The PDF file includes:

• Fig. S1. Development of a high-throughput evaluation system for Cas9-induced indel frequencies.
• Fig. S2. Overview of DeepSpCas9 development.
• Legend for table S1
• Table S2. Datasets used for this study.
• Legends for tables S3 to S6
• Legend for Supplementary Code

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). Datasets generated from the results of the high-throughput experiments.
• Table S3 (Microsoft Excel format). Datasets generated from the results of the experiments at endogenous target sites.
• Table S4 (Microsoft Excel format). Oligonucleotides used in this study.
• Table S5 (Microsoft Excel format). Model selection results.
• Table S6 (Microsoft Excel format). Confidence intervals for the values shown in the graphs.
• Supplementary Code (.zip format)