mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 445,558 | 0 | A | C | 50.0% | 6.8 / 17.5 | 22 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,604,344 | 0 | C | T | 47.8% | 32.9 / 31.7 | 46 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 42.9% | 28.8 / 15.7 | 28 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 42.1% | 42.6 / 20.6 | 38 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 40.6% | 26.7 / 22.1 | 32 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 33.3% | 42.3 / 17.5 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 501,564 | 0 | A | C | 32.4% | 51.5 / 17.2 | 34 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 650,809 | 0 | T | G | 29.3% | 70.3 / 13.2 | 41 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,105 | 0 | A | T | 28.2% | 86.3 / 10.9 | 39 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 28.1% | 110.2 / 17.8 | 57 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 28.1% | 110.3 / 17.3 | 57 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,380,679 | 0 | G | A | 27.3% | 72.1 / 27.5 | 44 | intergenic (‑36/+43) | menF/elaB | isochorismate synthase MenF/tail anchored inner membrane protein |
| * | NC_000913 | 29,496 | 0 | T | A | 26.2% | 95.9 / 11.9 | 42 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 25.8% | 126.6 / 17.3 | 62 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.5% | 82.4 / 11.1 | 34 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,763,608 | 0 | C | T | 23.4% | 122.4 / 33.9 | 64 | V134V (GTG→GTA) | sufB | Fe‑S cluster scaffold complex subunit SufB |
| * | NC_000913 | 3,274,865 | 0 | T | G | 22.4% | 133.3 / 11.6 | 58 | T15P (ACC→CCC) | garP | galactarate/glucarate/glycerate transporter GarP |
| * | NC_000913 | 3,492,013 | 1 | . | G | 22.2% | 119.2 / 50.7 | 54 | coding (285/573 nt) | ppiA | peptidyl‑prolyl cis‑trans isomerase A |
| * | NC_000913 | 2,760,525 | 0 | A | G | 21.5% | 259.3 / 72.8 | 130 | intergenic (+131/‑22) | yfjI/yfjJ | CP4‑57 prophage; protein YfjI/CP4‑57 prophage; protein YfjJ |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.100) | 4/200 | 5.0 | 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 | 4542682 = | 43 (0.600) | 7 (0.100) | 6/256 | 5.1 | 11.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 67 (1.000) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 5 (0.100) | 3/188 | 5.3 | 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 | 315401 = | NA (NA) | 5 (0.080) | 5/248 | 5.4 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 10 (0.150) | 5/258 | 5.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 8 (0.110) | 5/272 | 5.8 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 2049735 = | 52 (0.720) | 4 (0.060) | 4/256 | 6.0 | 8.2% | coding (4798/7077 nt) | yeeJ | inverse autotransporter adhesin |
| ? | NC_000913 | 2049872 = | 41 (0.610) | coding (4935/7077 nt) | yeeJ | inverse autotransporter adhesin | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 4 (0.060) | 4/266 | 6.1 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||
| * | ? | NC_000913 | = 1870520 | 51 (0.710) | 3 (0.040) | 3/264 | 6.6 | 5.6% | coding (136/1476 nt) | cdgI | putative c‑di‑GMP binding protein CdgI |
| ? | NC_000913 | 1870530 = | 52 (0.750) | coding (146/1476 nt) | cdgI | putative c‑di‑GMP binding protein CdgI | |||||
| * | ? | NC_000913 | 514751 = | 41 (0.570) | 3 (0.040) | 3/262 | 6.6 | 5.7% | coding (109/459 nt) | ybbJ | NfeD‑like family protein |
| ? | NC_000913 | 1027437 = | 60 (0.870) | coding (337/663 nt) | yccT | DUF2057 domain‑containing protein YccT | |||||