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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