Skip to main content

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).