<<include colors_fonts_patterns.conf>>
<<include /woldlab/castor/data00/proj/genome/programs/circos-0.60/etc/brewer.all.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>

<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 = 0.98r
r1 = 0.99r
</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 = 0.96r
r1 = 0.98r
</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 = 0.95r
r1 = 0.96r
</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 = 0.93r
r1 = 0.95r
</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 = 0.91r
r1 = 0.93r
</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>

type      = histogram
thickness = 0.5

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/ENCODE_mitochondria/2013-09-18-HA-mito/GM12878-PHB-sc28259-Rep10-130816-T-ED7-SL35767.chrM.v0.plus.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = ylorrd-6-seq-i
color   = ylgn-6-seq-2
min     = 0
max     = 6000
r0      = 0.80r
r1      = 0.90r
</plot>

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/ENCODE_mitochondria/2013-09-18-HA-mito/GM12878-PHB-sc28259-Rep10-130816-T-ED7-SL35767.chrM.v0.minus.wig
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = ylgn-6-seq-2
color   = ylorrd-6-seq-i
min     = 0
max     = 6000
r0      = 0.70r
r1      = 0.80r
</plot>

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/ENCODE_mitochondria/2013-09-18-HA-mito/GM12878-1PCR-Input-04.19.13-Rep10-SL31885.chrM.v0.plus.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = bupu-3-seq-3
color   = lyellow
min     = 0
max     = 4600
r0      = 0.60r
r1      = 0.70r
</plot>

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/ENCODE_mitochondria/2013-09-18-HA-mito/GM12878-1PCR-Input-04.19.13-Rep10-SL31885.chrM.v0.minus.wig
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = lyellow
color   = bupu-3-seq-3
min     = 0
max     = 4600
r0      = 0.50r
r1      = 0.60r
</plot>

<plot>
type = tile
file = /woldlab/castor/data02/ENCODE_data/Georgi_nonENCODE_datasets/Chan/circos_plots_TFAM/chrM.OsubL.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 24
padding = 6
orientation = out
stroke_thickness = 3
stroke_color = black
color = grey
r0 = 0.975r
r1 = 0.995r
</plot>

<plot>
type = tile
file = /woldlab/castor/data02/ENCODE_data/Georgi_nonENCODE_datasets/Chan/circos_plots_TFAM/chrM.Ori-b.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 24
padding = 6
orientation = out
stroke_thickness = 3
stroke_color = black
color = orange
r0 = 0.975r
r1 = 0.995r
</plot>

<plot>
type = tile
file = /woldlab/castor/data02/ENCODE_data/Georgi_nonENCODE_datasets/Chan/circos_plots_TFAM/chrM.OsubH.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 24
padding = 6
orientation = out
stroke_thickness = 3
stroke_color = black
color = yellow
r0 = 0.975r
r1 = 0.995r
</plot>

<plot>
type = tile
file = /woldlab/castor/data02/ENCODE_data/Georgi_nonENCODE_datasets/Chan/circos_plots_TFAM/chrM.LSP.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = red
color = yellow
r0 = 0.965r
r1 = 0.975r
</plot>

<plot>
type = tile
file = /woldlab/castor/data02/ENCODE_data/Georgi_nonENCODE_datasets/Chan/circos_plots_TFAM/chrM.HSP.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = black
color = black
r0 = 0.965r
r1 = 0.975r
</plot>

</plots>