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Table 3 Results of pipeline testing on real E. coli and K. pneumoniae data. Only samples with results different from expected are shown

From: BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing

SRA Run AC

Reported ST

Expected ST

Genes with multiple variants at the same position

ERR966604

95

73

SRR2767732

16

16

Icd

SRR2767734

21

21

Icd, mdh

SRR2970643

131

131

fumC

SRR2970737

131

131

adk, fumC, gyrB, mdh, recA, purA

SRR2970742

131

131

fumC

SRR2970753

131

131

fumC

SRR2970774

131

131

fumC

SRR2970775

131

131

fumC

SRR5973405

1164

1164

phoE

SRR5973308

1180

1180

phoE

SRR5973303

13

13

phoE

SRR5973253

133

133

phoE

SRR5973334

133

133

phoE

SRR5973324

1373

1373

phoE

SRR5973251

1426

1426

gapA, phoE

SRR5973269

147

147

gapA

SRR5973320

1876

1876

phoE

SRR5973351

188

188

gapA

SRR5973329

20

20

phoE

SRR5973408

2267

2276

phoE

SRR5973397

25

25

phoE

SRR5973248

258

258

gapA

SRR5973283

258

258

gapA

SRR5973279

258

258

gapA

SRR5973271

258

258

gapA

SRR5973336

258

258

gapA

SRR5973319

258

258

gapA

SRR5973317

258

258

gapA

SRR5973294

258

258

gapA

SRR5973291

258

258

gapA

SRR5973289

258

258

gapA

SRR5973400

258

258

gapA

SRR5973382

258

258

gapA

SRR5973381

258

258

gapA

SRR5973287

258

258

gapA

SRR5973240

307

307

phoE

SRR597324

307

307

phoE

SRR5973282

307

307

phoE

SRR5973280

307

307

phoE

SRR5973339

307

307

phoE

SRR5973322

307

307

phoE

SRR5973288

307

307

phoE

SRR5973396

307

307

phoE

SRR5973380

307

307

phoE

SRR5973379

307

307

phoE

SRR5973376

307

307

phoE

SRR5973373

307

307

phoE

SRR5973361

307

307

phoE

SRR5973355

307

307

phoE

SRR5973284

23

23

phoE

SRR5973332

35

35

phoE

SRR5973389

35

35

phoE

SRR5973368

35

35

phoE

SRR5973393

405

405

phoE

SRR5973311

412

412

phoE

SRR5973371

429

429

tonB

SRR5973327

466

466

phoE

SRR5973407

466

466

phoE

SRR5973239

492

492

phoE

SRR5973301

502

502

phoE

SRR5973348

753

753

phoE

SRR5973362

8

8

phoE