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 = 12032610 (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 = 1391495NA (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 = 19030722 (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 = 19727510 (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 = 2283591NA (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 = 36292460 (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