Table 3. MAF-stratified comparison of imputation software for EBB data.
MAF | Imputation Software | Sensitivity % | FPR % | #Variants |
---|---|---|---|---|
MAF <5% | Beagle5.4 | 99.538 | 1.252 | 72,493 |
Impute5 | 99.546 | 1.272 | 72,493 | |
Minimac4 | 99.496 | 1.201 | 72,493 | |
MAF >5% | Beagle5.4 | 97.951 | 3.282 | 429,884 |
Impute5 | 97.911 | 3.303 | 429,884 | |
Minimac4 | 97.841 | 3.408 | 429,884 |
MAF<5% indicates all the variants that are below or equal to 5% in minor allele frequencies and MAF>5% indicates all the variants above 5% in minor allele frequencies. A comparison of the sensitivity and false positive rate (FPR) of the imputation results, for each phasing-imputation combination, stratified in two MAF categories.