Table 2 Similarity of the predicted endogenous mitochondrial genome sequence to the original Neanderthal reference sequence, at various rates of simulated contamination with present-day human DNA. An endogenous consensus call was performed using schmutzi on all fragments, and using PMDtools followed by htslib on the fragments labeled by PMDtools as endogenous. For comparison, we generated a simple consensus by running htslib on all sequenced fragments. While this approach works well at low amounts of contamination, it produces an incorrect consensus at higher levels of contamination when the presence of contaminating fragments is not accounted for using approaches like PMDtools and schmutzi. The number of indels are reported as either insertions or deletions in either the predicted consensus or the Neanderthal reference; hence, discrepancies in the final sum may occur

From: Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA