For samples that do not make use of targeted capture, such as purified mtDNA or plasmid DNA, we have found that a PCR input of 40 amol of DNA produces an optimal peak family size of six when devoting eight million paired-end reads to a sample (i.e., ~5% sequencing capacity of a HiSeq2500 lane). For the 16.5-kb human mtDNA, this typically results in a depth of 500–1,000. Given the linear relationship between PCR input and lane fraction needed to keep the peak family size constant, 200 attomoles of input mtDNA for 25% of a HiSeq lane results in a depth of 2,500–5,000.
