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 27 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 | 42.4% | 101.0 / 77.2 | 106 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.7% | 119.2 / 109.6 | 106 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.5% | 292.6 / 26.9 | 151 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.4% | 83.6 / 31.7 | 57 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 28.4% | 151.6 / 26.9 | 74 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.2% | 200.1 / 38.3 | 78 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 27.1% | 145.1 / 29.1 | 70 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.1% | 247.4 / 64.9 | 119 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 27.1% | 215.5 / 50.2 | 107 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 26.9% | 96.2 / 16.1 | 52 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.2% | 172.5 / 31.1 | 65 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 650,809 | 0 | T | G | 25.7% | 161.0 / 15.3 | 74 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.6% | 114.5 / 17.1 | 57 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 24.1% | 113.4 / 12.8 | 54 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.7% | 281.7 / 33.4 | 118 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,001,918 | 0 | A | C | 23.6% | 134.6 / 12.2 | 55 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,628,625 | 0 | A | C | 23.5% | 155.3 / 26.1 | 68 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,556,205 | 0 | A | C | 23.5% | 125.2 / 11.4 | 51 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 22.9% | 248.0 / 26.1 | 110 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 4,111,752 | 0 | T | C | 22.8% | 164.2 / 13.7 | 79 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 22 (0.240) | 11/202 | 4.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 15 (0.120) +T |
13/274 | 5.4 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 11 (0.130) | 7/190 | 5.6 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4542690 | 91 (0.710) | 11 (0.090) | 10/258 | 6.0 | 9.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 133 (1.120) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 15 (0.120) +T |
11/274 | 6.0 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375225 = | NA (NA) | 16 (0.150) | 8/232 | 6.2 | NA | intergenic (+344/‑234) | 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 | 4542682 = | 89 (0.700) | 10 (0.080) | 9/258 | 6.3 | 8.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 135 (1.130) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375046 = | NA (NA) | 18 (0.140) +T |
10/274 | 6.3 | NA | noncoding (15/34 nt) | other | REP31c |
| ? | NC_000913 | 377508 = | NA (NA) | noncoding (15/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 1428524 = | 164 (1.280) | 36 (0.300) +GCA |
8/258 | 6.7 | 19.0% | noncoding (271/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2067082 | NA (NA) | noncoding (272/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1396312 = | NA (NA) | 11 (0.090) | 8/270 | 6.9 | 6.4% | noncoding (269/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1428524 = | 164 (1.280) | noncoding (271/1196 nt) | IS5 | repeat region | |||||