Genome-wide analysis of spontaneous mutations and mutations caused by tissue culture and Agrobacterium-mediated transformation. a, b Average numbers of SNVs and indels detected in three generations of wild type plants and four types of tissue culture-related control plants. Error bars indicate s.e.m. c, d Annotation of genome-wide distribution of mutations found in all control samples: WT, tissue culture only, Agro-infection, Cas9 backbone, and Cpf1 backbone. TE transposable element, CDS coding sequence. Error bars indicate s.e.m.