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 (highest frequency 20 of 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.5% | 63.0 / 40.9 | 65 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 789,037 | 0 | G | T | 36.2% | 113.7 / 75.0 | 69 | L315M (CTG→ATG) | galK | galactokinase |
| * | NC_000913 | 888,014 | 0 | T | G | 36.1% | 49.9 / 16.1 | 36 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.6% | 34.5 / 10.6 | 26 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,296,060 | 0 | C | T | 33.8% | 109.5 / 72.6 | 80 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,572 | 0 | A | C | 33.3% | 77.6 / 16.8 | 45 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 501,575 | 0 | A | C | 33.3% | 77.2 / 19.4 | 45 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.0% | 185.6 / 18.0 | 105 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 29,496 | 0 | T | A | 32.7% | 89.7 / 27.0 | 52 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.3% | 50.5 / 11.1 | 31 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 753,125 | 0 | T | A | 29.5% | 117.2 / 24.9 | 61 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 501,564 | 0 | A | C | 27.7% | 87.4 / 25.4 | 47 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,101,514 | 0 | G | T | 27.1% | 149.9 / 27.8 | 59 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.4% | 119.2 / 17.5 | 59 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.0% | 87.8 / 12.9 | 44 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.0% | 69.1 / 11.1 | 36 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.6% | 137.7 / 31.2 | 65 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 115,797 | 0 | C | A | 24.4% | 120.3 / 15.3 | 45 | E435* (GAA→TAA) | hofB | T2SSE family protein |
| * | NC_000913 | 753,114 | 0 | G | T | 21.9% | 174.3 / 12.2 | 64 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.4% | 228.3 / 22.1 | 98 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| 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 | 4542682 = | 51 (0.640) | 13 (0.170) | 12/258 | 3.5 | 17.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 79 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 19 (0.270) +GAACGCCTTATCCGGT |
9/244 | 4.1 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 20 (0.270) | 9/256 | 4.2 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 375204 = | NA (NA) | 15 (0.190) +T |
10/274 | 4.2 | NA | noncoding (16/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375103 = | NA (NA) | 25 (0.320) +T |
8/274 | 4.8 | NA | noncoding (16/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 9 (0.110) +T |
7/274 | 5.1 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 8 (0.110) | 5/260 | 5.7 | 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 | 3763871 = | NA (NA) | 4 (0.050) | 4/254 | 6.0 | 10.3% | coding (1689/4134 nt) | rhsA | rhs element protein RhsA |
| ? | NC_000913 | 3763989 = | 38 (0.480) | coding (1807/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 3620880 = | NA (NA) | 4 (0.050) | 4/254 | 6.0 | 10.5% | coding (1689/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620998 = | 37 (0.460) | coding (1807/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 731393 = | 79 (0.990) | 4 (0.050) | 4/262 | 6.1 | 5.1% | coding (1811/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 3620876 = | NA (NA) | coding (1685/4236 nt) | rhsB | rhs element protein RhsB | |||||