Sentence examples for between strains were calculated from inspiring English sources
Similarities between strains were calculated by using BioEdit (version 7.13, http://www.mbio.ncsu.eud/bioedit/bioedit.html).html
Identities between strains were calculated by using BioEdit version 7.09 (www.mbio.ncsu.edu/bioedit/bioedit.html) (Table 2).
Relative fold changes in gene expression between strains were calculated using the ΔΔ C T method [ 47].
Significance levels (p-values) between strains were calculated with MA-ANOVA, and within strains using the hierarchical t-test.
Following analysis by ANOVA, the magnitudes of differences in the normalized methylation levels between strains were calculated using Tukey's HSD test, with alpha set at 0.05.
The ANI between strains was calculated using JSpecies software package v1.2.1 using default parameters [ 74].
The Pearson's correlation coefficient of the distance to the Ori for orthologous genes between strains was calculated.
Statistical significance of the pairwise comparisons between strains was calculated using a post hoc Tukey test with p < 0.05.
Distance between strains was calculated with the Jaccard coefficient [ 108] and a tree was inferred using the neighbor joining reconstruction method including 100 bootstrap replicates.
Pairwise distances between two strains were calculated using the Kimura two-parameter model using all the aligned ORFs, and phylogenetic trees were constructed using the UPGMA method.
Significance levels (p-values) of differences between the four inbred strains were calculated for each probe-set using analysis of variance [ 65] for three pre-processing methods.
