Table 1.

Parameters used in the two experiments for each of the aligners tested

Mapper	Parameters
GNUMAP-bs	-m 17 -s 1 -T 20 -a 0.90 (-a 0.92) -b
Novoalign	-k 17 -s 2 -r -A 20 -t 75 (-t 90) -b2
BSMAP	-n 0 -w 100 -v 3
Bismark	-n 2 -l 50
Bismark-bt2	-N 1 -L 20 –bowtie2 –min-score L,0,-0.6
LAST	-Q1 -j1 -d120 -n20 -f1 | last-map-probs.py -s150 -m0.95
BRAT-BW	default settings for single-end reads

Parameters in parentheses were used for the human BSR dataset. Up to 3 to 4 sequencing errors or mutations were allowed in a 100-bp long BSR. Because the human genome contains many repeated genomic regions, 20 valid mapping locations were allowed for a given read when the alignment method supported this feature.