breseq  version 0.24  revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 649,391 T→A 100% I471F (ATC→TTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 683,496 A→C 100% V65G (GTT→GGT)  nagC ← DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine
RA 751,788 G→T 21.3% intergenic (+295/‑552) ybgG → / → cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA 1,329,516 C→T 100% H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC JC 1,733,647 IS150 (–) +3 bp 98.1% coding (683‑685/1413 nt) pykF → pyruvate kinase
RA 2,082,685 G→A 100% A494V (GCT→GTT)  yegI ← hypothetical protein
RA 3,762,741 A→T 100% K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,875,625 +T 100% intergenic (‑59/+294) glmU ← / ← atpC bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
MC JC 3,894,997 Δ6,934 bp 100% IS150‑mediated rbsD[yieO] rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
RA 4,100,655 C→T 100% M192I (ATG→ATA hslU ← ATP‑dependent protease ATP‑binding subunit
RA 4,192,978 G→C 100% intergenic (+146/+147) rrfE → / ← yjaB 5S ribosomal RNA/predicted acetyltransferase
RA 4,266,649 C→A 9.7% intergenic (‑345/‑48) acs ← / → nrfA acetyl‑coenzyme A synthetase/nitrite reductase, formate‑dependent, cytochrome

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 558852 558935 84 18 [16] [16] 18 ECB_00517/appY conserved hypothetical protein/DNA‑binding transcriptional activator
* * ÷ REL606 2330774 2330873 100 18 [17] [17] 18 elaD/yfbL predicted enzyme/putative aminopeptidase; b2271_1
* * ÷ REL606 3022856 3023168 313 18 [17] [14] 20 ECB_02821/ECB_02822 hypothetical protein/bifunctional Ribulose 5‑phosphate reductase/CDP‑ribitol pyrophosphorylase
* * ÷ REL606 3692587 3692708 122 19 [15] [16] 18 yiaY/selB predicted Fe‑containing alcohol dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 12231155 (1.100)9 (0.180) 6/58 NT 15.1% coding (227/855 nt) ampE predicted inner membrane protein
?REL606 1529589 = 46 (0.770)coding (19/1698 nt) sfcA malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
* ? REL606 553366 =10 (0.190)13 (0.250) 6/60 NT 44.1% coding (1526/2817 nt) ECB_00512 putative tail component of prophage
?REL606 4169224 = 23 (0.380)intergenic (+40/‑173) rpoC/htrC DNA‑directed RNA polymerase subunit beta'/heat shock protein
* ? REL606 555924 =0 (0.000)20 (0.380) 18/62 NT 100% coding (1209/2346 nt) ECB_00513 conserved hypothetical protein
?REL606 = 2035093 NA (NA)noncoding (1/768 nt) IS1 repeat region
* ? REL606 632818 =39 (0.760)7 (0.140) 4/60 NT 16.7% coding (17/297 nt) citD citrate lyase, acyl carrier (gamma) subunit
?REL606 1241885 = 31 (0.520)coding (337/1737 nt) ycgO potassium/proton antiporter
* ? REL606 640121 =40 (0.730)7 (0.130) 6/64 NT 16.9% intergenic (+39/+16) cspE/ccrB cold shock protein E/camphor resistance protein CrcB
?REL606 2994081 = 29 (0.480)coding (735/2136 nt) speC ornithine decarboxylase, constitutive
* ? REL606 = 103607327 (0.510)9 (0.170) 7/62 NT 26.9% intergenic (+45/+31) ycbG/ompA hypothetical protein/outer membrane protein A (3a;II*;G;d)
?REL606 = 2540943 22 (0.370)coding (38/1290 nt) uraA uracil transporter
* ? REL606 = 108121731 (0.520)7 (0.120) 6/70 NT 17.9% coding (892/1260 nt) yccE hypothetical protein
?REL606 = 3014302 33 (0.550)coding (883/1137 nt) ECB_02815 Capsule polysaccharide export inner‑membrane protein kpsE
* ? REL606 = 110605231 (0.600)4 (0.080) 4/60 NT 8.5% coding (91/2019 nt) ycdR predicted enzyme associated with biofilm formation
?REL606 3572096 = 55 (0.920)coding (545/1470 nt) yhiP predicted transporter
* ? REL606 1241529 =22 (0.460)4 (0.080) 3/56 NT 16.0% coding (693/1737 nt) ycgO potassium/proton antiporter
?REL606 = 2574504 20 (0.330)intergenic (+346/+472) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 1286705 =33 (0.690)8 (0.170) 4/56 NT 20.8% intergenic (+29/‑154) narI/ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
?REL606 3092577 = 28 (0.470)coding (756/927 nt) yqhG hypothetical protein
* ? REL606 = 185468326 (0.560)5 (0.110) 3/54 NT 14.5% coding (79/255 nt) yoaF conserved outer membrane protein
?REL606 = 4266654 33 (0.550)intergenic (‑350/‑43) acs/nrfA acetyl‑coenzyme A synthetase/nitrite reductase, formate‑dependent, cytochrome
* ? REL606 1946059 =37 (0.720)5 (0.100) 4/60 NT 11.5% coding (149/390 nt) cheY chemotaxis regulator transmitting signal to flagellar motor component
?REL606 = 3240660 40 (0.670)coding (392/1245 nt) mtr tryptophan transporter of high affinity
* ? REL606 = 208645149 (0.950)6 (0.120) 4/60 NT 10.8% intergenic (‑872/‑673) yegL/yegM hypothetical protein/multidrug efflux system, subunit A
?REL606 2752961 = 50 (0.830)coding (1009/2562 nt) mutS DNA mismatch repair protein
* ? REL606 = 221188548 (0.960)3 (0.060) 3/58 NT 4.9% coding (714/1692 nt) fruA fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
?REL606 = 2503593 69 (1.150)coding (13/1044 nt) ypfG hypothetical protein
* ? REL606 2353390 =27 (0.450)5 (0.080) 4/70 NT 17.0% coding (1554/1833 nt) yfbS predicted transporter
?REL606 3424865 = 22 (0.370)intergenic (+83/‑43) nirD/nirC nitrite reductase small subunit/nitrite transporter
* ? REL606 2448493 =23 (0.420)15 (0.270) 3/64 NT 39.5% intergenic (+24/+26) nupC/yfeA nucleoside (except guanosine) transporter/predicted diguanylate cyclase
?REL606 = 2774196 NA (NA)noncoding (1343/1343 nt) IS186 repeat region
* ? REL606 = 257451125 (0.520)6 (0.120) 5/56 NT 15.6% intergenic (+353/+465) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
?REL606 4395051 = 40 (0.670)intergenic (‑126/‑56) yjfO/yjfP hypothetical protein/predicted hydrolase
* ? REL606 = 257451125 (0.540)11 (0.240) 5/54 NT 27.5% intergenic (+353/+465) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
?REL606 4356096 = 33 (0.550)coding (338/537 nt) blc outer membrane lipoprotein (lipocalin)
* ? REL606 2753982 =48 (0.930)4 (0.080) 4/60 NT 8.7% coding (2030/2562 nt) mutS DNA mismatch repair protein
?REL606 = 4141016 36 (0.600)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 = 306111731 (0.600)3 (0.060) 3/60 NT 8.2% coding (752/1173 nt) ECB_02854 conserved hypothetical protein
?REL606 = 4141016 36 (0.600)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 = 320338026 (0.520)6 (0.120) 4/58 NT 16.2% intergenic (+828/+174) yhaC/garK hypothetical protein/glycerate kinase I
?REL606 = 4141016 36 (0.600)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 = 327811637 (0.620)6 (0.100) 6/70 NT 13.8% coding (46/576 nt) yrbK hypothetical protein
?REL606 4541608 = 38 (0.630)intergenic (‑14/‑236) yjiH/kptA conserved inner membrane protein/RNA 2'‑phosphotransferase‑like protein
* ? REL606 3289193 =52 (1.040)6 (0.120) 4/58 NT 12.1% coding (93/930 nt) yhcC predicted Fe‑S oxidoreductase
?REL606 3912273 = 35 (0.580)intergenic (+53/‑87) ilvL/ilvG ilvG operon leader peptide/acetolactate synthase II, valine insensitive, large subunit
* ? REL606 = 381468662 (1.130)6 (0.110) 5/64 NT 8.0% coding (834/1185 nt) emrD multidrug efflux system protein
?REL606 = 4414859 77 (1.280)intergenic (+305/‑4) fklB/cycA FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)/D‑alanine/D‑serine/glycine transporter