hub GCF_004193775.1 genome assembly
shortLabel wild soybean
longLabel wild soybean/Glycine soja/GCF_004193775.1_ASM419377v2 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_004193775.1_ASM419377v2.description.html

genome GCF_004193775.1
taxId 3848
groups groups.txt
description wild soybean
twoBitPath GCF_004193775.1.2bit
twoBitBptUrl GCF_004193775.1.2bit.bpt
chromSizes GCF_004193775.1.chrom.sizes.txt
chromAliasBb GCF_004193775.1.chromAlias.bb
chromAuthority ucsc
organism ASM419377v2 Feb. 2019
defaultPos NC_041019.1:19246692-19256692
scientificName Glycine soja
htmlPath html/GCF_004193775.1_ASM419377v2.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/193/775/GCF_004193775.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/193/775/GCF_004193775.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/193/775/GCF_004193775.1
liftOver.GCF_000004515.6 liftOver/GCF_004193775.1ToGCF_000004515.6.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_004193775.1_ASM419377v2.assembly.bb
type bigBed 6
html html/GCF_004193775.1_ASM419377v2.assembly
searchIndex name
searchTrix ixIxx/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.gc5Base.bw
html html/GCF_004193775.1_ASM419377v2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_004193775.1_ASM419377v2.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.tandemDups.bb
    type bigBed 12

track repeatMasker
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility dense
type bigBed 6 +
colorByStrand 50,50,150 150,50,50
maxWindowToDraw 10000000
spectrum on
html html/GCF_004193775.1_ASM419377v2.repeatMasker

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCF_004193775.1_ASM419377v2.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 6
    bigDataUrl bbi/GCF_004193775.1_ASM419377v2.rmsk.Low_complexity.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCF_004193775.1_ASM419377v2.rmsk.RNA.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_004193775.1_ASM419377v2.simpleRepeat.bb
html html/GCF_004193775.1_ASM419377v2.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 NCBI Glycine soja Annotation Release 100 (2019-05-07)
html html/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.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 ncbiRefSeqCurated
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Curated
        longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_004193775.1_ASM419377v2.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.ncbiRefSeqCurated.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 2

        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_004193775.1_ASM419377v2.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.ncbiRefSeqOther.bb
        type bigBed 12 +
        labelFields name
        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_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_004193775.1_ASM419377v2.windowMasker.bb
html html/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.allGaps.bb
html html/GCF_004193775.1_ASM419377v2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_004193775.1_ASM419377v2.augustus.bb
html html/GCF_004193775.1_ASM419377v2.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_004193775.1_ASM419377v2.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_004193775.1_ASM419377v2.xenoRefGene.ix
html html/GCF_004193775.1_ASM419377v2.xenoRefGene

##############################################################################
# GCF_000004515.6 - wild soybean - Glycine soja - taxId: 3848
##############################################################################
track chainNetGCF_000004515.6
compositeTrack on
shortLabel wild soybean Chain/Net
longLabel wild soybean (2019-02-21), 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_000004515.6
html html/GCF_004193775.1_ASM419377v2.chainNet

    track chainNetGCF_000004515.6Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_000004515.6
    spectrum on

        track chainGCF_000004515.6
        parent chainNetGCF_000004515.6Viewchain
        subGroups view=chain
        shortLabel wild soybean Chain
        longLabel wild soybean (2019-02-21) Chained Alignments
        type bigChain GCF_000004515.6
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.chainGCF_000004515.6.bb
        linkDataUrl bbi/GCF_004193775.1_ASM419377v2.chainGCF_000004515.6Link.bb
        priority 1

        track chainSynGCF_000004515.6
        parent chainNetGCF_000004515.6Viewchain
        subGroups view=chain
        shortLabel wild soybean synChain
        longLabel wild soybean (2019-02-21) Syntenic Chained Alignments
        type bigChain GCF_000004515.6
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.chainSynGCF_000004515.6.bb
        linkDataUrl bbi/GCF_004193775.1_ASM419377v2.chainSynGCF_000004515.6Link.bb
        priority 2

        track chainRBestGCF_000004515.6
        parent chainNetGCF_000004515.6Viewchain
        subGroups view=chain
        shortLabel wild soybean rbChain
        longLabel wild soybean (2019-02-21) Reciprocal Best Chained Alignments
        type bigChain GCF_000004515.6
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.chainRBestGCF_000004515.6.bb
        linkDataUrl bbi/GCF_004193775.1_ASM419377v2.chainRBestGCF_000004515.6Link.bb
        priority 3

    track mafNetGCF_000004515.6Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_000004515.6

        track netGCF_000004515.6
        parent mafNetGCF_000004515.6Viewnet
        subGroups view=net
        shortLabel wild soybean net
        longLabel wild soybean (2019-02-21) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.net.bb
        summary bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.net.summary.bb
        speciesOrder GCF_000004515.6
        priority 4

        track synNetGCF_000004515.6
        parent mafNetGCF_000004515.6Viewnet
        subGroups view=net
        shortLabel wild soybean synNet
        longLabel wild soybean (2019-02-21) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.synNet.bb
        summary bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.synNet.summary.bb
        speciesOrder GCF_000004515.6
        priority 5

        track rbestNetGCF_000004515.6
        parent mafNetGCF_000004515.6Viewnet
        subGroups view=net
        shortLabel wild soybean rbestNet
        longLabel wild soybean (2019-02-21) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.rbestNet.bb
        summary bbi/GCF_004193775.1_ASM419377v2.GCF_000004515.6.rbestNet.summary.bb
        speciesOrder GCF_000004515.6
        priority 6