Figure 2

Accuracy and precision of allele frequency estimates with low-coverage data. Estimates obtained by svgem from random samples of 100 diploid individuals, from populations with alternative allele frequencies between 0.01 and 0.5 (upper label of each plot; MAF, minor allele frequency), for mean coverage depths between 0.2 and 4. Each combination of allele frequency and depth of coverage was simulated 100 times. The red line indicates the true allele frequency, and the orange lines indicate the expected standard error of the true frequency, from a sample of 200 chromosomes.