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 427,415 Δ2 bp coding (54‑55/885 nt) tsx ← nucleoside‑specific channel‑forming protein Tsx
RA 690,117 C→T V99I (GTC→ATC)  miaB ← tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
JC 4,609,810 Δ72 bp coding (391‑462/1224 nt) deoB → phosphopentomutase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357574 594 2 [0] [1] 3 [lacA] [lacA]
* * ÷ NZ_CP009273 370665 370757–370716 52–93 3 [1] [1] 4 dmpG/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑(3‑hydroxy‑phenyl)propionate transporter
* * ÷ NZ_CP009273 396670 396680 11 2 [0] [1] 2 BW25113_RS25915/iraP hypothetical protein/anti‑adapter protein IraP
* * ÷ NZ_CP009273 414663 414678 16 2 [1] [0] 2 phoR/brnQ phosphate regulon sensor histidine kinase PhoR/branched‑chain amino acid transporter carrier protein BrnQ
* * ÷ NZ_CP009273 437903 437912 10 2 [1] [0] 2 thiI tRNA 4‑thiouridine(8) synthase ThiI
* * ÷ NZ_CP009273 564255 564281 27 3 [0] [1] 2 BW25113_RS25485 hypothetical protein
* * ÷ NZ_CP009273 579573 579588 16 4 [1] [1] 2 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 608874 608901 28 2 [1] [1] 2 fes enterochelin esterase
* * ÷ NZ_CP009273 642167 642246 80 2 [0] [0] 2 citG triphosphoribosyl‑dephospho‑CoA synthase CitG
* * ÷ NZ_CP009273 656058 656076 19 2 [1] [1] 2 ybeF YbeF family transcriptional regulator
* * ÷ NZ_CP009273 725196 725208–725204 9–13 2 [1] [0] 3 rhsC rhs element protein RhsC
* * ÷ NZ_CP009273 774498 774533 36 2 [1] [0] 3 [pal] [pal]
* * ÷ NZ_CP009273 803725 803821 97 2 [1] [1] 2 bioA adenosylmethionine‑‑8‑amino‑7‑oxononanoate transaminase
* * ÷ NZ_CP009273 830786 830798 13 2 [1] [1] 3 ybiB DNA‑binding protein YbiB
* * ÷ NZ_CP009273 836284 836353 70 2 [1] [1] 2 fiu catecholate siderophore receptor Fiu
* * ÷ NZ_CP009273 839633 839658 26 2 [0] [0] 2 ybiO mechanosensitive channel protein
* * ÷ NZ_CP009273 859429 859498 70 2 [1] [1] 3 fsa fructose‑6‑phosphate aldolase
* * ÷ NZ_CP009273 885077 885103 27 2 [1] [1] 2 ybjL aspartate:alanine antiporter
* * ÷ NZ_CP009273 969791 969854 64 2 [1] [1] 2 mukF chromosome partition protein MukF
* * ÷ NZ_CP009273 988185 988231 47 2 [1] [1] 3 pepN aminopeptidase N
* * ÷ NZ_CP009273 988405 988441 37 3 [1] [1] 2 pepN aminopeptidase N
* * ÷ NZ_CP009273 988565 988582 18 2 [1] [1] 4 pepN aminopeptidase N
* * ÷ NZ_CP009273 990973 990987 15 2 [1] [1] 2 ssuD FMNH2‑dependent alkanesulfonate monooxygenase
* * ÷ NZ_CP009273 998257 998270 14 2 [1] [1] 2 elfG fimbrial protein
* * ÷ NZ_CP009273 1003088 1003106 19 2 [1] [1] 2 ycbX/rlmKL 6‑N‑hydroxylaminopurine resistance protein YcbX/bifunctional 23S rRNA (guanine(2069)‑N(7))‑methyltransferase RlmK/23S rRNA (guanine(2445)‑N(2))‑methyltransferase RlmL
* * ÷ NZ_CP009273 1070848 1070868 21 2 [0] [1] 2 putA trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
* * ÷ NZ_CP009273 1074796 1074870 75 3 [1] [1] 3 putP sodium/proline symporter PutP
* * ÷ NZ_CP009273 1080297 1080341 45 2 [1] [1] 2 efeB/phoH iron uptake transporter deferrochelatase/peroxidase subunit/phosphate starvation‑inducible protein PhoH
* * ÷ NZ_CP009273 1088349 1088360 12 2 [1] [0] 2 dgcT GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1100140 1100200 61 2 [1] [1] 2 csgA curli major subunit CsgA
* * ÷ NZ_CP009273 1115826 1115855 30 2 [1] [1] 2 solA N‑methyl‑L‑tryptophan oxidase
* * ÷ NZ_CP009273 1139930 1139933 4 2 [0] [1] 2 rne/rluC ribonuclease E/23S rRNA pseudouridine(955/2504/2580) synthase RluC
* * ÷ NZ_CP009273 1168434 1168442 9 2 [1] [1] 2 mfd transcription‑repair coupling factor
* * ÷ NZ_CP009273 1172115 1172234 120 2 [1] [1] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1173161 1173169 9 2 [0] [1] 2 lolE lipoprotein‑releasing ABC transporter permease subunit LolE
* * ÷ NZ_CP009273 1178465 1178493 29 3 [0] [0] 3 potC spermidine/putrescine ABC transporter permease PotC
* * ÷ NZ_CP009273 1192488 1192534 47 2 [1] [0] 3 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1206653 1206676 24 3 [1] [1] 2 mcrA/BW25113_RS23640 5‑methylcytosine‑specific endonuclease McrA/isocitrate/isopropylmalate family dehydrogenase
* * ÷ NZ_CP009273 1207640 1207691 52 2 [1] [1] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1210191 1210207 17 2 [1] [1] 2 bluF blue light‑responsive regulator BluF
* * ÷ NZ_CP009273 1210566 1210612 47 2 [1] [1] 2 bluF blue light‑responsive regulator BluF
* * ÷ NZ_CP009273 1229158 1229164 7 4 [0] [1] 2 nhaB Na(+)/H(+) antiporter NhaB
* * ÷ NZ_CP009273 1264246 1264348 103 2 [1] [1] 2 kdsA 3‑deoxy‑8‑phosphooctulonate synthase
* * ÷ NZ_CP009273 1269200 1269204 5 2 [0] [1] 2 ychN/ychO DsrE/F sulfur relay family protein YchN/inverse autotransporter invasin YchO
* * ÷ NZ_CP009273 1275040 1275071 32 2 [1] [1] 2 narK/narG nitrate transporter NarK/nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1277039 1277059 21 2 [1] [1] 2 narG nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1277150 1277210 61 2 [1] [1] 2 narG nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1279571 1279602 32 2 [1] [1] 2 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1285411 1285422 12 2 [1] [1] 2 rssA patatin‑like phospholipase RssA
* * ÷ NZ_CP009273 1310589 1310651 63 3 [0] [1] 2 yciG/trpA general stress protein/tryptophan synthase subunit alpha
* * ÷ NZ_CP009273 1314944 1314981 38 2 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1326825 1326889 65 2 [0] [1] 2 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1347681 1347689 9 2 [0] [1] 2 sapD peptide ABC transporter ATP‑binding protein SapD
* * ÷ NZ_CP009273 1356397 1356412 16 2 [1] [0] 2 puuR HTH‑type transcriptional regulator PuuR
* * ÷ NZ_CP009273 1369129 1369145 17 2 [1] [0] 2 ycjP carbohydrate ABC transporter permease
* * ÷ NZ_CP009273 1369423 1369451 29 2 [1] [1] 2 ycjQ zinc‑binding alcohol dehydrogenase
* * ÷ NZ_CP009273 1393448 1393453 6 2 [1] [0] 2 fnr fumarate/nitrate reduction transcriptional regulator Fnr
* * ÷ NZ_CP009273 1398225 1398233 9 2 [0] [1] 2 abgA p‑aminobenzoyl‑glutamate hydrolase subunit AbgA
* * ÷ NZ_CP009273 1417984 1418005 22 2 [1] [1] 2 BW25113_RS26130/trkG hypothetical protein/Trk system potassium transporter TrkG
* * ÷ NZ_CP009273 1632746 1632782 37 2 [1] [1] 2 cspI cold shock protein CspI
* * ÷ NZ_CP009273 1733854 1733896 43 2 [1] [1] 2 punR DNA‑binding transcriptional activator PunR
* * ÷ NZ_CP009273 1781854 1781858 5 2 [1] [0] 2 ppsR posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR
* * ÷ NZ_CP009273 2005763 2005774 12 2 [1] [0] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2753605 2753686 82 2 [1] [1] 3 yfjI YfjI family protein
* * ÷ NZ_CP009273 2768289 2768291 3 3 [0] [0] 3 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 3575397 3575430 34 9 [0] [1] 2 hcp Hcp1 family type VI secretion system effector

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)43 (2.670) 28/168 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 =1 (0.060)7 (0.540) 7/136 0.5 83.3% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 2 (0.150)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)7 (0.440) 6/166 0.8 100% 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 = 19727510 (0.000)19 (1.180) 13/168 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 4532499 =7 (0.440)6 (0.420) 6/150 0.7 26.5% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 27 (1.880)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA