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 49,898 G→A A26T (GCC→ACC)  folA → type 3 dihydrofolate reductase
RA 49,910 T→G W30G (TGG→GGG)  folA → type 3 dihydrofolate reductase
RA 832,042 C→G A79G (GCG→GGG)  hcxB → hydroxycarboxylate dehydrogenase HcXB
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 243092 243129 38 2 [1] [1] 2 dinJ/yafL type II toxin‑antitoxin system antitoxin DinJ/C40 family peptidase
* * ÷ NZ_CP009273 356981 357569 589 5 [0] [1] 4 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 572470 572509 40 2 [0] [0] 2 BW25113_RS02855/essD porin/phage lysis protein EssD
* * ÷ NZ_CP009273 716429 716471 43 2 [1] [0] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 902986 902988 3 2 [0] [0] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 903031 903077 47 2 [0] [1] 4 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 993098 993158 61 4 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1010895 1010905 11 2 [1] [1] 2 pqiC membrane integrity‑associated transporter subunit PqiC
* * ÷ NZ_CP009273 1059773 1059785 13 2 [1] [0] 2 yccE YccE family protein
* * ÷ NZ_CP009273 1063315 1063351 37 2 [1] [1] 2 wrbA/ymdF NAD(P)H:quinone oxidoreductase/general stress protein
* * ÷ NZ_CP009273 1098936 1098983 48 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1099228 1099250 23 2 [0] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1310492 1310529 38 3 [1] [1] 3 yciG/trpA general stress protein/tryptophan synthase subunit alpha
* * ÷ NZ_CP009273 1370335 1370340 6 3 [1] [0] 2 ycjR sugar phosphate isomerase/epimerase
* * ÷ NZ_CP009273 1407142 1407167 26 3 [1] [1] 2 intR site‑specific integrase
* * ÷ NZ_CP009273 1455516 1455524 9 3 [1] [0] 2 paaJ bifunctional 3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
* * ÷ NZ_CP009273 1495881 1495884 4 4 [0] [1] 4 tehB tellurite resistance methyltransferase TehB
* * ÷ NZ_CP009273 1521166 1521178 13 2 [0] [1] 2 yncG/yncH glutathione S‑transferase family protein/YncH family protein
* * ÷ NZ_CP009273 1538972 1538982 11 2 [0] [1] 3 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539028 1539088 61 3 [1] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540349 1540373 25 2 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1556061 1556115 55 2 [1] [1] 2 ddpA ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 1592547 1592598 52 2 [1] [1] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1631643 1631651 9 2 [1] [0] 3 ydfO DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1748941 1748987 47 3 [1] [0] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1749399 1749409 11 5 [1] [0] 2 fumD/BW25113_RS26160 fumarate hydratase FumD/protein YnhH
* * ÷ NZ_CP009273 1973022 1973042 21 2 [0] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 1989138 1989181 44 2 [1] [1] 2 BW25113_RS25650 hypothetical protein
* * ÷ NZ_CP009273 2026978 2027036 59 2 [0] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2027336 2027454 119 2 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2034654 2034679 26 2 [1] [1] 2 msrQ/zinT protein‑methionine‑sulfoxide reductase heme‑binding subunit MsrQ/metal‑binding protein ZinT
* * ÷ NZ_CP009273 2099651 2099701 51 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2100182 2100215 34 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2400579 2400629 51 2 [1] [1] 3 lrhA/alaA transcriptional regulator LrhA/alanine transaminase AlaA
* * ÷ NZ_CP009273 2462910 2462941 32 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2753655 2753783 129 2 [1] [1] 3 [yfjI] [yfjI]
* * ÷ NZ_CP009273 2766757 2766787 31 3 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2897249 2897292 44 2 [0] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 3262283 3262288 6 2 [1] [0] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3354473 3354481 9 5 [0] [0] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 4241442 4241465 24 2 [1] [1] 4 BW25113_RS20970 SopA family protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)40 (1.780) 25/164 0.1 NA intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 NA (NA)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 = 19727511 (0.040)19 (0.850) 11/164 0.6 95.0% 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 4532499 =5 (0.220)4 (0.200) 4/146 1.4 35.6% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 10 (0.500)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA