Fig. 3

The positional and size distribution of indels, in relation to methylation status, insertion type, and orientation. a Percentage of reads with an indel at positions along the PacBio sequenced region. The same subset of reads used in Fig. 2a is included here (6-TG selected, both methylated and unmethylated, perfect match on the allele-defining SNVs and the surrounding portion of exon 1). Red arrowheads indicate the CRISPR/Cas9 cut sites. The purple bar marks the region of exon 1 surrounding the allele-defining SNVs. The distribution of indels is highest at the CRISPR/Cas9 cut sites, but many reads have indels within the CpG island as well. b Indel distributions at repair junctions of methylated (blue) or unmethylated (purple) alleles. c Indel distributions at repair junctions from events involving exogenous inserts (gray) or endogenous inserts (forward-oriented and inverted wild-type sequences; black). d Indel distributions at repair junctions from forward-oriented wild-type sequences (gray) or inverted wild-type sequences (black). The numbers of indels (y-axis) were scaled so that the maximum number for any indel size (x-axis) for a given distribution was one to allow easier comparison between distributions. Negative numbers for indel size represent deletions, positive numbers represent insertions, and sequences without any repair junction indels have an indel size of zero