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 5,144 G→A 65.4% intergenic (+124/‑90) thrC → / → yaaX L‑threonine synthase/DUF2502 family putative periplasmic protein
RA 7,905 A→C 12.5% Y19D (TAC→GAC)  yaaJ ← putative transporter
RA 10,444 G→T 83.0% F17L (TTC→TTA satP ← succinate‑acetate transporter
RA 12,901 G→A 100% D247N (GAT→AAT)  dnaK → chaperone Hsp70, with co‑chaperone DnaJ
RA 29,139 G→T 63.9% G256C (GGT→TGT)  dapB → dihydrodipicolinate reductase
RA 30,176 A→T 5.6% T176S (ACG→TCG)  carA → carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
RA 43,364 G→T 13.2% P59P (CCG→CCT fixB → putative electron transfer flavoprotein, NAD/FAD‑binding domain and ETFP adenine nucleotide‑binding domain‑like protein
RA 47,560 G→T 6.6% T105T (ACG→ACT kefF → potassium‑efflux system ancillary protein for KefC, glutathione‑regulated; quinone oxidoreductase, FMN‑dependent
RA 56,677 G→T 60.1% R145S (CGC→AGC)  lptD ← LPS assembly OM complex LptDE, beta‑barrel component
RA 65,335 G→T 7.3% P149Q (CCG→CAG)  polB ← DNA polymerase II
RA 72,337 C→A 15.4% D484Y (GAC→TAC)  sgrR ← transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA 72,392 G→T 34.4% F465L (TTC→TTA sgrR ← transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA 104,948 A→T 52.4% E61D (GAA→GAT secA → preprotein translocase subunit, ATPase
RA 105,563 C→A 14.9% D266E (GAC→GAA secA → preprotein translocase subunit, ATPase
RA 118,828 G→T 10.4% D84Y (GAT→TAT)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 118,873 G→T 88.9% D99Y (GAC→TAC)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 119,002 G→T 9.1% D142Y (GAT→TAT)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 123,870 G→T 44.0% P563P (CCG→CCT aceF → pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA 142,460 T→A 76.5% F298Y (TTC→TAC)  yadE → putative polysaccharide deacetylase lipoprotein
RA 142,829 G→T 7.4% A118E (GCG→GAG)  panD ← aspartate 1‑decarboxylase
RA 145,632 G→T 5.5% Q153K (CAG→AAG)  panB ← 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
RA 147,946 G→T 37.1% I47I (ATC→ATA yadK ← putative fimbrial‑like adhesin protein
RA 153,472 G→T 62.4% intergenic (‑102/+268) yadN ← / ← folK putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA 157,178 C→A 42.8% intergenic (‑87/+91) dksA ← / ← sfsA transcriptional regulator of rRNA transcription, DnaK suppressor protein/sugar fermentation stimulation protein A
RA 158,287 C→A 76.3% D78Y (GAC→TAC)  ligT ← 2'‑5' RNA ligase
RA 158,967 C→A 6.4% H126N (CAT→AAT)  hrpB → putative ATP‑dependent helicase
RA 161,068 A→C 12.0% intergenic (+47/‑149) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 161,171 G→T 18.4% intergenic (+150/‑46) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 170,868 C→A 12.2% V168F (GTT→TTT)  hemL ← glutamate‑1‑semialdehyde aminotransferase (aminomutase)
RA 180,358 A→C 5.3% N75K (AAT→AAG yaeH ← UPF0325 family protein
RA 198,022 C→A 41.3% R189S (CGT→AGT)  lpxD → UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase
RA 209,413 A→T 5.4% Q199L (CAG→CTG)  tilS → tRNA(Ile)‑lysidine synthetase
RA 230,561 G→A 5.8% P237S (CCT→TCT)  gloB ← hydroxyacylglutathione hydrolase
RA 230,579 C→T 100% E231K (GAA→AAA)  gloB ← hydroxyacylglutathione hydrolase
RA 232,860 G→T 82.8% D103Y (GAT→TAT)  dnaQ → DNA polymerase III epsilon subunit
RA 233,053 A→C 9.6% D167A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 238,195 G→T 65.1% V532V (GTC→GTA fadE ← acyl coenzyme A dehydrogenase
RA 241,773 A→T 19.1% Y174N (TAC→AAC)  yafK ← L,D‑transpeptidase‑related protein
RA 248,470 A→C 13.4% intergenic (+30/‑22) dinB → / → yafN DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA 249,629 G→A 8.6% R145Q (CGA→CAA)  yafP → putative acyl‑CoA transferase
RA 278,630 G→T 5.5% A214A (GCG→GCT yagE → 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA 281,469 A→T 9.1% T122S (ACC→TCC)  yagG → CP4‑6 prophage; putative sugar transporter
RA 283,278 A→T 9.0% Y260F (TAC→TTC)  yagH → CP4‑6 prophage; putative xylosidase/arabinosidase
RA 306,510 G→A 14.1% R180W (CGG→TGG)  ecpR ← putative transcriptional regulator for the ecp operon
RA 306,949 G→A 18.1% A33A (GCC→GCT ecpR ← putative transcriptional regulator for the ecp operon
RA 312,532 G→A 77.0% pseudogene (349/684 nt) ykgA ← pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA 320,920 G→A 66.5% S52S (AGC→AGT ykgH ← putative inner membrane protein
RA 334,250 G→T 17.4% R72L (CGT→CTT)  yahG → DUF1116 family protein
RA 339,660 C→T 5.5% intergenic (+16/‑227) yahK → / → yahL aldehyde reductase, NADPH‑dependent, Zn‑containing, broad specificity/uncharacterized protein
RA 341,060 C→A 12.7% intergenic (+358/‑55) yahL → / → yahM uncharacterized protein/uncharacterized protein
RA 351,359 G→T 15.5% G243C (GGT→TGT)  codB → cytosine transporter
RA 351,447 T→A 9.9% L272Q (CTG→CAG)  codB → cytosine transporter
RA 358,609 G→T 5.5% I94I (ATC→ATA lacY ← lactose permease
RA 360,752 A→G 100% V331A (GTG→GCG)  lacI ← DNA‑binding transcriptional repressor
JC 361,139 +GCCA 9.7% coding (605/1083 nt) lacI ← DNA‑binding transcriptional repressor
RA 361,806 G→A 100% intergenic (‑63/+14) lacI ← / ← mhpR DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA 362,159 G→T 63.6% I165I (ATC→ATA mhpR ← mhp operon transcriptional activator
RA 376,532 C→A 44.1% pseudogene (184/416 nt) yaiX ← pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
RA 379,943 C→T 8.7% G44R (GGA→AGA)  yaiS ← putative PIG‑L family deacetylase
RA 379,966 G→A 12.9% S36L (TCG→TTG)  yaiS ← putative PIG‑L family deacetylase
RA 389,725 G→T 11.1% pseudogene (1300/1449 nt) yaiT → pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA 401,729 G→A 5.4% intergenic (+51/‑132) yaiI → / → aroL UPF0178 family protein/shikimate kinase II
RA 402,340 G→T 86.8% V160V (GTG→GTT aroL → shikimate kinase II
RA 406,075 C→A 75.6% P159Q (CCG→CAG)  mak → manno(fructo)kinase
RA 411,027 G→T 81.2% L61L (CTC→CTA sbcC ← exonuclease, dsDNA, ATP‑dependent
RA 419,663 G→T 39.7% E564* (GAA→TAA)  malZ → maltodextrin glucosidase
RA 425,256 C→T 6.6% P99L (CCG→CTG)  secF → SecYEG protein translocase auxillary subunit
RA 433,551 G→T 82.3% S14Y (TCC→TAC)  yajO ← 2‑carboxybenzaldehyde reductase
RA 434,663 A→C 78.3% I324S (ATC→AGC)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 435,336 G→T 65.1% Q100K (CAG→AAG)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 437,672 T→A 66.0% V223E (GTG→GAG)  thiI → tRNA s(4)U8 sulfurtransferase
RA 442,299 G→T 15.7% S288* (TCG→TAG)  cyoE ← protoheme IX farnesyltransferase
RA 447,252 G→A 6.3% intergenic (‑186/+274) cyoA ← / ← ampG cytochrome o ubiquinol oxidase subunit II/muropeptide transporter
RA 456,588 G→T 82.6% D749Y (GAC→TAC)  lon → DNA‑binding ATP‑dependent protease La
RA 461,641 G→A 36.8% V376V (GTC→GTT ybaE ← putative ABC superfamily transporter periplasmic‑binding protein
RA 474,138 G→T 81.6% intergenic (‑65/+99) ylaB ← / ← ylaC putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA 479,244 C→A 62.2% A206S (GCC→TCC)  acrB ← multidrug efflux system protein
RA 480,820 C→T 83.0% D86N (GAC→AAC)  acrA ← multidrug efflux system
RA 495,504 A→T 39.8% intergenic (‑75/‑77) aes ← / → gsk acetyl esterase/inosine/guanosine kinase
RA 525,424 T→C 16.5% pseudogene (49/357 nt) ylbG ← pseudogene, DNA‑binding transcriptional regulator homology
RA 527,750 G→A 5.9% intergenic (‑73/‑157) allS ← / → allA allD operon transcriptional activator/ureidoglycolate lyase, releasing urea
RA 530,466 C→A 77.8% F365L (TTC→TTA gcl → glyoxylate carboligase
RA 535,589 G→T 5.9% M329I (ATG→ATT allB → allantoinase
RA 542,200 Δ1 bp 60.5% coding (65/1668 nt) fdrA → putative NAD(P)‑binding acyl‑CoA synthetase
RA 546,491 G→T 85.4% V199V (GTG→GTT ybcF → putative carbonate kinase
RA 549,397 G→T 83.0% intergenic (‑1/+2) lpxH ← / ← ppiB UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA 553,502 C→A 11.3% intergenic (‑305/‑166) folD ← / → sfmA bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase/FimA homolog
RA 565,299 T→G 9.7% N314K (AAT→AAG ybcK → DLP12 prophage; putative recombinase
RA 569,111 T→A 5.5% V95V (GTT→GTA rusA → DLP12 prophage; endonuclease RUS
RA 578,430 G→A 5.7% pseudogene (22/183 nt) tfaX → pseudogene, DLP12 prophage;Phage or Prophage Related
RA 579,710 G→A 32.9% A192T (GCA→ACA)  appY → global transcriptional activator; DLP12 prophage
RA 581,203 A→T 6.7% intergenic (‑114/‑310) ompT ← / → pauD DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA 583,341 T→G 83.6% S33R (AGT→CGT)  ybcH ← PRK09936 family protein
RA 595,736 C→A 5.5% R523S (CGT→AGT)  cusA → copper/silver efflux system, membrane component
RA 596,756 G→T 16.0% E863* (GAG→TAG)  cusA → copper/silver efflux system, membrane component
RA 601,154 T→A 12.1% L63F (TTA→TTT ybdF ← DUF419 family protein
RA 607,931 G→A 81.5% S7F (TCC→TTC)  fepA ← iron‑enterobactin outer membrane transporter
RA 608,174 G→A 20.4% intergenic (‑224/‑19) fepA ← / → fes iron‑enterobactin outer membrane transporter/enterobactin/ferric enterobactin esterase
RA 625,364 G→T 55.1% G5G (GGG→GGT cstA → carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA 632,406 T→A 44.0% K223N (AAA→AAT ybdO ← putative DNA‑binding transcriptional regulator
RA 639,231 G→A 79.3% L65F (CTT→TTT)  rnk ← regulator of nucleoside diphosphate kinase
RA 641,886 C→A 45.8% E51* (GAG→TAG)  citT ← citrate:succinate antiporter
RA 647,422 G→T 67.3% intergenic (‑110/‑269) citC ← / → citA [citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA 648,056 C→A 78.5% F122L (TTC→TTA citA → sensory histidine kinase in two‑component regulatory system with CitB
RA 652,865 Δ1 bp 80.4% coding (118/210 nt) cspE → constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA 657,177 C→T 5.4% A186A (GCG→GCA lipB ← octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase
RA 660,816 G→A 15.2% V318V (GTC→GTT mrdB ← cell wall shape‑determining protein
RA 662,631 C→A 61.8% R348L (CGC→CTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 663,449 G→T 6.1% N75K (AAC→AAA mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 668,211 C→A 10.4% V677F (GTT→TTT)  leuS ← leucyl‑tRNA synthetase
RA 705,588 C→A 60.9% intergenic (+16/+68) chiQ → / ← fur chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA 707,409 C→A 12.9% intergenic (‑55/+85) ybfE ← / ← ybfF LexA‑regulated protein, CopB family/acyl‑CoA esterase
RA 718,686 C→T 5.6% W395* (TGG→TGA kdpD ← fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA 731,316 A→T 7.1% T71S (ACA→TCA)  ybfC → putative periplasmic protein
RA 738,149 G→A 11.1% intergenic (‑137/‑134) dtpD ← / → ybgI dipeptide and tripeptide permease D/NIF3 family metal‑binding protein
RA 754,572 G→T 78.5% E137D (GAG→GAT sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 757,524 C→A 9.4% R183S (CGC→AGC)  sucB → dihydrolipoyltranssuccinase
RA 759,000 C→A 85.4% F177L (TTC→TTA sucC → succinyl‑CoA synthetase, beta subunit
RA 760,181 G→T 17.1% P182P (CCG→CCT sucD → succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit
RA 763,080 C→T 5.3% T547T (ACC→ACT mngA → fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
RA 766,563 G→A 11.1% intergenic (+496/‑351) mngB → / → cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA 773,443 C→A 9.4% A83E (GCG→GAG)  tolB → periplasmic protein
RA 788,902 G→T 82.8% R115S (CGT→AGT)  modF ← fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA 789,274 G→T 6.5% intergenic (‑30/+38) modF ← / ← modE fused molybdate transporter subunits of ABC superfamily: ATP‑binding components/transcriptional repressor for the molybdenum transport operon modABC
RA 800,779 G→T 81.2% E607D (GAG→GAT ybhJ → putative hydratase
RA 828,374 G→T 81.4% V11V (GTC→GTA ybiA ← DUF1768 family protein
RA 832,574 G→T 10.5% T256T (ACG→ACT ybiC → putative dehydrogenase
RA 868,618 G→T 13.3% E62* (GAA→TAA)  yliE → putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 871,072 C→A 10.5% V94V (GTC→GTA yliF → putative membrane‑anchored diguanylate cyclase
RA 874,768 G→T 15.8% E191* (GAA→TAA)  yliI → soluble aldose sugar dehydrogenase
RA 876,447 G→A 76.5% D89N (GAT→AAT)  dacC → D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA 879,085 G→T 79.7% intergenic (‑241/‑44) ybjG ← / → mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA 882,441 A→T 15.7% S119T (TCT→ACT)  ybjJ ← putative transporter
RA 920,469 G→T 14.4% G584C (GGT→TGT)  clpA → ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA 923,312 G→T 13.4% S447* (TCG→TAG)  cydC ← fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA 923,339 G→T 19.0% S438* (TCG→TAG)  cydC ← fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA 932,915 C→A 8.4% R30S (CGC→AGC)  lolA → lipoprotein chaperone
RA 939,763 C→A 6.6% S92* (TCG→TAG)  dmsC → dimethyl sulfoxide reductase, anaerobic, subunit C
RA 947,211 C→A 14.1% P600P (CCG→CCT pflB ← formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1
RA 948,890 C→A 8.2% E41* (GAG→TAG)  pflB ← formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1
RA 950,103 T→C 16.8% intergenic (‑181/+225) focA ← / ← ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
RA 961,946 T→A 8.7% F724Y (TTT→TAT)  ycaI → ComEC family inner membrane protein
RA 968,415 G→T 77.9% S148* (TCG→TAG)  ycbC ← DUF218 superfamily protein
RA 971,532 A→T 11.9% Q152L (CAG→CTG)  mukE → chromosome condensin MukBEF, MukE localization factor
RA 982,037 G→T 7.2% T134T (ACC→ACA ompF ← outer membrane porin 1a (Ia;b;F)
RA 1,006,218 G→T 14.0% E267* (GAG→TAG)  uup → putative transporter subunit of ABC superfamily: ATP‑binding component
RA 1,011,972 A→T 14.7% intergenic (‑46/+23) fabA ← / ← ycbZ beta‑hydroxydecanoyl thioester dehydrase/putative peptidase
RA 1,050,246 G→T 14.2% L463L (CTC→CTA torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,058,901 G→T 5.8% Q111K (CAA→AAA)  cbpA ← DnaK co‑chaperone; curved DNA‑binding protein
RA 1,077,911 A→C 79.3% K71N (AAA→AAC efeO → inactive ferrous ion transporter EfeUOB
RA 1,087,844 G→A 5.5% intergenic (‑99/‑488) pgaA ← / → ycdT biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/diguanylate cyclase, membrane‑anchored
RA 1,090,918 T→A 18.9% intergenic (‑25/‑43) insE1 ← / → ymdE IS3 transposase A/pseudogene
RA 1,116,964 A→G 80.9% intergenic (‑21/+53) dinI ← / ← pyrC DNA damage‑inducible protein I/dihydro‑orotase
RA 1,123,001 A→C 10.6% Q247P (CAG→CCG)  yceM → putative oxidoreductase
RA 1,129,363 G→A 17.3% A36T (GCG→ACG)  flgF → flagellar component of cell‑proximal portion of basal‑body rod
RA 1,136,758 T→A 7.0% A1022A (GCA→GCT rne ← fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein
RA 1,151,750 G→T 60.2% R178L (CGC→CTC)  holB → DNA polymerase III, delta prime subunit
RA 1,152,278 G→T 83.0% E16* (GAA→TAA)  ycfH → putative DNase
RA 1,192,525 C→T 11.5% S155N (AGC→AAC)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
RA 1,193,313 C→T 5.4% M127I (ATG→ATA ymfE ← e14 prophage; putative inner membrane protein
RA 1,193,873 G→T 84.1% intergenic (‑180/‑278) ymfE ← / → lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,194,365 G→T 15.9% W72L (TGG→TTG)  lit → e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,197,027 G→T 17.7% M25I (ATG→ATT ymfI → e14 prophage; uncharacterized protein
RA 1,210,957 C→A 9.1% intergenic (‑26/‑288) bluF ← / → ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA 1,211,142 C→T 9.0% intergenic (‑211/‑103) bluF ← / → ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA 1,215,174 G→T 36.7% pseudogene (118/2648 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,217,884 A→T 12.0% I69I (ATT→ATA ymgD ← uncharacterized protein
RA 1,220,996 G→T 81.6% R181R (CGG→AGG)  minC ← cell division inhibitor
RA 1,228,591 G→T 81.8% intergenic (‑105/+41) dsbB ← / ← nhaB oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA 1,228,879 A→C 18.6% L432R (CTG→CGG)  nhaB ← sodium:proton antiporter
RA 1,229,460 G→T 9.9% F238L (TTC→TTA nhaB ← sodium:proton antiporter
RA 1,243,278 G→A 18.2% S431S (AGC→AGT dhaM ← putative dihydroxyacetone‑specific PTS enzymes: HPr component/EI component
RA 1,247,376 G→T 17.6% V285V (GTG→GTT dhaR → dhaKLM operon transcription activator
RA 1,278,667 G→T 6.2% P1116P (CCG→CCT narG → nitrate reductase 1, alpha subunit
RA 1,282,421 A→T 6.7% intergenic (+439/+101) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,282,439 A→T 6.8% intergenic (+457/+83) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,283,124 G→A 7.5% intergenic (‑46/+114) tyrT ← / ← purU tRNA‑Tyr/formyltetrahydrofolate hydrolase
RA 1,306,244 G→A 5.3% S87L (TCG→TTG)  yciA ← acyl‑CoA esterase
RA 1,322,140 T→A 82.3% T159S (ACG→TCG)  btuR ← cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA 1,342,794 C→T 5.2% D126N (GAC→AAC)  rnb ← ribonuclease II
RA 1,365,202 C→A 13.5% H244N (CAT→AAT)  ycjM → alpha amylase catalytic domain family protein
RA 1,365,283 G→T 58.4% E271* (GAG→TAG)  ycjM → alpha amylase catalytic domain family protein
RA 1,368,566 T→G 13.0% F74V (TTC→GTC)  ycjP → inner membrane putative ABC superfamily sugar transporter permease
JC JC 1,376,043 IS5 (–) +4 bp 100% pseudogene (10‑13/126 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
RA 1,377,394 C→T 82.0% A275A (GCG→GCA ycjW ← LacI family putative transcriptional repressor
RA 1,386,008 G→T 55.1% Q35K (CAG→AAG)  ycjY ← S9 homolog non‑peptidase family protein
RA 1,388,406 G→T 56.8% R308L (CGC→CTC)  mppA → murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA 1,398,482 C→A 7.1% R114L (CGT→CTT)  abgA ← p‑aminobenzoyl‑glutamate hydrolase, A subunit
RA 1,413,956 G→T 5.1% intergenic (‑243/+66) ydaG ← / ← racR Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator
RA 1,469,291 C→A 5.0% L272I (CTT→ATT)  ydbC → putative NAD(P)‑binding oxidoreductase
RA 1,471,707 A→T 35.4% *769C (TGA→TGT ydbD → PF10971 family putative periplasmic methylglyoxal resistance protein
RA 1,502,324 C→A 5.8% T429T (ACC→ACA ydcP → putative peptidase
RA 1,503,048 G→T 5.0% intergenic (+49/+43) ydcP → / ← yncJ putative peptidase/uncharacterized protein
RA 1,510,179 G→T 5.2% A115A (GCG→GCT patD → gamma‑aminobutyraldehyde dehydrogenase
RA 1,519,349 T→A 79.0% K297* (AAA→TAA)  ansP ← L‑asparagine transporter
RA 1,524,654 G→T 10.3% W159L (TGG→TTG)  ydcD → uncharacterized protein
RA 1,538,906 G→A 16.4% pseudogene (116/381 nt) yddK ← pseudogene, leucine‑rich protein; putative glycoportein
RA 1,539,484 G→A 18.8% pseudogene (488/951 nt) yddK ← pseudogene, leucine‑rich protein; putative glycoportein
RA 1,548,144 G→T 80.1% intergenic (‑49/+85) adhP ← / ← maeA ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA 1,563,276 G→T 82.9% H491N (CAC→AAC)  gadC ← glutamate:gamma‑aminobutyric acid antiporter
RA 1,565,497 G→A 81.5% S269L (TCG→TTG)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,576,869 G→A 12.9% intergenic (‑88/+314) ydeN ← / ← ydeO putative Ser‑type periplasmic non‑aryl sulfatase/UV‑inducible global regulator, EvgA‑, GadE‑dependent
RA 1,599,970 T→A 5.3% D221E (GAT→GAA lsrB → autoinducer 2‑binding protein
RA 1,604,068 G→T 31.4% T290T (ACC→ACA uxaB ← altronate oxidoreductase, NAD‑dependent
RA 1,607,556 A→C 10.5% intergenic (‑48/+16) glsB ← / ← sad glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA 1,611,821 C→A 6.3% I179I (ATC→ATA ydeA → arabinose efflux transporter, arabinose‑inducible
RA 1,628,207 G→A 100% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,640,268 A→C 12.2% K39Q (AAG→CAG)  ydfV → Qin prophage; uncharacterized protein
RA 1,641,686 G→A 5.1% pseudogene (208/279 nt) ydfX ← pseudogene, Qin prophage;Phage or Prophage Related
RA 1,643,394 A→G 5.7% intergenic (+96/‑245) ydfC → / → dicF uncharacterized protein, Qin prophage/sRNA antisense regulator, inhibits ftsZ, Hfq‑dependent; Qin prophage
RA 1,649,456 C→T 36.8% intergenic (‑58/+148) rspA ← / ← ynfA bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein
RA 1,649,576 A→C 6.8% intergenic (‑178/+28) rspA ← / ← ynfA bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein
RA 1,658,420 C→A 8.2% S185R (AGC→AGA ynfH → oxidoreductase, membrane subunit
RA 1,661,763 C→A 82.5% P353P (CCG→CCT mlc ← glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA 1,671,110 C→A 8.0% D351Y (GAT→TAT)  pntA ← pyridine nucleotide transhydrogenase, alpha subunit
RA 1,703,062 T→A 10.4% R629R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,071 A→T 6.6% A632A (GCA→GCT rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,711,397 C→T 79.7% R28Q (CGA→CAA)  tyrS ← tyrosyl‑tRNA synthetase
RA 1,716,193 A→T 6.0% S225C (AGT→TGT)  ydhJ → putative membrane fusion protein (MFP) of YdhJK efflux pump
RA 1,726,289 A→T 10.0% P982P (CCA→CCT lhr → putative ATP‑dependent helicase
RA 1,748,094 T→A 19.1% intergenic (‑7/+14) ydhV ← / ← ydhY putative oxidoreductase subunit/putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex
RA 1,770,281 T→A 62.0% D146E (GAT→GAA ydiF → putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA 1,784,952 A→G 37.7% F184L (TTT→CTT)  ydiU ← UPF0061 family protein
RA 1,796,428 C→A 6.2% V134F (GTC→TTC)  thrS ← threonyl‑tRNA synthetase
RA 1,798,532 C→A 7.7% pseudogene (758/1476 nt) arpB → pseudogene, ankyrin repeats
RA 1,802,047 G→A 80.6% intergenic (+100/‑6) ydiZ → / → yniA uncharacterized protein/fructosamine kinase family protein
RA 1,807,639 G→A 13.1% intergenic (‑250/+39) ydjO ← / ← cedA uncharacterized protein/cell division modulator
RA 1,817,655 G→A 6.9% intergenic (+113/‑117) nadE → / → cho NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair
RA 1,832,413 C→A 64.9% L315L (CTC→CTA ynjC → inner membrane putative ABC superfamily transporter permease
RA 1,833,730 C→A 77.7% R3S (CGT→AGT)  ynjE → molybdopterin synthase sulfurtransferase
RA 1,849,412 T→A 15.7% T273S (ACT→TCT)  ydjG ← alpha‑Keto reductase, NADH‑dependent; can use methylglyoxal as substrate
RA 1,865,422 C→A 85.8% R261R (CGA→AGA)  yeaI → putative membrane‑anchored diguanylate cyclase
RA 1,872,520 G→T 74.2% P183P (CCG→CCT yeaP → diguanylate cyclase
RA 1,872,672 A→C 6.4% Q234P (CAG→CCG)  yeaP → diguanylate cyclase
RA 1,909,342 T→A 80.3% E150D (GAA→GAT proQ ← RNA chaperone, putative ProP translation regulator
RA 1,915,555 A→C 16.6% Q359P (CAG→CCG)  rsmF → 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
RA 1,924,898 T→A 8.6% D36V (GAT→GTT)  yebG ← DNA damage‑inducible protein regulated by LexA
RA 1,934,928 G→T 7.1% P322Q (CCG→CAG)  mepM ← murein DD‑endopeptidase, space‑maker hydrolase, septation protein
RA 1,944,177 C→A 55.6% L201L (CTG→CTT aspS ← aspartyl‑tRNA synthetase
RA 1,955,620 C→A 6.2% L434L (CTC→CTA argS → arginyl‑tRNA synthetase
RA 1,984,340 G→A 5.1% L393L (TTG→TTA tyrP → tyrosine transporter
RA 1,995,152 T→A 13.6% E40V (GAA→GTA)  fliA ← RNA polymerase, sigma 28 (sigma F) factor
RA 2,020,166 C→A 63.1% D445Y (GAC→TAC)  yedQ ← putative membrane‑anchored diguanylate cyclase
RA 2,048,571 A→T 9.8% P10P (CCA→CCT amn → AMP nucleosidase
RA 2,070,058 C→A 41.2% A90A (GCC→GCA yeeS → CP4‑44 prophage; putative DNA repair protein
RA 2,078,521 C→A 37.6% V162V (GTG→GTT yeeE ← UPF0394 family inner membrane protein
RA 2,084,482 C→T 5.9% S270S (AGC→AGT hisG → ATP phosphoribosyltransferase
RA 2,098,995 C→A 81.0% G182* (GGA→TGA)  wbbI ← d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA 2,114,911 A→T 61.5% L42Q (CTG→CAG)  wcaJ ← colanic biosynthesis UDP‑glucose lipid carrier transferase
RA 2,120,334 T→C 5.0% K113R (AAA→AGA)  wcaG ← bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase
RA 2,127,716 G→T 11.7% S473* (TCG→TAG)  wzc ← colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA 2,129,796 C→A 5.4% R310L (CGT→CTT)  wza ← colanic acid export protein; outer membrane auxillary lipoprotein
RA 2,136,421 A→G 19.9% D3D (GAT→GAC udk ← uridine/cytidine kinase
RA 2,139,910 G→T 81.3% R1055L (CGA→CTA)  yegE → putative diguanylate cyclase
RA 2,144,474 C→A 86.1% intergenic (‑8/‑192) yegI ← / → yegJ protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA 2,170,285 C→T 8.7% A133A (GCG→GCA gatY ← D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
RA 2,195,449 A→T 76.6% E564D (GAA→GAT yehI → DUF4132 domain‑containing protein
RA 2,216,296 C→A 70.2% I211I (ATC→ATA dld → D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA 2,237,098 G→T 66.7% H12N (CAT→AAT)  folE ← GTP cyclohydrolase I
RA 2,237,441 G→T 9.6% R18L (CGA→CTA)  yeiG → S‑formylglutathione hydrolase
RA 2,242,501 C→A 19.8% E199D (GAG→GAT yeiE ← putative DNA‑binding transcriptional regulator
RA 2,254,517 C→T 35.3% A125T (GCC→ACC)  fruA ← fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,258,182 A→T 12.4% K281* (AAG→TAG)  setB → lactose/glucose efflux system
RA 2,264,143 G→A 61.4% intergenic (+119/‑62) mepS → / → rtn murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 2,289,374 C→A 79.5% V142V (GTG→GTT ccmC ← heme exporter subunit
RA 2,293,295 C→T 5.7% V149I (GTT→ATT)  napG ← ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA 2,295,611 C→T 7.8% A208T (GCG→ACG)  napA ← nitrate reductase, periplasmic, large subunit
RA 2,298,128 C→T 5.1% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,492 A→G 5.1% intergenic (+620/+95) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,299,282 C→T 6.0% V318I (GTT→ATT)  mqo ← malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,302,650 C→A 8.2% M57I (ATG→ATT alkB ← oxidative demethylase of N1‑methyladenine or N3‑methylcytosine DNA lesions
RA 2,305,116 C→A 79.2% intergenic (‑103/+9) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,352,573 C→A 78.3% P353P (CCG→CCT rhmT ← putative L‑rhamnonate transporter
RA 2,359,673 G→T 87.4% M89I (ATG→ATT arnB → uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA 2,362,338 T→A 85.2% L274Q (CTG→CAG)  arnA → fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA 2,370,361:1 +G 78.0% coding (711/759 nt) menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,370,987 C→A 79.3% E29* (GAA→TAA)  menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,376,381 G→A 13.7% A64T (GCT→ACT)  elaD → protease, capable of cleaving an AMC‑ubiquitin model substrate
RA 2,390,862 C→A 12.8% V20V (GTG→GTT nuoH ← NADH:ubiquinone oxidoreductase, membrane subunit H
RA 2,405,946 T→G 83.3% Q43P (CAG→CCG)  yfbU ← UPF0304 family protein
RA 2,407,495 G→T 13.4% G183C (GGC→TGC)  ackA → acetate kinase A and propionate kinase 2
RA 2,407,538 T→G 5.8% L197R (CTG→CGG)  ackA → acetate kinase A and propionate kinase 2
RA 2,422,841 C→A 81.6% D293Y (GAT→TAT)  purF ← amidophosphoribosyltransferase
RA 2,424,074 C→T 78.2% D57N (GAC→AAC)  cvpA ← colicin V production membrane protein
RA 2,431,731 G→T 5.6% A101A (GCG→GCT flk → putative flagella assembly protein
RA 2,450,335 C→T 84.2% intergenic (‑44/+159) sixA ← / ← fadJ phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA 2,454,297 T→G 64.9% E39D (GAA→GAC yfcZ ← UPF0381 family protein
RA 2,474,418 G→T 84.3% S413* (TCA→TAA)  emrY ← putative multidrug efflux system
RA 2,493,151 C→A 10.5% V334V (GTC→GTA ypdA → sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
RA 2,493,283 C→A 21.8% N378K (AAC→AAA ypdA → sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system
RA 2,520,863 G→T 14.6% D187Y (GAC→TAC)  yfeH → putative inorganic ion transporter
RA 2,525,385 C→T 5.7% F188F (TTC→TTT cysZ → EI24 family inner membrane protein; putative sulfate transporter
RA 2,542,903 G→T 6.2% intergenic (+138/+102) yfeW → / ← yfeX penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic
RA 2,550,263 G→T 5.0% L132I (CTC→ATC)  eutC ← ethanolamine ammonia‑lyase, small subunit (light chain)
RA 2,551,235 C→T 5.8% A268A (GCG→GCA eutB ← ethanolamine ammonia‑lyase, large subunit, heavy chain
RA 2,553,563 T→G 17.1% intergenic (+138/‑53) intZ → / → yffL CPZ‑55 prophage; putative phage integrase/CPZ‑55 prophage; uncharacterized protein
RA 2,556,774 G→A 14.1% intergenic (+298/‑177) yffP → / → yffQ CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,576,325 C→A 77.9% E171D (GAG→GAT nudK ← GDP‑mannose pyrophosphatase
RA 2,587,029:1 +G 80.7% coding (101/699 nt) ypfH ← palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA 2,600,721 C→A 6.5% S149* (TCG→TAG)  hyfF → hydrogenase 4, membrane subunit
RA 2,605,882 C→A 6.9% S208R (AGC→AGA hyfR → hydrogenase‑4 transcriptional activator
RA 2,606,516 G→T 79.2% D420Y (GAC→TAC)  hyfR → hydrogenase‑4 transcriptional activator
RA 2,609,187 C→A 41.9% A18A (GCG→GCT yfgO ← putative UPF0118 family inner membrane permease
RA 2,614,168 C→A 76.4% D22Y (GAT→TAT)  upp ← uracil phosphoribosyltransferase
RA 2,643,286 C→A 5.0% A787A (GCG→GCT yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,651,665 G→T 75.2% G210G (GGC→GGA hscA ← DnaK‑like molecular chaperone specific for IscU
RA 2,653,668 G→T 16.9% intergenic (‑20/+8) iscU ← / ← iscS iron‑sulfur cluster assembly scaffold protein/cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,654,099 C→A 13.3% A264A (GCG→GCT iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,654,144 G→T 7.2% I249I (ATC→ATA iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,665,296 C→T 5.6% S238L (TCG→TTG)  hcaB → 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase
RA 2,667,539 C→T 5.5% R170Q (CGG→CAG)  yphB ← mutarotase superfamily protein, YphB family
RA 2,671,274 C→A 78.4% T149T (ACG→ACT yphE ← putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA 2,672,639 C→A 5.8% E30* (GAA→TAA)  yphF ← putative ABC superfamily sugar transporter periplasmic‑binding protein
RA 2,674,941 G→T 35.8% I388I (ATC→ATA yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,679,933 C→A 11.5% A247D (GCT→GAT)  hmp → fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA 2,681,873 T→A 79.3% Q97L (CAG→CTG)  glrR ← response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA 2,708,587 C→A 11.8% T31T (ACG→ACT yfiE ← putative DNA‑binding transcriptional regulator
JC 2,713,645 +CCTGCGC 9.0% coding (334/2661 nt) pka → protein lysine acetyltransferase
RA 2,715,643 G→T 87.1% E778* (GAA→TAA)  pka → protein lysine acetyltransferase
RA 2,718,953 G→T 41.7% I51I (ATC→ATA kgtP ← alpha‑ketoglutarate transporter
RA 2,719,426 T→C 100% intergenic (‑321/+2) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,733,753 C→T 100% E253K (GAG→AAG)  aroF ← 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA 2,740,398 C→T 5.4% D253N (GAT→AAT)  ffh ← Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)
RA 2,756,275 C→A 5.4% E209* (GAG→TAG)  yfjK ← DEAD/H helicase‑like protein, CP4‑57 putative defective prophage
RA 2,759,184 C→T 18.3% intergenic (‑49/‑93) yfjM ← / → rnlA CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; RNase LS
RA 2,767,403 G→A 12.7% D243N (GAT→AAT)  yfjW → CP4‑57 prophage; putative inner membrane protein
RA 2,771,358 G→A 62.8% intergenic (+217/+147) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA 2,775,830 C→T 37.3% D86N (GAT→AAT)  ypjA ← adhesin‑like autotransporter
RA 2,777,166 A→T 9.5% pseudogene (1205/1374 nt) ypjC ← pseudogene
RA 2,778,307 C→T 6.1% pseudogene (64/1374 nt) ypjC ← pseudogene
RA 2,802,110 T→A 6.9% pseudogene (436/1178 nt) ygaY → pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein
RA 2,804,103 G→A 6.6% intergenic (+65/‑26) ygaH → / → mprA putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA 2,818,527 A→T 6.4% Y137N (TAT→AAT)  mltB ← membrane‑bound lytic murein transglycosylase B
RA 2,825,783 C→T 74.2% intergenic (‑135/‑52) norR ← / → norV anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA 2,835,413 C→A 11.9% I355I (ATC→ATA ascB → cryptic 6‑phospho‑beta‑glucosidase
RA 2,850,790 C→A 79.5% I113I (ATC→ATA mutS → methyl‑directed mismatch repair protein
RA 2,873,087 G→T 83.9% V15V (GTC→GTA ygbT ← multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA 2,876,760 C→T 80.6% G246G (GGG→GGA casA ← CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA 2,878,668 G→T 66.8% V637V (GTC→GTA ygcB ← R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA 2,890,873 A→T 10.2% I119I (ATT→ATA ygcS ← putative transporter
RA 2,928,446 G→T 42.4% A285S (GCT→TCT)  fucP → L‑fucose transporter
RA 2,931,717 C→A 76.2% N307K (AAC→AAA fucK → L‑fuculokinase
RA 2,934,843 G→T 79.5% H50N (CAT→AAT)  ygdD ← UPF0382 family inner membrane protein
RA 2,936,672 C→A 10.8% intergenic (‑168/‑24) ygdI ← / → csdA DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA 2,975,955 C→A 5.3% P221P (CCG→CCT kduD ← hexuronate dehydrogenase; hexuronate utilization in high osmolarity
RA 2,983,868 G→T 38.3% intergenic (‑149/‑45) yqeK ← / → ygeF uncharacterized protein/pseudogene
RA 2,988,619 G→A 12.4% intergenic (‑168/+54) ygeK ← / ← ygeN pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA 2,988,774 C→A 17.2% pseudogene (346/447 nt) ygeN ← pseudogene
RA 2,989,295 C→A 84.5% pseudogene (85/261 nt) ygeN ← pseudogene
RA 2,993,211 C→A 82.7% V14L (GTG→TTG)  ygeR ← LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA 3,000,568 G→T 5.9% M316I (ATG→ATT ygeW → putative carbamoyltransferase
RA 3,001,919 C→A 21.5% H351N (CAT→AAT)  ygeX → 2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA 3,010,725 A→G 9.1% K436R (AAA→AGA)  ygfK → putative Fe‑S subunit oxidoreductase subunit
RA 3,020,228 G→T 9.6% A368A (GCG→GCT guaD → guanine deaminase
RA 3,020,629 C→A 42.3% I50I (ATC→ATA ygfQ → putative purine permease
RA 3,024,983 C→G 54.1% G86G (GGC→GGG uacT → uric acid permease
RA 3,033,430 G→T 13.9% D73Y (GAC→TAC)  fldB → flavodoxin 2
RA 3,044,464 G→A 77.9% intergenic (‑438/+10) gcvT ← / ← ubiI aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA 3,050,166 C→A 11.4% intergenic (+18/‑42) fau → / → sibC 5‑formyltetrahydrofolate cyclo‑ligase family protein/sRNA antisense regulator of toxic IbsC protein
RA 3,050,591 C→A 13.8% A393A (GCG→GCT serA ← D‑3‑phosphoglycerate dehydrogenase
RA 3,053,424 T→A 5.8% W105R (TGG→AGG)  argP → transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA 3,075,114 C→A 82.0% intergenic (‑120/‑158) tktA ← / → loiP transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA 3,076,526 C→A 63.3% D211Y (GAC→TAC)  speB ← agmatinase
RA 3,080,618 T→A 79.3% V185E (GTG→GAG)  metK → S‑adenosylmethionine synthetase
RA 3,094,183 G→A 6.0% intergenic (‑96/+80) ansB ← / ← yggN periplasmic L‑asparaginase 2/DUF2884 family putative periplasmic protein
RA 3,103,319 C→T 13.2% I136I (ATC→ATT yqgA → DUF554 family putative inner membrane protein
RA 3,105,207 G→T 12.3% pseudogene (243/963 nt) yghE ← pseudogene, secretion pathway protein, L‑type protein homology; putative general secretion pathway for protein export (GSP)
RA 3,111,434 C→A 77.8% A346A (GCG→GCT yghJ ← DUF4092 family putative lipoprotein peptidase
RA 3,116,216 G→T 5.8% R317S (CGT→AGT)  glcB ← malate synthase G
RA 3,120,216 C→A 80.2% D389Y (GAT→TAT)  glcD ← glycolate oxidase subunit, FAD‑linked
RA 3,131,302 C→A 5.4% D194Y (GAT→TAT)  gss ← fused glutathionylspermidine amidase/glutathionylspermidine synthetase
RA 3,158,037 C→T 6.6% K432K (AAG→AAA parC ← DNA topoisomerase IV, subunit A
RA 3,173,669 G→T 64.5% A189A (GCG→GCT ygiB → DUF1190 family protein
RA 3,174,009 G→T 5.1% R77L (CGC→CTC)  ygiC → ATP‑Grasp family ATPase
RA 3,209,857 C→A 6.0% intergenic (‑7/‑281) yqjH ← / → yqjI putative siderophore interacting protein/PadR family putative transcriptional regulator
RA 3,211,932 C→A 14.7% V168V (GTG→GTT aer ← fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA 3,212,068 A→C 5.8% I123S (ATC→AGC)  aer ← fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA 3,243,810 C→T 17.2% intergenic (+75/‑111) yqjK → / → yqjF uncharacterized protein/putative quinol oxidase subunit
RA 3,246,908 G→A 12.6% R222R (CGC→CGT yhaJ ← LysR family putative transcriptional regulator
RA 3,247,010 C→A 15.8% P188P (CCG→CCT yhaJ ← LysR family putative transcriptional regulator
RA 3,252,258 C→A 78.4% D251Y (GAT→TAT)  tdcG ← L‑serine dehydratase 3, anaerobic
RA 3,263,315 T→C 5.1% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,278,427 C→A 44.2% C128* (TGC→TGA agaC → N‑acetylgalactosamine‑specific enzyme IIC component of PTS
RA 3,302,027 G→T 64.4% S86* (TCG→TAG)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
RA 3,309,359 C→A 6.1% T5T (ACG→ACT infB ← translation initiation factor IF‑2
RA 3,311,854 G→T 7.6% intergenic (‑206/‑142) metY ← / → argG tRNA‑Met/argininosuccinate synthetase
RA 3,314,944 G→A 10.3% T10I (ACT→ATT)  yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,316,300 C→A 5.2% R377L (CGT→CTT)  glmM ← phosphoglucosamine mutase
RA 3,346,662 G→T 5.4% R250S (CGC→AGC)  yhcC ← putative Fe‑S oxidoreductase, Radical SAM superfamily protein
RA 3,354,405 C→T 80.9% intergenic (+430/‑130) gltD → / → gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA 3,371,372 G→T 33.3% I65I (ATC→ATA rpsI ← 30S ribosomal subunit protein S9
RA 3,373,985 C→A 81.1% intergenic (+37/‑117) yhcB → / → degQ DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA 3,375,260 G→T 80.8% D387Y (GAT→TAT)  degQ → serine endoprotease, periplasmic
RA 3,396,082 G→T 62.4% R204S (CGT→AGT)  csrD ← targeting factor for csrBC sRNA degradation
RA 3,422,390 C→A 17.3% intergenic (‑269/‑205) rrsD ← / → yrdA 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein
RA 3,440,151 G→T 63.9% I31I (ATC→ATA rpsN ← 30S ribosomal subunit protein S14
RA 3,440,444 G→T 77.7% S118S (TCC→TCA rplE ← 50S ribosomal subunit protein L5
RA 3,455,867 C→A 77.5% I55I (ATC→ATA gspJ → putative general secretory pathway component, cryptic
RA 3,460,036 T→A 5.2% N17Y (AAT→TAT)  bfr ← bacterioferritin, iron storage and detoxification protein
RA 3,471,787 C→A 11.7% D24Y (GAT→TAT)  slyD ← FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA 3,471,921 C→A 6.4% intergenic (‑65/+30) slyD ← / ← yheV FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)/DUF2387 family putative metal‑binding protein
RA 3,473,139 G→T 83.9% I276I (ATC→ATA kefB ← potassium:proton antiporter
RA 3,494,195 G→T 11.5% A309A (GCG→GCT frlA → putative fructoselysine transporter
RA 3,494,306 C→A 6.3% F346L (TTC→TTA frlA → putative fructoselysine transporter
RA 3,519,657 G→T 100% intergenic (‑149/‑171) nudE ← / → yrfF adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA 3,527,320 C→T 5.2% H382Y (CAC→TAC)  pck → phosphoenolpyruvate carboxykinase
RA 3,527,522 G→T 5.5% R449L (CGT→CTT)  pck → phosphoenolpyruvate carboxykinase
RA 3,530,481 G→T 11.6% R104L (CGT→CTT)  greB → transcript cleavage factor
RA 3,543,959 G→T 86.7% A625E (GCG→GAG)  malP ← maltodextrin phosphorylase
RA 3,555,325 T→C 11.8% intergenic (‑142/‑48) glpE ← / → glpD thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA 3,561,574 C→A 80.6% W372L (TGG→TTG)  glgC ← glucose‑1‑phosphate adenylyltransferase
RA 3,575,575 T→A 5.3% I118N (ATC→AAC)  yhhZ → putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA 3,609,368 T→A 7.5% F256L (TTT→TTA nikB → nickel transporter subunit
RA 3,622,519 C→A 40.9% R127L (CGA→CTA)  rbbA ← ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA 3,632,594 C→T 8.0% intergenic (+93/+151) pitA → / ← uspB phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA 3,635,421 C→T 9.2% G400G (GGC→GGT dtpB → dipeptide and tripeptide permease B
RA 3,636,207 T→A 12.7% T96S (ACT→TCT)  rsmJ ← 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA 3,662,801 T→A 6.4% intergenic (‑253/‑151) yhjA ← / → treF putative cytochrome C peroxidase/cytoplasmic trehalase
RA 3,664,370 G→T 6.9% A473A (GCG→GCT treF → cytoplasmic trehalase
RA 3,665,664 C→A 5.3% intergenic (‑410/‑110) yhjB ← / → yhjC putative DNA‑binding transcriptional response regulator/LysR family putative transcriptional regulator
RA 3,675,614 A→T 5.6% V398V (GTT→GTA dctA ← C4‑dicarboxylic acid, orotate and citrate transporter
RA 3,679,301 T→G 66.8% Q1078P (CAG→CCG)  bcsC ← cellulose synthase subunit
RA 3,679,324 C→A 82.6% M1070I (ATG→ATT bcsC ← cellulose synthase subunit
RA 3,681,219 C→A 36.4% A439S (GCG→TCG)  bcsC ← cellulose synthase subunit
RA 3,698,074 C→A 12.4% M16I (ATG→ATT dppC ← dipeptide/heme transporter
RA 3,721,480 T→G 7.0% T418P (ACG→CCG)  xylB ← xylulokinase
RA 3,721,485 T→G 11.6% Y416S (TAC→TCC)  xylB ← xylulokinase
RA 3,721,507 T→G 8.8% I409L (ATC→CTC)  xylB ← xylulokinase
RA 3,738,431 C→A 83.0% P90T (CCA→ACA)  yiaN → 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA 3,745,447 C→A 5.3% I32I (ATC→ATA yiaU → putative DNA‑binding transcriptional regulator
RA 3,748,366 C→A 8.0% V502V (GTG→GTT aldB ← aldehyde dehydrogenase B
RA 3,774,466 G→C 6.7% intergenic (+89/‑109) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,774,518 A→C 12.1% intergenic (+141/‑57) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,785,915 G→T 80.9% intergenic (‑4/+271) kbl ← / ← yibB glycine C‑acetyltransferase/YibB family protein, function unknown
RA 3,787,087 T→C 7.6% intergenic (‑44/‑260) yibB ← / → hldD YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding
RA 3,810,195 C→A 81.9% R54S (CGT→AGT)  yicC → UPF0701 family protein
RA 3,816,601 A→T 100% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,818,010 C→A 80.5% H46N (CAT→AAT)  trmH → tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA 3,825,702 C→A 77.7% K732N (AAG→AAT yicI ← putative alpha‑glucosidase
RA 3,830,311 G→T 61.9% intergenic (+395/‑2) yicT → / → setC pseudogene/putative arabinose efflux transporter
RA 3,837,177 C→T 43.6% intergenic (‑28/‑147) yicO ← / → ade putative adenine permease/cryptic adenine deaminase
RA 3,850,839 G→T 39.7% P309Q (CCG→CAG)  yidJ ← sulfatase/phosphatase superfamily protein
RA 3,860,159 C→A 86.3% P33P (CCG→CCT ibpB ← heat shock chaperone
RA 3,868,359 C→A 5.4% A54A (GCG→GCT dgoR ← putative DNA‑binding transcriptional regulator
RA 3,882,760 T→A 5.6% V224E (GTG→GAG)  tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,888,527 G→T 37.4% L172L (CTG→CTT chrR → chromate reductase, Class I, flavoprotein
RA 3,907,094 G→A 47.9% intergenic (‑66/+96) glmS ← / ← glmU L‑glutamine:D‑fructose‑6‑phosphate aminotransferase/fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase
RA 3,910,894 C→A 82.8% M244I (ATG→ATT atpG ← F1 sector of membrane‑bound ATP synthase, gamma subunit
RA 3,915,397 A→C 8.5% N5K (AAT→AAG atpB ← F0 sector of membrane‑bound ATP synthase, subunit a
RA 3,919,832 T→A 8.9% intergenic (‑17/+73) mioC ← / ← asnC FMN‑binding protein MioC/transcriptional activator of asnA; autorepressor
RA 3,923,700 G→T 6.3% R252S (CGC→AGC)  ravA ← hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA 3,930,583 A→T 6.9% intergenic (+55/‑71) rbsB → / → rbsK D‑ribose transporter subunit/ribokinase
RA 3,952,817 T→G 6.6% intergenic (+12/+75) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,954,751 G→T 5.3% V239L (GTG→TTG)  rep → DNA helicase and single‑stranded DNA‑dependent ATPase
RA 3,960,036 G→A 93.4% R87H (CGC→CAC)  rho → transcription termination factor
RA 3,964,617 A→T 6.0% S375S (TCA→TCT wecB → UDP‑N‑acetyl glucosamine‑2‑epimerase
RA 3,994,247 A→T 82.7% V57E (GTG→GAG)  yigE ← DUF2233 family protein
RA 4,007,147 A→C 5.4% E245D (GAA→GAC metE → 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase
RA 4,009,705 G→A 82.8% intergenic (‑176/‑86) ysgA ← / → udp putative carboxymethylenebutenolidase/uridine phosphorylase
RA 4,049,008 A→T 13.6% L231Q (CTG→CAG)  glnL ← sensory histidine kinase in two‑component regulatory system with GlnG
RA 4,056,018 T→A 84.6% F138I (TTC→ATC)  yihN → MFS transporter family protein
RA 4,062,424 G→T 84.6% I71I (ATC→ATA yihQ ← alpha‑glucosidase
RA 4,066,133 T→G 82.1% S267R (AGC→CGC)  yihU ← gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA 4,068,208 C→A 83.3% G60G (GGC→GGA yihW → DeoR family putative transcriptional regulator
RA 4,094,362 C→A 83.3% W181L (TGG→TTG)  cpxA ← sensory histidine kinase in two‑component regulatory system with CpxR
RA 4,096,163 G→T 6.5% R139L (CGA→CTA)  cpxP → inhibitor of the cpx response; periplasmic adaptor protein
RA 4,097,822 G→T 56.6% E115* (GAA→TAA)  pfkA → 6‑phosphofructokinase I
RA 4,127,022 T→G 78.8% E188D (GAA→GAC yijF ← DUF1287 family protein
RA 4,138,505 G→T 5.8% I563I (ATC→ATA eptC ← LPS heptose I phosphoethanolamine transferase
RA 4,142,369 A→T 16.8% Y220N (TAC→AAC)  ppc ← phosphoenolpyruvate carboxylase
RA 4,158,250 A→C 6.5% intergenic (+122/‑50) rrsB → / → gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA 4,175,869 T→A 11.5% C198S (TGC→AGC)  rpoC → RNA polymerase, beta prime subunit
RA 4,176,823 G→T 59.4% D516Y (GAC→TAC)  rpoC → RNA polymerase, beta prime subunit
RA 4,211,803 G→A 64.9% P205S (CCT→TCT)  arpA ← ankyrin repeat protein
RA 4,214,112 C→A 7.0% T119T (ACC→ACA metH → homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,230,913 A→T 64.3% W424R (TGG→AGG)  xylE ← D‑xylose transporter
RA 4,250,821 C→A 5.4% Q99K (CAG→AAG)  yjbM → uncharacterized protein
RA 4,259,875 G→T 5.0% S178S (TCG→TCT aphA → acid phosphatase/phosphotransferase, class B, non‑specific
RA 4,271,152 G→T 9.8% M415I (ATG→ATT yjcE → putative cation/proton antiporter
RA 4,273,158 A→T 11.1% intergenic (‑155/+23) yjcF ← / ← actP pentapeptide repeats protein/acetate transporter
RA 4,290,080 G→T 64.9% I256I (ATC→ATA mdtP ← outer membrane factor of efflux pump
RA 4,291,537 G→T 11.3% I453I (ATC→ATA mdtO ← membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA 4,295,721 A→G 16.3% Y232H (TAC→CAC)  yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,297,846 C→A 93.6% M150I (ATG→ATT alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,303,256 G→T 13.0% V30V (GTG→GTT rpiB → ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA 4,303,614 T→A 62.1% *150R (TGA→AGA)  rpiB → ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA 4,306,969 T→A 38.1% N23Y (AAC→TAC)  phnM ← ribophosphonate triphosphate hydrolase
RA 4,312,246 C→A 36.3% intergenic (‑7/+14) phnF ← / ← phnE putative DNA‑binding transcriptional regulator of phosphonate uptake and biodegradation/defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
RA 4,315,765 A→G 6.2% intergenic (‑207/+451) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,317,378 G→T 6.7% D143Y (GAT→TAT)  crfC → clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA 4,349,636 A→T 5.3% I71I (ATT→ATA cadB ← putative lysine/cadaverine transporter
RA 4,382,806 T→A 40.1% Q360L (CAA→CTA)  queG ← epoxyqueuosine reductase, cobalamine‑stimulated; queosine biosynthesis
RA 4,388,902 G→T 82.3% A558A (GCG→GCT mutL → methyl‑directed mismatch repair protein
RA 4,396,598 A→T 83.5% E43V (GAA→GTA)  rnr → exoribonuclease R, RNase R
RA 4,396,965 G→T 5.8% V165V (GTG→GTT rnr → exoribonuclease R, RNase R
RA 4,413,425 G→T 6.2% E255* (GAA→TAA)  ulaE → L‑xylulose 5‑phosphate 3‑epimerase
RA 4,434,159 G→A 7.3% L77L (CTG→CTA tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,436,661 C→A 14.8% N911K (AAC→AAA tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,458,254 T→A 79.9% V271V (GTT→GTA mgtA → magnesium transporter
RA 4,458,609 G→T 80.1% D390Y (GAT→TAT)  mgtA → magnesium transporter
RA 4,464,572 G→T 39.1% intergenic (+38/‑107) bdcR → / → tabA transcriptional repressor for divergent bdcA/biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily
RA 4,466,937 A→C 5.1% T562P (ACT→CCT)  yjgL → uncharacterized protein
RA 4,469,550 G→A 62.1% A2T (GCT→ACT)  yjgN → DUF898 family inner membrane protein
RA 4,470,017 G→A 74.8% M157I (ATG→ATA yjgN → DUF898 family inner membrane protein
RA 4,489,542 A→T 41.5% pseudogene (810/942 nt) yjgX ← pseudogene fragment
RA 4,502,777 G→A 5.1% N150N (AAC→AAT fecC ← iron‑dicitrate transporter subunit
RA 4,510,428 G→T 9.6% intergenic (‑287/+60) yjhU ← / ← yjhF putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA 4,511,877 G→A 40.8% intergenic (‑40/+67) yjhF ← / ← yjhG putative transporter/putative dehydratase
RA 4,512,693 T→A 87.7% K407* (AAG→TAG)  yjhG ← putative dehydratase
RA 4,525,234 G→A 79.2% pseudogene (415/1029 nt) yjhR → pseudogene, helicase family; putative frameshift suppressor
RA 4,531,143 A→T 81.0% I124F (ATT→TTT)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,556,296 C→T 41.9% Q256Q (CAG→CAA yjiN ← zinc‑type alcohol dehydrogenase‑like protein
RA 4,562,043 C→A 78.9% intergenic (+311/‑188) yjiS → / → yjiT DUF1127 family protein/pseudogene
RA 4,584,381 G→T 80.2% I53I (ATC→ATA yjjL ← L‑galactonate transporter
RA 4,601,014 T→C 36.7% intergenic (+194/‑199) prfC → / → osmY peptide chain release factor RF‑3/periplasmic protein
RA 4,626,235 G→T 40.4% E138* (GAA→TAA)  creB → response regulator in two‑component regulatory system with CreC
RA 4,629,622 C→A 6.1% A168S (GCC→TCC)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373836 375103 1268 231 [226] [229] 233 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100596 4101523 928 231 [225] [226] 232 [cdh]–tpiA [cdh],tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 312810302 (0.930)16 (0.050) 13/278 NT 5.0% pseudogene (71/684 nt) ykgA pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
?CP009273 = 1463497 NA (NA)noncoding (1/1331 nt) IS2 repeat region
* ? CP009273 360104 =321 (0.990)342 (1.060) 160/278 NT 51.6% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 = 360278NA (NA)9711 (31.890)
+TTAATTAA
195/262 NT 97.1% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 308 (0.950)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =377 (1.170)8524 (39.550)
+46 bp
186/186 NT 97.4% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 301 (0.930)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 376716 =NA (NA)112 (0.350) 77/278 NT 40.0% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 = 386403 168 (0.520)pseudogene (697/1458 nt) yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
* ? CP009273 376716 =NA (NA)287 (0.890) 163/278 NT 96.0% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 12 (0.040)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)116 (0.360) 82/278 NT 41.1% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 386399 = 166 (0.510)pseudogene (693/1458 nt) yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
* ? CP009273 = 378046NA (NA)360 (1.110) 170/278 NT 96.8% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 12 (0.040)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 1203246 =15 (0.050)236 (0.830) 124/246 NT 94.0% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 17 (0.060)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326114 (0.040)259 (0.910) 127/246 NT 94.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 17 (0.060)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 1462167 =NA (NA)4 (0.010) 3/278 NT NA noncoding (1331/1331 nt) IS2 repeat region
?CP009273 = 1463499 NA (NA)pseudogene (2/53 nt) ydbA pseudogene, autotransporter homolog; interrupted by IS2 and IS30
* ? CP009273 1635219 =54 (0.170)236 (0.740) 139/274 NT 81.4% intergenic (‑377/+377) essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
?CP009273 = 2063752 NA (NA)noncoding (1/1331 nt) IS2 repeat region
* ? CP009273 = 163522354 (0.170)276 (0.850) 142/278 NT 83.6% intergenic (‑381/+373) essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
?CP009273 = 1645805 NA (NA)intergenic (+11/‑3) insD1/intQ IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
* ? CP009273 = 4532507303 (0.940)16 (0.050) 11/260 NT 5.2% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 296 (0.980)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)