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 | 4,568,504 | 0 | T | G | 34.5% | 286.6 / 20.5 | 145 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.5% | 151.0 / 38.4 | 80 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.9% | 275.7 / 125.2 | 154 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.6% | 146.6 / 32.3 | 58 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 23.0% | 281.9 / 45.0 | 126 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 650,809 | 0 | T | G | 22.9% | 270.6 / 13.4 | 105 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 445,558 | 0 | A | C | 21.1% | 135.5 / 12.9 | 57 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 1,825,061 | 0 | G | A | 20.9% | 168.4 / 15.2 | 67 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1722616 = | 139 (0.910) | 5 (0.040) | 5/254 | 8.9 | 3.7% | coding (496/2013 nt) | ydhK | putative transporter YdhK |
| ? | NC_000913 | = 1722612 | 129 (0.920) | coding (492/2013 nt) | ydhK | putative transporter YdhK | |||||
| * | ? | NC_000913 | = 2518430 | 108 (0.750) | 8 (0.050) +ACAT |
4/252 | 9.4 | 6.5% | intergenic (‑199/‑37) | alaW/yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC |
| ? | NC_000913 | 2518431 = | 124 (0.810) | intergenic (‑200/‑36) | alaW/yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC | |||||
| * | ? | NC_000913 | = 1633410 | 0 (0.000) | 25 (0.170) +TTC |
4/252 | 9.4 | 100% | intergenic (+105/‑212) | ydfK/pinQ | Qin prophage; cold shock protein YdfK/Qin prophage; putative site‑specific recombinase |
| ? | NC_000913 | 1633411 = | 0 (0.000) | intergenic (+106/‑211) | ydfK/pinQ | Qin prophage; cold shock protein YdfK/Qin prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | = 1433876 | 3 (0.020) | 58 (0.390) +GAA |
4/252 | 9.4 | 95.0% | intergenic (‑202/+115) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/Rac prophage; uncharacterized protein YnaE |
| ? | NC_000913 | 1433877 = | 3 (0.020) | intergenic (‑203/+114) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/Rac prophage; uncharacterized protein YnaE | |||||
| * | ? | NC_000913 | 1433877 = | NA (NA) | 4 (0.030) | 4/264 | 9.6 | NA | intergenic (‑203/+114) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/Rac prophage; uncharacterized protein YnaE |
| ? | NC_000913 | 1633417 = | NA (NA) | intergenic (+112/‑205) | ydfK/pinQ | Qin prophage; cold shock protein YdfK/Qin prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | = 1585480 | 183 (1.250) | 6 (0.040) +CTTTC |
3/254 | 10.0 | 3.2% | coding (1007/2280 nt) | ydeP | putative oxidoreductase YdeP |
| ? | NC_000913 | 1585481 = | 189 (1.240) | coding (1006/2280 nt) | ydeP | putative oxidoreductase YdeP | |||||
| * | ? | NC_000913 | = 4542690 | 166 (1.080) | 3 (0.020) | 3/258 | 10.1 | 1.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 205 (1.430) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 171 (1.120) | 3 (0.020) | 3/258 | 10.1 | 1.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 205 (1.430) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4517588 | 71 (0.460) | 3 (0.020) | 3/264 | 10.2 | 4.4% | coding (130/954 nt) | fecR | regulator for fec operon, periplasmic |
| ? | NC_000913 | 4517595 = | 64 (0.440) | coding (123/954 nt) | fecR | regulator for fec operon, periplasmic | |||||
| * | ? | NC_000913 | 3426498 = | NA (NA) | 3 (0.020) | 3/264 | 10.2 | 2.0% | noncoding (286/2904 nt) | rrlD | 23S ribosomal RNA |
| ? | NC_000913 | 4037801 = | 156 (1.020) | noncoding (283/2905 nt) | rrlA | 23S ribosomal RNA | |||||