There is a significant amount of redundancy in the genetic code because most amino acids are encoded by multiple codons. Therefore, it is interesting to know the degeneracy of each codon position in all codons. In MEGA this information can be computed for any code table in the Genetic Code Selector. In addition to the degeneracy of the codon positions, MEGA writes the number of synonymous sites and the number of nonsynonymous sites for each codon using the Nei and Gojobori (1986) method. An example of the results obtained for the standard genetic code is given below:
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Code Table: Standard | |||||||
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Method: Nei-Gojobori (1986) methodology | |||||||
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S = No. of synonymous sites |
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N = No. of nonsynonymous sites |
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Codon |
No. of Sites for codon |
Redundancy | |||||
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|
S |
N |
Pos 1st |
Pos 2nd |
Pos 3rd | ||
|
UUU (F) |
0.333 |
2.667 |
0 |
0 |
2 | ||
|
UUC (F) |
0.333 |
2.667 |
0 |
0 |
2 | ||
|
UUA (L) |
0.667 |
2.333 |
2 |
0 |
2 | ||
|
UUG (L) |
0.667 |
2.333 |
2 |
0 |
2 | ||
|
UCU (S) |
1 |
2 |
0 |
0 |
4 | ||
|
UCC (S) |
1 |
2 |
0 |
0 |
4 | ||
|
UCA (S) |
1 |
2 |
0 |
0 |
4 | ||
|
UCG (S) |
1 |
2 |
0 |
0 |
4 | ||
|
UAU (Y) |
1 |
2 |
0 |
0 |
2 | ||
|
UAC (Y) |
1 |
2 |
0 |
0 |
2 | ||
|
UAA (*) |
0 |
3 |
0 |
0 |
0 | ||
|
UAG (*) |
0 |
3 |
0 |
0 |
0 | ||
|
UGU (C) |
0.5 |
2.5 |
0 |
0 |
2 | ||
|
UGC (C) |
0.5 |
2.5 |
0 |
0 |
2 | ||
|
UGA (*) |
0 |
3 |
0 |
0 |
0 | ||
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UGG (W) |
0 |
3 |
0 |
0 |
0 | ||
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CUU (L) |
1 |
2 |
0 |
0 |
4 | ||
|
CUC (L) |
1 |
2 |
0 |
0 |
4 | ||
|
CUA (L) |
1.333 |
1.667 |
2 |
0 |
4 | ||