track hprcCatGenes
shortLabel CAT Genes
longLabel CAT (Comparative Annotation Toolkit) gene annotations
type bigGenePred
bigDataUrl contrib/hprc2annot/catGenes.bb
group genes
priority 10
visibility pack
labelFields name,name2
defaultLabelFields name2
searchIndex name,name2
baseColorDefault genomicCodons
dataVersion HPRC Release 2, CAT genes v1.3
html contrib/hprc2annot/catGenes

track hprcLiftoffGenes
shortLabel Liftoff Genes
longLabel Liftoff RefSeq gene annotations
type bigGenePred
bigDataUrl contrib/hprc2annot/liftoffGenes.bb
group genes
priority 11
visibility dense
labelFields name,name2
defaultLabelFields name2
searchIndex name,name2
baseColorDefault genomicCodons
dataVersion HPRC Release 2, Liftoff genes v1.0
html contrib/hprc2annot/liftoffGenes

track hprcCensat
shortLabel cenSat
longLabel Centromere satellite annotation (cenSat)
type bigBed 9 +
bigDataUrl contrib/hprc2annot/censat.bb
group varRep
priority 20
visibility pack
itemRgb on
searchIndex name
dataVersion HPRC Release 2, cenSat v1.0
html contrib/hprc2annot/censat

track hprcActiveCentromeres
shortLabel Active Centromere
longLabel Active centromere regions
type bigBed 3
bigDataUrl contrib/hprc2annot/censatCentromeres.bb
group map
priority 21
visibility dense
color 220,20,60
dataVersion HPRC Release 2, cenSat centromeres v1.0
html contrib/hprc2annot/censatCentromeres

track hprcSegdups
shortLabel Seg Dups
longLabel Segmental duplications (SEDEF)
type bigBed 9 +
bigDataUrl contrib/hprc2annot/segdups.bb
group varRep
priority 22
visibility dense
itemRgb on
filterValues.original True,False
filterType.original multipleListOr
filterLabel.original SEDEF original call
mouseOver Duplicate of ${partner}<br>Identity: ${pctMatch}%<br>Aligned length: ${alnLen} bp<br>Satellite bases: ${satBases}
dataVersion HPRC Release 2, SEDEF segdups v1.1
html contrib/hprc2annot/segdups

track hprcPclai
shortLabel PCLAI Ancestry
longLabel Point cloud local ancestry inference (PCLAI)
type bigBed 9 +
bigDataUrl contrib/hprc2annot/pclai.bb
group compGeno
priority 30
visibility dense
onlyVisibility dense
denseClick on
itemRgb on
mouseOver Window ${window}<br>Window PC1,PC2: ${pca}<br>Ancestry centroid: ${centroid}<br>Confidence: ${score}
dataVersion HPRC Release 2, PCLAI v1.1
detailsScript.scatterPlot.pca {"dataUrl":"pclaiRefPanel.json","exportFields":["pca","centroid"],"title":"Position in ancestry space","xLabel":"PC1","yLabel":"PC2"}
html contrib/hprc2annot/pclai

track hprcMethylation
shortLabel Methylation
longLabel ONT 5mC CpG methylation
type bigWig 0 100
bigDataUrl contrib/hprc2annot/methylation.bw
group regulation
priority 40
visibility full
autoScale off
viewLimits 0:100
maxHeightPixels 100:40:8
color 0,0,200
dataVersion HPRC Release 2, ONT methylation v1.0
html contrib/hprc2annot/methylation