Table 2. Targeted mutation patterns in apple genome.

Target gene	Sequence	Mutation pattern	No. clone	Frequency (%)
MD05G1312300	AAGCTCCCTATCTTCTGTCAACCCTCGGCCTTCCCCCCCCCCAGTGTGCATTAATTAAGGAAGATTGACTTACTTTTAACCATTTTAAAAACACATTCAAACGAGCCCTTATTAGTTTCTACTAAGCATACGATAAGCTCCCTATCTTCTGTCAACCCTCGGCCT	WT	60	68.2
	-------ATTCAAACGAGCCCTTATTAGTTTCTACTAAGCATACGATAAGCTCCCTATCTTCTGTCAACCCTCGGCCT	−134 bp	22	25.0
	AAGCTCCCTAT------CTTCTGTCAACCCTCGGCCT	−134 bp	3	3.4
	------CAAACGAGCCCTTATTAGTTTCTACTAAGCATACGATAAGCTCCCTATCTTCTGTCAACCCTCGGCCT	−134 bp	1	1.1
	------CTTATTAGTTTCTACTAAGCATACGATAAGCTCCCTATCTTCTGTCAACCCTCGGCCT	−134 bp	1	1.1
	AAGCTCCCTATCTTCTGTC(+134bp)AACCCTCGGCCTTCCCCCCCCCCAGTGTGCATTAATTAAGGAAGATTGACTTACTTTTAACCATTTTAAAAACACATTCAAACGAGCCCTTATTAGTTTCTACTAAGCATACGATAAGCTCCCTATCTTCTGTCAACCCTCGGCCT	+134 bp	1	1.1
MD11G1251800	GGCCATGCATCTTGTGATCTGCTCTCTACATGCTCTCTCTCTTCTGTCATCCGTGGCTTTGTTTCTAGGCCATTAC	WT	74	98.7
	GGCCATGCATCTTGTGATCTGCTCTCTACATGCTCTCT------	−113 bp	1	1.3

The red characters indicate the 20 bp target sequences of SpCas9. The italicized characters indicate PAM sequences. The underlined characters indicate the predicted miR156 target sequences. The mutation frequencies were measured as the ratio of clones with mutation to the total number of sequenced clones.