Fig. 3: Mismatch count and CFD score as effective predictors of Cas9 cleavage efficiency.

a Number of mismatches in cut (n = 63) and uncut (n = 83) plants, mutations verified by Sanger sequencing. Statistical significance was evaluated by Students two-sided t-test, ***p-value < 0.001, assuming equal variances. b CFD score in cut (n = 63) and uncut (n = 83) plants. Statistical significance was evaluated by Students two-sided t-test, * p-value < 0.05, assuming equal variances. Data are presented as mean values ± SD. c Cas9 edits (cleavage efficiency) in phenotype-based selection (n = 66) and randomly selected plants (n = 80). Not significant by Students two-sided t-test (p-value = 0.064). Data are presented as mean values ± SD. d Cas9 cleavage efficiencies in two tomato backgrounds, M82 (n = 66) and Ailsa Craig (AC, n = 80). Data are presented as mean values ± SD. Not significant by Students two-sided t-test (p-value = 0.134). e CFD score in all library targets, divided into mismatch numbers: 0, 1, 2, and 3 or more mismatches. n number indicated in brackets below. Statistical significance was evaluated by one-way ANOVA and Tukey’s multiple comparison test, p-value < 0.0001. Data are presented as a box plot with the center by the median, box limits correspond to the 25th and 75th percentiles, whiskers extending to the minimum and maximum values. f Cas9 cleavage efficiencies in two tomato backgrounds, M82 (n = 66) and Ailsa Craig (AC, n = 80), among target genes with 0, 1 or 2 mismatches. “random” includes Cas9 cleavage efficiency data from independent plants randomly selected. “Phenotype” indicates phenotype-based selection and includes Cas9 cleavage efficiency data from plants selected based on observable phenotypes. Source data are provided as a Source Data file.