Adapters were trimmed from the sequencing data using fastx_clipper, part of the FASTX-Toolkit version 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) using parameters -Q 33 - 30. Levels of human DNA were determined by mapping reads to the human reference genome (GRCh37/hg19) or the revised Cambridge reference mitochondrial genome (32). Mapping was completed using BWA version 0.6.2 (33) with the following options: seed disabled (34) with terminal low-quality trimming (-q 15), before being aligned using BWA-0.6.2 aln with seed disabled. The mapped reads were sorted, and duplicates were removed and merged using SAMtools version 0.1.18 (35, 36).

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