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 30 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 | 44.1% | 123.7 / 117.2 | 145 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 37.2% | 163.6 / 59.0 | 86 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.7% | 117.8 / 35.1 | 72 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.1% | 362.0 / 40.6 | 187 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 646,747 | 0 | T | G | 30.4% | 139.8 / 48.9 | 79 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.2% | 90.7 / 38.1 | 63 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.7% | 217.2 / 69.8 | 115 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,125 | 0 | T | A | 28.2% | 158.3 / 31.1 | 78 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 28.2% | 151.7 / 22.9 | 71 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 26.5% | 191.4 / 13.8 | 83 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 26.0% | 142.5 / 28.3 | 73 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,207 | 0 | T | C | 26.0% | 146.2 / 16.8 | 73 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 26.0% | 164.6 / 17.0 | 73 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 445,558 | 0 | A | C | 23.5% | 151.3 / 27.6 | 68 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,111,752 | 0 | T | C | 23.1% | 203.6 / 20.9 | 104 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.5% | 293.8 / 28.4 | 120 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,223,593 | 0 | T | G | 22.4% | 295.0 / 12.4 | 118 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 650,809 | 0 | T | G | 22.1% | 230.3 / 16.6 | 95 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,608,719 | 0 | G | A | 22.1% | 163.4 / 12.8 | 77 | intergenic (+70/+32) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 1,315,936 | 0 | T | A | 21.1% | 360.6 / 30.9 | 147 | K34* (AAA→TAA) | yciG | protein YciG |
| Marginal new junction evidence (lowest skew 10 of 58 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 97 (0.890) | 20/190 | 3.8 | 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 | = 1207805 | 117 (0.740) | 31 (0.220) | 24/244 | 4.3 | 22.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 105 (0.750) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 88 (0.800) | 17/192 | 4.5 | 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 | = 375064 | NA (NA) | 18 (0.160) | 16/192 | 4.7 | 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 | 374922 = | NA (NA) | 44 (0.380) | 15/202 | 5.3 | 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 | 608007 = | NA (NA) | 36 (0.280) | 17/224 | 5.4 | 21.1% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 135 (1.050) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 375165 | NA (NA) | 10 (0.090) | 10/192 | 6.6 | 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 | = 375160 | NA (NA) | 64 (0.410) +T |
16/274 | 6.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375231 | NA (NA) | 11 (0.080) | 11/232 | 7.4 | NA | intergenic (+350/‑228) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | = 377522 | NA (NA) | noncoding (1/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 79 (0.580) | 11/238 | 7.5 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||