track NLv1a_genes
bigDataUrl bbi/NLv1a.anno.bb
shortLabel Gene models
longLabel Gene models published with NLv1a (Salk pangenome, primary high-confidence)
searchIndex name
type bigBed 12 +
visibility pack
group genes
priority 2

track cytoBandIdeo
bigDataUrl bbi/NLv1a.cytoBand.bb
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
type bigBed 4 +
visibility dense
group map

track NLv1a_gap
bigDataUrl bbi/NLv1a.gap.bb
shortLabel Gaps
longLabel Assembly gaps (runs of N) in NLv1a
type bigBed 3
color 0,0,0
visibility dense
group map

track NLv1a_gc
bigDataUrl bbi/NLv1a.gc.bw
shortLabel GC Percent
longLabel GC percent of NLv1a over non-N bases
type bigWig 0 100
viewLimits 25:55
autoScale off
windowingFunction mean
graphTypeDefault bar
maxHeightPixels 128:36:16
color 0,0,0
altColor 128,128,128
visibility dense
group map

track NLv1a_cannabinoid
bigDataUrl bbi/NLv1a.cannabinoid.bb
shortLabel Cannabinoid synthases
longLabel Full-length THCAS (red), CBDAS (blue) and CBCAS (green) copies (Salk pangenome)
type bigBed 9
itemRgb on
visibility pack
group genes
priority 30

track repeats
superTrack on show
shortLabel Repeats
longLabel Repeat annotation and masking for NLv1a
group varRep

track NLv1a_rmsk
parent repeats
bigDataUrl bbi/NLv1a.rmsk.bb
shortLabel RepeatMasker
longLabel RepeatMasker run published with NLv1a (Salk pangenome); colored by repeat class
itemRgb on
type bigBed 9 +
visibility dense
group varRep
priority 1

track NLv1a_maskunion
parent repeats
bigDataUrl bbi/NLv1a.maskunion.bb
shortLabel Aligner mask
longLabel Union of our four maskers: the soft-masking every panel alignment ran on
type bigBed 3
visibility dense
group varRep
priority 2

track NLv1a_dustmasker
parent repeats
bigDataUrl bbi/NLv1a.dustmasker.bb
shortLabel dustmasker
longLabel dustmasker (low-complexity), WF-B
type bigBed 3
visibility hide
group varRep

track NLv1a_windowmasker
parent repeats
bigDataUrl bbi/NLv1a.windowmasker.bb
shortLabel WindowMasker
longLabel WindowMasker (over-represented k-mers), WF-B
type bigBed 3
visibility hide
group varRep

track NLv1a_tantan
parent repeats
bigDataUrl bbi/NLv1a.tantan.bb
shortLabel tantan
longLabel tantan (tandem repeats), WF-B
type bigBed 3
visibility hide
group varRep

track NLv1a_fastan
parent repeats
bigDataUrl bbi/NLv1a.fastan.bb
shortLabel FasTAN
longLabel FasTAN (satellite and long tandem arrays), WF-B
type bigBed 3
visibility hide
group varRep