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 |
| RA | 123,061 | C→T | R15R (CGC→CGT) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| JC JC | 168,640 | IS2 (+) +5 bp | coding (1157‑1161/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 453,291 | G→A | L85L (CTC→CTT) | ampG ← | muropeptide transporter |
| RA | 909,353 | G→A | A566V (GCG→GTG) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| JC JC | 911,086 | IS2 (–) +5 bp | intergenic (‑37/+92) | poxB ← / ← hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent |
| RA | 1,158,881 | C→T | S338L (TCG→TTG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC JC | 1,290,476 | IS3 (–) +3 bp | coding (235‑237/1014 nt) | rssB → | PcnB‑degradosome interaction factor; response regulator |
| JC JC | 1,293,032 | IS1 (–) +8 bp | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| 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 | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,413,461 | G→A | intergenic (‑329/‑9) | yfbV ← / → ackA | UPF0208 family inner membrane protein/acetate kinase A and propionate kinase 2 |
| JC | 2,722,123 | Δ7 bp | coding (2171‑2177/2661 nt) | pka → | protein lysine acetyltransferase |
| 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 | 3,771,708 | IS3 (–) +4 bp :: +TC | coding (34‑37/363 nt) | yibI ← | DUF3302 family inner membrane protein |
| RA | 3,798,659 | (T)8→7 | coding (654/1074 nt) | waaU ← | lipopolysaccharide core biosynthesis |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta 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 | 123064 | 127536 | 4473 | 6 [4] | [5] 7 | [aceE]–[aceF] | [aceE],[aceF] |
| * | * | ÷ | NC_000913 | 1209603 | 1209618 | 16 | 29 [0] | [0] 27 | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| * | * | ÷ | NC_000913 | 2066289–2066464 | 2066606–2066468 | 5–318 | 7 [5] | [5] 8 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423753–3424234 | 3424519–3424238 | 5–767 | 8 [5] | [5] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1097245 = | NA (NA) | 5 (0.180) | 5/248 | 3.0 | 29.8% | intergenic (+416/+320) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097274 = | 12 (0.420) | intergenic (+445/+291) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 1 (0.030) | 20 (0.790) | 19/220 | 0.4 | 97.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.030) | 27 (1.070) | 25/220 | 0.2 | 98.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4040683 | 19 (0.660) | 16 (0.560) | 9/248 | 1.9 | 44.6% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4213162 | 21 (0.740) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||