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 | 4,027,436 | 0 | T | G | 56.2% | 23.6 / 42.6 | 32 | intergenic (+208/+173) | fre/fadA | flavin reductase/3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 37.6% | 180.4 / 17.6 | 102 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,765,752 | 0 | C | G | 34.6% | 233.6 / 252.1 | 202 | R1190R (CGC→CGG) | rhsA | rhs element protein RhsA |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 82.3 / 30.8 | 42 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.3% | 125.5 / 45.7 | 90 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 445,558 | 0 | A | C | 31.2% | 86.7 / 20.9 | 48 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.8% | 138.7 / 24.6 | 68 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.9% | 160.3 / 71.6 | 97 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,418,880 | 0 | G | T | 27.7% | 338.1 / 116.8 | 141 | intergenic (+269/‑162) | yhdV/yhdW | lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW |
| * | NC_000913 | 3,556,207 | 0 | T | C | 27.6% | 105.5 / 20.1 | 58 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 27.3% | 122.5 / 11.9 | 55 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 26.7% | 140.1 / 10.3 | 60 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 501,575 | 0 | A | C | 23.7% | 83.6 / 14.3 | 38 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,125 | 0 | T | A | 22.2% | 199.2 / 27.3 | 81 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 21.4% | 121.0 / 20.1 | 56 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 20.9% | 166.6 / 25.9 | 67 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | = 374958 | NA (NA) | 4 (0.050) | 4/202 | 6.0 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 8 (0.080) | 6/260 | 6.1 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 2765420 = | 203 (1.860) | 3 (0.040) | 3/188 | 6.2 | 2.0% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 149 (2.010) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 5 (0.050) +GAACGCCTTATCCGGT |
4/244 | 6.7 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 6 (0.060) +T |
5/274 | 6.7 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 166852 = | 104 (0.960) | 7 (0.060) | 5/276 | 6.7 | 6.6% | coding (2123/2535 nt) | mrcB | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| ? | NC_000913 | 166981 = | 95 (0.870) | coding (2252/2535 nt) | mrcB | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 3 (0.030) | 3/224 | 6.9 | 3.4% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 85 (0.960) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 374958 | NA (NA) | 5 (0.050) +T |
4/274 | 7.2 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 3 (0.030) | 3/250 | 7.3 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 382332 | NA (NA) | 3 (0.030) | 3/270 | 7.6 | NA | noncoding (1073/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 382336 = | NA (NA) | noncoding (1077/1331 nt) | IS2 | repeat region | |||||