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 49,910 T→G W30G (TGG→GGG)  folA → type 3 dihydrofolate reductase
RA 455,677 A→T D445V (GAT→GTT)  lon → endopeptidase La
RA 1,613,393 A→T D6V (GAT→GTT)  marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,511,988 C→A E146* (GAG→TAG)  aroK ← shikimate kinase AroK

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 255909 255930 22 3 [1] [1] 2 phoE/proB phosphoporin PhoE/glutamate 5‑kinase
* * ÷ NZ_CP009273 356981 357569 589 3 [0] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380412 380422 11 3 [1] [0] 3 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 396174 396179 6 2 [0] [1] 3 ddlA D‑alanine‑‑D‑alanine ligase
* * ÷ NZ_CP009273 396637 396679 43 2 [1] [1] 2 [BW25113_RS25915] [BW25113_RS25915]
* * ÷ NZ_CP009273 559279 559319 41 3 [1] [1] 2 [sfmF]–[fimZ] [sfmF],[fimZ]
* * ÷ NZ_CP009273 610518 610562 45 2 [1] [1] 2 entF enterobactin non‑ribosomal peptide synthetase EntF
* * ÷ NZ_CP009273 613529 613587 59 2 [1] [1] 3 entF/wzz(fepE) enterobactin non‑ribosomal peptide synthetase EntF/LPS O‑antigen length regulator Wzz(fepE)
* * ÷ NZ_CP009273 647495 647621 127 2 [0] [1] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 703461 703534 74 2 [1] [1] 2 glnS/chiP glutamine‑‑tRNA ligase/chitoporin
* * ÷ NZ_CP009273 716393 716519 127 2 [1] [1] 3 [kdpE] [kdpE]
* * ÷ NZ_CP009273 719703 719711 9 2 [0] [1] 2 kdpD two‑component system sensor histidine kinase KdpD
* * ÷ NZ_CP009273 724884 724894 11 4 [1] [1] 2 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 725085 725094 10 2 [0] [1] 2 rhsC rhs element protein RhsC
* * ÷ NZ_CP009273 744181 744192 12 3 [0] [1] 2 ybgO fimbrial protein
* * ÷ NZ_CP009273 835559 835569 11 3 [0] [0] 7 fiu catecholate siderophore receptor Fiu
* * ÷ NZ_CP009273 836233 836272 40 2 [0] [1] 2 fiu catecholate siderophore receptor Fiu
* * ÷ NZ_CP009273 839240 839268 29 2 [0] [1] 2 ybiO mechanosensitive channel protein
* * ÷ NZ_CP009273 903012 903039 28 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 950091 950254 164 3 [1] [1] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 982718 982811 94 2 [0] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982903 982948 46 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 989290 989367 78 4 [1] [1] 2 ssuB aliphatic sulfonates ABC transporter ATP‑binding protein
* * ÷ NZ_CP009273 991195 991195 1 2 [0] [0] 3 ssuD FMNH2‑dependent alkanesulfonate monooxygenase
* * ÷ NZ_CP009273 993139 993194 56 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1059487 1059497 11 2 [0] [0] 2 [yccE] [yccE]
* * ÷ NZ_CP009273 1068638 1068683 46 2 [1] [1] 2 rutA pyrimidine utilization protein A
* * ÷ NZ_CP009273 1073959 1074017 59 3 [1] [1] 2 putA trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1074889 1074949 61 2 [1] [1] 2 putP sodium/proline symporter PutP
* * ÷ NZ_CP009273 1088275 1088300 26 2 [1] [1] 2 pgaA/dgcT poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1123979 1124034 56 2 [1] [1] 2 murJ murein biosynthesis integral membrane protein MurJ
* * ÷ NZ_CP009273 1128349 1128383 35 2 [1] [1] 3 flgE flagellar hook protein FlgE
* * ÷ NZ_CP009273 1164381 1164451 71 3 [1] [1] 3 comR/bhsA TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
* * ÷ NZ_CP009273 1165661 1165750 90 3 [1] [1] 2 ldtC L,D‑transpeptidase LdtC
* * ÷ NZ_CP009273 1172286 1172393 108 2 [1] [1] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1172673 1172693 21 2 [1] [0] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1207775 1207803 29 3 [1] [1] 4 BW25113_RS25985/BW25113_RS25535 protein YmgK/hypothetical protein
* * ÷ NZ_CP009273 1209653 1209668 16 2 [0] [1] 3 bluR/bluF DNA‑binding transcriptional repressor BluR/blue light‑responsive regulator BluF
* * ÷ NZ_CP009273 1212148 1212194 47 2 [1] [1] 3 ariR/BW25113_RS06060 biofilm/acid‑resistance regulator AriR/hypothetical protein
* * ÷ NZ_CP009273 1215656 1215735 80 2 [0] [1] 2 BW25113_RS25990 autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1216670 1216696 27 4 [1] [1] 2 BW25113_RS25990 autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1225649 1225748 100 3 [1] [0] 2 hlyE hemolysin HlyE
* * ÷ NZ_CP009273 1225926 1226005 80 2 [1] [1] 3 hlyE/umuD hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit
* * ÷ NZ_CP009273 1229277 1229311 35 2 [1] [1] 3 nhaB Na(+)/H(+) antiporter NhaB
* * ÷ NZ_CP009273 1241775 1241842 68 2 [1] [1] 3 treA alpha,alpha‑trehalase
* * ÷ NZ_CP009273 1255533 1255550 18 2 [0] [1] 2 dauA C4‑dicarboxylic acid transporter DauA
* * ÷ NZ_CP009273 1259560 1259584 25 2 [1] [1] 3 hemA glutamyl‑tRNA reductase
* * ÷ NZ_CP009273 1290368 1290370 3 2 [0] [0] 2 BW25113_RS06460 IS4 family transposase
* * ÷ NZ_CP009273 1299537 1299547 11 2 [0] [1] 3 oppD murein tripeptide/oligopeptide ABC transporter ATP‑binding protein OppD
* * ÷ NZ_CP009273 1301384 1301399 16 2 [1] [0] 3 yciU HI1450 family dsDNA‑mimic protein
* * ÷ NZ_CP009273 1310172 1310216 45 2 [1] [1] 2 yciG general stress protein
* * ÷ NZ_CP009273 1318468 1318506 39 2 [0] [1] 2 yciO L‑threonylcarbamoyladenylate synthase
* * ÷ NZ_CP009273 1320837 1320905 69 2 [1] [0] 2 [yciQ] [yciQ]
* * ÷ NZ_CP009273 1327710 1327782 73 2 [0] [1] 2 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1357079 1357089 11 3 [1] [1] 3 puuC aldehyde dehydrogenase PuuC
* * ÷ NZ_CP009273 1357142 1357180 39 3 [1] [0] 2 puuC aldehyde dehydrogenase PuuC
* * ÷ NZ_CP009273 1357231 1357254 24 2 [0] [1] 2 puuC aldehyde dehydrogenase PuuC
* * ÷ NZ_CP009273 1374115 1374146 32 2 [1] [0] 2 ycjT kojibiose phosphorylase
* * ÷ NZ_CP009273 1375454 1375470 17 2 [1] [1] 2 BW25113_RS06905 ABC transporter ATP‑binding protein
* * ÷ NZ_CP009273 1379347 1379400 54 2 [1] [1] 2 ycjX YcjX family protein
* * ÷ NZ_CP009273 1394694 1394730 37 2 [1] [1] 2 abgT p‑aminobenzoyl‑glutamate transporter
* * ÷ NZ_CP009273 1412911 1412937 27 2 [1] [1] 2 [sieB] [sieB]
* * ÷ NZ_CP009273 1423672 1423778 107 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1434754 1434782 29 2 [0] [1] 2 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1437566 1437582 17 2 [1] [1] 2 ydbH YdbH family protein
* * ÷ NZ_CP009273 1459390 1459519 130 2 [1] [1] 2 BW25113_RS25580 BW25113_RS25580
* * ÷ NZ_CP009273 1500963 1501015 53 2 [1] [1] 2 [sutR] [sutR]
* * ÷ NZ_CP009273 1533651 1533670 20 2 [1] [1] 3 narZ nitrate reductase Z subunit alpha
* * ÷ NZ_CP009273 1539488 1539496 9 2 [0] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540202 1540217 16 3 [1] [0] 2 yddL porin
* * ÷ NZ_CP009273 1540260 1540276 17 2 [0] [1] 2 yddL porin
* * ÷ NZ_CP009273 1540404 1540433 30 2 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1592538 1592553 16 2 [1] [1] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1599851 1599942 92 2 [1] [1] 2 lsrB autoinducer 2 ABC transporter substrate‑binding protein LsrB
* * ÷ NZ_CP009273 1618908 1619008 101 2 [0] [1] 2 ydeI/ydeJ YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase
* * ÷ NZ_CP009273 1631969 1632120 152 2 [1] [1] 2 [gnsB] [gnsB]
* * ÷ NZ_CP009273 1652253 1652350 98 2 [1] [1] 2 [ynfE] [ynfE]
* * ÷ NZ_CP009273 1690592 1690596 5 2 [1] [0] 2 uidA/uidR beta‑glucuronidase/DNA‑binding transcriptional regulator UidR
* * ÷ NZ_CP009273 1692823 1692852 30 2 [1] [1] 2 malI mal regulon transcriptional regulator MalI
* * ÷ NZ_CP009273 1734591 1734601 11 2 [0] [1] 4 punC purine nucleoside transporter PunC
* * ÷ NZ_CP009273 1748945 1749036 92 2 [1] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1764342 1764390 49 2 [1] [1] 2 ydiK AI‑2E family transporter YdiK
* * ÷ NZ_CP009273 1774885 1774903 19 2 [0] [0] 2 ydiR electron transfer flavoprotein subunit alpha
* * ÷ NZ_CP009273 1781500 1781510 11 2 [0] [0] 2 ppsA/ppsR phosphoenolpyruvate synthase/posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR
* * ÷ NZ_CP009273 1797634 1797639 6 3 [1] [0] 2 espL1 type III secretion system effector EspL1
* * ÷ NZ_CP009273 1807423 1807440 18 2 [1] [0] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1811861 1811870 10 5 [0] [1] 2 celF 6‑phospho‑beta‑glucosidase
* * ÷ NZ_CP009273 1836378 1836398 21 2 [1] [1] 2 [ynjH] [ynjH]
* * ÷ NZ_CP009273 1888805 1888863 59 2 [1] [1] 3 [yoaH] [yoaH]
* * ÷ NZ_CP009273 1890752 1890780 29 4 [1] [1] 2 nudL CoA pyrophosphatase
* * ÷ NZ_CP009273 1951926 1951977 52 2 [1] [1] 3 torY NapC/NirT family cytochrome c
* * ÷ NZ_CP009273 1973023 1973047 25 3 [1] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 2001095 2001105 11 2 [0] [0] 3 amyA alpha‑amylase
* * ÷ NZ_CP009273 2011656 2011663 8 2 [1] [1] 3 fliJ flagellar export protein FliJ
* * ÷ NZ_CP009273 2027317 2027453 137 6 [1] [1] 6 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050725 2050751 27 3 [1] [0] 2 yeeN YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2062035 2062090 56 2 [1] [1] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2097136 2097183 48 2 [1] [1] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2097471 2097543 73 3 [1] [1] 3 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2099654 2099731 78 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2102573 2102598 26 2 [0] [0] 3 wzx O16 family O‑antigen flippase
* * ÷ NZ_CP009273 2185819 2185829 11 3 [1] [0] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2217688 2217700 13 2 [1] [1] 2 pbpG D‑alanyl‑D‑alanine endopeptidase
* * ÷ NZ_CP009273 2254510 2254532 23 2 [1] [0] 2 fruA PTS fructose transporter subunit IIBC
* * ÷ NZ_CP009273 2286424 2286478 55 2 [1] [0] 2 [dsbE]–[ccmF] [dsbE],[ccmF]
* * ÷ NZ_CP009273 2330355 2330362 8 3 [0] [0] 4 gyrA DNA topoisomerase (ATP‑hydrolyzing) subunit A
* * ÷ NZ_CP009273 2337801 2337886 86 2 [1] [1] 3 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2345589 2345599 11 5 [0] [1] 3 glpT glycerol‑3‑phosphate transporter
* * ÷ NZ_CP009273 2462811 2462819 9 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463143 2463190 48 2 [0] [1] 5 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463621 2463748 128 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2491902 2491920 19 3 [1] [1] 2 alaC/ypdA alanine transaminase/two‑component system sensor histidine kinase YpdA
* * ÷ NZ_CP009273 2505220 2505258 39 2 [0] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2511705 2511723 19 2 [1] [1] 2 [BW25113_RS12505] [BW25113_RS12505]
* * ÷ NZ_CP009273 2563823 2563847 25 2 [1] [1] 2 eutE aldehyde dehydrogenase EutE
* * ÷ NZ_CP009273 2599362 2599407 46 2 [1] [1] 2 hyfD hydrogenase 4 subunit HyfD
* * ÷ NZ_CP009273 2682717 2682784 68 2 [1] [1] 2 qseG two‑component system QseEF‑associated lipoprotein QseG
* * ÷ NZ_CP009273 2694318 2694331 14 3 [1] [1] 2 acpS holo‑ACP synthase
* * ÷ NZ_CP009273 2765245 2765283 39 2 [1] [0] 2 BW25113_RS13755/BW25113_RS26200 hypothetical protein/arsenate reductase
* * ÷ NZ_CP009273 2766442 2766468 27 2 [1] [1] 2 BW25113_RS13765 arsenic transporter
* * ÷ NZ_CP009273 2779433 2779435 3 2 [1] [0] 2 BW25113_RS13825/BW25113_RS26005 tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2975699 2975709 11 2 [1] [1] 3 araE/kduD arabinose‑proton symporter AraE/2‑dehydro‑3‑deoxy‑D‑gluconate 5‑dehydrogenase KduD
* * ÷ NZ_CP009273 3247097 3247151 55 2 [1] [0] 2 yhaJ DNA‑binding transcriptional regulator YhaJ
* * ÷ NZ_CP009273 3262610 3262641 32 2 [0] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3378658 3378770 113 2 [1] [1] 2 argR/yhcN transcriptional regulator ArgR/peroxide/acid stress response protein YhcN
* * ÷ NZ_CP009273 3763191 3763263 73 2 [0] [1] 3 BW25113_RS26240/yibH Imm57 family immunity protein/HlyD family secretion protein
* * ÷ NZ_CP009273 3792825 3792854 30 2 [1] [1] 2 waaZ 3‑deoxy‑D‑manno‑oct‑2‑ulosonate III transferase WaaZ
* * ÷ NZ_CP009273 3798330 3798404 75 3 [1] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3979644 3979660 17 2 [1] [1] 2 aslA/hemY arylsulfatase AslA/protoheme IX biogenesis protein HemY
* * ÷ NZ_CP009273 4241422 4241432 11 4 [1] [0] 2 BW25113_RS20970 SopA family protein
* * ÷ NZ_CP009273 4250365 4250380 16 2 [1] [0] 3 BW25113_RS21020 DUF2713 domain‑containing protein
* * ÷ NZ_CP009273 4294342 4294369 28 5 [1] [0] 2 ytcA/yjcS YtcA family lipoprotein/alkyl sulfatase YjcS
* * ÷ NZ_CP009273 4316729 4316750 22 2 [1] [1] 4 yjdM/crfC zinc ribbon domain‑containing protein YjdM/clamp‑binding protein CrfC

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 287112NA (NA)15 (1.130) 11/168 0.2 93.8% intergenic (‑55/‑99) BW25113_RS01405/BW25113_RS01410 IS1‑like element IS1B family transposase/hypothetical protein
?NZ_CP009273 1903038 = 1 (0.080)intergenic (‑15/‑144) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
* ? NZ_CP009273 360104 =NA (NA)30 (2.250) 18/168 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 = 1046001NA (NA)15 (1.130) 13/168 0.2 83.3% intergenic (+15/+418) BW25113_RS05135/cspH IS1‑like element IS1D family transposase/cold shock‑like protein CspH
?NZ_CP009273 = 1903046 3 (0.230)intergenic (‑23/‑136) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
* ? NZ_CP009273 1203246 =8 (0.600)3 (0.280) 3/136 1.0 30.8% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 7 (0.650)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032618 (0.600)4 (0.370) 3/136 1.0 37.2% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 7 (0.650)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)5 (0.380) 4/166 1.0 100% 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 = 19727510 (0.000)17 (1.280) 10/168 0.3 100% 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