breseq  version 0.25c  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 66,457 C→A 100% V32F (GTT→TTT)  araD ← L‑ribulose‑5‑phosphate 4‑epimerase
RA 97,880 C→T 100% S265F (TCC→TTC)  murD → UDP‑N‑acetylmuramoyl‑L‑alanine:D‑glutamate ligase
RA 167,632 C→A 100% P50Q (CCG→CAG)  fhuA → ferrichrome outer membrane transporter
RA 274,547 A→G 100% intergenic (‑206/‑2) insH ← / → mmuP IS5 transposase and trans‑activator/S‑methylmethionine transporter
MC JC 274,733 Δ97,240 bp 100% [mmuP][mhpD] 90 genes
RA 547,694 A→G 100% intergenic (+123/‑1156) fdrA → / → ylbF acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein
RA 547,831 +G 100% intergenic (+260/‑1019) fdrA → / → ylbF acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein
RA 556,858 A→T 100% L36Q (CTG→CAG)  folD ← bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA 569,996 G→C 100% intergenic (+345/‑120) ybcK → / → ybcL recombinase/kinase inhibitor
MC JC 654,214 Δ1,199 bp 100% insH insH
RA 749,354 C→A 100% P17P (CCG→CCT ybgO ← fimbrial‑like adhesin protein
RA 758,440 C→A 100% F110L (TTC→TTA sdhB → succinate dehydrogenase, FeS subunit
RA 887,234 C→A 100% A176A (GCG→GCT ybjJ ← transporter
RA 987,574 G→T 100% intergenic (‑170/+433) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA 1,093,686 T→C 100% V130A (GTA→GCA)  ycdT → diguanylate cyclase
RA 1,097,580 C→T 15.7% intergenic (+329/+226) ycdU → / ← serX inner membrane protein/tRNA‑Ser
RA 1,170,573 C→T 100% intergenic (‑164/‑77) ycfQ ← / → ycfR DNA‑binding transcriptional regulator/hypothetical protein
RA 1,197,797 C→T 2.2% H366H (CAC→CAT icd → isocitrate dehydrogenase,‑specific for NADP+
RA 1,197,809 C→T 1.9% T370T (ACC→ACT icd → isocitrate dehydrogenase,‑specific for NADP+
MC JC 1,301,041 Δ1,336 bp 100% insCinsD insC, insD
RA 1,303,904 A→G 6.7% N337D (AAC→GAC)  oppA → oligopeptide transporter subunit
RA 1,318,876 G→A 100% P21S (CCT→TCT)  trpA ← tryptophan synthase subunit alpha
MC JC 1,413,639 Δ23,060 bp 100% [ydaO]ynaE 30 genes
RA 1,483,588 G→A 100% L322L (CTG→CTA ynbD → phosphatase, inner membrane protein
RA 1,496,775 Δ1 bp 100% coding (11/924 nt) ydcI ← DNA‑binding transcriptional regulator
RA 1,615,814 C→A 100% D202Y (GAC→TAC)  yneI ← aldehyde dehydrogenase
RA 1,669,599 Δ1 bp 100% coding (680/1221 nt) dgsA ← DNA‑binding transcriptional repressor
RA 1,844,073 G→A 100% intergenic (‑224/‑12) ynjH ← / → gdhA hypothetical protein/glutamate dehydrogenase, NADP‑specific
RA 1,918,872 T→A 100% S301T (TCC→ACC)  yebS → inner membrane protein
RA 1,973,476 G→A 100% L310L (CTC→CTT tar ← methyl‑accepting chemotaxis protein II
RA 2,005,401 C→T 100% E115K (GAA→AAA)  fliC ← flagellar filament structural protein
RA 2,170,094 C→A 100% intergenic (‑437/+32) ogrK ← / ← yegR DNA‑binding transcriptional regulator/hypothetical protein
RA 2,178,210 A→C 3.8% intergenic (+179/+183) insH → / ← gatZ IS5 element protein/D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
MC JC 2,320,795 Δ1,336 bp 100% insDinsC insD, insC
RA 2,406,075 C→T 100% V51I (GTT→ATT)  nuoF ← NADH:ubiquinone oxidoreductase, chain F
RA 2,416,102 G→A 100% L233L (CTG→TTG)  yfbS ← transporter
RA 2,538,628 C→T 100% T258T (ACC→ACT cysK → cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
JC 2,865,274 +46 bp 26.7% coding (817/876 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor
JC 2,865,278 +92 bp 19.8% coding (813/876 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor
RA 2,866,111 A→G 100% intergenic (‑21/+159) rpoS ← / ← nlpD RNA polymerase, sigma S (sigma 38) factor/outer membrane lipoprotein
RA 3,003,330 G→A 100% L371L (CTC→CTT ygeV ← DNA‑binding transcriptional regulator
RA 3,049,815 G→T 100% R387S (CGC→AGC)  visC ← oxidoreductase
RA 3,397,813 C→G 100% D141H (GAT→CAT)  yhdE ← hypothetical protein
RA 3,450,056 C→A 63.4% A426S (GCA→TCA)  rpoC ← RNA polymerase, beta prime subunit
RA 3,689,274 G→A 2.4% W187* (TGG→TGA hdfR → DNA‑binding transcriptional regulator
MC JC 3,742,936 Δ1,336 bp 100% insDinsC insD, insC
MC JC 3,746,911 Δ1,199 bp 100% insH insH
RA 3,750,122 Δ1 bp 97.2% coding (365/1416 nt) tnaA ← tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,750,123 C→T 2.5% G122S (GGC→AGC)  tnaA ← tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,898,657 C→G 100% L259V (CTG→GTG)  yiaJ → DNA‑binding transcriptional repressor
MC JC 3,958,123 Δ34 bp 100% coding (1156‑1189/1287 nt) dctA → C4‑dicarboxylic acid, orotate and citrate transporter
RA 4,090,749 A→T 100% Q135L (CAG→CTG)  malQ → 4‑alpha‑glucanotransferase
RA 4,165,991 A→C 100% K43T (AAA→ACA)  rpsL → 30S ribosomal protein S12
MC JC 4,310,363 Δ1,199 bp 100% insH[alsK] insH, [alsK]
RA 4,371,271 Δ2 bp 100% intergenic (‑6/+299) dcuA ← / ← aspA C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA 4,371,467 Δ1 bp 1.9% intergenic (‑202/+104) dcuA ← / ← aspA C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA 4,546,535 T→A 100% intergenic (+296/‑182) fimB → / → fimE tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_007779 1288311–1288375 1288518–1288459 85–208 209 [205] [204] 207 ychS hypothetical protein
* * ÷ NC_007779 2176983–2178181 2178208 28–1226 303 [0] [0] 396 insH insH
* * ÷ NC_007779 3128818–3130002 3147473 17472–18656 207 [204] [0] 245 [yghO]–[yghZ] 19 genes
[yghO], insH, yghQ, yghR, yghS, yghT, pitB, gss, yghU, hybG, hybF, hybE, hybD, hybC, hybB, hybA, hybO, yghW, [yghZ]
* * ÷ NC_007779 3261134–3262332 3262337 6–1204 280 [0] [0] 310 insH–[tdcD] insH, [tdcD]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_007779 273179 =NA (NA)198 (0.760) 118/180 NT 77.0% coding (1109/1146 nt) ykfC hypothetical protein
?NC_007779 657877 = 59 (0.230)coding (164/210 nt) cspE DNA‑binding transcriptional repressor
* ? NC_007779 273211 =NA (NA)4 (0.020) 4/168 NT NA coding (1141/1146 nt) ykfC hypothetical protein
?NC_007779 273281 = NA (NA)intergenic (+65/+44) ykfC/insH hypothetical protein/IS5 transposase and trans‑activator
* ? NC_007779 = 274373NA (NA)156 (0.600) 97/180 NT 72.6% intergenic (‑32/‑176) insH/mmuP IS5 transposase and trans‑activator/S‑methylmethionine transporter
?NC_007779 = 657880 59 (0.230)coding (167/210 nt) cspE DNA‑binding transcriptional repressor
* ? NC_007779 = 274373NA (NA)10 (0.040) 3/180 NT 4.4% intergenic (‑32/‑176) insH/mmuP IS5 transposase and trans‑activator/S‑methylmethionine transporter
?NC_007779 679371 = 218 (0.840)coding (458/555 nt) ybeT outer membrane protein
* ? NC_007779 289856 =NA (NA)177 (1.080) 86/114 NT 100% intergenic (‑327/+17) argF/insB ornithine carbamoyltransferase 2, chain F/IS1 transposase InsAB'
?NC_007779 = 2176982 0 (0.000)intergenic (‑281/‑69) gatB/insH PTS system galactitol‑specific transporter subunit IIB/IS5 element protein
* ? NC_007779 380484 =NA (NA)288 (1.110) 136/180 NT NA intergenic (‑418/‑46) yaiO/insC hypothetical protein/IS2 insertion element repressor InsA
?NC_007779 = 381407 NA (NA)coding (510/906 nt) insD IS2 insertion element transposase InsAB'
* ? NC_007779 381401 =NA (NA)256 (1.010) 125/176 NT NA coding (504/906 nt) insD IS2 insertion element transposase InsAB'
?NC_007779 = 381812 NA (NA)coding (303/387 nt) yaiF hypothetical protein
* ? NC_007779 = 608570NA (NA)206 (0.820) 120/174 NT 75.5% intergenic (+170/+112) insL/entD IS186/IS421 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
?NC_007779 1305025 = 69 (0.270)coding (413/921 nt) oppB oligopeptide transporter subunit
* ? NC_007779 1209367 =196 (0.760)27 (0.130) 26/148 NT 14.1% coding (290/630 nt) ycfK hypothetical protein
?NC_007779 1211196 = 168 (0.790)intergenic (‑500/‑66) tfaE/pin tail fiber assembly protein/site‑specific DNA recombinase
* ? NC_007779 = 1209382190 (0.730)33 (0.150) 31/148 NT 16.9% coding (305/630 nt) ycfK hypothetical protein
?NC_007779 = 1211179 168 (0.790)intergenic (‑483/‑83) tfaE/pin tail fiber assembly protein/site‑specific DNA recombinase
* ? NC_007779 1221489 =3 (0.010)229 (0.900) 123/176 NT 98.7% intergenic (+711/+2393) ymgF/ymgD hypothetical protein/hypothetical protein
?NC_007779 1301041 = NA (NA)intergenic (+219/‑89) ychE/insC inner membrane protein/IS2 element protein
* ? NC_007779 = 12214950 (0.000)216 (0.830) 125/180 NT 100% intergenic (+717/+2387) ymgF/ymgD hypothetical protein/hypothetical protein
?NC_007779 = 1302369 NA (NA)intergenic (+11/‑527) insD/oppA IS2 element protein/oligopeptide transporter subunit
* ? NC_007779 = 130503768 (0.260)190 (0.770) 109/172 NT 74.5% coding (425/921 nt) oppB oligopeptide transporter subunit
?NC_007779 2519723 = NA (NA)intergenic (+33/‑54) nupC/insL nucleoside (except guanosine) transporter/transposase
* ? NC_007779 1397758 =NA (NA)240 (0.930) 122/180 NT 99.6% intergenic (‑122/‑32) ynaI/insH inner membrane protein/IS5 transposase and trans‑activator
?NC_007779 1672777 = 1 (0.000)intergenic (+111/‑313) ynfM/asr transporter/acid shock‑inducible periplasmic protein
* ? NC_007779 = 16727801 (0.000)250 (0.960) 124/180 NT 99.6% intergenic (+114/‑310) ynfM/asr transporter/acid shock‑inducible periplasmic protein
?NC_007779 1980209 = NA (NA)intergenic (‑289/+146) flhD/insH DNA‑binding transcriptional dual regulator/IS5 element protein
* ? NC_007779 1907280 =13 (0.050)213 (0.820) 119/180 NT 94.2% intergenic (+307/‑122) yobD/yebN inner membrane protein/inner membrane protein
?NC_007779 = 2412225 NA (NA)intergenic (‑55/‑782) insA/yfbQ IS1 element protein/aminotransferase
* ? NC_007779 = 19072887 (0.030)239 (0.920) 121/180 NT 97.2% intergenic (+315/‑114) yobD/yebN inner membrane protein/inner membrane protein
?NC_007779 2411458 = NA (NA)intergenic (‑147/+15) lrhA/insB DNA‑binding transcriptional repressor/IS1 element protein
* ? NC_007779 1980091 =1 (0.000)185 (0.710) 102/180 NT 99.5% intergenic (‑171/+264) flhD/insH DNA‑binding transcriptional dual regulator/IS5 element protein
?NC_007779 1980209 = NA (NA)intergenic (‑289/+146) flhD/insH DNA‑binding transcriptional dual regulator/IS5 element protein
* ? NC_007779 = 19800950 (0.000)261 (1.020) 126/178 NT 100% intergenic (‑175/+260) flhD/insH DNA‑binding transcriptional dual regulator/IS5 element protein
?NC_007779 2176984 = NA (NA)intergenic (‑283/‑67) gatB/insH PTS system galactitol‑specific transporter subunit IIB/IS5 element protein
* ? NC_007779 2178209 =0 (0.000)279 (1.080) 141/180 NT 100% intergenic (+178/+184) insH/gatZ IS5 element protein/D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
?NC_007779 = 2412225 NA (NA)intergenic (‑55/‑782) insA/yfbQ IS1 element protein/aminotransferase
* ? NC_007779 2320794 =NA (NA)214 (0.830) 105/180 NT 100% intergenic (+633/+11) rcsB/insD DNA‑binding response regulator in two‑component regulatory system with RcsC and YojN/IS2 element protein
?NC_007779 = 2589834 0 (0.000)intergenic (+470/‑69) acrD/yffB aminoglycoside/multidrug efflux system/hypothetical protein
* ? NC_007779 = 2322124NA (NA)285 (1.100) 141/180 NT 100% intergenic (‑91/‑2589) insC/atoS IS2 element protein/sensory histidine kinase in two‑component regulatory system with AtoC
?NC_007779 2589830 = 0 (0.000)intergenic (+466/‑73) acrD/yffB aminoglycoside/multidrug efflux system/hypothetical protein
* ? NC_007779 2411458 =NA (NA)6 (0.020) 6/180 NT 2.6% intergenic (‑147/+15) lrhA/insB DNA‑binding transcriptional repressor/IS1 element protein
?NC_007779 = 2643578 228 (0.880)intergenic (‑58/+91) ndk/pbpC multifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase/fused transglycosylase and transpeptidase
* ? NC_007779 2411458 =NA (NA)272 (1.050) 132/180 NT 96.5% intergenic (‑147/+15) lrhA/insB DNA‑binding transcriptional repressor/IS1 element protein
?NC_007779 = 2985055 10 (0.040)coding (553/1230 nt) yqeG transporter
* ? NC_007779 2411459 =NA (NA)29 (0.110) 26/178 NT 11.0% intergenic (‑148/+14) lrhA/insB DNA‑binding transcriptional repressor/IS1 element protein
?NC_007779 = 2941347 238 (0.920)intergenic (‑124/+227) gcvA/ygdI DNA‑binding transcriptional dual regulator/hypothetical protein
* ? NC_007779 = 2412225NA (NA)3 (0.010) 3/180 NT 1.3% intergenic (‑55/‑782) insA/yfbQ IS1 element protein/aminotransferase
?NC_007779 2643570 = 225 (0.870)intergenic (‑50/+99) ndk/pbpC multifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase/fused transglycosylase and transpeptidase
* ? NC_007779 = 2412225NA (NA)33 (0.130) 29/180 NT 12.0% intergenic (‑55/‑782) insA/yfbQ IS1 element protein/aminotransferase
?NC_007779 2941338 = 243 (0.940)intergenic (‑115/+236) gcvA/ygdI DNA‑binding transcriptional dual regulator/hypothetical protein
* ? NC_007779 = 2412225NA (NA)221 (0.850) 114/180 NT 95.3% intergenic (‑55/‑782) insA/yfbQ IS1 element protein/aminotransferase
?NC_007779 2985047 = 11 (0.040)coding (545/1230 nt) yqeG transporter
* ? NC_007779 3147474 =0 (0.000)226 (0.870) 128/180 NT 100% coding (922/1041 nt) yghZ aldo‑keto reductase
?NC_007779 = 3262328 NA (NA)coding (1188/1296 nt) tdcD propionate kinase/acetate kinase C, anaerobic
* ? NC_007779 = 3186081NA (NA)228 (0.890) 123/178 NT 87.5% coding (26/2466 nt) yqiG outer membrane usher protein
?NC_007779 3512753 = 33 (0.130)coding (529/1026 nt) cytR DNA‑binding transcriptional dual regulator
* ? NC_007779 = 32611330 (0.000)247 (1.020) 123/168 NT 100% intergenic (‑59/‑69) tdcE/insH pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase/IS5 element protein
?NC_007779 = 3748109 NA (NA)intergenic (+150/+962) insH/tnaA IS5 element protein/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
* ? NC_007779 3261134 =NA (NA)221 (0.850) 113/180 NT 100% intergenic (‑60/‑68) tdcE/insH pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase/IS5 element protein
?NC_007779 3265774 = 0 (0.000)coding (110/990 nt) tdcB catabolic threonine dehydratase, PLP‑dependent
* ? NC_007779 3261135 =NA (NA)255 (1.000) 130/178 NT 100% intergenic (‑61/‑67) tdcE/insH pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase/IS5 element protein
?NC_007779 3262338 = 0 (0.000)coding (1178/1296 nt) tdcD propionate kinase/acetate kinase C, anaerobic
* ? NC_007779 = 32657770 (0.000)276 (1.070) 134/180 NT 100% coding (107/990 nt) tdcB catabolic threonine dehydratase, PLP‑dependent
?NC_007779 3365411 = NA (NA)intergenic (+368/+146) yhcD/insH outer membrane protein/IS5 transposase and trans‑activator
* ? NC_007779 = 351275932 (0.120)230 (0.900) 120/178 NT 87.9% coding (535/1026 nt) cytR DNA‑binding transcriptional dual regulator
?NC_007779 = 3744262 NA (NA)intergenic (‑90/+31) insC/yidZ IS2 element protein/DNA‑binding transcriptional regulator
* ? NC_007779 = 3744263NA (NA)235 (0.910) 123/180 NT 100% intergenic (‑91/+30) insC/yidZ IS2 element protein/DNA‑binding transcriptional regulator
?NC_007779 3903274 = 0 (0.000)coding (37/825 nt) bax hypothetical protein
* ? NC_007779 3746911 =NA (NA)290 (1.120) 126/180 NT 100% intergenic (‑509/‑68) mdtL/insH multidrug efflux system protein/IS5 element protein
?NC_007779 = 3748646 0 (0.000)intergenic (+687/+425) insH/tnaA IS5 element protein/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
* ? NC_007779 = 3748105NA (NA)277 (1.070) 145/180 NT 100% intergenic (+146/+966) insH/tnaA IS5 element protein/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
?NC_007779 3748643 = 0 (0.000)intergenic (+684/+428) insH/tnaA IS5 element protein/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
* ? NC_007779 = 37505900 (0.000)250 (1.010) 123/172 NT 100% intergenic (‑104/‑69) tnaA/insH tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/IS5 element protein
?NC_007779 3751790 = 0 (0.000)intergenic (+151/+116) insH/tnaC IS5 element protein/tryptophanase leader peptide
* ? NC_007779 = 39032793 (0.010)275 (1.070) 141/178 NT 98.9% coding (42/825 nt) bax hypothetical protein
?NC_007779 = 4504190 NA (NA)intergenic (+10/‑89) insD/yjgW IS2 insertion element transposase InsAB'/hypothetical protein
* ? NC_007779 3987186 =NA (NA)265 (1.030) 135/178 NT 100% intergenic (‑732/‑31) slp/insH outer membrane lipoprotein/IS5 transposase and trans‑activator
?NC_007779 = 4009203 0 (0.000)coding (1379/1623 nt) yhiJ hypothetical protein
* ? NC_007779 = 3988379NA (NA)283 (1.090) 143/180 NT 100% coding (746/783 nt) yhiS hypothetical protein
?NC_007779 4009199 = 0 (0.000)coding (1375/1623 nt) yhiJ hypothetical protein
* ? NC_007779 4310363 =NA (NA)255 (0.980) 131/180 NT 100% intergenic (‑287/‑68) yjcS/insH alkyl sulfatase/IS5 element protein
?NC_007779 4353540 = 0 (0.000)intergenic (‑118/+453) dcuB/dcuR C4‑dicarboxylate antiporter/DNA‑binding response regulator in two‑component regulatory system with DcuS
* ? NC_007779 = 4311557NA (NA)273 (1.050) 135/180 NT 100% coding (921/1029 nt) alsK D‑allose kinase
?NC_007779 = 4353543 0 (0.000)intergenic (‑121/+450) dcuB/dcuR C4‑dicarboxylate antiporter/DNA‑binding response regulator in two‑component regulatory system with DcuS
* ? NC_007779 4355060 =1 (0.000)280 (1.080) 138/180 NT 99.6% coding (1281/1632 nt) dcuS sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
?NC_007779 4502861 = NA (NA)intergenic (+241/‑46) intB/insC integrase/IS2 insertion element repressor InsA
* ? NC_007779 = 43550664 (0.020)228 (0.900) 130/176 NT 98.3% coding (1275/1632 nt) dcuS sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
?NC_007779 = 4504189 NA (NA)intergenic (+9/‑90) insD/yjgW IS2 insertion element transposase InsAB'/hypothetical protein