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 | annotation | gene | description |
| RA | 28,427 | C→T | G18G (GGC→GGT) | dapB → | 4‑hydroxy‑tetrahydrodipicolinate reductase |
| RA | 31,826 | A→G | N337S (AAC→AGC) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | 39,838 | C→T | W183* (TGG→TGA) | caiA ← | crotonobetainyl‑CoA reductase |
| RA | 61,202 | A→G | L688P (CTG→CCG) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 62,678 | A→G | L196P (CTC→CCC) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 62,681 | A→G | L195P (CTG→CCG) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 66,691 | C→T | intergenic (‑141/+144) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase AraD/L‑arabinose isomerase |
| RA | 71,488 | A→G | G46G (GGA→GGG) | yabI → | DedA family protein YabI |
| RA | 83,579 | (A)7→8 | intergenic (‑50/+43) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 93,440 | A→G | E92G (GAG→GGG) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 130,378 | A→G | Y295H (TAC→CAC) | yacH ← | DUF3300 domain‑containing protein YacH |
| RA | 144,977 | (A)7→8 | coding (401/441 nt) | yadI → | putative PTS enzyme IIA component YadI |
| RA | 166,118 | A→G | K463K (AAA→AAG) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 166,897 | T→C | V723A (GTC→GCC) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 189,107 | A→G | Y134H (TAC→CAC) | map ← | methionine aminopeptidase |
| RA | 243,207 | A→G | W33R (TGG→CGG) | fadE ← | acyl‑CoA dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 272,712 | (G)5→6 | intergenic (+58/‑135) | eyeA → / → ykfC | CP4‑6 prophage; small RNA EyeA/CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 281,529 | T→C | H152R (CAC→CGC) | yagA ← | CP4‑6 prophage; integrase core domain‑containing protein YagA |
| RA | 325,411 | A→G | intergenic (‑47/+166) | ykgH ← / ← betA | uncharacterized protein YkgH/choline dehydrogenase |
| RA | 331,199 | A→G | G579G (GGA→GGG) | betT → | choline:H(+) symporter |
| RA | 352,317 | A→C | D368A (GAC→GCC) | prpD → | 2‑methylcitrate dehydratase |
| RA | 355,454 | G→A | G178D (GGC→GAC) | codB → | cytosine transporter |
| RA | 375,420 | C→T | intergenic (+539/‑39) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 388,948 | A→G | R260R (CGT→CGC) | hemB ← | porphobilinogen synthase |
| RA | 400,486 | A→G | R146R (CGT→CGC) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 413,449 | A→G | F769L (TTC→CTC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 422,427 | (C)5→4 | intergenic (+68/‑91) | proY → / → malZ | putative transporter ProY/maltodextrin glucosidase |
| RA | 453,249 | A→G | G99G (GGT→GGC) | ampG ← | muropeptide:H(+) symporter |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 534,368 | T→C | R151R (CGT→CGC) | gcl → | glyoxylate carboligase |
| RA | 538,610 | G→A | A326A (GCG→GCA) | ybbW → | putative allantoin transporter |
| RA | 545,990 | T→C | Q125R (CAG→CGG) | allD ← | ureidoglycolate dehydrogenase |
| RA | 592,390 | A→G | S263S (AGT→AGC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 602,962 | T→C | V335A (GTC→GCC) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 617,433 | T→C | S1093P (TCG→CCG) | entF → | apo‑serine activating enzyme |
| RA | 640,591 | A→G | Y280C (TAC→TGC) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
| RA | 640,716 | A→G | T322A (ACC→GCC) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
| RA | 645,367 | A→G | M405T (ATG→ACG) | citT ← | citrate:succinate antiporter |
| RA | 657,830 | T→C | T37A (ACG→GCG) | crcB ← | F(‑) channel |
| RA | 669,978 | G→A | P199S (CCG→TCG) | nadD ← | nicotinate‑mononucleotide adenylyltransferase |
| RA | 679,673 | A→G | T56A (ACT→GCT) | ybeU → | DUF1266 domain‑containing protein YbeU |
| RA | 685,941 | (C)6→7 | coding (729/741 nt) | gltJ ← | glutamate/aspartate ABC transporter membrane subunit GltJ |
| RA | 689,053 | A→G | intergenic (‑40/+290) | insH‑3 ← / ← lnt | IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase |
| RA | 710,861 | A→G | intergenic (‑136/+74) | uof ← / ← fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| RA | 717,125 | (G)6→8 | coding (1141/1320 nt) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 721,836 | C→T | G860E (GGG→GAG) | kdpD ← | sensory histidine kinase KdpD |
| RA | 757,649 | C→T | F581F (TTC→TTT) | sdhA → | succinate:quinone oxidoreductase, FAD binding protein |
| RA | 771,282 | A→G | intergenic (+671/‑176) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 789,358 | C→T | V208I (GTC→ATC) | galK ← | galactokinase |
| RA | 825,051 | G→A | A353V (GCC→GTC) | ybhR ← | putative ABC exporter membrane subunit YbhR |
| RA | 832,736 | A→G | M72T (ATG→ACG) | ybiA ← | N‑glycosidase YbiA |
| RA | 843,979 | A→G | L501P (CTA→CCA) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 856,822 | (GC)5→4 | coding (860‑861/1593 nt) | ybiT → | ABC transporter ATP‑binding protein YbiT |
| RA | 859,010 | T→C | I18V (ATC→GTC) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 866,902 | T→C | L112P (CTG→CCG) | iaaA → | isoaspartyl dipeptidase proenzyme |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 871,743 | A→G | G259G (GGA→GGG) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 910,426 | A→G | C208C (TGT→TGC) | poxB ← | pyruvate oxidase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 950,957 | T→C | T42A (ACC→GCC) | pflA ← | pyruvate formate‑lyase activating enzyme |
| RA | 961,476 | T→C | R92R (CGT→CGC) | cmk → | cytidylate kinase |
| RA | 975,737 | A→G | D39G (GAC→GGC) | mukE → | chromosome partitioning protein MukE |
| RA | 977,713 | A→G | Q463R (CAG→CGG) | mukB → | chromosome partitioning protein MukB |
| RA | 981,850 | (G)6→5 | coding (804/1848 nt) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,048,572 | G→A | G40G (GGC→GGT) | gfcC ← | capsule biosynthesis GfcC family protein |
| RA | 1,074,174 | A→G | intergenic (‑163/‑68) | rutA ← / → rutR | pyrimidine oxygenase/DNA‑binding transcriptional dual regulator RutR |
| RA | 1,081,596 | T→C | pseudogene (241/830 nt) | efeU → | inactive ferrous iron permease EfeU, N‑terminal fragment |
| RA | 1,104,948 | (T)8→9 | intergenic (+46/‑13) | csgA → / → csgC | curlin, major subunit/inhibitor of CsgA amyloid formation |
| RA | 1,105,994 | G→A | D59N (GAT→AAT) | ymdB → | 2'‑O‑acetyl‑ADP‑ribose deacetylase, regulator of RNase III activity |
| RA | 1,108,666 | A→G | G92G (GGT→GGC) | opgC ← | protein required for succinyl modification of osmoregulated periplasmic glucans |
| RA | 1,113,194 | Δ2 bp | coding (2332‑2333/2544 nt) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,148,066 | C→T | A149V (GCC→GTC) | plsX → | putative phosphate acyltransferase |
| RA | 1,153,353 | A→G | A18A (GCA→GCG) | pabC → | aminodeoxychorismate lyase |
| RA | 1,155,557 | T→C | V145A (GTT→GCT) | tmk → | hypothetical protein |
| RA | 1,170,791 | A→G | R1058R (CGT→CGC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,172,093 | A→G | R624R (CGT→CGC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,185,933 | C→T | G30G (GGC→GGT) | pepT → | peptidase T |
| 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 | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,230,806 | A→G | T14A (ACT→GCT) | umuD → | DNA polymerase V protein UmuD |
| RA | 1,252,660 | T→C | V532A (GTT→GCT) | dhaR → | DNA‑binding transcriptional dual regulator DhaR |
| RA | 1,262,453 | A→G | V142A (GTT→GCT) | ispE ← | 4‑(cytidine 5'‑diphospho)‑2‑C‑methyl‑D‑erythritol kinase |
| RA | 1,280,561 | Δ1 bp | coding (698/3744 nt) | narG → | nitrate reductase A subunit alpha |
| RA | 1,298,105 | A→G | V6A (GTC→GCC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,301,759 | T→C | V193A (GTG→GCG) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,346,840 | (T)8→7 | coding (45/105 nt) | ymiB → | putative protein YmiB |
| RA | 1,365,076 | A→G | N282S (AAC→AGC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,394,303 | A→G | E359E (GAA→GAG) | mppA → | murein tripeptide ABC transporter periplasmic binding protein |
| RA | 1,440,091 | A→G | Y232H (TAC→CAC) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,444,892 | A→G | G614G (GGA→GGG) | ydbH → | PF11739 family protein YdbH |
| RA | 1,453,575 | T→C | H23R (CAC→CGC) | paaZ ← | oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,460,012 | T→C | V320A (GTT→GCT) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase |
| RA | 1,464,032 | A→G | N165S (AAC→AGC) | paaX → | DNA‑binding transcriptional repressor PaaX |
| RA | 1,474,941 | T→C | W241R (TGG→CGG) | pdxI → | pyridoxine 4‑dehydrogenase |
| RA | 1,504,220 | A→G | K168K (AAA→AAG) | insQ → | putative insertion element transposase InsQ |
| RA | 1,518,956 | G→A | intergenic (‑110/‑71) | mnaT ← / → curA | L‑amino acid N‑acyltransferase/NADPH‑dependent curcumin/dihydrocurcumin reductase |
| RA | 1,521,536 | A→G | G510G (GGT→GGC) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,525,336 | (G)5→6 | coding (645/1500 nt) | ansP ← | L‑asparagine transporter |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,555,703 | G→A | intergenic (‑34/+123) | maeA ← / ← sra | malate dehydrogenase, NAD‑requiring/30S ribosomal subunit protein S22 |
| RA | 1,558,766 | T→C | K84K (AAA→AAG) | ddpD ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD |
| RA | 1,565,696 | (A)7→6 | coding (38/2400 nt) | dosP ← | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| RA | 1,570,600 | T→C | intergenic (‑111/+45) | gadC ← / ← gadB | L‑glutamate:4‑aminobutyrate antiporter/glutamate decarboxylase B |
| RA | 1,594,047 | T→C | pseudogene (4040/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,642,961 | T→C | Y94C (TAC→TGC) | ydfT ← | Qin prophage; putative antitermination protein Q |
| RA | 1,661,680 | G→A | W375* (TGG→TGA) | ynfF → | putative selenate reductase YnfF |
| RA | 1,666,271 | T→C | G319G (GGT→GGC) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,680,369 | T→C | G271G (GGT→GGC) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,682,372 | T→C | S72P (TCT→CCT) | rstA → | DNA‑binding transcriptional regulator RstA |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,707,905 | +C | coding (987/2223 nt) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,714,914 | G→A | A180T (GCA→ACA) | gstA → | glutathione S‑transferase GstA |
| RA | 1,733,200 | A→G | T1372A (ACG→GCG) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,760,153 | T→C | H124R (CAC→CGC) | sufS ← | L‑cysteine desulfurase |
| RA | 1,764,553 | T→C | intergenic (‑167/+160) | sufA ← / ← rydB | iron‑sulfur cluster insertion protein SufA/small regulatory RNA RydB |
| RA | 1,765,674 | (C)5→6 | coding (3012/3057 nt) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,766,131 | T→C | N852S (AAC→AGC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,770,856 | (T)6→5 | coding (242/357 nt) | ydiL → | DUF1870 domain‑containing protein YdiL |
| RA | 1,806,042 | (C)6→7 | coding (42/759 nt) | ydiY ← | acid‑inducible putative outer membrane protein YdiY |
| RA | 1,818,550 | (C)7→8 | intergenic (‑50/+55) | chbF ← / ← chbR | monoacetylchitobiose‑6‑phosphate hydrolase/DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,828,529 | T→C | G402G (GGA→GGG) | astD ← | aldehyde dehydrogenase |
| RA | 1,842,809 | (T)5→6 | coding (439/1344 nt) | gdhA → | glutamate dehydrogenase |
| RA | 1,855,756 | (T)7→8 | coding (216/981 nt) | ydjG ← | NADH‑dependent methylglyoxal reductase |
| RA | 1,858,955 | (C)5→4 | coding (1275/1380 nt) | ydjK ← | putative transporter YdjK |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,890,374 | A→C | G53G (GGT→GGG) | yeaY ← | Slp family lipoprotein YeaY |
| RA | 1,900,027 | G→A | intergenic (+2/+2) | pdeD → / ← yoaE | putative c‑di‑GMP phosphodiesterase PdeD/putative inner membrane protein |
| RA | 1,912,078 | A→G | S167P (TCC→CCC) | htpX ← | zinc dependent endoprotease |
| RA | 1,957,020 | G→A | intergenic (‑13/+12) | torZ ← / ← torY | trimethylamine N‑oxide reductase 2/cytochrome c quinol dehydrogenase TorY |
| RA | 1,957,999 | A→G | M45T (ATG→ACG) | torY ← | cytochrome c quinol dehydrogenase TorY |
| RA | 1,965,121 | T→C | G357G (GGA→GGG) | flhB ← | flagellar biosynthesis protein FlhB |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,022,686 | T→C | L24P (CTA→CCA) | fliQ → | flagellar biosynthesis protein FliQ |
| RA | 2,023,730 | A→G | intergenic (+52/‑238) | fliR → / → rcsA | flagellar biosynthesis protein FliR/DNA‑binding transcriptional activator RcsA |
| RA | 2,027,131 | T→C | H296R (CAT→CGT) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,028,495 | A→G | V291A (GTG→GCG) | yedI ← | conserved inner membrane protein YedI |
| RA | 2,043,483 | (G)5→6 | noncoding (75/90 nt) | serU ← | tRNA‑Ser |
| RA | 2,077,169 | T→C | W20R (TGG→CGG) | cbeA → | CP4‑44 prophage; cytoskeleton bundling‑enhancing antitoxin CbeA |
| RA | 2,077,174 | G→A | G21G (GGG→GGA) | cbeA → | CP4‑44 prophage; cytoskeleton bundling‑enhancing antitoxin CbeA |
| RA | 2,078,709 | G→A | A45A (GCG→GCA) | yoeF → | CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,089,275 | T→C | H64R (CAC→CGC) | yoeB ← | ribosome‑dependent mRNA interferase toxin YoeB |
| RA | 2,111,569 | T→C | E136E (GAA→GAG) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,153,889 | C→T | intergenic (+108/‑127) | sibB → / → mdtA | small RNA SibB/multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,173,803 | T→C | pseudogene (476/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,229,182 | (G)5→4 | intergenic (+117/+256) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,272,277 | T→C | W518R (TGG→CGG) | pdeN → | putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,302,553 | A→G | C67C (TGT→TGC) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,310,285 | A→G | S41P (TCT→CCT) | ada ← | DNA‑binding transcriptional dual regulator/DNA repair protein Ada |
| RA | 2,323,749 | T→C | G101G (GGT→GGC) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| RA | 2,326,589 | A→G | T161A (ACC→GCC) | atoB → | acetyl‑CoA acetyltransferase |
| RA | 2,330,784 | T→C | pseudogene (3619/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,342,454 | T→C | T572T (ACA→ACG) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,399,675 | T→C | Y164C (TAC→TGC) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,405,158 | (A)8→7 | intergenic (‑86/+545) | nuoA ← / ← lrhA | NADH:quinone oxidoreductase subunit A/DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,428,805 | G→A | F478F (TTC→TTT) | purF ← | amidophosphoribosyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,453,540 | T→C | pseudogene (1462/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,479,931 | T→C | L244L (TTG→CTG) | dsdA → | D‑serine ammonia‑lyase |
| RA | 2,490,509 | T→C | D481G (GAC→GGC) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,502,361 | A→G | C709R (TGC→CGC) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,509,057 | G→A | P124S (CCG→TCG) | glk ← | glucokinase |
| RA | 2,511,730 | A→C | V326G (GTG→GGG) | mntH ← | Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
| RA | 2,524,660 | A→T | H73Q (CAT→CAA) | xapA ← | xanthosine phosphorylase |
| RA | 2,527,795 | T→C | F284L (TTC→CTC) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,581,601 | G→A | A656T (GCA→ACA) | tktB → | transketolase 2 |
| RA | 2,591,633 | A→G | T9T (ACA→ACG) | dapE → | succinyl‑diaminopimelate desuccinylase |
| RA | 2,601,506 | C→T | S102S (AGC→AGT) | hyfA → | hydrogenase 4 component A |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,602,306 | T→C | A163A (GCT→GCC) | hyfB → | hydrogenase 4 component B |
| RA | 2,607,878 | A→G | N321S (AAC→AGC) | hyfF → | hydrogenase 4 component F |
| RA | 2,610,630 | T→C | V156A (GTC→GCC) | hyfH → | hydrogenase 4 component H |
| RA | 2,656,200 | A→G | G53G (GGT→GGC) | pepB ← | aminopeptidase B |
| RA | 2,692,928 | C→T | A872A (GCG→GCA) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,709,188 | T→C | T73A (ACA→GCA) | rseA ← | anti‑sigma factor |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| RA | 2,726,164 | A→G | noncoding (25/120 nt) | rrfG ← | 5S ribosomal RNA |
| RA | 2,734,543 | (C)8→10 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,749,819 | T→C | V349A (GTG→GCG) | yfjD → | putative inner membrane protein |
| RA | 2,777,401 | T→C | V96A (GTA→GCA) | yfjZ → | CP4‑57 prophage; putative antitoxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,779,192 | T→C | T1179A (ACC→GCC) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,786,387 | G→A | intergenic (‑550/‑10) | ileY ← / → ygaQ | tRNA‑Ile/putative uncharacterized protein YgaQ |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,832,101 | T→C | V63V (GTA→GTG) | norR ← | DNA‑binding transcriptional dual regulator NorR |
| RA | 2,845,589 | T→C | T295A (ACC→GCC) | hycE ← | formate hydrogenlyase subunit HycE |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,863,999 | T→C | V136A (GTG→GCG) | ygbL → | putative 3‑oxo‑tetronate 4‑phosphate decarboxylase YgbL |
| RA | 2,891,531 | T→C | E123G (GAA→GGA) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,906,062 | A→C | T118P (ACC→CCC) | ygcG → | protein YgcG |
| RA | 2,927,714 | T→C | intergenic (+42/‑515) | ppnN → / → sdaC | nucleotide 5'‑monophosphate nucleosidase/serine:H(+) symporter SdaC |
| RA | 2,937,272 | T→C | R563R (CGT→CGC) | fucI → | L‑fucose isomerase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,958,537 | A→G | G116G (GGT→GGC) | ptrA ← | protease 3 |
| RA | 2,988,044 | A→G | Y170C (TAT→TGT) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | 2,999,680 | (G)7→9 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,004,053 | A→G | A578A (GCT→GCC) | ygeV ← | putative sigma(54)‑dependent transcriptional regulator YgeV |
| RA | 3,011,406 | T→C | V460A (GTG→GCG) | hyuA → | phenylhydantoinase |
| RA | 3,046,876 | T→C | G722G (GGA→GGG) | gcvP ← | glycine decarboxylase |
| RA | 3,056,324 | T→C | Y28Y (TAT→TAC) | fau → | putative 5‑formyltetrahydrofolate cyclo‑ligase |
| RA | 3,058,859 | T→C | Y156C (TAC→TGC) | rpiA ← | ribose‑5‑phosphate isomerase A |
| RA | 3,060,042 | T→C | V97A (GTC→GCC) | argP → | DNA‑binding transcriptional dual regulator ArgP |
| RA | 3,063,040 | G→T | E18D (GAG→GAT) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,085,503 | A→G | S137P (TCC→CCC) | speA ← | arginine decarboxylase, biosynthetic |
| RA | 3,085,818 | C→T | A32T (GCC→ACC) | speA ← | arginine decarboxylase, biosynthetic |
| RA | 3,089,017 | A→G | N245S (AAC→AGC) | galP → | galactose:H(+) symporter |
| RA | 3,111,797 | G→A | pseudogene (192/861 nt) | yghE ← | putative type II secretion system L‑type protein |
| RA | 3,141,483 | T→C | T503A (ACC→GCC) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,142,568 | T→C | H141R (CAC→CGC) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,146,549 | G→A | R63R (CGC→CGT) | yghW ← | DUF2623 domain‑containing protein YghW |
| RA | 3,192,444 | (T)7→8 | coding (237/630 nt) | yqiJ → | putative inner membrane protein |
| RA | 3,208,251 | G→A | P76P (CCG→CCA) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,232,156 | C→T | S164S (TCC→TCT) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,252,476 | T→C | I58T (ATC→ACC) | yhaH → | putative inner membrane protein |
| RA | 3,253,881 | (A)5→4 | coding (334/897 nt) | yhaJ ← | DNA‑binding transcriptional activator YhaJ |
| RA | 3,272,461 | T→C | A97A (GCA→GCG) | garR ← | tartronate semialdehyde reductase |
| RA | 3,289,657 | T→C | L282L (TTG→CTG) | yraJ → | putative fimbrial usher protein YraJ |
| RA | 3,310,823 | T→C | T116A (ACC→GCC) | pnp ← | polynucleotide phosphorylase |
| RA | 3,322,662 | (A)7→8 | intergenic (‑157/+71) | secG ← / ← glmM | Sec translocon subunit SecG/phosphoglucosamine mutase |
| RA | 3,324,546 | T→C | E122E (GAA→GAG) | folP ← | dihydropteroate synthase |
| RA | 3,327,342 | G→A | A108V (GCA→GTA) | rlmE ← | 23S rRNA 2'‑O‑ribose U2552 methyltransferase |
| RA | 3,333,218 | A→G | R78R (CGT→CGC) | rplU ← | 50S ribosomal subunit protein L21 |
| RA | 3,337,189 | T→C | D23G (GAC→GGC) | mlaB ← | intermembrane phospholipid transport system protein MlaB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,368,963 | G→A | intergenic (+9/+51) | yhcG → / ← yhcH | DUF1016 domain‑containing protein YhcG/DUF386 domain‑containing protein YhcH |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,392,260 | C→T | intergenic (‑232/+198) | tldD ← / ← yhdP | metalloprotease TldD/AsmA2 domain‑containing protein |
| RA | 3,396,892 | T→C | T302A (ACC→GCC) | rng ← | RNase G |
| RA | 3,457,801 | G→A | G475G (GGG→GGA) | gspD → | Type II secretion system protein GspD |
| RA | 3,462,961 | T→C | V13A (GTA→GCA) | gspK → | Type II secretion system protein GspK |
| RA | 3,474,354 | T→C | I67V (ATC→GTC) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,484,088 | (C)6→7 | coding (887/1023 nt) | yheT → | putative hydrolase YheT |
| RA | 3,489,320 | A→G | G287G (GGT→GGC) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,511,233 | G→A | P64S (CCG→TCG) | yhfY ← | conserved protein YhfY |
| RA | 3,541,397 | T→C | F331L (TTC→CTC) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,544,403 | T→C | T148A (ACC→GCC) | bioH ← | pimeloyl‑acyl carrier protein methyl ester esterase |
| RA | 3,547,748 | G→A | G397D (GGC→GAC) | gntT → | high‑affinity gluconate transporter |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,563,647 | T→C | intergenic (+129/+77) | glpD → / ← yzgL | aerobic glycerol 3‑phosphate dehydrogenase/putative uncharacterized protein YzgL |
| RA | 3,565,249 | T→C | M445V (ATG→GTG) | glgP ← | glycogen phosphorylase |
| RA | 3,629,661 | A→C | R314R (CGT→CGG) | yhiI ← | putative membrane fusion protein YhiI |
| RA | 3,639,721 | A→G | intergenic (‑1/‑390) | uspB ← / → uspA | putative universal stress (ethanol tolerance) protein B/universal stress global stress response regulator |
| RA | 3,664,804 | A→G | intergenic (‑186/‑60) | gadW ← / → gadY | DNA‑binding transcriptional dual regulator GadW/small regulatory RNA GadY |
| RA | 3,670,288 | T→C | L233L (TTG→CTG) | treF → | cytoplasmic trehalase |
| RA | 3,673,175 | G→A | R254R (CGG→CGA) | yhjC → | putative DNA‑binding transcriptional regulator YhjC |
| RA | 3,684,903 | T→C | N239S (AAC→AGC) | pdeK ← | putative c‑di‑GMP phosphodiesterase PdeK |
| RA | 3,708,506 | C→T | intergenic (‑801/+110) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,757,729 | A→G | R33R (CGT→CGC) | yiaY ← | L‑threonine dehydrogenase |
| RA | 3,782,970 | G→A | A231V (GCG→GTG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase |
| RA | 3,784,960 | A→T | I19N (ATC→AAC) | yibN ← | putative sulfurtransferase YibN |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,903,168 | G→A | H178H (CAC→CAT) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,917,862 | G→A | A135V (GCC→GTC) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,927,392 | A→G | T80A (ACC→GCC) | asnA → | asparagine synthetase A |
| RA | 3,940,176 | A→G | V146A (GTG→GCG) | hsrA ← | putative transporter HsrA |
| RA | 3,946,671 | A→G | intergenic (+64/‑29) | rrlC → / → rrfC | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 3,949,385 | A→G | G195G (GGT→GGC) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,951,372 | A→G | pseudogene (813/1645 nt) | ilvG → | acetolactate synthase II subunit IlvG, N‑terminal fragment (pseudogene) |
| RA | 4,045,212 | T→C | Y338Y (TAT→TAC) | yihF → | uncharacterized protein YihF |
| RA | 4,045,596 | A→G | E466E (GAA→GAG) | yihF → | uncharacterized protein YihF |
| RA | 4,103,076 | T→C | G85G (GGT→GGC) | yiiM → | 2‑amino‑6‑N‑hydroxylaminopurine resistance protein |
| RA | 4,108,324 | T→C | V258A (GTG→GCG) | pfkA → | 6‑phosphofructokinase I |
| RA | 4,117,507 | C→T | G195D (GGC→GAC) | glpF ← | glycerol facilitator |
| RA | 4,153,570 | G→A | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,178,657 | A→G | T71A (ACC→GCC) | rplK → | 50S ribosomal subunit protein L11 |
| RA | 4,258,838 | A→G | Q366R (CAG→CGG) | dinF → | DNA damage‑inducible protein F |
| RA | 4,285,630 | T→C | N581S (AAC→AGC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,292,836 | A→G | Y442C (TAC→TGC) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,299,189 | G→A | P60S (CCG→TCG) | fdhF ← | formate dehydrogenase H |
| RA | 4,306,256 | A→G | G114G (GGT→GGC) | yjcS ← | alkyl sulfatase |
| RA | 4,353,616 | A→G | L368L (TTG→CTG) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,359,120 | A→G | G304G (GGT→GGC) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,370,118 | C→T | G99S (GGT→AGT) | yjeH ← | L‑methionine/branched chain amino acid exporter |
| RA | 4,376,294 | A→G | intergenic (+29/‑23) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,377,330 | G→A | C131C (TGC→TGT) | blc ← | outer membrane lipoprotein Blc |
| RA | 4,407,624 | A→G | Y324C (TAC→TGC) | rnr → | RNase R |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,472,524 | A→G | C4R (TGT→CGT) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,483,608 | A→G | V77A (GTC→GCC) | valS ← | valine‑‑tRNA ligase |
| RA | 4,486,769 | T→C | R184R (CGT→CGC) | lptF → | lipopolysaccharide transport system protein LptF |
| RA | 4,487,609 | A→G | T98A (ACC→GCC) | lptG → | lipopolysaccharide transport system protein LptG |
| RA | 4,509,831 | G→A | pseudogene (28/330 nt) | yjhV → | KpLE2 phage‑like element; putative uncharacterized protein YjhV |
| RA | 4,523,851 | C→T | A82T (GCG→ACG) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | 4,527,408 | T→C | T44A (ACG→GCG) | sgcE ← | KpLE2 phage‑like element; putative epimerase SgcE |
| RA | 4,537,169 | A→G | D142D (GAT→GAC) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,543,190 | A→G | T26A (ACG→GCG) | fimA → | type 1 fimbriae major subunit |
| RA | 4,560,459 | (C)5→4 | coding (222/684 nt) | yjiH ← | Gate family protein YjiH |
| RA | 4,565,730 | T→C | T41A (ACC→GCC) | yjiM ← | putative dehydratase subunit |
| RA | 4,568,337 | A→G | G61G (GGT→GGC) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 4,586,594 | (G)6→7 | coding (168/3513 nt) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 433032 | 433127 | 96 | 6 [5] | [5] 6 | nrdR | NrdR transcriptional repressor |
| * | * | ÷ | NC_000913 | 1196276 | 1211423 | 15148 | 7 [5] | [5] 6 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423794–3424230 | 3424523–3424240 | 11–730 | 6 [5] | [2] 6 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3945908–3946225 | 3946500–3946231 | 7–593 | 6 [3] | [5] 8 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 4 (0.140) | 3/204 | 3.0 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.150) | 4/192 | 2.5 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 43 (1.120) | 34/270 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 75 (1.890) | 73 (1.860) | 47/276 | 0.0 | 65.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.080) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 60 (1.510) | 41/278 | 0.1 | 96.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||