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
RA 216,852 G→A S51F (TCT→TTT)  yaeF ← putative lipoprotein
MC JC 257,908 Δ776 bp [crl] [crl]
RA 1,023,628 +G coding (256/2154 nt) yccS ← putative transporter, FUSC superfamily inner membrane protein
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 2,173,363 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 123049 127550 4502 21 [19] [18] 21 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 3423767–3424234 3424544–3424238 5–778 21 [20] [20] 21 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 905931 =58 (0.620)3340 (37.060) 278/272 -0.0 98.4% coding (823/1014 nt) ybjS putative NAD(P)H‑dependent oxidoreductase
?NC_000913 = 912978 54 (0.600)coding (837/1653 nt) hcp hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases
* ? NC_000913 911147 =NA (NA)54 (0.610) 28/266 2.1 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 1207790 =11 (0.120)36 (0.430) 34/252 1.4 83.0% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 5 (0.060)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780512 (0.130)50 (0.600) 46/252 0.7 86.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 5 (0.060)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)73 (0.800) 63/276 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
* ? NC_000913 3720633 =NA (NA)82 (0.870) 70/284 0.2 39.8% noncoding (1/1443 nt) IS150 repeat region
?NC_000913 = 4337579 124 (1.320)coding (351/762 nt) adiY adi system transcriptional activator