track chain_cs10
bigDataUrl bbi/cs10.bigChain.bb
linkDataUrl bbi/cs10.bigLink.bb
shortLabel cs10 chain
longLabel cs10 aligned to SMSQ
type bigChain
visibility pack
group compGeno
priority 7

track rbest_cs10
bigDataUrl bbi/cs10.rbestChain.bb
linkDataUrl bbi/cs10.rbestLink.bb
shortLabel cs10 rbest
longLabel cs10 reciprocal-best chains to SMSQ
type bigChain
visibility hide
group compGeno
priority 9

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

track SMSQ_cs10genes
bigDataUrl bbi/cs10.genes.bb
shortLabel Genes from cs10
longLabel cs10 RefSeq gene models lifted onto SMSQ through the cs10 chain (not its own annotation)
type bigBed 12
visibility hide
group genes

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

track SMSQ_gc
bigDataUrl bbi/SMSQ.gc.bw
shortLabel GC Percent
longLabel GC percent of SMSQ 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 repeats
superTrack on show
shortLabel Repeats
longLabel Repeat annotation and masking for SMSQ
group varRep

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

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

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

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

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