Fig. 7.

Robustness of the contamination estimate to lower coverage. The simulated dataset with a contamination rate of ∼47 % and single-stranded deamination patterns was subsampled at various coverages from 0 to 1250 ×. Top: Contamination rates were estimated across a range of coverages in simulated data for a Neanderthal, a Denisovan and an early modern human (Ust’-Ishim). Bottom: Contamination estimates when a high-quality mtDNA sequence from a closely related individual is used as the endogenous genome. Robust estimates can be made down to 5 × coverage even at 47 % contamination. For the early modern human, the contamination estimate provided was computed using the database alone and not the prediction of the contaminant genome thus leading to underestimates (see Table 4 for an example of the effect of using the predicted contaminant in the contamination estimate)