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 49,912 G→T W30C (TGG→TGT)  folA → type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356976 357584 609 2 [1] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 578967 579045 79 2 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 724910 724950 41 3 [1] [1] 2 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 761397 761407 11 2 [0] [1] 2 mngR/mngA mannosyl‑D‑glycerate transport/metabolism system transcriptional repressor MngR/PTS 2‑O‑a‑mannosyl‑D‑glycerate transporter subunit IIABC
* * ÷ NZ_CP009273 766335 766359 25 3 [1] [0] 2 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 896114 896170 57 5 [1] [1] 3 artJ/artM ABC transporter substrate‑binding protein ArtJ/arginine ABC transporter permease ArtM
* * ÷ NZ_CP009273 903013 903070 58 2 [1] [1] 3 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 950203 950254 52 2 [0] [0] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 982716 982741 26 4 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982921 982961 41 2 [0] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993105 993214 110 3 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1193127 1193244 118 2 [0] [0] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1310742 1310750 9 2 [0] [0] 2 trpA tryptophan synthase subunit alpha
* * ÷ NZ_CP009273 1323848 1323880 33 3 [1] [1] 2 sohB protease SohB
* * ÷ NZ_CP009273 1459488 1459511 24 2 [1] [0] 2 BW25113_RS25580/BW25113_RS07350 hypothetical protein/autotransporter domain‑containing protein
* * ÷ NZ_CP009273 1800500 1800529 30 2 [1] [1] 2 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 2027367 2027421 55 2 [0] [0] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2144484 2144509 26 4 [0] [0] 4 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2170705 2170735 31 2 [1] [1] 3 gatY/fbaB tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
* * ÷ NZ_CP009273 2337838 2337856 19 2 [0] [1] 2 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2778501 2778523 23 3 [1] [1] 2 BW25113_RS25705/BW25113_RS13825 DUF5507 domain‑containing protein/tRNA‑Ile
* * ÷ NZ_CP009273 3129929 3129954 26 2 [0] [0] 2 pitB/gss inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase
* * ÷ NZ_CP009273 3797710 3797726 17 3 [1] [0] 3 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3900164 3900171 8 2 [0] [1] 2 bglG/phoU transcriptional antiterminator BglG/phosphate signaling complex protein PhoU
* * ÷ NZ_CP009273 4225578 4225668 91 2 [1] [1] 2 pgi/yjbE glucose‑6‑phosphate isomerase/exopolysaccharide production protein YjbE
* * ÷ NZ_CP009273 4531449 4531515 67 3 [1] [1] 2 fimB/fimE type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE
* * ÷ NZ_CP009273 4532453 4532527 75 3 [1] [1] 2 fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 270859NA (NA)16 (0.740) 14/162 0.4 69.8% intergenic (‑67/‑177) BW25113_RS01325/mmuP IS5‑like element IS5 family transposase/S‑methylmethionine permease
?NZ_CP009273 = 481485 7 (0.320)coding (269/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
* ? NZ_CP009273 360104 =NA (NA)33 (1.500) 23/164 0.1 53.2% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 29 (1.320)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 481481 =5 (0.230)10 (0.460) 7/164 1.1 66.7% coding (265/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
?NZ_CP009273 570047 = NA (NA)intergenic (+252/+146) quuD/BW25113_RS02850 antitermination protein QuuD/IS5‑like element IS5 family transposase
* ? NZ_CP009273 = 1391494NA (NA)7 (0.320) 6/162 1.2 100% 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 = 19727510 (0.000)26 (1.180) 19/164 0.2 100% 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