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 |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,875,838 | 0 | A | C | 50.0% | ‑1.1 / 17.6 | 16 | T56P (ACC→CCC) | nimT | 2‑nitroimidazole exporter |
| * | NC_000913 | 395,294 | 0 | C | G | 47.1% | ‑6.4 / 25.2 | 17 | G332R (GGC→CGC) | ampH | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| * | NC_000913 | 395,288 | 0 | A | T | 41.2% | 4.9 / 23.2 | 17 | F334I (TTC→ATC) | ampH | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| * | NC_000913 | 2,318,354 | 0 | A | C | 38.1% | 25.3 / 13.4 | 21 | V508G (GTG→GGG) | rcsC | sensory histidine kinase RcsC |
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.5% | 44.5 / 60.3 | 56 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 395,291 | 0 | C | G | 36.8% | 13.8 / 20.8 | 19 | G333R (GGT→CGT) | ampH | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| * | NC_000913 | 2,223,410 | 0 | T | G | 35.0% | 26.8 / 10.9 | 20 | V409G (GTG→GGG) | dld | D‑lactate dehydrogenase |
| * | NC_000913 | 3,563,481 | 0 | T | G | 31.8% | 27.7 / 17.0 | 22 | V490G (GTG→GGG) | glpD | aerobic glycerol 3‑phosphate dehydrogenase |
| * | NC_000913 | 1,374,034 | 0 | G | . | 31.2% | 28.5 / 16.2 | 17 | coding (813/882 nt) | ycjO | putative ABC transporter membrane subunit YcjO |
| * | NC_000913 | 421,152 | 0 | A | . | 29.4% | 40.1 / 16.3 | 17 | coding (167/1374 nt) | proY | putative transporter ProY |
| * | NC_000913 | 1,374,038 | 0 | T | C | 28.6% | 30.1 / 11.5 | 21 | F273L (TTC→CTC) ‡ | ycjO | putative ABC transporter membrane subunit YcjO |
| * | NC_000913 | 421,151 | 0 | T | . | 27.8% | 46.3 / 16.0 | 18 | coding (166/1374 nt) | proY | putative transporter ProY |
| * | NC_000913 | 2,160,604 | 0 | A | C | 27.8% | 24.7 / 11.4 | 18 | Y740S (TAC→TCC) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 2,349,621 | 0 | A | C | 27.8% | 29.7 / 10.3 | 18 | intergenic (‑149/‑66) | inaA/yfaH | putative lipopolysaccharide kinase InaA/putative uncharacterized protein YfaH |
| * | NC_000913 | 2,710,279 | 0 | A | C | 25.9% | 51.9 / 15.7 | 27 | intergenic (‑115/‑141) | rseD/nadB | rpoE leader peptide/L‑aspartate oxidase |
| * | NC_000913 | 1,374,039 | 0 | T | G | 25.0% | 48.1 / 12.8 | 24 | F273C (TTC→TGC) ‡ | ycjO | putative ABC transporter membrane subunit YcjO |
| * | NC_000913 | 1,374,040 | 0 | C | T | 25.0% | 34.4 / 12.3 | 24 | F273F (TTC→TTT) ‡ | ycjO | putative ABC transporter membrane subunit YcjO |
| * | NC_000913 | 151,656 | 0 | T | G | 20.0% | 105.2 / 13.4 | 40 | A192A (GCA→GCC) | yadL | putative fimbrial protein YadL |
| * | NC_000913 | 421,141 | 0 | T | . | 20.0% | 56.5 / 10.9 | 20 | coding (156/1374 nt) | proY | putative transporter ProY |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 39 (0.980) | 5 (0.150) | 4/110 | 1.9 | 10.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 53 (1.550) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||