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 | 1,529,203 | C→A | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,731,621 | G→T | M845I (ATG→ATT) | lhr → | putative ATP‑dependent helicase |
| 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 |
| MC JC | 3,440,077 | Δ11 bp | coding (943‑953/990 nt) | rpoA ← | RNA polymerase, alpha 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 |
| RA | 4,234,667 | Δ1 bp | intergenic (‑1434/‑499) | 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 | 3423753–3424235 | 3424541–3424238 | 4–789 | 16 [15] | [15] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | 1216552 = | 17 (0.380) | 38 (0.850) | 30/278 | 0.6 | 69.1% | coding (184/267 nt) | ariR | RcsB connector protein for regulation of biofilm and acid‑resistance |
| ? | NC_000913_3_pae_pgi | = 1469240 | NA (NA) | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913_3_pae_pgi | = 1216556 | 19 (0.430) | 34 (0.760) | 26/278 | 1.0 | 64.1% | coding (188/267 nt) | ariR | RcsB connector protein for regulation of biofilm and acid‑resistance |
| ? | NC_000913_3_pae_pgi | = 1651548 | NA (NA) | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | = 1299498 | 0 (0.000) | 32 (0.740) | 27/270 | 0.8 | 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 | |||||