Comparisons of intravarietal and intersubspecific SNPs in rice chloroplast genomes. Intersubspecific SNPs are the ones found between japonica (Nipponbare-G) and indica (93-11). Intravarietal SNPs are those found within Nipponbare-G. The analysis was based on SNP types, including four transitions (G/A, C/T, T/C, and A/G) and eight transversions (A/T, T/A, A/C, C/A, G/C, C/G, G/T, and T/G). The oblique line (/) separates the major and minor genotypes in intravarietal SNPs and the major genotype in intersubspecific SNPs, respectively.