Skip to main content

Table 3 Comparison of VvDXS nucleotide diversity in different phenotypic classes

From: A candidate gene association study on muscat flavor in grapevine (Vitis viniferaL.)

Parameters Overall (coding/non-coding) Muscat (coding/non-coding) Neutral (coding/non-coding) Aromatic (coding/non-coding) Neutral Muscats (coding/non-coding) Muscat-like aromatic mutants (coding/non-coding)
Varieties 148 72 48 20 5 3
Number of polymorphic sites 102
(25/77)
77
(22/55)
99
(22/77)
64
(22/42)
48
(12/37)
26
(10/16)
Frequency of polymorphic sites 1 per 47 bp
(1 per 86 bp/1 per 35 bp)
1 per 62 bp
(1 per 98 bp/1 per 47 bp)
1 per 49 bp
(1 per 98 bp/1 per 35 bp)
1 per 76 bp
(1 per 98 bp/1 per 64 bp)
1 per 100 bp
(1 per 179 bp/1 per 73 bp)
1 per 191 bp
(1 per 215 bp/1 per 176 bp)
Synonymous changes 15 14 15 14 8 6
Non-synonymous changes 10 8 7 8 4 4
Synonymous vs non-synonymous mutations 1.5:1 1.75:1 2:1 1:75:1 2:1 1.5:1
Mean nucleotide diversity (π/θ) 0.0031/0.0034 0.0026/0.0029 0.0035/0.0040 0.0032/0.0034 0.0034/0.0036 0.0018/0.0023
C 10.8 1.999 16.605 9.9 nd nd
Mean Tajima D -0.19 -0.35 -0.42 0.67 nd nd
Fu and Li's D* 0.91 1.58* 1.15 1.30 nd nd
  1. π = nucleotide diversity per site, θ = Watterson's estimator; nd = not determined; C = recombination parameters * = this value is significantly (P < 0.05) different from its neutral expectation based on the critical values obtained after coalescent simulations, polymorphic sites include SNPs and INDELs.