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 | 1,184,613 | A→T | I207N (ATC→AAC) | phoQ ← | two‑component system sensor histidine kinase PhoQ |
RA | 1,613,627 | T→A | V84E (GTG→GAG) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357574 | 594 | 5 [0] | [1] 2 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 419798 | 419799 | 2 | 2 [0] | [0] 2 | acpH | ACP phosphodiesterase |
* | * | ÷ | NZ_CP009273 | 518495 | 518573 | 79 | 3 [0] | [1] 2 | ybbP/rhsD | ABC transporter permease/rhs element protein RhsD |
* | * | ÷ | NZ_CP009273 | 567352 | 567405 | 54 | 2 [1] | [1] 2 | ybcM | helix‑turn‑helix transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 578930 | 578967 | 38 | 2 [0] | [1] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 647590 | 647642 | 53 | 3 [1] | [1] 2 | citC/dpiB | [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB |
* | * | ÷ | NZ_CP009273 | 674902 | 674935 | 34 | 2 [0] | [1] 2 | ybeT/ybeU | tetratricopeptide repeat protein/DUF1266 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 699965 | 699976 | 12 | 3 [1] | [0] 2 | nagE | PTS N‑acetyl glucosamine transporter subunit IIABC |
* | * | ÷ | NZ_CP009273 | 716363 | 716390 | 28 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 716470 | 716509 | 40 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 717726 | 717741 | 16 | 2 [1] | [0] 2 | kdpD | two‑component system sensor histidine kinase KdpD |
* | * | ÷ | NZ_CP009273 | 724410 | 724449 | 40 | 2 [1] | [0] 2 | kdpF/ybfA | K(+)‑transporting ATPase subunit F/YbfA family protein |
* | * | ÷ | NZ_CP009273 | 748538 | 748541 | 4 | 2 [0] | [1] 2 | ybgD/gltA | fimbrial protein/citrate synthase |
* | * | ÷ | NZ_CP009273 | 798942 | 798973 | 32 | 2 [1] | [1] 2 | [ybhJ] | [ybhJ] |
* | * | ÷ | NZ_CP009273 | 859095 | 859104 | 10 | 4 [1] | [0] 2 | [fsa] | [fsa] |
* | * | ÷ | NZ_CP009273 | 869178 | 869198 | 21 | 2 [1] | [1] 3 | pdeI | EAL domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 962671 | 962672 | 2 | 4 [0] | [0] 2 | msbA | lipid A ABC transporter ATP‑binding protein/permease MsbA |
* | * | ÷ | NZ_CP009273 | 1007732 | 1007747 | 16 | 4 [1] | [0] 2 | pqiA | membrane integrity‑associated transporter subunit PqiA |
* | * | ÷ | NZ_CP009273 | 1021179 | 1021230 | 52 | 2 [0] | [1] 2 | helD | DNA helicase IV |
* | * | ÷ | NZ_CP009273 | 1028371 | 1028375 | 5 | 2 [0] | [0] 2 | hyaA | hydrogenase 1 small subunit |
* | * | ÷ | NZ_CP009273 | 1098942 | 1098980 | 39 | 2 [1] | [0] 2 | csgD/csgB | biofilm master transcriptional regulator CsgD/curli minor subunit CsgB |
* | * | ÷ | NZ_CP009273 | 1172143 | 1172253 | 111 | 3 [1] | [1] 3 | lolD | lipoprotein‑releasing ABC transporter ATP‑binding protein LolD |
* | * | ÷ | NZ_CP009273 | 1192377 | 1192477 | 101 | 3 [1] | [0] 3 | ymfD | class I SAM‑dependent methyltransferase |
* | * | ÷ | NZ_CP009273 | 1193061 | 1193144 | 84 | 2 [1] | [1] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1207318 | 1207327 | 10 | 2 [1] | [1] 2 | iraM | anti‑adapter protein IraM |
* | * | ÷ | NZ_CP009273 | 1208037 | 1208059 | 23 | 3 [1] | [1] 2 | BW25113_RS25535 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1242683 | 1242693 | 11 | 2 [0] | [0] 9 | treA | alpha,alpha‑trehalase |
* | * | ÷ | NZ_CP009273 | 1251605 | 1251637 | 33 | 2 [1] | [1] 2 | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
* | * | ÷ | NZ_CP009273 | 1298412 | 1298440 | 29 | 2 [1] | [1] 2 | oppC | oligopeptide ABC transporter permease OppC |
* | * | ÷ | NZ_CP009273 | 1320895 | 1320952 | 58 | 4 [0] | [1] 2 | [yciQ] | [yciQ] |
* | * | ÷ | NZ_CP009273 | 1327760 | 1327760 | 1 | 2 [0] | [0] 2 | topA | type I DNA topoisomerase |
* | * | ÷ | NZ_CP009273 | 1364410 | 1364419 | 10 | 5 [0] | [1] 2 | pspE/ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
* | * | ÷ | NZ_CP009273 | 1387385 | 1387399 | 15 | 2 [0] | [1] 2 | pgrR/mppA | DNA‑binding transcriptional regulator PgrR/murein tripeptide ABC transporter substrate‑binding protein MppA |
* | * | ÷ | NZ_CP009273 | 1400055 | 1400109 | 55 | 2 [1] | [1] 3 | abgR/smrA | LysR family transcriptional regulator/DNA endonuclease SmrA |
* | * | ÷ | NZ_CP009273 | 1453533 | 1453580 | 48 | 2 [1] | [1] 2 | paaC | 3‑hydroxyacyl‑CoA dehydrogenase PaaC |
* | * | ÷ | NZ_CP009273 | 1459420 | 1459534 | 115 | 2 [1] | [1] 3 | BW25113_RS25580 | BW25113_RS25580 |
* | * | ÷ | NZ_CP009273 | 1485607 | 1485634 | 28 | 2 [1] | [1] 2 | cybB | cytochrome b561 |
* | * | ÷ | NZ_CP009273 | 1514291 | 1514323 | 33 | 2 [0] | [1] 2 | [curA] | [curA] |
* | * | ÷ | NZ_CP009273 | 1521518 | 1521575 | 58 | 2 [0] | [1] 2 | yncH/BW25113_RS07645 | YncH family protein/RHS repeat protein |
* | * | ÷ | NZ_CP009273 | 1524271 | 1524373 | 103 | 2 [1] | [0] 2 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1525929 | 1525956 | 28 | 2 [1] | [1] 3 | BW25113_RS07655 | ISAs1 family transposase |
* | * | ÷ | NZ_CP009273 | 1540351 | 1540425 | 75 | 2 [1] | [1] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1573630 | 1573722 | 93 | 2 [1] | [1] 2 | yddA/BW25113_RS25610 | ABC transporter ATP‑binding protein/permease/protein YneP |
* | * | ÷ | NZ_CP009273 | 1610126 | 1610156 | 31 | 4 [1] | [0] 2 | yneK | putative protein YneK |
* | * | ÷ | NZ_CP009273 | 1618996 | 1619053 | 58 | 2 [1] | [1] 2 | [ydeJ] | [ydeJ] |
* | * | ÷ | NZ_CP009273 | 1621453 | 1621499 | 47 | 2 [1] | [1] 2 | dcp | peptidyl‑dipeptidase Dcp |
* | * | ÷ | NZ_CP009273 | 1631872 | 1632010 | 139 | 2 [1] | [1] 3 | gnsB | addiction module toxin, GnsA/GnsB family |
* | * | ÷ | NZ_CP009273 | 1633072 | 1633089 | 18 | 2 [1] | [1] 2 | cspI/rzpQ | cold shock protein CspI/DUF2514 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1634950 | 1635042 | 93 | 2 [1] | [1] 4 | essD/ynfU | phage lysis protein EssD/putative zinc‑binding protein YnfU |
* | * | ÷ | NZ_CP009273 | 1635288 | 1635319 | 32 | 2 [0] | [1] 3 | ynfU/cspB | putative zinc‑binding protein YnfU/cold shock‑like protein CspB |
* | * | ÷ | NZ_CP009273 | 1741246 | 1741254 | 9 | 2 [0] | [1] 2 | ydhR | monooxygenase |
* | * | ÷ | NZ_CP009273 | 1751464 | 1751479 | 16 | 3 [1] | [1] 2 | pykF/lpp | pyruvate kinase PykF/murein lipoprotein Lpp |
* | * | ÷ | NZ_CP009273 | 1783818 | 1783862 | 45 | 2 [1] | [1] 2 | aroH/hemP | 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP |
* | * | ÷ | NZ_CP009273 | 1807502 | 1807574 | 73 | 3 [1] | [1] 2 | BW25113_RS09050/cedA | hypothetical protein/cell division activator CedA |
* | * | ÷ | NZ_CP009273 | 1809774 | 1809788 | 15 | 2 [1] | [1] 3 | katE | catalase HPII |
* | * | ÷ | NZ_CP009273 | 1864853 | 1864892 | 40 | 2 [1] | [1] 2 | cdgI | GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1886961 | 1886991 | 31 | 3 [1] | [1] 2 | yoaA | ATP‑dependent DNA helicase |
* | * | ÷ | NZ_CP009273 | 1905346 | 1905378 | 33 | 2 [1] | [1] 3 | yebQ | MFS transporter |
* | * | ÷ | NZ_CP009273 | 1952557 | 1952615 | 59 | 2 [0] | [1] 2 | torY/cutC | NapC/NirT family cytochrome c/copper homeostasis protein CutC |
* | * | ÷ | NZ_CP009273 | 1973036 | 1973104 | 69 | 3 [1] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 2015784 | 2015794 | 11 | 2 [0] | [0] 3 | fliP | flagellar type III secretion system pore protein FliP |
* | * | ÷ | NZ_CP009273 | 2027367 | 2027423 | 57 | 2 [1] | [1] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2042217 | 2042228 | 12 | 2 [1] | [0] 2 | yeeJ | inverse autotransporter adhesin YeeJ |
* | * | ÷ | NZ_CP009273 | 2050125 | 2050269 | 145 | 2 [1] | [1] 2 | amn/yeeN | AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 2051091 | 2051131 | 41 | 2 [1] | [1] 2 | yeeN/BW25113_RS10360 | YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn |
* | * | ÷ | NZ_CP009273 | 2062036 | 2062082 | 47 | 2 [0] | [1] 2 | BW25113_RS10415/BW25113_RS24005 | IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2144491 | 2144494 | 4 | 2 [0] | [0] 4 | yegI/yegJ | protein kinase YegI/DUF2314 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2300312 | 2300381 | 70 | 3 [1] | [1] 4 | mqo/yojI | malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI |
* | * | ÷ | NZ_CP009273 | 2359194 | 2359210 | 17 | 3 [0] | [0] 2 | ais/arnB | lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
* | * | ÷ | NZ_CP009273 | 2449501 | 2449517 | 17 | 2 [0] | [1] 3 | yfcV/sixA | fimbrial protein/phosphohistidine phosphatase SixA |
* | * | ÷ | NZ_CP009273 | 2462911 | 2462924 | 14 | 2 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2463196 | 2463249 | 54 | 2 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2463656 | 2463794 | 139 | 2 [1] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2505237 | 2505285 | 49 | 3 [0] | [1] 2 | mntH | Nramp family divalent metal transporter |
* | * | ÷ | NZ_CP009273 | 2622404 | 2622470 | 67 | 2 [1] | [0] 2 | pdeF/BW25113_RS25940 | cyclic‑guanylate‑specific phosphodiesterase PdeF/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2622536 | 2622540 | 5 | 2 [0] | [1] 2 | BW25113_RS25940 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2623009 | 2623027 | 19 | 2 [1] | [1] 2 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2768270 | 2768282 | 13 | 2 [1] | [0] 4 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2877746 | 2877788 | 43 | 2 [1] | [0] 3 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 2988508 | 2988651 | 144 | 2 [1] | [1] 3 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3262628 | 3262746 | 119 | 2 [0] | [1] 2 | yhaC | YhaC family protein |
* | * | ÷ | NZ_CP009273 | 3354473 | 3354481 | 9 | 2 [0] | [0] 2 | gltD/gltF | glutamate synthase subunit GltD/DUF1120 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 3591174 | 3591186 | 13 | 2 [0] | [1] 2 | livK/panM | high‑affinity branched‑chain amino acid ABC transporter substrate‑binding protein LivK/aspartate 1‑decarboxylase autocleavage activator PanM |
* | * | ÷ | NZ_CP009273 | 3790424 | 3790457 | 34 | 3 [1] | [0] 2 | waaL | O‑antigen ligase |
* | * | ÷ | NZ_CP009273 | 3790495 | 3790549 | 55 | 2 [0] | [1] 2 | waaL | O‑antigen ligase |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 61 (3.750) | 34/168 | 0.0 | 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 | = 1391494 | NA (NA) | 12 (0.750) | 6/166 | 0.8 | 92.4% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 1 (0.060) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 18 (1.110) | 13/168 | 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 | 4532499 = | 2 (0.120) | 8 (0.550) | 8/150 | 0.5 | 50.3% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 14 (0.970) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
* | ? | NZ_CP009273 | = 4532507 | 2 (0.120) | 8 (0.550) | 7/150 | 0.6 | 50.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 14 (0.970) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |