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 | 42,566 | C→A | 5.5% | A55E (GCG→GAG) | fixA → | anaerobic carnitine reduction putative electron transfer flavoprotein subunit |
| RA | 48,827 | G→A | 5.3% | E353E (GAG→GAA) | kefC → | potassium:proton antiporter |
| RA | 75,208 | G→A | 11.9% | G367G (GGG→GGA) | setA → | broad specificity sugar efflux system |
| RA | 75,590 | G→T | 5.7% | N117K (AAC→AAA) | leuD ← | 3‑isopropylmalate dehydratase small subunit |
| RA | 89,224 | G→A | 8.0% | R442H (CGC→CAC) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3) |
| RA | 145,878 | C→A | 8.7% | A71S (GCC→TCC) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 171,709 | C→T | 8.0% | A39V (GCG→GTG) | clcA → | H(+)/Cl(‑) exchange transporter |
| RA | 189,173 | G→T | 8.1% | intergenic (+106/‑186) | pyrH → / → frr | uridylate kinase/ribosome recycling factor |
| RA | 222,173 | T→C | 6.2% | intergenic (+111/‑73) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA of rrnH operon |
| RA | 247,671 | G→A | 6.1% | R96H (CGC→CAC) | dinB → | DNA polymerase IV |
| RA | 249,874 | G→C | 15.1% | intergenic (+226/‑92) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 249,908 | A→G | 17.9% | intergenic (+260/‑58) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 258,104 | C→T | 8.3% | G297G (GGC→GGT) | proA → | gamma‑glutamylphosphate reductase |
| RA | 262,526 | C→T | 9.5% | pseudogene (153/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 262,529 | C→T | 10.2% | pseudogene (150/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 263,285 | G→A | 7.7% | D144D (GAC→GAT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,333 | G→C | 5.7% | L128L (CTC→CTG) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 267,804 | G→A | 5.2% | pseudogene (330/426 nt) | insN → | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 335,776 | C→T | 9.1% | intergenic (+322/‑100) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 350,026 | C→A | 8.3% | A537E (GCG→GAG) | prpE → | propionate‑‑CoA ligase |
| RA | 381,744 | G→T | 12.2% | E28* (GAG→TAG) | tauB → | taurine transporter subunit |
| RA | 423,515 | A→T | 6.6% | D138V (GAT→GTT) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 423,517 | A→C | 6.6% | M139L (ATG→CTG) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 423,521 | Δ1 bp | 6.9% | coding (419/1848 nt) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 423,524 | C→G | 7.0% | T141S (ACC→AGC) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 445,212 | C→T | 100% | G296S (GGT→AGT) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 446,280 | C→A | 5.7% | V263L (GTG→TTG) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 478,554 | C→A | 13.2% | G436W (GGG→TGG) | acrB ← | multidrug efflux system protein |
| RA | 519,282 | C→G | 5.4% | S189C (TCT→TGT) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 523,498 | C→A | 7.7% | pseudogene (91/708 nt) | rhsH → | pseudogene, Rhs familly protein |
| RA | 573,883 | G→C | 9.1% | T107T (ACG→ACC) R34P (CGG→CCG) |
rzpD → rzoD → |
DLP12 prophage; putative murein endopeptidase DLP12 prophage; putative lipoprotein |
| RA | 625,575 | G→C | 8.7% | D76H (GAC→CAC) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 664,088 | C→A | 9.6% | P28P (CCG→CCT) | rlmH ← | 23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent |
| RA | 702,494 | G→A | 6.3% | V316M (GTG→ATG) | glnS → | glutamyl‑tRNA synthetase |
| RA | 705,299 | G→T | 8.9% | A18A (GCG→GCT) | chiQ → | chitosugar‑induced verified lipoprotein |
| RA | 725,164 | G→A | 6.2% | G42G (GGG→GGA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,190 | G→A | 5.6% | K384K (AAG→AAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,848 | A→G | 5.4% | T604A (ACC→GCC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,325 | A→G | 5.3% | N763D (AAT→GAT) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,327 | T→A | 5.0% | N763K (AAT→AAA) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,329 | A→C | 5.2% | E764A (GAA→GCA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,369 | A→G | 7.9% | A777A (GCA→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 10.7% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,467 | T→C | 7.7% | I1143I (ATT→ATC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 733,915 | A→G | 5.6% | K123R (AAG→AGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 733,994 | C→T | 7.7% | S149S (TCC→TCT) | ybfD → | H repeat‑associated putative transposase |
| RA | 816,707 | G→T | 9.7% | A153A (GCG→GCT) | ybhM → | UPF0005 family inner membrane protein |
| RA | 868,982 | G→A | 14.3% | G183D (GGC→GAC) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 968,986 | G→T | 6.7% | intergenic (‑129/‑7) | ycbC ← / → smtA | DUF218 superfamily protein/putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 1,012,744 | C→A | 10.5% | E338* (GAG→TAG) | ycbZ ← | putative peptidase |
| RA | 1,033,634 | G→A | 5.4% | A147T (GCC→ACC) | cbdA → | cytochrome bd‑II oxidase, subunit I |
| RA | 1,045,764 | C→G | 20.0% | D94E (GAC→GAG) | insB1 → | IS1 transposase B |
| RA | 1,045,767 | G→C | 24.7% | V95V (GTG→GTC) | insB1 → | IS1 transposase B |
| RA | 1,045,771 | A→G | 16.1% | I97V (ATA→GTA) | insB1 → | IS1 transposase B |
| RA | 1,045,775 | G→A | 16.0% | W98* (TGG→TAG) | insB1 → | IS1 transposase B |
| RA | 1,045,806 | C→A | 12.8% | S108S (TCC→TCA) | insB1 → | IS1 transposase B |
| RA | 1,045,830 | A→T | 8.2% | V116V (GTA→GTT) | insB1 → | IS1 transposase B |
| RA | 1,062,181 | G→T | 7.2% | A381S (GCG→TCG) | agp → | glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,068,155 | G→A | 14.3% | T55T (ACC→ACT) | rutB ← | ureidoacrylate amidohydrolase |
| RA | 1,075,394 | T→C | 8.3% | F212L (TTT→CTT) | putP → | proline:sodium symporter |
| RA | 1,195,844 | A→G | 6.9% | L140P (CTT→CCT) | intE ← | e14 prophage; putative integrase |
| RA | 1,198,991 | G→T | 7.2% | D90Y (GAC→TAC) | ymfL → | e14 prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,219,339 | G→A | 5.5% | pseudogene (213/237 nt) | ycgI → | pseudogene |
| RA | 1,264,818 | G→T | 9.5% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| RA | 1,264,977 | G→A | 6.0% | intergenic (+132/+182) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,277,812 | G→A | 7.8% | A831A (GCG→GCA) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,279,968 | G→A | 14.8% | P303P (CCG→CCA) | narH → | nitrate reductase 1, beta (Fe‑S) subunit |
| RA | 1,282,249 | A→G | 12.6% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,439 | A→G | 7.0% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,454:1 | +C | 5.0% | intergenic (+472/+68) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,494 | T→G | 5.7% | intergenic (+512/+28) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,288,276 | C→A | 85.9% | V35F (GTT→TTT) | hns ← | global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,340,055 | C→T | 16.1% | G315G (GGG→GGA) | gmr ← | cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability |
| RA | 1,422,060 | G→C | 9.1% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 5.4% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,681 | A→G | 6.4% | pseudogene (303/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,798 | A→G | 5.1% | pseudogene (186/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,426,257 | A→G | 10.6% | T984T (ACA→ACG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,432,843 | C→T | 6.5% | G733G (GGG→GGA) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,461,113 | A→G | 6.2% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,471,475 | G→T | 9.1% | R692L (CGC→CTC) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
| RA | 1,471,890 | C→A | 8.4% | Q5K (CAG→AAG) | ynbA → | inner membrane protein |
| RA | 1,475,612 | G→T | 9.1% | L149L (CTG→CTT) | ynbD → | putative phosphatase inner membrane protein |
| RA | 1,481,402 | G→T | 5.0% | intergenic (+182/‑90) | hrpA → / → ydcF | putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding |
| RA | 1,487,324 | G→T | 12.1% | G200C (GGT→TGT) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,497,052 | C→A | 17.2% | T113T (ACC→ACA) | ydcL → | lipoprotein |
| RA | 1,509,778 | T→C | 7.0% | W254R (TGG→CGG) | ydcV → | putative spermidine/putrescine transporter subunit |
| RA | 1,523,601 | G→A | 8.6% | pseudogene (1443/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,523,604 | G→A | 9.1% | pseudogene (1446/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,527,189 | A→G | 7.2% | T373A (ACG→GCG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,544,249 | G→A | 7.1% | P864P (CCG→CCA) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,826 | T→A | 17.5% | S37T (TCC→ACC) | fdnH → | formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible |
| RA | 1,544,867 | G→A | 10.0% | S50S (TCG→TCA) | fdnH → | formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible |
| RA | 1,563,996 | C→A | 7.0% | V251F (GTT→TTT) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,605,684 | G→T | 11.8% | A143E (GCG→GAG) | yneF ← | putative membrane‑bound diguanylate cyclase |
| RA | 1,620,567 | C→A | 14.2% | K357N (AAG→AAT) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,659,962 | G→T | 17.6% | A131S (GCC→TCC) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,665,324 | C→T | 6.9% | intergenic (+115/‑309) | ynfM → / → asr | putative arabinose efflux transporter/acid shock‑inducible periplasmic protein |
| RA | 1,681,729 | G→A | 6.3% | R302R (CGC→CGT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,732 | A→G | 6.2% | I301I (ATT→ATC) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,885 | C→A | 5.2% | A250A (GCG→GCT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,699,312 | T→C | 16.0% | L36P (CTG→CCG) | cnu → | nucleoid‑associated oriC‑binding protein; H‑NS and StpA stabilizing factor |
| RA | 1,702,919 | C→G | 11.6% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,158 | A→T | 10.5% | R661R (CGA→CGT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,173 | A→G | 9.5% | K666K (AAA→AAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,741,287 | C→T | 12.5% | intergenic (+25/‑101) | ydhR → / → ydhS | putative monooxygenase/putative oxidoreductase |
| RA | 1,846,485 | T→A | 5.1% | N114K (AAT→AAA) | pncA → | nicotinamidase/pyrazinamidase |
| RA | 1,852,102 | T→C | 18.2% | E330G (GAG→GGG) | ydjJ ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,866,529 | G→T | 6.3% | E78* (GAA→TAA) | yeaJ → | putative diguanylate cyclase |
| RA | 1,879,041 | G→T | 6.5% | E40D (GAG→GAT) | yeaW → | putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster |
| RA | 1,891,477 | C→A | 13.6% | L97M (CTG→ATG) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,932,791 | C→T | 11.4% | P296S (CCG→TCG) | pykA → | pyruvate kinase II |
| RA | 1,991,191 | G→A | 7.2% | I35I (ATC→ATT) | yecC ← | putative ABC superfamily transporter ATP‑binding subunit |
| RA | 2,002,242 | G→T | 9.7% | G162V (GGC→GTC) | yedE → | UPF0394 family sulfur transport domain‑containing inner membrane protein |
| RA | 2,027,880 | G→T | 7.6% | pseudogene (349/663 nt) | yedS → | pseudogene, outer membrane protein homology; putative outer membrane protein |
| RA | 2,029,504 | C→T | 14.6% | T63T (ACC→ACT) | hchA → | glyoxalase III and Hsp31 molecular chaperone |
| RA | 2,059,656 | T→C | 5.9% | intergenic (‑21/+130) | yeeH ← / ← insH1 | pseudogene/IS5 transposase and trans‑activator |
| RA | 2,086,760 | C→A | 8.7% | D294E (GAC→GAA) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,141,742 | G→T | 6.4% | A196A (GCG→GCT) | yegD → | Hsp70 chaperone family protein |
| RA | 2,150,813 | G→C | 8.7% | W690C (TGG→TGC) | mdtB → | multidrug efflux system, subunit B |
| RA | 2,179,894 | G→T | 9.7% | G167C (GGT→TGT) | rcnA → | membrane protein conferring nickel and cobalt resistance |
| RA | 2,215,032 | G→T | 6.1% | A146E (GCG→GAG) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,271,518 | C→T | 11.8% | D67N (GAC→AAC) | yejG ← | uncharacterized protein |
| RA | 2,298,340 | T→G | 21.8% | intergenic (+468/+247) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,341 | C→G | 16.3% | intergenic (+469/+246) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,355 | G→A | 12.5% | intergenic (+483/+232) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,662 | G→T | 9.0% | N189K (AAC→AAA) | ompC ← | outer membrane porin protein C |
| RA | 2,329,010 | C→T | 14.8% | G372S (GGT→AGT) | yfaA ← | DUF2138 family protein, putative host defense protein |
| RA | 2,333,985 | C→A | 7.1% | V1222L (GTG→TTG) | yfaL ← | adhesin |
| RA | 2,363,970 | G→T | 7.4% | V158V (GTG→GTT) | arnD → | undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase |
| RA | 2,369,611 | G→A | 5.1% | R230C (CGC→TGC) | menB ← | dihydroxynaphthoic acid synthetase |
| RA | 2,397,608 | G→T | 8.5% | P162H (CCT→CAT) | nuoB ← | NADH:ubiquinone oxidoreductase, chain B |
| RA | 2,425,649 | G→A | 6.4% | A258V (GCC→GTC) | folC ← | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase |
| RA | 2,429,298 | G→A | 8.9% | N277N (AAC→AAT) | usg ← | putative semialdehyde dehydrogenase |
| RA | 2,433,927 | C→A | 8.2% | M386I (ATG→ATT) | fabB ← | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,434,989 | C→A | 10.2% | G32G (GGG→GGT) | fabB ← | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,439,360 | G→T | 16.1% | A168A (GCC→GCA) | mepA ← | murein DD‑endopeptidase |
| RA | 2,465,153 | T→C | 8.5% | pseudogene (449/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,488,470 | G→T | 14.0% | intergenic (+18/+59) | ypdI → / ← yfdY | putative lipoprotein involved in colanic acid biosynthesis/DUF2545 family putative inner membrane protein |
| RA | 2,547,258 | C→T | 6.7% | Y225Y (TAC→TAT) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,570,843 | C→T | 6.6% | A298A (GCG→GCA) | maeB ← | malic enzyme: putative oxidoreductase/putative phosphotransacetylase |
| RA | 2,604,168 | A→G | 9.5% | Y35C (TAC→TGC) | hyfI → | hydrogenase 4, Fe‑S subunit |
| RA | 2,640,133 | C→A | 7.4% | S184S (TCG→TCT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain |
| RA | 2,655,826 | T→C | 11.0% | intergenic (‑336/+116) | iscR ← / ← trmJ | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,663,322 | C→A | 7.9% | P311H (CCC→CAC) | hcaE → | 3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,677,505 | A→G | 14.3% | intergenic (+90/+108) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,677,506 | C→T | 14.3% | intergenic (+91/+107) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,677,509 | A→T | 14.8% | intergenic (+94/+104) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,677,510 | G→T | 14.9% | intergenic (+95/+103) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,677,511 | A→T | 14.8% | intergenic (+96/+102) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,677,512 | T→A | 12.1% | intergenic (+97/+101) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,536 | G→T | 38.9% | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,719,545 | G→A | 22.2% | noncoding (3/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,749,725 | G→A | 10.5% | D70N (GAT→AAT) | intA → | CP4‑57 prophage; integrase |
| RA | 2,761,407 | C→T | 9.9% | P113P (CCC→CCT) | yfjP → | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,761,410 | G→C | 9.8% | R114R (CGG→CGC) | yfjP → | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,771,529 | T→C | 13.1% | V1519V (GTA→GTG) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,793,713 | C→T | 8.2% | A70V (GCC→GTC) | ygaM → | DUF883 family protein, putative membrane‑anchored ribosome‑binding protein |
| RA | 2,804,924 | C→T | 7.3% | R47C (CGT→TGT) | emrA → | multidrug efflux system |
| RA | 2,839,358 | C→A | 16.3% | R158L (CGT→CTT) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,845,707 | G→T | 10.5% | V71V (GTG→GTT) | hypD → | hydrogenase maturation protein |
| RA | 2,903,090 | Δ1 bp | 6.3% | intergenic (‑65/+163) | pyrG ← / ← mazG | CTP synthetase/nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,903,091 | Δ1 bp | 6.2% | intergenic (‑66/+162) | pyrG ← / ← mazG | CTP synthetase/nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,903,092 | Δ1 bp | 6.2% | intergenic (‑67/+161) | pyrG ← / ← mazG | CTP synthetase/nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,904,970 | G→A | 9.7% | R681C (CGT→TGT) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,905,224 | C→A | 8.7% | R596L (CGC→CTC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,908,741 | A→G | 12.0% | Q109R (CAG→CGG) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,939,360 | C→A | 8.2% | intergenic (‑159/+80) | tcdA ← / ← mltA | tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A |
| RA | 3,000,170 | G→T | 5.6% | E184* (GAA→TAA) | ygeW → | putative carbamoyltransferase |
| RA | 3,005,829 | C→T | 16.0% | intergenic (+77/+144) | yqeA → / ← yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,005,830 | G→A | 16.0% | intergenic (+78/+143) | yqeA → / ← yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,005,832 | G→A | 14.8% | intergenic (+80/+141) | yqeA → / ← yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,064,718 | T→G | 16.5% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,072,806 | A→G | 100% | intergenic (‑117/+197) | cmtB ← / ← tktA | putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding |
| RA | 3,088,680 | C→A | 15.8% | T75K (ACA→AAA) | yggS → | UPF0001 family protein, PLP‑binding |
| RA | 3,092,899 | G→A | 10.0% | T9M (ACG→ATG) | yggM ← | DUF1202 family putative secreted protein |
| RA | 3,095,806 | G→T | 5.5% | R136S (CGC→AGC) | trmI ← | tRNA m(7)G46 methyltransferase, SAM‑dependent |
| RA | 3,096,855 | A→T | 7.1% | N162Y (AAT→TAT) | mutY → | adenine DNA glycosylase |
| RA | 3,115,752 | C→A | 9.3% | L471L (CTG→CTT) | glcB ← | malate synthase G |
| RA | 3,129,074 | C→G | 8.9% | A219A (GCG→GCC) ‡ | pitB ← | phosphate transporter |
| RA | 3,129,075 | G→A | 8.9% | A219V (GCG→GTG) ‡ | pitB ← | phosphate transporter |
| RA | 3,129,076 | C→T | 8.9% | A219T (GCG→ACG) ‡ | pitB ← | phosphate transporter |
| RA | 3,129,085 | C→G | 9.3% | V216L (GTT→CTT) | pitB ← | phosphate transporter |
| RA | 3,129,086 | A→G | 9.0% | I215I (ATT→ATC) | pitB ← | phosphate transporter |
| RA | 3,157,130 | C→A | 5.9% | D735Y (GAT→TAT) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,157,164 | G→A | 6.1% | R723R (CGC→CGT) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,210,552 | C→T | 23.5% | R139C (CGC→TGC) | yqjI → | PadR family putative transcriptional regulator |
| RA | 3,211,302 | A→G | 10.4% | R378R (CGT→CGC) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,305 | C→A | 10.6% | A377A (GCG→GCT) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,213,138 | G→T | 7.4% | V96L (GTG→TTG) | patA → | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| RA | 3,240,194 | G→A | 10.3% | V62I (GTC→ATC) | exuR → | hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,257,240 | G→A | 5.5% | A379A (GCC→GCT) | tdcC ← | L‑threonine/L‑serine transporter |
| RA | 3,274,891 | G→A | 6.8% | pseudogene (462/555 nt) | agaA → | pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase |
| RA | 3,408,537 | A→G | 5.5% | Y49C (TAT→TGT) | acrF → | multidrug efflux system protein |
| RA | 3,416,890 | T→G | 11.0% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 17.4% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,435,515 | C→A | 11.8% | A106S (GCA→TCA) | rpsM ← | 30S ribosomal subunit protein S13 |
| RA | 3,446,514 | G→T | 7.4% | P39Q (CCG→CAG) | rpsJ ← | 30S ribosomal subunit protein S10 |
| RA | 3,464,590 | G→A | 5.0% | T33T (ACC→ACT) | tufA ← | translation elongation factor EF‑Tu 1 |
| RA | 3,473,059 | G→A | 7.3% | A303V (GCG→GTG) | kefB ← | potassium:proton antiporter |
| RA | 3,536,567 | C→A | 8.2% | F14L (TTC→TTA) | yhgA → | transposase_31 family protein |
| RA | 3,542,080 | C→A | 13.8% | V450V (GTG→GTT) | malQ ← | 4‑alpha‑glucanotransferase (amylomaltase) |
| RA | 3,546,353 | T→A | 10.5% | intergenic (‑521/‑91) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,594,959 | T→C | 5.5% | D163G (GAT→GGT) | ftsX ← | inner membrane putative ABC superfamily transporter permease |
| RA | 3,614,441 | G→T | 6.0% | G630G (GGG→GGT) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,614,534 | T→C | 15.6% | L661L (CTT→CTC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,615,572 | G→A | 10.0% | R1007R (CGG→CGA) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,615,782 | C→G | 5.4% | A1077A (GCC→GCG) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,061 | T→C | 5.0% | Y1170Y (TAT→TAC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,121 | G→C | 6.4% | R1190R (CGG→CGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,618,160 | A→G | 6.9% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,635,961 | G→A | 11.4% | Q178* (CAG→TAG) | rsmJ ← | 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,636,203 | G→T | 5.7% | A97E (GCA→GAA) | rsmJ ← | 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,641,201 | C→T | 8.5% | intergenic (‑53/‑222) | dinQ ← / → agrA | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/Inactive antisense sRNA |
| RA | 3,642,356 | G→T | 9.5% | G21V (GGT→GTT) | arsB → | arsenite/antimonite transporter |
| RA | 3,693,119 | G→T | 7.5% | D516Y (GAC→TAC) | bcsG → | DUF3260 family inner membrane protein associated with cellulose production |
| RA | 3,695,359 | C→A | 7.7% | P290P (CCG→CCT) | dppF ← | dipeptide transporter |
| RA | 3,717,571 | C→T | 9.3% | E63K (GAA→AAA) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,717,835 | C→T | 5.5% | A282T (GCA→ACA) | glyQ ← | glycine tRNA synthetase, alpha subunit |
| RA | 3,747,137 | G→A | 8.2% | A108V (GCG→GTG) | yiaV ← | membrane fusion protein (MFP) component of efflux pump, signal anchor |
| RA | 3,758,773 | G→C | 6.1% | A1077A (GCG→GCC) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,758,971 | C→T | 6.0% | I1143I (ATC→ATT) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,772,814 | C→T | 8.5% | A134V (GCA→GTA) | lldR → | dual role activator/repressor for lldPRD operon |
| RA | 3,827,841 | C→T | 6.7% | P19P (CCG→CCA) | yicI ← | putative alpha‑glucosidase |
| RA | 3,859,358 | G→T | 5.2% | R92R (CGC→CGA) | yidE ← | putative transporter |
| RA | 3,868,004 | G→T | 5.1% | Q173K (CAG→AAG) | dgoR ← | putative DNA‑binding transcriptional regulator |
| RA | 3,911,530 | C→T | 6.4% | M32I (ATG→ATA) | atpG ← | F1 sector of membrane‑bound ATP synthase, gamma subunit |
| RA | 3,973,574:1 | +G | 10.5% | coding (259/741 nt) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,973,574:2 | +G | 10.5% | coding (259/741 nt) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,973,574:3 | +C | 10.5% | coding (259/741 nt) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,973,574:4 | +A | 10.5% | coding (259/741 nt) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,973,575:1 | +C | 10.5% | coding (260/741 nt) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,993,539 | G→T | 9.4% | intergenic (+34/+113) | uvrD → / ← yigE | DNA‑dependent ATPase I and helicase II/DUF2233 family protein |
| RA | 3,993,616 | T→C | 8.0% | intergenic (+111/+36) | uvrD → / ← yigE | DNA‑dependent ATPase I and helicase II/DUF2233 family protein |
| RA | 4,007,115 | C→T | 11.4% | Q235* (CAG→TAG) | metE → | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 4,034,757 | C→A | 21.3% | A13S (GCC→TCC) | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,076,606 | T→G | 14.3% | G859G (GGA→GGC) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,076,623 | A→T | 11.8% | F854I (TTT→ATT) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,077,245 | C→A | 11.8% | A646A (GCG→GCT) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,148,281 | G→T | 7.8% | noncoding (42/110 nt) | oxyS ← | sRNA antisense regulator activates genes that detoxify oxidative damage, Hfq‑dependent |
| RA | 4,153,912 | C→A | 8.2% | L116I (CTT→ATT) | btuB → | vitamin B12/cobalamin outer membrane transporter |
| RA | 4,165,449 | C→T | 27.2% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 27.2% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,173,148 | A→G | 7.3% | Q659R (CAG→CGG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,173,745 | G→A | 10.2% | G858D (GGT→GAT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,177,142 | A→G | 37.1% | D622G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,209 | C→T | 14.0% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,197,511 | G→T | 13.4% | intergenic (‑51/‑564) | purH ← / → rrsE | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon |
| RA | 4,202,979 | A→C | 18.2% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,236,118 | G→T | 6.0% | A77E (GCG→GAG) | malE ← | maltose transporter subunit |
| RA | 4,263,421 | G→T | 6.4% | L127M (CTG→ATG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,288,032 | G→A | 6.2% | S384S (AGC→AGT) | fdhF ← | formate dehydrogenase‑H, selenopolypeptide subunit |
| RA | 4,312,921 | C→A | 18.9% | pseudogene (127/426 nt) | phnE ← | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily |
| RA | 4,315,805 | G→T | 13.0% | intergenic (‑247/+411) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,905 | T→G | 6.3% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,955 | Δ1 bp | 6.1% | intergenic (‑397/+261) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,353,271 | G→T | 11.5% | P530Q (CCG→CAG) | dsbD ← | fused thiol:disulfide interchange protein: activator of DsbC/conserved protein |
| RA | 4,451,424:1 | +A | 5.4% | coding (1054/2139 nt) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,455,722 | C→A | 13.7% | Q92H (CAG→CAT) | treB ← | fused trehalose(maltose)‑specific PTS enzyme: IIB component/IIC component |
| RA | 4,463,488 | A→G | 6.9% | L128S (TTA→TCA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,472,667 | C→A | 9.8% | A330S (GCA→TCA) | valS ← | valyl‑tRNA synthetase |
| RA | 4,498,909 | G→T | 5.2% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,499,846 | C→A | 7.0% | pseudogene (226/330 nt) | yjhV → | pseudogene, KpLE2 phage‑like element |
| RA | 4,508,633 | A→G | 6.1% | pseudogene (96/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,651 | T→C | 8.1% | pseudogene (114/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,516,029 | A→G | 7.0% | L226P (CTA→CCA) | sgcR ← | putative DNA‑binding transcriptional regulator |
| RA | 4,521,810 | A→G | 10.8% | intergenic (‑342/+57) | sgcX ← / ← yjhY | putative endoglucanase with Zn‑dependent exopeptidase domain/pseudogene, zinc finger protein family |
| RA | 4,550,326 | G→T | 6.9% | L58M (CTG→ATG) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| RA | 4,551,778 | C→A | 7.2% | D239Y (GAT→TAT) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| RA | 4,561,269 | G→A | 80.9% | S41S (AGC→AGT) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| RA | 4,612,009 | G→T | 9.6% | V142L (GTG→TTG) | yjjJ → | putative protein kinase |
| RA | 4,619,818 | G→A | 14.3% | C174C (TGC→TGT) | yjjK ← | putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 4,626,934 | C→A | 8.3% | A141D (GCC→GAC) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB, regulator of the CreBC regulon |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2027120 | 2027506 | 387 | 6 [4] | [4] 5 | rseX | rseX |
| * | * | ÷ | CP009273 | 3448799 | 3448865 | 67 | 7 [4] | [3] 28 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 4323132 | 4323683 | 552 | 6 [4] | [4] 5 | basR | response regulator in two‑component regulatory system with BasS |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 311135 | NA (NA) | 3 (0.070) | 3/244 | NT | NA | coding (134/300 nt) | insE1 | IS3 transposase A |
| ? | CP009273 | 311327 = | NA (NA) | coding (30/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | CP009273 | 360104 = | 29 (0.620) | 33 (0.710) | 16/248 | NT | 53.2% | 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 | 1203246 = | 18 (0.390) | 34 (0.840) | 15/216 | NT | 76.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 5 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 14 (0.300) | 5 (0.120) | 4/216 | NT | 36.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 5 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||