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 | = 1972751 | 2 (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 | = 3628862 | 0 (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 |