track chain_cs10
bigDataUrl bbi/cs10.bigChain.bb
linkDataUrl bbi/cs10.bigLink.bb
shortLabel cs10 chain
longLabel cs10 aligned to SSLR
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 SSLR
type bigChain
visibility hide
group compGeno
priority 9

track SSLR_genes
bigDataUrl bbi/SSLR.anno.bb
shortLabel Gene models
longLabel Gene annotation for SSLR
type bigBed 12
visibility pack
group genes
priority 2

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

track SSLR_gc
bigDataUrl bbi/SSLR.gc.bw
shortLabel GC Percent
longLabel GC percent of SSLR 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 SSLR
group varRep

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

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

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

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