breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 119,295 A→T 5.7% T5T (ACA→ACT ampE → ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation
RA 219,763 T→C 5.6% N78S (AAT→AGT)  rcsF ← putative outer membrane protein
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 285,882 T→G 5.2% I163S (ATC→AGC)  yagG → CP4‑6 prophage; putative sugar transporter
RA 285,887 C→A 6.0% L165M (CTG→ATG)  yagG → CP4‑6 prophage; putative sugar transporter
RA 326,821 C→T 5.2% G143S (GGC→AGC)  betA ← choline dehydrogenase, a flavoprotein
RA 384,328 C→A 5.3% D97Y (GAT→TAT)  yaiS ← putative PIG‑L family deacetylase
JC JC 564,107 IS2 (+) +5 bp 100% coding (370‑374/633 nt) sfmZ ← response regulator family protein
RA 741,486 G→A 5.5% A357A (GCC→GCT dtpD ← dipeptide and tripeptide permease D
RA 756,303 C→A 92.4% R133S (CGC→AGC)  sdhA → succinate dehydrogenase, flavoprotein subunit
RA 786,623 T→C 5.1% W331R (TGG→CGG)  aroG → 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible
RA 875,401 G→T 6.9% A23S (GCC→TCC)  yliF → putative membrane‑anchored diguanylate cyclase
RA 897,081 C→T 5.8% H316H (CAC→CAT potH → putrescine ABC transporter permease
RA 942,026 C→G 5.5% A356A (GCC→GCG dmsA → dimethyl sulfoxide reductase, anaerobic, subunit A
RA 945,863 T→C 5.8% intergenic (‑306/‑8) ycaC ← / → ycaD putative isochorismatase family hydrolase/putative MFS transporter, inner membrane protein
RA 987,560 G→C 5.1% intergenic (‑578/+25) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA 987,561 G→C 5.1% intergenic (‑579/+24) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA 1,048,285 A→C 8.4% V136G (GTC→GGC)  gfcC ← putative O‑antigen capsule production periplasmic protein
RA 1,194,176 A→G 6.0% L38P (CTG→CCG)  nudJ ← bifunctional thiamine pyrimidine pyrophosphate hydrolase and thiamine pyrophosphate hydrolase
RA 1,221,641 T→A 7.4% pseudogene (2041/2574 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,224,829 A→G 5.5% L178P (CTG→CCG)  minD ← inhibitor of FtsZ ring polymerization; chromosome‑membrane tethering protein; membrane ATPase of the MinCDEE system
RA 1,286,766 T→G 9.0% intergenic (+240/+300) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,767 G→C 8.8% intergenic (+241/+299) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,768 C→A 9.4% intergenic (+242/+298) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,288,332 A→G 5.1% L98P (CTT→CCT)  purU ← formyltetrahydrofolate hydrolase
RA 1,314,261 C→T 6.5% P81L (CCG→CTG)  ompW → outer membrane protein W
RA 1,428,271 A→C 8.4% S152S (TCT→TCG insH1 ← IS5 transposase and trans‑activator
RA 1,452,259 C→T 5.9% G462R (GGG→AGG)  paaZ ← oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA 1,452,273 G→A 5.2% A457V (GCA→GTA)  paaZ ← oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA 1,466,891 C→T 5.4% pseudogene (1500/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,514,378 C→T 6.5% S183F (TCC→TTC)  ydcU → putative ABC transporter permease
RA 1,533,930 T→G 6.2% intergenic (‑79/‑94) yddH ← / → nhoA flavin reductase like‑protein/N‑hydroxyarylamine O‑acetyltransferase
RA 1,552,085 G→T 7.3% intergenic (+94/+313) fdnI → / ← yddM formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
RA 1,570,611 G→A 5.8% intergenic (‑122/+34) gadC ← / ← gadB glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent
RA 1,606,548 A→T 5.3% H150L (CAT→CTT)  lsrF → putative autoinducer‑2 (AI‑2) aldolase
RA 1,612,353 G→A 5.5% T300M (ACG→ATG)  glsB ← glutaminase 2
RA 1,612,716 C→T 5.1% G179D (GGC→GAC)  glsB ← glutaminase 2
RA 1,622,975 C→G 5.6% V292V (GTG→GTC dgcZ ← diguanylate cyclase, zinc‑sensing
RA 1,671,548 A→G 5.2% Q58R (CAG→CGG)  asr → acid shock‑inducible periplasmic protein
RA 1,715,919 T→G 5.6% intergenic (‑30/+29) pdxY ← / ← tyrS pyridoxamine kinase/tyrosyl‑tRNA synthetase
RA 1,715,920 T→A 5.2% intergenic (‑31/+28) pdxY ← / ← tyrS pyridoxamine kinase/tyrosyl‑tRNA synthetase
RA 1,729,944 T→C 6.7% L286L (CTT→CTC lhr → putative ATP‑dependent helicase
RA 1,733,378 A→G 10.2% N1431S (AAT→AGT)  lhr → putative ATP‑dependent helicase
RA 1,750,351 A→G 5.2% N221N (AAT→AAC ydhX ← putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex
RA 1,855,344 T→A 7.9% N210Y (AAT→TAT)  ydjG ← methylglyoxal reductase, NADH‑dependent
RA 1,862,688 A→G 5.0% intergenic (‑259/‑83) msrB ← / → gapA methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A
RA 1,900,088 Δ1 bp 5.2% coding (1498/1557 nt) yoaE ← putative membrane protein/conserved protein
RA 1,922,524 A→T 5.5% V149D (GTT→GAT)  pphA ← serine/threonine‑specific protein phosphatase 1
RA 1,929,318 T→C 5.1% Q130Q (CAA→CAG yebE ← DUF533 family inner membrane protein
RA 1,970,186 G→A 7.1% R267C (CGT→TGT)  tap ← methyl‑accepting protein IV
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 2,074,691 C→G 5.7% intergenic (+33/‑88) flu → / → yeeR CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein
RA 2,085,969 C→G 5.6% G365A (GGT→GCT)  plaP ← putrescine importer, low affinity
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,311,616 C→T 5.1% intergenic (‑82/+30) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,311,619 A→G 5.3% intergenic (‑85/+27) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,357,836 G→A 5.1% pseudogene (33/198 nt) ypaA → pseudogene, C‑terminal fragment, Transposase_31 family
RA 2,411,551 G→A 5.0% A180V (GCG→GTG)  yfbT ← sugar phosphatas
RA 2,443,811 T→C 6.0% intergenic (+41/+80) mnmC → / ← yfcL fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme/uncharacterized protein
RA 2,506,444 C→G 5.6% A63A (GCG→GCC ypdF ← Xaa‑Pro aminopeptidase
RA 2,516,520 C→T 7.4% G438D (GGT→GAT)  yfeA ← putative diguanylate cyclase
RA 2,549,601 T→G 6.1% intergenic (+195/+45) yfeW → / ← yfeX penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic
RA 2,552,185 A→T 5.2% intergenic (‑47/‑167) ypeA ← / → amiA GNAT family putative N‑acetyltransferase/N‑acetylmuramoyl‑l‑alanine amidase I
RA 2,560,985 C→A 21.2% intergenic (+87/‑383) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,609,522 C→T 5.1% Q346* (CAA→TAA)  hyfG → hydrogenase 4, subunit
RA 2,646,836 C→T 5.9% A164T (GCT→ACT)  pbpC ← penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein
RA 2,856,427 C→A 5.5% intergenic (+11/+26) fhlA → / ← ygbA formate hydrogenlyase transcriptional activator/uncharacterized protein
RA 2,918,497 G→A 5.1% Q297* (CAA→TAA)  gudD ← D‑glucarate dehydratase 1
RA 3,224,192 A→G 5.4% G520G (GGA→GGG ebgA → evolved beta‑D‑galactosidase, alpha subunit
RA 3,270,069 C→T 6.8% intergenic (+467/+147) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,569,442 C→T 5.6% E626E (GAG→GAA glgX ← glycogen debranching enzyme
RA 3,959,515 T→A 10.1% intergenic (+70/+17) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 4,182,929 A→T 100% E562V (GAA→GTA)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 27.8% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,323,257 Δ1 bp 5.4% intergenic (‑27/+79) phnE ← / ← phnD defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein
RA 4,357,644 T→A 5.4% K325I (AAA→ATA)  cadA ← lysine decarboxylase, acid‑inducible
RA 4,357,647 Δ1 bp 5.1% coding (971/2148 nt) cadA ← lysine decarboxylase, acid‑inducible
RA 4,606,239 A→G 15.7% noncoding (48/87 nt) leuP ← tRNA‑Leu

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 761497 762758 1262 27 [19] [25] 26 [sucA]–sucB [sucA],sucB
* * ÷ NC_000913 3423765–3424234 3424550–3424238 5–786 28 [24] [24] 26 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 381449 =NA (NA)4 (0.050) 3/242 NT NA noncoding (190/1331 nt) IS2 repeat region
?NC_000913 381470 = NA (NA)noncoding (211/1331 nt) IS2 repeat region
* ? NC_000913 1207790 =15 (0.170)44 (0.560) 38/214 NT 66.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 31 (0.400)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780514 (0.160)39 (0.500) 29/214 NT 64.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 31 (0.400)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1208513 =55 (0.610)4 (0.050) 4/234 NT 6.9% coding (382/414 nt) tfaP e14 prophage; uncharacterized protein
?NC_000913 1208541 = 56 (0.660)coding (410/414 nt)
coding (579/603 nt)
tfaP
tfaE
e14 prophage; uncharacterized protein
e14 prophage; putative tail fiber assembly protein
* ? NC_000913 = 12994980 (0.000)105 (1.210) 70/238 NT 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 1396531 =NA (NA)3 (0.040) 3/234 NT NA noncoding (488/1195 nt) IS5 repeat region
?NC_000913 = 1428264 NA (NA)noncoding (531/1196 nt) IS5 repeat region
* ? NC_000913 1972664 =72 (0.800)4 (0.050) 4/238 NT 5.2% coding (28/1662 nt) tar methyl‑accepting chemotaxis protein II
?NC_000913 1972676 = 76 (0.880)coding (16/1662 nt) tar methyl‑accepting chemotaxis protein II
* ? NC_000913 4357635 =112 (1.250)6 (0.070) 3/234 NT 5.5% coding (983/2148 nt) cadA lysine decarboxylase, acid‑inducible
?NC_000913 4357654 = 101 (1.180)coding (964/2148 nt) cadA lysine decarboxylase, acid‑inducible