Fig. 5

Inhibition of NHEJ leads to increased large fragment deletions. a Molecular structures of NHEJ inhibitors (M3814 and NU7441). b, c M3814 (b) or NU7441 (c) does not affect indel frequencies but significantly increases deletion indexes. d Visualization of changes in large deletions after inhibition of NHEJ or MMEJ repair pathways. Long PCR amplicons were aligned with references using Minimap2 and visualized with IGV. Deletions were calculated by (Read depth − Mean depth)/(Read depth). Unedited wildtype cells showed a background deletion. This noise was subtracted from the deletion of edited cells to obtain deletion indexes. e Schematic summary for the impact of DNA repair pathways on large deletions after CRISPR-Cas9 editing. The data in b and c were statistically analyzed by a two-way ANOVA test. Adjusted p values were indicated. “ns” means no significance (p > 0.05)