Microhomology (MH)–based deletions predominate in ku70 and lig4. (A) Distribution of deletions by length. (Error bars) Standard errors. (B) Distribution of deletions using no or 1–6 bp of MH. (Error bars) Standard errors. (C) Profile of 2- to 150-bp deletions. MH sequences contributing to large deletion peaks are indicated. (D) Distribution of deletions that use different 6 bp of MH around the ZFN site. The distances of the left MH sequence and the right MH sequence to the DSB are indicated in the parentheses and separated by a slash. Data for all panels were generated from protoplasts derived from Col, ku70, lig4, and smc6b plants that carried the same ADH1-ZFN-4 transgene. Protoplasts were treated with estradiol, and three independent biological replicates were used for 454 sequencing and analysis.