Table 3.
Reconstructed frequencies of common haplotypes for CWD positive animals and controls
| Haplotype definition | Frequency in (-) animals | Frequency in (+) animals |
| CCTAGGCCC | 33.0 | 39.8 |
| CCTAGGCTC | 28.1 | 31.6 |
| CCTAAGCTC | 12.2 | 2.6 |
| CTTAGGCCC | 10.3 | 16.3 |
| TCTCGGCCC | 4.6 | 0.0 |
| CCTAGGTCC | 3.9 | 2.8 |
| TCTAGGCCC | 1.4 | 1.8 |
| TCTAGGCCA | 1.3 | 0.0 |
| CCTCGGCCC | 1.1 | 1.5 |
Haplotypes were generated from unphased genotypes with the Bayesian (ELB) algorithim in Phase ver 2.1. The distribution of haplotype frequencies was significantly different between CWD positive and CWD negative animals (p < 0.01). Only haplotypes with frequencies greater than 1% are reported.