Ten potential off-target sites were identified by online tool Cas-OFFinder (http://www.rgenome.net/cas-offinder/) to identify potential off-target sites. Sequences surrounding these 10 sites and integrated −28 (A>G) mutation site were PCR amplified and deep sequenced using IlluminaHiseq 2500 PE150 as paired-end 150 reads. The primers for off-target site analysis can be found in Table S3. High-throughput sequencing data was analysed as reported. Briefly, Sample sequencing was done on an IlluminaHiSeq 2000 PE150 as paired-end 150 bp reads. The merged paired-end reads of each library were separated based on barcodes in primers (Table S5) by Python scripts and then submitted to cutadapt (v1.11) for trimming primer sequence. The trimmed reads were aligned to reference sequence by means of BWA with default parameters (v0.7.13). Samtools (v1.3, http://samtools.sourceforge.net) and Picard tools (v2.2.2, http://picard.sourceforge.net) were used to build indices and sort reads. GATK (The Genome Analysis ToolKit, version 3.5) Haplotype Caller and VarScan (v2.4.2, mpileup2snp and mpileup2indel with –min-reads2 10 –min-var-freq 0.01) were used to call variants for all samples and the combined variants of which were then divided into indels and SNVs by SelectVariants. Next, we aligned the reference and repaired sequence to the reads of each barcode by bowtie (version 1.1.2, http://bowtie-bio.sourceforge.net/index.shtmL) with no mismatch. The repair rate was equal to the number of repaired reads divided by the number of reference reads.