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 49,785 C→T intergenic (+154/‑38) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
JC 1,613,496 (CTGGATATTACCGCG)1→2 coding (120/435 nt) marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,754,231 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 307236 307279 44 2 [1] [1] 2 ecpR/BW25113_RS01515 ECP biosynthesis operon DNA‑binding transcriptional regulator EcpR/hypothetical protein
* * ÷ NZ_CP009273 356981 357580 600 2 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 382523 382541 19 2 [1] [1] 2 tauC taurine ABC transporter permease TauC
* * ÷ NZ_CP009273 404815 404821 7 2 [1] [0] 2 rdgC recombination‑associated protein RdgC
* * ÷ NZ_CP009273 578977 579059 83 2 [1] [0] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 587696 587714 19 2 [1] [1] 2 nrfB cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB
* * ÷ NZ_CP009273 716403 716449 47 2 [0] [1] 3 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 738358 738368 11 3 [0] [1] 2 ybgI radiation resistance protein YbgI
* * ÷ NZ_CP009273 785878 785890 13 2 [1] [1] 2 galT galactose‑1‑phosphate uridylyltransferase
* * ÷ NZ_CP009273 806178 806217 40 2 [1] [0] 2 bioF 8‑amino‑7‑oxononanoate synthase
* * ÷ NZ_CP009273 827485 827529 45 5 [0] [1] 2 rhlE ATP‑dependent RNA helicase RhlE
* * ÷ NZ_CP009273 877635 877658 24 2 [1] [1] 2 deoR DNA‑binding transcriptional repressor DeoR
* * ÷ NZ_CP009273 903003 903077 75 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 933389 933436 48 2 [0] [1] 2 lolA outer membrane lipoprotein chaperone LolA
* * ÷ NZ_CP009273 982945 982990 46 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993860 993904 45 2 [0] [1] 2 [elfA] [elfA]
* * ÷ NZ_CP009273 1088364 1088369 6 4 [0] [1] 2 dgcT GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1114555 1114663 109 3 [1] [1] 2 yceJ/BW25113_RS05515 cytochrome b/YceO family protein
* * ÷ NZ_CP009273 1115960 1115995 36 3 [0] [1] 2 solA N‑methyl‑L‑tryptophan oxidase
* * ÷ NZ_CP009273 1118164 1118176 13 2 [1] [1] 2 [yceB] [yceB]
* * ÷ NZ_CP009273 1148897 1148918 22 2 [1] [1] 2 pabC aminodeoxychorismate lyase
* * ÷ NZ_CP009273 1168969 1168992 24 2 [1] [1] 3 mfd transcription‑repair coupling factor
* * ÷ NZ_CP009273 1187379 1187392 14 2 [1] [0] 3 purB adenylosuccinate lyase
* * ÷ NZ_CP009273 1225285 1225323 39 2 [1] [0] 3 hlyE hemolysin HlyE
* * ÷ NZ_CP009273 1258945 1259003 59 2 [1] [0] 2 [lolB] [lolB]
* * ÷ NZ_CP009273 1265262 1265282–1265272 11–21 2 [0] [1] 2 [BW25113_RS06335] [BW25113_RS06335]
* * ÷ NZ_CP009273 1306010 1306029 20 2 [1] [1] 2 tonB TonB system transport protein TonB
* * ÷ NZ_CP009273 1314744 1314820 77 3 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1320930 1320946 17 3 [1] [1] 3 yciQ/rluB DUF2207 domain‑containing protein/23S rRNA pseudouridine(2605) synthase RluB
* * ÷ NZ_CP009273 1359123 1359181 59 4 [1] [0] 3 puuB gamma‑glutamylputrescine oxidase
* * ÷ NZ_CP009273 1370681 1370691 11 2 [0] [0] 2 ycjR sugar phosphate isomerase/epimerase
* * ÷ NZ_CP009273 1384013 1384109 97 2 [1] [1] 2 ycjG L‑Ala‑D/L‑Glu epimerase
* * ÷ NZ_CP009273 1398035 1398089 55 4 [1] [1] 3 abgA p‑aminobenzoyl‑glutamate hydrolase subunit AbgA
* * ÷ NZ_CP009273 1416798 1416814 17 2 [1] [1] 2 ydaV ATP‑binding protein
* * ÷ NZ_CP009273 1433059 1433137 79 2 [1] [1] 2 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1437779 1437813 35 2 [1] [1] 2 ydbH YdbH family protein
* * ÷ NZ_CP009273 1459454 1459482 29 2 [1] [0] 2 BW25113_RS25580 hypothetical protein
* * ÷ NZ_CP009273 1476858 1476882 25 2 [1] [1] 4 azoR FMN‑dependent NADH‑azoreductase
* * ÷ NZ_CP009273 1484045 1484061 17 2 [1] [1] 2 gap type I glyceraldehyde‑3‑phosphate dehydrogenase
* * ÷ NZ_CP009273 1499420 1499493 74 2 [1] [1] 3 ydcO BenE family transporter YdcO
* * ÷ NZ_CP009273 1540288 1540321 34 3 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1541306 1541313 8 2 [1] [1] 2 yddG aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1560914 1560971 58 2 [1] [1] 3 dosC diguanylate cyclase DosC
* * ÷ NZ_CP009273 1576819 1576841 23 2 [1] [1] 2 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1586351 1586363 13 6 [1] [1] 2 hipA type II toxin‑antitoxin system serine/threonine protein kinase toxin HipA
* * ÷ NZ_CP009273 1592539 1592553 15 2 [1] [1] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1598631 1598658 28 2 [0] [1] 3 lsrD autoinducer 2 ABC transporter permease LsrD
* * ÷ NZ_CP009273 1618470 1618485 16 2 [0] [1] 2 ydeI YdeI family stress tolerance OB fold protein
* * ÷ NZ_CP009273 1620493 1620531 39 3 [0] [1] 2 dcp peptidyl‑dipeptidase Dcp
* * ÷ NZ_CP009273 1646924 1646996 73 2 [1] [1] 2 [BW25113_RS25635] [BW25113_RS25635]
* * ÷ NZ_CP009273 1663580 1663600 21 2 [0] [0] 2 ynfL LysR family transcriptional regulator
* * ÷ NZ_CP009273 1663638 1663782 145 3 [1] [1] 2 ynfL LysR family transcriptional regulator
* * ÷ NZ_CP009273 1671486 1671495 10 2 [0] [0] 2 pntA Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha
* * ÷ NZ_CP009273 1681655 1681673 19 3 [1] [1] 2 fumB class I fumarate hydratase
* * ÷ NZ_CP009273 1681952 1681958 7 2 [0] [1] 4 fumB class I fumarate hydratase
* * ÷ NZ_CP009273 1699955 1699985 31 2 [1] [1] 3 ydgK/rsxA DUF2569 domain‑containing protein/electron transport complex subunit RsxA
* * ÷ NZ_CP009273 1731438 1731545 108 2 [1] [1] 3 ydhP MFS transporter
* * ÷ NZ_CP009273 1731671 1731698 28 2 [0] [1] 2 ydhP/ynhF MFS transporter/cytochrome bd‑I accessory subunit CydH
* * ÷ NZ_CP009273 1736312 1736338 27 2 [1] [1] 2 cfa cyclopropane fatty acyl phospholipid synthase
* * ÷ NZ_CP009273 1751448 1751517 70 2 [1] [1] 2 pykF/lpp pyruvate kinase PykF/murein lipoprotein Lpp
* * ÷ NZ_CP009273 1782269 1782320 52 2 [1] [1] 2 ppsR posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR
* * ÷ NZ_CP009273 1808815 1808873 59 2 [1] [1] 2 katE catalase HPII
* * ÷ NZ_CP009273 1819290 1819346 57 2 [1] [0] 2 ves/spy environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
* * ÷ NZ_CP009273 1820549 1820608 60 3 [1] [1] 2 astE succinylglutamate desuccinylase
* * ÷ NZ_CP009273 1823772 1823780 9 2 [1] [0] 2 astD succinylglutamate‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1828943 1828953 11 4 [0] [0] 2 ydjY lipoprotein YdjY
* * ÷ NZ_CP009273 1886959 1886963 5 2 [0] [0] 2 yoaA ATP‑dependent DNA helicase
* * ÷ NZ_CP009273 1888054 1888114 61 2 [1] [1] 2 yoaB/yoaC RidA family protein/DUF1889 family protein
* * ÷ NZ_CP009273 1917576 1917620 45 2 [1] [1] 2 pphA/yebY protein‑serine/threonine phosphatase/YebY family protein
* * ÷ NZ_CP009273 1934477 1934539 63 2 [0] [1] 2 lpxM/mepM lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM
* * ÷ NZ_CP009273 1977196 1977238 43 6 [1] [0] 2 araG arabinose ABC transporter ATP‑binding protein AraG
* * ÷ NZ_CP009273 1992562 1992600 39 4 [1] [1] 2 dcyD D‑cysteine desulfhydrase
* * ÷ NZ_CP009273 2001117 2001197 81 2 [1] [1] 2 [amyA]–[yedD] [amyA],[yedD]
* * ÷ NZ_CP009273 2005548 2005576 29 2 [1] [1] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2010340 2010350 11 2 [0] [1] 2 fliI flagellar protein export ATPase FliI
* * ÷ NZ_CP009273 2033140 2033236 97 2 [1] [1] 3 msrP protein‑methionine‑sulfoxide reductase catalytic subunit MsrP
* * ÷ NZ_CP009273 2051441 2051446 6 2 [1] [1] 2 yeeN/BW25113_RS10360 YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
* * ÷ NZ_CP009273 2081730 2081758 29 4 [1] [1] 2 [yeeY] [yeeY]
* * ÷ NZ_CP009273 2125989 2126064 76 2 [1] [1] 2 [wcaB]–[wcaA] [wcaB],[wcaA]
* * ÷ NZ_CP009273 2142461 2142502 42 2 [1] [1] 2 yegD molecular chaperone
* * ÷ NZ_CP009273 2144474 2144494 21 2 [1] [1] 2 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2156929 2156998 70 2 [1] [1] 2 baeS two‑component system sensor histidine kinase BaeS
* * ÷ NZ_CP009273 2192967 2193025 59 2 [1] [0] 2 BW25113_RS25680 WGR and DUF4132 domain‑containing protein
* * ÷ NZ_CP009273 2222156 2222196 41 2 [1] [0] 2 mdtQ multidrug resistance outer membrane protein MdtQ
* * ÷ NZ_CP009273 2269080 2269093 14 2 [1] [1] 2 yejE ABC transporter permease
* * ÷ NZ_CP009273 2303121 2303149 29 2 [0] [1] 2 ada bifunctional DNA‑binding transcriptional regulator/O6‑methylguanine‑DNA methyltransferase Ada
* * ÷ NZ_CP009273 2359238 2359265 28 2 [1] [1] 2 ais/arnB lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase
* * ÷ NZ_CP009273 2430276 2430281 6 2 [1] [0] 2 pdxB 4‑phosphoerythronate dehydrogenase PdxB
* * ÷ NZ_CP009273 2463180 2463190 11 2 [0] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2494953 2494963 11 3 [1] [1] 2 ypdC AraC family transcriptional regulator
* * ÷ NZ_CP009273 2495753 2495766 14 2 [0] [1] 2 ptsP phosphoenolpyruvate‑‑protein phosphotransferase
* * ÷ NZ_CP009273 2505243 2505270 28 2 [1] [0] 3 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2535184 2535199 16 3 [1] [0] 2 cysT sulfate/thiosulfate ABC transporter permease CysT
* * ÷ NZ_CP009273 2536216 2536231 16 2 [1] [1] 2 cysP thiosulfate/sulfate ABC transporter substrate‑binding protein CysP
* * ÷ NZ_CP009273 2559518 2559538 21 2 [1] [1] 2 eutA ethanolamine ammonia‑lyase reactivating factor EutA
* * ÷ NZ_CP009273 2578015 2578040 26 3 [1] [1] 2 aegA formate‑dependent uric acid utilization protein AegA
* * ÷ NZ_CP009273 2606472 2606496 25 2 [0] [0] 3 hyfR DNA‑binding transcriptional regulator HyfR
* * ÷ NZ_CP009273 2646452 2646460 9 2 [0] [1] 2 sseA 3‑mercaptopyruvate sulfurtransferase
* * ÷ NZ_CP009273 2673342 2673379 38 5 [0] [1] 2 yphG DUF5107 domain‑containing protein
* * ÷ NZ_CP009273 2753665 2753752 88 2 [1] [1] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2843842 2843857 16 2 [1] [1] 3 hycA/hypA formate hydrogenlyase regulator HycA/hydrogenase maturation nickel metallochaperone HypA
* * ÷ NZ_CP009273 3387048 3387067 20 2 [1] [1] 3 yhdP AsmA2 domain‑containing protein YhdP
* * ÷ NZ_CP009273 3628272 3629173 902 29 [0] [0] 2 yhiM DUF2776 domain‑containing protein
* * ÷ NZ_CP009273 3629221 3629650 430 2 [0] [1] 3 [yhiM]–[yhiN] [yhiM],[yhiN]
* * ÷ NZ_CP009273 3629816 3630037 222 2 [1] [1] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630043 3630280 238 2 [1] [1] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630313 3630498 186 2 [1] [1] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630584 3631227 644 2 [1] [1] 2 [yhiN]–[pitA] [yhiN],[pitA]
* * ÷ NZ_CP009273 3631230 3632286 1057 2 [1] [0] 2 pitA inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3632340 3633380 1041 2 [0] [0] 2 [pitA]–uspB [pitA],uspB
* * ÷ NZ_CP009273 3633465 3635559 2095 2 [0] [1] 2 uspA–[dtpB] uspA,BW25113_RS26225,BW25113_RS26230,[dtpB]
* * ÷ NZ_CP009273 3635650 3637210 1561 2 [1] [1] 2 [dtpB]–[prlC] [dtpB],rsmJ,[prlC]
* * ÷ NZ_CP009273 3637244 3637437 194 2 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637494 3637801 308 2 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637821 3638137 317 2 [1] [1] 3 prlC oligopeptidase A
* * ÷ NZ_CP009273 3638183 3638259 77 2 [0] [0] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3638338 3642591 4254 2 [0] [1] 2 [prlC]–[arsB] [prlC],rlmJ,gorA,dinQ,arsR,[arsB]
* * ÷ NZ_CP009273 3642651 3643525 875 2 [1] [1] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3643562 3644141 580 2 [1] [0] 2 [arsB]–arsC [arsB],arsC
* * ÷ NZ_CP009273 3644179 3644229 51 2 [0] [1] 2 arsC/BW25113_RS18155 glutaredoxin‑dependent arsenate reductase/hypothetical protein
* * ÷ NZ_CP009273 3644320 3646519–3645398 1079–2200 2 [1] [1] 3 BW25113_RS18155–[BW25113_RS18160] BW25113_RS18155,[BW25113_RS18160]
* * ÷ NZ_CP009273 3781416 3781427 12 2 [0] [1] 3 envC murein hydrolase activator EnvC
* * ÷ NZ_CP009273 4080276 4080295 20 2 [1] [1] 2 fdhD/yiiG formate dehydrogenase accessory sulfurtransferase FdhD/YiiG family protein
* * ÷ NZ_CP009273 4141268 4141300 33 2 [1] [1] 2 ppc phosphoenolpyruvate carboxylase
* * ÷ NZ_CP009273 4195347 4195352 6 2 [1] [0] 2 purD phosphoribosylamine‑‑glycine ligase
* * ÷ NZ_CP009273 4207538 4207558 21 2 [0] [1] 2 aceA isocitrate lyase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)15 (1.160) 8/168 0.4 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 =4 (0.310)9 (0.860) 9/136 0.2 80.9% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 1 (0.100)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032614 (0.310)7 (0.670) 5/136 0.6 76.8% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 1 (0.100)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727511 (0.080)10 (0.770) 7/168 0.5 90.9% 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 2282399 =NA (NA)29 (2.260) 18/166 0.0 100% pseudogene (2/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3628271 0 (0.000)coding (71/1053 nt) yhiM DUF2776 domain‑containing protein
* ? NZ_CP009273 4532499 =0 (0.000)5 (0.430) 5/150 0.6 58.8% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 7 (0.600)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325070 (0.000)6 (0.520) 6/150 0.5 63.2% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 7 (0.600)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA