mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
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] | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| 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 | 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 |
| RA | 3,735,339 | C→T | R121C (CGC→TGC) | xylR → | xylose divergent operon transcriptional activator |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 4,187,658 | T→G | L770R (CTC→CGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 568653 | 568978 | 326 | 49 [47] | [48] 49 | [ybcK] | [ybcK] |
| * | * | ÷ | NC_000913 | 583151 | 583850 | 700 | 58 [45] | [48] 49 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 1640620 | 1640775 | 156 | 60 [48] | [44] 72 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| * | * | ÷ | NC_000913 | 1978455 | 1979287 | 833 | 51 [48] | [48] 49 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2168263 | 2168481 | 219 | 51 [38] | [34] 56 | [yegR] | [yegR] |
| * | * | ÷ | NC_000913 | 2344238 | 2344419 | 182 | 50 [48] | [48] 49 | yfaL/nrdA | adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit |
| * | * | ÷ | NC_000913 | 3423756–3424234 | 3424547–3424238 | 5–792 | 49 [45] | [45] 49 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3653676 | 3653779 | 104 | 49 [47] | [42] 55 | [yhiS] | [yhiS] |
| * | * | ÷ | NC_000913 | 3769566 | 3770008 | 443 | 50 [48] | [44] 50 | [yibV]–[yibU] | [yibV], yibV, [yibU] |
| * | * | ÷ | NC_000913 | 4541560 | 4541926 | 367 | 59 [45] | [47] 53 | fimB/fimE | tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA |
| * | * | ÷ | NC_000913 | 4542569 | 4542924 | 356 | 50 [48] | [46] 58 | [fimE] | [fimE] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.170) | 189 (1.690) | 85/266 | 0.0 | 92.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.160) | 84 (0.750) | 53/266 | 0.7 | 84.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||