mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 887 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,222,233 | 0 | G | A | 49.2% | 55.8 / 41.9 | 65 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| * | NC_000913 | 2,676,106 | 0 | C | A | 47.5% | 105.6 / 68.7 | 101 | L240F (TTG→TTT) | yphD | putative sugar ABC transporter permease |
| * | NC_000913 | 1,356,201 | 0 | T | G | 47.1% | 93.4 / 18.8 | 69 | T304P (ACC→CCC) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| * | NC_000913 | 599,576 | 0 | T | G | 46.8% | 120.6 / 35.4 | 79 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 2,168,966 | 0 | A | C | 46.5% | 100.3 / 17.1 | 71 | I85I (ATA→ATC) | yegS | phosphatidylglycerol kinase, metal‑dependent |
| * | NC_000913 | 29,496 | 0 | T | A | 45.8% | 109.8 / 70.9 | 96 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 1,413,735 | 0 | A | T | 45.6% | 102.3 / 51.2 | 79 | Y2* (TAT→TAA) | ydaC | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| * | NC_000913 | 357,890 | 0 | C | A | 44.4% | 59.7 / 32.5 | 63 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 5,159 | 0 | G | A | 44.1% | 96.1 / 63.6 | 93 | intergenic (+139/‑75) | thrC/yaaX | L‑threonine synthase/DUF2502 family putative periplasmic protein |
| * | NC_000913 | 3,375,123 | 0 | T | G | 43.9% | 170.5 / 20.3 | 98 | G85G (GGT→GGG) | dcuD | putative transporter |
| * | NC_000913 | 2,483,268 | 0 | T | A | 43.8% | 137.4 / 63.7 | 112 | L24F (TTA→TTT) | emrK | multidrug resistance efflux pump membrane fusion protein |
| * | NC_000913 | 4,460,871 | 0 | T | G | 43.1% | 122.5 / 11.3 | 72 | Y597S (TAC→TCC) | nrdD | anaerobic ribonucleoside‑triphosphate reductase |
| * | NC_000913 | 4,346,675 | 0 | T | G | 42.6% | 183.8 / 22.1 | 108 | T218P (ACC→CCC) | fumB | anaerobic class I fumarate hydratase (fumarase B) |
| * | NC_000913 | 1,506,038 | 0 | A | C | 42.2% | 113.8 / 16.2 | 71 | F15V (TTT→GTT) | ydcO | BenE family inner membrane putative transporter |
| * | NC_000913 | 941,713 | 0 | T | G | 42.2% | 144.4 / 30.3 | 85 | V252G (GTG→GGG) | dmsA | dimethyl sulfoxide reductase, anaerobic, subunit A |
| * | NC_000913 | 535,901 | 0 | T | G | 42.1% | 119.5 / 13.7 | 78 | G64G (GGT→GGG) | hyi | hydroxypyruvate isomerase |
| * | NC_000913 | 40,515 | 0 | G | T | 41.9% | 111.0 / 43.5 | 86 | Q473K (CAA→AAA) | caiT | putative transporter |
| * | NC_000913 | 3,423,294 | 0 | T | C | 41.8% | 111.4 / 28.4 | 79 | intergenic (+100/+129) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 29,486 | 0 | C | A | 41.7% | 167.8 / 53.8 | 96 | intergenic (+291/‑165) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 3,350,844 | 0 | A | C | 41.4% | 186.3 / 18.0 | 99 | L728V (TTA→GTA) | arcB | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| 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 | 1207790 = | 82 (0.830) | 21 (0.240) | 20/266 | 8.5 | 22.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 68 (0.770) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 88 (0.890) | 20 (0.230) | 19/266 | 8.9 | 22.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 63 (0.710) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4542690 | 97 (0.980) | 8 (0.090) | 8/280 | 15.2 | 7.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 106 (1.140) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4542682 = | 102 (1.030) | 4 (0.040) | 4/280 | 18.3 | 3.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 107 (1.150) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1209618 | 74 (0.750) | 17 (0.190) | 3/268 | 18.7 | 18.3% | pseudogene (2/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| ? | NC_000913 | 2471897 = | 85 (0.950) | pseudogene (226/579 nt) | yfdL | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related | |||||