hub GCA_002759435.3 genome assembly
shortLabel budding yeast C.auris (B8441 2024)
longLabel budding yeast C.auris (B8441 2024)/Candidozyma auris/GCA_002759435.3_Cand_auris_B8441_V3 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_002759435.3_Cand_auris_B8441_V3.description.html

genome GCA_002759435.3
taxId 498019
groups groups.txt
description budding yeast C.auris (B8441 2024)
twoBitPath GCA_002759435.3.2bit
twoBitBptUrl GCA_002759435.3.2bit.bpt
chromSizes GCA_002759435.3.chrom.sizes.txt
chromAliasBb GCA_002759435.3.chromAlias.bb
chromAuthority ucsc
organism Cand_auris_B8441_V3 Apr. 2024
defaultPos CM076438.1:1385127-1395127
scientificName Candidozyma auris
htmlPath html/GCA_002759435.3_Cand_auris_B8441_V3.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/759/435/GCA_002759435.3
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/759/435/GCA_002759435.3
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/759/435/GCA_002759435.3
liftOver.GCA_002759435.2 liftOver/GCA_002759435.3ToGCA_002759435.2.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_002759435.3_Cand_auris_B8441_V3.assembly.bb
type bigBed 6
html html/GCA_002759435.3_Cand_auris_B8441_V3.assembly
searchIndex name
searchTrix ixIxx/GCA_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.gc5Base.bw
html html/GCA_002759435.3_Cand_auris_B8441_V3.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_002759435.3_Cand_auris_B8441_V3.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.rmsk.bb
xrefDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_002759435.3_Cand_auris_B8441_V3.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.simpleRepeat.bb
html html/GCA_002759435.3_Cand_auris_B8441_V3.simpleRepeat

track ncbiGene
longLabel Gene models submitted to GenBank, ENA, DDBJ
shortLabel NCBI GenBank
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.ncbiGene.bb
type bigGenePred
urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
html html/GCA_002759435.3_Cand_auris_B8441_V3.ncbiGene
searchIndex name
searchTrix ixIxx/GCA_002759435.3_Cand_auris_B8441_V3.ncbiGene.ix
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 dense
type bigBed 4 +
html html/GCA_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.windowMasker.bb
html html/GCA_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.allGaps.bb
html html/GCA_002759435.3_Cand_auris_B8441_V3.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.augustus.bb
html html/GCA_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.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_002759435.3_Cand_auris_B8441_V3.xenoRefGene.ix
html html/GCA_002759435.3_Cand_auris_B8441_V3.xenoRefGene

##############################################################################
# GCA_002759435.2 - budding yeasts & others - Candidozyma auris - taxId: 498019
##############################################################################
track chainNetGCA_002759435.2
compositeTrack on
shortLabel budding yeasts & others Chain/Net
longLabel budding yeasts & others (2024-04-22), 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_002759435.2
html html/GCA_002759435.3_Cand_auris_B8441_V3.chainNet

    track chainNetGCA_002759435.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_002759435.2
    spectrum on

        track chainGCA_002759435.2
        parent chainNetGCA_002759435.2Viewchain
        subGroups view=chain
        shortLabel budding yeasts & others Chain
        longLabel budding yeasts & others (2024-04-22) Chained Alignments
        type bigChain GCA_002759435.2
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainGCA_002759435.2.bb
        linkDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainGCA_002759435.2Link.bb
        priority 1

        track chainSynGCA_002759435.2
        parent chainNetGCA_002759435.2Viewchain
        subGroups view=chain
        shortLabel budding yeasts & others synChain
        longLabel budding yeasts & others (2024-04-22) Syntenic Chained Alignments
        type bigChain GCA_002759435.2
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainSynGCA_002759435.2.bb
        linkDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainSynGCA_002759435.2Link.bb
        priority 2

        track chainRBestGCA_002759435.2
        parent chainNetGCA_002759435.2Viewchain
        subGroups view=chain
        shortLabel budding yeasts & others rbChain
        longLabel budding yeasts & others (2024-04-22) Reciprocal Best Chained Alignments
        type bigChain GCA_002759435.2
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainRBestGCA_002759435.2.bb
        linkDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainRBestGCA_002759435.2Link.bb
        priority 3

        track chainLiftOverGCA_002759435.2
        parent chainNetGCA_002759435.2Viewchain
        subGroups view=chain
        shortLabel budding yeasts & others loChain
        longLabel budding yeasts & others (2024-04-22) Lift Over Chained Alignments
        type bigChain GCA_002759435.2
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainLiftOverGCA_002759435.2.bb
        linkDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.chainLiftOverGCA_002759435.2Link.bb
        priority 4

    track mafNetGCA_002759435.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_002759435.2

        track netGCA_002759435.2
        parent mafNetGCA_002759435.2Viewnet
        subGroups view=net
        shortLabel budding yeasts & others net
        longLabel budding yeasts & others (2024-04-22) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.net.bb
        summary bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.net.summary.bb
        speciesOrder GCA_002759435.2
        priority 5

        track synNetGCA_002759435.2
        parent mafNetGCA_002759435.2Viewnet
        subGroups view=net
        shortLabel budding yeasts & others synNet
        longLabel budding yeasts & others (2024-04-22) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.synNet.bb
        summary bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.synNet.summary.bb
        speciesOrder GCA_002759435.2
        priority 6

        track rbestNetGCA_002759435.2
        parent mafNetGCA_002759435.2Viewnet
        subGroups view=net
        shortLabel budding yeasts & others rbestNet
        longLabel budding yeasts & others (2024-04-22) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.rbestNet.bb
        summary bbi/GCA_002759435.3_Cand_auris_B8441_V3.GCA_002759435.2.rbestNet.summary.bb
        speciesOrder GCA_002759435.2
        priority 7