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 | 1,613,723 | G→C | G116A (GGC→GCC) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 233698 | 233724 | 27 | 2 [1] | [1] 2 | BW25113_RS01085/BW25113_RS01090 | tRNA‑Asp/lipoprotein |
* | * | ÷ | NZ_CP009273 | 295809 | 295829 | 21 | 3 [1] | [1] 2 | paoC | aldehyde oxidoreductase molybdenum‑binding subunit PaoC |
* | * | ÷ | NZ_CP009273 | 356956 | 357575 | 620 | 3 [1] | [0] 2 | lacA | lacA |
* | * | ÷ | NZ_CP009273 | 716342 | 716355 | 14 | 3 [0] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 903003 | 903045 | 43 | 2 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
* | * | ÷ | NZ_CP009273 | 917713 | 917722 | 10 | 4 [0] | [1] 2 | macB | macrolide ABC transporter ATP‑binding protein/permease MacB |
* | * | ÷ | NZ_CP009273 | 1415604 | 1415617 | 14 | 3 [1] | [0] 3 | ydaU | YdaU family protein |
* | * | ÷ | NZ_CP009273 | 1431318 | 1431331 | 14 | 2 [0] | [0] 2 | ompN/nifJ | porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase |
* | * | ÷ | NZ_CP009273 | 1521373 | 1521422 | 50 | 2 [1] | [0] 2 | [yncH] | [yncH] |
* | * | ÷ | NZ_CP009273 | 1540454 | 1540501 | 48 | 2 [1] | [1] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1576779 | 1576812 | 34 | 2 [1] | [1] 2 | [ydeN] | [ydeN] |
* | * | ÷ | NZ_CP009273 | 1618141 | 1618151 | 11 | 4 [0] | [0] 2 | dgcZ/ydeI | diguanylate cyclase DgcZ/YdeI family stress tolerance OB fold protein |
* | * | ÷ | NZ_CP009273 | 1631431 | 1631462 | 32 | 3 [1] | [1] 2 | ydfO | DUF1398 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1631942 | 1632026 | 85 | 2 [1] | [1] 3 | gnsB | addiction module toxin, GnsA/GnsB family |
* | * | ÷ | NZ_CP009273 | 1634968 | 1635001 | 34 | 2 [1] | [1] 2 | essD/ynfU | phage lysis protein EssD/putative zinc‑binding protein YnfU |
* | * | ÷ | NZ_CP009273 | 1643461 | 1643498 | 38 | 2 [0] | [1] 2 | BW25113_RS08235/dicB | hypothetical protein/cell division inhibition protein DicB |
* | * | ÷ | NZ_CP009273 | 1693102 | 1693164 | 63 | 2 [0] | [1] 4 | malI | mal regulon transcriptional regulator MalI |
* | * | ÷ | NZ_CP009273 | 1807557 | 1807562 | 6 | 2 [0] | [1] 2 | BW25113_RS09050/cedA | hypothetical protein/cell division activator CedA |
* | * | ÷ | NZ_CP009273 | 1972752 | 1972756 | 5 | 37 [0] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 1980190 | 1980210 | 21 | 2 [1] | [1] 2 | araF/ftnB | arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein |
* | * | ÷ | NZ_CP009273 | 2100368 | 2100413 | 46 | 2 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
* | * | ÷ | NZ_CP009273 | 2463644 | 2463713 | 70 | 2 [0] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2622952 | 2623095 | 144 | 2 [1] | [1] 4 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2768277 | 2768291 | 15 | 2 [1] | [1] 2 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3629488 | 3629670 | 183 | 16 [1] | [0] 2 | [yhiN] | [yhiN] |
* | * | ÷ | NZ_CP009273 | 3629706 | 3629898 | 193 | 2 [0] | [1] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
* | * | ÷ | NZ_CP009273 | 3629976 | 3630219 | 244 | 2 [1] | [1] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
* | * | ÷ | NZ_CP009273 | 3630535 | 3630761 | 227 | 2 [1] | [1] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
* | * | ÷ | NZ_CP009273 | 3630842 | 3630906 | 65 | 2 [1] | [1] 2 | yhiN/pitA | NAD(P)/FAD‑dependent oxidoreductase/inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631072 | 3631303 | 232 | 2 [0] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631638 | 3631642 | 5 | 4 [0] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631998 | 3632035 | 38 | 2 [1] | [1] 3 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3632316 | 3632383 | 68 | 2 [1] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3633302 | 3633338 | 37 | 2 [1] | [0] 3 | uspB/uspA | universal stress protein UspB/universal stress protein UspA |
* | * | ÷ | NZ_CP009273 | 3634201 | 3634215 | 15 | 2 [0] | [1] 2 | BW25113_RS26230/dtpB | protein YriB/dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3634326 | 3634468 | 143 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635163 | 3635268 | 106 | 2 [1] | [1] 3 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635574 | 3635645 | 72 | 2 [1] | [0] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635745 | 3635839 | 95 | 2 [1] | [1] 3 | rsmJ | 16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ |
* | * | ÷ | NZ_CP009273 | 3636010 | 3636121 | 112 | 2 [1] | [1] 4 | rsmJ | 16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ |
* | * | ÷ | NZ_CP009273 | 3636603 | 3636656 | 54 | 2 [1] | [0] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637502 | 3637604 | 103 | 2 [1] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3638002 | 3638048 | 47 | 2 [1] | [0] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3638382 | 3638440 | 59 | 4 [0] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3638586 | 3638644 | 59 | 2 [1] | [1] 2 | prlC/rlmJ | oligopeptidase A/23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
* | * | ÷ | NZ_CP009273 | 3638940 | 3639003 | 64 | 2 [0] | [0] 2 | rlmJ | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
* | * | ÷ | NZ_CP009273 | 3639197 | 3639463 | 267 | 2 [1] | [1] 2 | rlmJ | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
* | * | ÷ | NZ_CP009273 | 3639608 | 3639998 | 391 | 2 [1] | [0] 2 | [gorA] | [gorA] |
* | * | ÷ | NZ_CP009273 | 3640055 | 3640105 | 51 | 2 [0] | [1] 2 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640156 | 3640256 | 101 | 2 [1] | [1] 2 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640415 | 3640458 | 44 | 2 [1] | [0] 2 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640767 | 3640809 | 43 | 2 [1] | [1] 3 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3641219 | 3641256 | 38 | 2 [1] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3641405 | 3641456 | 52 | 3 [1] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3642064 | 3642086 | 23 | 2 [0] | [1] 2 | arsR | As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3643029 | 3643053 | 25 | 3 [1] | [0] 3 | arsB | arsenite/antimonite:H(+) antiporter ArsB |
* | * | ÷ | NZ_CP009273 | 3643443 | 3643525 | 83 | 2 [1] | [1] 2 | arsB | arsenite/antimonite:H(+) antiporter ArsB |
* | * | ÷ | NZ_CP009273 | 3643699 | 3643785 | 87 | 2 [1] | [1] 2 | arsC | glutaredoxin‑dependent arsenate reductase |
* | * | ÷ | NZ_CP009273 | 3643952 | 3643979 | 28 | 2 [0] | [0] 2 | arsC | glutaredoxin‑dependent arsenate reductase |
* | * | ÷ | NZ_CP009273 | 3644406 | 3644462 | 57 | 2 [1] | [1] 2 | arsC/BW25113_RS18155 | glutaredoxin‑dependent arsenate reductase/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644547 | 3644784 | 238 | 3 [1] | [1] 2 | [BW25113_RS18155] | [BW25113_RS18155] |
* | * | ÷ | NZ_CP009273 | 3644881 | 3644900 | 20 | 2 [1] | [0] 2 | BW25113_RS18155 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644954 | 3644972 | 19 | 2 [0] | [0] 2 | BW25113_RS18155 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3645122 | 3646527–3645396 | 275–1406 | 2 [0] | [1] 2 | [BW25113_RS18155]–BW25113_RS18160 | [BW25113_RS18155],BW25113_RS18160 |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 16 (0.950) | 10/168 | 0.4 | 44.4% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | 20 (1.190) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 37 (2.190) | 18/168 | 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 | 2282398 = | NA (NA) | 15 (0.890) | 11/168 | 0.4 | 93.8% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | = 3629487 | 1 (0.060) | intergenic (+234/+81) | yhiM/yhiN | DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase | |||||
* | ? | NZ_CP009273 | 3274233 = | 6 (0.360) | 3 (0.180) | 3/166 | 1.5 | 23.1% | pseudogene (174/372 nt) | BW25113_RS16250 | PTS sugar transporter subunit IIC |
? | NZ_CP009273 | = 3274505 | 14 (0.840) | pseudogene (79/558 nt) | BW25113_RS16255 | amidohydrolase family protein | |||||
* | ? | NZ_CP009273 | 4532499 = | 1 (0.060) | 11 (0.730) | 10/150 | 0.4 | 76.1% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 6 (0.400) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |