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Table 4 Levels of nucleotide variation at the two studied genes

From: Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

Gene Ecotype Indel SNP S πtot θtot dN/dS D D* F*
Wx Glutinous 6 1 23 0.0053 0.0043 - 1.7295 1.7295 1.8583
  Nonglutinous 17 7 31 0.0043 0.0033   1.1825 0.9145 1.369
OsC1 Colored 2 1 6 0.0023 0.0020 - 0.8109 1.0088 1.1449
  Colorless 3 8 10 0.0010 0.0021 1.00 −1.7683 −1.2847 −1.7178
  1. S, number of segregating sites; π, average number of nucleotide differences per site between two sequences [33] calculated on the total number of polymorphic sites (πtot); silent sites (πsil); synonymous sites (πsyn); nonsynonymous sites (πnonsyn); θ, Watterson’s estimator of nucleotide polymorphism per base pair [32] calculated on the total number of polymorphic sites (θtot); silent sites (θsil); synonymous sites (θsyn); nonsynonymous sites (θnonsyn); D, Tajima’s D[34]; D*, Fu and Li’s D*; F*, Fu and Li’s F* [35].
  2. Tajima’s D, *Fu and Li’s D* and F* not significant (P > 0.10).