hub GCF_000002775.5 genome assembly
shortLabel black cottonwood (v4.1 Nisqually-1 2022)
longLabel black cottonwood (v4.1 Nisqually-1 2022)/Populus trichocarpa/GCF_000002775.5_P.trichocarpa_v4.1 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_000002775.5_P.trichocarpa_v4.1.description.html

genome GCF_000002775.5
taxId 3694
groups groups.txt
description black cottonwood (v4.1 Nisqually-1 2022)
twoBitPath GCF_000002775.5.2bit
twoBitBptUrl GCF_000002775.5.2bit.bpt
chromSizes GCF_000002775.5.chrom.sizes.txt
chromAliasBb GCF_000002775.5.chromAlias.bb
chromAuthority ucsc
organism P.trichocarpa_v4.1 Oct. 2022
defaultPos NC_037285.2:16596193-16606193
scientificName Populus trichocarpa
htmlPath html/GCF_000002775.5_P.trichocarpa_v4.1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/775/GCF_000002775.5
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/775/GCF_000002775.5
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/775/GCF_000002775.5
liftOver.GCF_000002775.4 liftOver/GCF_000002775.5ToGCF_000002775.4.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_000002775.5_P.trichocarpa_v4.1.assembly.bb
type bigBed 6
html html/GCF_000002775.5_P.trichocarpa_v4.1.assembly
searchIndex name
searchTrix ixIxx/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.gap.bb
type bigBed 4
group map
html html/GCF_000002775.5_P.trichocarpa_v4.1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.gc5Base.bw
html html/GCF_000002775.5_P.trichocarpa_v4.1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000002775.5_P.trichocarpa_v4.1.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.rmsk.bb
xrefDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_000002775.5_P.trichocarpa_v4.1.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.simpleRepeat.bb
html html/GCF_000002775.5_P.trichocarpa_v4.1.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 Populus trichocarpa Annotation Release 102 (2023-06-06)
html html/GCF_000002775.5_P.trichocarpa_v4.1.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_000002775.5_P.trichocarpa_v4.1.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_000002775.5_P.trichocarpa_v4.1.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_000002775.5_P.trichocarpa_v4.1.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.windowMasker.bb
html html/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.allGaps.bb
html html/GCF_000002775.5_P.trichocarpa_v4.1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.augustus.bb
html html/GCF_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.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_000002775.5_P.trichocarpa_v4.1.xenoRefGene.ix
html html/GCF_000002775.5_P.trichocarpa_v4.1.xenoRefGene

##############################################################################
# GCF_000002775.4 - black cottonwood - Populus trichocarpa - taxId: 3694
##############################################################################
track chainNetGCF_000002775.4
compositeTrack on
shortLabel black cottonwood Chain/Net
longLabel black cottonwood (2022-10-20), 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_000002775.4
html html/GCF_000002775.5_P.trichocarpa_v4.1.chainNet

    track chainNetGCF_000002775.4Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_000002775.4
    spectrum on

        track chainGCF_000002775.4
        parent chainNetGCF_000002775.4Viewchain
        subGroups view=chain
        shortLabel black cottonwood Chain
        longLabel black cottonwood (2022-10-20) Chained Alignments
        type bigChain GCF_000002775.4
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainGCF_000002775.4.bb
        linkDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainGCF_000002775.4Link.bb
        priority 1

        track chainSynGCF_000002775.4
        parent chainNetGCF_000002775.4Viewchain
        subGroups view=chain
        shortLabel black cottonwood synChain
        longLabel black cottonwood (2022-10-20) Syntenic Chained Alignments
        type bigChain GCF_000002775.4
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainSynGCF_000002775.4.bb
        linkDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainSynGCF_000002775.4Link.bb
        priority 2

        track chainRBestGCF_000002775.4
        parent chainNetGCF_000002775.4Viewchain
        subGroups view=chain
        shortLabel black cottonwood rbChain
        longLabel black cottonwood (2022-10-20) Reciprocal Best Chained Alignments
        type bigChain GCF_000002775.4
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainRBestGCF_000002775.4.bb
        linkDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainRBestGCF_000002775.4Link.bb
        priority 3

        track chainLiftOverGCF_000002775.4
        parent chainNetGCF_000002775.4Viewchain
        subGroups view=chain
        shortLabel black cottonwood loChain
        longLabel black cottonwood (2022-10-20) Lift Over Chained Alignments
        type bigChain GCF_000002775.4
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainLiftOverGCF_000002775.4.bb
        linkDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.chainLiftOverGCF_000002775.4Link.bb
        priority 4

    track mafNetGCF_000002775.4Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_000002775.4

        track netGCF_000002775.4
        parent mafNetGCF_000002775.4Viewnet
        subGroups view=net
        shortLabel black cottonwood net
        longLabel black cottonwood (2022-10-20) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.net.bb
        summary bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.net.summary.bb
        speciesOrder GCF_000002775.4
        priority 5

        track synNetGCF_000002775.4
        parent mafNetGCF_000002775.4Viewnet
        subGroups view=net
        shortLabel black cottonwood synNet
        longLabel black cottonwood (2022-10-20) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.synNet.bb
        summary bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.synNet.summary.bb
        speciesOrder GCF_000002775.4
        priority 6

        track rbestNetGCF_000002775.4
        parent mafNetGCF_000002775.4Viewnet
        subGroups view=net
        shortLabel black cottonwood rbestNet
        longLabel black cottonwood (2022-10-20) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.rbestNet.bb
        summary bbi/GCF_000002775.5_P.trichocarpa_v4.1.GCF_000002775.4.rbestNet.summary.bb
        speciesOrder GCF_000002775.4
        priority 7


track evaSnp8
shortLabel EVA SNP Release 8
longLabel Short Genetic Variants from European Variant Archive Release 8
type bigBed 9 +
visibility dense
group varRep
itemRgb on
bigDataUrl contrib/evaSnp8/evaSnp8.bb
url https://www.ebi.ac.uk/eva/?variant&accessionID=$$
searchIndex name
mouseOver <b>Ref/Alt allele(s)</b>: $ref>$alt<br> <b>Var type</b>: $ucscClass<br> <b>AA change</b>: $aaChange
filterValues.varClass SNV|SNV,deletion|Deletion,indel|Indel,insertion|Insertion,MNV|MNV,sequence_alteration|Sequence alteration
filterLabel.varClass Variant class from EVA SO term
filterLabel.ucscClass Functional effect per UCSC Variant Annotation
filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant
filterType.ucscClass multipleListOnlyOr
filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants
filterLabel.itemRgb General variant types by color grouping
maxWindowCoverage 250000
maxItems 1000000
html contrib/evaSnp8/description