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 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 | 43.7% | 53.7 / 50.8 | 71 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.2% | 61.7 / 17.7 | 43 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 34.4% | 48.4 / 11.4 | 32 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,377,140 | 0 | A | C | 33.3% | 114.0 / 19.3 | 63 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 4,101,507 | 0 | T | G | 33.3% | 96.9 / 10.8 | 57 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 85.2 / 27.3 | 42 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,213,051 | 0 | A | C | 33.3% | 6.3 / 10.7 | 12 | noncoding (12/120 nt) | rrfE | 5S ribosomal RNA |
| * | NC_000913 | 3,556,207 | 0 | T | C | 31.4% | 54.1 / 10.3 | 35 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 31.0% | 131.5 / 27.5 | 58 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,101,525 | 0 | C | T | 30.2% | 112.8 / 13.9 | 63 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.9% | 150.7 / 47.0 | 83 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.6% | 209.8 / 14.2 | 105 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 650,809 | 0 | T | G | 28.4% | 142.0 / 12.0 | 68 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.8% | 92.3 / 23.1 | 55 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,401,459 | 0 | T | C | 27.8% | 136.8 / 16.7 | 72 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 3,206,444 | 0 | T | A | 26.4% | 112.7 / 15.5 | 53 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.2% | 140.7 / 52.8 | 80 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 753,125 | 0 | T | A | 25.4% | 143.4 / 17.6 | 59 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 29,496 | 0 | T | A | 24.5% | 114.0 / 12.5 | 49 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 175,694 | 0 | T | G | 24.3% | 160.1 / 18.1 | 74 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375124 = | NA (NA) | 20 (0.300) | 9/192 | 4.2 | NA | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 65 (0.680) | 13 (0.150) | 12/258 | 4.6 | 14.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 89 (1.000) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 54 (0.570) | 10 (0.110) | 10/258 | 5.1 | 12.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 86 (0.960) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 14 (0.180) | 8/224 | 5.1 | 14.4% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 83 (1.070) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 13 (0.190) | 7/202 | 5.1 | 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 | 375023 = | NA (NA) | 8 (0.120) | 6/192 | 5.2 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 359236 | 77 (0.810) | 10 (0.120) | 9/246 | 5.2 | 11.4% | coding (438/660 nt) | cynT | carbonic anhydrase 1 |
| ? | NC_000913 | = 359364 | 87 (1.020) | coding (566/660 nt) | cynT | carbonic anhydrase 1 | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 18 (0.190) +T |
10/274 | 5.4 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 13 (0.150) +GAACGCCTTATCCGGT |
8/244 | 5.5 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 27 (0.280) +T |
9/274 | 5.7 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||