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 | 10,659 | C→T | 6.2% | S233N (AGC→AAC) | yaaW ← | UPF0174 family protein |
| RA | 59,625 | G→A | 7.3% | intergenic (+346/+62) | yabP → / ← rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| RA | 59,626 | A→G | 7.7% | intergenic (+347/+61) | yabP → / ← rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| RA | 59,627 | C→T | 7.4% | intergenic (+348/+60) | yabP → / ← rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| RA | 59,628 | T→C | 7.6% | intergenic (+349/+59) | yabP → / ← rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| RA | 78,576 | G→A | 6.8% | G319D (GGC→GAC) | setA → | broad specificity sugar efflux system |
| RA | 111,016 | T→C | 5.4% | intergenic (+32/‑28) | secA → / → mutT | preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 125,817 | A→G | 11.0% | K41K (AAA→AAG) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,060 | A→G | 5.2% | E122E (GAA→GAG) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,093 | T→C | 11.1% | A133A (GCT→GCC) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,126 | G→A | 11.1% | K144K (AAG→AAA) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 163,417 | A→T | 10.7% | K438I (AAA→ATA) ‡ | hrpB → | putative ATP‑dependent helicase |
| RA | 163,418 | A→T | 9.6% | K438N (AAA→AAT) ‡ | hrpB → | putative ATP‑dependent helicase |
| RA | 163,419 | A→T | 9.9% | I439F (ATT→TTT) | hrpB → | putative ATP‑dependent helicase |
| RA | 201,032 | G→A | 6.2% | G21D (GGC→GAC) | lpxD → | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 256,915 | C→T | 5.1% | T130M (ACG→ATG) | frsA → | fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| RA | 256,926 | A→G | 5.5% | I134V (ATT→GTT) | frsA → | fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 464,354 | C→A | 8.1% | intergenic (+46/‑48) | ybaV → / → fadM | putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III |
| RA | 464,356 | A→T | 9.3% | intergenic (+48/‑46) | ybaV → / → fadM | putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III |
| RA | 464,358 | T→G | 11.8% | intergenic (+50/‑44) | ybaV → / → fadM | putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III |
| RA | 475,971 | C→G | 10.0% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 9.8% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 525,588 | A→G | 5.1% | K776K (AAA→AAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 543,748 | G→C | 6.9% | T100R (ACA→AGA) | allE ← | S‑ureidoglycine aminohydrolase |
| RA | 659,204 | C→T | 7.1% | intergenic (+54/+47) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,205 | A→T | 7.3% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 8.9% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 7.1% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 676,686 | T→A | 7.5% | intergenic (‑139/‑25) | ybeQ ← / → ybeR | Sel1 family TPR‑like repeat protein/uncharacterized protein |
| RA | 710,170 | C→T | 6.5% | intergenic (+54/+30) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 710,173 | A→G | 6.7% | intergenic (+57/+27) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 794,939 | T→C | 8.7% | intergenic (+17/‑150) | acrZ → / → modA | AcrAB‑TolC efflux pump accessory protein, membrane‑associated/molybdate ABC transporter periplasmic binding protein; chlorate resistance protein |
| RA | 808,205 | A→C | 22.1% | R351R (CGT→CGG) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 951,030 | G→A | 5.5% | D17D (GAC→GAT) | pflA ← | pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase |
| RA | 1,062,893 | A→G | 10.6% | S295P (TCG→CCG) | cbpA ← | DnaK co‑chaperone; curved DNA‑binding protein |
| RA | 1,129,394 | G→C | 7.9% | intergenic (+20/+20) | murJ → / ← flgN | putative lipid II flippase/export chaperone for FlgK and FlgL |
| RA | 1,141,150 | G→A | 6.4% | intergenic (+164/+32) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,141,151 | T→C | 7.0% | intergenic (+165/+31) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,141,153 | A→G | 6.5% | intergenic (+167/+29) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,243,335 | C→T | 6.4% | V52V (GTC→GTT) | emtA → | lytic murein endotransglycosylase E |
| RA | 1,449,799 | C→G | 9.0% | T517T (ACG→ACC) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,449,802 | A→G | 8.5% | A516A (GCT→GCC) ‡ | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,449,803 | G→C | 8.8% | A516G (GCT→GGT) ‡ | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,449,804 | C→T | 9.0% | A516T (GCT→ACT) ‡ | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,449,807 | C→G | 8.8% | G515R (GGT→CGT) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,460,565 | G→A | 6.2% | G32D (GGC→GAC) | paaI → | hydroxyphenylacetyl‑CoA thioesterase |
| RA | 1,466,144 | G→T | 10.7% | pseudogene (753/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 13.4% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,575,215 | C→T | 5.1% | intergenic (‑13/+32) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,575,216 | G→A | 5.2% | intergenic (‑14/+31) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,575,221 | T→C | 5.4% | intergenic (‑19/+26) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,596,499 | C→A | 9.0% | pseudogene (1489/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,602,990 | Δ1 bp | 8.3% | coding (1501/1536 nt) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,642,370 | C→G | 6.8% | intergenic (+303/+119) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,704,723 | T→C | 5.8% | intergenic (+47/‑226) | blr → / → cnu | beta‑lactam resistance membrane protein; divisome‑associated protein/nucleoid‑associated oriC‑binding protein; H‑NS and StpA stabilizing factor |
| RA | 1,784,808 | C→T | 7.0% | G769R (GGG→AGG) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,823,335 | G→C | 11.1% | intergenic (+50/‑180) | nadE → / → cho | NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair |
| RA | 1,823,338 | G→C | 11.5% | intergenic (+53/‑177) | nadE → / → cho | NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair |
| RA | 1,864,768 | T→C | 6.4% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,904,041 | A→T | 5.8% | A49A (GCA→GCT) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,982,500 | T→C | 6.5% | intergenic (‑113/+54) | otsB ← / ← araH | trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease |
| RA | 1,982,501 | T→C | 6.6% | intergenic (‑114/+53) | otsB ← / ← araH | trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease |
| RA | 1,982,505 | G→A | 6.1% | intergenic (‑118/+49) | otsB ← / ← araH | trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease |
| RA | 1,992,083 | G→C | 5.2% | noncoding (35/76 nt) | glyW ← | tRNA‑Gly |
| RA | 2,015,192 | A→G | 8.3% | S105G (AGC→GGC) | fliG → | flagellar motor switching and energizing component |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,044,721 | G→A | 8.1% | intergenic (+97/‑217) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,044,725 | T→A | 8.6% | intergenic (+101/‑213) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,044,727 | T→A | 7.7% | intergenic (+103/‑211) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,044,729 | T→A | 7.6% | intergenic (+105/‑209) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,044,733 | T→C | 7.8% | intergenic (+109/‑205) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,045,793 | C→T | 9.1% | L286L (CTG→TTG) | yeeJ → | putative adhesin |
| RA | 2,059,946 | T→A | 12.3% | intergenic (+20/+18) | asnU → / ← cbl | tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,059,948 | T→A | 11.4% | intergenic (+22/+16) | asnU → / ← cbl | tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,059,950 | T→A | 12.9% | intergenic (+24/+14) | asnU → / ← cbl | tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,139,716 | T→G | 6.8% | intergenic (+231/+43) | yegH → / ← asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,139,718 | T→A | 5.9% | intergenic (+233/+41) | yegH → / ← asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,139,720 | C→A | 6.5% | intergenic (+235/+39) | yegH → / ← asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,139,726 | T→G | 7.3% | intergenic (+241/+33) | yegH → / ← asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,139,727 | T→C | 5.8% | intergenic (+242/+32) | yegH → / ← asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic 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 | 2,231,175 | G→A | 8.1% | D53N (GAC→AAC) | yohK → | LrgB family inner membrane protein |
| RA | 2,310,322 | A→T | 9.9% | V28V (GTT→GTA) | ada ← | fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase |
| RA | 2,323,581 | C→T | 6.4% | R45R (CGC→CGT) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| RA | 2,352,779 | G→A | 6.1% | G45S (GGT→AGT) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,357,025 | A→G | 9.6% | N41S (AAC→AGC) ‡ | yfaD → | transposase_31 family protein |
| RA | 2,357,026 | C→G | 8.5% | N41K (AAC→AAG) ‡ | yfaD → | transposase_31 family protein |
| RA | 2,357,027 | C→T | 9.2% | L42L (CTG→TTG) | yfaD → | transposase_31 family protein |
| RA | 2,357,034 | C→G | 8.6% | T44S (ACC→AGC) | yfaD → | transposase_31 family protein |
| RA | 2,357,665 | G→A | 9.1% | G254G (GGG→GGA) | yfaD → | transposase_31 family protein |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,432,985 | A→G | 5.9% | intergenic (‑43/+27) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,990 | G→C | 6.6% | intergenic (‑48/+22) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,529,856 | T→C | 5.5% | K107K (AAA→AAG) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 2,536,370 | C→G | 7.9% | intergenic (+27/+16) | crr → / ← pdxK | glucose‑specific enzyme IIA component of PTS/pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| RA | 2,536,373 | C→G | 6.7% | intergenic (+30/+13) | crr → / ← pdxK | glucose‑specific enzyme IIA component of PTS/pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| RA | 2,564,635 | G→C | 6.6% | R38P (CGC→CCC) | yffS → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,564,640 | G→C | 6.9% | G40R (GGA→CGA) | yffS → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,597,699 | G→T | 7.4% | intergenic (‑81/+132) | purC ← / ← bamC | phosphoribosylaminoimidazole‑succinocarboxamide synthetase/BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,669,275 | C→A | 13.0% | L82I (CTC→ATC) | hcaE → | 3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,801,056 | A→T | 11.5% | N31I (AAT→ATT) | nrdI → | NrdEF cluster assembly flavodoxin |
| RA | 2,851,603 | C→T | 7.4% | S201S (AGC→AGT) | hypB → | GTP hydrolase involved in nickel liganding into hydrogenases |
| RA | 2,904,212 | G→A | 88.9% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,906,608 | G→C | 5.1% | intergenic (+25/+35) | ygcG → / ← eno | TPM domain protein, putative phosphatase/enolase |
| RA | 2,906,609 | G→C | 5.1% | intergenic (+26/+34) | ygcG → / ← eno | TPM domain protein, putative phosphatase/enolase |
| RA | 2,917,910 | T→C | 6.0% | intergenic (+97/+135) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,976,320 | T→G | 6.9% | noncoding (66/82 nt) | omrB ← | sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent |
| RA | 2,976,321 | C→A | 8.3% | noncoding (65/82 nt) | omrB ← | sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent |
| RA | 2,979,199 | C→A | 9.3% | P60H (CCT→CAT) | lysR → | transcriptional activator of lysA; autorepressor |
| RA | 3,020,821 | A→G | 6.1% | S94S (TCA→TCG) | ygfM → | putative oxidoreductase |
| RA | 3,156,591 | T→G | 7.6% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,171,852 | C→T | 6.3% | intergenic (+19/+27) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,171,857 | A→T | 6.5% | intergenic (+24/+22) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,171,858 | A→T | 6.5% | intergenic (+25/+21) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,171,863 | A→G | 6.4% | intergenic (+30/+16) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,194,875 | T→C | 11.8% | intergenic (‑10/+224) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,195,148 | A→C | 8.8% | noncoding (93/142 nt) K3T (AAG→ACG) |
sibE ← ibsE → |
sRNA antisense regulator of toxic IbsE protein toxic membrane protein |
| RA | 3,195,151 | T→G | 7.1% | noncoding (90/142 nt) L4R (CTC→CGC) |
sibE ← ibsE → |
sRNA antisense regulator of toxic IbsE protein toxic membrane protein |
| RA | 3,195,153 | G→T | 7.0% | noncoding (88/142 nt) V5F (GTC→TTC) |
sibE ← ibsE → |
sRNA antisense regulator of toxic IbsE protein toxic membrane protein |
| RA | 3,263,892 | A→G | 5.2% | W376R (TGG→CGG) | tdcC ← | L‑threonine/L‑serine transporter |
| RA | 3,269,917 | T→C | 7.9% | intergenic (+315/+299) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,440,923 | C→A | 18.7% | G36V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,441,061 | G→C | 5.8% | S205S (TCC→TCG) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,448,276 | T→A | 5.2% | intergenic (‑127/+38) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,505,096 | C→T | 7.5% | A309T (GCA→ACA) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| 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 | 3,623,820 | C→T | 5.5% | intergenic (+38/‑67) | yhhH → / → yrhC | putative NTF2 fold immunity protein for polymorphic toxin RhsB/pseudogene fragment |
| RA | 3,689,724 | G→C | 6.9% | P180A (CCC→GCC) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,689,728 | A→T | 7.0% | F178L (TTT→TTA) ‡ | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,689,729 | A→T | 6.8% | F178Y (TTT→TAT) ‡ | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,689,733 | G→C | 6.4% | R177G (CGT→GGT) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,732,136 | A→C | 5.6% | intergenic (+13/‑65) | xylF → / → xylG | D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase |
| RA | 3,817,940 | T→A | 5.5% | F61I (TTC→ATC) | dinD → | DNA damage‑inducible protein |
| RA | 3,817,948 | G→T | 5.1% | E63D (GAG→GAT) | dinD → | DNA damage‑inducible protein |
| RA | 3,817,949 | A→C | 5.6% | I64L (ATC→CTC) | dinD → | DNA damage‑inducible protein |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,891,506 | C→G | 6.2% | intergenic (+23/‑109) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,965,670 | C→T | 5.7% | intergenic (‑40/‑91) | rhlB ← / → trxA | ATP‑dependent RNA helicase/thioredoxin 1 |
| RA | 4,050,225 | A→T | 7.7% | L181M (TTG→ATG) | yihA ← | cell division GTP‑binding protein |
| RA | 4,051,262 | A→C | 7.2% | noncoding (227/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,060,261 | G→T | 7.0% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,060,264 | A→C | 8.7% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,155,881 | C→T | 5.2% | A294V (GCC→GTC) | argC → | N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding |
| RA | 4,296,060 | C→T | 42.8% | 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 | 4,326,072 | T→G | 8.8% | intergenic (‑331/+327) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,332,871 | A→C | 13.3% | S134R (AGT→AGG) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| RA | 4,353,170 | G→A | 5.3% | 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 | 5.9% | 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 | 5.3% | 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 | 6.2% | intergenic (+92/+27) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,362,581 | C→A | 37.3% | noncoding (46/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,415,525 | G→T | 11.3% | E417D (GAG→GAT) | aidB → | DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,448,424 | T→A | 5.8% | intergenic (+189/‑23) | ytfP → / → chpS | GGCT‑like protein/antitoxin of the ChpBS toxin‑antitoxin system |
| RA | 4,470,952 | T→C | 5.8% | intergenic (‑39/+34) | ridA ← / ← pyrI | enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit |
| RA | 4,470,958 | G→T | 7.3% | intergenic (‑45/+28) | ridA ← / ← pyrI | enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit |
| RA | 4,554,516 | A→G | 6.4% | intergenic (+155/‑60) | uxuB → / → uxuR | D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor |
| RA | 4,612,329 | A→G | 8.8% | intergenic (+40/‑82) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| RA | 4,612,330 | G→C | 8.5% | intergenic (+41/‑81) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| RA | 4,612,331 | C→T | 8.4% | intergenic (+42/‑80) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| RA | 4,633,743 | C→T | 38.1% | M1M (ATG→ATA) † | 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 | 772980 | 774221 | 1242 | 21 [19] | [19] 20 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037699 | 1039310 | 1612 | 20 [18] | [19] 21 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 3423733–3424234 | 3424549–3424238 | 5–817 | 20 [19] | [18] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 16653 | NA (NA) | 4 (0.070) | 4/262 | NT | NA | noncoding (1267/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 16691 | NA (NA) | noncoding (1305/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 274334 | NA (NA) | 4 (0.070) | 3/264 | NT | NA | noncoding (816/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274338 | NA (NA) | noncoding (812/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274347 = | NA (NA) | 3 (0.050) | 3/262 | NT | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 3 (0.050) | 3/258 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 315646 | NA (NA) | 4 (0.070) | 4/266 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 377834 | 55 (0.930) | 3 (0.050) | 3/264 | NT | 5.2% | coding (535/834 nt) | frmB | S‑formylglutathione hydrolase |
| ? | NC_000913 | = 377846 | 56 (0.990) | coding (523/834 nt) | frmB | S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 381663 = | NA (NA) | 3 (0.050) | 3/262 | NT | NA | noncoding (404/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381703 = | NA (NA) | noncoding (444/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 396419 = | 58 (0.980) | 4 (0.070) | 4/268 | NT | 6.8% | intergenic (‑132/‑220) | ampH/sbmA | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase/peptide antibiotic transporter |
| ? | NC_000913 | 396441 = | 54 (0.940) | intergenic (‑154/‑198) | ampH/sbmA | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase/peptide antibiotic transporter | |||||
| * | ? | NC_000913 | = 415136 | 55 (0.930) | 4 (0.070) | 4/268 | NT | 7.3% | coding (618/3147 nt) | sbcC | exonuclease, dsDNA, ATP‑dependent |
| ? | NC_000913 | = 415165 | 48 (0.830) | coding (589/3147 nt) | sbcC | exonuclease, dsDNA, ATP‑dependent | |||||
| * | ? | NC_000913 | 511333 = | 51 (0.860) | 3 (0.050) | 3/266 | NT | 5.9% | coding (47/2505 nt) | copA | copper transporter |
| ? | NC_000913 | 511361 = | 46 (0.810) | coding (19/2505 nt) | copA | copper transporter | |||||
| * | ? | NC_000913 | = 630079 | 41 (0.690) | 4 (0.070) | 4/262 | NT | 9.9% | coding (186/2106 nt) | cstA | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| ? | NC_000913 | = 630098 | 34 (0.600) | coding (205/2106 nt) | cstA | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein | |||||
| * | ? | NC_000913 | = 645068 | 60 (1.010) | 4 (0.070) | 3/254 | NT | 6.5% | intergenic (‑65/+49) | rna/citT | ribonuclease I/citrate/succinate antiporter; citrate carrier |
| ? | NC_000913 | = 645074 | 59 (1.080) | intergenic (‑71/+43) | rna/citT | ribonuclease I/citrate/succinate antiporter; citrate carrier | |||||
| * | ? | NC_000913 | = 730045 | NA (NA) | 3 (0.050) | 3/266 | NT | NA | coding (463/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 730067 | NA (NA) | coding (485/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 944904 = | 58 (0.980) | 4 (0.070) | 4/260 | NT | 6.9% | intergenic (+8/+27) | dmsC/ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase |
| ? | NC_000913 | 944926 = | 53 (0.950) | intergenic (+30/+5) | dmsC/ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase | |||||
| * | ? | NC_000913 | 1207790 = | 11 (0.190) | 15 (0.290) | 14/244 | NT | 52.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.200) | 20 (0.380) | 17/244 | NT | 59.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.020) | 75 (1.300) | 62/268 | NT | 99.4% | 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 | 1360160 = | 59 (1.000) | 4 (0.070) | 4/270 | NT | 6.5% | coding (749/1419 nt) | puuA | glutamate‑‑putrescine ligase |
| ? | NC_000913 | 1360180 = | 57 (0.980) | coding (729/1419 nt) | puuA | glutamate‑‑putrescine ligase | |||||
| * | ? | NC_000913 | 1825065 = | 68 (1.150) | 4 (0.070) | 4/262 | NT | 5.8% | intergenic (‑128/+75) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| ? | NC_000913 | 1825118 = | 65 (1.160) | intergenic (‑181/+22) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced | |||||
| * | ? | NC_000913 | = 1826224 | 56 (0.940) | 3 (0.050) | 3/264 | NT | 5.2% | coding (700/969 nt) | astE | succinylglutamate desuccinylase |
| ? | NC_000913 | = 1826327 | 56 (0.990) | coding (597/969 nt) | astE | succinylglutamate desuccinylase | |||||
| * | ? | NC_000913 | = 1828872 | 59 (1.000) | 4 (0.070) | 4/258 | NT | 6.4% | coding (863/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase |
| ? | NC_000913 | = 1828893 | 61 (1.100) | coding (842/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase | |||||
| * | ? | NC_000913 | = 2209958 | 55 (0.930) | 3 (0.050) | 3/260 | NT | 5.7% | pseudogene (859/2001 nt) | yehQ | pseudogene |
| ? | NC_000913 | = 2209979 | 48 (0.860) | pseudogene (880/2001 nt) | yehQ | pseudogene | |||||
| * | ? | NC_000913 | = 2385264 | 61 (1.030) | 3 (0.050) | 3/266 | NT | 5.1% | coding (459/1728 nt) | yfbK | Von Willebrand factor domain putative lipoprotein |
| ? | NC_000913 | = 2385282 | 54 (0.950) | coding (441/1728 nt) | yfbK | Von Willebrand factor domain putative lipoprotein | |||||
| * | ? | NC_000913 | = 2446595 | 53 (0.890) | 5 (0.090) | 3/268 | NT | 9.5% | coding (879/1086 nt) | aroC | chorismate synthase |
| ? | NC_000913 | = 2446636 | 44 (0.760) | coding (838/1086 nt) | aroC | chorismate synthase | |||||
| * | ? | NC_000913 | = 2455060 | 74 (1.250) | 6 (0.110) | 3/258 | NT | 7.7% | intergenic (‑59/+23) | yfcU/yfcV | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein/putative fimbrial‑like adhesin protein |
| ? | NC_000913 | = 2455066 | 75 (1.350) | intergenic (‑65/+17) | yfcU/yfcV | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein/putative fimbrial‑like adhesin protein | |||||
| * | ? | NC_000913 | = 2729452 | 32 (0.540) | 3 (0.050) | 3/256 | NT | 8.4% | intergenic (‑8/+164) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 4168342 = | 36 (0.660) | intergenic (+142/‑30) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 2729475 = | 38 (0.640) | 3 (0.050) | 3/256 | NT | 8.8% | intergenic (‑31/+141) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 4168363 | 27 (0.490) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | = 2900530 | 86 (1.450) | 5 (0.090) | 4/254 | NT | 5.6% | intergenic (‑257/‑62) | ygcW/yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| ? | NC_000913 | = 2900548 | 88 (1.610) | intergenic (‑275/‑44) | ygcW/yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein | |||||
| * | ? | NC_000913 | 3153895 = | 54 (0.910) | 3 (0.050) | 3/266 | NT | 5.7% | coding (333/660 nt) | yghB | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| ? | NC_000913 | 3153945 = | 47 (0.820) | coding (383/660 nt) | yghB | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter | |||||
| * | ? | NC_000913 | 3198857 = | 44 (0.740) | 4 (0.070) | 4/268 | NT | 9.1% | coding (785/2841 nt) | glnE | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| ? | NC_000913 | 3198892 = | 37 (0.640) | coding (750/2841 nt) | glnE | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase | |||||
| * | ? | NC_000913 | 3583431 = | NA (NA) | 4 (0.070) +CCC |
4/270 | NT | 100% | noncoding (4/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4640551 = | 0 (0.000) | intergenic (+9/‑391) | yjjY/yjtD | uncharacterized protein/putative methyltransferase | |||||
| * | ? | NC_000913 | 3605170 = | 79 (1.330) | 5 (0.090) | 5/254 | NT | 6.6% | coding (192/270 nt) | yhhL | DUF1145 family protein |
| ? | NC_000913 | 3605202 = | 69 (1.270) | coding (224/270 nt) | yhhL | DUF1145 family protein | |||||
| * | ? | NC_000913 | 3726887 = | 91 (1.540) | 5 (0.090) | 5/254 | NT | 5.6% | intergenic (+5/+37) | wecH/yiaA | O‑acetyltransferase for enterobacterial common antigen (ECA)/YiaAB family inner membrane protein, tandem domains |
| ? | NC_000913 | 3726917 = | 85 (1.560) | intergenic (+35/+7) | wecH/yiaA | O‑acetyltransferase for enterobacterial common antigen (ECA)/YiaAB family inner membrane protein, tandem domains | |||||
| * | ? | NC_000913 | 4326878 = | 99 (1.670) | 6 (0.110) | 6/258 | NT | 6.2% | intergenic (‑144/‑257) | yjdM/crfC | zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| ? | NC_000913 | 4326902 = | 88 (1.590) | intergenic (‑168/‑233) | yjdM/crfC | zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related | |||||