Figure 3

Effects of coverage depth at low and high divergence levels on variant call completeness. A) Percent of indels called correctly out of all indels for a reference-sample pair; B) Percent of SNPs called correctly out of all SNPs for a reference-sample pair. Squares and circles represent data points for low and high divergence samples, respectively. Best-fit linear relationships shown for low (solid lines) and high (dashed lines) divergence samples for A) and B). Equations and R² values for best-fit linear relationships are A) y = 3.9704x + 0.4293, R² = 0.92759 (low divergence); y = 2.8566x + 0.411, R² = 0.91455 (high divergence); B) y = 5.5174x + 2.3014, R² = 0.92406 (low divergence); y = 3.1491x + 1.6574, R² = 0.90764 (high divergence). Slopes for low versus high divergence samples are not significantly different in A) or B) at P < 0.05; however, percentage of variants found regressed on divergence level is significant at P < 0.05 and P < 0.001 for A) and B), respectively.