mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 860 | C→T | A175V (GCG→GTG) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 10,564 | C→T | intergenic (‑70/+79) | satP ← / ← yaaW | acetate/succinate:H(+) symporter/putative enzyme‑specific chaperone YaaW |
| RA | 23,291 | C→T | L301F (CTT→TTT) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 25,114 | C→T | T908T (ACC→ACT) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 47,652 | G→A | G136E (GGG→GAG) | kefF → | regulator of KefC‑mediated potassium transport and quinone oxidoreductase |
| JC JC | 57,276 | IS2 (+) +5 bp | intergenic (‑167/‑84) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 69,531 | G→A | S173F (TCT→TTT) | araB ← | ribulokinase |
| RA | 71,134 | G→A | G250S (GGT→AGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 81,556 | G→A | L135L (CTG→TTG) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 148,424 | C→T | P124P (CCG→CCA) | panC ← | pantothenate synthetase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 311,511 | G→A | intergenic (‑175/‑601) | matA ← / → ykgL | DNA‑binding transcriptional dual regulator MatA/uncharacterized protein YkgL |
| RA | 378,391 | C→T | intergenic (‑23/+71) | frmB ← / ← frmA | S‑formylglutathione hydrolase FrmB/S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | 390,948 | C→T | pseudogene (698/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 418,613 | C→T | A242V (GCG→GTG) | phoR → | sensor histidine kinase PhoR |
| RA | 432,880 | C→T | intergenic (‑29/‑122) | yajI ← / → nrdR | putative lipoprotein YajI/NrdR transcriptional repressor |
| RA | 438,623 | C→T | A519T (GCG→ACG) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 441,293 | C→T | E17E (GAG→GAA) | xseB ← | exodeoxyribonuclease VII subunit XseB |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,449 | IS2 (–) +5 bp | coding (135‑139/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 722,194 | G→A | L741L (CTG→TTG) | kdpD ← | sensor histidine kinase KdpD |
| RA | 736,420 | C→T | intergenic (+201/‑25) | ybfC → / → ybfQ | uncharacterized protein YbfC/inactive transposase YbfQ |
| RA | 781,595 | G→A | noncoding (19/76 nt) | lysQ → | tRNA‑Lys |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,290,881 | C→T | L214F (CTT→TTT) | rssB → | regulator of RpoS |
| MC JC | 1,294,035 | Δ141 bp | [tdk] | [tdk] | |
| JC | 1,303,073 | Δ12 bp | coding (175‑186/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,312,633 | C→T | A86A (GCG→GCA) | yciB ← | inner membrane protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,494,388 | Δ1 bp | coding (684/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,517,508 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,531,250 | C→T | intergenic (‑746/‑566) | yncO ← / → ydcC | protein YncO/H repeat‑associated putative transposase YdcC |
| RA | 1,556,938 | C→T | A105V (GCG→GTG) | osmC → | osmotically inducible peroxiredoxin OsmC |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| JC JC | 1,792,772 | IS2 (–) +5 bp | intergenic (‑41/+33) | nlpC ← / ← btuD | NlpC/P60 family lipoprotein NlpC/vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,179,326 | G→A | G169E (GGA→GAA) | yegT → | putative transporter YegT |
| RA | 2,242,121 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| JC JC | 2,269,876 | IS5 (+) +4 bp | intergenic (+309/‑100) | lpxT → / → mepS | lipid A‑core phosphotransferase/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| RA | 2,278,650 | G→A | P371S (CCG→TCG) | bcr ← | multidrug efflux pump Bcr |
| RA | 2,313,736 | C→T | S83S (TCC→TCT) | rcsD → | RcsD phosphotransferase |
| RA | 2,316,221 | C→T | V15V (GTC→GTT) | rcsB → | DNA‑binding transcriptional activator RcsB |
| RA | 2,316,753 | C→T | L193L (CTG→TTG) | rcsB → | DNA‑binding transcriptional activator RcsB |
| RA | 2,317,233 | C→T | D882N (GAT→AAT) | rcsC ← | histidine kinase RcsC |
| RA | 2,317,463 | C→T | S805N (AGC→AAC) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,319,850 | IS2 (+) +5 bp | coding (23‑27/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,320,552 | C→T | G170G (GGC→GGT) | atoS → | sensor histidine kinase AtoS |
| RA | 2,321,526 | C→T | A495V (GCC→GTC) | atoS → | sensor histidine kinase AtoS |
| RA | 2,324,745 | C→T | R213W (CGG→TGG) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit beta |
| RA | 2,327,447 | C→T | V233I (GTC→ATC) | yfaP ← | DUF2135 domain‑containing protein YfaP |
| RA | 2,397,444 | G→A | Q908* (CAA→TAA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,480,474 | G→A | G425R (GGA→AGA) | dsdA → | D‑serine ammonia‑lyase |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,666,074 | IS1 (+) +9 bp | coding (640‑648/1281 nt) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 2,784,599 | G→A | S138F (TCT→TTT) | ypjC ← | DUF5507 domain‑containing protein YpjC |
| RA | 2,789,285 | G→A | G101S (GGT→AGT) | glaH → | glutarate dioxygenase GlaH |
| RA | 2,794,383 | G→A | G44D (GGC→GAC) | gabP → | 4‑aminobutanoate:H(+) symporter |
| RA | 2,799,156 | G→A | intergenic (‑661/‑8) | stpA ← / → alaE | DNA‑binding transcriptional repressor StpA with RNA chaperone activity/L‑alanine exporter |
| RA | 2,799,342 | G→A | G60D (GGT→GAT) | alaE → | L‑alanine exporter |
| RA | 2,803,246 | G→A | A633A (GCG→GCA) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | 2,815,005 | G→A | P479S (CCG→TCG) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,816,433 | G→A | P3S (CCG→TCG) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,827,260 | T→C | V290A (GTC→GCC) | srlE → | sorbitol‑specific PTS enzyme IIBC1 component |
| RA | 2,845,115 | G→A | P453S (CCG→TCG) | hycE ← | formate hydrogenlyase subunit HycE |
| RA | 2,856,061 | G→A | G575E (GGG→GAG) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | 2,858,682 | G→A | E530E (GAG→GAA) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,862,253 | C→T | A275V (GCC→GTC) | ygbJ → | putative L‑threonate dehydrogenase |
| RA | 2,864,013 | C→T | P141S (CCG→TCG) | ygbL → | putative 3‑oxo‑tetronate 4‑phosphate decarboxylase YgbL |
| RA | 2,871,025 | G→A | P94S (CCG→TCG) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,878,239 | G→A | intergenic (+621/+330) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,885,029 | G→A | L731L (CTG→TTG) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 2,889,826 | T→C | T92A (ACC→GCC) | cysI ← | sulfite reductase, hemoprotein subunit |
| RA | 2,894,133 | G→A | W72* (TGG→TAG) | ygcO → | putative 4Fe‑4S cluster‑containing protein |
| RA | 2,899,661 | G→A | L205L (CTG→TTG) | ygcW ← | putative deoxygluconate dehydrogenase |
| RA | 2,926,071 | C→T | R242C (CGC→TGC) | queF → | 7‑cyano‑7‑deazaguanine reductase |
| RA | 2,930,384 | C→T | A270V (GCA→GTA) | sdaB → | L‑serine deaminase II |
| RA | 2,935,697 | C→T | A38A (GCC→GCT) | fucI → | L‑fucose isomerase |
| RA | 2,945,513 | C→T | T110T (ACG→ACA) | tcdA ← | tRNA threonylcarbamoyladenosine dehydratase |
| RA | 2,947,323 | C→T | intergenic (‑145/‑64) | mltA ← / → metZ | membrane‑bound lytic murein transglycosylase A/tRNA‑Met |
| RA | 2,949,648 | C→T | A136V (GCC→GTC) | argA → | N‑acetylglutamate synthase |
| RA | 2,949,800 | C→T | L187L (CTG→TTG) | argA → | N‑acetylglutamate synthase |
| RA | 2,953,166 | C→T | P946P (CCG→CCA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,958,080 | C→T | V269I (GTA→ATA) | ptrA ← | protease 3 |
| RA | 2,966,838 | C→T | E533K (GAG→AAG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,967,877 | C→T | W186* (TGG→TGA) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,983,800 | C→T | G109S (GGT→AGT) | kduI ← | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase |
| RA | 2,984,177 | C→T | intergenic (‑53/+234) | kduI ← / ← yqeF | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase/putative acyltransferase |
| RA | 2,985,807 | C→T | intergenic (‑215/‑40) | yqeF ← / → yqeG | putative acyltransferase/putative transporter YqeG |
| RA | 2,986,436 | C→T | S197L (TCG→TTG) | yqeG → | putative transporter YqeG |
| RA | 2,987,975 | C→T | T147I (ACC→ATC) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | 2,990,087 | C→T | E92K (GAA→AAA) | yqeK ← | protein YqeK |
| RA | 2,994,899 | C→T | intergenic (+1043/+1473) | ygeI → / ← insD4 | protein YgeI/IS2 insertion element protein InsB |
| RA | 3,008,693 | C→T | A395V (GCT→GTT) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,009,580 | G→A | E273K (GAA→AAA) | ygeY → | putative peptidase YgeY |
| RA | 3,010,747 | G→A | L240L (CTG→CTA) | hyuA → | phenylhydantoinase |
| RA | 3,012,153 | G→A | A231A (GCG→GCA) | yqeA → | putative amino acid kinase YqeA |
| RA | 3,022,051 | G→A | G246S (GGT→AGT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,042,914 | C→T | A79T (GCA→ACA) | yqfA ← | hemolysin‑III family protein YqfA |
| RA | 3,049,690 | C→T | A326A (GCG→GCA) | gcvT ← | aminomethyltransferase |
| RA | 3,056,165 | C→T | noncoding (183/183 nt) | ssrS → | 6S RNA |
| RA | 3,057,590 | C→T | S274N (AGC→AAC) | serA ← | phosphoglycerate dehydrogenase |
| RA | 3,061,808 | C→T | T320I (ACC→ATC) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,062,319 | C→T | A490A (GCC→GCT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,062,736 | C→T | R629R (CGC→CGT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,071,691 | C→T | G311D (GGC→GAC) | pgk ← | phosphoglycerate kinase |
| RA | 3,073,577 | C→T | A39T (GCG→ACG) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
| RA | 3,076,412 | C→T | V349M (GTG→ATG) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,082,464 | C→T | F184F (TTC→TTT) | loiP → | metalloprotease LoiP |
| RA | 3,087,433 | C→T | T243I (ACT→ATT) | metK → | methionine adenosyltransferase |
| RA | 3,093,260 | C→T | S108S (TCC→TCT) | yqgE → | DUF179 domain‑containing protein YqgE |
| RA | 3,099,265 | C→T | A101T (GCG→ACG) | yggM ← | DUF1202 domain‑containing protein YggM |
| RA | 3,099,484 | C→T | E28K (GAA→AAA) | yggM ← | DUF1202 domain‑containing protein YggM |
| RA | 3,100,557 | C→T | V58I (GTT→ATT) | ansB ← | L‑asparaginase 2 |
| RA | 3,112,243 | C→T | K269K (AAG→AAA) | yghF ← | putative type II secretion system C‑type protein YghF |
| RA | 3,114,520 | C→T | intergenic (‑168/+30) | pppA ← / ← yghJ | prepilin peptidase/putative lipoprotein YghJ |
| RA | 3,160,906 | C→T | A81T (GCC→ACC) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,164,048 | C→T | M642I (ATG→ATA) | parC ← | DNA topoisomerase IV subunit A |
| RA | 3,167,365 | C→T | W118* (TGG→TGA) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,173,521 | C→T | A626T (GCG→ACG) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,175,472 | C→T | D179N (GAT→AAT) | yqiA ← | esterase YqiA |
| RA | 3,175,628 | C→T | V127I (GTC→ATC) | yqiA ← | esterase YqiA |
| RA | 3,190,892 | G→A | M87I (ATG→ATA) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,193,282 | C→T | A140V (GCC→GTC) | yqiK → | flotillin family inner membrane protein YqiK |
| RA | 3,215,106 | C→T | W123* (TGG→TAG) | mug ← | stationary phase mismatch/uracil DNA glycosylase |
| RA | 3,218,479 | C→T | A200T (GCA→ACA) | aer ← | aerotaxis receptor |
| RA | 3,220,489 | C→T | T332T (ACC→ACT) | patA → | putrescine aminotransferase |
| RA | 3,232,319 | C→T | L219F (CTC→TTC) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,240,171 | G→A | G76G (GGG→GGA) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,243,005 | C→T | A104T (GCA→ACA) | uxaA ← | D‑altronate dehydratase |
| RA | 3,248,308 | C→T | P179L (CCG→CTG) | yqjA → | DedA family protein YqjA |
| RA | 3,248,681 | C→T | D81D (GAC→GAT) | mzrA → | modulator protein MzrA |
| RA | 3,251,737 | C→T | A238A (GCC→GCT) | yqjG → | glutathionyl‑hydroquinone reductase YqjG |
| RA | 3,254,120 | C→T | G32E (GGA→GAA) | yhaJ ← | DNA‑binding transcriptional activator YhaJ |
| RA | 3,254,853 | C→T | P179S (CCA→TCA) | yhaK → | bicupin‑related protein |
| RA | 3,255,992 | G→A | S220S (AGC→AGT) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| RA | 3,261,943 | G→A | P159L (CCG→CTG) | tdcE ← | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| RA | 3,268,852 | G→A | G146G (GGG→GGA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,273,052 | C→T | G169D (GGC→GAC) | garL ← | alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
| RA | 3,276,711 | C→T | T477I (ACC→ATC) | garD → | GarD |
| RA | 3,478,611 | C→T | G61E (GGG→GAG) | yheV ← | DUF2387 domain‑containing protein YheV |
| RA | 3,481,609 | G→A | G107G (GGG→GGA) | yheS → | putative ATP‑binding protein YheS |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,450 | C→T | P111S (CCG→TCG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,873 | C→T | P28L (CCC→CTC) | yhfK → | putative transporter YhfK |
| RA | 3,488,712 | C→T | A641V (GCC→GTC) | yhfK → | putative transporter YhfK |
| RA | 3,493,759 | C→T | intergenic (+10/‑252) | tsgA → / → nirB | putative transporter TsgA/nitrite reductase (NADH) large subunit |
| RA | 3,518,251 | G→A | A79V (GCT→GTT) | aroB ← | 3‑dehydroquinate synthase |
| RA | 3,519,801 | G→A | V301V (GTC→GTT) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,538,195 | G→A | A271T (GCG→ACG) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,538,357 | G→A | G325R (GGA→AGA) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,539,759 | G→A | intergenic (+53/‑404) | yhgF → / → feoA | putative RNA‑binding protein YhgF/ferrous iron transport protein A |
| RA | 3,548,459 | C→T | E538K (GAG→AAG) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,550,402 | C→T | G691D (GGC→GAC) | malP ← | maltodextrin phosphorylase |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,563,694 | C→T | intergenic (+176/+30) | glpD → / ← yzgL | aerobic glycerol 3‑phosphate dehydrogenase/putative uncharacterized protein YzgL |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,796,966 | C→T | L7F (CTT→TTT) | waaL → | O‑antigen ligase |
| RA | 3,814,113 | C→T | P62L (CCT→CTT) | dut → | dUTP diphosphatase |
| RA | 3,933,450 | C→T | P34S (CCC→TCC) | rbsD → | D‑ribose pyranase |
| RA | 3,934,173 | C→T | R132R (CGC→CGT) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 3,941,568 | G→A | intergenic (‑241/‑240) | yieP ← / → rrsC | DNA‑binding transcriptional regulator YieP/16S ribosomal RNA |
| RA | 3,942,034 | G→A | noncoding (227/1542 nt) | rrsC → | 16S ribosomal RNA |
| RA | 4,061,400 | C→T | A79V (GCC→GTC) | yihM → | putative TIM barrel domain‑containing protein YihM |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| JC JC | 4,135,180 | IS2 (–) +5 bp | coding (1346‑1350/2181 nt) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,214,131 | C→T | intergenic (‑8/‑149) | yjaB ← / → metA | peptidyl‑lysine N‑acetyltransferase YjaB/homoserine O‑succinyltransferase |
| RA | 4,218,867 | C→T | P91L (CCG→CTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,226,385 | C→T | P853L (CCG→CTG) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,250,729 | C→T | intergenic (+255/‑1777) | malM → / → ubiC | maltose regulon periplasmic protein/chorismate lyase |
| RA | 4,253,539 | C→T | A175V (GCC→GTC) | ubiA → | 4‑hydroxybenzoate octaprenyltransferase |
| RA | 4,259,194 | G→A | intergenic (+73/‑43) | dinF → / → yjbJ | DNA damage‑inducible protein F/putative stress response protein YjbJ |
| RA | 4,270,229 | G→A | intergenic (+102/‑9) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/PF01894 family protein YjbQ |
| RA | 4,277,732 | G→A | A88A (GCG→GCA) | soxR → | DNA‑binding transcriptional dual regulator SoxR |
| RA | 4,286,371 | G→A | P334L (CCC→CTC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,286,403 | G→A | C323C (TGC→TGT) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,290,944 | G→A | V157M (GTG→ATG) | nrfD → | putative menaquinol‑cytochrome c reductase subunit NrfD |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,298,639 | G→A | A243V (GCG→GTG) | fdhF ← | formate dehydrogenase H |
| RA | 4,302,032 | G→A | D349D (GAC→GAT) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| RA | 4,302,462 | G→A | A206V (GCA→GTA) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| RA | 4,303,109 | G→A | A334V (GCT→GTT) | mdtN ← | putative multidrug efflux pump membrane fusion protein |
| RA | 4,306,957 | G→A | A281A (GCC→GCT) | alsK ← | D‑allose kinase |
| RA | 4,310,026 | C→T | E319K (GAA→AAA) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,315,749 | C→T | A112T (GCG→ACG) | phnN ← | ribose 1,5‑bisphosphate phosphokinase |
| RA | 4,316,019 | C→T | E22K (GAA→AAA) | phnN ← | ribose 1,5‑bisphosphate phosphokinase |
| RA | 4,316,390 | C→T | G277S (GGC→AGC) | phnM ← | RPnTP hydrolase |
| RA | 4,316,898 | C→T | R107R (CGG→CGA) | phnM ← | RPnTP hydrolase |
| RA | 4,317,597 | C→T | R100H (CGC→CAC) | phnL ← | methylphosphonate degradation complex subunit PhnL |
| RA | 4,317,641 | C→T | V85V (GTG→GTA) | phnL ← | methylphosphonate degradation complex subunit PhnL |
| RA | 4,317,944 | C→T | intergenic (‑49/+62) | phnL ← / ← phnK | methylphosphonate degradation complex subunit PhnL/carbon‑phosphorus lyase subunit PhnK |
| RA | 4,318,776 | C→T | E277E (GAG→GAA) | phnJ ← | carbon‑phosphorus lyase core complex subunit PhnJ |
| RA | 4,319,494 | C→T | G38D (GGC→GAC) | phnJ ← | carbon‑phosphorus lyase core complex subunit PhnJ |
| RA | 4,325,150 | G→A | R6C (CGT→TGT) | phnC ← | phosphonate/phosphate ABC transporter ATP binding subunit |
| RA | 4,326,061 | G→A | intergenic (‑320/+338) | yjdN ← / ← yjdM | PF06983 family protein YjdN/zinc ribbon domain‑containing protein YjdM |
| RA | 4,329,790 | G→A | G144D (GGT→GAT) | rdcB → | regulator of diguanylate cyclase RdcB |
| RA | 4,336,958 | C→T | G25E (GGG→GAG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,339,222 | C→T | A434T (GCG→ACG) | adiA ← | arginine decarboxylase, degradative |
| RA | 4,342,807 | C→T | C299C (TGC→TGT) | melA → | alpha‑galactosidase |
| RA | 4,353,441 | C→T | G426D (GGT→GAT) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,360,665 | C→T | A424T (GCG→ACG) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,363,741 | C→T | W434* (TGG→TGA) | dsbD ← | thiol‑disulfide exchange protein DsbD |
| RA | 4,368,175 | C→T | M51I (ATG→ATA) | aspA ← | aspartate ammonia‑lyase |
| RA | 4,369,251 | C→T | V388I (GTC→ATC) | yjeH ← | L‑methionine/branched chain amino acid exporter |
| RA | 4,377,648 | C→T | P25P (CCG→CCA) | blc ← | outer membrane lipoprotein Blc |
| RA | 4,380,790 | C→T | G510D (GGC→GAC) | frdA ← | fumarate reductase flavoprotein subunit |
| RA | 4,380,900 | C→T | M473I (ATG→ATA) | frdA ← | fumarate reductase flavoprotein subunit |
| RA | 4,382,616 | C→T | intergenic (‑298/‑27) | frdA ← / → epmA | fumarate reductase flavoprotein subunit/EF‑P‑lysine lysyltransferase |
| RA | 4,382,970 | C→T | P110S (CCT→TCT) | epmA → | EF‑P‑lysine lysyltransferase |
| RA | 4,391,611 | C→T | A3V (GCC→GTC) | orn → | oligoribonuclease |
| RA | 4,393,631 | C→T | R146H (CGC→CAC) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,792 | C→T | T92T (ACG→ACA) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,787 | C→T | T241T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,399,104 | C→T | L565L (CTG→TTG) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,405,238 | C→T | Y184Y (TAC→TAT) | purA → | adenylosuccinate synthetase |
| RA | 4,410,409 | G→A | E93K (GAG→AAG) | yjfI → | DUF2170 domain‑containing protein YjfI |
| RA | 4,413,615 | G→A | Q196Q (CAG→CAA) | yjfC → | putative acid‑‑amine ligase YjfC |
| RA | 4,435,880 | G→A | S229F (TCT→TTT) | cpdB ← | 2',3'‑cyclic‑nucleotide 2'‑phosphodiesterase/3'‑nucleotidase |
| RA | 4,438,359 | G→A | G218D (GGC→GAC) | ytfI → | protein YtfI |
| RA | 4,438,403 | G→A | G233S (GGT→AGT) | ytfI → | protein YtfI |
| RA | 4,444,962 | G→A | S284N (AGC→AAC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,447,525 | G→A | M1138I (ATG→ATA) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,449,507 | G→A | A49V (GCG→GTG) | ppa ← | inorganic pyrophosphatase |
| RA | 4,461,722 | G→A | N313N (AAC→AAT) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,462,867 | G→A | intergenic (‑207/+187) | nrdD ← / ← treC | anaerobic ribonucleoside‑triphosphate reductase/trehalose‑6‑phosphate hydrolase |
| RA | 4,477,303 | G→A | intergenic (+52/+4) | yjgL → / ← argI | protein YjgL/ornithine carbamoyltransferase ArgI |
| RA | 4,479,109 | G→A | G143G (GGC→GGT) | yjgM ← | putative N‑acetyltransferase YjgM |
| RA | 4,479,694 | G→A | intergenic (‑157/‑36) | yjgM ← / → yjgN | putative N‑acetyltransferase YjgM/inner membrane protein YjgN |
| JC JC | 4,536,236 | IS5 (+) +4 bp | intergenic (‑2183/‑358) | topAI ← / → ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB |
| RA | 4,539,264 | C→T | V80I (GTT→ATT) | nanC ← | N‑acetylneuraminate outer membrane channel |
| RA | 4,542,683 | Δ1 bp | intergenic (+50/‑432) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| RA | 4,545,733 | G→A | S213N (AGT→AAT) | fimD → | type I fimbriae usher protein |
| RA | 4,559,285 | G→A | T81M (ACG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,561,613 | G→A | L355F (CTC→TTC) | yjiJ ← | putative transporter YjiJ |
| RA | 4,571,292 | G→A | L95L (CTG→TTG) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,572,651 | G→A | D80N (GAT→AAT) | yjiT → | putative uncharacterized protein YjiT |
| RA | 4,577,641 | G→A | N106N (AAC→AAT) | mcrC ← | Type IV methyl‑directed restriction enzyme EcoKMcrBC subunit |
| RA | 4,600,636 | G→A | H114Y (CAT→TAT) | dnaC ← | DNA replication protein DnaC |
| RA | 4,610,221 | G→A | D270N (GAT→AAT) | prfC → | peptide chain release factor RF3 |
| RA | 4,613,753 | G→A | K91K (AAG→AAA) | yjjV → | putative metal‑dependent hydrolase YjjV |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196304 | 1211472 | 15169 | 36 [34] | [35] 38 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 139 [0] | [0] 122 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423865–3424234 | 3424493–3424239 | 6–629 | 36 [35] | [35] 36 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 56 (0.550) | 41/598 | 1.4 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 34 (0.340) | 29/594 | 2.6 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 127 (1.270) | 76/590 | 0.1 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 138 (1.360) | 92/598 | 0.0 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 122 (1.200) | 78/598 | 0.1 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||