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 49,898 G→A A26T (GCC→ACC)  folA → 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 3,512,072 (T)6→5 coding (352/522 nt) aroK ← shikimate kinase AroK

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 42270 42287 18 2 [1] [1] 3 caiT/fixA L‑carnitine/gamma‑butyrobetaine antiporter/electron transfer flavoprotein FixA
* * ÷ NZ_CP009273 153494 153534 41 2 [0] [0] 2 yadN/folK fimbrial protein/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase
* * ÷ NZ_CP009273 211224 211247 24 2 [1] [0] 2 yaeQ YaeQ family protein
* * ÷ NZ_CP009273 247973 247991 19 3 [1] [1] 2 dinB DNA polymerase IV
* * ÷ NZ_CP009273 356981 357578 598 3 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 380412 380422 11 2 [0] [0] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 385441 385474 34 2 [0] [1] 2 hemB/BW25113_RS01915 porphobilinogen synthase/outer membrane autotransporter barrel domain‑containing protein
* * ÷ NZ_CP009273 447463 447475 13 2 [1] [0] 4 cyoA/ampG cytochrome o ubiquinol oxidase subunit II/muropeptide MFS transporter AmpG
* * ÷ NZ_CP009273 510155 510210 56 2 [1] [1] 3 ybbJ NfeD family protein
* * ÷ NZ_CP009273 518377 518451 75 2 [1] [1] 2 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 523122 523147 26 2 [1] [1] 2 ybbC YbbC/YhhH family protein
* * ÷ NZ_CP009273 569757 569777 21 2 [1] [1] 2 quuD antitermination protein QuuD
* * ÷ NZ_CP009273 572499 572506 8 3 [0] [0] 3 BW25113_RS02855/essD porin/phage lysis protein EssD
* * ÷ NZ_CP009273 574844 574851 8 2 [1] [0] 2 ybcV DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 578977 579073 97 3 [1] [0] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579243 579259 17 2 [1] [1] 2 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579961 580001 41 2 [1] [1] 3 appY/ompT DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT
* * ÷ NZ_CP009273 620328 620364 37 2 [1] [0] 2 [entC] [entC]
* * ÷ NZ_CP009273 647582 647606 25 2 [0] [1] 3 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 656878 656891 14 2 [1] [1] 2 ybeF/lipB YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB
* * ÷ NZ_CP009273 677592 677602 11 2 [0] [1] 3 hscC molecular chaperone HscC
* * ÷ NZ_CP009273 717593 717628 36 2 [1] [1] 2 kdpD two‑component system sensor histidine kinase KdpD
* * ÷ NZ_CP009273 719587 719588 2 2 [0] [0] 2 kdpD two‑component system sensor histidine kinase KdpD
* * ÷ NZ_CP009273 731696 731735 40 2 [0] [0] 3 BW25113_RS03640/ybfQ hypothetical protein/ISAs1 family transposase
* * ÷ NZ_CP009273 748284 748309 26 3 [1] [1] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 750327 750334 8 2 [1] [1] 2 BW25113_RS25495/sdhC hypothetical protein/succinate dehydrogenase cytochrome b556 subunit
* * ÷ NZ_CP009273 825312 825324 13 3 [1] [1] 3 hlyD secretion protein HlyD
* * ÷ NZ_CP009273 845159 845211 53 3 [1] [1] 2 rhtA threonine/homoserine exporter RhtA
* * ÷ NZ_CP009273 902895 902901 7 2 [1] [0] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 907646 907665 20 2 [1] [0] 4 hcp hydroxylamine reductase
* * ÷ NZ_CP009273 940818 940826 9 2 [0] [0] 2 ycaC hydrolase
* * ÷ NZ_CP009273 970334 970374 41 2 [1] [1] 2 mukF chromosome partition protein MukF
* * ÷ NZ_CP009273 982723 983070 348 2 [1] [1] 2 [asnS] [asnS]
* * ÷ NZ_CP009273 984082 984084 3 2 [1] [0] 2 asnS asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1040261 1040275 15 2 [1] [0] 2 gfcE polysaccharide export protein
* * ÷ NZ_CP009273 1059487 1059497 11 3 [1] [0] 2 [yccE] [yccE]
* * ÷ NZ_CP009273 1072176 1072192 17 2 [0] [1] 2 putA trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1072827 1072830 4 2 [0] [1] 2 putA trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1073397 1073411 15 2 [1] [1] 2 putA trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1080300 1080360 61 2 [0] [1] 3 efeB/phoH iron uptake transporter deferrochelatase/peroxidase subunit/phosphate starvation‑inducible protein PhoH
* * ÷ NZ_CP009273 1098636 1098639 4 2 [0] [0] 2 csgD biofilm master transcriptional regulator CsgD
* * ÷ NZ_CP009273 1098941 1099010 70 2 [1] [1] 3 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1116493 1116503 11 7 [0] [1] 3 bssS/dinI biofilm formation regulator BssS/DNA damage‑inducible protein I
* * ÷ NZ_CP009273 1123845 1123895 51 2 [1] [1] 2 murJ murein biosynthesis integral membrane protein MurJ
* * ÷ NZ_CP009273 1158176 1158228 53 2 [1] [1] 3 lpoB penicillin‑binding protein activator LpoB
* * ÷ NZ_CP009273 1158355 1158366 12 2 [1] [1] 2 lpoB penicillin‑binding protein activator LpoB
* * ÷ NZ_CP009273 1172297 1172344 48 2 [1] [1] 3 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1192726 1192775 50 2 [1] [1] 3 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1207758 1207801 44 2 [1] [1] 2 [BW25113_RS25985] [BW25113_RS25985]
* * ÷ NZ_CP009273 1218666 1218708 43 3 [1] [1] 2 BW25113_RS06100/BW25113_RS23645 hypothetical protein/hypothetical protein
* * ÷ NZ_CP009273 1225849 1225988 140 2 [1] [1] 2 [hlyE] [hlyE]
* * ÷ NZ_CP009273 1234924 1234937 14 3 [1] [0] 2 dadX catabolic alanine racemase DadX
* * ÷ NZ_CP009273 1242785 1242842 58 2 [1] [1] 2 [treA] [treA]
* * ÷ NZ_CP009273 1303153 1303153 1 3 [0] [0] 2 yciY YciY family protein
* * ÷ NZ_CP009273 1310438 1310463 26 2 [1] [0] 2 yciG/trpA general stress protein/tryptophan synthase subunit alpha
* * ÷ NZ_CP009273 1329154 1329164 11 2 [0] [0] 2 cysB/ymiA HTH‑type transcriptional regulator CysB/YmiA family putative membrane protein
* * ÷ NZ_CP009273 1334464 1334535 72 2 [1] [1] 2 [lapA] [lapA]
* * ÷ NZ_CP009273 1369511 1369521 11 2 [1] [0] 2 ycjQ zinc‑binding alcohol dehydrogenase
* * ÷ NZ_CP009273 1382390 1382394 5 2 [0] [1] 2 tyrR transcriptional regulator TyrR
* * ÷ NZ_CP009273 1432466 1432476 11 2 [0] [1] 2 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1459167 1459205 39 2 [1] [1] 2 paaY phenylacetic acid degradation protein PaaY
* * ÷ NZ_CP009273 1459470 1459518 49 2 [1] [0] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1518814 1518855 42 2 [0] [1] 2 ansP L‑asparagine permease
* * ÷ NZ_CP009273 1521218 1521313 96 2 [0] [1] 2 yncH YncH family protein
* * ÷ NZ_CP009273 1521404 1521434 31 2 [1] [0] 2 [yncH] [yncH]
* * ÷ NZ_CP009273 1537252 1537279 28 2 [1] [1] 3 narU nitrate/nitrite transporter NarU
* * ÷ NZ_CP009273 1539041 1539098 58 2 [1] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539164 1539254 91 2 [1] [1] 3 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539292 1539336 45 3 [0] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540397 1540468 72 2 [1] [1] 3 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1566539 1566585 47 2 [1] [1] 2 gadB/pqqL glutamate decarboxylase/insulinase family protein
* * ÷ NZ_CP009273 1596118 1596154 37 2 [1] [1] 2 lsrA autoinducer 2 ABC transporter ATP‑binding protein LsrA
* * ÷ NZ_CP009273 1606780 1606781 2 3 [0] [0] 4 glsB glutaminase B
* * ÷ NZ_CP009273 1626876 1626879 4 2 [0] [1] 2 ydfJ/BW25113_RS25615 MHS family MFS transporter/hypothetical protein
* * ÷ NZ_CP009273 1631547 1631587 41 2 [1] [0] 2 ydfO DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1632876 1632933 58 2 [1] [1] 2 [cspI] [cspI]
* * ÷ NZ_CP009273 1633180 1633269 90 2 [1] [1] 2 cspI/rzpQ cold shock protein CspI/DUF2514 domain‑containing protein
* * ÷ NZ_CP009273 1693217 1693238 22 2 [0] [1] 2 malI mal regulon transcriptional regulator MalI
* * ÷ NZ_CP009273 1723498 1723538 41 2 [0] [0] 3 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1772987 1773016 30 2 [1] [0] 2 ydiP AraC family transcriptional regulator
* * ÷ NZ_CP009273 1773577 1773611 35 2 [1] [1] 2 ydiP/ydiQ AraC family transcriptional regulator/electron transfer flavoprotein
* * ÷ NZ_CP009273 1820777 1820811 35 3 [1] [1] 3 astE succinylglutamate desuccinylase
* * ÷ NZ_CP009273 1822993 1823005 13 2 [0] [1] 2 astD succinylglutamate‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1825530 1825586 57 2 [1] [1] 2 astC succinylornithine/acetylornithine transaminase
* * ÷ NZ_CP009273 1831823 1831843 21 2 [1] [0] 2 ynjC ABC transporter permease subunit
* * ÷ NZ_CP009273 1835272 1835288 17 2 [1] [1] 2 ynjF CDP‑alcohol phosphatidyltransferase family protein
* * ÷ NZ_CP009273 1844096 1844134 39 2 [1] [0] 2 sppA signal peptide peptidase SppA
* * ÷ NZ_CP009273 1882329 1882373 45 2 [1] [1] 2 fadD long‑chain‑fatty‑acid‑‑CoA ligase FadD
* * ÷ NZ_CP009273 1882741 1882755 15 3 [1] [0] 2 fadD long‑chain‑fatty‑acid‑‑CoA ligase FadD
* * ÷ NZ_CP009273 1952515 1952546 32 2 [1] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1978963 1978987 25 2 [1] [1] 2 araF arabinose ABC transporter substrate‑binding protein AraF
* * ÷ NZ_CP009273 1980232 1980254 23 2 [1] [1] 3 araF/ftnB arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein
* * ÷ NZ_CP009273 2005838 2005861 24 2 [1] [0] 2 BW25113_RS10120/fliE DUF5503 domain‑containing protein/flagellar hook‑basal body complex protein FliE
* * ÷ NZ_CP009273 2026250 2026265 16 2 [1] [1] 2 yedJ phosphohydrolase
* * ÷ NZ_CP009273 2033242 2033259 18 2 [1] [1] 3 msrP protein‑methionine‑sulfoxide reductase catalytic subunit MsrP
* * ÷ NZ_CP009273 2093246 2093252 7 2 [0] [1] 2 ugd/gndA UDP‑glucose 6‑dehydrogenase/NADP‑dependent phosphogluconate dehydrogenase
* * ÷ NZ_CP009273 2097476 2097496 21 2 [1] [0] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2097568 2097592 25 2 [0] [0] 4 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2099604 2099620 17 2 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2100677 2100703 27 2 [1] [0] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2101496 2101619 124 2 [1] [1] 2 glf UDP‑galactopyranose mutase
* * ÷ NZ_CP009273 2103016 2103049 34 2 [1] [1] 2 wzx O16 family O‑antigen flippase
* * ÷ NZ_CP009273 2144447 2144473 27 2 [1] [0] 2 [yegI] [yegI]
* * ÷ NZ_CP009273 2170685 2170734 50 2 [1] [1] 3 gatY/fbaB tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
* * ÷ NZ_CP009273 2174739 2174767 29 2 [0] [1] 2 yegV carbohydrate kinase family protein
* * ÷ NZ_CP009273 2297293 2297314 22 3 [1] [1] 2 BW25113_RS25870/eco hypothetical protein/serine protease inhibitor ecotin
* * ÷ NZ_CP009273 2337840 2337887 48 2 [1] [1] 3 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2462736 2462966 231 3 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463679 2463762 84 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2483611 2483676 66 2 [1] [1] 2 [yfdV] [yfdV]
* * ÷ NZ_CP009273 2492124 2492140 17 2 [1] [0] 2 alaC/ypdA alanine transaminase/two‑component system sensor histidine kinase YpdA
* * ÷ NZ_CP009273 2563794 2563811 18 3 [1] [1] 2 eutE aldehyde dehydrogenase EutE
* * ÷ NZ_CP009273 2569341 2569349 9 2 [0] [0] 2 eutS/maeB ethanolamine utilization microcompartment protein EutS/NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase
* * ÷ NZ_CP009273 2584464 2584527 64 2 [1] [1] 2 ypfM/yffB protein YpfM/ArsC family reductase
* * ÷ NZ_CP009273 2605413 2605442 30 2 [1] [1] 3 hyfR DNA‑binding transcriptional regulator HyfR
* * ÷ NZ_CP009273 2622422 2622499 78 2 [1] [1] 2 [BW25113_RS25940] [BW25113_RS25940]
* * ÷ NZ_CP009273 2629245 2629275 31 2 [1] [1] 2 der ribosome biogenesis GTPase Der
* * ÷ NZ_CP009273 2687519 2687563 45 2 [0] [1] 2 purL phosphoribosylformylglycinamidine synthase
* * ÷ NZ_CP009273 2753634 2753715 82 2 [1] [1] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2779863 2779872 10 3 [0] [1] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2877733 2877776 44 3 [1] [0] 2 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 2897039 2897170 132 2 [1] [1] 3 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2981748 2981811 64 4 [1] [0] 2 yqeH/yqeI helix‑turn‑helix transcriptional regulator/transcriptional regulator
* * ÷ NZ_CP009273 2987451 2987527 77 2 [1] [1] 2 BW25113_RS14845 lytic transglycosylase domain‑containing protein
* * ÷ NZ_CP009273 3151235 3151238 4 2 [0] [1] 2 yqhG YbjP/YqhG family protein
* * ÷ NZ_CP009273 3184480 3184490 11 2 [1] [0] 2 yqiI fimbrial protein
* * ÷ NZ_CP009273 3261522 3261537 16 5 [1] [0] 2 BW25113_RS16190 hypothetical protein
* * ÷ NZ_CP009273 3262181 3262301 121 2 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3262565 3262613 49 3 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3627978 3628010 33 2 [0] [1] 2 BW25113_RS18065/yhiM YhiJ/YhiL family protein/DUF2776 domain‑containing protein
* * ÷ NZ_CP009273 3797724 3797784 61 2 [1] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3841887 3841893 7 2 [1] [0] 2 uhpC MFS transporter family glucose‑6‑phosphate receptor UhpC
* * ÷ NZ_CP009273 3995947 3995968 22 2 [1] [1] 2 yigF DUF2628 domain‑containing protein
* * ÷ NZ_CP009273 4272746 4272817 72 2 [1] [1] 2 espX5 T3SS effector pentapeptide repeat protein EspX5
* * ÷ NZ_CP009273 4427383 4427417 35 2 [0] [1] 2 cysQ/BW25113_RS21900 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein
* * ÷ NZ_CP009273 4546376 4546376 1 2 [0] [0] 5 yjiC/idlP YjfZ/YjiC family protein/iraD leader peptide IdlP

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)26 (1.850) 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 = 1391494NA (NA)7 (0.510) 6/164 0.7 100% 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 = 1391495NA (NA)5 (0.360) 5/166 0.8 33.3% intergenic (+146/‑127) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1853017 = 10 (0.710)coding (74/1044 nt) ydjJ NAD(P)‑dependent alcohol dehydrogenase
* ? NZ_CP009273 = 19727510 (0.000)38 (2.710) 21/166 0.0 100% 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