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 49,910 T→G W30G (TGG→GGG)  folA → type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 93786 93789 4 2 [0] [0] 2 murD UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase
* * ÷ NZ_CP009273 137740 137763 24 2 [1] [0] 2 gcd/hpt quinoprotein glucose dehydrogenase/hypoxanthine phosphoribosyltransferase
* * ÷ NZ_CP009273 233688 233708 21 2 [1] [1] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 356981 357570 590 2 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380439 380458 20 3 [1] [0] 3 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 428493 428567 75 2 [0] [1] 2 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 469319 469351 33 2 [1] [1] 4 amtB ammonium transporter AmtB
* * ÷ NZ_CP009273 502155 502165 11 2 [1] [0] 2 ybaK Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK
* * ÷ NZ_CP009273 506570 506594 25 3 [1] [1] 2 copA copper‑exporting P‑type ATPase CopA
* * ÷ NZ_CP009273 510075 510155 81 2 [1] [1] 2 ybbJ NfeD family protein
* * ÷ NZ_CP009273 686302 686342 41 2 [1] [1] 2 [lnt] [lnt]
* * ÷ NZ_CP009273 724884 724929 46 2 [1] [1] 2 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 772534 772585 52 2 [1] [1] 2 tolA cell envelope integrity protein TolA
* * ÷ NZ_CP009273 826666 826677 12 2 [0] [1] 3 rhlE ATP‑dependent RNA helicase RhlE
* * ÷ NZ_CP009273 827618 827676 59 2 [1] [1] 2 rhlE ATP‑dependent RNA helicase RhlE
* * ÷ NZ_CP009273 841248 841257 10 4 [1] [0] 2 glnQ glutamine ABC transporter ATP‑binding protein GlnQ
* * ÷ NZ_CP009273 896973 896995 23 2 [1] [1] 2 [artM]–[artQ] [artM],[artQ]
* * ÷ NZ_CP009273 981235 981255 21 2 [1] [1] 2 aspC/ompF aspartate transaminase/porin OmpF
* * ÷ NZ_CP009273 991030 991094 65 2 [1] [1] 2 ssuD FMNH2‑dependent alkanesulfonate monooxygenase
* * ÷ NZ_CP009273 1009079 1009092 14 2 [1] [1] 2 pqiB intermembrane transport protein PqiB
* * ÷ NZ_CP009273 1020977 1021016 40 2 [1] [1] 2 helD DNA helicase IV
* * ÷ NZ_CP009273 1032052 1032076 25 2 [1] [1] 2 hyaE hydrogenase‑1 operon protein HyaE
* * ÷ NZ_CP009273 1032558 1032600 43 2 [1] [1] 2 hyaF hydrogenase expression/formation protein
* * ÷ NZ_CP009273 1059498 1059515 18 3 [0] [1] 3 yccE YccE family protein
* * ÷ NZ_CP009273 1089282 1089321 40 2 [1] [0] 2 dgcT GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1118465 1118538 74 2 [1] [1] 2 yceB lipoprotein
* * ÷ NZ_CP009273 1128120 1128172 53 2 [0] [1] 3 flgE flagellar hook protein FlgE
* * ÷ NZ_CP009273 1138114 1138125 12 3 [1] [1] 5 rne ribonuclease E
* * ÷ NZ_CP009273 1144786 1144883 98 2 [1] [1] 2 fabH beta‑ketoacyl‑ACP synthase III
* * ÷ NZ_CP009273 1167692 1167715 24 2 [1] [0] 2 mfd transcription‑repair coupling factor
* * ÷ NZ_CP009273 1178506 1178567 62 3 [1] [1] 2 potC spermidine/putrescine ABC transporter permease PotC
* * ÷ NZ_CP009273 1189399 1189454 56 2 [1] [0] 2 nudJ phosphatase NudJ
* * ÷ NZ_CP009273 1192692 1192728 37 2 [1] [1] 2 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1193159 1193272 114 2 [1] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1230586 1230648 63 2 [0] [1] 2 fadR fatty acid metabolism transcriptional regulator FadR
* * ÷ NZ_CP009273 1236084 1236090 7 2 [0] [0] 2 cvrA potassium/proton antiporter
* * ÷ NZ_CP009273 1245711 1245719 9 2 [1] [0] 2 dhaK dihydroxyacetone kinase subunit DhaK
* * ÷ NZ_CP009273 1264327 1264406 80 2 [1] [1] 2 kdsA 3‑deoxy‑8‑phosphooctulonate synthase
* * ÷ NZ_CP009273 1274979 1275017 39 2 [1] [1] 2 narK/narG nitrate transporter NarK/nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1280516 1280561 46 2 [1] [1] 2 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1281922 1281923 2 2 [1] [0] 2 narI respiratory nitrate reductase subunit gamma
* * ÷ NZ_CP009273 1286244 1286264 21 4 [0] [1] 2 rssB two‑component system response regulator RssB
* * ÷ NZ_CP009273 1301070 1301147 78 2 [1] [1] 2 [yciU] [yciU]
* * ÷ NZ_CP009273 1303377 1303403 27 2 [1] [0] 2 kch voltage‑gated potassium channel protein
* * ÷ NZ_CP009273 1305425 1305438 14 3 [1] [1] 2 tonB TonB system transport protein TonB
* * ÷ NZ_CP009273 1321236 1321239 4 2 [0] [0] 2 rluB 23S rRNA pseudouridine(2605) synthase RluB
* * ÷ NZ_CP009273 1321442 1321508 67 2 [1] [1] 2 rluB 23S rRNA pseudouridine(2605) synthase RluB
* * ÷ NZ_CP009273 1333952 1333968 17 2 [0] [1] 2 pgpB phosphatidylglycerophosphatase B
* * ÷ NZ_CP009273 1360646 1360664 19 2 [1] [1] 2 puuE 4‑aminobutyrate transaminase
* * ÷ NZ_CP009273 1360961 1360973 13 2 [1] [0] 2 puuE 4‑aminobutyrate transaminase
* * ÷ NZ_CP009273 1362593 1362607 15 2 [1] [1] 2 pspA phage shock protein PspA
* * ÷ NZ_CP009273 1370894 1370897 4 2 [0] [1] 2 ycjR sugar phosphate isomerase/epimerase
* * ÷ NZ_CP009273 1378015 1378045 31 2 [1] [1] 2 ycjW LacI family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 1395505 1395543 39 2 [1] [1] 2 abgT p‑aminobenzoyl‑glutamate transporter
* * ÷ NZ_CP009273 1413661 1413689 29 2 [1] [0] 2 ydaF/racR YdaF family protein/DNA‑binding transcriptional repressor RacR
* * ÷ NZ_CP009273 1451680 1451734 55 2 [0] [1] 2 paaK phenylacetate‑CoA oxygenase/reductase subunit PaaK
* * ÷ NZ_CP009273 1497182 1497183 2 2 [0] [0] 3 ydcL DUF3313 domain‑containing protein
* * ÷ NZ_CP009273 1509348 1509376 29 2 [0] [0] 2 ydcV ABC transporter permease
* * ÷ NZ_CP009273 1540316 1540350 35 2 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1540434 1540460 27 2 [1] [0] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1556333 1556413 81 2 [1] [1] 2 ddpA ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 1592505 1592549 45 2 [1] [1] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1596124 1596147 24 3 [1] [0] 2 lsrA autoinducer 2 ABC transporter ATP‑binding protein LsrA
* * ÷ NZ_CP009273 1694304 1694338 35 2 [1] [1] 3 malX PTS maltose transporter subunit IICB
* * ÷ NZ_CP009273 1701678 1701740 63 2 [1] [1] 5 rsxC electron transport complex subunit RsxC
* * ÷ NZ_CP009273 1741228 1741286 59 2 [1] [1] 2 [ydhR] [ydhR]
* * ÷ NZ_CP009273 1746413 1746422 10 3 [1] [0] 2 ydhV aldehyde ferredoxin oxidoreductase
* * ÷ NZ_CP009273 1764407 1764483 77 2 [1] [0] 2 [ydiK] [ydiK]
* * ÷ NZ_CP009273 1776726 1776736 11 2 [0] [1] 2 ydiS FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 1814306 1814316 11 3 [1] [1] 2 chbC PTS N,N'‑diacetylchitobiose transporter subunit IIC
* * ÷ NZ_CP009273 1819025 1819094 70 2 [0] [1] 3 ves environmental stress‑induced protein Ves
* * ÷ NZ_CP009273 1835322 1835366 45 2 [1] [1] 3 ynjF CDP‑alcohol phosphatidyltransferase family protein
* * ÷ NZ_CP009273 1855724 1855731 8 3 [1] [0] 2 ydjL/yeaC zinc‑binding dehydrogenase/YeaC family protein
* * ÷ NZ_CP009273 1866625 1866634 10 2 [1] [0] 3 dgcJ diguanylate cyclase DgcJ
* * ÷ NZ_CP009273 1899007 1899008 2 4 [0] [1] 7 manZ/yobD PTS mannose transporter subunit IID/DUF986 family protein
* * ÷ NZ_CP009273 1923940 1923969 30 3 [1] [1] 2 [yebE] [yebE]
* * ÷ NZ_CP009273 1936639 1936672 34 2 [1] [0] 2 znuA zinc ABC transporter substrate‑binding protein ZnuA
* * ÷ NZ_CP009273 1940352 1940368 17 2 [0] [1] 2 ruvA/yobI Holliday junction branch migration protein RuvA/stress response small protein YobI
* * ÷ NZ_CP009273 1941059 1941079 21 2 [1] [1] 3 yebB YebB family permuted papain‑like enzyme
* * ÷ NZ_CP009273 1982055 1982120 66 2 [1] [0] 2 yecR/ftnA YecR‑like lipofamily protein/non‑heme ferritin
* * ÷ NZ_CP009273 2001533 2001543 11 3 [1] [1] 2 yedD lipoprotein
* * ÷ NZ_CP009273 2025560 2025591 32 2 [1] [1] 2 dcm DNA‑cytosine methyltransferase
* * ÷ NZ_CP009273 2062054 2062125 72 2 [1] [1] 3 [BW25113_RS24005] [BW25113_RS24005]
* * ÷ NZ_CP009273 2078971 2078994 24 2 [0] [1] 2 yeeE thiosulfate utilization transporter TsuA/YeeE
* * ÷ NZ_CP009273 2097482 2097640 159 2 [1] [1] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2120494 2120499 6 2 [0] [1] 3 fcl GDP‑L‑fucose synthase
* * ÷ NZ_CP009273 2156930 2156941 12 2 [1] [0] 2 baeS two‑component system sensor histidine kinase BaeS
* * ÷ NZ_CP009273 2157465 2157516 52 2 [1] [1] 2 baeS two‑component system sensor histidine kinase BaeS
* * ÷ NZ_CP009273 2169874 2169921 48 2 [1] [1] 2 gatY tagatose‑bisphosphate aldolase subunit GatY
* * ÷ NZ_CP009273 2173305 2173332 28 2 [1] [1] 2 yegT nucleoside permease
* * ÷ NZ_CP009273 2185801 2185918 118 3 [1] [0] 3 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2198848 2198867 20 8 [1] [1] 2 yehL MoxR family ATPase
* * ÷ NZ_CP009273 2250132 2250201 70 2 [0] [1] 2 psuT NupC/NupG family nucleoside CNT transporter
* * ÷ NZ_CP009273 2302896 2302924 29 3 [1] [1] 2 ada bifunctional DNA‑binding transcriptional regulator/O6‑methylguanine‑DNA methyltransferase Ada
* * ÷ NZ_CP009273 2317453 2317465 13 2 [0] [1] 2 atoD acetate CoA‑transferase subunit alpha
* * ÷ NZ_CP009273 2332449 2332504 56 2 [1] [1] 3 gyrA DNA topoisomerase (ATP‑hydrolyzing) subunit A
* * ÷ NZ_CP009273 2338919 2338996 78 2 [1] [1] 2 nrdA ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2370773 2370777 5 2 [1] [0] 2 menH 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
* * ÷ NZ_CP009273 2371542 2371578 37 3 [1] [1] 2 menD 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase
* * ÷ NZ_CP009273 2393003 2393032 30 4 [1] [1] 2 nuoG NADH‑quinone oxidoreductase subunit NuoG
* * ÷ NZ_CP009273 2462824 2462866 43 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2588485 2588533 49 2 [1] [1] 2 tmcA tRNA cytosine(34) acetyltransferase TmcA
* * ÷ NZ_CP009273 2613044 2613076 33 2 [1] [1] 2 uraA uracil permease
* * ÷ NZ_CP009273 2639234 2639279 46 2 [1] [1] 2 pbpC peptidoglycan glycosyltransferase PbpC
* * ÷ NZ_CP009273 2663125 2663132 8 2 [0] [0] 2 hcaE aromatic ring‑hydroxylating dioxygenase subunit alpha
* * ÷ NZ_CP009273 2706861 2706905 45 2 [1] [0] 3 srmB ATP‑dependent RNA helicase SrmB
* * ÷ NZ_CP009273 2826730 2826797 68 2 [1] [1] 2 norV anaerobic nitric oxide reductase flavorubredoxin
* * ÷ NZ_CP009273 2871511 2871545 35 2 [1] [1] 3 iap/cas2e alkaline phosphatase isozyme conversion aminopeptidase/type I‑E CRISPR‑associated endoribonuclease Cas2e
* * ÷ NZ_CP009273 3246091 3246186 96 3 [1] [1] 2 yhaH/yhaI DUF805 domain‑containing protein/DUF805 domain‑containing protein
* * ÷ NZ_CP009273 3285956 3285981 26 7 [1] [0] 3 rsmI 16S rRNA (cytidine(1402)‑2'‑O)‑methyltransferase
* * ÷ NZ_CP009273 3448808 3448836 29 2 [1] [1] 2 gspA/gspC type II secretion system protein GspA/type II secretion system protein GspC
* * ÷ NZ_CP009273 3608093 3608129 37 3 [1] [1] 2 nikA nickel ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 3792579 3792661 83 2 [0] [1] 2 waaU glycosyltransferase family 9 protein
* * ÷ NZ_CP009273 4225897 4225909 13 2 [1] [1] 2 yjbE exopolysaccharide production protein YjbE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)37 (2.930) 28/170 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 = 19727511 (0.080)17 (1.350) 13/170 0.1 94.4% 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 4532499 =3 (0.240)5 (0.440) 5/152 0.6 59.9% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 4 (0.350)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA