excellent at sites that were polymorphic in the population. For example, 3,558 of the 3,641 simulated polymorphic sites with MAF>0.5% were identified and, at these sites, alleles were called with an accuracy of 99.93% (see Tables VI and VII). For any given depth, imputed accuracy increased with the number of sequenced individuals (for example, accuracy at sites with MAF >0.5% was ~98.8% when 100 individuals were sequenced at 2 × coverage but increased to ~99.7% when 400 individuals were sequenced at the same depth; the number of errors per individual decreased similarly from 106.3 per individual to 40.3 per individual). In addition, the depth required to achieve a given accuracy decreased as the number of sequenced individuals increased: achieving 99.9% accuracy for sites with population MAF >0.5% requires ~8 × depth for 100 individuals, ~6 × depth in 200 individuals and only 4 × depth in 400 individuals. In each case, note that error rates are higher at heterozygous sites than at homozygous sites. Again, performance of the approach with larger numbers of individuals improves because the mosaic fragments described by our model increase in length and, thus, become easier to find. This is also reflected in the accuracy of
