Table 4.

Extracted read pairs crossing the Gt1 inserted site derived from original and modified TranSeq pipeline in artificial cisgenesis rice and WT.

	Artificial cisgenesis		Reason	WT (Xiushui 110)		Reason
	Not filtered	Filtered	Reason	Not filtered	Filtered	Reason
Chr 01: 32076358-32077341	20	20	Not really positives^a	20	20	Not really positives^a
Chr 01: 32076840-32078305	103	0	Not really positives^a	103	0	Not really positives^a
Chr 01: 32078413-32078798	13	13	Not really positives^a	13	13	Not really positives^a
Chr 04: 675093	1	1	noise sequences/alignment jitter	1	1	noise sequences/alignment jitter
Chr 05: 11030976-11031684	116	116	candidate	0	0
Chr 10: 13497001-13497784	65	65	Not really positives^a	65	65	Not really positives^a
Chr 10: 13497378-13499421	1008	0	Not really positives^a	508	0	Not really positives^a
Chr 10: 13499431-13499725	56	56	Not really positives^a	56	56	Not really positives^a

^a Homologous sequence between Gt1 and rice genome.