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 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,001,918 | 0 | A | C | 43.5% | 76.7 / 46.2 | 69 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 40.5% | 87.9 / 57.2 | 84 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 38.3% | 48.1 / 34.2 | 47 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.8% | 157.4 / 83.2 | 104 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,444 | 0 | T | A | 30.0% | 84.2 / 11.9 | 50 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.0% | 119.4 / 25.4 | 50 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 29,496 | 0 | T | A | 29.7% | 144.4 / 36.0 | 74 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.0% | 257.6 / 21.5 | 128 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.7% | 175.2 / 51.6 | 90 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 445,558 | 0 | A | C | 26.2% | 119.1 / 24.3 | 61 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 1,775,467 | 0 | A | C | 26.2% | 131.0 / 15.7 | 65 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 24.5% | 109.1 / 15.5 | 53 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.0% | 230.4 / 34.2 | 104 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,628,649 | 0 | A | C | 23.3% | 178.9 / 10.6 | 73 | 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 | 23.0% | 173.1 / 23.2 | 74 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 888,014 | 0 | T | G | 22.5% | 180.0 / 19.9 | 80 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 753,114 | 0 | G | T | 22.4% | 206.1 / 14.0 | 76 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 22.3% | 210.1 / 34.3 | 94 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 29,503 | 0 | T | C | 22.2% | 206.6 / 12.9 | 99 | intergenic (+308/‑148) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,628,625 | 0 | A | C | 21.7% | 146.2 / 13.5 | 60 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| Marginal new junction evidence (lowest skew 10 of 43 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 81 (0.850) | 16/216 | 3.7 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375118 | NA (NA) | 21 (0.220) | 12/216 | 4.6 | NA | noncoding (1/36 nt) | other | REP31d |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 43 (0.450) | 12/216 | 4.6 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 40 (0.330) +T |
15/274 | 4.9 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 11 (0.130) | 9/192 | 4.9 | NA | intergenic (+243/‑335) | 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 | = 4542690 | 84 (0.690) | 14 (0.120) | 13/258 | 5.1 | 14.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 88 (0.770) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 90 (0.740) | 13 (0.110) | 12/258 | 5.4 | 13.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 90 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 11 (0.130) | 7/192 | 5.6 | 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 | = 374958 | NA (NA) | 7 (0.080) | 7/202 | 5.9 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 17 (0.140) +T |
10/274 | 6.2 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||