Table 1 Mean precision, recall, and F-score on each empirical data set with each reference genome. Numbers in bold show the best precision, recall, and F-score for each species and reference genome

M. tuberculosis

17

H37Rv

BayesTyper

0.9995

0.9217

0.9579

GraphTyper

0.9997

0.8938

0.9422

Minos

0.9997

0.9181

0.9559

S. aureus

28

TW20

BayesTyper

0.9984

0.8669

0.9279

GraphTyper

0.9990

0.7530

0.8545

Minos

0.9988

0.8786

0.9347

USA300

BayesTyper

0.9993

0.8671

0.9283

GraphTyper

0.9995

0.7506

0.8534

Minos

0.9994

0.8792

0.9353

K. pneumoniae

17

GCF_000784945.1

BayesTyper

0.9990

0.9052

0.9495

GraphTyper

0.9999

0.9063

0.9505

Minos

0.9999

0.9143

0.9550

GCF_001952915.1

BayesTyper

0.9995

0.8800

0.9346

GraphTyper

0.9999

0.8788

0.9340

Minos

0.9994

0.8922

0.9417

GCF_003073315.1

BayesTyper

0.9996

0.9267

0.9617

GraphTyper

0.9999

0.9297

0.9634

Minos

0.9998

0.9367

0.9672

GCF_003076555.1

BayesTyper

0.9994

0.9397

0.9686

GraphTyper

0.9999

0.9387

0.9683

Minos

0.9999

0.9438

0.9710

GCF_011006575.1

BayesTyper

0.9995

0.9078

0.9511

GraphTyper

0.9999

0.9075

0.9513

Minos

0.9998

0.9238

0.9602