Table 2.
Positively selected codon sites in 103 South African G2P[4] pre- and post-RVA amino acid residues as identified by FEL, FUBAR and MEME analysis
|
Method |
Amino acid sites in the gene segments under positive selection |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
VP1 |
VP2 |
VP3 |
VP4 |
VP6 |
VP7 |
NSP1 |
NSP2 |
NSP3 |
NSP4 |
NSP5 |
|
MEME |
2,62,90, 97 128, 157 158, 187 332, 364 371, 406 546, 654,1033,1041 |
5,13, 14 , 723 869, 873 874, 877 878 |
7 ,25,133,153,322, 346 473, 704 788, 828 835 |
7 192, 625 627 |
13 |
315 |
10 212, 271 313 |
249 254 |
3, 6 , 16,27 |
2,3, 5 ,9,10, 16,17,51,79,170 |
3,7 |
|
FUBAR |
60 364 |
14 , 878 |
7 |
7 |
13 |
66 |
10,11, 103 380 402 |
75 254 |
6 |
5 |
– |
|
FEL |
– |
14 |
7 828 |
7 |
13 |
– |
319 |
254 |
6 |
5 ,9 |
– |
Bold and underlined sites are those identified by all the three methods: Fixed Effects Likelihood (FEL), Fast Unconstrained Bayesian AppRoximation (FUBAR) and Mixed Effects Model of Evolution (MEME). For MEME and FEL, statistical significance was assessed at P≤0.1 while for FUBAR it was assessed at posterior probability ≥0.9. The dash (-) sign indicates no site was identified. Further analysis reports are provided in the Supplementary Excelspreadsheet1.