Table 1.

NGS analysis of PCR amplicons of DNA and RNA of genome-edited lines.

Target gene	Line	Allele	No. of counts (DNA)	No. of counts (RNA)	Target 1		Target 2
					Sequence	In/Del	Sequence	In/Del
Gt5GT	WT	1	12,79–8	50,836	GTTAGAGGAAGAGGCCTTGC AGG	0	GCAAAAGGGCTCCTCGCGAG TGG	0
		2	11,604	26,024	GTTAGAGGAAGAGGCCTTGC AGG	0	GCAAAAGGGCTCCTCGCGAG TGG	0
	#47	1	9,611	6,443	GTTAGAGGAAGAGGCCTTGC AGG	0	GCAAAAGGGCT-----CGAG TGG	−5
		2	9,605	36,768	GTTAGAGGAAGAGGCCTTGC AGG	0	GCAAAAGGG---------AG TGG	−9
	#106	1	18,816	29,042	CGTTAGAGGAAGAGGCC-TGC AGG	−1	GCAAAAGGG-------CGAG TGG	−7
		2	30,010	261,382	CGTTAGAGGAAGAGGC----------------||----------------GAG TGG			−256
Gt3′GT	WT	1	5,666	4,852	CCT GGGATTCGACATATCTGTTC	0	AACGACGCTGCAGCTAAATT TGG	0
		2	5,419	2,055	CCT GGGATTCGACATATCTGTTC	0	AACGACGCTGCAGCTAAATT TGG	0
		3	5,825	2,018	CCT GGGATTCGACATATCTGTTC	0	AACGACGCTGCAGCTAAATT TGG	0
		4	4,852	22,326	CCT GGGATTCGACATATCTGTTC	0	AACGACGCTGCAGCTAAATT TGG	0
	#11*	1	20,194	35,543	CCT GGG------CATATCTGTTC	−6	AACGACGCTGCAGCT-AATT TGG	−1
		2	34,884	461,515	CCT GGG---------------------||--------------------AATT TGG			−221
		3
		4
	#35	1	7,186	3,004	CCT -------GACATATCTGTTC	−7	AACGACGCTGCAGCTAAATT TGG	0
		2	7,223	33,855	--||--ATTCGACATATCTGTTC	−10	AACGACGCTGCAGCTAAATT TGG	0
		3	—	—	not amplified	—	not amplified	—
		4	—	—	not amplified	—	not amplified	—
Gt5/3′AT	WT	1	15,403	12,453	CCT CTTTGTCTCTCACTCTAAAA	0	CCA TGCAAGACTATAAAGTGATC	0
		2	18,258	20,721	CCT CTTTGTCTCTCACTCTAAAA	0	CCA TGCAAGACTATAAAGTGATC	0
	#50	1	16,376	15,213	CCT CTTTGTCTCTCACTCTAAAA	0	------||-------AAGTGATC	−30
		2	19,913	11,267	CCT CTT-----||------ [202 base reversed] AGACTATAAAGTGATC			−27
	#60	1	7,872	1,272	CCT CTTTGTCTCTCACTCTAAAA	0	CCA TGC----CTATAAAGTGATC	−4
		2	6,874	22,102	CCT C---GTCTCTCACTCTAAAA	−3	CCA TGC–ACTATAAAGTGATC	−3

Double underlines show PAM sequences.

*Allele 2, 3 and 4 are indistinguishable from each other due to large deletion.