hub GCA_000188115.5 genome assembly
shortLabel tomato (SL4.0 Heinz 1706 2025 genbank)
longLabel tomato (SL4.0 Heinz 1706 2025 genbank)/Solanum lycopersicum/GCA_000188115.5_SL4.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_000188115.5_SL4.0.description.html

genome GCA_000188115.5
taxId 4081
groups groups.txt
description tomato (SL4.0 Heinz 1706 2025 genbank)
twoBitPath GCA_000188115.5.2bit
twoBitBptUrl GCA_000188115.5.2bit.bpt
chromSizes GCA_000188115.5.chrom.sizes.txt
chromAliasBb GCA_000188115.5.chromAlias.bb
chromAuthority ucsc
organism SL4.0 Feb. 2025
defaultPos CM001064.4:30287894-30297894
scientificName Solanum lycopersicum
htmlPath html/GCA_000188115.5_SL4.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/188/115/GCA_000188115.5
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/188/115/GCA_000188115.5
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/188/115/GCA_000188115.5
liftOver.GCF_000188115.2 liftOver/GCA_000188115.5ToGCF_000188115.2.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_000188115.5_SL4.0.assembly.bb
type bigBed 6
html html/GCA_000188115.5_SL4.0.assembly
searchIndex name
searchTrix ixIxx/GCA_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.gap.bb
type bigBed 4
group map
html html/GCA_000188115.5_SL4.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.gc5Base.bw
html html/GCA_000188115.5_SL4.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_000188115.5_SL4.0.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_000188115.5_SL4.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_000188115.5_SL4.0.rmsk.bb
xrefDataUrl bbi/GCA_000188115.5_SL4.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_000188115.5_SL4.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000188115.5_SL4.0.simpleRepeat.bb
html html/GCA_000188115.5_SL4.0.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_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_000188115.5_SL4.0.windowMasker.bb
html html/GCA_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.allGaps.bb
html html/GCA_000188115.5_SL4.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_000188115.5_SL4.0.augustus.bb
html html/GCA_000188115.5_SL4.0.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/GCA_000188115.5_SL4.0.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_000188115.5_SL4.0.xenoRefGene.ix
html html/GCA_000188115.5_SL4.0.xenoRefGene

##############################################################################
# GCF_000188115.2 - tomato - Solanum lycopersicum - taxId: 4081
##############################################################################
track chainNetGCF_000188115.2
compositeTrack on
shortLabel tomato Chain/Net
longLabel tomato (2011-02-08), 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_000188115.2
html html/GCA_000188115.5_SL4.0.chainNet

    track chainNetGCF_000188115.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_000188115.2
    spectrum on

        track chainGCF_000188115.2
        parent chainNetGCF_000188115.2Viewchain
        subGroups view=chain
        shortLabel tomato Chain
        longLabel tomato (2011-02-08) Chained Alignments
        type bigChain GCF_000188115.2
        bigDataUrl bbi/GCA_000188115.5_SL4.0.chainGCF_000188115.2.bb
        linkDataUrl bbi/GCA_000188115.5_SL4.0.chainGCF_000188115.2Link.bb
        priority 1

        track chainSynGCF_000188115.2
        parent chainNetGCF_000188115.2Viewchain
        subGroups view=chain
        shortLabel tomato synChain
        longLabel tomato (2011-02-08) Syntenic Chained Alignments
        type bigChain GCF_000188115.2
        bigDataUrl bbi/GCA_000188115.5_SL4.0.chainSynGCF_000188115.2.bb
        linkDataUrl bbi/GCA_000188115.5_SL4.0.chainSynGCF_000188115.2Link.bb
        priority 2

        track chainRBestGCF_000188115.2
        parent chainNetGCF_000188115.2Viewchain
        subGroups view=chain
        shortLabel tomato rbChain
        longLabel tomato (2011-02-08) Reciprocal Best Chained Alignments
        type bigChain GCF_000188115.2
        bigDataUrl bbi/GCA_000188115.5_SL4.0.chainRBestGCF_000188115.2.bb
        linkDataUrl bbi/GCA_000188115.5_SL4.0.chainRBestGCF_000188115.2Link.bb
        priority 3

        track chainLiftOverGCF_000188115.2
        parent chainNetGCF_000188115.2Viewchain
        subGroups view=chain
        shortLabel tomato loChain
        longLabel tomato (2011-02-08) Lift Over Chained Alignments
        type bigChain GCF_000188115.2
        bigDataUrl bbi/GCA_000188115.5_SL4.0.chainLiftOverGCF_000188115.2.bb
        linkDataUrl bbi/GCA_000188115.5_SL4.0.chainLiftOverGCF_000188115.2Link.bb
        priority 4

    track mafNetGCF_000188115.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_000188115.2

        track netGCF_000188115.2
        parent mafNetGCF_000188115.2Viewnet
        subGroups view=net
        shortLabel tomato net
        longLabel tomato (2011-02-08) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.net.bb
        summary bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.net.summary.bb
        speciesOrder GCF_000188115.2
        priority 5

        track synNetGCF_000188115.2
        parent mafNetGCF_000188115.2Viewnet
        subGroups view=net
        shortLabel tomato synNet
        longLabel tomato (2011-02-08) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.synNet.bb
        summary bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.synNet.summary.bb
        speciesOrder GCF_000188115.2
        priority 6

        track rbestNetGCF_000188115.2
        parent mafNetGCF_000188115.2Viewnet
        subGroups view=net
        shortLabel tomato rbestNet
        longLabel tomato (2011-02-08) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.rbestNet.bb
        summary bbi/GCA_000188115.5_SL4.0.GCF_000188115.2.rbestNet.summary.bb
        speciesOrder GCF_000188115.2
        priority 7