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. 2021 Sep 22;5:287. Originally published 2020 Dec 9. [Version 2] doi: 10.12688/wellcomeopenres.16320.2

Table 4. Metrics from Imputation bootstrapping (1,000 runs).

metric Number of
correct
genotypes		 Total
number of
genotypes		 No-call
number		 Correct
Proportion
of
genotypes		 Adjusted-
correct
proportion
of
genotypes		 Missing
proportion
of
genotypes		 Wild-Type Homozygote -α -3.7I Heterozygote -α -3.7I Homozygote
sensitivity specificity accuracy PPV sensitivity specificity accuracy PPV sensitivity specificity accuracy PPV
70% threshold
Minimum 1645 2936 54 0.560 0.746 0.018 0.582 0.826 0.796 0.582 0.486 0.787 0.710 0.486 0.256 0.910 0.889 0.256
1 st Qu 2173 2936 206.8 0.740 0.836 0.070 0.736 0.924 0.859 0.736 0.745 0.862 0.807 0.745 0.696 0.962 0.929 0.696
Median 2259 2936 274.5 0.769 0.854 0.093 0.770 0.938 0.872 0.770 0.776 0.877 0.827 0.776 0.755 0.970 0.938 0.755
Mean 2248 2936 296.2 0.766 0.852 0.101 0.765 0.934 0.871 0.765 0.772 0.875 0.825 0.772 0.747 0.968 0.937 0.747
SD 123.92 120.15 0.040 0.025 0.040 0.050 0.020 0.020 0.050 0.050 0.020 0.030 0.050 0.090 0.010 0.010 0.090
3 rd Qu 2334 2936 361.2 0.795 0.869 0.123 0.800 0.948 0.883 0.800 0.807 0.891 0.844 0.807 0.809 0.976 0.946 0.809
Maximum 2555 2936 1027 0.870 0.911 0.350 0.895 0.976 0.922 0.895 0.870 0.933 0.891 0.870 0.912 0.992 0.965 0.912
90% threshold
Minimum 1170 2936 215 0.399 0.771 0.073 0.453 0.851 0.754 0.453 0.302 0.829 0.639 0.302 0.134 0.932 0.876 0.134
1st Qu 1791 2936 589.8 0.610 0.861 0.201 0.640 0.940 0.833 0.640 0.597 0.902 0.760 0.597 0.517 0.976 0.918 0.517
Median 1938 2936 716 0.660 0.878 0.244 0.681 0.953 0.849 0.681 0.656 0.916 0.789 0.656 0.621 0.981 0.930 0.621
Mean 1919 2936 742.8 0.654 0.875 0.253 0.678 0.949 0.847 0.678 0.647 0.915 0.785 0.647 0.612 0.980 0.929 0.612
SD 194.51 212.13 0.066 0.025 0.072 0.062 0.018 0.022 0.062 0.081 0.020 0.038 0.081 0.137 0.008 0.017 0.137
3rd Qu 2059 2936 880 0.701 0893 0.300 0.721 0.961 0.862 0.721 0.706 0.929 0.813 0.706 0.717 0.985 0.941 0.717
Maximum 2436 2936 1544 0.830 0.925 0.526 0.840 0.981 0.901 0.840 0.830 0.960 0.873 0.830 0.887 0.997 0.965 0.887

Adjusted-correct proportion was calculated for each run by adjusting the total number of genotypes by the number of no-called genotypes (Underlying Data2 Table AD_Impute2_overall_summary).