Table 4.
(Imputation quality of the scenario ”entire SNP imputation using 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 SNPs |
IMPUTE2 Imputation score based on 10% overlapping masked SNPs |
|||||
|---|---|---|---|---|---|---|---|
| Data subset name | #SNPs | 10% | 20% | 50% | 10% | 20% | 50% |
| ALL |
9602 |
94.36+
|
94*+
|
91.63+
|
94.25+
|
93.77+
|
91.66
|
| LQ |
8472 |
94.33*
|
93.99*
|
91.61
|
94.14
|
93.68
|
91.68+
|
| NQ |
7923 |
94.27 |
93.82* |
91.33 |
94.13
|
93.50 |
91.39 |
| BQ |
6337 |
91.69* |
90.76* |
85.08 |
91.20 |
90.18 |
84.85 |
| HQ | 4658 | 91.22* | 90.2* | 83.64* | 90.21 | 88.97 | 82.42 |
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 faced letters. An asterisk (*) indicates whether MaCH or IMPUTE2 performed significantly better in the corresponding scenario.