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 49,780 C→T intergenic (+149/‑43) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
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 153596 153612 17 2 [1] [1] 3 yadN/folK fimbrial protein/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase
* * ÷ NZ_CP009273 153666 153744 79 3 [1] [1] 2 [folK] [folK]
* * ÷ NZ_CP009273 233670 233761 92 2 [1] [0] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 255911 255940 30 2 [0] [1] 3 phoE/proB phosphoporin PhoE/glutamate 5‑kinase
* * ÷ NZ_CP009273 356974 357574 601 2 [1] [1] 3 [lacA] [lacA]
* * ÷ NZ_CP009273 558633 558643 11 4 [1] [0] 2 fimH type 1 fimbria D‑mannose specific adhesin FimH
* * ÷ NZ_CP009273 579023 579080 58 2 [1] [1] 3 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 703507 703520 14 2 [1] [1] 2 glnS/chiP glutamine‑‑tRNA ligase/chitoporin
* * ÷ NZ_CP009273 712123 712138 16 2 [1] [1] 2 BW25113_RS03565/BW25113_RS03570 DUF2625 domain‑containing protein/winged helix‑turn‑helix domain‑containing protein
* * ÷ NZ_CP009273 716471 716526 56 2 [1] [1] 2 [kdpE] [kdpE]
* * ÷ NZ_CP009273 724755 724770 16 2 [0] [1] 2 ybfA YbfA family protein
* * ÷ NZ_CP009273 774511 774556 46 2 [1] [1] 2 [pal] [pal]
* * ÷ NZ_CP009273 823480 823492 13 3 [1] [1] 2 ybhF ATP‑binding cassette domain‑containing protein
* * ÷ NZ_CP009273 868459 868469 11 2 [1] [0] 2 pdeI EAL domain‑containing protein
* * ÷ NZ_CP009273 903000 903070 71 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 937017 937033 17 3 [1] [1] 2 dmsA dimethylsulfoxide reductase subunit A
* * ÷ NZ_CP009273 982911 983008 98 3 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993029 993035 7 2 [0] [0] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1000064 1000085 22 2 [1] [1] 2 ycbF fimbrial chaperone
* * ÷ NZ_CP009273 1038970 1038998 29 2 [1] [1] 2 etk tyrosine‑protein kinase
* * ÷ NZ_CP009273 1108084 1108125 42 2 [1] [1] 2 mdoH glucans biosynthesis glucosyltransferase MdoH
* * ÷ NZ_CP009273 1141844 1141865 22 2 [0] [1] 2 yceF 7‑methyl‑GTP pyrophosphatase
* * ÷ NZ_CP009273 1141961 1141964 4 3 [0] [1] 2 yceF 7‑methyl‑GTP pyrophosphatase
* * ÷ NZ_CP009273 1167786 1167805 20 3 [0] [1] 2 mfd transcription‑repair coupling factor
* * ÷ NZ_CP009273 1172121 1172186 66 3 [1] [1] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1174748 1174772 25 2 [0] [0] 3 nagK N‑acetylglucosamine kinase
* * ÷ NZ_CP009273 1187249 1187309 61 2 [1] [1] 2 purB adenylosuccinate lyase
* * ÷ NZ_CP009273 1207529 1207640 112 2 [1] [1] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1213758 1213773 16 3 [1] [1] 2 pdeG cyclic diguanylate phosphodiesterase
* * ÷ NZ_CP009273 1234835 1234868 34 2 [1] [1] 3 dadX catabolic alanine racemase DadX
* * ÷ NZ_CP009273 1287878 1287901 24 2 [0] [1] 2 galU/hns UTP‑‑glucose‑1‑phosphate uridylyltransferase GalU/DNA‑binding transcriptional regulator H‑NS
* * ÷ NZ_CP009273 1314757 1314809 53 2 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1327875 1327890 16 2 [1] [0] 4 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1341089 1341117 29 2 [1] [0] 2 BW25113_RS25050 hypothetical protein
* * ÷ NZ_CP009273 1368046 1368064 19 2 [0] [1] 2 ycjO sugar ABC transporter permease
* * ÷ NZ_CP009273 1369233 1369245 13 3 [1] [1] 3 ycjQ zinc‑binding alcohol dehydrogenase
* * ÷ NZ_CP009273 1403103 1403113 11 6 [1] [1] 4 zntB zinc transporter ZntB
* * ÷ NZ_CP009273 1407244 1407275 32 3 [1] [1] 2 intR site‑specific integrase
* * ÷ NZ_CP009273 1407946 1408003 58 2 [1] [1] 2 [rcbA]–[ralR] [rcbA],[ralR]
* * ÷ NZ_CP009273 1428684 1428754 71 3 [1] [1] 2 BW25113_RS25575/uspF hypothetical protein/universal stress protein UspF
* * ÷ NZ_CP009273 1431252 1431319 68 2 [1] [1] 2 ompN/nifJ porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1432842 1432869 28 2 [1] [1] 2 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1492448 1492489 42 2 [0] [1] 2 opgD glucan biosynthesis protein OpgD
* * ÷ NZ_CP009273 1535516 1535561 46 2 [1] [1] 2 narZ nitrate reductase Z subunit alpha
* * ÷ NZ_CP009273 1539195 1539211 17 2 [1] [1] 3 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539514 1539529 16 2 [0] [0] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1566539 1566581 43 2 [0] [1] 2 gadB/pqqL glutamate decarboxylase/insulinase family protein
* * ÷ NZ_CP009273 1592508 1592566 59 3 [1] [1] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1592816 1592882 67 2 [0] [0] 2 [lsrK] [lsrK]
* * ÷ NZ_CP009273 1606133 1606163 31 2 [1] [1] 2 [dgcF] [dgcF]
* * ÷ NZ_CP009273 1621367 1621373 7 2 [1] [1] 2 dcp peptidyl‑dipeptidase Dcp
* * ÷ NZ_CP009273 1623517 1623529 13 5 [1] [0] 2 ydfZ putative selenium delivery protein YdfZ
* * ÷ NZ_CP009273 1625162 1625191 30 2 [1] [1] 2 [ydfI] [ydfI]
* * ÷ NZ_CP009273 1631648 1631708 61 2 [0] [1] 5 ydfO DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1635213 1635285 73 4 [1] [1] 3 [ynfU] [ynfU]
* * ÷ NZ_CP009273 1663836 1663861 26 2 [0] [0] 2 [ynfL] [ynfL]
* * ÷ NZ_CP009273 1667397 1667452 56 2 [1] [1] 2 mdtJ multidrug/spermidine efflux SMR transporter subunit MdtJ
* * ÷ NZ_CP009273 1671494 1671572 79 3 [0] [1] 2 pntA Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha
* * ÷ NZ_CP009273 1704881 1704924 44 3 [1] [1] 2 rsxG electron transport complex subunit RsxG
* * ÷ NZ_CP009273 1722446 1722486 41 2 [1] [1] 2 gloA lactoylglutathione lyase
* * ÷ NZ_CP009273 1725504 1725529 26 2 [1] [1] 2 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1731702 1731723 22 2 [1] [1] 2 [ynhF] [ynhF]
* * ÷ NZ_CP009273 1749067 1749119 53 2 [1] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1766637 1766668 32 2 [1] [1] 2 ydiM/ydiN MFS transporter/MFS transporter
* * ÷ NZ_CP009273 1769327 1769351 25 2 [0] [1] 2 aroD type I 3‑dehydroquinate dehydratase
* * ÷ NZ_CP009273 1783521 1783741 221 3 [1] [1] 3 [aroH] [aroH]
* * ÷ NZ_CP009273 1800482 1800556 75 3 [1] [1] 2 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 1807071 1807152 82 2 [1] [1] 4 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1807352 1807490 139 2 [1] [1] 3 [BW25113_RS09050] [BW25113_RS09050]
* * ÷ NZ_CP009273 1819178 1819197 20 4 [1] [0] 2 [ves] [ves]
* * ÷ NZ_CP009273 1824612 1824614 3 2 [0] [0] 2 astA arginine N‑succinyltransferase
* * ÷ NZ_CP009273 1830160 1830175 16 2 [1] [1] 2 ynjA carboxymuconolactone decarboxylase family protein
* * ÷ NZ_CP009273 1864319 1864346 28 3 [1] [1] 2 yeaH YeaH/YhbH family protein
* * ÷ NZ_CP009273 1888079 1888119 41 2 [0] [0] 2 yoaB/yoaC RidA family protein/DUF1889 family protein
* * ÷ NZ_CP009273 1901723 1901724 2 3 [0] [1] 3 yobF DUF2627 domain‑containing protein
* * ÷ NZ_CP009273 1902633 1902667 35 2 [1] [1] 2 yebO YebO family protein
* * ÷ NZ_CP009273 1902948 1903002 55 3 [1] [1] 2 mgrB PhoP/PhoQ regulator MgrB
* * ÷ NZ_CP009273 1924785 1924796 12 2 [1] [1] 2 yebG DNA damage‑inducible protein YebG
* * ÷ NZ_CP009273 1981485 1981564 80 3 [1] [1] 2 azuC/yecR stress response protein AzuC/YecR‑like lipofamily protein
* * ÷ NZ_CP009273 1983677 1983687 11 2 [0] [1] 2 tyrP tyrosine transporter TyrP
* * ÷ NZ_CP009273 2004713 2004742 30 3 [1] [1] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2027114 2027129 16 2 [0] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2027297 2027372 76 4 [0] [0] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2034683 2034714 32 3 [1] [1] 2 msrQ/zinT protein‑methionine‑sulfoxide reductase heme‑binding subunit MsrQ/metal‑binding protein ZinT
* * ÷ NZ_CP009273 2035621 2035631 11 3 [1] [0] 2 zinT/yodB metal‑binding protein ZinT/cytochrome b
* * ÷ NZ_CP009273 2051100 2051162 63 3 [1] [0] 2 yeeN/BW25113_RS10360 YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
* * ÷ NZ_CP009273 2052494 2052542 49 4 [1] [1] 2 yeeO toxic metabolite efflux MATE transporter YeeO
* * ÷ NZ_CP009273 2062053 2062107 55 3 [1] [0] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2097092 2097175 84 2 [1] [1] 3 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2097542 2097577 36 2 [1] [0] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2100652 2100677 26 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2145165 2145207 43 2 [1] [1] 2 [pphC] [pphC]
* * ÷ NZ_CP009273 2243133 2243143 11 2 [0] [1] 2 yeiE/yeiH DNA‑binding transcriptional regulator YeiE/YeiH family protein
* * ÷ NZ_CP009273 2246118 2246126 9 3 [1] [0] 4 yeiI sugar kinase
* * ÷ NZ_CP009273 2285526 2285536 11 2 [0] [0] 3 ccmH cytochrome c‑type biogenesis thiol:disulfide oxidoreductase CcmH
* * ÷ NZ_CP009273 2337801 2337854 54 3 [1] [1] 2 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2345102 2345107 6 2 [1] [1] 2 glpT glycerol‑3‑phosphate transporter
* * ÷ NZ_CP009273 2409979 2410001 23 2 [1] [1] 4 pta phosphate acetyltransferase
* * ÷ NZ_CP009273 2418063 2418076 14 4 [0] [0] 2 hisM ABC transporter permease
* * ÷ NZ_CP009273 2463180 2463234 55 3 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463647 2463768 122 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2563805 2563857 53 2 [1] [1] 3 eutE aldehyde dehydrogenase EutE
* * ÷ NZ_CP009273 2590106 2590111 6 3 [0] [0] 2 ypfJ/purC neutral zinc metallopeptidase/phosphoribosylaminoimidazolesuccinocarboxamide synthase
* * ÷ NZ_CP009273 2646998 2647063 66 3 [1] [1] 3 sseA/timP 3‑mercaptopyruvate sulfurtransferase/small toxic inner membrane protein TimP
* * ÷ NZ_CP009273 2740237 2740263 27 2 [1] [1] 2 ffh signal recognition particle protein
* * ÷ NZ_CP009273 2745116 2745121 6 2 [0] [1] 2 nadK/recN NAD(+) kinase/DNA repair protein RecN
* * ÷ NZ_CP009273 2779433 2779449 17 4 [0] [0] 2 BW25113_RS13825/BW25113_RS26005 tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2784738 2784757 20 2 [1] [1] 2 gabD NADP‑dependent succinate‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 2897143 2897209 67 2 [1] [0] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2898964 2898995 32 2 [1] [0] 2 BW25113_RS14445 hypothetical protein
* * ÷ NZ_CP009273 3017591 3017601 11 2 [1] [1] 2 xdhD/xanQ molybdopterin‑dependent oxidoreductase Mo/Fe‑S‑binding subunit/xanthine/proton symporter XanQ
* * ÷ NZ_CP009273 3081376 3081415 40 2 [1] [1] 2 metK/galP methionine adenosyltransferase/galactose/proton symporter
* * ÷ NZ_CP009273 3262583 3262668 86 2 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3280599 3280635 37 2 [0] [1] 3 agaI/yraH galactosamine‑6‑phosphate isomerase/fimbrial protein
* * ÷ NZ_CP009273 3354287 3354309 23 2 [1] [0] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3463358 3463423 66 2 [1] [1] 2 chiA/tuf bifunctional chitinase/lysozyme/elongation factor Tu
* * ÷ NZ_CP009273 3505726 3505736 11 3 [1] [0] 6 BW25113_RS17530/trpS GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase
* * ÷ NZ_CP009273 3576442 3576452 11 3 [0] [1] 3 BW25113_RS17825 YrhA family protein
* * ÷ NZ_CP009273 3798382 3798455 74 2 [1] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 4089790 4089816 27 2 [1] [1] 2 rhaT L‑rhamnose/proton symporter RhaT
* * ÷ NZ_CP009273 4258422 4258501 80 3 [1] [1] 3 tyrB/BW25113_RS26020 aromatic amino acid transaminase/hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 287112NA (NA)7 (0.520) 6/168 0.7 100% intergenic (‑55/‑99) BW25113_RS01405/BW25113_RS01410 IS1‑like element IS1B family transposase/hypothetical protein
?NZ_CP009273 1903038 = 0 (0.000)intergenic (‑15/‑144) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
* ? NZ_CP009273 360104 =NA (NA)25 (1.870) 20/168 0.0 52.1% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 23 (1.720)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 = 1046001NA (NA)7 (0.520) 6/168 0.7 100% intergenic (+15/+418) BW25113_RS05135/cspH IS1‑like element IS1D family transposase/cold shock‑like protein CspH
?NZ_CP009273 = 1903046 0 (0.000)intergenic (‑23/‑136) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
* ? NZ_CP009273 1203246 =6 (0.450)5 (0.460) 4/136 0.8 45.8% 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 = 1391494NA (NA)9 (0.680) 5/166 0.8 100% 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)18 (1.350) 11/168 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