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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,529,175 | T→C | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| 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 | 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 | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,993,512 | Δ1 bp | coding (2360/2547 nt) | cyaA → | adenylate cyclase |
| RA | 4,158,929 | C→A | A147E (GCG→GAG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,233,708 | C→T | intergenic (‑475/‑1458) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,295,641 | +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_3_pae_pgi | 3423712–3424234 | 3424590–3424238 | 5–879 | 69 [67] | [67] 70 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913_3_pae_pgi | 4233746 | 4234675 | 930 | 69 [63] | [67] 71 | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 37 (0.280) | 61 (0.530) | 56/236 | 2.0 | 62.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 40 (0.350) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | = 1207805 | 38 (0.290) | 54 (0.470) | 50/236 | 2.7 | 59.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | = 1209602 | 40 (0.350) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | = 1299498 | 0 (0.000) | 138 (1.080) | 100/260 | 0.1 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_pae_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 1979270 | NA (NA) | 309 (2.360) | 167/268 | 0.0 | 69.3% | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913_3_pae_pgi | = 4259397 | 137 (1.040) | intergenic (‑134/‑184) | zur/yjbL | transcriptional repressor, Zn(II)‑binding/uncharacterized protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 3584195 | NA (NA) | 238 (1.810) | 147/268 | 0.0 | 67.4% | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E |
| ? | NC_000913_3_pae_pgi | 4221464 = | 115 (0.880) | coding (1024/2187 nt) | arpA | ankyrin repeat protein | |||||