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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.