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Table 1 Positive conditional selection pressure in HIV-1 protease

From: Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples

Codon Y

Codon X

NXaYa

NXaYs

(K a /K s )Y|Xa

NXoYa

NXoYs

(K a /K s )Y|Xo

(K a /K s )Y|X

LOD

p

90

73

1879

6

367.63

6842

628

12.79

28.74

>300

<0.001

82

24

564

0

277.79

3625

680

2.63

105.8

98.09

<0.001

90

95

161

1

189

7757

595

15.3

12.35

52.35

<0.001

82

48

483

2

118.95

3727

663

2.77

42.96

79.90

<0.001

82

53

366

2

90.13

4005

694

2.84

31.71

59.79

<0.001

82

55

332

2

81.76

3994

701

2.81

29.14

53.96

<0.001

30

88

1730

9

71.1

727

677

0.4

179

217.97

<0.001

63

50

132

1

65.01

22576

2037

5.46

11.91

21.31

<0.001

90

89

329

6

64.37

7677

524

17.2

3.74

100.28

<0.001

71

11

126

0

62.06

8775

964

4.48

13.84

21.91

<0.001

90

92

315

6

61.63

7706

575

15.73

3.92

95.67

<0.001

63

73

1711

14

60.2

20832

2016

5.09

11.83

269.97

<0.001

33

83

49

1

57.52

2436

803

3.56

16.15

15.09

<0.001

90

84

2039

45

53.19

6756

596

13.31

4

>300

<0.001

90

85

395

9

51.52

8361

627

15.65

3.29

117.75

<0.001

  1. Due to the long list of positive conditional selection pressure detected in the Specialty dataset, only the 15 positive selections with the strongest increase in (K a /K s )Y|Xa value after conditioning were showed here. Please see the Additional File for the complete list.
  2. Codon X: the codon site where the first mutation appears.
  3. Codon Y: the codon site where the second mutation appears.
  4. (K a /K s )Y|Xa: conditional selection pressure of codon Y in the presence of an amino acid mutation at codon X.
  5. (K a /K s )Y|Xo: conditional selection pressure of codon Y in the absence of any mutation at codon X.
  6. LOD: confidence score for (K a /K s )Y|Xa > 1.
  7. p: p-value for (K a /K s )Y|X > 1 to be random.