Table 3.
Mean allelic error rate of imputing SNP genotypes between different SNP chips obtained with IMPUTE2
| Scenario | Animals masked (%) | N animals total | N animal reference | N animals test | N SNP |
N |
% |
Mean allelic error rate (%) |
|---|---|---|---|---|---|---|---|---|
|
snp |
snp |
|||||||
| masked | masked | |||||||
| 15K by 50K |
25 |
1419 |
1065 |
354 |
1529 |
205 |
13 |
0.80 |
| 50 |
1419 |
710 |
709 |
1529 |
205 |
13 |
0.95 |
|
| 75 |
1419 |
355 |
1064 |
1529 |
205 |
13 |
1.40 |
|
| 50K by 15K |
25 |
1419 |
1065 |
354 |
1529 |
1324 |
87 |
2.85 |
| 50 |
1419 |
710 |
709 |
1529 |
1324 |
87 |
3.15 |
|
| 75 |
1419 |
355 |
1064 |
1529 |
1324 |
87 |
4.25 |
|
| 25K by 50K |
25 |
431 |
324 |
107 |
1652 |
328 |
20 |
1.50 |
| 50 |
431 |
216 |
215 |
1652 |
328 |
20 |
1.85 |
|
| 75 |
431 |
108 |
323 |
1652 |
328 |
20 |
2.75 |
|
| 50K by 25K | 25 |
431 |
324 |
107 |
1652 |
1324 |
80 |
2.75 |
| 50 |
431 |
216 |
215 |
1652 |
1324 |
80 |
2.75 |
|
| 75 | 431 | 108 | 323 | 1652 | 1324 | 80 | 4.55 |
The results are shown for three SNP chips viz. 15K, 25K and 50K and chromosome 20.