Gene

Gene position

α

β^{−}

q^{−}

β^{+}

P value

Log L

KF041236

2010

2011

2013


Prm


70^{£}

0

0

1.0

3916.54

.05

−8.79

S

S

A

A

NS3


10^{¥}

0

<.0001

1

278.84

.00

−11.26

P

P

P

Y

NS4B


130^{¥}

0

0

1

864.59

.04

−10.29

T

T

S

T

NS5


18^{¥}

0

0

.14

1888.34

.00

−11.51

N

N

S

N


440^{¥}

<.0001

<0.0001

1.0

233.06

.09

−8.46
    

610^{¥}

0

0

1

38.47

.08

−8.05

N

N

G

N


^{¥}Amino acid substitution sites newly reported in this study.

^{£}Amino acid substitution already reported in Pakistan [14].
 α The maximum likelihood estimate (MLE) of the synonymous substitution rate α.
 β^{+} The MLE of the unconstrained β nonsynonymous rate.
 β^{−}The maximum likelihood estimate (MLE) of the nonsynonymous rate for the branch class with β ≤ α.
 LRT Likelihood ratio test statistic for β^{+} = α (null) versus β^{+} unrestricted (alternative).
 p The pvalue for the LRT test, using the mixture distribution: 0.33 χ^{2}
_{0} + 0.30 χ^{2}
_{1} + 0.37 χ^{2}
_{2}
 q The qvalue for independent tests (upper bound on the false discovery rate), derived from the corresponding pvalue using Simes’ procedure.