Table 1.

Concordance between HISAT-genotype and Omixon on HLA-typing of 917 genomes from the CAAPA (Consortium on Asthma among African-ancestry Populations in the Americas) collection. Concordance is calculated as the total number of alleles matched between both programs divided by the total number of alleles. For example, for the HLA-A gene, HISAT-genotype and Omixon agree on the allele group (the first number of the HLA type) for both alleles for 913 genomes, agree on one allele for 4 genomes, and agree on no alleles for 0 genomes. Thus, the concordance for HLA-A is 0.998 = (913 × 2 + 4) / (917 × 2). HISAT-genotype reports HLA types with all four fields specified (e.g., A*24:02:01:01), while Omixon reports HLA types with either two numbers (e.g. A*69:01) or three numbers (A*24:02:01); therefore matches were evaluated using only the first two numbers.

	First number (e.g., A*01)				First and second numbers (e.g., A*01:01)
	Both alleles matched	One allele matched	No allele matched	Concordance	Both alleles matched	One allele matched	No allele matched	Concordance
HLA-A	913	4	0	0.998	883	33	1	0.981
HLA-B	911	6	0	0.997	877	40	0	0.978
HLA-C	915	2	0	0.999	880	34	3	0.978
HLA-DQA1	884	33	0	0.982	868	45	4	0.971
HLA-DQB1	917	0	0	1	753	164	0	0.911
HLA-DRB1	861	56	0	0.97	698	205	14	0.873