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 1,613,576 A→C D67A (GAC→GCC)  marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 235120 235139 20 3 [0] [1] 2 BW25113_RS01095 hypothetical protein
* * ÷ NZ_CP009273 356966 357567 602 2 [1] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 428519 428539 21 2 [1] [0] 2 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 472110 472125 16 2 [1] [0] 2 ffs/ybaA signal recognition particle sRNA small type/DUF1428 domain‑containing protein
* * ÷ NZ_CP009273 476533 476576 44 2 [1] [1] 2 tomB/acrB Hha toxicity modulator TomB/efflux RND transporter permease AcrB
* * ÷ NZ_CP009273 523342 523399 58 2 [1] [1] 3 ybbC YbbC/YhhH family protein
* * ÷ NZ_CP009273 532831 532837 7 2 [1] [1] 3 glxR 2‑hydroxy‑3‑oxopropionate reductase
* * ÷ NZ_CP009273 600235 600251 17 2 [0] [1] 2 nfsB oxygen‑insensitive NAD(P)H nitroreductase
* * ÷ NZ_CP009273 618484 618488 5 2 [1] [0] 2 entS enterobactin transporter EntS
* * ÷ NZ_CP009273 656858 656890 33 2 [1] [1] 2 ybeF/lipB YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB
* * ÷ NZ_CP009273 674899 674928 30 3 [1] [1] 2 ybeT/ybeU tetratricopeptide repeat protein/DUF1266 domain‑containing protein
* * ÷ NZ_CP009273 703923 703931 9 2 [1] [0] 4 chiP chitoporin
* * ÷ NZ_CP009273 716379 716416 38 2 [1] [0] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 769935 769972 38 2 [1] [1] 2 ybgE cyd operon protein YbgE
* * ÷ NZ_CP009273 772345 772355 11 2 [1] [0] 2 tolA cell envelope integrity protein TolA
* * ÷ NZ_CP009273 860465 860486 22 2 [0] [1] 3 moeB molybdopterin‑synthase adenylyltransferase MoeB
* * ÷ NZ_CP009273 864517 864575 59 2 [1] [1] 2 gsiA glutathione ABC transporter ATP‑binding protein GsiA
* * ÷ NZ_CP009273 868454 868516 63 2 [1] [0] 2 pdeI EAL domain‑containing protein
* * ÷ NZ_CP009273 950178 950212 35 2 [0] [1] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 993220 993267 48 3 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1016561 1016590 30 2 [1] [1] 2 sulA/sxy cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy
* * ÷ NZ_CP009273 1032517 1032589 73 2 [1] [1] 2 hyaF hydrogenase expression/formation protein
* * ÷ NZ_CP009273 1032702 1032717 16 2 [0] [1] 2 hyaF hydrogenase expression/formation protein
* * ÷ NZ_CP009273 1088096 1088106 11 2 [0] [1] 2 pgaA/dgcT poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1113803 1113816 14 2 [0] [1] 2 yceI YceI family protein
* * ÷ NZ_CP009273 1164353 1164420 68 2 [1] [1] 2 comR/bhsA TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
* * ÷ NZ_CP009273 1165713 1165750 38 2 [1] [0] 2 ldtC L,D‑transpeptidase LdtC
* * ÷ NZ_CP009273 1205059 1205074 16 15 [0] [0] 7 BW25113_RS06005 phage tail protein
* * ÷ NZ_CP009273 1211816 1211836 21 4 [1] [0] 4 [ariR] [ariR]
* * ÷ NZ_CP009273 1225762 1225785 24 2 [1] [1] 2 hlyE hemolysin HlyE
* * ÷ NZ_CP009273 1301408 1301418 11 2 [1] [0] 2 yciU/cls HI1450 family dsDNA‑mimic protein/cardiolipin synthase
* * ÷ NZ_CP009273 1433488 1433498 11 2 [0] [1] 2 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1445116 1445139 24 2 [1] [1] 2 tynA primary‑amine oxidase
* * ÷ NZ_CP009273 1461155 1461163 9 2 [1] [1] 2 BW25113_RS07350 autotransporter domain‑containing protein
* * ÷ NZ_CP009273 1476925 1476994 70 2 [1] [1] 3 azoR FMN‑dependent NADH‑azoreductase
* * ÷ NZ_CP009273 1486698 1486707 10 3 [0] [1] 2 BW25113_RS26140/trg hypothetical protein/methyl‑accepting chemotaxis protein Trg
* * ÷ NZ_CP009273 1524312 1524394 83 3 [1] [1] 2 BW25113_RS07645/BW25113_RS26145 RHS repeat protein/hypothetical protein
* * ÷ NZ_CP009273 1528460 1528497 38 2 [1] [0] 2 nhoA N‑hydroxyarylamine O‑acetyltransferase
* * ÷ NZ_CP009273 1595183 1595192 10 2 [1] [0] 2 lsrR transcriptional regulator LsrR
* * ÷ NZ_CP009273 1622885 1622899 15 2 [1] [1] 2 ydfH DNA‑binding transcriptional regulator rspR
* * ÷ NZ_CP009273 1658114 1658123 10 2 [1] [0] 2 ynfH dimethyl sulfoxide reductase anchor subunit
* * ÷ NZ_CP009273 1663836 1663920 85 2 [1] [1] 2 [ynfL] [ynfL]
* * ÷ NZ_CP009273 1725387 1725411 25 2 [0] [1] 2 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1725650 1725714 65 2 [1] [1] 2 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1800462 1800492 31 3 [0] [1] 2 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 1839514 1839538 25 2 [1] [1] 2 topB DNA topoisomerase III
* * ÷ NZ_CP009273 1841779 1841869 91 2 [1] [1] 2 selD selenide, water dikinase SelD
* * ÷ NZ_CP009273 1972752 1972760 9 16 [0] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 1982093 1982099 7 3 [0] [1] 2 yecR/ftnA YecR‑like lipofamily protein/non‑heme ferritin
* * ÷ NZ_CP009273 1994548 1994579 32 3 [1] [1] 2 [fliA] [fliA]
* * ÷ NZ_CP009273 2035752 2035796 45 3 [1] [1] 2 zinT/yodB metal‑binding protein ZinT/cytochrome b
* * ÷ NZ_CP009273 2078236 2078246 11 3 [1] [1] 2 yeeE thiosulfate utilization transporter TsuA/YeeE
* * ÷ NZ_CP009273 2152844 2152937 94 2 [1] [0] 2 mdtC multidrug efflux RND transporter permease subunit MdtC
* * ÷ NZ_CP009273 2243113 2243159 47 2 [1] [1] 2 yeiE/yeiH DNA‑binding transcriptional regulator YeiE/YeiH family protein
* * ÷ NZ_CP009273 2257456 2257481 26 3 [1] [0] 3 setB sugar efflux transporter SetB
* * ÷ NZ_CP009273 2337795 2337840 46 2 [1] [0] 2 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2348038 2348066 29 2 [1] [1] 3 glpB glycerol‑3‑phosphate dehydrogenase subunit GlpB
* * ÷ NZ_CP009273 2348322 2348330 9 2 [0] [0] 2 glpB glycerol‑3‑phosphate dehydrogenase subunit GlpB
* * ÷ NZ_CP009273 2371940 2371965 26 2 [1] [1] 2 menD 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase
* * ÷ NZ_CP009273 2376886 2376938 53 2 [1] [1] 2 elaD deubiquitinase ElaD
* * ÷ NZ_CP009273 2553589 2553610 22 4 [1] [1] 2 intZ/BW25113_RS12740 integrase arm‑type DNA‑binding domain‑containing protein/hypothetical protein
* * ÷ NZ_CP009273 2559185 2559190 6 2 [1] [0] 2 eutA ethanolamine ammonia‑lyase reactivating factor EutA
* * ÷ NZ_CP009273 2563818 2563838 21 2 [0] [1] 2 eutE aldehyde dehydrogenase EutE
* * ÷ NZ_CP009273 2590640 2590665 26 2 [0] [1] 2 purC phosphoribosylaminoimidazolesuccinocarboxamide synthase
* * ÷ NZ_CP009273 2608191 2608219 29 3 [1] [1] 3 yfgO AI‑2E family transporter
* * ÷ NZ_CP009273 2687778 2687812 35 2 [1] [1] 2 purL phosphoribosylformylglycinamidine synthase
* * ÷ NZ_CP009273 2767746 2767818 73 2 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2767936 2767962 27 2 [1] [1] 3 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2828071 2828115 45 2 [1] [1] 2 norW NADH:flavorubredoxin reductase NorW
* * ÷ NZ_CP009273 2897187 2897208 22 2 [1] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2899870 2899907 38 3 [0] [1] 2 ygcG YgcG family protein
* * ÷ NZ_CP009273 3129928 3129960 33 2 [0] [1] 2 pitB/gss inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase
* * ÷ NZ_CP009273 3227061 3227067 7 2 [0] [1] 2 fadH/higA NADPH‑dependent 2,4‑dienoyl‑CoA reductase/type II toxin‑antitoxin system antitoxin HigA
* * ÷ NZ_CP009273 3348744 3348748 5 4 [0] [1] 3 gltB glutamate synthase large subunit
* * ÷ NZ_CP009273 3354270 3354288 19 2 [1] [1] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3533012 3533018 7 3 [1] [0] 2 yhgF Tex family protein
* * ÷ NZ_CP009273 3629247 3631082 1836 22 [0] [0] 2 [yhiM]–[pitA] [yhiM],yhiN,[pitA]
* * ÷ NZ_CP009273 3631131 3631604 474 2 [0] [0] 2 pitA inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3631688 3633223 1536 2 [0] [1] 2 [pitA]–uspB [pitA],uspB
* * ÷ NZ_CP009273 3633261 3634583 1323 2 [1] [1] 2 uspA–[dtpB] uspA,BW25113_RS26225,BW25113_RS26230,[dtpB]
* * ÷ NZ_CP009273 3634600 3634697 98 2 [1] [0] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3634777 3635118 342 2 [0] [1] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3635206 3635298 93 2 [1] [1] 2 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3635389 3636121 733 2 [1] [1] 2 [dtpB]–[rsmJ] [dtpB],[rsmJ]
* * ÷ NZ_CP009273 3636202 3637124 923 2 [1] [1] 2 [rsmJ]–[prlC] [rsmJ],[prlC]
* * ÷ NZ_CP009273 3637215 3637414 200 2 [1] [0] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637475 3637634 160 2 [0] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637645 3637833 189 2 [1] [1] 3 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637897 3640799 2903 3 [1] [1] 2 [prlC]–[gorA] [prlC],rlmJ,[gorA]
* * ÷ NZ_CP009273 3640953 3641700 748 2 [1] [0] 2 [gorA]–dinQ [gorA],dinQ
* * ÷ NZ_CP009273 3641789 3643123 1335 2 [0] [1] 2 arsR–[arsB] arsR,[arsB]
* * ÷ NZ_CP009273 3643272 3644188 917 2 [1] [1] 2 [arsB]–arsC [arsB],arsC
* * ÷ NZ_CP009273 3644251 3644409 159 2 [1] [0] 2 arsC/BW25113_RS18155 glutaredoxin‑dependent arsenate reductase/hypothetical protein
* * ÷ NZ_CP009273 3644466 3644681 216 2 [0] [1] 2 [BW25113_RS18155] [BW25113_RS18155]
* * ÷ NZ_CP009273 3644721 3644830 110 2 [1] [1] 2 BW25113_RS18155 hypothetical protein
* * ÷ NZ_CP009273 3644886 3646532–3645398 513–1647 2 [1] [1] 2 [BW25113_RS18155]–BW25113_RS18160 [BW25113_RS18155],BW25113_RS18160
* * ÷ NZ_CP009273 3745310 3745325 16 4 [1] [0] 2 yiaT/yiaU MipA/OmpV family protein/LysR family transcriptional regulator
* * ÷ NZ_CP009273 3787053 3787104 52 2 [1] [0] 3 yibB/rfaD protein YibB/ADP‑glyceromanno‑heptose 6‑epimerase
* * ÷ NZ_CP009273 4205321 4205329 9 2 [0] [1] 2 metA/aceB homoserine O‑succinyltransferase/malate synthase A
* * ÷ NZ_CP009273 4532462 4532537 76 2 [0] [1] 3 fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)38 (2.520) 20/166 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 1203246 =0 (0.000)5 (0.410) 5/134 0.7 100% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 0 (0.000)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032610 (0.000)14 (1.150) 14/134 0.1 100% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 0 (0.000)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391495NA (NA)6 (0.400) 6/166 0.8 100% intergenic (+146/‑127) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1903069 = 0 (0.000)intergenic (‑46/‑113) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
* ? NZ_CP009273 = 19030720 (0.000)11 (0.730) 11/166 0.3 100% intergenic (‑49/‑110) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
?NZ_CP009273 = 2096424 NA (NA)intergenic (‑68/+3) BW25113_RS10605/wbbL IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL
* ? NZ_CP009273 = 19727510 (0.000)16 (1.060) 14/166 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
* ? NZ_CP009273 2282398 =NA (NA)23 (1.530) 13/166 0.2 92.0% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 3512437 = 2 (0.130)intergenic (‑14/+387) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 2283591NA (NA)27 (1.810) 18/164 0.1 93.2% intergenic (‑67/‑388) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
?NZ_CP009273 = 3512441 2 (0.130)intergenic (‑18/+383) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 36292460 (0.000)21 (1.390) 8/166 0.5 100% coding (1046/1053 nt) yhiM DUF2776 domain‑containing protein
?NZ_CP009273 3645396 = NA (NA)pseudogene (746/747 nt) BW25113_RS18155 hypothetical protein