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 49,791 G→A intergenic (+160/‑32) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 49,905 T→G L28R (CTC→CGC)  folA → type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 4,372,536 T→A I26N (ATC→AAC)  epmA → elongation factor P‑‑(R)‑beta‑lysine ligase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357574 594 2 [0] [1] 3 [lacA] [lacA]
* * ÷ NZ_CP009273 578921 579059 139 3 [1] [0] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 703504 703512 9 2 [1] [0] 2 glnS/chiP glutamine‑‑tRNA ligase/chitoporin
* * ÷ NZ_CP009273 993132 993216 85 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1098920 1099008 89 3 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1207580 1207617 38 2 [0] [1] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1207954 1208061 108 2 [0] [1] 2 [BW25113_RS25535] [BW25113_RS25535]
* * ÷ NZ_CP009273 1308145 1308210 66 2 [0] [1] 3 BW25113_RS25555/ompW YkgJ family cysteine cluster protein/outer membrane protein OmpW
* * ÷ NZ_CP009273 1337747 1337763 17 2 [1] [1] 2 osmB/yciT osmotically‑inducible lipoprotein OsmB/DNA‑binding transcriptional regulator YciT
* * ÷ NZ_CP009273 1400113 1400123 11 3 [0] [1] 2 abgR/smrA LysR family transcriptional regulator/DNA endonuclease SmrA
* * ÷ NZ_CP009273 1417964 1417969 6 2 [0] [0] 2 BW25113_RS26130/trkG hypothetical protein/Trk system potassium transporter TrkG
* * ÷ NZ_CP009273 1418012 1418045 34 2 [0] [1] 3 [trkG] [trkG]
* * ÷ NZ_CP009273 1459392 1459555 164 2 [1] [0] 2 BW25113_RS25580 BW25113_RS25580
* * ÷ NZ_CP009273 1524330 1524427 98 2 [1] [1] 2 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1525620 1525634 15 2 [1] [0] 3 BW25113_RS07655 ISAs1 family transposase
* * ÷ NZ_CP009273 1539292 1539295 4 2 [0] [0] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1550740 1550756 17 2 [1] [1] 2 bdm/osmC biofilm‑dependent modulation protein/peroxiredoxin OsmC
* * ÷ NZ_CP009273 1573669 1573722 54 2 [1] [0] 2 yddA/BW25113_RS25610 ABC transporter ATP‑binding protein/permease/protein YneP
* * ÷ NZ_CP009273 1576942 1577015 74 2 [1] [1] 2 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1631956 1631976 21 2 [1] [1] 2 gnsB addiction module toxin, GnsA/GnsB family
* * ÷ NZ_CP009273 1635234 1635276 43 2 [1] [1] 2 ynfU/cspB putative zinc‑binding protein YnfU/cold shock‑like protein CspB
* * ÷ NZ_CP009273 1708541 1708553 13 2 [1] [1] 2 dtpA/gstA dipeptide/tripeptide permease DtpA/glutathione transferase GstA
* * ÷ NZ_CP009273 1751659 1751668 10 2 [0] [0] 2 pykF/lpp pyruvate kinase PykF/murein lipoprotein Lpp
* * ÷ NZ_CP009273 1772983 1773046 64 2 [1] [1] 3 ydiP AraC family transcriptional regulator
* * ÷ NZ_CP009273 1807396 1807454 59 2 [1] [0] 4 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1864680 1864731 52 2 [1] [1] 2 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 2027397 2027407 11 2 [0] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2100158 2100278 121 2 [0] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2170747 2170783 37 2 [0] [1] 2 gatY/fbaB tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
* * ÷ NZ_CP009273 2337318 2337328 11 2 [1] [1] 2 yfaL AIDA‑I family autotransporter adhesin YfaL/EhaC
* * ÷ NZ_CP009273 2449360 2449463 104 2 [1] [1] 3 yfcV/sixA fimbrial protein/phosphohistidine phosphatase SixA
* * ÷ NZ_CP009273 2462809 2462846 38 2 [0] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2462971 2463011 41 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463196 2463239 44 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463719 2463743 25 2 [0] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2753660 2753704 45 5 [1] [0] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2984548 2984624 77 2 [0] [1] 2 BW25113_RS14825/ygeG hypothetical protein/tetratricopeptide repeat protein
* * ÷ NZ_CP009273 3262301 3262349 49 2 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3630898 3630956 59 2 [1] [1] 2 yhiN/pitA NAD(P)/FAD‑dependent oxidoreductase/inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3632746 3632800 55 2 [1] [1] 3 uspB universal stress protein UspB
* * ÷ NZ_CP009273 3634223 3634244 22 2 [1] [0] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3634312 3634327 16 2 [0] [1] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3635714 3635730 17 4 [0] [1] 2 dtpB/rsmJ dipeptide/tripeptide permease DtpB/16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ
* * ÷ NZ_CP009273 3635994 3636109 116 2 [1] [1] 4 rsmJ 16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ
* * ÷ NZ_CP009273 3636509 3636570 62 3 [1] [1] 3 prlC oligopeptidase A
* * ÷ NZ_CP009273 3636842 3636905 64 2 [1] [1] 3 prlC oligopeptidase A
* * ÷ NZ_CP009273 3636971 3637067 97 3 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637102 3637200 99 2 [1] [1] 3 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637269 3637313 45 3 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637600 3637730 131 2 [1] [0] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637840 3637912 73 2 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3640827 3640899 73 2 [1] [1] 2 gorA glutathione‑disulfide reductase
* * ÷ NZ_CP009273 3641567 3641580 14 2 [1] [0] 2 dinQ/arsR hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR
* * ÷ NZ_CP009273 3642818 3642900 83 2 [1] [0] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3642952 3642955 4 2 [0] [1] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3644461 3644476 16 2 [1] [0] 2 arsC/BW25113_RS18155 glutaredoxin‑dependent arsenate reductase/hypothetical protein
* * ÷ NZ_CP009273 3644901 3645109 209 2 [1] [1] 2 BW25113_RS18155 hypothetical protein
* * ÷ NZ_CP009273 3645200 3646523–3645391 192–1324 2 [1] [1] 2 [BW25113_RS18155]–BW25113_RS18160 [BW25113_RS18155],BW25113_RS18160
* * ÷ NZ_CP009273 3763096 3763106 11 4 [1] [1] 6 BW25113_RS26240 Imm57 family immunity protein
* * ÷ NZ_CP009273 3798332 3798376 45 3 [1] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3798467 3798496 30 2 [1] [0] 2 [rfaS] [rfaS]
* * ÷ NZ_CP009273 4466780 4466913 134 2 [1] [1] 5 BW25113_RS22080 hypothetical protein
* * ÷ NZ_CP009273 4532487 4532510 24 3 [1] [0] 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 360104 =NA (NA)26 (1.200) 20/164 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 1203246 =18 (0.830)4 (0.230) 4/132 1.3 26.3% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 8 (0.460)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)15 (0.700) 9/162 0.7 100% 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)29 (1.340) 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
* ? NZ_CP009273 2282398 =NA (NA)14 (0.640) 11/164 0.6 82.3% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3630786 3 (0.140)intergenic (‑16/‑216) yhiN/pitA NAD(P)/FAD‑dependent oxidoreductase/inorganic phosphate transporter PitA