mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 15,320:2 | +C | 5.1% | intergenic (+22/‑125) | dnaJ → / → insL1 | chaperone Hsp40, DnaK co‑chaperone/IS186 transposase |
| RA | 25,769 | G→T | 5.2% | intergenic (+68/‑57) | lspA → / → fkpB | prolipoprotein signal peptidase (signal peptidase II)/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 33,308 | C→T | 5.4% | A831V (GCG→GTG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 36,156 | C→A | 8.3% | E3* (GAA→TAA) | caiD ← | carnitinyl‑CoA dehydratase |
| RA | 62,253 | C→A | 6.0% | D338Y (GAT→TAT) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 62,703 | C→A | 5.1% | G188W (GGG→TGG) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 65,366 | G→T | 5.3% | R139S (CGT→AGT) | polB ← | DNA polymerase II |
| RA | 110,380 | G→A | 6.8% | P150P (CCG→CCA) | guaC → | GMP reductase |
| RA | 134,950 | C→T | 7.0% | P461S (CCG→TCG) | cueO → | multicopper oxidase (laccase) |
| RA | 204,992 | G→T | 5.3% | R1127L (CGG→CTG) | dnaE → | DNA polymerase III alpha subunit |
| RA | 209,669 | G→T | 8.3% | L284L (CTG→CTT) | tilS → | tRNA(Ile)‑lysidine synthetase |
| RA | 221,425 | T→C | 5.5% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 5.8% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 259,285 | C→T | 7.8% | Q32Q (CAG→CAA) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 259,297 | A→G | 5.7% | R28R (CGT→CGC) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 259,308 | A→G | 5.4% | L25L (TTA→CTA) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 259,327 | G→T | 5.5% | P18P (CCC→CCA) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 259,330 | T→C | 5.5% | S17S (TCA→TCG) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 263,231 | C→A | 5.4% | R162R (CGG→CGT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,234 | G→C | 5.5% | D161E (GAC→GAG) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 286,409 | T→A | 7.5% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 304,162 | C→A | 6.4% | A294A (GCG→GCT) | ecpC ← | ECP production outer membrane protein |
| RA | 347,277 | G→T | 5.9% | G118C (GGC→TGC) | prpD → | 2‑methylcitrate dehydratase |
| RA | 370,556:1 | +C | 5.9% | intergenic (+219/‑359) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 371,448 | G→A | 7.1% | P178P (CCG→CCA) | mhpT → | 3‑hydroxyphenylpropionic transporter |
| RA | 415,030 | C→A | 6.2% | intergenic (+390/‑17) | phoR → / → brnQ | sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 418,995 | T→G | 16.8% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 480,424 | G→T | 5.5% | Q218K (CAG→AAG) | acrA ← | multidrug efflux system |
| RA | 492,639 | C→A | 8.9% | I3I (ATC→ATA) | adk → | adenylate kinase |
| RA | 523,461 | G→A | 6.2% | pseudogene (54/708 nt) | rhsH → | pseudogene, Rhs familly protein |
| RA | 523,476 | G→T | 6.1% | pseudogene (69/708 nt) | rhsH → | pseudogene, Rhs familly protein |
| RA | 523,482 | A→G | 6.3% | pseudogene (75/708 nt) | rhsH → | pseudogene, Rhs familly protein |
| RA | 527,950 | C→A | 7.3% | A15D (GCT→GAT) | allA → | ureidoglycolate lyase, releasing urea |
| RA | 533,886 | G→T | 7.1% | L266L (CTG→CTT) | ybbW → | putative allantoin transporter |
| RA | 576,234 | G→A | 6.8% | intergenic (‑333/‑56) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| RA | 605,629 | A→C | 5.6% | intergenic (‑94/+81) | entD ← / ← fepA | phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex/iron‑enterobactin outer membrane transporter |
| RA | 628,454 | G→T | 7.3% | L160L (CTC→CTA) | ybdH ← | putative oxidoreductase |
| RA | 630,999 | G→T | 5.6% | P343T (CCA→ACA) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 693,582 | G→T | 5.7% | S351Y (TCT→TAT) | asnB ← | asparagine synthetase B |
| RA | 726,830 | G→A | 5.1% | A598T (GCC→ACC) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,831 | C→T | 5.2% | A598V (GCC→GTC) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,253 | A→G | 5.8% | T739A (ACG→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 732,499 | T→C | 6.5% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 742,940 | C→T | 6.0% | A96T (GCC→ACC) | abrB ← | regulator of aidB expression; inner membrane protein |
| RA | 768,256 | G→A | 5.2% | R448H (CGC→CAC) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 900,601 | C→A | 5.4% | P78Q (CCA→CAA) | amiD → | 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent; OM lipoprotein |
| RA | 930,967 | C→A | 9.3% | P763Q (CCG→CAG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 1,001,734 | G→A | 8.9% | P109P (CCG→CCA) | zapC → | FtsZ stabilizer |
| RA | 1,009,323 | C→A | 6.1% | F203L (TTC→TTA) | pqiB → | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| RA | 1,023,572 | C→T | 6.4% | G57G (GGC→GGT) | yccU → | putative CoA‑binding protein |
| RA | 1,027,272 | C→A | 5.5% | intergenic (‑104/‑323) | serT ← / → hyaA | tRNA‑Ser/hydrogenase 1, small subunit |
| RA | 1,045,283 | T→G | 5.9% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,050,522 | C→A | 5.1% | L371L (CTG→CTT) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,130,531 | G→A | 5.5% | R116H (CGT→CAT) | flgG → | flagellar component of cell‑distal portion of basal‑body rod |
| RA | 1,130,826 | G→A | 7.3% | L214L (CTG→CTA) | flgG → | flagellar component of cell‑distal portion of basal‑body rod |
| RA | 1,159,779 | C→A | 6.4% | R77S (CGC→AGC) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,203,106 | G→T | 6.0% | V50V (GTG→GTT) | stfP → | e14 prophage; uncharacterized protein |
| RA | 1,203,115 | A→C | 5.5% | A53A (GCA→GCC) | stfP → | e14 prophage; uncharacterized protein |
| RA | 1,225,749 | G→T | 9.4% | V34V (GTC→GTA) | hlyE ← | hemolysin E |
| RA | 1,231,187 | G→T | 5.8% | P504Q (CCG→CAG) | ycgB ← | SpoVR family stationary phase protein |
| RA | 1,265,353 | T→G | 8.8% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,282,249 | A→G | 9.9% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,421 | A→G | 8.4% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,430 | C→T | 8.1% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,439 | A→G | 10.1% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,325,829 | G→T | 8.7% | V175V (GTG→GTT) | topA → | DNA topoisomerase I, omega subunit |
| RA | 1,333,429 | G→T | 5.9% | intergenic (‑12/‑158) | ribA ← / → pgpB | GTP cyclohydrolase II/phosphatidylglycerophosphatase B |
| RA | 1,370,777 | C→A | 6.5% | R163S (CGC→AGC) | ycjR → | putative TIM alpha/beta barrel enzyme |
| RA | 1,379,249 | C→A | 5.4% | L292L (CTC→CTA) | ycjX → | DUF463 family protein, putative P‑loop NTPase |
| RA | 1,397,783 | C→T | 6.3% | W347* (TGG→TAG) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase, A subunit |
| RA | 1,422,040 | A→G | 6.0% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,252 | A→G | 7.3% | pseudogene (732/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 7.6% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,648 | G→C | 7.9% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,681 | A→G | 7.1% | pseudogene (303/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,444,044 | C→T | 5.1% | A521A (GCG→GCA) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,460,458 | T→C | 5.3% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,467 | G→A | 5.4% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 6.3% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,819 | G→A | 11.2% | pseudogene (1171/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,481,794 | C→A | 5.4% | I101I (ATC→ATA) | ydcF → | DUF218 superfamily protein, SAM‑binding |
| RA | 1,488,355 | C→A | 5.3% | F543L (TTC→TTA) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,522,209 | C→T | 7.4% | pseudogene (51/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,525,824 | C→A | 5.3% | pseudogene (243/315 nt) | yncI → | pseudogene |
| RA | 1,527,189 | A→G | 9.2% | T373A (ACG→GCG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,539,135 | C→A | 7.1% | pseudogene (837/951 nt) | yddK ← | pseudogene, leucine‑rich protein; putative glycoportein |
| RA | 1,624,086 | C→A | 9.5% | R362L (CGA→CTA) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,634,577 | C→A | 6.9% | E16* (GAG→TAG) | ydfR ← | Qin prophage; uncharacterized protein |
| RA | 1,657,607 | G→A | 5.3% | G121R (GGG→AGG) | ynfG → | oxidoreductase, Fe‑S subunit |
| RA | 1,665,715 | C→A | 5.6% | P28H (CCT→CAT) | asr → | acid shock‑inducible periplasmic protein |
| RA | 1,668,941 | T→C | 6.7% | F258L (TTC→CTC) | tqsA → | pheromone AI‑2 transporter |
| RA | 1,672,380 | C→A | 6.8% | intergenic (‑220/‑304) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,687,647 | C→A | 5.3% | G292C (GGT→TGT) | uidB ← | glucuronide transporter |
| RA | 1,719,078 | G→T | 5.2% | A271E (GCA→GAA) | ydhF ← | putative oxidoreductase |
| RA | 1,728,786 | G→T | 8.5% | R32M (AGG→ATG) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,730,099 | C→A | 6.2% | T155T (ACC→ACA) | sodB → | superoxide dismutase, Fe |
| RA | 1,746,843 | C→A | 8.7% | A415A (GCG→GCT) | ydhV ← | putative oxidoreductase subunit |
| RA | 1,829,789 | T→C | 5.2% | L6L (CTT→CTC) | ynjA → | carboxymuconolactone decarboxylase family protein |
| RA | 1,830,471 | C→A | 7.4% | R48S (CGC→AGC) | ynjB → | putative ABC superfamily transporter periplasmic‑binding protein |
| RA | 1,833,486 | C→A | 5.1% | F161L (TTC→TTA) | ynjD → | putative ABC superfamily transporter ATP‑binding subunit |
| RA | 1,870,372 | C→T | 5.2% | A148V (GCA→GTA) | yeaN → | putative transporter |
| RA | 1,878,275 | C→A | 11.8% | V277V (GTC→GTA) | yeaV → | putative transporter |
| RA | 1,882,553 | G→A | 8.0% | A484V (GCG→GTG) | fadD ← | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| RA | 1,895,294 | G→T | 5.5% | P183P (CCC→CCA) | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,900,961 | C→A | 8.9% | K119N (AAG→AAT) | rlmA ← | 23S rRNA m(1)G745 methyltransferase, SAM‑dependent |
| RA | 1,961,275 | T→C | 5.8% | K7R (AAA→AGA) | cheZ ← | chemotaxis regulator, protein phosphatase for CheY |
| RA | 1,964,631 | C→A | 5.8% | S204I (AGC→ATC) | tap ← | methyl‑accepting protein IV |
| RA | 1,984,025 | C→A | 8.2% | L288L (CTC→CTA) | tyrP → | tyrosine transporter |
| RA | 2,085,551 | C→A | 5.3% | P325Q (CCG→CAG) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| RA | 2,087,495 | C→T | 5.1% | Q183* (CAG→TAG) | hisB → | fused histidinol‑phosphatase/imidazoleglycerol‑phosphate dehydratase |
| RA | 2,150,962 | C→A | 5.3% | A740D (GCC→GAC) | mdtB → | multidrug efflux system, subunit B |
| RA | 2,196,141 | C→A | 5.7% | T795K (ACG→AAG) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,196,145 | C→G | 5.5% | F796L (TTC→TTG) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,196,148 | C→A | 5.6% | C797* (TGC→TGA) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,196,151 | Δ1 bp | 5.6% | coding (2394/3633 nt) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,249,462 | C→A | 5.4% | P210Q (CCG→CAG) | yeiL → | putative transcriptional regulator |
| RA | 2,249,621 | T→C | 8.2% | A398A (GCA→GCG) | psuT ← | putative nucleoside transporter |
| RA | 2,266,064 | C→T | 5.2% | G74G (GGC→GGT) | yejA → | microcin C transporter YejABEF, periplasmic binding protein; ABC family |
| RA | 2,275,962 | C→A | 5.7% | intergenic (+91/‑34) | yejH → / → rplY | putative ATP‑dependent DNA or RNA helicase/50S ribosomal subunit protein L25 |
| RA | 2,304,384 | C→T | 6.1% | S210S (TCG→TCA) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| RA | 2,320,948 | C→A | 5.7% | T225T (ACG→ACT) | yfaP ← | DUF2135 family protein, putative host defense protein |
| RA | 2,352,147 | G→T | 6.6% | Q60K (CAG→AAG) | rhmA ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| RA | 2,383,825 | G→T | 5.3% | P387Q (CCG→CAG) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,391,302 | C→A | 5.8% | P781P (CCG→CCT) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,465,390 | T→G | 7.5% | pseudogene (212/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,465,398 | C→A | 8.5% | pseudogene (204/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,465,404 | G→A | 9.1% | pseudogene (198/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,465,408 | A→G | 6.7% | pseudogene (194/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,497,475 | C→A | 6.8% | E164* (GAG→TAG) | fryA ← | putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component |
| RA | 2,503,891 | G→T | 6.7% | L261L (CTG→CTT) | yfeO → | putative ion channel protein |
| RA | 2,514,609 | Δ1 bp | 6.3% | intergenic (+2/‑3) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,514,610 | Δ1 bp | 6.3% | intergenic (+3/‑2) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,541,735 | C→T | 7.6% | A92V (GCC→GTC) | yfeW → | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity |
| RA | 2,549,778 | C→A | 5.3% | M293I (ATG→ATT) | eutC ← | ethanolamine ammonia‑lyase, small subunit (light chain) |
| RA | 2,587,120 | C→A | 5.6% | D4Y (GAC→TAC) | ypfH ← | palmitoyl‑CoA esterase activity, uncertain physiological substrate |
| RA | 2,641,359 | C→A | 8.1% | A1430S (GCG→TCG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,682,911 | A→T | 5.7% | intergenic (‑46/+119) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,707,680 | G→A | 5.7% | intergenic (+91/+118) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,707,703 | C→T | 6.7% | intergenic (+114/+95) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,715,079 | G→T | 8.2% | E590* (GAG→TAG) | pka → | protein lysine acetyltransferase |
| RA | 2,719,426 | T→C | 94.9% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,536 | G→T | 12.9% | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,742,425 | C→A | 11.4% | T98N (ACT→AAT) | yfjD → | UPF0053 family inner membrane protein |
| RA | 2,745,508 | G→T | 8.4% | E119* (GAA→TAA) | recN → | recombination and repair protein |
| RA | 2,748,152 | C→A | 7.6% | intergenic (‑29/‑103) | ratA ← / → smpB | toxic UPF0083 family protein inhibitor of 70S ribosome formation/trans‑translation protein |
| RA | 2,861,107 | C→A | 9.5% | E336* (GAA→TAA) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,876,051 | G→T | 11.4% | R483S (CGC→AGC) | casA ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| RA | 3,020,257 | G→T | 5.2% | G378V (GGC→GTC) | guaD → | guanine deaminase |
| RA | 3,027,995 | G→T | 5.5% | S180Y (TCC→TAC) | lysS ← | lysine tRNA synthetase, constitutive |
| RA | 3,043,956 | C→A | 6.1% | W24L (TGG→TTG) | gcvT ← | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex |
| RA | 3,064,718 | T→G | 10.4% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,080,755 | T→G | 7.1% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,096,890 | C→A | 5.6% | P173P (CCC→CCA) | mutY → | adenine DNA glycosylase |
| RA | 3,161,125 | G→T | 5.7% | intergenic (‑48/+85) | ygiS ← / ← mqsA | putative inner membrane ABC superfamily transporter permease/antitoxin for MqsR toxin; transcriptional repressor |
| RA | 3,181,434 | C→A | 5.7% | pseudogene (655/2445 nt) | yqiG → | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| RA | 3,199,759:1 | +C | 6.1% | intergenic (‑144/‑63) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,762 | T→A | 6.1% | intergenic (‑147/‑60) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,763 | T→G | 6.7% | intergenic (‑148/‑59) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,764 | T→G | 6.1% | intergenic (‑149/‑58) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,769:1 | +T | 6.2% | intergenic (‑154/‑53) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,769:2 | +G | 6.2% | intergenic (‑154/‑53) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,199,773 | A→C | 5.9% | intergenic (‑158/‑49) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,207,186 | C→T | 5.7% | L261L (CTG→TTG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,224,756 | C→A | 6.7% | intergenic (+158/‑268) | ygjK → / → fadH | alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,263,315 | T→C | 7.4% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,328,329 | G→T | 6.5% | G21V (GGA→GTA) | sfsB → | malPQ operon transcriptional activator |
| RA | 3,345,000 | C→A | 5.5% | G462V (GGC→GTC) | arcB ← | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,387,173 | C→A | 5.1% | A815A (GCG→GCT) | yhdP ← | DUF3971‑AsmA2 domains protein |
| RA | 3,416,899 | A→G | 8.1% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,465,459 | C→T | 6.0% | R472H (CGT→CAT) | fusA ← | protein chain elongation factor EF‑G, GTP‑binding |
| RA | 3,466,087 | G→T | 9.0% | L263M (CTG→ATG) | fusA ← | protein chain elongation factor EF‑G, GTP‑binding |
| RA | 3,539,549 | C→A | 5.5% | S189S (TCC→TCA) | nfuA → | Fe/S biogenesis protein; putative scaffold/chaperone for damaged Fe/S proteins |
| RA | 3,548,657 | C→A | 5.5% | Y738* (TAC→TAA) | malT → | mal regulon transcriptional activator |
| RA | 3,551,754 | G→T | 7.2% | R43L (CGA→CTA) | rtcR → | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| RA | 3,608,154 | A→T | 6.8% | K376N (AAA→AAT) | nikA → | nickel‑binding, heme‑binding periplasmic protein |
| RA | 3,616,199 | A→G | 5.3% | R1216R (CGA→CGG) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,618,160 | A→G | 5.6% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,670,805 | G→T | 8.8% | T302T (ACC→ACA) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,760,562 | G→T | 5.5% | intergenic (+23/‑19) | yibA → / → rhsJ | HEAT‑domain lethality reduction protein; putative immunity protein for putative polymorphic toxin RhsA/Rhs‑family protein |
| RA | 3,760,566 | A→G | 5.3% | intergenic (+27/‑15) | yibA → / → rhsJ | HEAT‑domain lethality reduction protein; putative immunity protein for putative polymorphic toxin RhsA/Rhs‑family protein |
| RA | 3,760,943 | G→A | 5.3% | pseudogene (363/945 nt) | rhsJ → | Rhs‑family protein |
| RA | 3,838,099 | C→A | 7.2% | S259Y (TCC→TAC) | ade → | cryptic adenine deaminase |
| RA | 3,869,212 | G→T | 7.7% | G139C (GGT→TGT) | yidX → | putative lipoprotein |
| RA | 3,877,923 | A→G | 100% | Q24R (CAG→CGG) | rnpA → | protein C5 component of RNase P |
| RA | 3,901,866 | C→G | 6.5% | intergenic (‑140/+43) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,901,867 | T→G | 7.1% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,918,853 | G→T | 5.8% | C47* (TGC→TGA) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,935,371 | G→T | 6.3% | noncoding (204/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,936,724 | T→A | 11.3% | intergenic (+15/‑71) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 3,950,334 | C→T | 6.0% | E283K (GAG→AAG) | ilvY ← | transcriptional activator of ilvC; autorepressor |
| RA | 3,950,336 | T→G | 6.0% | H282P (CAT→CCT) ‡ | ilvY ← | transcriptional activator of ilvC; autorepressor |
| RA | 3,950,337 | G→T | 6.0% | H282N (CAT→AAT) ‡ | ilvY ← | transcriptional activator of ilvC; autorepressor |
| RA | 3,952,869 | T→G | 18.3% | intergenic (+64/+23) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,016,182 | G→T | 5.1% | V29V (GTG→GTT) | tatC → | TatABCE protein translocation system subunit |
| RA | 4,019,993 | Δ1 bp | 100% | coding (107/702 nt) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,161,576 | A→C | 10.2% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,165,449 | C→T | 17.0% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 17.2% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,177,142 | A→T | 6.8% | D622V (GAC→GTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,177,586 | T→G | 81.8% | L770R (CTC→CGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,193,073 | C→A | 6.6% | A407D (GCC→GAC) | zraS → | sensory histidine kinase in two‑component regulatory system with ZraR |
| RA | 4,199,631 | T→A | 9.4% | intergenic (+15/‑71) | rrsE → / → gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu |
| RA | 4,202,979 | A→C | 10.8% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,269,099 | C→A | 5.5% | A231A (GCC→GCA) | yjcD → | inner membrane putative guanine permease |
| RA | 4,283,150 | C→A | 5.8% | V20V (GTC→GTA) | nrfF → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfF |
| RA | 4,315,765 | A→G | 7.6% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,336,205 | G→A | 5.1% | G313G (GGC→GGT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,238 | A→G | 6.5% | R302R (CGT→CGC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,241 | G→A | 5.7% | I301I (ATC→ATT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,361,922 | G→T | 6.1% | D361Y (GAC→TAC) | groL → | Cpn60 chaperonin GroEL, large subunit of GroESL |
| RA | 4,372,570 | G→T | 5.4% | E37D (GAG→GAT) | epmA → | Elongation Factor P Lys34 lysyltransferase |
| RA | 4,374,660 | G→T | 6.5% | P335P (CCG→CCT) | yjeM → | putative transporter |
| RA | 4,381,668 | G→T | 5.2% | R83L (CGG→CTG) | orn → | oligoribonuclease |
| RA | 4,391,954 | C→A | 7.2% | R34S (CGC→AGC) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 4,399,868 | T→C | 10.4% | intergenic (+45/‑82) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,400,031 | G→A | 7.7% | A28T (GCA→ACA) | yjfI → | DUF2170 family protein |
| RA | 4,449,764 | G→T | 7.3% | L140M (CTG→ATG) | nrdG ← | anaerobic ribonucleotide reductase activating protein |
| RA | 4,498,906 | T→C | 5.0% | pseudogene (81/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,909 | G→T | 5.3% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,660 | T→G | 5.4% | pseudogene (123/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,885 | T→A | 7.3% | pseudogene (348/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,516,519 | C→A | 9.3% | D63Y (GAC→TAC) | sgcR ← | putative DNA‑binding transcriptional regulator |
| RA | 4,604,253 | T→G | 7.7% | intergenic (+176/+244) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,320 | T→G | 7.1% | intergenic (+243/+177) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,322 | A→C | 6.0% | intergenic (+245/+175) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,617,948 | G→A | 8.9% | G273S (GGC→AGC) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,625,681 | C→A | 6.8% | S115* (TCG→TAG) | creA → | putative periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 463833 | 464308 | 476 | 24 [14] | [20] 21 | ybaO | ybaO |
| * | * | ÷ | CP009273 | 3448726 | 3448865 | 140 | 22 [19] | [9] 27 | [gspA] | [gspA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 87 (0.950) | 76 (0.830) | 34/250 | NT | 46.6% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1203246 = | 37 (0.410) | 43 (0.540) | 15/218 | NT | 60.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 23 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 36 (0.390) | 32 (0.400) | 12/218 | NT | 54.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 23 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972769 = | 6 (0.070) | 109 (1.200) | 40/248 | NT | 94.8% | intergenic (‑315/‑465) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 1972777 | 4 (0.040) | 78 (0.850) | 36/250 | NT | 95.1% | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||