Table 2.

Results of the metagenomic analysis of shotgun and target enrichment datasets using Kraken2 (Wood et al.¹⁷) and Metaphlan2 (Segata et al.¹⁸).

Sample ID	Type of data	Filtered reads	Kraken2							Metaphlan2
			% Reads identified	Identified reads	Yersinia hits	Yersinia PTB complex hits	Yersinia pestis hits	Yersinia Pseudotub. hits	% Yersinia hits	% Yersinia pestis
IMO2	Shotgun	47,690,216	5.43	2,589,579	743	454	50	11	0.029	0
	Capture Mapped (-n0.01 -q 30)	11,942	89.06	10,636	8694	7743	957	47	81.745	100
IMO3	Shotgun	53,694,249	4.84	2,598,802	126	12	1	3	0.005	0
IMO7	Shotgun	54,138,809	4.26	2,306,313	496	87	4	46	0.022	0

Kraken2 records the number of hits for each taxon and Metaphlan2 the abundance of identified reads assigned to each taxon. Mapped data denotes reads extracted from a mapping to the CO92 reference genome.