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 | 44.9% | 43.6 / 36.9 | 49 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.5% | 93.5 / 35.7 | 59 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.6% | 48.3 / 10.5 | 28 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 26.5% | 100.8 / 14.6 | 49 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.5% | 255.4 / 28.3 | 115 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.8% | 176.3 / 42.5 | 79 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 22.6% | 133.2 / 17.6 | 53 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 22.1% | 164.5 / 36.8 | 77 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 21.7% | 128.0 / 10.3 | 60 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,404,218 | 0 | T | G | 21.3% | 105.9 / 10.4 | 47 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,664,896 | 0 | T | G | 20.6% | 152.8 / 13.4 | 63 | G169G (GGT→GGG) | yfhR | putative peptidase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 20.6% | 151.9 / 10.7 | 68 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 2,583,424 | 0 | T | G | 20.6% | 162.6 / 11.5 | 68 | T19P (ACC→CCC) | nudK | GDP‑mannose hydrolase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 20.3% | 133.9 / 11.8 | 59 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,525,760 | 0 | G | A | 20.3% | 146.4 / 10.3 | 59 | S74L (TCG→TTG) | ansP | L‑asparagine transporter |
| 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 = | 72 (0.940) | 8 (0.110) | 8/258 | 4.9 | 10.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 64 (0.900) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 60 (0.790) | 4 (0.060) | 4/258 | 6.5 | 6.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 64 (0.900) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2744919 = | 95 (1.250) | 4 (0.050) | 4/264 | 6.6 | 4.2% | coding (421/768 nt) | trmD | tRNA m(1)G37 methyltransferase |
| ? | NC_000913 | = 2744915 | 90 (1.230) | coding (425/768 nt) | trmD | tRNA m(1)G37 methyltransferase | |||||
| * | ? | NC_000913 | 780554 = | 70 (0.920) | 3 (0.040) +GAAGTGGTGGGTGATGA |
3/242 | 6.8 | 4.8% | noncoding (1/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 2518169 = | 65 (0.850) | noncoding (63/76 nt) | alaW | tRNA‑Ala | |||||
| * | ? | NC_000913 | 780554 = | 70 (0.920) | 3 (0.040) +GAAGTGGTGGGTGATGA |
3/242 | 6.8 | 5.1% | noncoding (1/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 2518054 = | 58 (0.760) | noncoding (63/76 nt) | alaX | tRNA‑Ala | |||||
| * | ? | NC_000913 | = 4403120 | 82 (1.080) | 3 (0.040) | 3/270 | 7.2 | 3.6% | coding (1083/1260 nt) | hflK | regulator of FtsH protease |
| ? | NC_000913 | 4403124 = | 80 (1.070) | coding (1087/1260 nt) | hflK | regulator of FtsH protease | |||||
| * | ? | NC_000913 | 824306 = | 86 (1.130) | 3 (0.040) | 3/270 | 7.2 | 6.1% | coding (192/762 nt) | ybhP | endonuclease/exonuclease/phosphatase domain‑containing protein YbhP |
| ? | NC_000913 | 2066339 = | 8 (0.110) | noncoding (1015/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 688031 = | NA (NA) | 3 (0.040) | 3/270 | 7.2 | 3.4% | noncoding (1015/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 824306 = | 86 (1.130) | coding (192/762 nt) | ybhP | endonuclease/exonuclease/phosphatase domain‑containing protein YbhP | |||||