Table 2 Number of silent mutations of each dinucleotide at various codon positions.

From: Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames

Dinucleotide

Codon positions

Total

1 and 2

2 and 3

3 and 1

GT

0

8

30

38

GA

0

8

30

38

GC

0

8

30

38

GG

0

7

30

37

AG

4

4

32

40

AT

0

4

32

36

AC

0

4

32

36

AA

0

5

32

37

TG

1

7

33

41

TA

1

9

33

43

TC

2

9

33

44

TT

2

9

33

44

CG

2

12

33

47

CA

0

12

33

45

CT

2

12

33

47

CC

0

12

33

45

  1. When a dinucleotide is located at codon positions 1 and 2 or at codon positions 2 and 3, there are four codons that contain this dinucleotide. Theoretically, they can be mutated into any of the rest 60 codons. When a dinucleotide is located at codon positions 3 and 1, only the nucleotide at position 3 is considered to mutate. There are 16 codons containing this nucleotide. Theoretically, they can be mutated into any of the rest 48 codons. Therefore, values in the table are number of silent mutations out of 60, 60 and 48 mutations for a dinucleotide at codon positions 1 and 2, 2 and 3, or 3 and 1, respectively.
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