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Large Scale Sequence Analysis of Avian Influenza Isolates

Table S6. Supplementary Information.

Supplementary Information. Parameter values of each segment for MCMC phylogenetic analysis.

HA
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.095020   0.386495   0.044186   0.032415   0.402431   0.039453
Nucleotide frequencies:  A=0.308813   C=0.206636   G=0.209820   T=0.274731
Among site rates: 1st position=0.430885   2nd position=0.289711   3rd position=2.279404

M
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.071917   0.405091   0.035407   0.011031   0.446238   0.030316
Nucleotide frequencies: A=0.317634   C=0.188024   G=0.281314   T=0.213028
Among site rates: 1st position=0.231092   2nd position=0.128235   3rd position=2.640674

NA
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.086302   0.403849   0.038092   0.031448   0.402921   0.037389
Nucleotide frequencies: A=0.305587   C=0.207009   G=0.214727   T=0.272677
Among site rates: 1st position=0.415096   2nd position=0.271994   3rd position=2.312911

NP
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.061739   0.380992   0.040553   0.008337   0.480202   0.028177
Nucleotide frequencies: A=0.329376   C=0.200851   G=0.250785   T=0.218988
Among site rates: 1st position=0.238205   2nd position=0.107411   3rdposition=2.654384

NS
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.085436   0.369406   0.039046   0.017917   0.45161   0.036585
Nucleotide frequencies: A=0.344794   C=0.172993   G=0.245349   T=0.236864
Among site rates: 1st position=0.664188   2nd position=0.364234   3rd position=1.971578

PA
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.056426   0.394922   0.024101   0.005928   0.490545   0.028078
Nucleotide frequencies: A=0.32513   C=0.197694   G=0.241389   T=0.235787
Among site rates: 1st position=0.282766   2nd position=0.121805   3rd position=2.595429

PB1
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.046727   0.388934   0.023363   0.004626   0.509602   0.026748
Nucleotide frequencies: A=0.318226   C=0.209198   G=0.238192   T=0.234383
Among site rates: 1st position=0.227496   2nd position=0.104655   3rd position=2.667849

PB2
Rate matrix (A-C, A-G, A-T, C-G, C-T, G-T)
0.051345   0.350326   0.022916   0.006159   0.540647   0.028608
Nucleotide frequencies: A=0.346597   C=0.188611   G=0.243958   T=0.220834
Among site rates: 1st position=0.285579   2nd position=0.101938   3rd position=2.612483