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 | 4,604,344 | 0 | C | T | 41.7% | 84.5 / 60.1 | 84 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.6% | 134.1 / 20.6 | 90 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 32.6% | 64.6 / 27.3 | 49 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.9% | 69.2 / 22.0 | 47 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.6% | 124.5 / 26.9 | 49 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.7% | 60.2 / 14.6 | 37 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 29.4% | 96.6 / 47.0 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.5% | 97.8 / 25.1 | 51 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 25.5% | 94.7 / 19.1 | 47 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.8% | 179.1 / 47.9 | 84 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.5% | 199.5 / 23.8 | 71 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 22.2% | 136.3 / 19.2 | 54 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,032,731 | 0 | T | G | 22.2% | 146.5 / 13.0 | 72 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 1,645,023 | 0 | T | A | 21.0% | 155.6 / 18.8 | 62 | intergenic (‑121/+96) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 599,576 | 0 | T | G | 20.4% | 92.9 / 11.2 | 44 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 2,483,268 | 0 | T | A | 20.2% | 195.9 / 15.3 | 79 | L24F (TTA→TTT) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| * | NC_000913 | 786,855 | 0 | A | C | 20.0% | 122.3 / 10.5 | 55 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 66 (0.690) | 12 (0.130) | 12/258 | 4.5 | 14.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 76 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 271509 | 74 (0.780) | 23 (0.240) | 13/276 | 4.5 | 23.7% | noncoding (969/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1470264 | 0 (0.000) | 21 (0.220) | 11/276 | 5.0 | 100% | noncoding (969/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 271506 = | 68 (0.710) | 12 (0.130) | 11/276 | 5.0 | 15.0% | noncoding (966/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 275149 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 271506 = | 68 (0.710) | 9 (0.100) | 8/264 | 5.8 | 12.2% | noncoding (966/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1979340 | 34 (0.360) | 15 (0.160) | 6/276 | 6.7 | 30.6% | intergenic (‑125/‑413) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979337 = | 32 (0.340) | 5 (0.050) | 5/276 | 7.1 | 13.5% | intergenic (‑122/‑416) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2730489 | NA (NA) | 4 (0.040) | 4/270 | 7.5 | NA | noncoding (669/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2730493 = | NA (NA) | noncoding (665/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 3484544 = | 107 (1.120) | 3 (0.030) | 3/256 | 7.9 | 2.9% | coding (55/870 nt) | prkB | putative phosphoribulokinase |
| ? | NC_000913 | = 3484540 | 105 (1.190) | coding (51/870 nt) | prkB | putative phosphoribulokinase | |||||
| * | ? | NC_000913 | 381681 = | NA (NA) | 3 (0.030) | 3/258 | 7.9 | NA | noncoding (422/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381753 = | NA (NA) | noncoding (494/1331 nt) | IS2 | repeat region | |||||