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 = 19727510 (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