Table 1. Benchmark statistics for allele calls that could be achieved in a fully automated manner at three-field resolution (note that some of the reference samples only had two-field resolution, Supplementary Table S2).
| Allele call rate | |||||
|---|---|---|---|---|---|
| Locus | Genotypes available | Different alleles | Exact | Including alternatives | Mean alternatives/sample |
| A | 341 | 114 | 0.98 | 0.99 | 2.21 |
| B | 344 | 122 | 0.99 | 1.00 | 1.03 |
| C | 285 | 53 | 0.98 | 0.99 | 1.58 |
| DRB1 | 307 | 80 | 0.98 | 0.98 | 1.08 |
| DQA1 | 152 | 20 | 1.00 | 1.00 | 0.06 |
| DQB1 | 264 | 18 | 0.99 | 0.99 | 0.06 |
| DPA1 | 87 | 5 | 0.98 | 0.98 | 0.00 |
| DPB1 | 209 | 40 | 0.97 | 0.97 | 0.57 |
Columns - Locus: Lists the typed classical gene locus. Genotypes available: Shows the number of samples for which reference genotypes were available. Only alleles for which a reference call was available were used for calculating the call rate. Different alleles: Lists the number of different alleles within the reference data set for each locus. The automated calling generates two probable allele calls per diploid sample. Allele calling exact: Shows the validated allele call rate that was achieved by the automated calling. Allele calling including alternatives: Shows the call rate when including possible alternative alleles (ambiguities). Mean alternatives/sample: Shows the average number of alternative allele calls (ambiguities) per sample.