Table 4 Haplotype effects.
From: A selective genotyping approach identifies QTL in a simulated population
chr | Pos. (Mb) Start/End | Haplo. allele | Freq | Trait 1 | Trait 2 | Trait 3 | |||
|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | Effect | FDR P | Effect | FDR P | Effect | FDR P |
1 | 84.0 84.2 | 11222 | 0.21 | -48.7 | <10-4 | -0.5 | ns | 9.9*10-3 | <10-4 |
| Â | Â | 12121 | 0.24 | 32.5 | <10-4 | 0.9 | 2*10-2 | -4.1*10-3 | <10-4 |
| Â | Â | 12111 | 0.07 | 21.8 | 2*10-2 | -0.2 | ns | -7.0*10-3 | <10-4 |
| Â | Â | 11121 | 0.09 | 2.0 | ns | 0.3 | ns | 6.1*10-4 | ns |
| Â | Â | 12122 | 0.07 | 24.2 | 1*10-2 | -0.8 | ns | -9.8*10-3 | <10-4 |
| Â | Â | 21222 | 0.07 | -5.7 | ns | 0.1 | ns | 1.5*10-3 | ns |
1 | 14.5 14.7 | 11111 | 0.08 | -16.7 | 7*10-2 | -0.4 | ns | 2.1*10-3 | 8*10-2 |
| Â | Â | 12111 | 0.19 | 37.1 | <10-4 | 2.8 | <10-4 | 2.9*10-3 | 5*10-4 |
| Â | Â | 12112 | 0.18 | 18.1 | 4*10-3 | 0.5 | ns | -2.2*10-3 | 8*10-3 |
| Â | Â | 12121 | 0.14 | 0.5 | ns | 1.3 | 3*10-4 | 6.0*10-3 | <10-4 |
| Â | Â | 12212 | 0.32 | -25.5 | <10-4 | -2.3 | <10-4 | -4.0*10-3 | <10-4 |
2 | 46.7 46.9 | 11122 | 0.11 | -14.1 | ns | -0.5 | ns | 1.7*10-3 | ns |
| Â | Â | 11112 | 0.26 | -3.6 | ns | 0.4 | ns | 3.0*10-3 | <10-4 |
| Â | Â | 12111 | 0.23 | -17.9 | 4*10-3 | -1.0 | 2*10-3 | 4.3*10-4 | ns |
| Â | Â | 22111 | 0.19 | 8.4 | ns | 0.0 | ns | -2.4*10-3 | 6*10-3 |
2 | 76.9 77.1 | 11112 | 0.29 | -12.9 | 2*10-2 | -0.8 | 8*10-3 | 2.7*10-6 | ns |
| Â | Â | 21112 | 0.28 | 2.4 | ns | -0.1 | ns | -1.2*10-3 | ns |
| Â | Â | 22221 | 0.26 | 7.0 | ns | 0.8 | 1*10-2 | 1.3*10-3 | ns |
| Â | Â | 22112 | 0.07 | 25.0 | 1*10-2 | 0.2 | ns | -5.1*10-3 | 2*10-4 |
2 | 92.3 92.5 | 11111 | 0.39 | 13.1 | 2.*10-2 | 0.6 | 5*10-2 | -5.1*10-4 | ns |
| Â | Â | 22122 | 0.11 | 0.5 | ns | 0.1 | ns | 6.7*10-4 | ns |
| Â | Â | 22222 | 0.11 | -16.5 | 4*10-2 | -0.6 | ns | 1.6*10-3 | ns |
3 | 0.4 0.6 | 11121 | 0.11 | -22.1 | 8*10-3 | -1.5 | 1*10-4 | -1.7*10-5 | ns |
| Â | Â | 11122 | 0.27 | 10.1 | ns | -0.1 | ns | -3.2*10-3 | <10-4 |
| Â | Â | 22211 | 0.32 | 9.5 | ns | 1.4 | <10-4 | 3.5*10-3 | <10-4 |
| Â | Â | 22121 | 0.1 | -9.0 | ns | 0.2 | ns | 3.4*10-3 | 3*10-3 |
3 | 26.6 26.8 | 11121 | 0.38 | -17.3 | 4*10-4 | -0.9 | 4*10-4 | 7.4*10-4 | ns |
| Â | Â | 22212 | 0.22 | 31.7 | <10-4 | 1.2 | 2*10-4 | -3.3*10-3 | <10-4 |
| Â | Â | 11222 | 0.07 | -15.9 | ns | -0.9 | ns | -6.2*10-4 | ns |
| Â | Â | 22222 | 0.11 | -4.8 | ns | 0.2 | ns | 2.4*10-3 | ns |
3 | 36.9 37.1 | 11111 | 0.14 | 24.4 | 1*10-3 | -0.4 | ns | -1.0*10-2 | <10-4 |
| Â | Â | 21111 | 0.11 | -19.4 | 2*10-2 | 0.4 | ns | 7.4*10-3 | <10-4 |
| Â | Â | 21122 | 0.1 | 0.6 | ns | 0.6 | ns | 3.2*10-3 | 3*10-3 |
| Â | Â | 21112 | 0.08 | -2.3 | ns | -0.2 | ns | 7.5*10-4 | ns |
| Â | Â | 12111 | 0.16 | -4.0 | ns | -0.3 | ns | -1.1*10-1 | ns |
| Â | Â | 21222 | 0.19 | -2.7 | ns | 0.4 | ns | 3.6*10-3 | <10-4 |
4 | 7.7 7.9 | 11112 | 0.34 | 13.8 | 1*10-2 | 0.2 | ns | -2.3*10-3 | 8*10-4 |
| Â | Â | 11122 | 0.11 | -14.9 | 5*10-2 | -1.1 | 1*10-2 | -6.4*10-4 | ns |
| Â | Â | 12112 | 0.07 | -25.8 | 1*10-2 | -1.9 | 2*10-4 | -1.8*10-3 | ns |
| Â | Â | 22212 | 0.16 | -13.9 | 4*10-2 | 0.2 | ns | 4.7*10-3 | <10-4 |
4 | 24.9 25.3 | 11122 | 0.07 | -12.3 | ns | -1.8 | 1*10-4 | -3.8*10-3 | ns |
| Â | Â | 11211 | 0.15 | -24.5 | 1*10-4 | -1.3 | 1*10-4 | 8.2*10-4 | ns |
| Â | Â | 12121 | 0.07 | 49.8 | <10-4 | 3.0 | <10-4 | -6.0*10-4 | ns |
| Â | Â | 12122 | 0.23 | 35.8 | <10-4 | 2.6 | <10-4 | 1.5*10-3 | ns |
| Â | Â | 21111 | 0.14 | -37.9 | <10-4 | -2.5 | <10-4 | -2.2*10-5 | ns |
5 | 69.3 69.5 | 12121 | 0.35 | -27.7 | <10-4 | -1.6 | <10-4 | 5.2*10-4 | ns |
| Â | Â | 12112 | 0.15 | 20.2 | 2*10-3 | 0.8 | 4*10-2 | -2.5*10-3 | 1*10-2 |
| Â | Â | 12212 | 0.08 | 12.0 | ns | -0.1 | ns | -2.5*10-3 | 1*10-2 |
| Â | Â | 21212 | 0.19 | 15.3 | 1*10-2 | 1.1 | 2*10-3 | 8.6*10-4 | ns |
5 | 2.7 2.9 | 12111 | 0.19 | -11.4 | ns | -0.4 | ns | 1.3*10-3 | ns |
| Â | Â | 21221 | 0.16 | -27.3 | <10-4 | -0.4 | ns | 4.9*10-3 | <10-4 |
| Â | Â | 22111 | 0.19 | 26.3 | <10-4 | 0.8 | 5*10-2 | -3.0*10-3 | 1*10-4 |
| Â | Â | 22112 | 0.16 | 5.3 | ns | -0.3 | ns | -3.7*10-3 | <10-4 |