hub GCA_009873245.2 genome assembly
shortLabel blue whale (JJ_BM4_2016_0621 v2 2020)
longLabel blue whale (JJ_BM4_2016_0621 v2 2020)/Balaenoptera musculus/GCA_009873245.2_mBalMus1.v2 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_009873245.2_mBalMus1.v2.description.html

genome GCA_009873245.2
taxId 9771
groups groups.txt
description blue whale (JJ_BM4_2016_0621 v2 2020)
twoBitPath GCA_009873245.2.2bit
twoBitBptUrl GCA_009873245.2.2bit.bpt
chromSizes GCA_009873245.2.chrom.sizes.txt
chromAliasBb GCA_009873245.2.chromAlias.bb
chromAuthority ucsc
organism mBalMus1.v2 Feb. 2020
defaultPos CM020941.1:61719102-61729102
scientificName Balaenoptera musculus
htmlPath html/GCA_009873245.2_mBalMus1.v2.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/873/245/GCA_009873245.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/873/245/GCA_009873245.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/873/245/GCA_009873245.2
liftOver.GCF_001704415.2 liftOver/GCA_009873245.2ToGCF_001704415.2.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_009873245.2_mBalMus1.v2.assembly.bb
type bigBed 6
html html/GCA_009873245.2_mBalMus1.v2.assembly
searchIndex name
searchTrix ixIxx/GCA_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.gc5Base.bw
html html/GCA_009873245.2_mBalMus1.v2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_009873245.2_mBalMus1.v2.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_009873245.2_mBalMus1.v2.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.simpleRepeat.bb
html html/GCA_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.windowMasker.bb
html html/GCA_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.allGaps.bb
html html/GCA_009873245.2_mBalMus1.v2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.augustus.bb
html html/GCA_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.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_009873245.2_mBalMus1.v2.xenoRefGene.ix
html html/GCA_009873245.2_mBalMus1.v2.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2020_02
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.ensGene.bb
searchTrix ixIxx/GCA_009873245.2_mBalMus1.v2.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCA_009873245.2_mBalMus1.v2.ensGene

##############################################################################
# GCF_001704415.2 - Blue whale - Balaenoptera musculus - taxId: 9771
##############################################################################
track chainNetGCF_001704415.2
compositeTrack on
shortLabel Blue whale Chain/Net
longLabel Blue whale (2020-02-03), 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_001704415.2
html html/GCA_009873245.2_mBalMus1.v2.chainNet

    track chainNetGCF_001704415.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_001704415.2
    spectrum on

        track chainGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Blue whale Chain
        longLabel Blue whale (2020-02-03) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainGCF_001704415.2Link.bb
        priority 1

        track chainSynGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Blue whale synChain
        longLabel Blue whale (2020-02-03) Syntenic Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainSynGCF_001704415.2Link.bb
        priority 2

        track chainRBestGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Blue whale rbChain
        longLabel Blue whale (2020-02-03) Reciprocal Best Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainRBestGCF_001704415.2Link.bb
        priority 3

        track chainLiftOverGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Blue whale loChain
        longLabel Blue whale (2020-02-03) Lift Over Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCA_009873245.2_mBalMus1.v2.chainLiftOverGCF_001704415.2Link.bb
        priority 4

    track mafNetGCF_001704415.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_001704415.2

        track netGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Blue whale net
        longLabel Blue whale (2020-02-03) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.net.bb
        summary bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        priority 5

        track synNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Blue whale synNet
        longLabel Blue whale (2020-02-03) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.synNet.bb
        summary bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 6

        track rbestNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Blue whale rbestNet
        longLabel Blue whale (2020-02-03) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.rbestNet.bb
        summary bbi/GCA_009873245.2_mBalMus1.v2.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 7