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
JC JC 167,520 IS2 (–) +5 bp coding (37‑41/2244 nt) fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
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
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 2,149,615 G→T D457E (GAC→GAA yegI ← protein kinase‑related putative non‑specific DNA‑binding 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
RA 2,721,243 G→A G431R (GGA→AGA)  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
MC JC 3,625,592 Δ95,041 bp IS150‑mediated yhhJ[mokA] 82 genes
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 123045 127551 4507 11 [9] [9] 10 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 1196253 1211447 15195 11 [9] [9] 10 [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 3423776–3424234 3424580–3424238 5–805 10 [8] [9] 10 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 905931 =41 (1.010)2131 (55.280) 268/242 0.0 98.6% coding (823/1014 nt) ybjS putative NAD(P)H‑dependent oxidoreductase
?NC_000913 = 912978 21 (0.540)coding (837/1653 nt) hcp hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases
* ? NC_000913 911147 =NA (NA)22 (0.590) 17/236 1.2 NA noncoding (1/26 nt) REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 911173 = NA (NA)intergenic (‑124/+9) poxB/hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
* ? NC_000913 = 911155NA (NA)22 (0.590) 18/236 1.1 NA noncoding (9/26 nt) REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 = 911163 NA (NA)noncoding (17/26 nt) REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences
* ? NC_000913 = 12994980 (0.000)32 (0.820) 31/246 0.3 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein