mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 111,013 | G→A | 5.9% | intergenic (+29/‑31) | secA → / → mutT | preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 111,016 | T→C | 5.7% | intergenic (+32/‑28) | secA → / → mutT | preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 510,057 | C→T | 7.4% | V441V (GTG→GTA) | copA ← | copper transporter |
| RA | 623,054 | A→T | 6.4% | N252I (AAC→ATC) | entS → | enterobactin exporter, iron‑regulated |
| RA | 623,058 | G→C | 5.9% | W253C (TGG→TGC) | entS → | enterobactin exporter, iron‑regulated |
| RA | 623,062 | A→T | 5.6% | M255L (ATG→TTG) | entS → | enterobactin exporter, iron‑regulated |
| RA | 659,204 | C→T | 7.1% | intergenic (+54/+47) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,205 | A→T | 6.9% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 6.9% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 7.0% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 666,687 | Δ1 bp | 5.4% | coding (1531/1902 nt) | mrdA ← | penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis |
| RA | 773,446 | T→C | 5.9% | G135G (GGT→GGC) | cydB → | cytochrome d terminal oxidase, subunit II |
| RA | 927,369 | C→A | 5.4% | E22* (GAG→TAG) | aat ← | leucyl/phenylalanyl‑tRNA‑protein transferase |
| RA | 987,560 | G→C | 5.5% | intergenic (‑578/+25) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 987,561 | G→C | 6.3% | intergenic (‑579/+24) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,056,777 | C→T | 6.5% | P173S (CCC→TCC) | torT → | periplasmic sensory protein associated with the TorRS two‑component regulatory system |
| RA | 1,174,304 | C→A | 6.4% | V288F (GTT→TTT) | ycfT ← | inner membrane protein |
| RA | 1,208,443 | A→G | 5.1% | Q104Q (CAA→CAG) | tfaP → | e14 prophage; uncharacterized protein |
| RA | 1,217,116 | T→G | 5.8% | intergenic (+120/‑212) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,798 | T→C | 5.4% | intergenic (+30/+23) | oppF → / ← yciU | oligopeptide ABC transporter ATPase/UPF0263 family protein |
| RA | 1,306,807 | C→G | 5.5% | intergenic (+39/+14) | oppF → / ← yciU | oligopeptide ABC transporter ATPase/UPF0263 family protein |
| RA | 1,313,034 | A→G | 5.2% | S210S (TCT→TCC) | yciC ← | UPF0259 family inner membrane protein |
| RA | 1,408,537 | A→T | 5.9% | E163V (GAG→GTG) | ydaN → | putative Zn(II) transporter |
| RA | 1,408,546 | A→T | 5.7% | H166L (CAC→CTC) | ydaN → | putative Zn(II) transporter |
| RA | 1,679,331 | G→A | 5.5% | R302H (CGT→CAT) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,733,729 | G→A | 5.5% | intergenic (+26/+25) | lhr → / ← grxD | putative ATP‑dependent helicase/glutaredoxin‑4 |
| RA | 1,738,554 | G→A | 6.2% | P237P (CCG→CCA) | purR → | transcriptional repressor, hypoxanthine‑binding |
| JC JC | 1,806,309 | IS5 (+) +4 bp | 100% | intergenic (‑226/‑58) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| RA | 1,806,319 | C→T | 100% | intergenic (‑236/‑51) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| RA | 1,806,935 | A→T | 5.2% | K189I (AAA→ATA) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,806,982 | G→A | 82.5% | V205I (GTC→ATC) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,840,777 | T→C | 6.0% | intergenic (+3/+6) | ynjE → / ← ynjF | molybdopterin synthase sulfurtransferase/CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,988,048 | A→T | 6.5% | intergenic (‑89/‑174) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,049 | C→T | 6.5% | intergenic (‑90/‑173) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,050 | A→G | 6.7% | intergenic (‑91/‑172) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,051 | A→T | 7.9% | intergenic (‑92/‑171) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 2,070,230 | T→C | 5.9% | intergenic (‑50/‑47) | insC1 ← / → yoeA | IS2 repressor TnpA/CP4‑44 prophage; putative disrupted hemin or colicin receptor;Phage or Prophage Related; interrupted by IS2 and C‑terminal deletion |
| RA | 2,098,076 | C→T | 5.4% | A76T (GCC→ACC) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,120,246 | A→G | 5.3% | Y437H (TAC→CAC) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,200,106 | C→T | 5.9% | pseudogene (785/948 nt) | yehH → | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| RA | 2,252,012 | C→T | 6.0% | L105L (CTG→TTG) | yeiI → | putative kinase |
| RA | 2,294,209 | G→A | 6.4% | Y232Y (TAC→TAT) | ccmF ← | heme lyase, CcmF subunit |
| RA | 2,304,649 | C→T | 16.7% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,378,156 | G→A | 5.7% | G368G (GGC→GGT) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,398,261 | A→T | 5.3% | D635E (GAT→GAA) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,454,402 | C→T | 5.5% | pseudogene (600/2646 nt) | yfcU ← | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,539,241 | T→C | 5.0% | K115E (AAA→GAA) | cysM ← | cysteine synthase B (O‑acetylserine sulfhydrolase B) |
| RA | 2,560,996 | G→T | 22.0% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,589,065 | G→A | 6.1% | A491T (GCT→ACT) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,715,258 | A→G | 6.6% | A21A (GCT→GCC) ‡ | yfiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,715,259 | G→C | 7.3% | A21G (GCT→GGT) ‡ | yfiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,715,260 | C→T | 5.8% | A21T (GCT→ACT) ‡ | yfiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,866,488 | G→C | 5.1% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,918,017 | C→T | 7.5% | intergenic (+204/+28) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,019 | G→T | 7.2% | intergenic (+206/+26) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,020 | A→C | 7.3% | intergenic (+207/+25) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,918,022 | A→G | 7.6% | intergenic (+209/+23) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,951,471 | G→A | 5.5% | R331C (CGC→TGC) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 3,020,510 | G→T | 6.8% | intergenic (+21/‑30) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,511 | C→G | 6.5% | intergenic (+22/‑29) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,512 | A→C | 6.5% | intergenic (+23/‑28) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,037,787 | A→G | 6.4% | V107A (GTA→GCA) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,058,222 | G→A | 5.4% | T63T (ACC→ACT) | serA ← | D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,155,912 | T→G | 5.3% | R186R (CGT→CGG) | yqhD → | aldehyde reductase, NADPH‑dependent |
| RA | 3,234,024 | G→A | 5.3% | L41L (CTG→TTG) | higA ← | antitoxinof the HigB‑HigA toxin‑antitoxin system |
| 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 | 3,678,713 | C→T | 5.9% | D159N (GAT→AAT) | yhjH ← | cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| RA | 3,806,430 | C→A | 10.7% | R213L (CGC→CTC) | waaG ← | UDP‑glucose:(heptosyl)lipopolysaccharide alpha‑1,3‑glucosyltransferase; lipopolysaccharide core biosynthesis protein; lipopolysaccharide glucosyltransferase I |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,891,502 | C→G | 5.1% | intergenic (+19/‑113) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,891,506 | C→G | 5.1% | intergenic (+23/‑109) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 33.3% | 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 | 4,325,948 | A→G | 6.5% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,520,500 | Δ1 bp | 7.6% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 7.5% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423710–3424234 | 3424547–3424238 | 5–838 | 39 [36] | [36] 37 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107529 | 4108537 | 1009 | 37 [36] | [35] 39 | pfkA | pfkA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274620 = | NA (NA) | 5 (0.060) | 4/248 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 11 (0.120) | 9/266 | NT | 84.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1806304 | 2 (0.020) | intergenic (‑221/‑66) | ydiY/pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.300) | 49 (0.630) | 46/234 | NT | 64.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.300) | 44 (0.560) | 38/234 | NT | 62.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 4 (0.050) | 4/254 | NT | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1411899 = | 107 (1.210) | 23 (0.320) | 21/214 | NT | 21.9% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 78 (1.100) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3667894 | 73 (0.820) | 4 (0.050) | 4/256 | NT | 5.2% | coding (1295/1398 nt) | yhjA | putative cytochrome C peroxidase |
| ? | NC_000913 | = 3667902 | 77 (0.900) | coding (1287/1398 nt) | yhjA | putative cytochrome C peroxidase | |||||
| * | ? | NC_000913 | 4085413 = | 93 (1.050) | 5 (0.060) | 4/252 | NT | 5.3% | coding (410/3051 nt) | fdoG | formate dehydrogenase‑O, large subunit |
| ? | NC_000913 | 4085454 = | 91 (1.080) | coding (369/3051 nt) | fdoG | formate dehydrogenase‑O, large subunit | |||||
| * | ? | NC_000913 | = 4542690 | 131 (1.480) | 8 (0.100) | 8/248 | NT | 5.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 138 (1.670) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4593324 = | NA (NA) | 3 (0.040) | 3/244 | NT | NA | intergenic (+12/+37) | tsr/lgoT | methyl‑accepting chemotaxis protein I, serine sensor receptor/putative L‑galactonate:H+ symporter |
| ? | NC_000913 | 4593354 = | NA (NA) | intergenic (+42/+7) | tsr/lgoT | methyl‑accepting chemotaxis protein I, serine sensor receptor/putative L‑galactonate:H+ symporter | |||||