mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 226 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,386,862 | 0 | G | A | 61.5% | 12.7 / 36.2 | 39 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 57.9% | ‑1.8 / 54.1 | 57 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 345,328 | 0 | C | A | 56.1% | 45.0 / 94.7 | 57 | intergenic (+337/‑76) | yahL/yahM | uncharacterized protein/uncharacterized protein |
| * | NC_000913 | 357,890 | 0 | C | A | 54.5% | 3.6 / 25.7 | 22 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 4,604,350 | 0 | C | T | 54.4% | 10.7 / 58.8 | 57 | S64F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 281,089 | 0 | A | C | 53.2% | 55.3 / 74.0 | 48 | Y299D (TAT→GAT) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 3,423,294 | 0 | T | C | 52.6% | 27.8 / 49.7 | 38 | intergenic (+100/+129) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 1,826,370 | 0 | A | C | 52.4% | 41.5 / 54.2 | 42 | V185G (GTG→GGG) | astE | succinylglutamate desuccinylase |
| * | NC_000913 | 354,288 | 0 | T | G | 52.3% | 53.2 / 71.4 | 44 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 3,423,287 | 0 | G | C | 51.3% | 27.7 / 53.5 | 37 | intergenic (+93/+136) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 657,676 | 0 | A | C | 51.2% | 43.8 / 66.9 | 43 | V88G (GTG→GGG) | flc | fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 1,826,379 | 0 | T | C | 51.2% | 24.8 / 52.1 | 43 | E182G (GAG→GGG) | astE | succinylglutamate desuccinylase |
| * | NC_000913 | 2,332,823 | 0 | A | G | 50.0% | 48.5 / 17.5 | 53 | pseudogene (1580/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| * | NC_000913 | 3,423,297 | 0 | G | C | 50.0% | 44.3 / 24.5 | 38 | intergenic (+103/+126) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,665,698 | 0 | T | C | 49.2% | 37.8 / 46.7 | 67 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 29,496 | 0 | T | A | 48.9% | 34.8 / 37.1 | 47 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 3,640,981 | 0 | C | T | 48.7% | 17.1 / 23.3 | 39 | F40F (TTC→TTT) | dtpB | dipeptide and tripeptide permease B |
| * | NC_000913 | 3,423,290 | 0 | A | C | 48.6% | 24.4 / 13.2 | 37 | intergenic (+96/+133) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 3,556,207 | 0 | T | C | 48.6% | 30.4 / 18.0 | 37 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,665,702 | 0 | C | A | 48.6% | 33.2 / 53.9 | 70 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| Marginal new junction evidence (lowest skew 10 of 38 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 44 (0.870) | 5 (0.110) | 5/264 | 4.7 | 13.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 25 (0.550) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3858205 | 55 (1.090) | 6 (0.130) | 5/270 | 4.8 | 10.3% | coding (200/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | = 3858228 | 54 (1.170) | coding (177/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 3303996 | 54 (1.070) | 5 (0.110) | 5/274 | 4.9 | 9.6% | coding (549/1008 nt) | yhbW | putative luciferase‑like monooxygenase |
| ? | NC_000913 | = 3304188 | 44 (0.940) | coding (741/1008 nt) | yhbW | putative luciferase‑like monooxygenase | |||||
| * | ? | NC_000913 | 2721524 = | 42 (0.830) | 6 (0.130) | 5/276 | 4.9 | 11.9% | coding (1572/2661 nt) | pka | protein lysine acetyltransferase |
| ? | NC_000913 | 2721614 = | 50 (1.060) | coding (1662/2661 nt) | pka | protein lysine acetyltransferase | |||||
| * | ? | NC_000913 | 2197764 = | 66 (1.310) | 5 (0.110) | 5/274 | 4.9 | 7.5% | pseudogene (1291/2847 nt) | yehH | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| ? | NC_000913 | 2197796 = | 62 (1.320) | pseudogene (1323/2847 nt) | yehH | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function | |||||
| * | ? | NC_000913 | 761823 = | 43 (0.850) | 5 (0.110) | 5/274 | 4.9 | 11.8% | coding (302/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 761890 = | 35 (0.750) | coding (369/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | = 4115653 | 51 (1.010) | 5 (0.100) | 5/280 | 5.0 | 9.4% | intergenic (‑74/+61) | glpX/glpK | fructose 1,6‑bisphosphatase II/glycerol kinase |
| ? | NC_000913 | = 4115657 | NA (NA) | intergenic (‑78/+57) | glpX/glpK | fructose 1,6‑bisphosphatase II/glycerol kinase | |||||
| * | ? | NC_000913 | 843349 = | 37 (0.730) | 6 (0.120) | 5/282 | 5.0 | 14.9% | coding (2132/2226 nt) | ybiO | mechanosensitive channel protein, intermediate conductance |
| ? | NC_000913 | 843377 = | 33 (0.690) | coding (2104/2226 nt) | ybiO | mechanosensitive channel protein, intermediate conductance | |||||
| * | ? | NC_000913 | = 1207805 | 47 (0.930) | 4 (0.090) | 4/264 | 5.2 | 10.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.530) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4199344 | 50 (0.990) | 6 (0.120) | 4/282 | 5.5 | 10.8% | coding (555/672 nt) | nfi | endonuclease V; deoxyinosine 3' endonuclease |
| ? | NC_000913 | = 4199393 | 51 (1.060) | coding (604/672 nt) | nfi | endonuclease V; deoxyinosine 3' endonuclease | |||||