<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include chrM.ideogram.conf>>
<<include chrM.ticks.conf>>

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

karyotype   = chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

type      = histogram
thickness = 2

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.protein_coding_gene.plus.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = green
color = green
r0 = 0.99r
r1 = 0.97r
</plot>

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.protein_coding_gene.minus.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = orange
color = orange
r0 = 0.95r
r1 = 0.97r
</plot>

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.repeat.tiles
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = red
color = red
r0 = 0.91r
r1 = 0.95r
</plot>

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.rRNA.minus.tiles
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = blue
color = blue
r0 = 0.89r
r1 = 0.91r
</plot>

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.tRNA_gene.plus.tiles
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = purple
color = purple
r0 = 0.87r
r1 = 0.89r
</plot>

<plot>
type = tile
file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.tRNA_gene.minus.tiles
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = grey
color = grey
r0 = 0.85r
r1 = 0.87r
</plot>

</plots>

<links>

z      = 0
radius = 0.83r
bezier_radius = 0.1r

<link>
show         = yes
color        = vvdgrey
thickness    = 2
file         = GSM1078405-crh6-mutant-Hi-C.200bp.min2000bp-dist.links.chrM
record_limit = 2500
</link>

</links>
