hub GCA_900093555.2 genome assembly
shortLabel malaria parasite P. vivax (PvP01 2019)
longLabel malaria parasite P. vivax (PvP01 2019)/Plasmodium vivax/GCA_900093555.2_GCA_900093555 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_900093555.2_GCA_900093555.description.html

genome GCA_900093555.2
taxId 5855
groups groups.txt
description malaria parasite P. vivax (PvP01 2019)
twoBitPath GCA_900093555.2.2bit
twoBitBptUrl GCA_900093555.2.2bit.bpt
chromSizes GCA_900093555.2.chrom.sizes.txt
chromAliasBb GCA_900093555.2.chromAlias.bb
chromAuthority ucsc
organism GCA_900093555 Aug. 2019
defaultPos LT635623.1:1060921-1070921
scientificName Plasmodium vivax
htmlPath html/GCA_900093555.2_GCA_900093555.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/093/555/GCA_900093555.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/093/555/GCA_900093555.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/093/555/GCA_900093555.2
liftOver.GCF_000002415.2 liftOver/GCA_900093555.2ToGCF_000002415.2.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_900093555.2_GCA_900093555.assembly.bb
type bigBed 6
html html/GCA_900093555.2_GCA_900093555.assembly
searchIndex name
searchTrix ixIxx/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.gc5Base.bw
html html/GCA_900093555.2_GCA_900093555.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_900093555.2_GCA_900093555.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_900093555.2_GCA_900093555.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_900093555.2_GCA_900093555.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_900093555.2_GCA_900093555.simpleRepeat.bb
html html/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.ncbiGene.bb
type bigGenePred
html html/GCA_900093555.2_GCA_900093555.ncbiGene
searchIndex name
searchTrix ixIxx/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_900093555.2_GCA_900093555.windowMasker.bb
html html/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.allGaps.bb
html html/GCA_900093555.2_GCA_900093555.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_900093555.2_GCA_900093555.augustus.bb
html html/GCA_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.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_900093555.2_GCA_900093555.xenoRefGene.ix
html html/GCA_900093555.2_GCA_900093555.xenoRefGene

##############################################################################
# GCF_000002415.2 - malaria parasite P. vivax - Plasmodium vivax - taxId: 5855
##############################################################################
track chainNetGCF_000002415.2
compositeTrack on
shortLabel malaria parasite P. vivax Chain/Net
longLabel malaria parasite P. vivax (2019-08-01), 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 GCF_000002415.2
html html/GCA_900093555.2_GCA_900093555.chainNet

    track chainNetGCF_000002415.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_000002415.2
    spectrum on

        track chainGCF_000002415.2
        parent chainNetGCF_000002415.2Viewchain
        subGroups view=chain
        shortLabel malaria parasite P. vivax Chain
        longLabel malaria parasite P. vivax (2019-08-01) Chained Alignments
        type bigChain GCF_000002415.2
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.chainGCF_000002415.2.bb
        linkDataUrl bbi/GCA_900093555.2_GCA_900093555.chainGCF_000002415.2Link.bb
        priority 1

        track chainSynGCF_000002415.2
        parent chainNetGCF_000002415.2Viewchain
        subGroups view=chain
        shortLabel malaria parasite P. vivax synChain
        longLabel malaria parasite P. vivax (2019-08-01) Syntenic Chained Alignments
        type bigChain GCF_000002415.2
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.chainSynGCF_000002415.2.bb
        linkDataUrl bbi/GCA_900093555.2_GCA_900093555.chainSynGCF_000002415.2Link.bb
        priority 2

        track chainRBestGCF_000002415.2
        parent chainNetGCF_000002415.2Viewchain
        subGroups view=chain
        shortLabel malaria parasite P. vivax rbChain
        longLabel malaria parasite P. vivax (2019-08-01) Reciprocal Best Chained Alignments
        type bigChain GCF_000002415.2
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.chainRBestGCF_000002415.2.bb
        linkDataUrl bbi/GCA_900093555.2_GCA_900093555.chainRBestGCF_000002415.2Link.bb
        priority 3

        track chainLiftOverGCF_000002415.2
        parent chainNetGCF_000002415.2Viewchain
        subGroups view=chain
        shortLabel malaria parasite P. vivax loChain
        longLabel malaria parasite P. vivax (2019-08-01) Lift Over Chained Alignments
        type bigChain GCF_000002415.2
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.chainLiftOverGCF_000002415.2.bb
        linkDataUrl bbi/GCA_900093555.2_GCA_900093555.chainLiftOverGCF_000002415.2Link.bb
        priority 4

    track mafNetGCF_000002415.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_000002415.2

        track netGCF_000002415.2
        parent mafNetGCF_000002415.2Viewnet
        subGroups view=net
        shortLabel malaria parasite P. vivax net
        longLabel malaria parasite P. vivax (2019-08-01) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.net.bb
        summary bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.net.summary.bb
        speciesOrder GCF_000002415.2
        priority 5

        track synNetGCF_000002415.2
        parent mafNetGCF_000002415.2Viewnet
        subGroups view=net
        shortLabel malaria parasite P. vivax synNet
        longLabel malaria parasite P. vivax (2019-08-01) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.synNet.bb
        summary bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.synNet.summary.bb
        speciesOrder GCF_000002415.2
        priority 6

        track rbestNetGCF_000002415.2
        parent mafNetGCF_000002415.2Viewnet
        subGroups view=net
        shortLabel malaria parasite P. vivax rbestNet
        longLabel malaria parasite P. vivax (2019-08-01) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.rbestNet.bb
        summary bbi/GCA_900093555.2_GCA_900093555.GCF_000002415.2.rbestNet.summary.bb
        speciesOrder GCF_000002415.2
        priority 7