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 | 49,765 | C→T | intergenic (+134/‑58) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
RA | 49,884 | C→A | P21Q (CCG→CAG) | folA → | type 3 dihydrofolate reductase |
MC JC | 1,613,631 | Δ3 bp | coding (255‑257/435 nt) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 3,632,461 | T→G | L487R (CTT→CGT) | pitA → | inorganic phosphate transporter PitA |
RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357574 | 594 | 2 [0] | [1] 2 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 428519 | 428558 | 40 | 3 [0] | [0] 2 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 578839 | 578886 | 48 | 2 [1] | [1] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 633108 | 633147 | 40 | 2 [1] | [0] 2 | ybdO/dsbG | LysR family transcriptional regulator/thiol:disulfide interchange protein DsbG |
* | * | ÷ | NZ_CP009273 | 703470 | 703516 | 47 | 2 [1] | [0] 2 | glnS/chiP | glutamine‑‑tRNA ligase/chitoporin |
* | * | ÷ | NZ_CP009273 | 903022 | 903086 | 65 | 2 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
* | * | ÷ | NZ_CP009273 | 1058396 | 1058425 | 30 | 2 [1] | [0] 3 | cbpA | curved DNA‑binding protein |
* | * | ÷ | NZ_CP009273 | 1208108 | 1208199 | 92 | 2 [0] | [1] 2 | [ycgX] | [ycgX] |
* | * | ÷ | NZ_CP009273 | 1251641 | 1251666 | 26 | 2 [1] | [1] 2 | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
* | * | ÷ | NZ_CP009273 | 1521144 | 1521256 | 113 | 2 [1] | [1] 2 | [yncH] | [yncH] |
* | * | ÷ | NZ_CP009273 | 1524420 | 1524425 | 6 | 2 [0] | [0] 2 | BW25113_RS26145 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1540308 | 1540363 | 56 | 2 [1] | [0] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1540405 | 1540432 | 28 | 2 [0] | [1] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1629487 | 1629516 | 30 | 2 [1] | [1] 2 | stfQ | phage tail protein |
* | * | ÷ | NZ_CP009273 | 1631276 | 1631286 | 11 | 4 [0] | [0] 3 | ynfO/ydfO | YlcI/YnfO family protein/DUF1398 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1631433 | 1631462 | 30 | 2 [0] | [1] 4 | ydfO | DUF1398 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1631878 | 1631909 | 32 | 2 [0] | [1] 2 | gnsB | addiction module toxin, GnsA/GnsB family |
* | * | ÷ | NZ_CP009273 | 1652254 | 1652263 | 10 | 2 [0] | [1] 2 | ynfD/ynfE | DUF1161 domain‑containing protein/dimethyl sulfoxide reductase subunit A |
* | * | ÷ | NZ_CP009273 | 1748981 | 1749082 | 102 | 2 [1] | [1] 2 | ydhY/fumD | ferredoxin‑like protein/fumarate hydratase FumD |
* | * | ÷ | NZ_CP009273 | 1836625 | 1836626 | 2 | 2 [0] | [1] 2 | ynjH/gdhA | YnjH family protein/NADP‑specific glutamate dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1940369 | 1940434 | 66 | 2 [1] | [1] 2 | [yobI] | [yobI] |
* | * | ÷ | NZ_CP009273 | 1972996 | 1973133 | 138 | 2 [1] | [0] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 2027350 | 2027377 | 28 | 2 [1] | [0] 3 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2051119 | 2051141 | 23 | 3 [0] | [1] 2 | yeeN/BW25113_RS10360 | YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn |
* | * | ÷ | NZ_CP009273 | 2097547 | 2097578 | 32 | 2 [1] | [0] 6 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 2463180 | 2463190 | 11 | 3 [0] | [1] 3 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2897104 | 2897204 | 101 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 3178624 | 3178727 | 104 | 2 [1] | [1] 3 | ubiK/ygiL | ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein |
* | * | ÷ | NZ_CP009273 | 3268417 | 3268430 | 14 | 2 [1] | [1] 6 | garP/garD | galactarate/glucarate/glycerate transporter GarP/galactarate dehydratase |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 269666 = | NA (NA) | 17 (0.810) | 9/166 | 0.7 | 100% | intergenic (+2/+146) | ykfC/BW25113_RS01325 | reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase |
? | NZ_CP009273 | = 481436 | 0 (0.000) | coding (220/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR | |||||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 57 (2.710) | 24/166 | 0.1 | 64.8% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | 31 (1.470) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | 481433 = | 0 (0.000) | 32 (1.520) | 22/166 | 0.1 | 100% | coding (217/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR |
? | NZ_CP009273 | = 571241 | NA (NA) | coding (1041/1068 nt) | BW25113_RS02855 | porin | |||||
* | ? | NZ_CP009273 | 1203246 = | 29 (1.380) | 4 (0.240) | 4/134 | 1.2 | 21.4% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 6 (0.350) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 12 (0.580) | 8/164 | 0.8 | 100% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 0 (0.000) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 22 (1.040) | 19/166 | 0.1 | 100% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
* | ? | NZ_CP009273 | = 4532507 | 2 (0.090) | 5 (0.270) | 5/148 | 1.1 | 53.2% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 7 (0.370) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |