Genotyping performance on single-copy regions with or without CRISPR-Cas9-mediated repeat depletion starting from different amounts of sequencing data. (A) Number of genotyped positions. (B) Number of total variants identified. (C) Number of heterozygous variants identified. (D) Number of variants that were genotyped as reference (0/0) in the nondepleted sample and identified as homozygous (1/1) or heterozygous (1/0) alternative in the depleted sample. N = 3 at 6, 12, and 25 million fragments; N = 2 at 37, 50, and 63 million fragments.