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% | 87.2 / 54.9 | 84 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 39.4% | 36.2 / 16.4 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.5% | 135.2 / 14.9 | 80 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.0% | 30.2 / 12.0 | 25 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.0% | 87.6 / 18.8 | 50 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 27.5% | 111.1 / 18.8 | 51 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,645,034 | 0 | A | C | 27.4% | 107.6 / 21.6 | 62 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 650,809 | 0 | T | G | 26.9% | 83.1 / 15.2 | 52 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.8% | 173.4 / 59.2 | 97 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,844,219 | 0 | T | G | 25.3% | 178.0 / 16.0 | 83 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 646,747 | 0 | T | G | 22.6% | 112.2 / 16.6 | 53 | 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 | = 4542690 | 74 (0.980) | 12 (0.170) | 10/260 | 4.3 | 12.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 94 (1.340) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 8 (0.110) | 7/264 | 5.4 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 226685 | 24 (0.320) | 8 (0.110) | 7/264 | 5.4 | 26.0% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 4542682 = | 75 (1.000) | 5 (0.070) | 5/260 | 6.1 | 5.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 94 (1.340) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 972004 = | 69 (0.920) | 3 (0.040) | 3/262 | 7.2 | 4.4% | coding (253/894 nt) | ycbJ | putative phosphotransferase YcbJ |
| ? | NC_000913 | 972414 = | 65 (0.920) | coding (663/894 nt) | ycbJ | putative phosphotransferase YcbJ | |||||
| * | ? | NC_000913 | 3370838 = | 66 (0.880) | 3 (0.040) | 3/268 | 7.3 | 4.3% | coding (199/690 nt) | nanE | putative N‑acetylmannosamine‑6‑phosphate epimerase |
| ? | NC_000913 | 3370955 = | 69 (0.950) | coding (82/690 nt) | nanE | putative N‑acetylmannosamine‑6‑phosphate epimerase | |||||
| * | ? | NC_000913 | 2657858 = | 67 (0.890) | 3 (0.040) | 3/264 | 7.3 | 4.9% | coding (1078/1851 nt) | hscA | iron‑sulfur cluster biosynthesis chaperone HscA |
| ? | NC_000913 | 2657948 = | 54 (0.760) | coding (988/1851 nt) | hscA | iron‑sulfur cluster biosynthesis chaperone HscA | |||||
| * | ? | NC_000913 | = 1799799 | 50 (0.670) | 3 (0.040) | 3/270 | 7.4 | 5.5% | intergenic (‑50/+3) | rplT/rpmI | 50S ribosomal subunit protein L20/50S ribosomal subunit protein L35 |
| ? | NC_000913 | = 1799874 | 54 (0.740) | coding (126/198 nt) | rpmI | 50S ribosomal subunit protein L35 | |||||
| * | ? | NC_000913 | = 3492633 | 73 (0.970) | 3 (0.040) | 3/276 | 7.5 | 4.0% | coding (66/1182 nt) | tsgA | putative transporter TsgA |
| ? | NC_000913 | 3492637 = | 73 (0.980) | coding (70/1182 nt) | tsgA | putative transporter TsgA | |||||
| * | ? | NC_000913 | = 1466710 | 84 (1.120) | 3 (0.040) | 3/278 | 7.5 | 3.3% | pseudogene (1319/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | = 1467067 | 92 (1.220) | pseudogene (1676/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||