a, Transposon methylation in Col-0, ddm1-2, rdr6-15 and ddm1-2 rdr6-15 replicates. Scale: 1 = methylated cytosine; 0 = unmethylated cytosine. b–f, Total DNA methylation at transposons, grouped by superfamily in Col-0 (b), ddm1-2 (c), rdr6-15 (d) and ddm1-2 rdr6-15 (e, f) replicates. 1, LTR retrotransposon ATGYPSY; 2, LTR retrotransposon ATCOPIA; 3, non-LTR retrotransposons ATLINE; 4, non-LTR retrotransposon TSCL; 5, TIR DNA transposon MUDR; 6, non-TIR DNA transposon MuDR; 7, DNA transposon ENSPM; 8, DNA transposon HELITRON; 9, other repeats. Total methylation by total converted cytosine to thymine and non-converted cytosine counts (at least ten reads per cytosine). Scale: 0 = unmethylated; 1 = methylated. Boxplots indicate median, range and standard deviations (box). g, h, DNA methylation by CG (red), CHG (blue) and CHH+/− context (green) at ATHILA ORF1 (AT2G10280) (g) and ATCOPIA43 (AT1G36040) (h). Track order: 1, Col-0; 2, ddm1-2; 3, rdr6-15; 4, ddm1-2 rdr6-15.