Example for an asymmetric look-up table for 8 k-mers.

<p>The 8-mer ACGTCGCT (corresponds to key 7015) generates 7 other keys. The 8-mer ATGTCGTT (key 15215) from the BS-read can be looked up to find its referenced key as ACGTCGCT (key 7015), ACGTCGTT (key 7023), ATGTCGCT (key 15207) and ATGTCGTT (key 15215) but no others.</p

Distribution of cytosine sequence context.

<p>(A) Frequency of sequence context in the reference genome. (B) Frequency of sequence context of methylated C according to BiSS and A3M.</p

Global methylation level.

<p>Ratio of the number of mapped Cs divided by the number of mapped C plus T for all classified Cs. Black: Cs that are called methylated, White: C that are not called methylated.</p

Comparison of mapping results for BiSS and selected other aligning programs¹.

<p>Default parameters unless otherwise specified.</p>1<p>A3M – results reported by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041528#pone.0041528-Lister1" target="_blank">[4]</a>.</p>2<p>BSMAPv1 parameters: -p 8 -s 12 -r 2 -w 100 -n 1 -v 5 -g 5, recommended by the authors, maximal 5 mismatches.</p>3<p>RMAP parameters: -m 5 –v, default parameters.</p

Examples for validation by individual bisulfite sequencing.

<p>The plots show the correlation between calculated and validated methylation levels (C/(C+T)) from regions selected for congruency (A) or disagreement (B–D) between BiSS and A3M. Each point represents one cytosine position. The x-axis corresponds to the methylation levels calculated from either BiSS (filled circles and black regression lines) or A3M (open circles and dotted regression lines); the y-axis shows the result of individual bisulfite sequencing. The legends show the Pearson correlation coefficients. (A) Methylated region according to both methods (M/M). (B) A region called methylated by BiSS but not by A3M (M/U); the rectangles indicate experimentally validated Cs congruent to BiSS (filled) and discrepant to A3M (open). (C) A region called methylated by BiSS but not by A3M due to insufficient sequencing coverage (M/X). (D) A region called methylated by A3M but not by BiSS (U/M), the rectangle symbols are the same as in (B).</p

Congruency between methylation calling by A3M and BiSS.

<p>M: methylated, U: unmethylated, X: not determined due to lack of sufficient sequencing coverage. Percentages refer to the total number of genomic cytosines.</p