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breseq version 0.24 revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
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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 | ||||||||||
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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... | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | REL606 | = 122311 | 55 (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 | = 1036073 | 27 (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 | = 1081217 | 31 (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 | = 1106052 | 31 (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 | = 1854683 | 26 (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 | = 2086451 | 49 (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 | = 2211885 | 48 (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 | = 2574511 | 25 (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 | = 2574511 | 25 (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 | = 3061117 | 31 (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 | = 3203380 | 26 (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 | = 3278116 | 37 (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 | = 3814686 | 62 (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 |