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 22 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 | 42.8% | 144.1 / 114.3 | 152 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 40.0% | 94.4 / 32.9 | 65 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 37.3% | 68.9 / 41.8 | 59 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.7% | 68.1 / 27.5 | 49 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,207 | 0 | T | C | 33.3% | 93.4 / 27.4 | 66 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.6% | 146.8 / 33.9 | 62 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 30.0% | 102.5 / 21.2 | 60 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.8% | 105.1 / 15.9 | 52 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 650,809 | 0 | T | G | 26.4% | 252.4 / 27.6 | 110 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.1% | 343.1 / 17.6 | 160 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,667,126 | 0 | A | C | 25.0% | 226.9 / 25.7 | 104 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 888,014 | 0 | T | G | 23.5% | 192.2 / 15.1 | 85 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,943,488 | 0 | T | G | 23.2% | 144.7 / 17.4 | 69 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 753,125 | 0 | T | A | 22.7% | 211.5 / 23.8 | 88 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.6% | 356.7 / 94.1 | 168 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,209,827 | 0 | T | G | 22.5% | 133.0 / 17.4 | 71 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 445,558 | 0 | A | C | 22.4% | 111.4 / 18.1 | 49 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 1,335,691 | 0 | T | G | 21.6% | 278.4 / 19.6 | 116 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.5% | 230.4 / 33.4 | 93 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 21.4% | 300.9 / 42.3 | 126 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 119 (0.830) | 11 (0.080) | 8/258 | 7.3 | 7.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 153 (1.140) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 115 (0.800) | 9 (0.070) | 7/258 | 7.7 | 6.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 153 (1.140) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 324130 = | 170 (1.190) | 4 (0.030) | 4/258 | 9.1 | 2.8% | coding (373/696 nt) | ykgG | DUF162 domain‑containing lactate utilization protein YkgG |
| ? | NC_000913 | 324235 = | 120 (0.900) | coding (478/696 nt) | ykgG | DUF162 domain‑containing lactate utilization protein YkgG | |||||
| * | ? | NC_000913 | = 3000956 | 169 (1.180) | 4 (0.030) | 4/264 | 9.2 | 2.5% | coding (612/2259 nt) | xdhA | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| ? | NC_000913 | = 3000997 | 150 (1.100) | coding (653/2259 nt) | xdhA | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA | |||||
| * | ? | NC_000913 | 1466746 = | 164 (1.150) | 4 (0.030) | 4/260 | 9.2 | 2.5% | pseudogene (1355/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | 1466858 = | 160 (1.190) | pseudogene (1467/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 1466452 = | 125 (0.870) | 4 (0.030) | 4/260 | 9.2 | 2.8% | pseudogene (1061/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | 1466858 = | 160 (1.190) | pseudogene (1467/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 1514527 | 117 (0.850) | 8 (0.060) +TGC |
3/258 | 9.7 | 6.3% | coding (697/942 nt) | ydcU | putative ABC transporter membrane subunit YdcU |
| ? | NC_000913 | 1514528 = | 121 (0.840) | coding (698/942 nt) | ydcU | putative ABC transporter membrane subunit YdcU | |||||
| * | ? | NC_000913 | 3054424 = | 101 (0.710) | 3 (0.020) | 3/262 | 9.8 | 2.8% | coding (417/1326 nt) | pepP | proline aminopeptidase P II |
| ? | NC_000913 | 3054498 = | 116 (0.850) | coding (343/1326 nt) | pepP | proline aminopeptidase P II | |||||
| * | ? | NC_000913 | = 2041306 | 149 (1.040) | 3 (0.020) | 3/264 | 9.8 | 1.9% | intergenic (+188/‑69) | msrQ/zinT | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit/metal‑binding protein ZinT |
| ? | NC_000913 | = 2041355 | 160 (1.170) | intergenic (+237/‑20) | msrQ/zinT | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit/metal‑binding protein ZinT | |||||
| * | ? | NC_000913 | 4510797 = | 173 (1.210) | 3 (0.020) | 3/268 | 9.9 | 1.8% | coding (661/768 nt) | fecE | ferric citrate ABC transporter ATP binding subunit |
| ? | NC_000913 | = 4511007 | 162 (1.170) | coding (451/768 nt) | fecE | ferric citrate ABC transporter ATP binding subunit | |||||