breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 1,903 G→A E523K (GAA→AAA)  thrA → fused aspartate kinase/homoserine dehydrogenase 1
RA 10,696 C→T A221T (GCC→ACC)  yaaW ← putative enzyme‑specific chaperone YaaW
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 557,635 A→T L36Q (CTG→CAG)  folD ← bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
JC JC 1,105,376 IS2 (–) +5 bp intergenic (+83/‑34) csgC → / → ymdA curlin chaperone/uncharacterized protein YmdA
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,277 C→T N385N (AAC→AAT)  icd → isocitrate dehydrogenase
RA 1,196,280 G→C A386A (GCG→GCC)  icd → isocitrate dehydrogenase
RA 1,196,283 A→G K387K (AAA→AAG)  icd → isocitrate dehydrogenase
RA 1,196,292 C→T T390T (ACC→ACT)  icd → isocitrate dehydrogenase
RA 1,196,304 G→A E394E (GAG→GAA)  icd → isocitrate dehydrogenase
RA 1,196,316 T→A D398E (GAT→GAA)  icd → isocitrate dehydrogenase
JC JC 1,293,268 IS5 (–) +4 bp intergenic (‑346/‑256) hns ← / → tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
RA 1,301,998 A→G S273G (AGC→GGC)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
MC JC 1,397,239 Δ17,203 bp IS5‑mediated ynaJ–[recT] 23 genes
JC JC 1,492,211 IS150 (–) +3 bp intergenic (+36/‑257) sokB → / → trg putative small regulatory RNA antitoxin SokB/methyl‑accepting chemotaxis protein Trg
RA 1,507,867 G→A E363K (GAG→AAG)  rlhA → 23S rRNA 5‑hydroxycytidine C2501 synthase
JC JC 1,649,932 IS2 (+) +5 bp coding (139‑143/192 nt) ydfD → lysis protein
RA 2,032,423 G→A V219V (GTC→GTT)  yedJ ← putative HD superfamily phosphohydrolase YedJ
RA 2,173,363 Δ2 bp intergenic (‑490/+918) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
RA 2,299,162 G→A Y139Y (TAC→TAT)  napH ← ferredoxin‑type protein NapH
RA 2,410,419 G→A L312L (CTG→TTG)  yfbS ← putative transporter YfbS
RA 2,484,827 C→T L152F (CTT→TTT)  evgS → sensor histidine kinase EvgS
RA 2,510,609 C→T P327L (CCG→CTG)  yfeO → putative transport protein YfeO
RA 2,523,109 G→A L293L (CTG→TTG)  xapB ← xanthosine:H(+) symporter XapB
RA 2,725,858 G→A intergenic (‑112/‑67) kgtP ← / → yfiS alpha‑ketoglutarate:H(+) symporter/protein YfiS
RA 2,732,992 G→A I394I (ATC→ATT) 
I394I (ATC→ATT) 		 clpB ←
clpB ←		 chaperone protein ClpB
chaperone protein ClpB
RA 2,804,133 C→T S211F (TCT→TTT)  nrdF → ribonucleoside‑diphosphate reductase 2 subunit beta
RA 2,814,459 Δ1 bp coding (275/516 nt) luxS ← S‑ribosylhomocysteine lyase
RA 2,814,461 C→T L91L (CTG→CTA)  luxS ← S‑ribosylhomocysteine lyase
RA 2,817,197 G→A R103C (CGC→TGC)  yqaB ← fructose‑1‑phosphate phosphatase YqaB
RA 2,823,288 C→T G161D (GGC→GAC)  recA ← DNA recombination/repair protein RecA
RA 2,867,455 G→A Q33* (CAG→TAG)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,871,153 T→G N51T (AAC→ACC)  truD ← tRNA pseudouridine(13) synthase
RA 2,926,543 2 bp→TT coding (236‑237/1365 nt) ppnN → nucleotide 5'‑monophosphate nucleosidase
RA 2,926,772 C→A G155G (GGC→GGA)  ppnN → nucleotide 5'‑monophosphate nucleosidase
RA 3,486,205 C→A T29K (ACG→AAG)  crp → DNA‑binding transcriptional dual regulator CRP
RA 3,533,518 C→T S234F (TCC→TTC)  pck → phosphoenolpyruvate carboxykinase (ATP)
JC 3,553,460 (ATCTGG)1→2 coding (376/2706 nt) malT → DNA‑binding transcriptional activator MalT
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 4,182,791 A→T D516V (GAC→GTC)  rpoB → RNA polymerase subunit beta
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,395,743 T→C G53G (GGT→GGC)  tsaE → N(6)‑L‑threonylcarbamoyladenine synthase, TsaE subunit
RA 4,570,550 C→T S342N (AGC→AAC)  yjiR ← fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR
RA 4,571,280 C→T E99K (GAG→AAG)  yjiR ← fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR
RA 4,585,673 C→T W363* (TGG→TGA)  hsdR ← type I restriction enzyme EcoKI endonuclease subunit
RA 4,587,365 C→T S139S (AGC→AGT)  mrr → Type IV methyl‑directed restriction enzyme EcoKMrr
RA 4,604,517 C→T L120L (CTG→TTG)  bglJ → DNA‑binding transcriptional regulator BglJ
RA 4,630,295 C→T Q76Q (CAG→CAA)  ettA ← energy‑dependent translational throttle protein EttA
RA 4,636,925 G→C R77P (CGC→CCC)  creC → sensory histidine kinase CreC
RA 4,638,058 C→T L455L (CTG→TTG)  creC → sensory histidine kinase CreC
RA 4,638,240 G→A L21L (TTG→TTA)  creD → putative inner membrane protein CreD

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1196372 1209141 12770 3 [1] [1] 2 [icd]–tfaE [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE
* * ÷ NC_000913 1209385 1211412 2028 2 [1] [0] 2 pinE–mcrA pinE,mcrA
* * ÷ NC_000913 1650703 1658488 7786 21 [0] [1] 2 ynfP–[ynfE] ynfP,rspB,rspA,ynfA,ynfB,speG,ynfC,ynfD,[ynfE]
* * ÷ NC_000913 1658708 1665415 6708 2 [1] [1] 2 [ynfE]–[clcB] [ynfE],ynfF,ynfG,ynfH,dmsD,[clcB]
* * ÷ NC_000913 1665523 1670813 5291 2 [1] [0] 21 [clcB]–[ynfM] [clcB],bidA,mlc,ynfL,[ynfM]
* * ÷ NC_000913 1978495 1979159–1978504 10–665 22 [0] [1] 3 insB5–[insA5] insB5,[insA5]
* * ÷ NC_000913 2558699 2565480 6782 46 [0] [1] 2 intZ–yffS intZ,yffL,yffM,yffN,yffO,yffP,yffQ,yffR,yffS
* * ÷ NC_000913 3423903–3424232 3424404–3424238 7–502 3 [1] [0] 2 rrlD 23S ribosomal RNA
* * ÷ NC_000913 3927268 3931565 4298 58 [0] [0] 2 [asnA]–[kup] [asnA],viaA,ravA,[kup]
* * ÷ NC_000913 3931758 3932286 529 2 [0] [1] 2 kup K(+):H(+) symporter Kup
* * ÷ NC_000913 3932397 3938724 6328 2 [1] [0] 44 [kup]–[rbsR] [kup],rbsD,rbsA,rbsC,rbsB,rbsZ,rbsK,[rbsR]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 56677436 (0.880)10 (0.250) 5/482 2.3 25.4% pseudogene (91/93 nt) renD protein RenD
?NC_000913 568036 = 23 (0.570)pseudogene (2/213 nt) renD protein RenD
* ? NC_000913 = 12994980 (0.000)15 (0.370) 15/478 1.0 100% intergenic (+253/‑69) ychE/insH21 MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 1397238NA (NA)22 (0.540) 21/486 0.7 100% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 1978494 0 (0.000)intergenic (‑297/+24) flhD/insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
* ? NC_000913 = 16507020 (0.000)21 (0.520) 18/484 0.8 100% intergenic (+717/+2026) ydfD/ynfP lysis protein/protein YnfP
?NC_000913 1670814 = 0 (0.000)coding (1116/1254 nt) ynfM putative transporter YnfM
* ? NC_000913 1979271 =4 (0.100)19 (0.470) 17/486 0.9 82.6% intergenic (‑56/‑482) insA5/uspC IS1 family protein InsA/universal stress protein C
?NC_000913 = 2102947 NA (NA)pseudogene (443/446 nt) wbbL interrupted rhamnosyltransferase WbbL
* ? NC_000913 = 25586980 (0.000)46 (1.170) 41/470 0.1 98.9% intergenic (‑19/‑160) eutB/intZ ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ
?NC_000913 2565489 = 1 (0.030)coding (1396/1404 nt) eutA ethanolamine ammonia‑lyase reactivase EutA
* ? NC_000913 3652036 =NA (NA)44 (1.080) 41/484 0.2 100% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 3938725 = 0 (0.000)coding (499/993 nt) rbsR DNA‑binding transcriptional dual regulator RbsR
* ? NC_000913 = 3653230NA (NA)57 (1.400) 51/486 0.1 100% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3927267 0 (0.000)coding (113/993 nt) asnA asparagine synthetase A