mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 2,001,918 | 0 | A | C | 36.2% | 154.3 / 48.5 | 94 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.9% | 263.8 / 35.4 | 145 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 31.8% | 121.6 / 31.3 | 66 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 30.4% | 194.2 / 52.9 | 115 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.9% | 118.1 / 44.0 | 77 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.1% | 97.7 / 21.5 | 55 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.8% | 128.5 / 24.9 | 73 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.9% | 322.7 / 132.3 | 183 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,556,205 | 0 | A | C | 26.8% | 151.2 / 21.0 | 71 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.2% | 158.8 / 30.0 | 61 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.0% | 178.2 / 44.3 | 84 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.7% | 154.0 / 25.9 | 78 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 23.0% | 272.5 / 30.3 | 113 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 786,855 | 0 | A | C | 22.5% | 204.0 / 16.2 | 80 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 3,206,446 | 0 | C | A | 21.8% | 189.7 / 12.0 | 78 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,608,719 | 0 | G | A | 21.6% | 187.9 / 17.9 | 88 | intergenic (+70/+32) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 2,628,625 | 0 | A | C | 21.6% | 117.2 / 16.0 | 51 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,101,507 | 0 | T | G | 21.4% | 287.8 / 11.5 | 112 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 753,114 | 0 | G | T | 20.9% | 177.4 / 10.2 | 67 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 20.7% | 253.9 / 13.5 | 117 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 76 (0.490) | 33 (0.230) | 26/256 | 3.6 | 22.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 154 (1.060) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 93 (0.600) | 22 (0.150) | 15/256 | 5.8 | 15.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 158 (1.080) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4295966 = | NA (NA) | 5 (0.030) | 5/274 | 9.7 | NA | noncoding (18/37 nt) | other | REP321c |
| ? | NC_000913 | 4326020 = | NA (NA) | noncoding (19/36 nt) | other | REP325e | |||||
| * | ? | NC_000913 | = 359236 | 149 (0.950) | 5 (0.040) | 4/244 | 9.7 | 2.8% | coding (438/660 nt) | cynT | carbonic anhydrase 1 |
| ? | NC_000913 | = 359364 | 213 (1.530) | coding (566/660 nt) | cynT | carbonic anhydrase 1 | |||||
| * | ? | NC_000913 | 3617431 = | 133 (0.850) | 4 (0.030) | 4/250 | 9.8 | 2.9% | coding (417/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| ? | NC_000913 | 3617751 = | 144 (1.010) | coding (737/765 nt) | nikD | Ni(2(+)) ABC transporter ATP binding subunit NikD | |||||
| * | ? | NC_000913 | 2058023 = | 134 (0.860) | 3 (0.020) +22 bp |
3/230 | 10.0 | 2.7% | intergenic (+449/+4) | yeeN/asnW | putative transcriptional regulator YeeN/tRNA‑Asn |
| ? | NC_000913 | 2060006 = | 128 (0.820) | coding (909/951 nt) | cbl | DNA‑binding transcriptional activator Cbl | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.040) | 4/258 | 10.0 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 3745404 | 145 (0.930) | 4 (0.030) | 4/266 | 10.1 | 3.0% | coding (601/1278 nt) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| ? | NC_000913 | = 3745456 | 118 (0.780) | coding (653/1278 nt) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit | |||||
| * | ? | NC_000913 | 1151678 = | 173 (1.110) | 4 (0.030) | 4/266 | 10.1 | 2.3% | coding (64/237 nt) | acpP | acyl carrier protein |
| ? | NC_000913 | = 1151674 | 167 (1.100) | coding (60/237 nt) | acpP | acyl carrier protein | |||||
| * | ? | NC_000913 | = 3172965 | 113 (0.720) | 4 (0.030) | 4/272 | 10.2 | 3.5% | coding (436/582 nt) | mdaB | NADPH:quinone oxidoreductase MdaB |
| ? | NC_000913 | 3172969 = | 109 (0.700) | coding (440/582 nt) | mdaB | NADPH:quinone oxidoreductase MdaB | |||||