Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

Table 2 Bacterial isolate-derived sequencing read abundance (%) in metagenomes of varying sizes for detection of antimicrobial resistance genes in isolates with 3, 4, or 5 Mbp genomes

Metagenome Size^a (M)	Isolate Percentage in Metagenome^b
	3 Mbp		4 Mbp		5 Mbp
	5X (100000)	10X (200000)	5X (133333)	10X (266666)	5X (166666)	10X (333333)
5	2.00	4.00	2.67	5.33	3.33	6.67
10	1.00	2.00	1.33	2.67	1.67	3.33
40	0.25	0.50	0.33	0.67	0.42	0.83
50	0.25	0.40	0.27	0.53	0.33	0.67
100	0.1	0.20	0.13	0.27	0.17	0.33
125	0.8	0.16	0.11	0.21	0.13	0.27

Abbreviations: M million, Mbp million base pairs
^aMetagenome size refers to number of reads in metagenome
^bFor each genome size (3, 4, and 5 Mbp) 5- and 10-X genome coverage is estimated for read length of 150 bp (with number of reads to create specified coverage level in parentheses). Percentages are corresponding to metagenome size in the first column

ISSN: 1471-2180