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 49,912 G→T W30C (TGG→TGT)  folA → type 3 dihydrofolate reductase
RA 59,627 C→A intergenic (‑153/+60) BW25113_RS25400 ← / ← rluA transposase/bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA
RA 1,393,311 A→G I158T (ATC→ACC)  fnr ← fumarate/nitrate reduction transcriptional regulator Fnr
RA 1,613,588 T→C L71P (CTG→CCG)  marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,631,170 G→C A57P (GCG→CCG)  pitA → inorganic phosphate transporter PitA
RA 4,062,410 G→T P76Q (CCG→CAG)  yihQ ← sulfoquinovosidase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357567 587 4 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 716371 716459 89 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 923649 923717 69 2 [1] [1] 3 cydC cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC
* * ÷ NZ_CP009273 1020864 1020872 9 2 [0] [0] 2 helD DNA helicase IV
* * ÷ NZ_CP009273 1047121 1047133 13 2 [1] [0] 3 [cspG] [cspG]
* * ÷ NZ_CP009273 1108870 1108916 47 2 [1] [1] 3 mdoH/yceK glucans biosynthesis glucosyltransferase MdoH/YceK/YidQ family lipoprotein
* * ÷ NZ_CP009273 1112587 1112616 30 2 [0] [1] 4 trhO rhodanese‑related sulfurtransferase
* * ÷ NZ_CP009273 1183221 1183248 28 2 [1] [1] 2 roxA [50S ribosomal protein L16]‑arginine 3‑hydroxylase
* * ÷ NZ_CP009273 1298714 1298743 30 2 [1] [0] 2 oppC oligopeptide ABC transporter permease OppC
* * ÷ NZ_CP009273 1314785 1314859 75 2 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1315264 1315320 57 2 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1396563 1396586 24 2 [1] [1] 2 abgB p‑aminobenzoyl‑glutamate hydrolase subunit AbgB
* * ÷ NZ_CP009273 1428038–1428289 1428307 19–270 2 [1] [1] 3 [ydfK] [ydfK]
* * ÷ NZ_CP009273 1431317 1431367 51 2 [1] [0] 2 ompN/nifJ porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1532054 1532060 7 2 [0] [0] 2 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1534513 1534597 85 3 [0] [1] 2 narZ nitrate reductase Z subunit alpha
* * ÷ NZ_CP009273 1540348 1540425 78 3 [1] [0] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1648426 1648481 56 3 [1] [0] 2 rspA starvation‑sensing protein RspA
* * ÷ NZ_CP009273 1716847 1716961 115 2 [1] [1] 2 ydhK FUSC family protein
* * ÷ NZ_CP009273 1807470 1807533 64 2 [1] [1] 3 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1871594 1871653 60 2 [1] [1] 3 yoaF DUF333 domain‑containing lipoprotein YoaF
* * ÷ NZ_CP009273 1877547 1877598 52 2 [1] [1] 3 yeaV BCCT family transporter YeaV
* * ÷ NZ_CP009273 1897347 1897354 8 2 [0] [0] 2 manY PTS mannose transporter subunit IIC
* * ÷ NZ_CP009273 1917468 1917473 6 2 [1] [1] 3 pphA/yebY protein‑serine/threonine phosphatase/YebY family protein
* * ÷ NZ_CP009273 1973021 1973072 52 2 [1] [0] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 1976080 1976149 70 3 [1] [1] 2 araH arabinose ABC transporter permease AraH
* * ÷ NZ_CP009273 1990357 1990449 93 2 [0] [1] 3 sdiA/yecC transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC
* * ÷ NZ_CP009273 2009774 2009785 12 3 [1] [0] 3 fliH flagellar assembly protein FliH
* * ÷ NZ_CP009273 2133580 2133595 16 2 [0] [1] 2 asmA outer membrane assembly protein AsmA
* * ÷ NZ_CP009273 2144480 2144548 69 4 [1] [1] 2 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2268684 2268712 29 2 [0] [1] 2 yejB microcin C ABC transporter permease YejB
* * ÷ NZ_CP009273 2285536 2285600 65 2 [1] [1] 2 ccmH cytochrome c‑type biogenesis thiol:disulfide oxidoreductase CcmH
* * ÷ NZ_CP009273 2300309 2300341 33 3 [0] [1] 2 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2387066 2387100 35 2 [1] [1] 3 nuoL NADH‑quinone oxidoreductase subunit L
* * ÷ NZ_CP009273 2609999 2610010 12 2 [1] [1] 2 bepA beta‑barrel assembly‑enhancing protease
* * ÷ NZ_CP009273 2693354 2693367 14 2 [0] [0] 2 yfhL/shoB 4Fe‑4S dicluster ferredoxin YfhL/type I toxin‑antitoxin system toxin ShoB
* * ÷ NZ_CP009273 2768271 2768299 29 2 [1] [1] 3 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2779772 2779879 108 2 [1] [1] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2945193 2945250 58 2 [1] [1] 2 recD exodeoxyribonuclease V subunit alpha
* * ÷ NZ_CP009273 3116743 3116787 45 2 [0] [1] 2 glcB malate synthase G
* * ÷ NZ_CP009273 3798335 3798341 7 2 [0] [1] 2 rfaS LPS core biosynthesis protein RfaS

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =31 (2.020)40 (2.610) 31/258 0.0 56.3% 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 1972818 =2 (0.130)7 (0.460) 6/258 0.8 77.8% intergenic (‑364/‑416) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 2095230 = NA (NA)pseudogene (1/354 nt) wbbL N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL
* ? NZ_CP009273 = 19728211 (0.070)9 (0.590) 8/258 0.6 90.0% intergenic (‑367/‑413) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 = 2096424 NA (NA)intergenic (‑68/+3) BW25113_RS10605/wbbL IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL