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

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Figure

Fig. 1 Schematic illustration of mitochondrial sequences from an ancient DNA library. When DNA from an ancient human sample is sequenced,non-deaminated cytosines are represented ashandled the bone (contaminating fragments represented infragments are likely
Table 1 Inputs and outputs for the different programs describedin ‘Methods’. Overview of the three main programs, contDeam,endoCaller and mtCont, with the helper program splitEndo forthe iterative mode
Fig. 3 Effect of increasing contamination on endogenous genome sequence reconstruction and contaminant genome sequence reconstruction ofmore accurate at higher levels of present-day human contamination (simulated data
Table 2 Similarity of the predicted endogenous mitochondrial genome sequence to the original Neanderthal reference sequence, atvarious rates of simulated contamination with present-day human DNA
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