Fig. 4: Single basepair insertion outcomes.

a Most 1 bp insertions at the cut site matched the PAM-distal nucleotide in control cells. Dashed line represents Cas9 cutsite between 4th and 3rd basepair upstreams of the PAM sequence. First row represents the case in which basepairs flanking the cutsite are identical to each other, and to the inserted base. b Absolute frequency of 1 bp insertions in control cells, by cutsite flanking nucleotides and match between inserted nucleotide and flanking nucleotides. c Relationship between absolute 1 bp insertion frequency in control cells and relative frequency of PAM-proximal insertions. Only targets with differing flanking nucleotides included. d Relative frequency of PAM-proximal 1 bp insertion across knockouts. Bar height is mean, error bars are 95% bootstrap confidence intervals (N = 1000 bootstraping repeats). Grey horizontal band is 95% confidence interval of control cells. e Enrichment or depletion of 1 bp insertions across knockouts, segregated by match between insertion and flanking nucleotides. Frequency of 1 bp insertions matching the PAM-proximal nucleotide was diminished in the absence of Prkdc and Polm compared to controls, while PAM-distal insertions were not affected by these knockouts. f Single basepair insertions coloured by the match between inserted nucleotide and the cutsite flanking nucleotides, in UMAP projection. Only clusters 2, 3 and 4 are shown (90% of 1 bp insertion outcomes). g Relative frequency of targets within clusters, segregated by cutsite flanking nucleotides, in control cells. Only targets whose 1 bp insertion outcomes are >85% contained within a given target are included. h Enrichment or depletion of 1 bp insertions within clusters 2, 3 and 4 across knockouts. Source data are provided as a Source Data file.