Table 1 Analysis of nucleotide substitution and mutation distribution biases in MSV genome sequences derived from evolution experiments in maize (MSV-Kom, -Set and defective recombinant sequences) and sugarcane (MSV-Tas sequences).

Transversions

A → C

2

1.18

0.43

3

4.26

0.54

5

5.39

0.87

A → T

1

1.18

0.86

3

4.26

0.54

4

5.39

0.55

C → A

0

1.08

0.28

2

3.65

0.39

2

4.62

0.22

C → G

1

1.08

0.94

5

3.65

0.48

6

4.62

0.52

G → C

1

1.22

0.84

4

3.87

0.95

5

4.90

0.96

G → T

3

1.22

0.09

13

3.87

< 10 ^-8

16

4.90

5.4 × 10 ^-7

T → A

0

1.19

0.25

3

4.26

0.54

3

5.39

0.30

T → G

0

1.19

0.25

4

4.26

0.90

4

5.39

0.55

Transitions

A → G

3

1.18

0.08

4

4.26

0.90

7

5.39

0.48

C → T

1

1.08

0.94

3

3.65

073

4

4.62

0.77

G → A

2

1.22

0.46

3

3.87

0.66

5

4.90

0.96

T → C

0

1.19

0.25

2

4.26

0.27

2

5.39

0.14

Ins

0

1

1

Del

1

1

2

GC Content

A/T→G/C

5

4.7

0.50

13

17

0.07

18

21.6

0.05

G/C→A/T

6

4.6

0.50

21

15

0.07

27

19.0

0.05

Transitions (Ts) vs transversions (Tv)

Tv

8

9.3

0.45

37

32.7

0.19

45

42

0.42

Ts

6

4.7

0.45

12

16.3

0.19

18

21

0.42

Ts/Tv

0.75

0.5

0.32

0.5

0.40

0.5

Coding vs non-coding genome regions

Coding

13

12.4

0.67

42

42.1

0.99

55

54.4

0.85

Non-coding

2

2.6

0.67

9

9.9

0.99

11

11.6

0.85

Synonymous (S) vs non-synonymous (N) mutations

N

6

10.1

6 × 10 ^-3

27

30.4

0.18

33

40.5

0.012

S

7

2.9

6 × 10 ^-3

12

8.6

0.18

19

11.5

0.012

dN/dS

0.24

1.0

0.64

1.0

0.49

1.0