2.5. Genome Mutation Heterogeneity Analyses
All short reads were mapped to the Cricetulus griseusmitochondrion complete genome
(gi|186694636|gb|EU660217.1|) using
HISAT2 v. 2.0.5 (Kim, Langmead, & Salzberg, 2015). PCR duplicate
removal, and SNP (single nucleotide polymorphism) and short indel
(insertion or deletion) calling were performed with the SAMtools v.
1.8.0 utilities, rmdup and mpileup, respectively (H. Li et al., 2009).
The called variant loci were annotated as “heteroplasmy,” “homo
alternative,” “homo reference,” or “low coverage.” A correlation
test between the culture time (Days) and the hetero/homo ratio was
performed with the R Stats Package v. 3.2.2.