hub GCF_000002845.2 genome assembly
shortLabel Leishmania braziliensis (MHOM/BR/75/M2904 2011 kinetoplastids)
longLabel Leishmania braziliensis (MHOM/BR/75/M2904 2011 kinetoplastids)/Leishmania braziliensis MHOM/BR/75/M2904/GCF_000002845.2_ASM284v2 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_000002845.2_ASM284v2.description.html

genome GCF_000002845.2
taxId 420245
groups groups.txt
description Leishmania braziliensis (MHOM/BR/75/M2904 2011 kinetoplastids)
twoBitPath GCF_000002845.2.2bit
twoBitBptUrl GCF_000002845.2.2bit.bpt
chromSizes GCF_000002845.2.chrom.sizes.txt
chromAliasBb GCF_000002845.2.chromAlias.bb
chromAuthority ucsc
organism ASM284v2 Nov. 2011
defaultPos NC_009327.2:895547-905547
scientificName Leishmania braziliensis MHOM/BR/75/M2904
htmlPath html/GCF_000002845.2_ASM284v2.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/845/GCF_000002845.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/845/GCF_000002845.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/845/GCF_000002845.2
liftOver.GCA_000340355.2 liftOver/GCF_000002845.2ToGCA_000340355.2.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/GCF_000002845.2_ASM284v2.assembly.bb
type bigBed 6
html html/GCF_000002845.2_ASM284v2.assembly
searchIndex name
searchTrix ixIxx/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.gc5Base.bw
html html/GCF_000002845.2_ASM284v2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000002845.2_ASM284v2.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_000002845.2_ASM284v2.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_000002845.2_ASM284v2.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002845.2_ASM284v2.simpleRepeat.bb
html html/GCF_000002845.2_ASM284v2.simpleRepeat

track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq gene predictions from NCBI
group genes
visibility pack
type bigBed
dragAndDrop subTracks
allButtonPair on
dataVersion GCF_000002845.2_ASM284v2 (2021-09-26)
html html/GCF_000002845.2_ASM284v2.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        altColor 120,12,12
        shortLabel RefSeq All
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002845.2_ASM284v2.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.ncbiRefSeq.bb
        longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
        idXref ncbiRefSeqLink mrnaAcc name
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 1

        track ncbiRefSeqPredicted
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Predicted
        longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002845.2_ASM284v2.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.ncbiRefSeqPredicted.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 3

        track ncbiRefSeqOther
        color 32,32,32
        parent refSeqComposite on
        shortLabel RefSeq Other
        longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
        priority 4
        searchIndex name
        searchTrix ixIxx/GCF_000002845.2_ASM284v2.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.ncbiRefSeqOther.bb
        type bigBed 12 +
        labelFields gene
        skipEmptyFields on
        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"

        track ncbiRefSeqPsl
        priority 5
        parent refSeqComposite off
        shortLabel RefSeq Alignments
        longLabel RefSeq Alignments of RNAs
        type bigPsl
        searchIndex name
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.bigPsl.bb
        indelDoubleInsert on
        indelQueryInsert on
        showDiffBasesAllScales .
        showDiffBasesMaxZoom 10000.0
        showCdsMaxZoom 10000.0
        showCdsAllScales .
        baseColorDefault diffCodons
        pslSequence no
        baseColorUseSequence lfExtra
        baseColorUseCds table given
        color 0,0,0

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/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000002845.2_ASM284v2.windowMasker.bb
html html/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.allGaps.bb
html html/GCF_000002845.2_ASM284v2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000002845.2_ASM284v2.augustus.bb
html html/GCF_000002845.2_ASM284v2.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/GCF_000002845.2_ASM284v2.xenoRefGene.bb
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_000002845.2_ASM284v2.xenoRefGene.ix
html html/GCF_000002845.2_ASM284v2.xenoRefGene

##############################################################################
# GCA_000340355.2 - kinetoplastids - Leishmania braziliensis MHOM/BR/75/M2904 - taxId: 420245
##############################################################################
track chainNetGCA_000340355.2
compositeTrack on
shortLabel kinetoplastids Chain/Net
longLabel kinetoplastids (2011-11-07), 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_000340355.2
html html/GCF_000002845.2_ASM284v2.chainNet

    track chainNetGCA_000340355.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_000340355.2
    spectrum on

        track chainGCA_000340355.2
        parent chainNetGCA_000340355.2Viewchain
        subGroups view=chain
        shortLabel kinetoplastids Chain
        longLabel kinetoplastids (2011-11-07) Chained Alignments
        type bigChain GCA_000340355.2
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.chainGCA_000340355.2.bb
        linkDataUrl bbi/GCF_000002845.2_ASM284v2.chainGCA_000340355.2Link.bb
        priority 1

        track chainSynGCA_000340355.2
        parent chainNetGCA_000340355.2Viewchain
        subGroups view=chain
        shortLabel kinetoplastids synChain
        longLabel kinetoplastids (2011-11-07) Syntenic Chained Alignments
        type bigChain GCA_000340355.2
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.chainSynGCA_000340355.2.bb
        linkDataUrl bbi/GCF_000002845.2_ASM284v2.chainSynGCA_000340355.2Link.bb
        priority 2

        track chainRBestGCA_000340355.2
        parent chainNetGCA_000340355.2Viewchain
        subGroups view=chain
        shortLabel kinetoplastids rbChain
        longLabel kinetoplastids (2011-11-07) Reciprocal Best Chained Alignments
        type bigChain GCA_000340355.2
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.chainRBestGCA_000340355.2.bb
        linkDataUrl bbi/GCF_000002845.2_ASM284v2.chainRBestGCA_000340355.2Link.bb
        priority 3

        track chainLiftOverGCA_000340355.2
        parent chainNetGCA_000340355.2Viewchain
        subGroups view=chain
        shortLabel kinetoplastids loChain
        longLabel kinetoplastids (2011-11-07) Lift Over Chained Alignments
        type bigChain GCA_000340355.2
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.chainLiftOverGCA_000340355.2.bb
        linkDataUrl bbi/GCF_000002845.2_ASM284v2.chainLiftOverGCA_000340355.2Link.bb
        priority 4

    track mafNetGCA_000340355.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_000340355.2

        track netGCA_000340355.2
        parent mafNetGCA_000340355.2Viewnet
        subGroups view=net
        shortLabel kinetoplastids net
        longLabel kinetoplastids (2011-11-07) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.net.bb
        summary bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.net.summary.bb
        speciesOrder GCA_000340355.2
        priority 5

        track synNetGCA_000340355.2
        parent mafNetGCA_000340355.2Viewnet
        subGroups view=net
        shortLabel kinetoplastids synNet
        longLabel kinetoplastids (2011-11-07) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.synNet.bb
        summary bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.synNet.summary.bb
        speciesOrder GCA_000340355.2
        priority 6

        track rbestNetGCA_000340355.2
        parent mafNetGCA_000340355.2Viewnet
        subGroups view=net
        shortLabel kinetoplastids rbestNet
        longLabel kinetoplastids (2011-11-07) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.rbestNet.bb
        summary bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.rbestNet.summary.bb
        speciesOrder GCA_000340355.2
        priority 7

        track liftOverNetGCA_000340355.2
        parent mafNetGCA_000340355.2Viewnet
        subGroups view=net
        shortLabel kinetoplastids liftOverNet
        longLabel kinetoplastids (2011-11-07) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.liftOverNet.bb
        summary bbi/GCF_000002845.2_ASM284v2.GCA_000340355.2.liftOverNet.summary.bb
        speciesOrder GCA_000340355.2
        priority 8