Fig. 3

Effect of increasing contamination on endogenous genome sequence reconstruction and contaminant genome sequence reconstruction of simulated data. Accuracy of the ancient (a) and present-day contaminant (b) mitochondrial consensus sequences produced by schmutzi on simulated data for an early modern human, a Neanderthal and a Denisovan mitochondrial genome. We define an error as either a mismatch or an indel between the predicted endogenous sequence and the published mitochondrial sequence used for simulations. As contamination increases, inference of the endogenous mitochondrial genome becomes more difficult (a). In contrast, the prediction of the contaminant genome becomes more accurate at higher levels of present-day human contamination (b)