track assembly
longLabel Assembly
shortLabel Assembly
visibility pack
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.assembly.bb
type bigBed 6
html html/GCA_001624185.1_129S1_SvImJ_v1.assembly
searchIndex name
searchTrix ixIxx/GCA_001624185.1_129S1_SvImJ_v1.assembly.ix
url http://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility dense
color 0,0,0
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.gap.bb
type bigBed 4
group map
html html/GCA_001624185.1_129S1_SvImJ_v1.gap

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility full
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_001624185.1_129S1_SvImJ_v1.gc5Base.bw
html html/GCA_001624185.1_129S1_SvImJ_v1.gc5Base

track repeatMasker
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility dense
type bed 3 .
noInherit on
html html/GCA_001624185.1_129S1_SvImJ_v1.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    priority 1
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    priority 2
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    priority 3
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    priority 4
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    priority 5
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    priority 6
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    priority 7
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    priority 8
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    priority 9
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.simpleRepeat.bb
html html/GCA_001624185.1_129S1_SvImJ_v1.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility pack
type bed 3 .
noInherit on
html html/GCA_001624185.1_129S1_SvImJ_v1.cpgIslands

    track cpgIslandExt
    parent cpgIslands
    shortLabel CpG Islands
    longLabel CpG Islands (Islands < 300 Bases are Light Green)
    priority 1
    type bigBed 4 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.cpgIslandExt.bb

    track cpgIslandExtUnmasked
    parent cpgIslands
    shortLabel Unmasked CpG
    longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
    priority 2
    type bigBed 4 +
    bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.windowMasker.bb
html html/GCA_001624185.1_129S1_SvImJ_v1.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.allGaps.bb
html html/GCA_001624185.1_129S1_SvImJ_v1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.augustus.bb
html html/GCA_001624185.1_129S1_SvImJ_v1.augustus

track gapOverlap
shortLabel Gap Overlaps
longLabel Exactly identical sequence on each side of a gap
group map
visibility hide
type bigBed 12 .
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.gapOverlap.bb
html html/GCA_001624185.1_129S1_SvImJ_v1.gapOverlap

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes v86
group genes
priority 40
visibility pack
color 150,0,0
type bigBed 12 .
bigDataUrl bbi/GCA_001624185.1_129S1_SvImJ_v1.ensGene.bb
searchIndex name
searchTrix ixIxx/GCA_001624185.1_129S1_SvImJ_v1.ensGene.name.ix
html html/GCA_001624185.1_129S1_SvImJ_v1.ensGene

include rnaSeqData/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt
include GCA_001624185.1_129S1_SvImJ_v1.bigMaf.trackDb.txt
