Table 3.

Observed frequency of the CRISPR/Cas9 adenosine insertion, specific to the GE rice line in crop mixture samples (n°18–19). (A) The samples were composed of 0.1% of the GE rice line (corresponding to 14 estimated haploid genome copies), 0.1% of the parental rice line (corresponding to 14 estimated haploid genome copies), and 99.8% of WT maize (sample n°12) or WT soybean (sample n°13) (corresponding to 13,972 estimated haploid genome copies). (B) For each sample, the copy number associated with the GE rice line, previously measured using a 2-plex ddPCR method [16], is indicated (Table S1). Additionally, regarding the rice ingredient, the rice ratio of the GE rice line is specified. The targeted high-throughput sequencing approach was performed in quadruplicate for each sample, allowing us to subsequently determine the allele frequency of the CRISPR/Cas9 adenosine insertion specific to the GE rice line. The associated depth of coverage of the reference at the position of this specific indel (bp 679,646) is indicated.

(A)
Sample Composition
Sample n°18	0.1 % GE rice line (14 estimated haploid genome copies)
	0.1 % parental rice line (14 estimated haploid genome copies)
	99.8 % WT maize (113,972 estimated haploid genome copies)
Sample n°19	0.1 % GE rice line (14 estimated haploid genome copies)
	0.1 % parental rice line (14 estimated haploid genome copies)
	99.8 % WT soybean (113,972 estimated haploid genome copies)
( B )
Crop Mixture Sample Description			CRISPR/Cas9 Adenosine Insertion
Sample n°	GE Rice Line Content		Allele Frequency ~			Depth of Coverage ~
	Copy Number	Rice Ratio *	Detection	Percentage	StDev	Value	StDev
18	10.6	50	+	40.46	10.78	533	50
19	9.3	50	+	48.52	18.12	23,124	3181

~ For each sample, the average value of the 4 replicates and the associated standard deviation (StDev) are indicated. * The rice ratio of the GE rice line is determined according to the total amount of rice (ingredient) present in the investigated samples.