breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 124,447 G→A 5.5% P477P (CCG→CCA aceE → pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA 128,803 G→A 5.9% D298N (GAC→AAC)  lpd → dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 287,437 T→A 5.2% S217T (TCC→ACC)  yagH → CP4‑6 prophage; putative xylosidase/arabinosidase
RA 399,993 C→A 11.0% V311L (GTG→TTG)  ddlA ← D‑alanine‑D‑alanine ligase A
RA 420,941 T→A 5.2% intergenic (+31/‑45) brnQ → / → proY branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA 420,942 G→T 5.1% intergenic (+32/‑44) brnQ → / → proY branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA 420,945 A→C 5.9% intergenic (+35/‑41) brnQ → / → proY branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA 420,946 T→A 5.3% intergenic (+36/‑40) brnQ → / → proY branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA 460,110 A→G 6.1% Q408R (CAG→CGG)  lon → DNA‑binding ATP‑dependent protease La
RA 514,229 C→T 5.7% D79D (GAC→GAT cueR → copper‑responsive regulon transcriptional regulator
RA 725,523 T→A 6.0% Q505L (CAG→CTG)  kdpB ← potassium translocating ATPase, subunit B
RA 894,627 A→G 5.2% M282V (ATG→GTG)  potF → putrescine ABC transporter periplasmic binding protein
RA 894,952 T→A 5.1% intergenic (+56/‑39) potF → / → potG putrescine ABC transporter periplasmic binding protein/putrescine ABC transporter ATPase
RA 911,690 A→G 6.0% V154A (GTT→GCT)  hcr ← HCP oxidoreductase, NADH‑dependent
RA 1,019,626 A→T 5.6% V143D (GTC→GAC)  ompA ← outer membrane protein A (3a;II*;G;d)
RA 1,032,082 T→C 5.5% intergenic (‑370/‑57) serT ← / → hyaA tRNA‑Ser/hydrogenase 1, small subunit
RA 1,053,860 Δ1 bp 7.2% coding (2319/2745 nt) torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,065,890 G→A 7.1% P102P (CCG→CCA agp → glucose‑1‑phosphatase/inositol phosphatase
RA 1,072,982 C→T 5.8% E344K (GAA→AAA)  rutA ← pyrimidine oxygenase, FMN‑dependent
RA 1,073,609 G→T 5.5% L135I (CTC→ATC)  rutA ← pyrimidine oxygenase, FMN‑dependent
RA 1,137,952 C→T 5.5% G194G (GGC→GGT flgJ → flagellar rod assembly protein and murein hydrolase; flagellum‑specific muramidase
RA 1,183,782 C→T 5.1% A221A (GCG→GCA potB ← spermidine/putrescine ABC transporter permease
RA 1,339,336 T→C 5.0% S3P (TCG→CCG)  pgpB → phosphatidylglycerophosphatase B
RA 1,377,597 G→A 5.0% A256T (GCA→ACA)  ycjS → putative NADH‑binding oxidoreductase
RA 1,395,089 G→T 6.0% F278L (TTC→TTA) ‡ ynaI ← mechanosensitive channel protein, very small conductance
RA 1,395,091 A→T 6.2% F278I (TTC→ATC) ‡ ynaI ← mechanosensitive channel protein, very small conductance
RA 1,395,094 A→C 5.5% Y277D (TAT→GAT)  ynaI ← mechanosensitive channel protein, very small conductance
RA 1,396,083 T→A 6.1% V3D (GTC→GAC)  insH1 → IS5 transposase and trans‑activator
RA 1,413,829 G→A 5.6% C33C (TGC→TGT ralR ← Rac prophage; restriction alleviation protein
RA 1,662,350 C→T 100% P599S (CCC→TCC)  ynfF → S‑ and N‑oxide reductase, A subunit, periplasmic
RA 1,708,805 T→A 30.1% R629R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,765,160 C→G 5.8% intergenic (‑38/+62) ydiH ← / ← menI uncharacterized protein/1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase
RA 1,806,340 C→T 100% intergenic (‑257/‑30) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA 1,806,700 G→A 100% A111T (GCG→ACG)  pfkB → 6‑phosphofructokinase II
RA 1,864,997 C→T 5.3% E214K (GAA→AAA)  yeaE ← aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA 1,869,015 C→T 6.0% R21C (CGT→TGT)  yeaH → UPF0229 family protein
RA 1,963,048 T→C 5.2% Q668R (CAG→CGG)  flhA ← putative flagellar export pore protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 1,985,112 C→G 5.6% intergenic (‑43/+27) araG ← / ← araF L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA 2,148,023 G→A 7.1% G117D (GGC→GAC)  yegD → Hsp70 chaperone family protein
RA 2,149,510 T→C 5.9% E492E (GAA→GAG yegI ← protein kinase‑related putative non‑specific DNA‑binding protein
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 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 2,189,705 A→G 5.3% D402D (GAT→GAC yehB ← putative outer membrane protein
RA 2,248,399 T→A 5.5% Q45L (CAG→CTG)  lysP ← lysine transporter
RA 2,273,931 T→A 5.3% I523N (ATC→AAC)  yejA → microcin C ABC transporter periplasmic binding protein
RA 2,342,538 G→C 5.7% G544G (GGC→GGG yfaL ← adhesin
RA 2,357,653 A→G 6.5% L250L (CTA→CTG yfaD → transposase_31 family protein
RA 2,357,836 G→A 7.0% pseudogene (33/198 nt) ypaA → pseudogene, C‑terminal fragment, Transposase_31 family
RA 2,486,190 A→G 5.8% E606G (GAA→GGA)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA 2,586,450 C→A 6.1% L240L (CTC→CTA narQ → sensory histidine kinase in two‑component regulatory system with NarP
RA 2,596,873 Δ1 bp 5.1% intergenic (‑136/+32) ypfJ ← / ← purC putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA 2,596,878:1 +G 5.3% intergenic (‑141/+27) ypfJ ← / ← purC putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA 2,616,314 A→G 5.8% Q74R (CAA→CGA)  bepA → OM protein maintenance and assembly metalloprotease and chaperone, periplasmic
RA 2,649,275 C→T 5.5% A1005T (GCA→ACA)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,656,820 C→G 5.9% Q88H (CAG→CAC fdx ← [2Fe‑2S] ferredoxin
RA 2,662,549 A→G 5.3% intergenic (‑418/+34) iscR ← / ← trmJ isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
RA 2,662,550 A→C 5.0% intergenic (‑419/+33) iscR ← / ← trmJ isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
RA 2,662,556 A→G 5.1% intergenic (‑425/+27) iscR ← / ← trmJ isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
RA 2,662,560 C→T 7.8% intergenic (‑429/+23) iscR ← / ← trmJ isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
RA 2,691,173 A→T 7.1% noncoding (168/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,932,437 C→T 5.3% G193S (GGT→AGT)  fucO ← L‑1,2‑propanediol oxidoreductase
RA 2,962,391 A→G 5.5% L13P (CTG→CCG)  recC ← exonuclease V (RecBCD complex), gamma chain
RA 2,984,802 G→A 7.4% A264V (GCA→GTA)  yqeF ← short chain acyltransferase
RA 3,154,675 T→A 5.1% I182F (ATC→TTC)  yqhC ← transcriptional activator of yqhD
RA 3,183,345:1 +T 5.7% intergenic (+22/+468) zupT → / ← ribB zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA 3,183,350 Δ1 bp 5.7% intergenic (+27/+463) zupT → / ← ribB zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA 3,270,193 C→T 6.7% intergenic (+591/+23) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,194 G→T 9.3% intergenic (+592/+22) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,195 A→C 7.3% intergenic (+593/+21) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,196 A→G 6.0% intergenic (+594/+20) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,386,794 G→C 6.3% T465T (ACC→ACG aaeB ← p‑hydroxybenzoic acid efflux system component
RA 3,560,455:1 +G 100% 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
JC JC 3,560,930 IS5 (+) +4 bp 100% coding (520‑523/831 nt) glpG ← rhomboid intramembrane serine protease
RA 3,663,547 T→C 5.4% intergenic (+20/+343) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,663,553 A→C 5.3% intergenic (+26/+337) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,663,555 G→T 5.6% intergenic (+28/+335) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,663,556 A→C 5.5% intergenic (+29/+334) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,663,558 G→T 5.3% intergenic (+31/+332) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,663,564 G→A 5.4% intergenic (+37/+326) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,691,089 G→T 5.2% Q507K (CAG→AAG)  bcsB ← regulator of cellulose synthase, cyclic di‑GMP binding
RA 3,864,621 A→T 5.4% S551R (AGT→AGA yidE ← putative transporter
RA 3,959,515 T→A 7.8% intergenic (+70/+17) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 4,187,214 A→C 100% D622A (GAC→GCC)  rpoC → RNA polymerase, beta prime subunit
RA 4,195,080 A→G 7.0% Y340Y (TAT→TAC thiC ← phosphomethylpyrimidine synthase
RA 4,296,060 C→T 34.5% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,303,758 A→G 5.3% S118P (TCG→CCG)  mdtN ← membrane fusion protein of efflux pump
RA 4,426,592 T→A 7.0% intergenic (+35/+36) rplI → / ← yjfZ 50S ribosomal subunit protein L9/uncharacterized protein
RA 4,606,239 A→G 25.0% noncoding (48/87 nt) leuP ← tRNA‑Leu

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423764–3424234 3424573–3424238 5–810 35 [29] [30] 31 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107539 4108512 974 31 [30] [29] 31 [pfkA] [pfkA]
* * ÷ NC_000913 4144034 4147099 3066 32 [30] [30] 31 [pflD]–[pflC] [pflD],[pflC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 212286 =73 (0.890)4 (0.050) 4/250 NT 5.6% intergenic (+20/‑45) yaeR/tilS putative lyase/tRNA(Ile)‑lysidine synthetase
?NC_000913 212307 = 66 (0.850)intergenic (+41/‑24) yaeR/tilS putative lyase/tRNA(Ile)‑lysidine synthetase
* ? NC_000913 274347 =NA (NA)4 (0.050) 4/250 NT NA noncoding (803/1195 nt) IS5 repeat region
?NC_000913 274410 = NA (NA)noncoding (740/1195 nt) IS5 repeat region
* ? NC_000913 1097172 =NA (NA)5 (0.060) 5/258 NT 13.4% intergenic (+343/+393) ycdU/serX putative inner membrane protein/tRNA‑Ser
?NC_000913 1097188 = 33 (0.400)intergenic (+359/+377) ycdU/serX putative inner membrane protein/tRNA‑Ser
* ? NC_000913 1207790 =49 (0.600)28 (0.390) 27/232 NT 41.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 37 (0.510)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780549 (0.600)29 (0.400) 26/232 NT 42.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 37 (0.510)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)98 (1.230) 75/256 NT 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 2035286 =71 (0.860)4 (0.050) 4/240 NT 5.9% intergenic (+43/‑549) yedS/hchA pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone
?NC_000913 2035318 = 64 (0.860)intergenic (+75/‑517) yedS/hchA pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone
* ? NC_000913 = 228374043 (0.520)4 (0.050) 4/250 NT 8.9% coding (208/1008 nt) yejK spermidine nucleoid‑associated protein
?NC_000913 = 2283746 41 (0.530)coding (202/1008 nt) yejK spermidine nucleoid‑associated protein
* ? NC_000913 = 251807238 (0.460)5 (0.060) 4/262 NT 10.2% noncoding (45/76 nt) alaX tRNA‑Ala
?NC_000913 = 2518206 50 (0.610)noncoding (26/76 nt) alaW tRNA‑Ala
* ? NC_000913 = 27262050 (0.000)3 (0.040) 3/252 NT 100% intergenic (‑17/+76) rrfG/rrlG 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
?NC_000913 = 2726217 NA (NA)intergenic (‑29/+64) rrfG/rrlG 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
* ? NC_000913 = 285563375 (0.910)5 (0.060) 3/248 NT 6.6% coding (1296/2079 nt) fhlA formate hydrogenlyase transcriptional activator
?NC_000913 = 2855651 71 (0.920)coding (1314/2079 nt) fhlA formate hydrogenlyase transcriptional activator
* ? NC_000913 3261397 =78 (0.950)4 (0.050) 3/256 NT 5.0% coding (1022/2295 nt) tdcE pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
?NC_000913 3261423 = 75 (0.940)coding (996/2295 nt) tdcE pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
* ? NC_000913 3423376 =96 (1.170)11 (0.140)
+TTGATGT
5/250 NT 11.9% intergenic (+182/+47) yhdZ/rrfF putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
?NC_000913 3423672 = 76 (0.920)noncoding (116/120 nt) rrfD 5S ribosomal RNA of rrnD operon
* ? NC_000913 3427078 =NA (NA)3 (0.040) 3/246 NT 100% noncoding (75/77 nt) ileU tRNA‑Ile
?NC_000913 = 4037236 0 (0.000)intergenic (+19/‑24) ileT/alaT tRNA‑Ile/tRNA‑Ala
* ? NC_000913 3650712 =NA (NA)3 (0.040) 3/250 NT NA noncoding (1/100 nt) RIP262 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP262 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
?NC_000913 3650744 = NA (NA)noncoding (33/100 nt) RIP262 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP262 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
* ? NC_000913 3832178 =NA (NA)3 (0.040) 3/244 NT NA noncoding (1/27 nt) REP277 (repetitive extragenic palindromic) element; contains 1 REP sequences REP277 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 3832205 = NA (NA)intergenic (+39/+14) yicH/yicI putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
* ? NC_000913 = 387611195 (1.150)5 (0.070) 5/244 NT 5.4% intergenic (+17/+29) yidX/yidA putative lipoprotein/sugar phosphate phosphatase
?NC_000913 = 3876122 88 (1.160)intergenic (+28/+18) yidX/yidA putative lipoprotein/sugar phosphate phosphatase
* ? NC_000913 3898629 =NA (NA)3 (0.040) 3/248 NT NA intergenic (+20/+42) cbrC/yieK UPF0167 family protein/putative 6‑phosphogluconolactonase
?NC_000913 3898659 = NA (NA)intergenic (+50/+12) cbrC/yieK UPF0167 family protein/putative 6‑phosphogluconolactonase
* ? NC_000913 = 398661486 (1.040)5 (0.070) 5/242 NT 5.8% noncoding (183/207 nt) glmZ sRNA antisense activator of glmS mRNA, Hfq‑dependent
?NC_000913 = 3986622 83 (1.100)noncoding (191/207 nt) glmZ sRNA antisense activator of glmS mRNA, Hfq‑dependent
* ? NC_000913 = 404068369 (0.840)9 (0.110) 4/260 NT 9.7% intergenic (+47/+223) rrfA/mobB 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
?NC_000913 = 4213162 100 (1.230)intergenic (+3/‑72) rrfE/yjaA 5S ribosomal RNA of rrnE operon/stress‑induced protein
* ? NC_000913 = 416834146 (0.560)3 (0.040) 3/244 NT 7.1% intergenic (+141/‑31) rrsB/gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
?NC_000913 = 4168363 36 (0.470)intergenic (+163/‑9) rrsB/gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
* ? NC_000913 4200145 =78 (0.950)4 (0.050) 3/242 NT 5.2% intergenic (+51/‑136) yjaG/hupA DUF416 domain protein/HU, DNA‑binding transcriptional regulator, alpha subunit
?NC_000913 4200182 = 75 (0.990)intergenic (+88/‑99) yjaG/hupA DUF416 domain protein/HU, DNA‑binding transcriptional regulator, alpha subunit