breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 53,376 G→A 6.9% P14L (CCC→CTC)  pdxA ← 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA 53,379 T→C 6.6% E13G (GAG→GGG)  pdxA ← 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA 83,587 A→C 7.1% intergenic (‑58/+35) leuA ← / ← leuL 2‑isopropylmalate synthase/leu operon leader peptide
RA 83,590 G→T 6.8% intergenic (‑61/+32) leuA ← / ← leuL 2‑isopropylmalate synthase/leu operon leader peptide
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 299,652 T→A 6.1% E428V (GAG→GTG)  paoC ← PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA 328,486 T→C 5.3% N83S (AAT→AGT)  betB ← betaine aldehyde dehydrogenase, NAD‑dependent
RA 360,352 A→G 6.3% T121A (ACG→GCG)  cynX → putative cyanate transporter
RA 434,375 A→G 5.7% A307A (GCA→GCG ribD → fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
RA 511,475 A→G 5.4% intergenic (‑96/‑166) copA ← / → glsA copper transporter/glutaminase 1
RA 538,646 C→T 6.8% A338A (GCC→GCT ybbW → putative allantoin transporter
RA 556,492 T→C 7.1% K21R (AAA→AGA)  ybcI ← DUF457 family inner membrane protein
RA 778,380 T→A 5.1% L214Q (CTG→CAG)  tolB → periplasmic protein
RA 779,901 A→G 5.9% S102G (AGC→GGC)  ybgF → periplasmic TolA‑binding protein
RA 808,398 A→G 6.0% L287P (CTC→CCC)  bioA ← 7,8‑diaminopelargonic acid synthase, PLP‑dependent
RA 819,215 C→T 5.3% N56N (AAC→AAT moaD → molybdopterin synthase, small subunit
RA 893,111 A→T 5.4% D52V (GAT→GTT)  ybjN → negative regulator of motility; multicopy suppressor of coaA(Ts)
RA 933,515 T→C 7.0% W98R (TGG→CGG)  ftsK → DNA translocase at septal ring sorting daughter chromsomes
RA 1,010,169 C→T 5.0% A69V (GCG→GTG)  uup → replication regulatory ABC‑F family DNA‑binding ATPase
RA 1,067,130 T→C 5.2% A193A (GCA→GCG wrbA ← NAD(P)H:quinone oxidoreductase
RA 1,068,774 C→T 7.5% A356T (GCA→ACA)  rutG ← pyrimidine permease
RA 1,112,578 T→C 5.6% A572A (GCT→GCC opgH → OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA 1,287,009 A→T 11.9% intergenic (+483/+57) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,294,583 G→A 8.1% pseudogene (410/567 nt) insZ ← pseudogene, transposase homolog
RA 1,295,598 T→C 5.4% T842A (ACC→GCC)  adhE ← fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,315,800 A→G 5.2% intergenic (‑30/+56) yciF ← / ← yciG putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA 1,315,803 C→T 6.4% intergenic (‑33/+53) yciF ← / ← yciG putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA 1,332,366 C→T 6.2% A440V (GCG→GTG)  topA → DNA topoisomerase I, omega subunit
JC JC 1,335,762 IS5 (–) +4 bp 100% intergenic (+304/‑66) yciX → / → acnA uncharacterized protein/aconitate hydratase 1; aconitase A
RA 1,388,549 G→A 6.1% P88L (CCG→CTG)  tpx ← lipid hydroperoxide peroxidase
RA 1,419,711 T→C 6.3% intergenic (‑255/+54) ydaG ← / ← racR Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator
RA 1,429,021 T→A 6.1% intergenic (+37/‑28) lomR → / → stfR pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein
RA 1,429,022 T→A 6.3% intergenic (+38/‑27) lomR → / → stfR pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein
RA 1,429,024 A→C 6.1% intergenic (+40/‑25) lomR → / → stfR pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein
RA 1,436,497 C→A 5.9% G133C (GGC→TGC)  ompN ← outer membrane pore protein N, non‑specific
RA 1,484,651 C→T 5.8% R531C (CGC→TGC)  hrpA → putative ATP‑dependent helicase
RA 1,698,695 A→G 6.7% V162V (GTT→GTC malI ← transcriptional repressor of Mal regulon
RA 1,761,309 C→T 7.7% V161V (GTG→GTA sufD ← component of SufBCD Fe‑S cluster assembly scaffold
RA 1,779,211 G→C 5.6% P31A (CCA→GCA)  ydiP ← putative DNA‑binding transcriptional regulator
RA 1,806,380 T→C 5.9% I4T (ATC→ACC)  pfkB → 6‑phosphofructokinase II
RA 1,820,565 A→G 6.1% I217T (ATC→ACC)  chbC ← N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS
RA 1,829,556 T→C 5.4% E60G (GAA→GGA)  astD ← succinylglutamic semialdehyde dehydrogenase
RA 1,846,605 A→G 5.5% L119P (CTG→CCG)  topB ← DNA topoisomerase III
RA 1,853,342 G→A 5.6% A213V (GCA→GTA)  ydjE ← putative MFS sugar transporter, membrane protein
RA 1,860,504 C→A 6.6% G277* (GGA→TGA)  ydjL ← putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA 1,888,807 G→A 5.0% L314L (CTG→TTG)  fadD ← acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA 1,920,826 G→A 6.6% V202M (GTG→ATG)  rsmF → 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
RA 1,935,902 G→T 5.2% A138D (GCT→GAT)  zwf ← glucose‑6‑phosphate 1‑dehydrogenase
RA 1,961,207 C→T 5.5% T382T (ACC→ACT argS → arginyl‑tRNA synthetase
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 1,980,240 C→A 6.7% S458I (AGC→ATC) ‡ otsA ← trehalose‑6‑phosphate synthase
RA 1,980,241 T→A 6.8% S458C (AGC→TGC) ‡ otsA ← trehalose‑6‑phosphate synthase
RA 1,980,242 T→G 6.9% R457R (CGA→CGC otsA ← trehalose‑6‑phosphate synthase
RA 1,985,112 C→G 9.3% intergenic (‑43/+27) araG ← / ← araF L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA 2,017,871 G→A 5.5% A440T (GCG→ACG)  fliI → flagellum‑specific ATP synthase
RA 2,100,879 A→G 5.5% G130G (GGT→GGC gnd ← 6‑phosphogluconate dehydrogenase, decarboxylating
RA 2,121,394 A→T 6.3% I54N (ATT→AAT)  wcaJ ← colanic biosynthesis UDP‑glucose lipid carrier transferase
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,169,100 A→G 5.6% N130S (AAC→AGC)  yegS → phosphatidylglycerol kinase, metal‑dependent
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 2,204,390 T→C 5.7% intergenic (+101/‑206) yehK → / → yehL uncharacterized protein/putative hexameric AAA+ MoxR family ATPase
RA 2,216,060 C→T 5.0% A139A (GCG→GCA yehW ← putative ABC transporter permease
RA 2,294,591 C→T 5.2% G105D (GGC→GAC)  ccmF ← heme lyase, CcmF subunit
RA 2,304,649 C→T 23.5% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,307,304 G→T 5.9% L438I (CTT→ATT)  yojI ← microcin J25 efflux ABC transporter permease/ATPase
RA 2,316,369 G→A 5.5% G65S (GGC→AGC)  rcsB → response regulator in two‑component regulatory system with RcsC and YojN
RA 2,364,995 T→G 5.0% intergenic (+16/+23) nudI → / ← ais nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA 2,364,998 C→A 5.1% intergenic (+19/+20) nudI → / ← ais nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA 2,409,215 G→A 5.5% P118P (CCG→CCA yfbR → 5'‑nucleotidase
RA 2,433,237 C→T 5.5% P230P (CCG→CCA accD ← acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,525,907 G→A 7.0% intergenic (+16/+23) yfeN → / ← yfeR putative outer membrane protein/transcriptional regulator of yefH
RA 2,525,908 C→G 7.8% intergenic (+17/+22) yfeN → / ← yfeR putative outer membrane protein/transcriptional regulator of yefH
RA 2,556,903 A→G 7.5% L132P (CTC→CCC)  eutC ← ethanolamine ammonia‑lyase, small subunit (light chain)
RA 2,560,996 G→T 19.3% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,632,586 G→C 5.0% intergenic (‑51/+18) guaA ← / ← guaB GMP synthetase (glutamine aminotransferase)/IMP dehydrogenase
RA 2,671,594 G→A 5.2% A124T (GCA→ACA)  hcaB → 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase
RA 2,914,929 G→A 5.1% L24L (CTC→CTT rlmD ← 23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
RA 2,972,260 G→C 5.7% V222L (GTC→CTC)  tas → putative NADP(H)‑dependent aldo‑keto reductase
RA 3,078,568 A→G 5.9% F98L (TTC→CTC)  cmtA ← putative mannitol‑specific PTS IIB and IIC components
RA 3,094,906 T→C 5.3% I59V (ATA→GTA)  yggR ← putative PilT family AAA+ ATPase
RA 3,096,244 G→A 5.0% R142H (CGC→CAC)  yggT → putative inner membrane protein; compensates for loss in K+ uptake
RA 3,105,253 T→A 5.3% L274Q (CTG→CAG)  mltC → membrane‑bound lytic murein transglycosylase C
RA 3,210,894 T→C 5.5% Y38Y (TAT→TAC rpsU → 30S ribosomal subunit protein S21
RA 3,214,951 T→G 6.7% intergenic (+63/+16) rpoD → / ← mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,214,952 T→A 6.2% intergenic (+64/+15) rpoD → / ← mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,214,953 T→A 6.2% intergenic (+65/+14) rpoD → / ← mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,214,954 T→A 6.7% intergenic (+66/+13) rpoD → / ← mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,214,955 C→A 6.8% intergenic (+67/+12) rpoD → / ← mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA 3,282,866 T→C 6.0% A297A (GCT→GCC agaS → tagatose‑6‑phosphate ketose/aldose isomerase
RA 3,368,180 A→G 5.5% T118T (ACA→ACG yhcG → DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA 3,368,181 C→G 5.5% P119A (CCG→GCG) ‡ yhcG → DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA 3,368,182 C→T 5.4% P119L (CCG→CTG) ‡ yhcG → DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA 3,368,189 A→G 6.2% A121A (GCA→GCG yhcG → DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA 3,390,969 A→T 6.3% S354T (TCC→ACC)  tldD ← putative peptidase
RA 3,432,812 A→T 5.8% L250* (TTG→TAG)  smf ← DNA recombination‑mediator A family protein
RA 3,439,588 G→C 5.4% intergenic (‑79/+28) yhdN ← / ← rplQ DUF1992 family protein/50S ribosomal subunit protein L17
RA 3,439,589 G→C 5.3% intergenic (‑80/+27) yhdN ← / ← rplQ DUF1992 family protein/50S ribosomal subunit protein L17
RA 3,504,875 T→G 5.2% intergenic (+92/+60) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,525,436 T→C 5.5% intergenic (+13/+153) mrcA → / ← nudE penicillin‑binding protein 1a, murein transglycosylase and transpeptidase/adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,525,437 T→G 5.2% intergenic (+14/+152) mrcA → / ← nudE penicillin‑binding protein 1a, murein transglycosylase and transpeptidase/adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,525,438 C→A 5.4% intergenic (+15/+151) mrcA → / ← nudE penicillin‑binding protein 1a, murein transglycosylase and transpeptidase/adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,525,439 G→A 5.4% intergenic (+16/+150) mrcA → / ← nudE penicillin‑binding protein 1a, murein transglycosylase and transpeptidase/adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,534,738 T→C 5.5% G377G (GGA→GGG envZ ← sensory histidine kinase in two‑component regulatory system with OmpR
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 3,606,114 T→A 6.3% W122R (TGG→AGG)  yhhN → TMEM86 family putative inner membrane protein
RA 3,693,326 C→G 100% R637R (CGG→CGC bcsA ← cellulose synthase, catalytic subunit
RA 3,777,919 G→A 5.5% G174D (GGC→GAC)  lldP → L‑lactate permease
RA 3,792,765 C→T 5.2% intergenic (‑214/+61) kbl ← / ← yibB glycine C‑acetyltransferase/YibB family protein, function unknown
RA 3,806,430 C→A 9.3% R213L (CGC→CTC)  waaG ← UDP‑glucose:(heptosyl)lipopolysaccharide alpha‑1,3‑glucosyltransferase; lipopolysaccharide core biosynthesis protein; lipopolysaccharide glucosyltransferase I
JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,873,365 A→G 6.0% L83P (CTC→CCC)  dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,873,370 A→T 6.7% C81* (TGT→TGA dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,873,375 C→T 7.4% G80S (GGC→AGC)  dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,927,717 C→T 5.1% A188V (GCG→GTG)  asnA → asparagine synthetase A
RA 3,930,341 A→C 5.2% R251R (CGT→CGG ravA ← hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA 3,959,925 A→T 5.7% intergenic (‑112/+87) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA 3,959,926 A→T 5.5% intergenic (‑113/+86) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA 3,997,433 T→A 6.2% M84K (ATG→AAG)  yigB → 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,173,658 G→A 5.8% G193S (GGC→AGC)  birA → bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,295,929 T→C 7.3% intergenic (+135/+507) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,060 C→T 32.1% 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 4,367,339 G→A 5.2% P330L (CCG→CTG)  aspA ← aspartate ammonia‑lyase
RA 4,388,496 T→A 5.2% Q292L (CAG→CTG)  mscM ← mechanosensitive channel protein, miniconductance
RA 4,388,502 G→C 5.2% A290G (GCC→GGC)  mscM ← mechanosensitive channel protein, miniconductance
RA 4,388,508 T→A 6.1% Q288L (CAG→CTG)  mscM ← mechanosensitive channel protein, miniconductance
RA 4,559,342 G→A 5.5% P62L (CCA→CTA)  iadA ← isoaspartyl dipeptidase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 131574 134211 2638 30 [28] [28] 30 [acnB] [acnB]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 127338 =69 (0.870)4 (0.050) 4/252 NT 5.4% coding (1644/1893 nt) aceF pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
?NC_000913 127444 = 73 (0.950)coding (1750/1893 nt) aceF pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
* ? NC_000913 = 381669NA (NA)4 (0.050) 3/246 NT NA noncoding (410/1331 nt) IS2 repeat region
?NC_000913 = 381695 NA (NA)noncoding (436/1331 nt) IS2 repeat region
* ? NC_000913 1207790 =31 (0.390)43 (0.620) 38/228 NT 59.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 32 (0.460)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780527 (0.340)36 (0.520) 31/228 NT 56.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 32 (0.460)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 141662273 (0.920)5 (0.070) 5/246 NT 6.4% coding (765/2601 nt) recE Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
?NC_000913 = 1416637 76 (1.020)coding (750/2601 nt) recE Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
* ? NC_000913 = 3943635NA (NA)5 (0.070) 5/246 NT 8.1% intergenic (+125/‑69) gltU/rrlC tRNA‑Glu/23S ribosomal RNA of rrnC operon
?NC_000913 = 4037446 60 (0.760)intergenic (+111/‑73) alaT/rrlA tRNA‑Ala/23S ribosomal RNA of rrnA operon
* ? NC_000913 4295853 =NA (NA)4 (0.060)
+TTAAGCGTCGC
4/238 NT NA noncoding (19/600 nt) RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
?NC_000913 4295861 = NA (NA)noncoding (27/600 nt) RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
* ? NC_000913 = 463814669 (0.870)5 (0.070) 5/238 NT 7.1% intergenic (+26/‑32) creC/creD sensory histidine kinase in two‑component regulatory system with CreB or PhoB/inner membrane protein
?NC_000913 = 4638170 67 (0.930)intergenic (+50/‑8) creC/creD sensory histidine kinase in two‑component regulatory system with CreB or PhoB/inner membrane protein