Table 4.

Mutation rate assay by targeted deep sequencing in MLO-7, DIPM 1, 2, and 4.

Target gene	Sample name	Number of Reads (more than minimum frequency)			Number of insertion mutations			Number of deletion mutations			Indel ratio (average, %)
		1	2	3	1	2	3	1	2	3
MLO-7 (RG4, grape)	sgRNA only	56302	52455	54565	0	0	0	0	0	0	0.00
	Cas9 only	9924	10123	10001	0	0	0	0	0	0	0.00
	Cas9: sgRNA, 1:1	51558	52015	52206	0	0	0	49	55	64	0.10
	Cas9; sgRNA, 1:3	56546	55432	56421	2	4	6	71	74	69	0.10
	Cas9; sgRNA, 3:1	67286	64532	66876	42	57	68	10	12	9	0.10
DIPM1 (RG2, apple)	sgRNA only	58020	57987	58911	0	0	0	2	0	1	0.00
	Cas9 only	53727	54455	55432	0	0	0	5	7	8	0.00
	Cas9: sgRNA, 1:1	60903	60467	60787	0	0	0	16	22	13	0.00
	Cas9; sgRNA, 1:3	65674	64678	65632	0	0	0	15	19	22	0.00
	Cas9; sgRNA, 3:1	61565	62639	60166	0	0	0	4150	4500	3989	6.70
DIPM2 (RG4, apple)	sgRNA only	22397	22565	22001	0	0	0	0	0	0	0.00
	Cas9 only	16021	17089	17345	0	0	0	0	0	0	0.00
	Cas9: sgRNA, 1:1	17847	18945	17923	447	565	472	140	167	178	3.30
	Cas9; sgRNA, 1:3	17965	17456	17989	80	74	92	2	4	5	0.50
	Cas9; sgRNA, 3:1	17005	17233	17565	291	300	267	271	288	298	3.30
DIPM4 (RG7, apple)	sgRNA only	20239	20679	20899	0	0	0	0	0	0	0.00
	Cas9 only	32096	32198	32345	0	0	0	0	0	0	0.00
	Cas9: sgRNA, 1:1	42871	43211	43001	691	701	719	2253	2300	2310	6.90
	Cas9; sgRNA, 1:3	22055	22100	22189	0	0	0	555	567	590	2.50
	Cas9; sgRNA, 3:1	30240	31000	30319	0	0	0	1835	2000	2187	6.10