Extended Data Table 1:

Frequency of gRNAs in the human genome with denoted Cas9-mediated outcome precision.

	inDelphi trained on Lib-A data from mESCs for 1-bp ins. module			inDelphi trained on Lib-A data from U2OS cells for 1-bp ins. module
Precision-X threshold (%)	Precise product is a deletion (% of gRNAs)	Precise product is a 1-bp insertion (% of gRNAs)	Total % of gRNAs that are precise-X	Precise product is a deletion (% of gRNAs)	Precise product is a 1-bp insertion (% of gRNAs)	Total % of gRNAs that are precise-X
10	82	38	93	70	78	97
15	61	23	75	44	64	87
20	43	15	55	27	53	72
25	30	10	39	17	44	58
30	21	6.6	28	11	36	46
35	15	4.4	19	6.9	28	34
40	10	2.9	13	4.1	21	25
45	6.5	1.9	8.4	2.4	15	18
50	4.3	1.3	5.6	1.4	10	12
55	2.8	0.8	3.6	0.8	6.7	7.5
60	1.8	0.5	2.3	0.5	4.0	4.4
65	1.1	0.3	1.5	0.2	2.2	2.4
70	0.7	0.2	0.9	0.1	1.1	1.2
75	0.4	0.1	0.5	0.04	0.5	0.5
80	0.2	0.08	0.3	0.01	0.2	0.2
85	0.08	0.04	0.1	0.003	0.07	0.08
90	0.03	0.02	0.05	0.0007	0.03	0.03

SpCas9 gRNAs in human exons and introns in mESCs (n = 1,003,524 SpCas9 gRNAs) and U2OS cells (n = 4,498,780 SpCas9 gRNAs). Predictions were smoothed with Gaussian noise (Supplementary Methods).