When performing targeted capture, a PCR input amount of 4 amol of target DNA is used for ~8 million paired-end reads (i.e., ~5% sequencing capacity of a HiSeq2500 lane). However, in contrast to a noncapture sample, this value refers specifically to the amount of target DNA being captured in the sample, which is generally much less than the amount of total DNA. The amount of total DNA used in the PCR is dependent on its relative copy number and the size of the genomic target, and it can be estimated by the following formula: Total DNA=mGNT Where m is the desired amount of target DNA in attomoles of fragments (Table 2), G is the size of total genome in base pairs, T is the size of the target DNA in base pairs and N is the number of copies of the target per copy of the nontarget portion of the genome. For single-copy genes, N will have a value of 1 and can be ignored. However, in the case of multicopy targets such as mtDNA or ribosomal genes, N can
