From: Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis
 |  | Two marker test | Intersection test | Interval mapping | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Chromosome | Marker | Frequency M2N2 | M2N2 df | M2N2 p-value | Frequency M2 | Frequency N2 | M2 df | N2 df | M2 p-value | N2 p-value | p-value |
1 | 3E-4F | 0.67 | 94 | 0.029 | 0.67 | 0.86 | 96 | 95 | 0.14 | 0.0256 | 0.0242 |
 | 4F-5D | 0.81 | 93 | 0.032 | 0.86 | 0.84 | 95 | 96 | 0.0256 | 0.056 | 0.0226 |
 | 6E-7D | 0.7 | 93 | 0.0499 | 0.83 | 0.74 | 96 | 95 | 0.069 | 0.1 | 0.0373 |
2 | 35B-38A | 0.69 | 82 | 0.028 | 0.81 | 0.83 | 89 | 84 | 0.33 | 0.017 | 0.3036 |
 | 38A-38E | 0.7 | 77 | 0.017 | 0.83 | 0.88 | 84 | 87 | 0.017 | 0.028 | 0.0105 |
 | 38E-43A | 0.71 | 78 | 0.028 | 0.88 | 0.84 | 87 | 84 | 0.028 | 0.038 | 0.0083 |
 | 43A-43E | 0.73 | 79 | 0.03 | 0.84 | 0.9 | 84 | 87 | 0.038 | 0.034 | 0.0177 |
 | 43E-46C | 0.8 | 85 | 0.038 | 0.90 | 0.89 | 87 | 89 | 0.034 | 0.073 | 0.0339 |
3 | 63A-65A | 0.29 | 85 | 0.075 | 0.49 | 0.38 | 94 | 89 | 0.227 | 0.0249 | 0.0187 |
 | 65A-65D | 0.3 | 86 | 0.035 | 0.38 | 0.51 | 89 | 93 | 0.0249 | 0.13 | 0.0207 |
 | 65D-67D | 0.42 | 90 | 0.021 | 0.51 | 0.51 | 93 | 94 | 0.13 | 0.004 | 0.0031 |
 | 67D-68B | 0.44 | 91 | 0.00004 | 0.51 | 0.58 | 94 | 94 | 0.004 | 0 | 0 |
 | 68B-68C | 0.46 | 90 | 0.00003 | 0.58 | 0.49 | 94 | 92 | 0 | 0.002 | 0 |
 | 68C-69D | 0.41 | 89 | 0.002 | 0.49 | 0.46 | 92 | 94 | 0.002 | 0.007 | 0.0013 |
 | 69D-70C | 0.34 | 86 | 0.0007 | 0.46 | 0.45 | 94 | 90 | 0.007 | 0.0008 | 0.001 |
 | 70C-71E | 0.35 | 84 | 0.0002 | 0.45 | 0.38 | 90 | 89 | 0.0008 | 0.0006 | 0.0009 |
 | 71E-72A | 0.35 | 84 | 0.0002 | 0.39 | 0.42 | 89 | 90 | 0.0006 | 0.0007 | 0.0016 |
 | 72A-73D | 0.39 | 88 | 0.0001 | 0.42 | 0.46 | 90 | 90 | 0.0007 | 0.0003 | 0.001 |
 | 73D-76A | 0.34 | 83 | 0.0001 | 0.46 | 0.37 | 90 | 87 | 0.0003 | 0.0001 | 0.0007 |
 | 76A-76B | 0.34 | 85 | 0.0001 | 0.37 | 0.45 | 87 | 92 | 0.0001 | 0.0009 | 0.0005 |
 | 76B-77A | 0.41 | 90 | 0.0008 | 0.45 | 0.44 | 92 | 92 | 0.0009 | 0.0009 | 0.0009 |
 | 77A-82D | 0.34 | 83 | 0.0002 | 0.44 | 0.38 | 92 | 87 | 0.0009 | 0.0003 | 0.0011 |
 | 82D-85F | 0.31 | 84 | 0.0006 | 0.38 | 0.38 | 87 | 90 | 0.0003 | 0.0012 | 0.0006 |
 | 85F-87B | 0.27 | 84 | 0.0019 | 0.38 | 0.32 | 90 | 89 | 0.0012 | 0.003 | 0.0012 |
 | 87B-87E | 0.28 | 85 | 0.008 | 0.32 | 0.34 | 89 | 91 | 0.003 | 0.01 | 0.0028 |
 | 87E-87F | 0.27 | 84 | 0.006 | 0.34 | 0.30 | 91 | 89 | 0.011 | 0.004 | 0.0066 |
 | 87F-88E | 0.23 | 85 | 0.13 | 0.3 | 0.32 | 89 | 88 | 0.004 | 0.11 | 0.0061 |
 | 96A-96F | 0.2 | 87 | 0.066 | 0.32 | 0.27 | 94 | 90 | 0.21 | 0.013 | 0.0176 |
 | 96F-97D | 0.23 | 86 | 0.013 | 0.27 | 0.36 | 90 | 92 | 0.013 | 0.048 | 0.0168 |
 | 97D-97E | 0.3 | 88 | 0.024 | 0.36 | 0.32 | 92 | 90 | 0.048 | 0.02 | 0.053 |
 | 97E-98A | 0.26 | 88 | 0.013 | 0.32 | 0.34 | 90 | 94 | 0.02 | 0.018 | 0.016 |
 | 98A-99A | 0.27 | 88 | 0.0001 | 0.34 | 0.4 | 94 | 90 | 0.018 | 0 | 0.0001 |
 | 99A-99B | 0.34 | 88 | 0 | 0.40 | 0.43 | 90 | 90 | 0 | 0.0000 | 0 |
 | 99B-99E | 0.32 | 88 | 0 | 0.43 | 0.33 | 90 | 94 | 0 | 0.0000 | 0 |
 | 99E-100A | 0.33 | 93 | 0 | 0.33 | 0.34 | 94 | 95 | 0 | 0.0000 | 0 |