mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 612,648 | G→T | intergenic (‑154/‑89) | fepA ← / → fes | ferrienterobactin outer membrane transporter/enterobactin/ferrienterobactin esterase |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/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 | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,810,956 | A→C | T63P (ACG→CCG) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 3,413,571 | T→C | intergenic (‑106/‑293) | acrS ← / → acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| RA | 3,560,455 | +G | 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 |
| MC JC | 3,580,295 | Δ3,133 bp | IS1‑mediated | [yhhX]–yrhA | [yhhX], ryhB, yhhY, yhhZ, yrhA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 300103 | 300107 | 5 | 4 [0] | [1] 2 | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | * | ÷ | NC_000913 | 493073 | 493091 | 19 | 2 [1] | [0] 3 | dnaX | DNA polymerase III/DNA elongation factor III, tau and gamma subunits |
| * | * | ÷ | NC_000913 | 600407 | 600429 | 23 | 5 [1] | [1] 2 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | NC_000913 | 723877 | 723894 | 18 | 2 [0] | [1] 2 | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| * | * | ÷ | NC_000913 | 1429977 | 1429984 | 8 | 2 [0] | [1] 2 | stfR | Rac prophage; putative tail fiber protein |
| * | * | ÷ | NC_000913 | 2118841 | 2118858 | 18 | 2 [1] | [1] 2 | wzxC | putative colanic acid exporter |
| * | * | ÷ | NC_000913 | 2377218 | 2377280 | 63 | 3 [1] | [1] 2 | menH | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| * | * | ÷ | NC_000913 | 2995187 | 2995243 | 57 | 2 [1] | [1] 2 | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| * | * | ÷ | NC_000913 | 3423723–3424234 | 3424588–3424238 | 5–866 | 2 [0] | [0] 4 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3470008 | 3470030 | 23 | 2 [0] | [0] 3 | chiA/tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| * | * | ÷ | NC_000913 | 3500634 | 3500638 | 5 | 5 [0] | [1] 2 | frlA | putative fructoselysine transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 871062 | 16 (0.820) | 4 (0.230) | 3/118 | 1.6 | 20.9% | coding (96/921 nt) | gsiC | glutathione ABC transporter permease |
| ? | NC_000913 | = 871080 | 16 (0.920) | coding (114/921 nt) | gsiC | glutathione ABC transporter permease | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.770) | 6 (0.410) | 5/100 | 0.8 | 36.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.680) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.770) | 8 (0.550) | 8/100 | 0.4 | 42.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.680) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 20 (1.100) | 17/124 | 0.1 | 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 | = 2962469 | 16 (0.820) | 4 (0.240) | 3/114 | 1.5 | 23.7% | coding (296/324 nt) | ppdC | putative prepilin peptidase‑dependent protein |
| ? | NC_000913 | = 2962525 | 12 (0.720) | coding (240/324 nt) | ppdC | putative prepilin peptidase‑dependent protein | |||||