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 | 1,613,576 | A→C | D67A (GAC→GCC) | 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 | 234687 | 234687 | 1 | 2 [0] | [0] 2 | BW25113_RS01090/BW25113_RS01095 | lipoprotein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 356981 | 357574 | 594 | 2 [0] | [1] 2 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 428536 | 428536 | 1 | 2 [0] | [0] 2 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 536743 | 536784 | 42 | 2 [1] | [1] 2 | ybbY | uracil/xanthine transporter |
* | * | ÷ | NZ_CP009273 | 566191 | 566211 | 21 | 2 [1] | [0] 4 | ybcK/ybcL | recombinase family protein/Raf kinase inhibitor‑like protein YbcL |
* | * | ÷ | NZ_CP009273 | 578764 | 578778 | 15 | 2 [0] | [1] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 578869 | 578877 | 9 | 2 [1] | [0] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 578977 | 579139 | 163 | 2 [0] | [1] 2 | [appY] | [appY] |
* | * | ÷ | NZ_CP009273 | 647620 | 647648 | 29 | 2 [0] | [1] 5 | citC/dpiB | [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB |
* | * | ÷ | NZ_CP009273 | 674902 | 674922 | 21 | 5 [1] | [1] 2 | ybeT/ybeU | tetratricopeptide repeat protein/DUF1266 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 716416 | 716496 | 81 | 2 [1] | [1] 3 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 766298 | 766383 | 86 | 2 [1] | [1] 2 | mngB/cydA | mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I |
* | * | ÷ | NZ_CP009273 | 869156 | 869183 | 28 | 2 [1] | [1] 3 | pdeI | EAL domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 950122 | 950245 | 124 | 3 [1] | [1] 5 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 970147 | 970168 | 22 | 2 [1] | [0] 2 | mukF | chromosome partition protein MukF |
* | * | ÷ | NZ_CP009273 | 982933 | 982981 | 49 | 2 [1] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 993226 | 993267 | 42 | 2 [0] | [1] 3 | ssuE/elfA | NADPH‑dependent FMN reductase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1001223 | 1001254 | 32 | 4 [1] | [1] 2 | [pyrD] | [pyrD] |
* | * | ÷ | NZ_CP009273 | 1098840 | 1098925 | 86 | 2 [1] | [1] 3 | csgD/csgB | biofilm master transcriptional regulator CsgD/curli minor subunit CsgB |
* | * | ÷ | NZ_CP009273 | 1158337 | 1158337 | 1 | 2 [0] | [0] 2 | lpoB | penicillin‑binding protein activator LpoB |
* | * | ÷ | NZ_CP009273 | 1164348 | 1164386 | 39 | 2 [1] | [1] 2 | comR/bhsA | TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA |
* | * | ÷ | NZ_CP009273 | 1206611 | 1206713 | 103 | 4 [1] | [1] 2 | [mcrA] | [mcrA] |
* | * | ÷ | NZ_CP009273 | 1208074 | 1208204 | 131 | 2 [1] | [1] 6 | [BW25113_RS25535]–[ycgX] | [BW25113_RS25535],[ycgX] |
* | * | ÷ | NZ_CP009273 | 1225894 | 1225938 | 45 | 2 [0] | [1] 3 | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit |
* | * | ÷ | NZ_CP009273 | 1240579 | 1240616 | 38 | 3 [1] | [1] 6 | [BW25113_RS06225] | [BW25113_RS06225] |
* | * | ÷ | NZ_CP009273 | 1345837 | 1345897 | 61 | 2 [1] | [1] 4 | ycjD | DUF559 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1395650 | 1395652 | 3 | 2 [0] | [1] 4 | abgT | p‑aminobenzoyl‑glutamate transporter |
* | * | ÷ | NZ_CP009273 | 1521141 | 1521201 | 61 | 2 [1] | [1] 2 | [yncH] | [yncH] |
* | * | ÷ | NZ_CP009273 | 1524369 | 1524394 | 26 | 2 [0] | [1] 2 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1539076 | 1539110 | 35 | 2 [0] | [1] 2 | BW25113_RS07710 | leucine‑rich repeat domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1539239 | 1539274 | 36 | 2 [0] | [1] 2 | BW25113_RS07710 | leucine‑rich repeat domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1560758 | 1560816 | 59 | 2 [1] | [0] 2 | dosC | diguanylate cyclase DosC |
* | * | ÷ | NZ_CP009273 | 1566565 | 1566645 | 81 | 3 [1] | [1] 2 | gadB/pqqL | glutamate decarboxylase/insulinase family protein |
* | * | ÷ | NZ_CP009273 | 1573719 | 1573722 | 4 | 2 [0] | [0] 2 | yddA/BW25113_RS25610 | ABC transporter ATP‑binding protein/permease/protein YneP |
* | * | ÷ | NZ_CP009273 | 1577927 | 1578028 | 102 | 3 [1] | [1] 2 | [ydeO]–[safA] | [ydeO],[safA] |
* | * | ÷ | NZ_CP009273 | 1580914 | 1580975 | 62 | 3 [0] | [1] 3 | ydeP/ydeQ | acid resistance putative oxidoreductase YdeP/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1652270 | 1652324 | 55 | 2 [1] | [1] 3 | ynfD/ynfE | DUF1161 domain‑containing protein/dimethyl sulfoxide reductase subunit A |
* | * | ÷ | NZ_CP009273 | 1762564 | 1762574 | 11 | 2 [0] | [1] 2 | ydiJ | FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1800514 | 1800557 | 44 | 3 [1] | [0] 2 | ydiY/pfkB | YdiY family protein/6‑phosphofructokinase II |
* | * | ÷ | NZ_CP009273 | 1806960 | 1806973 | 14 | 2 [1] | [0] 2 | BW25113_RS09050 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1902201 | 1902217 | 17 | 2 [1] | [1] 2 | yobF/yebO | DUF2627 domain‑containing protein/YebO family protein |
* | * | ÷ | NZ_CP009273 | 1972752 | 1972773 | 22 | 50 [0] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 1972982 | 1973101 | 120 | 2 [1] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 1980214 | 1980255 | 42 | 2 [1] | [1] 4 | araF/ftnB | arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein |
* | * | ÷ | NZ_CP009273 | 2021541 | 2021556 | 16 | 2 [0] | [1] 2 | yedQ/yodC | cellulose biosynthesis regulator diguanylate cyclase DgcQ/DUF2158 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2027311 | 2027357 | 47 | 4 [0] | [1] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2027556 | 2027627 | 72 | 2 [1] | [1] 2 | ompC | porin OmpC |
* | * | ÷ | NZ_CP009273 | 2096929 | 2096987 | 59 | 2 [1] | [1] 2 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 2144495 | 2144537 | 43 | 2 [0] | [1] 2 | yegI/yegJ | protein kinase YegI/DUF2314 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2161765 | 2161862 | 98 | 3 [1] | [1] 3 | [BW25113_RS10880] | [BW25113_RS10880] |
* | * | ÷ | NZ_CP009273 | 2176581 | 2176599 | 19 | 2 [1] | [1] 2 | yegX | glycoside hydrolase family 25 protein |
* | * | ÷ | NZ_CP009273 | 2297159 | 2297197 | 39 | 2 [1] | [1] 5 | BW25113_RS25870 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2337830 | 2337866 | 37 | 2 [0] | [1] 2 | yfaL/nrdA | AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 2379246 | 2379286 | 41 | 2 [1] | [0] 2 | yfbK/yfbL | VWA domain‑containing protein/M28 family metallopeptidase |
* | * | ÷ | NZ_CP009273 | 2380309 | 2380379 | 71 | 2 [1] | [1] 2 | [yfbL] | [yfbL] |
* | * | ÷ | NZ_CP009273 | 2462921 | 2462945 | 25 | 2 [0] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2536898 | 2536929 | 32 | 2 [1] | [1] 2 | cysP/ucpA | thiosulfate/sulfate ABC transporter substrate‑binding protein CysP/SDR family oxidoreductase UcpA |
* | * | ÷ | NZ_CP009273 | 2563823 | 2563835 | 13 | 2 [0] | [1] 2 | eutE | aldehyde dehydrogenase EutE |
* | * | ÷ | NZ_CP009273 | 2584452 | 2584495 | 44 | 4 [1] | [0] 2 | ypfM/yffB | protein YpfM/ArsC family reductase |
* | * | ÷ | NZ_CP009273 | 2622475 | 2622490 | 16 | 2 [1] | [1] 2 | [BW25113_RS25940] | [BW25113_RS25940] |
* | * | ÷ | NZ_CP009273 | 2753666 | 2753730 | 65 | 2 [0] | [0] 2 | yfjI | YfjI family protein |
* | * | ÷ | NZ_CP009273 | 2766681 | 2766704 | 24 | 2 [1] | [1] 2 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2778850 | 2778854 | 5 | 3 [0] | [0] 3 | BW25113_RS25705/BW25113_RS13825 | DUF5507 domain‑containing protein/tRNA‑Ile |
* | * | ÷ | NZ_CP009273 | 2877632 | 2877660 | 29 | 3 [1] | [0] 2 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 2877715 | 2877788 | 74 | 2 [0] | [1] 5 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 2897034 | 2897069 | 36 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2897156 | 2897216 | 61 | 2 [1] | [0] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2898952 | 2899003 | 52 | 3 [0] | [1] 2 | BW25113_RS14445 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3178632 | 3178669 | 38 | 2 [1] | [1] 2 | ubiK/ygiL | ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein |
* | * | ÷ | NZ_CP009273 | 3262447 | 3262459 | 13 | 2 [0] | [1] 3 | yhaC | YhaC family protein |
* | * | ÷ | NZ_CP009273 | 3262697 | 3262714 | 18 | 3 [1] | [1] 2 | yhaC | YhaC family protein |
* | * | ÷ | NZ_CP009273 | 3403484 | 3403498 | 15 | 2 [1] | [1] 2 | prmA/dusB | 50S ribosomal protein L11 methyltransferase/tRNA dihydrouridine synthase DusB |
* | * | ÷ | NZ_CP009273 | 3578076 | 3578097 | 22 | 2 [1] | [1] 2 | BW25113_RS25760/yrhB | hypothetical protein/YrhB family protein |
* | * | ÷ | NZ_CP009273 | 3627855 | 3627909 | 55 | 2 [1] | [1] 2 | BW25113_RS18065/yhiM | YhiJ/YhiL family protein/DUF2776 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 3629247 | 3629935 | 689 | 17 [0] | [0] 2 | [yhiM]–[yhiN] | [yhiM],[yhiN] |
* | * | ÷ | NZ_CP009273 | 3629991 | 3633217 | 3227 | 2 [0] | [1] 2 | [yhiN]–uspB | [yhiN],pitA,uspB |
* | * | ÷ | NZ_CP009273 | 3633250 | 3633369 | 120 | 2 [1] | [1] 2 | uspB/uspA | universal stress protein UspB/universal stress protein UspA |
* | * | ÷ | NZ_CP009273 | 3633428 | 3633597 | 170 | 2 [1] | [0] 2 | [uspA] | [uspA] |
* | * | ÷ | NZ_CP009273 | 3633658 | 3638035 | 4378 | 2 [0] | [0] 2 | [uspA]–[prlC] | [uspA],BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,[prlC] |
* | * | ÷ | NZ_CP009273 | 3638102 | 3643425 | 5324 | 2 [0] | [1] 2 | [prlC]–[arsB] | [prlC],rlmJ,gorA,dinQ,arsR,[arsB] |
* | * | ÷ | NZ_CP009273 | 3643515 | 3646525–3645396 | 1882–3011 | 2 [1] | [1] 2 | [arsB]–BW25113_RS18160 | [arsB],arsC,BW25113_RS18155,BW25113_RS18160 |
* | * | ÷ | NZ_CP009273 | 3745299 | 3745330 | 32 | 2 [1] | [0] 2 | yiaT/yiaU | MipA/OmpV family protein/LysR family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 3792820 | 3792847 | 28 | 2 [0] | [1] 2 | waaZ | 3‑deoxy‑D‑manno‑oct‑2‑ulosonate III transferase WaaZ |
* | * | ÷ | NZ_CP009273 | 3794251 | 3794257 | 7 | 2 [0] | [0] 2 | rfaY | lipopolysaccharide core heptose(II) kinase RfaY |
* | * | ÷ | NZ_CP009273 | 3798228 | 3798291 | 64 | 2 [1] | [1] 2 | rfaS | LPS core biosynthesis protein RfaS |
* | * | ÷ | NZ_CP009273 | 3881647 | 3881667 | 21 | 2 [1] | [1] 3 | mnmE/tnaC | tRNA uridine‑5‑carboxymethylaminomethyl(34) synthesis GTPase MnmE/tryptophanase leader peptide |
* | * | ÷ | NZ_CP009273 | 4272224 | 4272251 | 28 | 2 [1] | [0] 2 | espX5 | T3SS effector pentapeptide repeat protein EspX5 |
* | * | ÷ | NZ_CP009273 | 4531655 | 4531673 | 19 | 2 [0] | [1] 2 | fimB/fimE | type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE |
* | * | ÷ | NZ_CP009273 | 4532501 | 4532543 | 43 | 2 [1] | [0] 2 | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
* | * | ÷ | NZ_CP009273 | 4532585 | 4532602 | 18 | 2 [0] | [0] 2 | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
* | * | ÷ | NZ_CP009273 | 4546145 | 4546149 | 5 | 3 [1] | [1] 3 | yjiC/idlP | YjfZ/YjiC family protein/iraD leader peptide IdlP |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 24 (1.330) | 14/164 | 0.2 | 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 = | 0 (0.000) | 13 (0.900) | 9/132 | 0.4 | 92.9% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 2 (0.140) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1203261 | 0 (0.000) | 15 (1.030) | 12/132 | 0.2 | 93.8% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | = 1205058 | 2 (0.140) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391495 | NA (NA) | 25 (1.380) | 15/164 | 0.2 | 100% | intergenic (+146/‑127) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1903069 = | 0 (0.000) | intergenic (‑46/‑113) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein | |||||
* | ? | NZ_CP009273 | = 1903072 | 2 (0.110) | 18 (1.000) | 15/164 | 0.2 | 90.0% | intergenic (‑49/‑110) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein |
? | NZ_CP009273 | = 2096424 | NA (NA) | intergenic (‑68/+3) | BW25113_RS10605/wbbL | IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 50 (2.770) | 32/164 | 0.0 | 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) | 27 (1.490) | 14/164 | 0.2 | 100% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | 3512437 = | 0 (0.000) | intergenic (‑14/+387) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
* | ? | NZ_CP009273 | = 2283591 | NA (NA) | 17 (0.950) | 14/162 | 0.2 | 100% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
? | NZ_CP009273 | = 3512441 | 0 (0.000) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
* | ? | NZ_CP009273 | = 3629246 | 0 (0.000) | 16 (0.890) | 12/164 | 0.4 | 100% | coding (1046/1053 nt) | yhiM | DUF2776 domain‑containing protein |
? | NZ_CP009273 | 3645396 = | NA (NA) | pseudogene (746/747 nt) | BW25113_RS18155 | hypothetical protein |