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
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 pack
labelFields name,name2
defaultLabelFields name2
searchIndex name,name2
baseColorDefault genomicCodons
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
html contrib/hprc2annot/censat

track hprcActiveCentromeres
shortLabel Active centromeres
longLabel Active centromere regions
type bigBed 3
bigDataUrl contrib/hprc2annot/censatCentromeres.bb
group map
priority 21
visibility dense
color 220,20,60
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 pack
itemRgb on
mouseOver Duplicate of ${partner}<br>Identity: ${fracMatch}<br>Aligned length: ${alnLen} bp<br>Satellite bases: ${satBases}
html contrib/hprc2annot/segdups

track hprcPclai
shortLabel pcLAI ancestry
longLabel Pangenome local ancestry inference (pcLAI)
type bigBed 9 +
bigDataUrl contrib/hprc2annot/pclai.bb
group compGeno
priority 30
visibility dense
itemRgb on
mouseOver Window ${window}<br>PCA coordinates (PC1,PC2): ${pca}<br>Segment PCA: ${pcaSegment}<br>Confidence: ${score}
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
html contrib/hprc2annot/methylation