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 | 565,343 | A→C | T212T (ACT→ACG) | intD ← | DLP12 prophage; putative phage integrase |
| RA | 1,261,481 | G→C | A132G (GCT→GGT) | prs ← | phosphoribosylpyrophosphate synthase |
| JC JC | 1,293,033 | IS1 (+) +9 bp | intergenic (‑111/‑486) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,393,457 | IS186 (–) +5 bp | coding (231‑235/1614 nt) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,615,076 | T→A | F91L (TTT→TTA) | yneJ → | putative DNA‑binding transcriptional regulator |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | V359I (GTC→ATC) | fliK → | flagellar hook‑length control 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 | 2,317,667 | T→G | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,632,046 | G→T | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 3,002,530 | G→A | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| 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 |
| JC JC | 3,890,075 | IS5 (–) +4 bp | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| 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 | 3423751–3424234 | 3424554–3424238 | 5–804 | 49 [48] | [47] 49 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514354 | 3515094 | 741 | 49 [48] | [45] 52 | [gph]–[dam] | [gph],rpe,[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 24 (0.190) | 62 (0.550) | 52/248 | 1.5 | 69.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 34 (0.300) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.190) | 49 (0.440) | 39/248 | 2.8 | 63.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 34 (0.300) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 188 (1.530) | 123/272 | 0.0 | 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 | |||||