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 | 5.5% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 5.2% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 164,581 | A→C | 15.3% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 254,223 | A→T | 5.3% | intergenic (+21/+36) | prfH → / ← pepD | pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D) |
| RA | 254,228 | A→T | 5.4% | intergenic (+26/+31) | prfH → / ← pepD | pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D) |
| RA | 254,233 | A→T | 6.6% | intergenic (+31/+26) | prfH → / ← pepD | pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D) |
| RA | 254,238 | A→T | 6.1% | intergenic (+36/+21) | prfH → / ← pepD | pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D) |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 281,946 | A→T | 7.2% | M13K (ATG→AAG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 349,717 | T→C | 5.8% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 357,775 | A→T | 7.6% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 357,778 | C→T | 7.3% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 572,058 | A→T | 8.6% | E202V (GAG→GTG) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 580,727 | G→T | 9.4% | intergenic (‑282/‑107) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| RA | 781,238 | T→A | 6.1% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 8.6% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,269 | C→T | 7.2% | intergenic (+47/‑100) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,668 | C→T | 6.0% | intergenic (+16/‑417) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 781,670 | A→T | 6.0% | intergenic (+18/‑415) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 781,672 | A→G | 6.6% | intergenic (+20/‑413) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 857,576 | T→C | 5.6% | intergenic (+21/+220) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,578 | C→G | 6.5% | intergenic (+23/+218) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,580 | G→A | 5.5% | intergenic (+25/+216) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 915,226 | T→G | 10.0% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,015,912 | T→A | 5.5% | intergenic (+30/+40) | rmf → / ← fabA | ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase |
| RA | 1,052,257 | C→T | 5.8% | intergenic (+17/+32) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,260 | T→C | 6.0% | intergenic (+20/+29) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,261 | G→A | 5.6% | intergenic (+21/+28) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,264 | A→G | 5.8% | intergenic (+24/+25) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,151,888 | T→G | 17.8% | intergenic (+37/‑51) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,151,889 | T→G | 22.7% | intergenic (+38/‑50) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,151,890 | T→G | 20.3% | intergenic (+39/‑49) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,169,380 | T→C | 5.9% | intergenic (+50/+32) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,382 | C→G | 6.0% | intergenic (+52/+30) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,384 | G→A | 6.2% | intergenic (+54/+28) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,287,149 | G→A | 6.9% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,292,472 | G→A | 5.7% | intergenic (+107/+37) | galU → / ← hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,292,473 | C→G | 5.8% | intergenic (+108/+36) | galU → / ← hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,292,474 | T→C | 5.7% | intergenic (+109/+35) | galU → / ← hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,351,228 | G→C | 7.9% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,388,283 | C→T | 5.8% | 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 | 6.1% | 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 | 6.0% | intergenic (+24/+20) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,466,210 | G→A | 6.0% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,336 | C→G | 7.7% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 8.5% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,495 | C→T | 6.2% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 5.3% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,604 | G→A | 6.5% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,630 | G→C | 6.0% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,639 | C→T | 7.0% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,708,709 | T→A | 8.3% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 8.0% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 5.5% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,715,919 | T→G | 5.5% | intergenic (‑30/+29) | pdxY ← / ← tyrS | pyridoxamine kinase/tyrosyl‑tRNA synthetase |
| 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 | 5.9% | 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 | 6.9% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,008,698 | T→G | 6.4% | I141S (ATT→AGT) | yedE → | UPF0394 family sulphur transport domain‑containing inner membrane protein |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,028,158 | G→C | 5.6% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 5.8% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 6.2% | 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 | 14.6% | 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 | 12.9% | 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 | 14.3% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,282,830 | T→C | 5.0% | intergenic (+29/+110) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,831 | C→G | 5.0% | intergenic (+30/+109) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,832 | C→G | 5.2% | intergenic (+31/+108) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,833 | G→A | 5.2% | intergenic (+32/+107) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,304,522 | G→T | 6.0% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,523 | G→C | 7.3% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,649 | C→T | 8.9% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,680 | T→C | 7.3% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,688 | A→G | 7.3% | intergenic (+295/+420) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,762 | T→C | 5.5% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 5.8% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,409,191 | A→C | 5.7% | E110D (GAA→GAC) | yfbR → | 5'‑nucleotidase |
| RA | 2,432,985 | A→G | 6.8% | intergenic (‑43/+27) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,990 | G→C | 6.3% | intergenic (‑48/+22) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,995 | C→T | 6.0% | intergenic (‑53/+17) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,462,677 | A→T | 5.7% | intergenic (+31/‑335) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,678 | T→A | 5.2% | intergenic (+32/‑334) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,679 | A→T | 5.2% | intergenic (+33/‑333) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,470,427 | C→A | 18.5% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,431 | G→T | 12.0% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,441 | C→A | 5.9% | D437E (GAC→GAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,481,771 | G→T | 12.3% | P136T (CCG→ACG) | emrY ← | putative multidrug efflux system |
| RA | 2,731,581 | G→T | 5.1% | intergenic (‑424/+19) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,768,609 | T→C | 5.1% | intergenic (+36/‑56) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,768,614 | A→C | 5.3% | intergenic (+41/‑51) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,818,046 | A→G | 5.3% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,049 | T→A | 5.8% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,980,742 | A→G | 6.0% | intergenic (‑107/+22) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 2,980,744 | A→T | 6.0% | intergenic (‑109/+20) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 2,980,746 | C→T | 6.1% | intergenic (‑111/+18) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 3,046,068 | T→A | 9.4% | intergenic (‑167/+100) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,054,905 | T→G | 8.6% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein |
| RA | 3,057,140 | A→G | 5.2% | intergenic (+152/+38) | sibC → / ← serA | sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,239,609 | T→G | 9.4% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,270,101 | C→A | 7.6% | intergenic (+499/+115) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,324,952 | A→G | 5.0% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 5.3% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,392,157 | A→T | 5.2% | intergenic (‑129/+301) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,392,212 | C→G | 5.0% | intergenic (‑184/+246) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,423,375 | G→A | 7.8% | intergenic (+181/+48) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,439,588 | G→C | 5.4% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 5.3% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| 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 | 3,781,038 | T→A | 13.4% | intergenic (+21/‑177) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,051 | C→G | 6.5% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,131 | T→G | 5.2% | intergenic (+114/‑84) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,158 | A→C | 6.3% | intergenic (+141/‑57) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,790,300 | A→T | 5.3% | intergenic (‑219/+20) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,959,457 | T→G | 7.2% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,501 | T→A | 7.9% | intergenic (+56/+31) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 9.6% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,060,261 | G→T | 5.0% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,060,264 | A→C | 5.5% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,296,060 | C→T | 33.8% | 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 | 4,353,170 | G→A | 5.4% | intergenic (+89/+30) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,353,171 | C→G | 5.4% | intergenic (+90/+29) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,353,172 | C→G | 5.4% | intergenic (+91/+28) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,353,173 | T→C | 5.4% | intergenic (+92/+27) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,362,528 | G→A | 5.8% | intergenic (‑175/+23) | yjdQ ← / ← pheU | pseudogene, P4‑like integrase remnant/tRNA‑Phe |
| RA | 4,362,529 | T→C | 5.9% | intergenic (‑176/+22) | yjdQ ← / ← pheU | pseudogene, P4‑like integrase remnant/tRNA‑Phe |
| RA | 4,362,581 | C→A | 5.7% | noncoding (46/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,366,854 | T→G | 9.8% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,366,855 | C→A | 9.0% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,520,500 | Δ1 bp | 6.0% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 5.9% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,591,859 | A→C | 5.1% | N68T (AAC→ACC) | tsr → | methyl‑accepting chemotaxis protein I, serine sensor receptor |
| RA | 4,596,812 | C→A | 5.7% | H275N (CAT→AAT) | lgoD → | L‑galactonate oxidoreductase; L‑gulonate oxidoreductase |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 772977 | 774231 | 1255 | 193 [186] | [186] 188 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037678 | 1039343 | 1666 | 191 [184] | [182] 188 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 1166013 | 1167438 | 1426 | 188 [181] | [185] 188 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423720–3424234 | 3424577–3424238 | 5–858 | 190 [186] | [187] 190 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 224368 = | NA (NA) | 4 (0.010) | 3/264 | NT | NA | noncoding (598/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 224411 = | NA (NA) | noncoding (641/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 258469 = | NA (NA) | 7 (0.020) | 4/260 | NT | 9.2% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 279818 = | 74 (0.230) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 274038 = | NA (NA) | 5 (0.020) | 4/266 | NT | NA | noncoding (1112/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274083 = | NA (NA) | noncoding (1067/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 10 (0.030) | 5/260 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 274695 | NA (NA) | 7 (0.020) | 3/270 | NT | NA | noncoding (455/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274727 | NA (NA) | noncoding (423/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 315838 | NA (NA) | 8 (0.030) | 4/274 | NT | NA | noncoding (610/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315862 | NA (NA) | noncoding (634/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 316099 = | NA (NA) | 4 (0.010) | 3/262 | NT | NA | noncoding (871/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 316185 = | NA (NA) | noncoding (957/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 357544 | NA (NA) | 9 (0.030) | 7/264 | NT | NA | noncoding (61/79 nt) | REP27 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP27 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 357555 | NA (NA) | noncoding (72/79 nt) | REP27 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP27 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 381663 = | NA (NA) | 5 (0.020) | 3/264 | NT | NA | noncoding (404/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381703 = | NA (NA) | noncoding (444/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 5 (0.020) | 3/260 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382323 | NA (NA) | 3 (0.010) | 3/268 | NT | NA | noncoding (1064/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382348 | NA (NA) | noncoding (1089/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 715264 = | NA (NA) | 5 (0.020) | 3/264 | NT | NA | noncoding (1/98 nt) | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 715289 = | NA (NA) | noncoding (26/98 nt) | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 715264 = | NA (NA) | 8 (0.030) | 3/264 | NT | NA | noncoding (1/98 nt) | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 899768 | NA (NA) | noncoding (73/98 nt) | RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 781369 = | 233 (0.720) | 27 (0.090) +GAAG |
10/270 | NT | 10.2% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 257 (0.790) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1068490 | NA (NA) | 6 (0.020) | 5/262 | NT | NA | intergenic (+236/+21) | ymdF/rutG | KGG family protein/pyrimidine permease |
| ? | NC_000913 | = 1068495 | NA (NA) | intergenic (+241/+16) | ymdF/rutG | KGG family protein/pyrimidine permease | |||||
| * | ? | NC_000913 | 1097287 = | 53 (0.160) | 6 (0.020) | 4/262 | NT | 10.5% | intergenic (+458/+278) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097464 = | 52 (0.170) | intergenic (+635/+101) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1097456 = | 70 (0.220) | 5 (0.020) | 3/262 | NT | 7.8% | intergenic (+627/+109) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097476 = | 53 (0.170) | intergenic (+647/+89) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 215 (0.660) | 68 (0.240) | 50/246 | NT | 26.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 179 (0.620) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 202 (0.620) | 98 (0.340) | 67/246 | NT | 35.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 179 (0.620) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 295 (0.940) | 140/270 | 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 | = 1823410 | NA (NA) | 7 (0.020) | 5/268 | NT | NA | noncoding (80/98 nt) | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 1823421 | NA (NA) | noncoding (91/98 nt) | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 1843797 | NA (NA) | 8 (0.030) | 6/266 | NT | NA | noncoding (74/93 nt) | REP131 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP131 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 1843810 | NA (NA) | noncoding (87/93 nt) | REP131 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP131 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 2304902 | 86 (0.270) | 4 (0.020) +33 bp |
4/212 | NT | 5.8% | noncoding (486/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2305065 | NA (NA) | noncoding (649/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 2888334 = | NA (NA) | 4 (0.010) | 4/264 | NT | NA | noncoding (1/37 nt) | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 2888367 = | NA (NA) | noncoding (34/37 nt) | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | = 3070082 | NA (NA) | 11 (0.040) | 6/264 | NT | NA | noncoding (80/98 nt) | RIP213 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP213 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3740971 = | NA (NA) | noncoding (8/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 3304504 | NA (NA) | 6 (0.020) | 6/266 | NT | NA | noncoding (1/29 nt) | REP241 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP241 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 3304536 | NA (NA) | intergenic (+81/+37) | yhbW/mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity | |||||
| * | ? | NC_000913 | 3423373 = | 228 (0.700) | 16 (0.050) +ATGT |
9/270 | NT | 6.7% | intergenic (+179/+50) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913 | 3423672 = | NA (NA) | noncoding (116/120 nt) | rrfD | 5S ribosomal RNA of rrnD operon | |||||
| * | ? | NC_000913 | 3620119 = | NA (NA) | 5 (0.020) | 3/266 | NT | 100% | coding (928/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3620146 = | 0 (0.000) | coding (955/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3962703 | NA (NA) | 5 (0.020) | 4/266 | NT | NA | noncoding (4/36 nt) | REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 3962735 | NA (NA) | noncoding (36/36 nt) | REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | = 4040686 | 198 (0.610) | 20 (0.060) +ATGT |
9/270 | NT | 7.5% | intergenic (+50/+220) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4213155 | 313 (0.970) | noncoding (116/120 nt) | rrfE | 5S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | = 4209893 | 19 (0.060) | 3 (0.010) | 3/256 | NT | 14.6% | intergenic (+44/‑150) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon |
| ? | NC_000913 | = 4209911 | NA (NA) | intergenic (+62/‑132) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | 4542682 = | 249 (0.770) | 25 (0.080) | 18/260 | 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 = | 284 (0.940) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 247 (0.760) | 27 (0.090) | 14/260 | NT | 9.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 284 (0.940) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||