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Ahmed Supplementary Figure 1. a. b. c. Ahmed Supplementary Figure 2. a. b. c. CG GC. d. CHG GHC. -log(p-value). Methylation difference. Ahmed Supplementary Figure 3. met1. a. Methylation density. ddc. Methylation density. b. TE sequence. TE sequence. TE sequence.

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Ahmed Supplementary Figure 2

a

b

c

CG

GC

d

CHG

GHC

-log(p-value)

Methylation difference


Ahmed Supplementary Figure 3

met1

a

Methylation density

ddc

Methylation density

b

TE sequence

TE sequence

TE sequence

5’ flank

5’ flank

5’ flank

3’ flank

3’ flank

3’ flank

TE end

TE end

TE end

TE start

TE start

TE start

rdd

800bp

800bp

800bp

600bp

600bp

600bp

400bp

400bp

400bp

200bp

200bp

200bp

200bp

200bp

200bp

400bp

400bp

400bp

600bp

600bp

600bp

800bp

800bp

800bp

1kb

1kb

1kb

1kb

1kb

1kb

Methylation density

c


Ahmed Supplementary Figure 4

CG

Methylation density

TE sequence

TE sequence

TE sequence

CHG

3’ flank

3’ flank

3’ flank

Methylation density

5’ flank

5’ flank

5’ flank

TE start

TE start

TE start

TE end

TE end

TE end

CHH

Methylation density


Ahmed Supplementary Figure 5

a

b

g

h

Methylation density

Methylation density

Methylation density

Methylation density

5’ flank

TE

5’ flank

TE

5’ flank

5’ flank

TE

TE

TE

3’ flank

5’ flank

5’ flank

TE

TE

TE

3’ flank

i

j

c

d

Methylation density

Methylation density

Methylation density

Methylation density

TE

3’ flank

TE

3’ flank

f

k

l

e

Methylation density

Methylation density

Methylation density

Methylation density

TE

3’ flank

TE

3’ flank


Ahmed Supplementary Figure 6

Cm = methyl-cytosine

N = # cytosines in context having sufficient sequencing depths

CG = 100%

CHG = 100%

CHH = 51%

Pattern Assigned = MMM (Methylated CG, Methylated CHG, Methylated CHH)

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

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x

x

x

x

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