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 | 4,153,616 | 0 | C | T | 65.2% | 19.5 / 17.1 | 23 | intergenic (‑518/+80) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| * | NC_000913 | 3,363,770 | 0 | A | G | 48.1% | ‑1.8 / 224.8 | 158 | T322A (ACC→GCC) | yhcD | putative fimbrial usher protein YhcD |
| * | NC_000913 | 4,111,747 | 0 | G | T | 47.8% | 21.4 / 19.7 | 23 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,153,595 | 0 | A | C | 45.8% | 2.2 / 44.2 | 24 | intergenic (‑497/+101) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| * | NC_000913 | 4,153,535 | 0 | T | C | 38.9% | 11.1 / 15.2 | 18 | intergenic (‑437/+161) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 38.2% | 39.7 / 15.5 | 34 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,604,344 | 0 | C | T | 37.2% | 43.0 / 23.9 | 43 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,434,642 | 0 | G | A | 36.1% | 145.6 / 109.5 | 108 | intergenic (‑236/+316) | ynaM/ttcC | Rac prophage; protein YnaM/putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| * | NC_000913 | 501,564 | 0 | A | C | 32.0% | 33.5 / 10.4 | 25 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 29,496 | 0 | T | A | 31.4% | 64.5 / 14.0 | 35 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 888,014 | 0 | T | G | 28.3% | 84.8 / 10.1 | 46 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.6% | 48.3 / 10.1 | 29 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,125 | 0 | T | A | 26.9% | 117.5 / 18.3 | 52 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 646,747 | 0 | T | G | 26.7% | 80.4 / 19.0 | 45 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.5% | 128.8 / 16.0 | 53 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.8% | 118.8 / 11.0 | 58 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,577,123 | 0 | A | C | 21.5% | 173.3 / 12.6 | 79 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| * | NC_000913 | 753,096 | 0 | A | T | 21.1% | 155.3 / 11.2 | 57 | intergenic (‑301/+89) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.7% | 123.8 / 10.6 | 58 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| 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 | = 375165 | NA (NA) | 7 (0.180) | 6/192 | 3.4 | NA | noncoding (33/34 nt) | other | REP31e |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4373296 | NA (NA) | 8 (0.150) | 8/256 | 3.8 | NA | noncoding (1/34 nt) | other | REP328b |
| ? | NC_000913 | = 4374496 | NA (NA) | intergenic (‑262/+133) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 4 (0.100) | 4/192 | 4.2 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 7 (0.170) | 4/202 | 4.4 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 6 (0.120) +GAACGCCTTATCCGGT |
5/244 | 4.6 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375103 = | NA (NA) | 12 (0.210) +T |
5/274 | 5.1 | NA | noncoding (16/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375204 = | NA (NA) | 5 (0.090) +T |
4/274 | 5.5 | NA | noncoding (16/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 3193155 = | 64 (1.130) | 3 (0.050) | 3/266 | 5.9 | 4.6% | coding (292/1662 nt) | yqiK | protein YqiK |
| ? | NC_000913 | = 3193151 | 62 (1.140) | coding (288/1662 nt) | yqiK | protein YqiK | |||||
| * | ? | NC_000913 | 366291 = | 46 (0.810) | 3 (0.050) +CCAAG |
3/266 | 5.9 | 6.3% | coding (15/3075 nt) | lacZ | beta‑galactosidase |
| ? | NC_000913 | 1432659 = | NA (NA) | coding (249/576 nt) | tfaR | Rac prophage; putative tail fiber assembly protein TfaR | |||||