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 | 53,376 | G→A | 5.8% | P14L (CCC→CTC) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 53,379 | T→C | 5.6% | E13G (GAG→GGG) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 289,255 | T→A | 10.1% | intergenic (‑93/+46) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 357,578 | T→C | 5.3% | intergenic (+124/+213) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 420,941 | T→A | 5.3% | intergenic (+31/‑45) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 420,942 | G→T | 5.3% | intergenic (+32/‑44) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 420,945 | A→C | 5.2% | intergenic (+35/‑41) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 420,946 | T→A | 5.1% | intergenic (+36/‑40) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 556,019 | T→A | 5.3% | intergenic (+23/+13) | cysS → / ← ybcI | cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein |
| RA | 681,694 | A→G | 6.5% | intergenic (+31/+29) | djlC → / ← hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 758,459 | G→A | 5.3% | intergenic (+54/‑247) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 758,466 | G→T | 5.7% | intergenic (+61/‑240) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 758,467 | A→C | 5.1% | intergenic (+62/‑239) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 758,473 | T→G | 5.1% | intergenic (+68/‑233) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 781,254 | A→T | 7.3% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,269 | C→T | 7.8% | 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 | 1,015,912 | T→A | 7.7% | intergenic (+30/+40) | rmf → / ← fabA | ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase |
| RA | 1,146,625 | T→C | 5.4% | noncoding (37/169 nt) | psrD → | novel Novel sRNA, function unknown |
| RA | 1,151,890 | T→G | 5.6% | intergenic (+39/‑49) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,224,239 | A→T | 5.2% | intergenic (+332/+40) | ycgI → / ← minE | pseudogene/cell division topological specificity factor |
| RA | 1,224,242 | A→T | 5.4% | intergenic (+335/+37) | ycgI → / ← minE | pseudogene/cell division topological specificity factor |
| RA | 1,286,965 | A→T | 13.9% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,149 | G→A | 9.2% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,466,201 | T→C | 5.7% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 6.4% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,495 | C→T | 6.5% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,639 | C→T | 5.0% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,668 | G→A | 5.6% | pseudogene (1277/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,666,466 | T→G | 8.8% | Y384* (TAT→TAG) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,666,468 | A→T | 8.6% | Q385L (CAG→CTG) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,666,470 | C→A | 8.3% | L386I (CTA→ATA) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,708,709 | T→A | 11.1% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 5.5% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→A | 11.5% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,864,758 | G→A | 5.2% | 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 | 6.5% | 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 | 6.8% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,880,851 | T→A | 7.2% | intergenic (‑92/+35) | leuE ← / ← dmlR | leucine efflux protein/transcriptional activator of dmlA |
| RA | 1,880,852 | T→A | 7.7% | intergenic (‑93/+34) | leuE ← / ← dmlR | leucine efflux protein/transcriptional activator of dmlA |
| RA | 1,932,094 | C→G | 6.1% | 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 | 6.0% | 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 | 5.9% | 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 | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,028,158 | G→C | 8.6% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 8.6% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 8.7% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,079,004 | G→C | 7.5% | intergenic (+73/+28) | yoeF → / ← yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein |
| RA | 2,090,122 | A→G | 5.8% | intergenic (+76/‑70) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,124 | C→G | 5.8% | intergenic (+78/‑68) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,126 | C→T | 6.0% | intergenic (+80/‑66) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| 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 | 17.0% | 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 | 14.7% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,279 | C→A | 9.3% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,296 | G→T | 9.4% | intergenic (‑92/+216) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,229,177 | A→C | 17.3% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,229,322 | C→G | 5.4% | intergenic (+257/+116) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,229,323 | C→G | 5.5% | intergenic (+258/+115) | 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 | 2,304,680 | T→C | 6.4% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,311,619 | A→G | 5.4% | intergenic (‑85/+27) | apbE ← / ← ompC | putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,383,956 | A→T | 5.7% | 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 | 5.8% | intergenic (+35/+36) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,407,898 | A→C | 5.2% | Q113P (CAG→CCG) | alaA → | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,560,317 | A→C | 7.2% | N21H (AAT→CAT) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,560,321 | C→T | 7.7% | A22V (GCT→GTT) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,560,326 | A→G | 7.2% | T24A (ACA→GCA) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,560,330 | G→T | 7.2% | C25F (TGC→TTC) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,655,051 | T→A | 5.2% | intergenic (‑118/+24) | sseB ← / ← pepB | rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B |
| RA | 2,655,052 | T→A | 5.1% | intergenic (‑119/+23) | sseB ← / ← pepB | rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B |
| RA | 2,655,058 | G→T | 5.0% | intergenic (‑125/+17) | sseB ← / ← pepB | rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B |
| RA | 2,655,059 | C→T | 5.0% | intergenic (‑126/+16) | sseB ← / ← pepB | rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B |
| RA | 2,704,304 | A→G | 7.0% | intergenic (‑241/+31) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,306 | A→T | 7.0% | intergenic (‑243/+29) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,308 | C→T | 7.1% | intergenic (‑245/+27) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,716,030 | T→G | 5.0% | intergenic (+20/+36) | eamB → / ← grcA | cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor |
| RA | 2,761,620 | T→G | 7.5% | K641Q (AAG→CAG) | yfjK ← | radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage |
| RA | 2,761,623 | C→A | 8.1% | V640L (GTA→TTA) | yfjK ← | radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage |
| RA | 2,768,609 | T→C | 5.8% | 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 | 6.4% | intergenic (+41/‑51) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,768,615 | G→T | 6.0% | intergenic (+42/‑50) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,768,620 | G→A | 6.1% | intergenic (+47/‑45) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,817,916 | T→G | 11.1% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,046 | A→G | 5.7% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,049 | T→A | 7.3% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,866,487 | G→C | 7.1% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,866,488 | G→C | 7.1% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 3,156,590 | C→A | 5.7% | intergenic (+72/‑33) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,233,660 | A→C | 6.1% | T666P (ACA→CCA) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,239,609 | T→G | 12.8% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,610 | C→G | 8.8% | intergenic (+65/‑334) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,611 | C→A | 9.6% | intergenic (+66/‑333) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,270,082 | A→C | 5.2% | intergenic (+480/+134) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,143 | C→T | 6.9% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,313,207 | G→A | 5.9% | intergenic (‑29/+135) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,313,208 | T→A | 5.9% | intergenic (‑30/+134) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,313,209 | T→C | 5.9% | intergenic (‑31/+133) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,334,703 | A→G | 6.8% | intergenic (+22/‑206) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,704 | G→C | 6.7% | intergenic (+23/‑205) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,705 | C→T | 6.3% | intergenic (+24/‑204) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon 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 | 8.3% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,608,721 | A→C | 13.4% | intergenic (+72/+30) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,657,599 | T→A | 5.5% | intergenic (+32/+387) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,601 | G→C | 5.1% | intergenic (+34/+385) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,603 | T→A | 5.5% | intergenic (+36/+383) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,781,022 | T→G | 8.4% | intergenic (+5/‑193) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,051 | C→G | 6.0% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,145 | C→G | 6.9% | intergenic (+128/‑70) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,877,558 | G→C | 5.4% | intergenic (‑93/+147) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,908,507 | T→G | 6.8% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| RA | 3,959,480 | A→T | 5.3% | intergenic (+35/+52) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,481 | C→G | 5.4% | intergenic (+36/+51) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,060,261 | G→T | 6.5% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,060,264 | A→C | 7.0% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,070,457 | G→T | 8.3% | intergenic (‑56/+58) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,462 | T→A | 7.8% | intergenic (‑61/+53) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,463 | T→A | 7.0% | intergenic (‑62/+52) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,464 | T→A | 8.1% | intergenic (‑63/+51) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,469 | A→C | 10.8% | intergenic (‑68/+46) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,088,091 | G→C | 6.1% | intergenic (+34/+16) | yiiG → / ← frvR | DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,153,447 | A→G | 5.9% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,296,060 | C→T | 26.9% | 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 | 4,326,248 | G→A | 7.2% | intergenic (‑507/+151) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,366,854 | T→G | 5.7% | intergenic (‑81/+37) | 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 | 4,596,812 | C→A | 9.3% | H275N (CAT→AAT) | lgoD → | L‑galactonate oxidoreductase; L‑gulonate oxidoreductase |
| RA | 4,633,634 | C→T | 89.2% | E38K (GAG→AAG) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| 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 | 772996 | 774216 | 1221 | 92 [90] | [90] 95 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037697 | 1039332 | 1636 | 94 [88] | [88] 91 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 1166013 | 1167448 | 1436 | 93 [90] | [88] 91 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423733–3424560 | 3424560 | 1–828 | 93 [88] | [80] 93 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 213086 | 213 (1.110) | 12 (0.060) | 4/270 | NT | 5.2% | coding (756/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase |
| ? | NC_000913 | = 213115 | 233 (1.250) | coding (785/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase | |||||
| * | ? | NC_000913 | 781369 = | 127 (0.660) | 22 (0.120) +GAAG |
15/270 | NT | 15.1% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 127 (0.660) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 1207790 = | 136 (0.710) | 46 (0.270) | 29/246 | NT | 28.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 112 (0.660) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 130 (0.680) | 76 (0.450) | 43/246 | NT | 40.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 112 (0.660) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 166 (0.890) | 82/270 | 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 | 1360805 = | 147 (0.760) | 8 (0.040) | 3/260 | NT | 5.4% | coding (104/1419 nt) | puuA | glutamate‑‑putrescine ligase |
| ? | NC_000913 | 1360853 = | 145 (0.810) | coding (56/1419 nt) | puuA | glutamate‑‑putrescine ligase | |||||
| * | ? | NC_000913 | 1484624 = | 164 (0.850) | 10 (0.050) | 6/270 | NT | 5.8% | coding (1564/3903 nt) | hrpA | putative ATP‑dependent helicase |
| ? | NC_000913 | 1484660 = | 167 (0.890) | coding (1600/3903 nt) | hrpA | putative ATP‑dependent helicase | |||||
| * | ? | NC_000913 | = 2817942 | 124 (0.640) | 14 (0.090) | 8/238 | NT | 10.5% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 133 (0.810) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | 3217434 = | NA (NA) | 8 (0.040) | 3/264 | NT | NA | noncoding (1/89 nt) | REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 3217467 = | NA (NA) | noncoding (34/89 nt) | REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 3392102 | 241 (1.250) | 10 (0.070) | 10/212 | NT | 5.5% | noncoding (27/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences |
| ? | NC_000913 | 3392377 = | 160 (1.090) | noncoding (302/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | |||||
| * | ? | NC_000913 | 3667192 = | 0 (0.000) | 5 (0.030) | 3/266 | NT | 16.9% | coding (389/1401 nt) | gadA | glutamate decarboxylase A, PLP‑dependent |
| ? | NC_000913 | 3667233 = | 49 (0.270) | coding (348/1401 nt) | gadA | glutamate decarboxylase A, PLP‑dependent | |||||
| * | ? | NC_000913 | 4235376 = | NA (NA) | 3 (0.020) | 3/256 | NT | NA | coding (1619/1650 nt) | pgi | glucosephosphate isomerase |
| ? | NC_000913 | 4235411 = | NA (NA) | intergenic (+4/‑495) | pgi/yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein | |||||
| * | ? | NC_000913 | 4542682 = | 141 (0.730) | 15 (0.080) | 8/260 | NT | 9.3% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 162 (0.900) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 135 (0.700) | 10 (0.060) | 8/260 | NT | 6.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 162 (0.900) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4549784 | NA (NA) | 10 (0.050) | 5/266 | NT | NA | noncoding (2/36 nt) | REP345 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP345 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 4549822 | NA (NA) | intergenic (+112/+131) | fimH/gntP | minor component of type 1 fimbriae/fructuronate transporter | |||||