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

Table 11 In silico mining of SNPs within OakContigV1

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%

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.

ISSN: 1471-2164