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
RA 37,693 A→C N44K (AAT→AAG caiC ← putative crotonobetaine/carnitine‑CoA ligase
RA 100,657 T→G I338M (ATT→ATG murG → N‑acetylglucosaminyl transferase
JC 111,028 +46 bp intergenic (+44/‑16) secA → / → mutT preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA 140,169 T→G T353P (ACC→CCC)  gcd ← glucose dehydrogenase
RA 146,136 T→G F352L (TTT→TTG yadE → putative polysaccharide deacetylase lipoprotein
MC JC 257,908 Δ776 bp [crl] [crl]
RA 522,892 A→C intergenic (+62/‑369) ybbP → / → rhsD putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 532,886 A→C N146H (AAC→CAC)  allA → ureidoglycolate lyase, releasing urea
RA 707,238 T→G F382L (TTT→TTG glnS → glutamyl‑tRNA synthetase
RA 943,261 T→G L768R (CTG→CGG)  dmsA → dimethyl sulfoxide reductase, anaerobic, subunit A
RA 1,343,574 T→G intergenic (‑246/+23) osmB ← / ← yciT osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family
RA 1,356,671 T→G Y147S (TAC→TCC)  sapA ← antimicrobial peptide transport ABC transporter periplasmic binding protein
JC JC 1,425,236 IS5 (–) +4 bp coding (1455‑1458/1458 nt) trkG → Rac prophage; potassium transporter subunit
RA 1,502,324 T→G intergenic (+169/‑133) tehB → / → ydcL tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein/lipoprotein
RA 1,583,769 T→G Q64P (CAA→CCA)  safA ← two‑component system connector membrane protein, EvgSA to PhoQP
RA 1,614,214 T→G N164H (AAT→CAT)  sad ← succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA 1,756,083 T→C L129P (CTG→CCG)  pykF → pyruvate kinase I
RA 1,821,514 T→G I36L (ATT→CTT)  chbB ← N,N'‑diacetylchitobiose‑specific enzyme IIB component of PTS
RA 1,903,203 T→G I41S (ATC→AGC)  manY → mannose‑specific enzyme IIC component of PTS
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
RA 2,085,510 A→C L6V (TTA→GTA)  yeeE ← UPF0394 family inner membrane protein
RA 2,133,868 A→C A595A (GCT→GCG wzc ← colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
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 2,173,468 A→C pseudogene (811/914 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,343,454 T→G Y239S (TAT→TCT)  yfaL ← adhesin
RA 2,406,260 A→C L128V (TTA→GTA)  lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes
RA 2,495,641 A→C intergenic (‑349/‑4) yfdY ← / → lpxP DUF2545 family putative inner membrane protein/palmitoleoyl‑acyl carrier protein (ACP)‑dependent acyltransferase
RA 2,511,580 A→C L376W (TTG→TGG)  mntH ← manganese/divalent cation transporter
RA 2,583,262 T→G N73H (AAT→CAT)  nudK ← GDP‑mannose pyrophosphatase
RA 2,591,492 A→C L82F (TTA→TTC yffB → putative ArsC family reductase
RA 2,751,315 T→G F162C (TTC→TGC)  nadK → NAD kinase
RA 2,828,281 T→G L182R (CTG→CGG)  srlD → sorbitol‑6‑phosphate dehydrogenase
RA 3,000,850 A→C Q169P (CAG→CCG)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
RA 3,021,392 T→G L26W (TTG→TGG)  xdhD → putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA 3,067,245 T→G intergenic (‑72/+95) ygfI ← / ← yggE putative DNA‑binding transcriptional regulator/oxidative stress defense protein
RA 3,378,200 T→G E3A (GAA→GCA)  rpsI ← 30S ribosomal subunit protein S9
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 3,927,462 A→C E103A (GAA→GCA)  asnA → asparagine synthetase A
RA 3,989,853 T→G E305A (GAA→GCA)  hemC ← hydroxymethylbilane synthase
RA 4,032,395 A→C E412A (GAA→GCA)  pepQ → proline dipeptidase
RA 4,153,955 A→C L298R (CTG→CGG)  argE ← acetylornithine deacetylase
RA 4,180,393 A→C E133A (GAA→GCA)  rplJ → 50S ribosomal subunit protein L10
RA 4,182,313 A→C N357H (AAC→CAC)  rpoB → RNA polymerase, beta subunit
RA 4,187,214 A→T D622V (GAC→GTC)  rpoC → RNA polymerase, beta prime subunit
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,586,506 A→C L86V (TTA→GTA)  hsdR ← endonuclease R Type I restriction enzyme
RA 4,609,163 T→G M173R (ATG→AGG)  yjjG → dUMP phosphatase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423693–3424234 3424588–3424238 5–896 38 [35] [37] 38 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =6 (0.080)50 (0.770) 42/266 1.0 87.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 9 (0.140)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078056 (0.080)55 (0.850) 43/266 0.9 88.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 9 (0.140)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)64 (0.910) 54/290 0.5 100% 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