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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