track gcPercent
shortLabel GC Content
longLabel GC content in 200 bp windows
type bigWig
bigDataUrl gcPercent.bw
visibility full
priority 1.1
group map
html gcPercent.html
autoScale on
viewLimits 0:63.03
graphTypeDefault points
windowingFunction mean

track seqEntropy
shortLabel Sequence Entropy
longLabel Shannon sequence entropy in 200 bp windows
type bigWig
bigDataUrl seqEntropy.bw
visibility full
priority 1.2
group map
html seqEntropy.html
autoScale on
viewLimits 0:1.99
graphTypeDefault points
windowingFunction mean

track nonBdna
shortLabel Non-B DNA
longLabel Non-B DNA motifs: G-quadruplexes, Z-DNA, triplex and repeat-based structures
type bigBed 9
bigDataUrl nonBdna.bb
visibility dense
priority 1.3
group varRep
html nonBdna.html
itemRgb on
maxWindowToDraw 26799200

track readCoverage
superTrack on show
shortLabel Read Coverage
longLabel Long-read sequencing coverage
priority 2
group map
html readCoverage.html

    track covHifi
    parent readCoverage
    shortLabel HiFi Coverage
    longLabel PacBio HiFi read coverage
    type bigWig
    bigDataUrl covHifi.bw
    visibility full
    priority 2.1
    html covHifi.html
    autoScale on
    viewLimits 0:240.128
    graphTypeDefault bar
    windowingFunction mean

    track covOnt
    parent readCoverage
    shortLabel ONT Coverage
    longLabel Oxford Nanopore read coverage
    type bigWig
    bigDataUrl covOnt.bw
    visibility full
    priority 2.2
    html covOnt.html
    autoScale on
    viewLimits 0:290.112
    graphTypeDefault bar
    windowingFunction mean

    track covClr
    parent readCoverage
    shortLabel CLR Coverage
    longLabel PacBio CLR read coverage from the earlier bTaeGut1.4 individual
    type bigWig
    bigDataUrl covClr.bw
    visibility full
    priority 2.3
    html covClr.html
    autoScale on
    viewLimits 0:562.551
    graphTypeDefault bar
    windowingFunction mean

track genes
superTrack on show
shortLabel Genes and Retrocopies
longLabel Gene models and processed retrocopies
priority 3
group genes
html genes.html

    track egapx
    parent genes
    shortLabel EGAPx Genes
    longLabel Protein-coding and lncRNA gene models from NCBI EGAPx
    type bigGenePred
    bigDataUrl egapx.bb
    visibility pack
    priority 3.1
    html egapx.html

    track retrocopies
    parent genes
    shortLabel Retrocopies
    longLabel Processed retrocopies identified with RCPedia
    type bigGenePred
    bigDataUrl retrocopies.bb
    visibility pack
    priority 3.2
    html retrocopies.html

track repeats
superTrack on show
shortLabel Repeats
longLabel Transposable elements, tandem repeats and satellite arrays
priority 4
group varRep
html repeats.html

    track transposons
    parent repeats
    shortLabel Transposable Elements
    longLabel Transposable elements and interspersed repeats from EDTA2
    type bigBed 9 +
    bigDataUrl transposons.bb
    visibility dense
    priority 4.1
    html transposons.html
    maxWindowToDraw 809629799
    itemRgb on

    track tandemRepeats
    parent repeats
    shortLabel Tandem Repeats
    longLabel Tandem repeat arrays from Tandem Repeats Finder
    type bigBed 6 +
    bigDataUrl tandemRepeats.bb
    visibility dense
    priority 4.2
    html tandemRepeats.html
    maxWindowToDraw 11605447

    track satellome
    parent repeats
    shortLabel Satellite Repeats
    longLabel Satellite repeat arrays from the Satellome catalog
    type bigBed 6
    bigDataUrl satellome.bb
    visibility pack
    priority 4.3
    html satellome.html

track centroTelo
superTrack on show
shortLabel Centromeres and Telomeres
longLabel Centromere cores and markers, telomeres and interstitial telomeric sequences
priority 5
group map
html centroTelo.html

    track centroSat
    parent centroTelo
    shortLabel Centromeric Satellites
    longLabel Centromeric satellite arrays from a curated satellite library
    type bigBed 9 +
    bigDataUrl centroSat.bb
    visibility pack
    priority 5.1
    html centroSat.html
    itemRgb on

    track centroCores
    parent centroTelo
    shortLabel Centromere Cores
    longLabel Centromere core regions predicted by Centromere Detector
    type bigBed 9 +
    bigDataUrl centroCores.bb
    visibility pack
    priority 5.2
    html centroCores.html
    itemRgb on

    track centroMarkers
    parent centroTelo
    shortLabel Centromere Markers
    longLabel Mapped positions of published centromeric and distal primer pairs
    type bigBed 4
    bigDataUrl centroMarkers.bb
    visibility pack
    priority 5.3
    html centroMarkers.html

    track telomeres
    parent centroTelo
    shortLabel Telomeres
    longLabel Terminal TTAGGG telomere arrays
    type bigBed 4 +
    bigDataUrl telomeres.bb
    visibility pack
    priority 5.4
    html telomeres.html

    track itsRepeats
    parent centroTelo
    shortLabel Interstitial Telomeres
    longLabel Interstitial telomeric sequences away from the chromosome ends
    type bigBed 3
    bigDataUrl itsRepeats.bb
    visibility pack
    priority 5.5
    html itsRepeats.html

track structVar
superTrack on show
shortLabel Structural Variation
longLabel Previously unassembled regions and large inter-haplotype variants
priority 6
group varRep
html structVar.html

    track newRegions
    parent structVar
    shortLabel Previously Unassembled
    longLabel Regions missing or collapsed in the earlier bTaeGut1.4 reference
    type bigBed 3
    bigDataUrl newRegions.bb
    visibility pack
    priority 6.1
    html newRegions.html

    track largeSv
    parent structVar
    shortLabel Large SVs
    longLabel Large structural variants between the maternal and paternal haplotypes
    type bigBed 4
    bigDataUrl largeSv.bb
    visibility pack
    priority 6.2
    html largeSv.html

track chromatin
superTrack on show
shortLabel Methylation and 3D Chromatin
longLabel CpG methylation and Hi-C A/B compartments
priority 7
group regulation
html chromatin.html

    track methyl5mC
    parent chromatin
    shortLabel 5mC Methylation
    longLabel CpG 5-methylcytosine probability from PacBio HiFi reads
    type bigWig
    bigDataUrl methyl5mC.bw
    visibility full
    priority 7.1
    html methyl5mC.html
    autoScale on
    viewLimits 0:94.529
    graphTypeDefault bar
    windowingFunction mean

    track compartE1
    parent chromatin
    shortLabel Compartment E1
    longLabel Hi-C first eigenvector at 200 kb, positive in the active A compartment
    type bigWig
    bigDataUrl compartE1.bw
    visibility full
    priority 7.2
    html compartE1.html
    autoScale on
    viewLimits -1.143:1.67
    windowingFunction mean

    track compartAB
    parent chromatin
    shortLabel A/B Compartments
    longLabel Hi-C A and B compartment intervals at 200 kb
    type bigBed 9
    bigDataUrl compartAB.bb
    visibility dense
    priority 7.3
    html compartAB.html
    itemRgb on
