breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
---|---|---|---|---|---|
evidence | position | mutation | annotation | gene | description |
RA | 278,744 | +A | intergenic (‑239/+75) | PP_0224 ← / ← sctC | Monooxygenase, DszC family/sulfur compound ABC transporter ‑ ATP‑binding subunit |
RA | 307,866 | +C | intergenic (+881/‑988) | hslO → / → PP_0254 | 33 kDa chaperonin/conserved protein of unknown function |
RA | 336,125 | +T | coding (210/237 nt) | PP_0278 → | conserved protein of unknown function |
RA | 353,067 | A→G | intergenic (+34/+84) | hisF → / ← cbcV | Imidazole glycerol phosphate synthase subunit HisF/choline / betaine / carnitine ABC transporter ‑ ATP binding subunit |
RA | 499,203 | A→G | intergenic (+47/‑249) | uhpA → / → PP_0411 | DNA‑binding response regulator UhpA/Polyamine ABC transporter, ATP‑binding protein |
RA | 1,070,248 | +GA | intergenic (+48/+94) | aroP‑I → / ← PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger related‑protein |
RA | 1,126,647 | +C | intergenic (‑101/+48) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
RA | 1,419,549 | +C | intergenic (‑38/+98) | PP_1242 ← / ← PP_1244 | conserved protein of unknown function/conserved protein of unknown function |
RA | 1,499,480 | 2 bp→AC | intergenic (+57/‑106) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
RA | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
RA | 1,499,508 | +C | intergenic (+85/‑79) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
RA | 1,932,640 | +C | intergenic (‑107/+43) | rluA ← / ← minE | 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor |
RA | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/Transcriptional regulator, LysR family |
RA | 3,951,159 | T→C | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
RA | 3,951,161 | A→T | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
RA | 4,586,030 | 2 bp→TC | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
RA | 4,586,035 | +G | intergenic (+118/+97) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
RA | 4,586,057 | +C | intergenic (+140/+75) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
RA | 4,740,811 | (T)7→6 | intergenic (+48/+705) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,740,816 | T→G | intergenic (+53/+700) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,740,819 | 2 bp→CT | intergenic (+56/+696) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,229 | A→C | intergenic (+466/+287) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,231 | C→G | intergenic (+468/+285) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,234 | C→T | intergenic (+471/+282) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,236 | 2 bp→TG | intergenic (+473/+279) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,239 | A→G | intergenic (+476/+277) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,243 | 3 bp→TGC | intergenic (+480/+271) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,255 | C→T | intergenic (+492/+261) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,257 | A→C | intergenic (+494/+259) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,260 | 2 bp→GC | intergenic (+497/+255) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,263 | A→C | intergenic (+500/+253) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,272 | A→G | intergenic (+509/+244) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,274 | A→C | intergenic (+511/+242) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,276 | G→C | intergenic (+513/+240) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,278 | C→T | intergenic (+515/+238) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,283 | +T | intergenic (+520/+233) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,289 | C→G | intergenic (+526/+227) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,292 | C→T | intergenic (+529/+224) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,294 | C→G | intergenic (+531/+222) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,296 | A→C | intergenic (+533/+220) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
RA | 4,741,298 | C→T | intergenic (+535/+218) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
JC | 4,980,585 | +GGC | intergenic (‑24/+44) | PP_4387 ← / ← flgE | conserved exported protein of unknown function/Flagellar hook protein FlgE |
JC | 5,555,608 | +GCC | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer |
RA | 5,674,751 | +G | intergenic (+113/+27) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
RA | 5,674,753 | G→C | intergenic (+115/+25) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
JC | 5,681,415 | +CGGG | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | Channel protein, hemolysin III family/putative Chemotaxis protein |
RA | 6,013,885 | T→C | intergenic (+90/+20) | xpt → / ← PP_5266 | Xanthine phosphoribosyltransferase/putative acetyl‑CoA hydrolase family protein |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | AE015451 | 432344 | 432365 | 22 | 10 [3] | [3] 5 | PP_0354/PP_0355 | CBS domain protein/Response regulator |
* | * | ÷ | AE015451 | 441181 | 441359 | 179 | 4 [3] | [2] 4 | bioF | 8‑amino‑7‑oxononanoate synthase |
* | * | ÷ | AE015451 | 486311 | 486429 | 119 | 4 [2] | [2] 4 | [apaG] | [apaG] |
* | * | ÷ | AE015451 | 726774 | 726878 | 105 | 4 [3] | [2] 4 | PP_0620/PP_0621 | GntR family transcriptional regulator/conserved protein of unknown function |
* | * | ÷ | AE015451 | 747579 | 747655 | 77 | 4 [3] | [2] 4 | PP_0638/PP_5448 | transposase/conserved protein of unknown function |
* | * | ÷ | AE015451 | 790210 | 790338 | 129 | 4 [3] | [2] 4 | PP_0676 | putative Transcription elongation factor |
* | * | ÷ | AE015451 | 926424 | 926527 | 104 | 4 [3] | [3] 4 | PP_0805 | Outer membrane efflux protein |
* | * | ÷ | AE015451 | 965605 | 965676 | 72 | 4 [3] | [3] 7 | ptxC | putative phosphonate transport system permease protein PtxC |
* | * | ÷ | AE015451 | 968779 | 968815 | 37 | 4 [2] | [3] 5 | PP_0831/PP_t68 | hypothetical protein/tRNA‑Leu |
* | * | ÷ | AE015451 | 1156204 | 1156282 | 79 | 4 [2] | [2] 8 | PP_1013 | Sensor histidine kinase |
* | * | ÷ | AE015451 | 1348660 | 1348748 | 89 | 4 [3] | [3] 4 | galP‑I/PP_1174 | porin‑like protein/conserved protein of unknown function |
* | * | ÷ | AE015451 | 1367572 | 1367798 | 227 | 5 [3] | [2] 4 | PP_1193 | conserved membrane protein of unknown function |
* | * | ÷ | AE015451 | 1421780 | 1422001 | 222 | 4 [3] | [2] 9 | PP_1246 | conserved exported protein of unknown function |
* | * | ÷ | AE015451 | 1544307 | 1544427 | 121 | 5 [3] | [2] 4 | mdfA | putative multidrug efflux MFS transporter |
* | * | ÷ | AE015451 | 1637426 | 1637550 | 125 | 4 [2] | [3] 5 | PP_1437 | Heavy metal sensor histidine kinase |
* | * | ÷ | AE015451 | 1644725 | 1644826 | 102 | 4 [3] | [3] 4 | [lon‑I] | [lon‑I] |
* | * | ÷ | AE015451 | 1664506 | 1664590 | 85 | 5 [2] | [3] 5 | yhjE/PP_1459 | putative inner membrane metabolite transport protein YhjE/CBS domain protein |
* | * | ÷ | AE015451 | 1691059 | 1691251 | 193 | 4 [2] | [3] 4 | PP_1487 | conserved protein of unknown function |
* | * | ÷ | AE015451 | 1907203 | 1907303 | 101 | 4 [3] | [3] 4 | PP_1707 | D‑isomer specific 2‑hydroxyacid dehydrogenase family protein |
* | * | ÷ | AE015451 | 2027322 | 2027481 | 160 | 4 [2] | [1] 5 | wbpL | Glycosyl transferase WbpL |
* | * | ÷ | AE015451 | 2029898 | 2030014 | 117 | 5 [3] | [2] 4 | wbpM | Polysaccharide biosynthesis protein |
* | * | ÷ | AE015451 | 2038239 | 2038385 | 147 | 5 [3] | [3] 4 | [rffE] | [rffE] |
* | * | ÷ | AE015451 | 2039509 | 2039668 | 160 | 4 [3] | [3] 4 | [PP_1812] | [PP_1812] |
* | * | ÷ | AE015451 | 2053476 | 2053596 | 121 | 4 [2] | [3] 4 | PP_1828 | conserved protein of unknown function |
* | * | ÷ | AE015451 | 2073369 | 2073477 | 109 | 5 [3] | [3] 11 | [PP_1847] | [PP_1847] |
* | * | ÷ | AE015451 | 2083885 | 2083995 | 111 | 4 [3] | [3] 4 | PP_1862 | conserved membrane protein of unknown function |
* | * | ÷ | AE015451 | 2095205 | 2095250 | 46 | 4 [2] | [2] 5 | htpX/alaA | Protease HtpX/glutamate‑pyruvate aminotransferase |
* | * | ÷ | AE015451 | 2142378 | 2142467 | 90 | 5 [3] | [3] 5 | PP_1897 | DNA internalization‑related competence protein ComEC/Rec2 |
* | * | ÷ | AE015451 | 2388272 | 2388337 | 66 | 4 [2] | [3] 5 | pyrD/rmf | Dihydroorotate dehydrogenase (quinone)/ribosome modulation factor |
* | * | ÷ | AE015451 | 2478389 | 2478515 | 127 | 4 [2] | [3] 4 | PP_2172 | conserved exported protein of unknown function |
* | * | ÷ | AE015451 | 2563975 | 2564017 | 43 | 5 [3] | [0] 4 | PP_2248 | putative transporter |
* | * | ÷ | AE015451 | 2569413 | 2569605 | 193 | 5 [2] | [2] 4 | [PP_2252] | [PP_2252] |
* | * | ÷ | AE015451 | 2865424 | 2865506 | 83 | 4 [2] | [3] 4 | gllP/glllA | porin‑like protein/gallate dioxygenase |
* | * | ÷ | AE015451 | 2960765 | 2961011 | 247 | 4 [3] | [3] 4 | PP_2590 | Outer membrane ferric siderophore receptor |
* | * | ÷ | AE015451 | 2975872 | 2975997 | 126 | 5 [3] | [3] 4 | ligC | putative 4‑carboxy‑2‑hydroxymuconate‑6‑semialdehyde dehydrogenase |
* | * | ÷ | AE015451 | 2997207 | 2997259 | 53 | 4 [3] | [2] 4 | PP_2621 | conserved protein of unknown function |
* | * | ÷ | AE015451 | 3157723 | 3157850 | 128 | 4 [2] | [3] 4 | PP_2773/opuA | conserved protein of unknown function/glycine betaine ABC transporter, ATPase/permease fusion protein |
* | * | ÷ | AE015451 | 3178888 | 3178931 | 44 | 4 [1] | [1] 5 | PP_2790 | Sigma‑54 dependent sensory box protein |
* | * | ÷ | AE015451 | 3276157 | 3276200 | 44 | 4 [3] | [3] 4 | PP_2874 | conserved protein of unknown function |
* | * | ÷ | AE015451 | 3287123 | 3287265 | 143 | 5 [3] | [3] 4 | [PP_2889] | [PP_2889] |
* | * | ÷ | AE015451 | 3443466 | 3443610 | 145 | 4 [3] | [2] 5 | PP_3062 | putative Pyocin R2_PP, tail length determination protein |
* | * | ÷ | AE015451 | 3461014 | 3461091 | 78 | 4 [3] | [2] 4 | PP_3076 | putative ABC transporter permease protein |
* | * | ÷ | AE015451 | 3579963 | 3580041 | 79 | 4 [1] | [1] 4 | benR | BenABC operon transcriptional activator |
* | * | ÷ | AE015451 | 3839772 | 3839921 | 150 | 4 [3] | [2] 4 | PP_3389 | conserved membrane protein of unknown function |
* | * | ÷ | AE015451 | 3848874 | 3848917 | 44 | 4 [0] | [1] 5 | PP_3397 | conserved exported protein of unknown function |
* | * | ÷ | AE015451 | 3852871 | 3852972 | 102 | 6 [2] | [3] 5 | alkB | alpha‑ketoglutarate‑ and Fe(II)‑dependent dioxygenase |
* | * | ÷ | AE015451 | 3872787 | 3872826 | 40 | 5 [1] | [3] 5 | PP_3421 | Sensor histidine kinase |
* | * | ÷ | AE015451 | 3929687 | 3929892 | 206 | 4 [2] | [1] 4 | [PP_3464]–[PP_5603] | [PP_3464],[PP_5603] |
* | * | ÷ | AE015451 | 3975746 | 3975967 | 222 | 4 [3] | [3] 4 | [PP_3505]–[PP_3506] | [PP_3505],[PP_3506] |
* | * | ÷ | AE015451 | 3985633 | 3985742 | 110 | 5 [0] | [3] 4 | [oplB] | [oplB] |
* | * | ÷ | AE015451 | 4515353 | 4515502 | 150 | 4 [2] | [3] 4 | [aat] | [aat] |
* | * | ÷ | AE015451 | 4648211 | 4648305 | 95 | 5 [3] | [3] 4 | PP_4112 | Sulphate transporter |
* | * | ÷ | AE015451 | 4705297 | 4705365 | 69 | 4 [2] | [3] 4 | kdpF/PP_4162 | potassium‑transporting ATPase F/conserved membrane protein of unknown function |
* | * | ÷ | AE015451 | 4805264 | 4805351 | 88 | 4 [3] | [3] 7 | PP_4234 | Aldehyde oxidase and xanthine dehydrogenase |
* | * | ÷ | AE015451 | 4839237 | 4839336 | 100 | 4 [2] | [2] 4 | ccoP‑I/PP_4254 | cytochrome c oxidase subunit, cbb3‑type/conserved protein of unknown function |
* | * | ÷ | AE015451 | 5168109 | 5168200 | 92 | 4 [2] | [3] 4 | hrpA/PP_4547 | ATP‑dependent helicase HrpA/putative Glutamine synthetase |
* | * | ÷ | AE015451 | 5291046 | 5291112 | 67 | 4 [3] | [3] 4 | PP_4664 | Transcriptional regulator, LysR family |
* | * | ÷ | AE015451 | 5343554 | 5343613 | 60 | 5 [3] | [3] 4 | pgi‑II | glucose‑6‑phosphate isomerase |
* | * | ÷ | AE015451 | 5389437 | 5389568 | 132 | 4 [2] | [3] 4 | dld2/PP_4738 | D‑lactate dehydrogenase/conserved exported protein of unknown function |
* | * | ÷ | AE015451 | 5401503 | 5401516 | 14 | 5 [0] | [2] 4 | PP_4743/PP_4745 | conserved protein of unknown function/transposase |
* | * | ÷ | AE015451 | 5660620 | 5660662 | 43 | 4 [1] | [1] 4 | ligB | DNA ligase B |
* | * | ÷ | AE015451 | 5696601 | 5696757 | 157 | 8 [3] | [2] 4 | pyrC'/hslV | dihydroorotase‑like protein/peptidase component of the ATP‑dependent HslVU protease |
* | * | ÷ | AE015451 | 5812277 | 5812372 | 96 | 4 [3] | [2] 4 | priA | primosome assembly protein |
* | * | ÷ | AE015451 | 5812409 | 5812502 | 94 | 4 [2] | [3] 4 | priA | primosome assembly protein |
* | * | ÷ | AE015451 | 5816950 | 5817153 | 204 | 4 [3] | [3] 5 | pilT | twitching motility protein |
* | * | ÷ | AE015451 | 5835165 | 5835279 | 115 | 5 [3] | [3] 4 | [PP_5113]–[PP_5114] | [PP_5113],[PP_5114] |
* | * | ÷ | AE015451 | 5858373 | 5858471 | 99 | 4 [2] | [3] 4 | PP_5134 | conserved protein of unknown function |
* | * | ÷ | AE015451 | 6005849 | 6005924 | 76 | 5 [3] | [2] 4 | ydcJ | metalloprotein, putative enzyme |
* | * | ÷ | AE015451 | 6008612 | 6008748 | 137 | 4 [0] | [3] 4 | norM | Probable multidrug resistance protein NorM |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | AE015451 | 1737987 = | 20 (0.890) | 4 (0.200) | 3/282 | 2.4 | 21.7% | coding (32/348 nt) | yffB | putative glutathione‑dependent thiol reductase |
? | AE015451 | = 1777401 | 11 (0.550) | intergenic (+135/+157) | PP_5476/PP_1585 | conserved protein of unknown function/putative Antidote protein | |||||
* | ? | AE015451 | = 1780066 | 17 (0.760) | 10 (0.470) | 10/302 | 0.9 | 37.6% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative |
? | AE015451 | 1780129 = | 17 (0.790) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative | |||||
* | ? | AE015451 | 2301453 = | 19 (0.850) | 5 (0.230) | 4/310 | 2.3 | 21.1% | intergenic (‑97/‑234) | sbcD/PP_5497 | Exonuclease SbcD/conserved protein of unknown function with rhs repeat‑associated core domain |
? | AE015451 | 2925429 = | NA (NA) | intergenic (‑177/+388) | PP_2563/PP_2564 | putative Antibiotic biosynthesis protein/putative Quercetin 2,3‑dioxygenase | |||||
* | ? | AE015451 | 4808174 = | 0 (0.000) | 4 (0.230) | 3/246 | 2.2 | 42.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | AE015451 | = 5988935 | 11 (0.630) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | AE015451 | = 4808179 | 0 (0.000) | 8 (0.390) | 4/292 | 2.2 | 61.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | AE015451 | 5988765 = | 10 (0.480) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | AE015451 | = 5201567 | 9 (0.400) | 15 (0.680) | 15/310 | 0.5 | 59.0% | intergenic (‑53/‑127) | PP_4582/PP_4583 | conserved membrane protein of unknown function/putative Peptidase |
? | AE015451 | 5201666 = | 12 (0.550) | intergenic (‑152/‑28) | PP_4582/PP_4583 | conserved membrane protein of unknown function/putative Peptidase | |||||
* | ? | AE015451 | = 5988757 | 11 (0.490) | 7 (0.330) | 7/300 | 1.4 | 35.5% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | AE015451 | 5988979 = | 15 (0.700) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |