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. 2022 Oct 19;17(10):e0260177. doi: 10.1371/journal.pone.0260177

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.