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 | Â | 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 |