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 1,613,378 T→C M1A (GTG→GCG) † marR → multiple antibiotic resistance transcriptional regulator MarR
RA 1,902,956 A→T V23E (GTA→GAA)  mgrB ← PhoP/PhoQ regulator MgrB
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 29403 29439 37 2 [1] [0] 2 dapB/carA 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
* * ÷ NZ_CP009273 118393 118439 47 2 [0] [1] 2 aroP/pdhR aromatic amino acid transporter AroP/pyruvate dehydrogenase complex transcriptional repressor PdhR
* * ÷ NZ_CP009273 233586 233674 89 2 [1] [1] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 327564 327570 7 2 [0] [0] 2 BW25113_RS25450 protein YahV
* * ÷ NZ_CP009273 356971 357574 604 2 [1] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 380361 380383 23 3 [1] [1] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 396637 396678 42 2 [1] [1] 2 [BW25113_RS25915] [BW25113_RS25915]
* * ÷ NZ_CP009273 510053 510096 44 2 [0] [1] 2 ybbJ NfeD family protein
* * ÷ NZ_CP009273 518507 518592 86 2 [1] [1] 2 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 578956 579064 109 3 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 613823 613837 15 2 [1] [1] 2 wzz(fepE) LPS O‑antigen length regulator Wzz(fepE)
* * ÷ NZ_CP009273 632219 632251 33 2 [1] [1] 2 ybdO LysR family transcriptional regulator
* * ÷ NZ_CP009273 647607 647627 21 3 [0] [0] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 674899 674918 20 2 [1] [1] 2 ybeT/ybeU tetratricopeptide repeat protein/DUF1266 domain‑containing protein
* * ÷ NZ_CP009273 724902 724993 92 3 [1] [0] 3 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 734360 734411 52 2 [1] [1] 2 ybfD/ybgA ISAs1 family transposase/YbgA family protein
* * ÷ NZ_CP009273 808696 808711 16 3 [0] [1] 4 bioD/uvrB dethiobiotin synthase/excinuclease ABC subunit UvrB
* * ÷ NZ_CP009273 841597 841619 23 2 [1] [1] 2 glnQ glutamine ABC transporter ATP‑binding protein GlnQ
* * ÷ NZ_CP009273 864164 864170 7 2 [0] [0] 2 gsiA glutathione ABC transporter ATP‑binding protein GsiA
* * ÷ NZ_CP009273 896203 896212 10 2 [1] [1] 4 artJ/artM ABC transporter substrate‑binding protein ArtJ/arginine ABC transporter permease ArtM
* * ÷ NZ_CP009273 902997 903087 91 3 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 908342 908357 16 2 [1] [1] 2 hcp hydroxylamine reductase
* * ÷ NZ_CP009273 914302 914327 26 2 [0] [1] 2 ybjX VirK/YbjX family protein
* * ÷ NZ_CP009273 950054 950131 78 2 [1] [1] 3 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 952932 952960 29 3 [1] [1] 2 ycaP/serC DUF421 domain‑containing protein/3‑phosphoserine/phosphohydroxythreonine transaminase
* * ÷ NZ_CP009273 970587 970595 9 3 [1] [1] 2 mukF chromosome partition protein MukF
* * ÷ NZ_CP009273 993113 993125 13 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 993216 993230 15 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1032560 1032604 45 2 [1] [1] 3 hyaF hydrogenase expression/formation protein
* * ÷ NZ_CP009273 1098840 1098941 102 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1193939 1193966 28 2 [1] [1] 2 BW25113_RS05920/lit hypothetical protein/cell death peptidase Lit
* * ÷ NZ_CP009273 1207466 1207466 1 2 [0] [0] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1208070 1208119 50 2 [1] [0] 2 [BW25113_RS25535] [BW25113_RS25535]
* * ÷ NZ_CP009273 1209636 1209735 100 2 [1] [1] 2 [bluF] [bluF]
* * ÷ NZ_CP009273 1211105 1211180 76 2 [1] [1] 3 bluF/ycgZ blue light‑responsive regulator BluF/regulatory protein YcgZ
* * ÷ NZ_CP009273 1218591 1218657 67 2 [1] [1] 2 [BW25113_RS06100] [BW25113_RS06100]
* * ÷ NZ_CP009273 1225796 1225932 137 2 [1] [1] 3 [hlyE] [hlyE]
* * ÷ NZ_CP009273 1230181 1230261 81 2 [1] [1] 2 nhaB/fadR Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR
* * ÷ NZ_CP009273 1241611 1241679 69 2 [0] [1] 2 treA alpha,alpha‑trehalase
* * ÷ NZ_CP009273 1279560 1279581 22 2 [1] [1] 2 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1309994 1310004 11 2 [0] [1] 2 yciF ferritin‑like domain‑containing protein
* * ÷ NZ_CP009273 1310582 1310635 54 2 [1] [1] 2 yciG/trpA general stress protein/tryptophan synthase subunit alpha
* * ÷ NZ_CP009273 1313792 1313817 26 2 [1] [1] 5 trpCF bifunctional indole‑3‑glycerol‑phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF
* * ÷ NZ_CP009273 1315222 1315303 82 4 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1393393 1393408 16 2 [0] [1] 2 fnr fumarate/nitrate reduction transcriptional regulator Fnr
* * ÷ NZ_CP009273 1408165 1408175 11 2 [1] [1] 2 ralR type I toxin‑antitoxin system endodeoxyribonuclease toxin RalR
* * ÷ NZ_CP009273 1417991 1418064 74 2 [1] [1] 2 [trkG] [trkG]
* * ÷ NZ_CP009273 1424353 1424394 42 3 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1452830 1452845 16 2 [1] [0] 4 paaG 2‑(1,2‑epoxy‑1,2‑dihydrophenyl)acetyl‑CoA isomerase PaaG
* * ÷ NZ_CP009273 1459351 1459366 16 2 [1] [1] 2 paaY/BW25113_RS25580 phenylacetic acid degradation protein PaaY/hypothetical protein
* * ÷ NZ_CP009273 1489371 1489413 43 2 [1] [1] 2 ydcI/ydcJ LysR substrate‑binding domain‑containing protein/VOC family protein
* * ÷ NZ_CP009273 1524422 1524509 88 2 [1] [1] 2 BW25113_RS26145 hypothetical protein
* * ÷ NZ_CP009273 1539715 1539740 26 2 [0] [1] 3 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540302 1540419 118 3 [1] [0] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1572625 1572682 58 3 [1] [1] 2 yddA ABC transporter ATP‑binding protein/permease
* * ÷ NZ_CP009273 1576320 1576368 49 2 [1] [1] 3 ydeN sulfatase
* * ÷ NZ_CP009273 1576937 1576981 45 2 [0] [1] 2 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1580799 1580839 41 2 [0] [1] 3 ydeP/ydeQ acid resistance putative oxidoreductase YdeP/fimbrial protein
* * ÷ NZ_CP009273 1581964 1582000 37 2 [1] [1] 2 [ydeQ] [ydeQ]
* * ÷ NZ_CP009273 1607922 1607951 30 3 [0] [1] 2 sad succinate‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1632920 1632959 40 2 [0] [1] 3 [cspI] [cspI]
* * ÷ NZ_CP009273 1635032 1635034 3 3 [0] [0] 2 essD/ynfU phage lysis protein EssD/putative zinc‑binding protein YnfU
* * ÷ NZ_CP009273 1635235 1635285 51 2 [1] [1] 2 ynfU/cspB putative zinc‑binding protein YnfU/cold shock‑like protein CspB
* * ÷ NZ_CP009273 1651498 1651575 78 2 [1] [1] 2 ynfC YnfC family lipoprotein
* * ÷ NZ_CP009273 1697072 1697074 3 2 [1] [0] 6 add adenosine deaminase
* * ÷ NZ_CP009273 1713963 1714003 41 2 [1] [1] 2 anmK/slyB anhydro‑N‑acetylmuramic acid kinase/outer membrane lipoprotein SlyB
* * ÷ NZ_CP009273 1725629 1725648 20 2 [0] [1] 2 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1754207 1754224 18 2 [1] [1] 2 sufS cysteine desulfurase SufS
* * ÷ NZ_CP009273 1772983 1773022 40 2 [1] [1] 2 ydiP AraC family transcriptional regulator
* * ÷ NZ_CP009273 1781647 1781774 128 2 [1] [1] 2 [ppsR] [ppsR]
* * ÷ NZ_CP009273 1807084 1807135 52 2 [1] [1] 7 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1815460 1815501 42 2 [0] [1] 2 [chbC] [chbC]
* * ÷ NZ_CP009273 1839021 1839125 105 2 [1] [1] 2 ynjI DUF1266 domain‑containing protein
* * ÷ NZ_CP009273 1864723 1864769 47 2 [1] [0] 3 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1871908 1871982 75 2 [1] [0] 2 [dgcP] [dgcP]
* * ÷ NZ_CP009273 1940370 1940507 138 3 [1] [1] 3 yobI yobI
* * ÷ NZ_CP009273 1952422 1952456 35 2 [1] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1952610 1952627 18 3 [0] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1972989 1973024 36 2 [1] [1] 3 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 2021075 2021125 51 4 [1] [1] 4 yedQ cellulose biosynthesis regulator diguanylate cyclase DgcQ
* * ÷ NZ_CP009273 2027328 2027395 68 2 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2031205 2031248 44 2 [1] [1] 2 hprS two‑component system sensor histidine kinase HprS
* * ÷ NZ_CP009273 2036510 2036575 66 2 [1] [1] 2 yodB/BW25113_RS10320 cytochrome b/tRNA‑Ser
* * ÷ NZ_CP009273 2062051 2062107 57 2 [1] [1] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2091870 2091893 24 2 [1] [1] 2 wzzB/ugd LPS O‑antigen chain length determinant protein WzzB/UDP‑glucose 6‑dehydrogenase
* * ÷ NZ_CP009273 2096915 2097027 113 2 [0] [1] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2097435 2097539 105 3 [1] [1] 3 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2099671 2099742 72 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2103002 2103062 61 2 [1] [1] 2 wzx O16 family O‑antigen flippase
* * ÷ NZ_CP009273 2113246 2113258 13 5 [0] [1] 4 wzxC colanic acid undecaprenyl disphosphate flippase WzxC
* * ÷ NZ_CP009273 2113737 2113757 21 2 [1] [1] 2 wcaJ UDP‑glucose‑‑undecaprenyl‑phosphate glucose‑1‑phosphate transferase
* * ÷ NZ_CP009273 2185742 2185848 107 2 [1] [1] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2193829 2193871 43 3 [1] [1] 2 BW25113_RS11045 DUF4132 domain‑containing protein
* * ÷ NZ_CP009273 2224827 2224878 52 2 [1] [1] 2 yohK CidB/LrgB family autolysis modulator
* * ÷ NZ_CP009273 2300371 2300376 6 2 [0] [0] 2 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2357851 2357912 62 3 [1] [1] 2 yfaZ/nudI YfaZ family protein/nucleoside triphosphatase NudI
* * ÷ NZ_CP009273 2381905 2381941 37 4 [1] [1] 2 [BW25113_RS11875] [BW25113_RS11875]
* * ÷ NZ_CP009273 2439785 2439815 31 2 [1] [1] 3 mepA penicillin‑insensitive murein endopeptidase
* * ÷ NZ_CP009273 2449153 2449173 21 2 [0] [1] 3 yfcV/sixA fimbrial protein/phosphohistidine phosphatase SixA
* * ÷ NZ_CP009273 2463106 2463122 17 4 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463206 2463255 50 2 [0] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463684 2463820 137 3 [1] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2547889 2547896 8 4 [1] [0] 3 eutR HTH‑type transcriptional regulator EutR
* * ÷ NZ_CP009273 2568886 2568937 52 2 [1] [1] 2 eutS ethanolamine utilization microcompartment protein EutS
* * ÷ NZ_CP009273 2569343 2569351 9 2 [0] [0] 2 eutS/maeB ethanolamine utilization microcompartment protein EutS/NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase
* * ÷ NZ_CP009273 2576272 2576288 17 2 [1] [1] 2 nudK GDP‑mannose pyrophosphatase NudK
* * ÷ NZ_CP009273 2623010 2623042 33 3 [1] [0] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2623095 2623096 2 2 [0] [1] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2646928 2647009 82 2 [1] [1] 2 sseA/timP 3‑mercaptopyruvate sulfurtransferase/small toxic inner membrane protein TimP
* * ÷ NZ_CP009273 2672224 2672259 36 2 [1] [1] 3 yphF substrate‑binding domain‑containing protein
* * ÷ NZ_CP009273 2694138 2694196 59 2 [1] [1] 3 acpS holo‑ACP synthase
* * ÷ NZ_CP009273 2701149 2701190 42 2 [0] [1] 5 [rseC]–[rseB] [rseC],[rseB]
* * ÷ NZ_CP009273 2753612 2753686 75 3 [1] [0] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2767899 2767959 61 2 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2792335 2792398 64 2 [0] [1] 2 stpA/alaE DNA‑binding protein StpA/L‑alanine exporter AlaE
* * ÷ NZ_CP009273 2897103 2897219 117 2 [1] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2981773 2981778 6 2 [0] [0] 2 yqeH/yqeI helix‑turn‑helix transcriptional regulator/transcriptional regulator
* * ÷ NZ_CP009273 2985443 2985490 48 2 [1] [0] 2 [ygeH] [ygeH]
* * ÷ NZ_CP009273 2988672 2988681 10 2 [1] [1] 2 [BW25113_RS26010] [BW25113_RS26010]
* * ÷ NZ_CP009273 3129909 3129962 54 2 [1] [1] 2 pitB/gss inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase
* * ÷ NZ_CP009273 3176928 3176985 58 3 [1] [1] 3 BW25113_RS25885/ribB hypothetical protein/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
* * ÷ NZ_CP009273 3260843 3260878 36 2 [1] [0] 3 tdcR transcriptional activator TdcR
* * ÷ NZ_CP009273 3367961 3368027 67 3 [1] [1] 2 nanR/dcuC transcriptional regulator NanR/anaerobic C4‑dicarboxylate transporter DcuC
* * ÷ NZ_CP009273 3411570 3411573 4 2 [1] [0] 2 acrF/BW25113_RS16940 multidrug efflux RND transporter permease subunit AcrF/membrane protein
* * ÷ NZ_CP009273 3763203 3763248 46 2 [0] [1] 2 BW25113_RS26240/yibH Imm57 family immunity protein/HlyD family secretion protein
* * ÷ NZ_CP009273 3792666 3792692 27 2 [1] [1] 2 [waaU] [waaU]
* * ÷ NZ_CP009273 3792812 3792866 55 2 [1] [0] 2 waaZ 3‑deoxy‑D‑manno‑oct‑2‑ulosonate III transferase WaaZ
* * ÷ NZ_CP009273 3798469 3798492 24 2 [1] [0] 2 [rfaS] [rfaS]
* * ÷ NZ_CP009273 3881612 3881641 30 2 [0] [1] 2 mnmE/tnaC tRNA uridine‑5‑carboxymethylaminomethyl(34) synthesis GTPase MnmE/tryptophanase leader peptide
* * ÷ NZ_CP009273 3900133 3900202 70 2 [1] [0] 2 bglG/phoU transcriptional antiterminator BglG/phosphate signaling complex protein PhoU
* * ÷ NZ_CP009273 4227068 4227076 9 2 [0] [1] 2 yjbG capsule biosynthesis GfcC family protein
* * ÷ NZ_CP009273 4241741 4241762 22 3 [1] [1] 2 BW25113_RS20970 SopA family protein
* * ÷ NZ_CP009273 4316729 4316824 96 2 [1] [1] 2 yjdM/crfC zinc ribbon domain‑containing protein YjdM/clamp‑binding protein CrfC
* * ÷ NZ_CP009273 4531411 4531498 88 3 [0] [1] 2 fimB/fimE type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)18 (1.310) 14/168 0.1 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)7 (0.630) 7/136 0.4 66.7% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 7 (0.630)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032610 (0.000)7 (0.630) 6/136 0.5 66.7% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 7 (0.630)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727511 (0.070)21 (1.530) 16/168 0.1 95.5% 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