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 | 4,213,051 | 0 | A | C | 46.2% | ‑4.5 / 19.9 | 14 | noncoding (12/120 nt) | rrfE | 5S ribosomal RNA |
| * | NC_000913 | 3,556,207 | 0 | T | C | 44.4% | 17.1 / 15.6 | 27 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 39.4% | 46.5 / 14.9 | 33 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.5% | 62.4 / 25.0 | 52 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 35.6% | 61.1 / 24.0 | 45 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.6% | 73.5 / 18.3 | 45 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 34.3% | 182.6 / 21.8 | 100 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 501,575 | 0 | A | C | 30.6% | 68.1 / 14.6 | 36 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.9% | 60.6 / 17.3 | 38 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.6% | 99.7 / 17.6 | 42 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 27.4% | 132.6 / 12.6 | 62 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,568,512 | 0 | C | A | 26.3% | 200.8 / 33.2 | 76 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,101,514 | 0 | G | T | 26.2% | 154.2 / 26.5 | 61 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 445,558 | 0 | A | C | 25.0% | 64.0 / 12.0 | 32 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,240,985 | 0 | T | G | 25.0% | 111.3 / 17.6 | 52 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.5% | 184.4 / 55.3 | 94 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 24.2% | 65.8 / 17.1 | 33 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.3% | 97.8 / 16.0 | 43 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 22.7% | 152.5 / 18.9 | 75 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 29,496 | 0 | T | A | 22.4% | 108.0 / 17.1 | 49 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 50 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375023 = | NA (NA) | 37 (0.650) | 10/192 | 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 | 374922 = | NA (NA) | 20 (0.330) | 11/202 | 3.3 | 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 | 374921 = | NA (NA) | 40 (0.710) | 9/190 | 3.6 | 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 | = 4296059 | NA (NA) | 18 (0.250) +TGCCTGATGCGACGCTTGC |
12/238 | 3.7 | NA | intergenic (+265/+377) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | = 4326120 | NA (NA) | noncoding (19/36 nt) | other | REP325g | |||||
| * | ? | NC_000913 | 375304 = | NA (NA) | 15 (0.220) | 11/232 | 3.8 | NA | noncoding (17/36 nt) | other | REP31h |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 34 (0.420) +T |
14/274 | 3.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 29 (0.410) | 11/238 | 3.9 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4296059 | NA (NA) | 16 (0.230) +TGCCTGATGCGACGCTTGC |
10/238 | 4.2 | NA | intergenic (+265/+377) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | = 4326320 | NA (NA) | noncoding (19/36 nt) | other | REP325k | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 37 (0.520) | 10/238 | 4.2 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375100 | NA (NA) | 12 (0.170) | 10/238 | 4.2 | NA | noncoding (19/36 nt) | other | REP31d |
| ? | NC_000913 | = 377352 | NA (NA) | noncoding (17/37 nt) | other | REP32a | |||||