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 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 45.6% | 30.9 / 46.0 | 57 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,363,151 | 0 | T | C | 44.3% | 70.3 / 242.4 | 192 | G115G (GGT→GGC) | yhcD | putative fimbrial usher protein YhcD |
| * | NC_000913 | 3,556,207 | 0 | T | C | 36.4% | 63.2 / 14.8 | 44 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.2% | 55.6 / 14.0 | 38 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.8% | 72.5 / 11.1 | 44 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.4% | 70.7 / 17.2 | 46 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.1% | 215.7 / 14.9 | 111 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 29,496 | 0 | T | A | 28.3% | 99.0 / 18.2 | 46 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.3% | 106.5 / 15.9 | 46 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.2% | 94.4 / 12.2 | 39 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 28.1% | 51.5 / 14.4 | 32 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,404,218 | 0 | T | G | 27.8% | 105.7 / 13.8 | 54 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 27.1% | 115.9 / 14.3 | 59 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 25.9% | 121.6 / 12.2 | 58 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.8% | 126.6 / 27.7 | 66 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.6% | 171.9 / 20.3 | 82 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,032,731 | 0 | T | G | 25.4% | 114.7 / 12.7 | 59 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 96.6 / 11.1 | 40 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 332,991 | 0 | G | T | 24.4% | 207.3 / 27.0 | 82 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 4,287,719 | 0 | T | A | 24.2% | 156.2 / 19.8 | 66 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| 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 | 608007 = | NA (NA) | 6 (0.080) | 4/224 | 7.1 | 5.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 97 (1.330) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374945 = | NA (NA) | 4 (0.050) +TACGCCGCATCCGGT |
4/246 | 7.5 | NA | noncoding (15/34 nt) | other | REP31a |
| ? | NC_000913 | 377422 = | NA (NA) | noncoding (1/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | = 2973537 | 89 (0.990) | 3 (0.030) | 3/270 | 8.6 | 3.4% | coding (326/1194 nt) | lplT | lysophospholipid transporter |
| ? | NC_000913 | 2973541 = | 84 (0.950) | coding (322/1194 nt) | lplT | lysophospholipid transporter | |||||
| * | ? | NC_000913 | = 2173362 | 64 (0.710) | 7 (0.080) | 3/272 | 8.6 | 9.4% | pseudogene (917/1358 nt) | gatC | galactitol‑specific PTS enzyme IIC component |
| ? | NC_000913 | 2173368 = | 72 (0.810) | pseudogene (911/1358 nt) | gatC | galactitol‑specific PTS enzyme IIC component | |||||
| * | ? | NC_000913 | 339772 = | NA (NA) | 3 (0.030) +T |
3/274 | 8.6 | NA | noncoding (15/34 nt) | other | REP23a |
| ? | NC_000913 | 377408 = | NA (NA) | noncoding (15/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | 511043 = | 76 (0.840) | 3 (0.030) | 3/276 | 8.7 | 3.8% | coding (337/2505 nt) | copA | Cu(+) exporting P‑type ATPase |
| ? | NC_000913 | 511081 = | 78 (0.860) | coding (299/2505 nt) | copA | Cu(+) exporting P‑type ATPase | |||||