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 | = 1391494 | NA (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 | = 1972751 | 0 (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 |