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 | 47.8% | 22.4 / 35.7 | 46 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 753,125 | 0 | T | A | 34.1% | 73.8 / 23.8 | 44 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 501,564 | 0 | A | C | 33.3% | 36.9 / 18.7 | 30 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 34.0 / 18.5 | 30 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 51.3 / 12.4 | 24 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.8% | 102.5 / 10.6 | 65 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,926,366 | 0 | A | C | 27.6% | 146.8 / 19.8 | 76 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.5% | 86.1 / 22.2 | 47 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 599,576 | 0 | T | G | 25.0% | 48.4 / 11.4 | 28 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.0% | 92.8 / 12.4 | 48 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.8% | 116.3 / 15.0 | 57 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,782,509 | 0 | A | C | 22.1% | 183.7 / 14.9 | 86 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,492,013 | 1 | . | G | 20.8% | 109.5 / 42.0 | 48 | coding (285/573 nt) | ppiA | peptidyl‑prolyl cis‑trans isomerase A |
| 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 = | 68 (1.030) | 8 (0.130) | 8/258 | 4.2 | 10.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 76 (1.230) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 723100 = | 59 (0.890) | 5 (0.080) | 5/256 | 5.3 | 8.1% | coding (1315/2685 nt) | kdpD | sensory histidine kinase KdpD |
| ? | NC_000913 | = 723096 | 59 (0.960) | coding (1319/2685 nt) | kdpD | sensory histidine kinase KdpD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.060) | 3/202 | 5.3 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1639183 | 46 (0.690) | 6 (0.090) | 5/270 | 5.5 | 11.7% | coding (345/498 nt) coding (152/255 nt) |
rzpQ rzoQ |
Qin prophage; DUF2514 domain‑containing protein RzpQ Qin prophage; putative lipoprotein RzoQ |
| ? | NC_000913 | 1639187 = | 46 (0.710) | coding (341/498 nt) coding (148/255 nt) |
rzpQ rzoQ |
Qin prophage; DUF2514 domain‑containing protein RzpQ Qin prophage; putative lipoprotein RzoQ |
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| * | ? | NC_000913 | = 4542690 | 70 (1.060) | 5 (0.080) | 4/258 | 5.7 | 6.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 76 (1.230) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2821795 | 56 (0.850) | 4 (0.060) | 4/270 | 5.9 | 6.7% | coding (217/2631 nt) | alaS | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| ? | NC_000913 | 2821799 = | 56 (0.860) | coding (213/2631 nt) | alaS | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor | |||||
| * | ? | NC_000913 | = 382235 | NA (NA) | 3 (0.050) | 3/272 | 6.4 | NA | noncoding (976/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 382239 = | NA (NA) | noncoding (980/1331 nt) | IS2 | repeat region | |||||