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 24 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 | 38.7% | 135.9 / 82.6 | 120 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 34.5% | 189.5 / 134.8 | 139 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.3% | 102.3 / 33.9 | 62 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 445,558 | 0 | A | C | 32.0% | 76.9 / 28.6 | 50 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 753,125 | 0 | T | A | 32.0% | 80.1 / 23.9 | 50 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 31.4% | 83.8 / 26.0 | 51 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.0% | 91.4 / 18.3 | 50 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.6% | 256.2 / 30.3 | 136 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,287,719 | 0 | T | A | 28.4% | 196.7 / 53.4 | 102 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 27.6% | 162.1 / 10.2 | 76 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.7% | 101.7 / 27.7 | 60 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 26.3% | 126.7 / 19.9 | 57 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.9% | 95.2 / 14.3 | 54 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 25.8% | 174.9 / 32.0 | 66 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,105 | 0 | A | T | 25.4% | 111.9 / 14.5 | 55 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.0% | 195.4 / 42.0 | 93 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 24.7% | 167.4 / 14.1 | 81 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 24.5% | 107.1 / 12.4 | 53 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,209,827 | 0 | T | G | 23.3% | 118.1 / 12.4 | 60 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 4,101,514 | 0 | G | T | 21.4% | 193.3 / 17.7 | 70 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 94 (0.780) | 26 (0.230) | 23/258 | 3.1 | 23.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 85 (0.750) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 83 (0.690) | 19 (0.170) | 14/258 | 4.9 | 19.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 83 (0.740) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 16 (0.150) | 8/238 | 6.3 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1207805 | 105 (0.870) | 11 (0.100) | 8/244 | 6.4 | 9.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 107 (1.000) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 374987 = | NA (NA) | 12 (0.110) | 8/250 | 6.5 | NA | noncoding (31/36 nt) | other | REP31b |
| ? | NC_000913 | 377366 = | NA (NA) | noncoding (31/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 8 (0.100) | 4/192 | 7.0 | 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 | 2765412 = | 12 (0.100) | 5 (0.050) | 5/220 | 7.2 | 46.4% | intergenic (‑259/+101) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765435 | 2 (0.020) | intergenic (‑282/+78) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 11 (0.090) +T |
7/274 | 7.4 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 9 (0.090) | 5/238 | 7.6 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 3 (0.040) | 3/192 | 7.6 | 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 | |||||