breseq  version 0.29.0  revision 8f9c342918e4
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 657,215 Δ25 bp intergenic (+98/‑53) pagP → / → cspE phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
JC JC 700,680 IS1 (+) +9 bp coding (907‑915/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
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 2,725,370 A→C L126* (TTA→TGA)  kgtP ← alpha‑ketoglutarate transporter
MC JC 2,765,456 (TATGGCAC)6→5 intergenic (‑303/+50) yfjL ← / ← yfjM CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein
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
RA 3,823,105 C→A R236S (CGC→AGC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 4,296,381 +GC intergenic (+587/+55) 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 3423714–3424234 3424580–3424238 5–867 33 [32] [31] 33 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =6 (0.090)40 (0.710) 38/266 0.9 85.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 8 (0.140)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078056 (0.090)59 (1.040) 55/266 0.1 89.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 8 (0.140)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related