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
RA 167,843 +T coding (360/2244 nt) fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
RA 909,422 G→A A543V (GCC→GTC)  poxB ← pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
JC JC 911,086 IS2 (–) +5 bp intergenic (‑37/+92) poxB ← / ← hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
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 insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,173,363 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 2,720,868 (CGCTGG)2→3 coding (916/2661 nt) pka → protein lysine acetyltransferase
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 3,768,131 A→T pseudogene (911/945 nt) rhsJ → Rhs‑family protein
RA 3,964,929 C→T E234E (GAG→GAA)  rhlB ← ATP‑dependent RNA helicase
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 123052 127528 4477 6 [3] [4] 5 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 3423756–3424234 3424529–3424238 5–774 5 [4] [4] 5 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3619373–3622295 3669572 47278–50200 5 [4] [4] 5 [rhsB]–yhjA [rhsB],yhhH,yrhC,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,insH1,yhiS,slp,dctR,yhiD,hdeB,hdeA,hdeD,arrS,gadE,mdtE,mdtF,gadW,gadY,gadX,gadA,yhjA
* * ÷ NC_000913 3669673 3688673 19001 5 [4] [0] 29 [treF]–[bcsC] [treF],yhjB,yhjC,yhjD,yhjE,yhjG,yhjH,kdgK,yhjJ,dctA,yhjK,[bcsC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =0 (0.000)20 (0.720) 19/238 0.5 85.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 7 (0.250)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078050 (0.000)30 (1.070) 26/238 0.2 89.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 7 (0.250)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 3688674 =0 (0.000)29 (0.920) 26/268 0.3 60.4% coding (500/3474 nt) bcsC cellulose synthase subunit
?NC_000913 = 4506221 38 (1.210)coding (935/1119 nt) yjhC GFO/IDH/MOCA family putative oxidoreductase. NAD(P)‑dependent