Fig. 2.

Effects of penalty value on domain demarcation. a Effects of penalty value on domain length distribution. CpG sites covered by at least ten reads were used for calculation. b Domain demarcation patterns are shown for a genomic region around FOXD2 gene (chr1, 47,880,913–47,915,913) under five different penalty values. Arrowheads indicate small domains that were missed unless low penalty value were used. The bottom track indicates the maximum penalty value above which each changepoint cannot be detected