Table 2. Concordance rate and call rate for each imputation program.
| European Americans | African Americans | ||||
|---|---|---|---|---|---|
| Allele | Imputation Program | Concordance Rate | Call Rate | Concordance Rate | Call Rate |
| HLA-A | SNP2HLA | 0.983 | 0.999 | 0.969 | 0.995 |
| HLA*IMP:02 | 0.963 | 0.997 | 0.675 | 0.855 | |
| HIBAG | 0.986 | 0.996 | 0.960 | 0.796 | |
| HLA-B | SNP2HLA | 0.969 | 1.00 | 0.884 | 1.00 |
| HLA*IMP:02 | 0.952 | 0.979 | 0.423 | 0.752 | |
| HIBAG | 0.978 | 0.967 | 0.953 | 0.403 | |
| HLA-C | SNP2HLA | 0.987 | 1.00 | 0.884 | 1.00 |
| HLA*IMP:02 | 0.984 | 0.994 | 0.792 | 0.741 | |
| HIBAG | 0.987 | 0.992 | 0.957 | 0.619 | |
| HLA-DPB1 | SNP2HLA | 0.957 | 1.00 | 0.945 | 1.00 |
| HLA*IMP:02 | 0.829 | 0.987 | 0.567 | 0.708 | |
| HIBAG | 0.957 | 0.975 | 0.834 | 0.475 | |
| HLA-DQB1 | SNP2HLA | 0.988 | 1.00 | 0.907 | 1.00 |
| HLA*IMP:02 | 0.983 | 0.993 | 0.845 | 0.761 | |
| HIBAG | 0.988 | 0.990 | 0.904 | 0.654 | |
| HLA-DRB1 | SNP2HLA | 0.964 | 1.00 | 0.920 | 1.00 |
| HLA*IMP:02 | 0.924 | 0.961 | 0.414 | 0.791 | |
| HIBAG | 0.959 | 0.946 | 0.946 | 0.557 | |
Concordance and call rates generated from imputed alleles with posterior probability>0.50 versus sequenced alleles after combining data for HumanOmni1-QUAD and HumanOmni5-QUAD platforms by HLA locus and race/ethnicity.