Table I.

Minor genotype frequency of each SNP type among three chloroplast genomes

SNP type in 93-11/ PA64S & Nip-GMF in 93-11MF in PA64SMF in Nip-G
%
G/A4.3 (1,583)2.4 (1,384)2.5 (2,961)
C/T5.1 (1,014)3.9 (934)2.7 (1,875)
A/G4.5 (2,207)1.5 (882)2.9 (1,978)
T/C4.5 (1,591)1.8 (529)2.6 (1,375)
A/T3.9 (2,224)2.4 (660)0.7 (848)
T/A2.3 (911)2.4 (1,667)0.9 (2,109)
A/C6.6 (1,219)3.0 (568)2.9 (1,415)
C/A4.2 (1,154)1.4 (709)1.9 (1,442)
G/C000
C/G9.8 (384)01.2 (482)
G/T6.0 (990)3.7 (859)2.5 (1,760)
T/G5.2 (1,485)0.5 (610)2.2 (1,051)
  • The intersubspecific SNP types and their respective minor genotype frequencies among three varieties, 93-11, PA64S, and Nipponbare-G (Nip-G), are listed. The oblique line in the first column (/) separates the major genotype in 93-11 and PA64S /Nipponbare-G. Minor genotype frequencies (MF) were indicated as percentage of the minor genotype in each SNP type. The statistics was based on the total sites of each SNP type in a given variety. The number in the parenthesis shows the total number of the surveyed sequence traces covering the SNP loci of a given type. MF in 93-11 is about twice as high as that of PA64S or Nipponbare-G chloroplast genome.