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Table 1 Nucleotide and haplotype diversity in grapevine

From: High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology

Parameter

Overall

(coding/non-coding)

Number of fragments

230

 

Average sample size1

10.0

 

Average fragment size, kb

0.437

 

Total size of amplicons, kb

100.5

81.4/19.1

Total bases sequenced, kb2

~2010

 

Number of SNPs

1573

1170/403

Frequency of SNP

1 per 64 bp

1 per 69 bp/1 per 47 bp

Number of indels

52

9/43

Frequency of indels

1 per 1932 bp

1 per 9055 bp/1 per 444 bp

Mean nucleotide diversity (π/θ)

0.0051/0.0046

 

Maximum nucleotide diversity (π/θ)

0.0246/0.0173

 

Minimum nucleotide diversity (π/θ)

0.0004/0.004

 

Mean gene diversity

0.30

0.30/0.30

Mean haplotype diversity

0.64

 

Mean Tajima D

0.29

 

Mean observed haplotypes

6.6

 

Mean expected haplotypes

5.8

 
  1. 1Average number of cultivars analyzed through the 230 fragments. 2Estimation based on (Total size of amplicons, kb) × (Average sample size) × (two DNA strands).