Fig. 3: Tests of aPE performance in deletions and insertions.

a Alignment of the HEK3 reference sequence and representative deletion variants spanning from the +1 position to +6. Numbers above the reference indicate positions relative to the SpCas9 nicking site. Dashed lines represent deleted nucleotides in each variant. b Editing efficiency of PE and aPE2-induced deletions at HEK3 site. c, Indels formation of PE and aPE2-induced deletions at HEK3 site. d Comprehensive editing efficiency comparison of PE2 and aPE2-induced deletions for edits of HEK2, HEK3, HEK5, and HEK6. e Comprehensive indels comparison of PE2 and aPE2-induced deletions for edits of of HEK2, HEK3, HEK5, and HEK6. f Alignment of the HEK3 reference sequence and representative insertion variants at +1 position, with inserted sequences ranging from 1 to 6 nucleotides. Numbers above the reference indicate positions relative to the SpCas9 nicking site. Inserted nucleotides are shown in red for clarity. g Editing efficiency of PE and aPE2-induced insertions at HEK3 site. h Indels formation of PE and aPE2-induced insertions at HEK3 site. i Comprehensive editing efficiency comparison of PE2 and aPE2-induced insertions for edits of HEK2, HEK3, HEK5, and HEK6. j Comprehensive indels comparison of PE2 and aPE2-induced insertions for edits of of HEK2, HEK3, HEK5, and HEK6. All experiments were conducted in HEK293T cells. The data in (b, c, g, h) were obtained from n = 3 independent biological replicates. Bars represent mean ± s.d. P values were calculated using the two-tailed Student’s t-test. Source data are provided as a Source Data file.