mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 172,545 | G→A | 5.2% | V362M (GTG→ATG) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 349,615 | T→C | 13.5% | intergenic (+43/‑397) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,624 | C→T | 10.3% | intergenic (+52/‑388) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,642 | A→G | 9.1% | intergenic (+70/‑370) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 564,303 | G→A | 6.2% | P60S (CCC→TCC) | sfmZ ← | response regulator family protein |
| RA | 629,270 | C→T | 5.3% | V240V (GTC→GTT) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| RA | 898,300 | C→T | 5.0% | A104A (GCC→GCT) | ybjO → | DUF2593 family inner membrane protein |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,544,021:1 | +A | 79.7% | coding (40/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,544,022 | C→A | 100% | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| RA | 1,722,472 | G→A | 7.3% | V118I (GTC→ATC) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,091,738 | C→T | 7.2% | V214V (GTC→GTT) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| 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 | 2,304,522 | G→T | 7.4% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,440,435 | C→A | 36.5% | D199Y (GAC→TAC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,440,923 | C→T | 45.2% | G36D (GGC→GAC) | rpoA ← | RNA polymerase, alpha subunit |
| 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 | 3,563,755 | T→C | 6.7% | intergenic (+237/+32) | glpD → / ← yzgL | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology |
| RA | 3,979,412 | C→T | 5.4% | P271L (CCG→CTG) | wzyE → | putative ECA polysaccharide chain elongation protein |
| RA | 4,111,596 | G→A | 100% | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| RA | 4,295,976 | C→T | 32.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,296:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,632 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_pae_tpiA | 3423746–3424539 | 3424539 | 1–794 | 26 [25] | [25] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 404104 = | 58 (0.730) | 3 (0.040) | 3/270 | NT | 5.1% | coding (402/1116 nt) | yaiC | diguanylate cyclase, cellulose regualtor |
| ? | NC_000913_3_pae_tpiA | 404127 = | 54 (0.690) | coding (425/1116 nt) | yaiC | diguanylate cyclase, cellulose regualtor | |||||
| * | ? | NC_000913_3_pae_tpiA | 1207790 = | 59 (0.740) | 15 (0.210) | 14/242 | NT | 24.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | 1209619 = | 43 (0.610) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1207805 | 58 (0.730) | 16 (0.230) | 13/242 | NT | 25.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | = 1209602 | 43 (0.610) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1299498 | 0 (0.000) | 60 (0.780) | 51/266 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_pae_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||