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Table 4 Codon usage bias across all possible quantitative relationships among positional purine contents

From: Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

Purine content

GC content = 0.3

GC content = 0.5

GC content = 0.7

1st

2nd

3rd

CDC

Scaled

N c

Scaled

N c '

CDC

Scaled

N c

Scaled

N c '

CDC

Scaled

N c

Scaled

N c '

0.3

0.5

0.7

0.01743

0.35780

0.18606

0.01023

0.15974

0.17789

0.00232

0.34949

0.17267

0.3

0.7

0.5

0.01836

0.21922

0.01880

0.01036

0.01515

0.01520

0.00263

0.24157

0.00941

0.5

0.3

0.7

0.00616

0.38200

0.16209

0.00294

0.15248

0.16112

0.00063

0.33321

0.16601

0.5

0.7

0.3

0.00566

0.31973

0.15002

0.00302

0.16556

0.15842

0.00061

0.37234

0.15754

0.7

0.3

0.5

0.00182

0.27781

0.02340

0.00079

0.02564

0.02805

0.00026

0.21360

0.02756

0.7

0.5

0.3

0.00179

0.35410

0.15793

0.00087

0.16099

0.15939

0.00024

0.35439

0.15404

  1. Sequences with 100000 codons were simulated. The compositions in the Med-1 set (0.3, 0.5 and 0.7) were used. Purine content was considered non-uniform at three codon positions, whereas GC content was set uniform at three codon positions. The expected value of codon usage bias is zero so that these estimated values are also the deviations from the expected.