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