Table 3. Verification of gene-chip predicted SFPs by sequence information.
| (a) SFP in CP&LG | |||
| Sequence information | Gene-chip | ||
| 5376 SFP(9.5% FDR) | 9093 SFP (11.9% FDR) | ||
| Total probe sequence | 186 | 78 | 85 |
| Polymorphism | 104 | 77 | 82 |
| Non-polymorphism | 82 | 1 | 3 |
| SFP detection sensitivity | 74% | 79% | |
| FDR after sequencing | 1% | 3% | |
| (b) SFP in CP&RT | |||
| Sequence information | Gene-chip | ||
| 25325 SFP(9% FDR) | 61055 SFP(10% FDR) | ||
| Total probe sequence | 603 | 204 | 257 |
| Polymorphism | 245 | 180 | 207 |
| Non-polymorphism | 358 | 24 | 50 |
| SFP detection sensitivity | 73% | 84% | |
| FDR after sequencing | 12% | 20% | |
CP = Cypress, LG = LaGrue and RT = RT0034.