA_001949185.1_Rvar_4.0.simpleRepeat

track ncbiGene
longLabel Gene models submitted to NCBI
shortLabel Gene models
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.ncbiGene.bb
type bigGenePred
html html/GCA_001949185.1_Rvar_4.0.ncbiGene
searchIndex name
searchTrix ixIxx/GCA_001949185.1_Rvar_4.0.ncbiGene.ix
url https://www.ncbi.nlm.nih.gov/gene/?term=$$
urlLabel Entrez gene
labelFields geneName,geneName2
defaultLabelFields geneName2
group genes

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_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.windowMasker.bb
html html/GCA_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.allGaps.bb
html html/GCA_001949185.1_Rvar_4.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.augustus.bb
html html/GCA_001949185.1_Rvar_4.0.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_001949185.1_Rvar_4.0.xenoRefGene.bb
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_001949185.1_Rvar_4.0.xenoRefGene.ix
html html/GCA_001949185.1_Rvar_4.0.xenoRefGene

##############################################################################
# GCA_002082055.1 - tardigrades - Ramazzottius varieornatus - taxId: 947166
##############################################################################
track chainNetGCA_002082055.1
compositeTrack on
shortLabel tardigrades Chain/Net
longLabel tardigrades (2016-11-09), 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_002082055.1
html html/GCA_001949185.1_Rvar_4.0.chainNet

    track chainNetGCA_002082055.1Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_002082055.1
    spectrum on

        track chainGCA_002082055.1
        parent chainNetGCA_002082055.1Viewchain
        subGroups view=chain
        shortLabel tardigrades Chain
        longLabel tardigrades (2016-11-09) Chained Alignments
        type bigChain GCA_002082055.1
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainGCA_002082055.1.bb
        linkDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainGCA_002082055.1Link.bb
        priority 1

        track chainSynGCA_002082055.1
        parent chainNetGCA_002082055.1Viewchain
        subGroups view=chain
        shortLabel tardigrades synChain
        longLabel tardigrades (2016-11-09) Syntenic Chained Alignments
        type bigChain GCA_002082055.1
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainSynGCA_002082055.1.bb
        linkDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainSynGCA_002082055.1Link.bb
        priority 2

        track chainRBestGCA_002082055.1
        parent chainNetGCA_002082055.1Viewchain
        subGroups view=chain
        shortLabel tardigrades rbChain
        longLabel tardigrades (2016-11-09) Reciprocal Best Chained Alignments
        type bigChain GCA_002082055.1
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainRBestGCA_002082055.1.bb
        linkDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainRBestGCA_002082055.1Link.bb
        priority 3

        track chainLiftOverGCA_002082055.1
        parent chainNetGCA_002082055.1Viewchain
        subGroups view=chain
        shortLabel tardigrades loChain
        longLabel tardigrades (2016-11-09) Lift Over Chained Alignments
        type bigChain GCA_002082055.1
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainLiftOverGCA_002082055.1.bb
        linkDataUrl bbi/GCA_001949185.1_Rvar_4.0.chainLiftOverGCA_002082055.1Link.bb
        priority 4

    track mafNetGCA_002082055.1Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_002082055.1

        track netGCA_002082055.1
        parent mafNetGCA_002082055.1Viewnet
        subGroups view=net
        shortLabel tardigrades net
        longLabel tardigrades (2016-11-09) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.net.bb
        summary bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.net.summary.bb
        speciesOrder GCA_002082055.1
        priority 5

        track synNetGCA_002082055.1
        parent mafNetGCA_002082055.1Viewnet
        subGroups view=net
        shortLabel tardigrades synNet
        longLabel tardigrades (2016-11-09) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.synNet.bb
        summary bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.synNet.summary.bb
        speciesOrder GCA_002082055.1
        priority 6

        track rbestNetGCA_002082055.1
        parent mafNetGCA_002082055.1Viewnet
        subGroups view=net
        shortLabel tardigrades rbestNet
        longLabel tardigrades (2016-11-09) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.rbestNet.bb
        summary bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.rbestNet.summary.bb
        speciesOrder GCA_002082055.1
        priority 7

        track liftOverNetGCA_002082055.1
        parent mafNetGCA_002082055.1Viewnet
        subGroups view=net
        shortLabel tardigrades liftOverNet
        longLabel tardigrades (2016-11-09) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.liftOverNet.bb
        summary bbi/GCA_001949185.1_Rvar_4.0.GCA_002082055.1.liftOverNet.summary.bb
        speciesOrder GCA_002082055.1
        priority 8