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 855 T→G 5.1% R173R (CGT→CGG thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 864 A→T 5.3% A176A (GCA→GCT thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 865 A→T 5.3% S177C (AGC→TGC)  thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 872 T→A 6.0% I179N (ATT→AAT)  thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 874 C→A 6.4% P180T (CCG→ACG)  thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 43,677 G→A 5.0% E164K (GAA→AAA)  fixB → putative electron transfer flavoprotein, NAD/FAD‑binding domain and ETFP adenine nucleotide‑binding domain‑like protein
RA 89,152 A→T 5.1% intergenic (+120/‑482) cra → / → mraZ transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA 139,246 A→G 5.6% F660F (TTT→TTC gcd ← glucose dehydrogenase
RA 164,558 T→A 5.4% intergenic (+24/‑172) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 194,272 A→G 5.8% H251R (CAC→CGC)  dxr → 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 285,197 A→G 6.9% intergenic (+29/‑198) yagF → / → yagG CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
RA 285,199 T→A 7.0% intergenic (+31/‑196) yagF → / → yagG CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
RA 285,202 T→A 7.9% intergenic (+34/‑193) yagF → / → yagG CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
RA 285,204 C→T 7.0% intergenic (+36/‑191) yagF → / → yagG CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
RA 334,215 G→T 5.1% T73T (ACC→ACA yahB ← putative DNA‑bindng transcriptional regulator
RA 337,740 G→A 6.0% L321L (CTG→CTA yahF → putative NAD(P)‑binding succinyl‑CoA synthase
RA 366,833 A→T 6.0% F226L (TTT→TTA lacI ← lactose‑inducible lac operon transcriptional repressor
RA 414,832 G→T 5.4% H308N (CAT→AAT)  sbcC ← exonuclease, dsDNA, ATP‑dependent
RA 475,971 C→G 7.7% intergenic (+20/+11) ybaY → / ← ybaZ outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA 475,972 C→G 6.6% intergenic (+21/+10) ybaY → / ← ybaZ outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA 517,383 A→T 6.9% intergenic (+21/+42) fetB → / ← ybbN iron export ABC transporter permease; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein
JC JC 523,077 IS2 (+) +5 bp 25.9% intergenic (+247/‑180) ybbP → / → rhsD putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 525,924 C→T 6.8% Y888Y (TAC→TAT rhsD → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA 544,323 C→G 5.1% D324H (GAC→CAC)  allC ← allantoate amidohydrolase
RA 578,331 G→T 7.8% A75A (GCG→GCT
R2L (CGA→CTA) 
rzpD →
rzoD →
DLP12 prophage; putative murein endopeptidase
DLP12 prophage; putative lipoprotein
RA 578,809 T→C 5.4% T29A (ACA→GCA)  borD ← DLP12 prophage; putative lipoprotein
RA 580,020 G→A 5.5% R47R (AGG→AGA ybcW → DLP12 prophage; uncharacterized protein
RA 580,115 C→T 7.5% intergenic (+29/+136) ybcW → / ← ylcI DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage
RA 580,119 A→G 7.3% intergenic (+33/+132) ybcW → / ← ylcI DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage
RA 580,120 C→T 7.2% intergenic (+34/+131) ybcW → / ← ylcI DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage
RA 581,042 T→G 9.5% L70R (CTG→CGG)  nohD → DLP12 prophage; DNA packaging protein
RA 696,410 C→T 6.5% intergenic (+134/+20) ubiF → / ← glnX 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA 696,411 G→T 6.6% intergenic (+135/+19) ubiF → / ← glnX 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA 696,412 A→C 7.5% intergenic (+136/+18) ubiF → / ← glnX 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA 696,413 A→G 6.7% intergenic (+137/+17) ubiF → / ← glnX 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA 733,154 T→C 5.6% L1191P (CTG→CCG)  rhsC → Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA 755,646 C→A 7.6% Y29* (TAC→TAA sdhD → succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA 756,054 C→T 42.8% Q50* (CAA→TAA)  sdhA → succinate dehydrogenase, flavoprotein subunit
JC 756,291 Δ11 bp 18.8% coding (385‑395/1767 nt) sdhA → succinate dehydrogenase, flavoprotein subunit
RA 756,423 C→T 24.3% Q173* (CAG→TAG)  sdhA → succinate dehydrogenase, flavoprotein subunit
RA 757,857 G→T 9.1% E57* (GAA→TAA)  sdhB → succinate dehydrogenase, FeS subunit
RA 816,956 C→A 5.4% intergenic (‑309/‑88) ybhK ← / → moaA putative CofD superfamily transferase/molybdopterin biosynthesis protein A
RA 854,868 C→T 5.1% E293K (GAA→AAA)  ldtB ← L,D‑transpeptidase linking Lpp to murein
RA 944,073 C→T 5.9% T14M (ACG→ATG)  dmsC → dimethyl sulfoxide reductase, anaerobic, subunit C
RA 1,046,842 C→A 5.1% T368T (ACG→ACT gfcD ← putative O‑antigen capsule production periplasmic protein
RA 1,071,029 G→A 5.9% T246M (ACG→ATG)  rutD ← putative reactive intermediate detoxifying aminoacrylate hydrolase
RA 1,071,673 C→T 6.2% P31P (CCG→CCA rutD ← putative reactive intermediate detoxifying aminoacrylate hydrolase
RA 1,097,348 A→G 7.8% intergenic (+519/+217) ycdU → / ← serX putative inner membrane protein/tRNA‑Ser
RA 1,149,544 Δ1 bp 5.4% coding (786/954 nt) fabH → 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III
RA 1,287,024 G→A 5.3% intergenic (+498/+42) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,287,047 C→T 5.7% intergenic (+521/+19) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,355,187 A→G 5.5% V95A (GTG→GCG) ‡ sapB ← antimicrobial peptide transport ABC transporter permease
RA 1,355,188 C→T 5.5% V95M (GTG→ATG) ‡ sapB ← antimicrobial peptide transport ABC transporter permease
RA 1,375,962 C→G 5.1% Q334E (CAG→GAG)  ycjQ → putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA 1,429,021 T→A 7.2% 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 7.1% 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 7.1% 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 1,429,027 C→T 7.4% intergenic (+43/‑22) 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 1,429,069 T→A 10.7% G7G (GGT→GGA stfR → Rac prophage; putative tail fiber protein
RA 1,429,072 A→C 10.1% V8V (GTA→GTC stfR → Rac prophage; putative tail fiber protein
RA 1,429,111 A→C 12.3% T21T (ACA→ACC stfR → Rac prophage; putative tail fiber protein
RA 1,429,114 C→T 12.6% I22I (ATC→ATT stfR → Rac prophage; putative tail fiber protein
RA 1,429,126 A→C 11.2% A26A (GCA→GCC stfR → Rac prophage; putative tail fiber protein
RA 1,429,128 A→G 11.4% K27R (AAA→AGA)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,160 C→G 8.7% L38V (CTG→GTG)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,164 C→G 8.5% A39G (GCC→GGC)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,171 A→G 7.5% E41E (GAA→GAG stfR → Rac prophage; putative tail fiber protein
RA 1,429,204 C→T 7.7% D52D (GAC→GAT stfR → Rac prophage; putative tail fiber protein
RA 1,429,816 C→T 6.7% S256S (AGC→AGT stfR → Rac prophage; putative tail fiber protein
RA 1,429,820 A→G 6.8% S258G (AGT→GGT)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,823 A→C 6.8% S259R (AGT→CGT)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,851 G→A 6.1% G268E (GGA→GAA)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,858 C→T 6.5% S270S (TCC→TCT stfR → Rac prophage; putative tail fiber protein
RA 1,429,861 G→C 6.3% A271A (GCG→GCC stfR → Rac prophage; putative tail fiber protein
RA 1,429,863 A→G 6.3% K272R (AAG→AGG)  stfR → Rac prophage; putative tail fiber protein
RA 1,429,888 C→T 5.5% N280N (AAC→AAT stfR → Rac prophage; putative tail fiber protein
RA 1,429,897 T→A 5.3% S283S (TCT→TCA stfR → Rac prophage; putative tail fiber protein
RA 1,429,906 G→A 5.9% T286T (ACG→ACA stfR → Rac prophage; putative tail fiber protein
RA 1,429,914 G→A 5.9% G289E (GGA→GAA)  stfR → Rac prophage; putative tail fiber protein
RA 1,567,466 G→C 6.0% intergenic (‑326/+38) dosC ← / ← yddW diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog
RA 1,567,467 G→T 5.5% intergenic (‑327/+37) dosC ← / ← yddW diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog
RA 1,567,469 A→T 6.0% intergenic (‑329/+35) dosC ← / ← yddW diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog
RA 1,567,471 A→C 7.7% intergenic (‑331/+33) dosC ← / ← yddW diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog
RA 1,567,472 G→C 5.6% intergenic (‑332/+32) dosC ← / ← yddW diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog
RA 1,585,149 Δ1 bp 5.3% coding (1338/2280 nt) ydeP ← putative oxidoreductase
RA 1,592,875 C→T 5.3% pseudogene (1251/1461 nt) yneO ← pseudogene, AidA homolog
RA 1,603,934 C→T 7.0% R306C (CGC→TGC)  lsrC → autoinducer 2 import system permease protein
RA 1,612,094 T→A 6.2% T78S (ACC→TCC)  yneG ← DUF4186 family protein
RA 1,636,690 C→T 5.5% intergenic (‑323/‑66) nohQ ← / → ynfO pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage
RA 1,655,299 G→A 5.9% intergenic (‑158/+48) rspA ← / ← ynfA bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein
RA 1,662,350 C→T 100% P599S (CCC→TCC)  ynfF → S‑ and N‑oxide reductase, A subunit, periplasmic
RA 1,663,395 G→A 6.0% G136R (GGG→AGG)  ynfG → oxidoreductase, Fe‑S subunit
RA 1,674,955 A→T 5.7% intergenic (+8/+17) tqsA → / ← pntB pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit
RA 1,678,903 T→C 5.4% D159D (GAT→GAC ydgH → DUF1471 family periplasmic protein
RA 1,721,397 T→A 5.6% V45D (GTT→GAT)  ydhJ → putative membrane fusion protein (MFP) of YdhJK efflux pump
RA 1,867,030 G→A 5.2% R41R (CGG→CGA yeaG → protein kinase, endogenous substrate unidentified; autokinase
RA 1,925,473 G→C 5.3% E12Q (GAG→CAG)  yobB → C‑N hydrolase family protein
RA 1,932,094 C→G 7.6% intergenic (+35/+21) purT → / ← eda phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA 1,932,095 T→A 7.4% intergenic (+36/+20) purT → / ← eda phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA 1,932,096 C→G 7.3% intergenic (+37/+19) purT → / ← eda phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
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 2,216,776 C→T 5.2% G211D (GGT→GAT)  yehX ← putative ABC transporter ATPase
RA 2,304,649 C→T 21.4% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,085 A→G 6.5% intergenic (+692/+23) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,086 C→G 6.2% intergenic (+693/+22) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,087 C→T 6.4% intergenic (+694/+21) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,357,653 A→G 7.0% L250L (CTA→CTG yfaD → transposase_31 family protein
RA 2,412,639 T→A 5.3% intergenic (‑45/+38) yfbU ← / ← yfbV UPF0304 family protein/UPF0208 family inner membrane protein
RA 2,412,640 G→T 5.3% intergenic (‑46/+37) yfbU ← / ← yfbV UPF0304 family protein/UPF0208 family inner membrane protein
RA 2,412,642 G→C 5.1% intergenic (‑48/+35) yfbU ← / ← yfbV UPF0304 family protein/UPF0208 family inner membrane protein
RA 2,432,985 A→G 6.7% intergenic (‑43/+27) folC ← / ← accD bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,432,990 G→C 6.3% intergenic (‑48/+22) folC ← / ← accD bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,432,995 C→T 5.9% intergenic (‑53/+17) folC ← / ← accD bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA 2,440,295 A→T 6.6% intergenic (‑175/+90) yfcJ ← / ← fabB putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA 2,440,296 T→G 6.7% intergenic (‑176/+89) yfcJ ← / ← fabB putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA 2,440,297 C→A 6.8% intergenic (‑177/+88) yfcJ ← / ← fabB putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA 2,440,298 A→T 6.7% intergenic (‑178/+87) yfcJ ← / ← fabB putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA 2,462,677 A→T 5.8% intergenic (+31/‑335) fadL → / → yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA 2,462,678 T→A 5.6% intergenic (+32/‑334) fadL → / → yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA 2,462,679 A→T 5.6% intergenic (+33/‑333) fadL → / → yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA 2,533,418 T→A 5.3% intergenic (+38/‑346) cysK → / → ptsH cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA 2,560,996 G→T 16.2% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,607,935 C→A 6.5% A340E (GCG→GAG)  hyfF → hydrogenase 4, membrane subunit
RA 2,642,793 G→T 5.4% R18S (CGC→AGC)  rodZ ← MreB assembly cytoskeletal protein
RA 2,666,510 T→A 5.1% L359* (TTA→TAA)  csiE → stationary phase inducible protein
RA 2,684,983 A→T 5.5% S175S (TCT→TCA glyA ← serine hydroxymethyltransferase
RA 2,691,169 A→T 6.1% noncoding (172/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,691,171 T→A 5.9% noncoding (170/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,691,173 A→T 5.9% noncoding (168/184 nt) glmY ← sRNA activator of glmS mRNA, glmZ processing antagonist
RA 2,704,304 A→G 5.6% intergenic (‑241/+31) rnc ← / ← lepB RNase III/leader peptidase (signal peptidase I)
RA 2,704,306 A→T 5.7% intergenic (‑243/+29) rnc ← / ← lepB RNase III/leader peptidase (signal peptidase I)
RA 2,704,308 C→T 5.8% intergenic (‑245/+27) rnc ← / ← lepB RNase III/leader peptidase (signal peptidase I)
RA 2,771,583 C→T 5.4% L146L (CTG→TTG)  yfjT → CP4‑57 prophage; putative periplasmic protein
RA 2,947,465 Δ1 bp 16.7% intergenic (+2/‑32) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 2,947,467 A→C 16.7% intergenic (+4/‑30) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 2,981,039 T→C 5.0% I382V (ATC→GTC)  araE ← arabinose transporter
RA 3,031,616 G→A 5.6% G84S (GGT→AGT)  uacT → uric acid permease
RA 3,125,574 A→C 5.9% F317V (TTT→GTT)  glcE ← glycolate oxidase FAD binding subunit
RA 3,157,277 C→A 5.3% R219S (CGC→AGC)  dkgA → 2,5‑diketo‑D‑gluconate reductase A
RA 3,165,154 T→A 5.8% M274L (ATG→TTG)  parC ← DNA topoisomerase IV, subunit A
RA 3,165,155 T→A 5.8% Q273H (CAA→CAT parC ← DNA topoisomerase IV, subunit A
RA 3,239,609 T→G 6.2% intergenic (+64/‑335) alx → / → sstT putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA 3,239,610 C→G 6.7% intergenic (+65/‑334) alx → / → sstT putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA 3,239,611 C→A 6.5% intergenic (+66/‑333) alx → / → sstT putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA 3,253,616 A→G 5.0% I200T (ATT→ACT)  yhaJ ← LysR family putative transcriptional regulator
RA 3,439,588 G→C 5.8% intergenic (‑79/+28) yhdN ← / ← rplQ DUF1992 family protein/50S ribosomal subunit protein L17
RA 3,439,589 G→C 6.0% intergenic (‑80/+27) yhdN ← / ← rplQ DUF1992 family protein/50S ribosomal subunit protein L17
RA 3,530,672 G→C 8.0% intergenic (+20/+43) hslO → / ← yhgE heat shock protein Hsp33/DUF4153 family putative inner membrane protein
RA 3,533,559 G→A 6.3% G248S (GGC→AGC)  pck → phosphoenolpyruvate carboxykinase [ATP]
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 3,690,623 G→A 5.7% A662V (GCG→GTG)  bcsB ← regulator of cellulose synthase, cyclic di‑GMP binding
RA 3,809,681 T→A 6.8% V381D (GTT→GAT) ‡ waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA 3,809,682 T→A 6.8% V381V (GTT→GTA) ‡ waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA 3,809,683 T→A 6.8% S382T (TCC→ACC)  waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
JC 3,815,859 Δ82 bp 48.8% [rph][rph] [rph], [rph]
RA 3,819,816 A→C 5.2% L452R (CTT→CGT)  ligB ← DNA ligase, NAD(+)‑dependent
RA 4,175,146 Δ1 bp 100% intergenic (‑120/‑242) coaA ← / → thrU pantothenate kinase/tRNA‑Thr
RA 4,296,060 C→T 42.1% 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 4,312,080 G→C 5.3% intergenic (‑38/+21) alsB ← / ← alsR D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA 4,356,445 A→T 6.7% intergenic (‑34/+25) dtpC ← / ← cadA dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA 4,356,446 A→T 6.7% intergenic (‑35/+24) dtpC ← / ← cadA dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA 4,599,416 A→G 5.2% L9P (CTT→CCT)  opgB ← OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 131572 134236 2665 37 [35] [35] 37 acnB acnB
* * ÷ NC_000913 3423760–3424234 3424591–3424238 5–832 37 [36] [36] 39 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 7338252 (0.590)5 (0.060) 5/244 NT 8.9% coding (1140/1611 nt) thiP thiamine/thiamine pyrophosphate ABC transporter permease
?NC_000913 = 73393 53 (0.640)coding (1129/1611 nt) thiP thiamine/thiamine pyrophosphate ABC transporter permease
* ? NC_000913 79973 =65 (0.740)4 (0.050) 4/242 NT 6.8% coding (892/1401 nt) leuC 3‑isopropylmalate dehydratase large subunit
?NC_000913 80003 = 48 (0.580)coding (862/1401 nt) leuC 3‑isopropylmalate dehydratase large subunit
* ? NC_000913 244129 =NA (NA)5 (0.060) 5/246 NT 6.5% noncoding (1/135 nt) REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences
?NC_000913 244213 = 72 (0.860)noncoding (85/135 nt) REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences
* ? NC_000913 = 315838NA (NA)3 (0.030) 3/254 NT NA noncoding (610/1255 nt) IS3 repeat region
?NC_000913 = 315862 NA (NA)noncoding (634/1255 nt) IS3 repeat region
* ? NC_000913 1155242 =60 (0.680)7 (0.080) 7/256 NT 9.6% coding (119/642 nt) tmk thymidylate kinase
?NC_000913 = 1560603 73 (0.840)coding (327/1023 nt) ddpB D,D‑dipeptide ABC transporter permease
* ? NC_000913 1170033 =80 (0.910)5 (0.060) 5/256 NT 6.1% coding (342/963 nt) ldtC L,D‑transpeptidase linking Lpp to murein
?NC_000913 = 1340069 75 (0.860)coding (740/765 nt) pgpB phosphatidylglycerophosphatase B
* ? NC_000913 1207790 =38 (0.430)47 (0.610) 41/226 NT 55.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 41 (0.530)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780538 (0.430)39 (0.510) 37/226 NT 51.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 41 (0.530)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)122 (1.440) 92/250 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 1570598 =111 (1.270)7 (0.090)
+CCGTTACCGTTAAAC
7/228 NT 6.7% intergenic (‑109/+47) gadC/gadB glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent
?NC_000913 3666176 = 111 (1.270)intergenic (‑366/+4) gadX/gadA acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent
* ? NC_000913 1592628 =NA (NA)4 (0.050) 4/236 NT NA intergenic (‑186/+37) hipB/yneO antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
?NC_000913 1592659 = NA (NA)intergenic (‑217/+6) hipB/yneO antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
* ? NC_000913 2729475 =50 (0.570)5 (0.060) 4/238 NT 10.4% intergenic (‑31/+141) gltW/rrsG tRNA‑Glu/16S ribosomal RNA of rrnG operon
?NC_000913 = 4168363 40 (0.490)intergenic (+163/‑9) rrsB/gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
* ? NC_000913 = 341141395 (1.080)11 (0.140) 10/236 NT 11.6% coding (143/297 nt) fis global DNA‑binding transcriptional dual regulator
?NC_000913 3411671 = 81 (1.010)coding (19/885 nt) yhdJ DNA adenine methyltransferase, SAM‑dependent
* ? NC_000913 = 418850064 (0.730)4 (0.050) 4/244 NT 5.9% coding (3151/4224 nt) rpoC RNA polymerase, beta prime subunit
?NC_000913 = 4188510 66 (0.800)coding (3161/4224 nt) rpoC RNA polymerase, beta prime subunit
* ? NC_000913 4542682 =79 (0.900)40 (0.490) 36/240 NT 34.0% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 82 (1.010)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 454269078 (0.890)53 (0.650) 46/240 NT 40.7% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 82 (1.010)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)