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Table 3 Descriptive parameters of coding SNPs

From: Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs

Parameter Blastx/Uniprot proteins
e-value < 1e-10
Blastx/Arabidopsis proteins
e-value < 1e-10
Diogenes ORF Brassicaceae trained
p-value < 1e-08
Diogenes ORF Pinaceae trained
p-value < 1e-08
Dataset of 205 ORF predicted by Diogenes but with no match in Uniprot e-value < 1e-10 Combination of all methods
Contigs with a putative coding sequence assigned 3,140 3,080 2,823 2,065 205 3,374
Contigs with no coding region assigned 450 510 767 1,525 - 196
Unclassified SNPs 3,910 3,853 3,202 2,626   3,923
Synonymous SNPs (1) 2,013 1,951 2,072 1,468 132 2,282
Nonsynonymous SNPs (2) 1,339 1,309 1,347 972 89 1,507
Total coding SNPs 3,352 3,260 3,419 2,440 221 3,789
synonymous/nonsynonymous SNPs 1.50 1.49 1.54 1.51 1.48 1.51
Number of nonsynonymous sites (La) 1,529,942.94 1,493,852.65 1,501,524.04 1,060,194.41 80,471.00 1676414.38
Number of synonymous sites (Ls) 401,769.06 391,332.35 393,089.96 277,718.59 21339.01 440352.62
Total number of coding sites (La+Ls) 1,931,712 1,885,185 1,894,614 1,337,913 101,811 2116767
Rate of nonsynonymous SNP per site (2)/La (Ka) 0.00087 0.00087 0.00090 0.00092 0.00110 0.00089
Rate of synonymous SNP per site (1)/Ls (Ks) 0.00501 0.00498 0.00527 0.00528 0.0062 0.00518
Ratio Ka/Ks 0.174 0.175 0.170 0.174 0.179 0.172