<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include hg19.ideogram.conf>>
<<include hg19.ticks.conf>>

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

karyotype   = hg19.chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

type      = histogram
thickness = 2

<plot>
show    = yes
file    = hg19.36mers.hg19-female.bowtie.v2.unique.chrM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = dred
color   = dred
min     = 0
max     = 36
r0      = 0.88r
r1      = 0.98r
</plot>

<plot>
type = tile
file = hg19.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 = 0.85r
r1 = 0.86r
</plot>

<plot>
type = tile
file = hg19.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 = 0.83r
r1 = 0.85r
</plot>

<plot>
type = tile
file = hg19.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 = 0.82r
r1 = 0.83r
</plot>

<plot>
type = tile
file = hg19.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 = 0.80r
r1 = 0.82r
</plot>

<plot>
type = tile
file = hg19.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 = 0.78r
r1 = 0.80r
</plot>

<plot>
type = text
file = hg19.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 = hg19.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>

<plot>
type = tile
file = hg19.chrM.D-loop.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = black
color = black
r0 = 0.86r
r1 = 0.87r
</plot>


<plot>
show    = yes
file    = 7-KSV-Homo_sapiens/ChIPseq_H3K4me3_iSLK219-GSM1359503.36mers.chrM.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = ylorrd-9-seq-7
color   = ylorrd-9-seq-9
min     = 0
max     = 25547
r0      = 0.68r
r1      = 0.73r
</plot>


<plot>
show    = yes
file    = 7-KSV-Homo_sapiens/ChIPseq_H3K4me3_iSLK219-GSM1359503.36mers.chrM.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = ylorrd-9-seq-9
color   = ylorrd-9-seq-7
min     = 0
max     = 29927
r0      = 0.73r
r1      = 0.78r
</plot>


<plot>
show    = yes
file    = 7-KSV-Homo_sapiens/ChIPseq_IgG_iSLK219-GSM1359509.36mers.chrM.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = greens-9-seq-2
color   = purd-9-seq-5
min     = 0
max     = 12593
r0      = 0.58r
r1      = 0.63r
</plot>


<plot>
show    = yes
file    = 7-KSV-Homo_sapiens/ChIPseq_IgG_iSLK219-GSM1359509.36mers.chrM.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = purd-9-seq-5
color   = greens-9-seq-2
min     = 0
max     = 19585
r0      = 0.63r
r1      = 0.68r
</plot>

</plots>
