Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

Table 3 Correlation analysis of three types of mutation

Comparison	CSA	CIA	CWN
Repeats and Substitutions
Correlation between repeats and substitutions (r)	0.033	0.049	0.028
Significance of correlation (t)	0.103**	0.103**	0.145**
Coefficient of determination (r²)	0.0011	0.0024	0.0008
Indels and Substitutions
Correlation between indels and substitutions (r)	0.207	0.435	0.165
Significance of correlation (t)	0.158**	0.195**	0.144**
Coefficient of determination (r²)	0.043	0.189	0.0273
Repeats and Indels
Correlation between repeats and indels (r)	0.090	0.099	0.120
Significance of correlation (t)	0.195**	0.221**	0.268**
Coefficient of determination (r²)	0.0081	0.0098	0.0145

Comparisons among the pairwise alignments (CSS taken as a Reference) to calculate the correlations between Repeats and Substitutions, Insertion-Deletions (Indels) and Substitutions, and Repeats and Indels. The alignments were partitioned into 630 nonoverlapping bins of 250 bp size each to calculate these correlations. ** indicated high significance. CWN ‘Wuyi narcissus’ cultivar of C. sinensis var. sinensis (natural triploid Chinary type tea), CSS C. sinensis var. sinensis (diploid Chinary type tea), CSA C. sinensis var. assamica (diploid Chinese Assamica type tea), CIA C. sinensis var. assamica (diploid Indian Assamica type tea)