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 |
| RA | 123,061 | C→T | R15R (CGC→CGT) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 168,660 | C→T | Q393* (CAG→TAG) | fhuA → | ferrichrome outer membrane transporter |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| JC JC | 911,086 | IS2 (–) +5 bp | intergenic (‑37/+92) | poxB ← / ← hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent |
| RA | 1,159,287 | C→A | Y473* (TAC→TAA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| 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 | 1,649,718 | A→G | E37G (GAA→GGA) | dicB → | Qin prophage; cell division inhibition protein |
| RA | 1,667,529 | T→A | K346* (AAA→TAA) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| 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 | 2,042,457 | C→A | G30G (GGC→GGA) | yodB → | cytochrome b561 homolog |
| 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 |
| JC JC | 2,415,938 | IS2 (–) +5 bp | coding (1192‑1196/2145 nt) | pta → | phosphate acetyltransferase |
| JC | 2,721,224 | (GGCTGCCG)1→2 | coding (1272/2661 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 |
| RA | 3,768,131 | A→T | pseudogene (911/945 nt) | rhsJ → | Rhs‑family protein |
| RA | 3,964,929 | C→T | E234E (GAG→GAA) | rhlB ← | ATP‑dependent RNA helicase |
| 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 | 123066 | 127551 | 4486 | 7 [6] | [6] 8 | [aceE]–[aceF] | [aceE],[aceF] |
| * | * | ÷ | NC_000913 | 3423782–3424230 | 3424544–3424238 | 9–763 | 7 [5] | [6] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 202637 = | 26 (0.760) | 12 (0.360) | 12/270 | 1.7 | 26.2% | coding (78/789 nt) | lpxA | UDP‑N‑acetylglucosamine acetyltransferase |
| ? | NC_000913 | = 4542986 | 42 (1.250) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1207790 = | 3 (0.090) | 28 (0.920) | 27/244 | 0.2 | 88.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.090) | 21 (0.690) | 17/244 | 0.9 | 84.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||