hub GCF_000004515.6 genome assembly
shortLabel soybean (US DOE JGI-PGF v2 2021)
longLabel soybean (US DOE JGI-PGF v2 2021)/Glycine max/GCF_000004515.6_Glycine_max_v4.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_000004515.6_Glycine_max_v4.0.description.html

genome GCF_000004515.6
taxId 3847
groups groups.txt
description soybean (US DOE JGI-PGF v2 2021)
twoBitPath GCF_000004515.6.2bit
twoBitBptUrl GCF_000004515.6.2bit.bpt
chromSizes GCF_000004515.6.chrom.sizes.txt
chromAliasBb GCF_000004515.6.chromAlias.bb
chromAuthority ucsc
organism Glycine_max_v4.0 Mar. 2021
defaultPos NC_038254.2:19428756-19438756
scientificName Glycine max
htmlPath html/GCF_000004515.6_Glycine_max_v4.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/004/515/GCF_000004515.6
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/004/515/GCF_000004515.6
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/004/515/GCF_000004515.6
liftOver.GCF_004193775.1 liftOver/GCF_000004515.6ToGCF_004193775.1.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/GCF_000004515.6_Glycine_max_v4.0.assembly.bb
type bigBed 6
html html/GCF_000004515.6_Glycine_max_v4.0.assembly
searchIndex name
searchTrix ixIxx/GCF_000004515.6_Glycine_max_v4.0.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility hide
color 0,0,0
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.gap.bb
type bigBed 4
group map
html html/GCF_000004515.6_Glycine_max_v4.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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/GCF_000004515.6_Glycine_max_v4.0.gc5Base.bw
html html/GCF_000004515.6_Glycine_max_v4.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000004515.6_Glycine_max_v4.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.rmsk.bb
xrefDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_000004515.6_Glycine_max_v4.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.simpleRepeat.bb
html html/GCF_000004515.6_Glycine_max_v4.0.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 RefSeq GCF_000004515.6-RS_2025_01 (2025-01-31)
html html/GCF_000004515.6_Glycine_max_v4.0.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        shortLabel RefSeq All
        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/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000004515.6_Glycine_max_v4.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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
        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/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000004515.6_Glycine_max_v4.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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
        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/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000004515.6_Glycine_max_v4.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.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 dense
type bigBed 4 +
html html/GCF_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.windowMasker.bb
html html/GCF_000004515.6_Glycine_max_v4.0.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/GCF_000004515.6_Glycine_max_v4.0.allGaps.bb
html html/GCF_000004515.6_Glycine_max_v4.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.augustus.bb
html html/GCF_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.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_000004515.6_Glycine_max_v4.0.xenoRefGene.ix
html html/GCF_000004515.6_Glycine_max_v4.0.xenoRefGene

##############################################################################
# GCF_004193775.1 - soybean - Glycine max - taxId: 3847
##############################################################################
track chainNetGCF_004193775.1
compositeTrack on
shortLabel soybean Chain/Net
longLabel soybean (2021-03-10), 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_004193775.1
html html/GCF_000004515.6_Glycine_max_v4.0.chainNet

    track chainNetGCF_004193775.1Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_004193775.1
    spectrum on

        track chainGCF_004193775.1
        parent chainNetGCF_004193775.1Viewchain
        subGroups view=chain
        shortLabel soybean Chain
        longLabel soybean (2021-03-10) Chained Alignments
        type bigChain GCF_004193775.1
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainGCF_004193775.1.bb
        linkDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainGCF_004193775.1Link.bb
        priority 1

        track chainSynGCF_004193775.1
        parent chainNetGCF_004193775.1Viewchain
        subGroups view=chain
        shortLabel soybean synChain
        longLabel soybean (2021-03-10) Syntenic Chained Alignments
        type bigChain GCF_004193775.1
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainSynGCF_004193775.1.bb
        linkDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainSynGCF_004193775.1Link.bb
        priority 2

        track chainRBestGCF_004193775.1
        parent chainNetGCF_004193775.1Viewchain
        subGroups view=chain
        shortLabel soybean rbChain
        longLabel soybean (2021-03-10) Reciprocal Best Chained Alignments
        type bigChain GCF_004193775.1
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainRBestGCF_004193775.1.bb
        linkDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.chainRBestGCF_004193775.1Link.bb
        priority 3

    track mafNetGCF_004193775.1Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_004193775.1

        track netGCF_004193775.1
        parent mafNetGCF_004193775.1Viewnet
        subGroups view=net
        shortLabel soybean net
        longLabel soybean (2021-03-10) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.net.bb
        summary bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.net.summary.bb
        speciesOrder GCF_004193775.1
        priority 4

        track synNetGCF_004193775.1
        parent mafNetGCF_004193775.1Viewnet
        subGroups view=net
        shortLabel soybean synNet
        longLabel soybean (2021-03-10) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.synNet.bb
        summary bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.synNet.summary.bb
        speciesOrder GCF_004193775.1
        priority 5

        track rbestNetGCF_004193775.1
        parent mafNetGCF_004193775.1Viewnet
        subGroups view=net
        shortLabel soybean rbestNet
        longLabel soybean (2021-03-10) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.rbestNet.bb
        summary bbi/GCF_000004515.6_Glycine_max_v4.0.GCF_004193775.1.rbestNet.summary.bb
        speciesOrder GCF_004193775.1
        priority 6