Table 2.

Sites identified with significantly different indels located within 10 bp of a nominated cut site in the WGS.

				Distance from cut site	Untreated		EBT-001
Guide and nominated site ID	Monkey	Ref	SNP		Freq	Depth	Freq	Depth	Diff %
SIV_031_6MM_gag_03	CH97	G	+T	7	100%	19	95.8%	24	−4.2
SIV_031_6MM_gag_03	CK49	G	+T	7	68.0%	25	91.7%	24	23.7
SIV_052_4MM_ltr_13	CH97	T	+A	−10	35.9%	53	34.4%	96	−1.5
SIV_052_4MM_ltr_13	CK49	T	+A	−10	39.3%	56	43.5%	85	+4.2
SIV_093_5MM_ltr_44	CK49	A	+T	−10	65.6%	32	85.2%	27	19.6
SIV_093_5MM_ltr_44	CH97	A	+T	−10	95.2%	21	90.0%	10	−5.2
SIV_130_5MM_ltr_73	CK49	G	–	7	30.5%	584	26.4%	606	−4.1
SIV_130_5MM_ltr_73	CH97	G	–	7	24.7%	663	29.2%	634	+4.4
SIV_135_4MM_gag_03	CK49	A	+C	10	13.4%	739	11.5%	861	−1.9
SIV_135_4MM_gag_03	CH97	A	+C	10	12.3%	1023	13.0%	864	+0.7

Each location had a SNP rate compared to the reference genome in untreated and CRISPR-treated samples, which varied between NHP. The direction of change at each site alternates between the monkeys—a positive change is seen with one NHP, while a negative change is seen in the other—which is more consistent with sequencing noise, as seen in the alignments. Distance in nucleotides is given, as the SNPs are also not overlapping the nominated cut sites. Negative numbers are 5′ from the cut site.

Diff difference, Freq, frequency, Ref reference, SNP single nucleotide polymorphism.