*3.4. Detection of Structural Variants*

Detection of structural variants in the mitochondrial genome was performed using the approach described by [52]. It consists of two main steps: Mapping by NGMLR 0.2.8 and then structural variant detection by Sniffles 1.0.11. NGMLR was run with the option made for typical PacBio reads ("presets pacbio"), as it has no dedicated option for PacBio CCS reads.
