hub GCF_016699485.2 genome assembly
shortLabel chicken white leghorn layer X broiler (v2 broiler haplotype 2021 2021)
longLabel chicken white leghorn layer X broiler (v2 broiler haplotype 2021 2021)/Gallus gallus/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.description.html

genome GCF_016699485.2
taxId 9031
groups groups.txt
description chicken white leghorn layer X broiler (v2 broiler haplotype 2021 2021)
twoBitPath GCF_016699485.2.2bit
twoBitBptUrl GCF_016699485.2.2bit.bpt
chromSizes GCF_016699485.2.chrom.sizes.txt
chromAliasBb GCF_016699485.2.chromAlias.bb
chromAuthority ucsc
organism bGalGal1.mat.broiler.GRCg7b Jan. 2021
defaultPos NC_052532.1:65483052-65493052
scientificName Gallus gallus
htmlPath html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/699/485/GCF_016699485.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/699/485/GCF_016699485.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/699/485/GCF_016699485.2
liftOver.GCF_002263795.3 liftOver/GCF_016699485.2ToGCF_002263795.3.over.chain.gz
liftOver.GCF_014805655.1 liftOver/GCF_016699485.2ToGCF_014805655.1.over.chain.gz
liftOver.galGal5 liftOver/GCF_016699485.2ToGalGal5.over.chain.gz
liftOver.galGal6 liftOver/GCF_016699485.2ToGalGal6.over.chain.gz
liftOver.hg38 liftOver/GCF_016699485.2ToHg38.over.chain.gz
liftOver.mm10 liftOver/GCF_016699485.2ToMm10.over.chain.gz
liftOver.mm39 liftOver/GCF_016699485.2ToMm39.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.assembly.bb
type bigBed 6
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.assembly
searchIndex name
searchTrix ixIxx/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.gap.bb
type bigBed 4
group map
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.gc5Base.bw
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rmsk.bb
xrefDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rModel.bb
xrefDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.simpleRepeat.bb
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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 Gallus gallus Annotation Release 106 (2022-03-04)
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.windowMasker.bb
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.allGaps.bb
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.augustus.bb
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.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_016699485.2_bGalGal1.mat.broiler.GRCg7b.xenoRefGene.ix
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2022_01
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.ensGene.bb
searchTrix ixIxx/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.ensGene

track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=galGal6 s001=galGal5 s002=GCF_014805655.1 s003=hg38 s004=GCF_002263795.3 s005=mm39 s006=mm10
subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=chainType dimensionY=species
sortOrder species=+ view=+ chainType=+
configurable on
html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet

    track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet
    spectrum on

        track chainGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Chicken/galGal6 Chain
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigChain galGal6
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGalGal6.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGalGal6Link.bb
        otherDb galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track chainGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Chicken/galGal5 Chain
        longLabel Chicken/galGal5/galGal5 (Dec 2015) Chained Alignments
        type bigChain galGal5
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGalGal5.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGalGal5Link.bb
        otherDb galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track chainGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel Eurasian tree sparrow Chain
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigChain GCF_014805655.1
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGCF_014805655.1.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGCF_014805655.1Link.bb
        otherDb GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track chainHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s003 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainHg38.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainHg38Link.bb
        otherDb hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track chainGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s004 chainType=c00
        shortLabel cattle Chain
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track chainMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s005 chainType=c00
        shortLabel Mouse/mm39 Chain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainMm39.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainMm39Link.bb
        otherDb mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track chainMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewchain off
        subGroups view=chain species=s006 chainType=c00
        shortLabel Mouse/mm10 Chain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainMm10.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainMm10Link.bb
        otherDb mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639

    track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet
    spectrum on

        track chainSynGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Chicken/galGal6 synChain
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigChain galGal6
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGalGal6.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGalGal6Link.bb
        otherDb galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track chainSynGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Chicken/galGal5 synChain
        longLabel Chicken/galGal5/galGal5 (Dec 2015) Chained Alignments
        type bigChain galGal5
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGalGal5.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGalGal5Link.bb
        otherDb galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track chainSynGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel Eurasian tree sparrow synChain
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigChain GCF_014805655.1
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGCF_014805655.1.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGCF_014805655.1Link.bb
        otherDb GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track chainSynHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s003 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38_ASM1480565v1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynHg38.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynHg38Link.bb
        otherDb hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track chainSynGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s004 chainType=c01
        shortLabel cattle synChain
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track chainSynMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s005 chainType=c01
        shortLabel Mouse/mm39 synChain
        longLabel Mouse/mm39/mm39_ARS-UCD2.0 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynMm39.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynMm39Link.bb
        otherDb mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track chainSynMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewSynTen off
        subGroups view=synten species=s006 chainType=c01
        shortLabel Mouse/mm10 synChain
        longLabel Mouse/mm10/mm10_ARS-UCD2.0 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynMm10.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainSynMm10Link.bb
        otherDb mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639

    track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet
    spectrum on

        track chainRBestGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Chicken/galGal6 rbChain
        longLabel Chicken/galGal6/galGal6_ARS-UCD2.0 (Mar. 2018) Chained Alignments
        type bigChain galGal6
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGalGal6.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGalGal6Link.bb
        otherDb galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track chainRBestGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Chicken/galGal5 rbChain
        longLabel Chicken/galGal5/galGal5_ARS-UCD2.0 (Dec 2015) Chained Alignments
        type bigChain galGal5
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGalGal5.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGalGal5Link.bb
        otherDb galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track chainRBestGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel Eurasian tree sparrow rbChain
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigChain GCF_014805655.1
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGCF_014805655.1.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGCF_014805655.1Link.bb
        otherDb GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track chainRBestHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s003 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38_ASM1480565v1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestHg38.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track chainRBestGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s004 chainType=c02
        shortLabel cattle rbChain
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track chainRBestMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s005 chainType=c02
        shortLabel Mouse/mm39 rbChain
        longLabel Mouse/mm39/mm39_ARS-UCD2.0 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestMm39.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestMm39Link.bb
        otherDb mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track chainRBestMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewRBest off
        subGroups view=rbest species=s006 chainType=c02
        shortLabel Mouse/mm10 rbChain
        longLabel Mouse/mm10/mm10_ARS-UCD2.0 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestMm10.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639

    track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet
    spectrum on

        track chainLiftOverGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Chicken/galGal6 loChain
        longLabel Chicken/galGal6/galGal6_ARS-UCD2.0 (Mar. 2018) Chained Alignments
        type bigChain galGal6
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGalGal6.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGalGal6Link.bb
        otherDb galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track chainLiftOverGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel Eurasian tree sparrow loChain
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigChain GCF_014805655.1
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGCF_014805655.1.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGCF_014805655.1Link.bb
        otherDb GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track chainLiftOverGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNetViewLiftOver off
        subGroups view=liftover species=s004 chainType=c03
        shortLabel cattle loChain
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainLiftOverGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

    track GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bChainNet

        track netGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Chicken/galGal6 mafNet
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.net.summary.bb
        speciesOrder galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track synNetGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Chicken/galGal6 synNet
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.synNet.summary.bb
        speciesOrder galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track rbestNetGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Chicken/galGal6 rbestNet
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.rbestNet.summary.bb
        speciesOrder galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track liftOverNetGalGal6
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s000 chainType=c07
        shortLabel Chicken/galGal6 liftOverNet
        longLabel Chicken/galGal6/galGal6 (Mar. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.liftOverNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal6.liftOverNet.summary.bb
        speciesOrder galGal6
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.479

        track netGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Chicken/galGal5 mafNet
        longLabel Chicken/galGal5/galGal5 (Dec 2015) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.net.summary.bb
        speciesOrder galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track synNetGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Chicken/galGal5 synNet
        longLabel Chicken/galGal5/galGal5 (Dec 2015) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.synNet.summary.bb
        speciesOrder galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track rbestNetGalGal5
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Chicken/galGal5 rbestNet
        longLabel Chicken/galGal5/galGal5 (Dec 2015) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.galGal5.rbestNet.summary.bb
        speciesOrder galGal5
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 1.573

        track netGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s002 chainType=c04
        shortLabel Eurasian tree sparrow mafNet
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.net.summary.bb
        speciesOrder GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track synNetGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s002 chainType=c05
        shortLabel Eurasian tree sparrow synNet
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.synNet.summary.bb
        speciesOrder GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track rbestNetGCF_014805655.1
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s002 chainType=c06
        shortLabel Eurasian tree sparrow rbestNet
        longLabel Eurasian tree sparrow/GCF_014805655.1_ASM1480565v1 (2020-09-30) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_014805655.1.rbestNet.summary.bb
        speciesOrder GCF_014805655.1
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 28.668

        track netHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s003 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track synNetHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s003 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track rbestNetHg38
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s003 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 88.635

        track netGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s004 chainType=c04
        shortLabel cattle mafNet
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.net.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track synNetGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s004 chainType=c05
        shortLabel cattle synNet
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.synNet.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track rbestNetGCF_002263795.3
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s004 chainType=c06
        shortLabel cattle rbestNet
        longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.GCF_002263795.3.rbestNet.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 93.758

        track netMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s005 chainType=c04
        shortLabel Mouse/mm39 mafNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.net.summary.bb
        speciesOrder mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track synNetMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s005 chainType=c05
        shortLabel Mouse/mm39 synNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.synNet.summary.bb
        speciesOrder mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track rbestNetMm39
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s005 chainType=c06
        shortLabel Mouse/mm39 rbestNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm39.rbestNet.summary.bb
        speciesOrder mm39
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.636

        track netMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s006 chainType=c04
        shortLabel Mouse/mm10 mafNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.net.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.net.summary.bb
        speciesOrder mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639

        track synNetMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s006 chainType=c05
        shortLabel Mouse/mm10 synNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.synNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639

        track rbestNetMm10
        parent GCF_016699485.2_bGalGal1.mat.broiler.GRCg7bMafNetViewnet off
        subGroups view=align species=s006 chainType=c06
        shortLabel Mouse/mm10 rbestNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.rbestNet.bb
        summary bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chainNet
        priority 94.639


track TOGAv2
shortLabel TOGA V2
longLabel TOGA 2.0 annotations, multiple reference
group genes
visibility hide
type bigBed 12 +
superTrack on
html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLrisTri2v2
    parent TOGAv2
    shortLabel TOGA2 kittiwake annotations
    longLabel TOGA 2.0 annotations using Black-legged kittiwake HLrisTri2 as reference
    group genes
    priority 4
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_028500815.1v2/HLTOGAannotVsHLrisTri2v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_028500815.1v2/HLTOGAannotVsHLrisTri2v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_028500815.1v2/HLTOGAannotVsHLrisTri2v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLcorHaw3v2
    parent TOGAv2
    shortLabel TOGA2 crow annotations
    longLabel TOGA 2.0 annotations using Hawaiian crow HLcorHaw3 as reference
    group genes
    priority 5
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_020740725.1v2/HLTOGAannotVsHLcorHaw3v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_020740725.1v2/HLTOGAannotVsHLcorHaw3v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_020740725.1v2/HLTOGAannotVsHLcorHaw3v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLtaeGut5v2
    parent TOGAv2
    shortLabel TOGA2 zebrafinch annotations
    longLabel TOGA 2.0 annotations using zebrafinch taeGut5 as reference
    group genes
    priority 3
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_003957565.2v2/HLTOGAannotVsHLtaeGut5v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_003957565.2v2/HLTOGAannotVsHLtaeGut5v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_003957565.2v2/HLTOGAannotVsHLtaeGut5v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLdroNov3v2
    parent TOGAv2
    shortLabel TOGA2 emu annotations
    longLabel TOGA 2.0 annotations using emu HLdroNov3 as reference
    group genes
    priority 6
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_036370855.1v2/HLTOGAannotVsHLdroNov3v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_036370855.1v2/HLTOGAannotVsHLdroNov3v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_036370855.1v2/HLTOGAannotVsHLdroNov3v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

track VEuPathDBGeneModels
shortLabel VEuPathDB Genes
longLabel Gene Models mirrored from VEuPathDB
group genes
type bigBed 12 .
visibility pack
labelFields name
searchIndex name
bigDataUrl contrib/VEuPathDB/veupathGenes.bb
colorByStrand 0,0,122 157,60,32
dataVersion VEuPathDB release 68
html contrib/VEuPathDB/VEuPathDB

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