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 | 66,534 | T→G | 6.3% | K6T (AAA→ACA) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 83,587 | A→C | 10.9% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 8.9% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 107,554 | G→T | 11.9% | intergenic (+80/‑151) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 127,605 | A→C | 5.1% | intergenic (+18/‑307) | aceF → / → lpd | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2/dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase |
| RA | 164,581 | A→C | 22.6% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 231,868 | T→G | 6.9% | A249A (GCT→GCG) | yafD → | endo/exonuclease/phosphatase family protein |
| RA | 238,507 | G→T | 8.0% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 285,882 | T→G | 6.0% | I163S (ATC→AGC) | yagG → | CP4‑6 prophage; putative sugar transporter |
| RA | 285,887 | C→A | 5.8% | L165M (CTG→ATG) | yagG → | CP4‑6 prophage; putative sugar transporter |
| RA | 289,256 | G→C | 7.4% | intergenic (‑94/+45) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 289,257 | T→A | 7.7% | intergenic (‑95/+44) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 357,775 | A→T | 5.8% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 475,971 | C→G | 7.6% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 7.6% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 632,070 | T→G | 6.9% | intergenic (+71/‑112) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,075 | G→A | 6.1% | intergenic (+76/‑107) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,076 | G→C | 6.5% | intergenic (+77/‑106) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,077 | T→C | 6.5% | intergenic (+78/‑105) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,082 | C→A | 6.5% | intergenic (+83/‑100) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 780,841:1 | +T | 7.0% | intergenic (+1/‑2) | valT → / → lysW | tRNA‑Val/tRNA‑Lys |
| RA | 781,238 | T→A | 7.5% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 5.3% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,269 | C→T | 5.3% | intergenic (+47/‑100) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 915,215 | T→G | 8.6% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 950,313 | C→T | 5.6% | intergenic (+55/+27) | ycaK → / ← pflA | putative NAD(P)H‑dependent oxidoreductase/pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase |
| RA | 950,314 | A→T | 5.7% | intergenic (+56/+26) | ycaK → / ← pflA | putative NAD(P)H‑dependent oxidoreductase/pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase |
| RA | 950,317 | A→T | 5.8% | intergenic (+59/+23) | ycaK → / ← pflA | putative NAD(P)H‑dependent oxidoreductase/pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase |
| RA | 950,318 | A→G | 5.7% | intergenic (+60/+22) | ycaK → / ← pflA | putative NAD(P)H‑dependent oxidoreductase/pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase |
| RA | 962,213 | C→T | 5.1% | D73D (GAC→GAT) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,169,380 | T→C | 5.2% | intergenic (+50/+32) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,382 | C→G | 5.2% | intergenic (+52/+30) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,384 | G→A | 5.4% | intergenic (+54/+28) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,351,228 | G→C | 7.2% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,388,283 | C→T | 5.4% | intergenic (+22/+22) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,388,284 | A→T | 5.8% | intergenic (+23/+21) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,388,285 | A→G | 5.5% | intergenic (+24/+20) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,389,007 | A→C | 8.2% | E26D (GAA→GAC) | ycjG → | L‑Ala‑D/L‑Glu epimerase |
| RA | 1,466,336 | C→G | 7.4% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 7.1% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,562 | G→A | 5.4% | pseudogene (1171/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,639 | C→T | 5.8% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,543,229 | G→T | 7.3% | L278M (CTG→ATG) | narU ← | nitrate/nitrite transporter |
| RA | 1,543,230 | C→G | 7.5% | M277I (ATG→ATC) ‡ | narU ← | nitrate/nitrite transporter |
| RA | 1,543,231 | A→C | 7.5% | M277R (ATG→AGG) ‡ | narU ← | nitrate/nitrite transporter |
| RA | 1,636,476 | T→A | 8.1% | intergenic (‑109/‑280) | nohQ ← / → ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| RA | 1,642,370 | C→G | 5.7% | intergenic (+303/+119) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,642,373 | C→G | 5.5% | intergenic (+306/+116) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,708,709 | T→A | 5.8% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 9.5% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| 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 | 1,985,112 | C→G | 5.3% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,028,158 | G→C | 6.8% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 7.1% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 6.8% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| 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 | 19.3% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 19.5% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,229,177 | A→C | 19.7% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,286,313 | T→A | 5.0% | intergenic (+26/+77) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,286,315 | C→G | 5.7% | intergenic (+28/+75) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,304,649 | C→T | 7.1% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,462,677 | A→T | 6.0% | intergenic (+31/‑335) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,470,441 | C→A | 9.7% | D437E (GAC→GAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,704,304 | A→G | 5.4% | intergenic (‑241/+31) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,306 | A→T | 5.4% | intergenic (‑243/+29) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,308 | C→T | 5.4% | intergenic (‑245/+27) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,725,850 | T→A | 8.6% | intergenic (‑104/+219) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,731,580 | C→T | 5.1% | intergenic (‑423/+20) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,817,916 | T→G | 6.6% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,866,487 | G→C | 6.1% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,866,488 | G→C | 5.9% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,907,998 | A→T | 5.2% | intergenic (‑57/+31) | eno ← / ← pyrG | enolase/CTP synthetase |
| RA | 2,972,652 | A→T | 6.2% | intergenic (+15/+17) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter |
| RA | 2,972,653 | A→T | 6.2% | intergenic (+16/+16) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter |
| RA | 3,020,512 | A→C | 5.1% | intergenic (+23/‑28) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,046,050 | T→G | 7.9% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,046,068 | T→A | 14.9% | intergenic (‑167/+100) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,066,310 | A→T | 5.0% | H288Q (CAT→CAA) | ygfI ← | putative DNA‑binding transcriptional regulator |
| RA | 3,180,505 | G→T | 5.2% | E29* (GAG→TAG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,180,506 | A→C | 5.4% | E29A (GAG→GCG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,239,609 | T→G | 11.3% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,269,956 | T→C | 10.0% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,969 | A→C | 5.4% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,143 | C→T | 7.8% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,334,703 | A→G | 7.9% | intergenic (+22/‑206) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,704 | G→C | 7.9% | intergenic (+23/‑205) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,705 | C→T | 7.2% | intergenic (+24/‑204) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,437,908 | T→A | 5.6% | intergenic (+14/‑116) | trkA → / → mscL | NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance |
| RA | 3,437,909 | A→T | 5.1% | intergenic (+15/‑115) | trkA → / → mscL | NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance |
| RA | 3,437,910 | A→T | 5.6% | intergenic (+16/‑114) | trkA → / → mscL | NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance |
| RA | 3,437,911 | T→A | 6.0% | intergenic (+17/‑113) | trkA → / → mscL | NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance |
| RA | 3,458,110 | C→A | 100% | T578T (ACC→ACA) | gspD → | general secretory pathway component, cryptic |
| RA | 3,482,325 | G→A | 100% | R346H (CGC→CAC) | yheS → | ABC‑F family protein predicted regulatory ATPase |
| RA | 3,554,283 | T→A | 9.0% | L400Q (CTG→CAG) | malT → | mal regulon transcriptional activator |
| 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 | 3,608,695 | C→G | 14.1% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,657,599 | T→A | 6.4% | intergenic (+32/+387) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,601 | G→C | 6.4% | intergenic (+34/+385) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,603 | T→A | 6.7% | intergenic (+36/+383) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,708,427 | G→A | 5.4% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,428 | T→A | 5.3% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,429 | T→C | 5.5% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,595 | G→A | 7.2% | intergenic (‑890/+21) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,596 | T→A | 7.6% | intergenic (‑891/+20) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,597 | T→C | 7.2% | intergenic (‑892/+19) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,774,207 | C→T | 5.3% | intergenic (+13/‑217) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,214 | C→T | 5.3% | intergenic (+20/‑210) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,215 | A→G | 5.5% | intergenic (+21/‑209) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,774,222 | A→G | 5.3% | intergenic (+28/‑202) | mtlA → / → mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,781,051 | C→G | 6.2% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,828,980 | A→C | 8.1% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,959,457 | T→G | 12.3% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,482 | A→C | 5.1% | intergenic (+37/+50) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 9.2% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,984,542 | T→A | 7.5% | Q489L (CAG→CTG) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 4,040,752 | A→C | 5.0% | intergenic (+116/+154) | rrfA → / ← mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,094,415 | T→G | 5.1% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,213,131 | C→T | 5.5% | noncoding (92/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,236,226 | T→C | 5.7% | intergenic (+78/‑36) | yjbE → / → yjbF | extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein |
| RA | 4,236,227 | C→G | 5.7% | intergenic (+79/‑35) | yjbE → / → yjbF | extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein |
| RA | 4,236,228 | C→G | 5.9% | intergenic (+80/‑34) | yjbE → / → yjbF | extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein |
| RA | 4,236,229 | G→A | 5.8% | intergenic (+81/‑33) | yjbE → / → yjbF | extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein |
| RA | 4,296,060 | C→T | 31.8% | intergenic (+266/+376) | 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 | 4,412,785 | A→T | 6.3% | G133G (GGA→GGT) | yjfM → | DUF1190 family protein |
| RA | 4,473,927 | C→A | 100% | A43S (GCC→TCC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,520,500 | Δ1 bp | 5.4% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 5.2% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 448611 | 450692 | 2082 | 131 [125] | [123] 129 | [cyoC]–[cyoA] | [cyoC],cyoB,[cyoA] |
| * | * | ÷ | NC_000913 | 2403888 | 2404667 | 780 | 128 [124] | [127] 132 | nuoB–[nuoA] | nuoB,[nuoA] |
| * | * | ÷ | NC_000913 | 3423742–3424234 | 3424560–3424238 | 5–819 | 130 [122] | [118] 128 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274038 = | NA (NA) | 3 (0.010) | 3/266 | NT | NA | noncoding (1112/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274083 = | NA (NA) | noncoding (1067/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274384 = | NA (NA) | 7 (0.030) | 3/272 | NT | NA | noncoding (766/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274422 = | NA (NA) | noncoding (728/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 4 (0.020) | 3/260 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 781369 = | 183 (0.730) | 32 (0.130) +G |
7/276 | NT | 15.2% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521128 | 178 (0.710) | intergenic (+2/‑45) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | 781577 = | 142 (0.560) | 39 (0.160) +GAAG |
10/270 | NT | 20.6% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 168 (0.670) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 1097245 = | NA (NA) | 3 (0.010) | 3/274 | NT | 6.8% | intergenic (+416/+320) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097274 = | 42 (0.170) | intergenic (+445/+291) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 107 (0.420) | 89 (0.400) | 62/246 | NT | 45.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 115 (0.520) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 102 (0.400) | 114 (0.510) | 67/246 | NT | 52.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 115 (0.520) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1287084 | 110 (0.440) | 8 (0.040) | 6/238 | NT | 7.0% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | NC_000913 | 1287557 = | 120 (0.560) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 191 (0.780) | 101/270 | 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 | = 2817942 | 194 (0.770) | 17 (0.080) | 13/238 | NT | 8.2% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 214 (0.990) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | 3943411 = | NA (NA) | 5 (0.020) | 3/266 | NT | 7.1% | intergenic (+62/‑24) | rrsC/gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| ? | NC_000913 | 3943511 = | 68 (0.270) | intergenic (+1/‑193) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | = 4040683 | 204 (0.810) | 24 (0.100) | 9/274 | NT | 9.6% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4213162 | 249 (1.000) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913 | = 4254000 | NA (NA) | 3 (0.010) | 3/264 | NT | NA | noncoding (100/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site |
| ? | NC_000913 | = 4254030 | NA (NA) | noncoding (130/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4542682 = | 188 (0.750) | 25 (0.110) | 16/260 | NT | 12.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 192 (0.820) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 189 (0.750) | 16 (0.070) | 10/260 | NT | 8.0% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 192 (0.820) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||