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 | 4,604,344 | 0 | C | T | 40.0% | 103.1 / 68.4 | 95 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.0% | 103.9 / 46.6 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 36.0% | 70.9 / 18.4 | 50 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 35.6% | 88.5 / 30.4 | 59 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,207 | 0 | T | C | 34.0% | 72.1 / 17.9 | 50 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.7% | 196.2 / 103.5 | 127 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.5% | 142.1 / 57.2 | 95 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 29.3% | 131.5 / 35.4 | 82 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 445,558 | 0 | A | C | 28.8% | 103.2 / 36.8 | 66 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.8% | 302.0 / 30.8 | 164 | 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 | 25.0% | 119.8 / 23.3 | 60 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 25.0% | 134.4 / 14.5 | 48 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.4% | 215.1 / 29.5 | 78 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 23.4% | 136.2 / 10.2 | 64 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,628,649 | 0 | A | C | 23.3% | 127.7 / 11.5 | 60 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 753,125 | 0 | T | A | 22.9% | 197.7 / 26.2 | 84 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 888,014 | 0 | T | G | 21.4% | 211.0 / 21.7 | 103 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 29,496 | 0 | T | A | 21.2% | 161.2 / 22.2 | 66 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,444 | 0 | T | A | 20.6% | 146.3 / 14.9 | 63 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,401,459 | 0 | T | C | 20.2% | 239.5 / 14.5 | 104 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| Marginal new junction evidence (lowest skew 10 of 31 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 13 (0.140) | 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 | 375023 = | NA (NA) | 14 (0.150) | 7/192 | 6.8 | 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 | 375248 = | NA (NA) | 16 (0.140) | 8/238 | 7.6 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 16 (0.130) | 8/260 | 8.1 | 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 | = 375165 | NA (NA) | 5 (0.050) | 4/192 | 8.4 | NA | noncoding (33/34 nt) | other | REP31e |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 112 (0.840) | 7 (0.060) | 7/258 | 8.5 | 5.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 130 (1.050) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 10 (0.090) | 5/224 | 8.7 | 7.9% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 117 (1.080) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 1462089 = | 120 (0.900) | 6 (0.050) | 6/252 | 8.9 | 4.4% | coding (1197/1206 nt) | paaJ | beta‑ketoadipyl‑CoA thiolase |
| ? | NC_000913 | 1462223 = | 153 (1.260) | coding (99/1314 nt) | paaK | phenylacetate‑CoA ligase | |||||
| * | ? | NC_000913 | 226608 = | NA (NA) | 5 (0.040) | 5/262 | 9.6 | NA | noncoding (850/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 226686 = | NA (NA) | noncoding (928/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 374987 = | NA (NA) | 3 (0.030) +28 bp |
3/220 | 9.8 | NA | noncoding (31/36 nt) | other | REP31b |
| ? | NC_000913 | 377321 = | NA (NA) | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||