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Table 11 In silico mining of SNPs within OakContigV1

From: Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

SNP type Allele Number of SNPs Percentage
Transition A/G 11757 32.29%
  G/C 12703 34.89%
Transversion A/C 2814 7.73%
  A/T 3898 10.71%
  T/G 2814 7.73%
  G/C 2313 6.35%
Tri-nucleotide   112 0.31%
Total   36411 100.00%
Synonymous (a)   17622 36.52%
Non-synonymous (b)   10140 21.02%
Coding (a)+(b)   27762 57.54%
Non-coding   20485 42.46%
Total   48247 100.00%
  1. Peptides were predicted by FrameDP, which often produces multiple peptide for a single unigene elements. Because location of SNP sites (coding/non-coding) were estimated for each predicted peptide, the sum of coding and non-coding SNPs exceeded the total number (36,411) of SNPs. Tri-nucleotides are polymorphic sites with three alleles.