Table 3.

Summary of accuracies of the human leukocyte antigen (HLA) interpretation programs for 1000 Genomes samples.

Program	Number of alleles	Correct (all alleles)	Accuracy (all alleles) (%)	Missing alleles (%)	Correct (intersection N = 164)	Accuracy (intersection) (%)
HLAreporter	630	202	32.06	190 (30.16)	91	55.49
ATHLATES	630	468	74.29	78 (12.38)	137	83.54
Optitype	378	372	98.41	0 (0.00)	161	98.17

Missing allele refers to either a completely missing call or one for which no consensus could be formed based on a list of detected alleles. Intersection denotes the set of alleles for all sample–gene pairs that had a non-missing typing in all tested typing programs. No results could be achieved using HLAssign.