From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle
Concordance rate | Allelic R ^{2} | ||||
---|---|---|---|---|---|
Source | Mean | Scheffé test ^{3} | Source | Mean | Scheffé test ^{3} |
Step ^{4} (P-value < 0.0001) | Step ^{4} (P-value < 0.0001) | ||||
Two-step | 1.231 | a | Two-step | 1.125 | a |
One-step | 1.110 | b | One-step | 0.997 | b |
Algorithm ^{5} (P-value < 0.0001) | Algorithm ^{4} (P-valeu 0.0001) | ||||
FImpute | 1.202 | a | FImpute | 1.080 | a |
Beagle | 1.140 | b | Beagle | 0.997 | b |
Panel ^{6} (P-value < 0.0001) | Panel ^{6} (P-value < 0.0001) | ||||
15K | 1.236 | a | 15K | 1.130 | a |
20K | 1.229 | b | 20K | 1.120 | a |
8K | 1.180 | c | 8K | 1.052 | b |
6K | 1.167 | d | 6K | 1.034 | c |
3K | 1.042 | e | 3K | 0.855 | d |
Scenario ^{7} (P-value 0.7638) | Scenario ^{7} (P-value 0.9983) | ||||
NE-NP | 1.171 | a | NE-NP | 1.038 | a |
NE-P | 1.170 | a | NE-P | 1.038 | a |
Step*Algorithm (P-value < 0.0001) | Step*Algorithm (P-value < 0.0001) | ||||
Two-step - FImpute | 1.254 | a | Two-step - FImpute | 1.154 | a |
Two-step - Beagle | 1.208 | b | Two-step - Beagle | 1.095 | b |
One-step - FImpute | 1.149 | c | One-step - FImpute | 1.006 | c |
One-step - Beagle | 1.072 | d | One-step - Beagle | 0.898 | d |
Step*Panel (P-value < 0.0001) | Step*Panel (P-value < 0.0001) | ||||
Two-step - 15K | 1.274 | a | Two-step - 15K | 1.183 | a |
Two-step - 20K | 1.247 | b | Two-step - 20K | 1.147 | b |
Two-step - 8K | 1.246 | b | Two-step - 8K | 1.145 | b |
Two-step - 6K | 1.239 | b | Two-step - 6K | 1.136 | b |
One-step - 20K | 1.210 | c | One-step - 20K | 1.094 | c |
One-step - 15K | 1.198 | c | One-step - 15K | 1.078 | c |
Two-step - 3K | 1.149 | d | Two-step - 3K | 1.013 | d |
One-step - 8K | 1.114 | e | One-step - 8K | 0.960 | e |
One-step - 6K | 1.094 | f | One-step - 6K | 0.932 | e |
One-step - 3K | 0.936 | g | One-step - 3K | 0.696 | f |