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 49,883 C→T P21S (CCG→TCG)  folA → type 3 dihydrofolate reductase
RA 214,743 A→C Y174D (TAC→GAC)  proS ← proline‑‑tRNA ligase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase
RA 4,267,454 C→T R20C (CGC→TGC)  soxR → redox‑sensitive transcriptional activator SoxR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 233750 233763 14 3 [1] [1] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 323589 323631 43 3 [1] [1] 2 betB betaine‑aldehyde dehydrogenase
* * ÷ NZ_CP009273 356958 357579 622 2 [1] [1] 3 lacA lacA
* * ÷ NZ_CP009273 380237 380264 28 3 [1] [1] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 396622 396681 60 2 [1] [1] 2 [BW25113_RS25915] [BW25113_RS25915]
* * ÷ NZ_CP009273 518578 518634 57 3 [0] [1] 2 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 578866 578887 22 3 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 748526 748538 13 3 [1] [1] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 902997 903082 86 2 [1] [1] 3 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 982567 982611 45 3 [1] [0] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982810 982861 52 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982911 982966 56 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1098834 1098917 84 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1205309 1205336 28 2 [0] [1] 2 pinE site‑specific DNA recombinase
* * ÷ NZ_CP009273 1225878 1225962 85 2 [1] [1] 2 hlyE/umuD hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit
* * ÷ NZ_CP009273 1253801 1253812 12 2 [1] [1] 2 pth aminoacyl‑tRNA hydrolase
* * ÷ NZ_CP009273 1264539 1264692–1264551 13–154 2 [1] [1] 2 [BW25113_RS06330] [BW25113_RS06330]
* * ÷ NZ_CP009273 1358317 1358343 27 2 [0] [1] 2 puuC aldehyde dehydrogenase PuuC
* * ÷ NZ_CP009273 1384235 1384256 22 2 [1] [0] 2 mpaA murein tripeptide amidase MpaA
* * ÷ NZ_CP009273 1526036 1526056 21 3 [1] [0] 2 BW25113_RS07655/BW25113_RS07660 ISAs1 family transposase/ISAs1‑like element ISEc5 family transposase
* * ÷ NZ_CP009273 1826953 1826967 15 2 [0] [1] 2 xthA exodeoxyribonuclease III
* * ÷ NZ_CP009273 1973115 1973126 12 2 [1] [0] 3 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 2010421 2010447 27 2 [1] [0] 2 fliI flagellar protein export ATPase FliI
* * ÷ NZ_CP009273 2035741 2035786 46 2 [1] [0] 2 zinT/yodB metal‑binding protein ZinT/cytochrome b
* * ÷ NZ_CP009273 2100617 2100701 85 2 [1] [1] 5 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2491965 2491982 18 2 [1] [1] 2 alaC/ypdA alanine transaminase/two‑component system sensor histidine kinase YpdA
* * ÷ NZ_CP009273 2768281 2768328 48 4 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2912215 2912251 37 3 [1] [1] 2 gudD glucarate dehydratase
* * ÷ NZ_CP009273 3628863 3630061 1199 28 [0] [1] 2 [yhiM]–[yhiN] [yhiM],[yhiN]
* * ÷ NZ_CP009273 3630096 3631276 1181 2 [1] [0] 2 [yhiN]–[pitA] [yhiN],[pitA]
* * ÷ NZ_CP009273 3631317 3631546 230 2 [0] [1] 2 pitA inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3631605 3633664 2060 2 [1] [0] 2 [pitA]–[uspA] [pitA],uspB,[uspA]
* * ÷ NZ_CP009273 3633714 3634913 1200 2 [0] [0] 2 [uspA]–[dtpB] [uspA],BW25113_RS26225,BW25113_RS26230,[dtpB]
* * ÷ NZ_CP009273 3634991 3635685 695 2 [0] [1] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3635724 3646507–3645393 9670–10784 2 [1] [0] 2 rsmJ–[BW25113_RS18160] rsmJ,prlC,rlmJ,gorA,dinQ,arsR,arsB,arsC,BW25113_RS18155,[BW25113_RS18160]
* * ÷ NZ_CP009273 3792589 3792698 110 3 [1] [1] 2 [waaU] [waaU]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)20 (0.970) 14/168 0.3 52.6% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 18 (0.870)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 1203246 =10 (0.480)5 (0.300) 5/136 1.0 47.5% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 3 (0.180)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727512 (0.100)23 (1.110) 19/168 0.1 92.0% 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 = 36288620 (0.000)28 (1.350) 13/168 0.4 100% coding (662/1053 nt) yhiM DUF2776 domain‑containing protein
?NZ_CP009273 3645396 = NA (NA)pseudogene (746/747 nt) BW25113_RS18155 hypothetical protein