| Site Class | Proportion | B1 | B2 | B3 | B4 | B5 |
| Scheme NC1 (model A with ω2 = 1 and B5 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B5 | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 1.0 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NC2 (model A with ω2 = 1 and B1 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B1 | 0.15 | 1.0 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NI | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Relaxed constraint on B1 and B2 | 0.2 | 1.0 | 1.0 | 0.1 | 0.2 | 0.2 |
| Scheme SC | ||||||
| Model A with ω2 = 4 on B5 | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: positive selection | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 4.0 |
| Class 2b: positive selection | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 4.0 |
| Scheme SI1 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B5 | 0.2 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Scheme SI2 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on 5 | 0.1 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Positive selection on 1 | 0.1 | 5.0 | 0.3 | 0.1 | 0.2 | 0.3 |
| Scheme SI3 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B1-4 | 0.2 | 5.0 | 5.0 | 5.0 | 5.0 | 0.8 |
| Site Class | Proportion | B1 | B2 | B3 | B4 | B5 |
| Scheme NC1 (model A with ω2 = 1 and B5 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B5 | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 1.0 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NC2 (model A with ω2 = 1 and B1 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B1 | 0.15 | 1.0 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NI | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Relaxed constraint on B1 and B2 | 0.2 | 1.0 | 1.0 | 0.1 | 0.2 | 0.2 |
| Scheme SC | ||||||
| Model A with ω2 = 4 on B5 | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: positive selection | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 4.0 |
| Class 2b: positive selection | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 4.0 |
| Scheme SI1 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B5 | 0.2 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Scheme SI2 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on 5 | 0.1 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Positive selection on 1 | 0.1 | 5.0 | 0.3 | 0.1 | 0.2 | 0.3 |
| Scheme SI3 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B1-4 | 0.2 | 5.0 | 5.0 | 5.0 | 5.0 | 0.8 |
NOTE.—values of ω greater than 1 are shown in bold.
| Site Class | Proportion | B1 | B2 | B3 | B4 | B5 |
| Scheme NC1 (model A with ω2 = 1 and B5 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B5 | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 1.0 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NC2 (model A with ω2 = 1 and B1 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B1 | 0.15 | 1.0 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NI | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Relaxed constraint on B1 and B2 | 0.2 | 1.0 | 1.0 | 0.1 | 0.2 | 0.2 |
| Scheme SC | ||||||
| Model A with ω2 = 4 on B5 | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: positive selection | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 4.0 |
| Class 2b: positive selection | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 4.0 |
| Scheme SI1 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B5 | 0.2 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Scheme SI2 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on 5 | 0.1 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Positive selection on 1 | 0.1 | 5.0 | 0.3 | 0.1 | 0.2 | 0.3 |
| Scheme SI3 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B1-4 | 0.2 | 5.0 | 5.0 | 5.0 | 5.0 | 0.8 |
| Site Class | Proportion | B1 | B2 | B3 | B4 | B5 |
| Scheme NC1 (model A with ω2 = 1 and B5 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B5 | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 1.0 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NC2 (model A with ω2 = 1 and B1 to be foreground) | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: variable on B1 | 0.15 | 1.0 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 2b = class 1 | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Scheme NI | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Relaxed constraint on B1 and B2 | 0.2 | 1.0 | 1.0 | 0.1 | 0.2 | 0.2 |
| Scheme SC | ||||||
| Model A with ω2 = 4 on B5 | ||||||
| Class 0: conserved | 0.6 | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
| Class 1: neutral | 0.2 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Class 2a: positive selection | 0.15 | 0.3 | 0.3 | 0.3 | 0.3 | 4.0 |
| Class 2b: positive selection | 0.05 | 1.0 | 1.0 | 1.0 | 1.0 | 4.0 |
| Scheme SI1 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B5 | 0.2 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Scheme SI2 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on 5 | 0.1 | 0.3 | 0.3 | 0.1 | 0.2 | 4.0 |
| Positive selection on 1 | 0.1 | 5.0 | 0.3 | 0.1 | 0.2 | 0.3 |
| Scheme SI3 | ||||||
| Conserved class 1 | 0.3 | 0.0 | 0.0 | 0.1 | 0.2 | 0.3 |
| Conserved class 2 | 0.3 | 0.5 | 0.4 | 0.3 | 0.2 | 0.1 |
| Nearly neutral class | 0.2 | 0.7 | 0.8 | 0.9 | 1.0 | 1.0 |
| Positive selection on B1-4 | 0.2 | 5.0 | 5.0 | 5.0 | 5.0 | 0.8 |
NOTE.—values of ω greater than 1 are shown in bold.
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