mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 9,907 | A→C | 7.5% | intergenic (+14/+21) | mog → / ← satP | molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter |
| RA | 9,908 | G→T | 7.6% | intergenic (+15/+20) | mog → / ← satP | molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter |
| RA | 36,358 | C→A | 9.0% | A489A (GCG→GCT) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 83,587 | A→C | 6.2% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 6.2% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 120,154 | Δ1 bp | 5.4% | intergenic (+19/+24) | ampE → / ← aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| RA | 120,158:1 | +A | 5.6% | intergenic (+23/+20) | ampE → / ← aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| RA | 252,589 | G→C | 5.5% | A97P (GCA→CCA) | yafO → | mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system |
| RA | 252,594 | G→C | 5.5% | W98C (TGG→TGC) | yafO → | mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system |
| RA | 256,449 | T→C | 7.7% | intergenic (+14/‑78) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| RA | 256,454 | C→G | 8.2% | intergenic (+19/‑73) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| RA | 256,459 | G→A | 8.2% | intergenic (+24/‑68) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 289,256 | G→C | 6.7% | intergenic (‑94/+45) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 289,257 | T→A | 7.4% | intergenic (‑95/+44) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 292,302 | C→G | 6.5% | intergenic (+71/+20) | yagJ → / ← yagK | CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 475,971 | C→G | 6.0% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 5.9% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 481,225 | T→G | 6.9% | intergenic (‑517/+29) | tomB ← / ← acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| RA | 481,228 | C→A | 6.8% | intergenic (‑520/+26) | tomB ← / ← acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| RA | 774,356 | C→G | 5.1% | P16P (CCC→CCG) | ybgE → | putative inner membrane protein in cydABX‑ybgE operon |
| RA | 915,080 | G→C | 5.2% | intergenic (‑223/+272) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 915,081 | G→C | 6.0% | intergenic (‑224/+271) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 987,560 | G→C | 5.5% | intergenic (‑578/+25) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 987,561 | G→C | 5.5% | intergenic (‑579/+24) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,015,912 | T→A | 7.1% | intergenic (+30/+40) | rmf → / ← fabA | ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase |
| RA | 1,018,983 | A→T | 5.3% | intergenic (+46/+30) | matP → / ← ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| RA | 1,018,986 | A→T | 5.2% | intergenic (+49/+27) | matP → / ← ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| RA | 1,141,148 | C→T | 5.6% | intergenic (+162/+34) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,141,150 | G→A | 6.2% | intergenic (+164/+32) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,141,151 | T→C | 5.8% | intergenic (+165/+31) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,141,153 | A→G | 5.9% | intergenic (+167/+29) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,147,548 | T→G | 5.3% | intergenic (+8/‑73) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,147,549 | C→A | 5.2% | intergenic (+9/‑72) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,174,077 | G→A | 6.3% | intergenic (‑113/+15) | mfd ← / ← ycfT | transcription‑repair coupling factor/inner membrane protein |
| RA | 1,174,080 | T→C | 6.3% | intergenic (‑116/+12) | mfd ← / ← ycfT | transcription‑repair coupling factor/inner membrane protein |
| RA | 1,211,610 | A→G | 6.7% | intergenic (+33/+70) | icdC → / ← iraM | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor |
| RA | 1,211,612 | A→T | 6.8% | intergenic (+35/+68) | icdC → / ← iraM | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor |
| RA | 1,211,614 | C→T | 6.7% | intergenic (+37/+66) | icdC → / ← iraM | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor |
| JC JC | 1,293,015 | IS1 (–) +8 bp | 7.5% | intergenic (‑93/‑505) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,091 | IS5 (+) +4 bp | 11.4% | intergenic (‑169/‑433) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,311,830 | A→G | 6.5% | intergenic (+22/+18) | tonB → / ← yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| RA | 1,311,831 | C→T | 6.3% | intergenic (+23/+17) | tonB → / ← yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| RA | 1,324,839 | G→T | 5.3% | E32* (GAA→TAA) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,330,396:1 | +T | 6.0% | intergenic (+15/+21) | sohB → / ← yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| RA | 1,330,399 | A→T | 6.0% | intergenic (+18/+18) | sohB → / ← yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| RA | 1,330,402 | Δ1 bp | 5.9% | intergenic (+21/+15) | sohB → / ← yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| RA | 1,344,033 | A→G | 5.5% | L105P (CTG→CCG) | yciT ← | global regulator of transcription; DeoR family |
| RA | 1,344,036 | G→C | 5.6% | T104S (ACT→AGT) | yciT ← | global regulator of transcription; DeoR family |
| RA | 1,344,039 | C→T | 5.8% | R103Q (CGG→CAG) | yciT ← | global regulator of transcription; DeoR family |
| RA | 1,449,050 | T→A | 7.8% | intergenic (+32/+26) | feaB → / ← tynA | phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring |
| RA | 1,603,724 | A→C | 5.4% | T236P (ACC→CCC) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,603,735 | G→T | 5.3% | G239G (GGG→GGT) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,608,704 | A→G | 5.0% | S107P (TCG→CCG) | yneE ← | bestrophin family putative inner membrane protein |
| RA | 1,625,976 | A→C | 30.4% | F469V (TTC→GTC) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,685,527 | A→G | 100% | G354G (GGT→GGC) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,689,817 | C→A | 7.3% | intergenic (+66/‑35) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,689,819 | A→T | 7.2% | intergenic (+68/‑33) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,689,821 | T→G | 7.3% | intergenic (+70/‑31) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,799,370 | Δ1 bp | 5.7% | intergenic (‑100/+23) | pheM ← / ← rplT | phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20 |
| RA | 1,799,374:1 | +T | 5.8% | intergenic (‑104/+19) | pheM ← / ← rplT | phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20 |
| RA | 1,865,682 | G→C | 7.7% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| RA | 1,932,094 | C→G | 5.3% | intergenic (+35/+21) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,095 | T→A | 5.3% | intergenic (+36/+20) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,096 | C→G | 5.3% | intergenic (+37/+19) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,985,112 | C→G | 6.9% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,020,838 | T→C | 8.7% | V251A (GTG→GCG) | fliM → | flagellar motor switching and energizing component |
| RA | 2,020,841 | G→A | 9.3% | R252H (CGC→CAC) | fliM → | flagellar motor switching and energizing component |
| RA | 2,028,158 | G→C | 5.3% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 5.1% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 5.3% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,032,336 | G→C | 5.9% | intergenic (‑19/+48) | dcm ← / ← yedJ | DNA cytosine methyltransferase/putative HD superfamily phosphohydrolase |
| RA | 2,044,729 | T→A | 5.1% | intergenic (+105/‑209) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,062,354 | T→A | 5.9% | intergenic (+19/+37) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,062,355 | T→G | 5.9% | intergenic (+20/+36) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,062,356 | C→A | 5.9% | intergenic (+21/+35) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,062,357 | T→A | 5.9% | intergenic (+22/+34) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,081,688 | A→T | 5.1% | I287N (ATT→AAT) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b |
| RA | 2,145,313 | C→A | 100% | S683Y (TCC→TAC) | yegE → | putative diguanylate cyclase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,286,313 | T→A | 5.2% | intergenic (+26/+77) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,286,315 | C→G | 5.2% | intergenic (+28/+75) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,305,085 | A→G | 5.3% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 5.4% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 5.4% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,314,800 | A→C | 5.1% | Q438P (CAG→CCG) ‡ | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,314,801 | G→T | 5.0% | Q438H (CAG→CAT) ‡ | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,318,095 | C→G | 100% | L594F (TTG→TTC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,364,995 | T→G | 6.8% | intergenic (+16/+23) | nudI → / ← ais | nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase |
| RA | 2,364,998 | C→A | 6.4% | intergenic (+19/+20) | nudI → / ← ais | nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase |
| RA | 2,462,677 | A→T | 5.1% | intergenic (+31/‑335) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,678 | T→A | 5.4% | intergenic (+32/‑334) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,561,205 | A→T | 6.0% | intergenic (+307/‑163) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,561,206 | A→T | 5.6% | intergenic (+308/‑162) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,653,367 | G→A | 5.4% | intergenic (+28/‑488) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,372 | T→C | 5.1% | intergenic (+33/‑483) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,704,304 | A→G | 6.3% | intergenic (‑241/+31) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,306 | A→T | 6.2% | intergenic (‑243/+29) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,308 | C→T | 6.6% | intergenic (‑245/+27) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,725,630 | Δ1 bp | 88.3% | coding (117/1299 nt) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,731,073 | A→T | 7.8% | noncoding (85/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,731,074 | A→T | 7.7% | noncoding (84/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,775,093 | G→A | 5.7% | intergenic (+72/‑452) | yfjW → / → ypjI | CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related |
| RA | 2,801,056 | A→T | 5.1% | N31I (AAT→ATT) | nrdI → | NrdEF cluster assembly flavodoxin |
| RA | 2,838,222 | A→T | 6.6% | intergenic (‑117/+32) | hydN ← / ← ascG | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,838,231 | A→T | 6.6% | intergenic (‑126/+23) | hydN ← / ← ascG | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,873,915 | A→G | 5.2% | H26H (CAT→CAC) ‡ | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,873,917 | G→C | 5.7% | H26D (CAT→GAT) ‡ | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,873,919 | C→T | 5.2% | G25D (GGT→GAT) | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,918,017 | C→T | 5.4% | intergenic (+204/+28) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,019 | G→T | 5.2% | intergenic (+206/+26) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,020 | A→C | 5.6% | intergenic (+207/+25) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,022 | A→G | 6.2% | intergenic (+209/+23) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,971,146 | T→C | 5.8% | intergenic (+13/‑125) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,971,151 | T→C | 5.4% | intergenic (+18/‑120) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,971,154 | G→A | 5.6% | intergenic (+21/‑117) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,971,159 | G→A | 6.2% | intergenic (+26/‑112) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 3,020,510 | G→T | 7.1% | intergenic (+21/‑30) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,511 | C→G | 7.4% | intergenic (+22/‑29) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,512 | A→C | 7.8% | intergenic (+23/‑28) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,061,817 | G→C | 6.3% | W323S (TGG→TCG) ‡ | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,061,818 | G→C | 6.3% | W323C (TGG→TGC) ‡ | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,156,590 | C→A | 6.6% | intergenic (+72/‑33) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,156,591 | T→G | 6.6% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,160,640 | G→C | 5.3% | T169T (ACC→ACG) | ygiQ ← | Radical SAM superfamily protein |
| RA | 3,171,863 | A→G | 5.0% | intergenic (+30/+16) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,180,505 | G→T | 6.1% | E29* (GAG→TAG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,180,506 | A→C | 6.6% | E29A (GAG→GCG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,183,345:1 | +T | 5.9% | intergenic (+22/+468) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,183,350 | Δ1 bp | 5.8% | intergenic (+27/+463) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,239,609 | T→G | 5.7% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,256,442 | G→C | 6.6% | G70G (GGC→GGG) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,328,182 | A→T | 6.3% | intergenic (+99/+57) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,328,183 | T→A | 6.1% | intergenic (+100/+56) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,328,184 | A→T | 5.8% | intergenic (+101/+55) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,368,982 | G→C | 5.9% | intergenic (+28/+32) | yhcG → / ← yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily |
| RA | 3,407,293 | T→A | 6.1% | intergenic (+27/‑82) | accC → / → yhdT | acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein |
| RA | 3,407,294 | T→A | 6.0% | intergenic (+28/‑81) | accC → / → yhdT | acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein |
| RA | 3,407,295 | T→A | 6.0% | intergenic (+29/‑80) | accC → / → yhdT | acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein |
| RA | 3,418,628 | G→A | 6.0% | intergenic (+17/‑414) | yhdV → / → yhdW | putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily |
| RA | 3,418,629 | T→C | 6.1% | intergenic (+18/‑413) | yhdV → / → yhdW | putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily |
| RA | 3,423,229 | T→G | 5.9% | intergenic (+35/+194) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,230 | T→A | 5.9% | intergenic (+36/+193) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,231 | T→A | 6.3% | intergenic (+37/+192) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,232 | C→A | 5.8% | intergenic (+38/+191) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,458,556 | C→A | 64.4% | S73* (TCG→TAG) | gspE → | general secretory pathway component, cryptic |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,642,358 | T→A | 6.1% | intergenic (+27/+22) | dtpB → / ← rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,642,361 | T→A | 6.1% | intergenic (+30/+19) | dtpB → / ← rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,708,595 | G→A | 5.4% | intergenic (‑890/+21) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,596 | T→A | 5.5% | intergenic (‑891/+20) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,597 | T→C | 5.4% | intergenic (‑892/+19) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,774,207 | C→T | 5.6% | intergenic (+13/‑217) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,214 | C→T | 5.9% | intergenic (+20/‑210) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,215 | A→G | 6.0% | intergenic (+21/‑209) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,222 | A→G | 5.3% | intergenic (+28/‑202) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,781,051 | C→G | 7.2% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,790,300 | A→T | 6.0% | intergenic (‑219/+20) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,790,303 | A→T | 5.9% | intergenic (‑222/+17) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| JC JC | 3,922,629 | IS5 (–) +4 bp | 15.1% | intergenic (‑189/+425) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| RA | 3,959,515 | T→A | 6.2% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,127,252 | A→G | 5.5% | intergenic (+27/+34) | rpmE → / ← yiiX | 50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein |
| RA | 4,291,512 | G→A | 5.7% | M1M (GTG→ATG) †‡ | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| RA | 4,291,513 | T→C | 5.3% | M1A (GTG→GCG) †‡ | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| RA | 4,296,060 | C→T | 19.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,307,294 | A→T | 5.2% | L169Q (CTG→CAG) | alsK ← | D‑allose kinase |
| RA | 4,335,654 | T→A | 5.9% | intergenic (‑64/+40) | eptA ← / ← adiC | lipid A phosphoethanolamine transferase/arginine:agmatine antiporter |
| RA | 4,335,655 | T→A | 5.9% | intergenic (‑65/+39) | eptA ← / ← adiC | lipid A phosphoethanolamine transferase/arginine:agmatine antiporter |
| RA | 4,362,528 | G→A | 5.9% | intergenic (‑175/+23) | yjdQ ← / ← pheU | pseudogene, P4‑like integrase remnant/tRNA‑Phe |
| RA | 4,362,529 | T→C | 6.4% | intergenic (‑176/+22) | yjdQ ← / ← pheU | pseudogene, P4‑like integrase remnant/tRNA‑Phe |
| RA | 4,426,592 | T→A | 6.1% | intergenic (+35/+36) | rplI → / ← yjfZ | 50S ribosomal subunit protein L9/uncharacterized protein |
| RA | 4,479,012 | A→T | 5.8% | intergenic (+123/+22) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,016 | G→C | 5.6% | intergenic (+127/+18) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,020 | A→T | 5.6% | intergenic (+131/+14) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,520,500 | Δ1 bp | 9.8% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 9.1% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423750–3424554 | 3424554 | 1–805 | 96 [93] | [93] 96 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 224891 = | NA (NA) | 4 (0.020) | 3/290 | NT | NA | noncoding (1121/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 224923 = | NA (NA) | noncoding (1153/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 274038 = | NA (NA) | 4 (0.020) | 4/286 | NT | NA | noncoding (1112/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274083 = | NA (NA) | noncoding (1067/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 3 (0.020) | 3/280 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 474269 = | NA (NA) | 4 (0.020) | 4/286 | NT | NA | intergenic (+17/+32) | amtB/tesB | ammonium transporter/acyl‑CoA thioesterase 2 |
| ? | NC_000913 | 474296 = | NA (NA) | intergenic (+44/+5) | amtB/tesB | ammonium transporter/acyl‑CoA thioesterase 2 | |||||
| * | ? | NC_000913 | 1207790 = | 95 (0.500) | 100 (0.590) | 71/266 | NT | 55.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 78 (0.460) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 94 (0.490) | 86 (0.510) | 71/266 | NT | 51.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 78 (0.460) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 142 (0.770) | 101/290 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1392552 | 64 (0.340) | 140 (0.740) | 112/298 | NT | 68.6% | coding (562/900 nt) | pgrR | murein peptide degradation regulator |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3091097 | 170 (0.890) | 9 (0.050) | 7/280 | NT | 5.3% | intergenic (+43/‑37) | endA/rsmE | DNA‑specific endonuclease I/16S rRNA m(3)U1498 methyltransferase, SAM‑dependent |
| ? | NC_000913 | = 3091103 | 162 (0.910) | intergenic (+49/‑31) | endA/rsmE | DNA‑specific endonuclease I/16S rRNA m(3)U1498 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | 3423376 = | 180 (0.950) | 17 (0.090) | 9/294 | NT | 8.8% | intergenic (+182/+47) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913 | = 4213162 | 173 (0.920) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 9 (0.050) | 7/280 | NT | 100% | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619892 = | 0 (0.000) | coding (701/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3721045 = | 228 (1.200) | 498 (2.640) | 226/296 | NT | 69.0% | noncoding (413/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3839774 | 222 (1.180) | coding (220/819 nt) | nlpA | cytoplasmic membrane lipoprotein‑28 | |||||
| * | ? | NC_000913 | = 4168341 | 141 (0.740) | 7 (0.040) | 6/278 | NT | 5.2% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu |
| ? | NC_000913 | = 4168363 | 125 (0.700) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 4614608 = | 137 (0.720) | 8 (0.040) | 7/284 | NT | 5.8% | noncoding (352/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913 | 4614641 = | 131 (0.720) | noncoding (385/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||