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
   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 = 1391494NA (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 = 19727510 (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 = 45325072 (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