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 | 4,604,344 | 0 | C | T | 44.9% | 42.2 / 51.4 | 69 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 34.5% | 37.2 / 12.1 | 29 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 92.5 / 21.7 | 42 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.1% | 38.0 / 11.0 | 28 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.7% | 140.4 / 14.4 | 84 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.6% | 44.5 / 11.0 | 27 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,628,649 | 0 | A | C | 29.5% | 84.3 / 13.6 | 44 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.1% | 141.2 / 20.7 | 57 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.0% | 125.9 / 13.5 | 56 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,843,904 | 0 | C | A | 24.7% | 194.8 / 47.6 | 73 | intergenic (‑115/‑60) | adeQ/adeD | adenine transporter/adenine deaminase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.8% | 94.3 / 12.5 | 42 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 888,014 | 0 | T | G | 22.9% | 140.4 / 11.8 | 61 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,168,966 | 0 | A | C | 22.5% | 160.5 / 12.5 | 71 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 22.2% | 142.6 / 12.0 | 63 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.7% | 152.6 / 15.9 | 69 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 753,125 | 0 | T | A | 21.6% | 125.8 / 10.3 | 51 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.3% | 138.2 / 24.8 | 61 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.6% | 164.1 / 12.2 | 68 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,240,985 | 0 | T | G | 20.0% | 147.6 / 10.3 | 60 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| 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 | 608007 = | NA (NA) | 3 (0.050) | 3/226 | 6.6 | 4.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 59 (0.980) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 484269 = | 102 (1.370) | 7 (0.100) | 4/270 | 6.8 | 7.1% | coding (135/3150 nt) | acrB | multidrug efflux pump RND permease AcrB |
| ? | NC_000913 | 484327 = | 84 (1.160) | coding (77/3150 nt) | acrB | multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | 3621432 = | NA (NA) | 3 (0.040) | 3/270 | 7.4 | NA | coding (2241/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621840 | NA (NA) | coding (2649/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 1879834 | 2 (0.030) | 3 (0.040) | 3/272 | 7.4 | 60.0% | coding (115/360 nt) | yeaR | DUF1971 domain‑containing protein YeaR |
| ? | NC_000913 | 2514274 = | NA (NA) | noncoding (2/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 1747182 = | 85 (1.140) | 3 (0.040) | 3/276 | 7.5 | 3.8% | coding (52/1605 nt) | ydhS | FAD/NAD(P) binding domain‑containing protein YdhS |
| ? | NC_000913 | 1747232 = | 69 (0.930) | coding (102/1605 nt) | ydhS | FAD/NAD(P) binding domain‑containing protein YdhS | |||||
| * | ? | NC_000913 | = 224567 | NA (NA) | 3 (0.040) | 3/276 | 7.5 | NA | noncoding (797/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | = 224628 | NA (NA) | noncoding (858/1542 nt) | rrsH | 16S ribosomal RNA | |||||