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 | ||||||||||
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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 | = 1972751 | 1 (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 |