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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.5% | 133.8 / 103.3 | 107 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.7% | 124.9 / 53.5 | 92 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.6% | 76.9 / 20.5 | 46 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.3% | 118.9 / 30.9 | 65 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 32.1% | 95.1 / 28.4 | 53 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 445,558 | 0 | A | C | 31.7% | 63.6 / 22.6 | 41 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 888,014 | 0 | T | G | 28.8% | 137.7 / 19.6 | 73 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,556,205 | 0 | A | C | 26.0% | 111.4 / 12.4 | 50 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 26.0% | 93.7 / 13.5 | 50 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 753,114 | 0 | G | T | 25.3% | 200.9 / 13.3 | 75 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 150.2 / 25.0 | 68 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 24.7% | 162.5 / 22.2 | 73 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 24.6% | 157.8 / 11.6 | 69 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,628,649 | 0 | A | C | 23.9% | 173.9 / 11.8 | 71 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.4% | 94.0 / 17.4 | 47 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,536 | 0 | C | A | 21.9% | 182.7 / 16.6 | 64 | intergenic (+106/‑154) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.6% | 252.1 / 17.4 | 97 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 372,640 | 0 | T | G | 20.0% | 136.6 / 12.0 | 55 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,335,691 | 0 | T | G | 20.0% | 219.9 / 13.8 | 90 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 1,679,688 | 0 | T | G | 20.0% | 220.6 / 12.9 | 85 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 78 (0.770) | 20 (0.220) | 16/246 | 4.6 | 20.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 82 (0.920) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 71 (0.700) | 8 (0.080) | 8/260 | 7.8 | 9.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 84 (0.890) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 614760 | 96 (0.950) | 7 (0.070) | 7/274 | 8.6 | 7.4% | coding (604/3882 nt) | entF | apo‑serine activating enzyme |
| ? | NC_000913 | = 615179 | 80 (0.800) | coding (1023/3882 nt) | entF | apo‑serine activating enzyme | |||||
| * | ? | NC_000913 | = 340006 | NA (NA) | 5 (0.060) +29 bp |
4/218 | 8.8 | NA | noncoding (18/29 nt) | other | REPv23f |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339913 | NA (NA) | 3 (0.040) +29 bp |
3/218 | 9.5 | NA | noncoding (18/29 nt) | other | REPv23d |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339820 | NA (NA) | 3 (0.040) +29 bp |
3/218 | 9.5 | NA | noncoding (18/29 nt) | other | REPv23b |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 762116 = | 49 (0.490) | 5 (0.060) | 4/250 | 9.7 | 7.6% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinylase |
| ? | NC_000913 | 762340 = | 77 (0.850) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinylase | |||||
| * | ? | NC_000913 | = 2340349 | NA (NA) | 3 (0.030) | 3/240 | 10.1 | NA | noncoding (36/37 nt) | other | REP163a |
| ? | NC_000913 | 4295985 = | NA (NA) | noncoding (37/37 nt) | other | REP321c | |||||
| * | ? | NC_000913 | = 1209618 | 82 (0.810) | 3 (0.030) | 3/248 | 10.3 | 3.8% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 80 (0.890) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | 1947995 = | 115 (1.140) | 5 (0.050) | 3/252 | 10.4 | 4.3% | coding (157/741 nt) | yebC | putative transcriptional regulator YebC |
| ? | NC_000913 | 1948948 = | 118 (1.290) | coding (1575/1773 nt) | aspS | aspartate‑‑tRNA ligase | |||||