mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 1,413 | T→A | S359R (AGT→AGA) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 450,073 | C→T | W190* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 932,321 | C→T | intergenic (‑271/‑274) | trxB ← / → lrp | thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,818,103 | A→T | V133E (GTA→GAA) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 | 2,599,861 | (T)8→7 | intergenic (‑101/‑45) | dapA ← / → gcvR | dihydrodipicolinate synthase/transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,907,364 | A→T | L193Q (CTG→CAG) | eno ← | enolase |
| RA | 2,942,635 | (T)7→6 | intergenic (‑68/+283) | gcvA ← / ← ygdI | glycine cleavage system transcriptional activator; autorepressor/DUF903 family verified lipoprotein |
| RA | 3,514,455 | A→G | I202T (ATC→ACC) | rpe ← | D‑ribulose‑5‑phosphate 3‑epimerase |
| 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 | 3,966,676 | G→T | R87L (CGC→CTC) | rho → | transcription termination factor |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,428,871 | T→C | intergenic (‑154/‑64) | ytfB ← / → fklB | OapA family protein/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1896869 | 1898346 | 1478 | 49 [48] | [48] 49 | sdaA | sdaA |
| * | * | ÷ | NC_000913 | 2684207 | 2685564 | 1358 | 50 [48] | [47] 49 | glyA | glyA |
| * | * | ÷ | NC_000913 | 2929509 | 2930998 | 1490 | 50 [47] | [48] 51 | [sdaC]–sdaB | [sdaC], sdaB |
| * | * | ÷ | NC_000913 | 3258227 | 3259736 | 1510 | 49 [48] | [48] 49 | tdcG–[tdcF] | tdcG, [tdcF] |
| * | * | ÷ | NC_000913 | 3423695–3424234 | 3424559–3424238 | 5–865 | 50 [48] | [47] 49 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 16 (0.180) | 72 (0.920) | 60/268 | 0.4 | 81.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.180) | 72 (0.920) | 63/268 | 0.3 | 81.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||