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 (highest frequency 20 of 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 908,794 | 0 | A | G | 74.5% | 87.5 / 29.0 | 51 | G167G (GGT→GGC) | ltaE | low‑specificity L‑threonine aldolase |
| * | NC_000913 | 3,921,947 | 1 | . | G | 60.7% | 189.3 / 129.5 | 89 | coding (105/816 nt) | atpB | ATP synthase Fo complex subunit a |
| * | NC_000913 | 3,499,651 | 0 | G | A | 56.2% | 12.2 / 80.0 | 65 | intergenic (+36/‑259) | yhfL/frlA | DUF4223 domain‑containing lipoprotein YhfL/fructoselysine/psicoselysine transporter |
| * | NC_000913 | 4,604,344 | 0 | C | T | 52.9% | 21.1 / 89.3 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 711,026 | 0 | T | C | 39.8% | 63.0 / 118.7 | 103 | D147G (GAC→GGC) | fldA | flavodoxin 1 |
| * | NC_000913 | 3,556,207 | 0 | T | C | 38.2% | 40.4 / 14.0 | 34 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 36.2% | 53.3 / 31.5 | 47 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.3% | 49.9 / 15.5 | 35 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,489,637 | 0 | C | T | 33.3% | 103.4 / 81.2 | 90 | D143N (GAT→AAT) | yjgR | DUF853 domain‑containing protein YjgR |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.5% | 88.6 / 19.1 | 40 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 31.5% | 107.7 / 20.2 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 753,105 | 0 | A | T | 29.8% | 119.5 / 17.9 | 57 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.9% | 98.0 / 17.6 | 45 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 28.6% | 99.1 / 15.0 | 49 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.7% | 98.0 / 12.1 | 47 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.6% | 133.0 / 53.2 | 76 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.6% | 175.1 / 15.5 | 87 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.5% | 135.4 / 33.3 | 69 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 27.1% | 103.7 / 11.2 | 48 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 646,747 | 0 | T | G | 25.9% | 123.0 / 21.9 | 58 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | 4542682 = | 64 (0.770) | 18 (0.230) | 16/258 | 3.2 | 23.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 61 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 52 (0.630) | 10 (0.130) | 9/258 | 4.9 | 15.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 61 (0.790) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375165 | NA (NA) | 3 (0.050) | 3/192 | 6.2 | 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 | 374922 = | NA (NA) | 6 (0.100) | 3/202 | 6.4 | 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 | 4498181 = | NA (NA) | 5 (0.060) | 3/276 | 7.7 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+12/+81) | insD‑6/yjgX | KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment | |||||
| * | ? | NC_000913 | 381258 = | NA (NA) | 4 (0.050) | 3/274 | 7.7 | NA | pseudogene (3/417 nt) | yaiX | putative acyltransferase, N‑terminal fragment |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||