Figure 4

Effects of coverage depth on ratio of homozygous to heterozygous variant calls. Ratios of observed homozygous:heterozygous to true homozygous:heterozygous variant call ratios. Squares and circles represent data points for low and high divergence samples, respectively, for A) indel variant calls and B) SNP variant calls. Equations and R² values for best-fit linear relationship are A) y = -0.1288 + 4.3862, R² = 0.15353 for low divergence samples (solid line); y = -0.1712x + 4.3267, R² = 0.65332 for high divergence samples (dashed line); B) y = -0.1899x + 4.4411, R² = 0.21871 for low divergence samples (solid line); y = -0.1835x + 3.8176, R² = 0.64356 for high divergence samples (dashed line). Dashed grey line added at unity for observed hom:het / true hom:het for visual clarity.