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 | 1,875 | A→G | V513V (GTA→GTG) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 7,390 | C→T | L190L (CTG→CTA) | yaaJ ← | putative transporter YaaJ |
| RA | 70,424 | A→G | Y13C (TAC→TGC) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 80,625 | A→G | R80R (CGT→CGC) | leuC ← | 3‑isopropylmalate dehydratase subunit LeuC |
| RA | 112,873 | A→G | V116A (GTA→GCA) | coaE ← | dephospho‑CoA kinase |
| RA | 114,907 | G→A | T273I (ACA→ATA) | hofC ← | inner membrane protein HofC |
| RA | 120,112 | A→G | T278A (ACG→GCG) | ampE → | protein AmpE |
| RA | 140,924 | C→T | G101D (GGC→GAC) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 189,159 | A→G | G116G (GGT→GGC) | map ← | methionine aminopeptidase |
| RA | 202,893 | G→A | G112S (GGC→AGC) | lpxA → | UDP‑N‑acetylglucosamine acyltransferase |
| RA | 205,353 | G→A | L76L (CTG→CTA) | dnaE → | DNA polymerase III subunit alpha |
| RA | 219,654 | A→G | G114G (GGT→GGC) | rcsF ← | outer membrane lipoprotein RcsF |
| RA | 234,139 | (A)7→8 | coding (644/756 nt) | gloB ← | hydroxyacylglutathione hydrolase GloB |
| RA | 240,779 | G→A | S146N (AGC→AAC) | ivy → | periplasmic chaperone, inhibitor of vertebrate C‑type lysozyme |
| RA | 256,049 | C→T | P25S (CCT→TCT) | gpt → | xanthine‑guanine phsophoribosyltransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 272,498 | T→C | intergenic (+308/‑82) | insN → / → eyeA | CP4‑6 prophage; IS911A regulator fragment/CP4‑6 prophage; small RNA EyeA |
| RA | 285,647 | (G)6→7 | coding (253/1383 nt) | yagG → | putative D‑xylonate transporter YagG |
| RA | 291,343 | C→T | A2T (GCT→ACT) | insA‑3 ← | IS1 protein InsA |
| RA | 294,752 | (T)7→6 | coding (48/855 nt) | yagM ← | CP4‑6 prophage; protein YagM |
| RA | 297,827 | T→C | E300E (GAA→GAG) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 310,057 | (G)6→7 | intergenic (‑31/+27) | ecpB ← / ← ecpA | putative fimbrial chaperone EcpB/common pilus major subunit |
| RA | 316,612 | A→G | pseudogene (525/687 nt) | ykgA ← | putative DNA‑binding transcriptional regulator YkgA |
| RA | 329,082 | C→T | E85K (GAG→AAG) | betI ← | DNA‑binding transcriptional repressor BetI |
| RA | 330,537 | T→C | F359L (TTT→CTT) | betT → | choline:H(+) symporter |
| RA | 334,301 | T→C | T45A (ACG→GCG) | yahB ← | putative LysR‑type DNA‑binding transcriptional regulator YahB |
| RA | 354,768 | A→G | intergenic (+176/‑154) | prpE → / → codB | propionyl‑CoA synthetase/cytosine transporter |
| RA | 364,824 | G→A | T494T (ACC→ACT) | lacZ ← | beta‑galactosidase |
| RA | 371,379 | T→C | G47G (GGT→GGC) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 379,940 | A→G | intergenic (‑59/+129) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 391,703 | (G)6→7 | pseudogene (1453/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 421,903 | C→T | G306G (GGC→GGT) | proY → | putative transporter ProY |
| RA | 422,427 | (C)5→7 | intergenic (+68/‑91) | proY → / → malZ | putative transporter ProY/maltodextrin glucosidase |
| RA | 426,301 | C→T | L55L (CTC→CTT) | tgt → | tRNA‑guanine transglycosylase |
| RA | 466,851 | G→A | G154G (GGC→GGT) | ybaE ← | putative protein YbaE |
| RA | 474,447 | A→G | F239L (TTT→CTT) | tesB ← | acyl‑CoA thioesterase II |
| RA | 503,439 | A→G | intergenic (‑201/+37) | ybaL ← / ← fsr | putative transporter YbaL/fosmidomycin efflux pump |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 530,394 | T→C | Y278C (TAT→TGT) | selU ← | tRNA 2‑selenouridine synthase |
| RA | 592,150 | T→G | K343N (AAA→AAC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 595,667 | A→G | D23G (GAT→GGT) | cusC → | copper/silver export system outer membrane channel |
| RA | 627,410 | C→T | I447I (ATC→ATT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| RA | 640,890 | C→T | H380Y (CAC→TAC) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
| RA | 649,194 | A→G | G126G (GGT→GGC) | citF ← | citrate lyase alpha subunit |
| RA | 657,549 | (T)8→7 | intergenic (+48/+6) | cspE → / ← crcB | transcription antiterminator and regulator of RNA stability/F(‑) channel |
| RA | 660,412 | T→C | intergenic (‑196/+13) | lipA ← / ← ybeF | lipoyl synthase/putative LysR‑type DNA‑binding transcriptional regulator YbeF |
| RA | 684,415 | T→C | intergenic (‑3/+115) | rihA ← / ← gltL | pyrimidine‑specific ribonucleoside hydrolase RihA/glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 691,798 | T→G | intergenic (‑14/+76) | ybeX ← / ← ybeY | CorC‑HlyC family protein YbeX/endoribonuclease YbeY |
| RA | 692,306 | A→G | C12C (TGT→TGC) | ybeY ← | endoribonuclease YbeY |
| RA | 710,005 | A→G | V72V (GTA→GTG) | chiQ → | lipoprotein ChiQ |
| RA | 715,004 | A→G | T483A (ACT→GCT) | pgm → | phosphoglucomutase |
| RA | 722,788 | A→G | F543L (TTT→CTT) | kdpD ← | sensory histidine kinase KdpD |
| RA | 742,314 | (C)5→4 | coding (243/1482 nt) | dtpD ← | dipeptide:H(+) symporter DtpD |
| RA | 771,858 | C→T | A134V (GCG→GTG) | cydA → | cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 784,802 | T→C | T8A (ACG→GCG) | zitB ← | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter |
| RA | 814,014 | C→T | V163V (GTC→GTT) | uvrB → | excision nuclease subunit B |
| RA | 829,181 | A→G | Y264Y (TAT→TAC) | ybhG ← | HlyD_D23 family protein YbhG |
| RA | 838,323 | G→A | P45L (CCC→CTC) | ybiI ← | zinc finger domain‑containing protein YbiI |
| RA | 858,438 | T→C | A208A (GCA→GCG) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 862,465 | T→A | I48F (ATC→TTC) | ybiW ← | putative pyruvate formate lyase |
| RA | 886,100 | T→C | D11G (GAT→GGT) | ybjI ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 915,319 | (A)7→8 | intergenic (‑462/+33) | lysO ← / ← aqpZ | L‑lysine exporter/water channel AqpZ |
| RA | 929,457 | A→G | N502N (AAT→AAC) | cydD ← | glutathione/L‑cysteine ABC exporter subunit CydD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 934,388 | C→T | P389S (CCT→TCT) | ftsK → | cell division DNA translocase FtsK |
| RA | 943,761 | T→C | Y116Y (TAT→TAC) | dmsB → | dimethyl sulfoxide reductase subunit B |
| RA | 1,010,725 | A→G | L254L (TTA→TTG) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,016,702 | A→G | V533A (GTG→GCG) | ycbZ ← | putative ATP‑dependent protease YcbZ |
| RA | 1,045,000 | C→T | T268T (ACG→ACA) | gfcE ← | putative exopolysaccharide export lipoprotein GfcE |
| RA | 1,048,903 | T→C | T144A (ACT→GCT) | gfcB ← | lipoprotein GfcB |
| RA | 1,054,270 | C→T | A637T (GCC→ACC) | torS ← | sensory histidine kinase TorS |
| RA | 1,057,108 | A→G | E283G (GAA→GGA) | torT → | periplasmic trimethylamine‑N‑oxide binding protein |
| RA | 1,087,643 | A→G | A68A (GCT→GCC) | pgaC ← | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,206,680 | A→G | pseudogene (550/792 nt) | jayE → | e14 prophage; putative protein JayE |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,215,983 | A→G | E65E (GAA→GAG) | ycgZ → | putative two‑component system connector protein YcgZ |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,222,729 | A→G | V87A (GTT→GCT) | ymgG ← | PF13488 family protein YmgG |
| RA | 1,227,593 | (G)6→7 | intergenic (‑121/‑88) | pliG ← / → ycgL | inhibitor of g‑type lysozyme/PF05166 family protein YcgL |
| RA | 1,237,673 | (G)5→6 | coding (103/1299 nt) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,266,239 | A→G | D49G (GAC→GGC) | prmC → | protein‑(glutamine‑N(5)) methyltransferase |
| RA | 1,269,425 | (C)5→4 | intergenic (+36/+278) | rdlA → / ← ldrB | putative antisense RNA regulator of LdrA/small toxic polypeptide LdrB |
| RA | 1,296,183 | A→G | C647R (TGT→CGT) | adhE ← | aldehyde‑alcohol dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,326,396 | A→G | T551A (ACA→GCA) | yciQ → | DUF2207 domain‑containing protein YciQ |
| RA | 1,331,358 | A→G | D104G (GAC→GGC) | topA → | DNA topoisomerase 1 |
| RA | 1,336,451 | A→G | T207T (ACA→ACG) | acnA → | aconitate hydratase 1 |
| RA | 1,351,196 | (G)7→6 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,357,671 | T→G | intergenic (‑3/+131) | ymjA ← / ← puuP | DUF2543 domain‑containing protein YmjA/putrescine:H(+) symporter PuuP |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,417,546 | (T)8→7 | coding (218/276 nt) | racC ← | Rac prophage; protein RacC |
| RA | 1,420,131 | T→C | Q37Q (CAA→CAG) | racR ← | Rac prophage; DNA‑binding transcriptional repressor RacR |
| RA | 1,423,575 | A→G | pseudogene (231/300 nt) N59S (AAC→AGC) |
rzpR → rzoR → |
Rac prophage; putative endopeptidase RzpR Rac prophage; putative lipoprotein |
| RA | 1,434,347 | A→G | A20A (GCT→GCC) | ynaM ← | Rac prophage; protein YnaM |
| RA | 1,440,632 | T→C | T51T (ACA→ACG) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,485,031 | T→C | G657G (GGT→GGC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,488,314 | A→G | N28S (AAC→AGC) | aldA → | aldehyde dehydrogenase A |
| RA | 1,491,291 | A→G | V130V (GTA→GTG) | cybB → | cytochrome b561 |
| RA | 1,535,988 | C→T | A210A (GCG→GCA) | narV ← | nitrate reductase Z subunit gamma |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,564,808 | T→C | H309R (CAC→CGC) | dosP ← | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| RA | 1,587,901 | G→A | I132I (ATC→ATT) | ydeR ← | putative fimbrial protein YdeR |
| RA | 1,591,925 | T→C | R84R (AGA→AGG) | hipA ← | serine/threonine kinase HipA |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,596,091 | A→G | pseudogene (1996/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→9 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,601,771 | A→G | E94E (GAA→GAG) | lsrA → | Autoinducer‑2 ABC transporter ATP binding subunit |
| RA | 1,632,303 | (T)6→5 | intergenic (‑18/‑587) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,671,708 | Δ1 bp | intergenic (+24/‑69) | asr → / → ydgU | acid shock protein/uncharacterized protein YdgU |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,705,751 | (T)6→5 | intergenic (+61/‑16) | ydgK → / → rsxA | conserved inner membrane protein YdgK/SoxR [2Fe‑2S] reducing system protein RsxA |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,714,584 | A→G | M70V (ATG→GTG) | gstA → | glutathione S‑transferase GstA |
| RA | 1,735,284 | T→C | intergenic (+34/‑94) | mepH → / → sodB | peptidoglycan DD‑endopeptidase MepH/superoxide dismutase (Fe) |
| RA | 1,738,197 | T→C | G118G (GGT→GGC) | purR → | DNA‑binding transcriptional repressor PurR |
| RA | 1,784,065 | G→A | V363V (GTG→GTA) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,799,072 | T→C | intergenic (‑130/+154) | pheS ← / ← pheM | phenylalanine‑‑tRNA ligase subunit alpha/pheST‑ihfA operon leader peptide |
| MC JC | 1,834,817 | (ATG)4→3 | coding (10‑12/708 nt) | ydjZ → | DedA family protein YdjZ |
| RA | 1,849,930 | T→C | V365A (GTG→GCG) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,870,094 | T→C | R380R (CGT→CGC) | yeaH → | DUF444 domain‑containing protein YeaH |
| 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 | 1,892,882 | (C)6→7 | coding (354/1911 nt) | yoaA ← | putative 5' to 3' DNA helicase implicated in DNA repair |
| RA | 1,926,868 | G→A | R658C (CGC→TGC) | ptrB ← | oligopeptidase B |
| RA | 1,928,699 | A→G | G47G (GGT→GGC) | ptrB ← | oligopeptidase B |
| RA | 1,928,733 | A→G | V36A (GTC→GCC) | ptrB ← | oligopeptidase B |
| RA | 1,945,866 | T→C | E37E (GAA→GAG) | ruvA ← | Holliday junction branch migration complex subunit RuvA |
| RA | 1,947,257 | A→C | D40E (GAT→GAG) | ruvC ← | crossover junction endodeoxyribonuclease RuvC |
| RA | 1,955,459 | T→C | T517A (ACC→GCC) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,956,871 | G→A | A46V (GCG→GTG) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,974,960 | G→A | A122V (GCC→GTC) | cheA ← | chemotaxis protein CheA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,986,976 | T→C | F18L (TTT→CTT) | ftnB → | putative ferritin‑like protein |
| RA | 2,015,075 | T→C | F66L (TTT→CTT) | fliG → | flagellar motor switch protein FliG |
| RA | 2,017,886 | T→C | S445P (TCT→CCT) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,024,436 | C→T | Q157* (CAA→TAA) | rcsA → | DNA‑binding transcriptional activator RcsA |
| RA | 2,095,695 | T→C | C191R (TGC→CGC) | hisA → | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino]imidazole‑4‑ carboxamide isomerase |
| RA | 2,096,038 | G→A | W65* (TGG→TGA) | hisF → | imidazole glycerol phosphate synthase subunit HisF |
| RA | 2,096,351 | G→A | G170S (GGT→AGT) | hisF → | imidazole glycerol phosphate synthase subunit HisF |
| RA | 2,124,085 | T→C | T146A (ACC→GCC) | cpsB ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 2,127,723 | T→C | T198A (ACC→GCC) | gmd ← | GDP‑mannose 4,6‑dehydratase |
| RA | 2,135,234 | G→A | T140I (ACC→ATC) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,146,949 | T→C | I198V (ATA→GTA) | alkA ← | DNA‑3‑methyladenine glycosylase 2 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,187,323 | (G)5→6 | intergenic (+25/+57) | rcnB → / ← yehA | periplasmic protein involved in nickel/cobalt export/putative fimbrial adhesin YehA |
| RA | 2,197,183 | T→C | V237A (GTA→GCA) | yehF → | putative protein YehF |
| RA | 2,206,448 | A→G | M252V (ATG→GTG) | yehM → | putative YehN |
| RA | 2,224,365 | A→G | V169A (GTG→GCG) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,233,659 | C→T | F20F (TTC→TTT) | yeiS → | DUF2542 domain‑containing protein YeiS |
| RA | 2,234,448 | C→T | A139V (GCC→GTC) | preT → | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreT |
| RA | 2,291,359 | (T)5→6 | coding (1052/1053 nt) | ccmH ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmH |
| RA | 2,297,738 | T→C | K174K (AAA→AAG) | napC ← | periplasmic nitrate reductase cytochrome c protein |
| RA | 2,301,107 | T→C | V549V (GTA→GTG) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,312,343 | T→C | Y136C (TAC→TGC) | ompC ← | outer membrane porin C |
| RA | 2,362,013 | T→C | T67A (ACC→GCC) | yfaX ← | putative DNA‑binding transcriptional regulator YfaX |
| RA | 2,362,203 | T→C | E3E (GAA→GAG) | yfaX ← | putative DNA‑binding transcriptional regulator YfaX |
| RA | 2,378,828 | G→A | P144P (CCC→CCT) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| RA | 2,402,588 | T→C | T420A (ACC→GCC) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,415,078 | T→C | V111A (GTC→GCC) | pta → | phosphate acetyltransferase |
| RA | 2,432,681 | G→A | R88C (CGT→TGT) | folC ← | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase |
| RA | 2,442,660 | (C)5→6 | coding (897/2007 nt) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,456,619 | T→C | D65G (GAT→GGT) | sixA ← | phosphohistidine phosphatase |
| RA | 2,462,324 | T→C | F340S (TTC→TCC) | fadL → | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,464,242 | (T)6→7 | intergenic (+172/+10) | yfdF → / ← mlaA | protein YfdF/intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA |
| RA | 2,504,414 | T→C | E24E (GAA→GAG) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,510,853 | T→C | R408R (CGT→CGC) | yfeO → | putative transport protein YfeO |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,556,929 | T→C | V123V (GTA→GTG) | eutC ← | ethanolamine ammonia‑lyase subunit beta |
| RA | 2,570,274 | T→C | T22A (ACG→GCG) | eutJ ← | putative chaperonin, ethanolamine utilization protein |
| RA | 2,602,017 | (C)7→9 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,602,375 | +G | coding (558/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,638,026 | (C)6→5 | coding (627/1179 nt) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,638,481 | T→C | N58D (AAC→GAC) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,662,353 | A→G | intergenic (‑222/+230) | iscR ← / ← trmJ | DNA‑binding transcriptional dual regulator IscR/tRNA Cm32/Um32 methyltransferase |
| RA | 2,670,928 | T→C | C7C (TGT→TGC) | hcaC → | putative 3‑phenylpropionate/cinnamate dioxygenase ferredoxin subunit |
| RA | 2,710,742 | T→C | I108T (ATT→ACT) | nadB → | L‑aspartate oxidase |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| RA | 2,731,822 | T→C | K784K (AAA→AAG) | clpB ← | ClpB chaperone |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,740,857 | T→C | K98K (AAA→AAG) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,767,085 | G→A | T34T (ACG→ACA) | rnlB → | CP4‑57 prophage; antitoxin RnlB |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,926 | (C)6→7 | coding (828/1140 nt) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,877,685 | T→C | intergenic (+67/+884) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,878,876 | A→G | D299D (GAT→GAC) | cas1 ← | multifunctional nuclease Cas1 |
| RA | 2,892,952 | T→C | V99A (GTA→GCA) | ygcN → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 2,901,848 | (C)5→6 | coding (1257/1278 nt) | yqcE → | putative transport protein YqcE |
| RA | 2,903,363 | T→C | S490P (TCG→CCG) | ygcE → | putative sugar kinase YgcE |
| RA | 2,909,569 | C→T | G33D (GGC→GAC) | pyrG ← | CTP synthetase |
| RA | 2,910,165 | T→C | D174G (GAC→GGC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,920,251 | T→C | N166D (AAT→GAT) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,955,096 | T→C | E303G (GAA→GGA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,955,841 | T→C | T55A (ACC→GCC) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,970,436 | T→C | I6T (ATA→ACA) | ygdQ → | UPF0053 inner membrane protein YgdQ |
| RA | 2,973,182 | T→C | L227L (TTA→TTG) | lplT ← | lysophospholipid transporter |
| RA | 2,973,904 | A→G | F704S (TTT→TCT) | aas ← | acyltransferase |
| RA | 2,977,018 | T→C | G140G (GGT→GGC) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 2,989,323 | (A)8→7 | coding (20/483 nt) | yqeJ → | protein YqeJ |
| RA | 3,004,535 | C→T | A418T (GCC→ACC) | ygeV ← | putative sigma(54)‑dependent transcriptional regulator YgeV |
| RA | 3,006,380 | A→G | D40G (GAC→GGC) | ygeW → | putative carbamoyltransferase YgeW |
| RA | 3,026,179 | G→A | A138A (GCG→GCA) | guaD → | guanine deaminase |
| RA | 3,038,005 | T→C | G34G (GGA→GGG) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,043,737 | G→A | G26S (GGC→AGC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,045,063 | T→C | Y468H (TAC→CAC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,057,643 | T→C | K256K (AAA→AAG) | serA ← | phosphoglycerate dehydrogenase |
| RA | 3,066,127 | C→T | A442A (GCC→GCT) | scpC → | propionyl‑CoA:succinate CoA transferase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,068,406 | T→C | S135G (AGC→GGC) | argO ← | L‑arginine exporter |
| RA | 3,107,477 | T→C | D560G (GAT→GGT) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,122,917 | T→C | T297A (ACT→GCT) | glcB ← | malate synthase G |
| RA | 3,154,600 | T→C | T207A (ACT→GCT) | yqhC ← | DNA‑binding transcriptional activator YqhC |
| RA | 3,207,655 | C→T | G95G (GGC→GGT) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,230,399 | C→T | G504G (GGC→GGT) | ygjK → | glycoside hydrolase |
| RA | 3,266,958 | C→T | P36P (CCG→CCA) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,327,834 | A→G | A15A (GCA→GCG) | yhbY → | ribosome assembly factor YhbY |
| RA | 3,329,249 | T→C | V96A (GTA→GCA) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,348,279 | (C)6→7 | intergenic (+41/‑173) | npr → / → yrbL | phosphorelay protein Npr/protein kinase‑like domain‑containing protein YrbL |
| RA | 3,350,184 | (C)7→8 | coding (276/654 nt) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,354,811 | G→A | V29V (GTG→GTA) | gltB → | glutamate synthase subunit GltB |
| RA | 3,360,574 | T→C | G459G (GGT→GGC) | gltD → | glutamate synthase subunit GltD |
| RA | 3,367,500 | T→C | V192A (GTA→GCA) | yhcF → | DUF1120 domain‑containing protein YhcF |
| RA | 3,382,394 | T→C | G65G (GGT→GGC) | degS → | serine endoprotease |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,402,255 | T→C | T360A (ACC→GCC) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,423,701 | A→G | noncoding (87/120 nt) | rrfD ← | 5S ribosomal RNA |
| RA | 3,494,433 | C→T | C141C (TGC→TGT) | nirB → | nitrite reductase catalytic subunit NirB |
| RA | 3,504,971 | C→T | V350V (GTG→GTA) | yhfS ← | putative aminotransferase YhfS |
| RA | 3,521,245 | C→T | E69K (GAG→AAG) | hofO ← | DNA utilization protein HofO |
| RA | 3,524,518 | T→C | F550L (TTC→CTC) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,569,795 | T→C | T509A (ACG→GCG) | glgX ← | limit dextrin alpha‑1,6‑glucohydrolase |
| RA | 3,586,429 | T→C | N132S (AAC→AGC) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,601,749 | A→G | V113A (GTT→GCT) | ftsX ← | cell division protein FtsX |
| RA | 3,611,879 | A→G | Q5Q (CAA→CAG) | yhhT → | putative transporter YhhT |
| RA | 3,648,289 | A→G | intergenic (+143/‑5) | agrA → / → agrB | small RNA AgrA/small RNA AgrB |
| RA | 3,651,664 | (A)7→6 | pseudogene (374/746 nt) | yhiS → | putative uncharacterized protein YhiS |
| RA | 3,667,921 | T→C | D423G (GAC→GGC) | ccp ← | cytochrome c peroxidase |
| RA | 3,690,189 | A→G | W25R (TGG→CGG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,731,244 | A→G | E38E (GAA→GAG) | xylF → | xylose ABC transporter periplasmic binding protein |
| RA | 3,763,972 | A→G | N597S (AAC→AGC) | rhsA → | rhs element protein RhsA |
| RA | 3,765,830 | G→A | R1216R (CGG→CGA) | rhsA → | rhs element protein RhsA |
| RA | 3,765,854 | G→A | G1224G (GGG→GGA) | rhsA → | rhs element protein RhsA |
| RA | 3,770,236 | (C)6→8 | intergenic (+556/+7) | yibV → / ← yibH | PF15596 family protein YibV/inner membrane protein YibH |
| RA | 3,773,042 | T→C | G254G (GGT→GGC) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,852,262 | G→A | Q175* (CAA→TAA) | ilvB ← | acetohydroxy acid synthase I subunit IlvB |
| RA | 3,854,735 | A→G | T272A (ACG→GCG) | emrD → | multidrug efflux pump EmrD |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,870,024 | T→C | G216G (GGT→GGC) | cbrA → | colicin M resistance protein |
| RA | 3,876,744 | T→C | N70S (AAC→AGC) | yidA ← | sugar phosphatase YidA |
| RA | 3,917,313 | A→G | D21D (GAT→GAC) | atpD ← | ATP synthase F1 complex subunit beta |
| RA | 3,924,387 | T→C | D416G (GAC→GGC) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,931,868 | T→C | L185L (TTA→CTA) | kup → | K(+):H(+) symporter Kup |
| RA | 3,939,901 | A→G | L238L (TTA→CTA) | hsrA ← | putative transporter HsrA |
| RA | 3,941,955 | (G)5→6 | noncoding (148/1542 nt) | rrsC → | 16S ribosomal RNA |
| RA | 3,950,476 | (T)8→7 | intergenic (+56/‑31) | ilvL → / → ilvX | ilvXGMEDA operon leader peptide/uncharacterized protein IlvX |
| RA | 3,969,180 | (T)6→7 | coding (150/1047 nt) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,983,835 | A→G | D293G (GAC→GGC) | aslB → | putative anaerobic sulfatase maturation enzyme AslB |
| RA | 3,994,386 | T→A | intergenic (+51/‑136) | yzcX → / → yifL | protein YzcX/putative lipoprotein YifL |
| RA | 4,050,225 | A→G | L181L (TTG→CTG) | yihA ← | GTP‑binding protein YihA |
| RA | 4,058,537 | A→G | D44G (GAC→GGC) | bipA → | ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,060,280 | (T)9→8 | intergenic (+50/‑167) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,094,683 | C→T | intergenic (‑411/+40) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,094,691 | G→T | intergenic (‑419/+32) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,094,700 | G→A | intergenic (‑428/+23) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,094,703 | C→T | intergenic (‑431/+20) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,094,705 | C→T | intergenic (‑433/+18) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,128,747 | C→T | P26S (CCG→TCG) | metB → | O‑succinylhomoserine(thiol)‑lyase/O‑ succinylhomoserine lyase |
| RA | 4,155,010 | A→G | T4A (ACG→GCG) | argC → | N‑acetylglutamylphosphate reductase |
| RA | 4,168,571 | G→A | intergenic (+124/‑70) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA |
| RA | 4,217,424 | T→C | Y106H (TAT→CAT) | aceA → | isocitrate lyase |
| RA | 4,219,263 | (T)5→4 | coding (668/1737 nt) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,250,878 | A→G | pseudogene (176/1581 nt) | yjbI → | pentapeptide repeats‑containing protein YjbI |
| RA | 4,263,602 | C→T | V210V (GTG→GTA) | qorA ← | putative quinone oxidoreductase 1 |
| RA | 4,269,672 | (A)7→6 | coding (259/714 nt) | aphA → | acid phosphatase/phosphotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,305,427 | A→G | Y391H (TAC→CAC) | yjcS ← | alkyl sulfatase |
| RA | 4,343,821 | (T)7→6 | coding (453/1422 nt) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,348,470 | A→G | V92A (GTC→GCC) | dcuB ← | anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,360,830 | A→G | S369P (TCC→CCC) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,363,323 | T→C | intergenic (‑15/+22) | yjdC ← / ← dsbD | putative DNA‑binding transcriptional regulator YjdC/protein disulfide oxidoreductase ‑ DsbDreduced |
| RA | 4,384,173 | C→T | T112I (ACA→ATA) | yjeM → | putative transporter YjeM |
| RA | 4,394,870 | (G)5→4 | coding (805/1548 nt) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,403,092 | T→C | V352A (GTT→GCT) | hflK → | regulator of FtsH protease |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,446,347 | A→G | T746A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,449,311 | C→T | L114L (CTG→CTA) | ppa ← | inorganic pyrophosphatase |
| RA | 4,467,292 | A→G | intergenic (‑46/‑139) | treR ← / → mgtL | DNA‑binding transcriptional repressor TreR/leader peptide MgtL |
| RA | 4,482,396 | A→G | L481P (CTG→CCG) | valS ← | valine‑‑tRNA ligase |
| RA | 4,500,982 | (C)5→6 | intergenic (‑191/‑278) | yjgX ← / → yjgZ | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment/KpLE2 phage‑like element; uncharacterized protein YjgZ |
| RA | 4,511,541 | (G)5→6 | coding (874/957 nt) | fecD ← | ferric citrate ABC transporter membrane subunit FecD |
| RA | 4,516,073 | A→G | V202A (GTC→GCC) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,517,951 | (C)6→7 | coding (285/522 nt) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,524,555 | A→G | R152R (CGT→CGC) | yjhH ← | KpLE2 phage‑like element; putative 2‑dehydro‑3‑deoxy‑D‑pentonate aldolase |
| RA | 4,551,005 | G→A | R98C (CGC→TGC) | gntP ← | fructuronate transporter |
| RA | 4,558,867 | +A | coding (660/1173 nt) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,559,164 | A→G | R121R (CGT→CGC) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,568,725 | C→T | intergenic (‑206/‑273) | mdtM ← / → rpnD | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter/truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,582,379 | G→A | L224L (CTG→TTG) | hsdM ← | type I restriction enzyme EcoKI methyltransferase component |
| RA | 4,585,372 | G→A | Q464* (CAA→TAA) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,599,590 | A→G | intergenic (‑149/+105) | opgB ← / ← yjjA | phosphoglycerol transferase I/DUF2501 domain‑containing protein YjjA |
| RA | 4,606,215 | (G)8→10 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,622,890 | C→T | S374S (AGC→AGT) | yjjJ → | toxin YjjJ |
| RA | 4,634,532 | T→C | D260G (GAT→GGT) | rob ← | DNA‑binding transcriptional dual regulator Rob |
| RA | 4,636,119 | C→T | P38L (CCG→CTG) | creB → | DNA‑binding transcriptional regulator CreB |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1433355 | 1433529–1433373 | 19–175 | 18 [9] | [9] 12 | pinR | Rac prophage; putative site‑specific recombinase |
| * | * | ÷ | NC_000913 | 1433778–1434069 | 1434256–1434079 | 11–479 | 13 [10] | [10] 13 | ynaE | ynaE |
| * | * | ÷ | NC_000913 | 1633339–1633616 | 1633798–1633630 | 15–460 | 13 [9] | [10] 11 | [pinQ] | [pinQ] |
| * | * | ÷ | NC_000913 | 1634052 | 1634907–1634643 | 592–856 | 11 [8] | [10] 11 | [pinQ]–[ydfN] | [pinQ],tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423766–3424233 | 3424530–3424238 | 6–765 | 11 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619361–3621079 | 3622178–3621086 | 8–2818 | 11 [10] | [9] 13 | rhsB | rhs element protein RhsB |
| * | * | ÷ | NC_000913 | 3764173–3765288 | 3765789–3765672 | 385–1617 | 11 [8] | [10] 13 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 3944154–3946508 | 3946508 | 1–2355 | 12 [10] | [8] 13 | rrlC | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4037963–4038688 | 4039280–4038730 | 43–1318 | 11 [10] | [9] 12 | rrlA | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4094415 | 4094673 | 259 | 11 [9] | [9] 11 | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 86 (1.690) | 69 (1.360) | 42/274 | 0.1 | 61.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 52 (1.020) | 46/276 | 0.1 | 92.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.080) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 33 (0.650) | 12 (0.250) | 11/258 | 2.3 | 21.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 58 (1.220) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||