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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,568,504 | 0 | T | G | 37.4% | 337.9 / 38.5 | 181 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.8% | 239.3 / 50.3 | 119 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 31.2% | 278.1 / 87.5 | 173 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.9% | 165.4 / 44.9 | 94 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.6% | 91.6 / 11.3 | 49 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.3% | 138.5 / 27.4 | 55 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 295.4 / 94.0 | 144 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,628,625 | 0 | A | C | 24.7% | 223.5 / 25.9 | 93 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 650,809 | 0 | T | G | 24.1% | 292.9 / 23.7 | 116 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.5% | 213.1 / 35.8 | 98 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,775,467 | 0 | A | C | 21.9% | 227.5 / 11.6 | 96 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 501,575 | 0 | A | C | 21.2% | 172.0 / 15.7 | 66 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 176 (1.020) | 15 (0.090) | 13/258 | 6.5 | 7.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 198 (1.230) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 274752 | NA (NA) | 5 (0.030) | 5/272 | 9.8 | NA | noncoding (398/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274756 = | NA (NA) | noncoding (394/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 186 (1.080) | 4 (0.020) | 4/258 | 10.1 | 2.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 198 (1.230) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 802584 = | 162 (0.940) | 4 (0.020) | 4/266 | 10.2 | 2.5% | coding (698/1434 nt) | ybhI | putative tricarboxylate transporter |
| ? | NC_000913 | = 802580 | 159 (0.960) | coding (694/1434 nt) | ybhI | putative tricarboxylate transporter | |||||
| * | ? | NC_000913 | = 1005510 | 149 (0.860) | 4 (0.020) | 4/276 | 10.4 | 2.6% | coding (743/1011 nt) | pyrD | dihydroorotate dehydrogenase, type 2 |
| ? | NC_000913 | 1005514 = | 155 (0.900) | coding (747/1011 nt) | pyrD | dihydroorotate dehydrogenase, type 2 | |||||
| * | ? | NC_000913 | = 722725 | 133 (0.770) | 4 (0.020) | 4/274 | 10.4 | 3.0% | coding (1690/2685 nt) | kdpD | sensory histidine kinase KdpD |
| ? | NC_000913 | 722729 = | 131 (0.770) | coding (1686/2685 nt) | kdpD | sensory histidine kinase KdpD | |||||
| * | ? | NC_000913 | 3641604 = | 203 (1.180) | 3 (0.020) | 3/266 | 10.8 | 1.5% | coding (743/1470 nt) | dtpB | dipeptide/tripeptide:H(+) symporter DtpB |
| ? | NC_000913 | = 3641600 | 199 (1.200) | coding (739/1470 nt) | dtpB | dipeptide/tripeptide:H(+) symporter DtpB | |||||
| * | ? | NC_000913 | 2166837 = | 167 (0.970) | 3 (0.020) | 3/262 | 10.8 | 1.9% | coding (1170/1362 nt) | yegQ | putative peptidase YegQ |
| ? | NC_000913 | = 3546914 | 144 (0.880) | coding (356/1317 nt) | gntT | high‑affinity gluconate transporter | |||||
| * | ? | NC_000913 | 2063913 = | 195 (1.130) | 3 (0.020) | 3/264 | 10.8 | 1.6% | coding (555/1080 nt) | cobT | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| ? | NC_000913 | = 2063909 | 177 (1.070) | coding (559/1080 nt) | cobT | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase | |||||
| * | ? | NC_000913 | 620568 = | 133 (0.770) | 4 (0.020) | 3/264 | 10.8 | 3.0% | coding (621/993 nt) | fepG | ferric enterobactin ABC transporter membrane subunit FepG |
| ? | NC_000913 | = 620564 | 129 (0.780) | coding (625/993 nt) | fepG | ferric enterobactin ABC transporter membrane subunit FepG | |||||