TABLE 1.

The percentage of concordantly typed (WGS and microarray identify a gene as present or absent, respectively) and discrepantly typed results (either only WGS or only microarray identifies a gene as present) for each functional target category^a

Result category	Result caused by		Result by functional category of genes (no.)				Total no.	Total, %
			Identification	Regulation	Resistance	Virulence
Concordant (n = 27,119; 96.8 %)
Positive	Microarray and WGS (de novo)		829	990	1,060	8,495	11,374	40.6
Negative	Microarray and WGS (de novo)		0	1,159	8,100	6,486	15,745	56.2
Discrepant (n = 909; 3.2 %)
False positive	Microarray	Mishybridizations	0	78	21	103	202	0.7
	LFM	Misprediction	0	17	2	9	28	0.1
False negative	Microarray	Polymorphisms	0	3	14	140	157	0.6
	LFM	Misprediction	0	0	0	5	5	<0.1
	WGS	Assembly error	88	42	16	164	310	1.1
		Cropped contig	1	12	15	28	56	0.2
		Not sequenced or aberrant allele	6	9	8	100	123	0.4
Unknown			0	0	4	24	28	0.1
Total no. of typing results			924	2,310	9,235	15,554	28,028	100

^aComparison of typing concordance of WGS typing and the traditional DNA microarray. In total, 182 targets in 154 samples were analyzed, resulting in 28,028 individual typing results. The discrepant results are subdivided by false-positive and false-negative typing results and different causes of error. Results that were assumed to be false negatively typed by the two methods are not considered in this table (n = 4).