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]
JC JC 701,889 IS1 (+) +9 bp coding (855‑863/1149 nt) nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,728,425 G→A A27T (GCC→ACC)  rnt → RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair
MC JC 1,978,503 Δ776 bp insB1–insA 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
JC 2,672,981 (CGCTAC)2→1 coding (935‑940/1203 nt) hcaD → phenylpropionate dioxygenase, ferredoxin reductase subunit
JC 2,724,732 (AAAAGC)1→2 coding (1015/1299 nt) kgtP ← alpha‑ketoglutarate transporter
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 3,823,139 T→A M247K (ATG→AAG)  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 3423744–3424234 3424557–3424238 5–814 36 [35] [35] 39 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 120780552 (0.600)40 (0.520) 34/266 2.2 52.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 27 (0.350)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related