hub GCF_016772045.2 genome assembly
shortLabel sheep (OAR_USU_Benz2616 2023)
longLabel sheep (OAR_USU_Benz2616 2023)/Ovis aries/GCF_016772045.2_ARS-UI_Ramb_v3.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_016772045.2_ARS-UI_Ramb_v3.0.description.html

genome GCF_016772045.2
taxId 9940
groups groups.txt
description sheep (OAR_USU_Benz2616 2023)
twoBitPath GCF_016772045.2.2bit
twoBitBptUrl GCF_016772045.2.2bit.bpt
chromSizes GCF_016772045.2.chrom.sizes.txt
chromAliasBb GCF_016772045.2.chromAlias.bb
chromAuthority ucsc
organism ARS-UI_Ramb_v3.0 Jul. 2023
defaultPos NC_056054.1:92872400-92882400
scientificName Ovis aries
htmlPath html/GCF_016772045.2_ARS-UI_Ramb_v3.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/772/045/GCF_016772045.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/772/045/GCF_016772045.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/016/772/045/GCF_016772045.2
liftOver.GCA_005887515.3 liftOver/GCF_016772045.2ToGCA_005887515.3.over.chain.gz
liftOver.GCA_014523465.1 liftOver/GCF_016772045.2ToGCA_014523465.1.over.chain.gz
liftOver.GCF_001704415.2 liftOver/GCF_016772045.2ToGCF_001704415.2.over.chain.gz
liftOver.GCF_002263795.3 liftOver/GCF_016772045.2ToGCF_002263795.3.over.chain.gz
liftOver.GCF_016772045.1 liftOver/GCF_016772045.2ToGCF_016772045.1.over.chain.gz
liftOver.bosTau9 liftOver/GCF_016772045.2ToBosTau9.over.chain.gz
liftOver.hg38 liftOver/GCF_016772045.2ToHg38.over.chain.gz
liftOver.mm10 liftOver/GCF_016772045.2ToMm10.over.chain.gz
liftOver.oviAri3 liftOver/GCF_016772045.2ToOviAri3.over.chain.gz
liftOver.susScr11 liftOver/GCF_016772045.2ToSusScr11.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_016772045.2_ARS-UI_Ramb_v3.0.assembly.bb
type bigBed 6
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.assembly
searchIndex name
searchTrix ixIxx/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.gc5Base.bw
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.rmsk.bb
xrefDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.simpleRepeat.bb
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2-RS_2023_10 (2023-10-30)
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_016772045.2_ARS-UI_Ramb_v3.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_016772045.2_ARS-UI_Ramb_v3.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_016772045.2_ARS-UI_Ramb_v3.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.windowMasker.bb
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.allGaps.bb
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.augustus.bb
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.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_016772045.2_ARS-UI_Ramb_v3.0.xenoRefGene.ix
html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.xenoRefGene

track GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_016772045.2_ARS-UI_Ramb_v3.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCF_016772045.1 s001=GCA_014523465.1 s002=GCF_001704415.2 s003=oviAri3 s004=GCF_002263795.3 s005=GCA_005887515.3 s006=bosTau9 s007=susScr11 s008=hg38 s009=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_016772045.2_ARS-UI_Ramb_v3.0.chainNet

    track GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet
    spectrum on

        track chainGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Rambouillet sheep Chain
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigChain GCF_016772045.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_016772045.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_016772045.1Link.bb
        otherDb GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track chainGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Asiatic mouflon Chain
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigChain GCA_014523465.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCA_014523465.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCA_014523465.1Link.bb
        otherDb GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track chainGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel goat Chain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track chainOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s003 chainType=c00
        shortLabel Sheep/oviAri3 Chain
        longLabel Sheep/oviAri3/oviAri3 (Aug. 2012) Chained Alignments
        type bigChain oviAri3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainOviAri3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainOviAri3Link.bb
        otherDb oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track chainGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain 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_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track chainGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s005 chainType=c00
        shortLabel domestic yak Chain
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigChain GCA_005887515.3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCA_005887515.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainGCA_005887515.3Link.bb
        otherDb GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track chainBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s006 chainType=c00
        shortLabel Cow/bosTau9 Chain
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainBosTau9.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track chainSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s007 chainType=c00
        shortLabel Pig/susScr11 Chain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSusScr11.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSusScr11Link.bb
        otherDb susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track chainHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s008 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainHg38.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainHg38Link.bb
        otherDb hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track chainMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewchain off
        subGroups view=chain species=s009 chainType=c00
        shortLabel Mouse/mm10 Chain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainMm10.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainMm10Link.bb
        otherDb mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942

    track GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet
    spectrum on

        track chainSynGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Rambouillet sheep synChain
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigChain GCF_016772045.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_016772045.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_016772045.1Link.bb
        otherDb GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track chainSynGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Asiatic mouflon synChain
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigChain GCA_014523465.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCA_014523465.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCA_014523465.1Link.bb
        otherDb GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track chainSynGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel goat synChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track chainSynOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s003 chainType=c01
        shortLabel Sheep/oviAri3 synChain
        longLabel Sheep/oviAri3/oviAri3_ARS1.2 (Aug. 2012) Chained Alignments
        type bigChain oviAri3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynOviAri3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynOviAri3Link.bb
        otherDb oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track chainSynGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen 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_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track chainSynGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s005 chainType=c01
        shortLabel domestic yak synChain
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigChain GCA_005887515.3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCA_005887515.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynGCA_005887515.3Link.bb
        otherDb GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track chainSynBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s006 chainType=c01
        shortLabel Cow/bosTau9 synChain
        longLabel Cow/bosTau9/bosTau9_BosGru3.1 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynBosTau9.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track chainSynSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s007 chainType=c01
        shortLabel Pig/susScr11 synChain
        longLabel Pig/susScr11/susScr11_BosGru3.1 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynSusScr11.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynSusScr11Link.bb
        otherDb susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track chainSynHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s008 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38_BosGru3.1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynHg38.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynHg38Link.bb
        otherDb hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track chainSynMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewSynTen off
        subGroups view=synten species=s009 chainType=c01
        shortLabel Mouse/mm10 synChain
        longLabel Mouse/mm10/mm10_BosGru3.1 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynMm10.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainSynMm10Link.bb
        otherDb mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942

    track GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet
    spectrum on

        track chainRBestGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Rambouillet sheep rbChain
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigChain GCF_016772045.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_016772045.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_016772045.1Link.bb
        otherDb GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track chainRBestGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Asiatic mouflon rbChain
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigChain GCA_014523465.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCA_014523465.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCA_014523465.1Link.bb
        otherDb GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track chainRBestGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel goat rbChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track chainRBestOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s003 chainType=c02
        shortLabel Sheep/oviAri3 rbChain
        longLabel Sheep/oviAri3/oviAri3_ARS1.2 (Aug. 2012) Chained Alignments
        type bigChain oviAri3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestOviAri3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestOviAri3Link.bb
        otherDb oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track chainRBestGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest 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_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track chainRBestGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s005 chainType=c02
        shortLabel domestic yak rbChain
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigChain GCA_005887515.3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCA_005887515.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestGCA_005887515.3Link.bb
        otherDb GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track chainRBestBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s006 chainType=c02
        shortLabel Cow/bosTau9 rbChain
        longLabel Cow/bosTau9/bosTau9_BosGru3.1 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestBosTau9.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track chainRBestSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s007 chainType=c02
        shortLabel Pig/susScr11 rbChain
        longLabel Pig/susScr11/susScr11_BosGru3.1 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestSusScr11.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestSusScr11Link.bb
        otherDb susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track chainRBestHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s008 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38_BosGru3.1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestHg38.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track chainRBestMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewRBest off
        subGroups view=rbest species=s009 chainType=c02
        shortLabel Mouse/mm10 rbChain
        longLabel Mouse/mm10/mm10_BosGru3.1 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestMm10.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942

    track GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet
    spectrum on

        track chainLiftOverGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Rambouillet sheep loChain
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigChain GCF_016772045.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_016772045.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_016772045.1Link.bb
        otherDb GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track chainLiftOverGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Asiatic mouflon loChain
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigChain GCA_014523465.1
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCA_014523465.1.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCA_014523465.1Link.bb
        otherDb GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track chainLiftOverGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel goat loChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track chainLiftOverGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver 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_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_002263795.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCF_002263795.3Link.bb
        otherDb GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track chainLiftOverGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s005 chainType=c03
        shortLabel domestic yak loChain
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigChain GCA_005887515.3
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCA_005887515.3.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverGCA_005887515.3Link.bb
        otherDb GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track chainLiftOverBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s006 chainType=c03
        shortLabel Cow/bosTau9 loChain
        longLabel Cow/bosTau9/bosTau9_BosGru3.1 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverBosTau9.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track chainLiftOverSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s007 chainType=c03
        shortLabel Pig/susScr11 loChain
        longLabel Pig/susScr11/susScr11_BosGru3.1 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverSusScr11.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverSusScr11Link.bb
        otherDb susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track chainLiftOverHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s008 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38_BosGru3.1 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverHg38.bb
        linkDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

    track GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_016772045.2_ARS-UI_Ramb_v3.0ChainNet

        track netGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Rambouillet sheep mafNet
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.net.summary.bb
        speciesOrder GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track synNetGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Rambouillet sheep synNet
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.synNet.summary.bb
        speciesOrder GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track rbestNetGCF_016772045.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Rambouillet sheep rbestNet
        longLabel Rambouillet sheep/GCF_016772045.1_ARS-UI_Ramb_v2.0 (2021-02-03) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_016772045.1.rbestNet.summary.bb
        speciesOrder GCF_016772045.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 0.460

        track netGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Asiatic mouflon mafNet
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.net.summary.bb
        speciesOrder GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track synNetGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Asiatic mouflon synNet
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.synNet.summary.bb
        speciesOrder GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track rbestNetGCA_014523465.1
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Asiatic mouflon rbestNet
        longLabel Asiatic mouflon/GCA_014523465.1_CAU_Oori_1.0 (2020-09-11) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_014523465.1.rbestNet.summary.bb
        speciesOrder GCA_014523465.1
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 1.156

        track netGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c04
        shortLabel goat mafNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track synNetGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c05
        shortLabel goat synNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track rbestNetGCF_001704415.2
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c06
        shortLabel goat rbestNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 2.154

        track netOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c04
        shortLabel Sheep/oviAri3 mafNet
        longLabel Sheep/oviAri3/oviAri3 (Aug. 2012) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.net.summary.bb
        speciesOrder oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track synNetOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c05
        shortLabel Sheep/oviAri3 synNet
        longLabel Sheep/oviAri3/oviAri3 (Aug. 2012) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.synNet.summary.bb
        speciesOrder oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track rbestNetOviAri3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c06
        shortLabel Sheep/oviAri3 rbestNet
        longLabel Sheep/oviAri3/oviAri3 (Aug. 2012) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.oviAri3.rbestNet.summary.bb
        speciesOrder oviAri3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 4.860

        track netGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet 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_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.net.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track synNetGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet 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_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.synNet.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track rbestNetGCF_002263795.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet 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_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCF_002263795.3.rbestNet.summary.bb
        speciesOrder GCF_002263795.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 9.043

        track netGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c04
        shortLabel domestic yak mafNet
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.net.summary.bb
        speciesOrder GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track synNetGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c05
        shortLabel domestic yak synNet
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.synNet.summary.bb
        speciesOrder GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track rbestNetGCA_005887515.3
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c06
        shortLabel domestic yak rbestNet
        longLabel domestic yak/GCA_005887515.3_BosGru3.1 (2019-06-10) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.GCA_005887515.3.rbestNet.summary.bb
        speciesOrder GCA_005887515.3
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.179

        track netBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c04
        shortLabel Cow/bosTau9 mafNet
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.net.summary.bb
        speciesOrder bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track synNetBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c05
        shortLabel Cow/bosTau9 synNet
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.synNet.summary.bb
        speciesOrder bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track rbestNetBosTau9
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c06
        shortLabel Cow/bosTau9 rbestNet
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.bosTau9.rbestNet.summary.bb
        speciesOrder bosTau9
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 11.634

        track netSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c04
        shortLabel Pig/susScr11 mafNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.net.summary.bb
        speciesOrder susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track synNetSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c05
        shortLabel Pig/susScr11 synNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.synNet.summary.bb
        speciesOrder susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track rbestNetSusScr11
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c06
        shortLabel Pig/susScr11 rbestNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.susScr11.rbestNet.summary.bb
        speciesOrder susScr11
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 41.989

        track netHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track synNetHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track rbestNetHg38
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 49.896

        track netMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s009 chainType=c04
        shortLabel Mouse/mm10 mafNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.net.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.net.summary.bb
        speciesOrder mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942

        track synNetMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s009 chainType=c05
        shortLabel Mouse/mm10 synNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.synNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942

        track rbestNetMm10
        parent GCF_016772045.2_ARS-UI_Ramb_v3.0MafNetViewnet off
        subGroups view=align species=s009 chainType=c06
        shortLabel Mouse/mm10 rbestNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.rbestNet.bb
        summary bbi/GCF_016772045.2_ARS-UI_Ramb_v3.0.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCF_016772045.2_ARS-UI_Ramb_v3.0.chainNet
        priority 73.942


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 HLTOGAannotvsHLbosTau10v2
    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/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsMm10v2
    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/TOGAvMm10v2/HLTOGAannotVsMm10v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvMm10v2/HLTOGAannotVsMm10v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvMm10v2/HLTOGAannotVsMm10v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLeleMaxInd3Av2
    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_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHg38v2
    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/TOGAvHg38v2/HLTOGAannotVsHg38v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvHg38v2/HLTOGAannotVsHg38v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvHg38v2/HLTOGAannotVsHg38v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

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

track Tiberius
bigDataUrl contrib/tiberius/tiberius.bigGenePred.bb
shortLabel Tiberius genes
longLabel Tiberius ab initio gene prediction
type bigGenePred
visibility pack
color 0,102,204
noScoreFilter on
html contrib/tiberius/Tiberius.html
group genes
dataVersion Tiberius version 2025-01-07
baseColorDefault genomicCodons