Targeted deep sequencing
Target sites were first amplified to a size of ~500 bp from extracted genomic DNA using KAPA HiFi HotStart DNA polymerase (Roche, Cat. no. #KK2502) according to the manufacturer’s protocols. Then, amplicons were amplified again to a size of ~230 bp, after which the amplicons were amplified using TruSeq HT dual index-containing primers to add adaptor and index sequences for Illumina sequencing platforms to each sample [20]. Primers used in this study are listed in Supplementary Table 3. Pooled PCR amplicons were purified using a PCR purification kit (MGmed) and sequenced on a MiniSeq (Illumina) with paired-end sequencing systems (2x150 bp). Cas-Analyzer (http://www.rgenome.net/cas-analyzer/#!) was used to quantify the indel frequencies from deep sequencing data [20].