2.6　Methylation modification

Pacific Biosciences'SMRTPortal analysis platform v.1.3.1 was used to identify modified positions.At each genomic position，modification quality values(modQV)were computed as the—10 log(p-value)for representing a modified base position，based on the distributions of the kinetics of interpulse durations(IPD ratios)from all reads covering this position and from in silico kinetic reference values(Feng et al.，2013).A value of 20 is the minimum default threshold and corresponds to a p-value of 0.01.DNA methylation on both mtDNA strands was assessed independently and represented by modQV，which comprises base incorporation rates differing from that of the unmodified reference sequences.The RS_Modification_and_Motif_Analysis.1 protocol of the SMRT analysis v2.0 was used to identify methylation and the corresponding motifs of the responsible DNA methylases.(https://www.daowen.com)