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 | 83,587 | A→C | 8.8% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 8.0% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 299,984 | T→G | 6.4% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 317,571 | T→C | 5.7% | intergenic (+4/+155) | ykgQ → / ← rclC | pseudogene, putative dehydrogenase/reactive chlorine species (RCS) stress resistance inner membrane protein |
| RA | 357,775 | A→T | 5.0% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 357,806 | T→C | 5.9% | G295G (GGA→GGG) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 357,827 | A→C | 6.1% | D288E (GAT→GAG) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 659,205 | A→T | 5.0% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 5.0% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 6.2% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 756,968 | C→G | 7.4% | H354Q (CAC→CAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 759,250 | G→T | 83.9% | R182L (CGC→CTC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 779,660 | C→G | 5.2% | P21P (CCC→CCG) | ybgF → | periplasmic TolA‑binding protein |
| RA | 781,061 | C→T | 8.7% | intergenic (+143/‑7) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 781,234 | A→G | 5.6% | intergenic (+12/‑135) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,237 | C→G | 5.4% | intergenic (+15/‑132) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,238 | T→A | 6.3% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 6.5% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 838,930 | T→A | 5.1% | Y93F (TAT→TTT) | ybiX ← | Fe(II)‑dependent oxygenase superfamily protein |
| RA | 845,575 | G→A | 6.0% | intergenic (‑95/+166) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,576 | G→C | 5.9% | intergenic (‑96/+165) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,577 | G→C | 5.9% | intergenic (‑97/+164) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,578 | T→C | 5.9% | intergenic (‑98/+163) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 931,298 | C→T | 7.3% | A251A (GCG→GCA) | trxB ← | thioredoxin reductase, FAD/NAD(P)‑binding |
| RA | 1,005,268 | A→G | 6.2% | G167G (GGA→GGG) | pyrD → | dihydro‑orotate oxidase, FMN‑linked |
| RA | 1,147,583 | G→T | 6.0% | intergenic (+43/‑38) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,147,584 | C→T | 6.2% | intergenic (+44/‑37) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,147,585 | A→G | 6.3% | intergenic (+45/‑36) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,147,586 | A→C | 6.9% | intergenic (+46/‑35) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,169,380 | T→C | 5.5% | intergenic (+50/+32) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,382 | C→G | 5.3% | intergenic (+52/+30) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,384 | G→A | 5.7% | intergenic (+54/+28) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,212,555 | C→A | 7.8% | intergenic (‑552/+148) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,286,965 | A→G | 10.9% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,143 | G→T | 10.8% | noncoding (94/171 nt) P12T (CCA→ACA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,149 | G→A | 5.8% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,315,807 | C→T | 5.5% | intergenic (‑37/+49) | yciF ← / ← yciG | putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein |
| RA | 1,324,837 | A→C | 5.4% | Y31S (TAT→TCT) ‡ | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,324,838 | T→A | 6.2% | Y31* (TAT→TAA) ‡ | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,324,839 | G→T | 5.7% | E32* (GAA→TAA) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,426,706 | G→T | 5.8% | pseudogene (253/933 nt) | tmpR → | Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein |
| RA | 1,466,336 | C→G | 10.1% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 5.6% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,495 | C→T | 8.9% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 8.4% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,568,915 | G→A | 5.8% | intergenic (‑92/+39) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,568,917 | A→T | 6.0% | intergenic (‑94/+37) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,568,919 | T→C | 6.7% | intergenic (‑96/+35) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,650,147 | G→A | 5.1% | pseudogene (70/765 nt) | ydfE → | Qin prophage; pseudogene;Phage or Prophage Related |
| RA | 1,650,148 | T→C | 5.2% | pseudogene (71/765 nt) | ydfE → | Qin prophage; pseudogene;Phage or Prophage Related |
| RA | 1,657,901 | A→T | 5.6% | intergenic (+31/‑168) | ynfD → / → ynfE | DUF1161 family periplasmic protein/putative selenate reductase, periplasmic |
| RA | 1,708,718 | G→A | 6.8% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 9.4% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 13.8% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,752,027 | C→T | 7.9% | A602T (GCA→ACA) | ydhV ← | putative oxidoreductase subunit |
| RA | 1,864,758 | G→A | 5.9% | intergenic (+24/+24) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,763 | A→T | 8.2% | intergenic (+29/+19) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,768 | T→C | 7.5% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,932,094 | C→G | 6.4% | intergenic (+35/+21) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,095 | T→A | 7.1% | intergenic (+36/+20) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,096 | C→G | 7.1% | intergenic (+37/+19) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,028,158 | G→C | 6.4% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 6.6% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 6.3% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,032,336 | G→C | 6.0% | intergenic (‑19/+48) | dcm ← / ← yedJ | DNA cytosine methyltransferase/putative HD superfamily phosphohydrolase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,177,234 | C→A | 8.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,229,177 | A→C | 18.9% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,304,649 | C→T | 7.6% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,688 | A→G | 8.8% | intergenic (+295/+420) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 5.9% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,085 | A→G | 7.4% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 6.8% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 6.8% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,383,956 | A→T | 6.2% | intergenic (+32/+39) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,383,959 | A→T | 6.2% | intergenic (+35/+36) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,470,427 | C→A | 18.9% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,441 | C→A | 11.5% | D437E (GAC→GAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,486,083 | T→C | 5.5% | D570D (GAT→GAC) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,679,430 | Δ1 bp | 6.3% | intergenic (‑63/+34) | yphF ← / ← yphG | putative sugar ABC transporter periplasmic binding protein/DUF4380 domain‑containing TPR repeat protein |
| RA | 2,679,434:1 | +C | 6.2% | intergenic (‑67/+30) | yphF ← / ← yphG | putative sugar ABC transporter periplasmic binding protein/DUF4380 domain‑containing TPR repeat protein |
| RA | 2,778,124 | A→C | 5.3% | intergenic (+342/+22) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter |
| RA | 2,818,049 | T→A | 5.2% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,828,533 | A→T | 5.7% | intergenic (+17/‑88) | srlD → / → srlM | sorbitol‑6‑phosphate dehydrogenase/sorbitol=responsive srl operon transcriptional activator |
| RA | 2,828,535 | T→A | 5.9% | intergenic (+19/‑86) | srlD → / → srlM | sorbitol‑6‑phosphate dehydrogenase/sorbitol=responsive srl operon transcriptional activator |
| RA | 2,828,537 | A→T | 5.7% | intergenic (+21/‑84) | srlD → / → srlM | sorbitol‑6‑phosphate dehydrogenase/sorbitol=responsive srl operon transcriptional activator |
| RA | 2,900,322 | C→T | 6.0% | intergenic (‑49/‑270) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,900,324 | G→T | 6.1% | intergenic (‑51/‑268) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,900,327 | A→C | 6.4% | intergenic (‑54/‑265) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,993,889 | T→A | 6.1% | intergenic (+33/‑50) | ygeI → / → pbl | uncharacterized protein/pseudogene, peptidoglycan‑binding enzyme family |
| RA | 2,993,896 | T→A | 6.1% | intergenic (+40/‑43) | ygeI → / → pbl | uncharacterized protein/pseudogene, peptidoglycan‑binding enzyme family |
| RA | 3,046,050 | T→G | 12.3% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,114,526 | G→T | 5.0% | intergenic (‑174/+24) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,114,527 | A→C | 5.0% | intergenic (‑175/+23) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,114,533 | T→G | 5.5% | intergenic (‑181/+17) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,114,534 | T→C | 5.2% | intergenic (‑182/+16) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,180,505 | G→T | 6.0% | E29* (GAG→TAG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,180,506 | A→C | 7.0% | E29A (GAG→GCG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,195,008 | C→G | 5.0% | intergenic (‑143/+91) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,239,609 | T→G | 7.3% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,269,969 | A→C | 5.4% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,313,208 | T→A | 5.4% | intergenic (‑30/+134) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,313,209 | T→C | 5.0% | intergenic (‑31/+133) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,316,890 | C→G | 22.9% | V213L (GTG→CTG) | nusA ← | transcription termination/antitermination L factor |
| RA | 3,324,952 | A→G | 5.4% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 5.5% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,959 | C→T | 5.3% | intergenic (‑48/+42) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,334,703 | A→C | 6.8% | intergenic (+22/‑206) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,368,173 | C→T | 5.2% | P116L (CCG→CTG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,180 | A→G | 5.3% | T118T (ACA→ACG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,181 | C→G | 5.9% | P119A (CCG→GCG) ‡ | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,182 | C→T | 5.3% | P119L (CCG→CTG) ‡ | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,189 | A→G | 5.3% | A121A (GCA→GCG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,377,768 | C→T | 5.9% | intergenic (‑348/+47) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,377,769 | G→T | 5.3% | intergenic (‑349/+46) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,377,770 | A→C | 5.8% | intergenic (‑350/+45) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,377,771 | A→G | 5.8% | intergenic (‑351/+44) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,423,531 | T→G | 5.8% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,458,110 | C→A | 100% | T578T (ACC→ACA) | gspD → | general secretory pathway component, cryptic |
| RA | 3,471,361 | T→G | 5.1% | intergenic (‑32/+39) | tufA ← / ← fusA | translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding |
| RA | 3,482,325 | G→A | 100% | R346H (CGC→CAC) | yheS → | ABC‑F family protein predicted regulatory ATPase |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,608,696 | T→G | 5.4% | intergenic (+47/+55) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,657,603 | T→A | 5.1% | intergenic (+36/+383) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,728,125 | T→G | 11.0% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,790,300 | A→T | 5.1% | intergenic (‑219/+20) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,877,617 | T→A | 6.5% | intergenic (‑152/+88) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
| RA | 3,908,506 | C→G | 6.8% | intergenic (‑140/+43) | pstB ← / ← pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| RA | 3,947,048 | G→T | 5.3% | intergenic (+16/+80) | trpT → / ← hdfR | tRNA‑Trp/flhDC operon transcriptional repressor |
| RA | 3,947,049 | A→T | 5.4% | intergenic (+17/+79) | trpT → / ← hdfR | tRNA‑Trp/flhDC operon transcriptional repressor |
| RA | 3,947,050 | A→T | 5.2% | intergenic (+18/+78) | trpT → / ← hdfR | tRNA‑Trp/flhDC operon transcriptional repressor |
| RA | 3,947,051 | A→C | 5.2% | intergenic (+19/+77) | trpT → / ← hdfR | tRNA‑Trp/flhDC operon transcriptional repressor |
| RA | 3,959,515 | T→A | 11.6% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,966,943 | T→G | 6.8% | I176S (ATT→AGT) | rho → | transcription termination factor |
| RA | 3,967,011 | C→G | 8.8% | H199D (CAC→GAC) | rho → | transcription termination factor |
| RA | 3,967,609 | T→A | 8.2% | F398Y (TTC→TAC) | rho → | transcription termination factor |
| RA | 4,153,447 | A→G | 8.6% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,296,060 | C→T | 24.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,155 | T→C | 10.4% | intergenic (+361/+281) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,473,927 | C→A | 100% | A43S (GCC→TCC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,614,580 | G→A | 6.2% | intergenic (+320/+100) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 448617 | 450659 | 2043 | 61 [59] | [58] 62 | [cyoC]–cyoB | [cyoC],cyoB |
| * | * | ÷ | NC_000913 | 1166040 | 1167421 | 1382 | 61 [59] | [59] 65 | ndh | ndh |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 227446 | NA (NA) | 5 (0.030) | 4/272 | NT | NA | noncoding (1688/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 227462 | NA (NA) | noncoding (1704/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 381669 | NA (NA) | 3 (0.020) | 3/264 | NT | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 603390 | 158 (0.910) | 8 (0.050) | 5/250 | NT | 5.0% | intergenic (+55/+26) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance |
| ? | NC_000913 | = 603395 | 161 (1.030) | intergenic (+60/+21) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance | |||||
| * | ? | NC_000913 | 1207790 = | 45 (0.260) | 72 (0.470) | 40/246 | NT | 63.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 44 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 43 (0.250) | 91 (0.590) | 51/246 | NT | 68.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 44 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 114 (0.680) | 65/270 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2654970 = | NA (NA) | 7 (0.040) | 3/264 | NT | NA | noncoding (1/97 nt) | RIP183 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP183 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 4080092 | NA (NA) | noncoding (73/98 nt) | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 4168373 | 102 (0.590) | 9 (0.100) +66 bp |
3/146 | NT | 9.5% | noncoding (2/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | = 4209753 | 225 (1.290) | intergenic (+65/‑21) | rrsE/gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 4542682 = | 171 (0.980) | 15 (0.090) | 10/260 | NT | 8.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 152 (0.930) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 173 (0.990) | 19 (0.120) | 12/260 | NT | 10.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 152 (0.930) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||