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 83,355 G→A 6.7% Q59* (CAA→TAA)  leuA ← 2‑isopropylmalate synthase
RA 95,070 G→A 5.3% V141I (GTA→ATA) ‡ murF → UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA 95,071 T→C 5.3% V141A (GTA→GCA) ‡ murF → UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA 155,285 T→C 6.1% I48V (ATT→GTT)  htrE ← putative outer membrane usher protein
RA 164,557 G→C 6.0% intergenic (+23/‑173) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 164,558 T→A 5.8% intergenic (+24/‑172) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 218,459 A→G 9.3% L106P (CTC→CCC)  proS ← prolyl‑tRNA synthetase
RA 243,632 T→C 6.1% I30I (ATT→ATC gmhA → D‑sedoheptulose 7‑phosphate isomerase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 263,316 T→C 5.2% intergenic (‑104/+12) ykfN ← / ← ykfI pseudogene, YdiA family/CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system
RA 285,846 T→A 6.2% F151Y (TTC→TAC)  yagG → CP4‑6 prophage; putative sugar transporter
RA 292,302 C→G 7.3% intergenic (+71/+20) yagJ → / ← yagK CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein
RA 299,635 C→T 9.1% G434S (GGT→AGT)  paoC ← PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA 324,133 C→T 5.5% Q126* (CAG→TAG)  ykgG → LutC family protein; putative electron transport chain YkgEFG component
RA 394,892 C→T 9.0% R129R (CGC→CGT yaiV → putative transcriptional regulator
RA 411,489 T→A 9.3% I331I (ATA→ATT araJ ← L‑arabinose‑inducible putative transporter, MFS family
RA 423,989 A→C 7.0% N491T (AAC→ACC) ‡ malZ → maltodextrin glucosidase
RA 423,990 C→G 6.8% N491K (AAC→AAG) ‡ malZ → maltodextrin glucosidase
RA 464,354 C→A 6.7% intergenic (+46/‑48) ybaV → / → fadM putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA 464,356 A→T 6.7% intergenic (+48/‑46) ybaV → / → fadM putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA 464,358 T→G 6.3% intergenic (+50/‑44) ybaV → / → fadM putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA 508,601 C→A 5.3% intergenic (+42/+274) ybaQ → / ← copA putative DNA‑binding transcriptional regulator/copper transporter
RA 516,487 C→T 6.2% A190V (GCC→GTC)  fetA → iron export ABC transporter ATPase; peroxide resistance protein
RA 531,581 A→G 6.7% L214S (TTG→TCG)  allS ← allD operon transcriptional activator
RA 531,584 C→T 6.7% R213Q (CGA→CAA)  allS ← allD operon transcriptional activator
RA 553,495 C→T 6.0% R149H (CGC→CAC)  lpxH ← UDP‑2,3‑diacylglucosamine pyrophosphohydrolase
RA 594,946 C→A 7.7% Q166H (CAG→CAT) ‡ cusR ← response regulator in two‑component regulatory system with CusS
RA 594,948 G→C 7.7% Q166E (CAG→GAG) ‡ cusR ← response regulator in two‑component regulatory system with CusS
RA 594,950 T→G 7.6% H165P (CAT→CCT)  cusR ← response regulator in two‑component regulatory system with CusS
RA 600,179 C→T 6.7% A489V (GCG→GTG)  cusA → copper/silver efflux system, membrane component
RA 610,711 G→A 6.3% P595L (CCG→CTG)  fepA ← ferrienterobactin outer membrane transporter
RA 611,329 G→A 6.4% T389M (ACG→ATG)  fepA ← ferrienterobactin outer membrane transporter
RA 658,577 G→A 5.5% pseudogene (353/594 nt) ybeM → pseudogene, C‑N hydrolase superfamily homology;putative enzyme; Not classified; putative amidase
RA 690,901 Δ1 bp 5.1% intergenic (‑20/+5) lnt ← / ← ybeX apolipoprotein N‑acyltransferase/putative ion transport
RA 699,556 C→T 8.3% intergenic (‑379/+18) asnB ← / ← umpH asparagine synthetase B/UMP phosphatase
RA 699,559 A→G 8.2% intergenic (‑382/+15) asnB ← / ← umpH asparagine synthetase B/UMP phosphatase
RA 701,130 T→C 5.2% P155P (CCA→CCG nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 716,572 T→C 5.9% pseudogene (26/651 nt) ybfG ← pseudogene
RA 781,668 C→T 7.3% intergenic (+16/‑417) lysQ → / → nadA tRNA‑Lys/quinolinate synthase, subunit A
RA 781,670 A→T 7.2% intergenic (+18/‑415) lysQ → / → nadA tRNA‑Lys/quinolinate synthase, subunit A
RA 781,672 A→G 6.9% intergenic (+20/‑413) lysQ → / → nadA tRNA‑Lys/quinolinate synthase, subunit A
RA 807,018 G→A 5.8% G88G (GGC→GGT ybhC ← acyl‑CoA thioesterase, lipoprotein
RA 818,694 C→T 5.8% A42V (GCG→GTG)  moaC → molybdopterin biosynthesis, protein C
RA 843,342 A→T 8.2% V713V (GTT→GTA) ‡ ybiO ← mechanosensitive channel protein, intermediate conductance
RA 843,343 A→T 8.2% V713D (GTT→GAT) ‡ ybiO ← mechanosensitive channel protein, intermediate conductance
RA 843,347 C→G 8.5% G712R (GGC→CGC)  ybiO ← mechanosensitive channel protein, intermediate conductance
RA 853,467 G→A 8.0% T95T (ACG→ACA mntR → Mn(2+)‑responsive manganese regulon transcriptional regulator
RA 857,576 T→C 5.7% intergenic (+21/+220) ybiT → / ← ybiU ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA 857,578 C→G 5.7% intergenic (+23/+218) ybiT → / ← ybiU ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA 875,531 C→T 10.2% T66M (ACG→ATG)  yliF → putative membrane‑anchored diguanylate cyclase
RA 928,207 T→A 7.8% Q330L (CAA→CTA)  cydC ← glutathione/cysteine ABC transporter export permease/ATPase
RA 930,998 C→T 6.9% intergenic (‑36/+87) cydD ← / ← trxB glutathione/cysteine ABC transporter export permease/ATPase/thioredoxin reductase, FAD/NAD(P)‑binding
RA 975,202 G→A 5.5% R295H (CGC→CAC)  mukF → chromosome condensin MukBEF, kleisin‑like subunit, binds calcium
RA 1,000,101 G→T 5.7% A296S (GCC→TCC)  elfC → putative outer membrane fimbrial subunit export usher protein
RA 1,018,983 A→T 11.9% intergenic (+46/+30) matP → / ← ompA Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA 1,018,986 A→T 11.8% intergenic (+49/+27) matP → / ← ompA Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA 1,069,287 G→T 6.3% L185M (CTG→ATG)  rutG ← pyrimidine permease
RA 1,085,592 G→C 8.9% V201L (GTC→CTC)  phoH → ATP‑binding protein; putative PhoH family P‑loop ATPase
RA 1,153,208 T→C 10.5% intergenic (+28/‑92) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,213 T→A 8.2% intergenic (+33/‑87) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,214 T→A 8.3% intergenic (+34/‑86) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,219 G→A 8.1% intergenic (+39/‑81) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,174,077 G→A 9.5% intergenic (‑113/+15) mfd ← / ← ycfT transcription‑repair coupling factor/inner membrane protein
RA 1,174,080 T→C 9.5% intergenic (‑116/+12) mfd ← / ← ycfT transcription‑repair coupling factor/inner membrane protein
RA 1,177,156 A→G 6.7% N180D (AAC→GAC)  lolD → outer membrane‑specific lipoprotein transporter subunit
RA 1,196,319 C→G 5.9% G399G (GGC→GGG icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,198,675 A→G 5.5% intergenic (‑438/‑20) ymfE ← / → lit e14 prophage; putative inner membrane protein/T4 phage exclusion protein; cell death peptidase, e14 prophage
RA 1,224,724 T→C 6.0% E213G (GAG→GGG)  minD ← inhibitor of FtsZ ring polymerization; chromosome‑membrane tethering protein; membrane ATPase of the MinCDEE system
RA 1,260,904 A→G 5.4% intergenic (‑101/+24) dauA ← / ← prs C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA 1,281,545 T→C 5.7% M561T (ATG→ACG)  narG → nitrate reductase 1, alpha subunit
RA 1,296,331 G→A 6.8% T597T (ACC→ACT 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 1,333,941 A→G 5.7% S29S (TCA→TCG cysB → N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor
RA 1,346,451 C→T 6.0% D98N (GAC→AAC)  gmr ← cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability
RA 1,354,905 G→T 6.5% T189N (ACC→AAC)  sapB ← antimicrobial peptide transport ABC transporter permease
RA 1,372,052 A→G 6.6% K48K (AAA→AAG ycjN → putative ABC sugar transporter periplasmic binding protein
RA 1,444,587 G→A 6.1% G513R (GGG→AGG)  ydbH → putative membrane‑anchored protein, function unknown
RA 1,446,411 C→A 8.3% M291I (ATG→ATT feaR ← transcriptional activator for tynA and feaB
RA 1,493,194 G→C 5.5% S242T (AGT→ACT)  trg → methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor
RA 1,499,361 A→G 8.4% N142D (AAC→GAC)  rimL → ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA 1,499,365 A→T 9.1% Q143L (CAG→CTG)  rimL → ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA 1,499,369 C→T 8.9% V144V (GTC→GTT rimL → ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA 1,501,769 C→T 6.5% R70C (CGC→TGC)  tehB → tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein
RA 1,523,429 A→G 6.0% K41K (AAA→AAG yncE → ATP‑binding protein, periplasmic, function unknown
RA 1,539,982 C→T 5.9% R870H (CGC→CAC)  narZ ← nitrate reductase 2 (NRZ), alpha subunit
RA 1,559,537 G→A 6.7% A125V (GCA→GTA)  ddpC ← D,D‑dipeptide ABC transporter permease
RA 1,654,745 C→T 6.5% D133N (GAT→AAT)  rspA ← bifunctional D‑altronate/D‑mannonate dehydratase
RA 1,685,527 A→G 100% G354G (GGT→GGC fumC ← fumarate hydratase (fumarase C),aerobic Class II
RA 1,689,817 C→A 5.4% intergenic (+66/‑35) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,689,819 A→T 5.4% intergenic (+68/‑33) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,689,821 T→G 5.6% intergenic (+70/‑31) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,701,108 A→T 7.7% N51I (AAT→ATT)  malY → PLP‑dependent beta‑cystathionase and maltose regulon regulator
RA 1,757,688 T→A 8.8% intergenic (+31/+33) lpp → / ← ldtE murein lipoprotein/murein L,D‑transpeptidase
RA 1,797,388 G→T 8.7% P186Q (CCG→CAG)  pheT ← phenylalanine tRNA synthetase, beta subunit
RA 1,797,391 A→C 8.9% L185R (CTG→CGG)  pheT ← phenylalanine tRNA synthetase, beta subunit
RA 1,827,811 T→G 5.7% K150T (AAA→ACA)  astB ← succinylarginine dihydrolase
RA 1,827,816 C→A 5.1% L148L (CTG→CTT astB ← succinylarginine dihydrolase
RA 1,864,681 A→G 11.3% T278A (ACC→GCC)  yeaD → D‑hexose‑6‑phosphate epimerase‑like protein
RA 1,864,768 T→C 8.9% intergenic (+34/+14) yeaD → / ← yeaE D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA 1,888,030 Δ1 bp 6.1% intergenic (‑39/+31) rnd ← / ← fadD ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA 1,888,034:1 +T 6.1% intergenic (‑43/+27) rnd ← / ← fadD ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA 1,936,823 A→G 5.1% M58V (ATG→GTG)  yebK → putative DNA‑binding transcriptional regulator
RA 1,963,758 A→G 7.5% D431D (GAT→GAC flhA ← putative flagellar export pore protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 1,987,442 Δ1 bp 7.7% intergenic (+14/+65) ftnB → / ← yecJ ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA 1,987,450:1 +A 5.5% intergenic (+22/+57) ftnB → / ← yecJ ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA 2,008,558 A→T 8.5% A94A (GCA→GCT yedE → UPF0394 family sulphur transport domain‑containing inner membrane protein
RA 2,145,313 C→A 100% S683Y (TCC→TAC)  yegE → putative diguanylate cyclase
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 2,180,783 A→C 5.9% D230A (GAC→GCC)  yegU → ADP‑ribosylglycohydrolase family protein
RA 2,218,893 C→T 6.0% G197S (GGC→AGC)  osmF ← putative ABC transporter periplasmic binding protein
RA 2,236,306 G→A 10.8% G348R (GGA→AGA)  preA → dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C
RA 2,259,686 A→G 12.1% intergenic (‑390/+33) psuK ← / ← fruA pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,259,690 G→A 8.5% intergenic (‑394/+29) psuK ← / ← fruA pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,259,693 A→T 8.1% intergenic (‑397/+26) psuK ← / ← fruA pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,259,696 T→C 8.1% intergenic (‑400/+23) psuK ← / ← fruA pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,259,700 C→T 9.2% intergenic (‑404/+19) psuK ← / ← fruA pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,287,682 C→A 5.3% pseudogene (1233/2525 nt) yejO ← pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA 2,305,085 A→G 15.4% intergenic (+692/+23) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,086 C→G 15.4% intergenic (+693/+22) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,087 C→T 14.9% intergenic (+694/+21) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,311,616 C→T 6.3% intergenic (‑82/+30) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,311,619 A→G 6.3% intergenic (‑85/+27) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,318,095 C→G 100% L594F (TTG→TTC rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,324,596 C→T 7.1% A163V (GCG→GTG)  atoA → acetyl‑CoA:acetoacetyl‑CoA transferase, beta subunit
RA 2,364,995 T→G 6.4% intergenic (+16/+23) nudI → / ← ais nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA 2,364,998 C→A 6.8% intergenic (+19/+20) nudI → / ← ais nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA 2,368,320 G→A 7.1% Q94Q (CAG→CAA arnA → fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA 2,432,985 A→G 6.5% intergenic (‑43/+27) folC ← / ← accD bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,432,990 G→C 6.4% intergenic (‑48/+22) folC ← / ← accD bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,434,956 C→T 6.3% L227L (TTG→TTA truA ← tRNA pseudouridine(38‑40) synthase
RA 2,596,873 Δ1 bp 10.2% intergenic (‑136/+32) ypfJ ← / ← purC putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA 2,596,878:1 +G 10.0% intergenic (‑141/+27) ypfJ ← / ← purC putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA 2,638,584 A→T 8.3% F23L (TTT→TTA bamB ← BamABCDE complex OM biogenesis lipoprotein
RA 2,732,027 A→G 6.8% M716T (ATG→ACG)  clpB ← protein disaggregation chaperone
RA 2,757,961 C→T 5.6% A214T (GCA→ACA)  yfjH ← CP4‑57 prophage; uncharacterized protein
RA 2,761,620 T→G 5.4% K641Q (AAG→CAG)  yfjK ← radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA 2,761,623 C→A 5.4% V640L (GTA→TTA)  yfjK ← radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA 2,859,242 A→G 5.7% N717S (AAT→AGT)  mutS → methyl‑directed mismatch repair protein
RA 2,863,768 A→G 6.8% Q59R (CAG→CGG)  ygbL → putative class II aldolase
RA 2,863,772 G→A 7.8% R60R (CGG→CGA ygbL → putative class II aldolase
RA 2,863,777 C→G 5.3% S62C (TCC→TGC) ‡ ygbL → putative class II aldolase
RA 2,863,778 C→G 6.6% S62S (TCC→TCG) ‡ ygbL → putative class II aldolase
RA 2,863,783 T→C 5.3% V64A (GTC→GCC)  ygbL → putative class II aldolase
RA 2,863,787 C→T 5.3% A65A (GCC→GCT ygbL → putative class II aldolase
RA 2,868,804 A→T 6.5% intergenic (‑51/+89) nlpD ← / ← pcm activator of AmiC murein hydrolase activity, lipoprotein/L‑isoaspartate protein carboxylmethyltransferase type II
RA 2,907,316 T→C 6.2% E209G (GAA→GGA)  eno ← enolase
RA 2,929,056 A→G 7.3% A276A (GCA→GCG sdaC → putative serine transporter
RA 2,958,119 G→A 11.3% P256S (CCG→TCG)  ptrA ← protease III
RA 2,961,248 A→T 8.3% L394Q (CTG→CAG)  recC ← exonuclease V (RecBCD complex), gamma chain
RA 2,961,251 A→T 8.4% L393Q (CTG→CAG)  recC ← exonuclease V (RecBCD complex), gamma chain
RA 2,968,103 A→G 6.2% L111S (TTA→TCA)  ptsP ← PEP‑protein phosphotransferase enzyme I; GAF domain containing protein
RA 3,006,513 G→A 5.5% L84L (CTG→CTA ygeW → putative carbamoyltransferase
RA 3,009,617 T→C 5.9% V285A (GTA→GCA)  ygeY → putative peptidase
RA 3,023,295 G→T 5.1% P660P (CCG→CCT xdhD → putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA 3,082,040 C→A 5.9% A43E (GCG→GAG)  loiP → Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein
RA 3,096,388 T→C 5.5% N2N (AAT→AAC yggU → UPF0235 family protein
RA 3,132,926 G→T 5.9% P96Q (CCG→CAG)  yghR ← putative ATP‑binding protein
RA 3,162,811 A→G 9.6% I224T (ATA→ACA)  plsC ← 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase
RA 3,162,815 A→T 10.1% S223T (TCG→ACG)  plsC ← 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase
RA 3,162,816 A→T 10.4% R222R (CGT→CGA plsC ← 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase
RA 3,162,820 C→T 10.3% C221Y (TGT→TAT)  plsC ← 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase
RA 3,176,799 T→C 6.1% E12G (GAG→GGG)  cpdA ← 3',5' cAMP phosphodiesterase
RA 3,216,435 T→A 7.2% E19D (GAA→GAT yqjH ← putative siderophore interacting protein
RA 3,288,032 C→A 5.2% intergenic (+22/‑58) yraH → / → yraI putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA 3,299,574 C→A 7.1% P114P (CCG→CCT yhbP ← UPF0306 family protein
RA 3,322,672 C→G 5.4% intergenic (‑167/+61) secG ← / ← glmM preprotein translocase membrane subunit/phosphoglucosamine mutase
RA 3,326,411 G→C 6.2% S175R (AGC→AGG ftsH ← protease, ATP‑dependent zinc‑metallo
RA 3,330,415 Δ1 bp 6.3% intergenic (+19/+167) dacB → / ← obgE D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA 3,330,419:1 +T 6.7% intergenic (+23/+163) dacB → / ← obgE D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA 3,418,629 T→C 5.3% intergenic (+18/‑413) yhdV → / → yhdW putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA 3,423,405 A→G 6.9% intergenic (+211/+18) yhdZ → / ← rrfF putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
RA 3,437,908 T→A 5.6% intergenic (+14/‑116) trkA → / → mscL NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA 3,437,909 A→T 5.6% intergenic (+15/‑115) trkA → / → mscL NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA 3,437,910 A→T 5.2% intergenic (+16/‑114) trkA → / → mscL NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA 3,437,911 T→A 5.6% intergenic (+17/‑113) trkA → / → mscL NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA 3,478,932 A→G 6.5% L559P (CTC→CCC)  kefB ← potassium:proton antiporter
RA 3,490,177 C→T 5.5% A2T (GCA→ACA)  argD ← bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase
RA 3,505,785 A→T 6.1% I79N (ATT→AAT)  yhfS ← FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,508,092 C→A 5.6% E167* (GAG→TAG)  php ← phosphotriesterase homology protein
RA 3,529,926 G→A 5.7% A51A (GCG→GCA hslO → heat shock protein Hsp33
RA 3,544,096 A→G 6.2% V250A (GTG→GCG)  bioH ← pimeloyl‑ACP methyl ester carboxylesterase
RA 3,556,119 T→C 5.9% N244S (AAT→AGT)  rtcA ← RNA 3'‑terminal phosphate cyclase
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 3,569,431 A→G 9.7% I630T (ATT→ACT)  glgX ← glycogen debranching enzyme
RA 3,569,436 G→A 9.5% H628H (CAC→CAT) ‡ glgX ← glycogen debranching enzyme
RA 3,569,437 T→C 9.3% H628R (CAC→CGC) ‡ glgX ← glycogen debranching enzyme
RA 3,569,442 C→T 9.0% E626E (GAG→GAA glgX ← glycogen debranching enzyme
RA 3,581,121 C→T 5.1% intergenic (‑105/‑17) ryhB ← / → yhhY sRNA antisense regulator mediating positive Fur regulon response, Hfq‑dependent; global iron regulator/aminoacyl nucleotide detoxifying acetyltransferase
RA 3,632,645 G→T 6.2% intergenic (‑55/+207) yhiJ ← / ← yhiL DUF4049 family protein/pseudogene, DUF4049 family protein
RA 3,671,075 A→G 6.1% K495R (AAG→AGG)  treF → cytoplasmic trehalase
RA 3,722,300 G→T 5.3% intergenic (+195/+28) sokA → / ← glyS pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
RA 3,781,051 C→G 6.8% intergenic (+34/‑164) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,845,746 G→A 8.2% intergenic (+16/+30) adeD → / ← uhpT cryptic adenine deaminase/hexose phosphate transporter
RA 3,845,748 C→G 8.3% intergenic (+18/+28) adeD → / ← uhpT cryptic adenine deaminase/hexose phosphate transporter
RA 3,845,750 T→C 8.6% intergenic (+20/+26) adeD → / ← uhpT cryptic adenine deaminase/hexose phosphate transporter
RA 3,852,553 C→A 6.7% A78S (GCG→TCG)  ilvB ← acetolactate synthase 2 large subunit
RA 3,852,558 T→A 7.0% K76I (AAA→ATA) ‡ ilvB ← acetolactate synthase 2 large subunit
RA 3,852,559 T→A 7.0% K76* (AAA→TAA) ‡ ilvB ← acetolactate synthase 2 large subunit
RA 3,877,558 G→C 8.0% intergenic (‑93/+147) yidB ← / ← gyrB DUF937 family protein/DNA gyrase, subunit B
RA 3,888,245 T→G 6.7% intergenic (+53/‑190) mnmE → / → tnaC tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide
RA 3,891,502 C→G 6.3% intergenic (+19/‑113) tnaB → / → mdtL tryptophan transporter of low affinity/multidrug efflux system protein
RA 3,891,504 T→A 6.2% intergenic (+21/‑111) tnaB → / → mdtL tryptophan transporter of low affinity/multidrug efflux system protein
RA 3,891,506 C→G 6.0% intergenic (+23/‑109) tnaB → / → mdtL tryptophan transporter of low affinity/multidrug efflux system protein
RA 3,907,100 T→C 6.0% E160G (GAA→GGA)  phoU ← negative regulator of PhoR/PhoB two‑component regulator
RA 3,912,161 A→G 6.1% L503P (CTG→CCG)  glmS ← L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA 3,948,276 G→A 5.2% C64Y (TGC→TAC)  yifE → UPF0438 family protein
RA 3,956,465 A→G 6.9% I379V (ATC→GTC)  ilvA → l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
RA 3,959,924 A→T 7.7% intergenic (‑111/+88) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA 3,959,925 A→T 7.7% intergenic (‑112/+87) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA 3,959,926 A→T 7.8% intergenic (‑113/+86) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA 3,991,331 G→T 27.8% G60V (GGC→GTC)  cyaA → adenylate cyclase
RA 3,992,392 G→T 25.6% D414Y (GAT→TAT)  cyaA → adenylate cyclase
JC JC 3,992,705 IS5 (+) +4 bp 47.1% coding (1553‑1556/2547 nt) cyaA → adenylate cyclase
RA 4,000,304 Δ1 bp 8.0% coding (753/765 nt) yigE ← DUF2233 family protein
RA 4,000,308:1 +G 7.7% coding (749/765 nt) yigE ← DUF2233 family protein
RA 4,028,758 G→A 5.5% V5V (GTC→GTT fadA ← 3‑ketoacyl‑CoA thiolase (thiolase I)
RA 4,060,261 G→T 5.3% intergenic (+31/‑186) typA → / → yihL GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA 4,060,264 A→C 5.1% intergenic (+34/‑183) typA → / → yihL GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA 4,062,371 A→T 5.6% N42I (AAT→ATT)  yihN → MFS transporter family protein
RA 4,072,411 C→T 5.3% A81T (GCC→ACC)  yihT ← 6‑deoxy‑6‑sulphofructose‑1‑phosphate aldolase
RA 4,088,377 A→G 8.3% G493G (GGT→GGC frvR ← putative frv operon regulator; contains a PTS EIIA domain
RA 4,096,388 C→A 5.7% R354L (CGG→CTG)  rhaB ← rhamnulokinase
RA 4,116,528 C→T 25.0% G232D (GGC→GAC)  glpK ← glycerol kinase
RA 4,117,005 T→G 72.0% D73A (GAT→GCT)  glpK ← glycerol kinase
RA 4,117,122 C→T 9.7% R34H (CGC→CAC)  glpK ← glycerol kinase
RA 4,117,687 A→G 6.2% F135S (TTC→TCC)  glpF ← glycerol facilitator
RA 4,161,974 T→A 7.3% A68A (GCT→GCA yijD → DUF1422 family inner membrane protein
RA 4,189,525 C→G 6.3% S1392R (AGC→AGG rpoC → RNA polymerase, beta prime subunit
RA 4,227,560 T→C 5.3% intergenic (+49/‑171) metH → / → yjbB homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA 4,280,402 Δ1 bp 6.9% coding (423/1650 nt) yjcE → putative cation/proton antiporter
RA 4,296,060 C→T 20.9% 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 4,312,080 G→C 5.1% intergenic (‑38/+21) alsB ← / ← alsR D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA 4,312,083 G→C 5.4% intergenic (‑41/+18) alsB ← / ← alsR D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA 4,312,089 A→G 5.1% intergenic (‑47/+12) alsB ← / ← alsR D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA 4,326,341 T→C 8.5% intergenic (‑600/+58) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,348,977 C→T 6.2% intergenic (‑233/+338) dcuB ← / ← dcuR C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor/response regulator in two‑component regulatory system with DcuS
RA 4,356,445 A→T 6.6% intergenic (‑34/+25) dtpC ← / ← cadA dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA 4,356,446 A→T 6.6% intergenic (‑35/+24) dtpC ← / ← cadA dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA 4,362,528 G→A 5.8% intergenic (‑175/+23) yjdQ ← / ← pheU pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA 4,362,529 T→C 5.8% intergenic (‑176/+22) yjdQ ← / ← pheU pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA 4,376,819 A→T 6.1% intergenic (+120/‑56) ecnB → / → sugE entericidin B membrane lipoprotein/multidrug efflux system protein
RA 4,376,822 A→T 6.1% intergenic (+123/‑53) ecnB → / → sugE entericidin B membrane lipoprotein/multidrug efflux system protein
RA 4,405,056 G→A 5.4% A124T (GCG→ACG)  purA → adenylosuccinate synthetase
RA 4,422,887 G→A 10.4% A14A (GCG→GCA ulaE → L‑xylulose 5‑phosphate 3‑epimerase
RA 4,422,895 C→G 9.6% A17G (GCC→GGC)  ulaE → L‑xylulose 5‑phosphate 3‑epimerase
RA 4,432,953 A→T 5.3% M35K (ATG→AAG)  ytfF ← DMT transporter family inner membrane protein
RA 4,439,845 T→A 6.2% intergenic (+52/+27) ytfK → / ← ytfL DUF1107 family protein/UPF0053 family inner membrane protein
RA 4,443,212 C→T 5.9% D277D (GAC→GAT tamA → translocation and assembly module for autotransporter export, outer membrane subunit
RA 4,468,881 A→G 5.1% T419T (ACA→ACG mgtA → magnesium transporter
RA 4,520,500 Δ1 bp 7.3% intergenic (‑176/+171) yjhU ← / ← yjhF putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA 4,520,504:1 +T 7.1% intergenic (‑180/+167) yjhU ← / ← yjhF putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA 4,541,195 C→A 5.4% P80Q (CCG→CAG)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,580,619 T→C 5.6% K282E (AAA→GAA)  hsdS ← specificity determinant for hsdM and hsdR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423736–3424234 3424575–3424239 6–840 28 [27] [27] 28 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 24161 =70 (1.060)4 (0.060) 3/268 NT 5.8% coding (1771/2817 nt) ileS isoleucyl‑tRNA synthetase
?NC_000913 24182 = 61 (0.930)coding (1792/2817 nt) ileS isoleucyl‑tRNA synthetase
* ? NC_000913 = 228108NA (NA)8 (0.120) 7/262 NT NA noncoding (2350/2904 nt) rrlH 23S ribosomal RNA of rrnH operon
?NC_000913 = 228124 NA (NA)noncoding (2366/2904 nt) rrlH 23S ribosomal RNA of rrnH operon
* ? NC_000913 726472 =39 (0.590)3 (0.050) 3/260 NT 6.7% coding (565/2049 nt) kdpB potassium translocating ATPase, subunit B
?NC_000913 726511 = 46 (0.720)coding (526/2049 nt) kdpB potassium translocating ATPase, subunit B
* ? NC_000913 765068 =60 (0.910)3 (0.050) 3/258 NT 5.2% intergenic (+19/+85) sucD/mngR succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
?NC_000913 765107 = 51 (0.810)intergenic (+58/+46) sucD/mngR succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
* ? NC_000913 1207790 =22 (0.330)37 (0.640) 25/238 NT 57.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 36 (0.620)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780527 (0.410)31 (0.530) 26/238 NT 50.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 36 (0.620)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 132678047 (0.710)4 (0.070) 4/246 NT 8.1% intergenic (+139/‑72) yciQ/rluB enhancer of membrane protein expression; putative inner membrane protein/23S rRNA pseudouridine(2605) synthase
?NC_000913 = 1326787 48 (0.800)intergenic (+146/‑65) yciQ/rluB enhancer of membrane protein expression; putative inner membrane protein/23S rRNA pseudouridine(2605) synthase
* ? NC_000913 1512011 =42 (0.640)3 (0.050) 3/262 NT 6.1% coding (358/1146 nt) ydcS putative ABC transporter periplasmic binding protein
?NC_000913 1512028 = 51 (0.790)coding (375/1146 nt) ydcS putative ABC transporter periplasmic binding protein
* ? NC_000913 = 248798258 (0.880)3 (0.050) 3/252 NT 5.1% intergenic (+15/+41) evgS/yfdE hybrid sensory histidine kinase in two‑component regulatory system with EvgA/acetyl‑CoA:oxalate CoA‑transferase
?NC_000913 = 2487991 57 (0.920)intergenic (+24/+32) evgS/yfdE hybrid sensory histidine kinase in two‑component regulatory system with EvgA/acetyl‑CoA:oxalate CoA‑transferase
* ? NC_000913 3214941 =NA (NA)4 (0.070) 3/250 NT 8.9% intergenic (+53/+26) rpoD/mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
?NC_000913 3214966 = 41 (0.670)intergenic (+78/+1) rpoD/mug RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
* ? NC_000913 = 337776770 (1.060)5 (0.080) 5/250 NT 7.0% intergenic (‑347/+48) sspA/rpsI stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9
?NC_000913 4189605 = 69 (1.130)intergenic (+32/‑181) rpoC/yjaZ RNA polymerase, beta prime subunit/stationary phase growth adaptation protein
* ? NC_000913 3721045 =94 (1.420)172 (2.620) 109/268 NT 68.2% noncoding (413/1443 nt) IS150 repeat region
?NC_000913 = 3839774 67 (1.020)coding (220/819 nt) nlpA cytoplasmic membrane lipoprotein‑28
* ? NC_000913 = 37642280 (0.000)3 (0.050) 3/260 NT 100% coding (2046/4134 nt) rhsA Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
?NC_000913 = 3764260 NA (NA)coding (2078/4134 nt) rhsA Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
* ? NC_000913 = 397760352 (0.790)5 (0.080) 3/260 NT 8.9% coding (79/1080 nt) wecF TDP‑Fuc4NAc:lipidIIFuc4NAc transferase
?NC_000913 = 3977623 52 (0.820)coding (99/1080 nt) wecF TDP‑Fuc4NAc:lipidIIFuc4NAc transferase
* ? NC_000913 = 404072726 (0.390)4 (0.060) 4/252 NT 14.7% intergenic (+91/+179) rrfA/mobB 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
?NC_000913 = 4040732 22 (0.360)intergenic (+96/+174) rrfA/mobB 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
* ? NC_000913 = 416833048 (0.730)3 (0.050) 3/270 NT 7.2% intergenic (+130/‑42) rrsB/gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
?NC_000913 = 4168374 29 (0.440)noncoding (3/76 nt) gltT tRNA‑Glu