breseq  version 0.35.4  revision f352f80f4bc9
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]
RA 555,478 C→A R290S (CGT→AGT)  cysS → cysteinyl‑tRNA synthetase
RA 1,196,220 C→T H366H (CAC→CAT icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,232 C→T T370T (ACC→ACT icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,247 A→G L375M (TTA→CTG icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
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 1,806,340 C→T intergenic (‑257/‑30) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA 1,807,117 A→G S250G (AGT→GGT)  pfkB → 6‑phosphofructokinase II
MC JC 1,978,503 Δ776 bp insB1insA 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 2,661,691 C→A A147A (GCG→GCT iscR ← isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor
MC JC 3,559,357 Δ1,629 bp [rtcR][glpG] [rtcR], glpR, glpR, [glpG]
MC JC 3,815,859 Δ82 bp [rph][rph] [rph], [rph]
MC 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 4,296,381 +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 1196263 1211427 15165 9 [8] [8] 9 [icd]–[icdC] [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 2066286–2066577 2066577 1–292 10 [8] [7] 9 [insH1] [insH1]
* * ÷ NC_000913 3423765–3424234 3424547–3424238 5–783 9 [8] [8] 9 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107543 4108522 980 9 [8] [8] 9 pfkA pfkA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3423376 =36 (1.040)15 (0.460)
+TTGATGT
11/232 2.0 34.3% intergenic (+182/+47) yhdZ/rrfF putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
?NC_000913 = 4213155 25 (0.720)noncoding (116/120 nt) rrfE 5S ribosomal RNA of rrnE operon