Table 1.

COPLA accuracy for a set of 1000 plasmids

Outcome	Enterobacterales	Lactobacillales	Bacillales	All samples
PTU correctly assigned	230 (89%)	88 (92%)	107 (94%)	935 (94%)
Cluster reconstructeda	4 (2%)	5 (5%)	3 (3%)	31 (3%)
Total correct predictions	234 (91%)	93 (97%)	110 (96%)	966 (97%)

1000 plasmids were randomly removed from the reference dataset (RefSeq84), consisting on 9894 plasmids. COPLA was run using each of these plasmids as query. The table indicates the number of cases (and percentage) for each prediction outcome for all samples and selected bacterial orders. The individual results can be found in Additional file 2

^aAs a result of the elimination of 1000 plasmids from the RefSeq84 sHSBM network, some PTUs containing 4–5 members fell below the threshold for PTU definition (at least four members). Thus, when a plasmid was assigned to one of these clusters, a PTU assignation did not follow (or resulted in a “new PTU assignation”), but in fact the result was correct, since the plasmid was assigned to the correct cluster