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 | 4,101,507 | 0 | T | G | 39.2% | 71.2 / 17.2 | 53 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.8% | 99.0 / 37.7 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 646,747 | 0 | T | G | 32.6% | 63.0 / 28.0 | 43 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.4% | 67.2 / 20.3 | 34 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.1% | 74.9 / 18.1 | 45 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.4% | 162.6 / 11.4 | 89 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 27.9% | 89.8 / 15.6 | 43 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 29,496 | 0 | T | A | 27.0% | 72.9 / 13.9 | 37 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.4% | 110.3 / 17.0 | 53 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 1,491,098 | 0 | A | C | 24.6% | 136.7 / 10.4 | 65 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 646,760 | 0 | T | C | 24.0% | 99.8 / 14.4 | 50 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.0% | 125.1 / 17.4 | 50 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 175,694 | 0 | T | G | 23.9% | 167.9 / 12.1 | 71 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.7% | 76.9 / 12.2 | 38 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.6% | 163.9 / 18.2 | 72 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.3% | 165.4 / 26.4 | 73 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,525,760 | 0 | G | A | 22.0% | 133.0 / 13.2 | 59 | S74L (TCG→TTG) | ansP | L‑asparagine transporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 21.1% | 173.7 / 13.6 | 71 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| 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 | = 374963 | NA (NA) | 5 (0.080) | 5/190 | 5.2 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 15 (0.190) | 8/256 | 5.3 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 377351 = | NA (NA) | 5 (0.070) +29 bp |
4/218 | 6.3 | NA | noncoding (16/37 nt) | other | REP32a |
| ? | NC_000913 | 4325850 = | NA (NA) | intergenic (‑109/+549) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | 339959 = | NA (NA) | 6 (0.090) +28 bp |
3/220 | 6.9 | NA | coding (167/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377433 = | NA (NA) | intergenic (+122/+102) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4542690 | 65 (0.750) | 4 (0.050) | 4/258 | 7.0 | 5.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 81 (1.000) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1731964 = | 69 (0.800) | 3 (0.040) | 3/256 | 7.5 | 4.7% | coding (2878/4617 nt) | lhr | putative ATP‑dependent helicase Lhr |
| ? | NC_000913 | 1732069 = | 58 (0.720) | coding (2983/4617 nt) | lhr | putative ATP‑dependent helicase Lhr | |||||
| * | ? | NC_000913 | = 3781055 | 58 (0.670) | 3 (0.030) | 3/276 | 7.9 | 5.0% | intergenic (+38/‑160) | lldD/trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| ? | NC_000913 | 3781059 = | 57 (0.660) | intergenic (+42/‑156) | lldD/trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase | |||||