Table 5.
(Software specific quality scores for the scenario “Entire SNP imputation using external HapMap reference”): percentages of SNPs above a quality cut-off of 0.3 for both MaCH-rsq and IMPUTE-info score are provided
|
Datasets |
MaCH Imputation score observing 10% overlapping masked SNPs |
IMPUTE2 Imputation score observing 10% overlapping masked SNPs |
|||||
|---|---|---|---|---|---|---|---|
| Data subset name | #SNPs | 10% | 20% | 50% | 10% | 20% | 50% |
| ALL |
9602 |
98.29
|
98.72+
|
98.07+
|
99.57+
|
99.57+
|
99.36
|
| LQ |
8472 |
98.29
|
98.50
|
98.07
|
99.57
|
99.57
|
99.57+
|
| NQ |
7923 |
98.50+
|
98.50
|
97.64
|
99.57
|
99.57
|
99.36
|
| BQ |
6337 |
96.57 |
96.57 |
92.72 |
99.14
|
98.93
|
97.43 |
| HQ | 4658 | 96.36 | 96.36 | 91.65 | 98.50 | 98.07 | 96.36 |
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. Note that MaCH-Rsq and IMPUTE-info scores are defined differently and cannot be compared directly.