Table 5.
Nucleotide replacement matrices at (NRMs) three codon positions for human mouse orthologs of high-, medium-, and low-GC groups under study
| Human |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Group | First codon position | Second codon position | Third codon position | |||||||||||
| Mouse | A | T | G | C | A | T | G | C | A | T | G | C | ||
| High-GC group | A | ― | 1.00 | 1.13 | 1.16 | ― | 1.01 | 1.08 | 1.06 | ― | 1.00 | 1.86 | 1.71 | |
| T | 1.00 | ― | 1.11 | 1.19 | 0.99 | ― | 1.06 | 1.06 | 1.00 | ― | 1.69 | 1.86 | ||
| G | 0.88 | 0.90 | ― | 1.01 | 0.92 | 0.95 | ― | 0.98 | 0.54 | 0.59 | ― | 1.01 | ||
| C | 0.86 | 0.84 | 0.99 | ― | 0.94 | 0.95 | 1.02 | ― | 0.58 | 0.54 | 0.99 | ― | ||
| Medium-GC group | A | ― | 1.01 | 1.02 | 1.03 | ― | 0.99 | 1.01 | 1.01 | ― | 1.00 | 1.04 | 1.01 | |
| T | 0.99 | ― | 1.03 | 1.02 | 1.01 | ― | 1.02 | 1.02 | 1.00 | ― | 1.02 | 1.03 | ||
| G | 0.98 | 0.97 | ― | 1.00 | 0.99 | 0.98 | ― | 1.00 | 0.97 | 0.98 | ― | 1.00 | ||
| C | 0.97 | 0.98 | 1.00 | ― | 0.99 | 0.98 | 1.00 | ― | 0.99 | 0.97 | 1.00 | ― | ||
| Low-GC group | A | ― | 1.01 | 0.93 | 0.90 | ― | 0.99 | 0.90 | 0.94 | ― | 0.99 | 0.64 | 0.65 | |
| T | 0.99 | ― | 0.93 | 0.83 | 1.01 | ― | 0.94 | 0.95 | 1.01 | ― | 0.70 | 0.62 | ||
| G | 1.08 | 1.07 | ― | 0.97 | 1.11 | 1.06 | ― | 1.02 | 1.56 | 1.42 | ― | 0.96 | ||
| C | 1.11 | 1.20 | 1.03 | ― | 1.07 | 1.06 | 0.98 | ― | 1.53 | 1.62 | 1.04 | ― | ||
Each element rij in the NRM represents the ratio of number of replacements of the nucleotide i by the nucleotide j in the forward direction (mouse to human) to that in the reverse direction. This means that if rij > 1, the number of (i)Mouse → (j)Human replacements is higher than the number of (j)Mouse → (i)Human replacements and if rij < 1, the reverse is true. Bold and bold-italics ratios signifies the directional bias at p < 0.0001 and 0.001, respectively.