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 |
| 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 | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,188,870 | C→T | 35.5% | A303T (GCT→ACT) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,466,210 | G→A | 10.9% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,544,021:1 | +A | 78.1% | coding (40/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,544,022 | C→A | 100% | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,679,525 | 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 | 3,528,907 | A→T | 24.1% | D80V (GAT→GTT) | yrfG → | GMP/IMP nucleotidase |
| 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 | 4,110,747 | G→T | 28.7% | intergenic (+62/+784) | cdh → / ← yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein |
| RA | 4,241,676 | A→G | 8.9% | S165S (TCT→TCC) | xylE ← | D‑xylose transporter |
| RA | 4,295,976 | C→T | 14.8% | 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 | 4,366,770 | T→G | 14.4% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,366,771 | C→A | 15.8% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| 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 | 365872 | 366480 | 609 | 14 [13] | [13] 14 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3423761–3424234 | 3424542–3424238 | 5–782 | 15 [12] | [13] 14 | [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 | = 1299498 | 0 (0.000) | 56 (1.480) | 45/268 | 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 | |||||
| * | ? | NC_000913_3_pae_tpiA | 1399590 = | 38 (0.970) | 3 (0.080) | 3/276 | NT | 7.3% | intergenic (‑64/+131) | fnr/ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| ? | NC_000913_3_pae_tpiA | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913_3_pae_tpiA | 1483726 = | 15 (0.380) | 11 (0.280) | 10/274 | NT | 42.5% | coding (666/3903 nt) | hrpA | putative ATP‑dependent helicase |
| ? | NC_000913_3_pae_tpiA | 2101750 = | NA (NA) | intergenic (‑6/+145) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1483730 | 16 (0.410) | 11 (0.280) | 10/276 | NT | 40.7% | coding (670/3903 nt) | hrpA | putative ATP‑dependent helicase |
| ? | NC_000913_3_pae_tpiA | = 2290113 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913_3_pae_tpiA | 3186098 = | NA (NA) | 3 (0.080) | 3/272 | NT | 8.2% | intergenic (+8/‑89) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913_3_pae_tpiA | = 3546580 | 34 (0.870) | coding (22/1317 nt) | gntT | gluconate transporter, high‑affinity GNT I system | |||||