Table 5.
Results of codon based Z- test of selection for group 1 and group 2
| n | dN | dS | Z | P | |
|---|---|---|---|---|---|
| |
Group 1 |
|
|
|
|
|
ABS |
18 |
0.171 ± 0.135 |
0.016 ± 0.03 |
1.244 |
0.108 |
|
Non-ABS |
194 |
0.067 ± 0.014 |
0.112 ± 0.034 |
−1.218 |
1 |
|
PSS |
9 |
0.152 ± 0.101 |
0.038 ± 0.039 |
1.493 |
0.069 |
|
Non-PSS |
203 |
0.065 ± 0.014 |
0.115 ± 0.036 |
−1.254 |
1 |
|
All |
212 |
0.075 ± 0.015 |
0.103 ± 0.032 |
−0.788 |
1 |
| |
Group 2 |
|
|
|
|
| |
|
|
|
||
|
ABS |
18 |
0.578 ± 0.132 |
0.134 ± 0.068 |
3.694 |
<0.001 |
|
Non-ABS |
203 |
0.054 ± 0.011 |
0.128 ± 0.032 |
−2.106 |
1 |
|
PSS |
27 |
0.492 ± 0.092 |
0.069 ± 0.051 |
5.801 |
<0.001 |
|
Non-PSS |
194 |
0.043 ± 0.009 |
0.136 ± 0.034 |
−2.686 |
1 |
| All | 221 | 0.085 ± 0.017 | 0.126 ± 0.029 | −1.158 | 1 |
The rates of non-synonymous mutations (dN) and synonymous mutations (dS) were computed using Nei-Gojobari method and Jukes-Cantor correction. The standard errors were obtained through 1000 bootstraps replicates. Z test of selection estimated dN-dS (indicated as Z) and computed a1-tailed test to determine whether dN > dS (indicated as P). n is the number of nucleotides representing antigen binding sites (ABS), non antigen binding sites (Non-ABS), positively selected sites (PSS), non positively selected sites (Non-PSS) and all sites in Group 1 and Group 2. ABS were detected by superimposing the chicken Mhc class I sequences and assuming concordance. Significant p-values are bold.