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 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 445,558 | 0 | A | C | 40.6% | 36.3 / 21.7 | 32 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.0% | 115.2 / 53.4 | 89 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 35.0% | 75.9 / 37.5 | 60 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.9% | 117.1 / 34.1 | 65 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,775,467 | 0 | A | C | 31.1% | 106.6 / 14.8 | 61 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 501,575 | 0 | A | C | 30.8% | 79.8 / 11.8 | 39 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,943,488 | 0 | T | G | 30.2% | 70.2 / 13.5 | 43 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 650,809 | 0 | T | G | 30.1% | 139.6 / 25.3 | 73 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.4% | 238.6 / 21.1 | 121 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.3% | 103.8 / 22.8 | 58 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.0% | 139.6 / 34.7 | 62 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.6% | 182.7 / 76.2 | 105 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,628,625 | 0 | A | C | 28.3% | 98.8 / 15.2 | 46 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,101,507 | 0 | T | G | 26.0% | 219.9 / 12.8 | 96 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,729,391 | 0 | A | C | 25.3% | 151.4 / 13.2 | 75 | noncoding (54/76 nt) | gltW | tRNA‑Glu |
| * | NC_000913 | 3,926,366 | 0 | A | C | 24.6% | 262.7 / 34.9 | 114 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 29,496 | 0 | T | A | 24.1% | 194.2 / 29.0 | 83 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,752 | 0 | T | C | 24.0% | 148.9 / 10.6 | 75 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.6% | 216.5 / 38.8 | 89 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 23.1% | 135.6 / 12.1 | 65 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375023 = | NA (NA) | 20 (0.250) | 15/192 | 3.3 | 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) | 26 (0.330) | 14/192 | 3.6 | 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) | 21 (0.220) | 14/232 | 4.4 | NA | noncoding (17/36 nt) | other | REP31h |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4542690 | 123 (1.080) | 19 (0.180) | 16/258 | 4.5 | 13.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 120 (1.130) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 18 (0.180) | 14/238 | 4.5 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 4542682 = | 132 (1.160) | 14 (0.130) | 14/258 | 4.9 | 10.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 120 (1.130) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 14 (0.150) | 10/222 | 5.3 | 14.5% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2515618 = | 83 (0.900) | intergenic (+175/+25) | insL‑3/pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA | |||||
| * | ? | NC_000913 | 377353 = | NA (NA) | 15 (0.170) +30 bp |
9/216 | 5.5 | 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 | 374922 = | NA (NA) | 28 (0.340) | 8/202 | 5.6 | 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) | 13 (0.140) | 9/224 | 5.7 | 12.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 93 (1.010) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||