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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 29,496 | 0 | T | A | 42.9% | 34.8 / 14.8 | 28 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 41.7% | 12.9 / 17.1 | 24 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.6% | 49.2 / 19.3 | 41 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 35.7% | 58.0 / 12.7 | 28 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 34.4% | 57.6 / 11.3 | 32 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.6% | 67.2 / 13.1 | 38 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,068,173 | 0 | T | G | 31.1% | 78.8 / 11.4 | 45 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,404,215 | 0 | T | G | 28.3% | 87.7 / 15.7 | 46 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.9% | 78.6 / 20.3 | 43 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,431,769 | 0 | C | T | 25.0% | 54.3 / 16.9 | 32 | G907G (GGC→GGT) | stfR | Rac prophage; putative membrane protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 98.1 / 30.4 | 52 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,315,936 | 0 | T | A | 24.0% | 113.6 / 11.8 | 50 | K34* (AAA→TAA) | yciG | protein YciG |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 40 (0.800) | 7 (0.150) | 7/258 | 3.4 | 16.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 34 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 10 (0.200) +T |
7/274 | 3.5 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 7 (0.170) | 5/224 | 3.6 | 9.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 66 (1.630) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 8 (0.190) | 4/238 | 4.1 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 4295872 = | NA (NA) | noncoding (37/37 nt) | other | REP321a | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 4 (0.090) +GAACGCCTTATCCGGT |
4/244 | 4.2 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 1462089 = | 54 (1.080) | 4 (0.090) | 4/252 | 4.3 | 7.3% | coding (1197/1206 nt) | paaJ | beta‑ketoadipyl‑CoA thiolase |
| ? | NC_000913 | 1462223 = | 52 (1.140) | coding (99/1314 nt) | paaK | phenylacetate‑CoA ligase | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 7 (0.170) | 3/232 | 4.5 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 4296324 = | NA (NA) | noncoding (37/37 nt) | other | REP321i | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 7 (0.170) | 3/232 | 4.5 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 4295985 = | NA (NA) | noncoding (37/37 nt) | other | REP321c | |||||
| * | ? | NC_000913 | = 2583209 | 64 (1.280) | 3 (0.060) | 3/268 | 5.0 | 4.6% | coding (270/576 nt) | nudK | GDP‑mannose hydrolase |
| ? | NC_000913 | = 2583273 | 61 (1.260) | coding (206/576 nt) | nudK | GDP‑mannose hydrolase | |||||