<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include mm9.ideogram.conf>>
<<include mm9.ticks.conf>>

<image>
<<include etc/image.conf>>
</image>

karyotype   = mm9.chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

<plot>
type = tile
file = mm9.chrM.minus.protein_coding.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = dorange
color = dorange
r0 = 0.98r
r1 = 0.99r
</plot>

<plot>
type = tile
file = mm9.chrM.plus.protein_coding.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = green
color = green
r0 = 0.96r
r1 = 0.98r
</plot>

<plot>
type = tile
file = mm9.chrM.plus.rRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = blue
color = blue
r0 = 0.95r
r1 = 0.96r
</plot>

<plot>
type = tile
file = mm9.chrM.plus.tRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = purple
color = purple
r0 = 0.93r
r1 = 0.95r
</plot>

<plot>
type = tile
file = mm9.chrM.minus.tRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = gpos75
color = gpos75
r0 = 0.91r
r1 = 0.93r
</plot>

<plot>
type = text
file = mm9.chrM.protein_coding.text
color      = black
label_font = bold
label_size = 36p
label_parallel   = no
padding = 15p
rpadding = 15p
z       = 1
r0 = 1.02r
r1 = 1.22r
</plot>

<plot>
type = text
file = mm9.chrM.tRNA.text
color      = black
label_font = bold
label_size = 30p
label_parallel   = yes
padding = 2p
rpadding = 2p
z       = 2
r0 = 1.03r
r1 = 1.08r
</plot>

type      = histogram
thickness = 0.5

</plots>

<links>

z      = 0
radius = 0.95r
bezier_radius = 0.1r

<link>
show         = yes
color        = vvdgrey
thickness    = 2
file         = GSM1192206-HiC-mNSC-Rad21-floxed-G1-rep1.50bp.min1000bp-dist.links
record_limit = 2500
</link>

</links>
