mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 248 | C→T | 9.6% | A20V (GCG→GTG) | thrL → | thr operon leader peptide |
| RA | 12,110 | C→A | 5.6% | intergenic (‑324/‑53) | yaaI ← / → dnaK | UPF0412 family protein/chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 75,348 | G→A | 5.1% | A198V (GCG→GTG) | leuD ← | 3‑isopropylmalate dehydratase small subunit |
| RA | 94,323 | G→T | 5.9% | R250R (CGG→CGT) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine:D‑glutamate ligase |
| RA | 96,239 | C→A | 5.4% | R37S (CGC→AGC) | murG → | N‑acetylglucosaminyl transferase |
| RA | 104,013 | C→A | 14.6% | intergenic (+52/‑179) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 114,800 | G→T | 6.8% | S111S (TCC→TCA) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,842 | G→T | 6.9% | V97V (GTC→GTA) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 121,390 | C→A | 12.0% | S629S (TCC→TCA) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 142,444 | C→A | 8.6% | R293S (CGC→AGC) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 153,209 | G→T | 6.6% | I54I (ATC→ATA) | yadN ← | putative fimbrial‑like adhesin protein |
| RA | 165,108 | G→A | 6.9% | V380I (GTT→ATT) | fhuA → | ferrichrome outer membrane transporter |
| RA | 177,670 | C→T | 6.8% | G100G (GGC→GGT) | degP → | serine endoprotease (protease Do), membrane‑associated |
| RA | 185,449 | T→C | 6.1% | Q182R (CAG→CGG) | map ← | methionine aminopeptidase |
| RA | 189,367 | C→T | 6.6% | S3S (AGC→AGT) | frr → | ribosome recycling factor |
| RA | 200,351 | C→A | 11.4% | P173T (CCA→ACA) | lpxB → | tetraacyldisaccharide‑1‑P synthase |
| RA | 221,402 | A→C | 5.7% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 235,769 | G→T | 8.3% | pseudogene (177/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 238,320 | Δ1 bp | 8.9% | coding (1471/2445 nt) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,321 | Δ1 bp | 8.7% | coding (1470/2445 nt) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,324 | G→A | 8.7% | G489G (GGC→GGT) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,327 | C→A | 8.7% | Q488H (CAG→CAT) ‡ | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,328 | T→C | 8.8% | Q488R (CAG→CGG) ‡ | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,330 | G→A | 8.7% | Y487Y (TAC→TAT) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,333 | A→C | 9.8% | A486A (GCT→GCG) ‡ | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,334 | G→C | 9.8% | A486G (GCT→GGT) ‡ | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 238,337 | Δ1 bp | 9.8% | coding (1454/2445 nt) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 242,325 | G→A | 7.5% | intergenic (‑33/+123) | yafK ← / ← yafQ | L,D‑transpeptidase‑related protein/translation inhibitor toxin of toxin‑antitoxin pair YafQ/DinJ |
| RA | 243,622 | G→T | 11.7% | D142Y (GAT→TAT) | yafL → | putative lipoprotein and C40 family peptidase |
| RA | 256,248 | G→T | 10.7% | S50S (TCG→TCT) | proB → | gamma‑glutamate kinase |
| RA | 262,526 | C→T | 8.9% | pseudogene (153/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 262,529 | C→T | 8.8% | pseudogene (150/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 262,691 | G→A | 7.4% | intergenic (‑13/+204) | ykfK ← / ← yafZ | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 262,692 | T→G | 7.3% | intergenic (‑14/+203) | ykfK ← / ← yafZ | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 263,285 | G→A | 14.8% | D144D (GAC→GAT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,324 | A→G | 8.4% | G131G (GGT→GGC) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 292,279 | C→A | 7.7% | G177* (GGA→TGA) | intF ← | CP4‑6 prophage; putative phage integrase |
| RA | 296,628 | G→A | 5.8% | P6P (CCC→CCT) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 315,164 | C→A | 9.5% | K183N (AAG→AAT) | rclA ← | reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 322,367 | C→T | 5.8% | A198T (GCC→ACC) | betA ← | choline dehydrogenase, a flavoprotein |
| RA | 331,147 | G→T | 10.9% | A53S (GCT→TCT) | yahD → | ankyrin repeat protein |
| RA | 335,689 | A→G | 7.7% | intergenic (+235/‑187) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 335,690 | G→A | 9.3% | intergenic (+236/‑186) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 335,696 | C→T | 7.4% | intergenic (+242/‑180) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 335,703 | C→T | 9.0% | intergenic (+249/‑173) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 335,710 | C→T | 7.0% | intergenic (+256/‑166) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 340,599 | G→T | 9.3% | R238I (AGA→ATA) | yahL → | uncharacterized protein |
| RA | 345,326 | T→C | 5.3% | intergenic (+43/‑397) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 346,154 | C→A | 6.1% | S144R (AGC→AGA) | prpC → | 2‑methylcitrate synthase |
| RA | 364,470 | C→A | 6.1% | R543S (CGC→AGC) | mhpA → | 3‑(3‑hydroxyphenyl)propionate hydroxylase |
| RA | 370,415 | C→T | 5.4% | intergenic (+78/‑500) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 372,599 | C→A | 7.1% | V124V (GTC→GTA) | yaiL → | DUF2058 family protein |
| RA | 372,807 | Δ1 bp | 6.4% | intergenic (+40/+184) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,808 | G→A | 6.6% | intergenic (+41/+183) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,906 | T→A | 5.3% | intergenic (+139/+85) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,930 | C→T | 8.1% | intergenic (+163/+61) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,934 | C→T | 9.0% | intergenic (+167/+57) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,948 | G→A | 7.4% | intergenic (+181/+43) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 379,901 | C→A | 8.8% | G58C (GGC→TGC) | yaiS ← | putative PIG‑L family deacetylase |
| RA | 408,943 | G→A | 6.0% | T756I (ACC→ATC) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 449,252 | C→A | 10.1% | A124A (GCG→GCT) | yajG ← | putative lipoprotein |
| RA | 465,800 | G→A | 6.1% | E492K (GAA→AAA) | mdlA → | putative multidrug transporter subunit of ABC superfamily, ATP‑binding component |
| RA | 484,485 | G→T | 5.5% | E832* (GAA→TAA) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 497,644 | G→T | 5.1% | L351M (CTG→ATG) | ybaL ← | inner membrane putative NAD(P)‑binding transporter |
| RA | 507,612 | C→A | 6.7% | A172A (GCC→GCA) | glsA → | glutaminase 1 |
| RA | 507,734 | C→A | 5.2% | A213E (GCG→GAG) | glsA → | glutaminase 1 |
| RA | 527,360 | C→T | 9.3% | Q106Q (CAG→CAA) | allS ← | allD operon transcriptional activator |
| RA | 546,321 | C→A | 8.0% | Q143K (CAG→AAG) | ybcF → | putative carbonate kinase |
| RA | 628,446 | G→T | 19.0% | P163Q (CCG→CAG) | ybdH ← | putative oxidoreductase |
| RA | 629,236 | C→A | 8.7% | P65P (CCC→CCA) | ybdL → | methionine aminotransferase, PLP‑dependent |
| RA | 631,455 | G→T | 10.5% | P191T (CCC→ACC) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 639,144 | C→A | 6.6% | V94L (GTA→TTA) | rnk ← | regulator of nucleoside diphosphate kinase |
| RA | 647,263 | T→C | 5.7% | K17R (AAA→AGA) | citC ← | [citrate [pro‑3S]‑lyase] ligase |
| RA | 699,972 | G→T | 6.6% | Q191H (CAG→CAT) | nagE → | fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components |
| RA | 710,750 | A→C | 14.9% | intergenic (+96/‑118) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,751 | G→A | 14.8% | intergenic (+97/‑117) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,753 | A→C | 15.4% | intergenic (+99/‑115) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,755 | G→C | 15.4% | intergenic (+101/‑113) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,756 | G→C | 15.4% | intergenic (+102/‑112) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,774 | A→T | 12.9% | intergenic (+120/‑94) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,775 | A→C | 12.9% | intergenic (+121/‑93) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,776 | G→A | 11.1% | intergenic (+122/‑92) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,777 | C→T | 10.5% | intergenic (+123/‑91) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 710,779 | A→C | 11.0% | intergenic (+125/‑89) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 714,905 | G→T | 8.3% | L338M (CTG→ATG) | speF ← | ornithine decarboxylase isozyme, inducible |
| RA | 723,488 | C→T | 7.7% | G234D (GGC→GAC) | kdpA ← | potassium translocating ATPase, subunit A |
| RA | 725,257 | T→C | 8.4% | I73I (ATT→ATC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,319 | G→C | 5.7% | A427A (GCG→GCC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,848 | A→G | 5.1% | T604A (ACC→GCC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,207 | C→T | 6.2% | R723R (CGC→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 8.1% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,446 | A→G | 7.5% | V1136V (GTA→GTG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,467 | T→C | 8.2% | I1143I (ATT→ATC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 732,050 | C→T | 10.0% | pseudogene (150/240 nt) | ybfQ → | pseudogene, H repeat‑associated protein |
| RA | 732,499 | T→C | 9.1% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 734,222 | T→C | 6.4% | I225I (ATT→ATC) | ybfD → | H repeat‑associated putative transposase |
| RA | 749,509 | G→A | 7.4% | T139I (ACC→ATC) | gltA ← | citrate synthase |
| RA | 776,710 | A→T | 8.5% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 785,106 | G→T | 14.0% | F110L (TTC→TTA) | galK ← | galactokinase |
| RA | 813,288 | G→A | 5.3% | L263L (CTG→CTA) | moaA → | molybdopterin biosynthesis protein A |
| RA | 814,665 | C→A | 7.8% | A54A (GCC→GCA) | moaD → | molybdopterin synthase, small subunit |
| RA | 835,682 | C→T | 5.7% | G436S (GGC→AGC) | fiu ← | catecholate siderophore receptor Fiu |
| RA | 847,291 | C→A | 7.5% | D255Y (GAC→TAC) | ybiP ← | putative EptAB family phosphoethanolamine transferase, inner membrane protein |
| RA | 851,355:1 | +G | 5.5% | intergenic (‑155/‑64) | ldtB ← / → ybiT | L,D‑transpeptidase linking Lpp to murein/putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 851,355:2 | +C | 5.5% | intergenic (‑155/‑64) | ldtB ← / → ybiT | L,D‑transpeptidase linking Lpp to murein/putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 851,355:3 | +T | 5.5% | intergenic (‑155/‑64) | ldtB ← / → ybiT | L,D‑transpeptidase linking Lpp to murein/putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 860,939 | G→T | 6.4% | F294L (TTC→TTA) | moeA ← | molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein |
| RA | 916,429 | G→T | 5.3% | Q209H (CAG→CAT) | macB → | fused macrolide transporter subunits of ABC superfamily: ATP‑binding component/membrane component |
| RA | 944,862 | G→T | 7.4% | R55R (CGA→AGA) | ycaN ← | LysR family putative transcriptional regulator |
| RA | 956,649 | A→G | 9.2% | intergenic (+165/‑8) | ycaL → / → cmk | putative peptidase‑related chaperone/cytidylate kinase |
| RA | 960,135 | G→T | 7.7% | P120P (CCG→CCT) | ycaI → | ComEC family inner membrane protein |
| RA | 972,699 | G→A | 8.9% | Q306Q (CAG→CAA) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 973,565 | A→G | 6.7% | Q595R (CAG→CGG) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 979,098 | G→T | 7.8% | intergenic (+19/‑8) | ycbK → / → ycbL | M15A protease‑related family periplasmic protein/putative metal‑binding enzyme |
| RA | 980,635 | G→T | 8.2% | F177L (TTC→TTA) | aspC ← | aspartate aminotransferase, PLP‑dependent |
| RA | 981,730 | C→T | 5.7% | A237T (GCT→ACT) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| RA | 990,013 | C→A | 9.0% | W92C (TGG→TGT) | ssuC ← | putative alkanesulfonate transporter subunit |
| RA | 997,443 | G→T | 7.5% | G61W (GGG→TGG) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,005,202 | C→A | 7.0% | H635N (CAT→AAT) | rlmL → | fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent |
| RA | 1,012,498 | G→T | 8.8% | P420T (CCC→ACC) | ycbZ ← | putative peptidase |
| RA | 1,063,559 | C→A | 6.6% | S8Y (TCC→TAC) | ymdF → | KGG family protein |
| RA | 1,064,481 | C→A | 8.2% | G272V (GGG→GTG) | rutG ← | pyrimidine permease |
| RA | 1,127,021 | G→T | 9.1% | R43L (CGG→CTG) | flgC → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,127,693 | G→A | 9.5% | L128L (CTG→CTA) | flgD → | flagellar hook assembly protein |
| RA | 1,129,692 | G→A | 6.2% | A145A (GCG→GCA) | flgF → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,139,290 | C→A | 14.8% | E178D (GAG→GAT) | rne ← | fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein |
| RA | 1,141,503 | C→T | 6.0% | M183I (ATG→ATA) | yceF ← | Maf‑like protein |
| RA | 1,191,748 | C→T | 7.7% | T390T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,218,936 | C→T | 5.3% | intergenic (+31/‑84) | ymgJ → / → ycgI | uncharacterized protein/pseudogene |
| RA | 1,219,041 | G→A | 5.1% | pseudogene (22/108 nt) | ycgI → | pseudogene |
| RA | 1,219,085 | T→C | 5.3% | pseudogene (66/108 nt) | ycgI → | pseudogene |
| RA | 1,264,818 | G→T | 9.4% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| RA | 1,265,888 | T→G | 5.3% | noncoding (40/68 nt) | rdlC → | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC |
| RA | 1,266,001 | G→T | 9.4% | intergenic (+85/+204) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,277,758 | G→T | 11.8% | A813A (GCG→GCT) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,282,249 | A→G | 17.9% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,283,409 | C→A | 8.2% | L224L (CTG→CTT) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,296,971 | C→A | 9.7% | Y511* (TAC→TAA) | oppA → | oligopeptide transporter subunit |
| RA | 1,297,112 | G→T | 6.3% | intergenic (+42/‑44) | oppA → / → oppB | oligopeptide transporter subunit/oligopeptide transporter subunit |
| RA | 1,298,034 | C→A | 6.5% | V293V (GTC→GTA) | oppB → | oligopeptide transporter subunit |
| RA | 1,298,059 | C→A | 6.4% | P302T (CCG→ACG) | oppB → | oligopeptide transporter subunit |
| RA | 1,341,727 | G→T | 10.5% | P481P (CCC→CCA) | rnb ← | ribonuclease II |
| RA | 1,347,987 | C→T | 6.4% | P263P (CCG→CCA) | sapC ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,363,269 | G→T | 8.6% | W71L (TGG→TTG) | pspB → | psp operon transcription co‑activator |
| RA | 1,363,596 | C→A | 5.2% | V105V (GTC→GTA) | pspC → | psp operon transcription co‑activator |
| RA | 1,367,098 | G→T | 7.7% | E311D (GAG→GAT) | ycjN → | putative ABC superfamily sugar transporter periplasmic‑binding protein |
| RA | 1,384,753 | G→T | 10.3% | P35T (CCT→ACT) | mpaA ← | murein peptide amidase A |
| RA | 1,422,040 | A→G | 5.8% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,098 | G→A | 8.2% | pseudogene (886/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,132 | C→T | 5.9% | pseudogene (852/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,150 | C→T | 5.4% | pseudogene (834/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,168 | A→C | 5.2% | pseudogene (816/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,252 | A→G | 7.3% | pseudogene (732/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 9.1% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,648 | G→C | 7.0% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,432,890 | G→T | 7.7% | P718T (CCT→ACT) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,460,467 | G→A | 7.1% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,483,438 | C→A | 18.3% | P317H (CCC→CAC) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,516,426 | C→A | 5.6% | M299I (ATG→ATT) | yncD ← | putative iron outer membrane transporter |
| RA | 1,527,113 | T→G | 9.7% | D347E (GAT→GAG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,536,006 | A→G | 8.3% | I281T (ATT→ACT) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,541,970 | G→T | 9.7% | E105* (GAA→TAA) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,819 | C→A | 5.8% | I34I (ATC→ATA) | fdnH → | formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible |
| RA | 1,588,049 | C→A | 5.8% | pseudogene (4196/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,629,321 | G→T | 7.7% | H262N (CAC→AAC) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,664,783 | G→T | 5.2% | V276V (GTG→GTT) | ynfM → | putative arabinose efflux transporter |
| RA | 1,668,943 | C→A | 5.6% | F258L (TTC→TTA) | tqsA → | pheromone AI‑2 transporter |
| RA | 1,679,430 | G→A | 7.4% | L305L (CTG→CTA) | tus → | inhibitor of replication at Ter, DNA‑binding protein |
| RA | 1,685,588 | C→A | 8.3% | P494T (CCG→ACG) | ydgA → | DUF945 family protein |
| RA | 1,691,520 | C→A | 8.6% | intergenic (‑211/+10) | uidR ← / ← hdhA | transcriptional repressor/7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent |
| RA | 1,700,347 | G→T | 6.9% | P108P (CCG→CCT) | rsxA → | SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex |
| RA | 1,720,698 | C→A | 6.2% | A140E (GCG→GAG) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,720,789 | G→T | 13.0% | A170A (GCG→GCT) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,743,166 | C→A | 8.3% | T217T (ACG→ACT) | ydhT ← | FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,757,890 | G→A | 9.2% | A126V (GCG→GTG) | sufB ← | component of SufBCD Fe‑S cluster assembly scaffold |
| RA | 1,772,524 | G→T | 7.8% | E358* (GAA→TAA) | ydiO → | putative acyl‑CoA dehydrogenase |
| RA | 1,785,446 | G→A | 6.1% | A19V (GCA→GTA) | ydiU ← | UPF0061 family protein |
| RA | 1,789,351 | G→A | 23.1% | S20L (TCA→TTA) | btuC ← | vitamin B12 transporter subunit: membrane component of ABC superfamily |
| RA | 1,829,328 | C→A | 6.4% | A88A (GCC→GCA) | ydjZ → | TVP38/TMEM64 family inner membrane protein |
| RA | 1,835,917 | G→T | 7.0% | L57L (CTG→CTT) | nudG → | CTP pyrophosphohydrolase; also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP |
| RA | 1,843,183 | C→A | 12.6% | F30L (TTC→TTA) | sppA → | protease IV (signal peptide peptidase) |
| RA | 1,849,640 | G→T | 10.9% | R197R (CGG→AGG) | ydjG ← | alpha‑Keto reductase, NADH‑dependent; can use methylglyoxal as substrate |
| RA | 1,876,522 | G→T | 6.4% | P118P (CCG→CCT) | dmlA → | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| RA | 1,879,285 | C→A | 12.1% | L122M (CTG→ATG) | yeaW → | putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster |
| RA | 1,894,952 | C→T | 5.5% | S297S (TCG→TCA) | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,897,932 | C→A | 5.4% | I198I (ATC→ATA) | manY → | mannose‑specific enzyme IIC component of PTS |
| RA | 1,922,023 | C→A | 9.1% | P358P (CCG→CCT) | ptrB ← | protease II |
| RA | 1,924,208 | A→G | 8.7% | intergenic (‑244/+83) | yebE ← / ← yebF | DUF533 family inner membrane protein/extracellular Colicin M immunity family protein |
| RA | 1,928,233 | G→T | 8.5% | S210* (TCA→TAA) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,930,463 | C→A | 8.5% | G37C (GGT→TGT) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| RA | 1,936,274 | C→T | 20.7% | T189T (ACG→ACA) | znuA ← | zinc transporter subunit: periplasmic‑binding component of ABC superfamily |
| RA | 1,941,388 | G→T | 5.6% | G82G (GGC→GGA) | ruvC ← | component of RuvABC resolvasome, endonuclease |
| RA | 1,992,667 | G→A | 13.6% | L99L (CTG→TTG) | dcyD ← | D‑cysteine desulfhydrase, PLP‑dependent |
| RA | 2,033,508 | G→T | 10.9% | A184S (GCA→TCA) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| RA | 2,039,935 | T→A | 5.4% | V506D (GTC→GAC) | yeeJ → | putative adhesin |
| RA | 2,066,171 | C→A | 7.5% | G384G (GGC→GGA) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,074,417 | G→T | 7.5% | P109P (CCC→CCA) | sbmC ← | DNA gyrase inhibitor |
| RA | 2,077,127 | G→T | 7.0% | P297P (CCG→CCT) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,082,069 | C→A | 6.1% | G181C (GGT→TGT) | yeeZ ← | putative epimerase |
| RA | 2,087,757 | C→A | 6.7% | A270E (GCG→GAG) | hisB → | fused histidinol‑phosphatase/imidazoleglycerol‑phosphate dehydratase |
| RA | 2,088,363 | G→T | 6.4% | M116I (ATG→ATT) | hisH → | imidazole glycerol phosphate synthase, glutamine amidotransferase subunit with HisF |
| RA | 2,090,712 | G→T | 13.3% | intergenic (+6/+90) | hisI → / ← wzzB | fused phosphoribosyl‑AMP cyclohydrolase/phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,114,428 | C→A | 8.3% | G203V (GGC→GTC) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,134,522 | C→A | 8.0% | R191L (CGG→CTG) | asmA ← | suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,198,216 | C→A | 7.6% | L48I (CTT→ATT) | yehL → | putative ABC superfamily transporter ATP‑binding subunit |
| RA | 2,207,425 | C→A | 14.9% | M233I (ATG→ATT) | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| RA | 2,212,592 | G→T | 13.2% | P123P (CCC→CCA) | osmF ← | putative ABC superfamily transporter periplasmic‑binding protein |
| RA | 2,227,142 | G→T | 6.1% | E22* (GAA→TAA) | yeiS → | DUF2542 family protein |
| RA | 2,249,666 | G→A | 8.3% | R383R (CGC→CGT) | psuT ← | putative nucleoside transporter |
| RA | 2,249,669 | T→G | 8.3% | K382N (AAA→AAC) ‡ | psuT ← | putative nucleoside transporter |
| RA | 2,249,671 | T→G | 8.3% | K382Q (AAA→CAA) ‡ | psuT ← | putative nucleoside transporter |
| RA | 2,325,658 | G→T | 5.9% | pseudogene (2224/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,337,131 | C→T | 5.6% | G173D (GGC→GAC) | yfaL ← | adhesin |
| RA | 2,345,469 | G→T | 9.8% | L129I (CTC→ATC) | glpT ← | sn‑glycerol‑3‑phosphate transporter |
| RA | 2,347,820 | T→C | 9.9% | L26P (CTG→CCG) | glpB → | sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit |
| RA | 2,349,059 | G→A | 5.5% | P20P (CCG→CCA) | glpC → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| RA | 2,349,887 | C→A | 7.0% | H296Q (CAC→CAA) | glpC → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| RA | 2,379,637 | A→G | 5.9% | Y100C (TAT→TGT) | yfbL → | putative peptidase |
| RA | 2,395,893 | C→A | 8.0% | E478* (GAG→TAG) | nuoC ← | NADH:ubiquinone oxidoreductase, fused CD subunit |
| RA | 2,436,464 | C→A | 9.6% | P408T (CCA→ACA) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,450,011 | G→T | 8.7% | A94E (GCG→GAG) | sixA ← | phosphohistidine phosphatase |
| RA | 2,457,936 | T→A | 9.7% | K184I (AAA→ATA) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,464,610 | A→T | 7.5% | T129T (ACT→ACA) | yfdK ← | CPS‑53 (KpLE1) prophage; conserved protein |
| RA | 2,465,527 | C→T | 6.4% | pseudogene (75/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,492,873 | G→A | 13.3% | D242N (GAT→AAT) | ypdA → | sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system |
| RA | 2,493,691 | G→T | 7.5% | P514P (CCG→CCT) | ypdA → | sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system |
| RA | 2,503,245 | C→A | 8.5% | P46Q (CCG→CAG) | yfeO → | putative ion channel protein |
| RA | 2,503,453 | C→A | 5.4% | V115V (GTC→GTA) | yfeO → | putative ion channel protein |
| RA | 2,514,609 | Δ1 bp | 14.0% | intergenic (+2/‑3) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,545,478 | C→T | 8.0% | R7H (CGC→CAC) | ypeA ← | putative acyl‑CoA transferase |
| RA | 2,603,210 | C→A | 6.7% | F455L (TTC→TTA) | hyfG → | hydrogenase 4, subunit |
| RA | 2,613,836 | C→A | 5.6% | M132I (ATG→ATT) | upp ← | uracil phosphoribosyltransferase |
| RA | 2,620,217 | C→T | 5.3% | R694Q (CGA→CAA) | yfgF ← | cyclic‑di‑GMP phosphodiesterase, anaerobic |
| RA | 2,643,036 | G→T | 6.6% | P871T (CCC→ACC) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,666,996 | C→A | 7.1% | H98N (CAT→AAT) | yphA → | DoxX family inner membrane protein |
| RA | 2,669,347 | C→A | 9.8% | G280C (GGT→TGT) | yphD ← | inner membrane putative ABC superfamily sugar transporter permease |
| RA | 2,682,911 | A→T | 6.2% | intergenic (‑46/+119) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,682,916 | C→T | 5.5% | intergenic (‑51/+114) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,688,637 | G→T | 6.9% | S89* (TCG→TAG) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,719,426 | T→C | 86.8% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,764,424 | C→A | 7.4% | H129N (CAT→AAT) | yfjS → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,782,570 | C→T | 6.6% | A76V (GCG→GTG) | csiD → | carbon starvation protein |
| RA | 2,811,122 | T→C | 5.2% | intergenic (‑260/+21) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,811,129 | G→A | 5.5% | intergenic (‑267/+14) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,811,131 | Δ1 bp | 5.3% | intergenic (‑269/+12) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,811,136 | G→T | 5.3% | intergenic (‑274/+7) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,837,370 | C→A | 5.6% | R67L (CGA→CTA) | hycG ← | hydrogenase 3 and formate hydrogenase complex, HycG subunit |
| RA | 2,842,651 | C→A | 16.5% | T186T (ACG→ACT) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,851,839 | T→C | 5.3% | L463P (CTG→CCG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,878,529 | T→A | 6.0% | T684S (ACC→TCC) | ygcB ← | R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity |
| RA | 2,887,488 | C→A | 7.1% | Q71K (CAG→AAG) | ygcO → | putative 4Fe‑4S cluster‑containing protein |
| RA | 2,913,215 | C→A | 10.7% | M297I (ATG→ATT) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 2,959,246 | C→A | 11.1% | G51C (GGC→TGC) | lgt ← | phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase |
| RA | 2,978,427 | C→A | 5.3% | Q175H (CAG→CAT) | yqeF ← | short chain acyltransferase |
| RA | 2,985,157 | C→A | 8.9% | intergenic (+39/‑296) | ygeG → / → ygeH | SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator |
| RA | 3,006,103 | C→A | 19.1% | R499L (CGT→CTT) | yqeB ← | XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,013,084 | G→T | 6.4% | E189* (GAG→TAG) | ssnA → | putative chlorohydrolase/aminohydrolase |
| RA | 3,015,849 | C→A | 7.0% | P392Q (CCG→CAG) | xdhD → | putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding |
| RA | 3,021,589 | C→A | 8.9% | P370P (CCC→CCA) | ygfQ → | putative purine permease |
| RA | 3,064,718 | T→G | 21.7% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,065,273 | C→A | 7.5% | D237Y (GAC→TAC) | pgk ← | phosphoglycerate kinase |
| RA | 3,071,761 | G→T | 12.8% | P153Q (CCG→CAG) | cmtA ← | putative mannitol‑specific PTS enzymes: IIB component/IIC component |
| RA | 3,073,350 | G→T | 5.5% | Q549K (CAG→AAG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,083,695 | C→A | 6.7% | intergenic (+84/‑11) | yggI → / → endA | Zn‑dependent metalloprotease‑related protein/DNA‑specific endonuclease I |
| RA | 3,088,806 | C→A | 6.5% | P117Q (CCG→CAG) | yggS → | UPF0001 family protein, PLP‑binding |
| RA | 3,100,937 | G→T | 5.6% | C526* (TGC→TGA) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,105,440 | G→T | 6.7% | pseudogene (10/963 nt) | yghE ← | pseudogene, secretion pathway protein, L‑type protein homology; putative general secretion pathway for protein export (GSP) |
| RA | 3,111,002 | C→A | 6.2% | V490V (GTG→GTT) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,118,773 | Δ1 bp | 7.4% | coding (46/1224 nt) | glcF ← | glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit |
| RA | 3,118,774 | Δ1 bp | 7.4% | coding (45/1224 nt) | glcF ← | glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit |
| RA | 3,120,172 | G→T | 9.3% | P403P (CCC→CCA) | glcD ← | glycolate oxidase subunit, FAD‑linked |
| RA | 3,125,638 | C→A | 8.9% | G44C (GGT→TGT) | yghQ ← | putative inner membrane polysaccharide flippase |
| RA | 3,126,992 | G→A | 5.1% | R109C (CGC→TGC) | yghS ← | putative ATP‑binding protein |
| RA | 3,130,437 | G→T | 7.6% | P482Q (CCG→CAG) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,145,823 | G→T | 11.3% | G77C (GGC→TGC) | metC → | cystathionine beta‑lyase, PLP‑dependent |
| RA | 3,192,205 | C→A | 7.4% | D266Y (GAT→TAT) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,206,139 | G→A | 7.1% | E558E (GAG→GAA) | dnaG → | DNA primase |
| RA | 3,206,241 | G→T | 5.1% | intergenic (+30/‑165) | dnaG → / → rpoD | DNA primase/RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,216,558 | G→T | 6.3% | Q189H (CAG→CAT) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,273,750 | C→T | 9.5% | R59C (CGT→TGT) | agaV → | N‑acetylgalactosamine‑specific enzyme IIB component of PTS |
| RA | 3,298,217 | C→A | 6.1% | V320V (GTG→GTT) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,307,639 | C→A | 7.4% | G579C (GGT→TGT) | infB ← | translation initiation factor IF‑2 |
| RA | 3,308,524 | C→A | 8.0% | G284C (GGC→TGC) | infB ← | translation initiation factor IF‑2 |
| RA | 3,317,714 | G→T | 8.5% | P186H (CCC→CAC) | folP ← | 7,8‑dihydropteroate synthase |
| RA | 3,331,496 | C→A | 5.6% | E109* (GAA→TAA) | mlaD ← | ABC transporter maintaining OM lipid asymmetry, anchored periplasmic binding protein |
| RA | 3,336,004 | G→T | 5.4% | D125Y (GAT→TAT) | kdsC → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| RA | 3,346,586 | C→A | 7.0% | W275L (TGG→TTG) | yhcC ← | putative Fe‑S oxidoreductase, Radical SAM superfamily protein |
| RA | 3,349,210 | G→A | 9.1% | G376D (GGT→GAT) | gltB → | glutamate synthase, large subunit |
| RA | 3,350,612 | C→A | 9.1% | V843V (GTC→GTA) | gltB → | glutamate synthase, large subunit |
| RA | 3,385,928 | C→A | 12.5% | L1230L (CTG→CTT) | yhdP ← | DUF3971‑AsmA2 domains protein |
| RA | 3,395,730 | G→A | 5.4% | A321V (GCA→GTA) | csrD ← | targeting factor for csrBC sRNA degradation |
| RA | 3,397,319 | C→T | 6.5% | V159V (GTC→GTT) | acuI → | putative acryloyl‑CoA reductase |
| RA | 3,416,899 | A→G | 7.2% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,424,994 | G→A | 5.2% | R110W (CGG→TGG) | yrdD ← | putative DNA topoisomerase |
| RA | 3,462,341 | G→T | 5.7% | P291H (CCT→CAT) | chiA ← | periplasmic endochitinase |
| RA | 3,485,651 | G→T | 8.9% | F2L (TTC→TTA) | ppiA ← | peptidyl‑prolyl cis‑trans isomerase A (rotamase A) |
| RA | 3,523,042 | G→T | 5.5% | P112P (CCG→CCT) | hslR → | ribosome‑associated heat shock protein Hsp15 |
| RA | 3,537,916 | G→T | 5.9% | P96P (CCC→CCA) | bioH ← | pimeloyl‑ACP methyl ester carboxylesterase |
| RA | 3,550,165 | C→A | 6.9% | G15V (GGC→GTC) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| RA | 3,552,763 | Δ1 bp | 8.2% | coding (1137/1599 nt) | rtcR → | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| RA | 3,559,474 | G→T | 18.2% | F156L (TTC→TTA) | glgP ← | glycogen phosphorylase |
| RA | 3,581,713 | C→A | 15.5% | M276I (ATG→ATT) | ugpC ← | glycerol‑3‑phosphate transporter subunit |
| RA | 3,596,692 | C→A | 13.8% | V304V (GTG→GTT) | ftsY ← | Signal Recognition Particle (SRP) receptor |
| RA | 3,701,364 | C→A | 11.0% | intergenic (‑299/+612) | dppA ← / ← proK | dipeptide transporter/tRNA‑Pro |
| RA | 3,705,231 | C→A | 5.3% | S46I (AGC→ATC) | yhjX ← | pyruvate‑inducible inner membrane protein, putative transporter |
| RA | 3,729,074 | G→A | 5.7% | A246T (GCG→ACG) | xylR → | xylose divergent operon transcriptional activator |
| RA | 3,732,734 | C→T | 5.1% | S626S (AGC→AGT) | malS → | alpha‑amylase |
| RA | 3,759,052 | C→T | 6.5% | Y1170Y (TAC→TAT) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,759,248 | T→C | 5.1% | L1236L (TTG→CTG) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,767,150 | G→T | 7.7% | G504C (GGT→TGT) | mtlA → | fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components |
| RA | 3,772,935 | G→A | 5.3% | L174L (CTG→CTA) | lldR → | dual role activator/repressor for lldPRD operon |
| RA | 3,824,326 | C→A | 7.8% | A170A (GCC→GCA) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,827,542 | G→T | 6.3% | S119* (TCA→TAA) | yicI ← | putative alpha‑glucosidase |
| RA | 3,877,923 | A→G | 90.2% | Q24R (CAG→CGG) | rnpA → | protein C5 component of RNase P |
| RA | 3,879,272 | G→T | 6.4% | L279L (CTG→CTT) | yidC → | membrane protein insertase |
| RA | 3,911,338 | G→T | 6.9% | F96L (TTC→TTA) | atpG ← | F1 sector of membrane‑bound ATP synthase, gamma subunit |
| RA | 3,918,498 | C→T | 6.4% | G166S (GGT→AGT) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,918,630:1 | +G | 7.0% | coding (364/1890 nt) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,918,630:2 | +A | 7.0% | coding (364/1890 nt) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,918,630:3 | +A | 7.0% | coding (364/1890 nt) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,918,630:4 | +G | 7.0% | coding (364/1890 nt) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,918,630:5 | +A | 7.0% | coding (364/1890 nt) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,923,871 | C→A | 12.0% | D195Y (GAT→TAT) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,935,371 | G→T | 5.9% | noncoding (204/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,936,724 | T→A | 6.9% | intergenic (+15/‑71) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 3,977,554 | A→G | 6.2% | intergenic (+1/+158) | aslB → / ← aslA | putative AslA‑specific sulfatase‑maturating enzyme/putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 3,993,815 | Δ1 bp | 8.2% | coding (602/765 nt) | yigE ← | DUF2233 family protein |
| RA | 3,993,816 | Δ1 bp | 8.0% | coding (601/765 nt) | yigE ← | DUF2233 family protein |
| RA | 4,004,549 | G→T | 6.6% | L38L (CTG→CTT) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,019,993 | Δ1 bp | 75.7% | coding (107/702 nt) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,024,042 | C→T | 5.3% | R97H (CGC→CAC) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,037,133 | A→G | 8.7% | Q119R (CAG→CGG) | dsbA → | periplasmic protein disulfide isomerase I |
| RA | 4,037,217 | G→T | 11.1% | S147I (AGC→ATC) | dsbA → | periplasmic protein disulfide isomerase I |
| RA | 4,051,827 | C→A | 8.9% | L21M (CTG→ATG) | typA → | GTP‑binding protein |
| RA | 4,075,821 | C→T | 7.4% | C100Y (TGT→TAT) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,096,194 | G→A | 5.7% | W149* (TGG→TGA) | cpxP → | inhibitor of the cpx response; periplasmic adaptor protein |
| RA | 4,104,821 | G→A | 9.2% | N229N (AAC→AAT) | glpX ← | fructose 1,6‑bisphosphatase II |
| RA | 4,125,115 | C→A | 6.3% | I451I (ATC→ATA) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,131,966 | C→T | 5.3% | D62N (GAT→AAT) | frwA ← | putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component |
| RA | 4,140,442 | G→T | 5.3% | P862H (CCT→CAT) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,445:1 | +A | 5.3% | coding (2582/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,445:2 | +C | 5.3% | coding (2582/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,445:3 | +G | 5.3% | coding (2582/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,448:1 | +C | 5.1% | coding (2579/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,448:2 | +A | 5.1% | coding (2579/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,450 | T→G | 5.1% | E859D (GAA→GAC) ‡ | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,451 | T→C | 5.1% | E859G (GAA→GGA) ‡ | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,140,452 | C→G | 5.1% | E859Q (GAA→CAA) ‡ | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,165,449 | C→T | 18.9% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 18.9% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,460 | G→T | 5.2% | noncoding (61/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,166,006 | C→T | 12.0% | R45R (CGC→CGT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,177,586 | T→C | 88.9% | L770P (CTC→CCC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,180,725 | C→A | 13.1% | G358C (GGT→TGT) | thiH ← | tyrosine lyase, involved in thiamine‑thiazole moiety synthesis |
| RA | 4,196,303 | C→T | 8.3% | L386L (CTG→CTA) | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,202,979 | A→C | 26.3% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,218,959 | G→T | 11.2% | R434L (CGG→CTG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,223,539 | G→T | 5.7% | intergenic (‑378/‑147) | lysC ← / → pgi | lysine‑sensitive aspartokinase 3/glucosephosphate isomerase |
| RA | 4,223,964 | C→A | 7.2% | N93K (AAC→AAA) | pgi → | glucosephosphate isomerase |
| RA | 4,257,146 | G→T | 10.9% | L35L (CTG→CTT) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,266,568 | T→C | 6.8% | I390I (ATT→ATC) | yjcC → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 4,269,394 | G→T | 5.8% | G330C (GGC→TGC) | yjcD → | inner membrane putative guanine permease |
| RA | 4,279,429 | C→A | 5.2% | S86* (TCA→TAA) | nrfB → | nitrite reductase, formate‑dependent, penta‑heme cytochrome c |
| RA | 4,296,235 | G→A | 7.4% | D60D (GAC→GAT) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,305,988 | C→A | 5.9% | G350C (GGC→TGC) | phnM ← | ribophosphonate triphosphate hydrolase |
| RA | 4,315,905 | T→G | 7.6% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,938 | C→T | 7.0% | intergenic (‑380/+278) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,939 | A→C | 5.8% | intergenic (‑381/+277) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,951 | A→T | 6.3% | intergenic (‑393/+265) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,956 | Δ1 bp | 6.3% | intergenic (‑398/+260) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,959 | G→T | 6.4% | intergenic (‑401/+257) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,965:1 | +A | 6.1% | intergenic (‑407/+251) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,966 | T→A | 6.1% | intergenic (‑408/+250) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,316,005 | G→T | 7.2% | intergenic (‑447/+211) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,340,336 | G→T | 9.1% | Q382K (CAG→AAG) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,362,494 | C→A | 10.9% | intergenic (+6/‑132) | groL → / → yjeI | Cpn60 chaperonin GroEL, large subunit of GroESL/DUF4156 family lipoprotein |
| RA | 4,363,098 | T→C | 5.4% | intergenic (+119/+84) | yjeI → / ← yjeJ | DUF4156 family lipoprotein/uncharacterized protein |
| RA | 4,398,431 | T→G | 8.9% | V654G (GTC→GGC) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,432 | C→G | 9.3% | V654V (GTC→GTG) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,435 | Δ1 bp | 9.4% | coding (1965/2442 nt) | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,436 | Δ1 bp | 9.4% | coding (1966/2442 nt) | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,437 | Δ1 bp | 9.4% | coding (1967/2442 nt) | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,438 | C→A | 9.4% | G656G (GGC→GGA) | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,440 | T→A | 9.4% | F657Y (TTT→TAT) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,441 | T→G | 9.4% | F657L (TTT→TTG) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,442 | G→C | 9.4% | G658R (GGC→CGC) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,398,443 | G→C | 9.2% | G658A (GGC→GCC) ‡ | rnr → | exoribonuclease R, RNase R |
| RA | 4,399,668 | C→T | 8.9% | L193L (CTG→TTG) | rlmB → | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 4,402,207 | G→T | 8.6% | A2S (GCC→TCC) | yjfM → | DUF1190 family protein |
| RA | 4,431,948 | G→T | 8.2% | L16M (CTG→ATG) | msrA ← | methionine sulfoxide reductase A |
| RA | 4,437,157 | G→T | 13.4% | A1077S (GCC→TCC) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,468,398 | C→A | 8.7% | H37N (CAT→AAT) | rraB → | protein inhibitor of RNase E |
| RA | 4,486,551 | G→T | 5.8% | pseudogene (60/1266 nt) | intB → | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase |
| RA | 4,498,981 | G→A | 7.0% | pseudogene (156/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,499,008 | C→T | 6.2% | pseudogene (183/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,499,011 | T→C | 5.4% | pseudogene (186/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,444 | C→A | 5.3% | P34H (CCT→CAT) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,508,445 | T→C | 5.4% | P34P (CCT→CCC) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,508,466 | A→G | 5.5% | L41L (CTA→CTG) | insA → | IS1 repressor TnpA |
| RA | 4,508,484 | C→T | 8.6% | A47A (GCC→GCT) | insA → | IS1 repressor TnpA |
| RA | 4,508,490 | G→A | 9.1% | Q49Q (CAG→CAA) | insA → | IS1 repressor TnpA |
| RA | 4,508,498 | A→C | 7.1% | K52T (AAG→ACG) | insA → | IS1 repressor TnpA |
| RA | 4,514,221 | G→A | 9.5% | L203L (CTG→TTG) | yjhH ← | putative lyase/synthase |
| RA | 4,523,165 | G→T | 6.8% | P146Q (CCG→CAG) | yjhQ ← | putative acetyltransferase |
| RA | 4,534,041 | G→A | 6.0% | G166D (GGC→GAC) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,538,741 | C→A | 5.3% | A39A (GCC→GCA) | fimH → | minor component of type 1 fimbriae |
| RA | 4,560,372 | G→T | 10.9% | I340I (ATC→ATA) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| RA | 4,571,155 | G→T | 8.4% | P42H (CCT→CAT) | hsdS ← | specificity determinant for hsdM and hsdR |
| RA | 4,599,641 | C→A | 5.4% | I137I (ATC→ATA) | prfC → | peptide chain release factor RF‑3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 463819 | 464287 | 469 | 10 [9] | [9] 11 | [ybaO] | [ybaO] |
| * | * | ÷ | CP009273 | 2027284 | 2027418 | 135 | 10 [8] | [7] 10 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2622923 | 2623068 | 146 | 10 [8] | [9] 13 | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| * | * | ÷ | CP009273 | 3448791 | 3448865 | 75 | 10 [8] | [2] 11 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3792511 | 3792780 | 270 | 11 [8] | [8] 10 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | CP009273 | 3797648 | 3797831 | 184 | 14 [9] | [6] 11 | waaS | lipopolysaccharide core biosynthesis protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 335717 | 65 (1.120) | 6 (0.130) +29 bp |
3/188 | NT | 10.7% | noncoding (250/358 nt) | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | CP009273 | = 372985 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 360104 = | 55 (0.940) | 55 (0.940) | 21/248 | NT | 50.0% | 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 | = 370385 | 86 (2.020) | 16 (0.420) | 7/162 | NT | 17.1% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 370419 | 119 (2.030) | 7 (0.120) | 3/240 | NT | 6.2% | noncoding (34/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | = 372843 | 97 (1.710) | noncoding (53/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 372944 = | 55 (0.940) | 26 (0.520) | 5/210 | NT | 34.3% | noncoding (154/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | CP009273 | 4315902 = | 53 (1.070) | noncoding (284/583 nt) | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | CP009273 | = 627604 | NA (NA) | 3 (0.070) | 3/176 | NT | 5.8% | noncoding (34/34 nt) | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | CP009273 | = 4398969 | 49 (1.160) | intergenic (+57/‑123) | rnr/rlmB | exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | CP009273 | = 1046001 | 88 (1.500) | 48 (0.820) | 19/248 | NT | 49.7% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | = 1972777 | 9 (0.150) | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 20 (0.340) | 44 (0.860) | 20/216 | NT | 73.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 15 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 18 (0.310) | 32 (0.630) | 15/216 | NT | 67.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 15 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972769 = | 4 (0.070) | 46 (0.790) | 26/246 | NT | 92.1% | intergenic (‑315/‑465) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||