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 | 42.3% | 142.9 / 116.9 | 149 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 39.3% | 94.3 / 66.2 | 89 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,205 | 0 | A | C | 32.8% | 122.3 / 17.0 | 61 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 445,558 | 0 | A | C | 31.5% | 132.5 / 40.2 | 73 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,556,207 | 0 | T | C | 30.6% | 103.9 / 20.0 | 62 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.6% | 175.4 / 66.8 | 98 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.7% | 341.5 / 27.7 | 167 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.8% | 153.6 / 25.8 | 73 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.7% | 156.8 / 43.7 | 94 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,507 | 0 | T | G | 27.4% | 187.7 / 12.8 | 84 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 888,014 | 0 | T | G | 27.0% | 153.6 / 22.6 | 74 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 753,125 | 0 | T | A | 25.8% | 147.1 / 20.5 | 66 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 24.6% | 245.1 / 18.8 | 127 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,206,446 | 0 | C | A | 24.2% | 209.9 / 21.3 | 95 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 501,575 | 0 | A | C | 23.9% | 173.6 / 18.3 | 71 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 501,564 | 0 | A | C | 23.9% | 155.2 / 27.1 | 67 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 650,809 | 0 | T | G | 23.5% | 195.2 / 17.8 | 85 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 23.3% | 204.7 / 27.1 | 91 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.2% | 268.1 / 30.5 | 112 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.0% | 357.6 / 46.4 | 152 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (lowest skew 10 of 52 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 110 (0.970) | 22/216 | 3.1 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375219 | NA (NA) | 33 (0.290) | 19/216 | 3.7 | NA | noncoding (1/36 nt) | other | REP31f |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 377353 = | NA (NA) | 24 (0.210) +30 bp |
17/216 | 4.1 | NA | noncoding (18/37 nt) | other | REP32a |
| ? | NC_000913 | 4325850 = | NA (NA) | intergenic (‑109/+549) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 24 (0.240) | 14/192 | 4.2 | 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 | 375304 = | NA (NA) | 27 (0.220) | 17/232 | 4.4 | NA | noncoding (17/36 nt) | other | REP31h |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 17 (0.170) | 11/192 | 5.0 | 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 | 608007 = | NA (NA) | 29 (0.250) | 12/224 | 5.4 | 19.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 122 (1.030) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 23 (0.220) | 9/202 | 5.9 | 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 | = 375246 | NA (NA) | 23 (0.180) +GAACGCCTTATCCGGT |
11/244 | 6.1 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 22 (0.150) +T |
12/274 | 6.4 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||