a b

c

Ahmed Supplementary Figure 1

ba

CGGC

CHGGHC

Ahmed Supplementary Figure 2

c

d

Methylation difference

-log(

p-va

lue)

Ahmed Supplementary Figure 3

ddc

a

rdd

met1

b

c

3’ flankTE sequence5’ flank

3’ flankTE sequence5’ flank

3’ flankTE sequence5’ flank

Ahmed Supplementary Figure 4

5’ flankTE start TE end

3’ flankTE sequence

5’ flankTE start TE end

3’ flankTE sequence

5’ flankTE start TE end

3’ flankTE sequence

CHH

CG

CHG

a b

dc

e f k l

ji

g h

Ahmed Supplementary Figure 5

3’ flankTE5’ flank TE 5’ flank TE 3’ flankTE

3’ flankTE3’ flankTE5’ flank TE

5’ flank TE 5’ flank TE 3’ flankTE 3’ flankTE

5’ flank TE

Ahmed Supplementary Figure 6

CG = 100%CHG = 100%CHH = 51%Pattern Assigned = MMM (Methylated CG, Methylated CHG, Methylated CHH)

Cm = methyl-cytosine

N = # cytosines in context having sufficient sequencing depths

xx

x x

x x

xx x

xx

xx x

x x

x

x x

xx

x

xx

xxx x xxx x