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.