hub GCF_014441545.1 genome assembly
shortLabel dog (labrador SID07034 2020)
longLabel dog (labrador SID07034 2020)/Canis lupus familiaris/GCF_014441545.1_ROS_Cfam_1.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_014441545.1_ROS_Cfam_1.0.description.html

genome GCF_014441545.1
taxId 9615
groups groups.txt
description dog (labrador SID07034 2020)
twoBitPath GCF_014441545.1.2bit
twoBitBptUrl GCF_014441545.1.2bit.bpt
chromSizes GCF_014441545.1.chrom.sizes.txt
chromAliasBb GCF_014441545.1.chromAlias.bb
chromAuthority ucsc
organism ROS_Cfam_1.0 Sep. 2020
defaultPos NC_051843.1:42356539-42366539
scientificName Canis lupus familiaris
htmlPath html/GCF_014441545.1_ROS_Cfam_1.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/014/441/545/GCF_014441545.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/014/441/545/GCF_014441545.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/014/441/545/GCF_014441545.1
liftOver.GCF_001704415.2 liftOver/GCF_014441545.1ToGCF_001704415.2.over.chain.gz
liftOver.canFam2 liftOver/GCF_014441545.1ToCanFam2.over.chain.gz
liftOver.canFam3 liftOver/GCF_014441545.1ToCanFam3.over.chain.gz
liftOver.canFam4 liftOver/GCF_014441545.1ToCanFam4.over.chain.gz
liftOver.canFam6 liftOver/GCF_014441545.1ToCanFam6.over.chain.gz
liftOver.hg19 liftOver/GCF_014441545.1ToHg19.over.chain.gz
liftOver.hg38 liftOver/GCF_014441545.1ToHg38.over.chain.gz
liftOver.mm10 liftOver/GCF_014441545.1ToMm10.over.chain.gz
liftOver.rheMac10 liftOver/GCF_014441545.1ToRheMac10.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_014441545.1_ROS_Cfam_1.0.assembly.bb
type bigBed 6
html html/GCF_014441545.1_ROS_Cfam_1.0.assembly
searchIndex name
searchTrix ixIxx/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.gc5Base.bw
html html/GCF_014441545.1_ROS_Cfam_1.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_014441545.1_ROS_Cfam_1.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.gapOverlap.bb
    type bigBed 12

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_014441545.1_ROS_Cfam_1.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.simpleRepeat.bb
html html/GCF_014441545.1_ROS_Cfam_1.0.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 Canis lupus familiaris Annotation Release 106 (2021-01-11)
html html/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.windowMasker.bb
html html/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.allGaps.bb
html html/GCF_014441545.1_ROS_Cfam_1.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.augustus.bb
html html/GCF_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.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_014441545.1_ROS_Cfam_1.0.xenoRefGene.ix
html html/GCF_014441545.1_ROS_Cfam_1.0.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2020_10
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.ensGene.bb
searchTrix ixIxx/GCF_014441545.1_ROS_Cfam_1.0.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCF_014441545.1_ROS_Cfam_1.0.ensGene

track GCF_014441545.1_ROS_Cfam_1.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_014441545.1_ROS_Cfam_1.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=canFam4 s001=canFam3 s002=canFam2 s003=canFam6 s004=hg38 s005=hg19 s006=rheMac10 s007=GCF_001704415.2 s008=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_014441545.1_ROS_Cfam_1.0.chainNet

    track GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_014441545.1_ROS_Cfam_1.0ChainNet
    spectrum on

        track chainCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Dog/canFam4 Chain
        longLabel Dog/canFam4/canFam4 (Mar. 2020) Chained Alignments
        type bigChain canFam4
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam4.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam4Link.bb
        otherDb canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track chainCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Dog/canFam3 Chain
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigChain canFam3
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam3.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam3Link.bb
        otherDb canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track chainCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel Dog/canFam2 Chain
        longLabel Dog/canFam2/canFam2 (May 2005) Chained Alignments
        type bigChain canFam2
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam2Link.bb
        otherDb canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track chainCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s003 chainType=c00
        shortLabel Dog/canFam6 Chain
        longLabel Dog/canFam6/canFam6 (Oct. 2020) Chained Alignments
        type bigChain canFam6
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam6.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainCanFam6Link.bb
        otherDb canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track chainHg38
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s004 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainHg38.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainHg38Link.bb
        otherDb hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track chainHg19
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s005 chainType=c00
        shortLabel Human/hg19 Chain
        longLabel Human/hg19/hg19 (Feb. 2009) Chained Alignments
        type bigChain hg19
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainHg19.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainHg19Link.bb
        otherDb hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track chainRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s006 chainType=c00
        shortLabel Rhesus/rheMac10 Chain
        longLabel Rhesus/rheMac10/rheMac10 (Feb. 2019) Chained Alignments
        type bigChain rheMac10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRheMac10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRheMac10Link.bb
        otherDb rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track chainGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s007 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_014441545.1_ROS_Cfam_1.0.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track chainMm10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewchain off
        subGroups view=chain species=s008 chainType=c00
        shortLabel Mouse/mm10 Chain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainMm10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainMm10Link.bb
        otherDb mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

    track GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_014441545.1_ROS_Cfam_1.0ChainNet
    spectrum on

        track chainSynCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Dog/canFam4 synChain
        longLabel Dog/canFam4/canFam4 (Mar. 2020) Chained Alignments
        type bigChain canFam4
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam4.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam4Link.bb
        otherDb canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track chainSynCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Dog/canFam3 synChain
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigChain canFam3
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam3.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam3Link.bb
        otherDb canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track chainSynCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel Dog/canFam2 synChain
        longLabel Dog/canFam2/canFam2 (May 2005) Chained Alignments
        type bigChain canFam2
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam2Link.bb
        otherDb canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track chainSynCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s003 chainType=c01
        shortLabel Dog/canFam6 synChain
        longLabel Dog/canFam6/canFam6 (Oct. 2020) Chained Alignments
        type bigChain canFam6
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam6.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynCanFam6Link.bb
        otherDb canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track chainSynHg38
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s004 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynHg38.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynHg38Link.bb
        otherDb hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track chainSynHg19
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s005 chainType=c01
        shortLabel Human/hg19 synChain
        longLabel Human/hg19/hg19 (Feb. 2009) Chained Alignments
        type bigChain hg19
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynHg19.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynHg19Link.bb
        otherDb hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track chainSynRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s006 chainType=c01
        shortLabel Rhesus/rheMac10 synChain
        longLabel Rhesus/rheMac10/rheMac10 (Feb. 2019) Chained Alignments
        type bigChain rheMac10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynRheMac10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynRheMac10Link.bb
        otherDb rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track chainSynGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s007 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_014441545.1_ROS_Cfam_1.0.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track chainSynMm10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewSynTen off
        subGroups view=synten species=s008 chainType=c01
        shortLabel Mouse/mm10 synChain
        longLabel Mouse/mm10/mm10_ARS1.2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynMm10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainSynMm10Link.bb
        otherDb mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

    track GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_014441545.1_ROS_Cfam_1.0ChainNet
    spectrum on

        track chainRBestCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Dog/canFam4 rbChain
        longLabel Dog/canFam4/canFam4_ARS1.2 (Mar. 2020) Chained Alignments
        type bigChain canFam4
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam4.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam4Link.bb
        otherDb canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track chainRBestCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Dog/canFam3 rbChain
        longLabel Dog/canFam3/canFam3_ARS1.2 (Sep. 2011) Chained Alignments
        type bigChain canFam3
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam3.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam3Link.bb
        otherDb canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track chainRBestCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel Dog/canFam2 rbChain
        longLabel Dog/canFam2/canFam2_ARS1.2 (May 2005) Chained Alignments
        type bigChain canFam2
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam2Link.bb
        otherDb canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track chainRBestCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s003 chainType=c02
        shortLabel Dog/canFam6 rbChain
        longLabel Dog/canFam6/canFam6_ARS1.2 (Oct. 2020) Chained Alignments
        type bigChain canFam6
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam6.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestCanFam6Link.bb
        otherDb canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track chainRBestHg38
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s004 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38_ARS1.2 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestHg38.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track chainRBestHg19
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s005 chainType=c02
        shortLabel Human/hg19 rbChain
        longLabel Human/hg19/hg19_ARS1.2 (Feb. 2009) Chained Alignments
        type bigChain hg19
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestHg19.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestHg19Link.bb
        otherDb hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track chainRBestRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s006 chainType=c02
        shortLabel Rhesus/rheMac10 rbChain
        longLabel Rhesus/rheMac10/rheMac10_ARS1.2 (Feb. 2019) Chained Alignments
        type bigChain rheMac10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestRheMac10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestRheMac10Link.bb
        otherDb rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track chainRBestGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s007 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_014441545.1_ROS_Cfam_1.0.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track chainRBestMm10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewRBest off
        subGroups view=rbest species=s008 chainType=c02
        shortLabel Mouse/mm10 rbChain
        longLabel Mouse/mm10/mm10_ARS1.2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestMm10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

    track GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_014441545.1_ROS_Cfam_1.0ChainNet
    spectrum on

        track chainLiftOverCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Dog/canFam4 loChain
        longLabel Dog/canFam4/canFam4_ARS1.2 (Mar. 2020) Chained Alignments
        type bigChain canFam4
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam4.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam4Link.bb
        otherDb canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track chainLiftOverCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Dog/canFam3 loChain
        longLabel Dog/canFam3/canFam3_ARS1.2 (Sep. 2011) Chained Alignments
        type bigChain canFam3
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam3.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam3Link.bb
        otherDb canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track chainLiftOverCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s003 chainType=c03
        shortLabel Dog/canFam6 loChain
        longLabel Dog/canFam6/canFam6_ARS1.2 (Oct. 2020) Chained Alignments
        type bigChain canFam6
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam6.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverCanFam6Link.bb
        otherDb canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track chainLiftOverHg38
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s004 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38_ARS1.2 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverHg38.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track chainLiftOverRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s006 chainType=c03
        shortLabel Rhesus/rheMac10 loChain
        longLabel Rhesus/rheMac10/rheMac10_ARS1.2 (Feb. 2019) Chained Alignments
        type bigChain rheMac10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverRheMac10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverRheMac10Link.bb
        otherDb rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track chainLiftOverGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s007 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_014441545.1_ROS_Cfam_1.0.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track chainLiftOverMm10
        parent GCF_014441545.1_ROS_Cfam_1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s008 chainType=c03
        shortLabel Mouse/mm10 loChain
        longLabel Mouse/mm10/mm10_ARS1.2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverMm10.bb
        linkDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.chainLiftOverMm10Link.bb
        otherDb mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

    track GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_014441545.1_ROS_Cfam_1.0ChainNet

        track netCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Dog/canFam4 mafNet
        longLabel Dog/canFam4/canFam4 (Mar. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.net.summary.bb
        speciesOrder canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track synNetCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Dog/canFam4 synNet
        longLabel Dog/canFam4/canFam4 (Mar. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.synNet.summary.bb
        speciesOrder canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track rbestNetCanFam4
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Dog/canFam4 rbestNet
        longLabel Dog/canFam4/canFam4 (Mar. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam4.rbestNet.summary.bb
        speciesOrder canFam4
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.385

        track netCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Dog/canFam3 mafNet
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.net.summary.bb
        speciesOrder canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track synNetCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Dog/canFam3 synNet
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.synNet.summary.bb
        speciesOrder canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track rbestNetCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Dog/canFam3 rbestNet
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.rbestNet.summary.bb
        speciesOrder canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track liftOverNetCanFam3
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c07
        shortLabel Dog/canFam3 liftOverNet
        longLabel Dog/canFam3/canFam3 (Sep. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.liftOverNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam3.liftOverNet.summary.bb
        speciesOrder canFam3
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.859

        track netCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c04
        shortLabel Dog/canFam2 mafNet
        longLabel Dog/canFam2/canFam2 (May 2005) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.net.summary.bb
        speciesOrder canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track synNetCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c05
        shortLabel Dog/canFam2 synNet
        longLabel Dog/canFam2/canFam2 (May 2005) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.synNet.summary.bb
        speciesOrder canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track rbestNetCanFam2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c06
        shortLabel Dog/canFam2 rbestNet
        longLabel Dog/canFam2/canFam2 (May 2005) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam2.rbestNet.summary.bb
        speciesOrder canFam2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 1.937

        track netCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c04
        shortLabel Dog/canFam6 mafNet
        longLabel Dog/canFam6/canFam6 (Oct. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.net.summary.bb
        speciesOrder canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track synNetCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c05
        shortLabel Dog/canFam6 synNet
        longLabel Dog/canFam6/canFam6 (Oct. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.synNet.summary.bb
        speciesOrder canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track rbestNetCanFam6
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c06
        shortLabel Dog/canFam6 rbestNet
        longLabel Dog/canFam6/canFam6 (Oct. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.canFam6.rbestNet.summary.bb
        speciesOrder canFam6
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 2.732

        track netHg38
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track synNetHg38
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track rbestNetHg38
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.484

        track netHg19
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c04
        shortLabel Human/hg19 mafNet
        longLabel Human/hg19/hg19 (Feb. 2009) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.net.summary.bb
        speciesOrder hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track synNetHg19
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c05
        shortLabel Human/hg19 synNet
        longLabel Human/hg19/hg19 (Feb. 2009) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.synNet.summary.bb
        speciesOrder hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track rbestNetHg19
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s005 chainType=c06
        shortLabel Human/hg19 rbestNet
        longLabel Human/hg19/hg19 (Feb. 2009) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.hg19.rbestNet.summary.bb
        speciesOrder hg19
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.560

        track netRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c04
        shortLabel Rhesus/rheMac10 mafNet
        longLabel Rhesus/rheMac10/rheMac10 (Feb. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.net.summary.bb
        speciesOrder rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track synNetRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c05
        shortLabel Rhesus/rheMac10 synNet
        longLabel Rhesus/rheMac10/rheMac10 (Feb. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.synNet.summary.bb
        speciesOrder rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track rbestNetRheMac10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s006 chainType=c06
        shortLabel Rhesus/rheMac10 rbestNet
        longLabel Rhesus/rheMac10/rheMac10 (Feb. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.rheMac10.rbestNet.summary.bb
        speciesOrder rheMac10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 38.996

        track netGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c04
        shortLabel goat mafNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track synNetGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c05
        shortLabel goat synNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track rbestNetGCF_001704415.2
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s007 chainType=c06
        shortLabel goat rbestNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 41.381

        track netMm10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c04
        shortLabel Mouse/mm10 mafNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.net.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.net.summary.bb
        speciesOrder mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

        track synNetMm10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c05
        shortLabel Mouse/mm10 synNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.synNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090

        track rbestNetMm10
        parent GCF_014441545.1_ROS_Cfam_1.0MafNetViewnet off
        subGroups view=align species=s008 chainType=c06
        shortLabel Mouse/mm10 rbestNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.rbestNet.bb
        summary bbi/GCF_014441545.1_ROS_Cfam_1.0.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCF_014441545.1_ROS_Cfam_1.0.chainNet
        priority 68.090


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 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

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