Figure 2.

Effect of missing data and quality threshold on the detection of polymorphic sites. Estimates of the number of polymorphic sites as a function of the proportion of missing data for different quality thresholds (red = 100%, magenta = 90%, green = 50%, blue = 10%). The simulations parameters are as follow: number of segregating sites = 30; sample size = 40; only polymorphic sites are generated and analyzed; for each value of the proportion of mission data, nucleotides are replaced by N's by random sampling without replacement. Each point represents the average over 5000 repetitions.

De Mita and Siol BMC Genetics 2012 13:27   doi:10.1186/1471-2156-13-27
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