Table 3.
(Imputation quality of the scenario “Hole-filling with external HapMap reference”): percentages of overlapping masked genotypes imputed with good Hellinger score (≥0.6) are presented
|
Datasets |
MACH Imputation score based on 10% overlapping masked genotypes |
IMPUTE2 Imputation score based on 10% overlapping masked genotypes |
|||||
|---|---|---|---|---|---|---|---|
| Data subset name | #SNPs | 10% | 20% | 50% | 10% | 20% | 50% |
| ALL |
9602 |
94.03*+
|
93.44*
|
91.03*+
|
93.12+
|
92.42+
|
89.74
|
| LQ |
8472 |
94.01*
|
93.45*+
|
91.01*
|
93.10
|
92.41
|
89.85+
|
| NQ |
7923 |
93.83* |
93.15* |
90.61* |
92.90 |
92.11 |
89.32 |
| BQ |
6337 |
90.85* |
89.62* |
83.34* |
89.85 |
88.61 |
82.47 |
| HQ | 4658 | 90.47* | 89.05* | 81.84* | 89.00 | 87.55 | 80.57 |
Datasets of different pre-imputation quality filtering were considered and different percentages of genotypes were masked. Results of the optimal imputation scenarios are described with (+). Results of the filtering scenarios which are not significantly inferior compared to the best scenario, are described with Italic-bold letters. An asterisk (*) indicates whether MaCH or IMPUTE2 performed significantly better in the corresponding scenario.