hub GCA_003957565.2 genome assembly
shortLabel zebra finch (v1 Black17 male 2019 genbank)
longLabel zebra finch (v1 Black17 male 2019 genbank)/Taeniopygia guttata/GCA_003957565.2_bTaeGut1_v1.p genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_003957565.2_bTaeGut1_v1.p.description.html

genome GCA_003957565.2
taxId 59729
groups groups.txt
description zebra finch (v1 Black17 male 2019 genbank)
twoBitPath GCA_003957565.2.2bit
twoBitBptUrl GCA_003957565.2.2bit.bpt
chromSizes GCA_003957565.2.chrom.sizes.txt
chromAliasBb GCA_003957565.2.chromAlias.bb
chromAuthority ucsc
organism bTaeGut1_v1.p May 2019
defaultPos CM012083.1:50229599-50239599
scientificName Taeniopygia guttata
htmlPath html/GCA_003957565.2_bTaeGut1_v1.p.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/003/957/565/GCA_003957565.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/003/957/565/GCA_003957565.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/003/957/565/GCA_003957565.2

track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.assembly.bb
type bigBed 6
html html/GCA_003957565.2_bTaeGut1_v1.p.assembly
searchIndex name
searchTrix ixIxx/GCA_003957565.2_bTaeGut1_v1.p.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/GCA_003957565.2_bTaeGut1_v1.p.cytoBand.bb

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
autoScale Off
maxHeightPixels 128:36:16
graphTypeDefault Bar
gridDefault OFF
windowingFunction Mean
color 0,0,0
altColor 128,128,128
viewLimits 30:70
type bigWig 0 100
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.gc5Base.bw
html html/GCA_003957565.2_bTaeGut1_v1.p.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_003957565.2_bTaeGut1_v1.p.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.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/GCA_003957565.2_bTaeGut1_v1.p.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_003957565.2_bTaeGut1_v1.p.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.simpleRepeat.bb
html html/GCA_003957565.2_bTaeGut1_v1.p.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility dense
type bigBed 4 +
html html/GCA_003957565.2_bTaeGut1_v1.p.cpgIslands

    track cpgIslandExt
    parent cpgIslands off
    shortLabel CpG Islands
    longLabel CpG Islands (Islands < 300 Bases are Light Green)
    type bigBed 4 +
    priority 1
    bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.cpgIslandExt.bb

    track cpgIslandExtUnmasked
    parent cpgIslands on
    shortLabel Unmasked CpG
    longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
    type bigBed 4 +
    priority 2
    bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.windowMasker.bb
html html/GCA_003957565.2_bTaeGut1_v1.p.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility hide
type bigBed 3
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.allGaps.bb
html html/GCA_003957565.2_bTaeGut1_v1.p.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.augustus.bb
html html/GCA_003957565.2_bTaeGut1_v1.p.augustus

track xenoRefGene
shortLabel RefSeq mRNAs
longLabel RefSeq mRNAs mapped to this assembly
group rna
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_003957565.2_bTaeGut1_v1.p.xenoRefGene.ix
html html/GCA_003957565.2_bTaeGut1_v1.p.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2019_05
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_003957565.2_bTaeGut1_v1.p.ensGene.bb
searchTrix ixIxx/GCA_003957565.2_bTaeGut1_v1.p.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCA_003957565.2_bTaeGut1_v1.p.ensGene


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

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

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

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

    track HLTOGAannotvsHLgalGal7v2
    parent TOGAv2
    shortLabel TOGA2 chicken annotations
    longLabel TOGA 2.0 annotations using chicken galGal7 as reference
    group genes
    priority 2
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_016699485.2v2/HLTOGAannotVsHLgalGal7v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_016699485.2v2/HLTOGAannotVsHLgalGal7v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_016699485.2v2/HLTOGAannotVsHLgalGal7v2.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