Table 2

Neutrality tests and test of positive selection for the human 2009 H1N1 pandemic.

Model

p-MKT

pD

np

ln L

p-value

ω

pω

sites (95%)


PB2

H0

108

-10489.98

0.037

0.967

na

H1

0.770

0.573

109

-10489.98

1.000

1.000

0.000

none

PB1

H0

116

-10151.99

0.023

0.940

na

H1

0.671

0.072

117

-10151.99

1.000

0.023

0.940

none

PA

H0

110

-9736.96

0.032

0.955

na

H1

0.327

0.169

111

-9736.96

0.999

0.032

0.955

none

HA

H0

158

-10294.19

0.067

0.862

na

H1

0.844

0.026

159

-10293.78

0.362

1.000

0.007

none

NP

H0

110

-6402.29

0.039

0.969

na

H1

0.982

0.392

111

-6402.29

0.989

1.000

0.000

none

NA

H0

154

-8085.11

0.075

0.846

na

H1

0.015

0.034

155

-8085.01

0.655

2.345

0.001

none

M2

H0

224

-1699.98

0.132

0.000

na

H1

0.436

0.007

225

-1699.98

0.976

1.171

0.384

none

M1

H0

142

-3175.82

0.025

0.973

na

H1

0.894

0.101

143

-3175.82

1.000

1.000

0.000

none

NS2

H0

286

-2341.50

0.082

0.865

na

H1

0.901

0.005

287

-2341.50

0.984

1.000

0.000

none

NS1

H0

182

-4142.63

0.125

0.696

na

H1

0.271

0.011

183

-4142.63

1.000

1.000

0.001

none


Results of the McDonald-Kreitman test (MKT; p-value), Tajima's D test (pD), as well as log-likelihood values (ln L), parameter estimates and p-values for the ten standard protein-coding genes of 2009 H1N1 Influenza A genomes. H0 is the null branch-site codon model, without positive selection; H1 is the alternative model that allows for positive selection at sites in the foreground branches. The p-values are derived from a <a onClick="popup('http://www.biomedcentral.com/1471-2148/11/6/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2148/11/6/mathml/M2">View MathML</a> distribution (see Methods). Parameter estimates for ω and its proportion of sites pω are for rate categories ω < 1 under H0, and ω ≥ 1 under H1.

Notes--na: not applicable; nfd: no fixed differences. Sites in boldface are those for which the LRT rejects H0 at the 1% level.

Abdussamad and Aris-Brosou BMC Evolutionary Biology 2011 11:6   doi:10.1186/1471-2148-11-6

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