Table 2. Reference strains relative abundances expected and computed by StrainFLAIR or Kraken2 for each simulated experiment with variable coverage of the K-12 strain.

Best results are shown in bold. For StrainFLAIR, the proportion of specific genes detected is shown in parentheses. Complete results are presented Section S1.6.

#reads K-12	Method	O104:H4	IAI39	K-12	Sakai	SE15	Santai	RM8426
1,000	Expected	59.88	39.92	0.2	0	0	0	0
	StrainFLAIR	56.47	43.53	0	0	0	0	0
		(0.995)	(0.989)	(0.309)	(0.189)	(0.151)	(0.188)	(0.212)
	Kraken2	38.91	60.72	0.22	0.04	0.07	0.03	0.02
25,000	Expected	57.14	38.1	4.76	0	0	0	0
	StrainFLAIR	52.14	40.58	7.27	0	0	0	0
		(0.994)	(0.989)	(0.878)	(0.208)	(0.153)	(0.215)	(0.234)
	Kraken2	37.23	58.1	4.51	0.04	0.07	0.03	0.02
200,000	Expected	42.86	28.57	28.57	0	0	0	0
	StrainFLAIR	38.12	29.81	32.08	0	0	0	0
		(0.993)	(0.988)	(0.99)	(0.211)	(0.159)	(0.219)	(0.237)
	Kraken2	28.31	44.18	27.35	0.04	0.08	0.03	0.02