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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,825,061 | 0 | G | A | 36.8% | 117.6 / 46.7 | 87 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.2% | 229.0 / 97.9 | 174 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.0% | 353.2 / 37.4 | 196 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,205 | 0 | A | C | 32.7% | 100.8 / 17.9 | 56 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.8% | 136.6 / 44.0 | 84 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.3% | 97.9 / 18.4 | 58 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 888,014 | 0 | T | G | 28.7% | 211.3 / 24.5 | 108 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 501,575 | 0 | A | C | 28.0% | 161.5 / 17.2 | 75 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 372,640 | 0 | T | G | 27.7% | 184.8 / 29.0 | 94 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,564 | 0 | A | C | 26.9% | 159.0 / 32.6 | 78 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,101,507 | 0 | T | G | 26.3% | 254.0 / 18.0 | 118 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,745,397 | 0 | A | C | 26.1% | 212.1 / 21.9 | 116 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.9% | 296.7 / 43.8 | 136 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 445,558 | 0 | A | C | 25.7% | 149.1 / 32.3 | 74 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 1,377,140 | 0 | A | C | 25.6% | 190.9 / 12.8 | 90 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.5% | 447.0 / 126.2 | 217 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 23.5% | 189.0 / 25.8 | 81 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 23.2% | 189.1 / 14.6 | 82 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.0% | 308.6 / 54.4 | 135 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.9% | 287.1 / 35.1 | 109 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 125 (0.820) | 40 (0.300) | 29/246 | 3.0 | 26.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 111 (0.820) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 147 (0.960) | 31 (0.220) | 25/260 | 3.9 | 18.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 140 (0.980) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 115 (0.750) | 19 (0.140) | 18/246 | 5.0 | 15.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 108 (0.800) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 150 (0.980) | 18 (0.130) | 18/260 | 5.3 | 11.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 142 (0.990) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1396044 = | NA (NA) | 7 (0.050) +CTAA |
7/270 | 9.0 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1979271 = | 0 (0.000) | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 4492090 | 189 (1.230) | 6 (0.040) | 6/276 | 9.6 | 3.2% | coding (436/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter |
| ? | NC_000913 | = 4492168 | 173 (1.140) | coding (358/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter | |||||
| * | ? | NC_000913 | 226608 = | NA (NA) | 5 (0.030) | 5/264 | 9.9 | NA | noncoding (850/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 226686 = | NA (NA) | noncoding (928/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3597640 | 180 (1.170) | 4 (0.030) | 4/264 | 10.5 | 2.4% | intergenic (‑80/‑344) | livK/panZ | L‑leucine/L‑phenylalanine ABC transporter periplasmic binding protein/PanD maturation factor |
| ? | NC_000913 | = 3597672 | 159 (1.090) | intergenic (‑112/‑312) | livK/panZ | L‑leucine/L‑phenylalanine ABC transporter periplasmic binding protein/PanD maturation factor | |||||
| * | ? | NC_000913 | = 484317 | 150 (0.980) | 6 (0.040) +AACGATCTCCGCCTC |
3/248 | 10.7 | 3.5% | coding (87/3150 nt) | acrB | multidrug efflux pump RND permease AcrB |
| ? | NC_000913 | 3415176 = | 217 (1.420) | coding (144/3105 nt) | acrF | multidrug efflux pump RND permease AcrF | |||||
| * | ? | NC_000913 | = 2704109 | 134 (0.870) | 4 (0.030) | 3/252 | 10.8 | 3.0% | intergenic (‑46/+226) | rnc/lepB | RNase III/signal peptidase I |
| ? | NC_000913 | = 2704177 | 133 (0.960) | intergenic (‑114/+158) | rnc/lepB | RNase III/signal peptidase I | |||||