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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,556,207 | 0 | T | C | 37.9% | 83.6 / 34.9 | 66 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.7% | 94.7 / 43.9 | 69 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 34.9% | 105.4 / 25.7 | 63 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.6% | 198.9 / 75.0 | 131 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.0% | 161.7 / 40.6 | 71 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.4% | 312.8 / 29.1 | 160 | 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 | 29.8% | 138.3 / 44.7 | 84 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.5% | 130.8 / 24.4 | 69 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.7% | 198.3 / 20.9 | 86 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,206,444 | 0 | T | A | 26.2% | 162.8 / 24.1 | 84 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 25.6% | 175.1 / 25.8 | 78 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.3% | 168.7 / 16.5 | 75 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,489,174 | 0 | G | T | 25.0% | 216.7 / 21.0 | 80 | G315C (GGT→TGT) | aldA | aldehyde dehydrogenase A |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.0% | 233.8 / 33.7 | 88 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,223,593 | 0 | T | G | 23.9% | 271.0 / 14.3 | 113 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 4,209,827 | 0 | T | G | 23.3% | 117.9 / 13.8 | 60 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 29,496 | 0 | T | A | 23.1% | 188.2 / 29.0 | 78 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 888,014 | 0 | T | G | 22.4% | 203.8 / 19.4 | 85 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,401,459 | 0 | T | C | 22.0% | 246.5 / 28.8 | 118 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,032,731 | 0 | T | G | 21.7% | 197.6 / 20.4 | 83 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 18 (0.180) | 10/190 | 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 | 374922 = | NA (NA) | 32 (0.230) | 14/260 | 6.0 | 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 | = 375064 | NA (NA) | 8 (0.080) | 8/192 | 6.4 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 28 (0.280) | 7/190 | 6.7 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 12 (0.110) | 7/202 | 7.1 | 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) | 27 (0.190) +T |
11/274 | 7.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 26 (0.260) | 6/192 | 7.2 | NA | intergenic (+142/‑436) | 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 | 340035 = | NA (NA) | 26 (0.180) | 10/274 | 7.5 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 66 (0.450) | 8 (0.060) | 8/258 | 7.9 | 8.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 122 (0.900) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374958 | NA (NA) | 4 (0.040) | 4/202 | 8.5 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||