Global CRISPResso indel analysis

To analyze CRISPR action on both Tmc1^Bth and Tmc1^WT alleles, we subjected the fastq files to CRISPResso analysis without segregating them to mutant and WT reads (Extended Data Fig. 9b). Briefly, reads were split to read 1 and read 2 then merged using flash v1.2.11 (parameters: min overlap: 4, max overlap: 126, max mismatch density: 0.250000, allow “outie” pairs: true, cap mismatch quals: false, combiner threads: 8, input format: fastq, phred_offset=33, output format: fastq, phred_offset=33). Next, CRISPResso was run with the following parameters: CRISPResso -r1 <fastq_file> --split_paired_end -w 5 -c <protein_coding_sequence> --ignore_substitutions -a <amplicon_sequence> -g <gRNA_sequence>.