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We used Schmutzi (35) to determine the endogenous consensus mtDNA sequences. Reads were mapped to the Cambridge reference sequence and filtered for MAPQ ≥ 30. Haploid variants were called using the endoCaller program implemented in Schmutzi (35), and only variants with a posterior probability exceeding 50 on the PHRED scale (probability of error: 1/100,000) were retained. We then used Haplogrep 2.2 (36) to determine the mtDNA haplogroups, specifying PhyloTree (build 17) as the reference phylogeny (37).
Copyright and License information: ©2019 the Author(s). Published by PNAS.
This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
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