breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp [crl] [crl]
MC JC 417,368 Δ5 bp coding (227‑231/690 nt) phoB → response regulator in two‑component regulatory system with PhoR
RA 701,378 +T coding (217/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 704,008 C→A P22Q (CCG→CAG)  nagE → N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components
RA 1,157,900 +A coding (32/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
RA 1,726,169 T→G F49L (TTT→TTG)  nemR → transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
JC JC 1,755,755 IS5 (+) +4 bp coding (58‑61/1413 nt) pykF → pyruvate kinase I
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
MC JC 3,909,312 Δ774 bp [pstA]–[pstC] [pstA], [pstC]
JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,382 +C intergenic (+588/+54) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 365849 365965 117 4 [3] [3] 4 lacZ beta‑D‑galactosidase
* * ÷ NC_000913 1293040 1303173 10134 29 [0] [0] 20 tdk–[oppB] tdk,insZ,insZ,insZ,adhE,ychE,oppA,[oppB]
* * ÷ NC_000913 3423755–3424233 3424533–3424239 7–779 4 [3] [3] 4 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4110750 4111496 747 4 [3] [3] 5 tpiA triosephosphate isomerase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)28 (1.400) 25/284 0.0 100% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 = 258675NA (NA)20 (1.010) 19/282 0.1 100% noncoding (1/768 nt) IS1 repeat region
?NC_000913 1303174 = 0 (0.000)coding (276/921 nt) oppB oligopeptide ABC transporter permease
* ? NC_000913 1207790 =3 (0.150)10 (0.560) 8/252 0.9 77.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 3 (0.170)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078053 (0.150)12 (0.680) 11/252 0.5 80.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 3 (0.170)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related