Table 2.
The 11 SNP core haplotype shown by Sweep (v1.1) to be in LD in region 2 (Table 1 ) on chromosome 1
| SNP ID | Chr | Position | Platform | SNP | Haplotype | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (Derived/ancestral) | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | ||||
| OAR1_93117979 | 1 | 87702641 | Sequenom® | T/C | C | C | C | C | C | C | C | T |
| OAR1_93118073 | 1 | 87702735 | Sequenom® | C/T | T | T | T | T | T | T | T | C |
| OAR1_93124341.1 | 1 | 87709264 | SNP50 BeadChip | T/C | C | C | C | C | C | T | T | T |
| OAR1_93154178 | 1 | 87740396 | Sequenom® | A/G | A | G | G | G | G | A | G | A |
| s50853 | 1 | 87751371 | Sequenom® | G/C | G | C | C | G | G | C | C | C |
| OAR1_93166689.1 | 1 | 87753155 | SNP50 BeadChip | G/T | T | T | T | T | T | T | T | G |
| OAR1_93219257.1 | 1 | 87791568 | SNP50 BeadChip | C/T | C | C | C | C | C | C | C | T |
| OAR1_93226648 | 1 | 87801889 | Sequenom® | A/G | G | G | G | G | G | G | G | A |
| OAR1_93231706 | 1 | 87807624 | Sequenom® | G/T | T | T | T | G | T | T | T | T |
| OAR1_93231813 | 1 | 87807731 | Sequenom® | T/C | T | T | T | C | T | C | T | T |
| s57213.1 | 1 | 87826285 | SNP50 BeadChip | C/T | C | C | T | C | T | C | C | T |
| OAR1_93251748 | 1 | 87828912 | Sequenom® | A/G | - | - | - | - | - | - | - | - |
| Selection line | Haplotype frequency | |||||||||||
| Romney resistant | - | - | - | 0.3211 | - | - | - | 0.6789 | ||||
| Romney susceptible | - | - | - | 0.8841 | - | - | - | 0.0976 | ||||
| Perendale resistant | 0.0203 | - | 0.0203 | 0.6554 | 0.0338 | 0.0203 | 0.0405 | - | ||||
| Perendale susceptible | - | 0.0278 | - | 0.3264 | 0.0764 | - | - | 0.5417 | ||||
Haplotypes 1–8 were present in either the Romney or Perendale animals, or both. Haplotype frequencies are given for each selection line.