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 298 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 357,890 | 0 | C | A | 50.0% | 14.9 / 14.3 | 26 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 646,747 | 0 | T | G | 46.9% | 61.8 / 17.1 | 49 | T255P (ACC→CCC) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| * | NC_000913 | 4,536,197 | 0 | A | T | 46.7% | 67.1 / 68.0 | 75 | intergenic (+166/+417) | yjhR/nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| * | NC_000913 | 357,880 | 0 | T | C | 44.4% | 28.5 / 10.5 | 27 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 941,713 | 0 | T | G | 43.3% | 89.4 / 18.6 | 60 | V252G (GTG→GGG) | dmsA | dimethyl sulfoxide reductase, anaerobic, subunit A |
| * | NC_000913 | 925,900 | 0 | A | G | 42.6% | 78.9 / 24.7 | 61 | noncoding (72/88 nt) | serW | tRNA‑Ser |
| * | NC_000913 | 29,496 | 0 | T | A | 42.1% | 144.4 / 72.3 | 114 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 41.9% | 72.4 / 43.1 | 63 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 1,478,324 | 0 | T | G | 41.8% | 78.6 / 23.6 | 56 | G33G (GGT→GGG) | ynbB | putative CDP‑diglyceride synthase |
| * | NC_000913 | 1,510,391 | 0 | T | A | 41.7% | 41.5 / 19.4 | 37 | V130E (GTA→GAA) | ydcR | putative DNA‑binding transcriptional regulator and putative aminotransferase |
| * | NC_000913 | 2,903,692 | 0 | C | A | 41.5% | 85.3 / 27.6 | 53 | intergenic (+318/+1055) | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| * | NC_000913 | 1,268,870 | 0 | C | G | 41.3% | 81.0 / 12.8 | 47 | L236V (CTG→GTG) | kdsA | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
| * | NC_000913 | 2,040,075 | 0 | C | G | 41.1% | 78.0 / 25.3 | 59 | L200V (CTG→GTG) | yedY | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 40.7% | 96.8 / 12.7 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| * | NC_000913 | 907,580 | 0 | T | G | 40.5% | 60.4 / 16.9 | 42 | I235L (ATC→CTC) | ybjT | putative NAD‑dependent oxidoreductase |
| * | NC_000913 | 3,850,007 | 0 | G | A | 40.0% | 53.0 / 18.7 | 45 | P44S (CCG→TCG) | uhpB | sensory histidine kinase in two‑component regulatory sytem with UhpA |
| * | NC_000913 | 4,536,212 | 0 | T | A | 40.0% | 123.8 / 33.2 | 76 | intergenic (+181/+402) | yjhR/nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 39.3% | 81.0 / 36.5 | 62 | intergenic (‑108/+33) | uspF/ompN | stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific |
| * | NC_000913 | 366,526 | 0 | T | G | 39.3% | 89.5 / 21.0 | 58 | T329P (ACC→CCC) | lacI | lactose‑inducible lac operon transcriptional repressor |
| * | NC_000913 | 3,270,455 | 0 | G | T | 39.1% | 62.7 / 19.2 | 46 | intergenic (+853/+170) | yhaC/garK | pentapetide repeats‑related protein/glycerate kinase I |
| 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 | 63 (0.960) | 6 (0.100) | 6/280 | 9.6 | 8.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 70 (1.130) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4542682 = | 69 (1.050) | 6 (0.100) | 6/280 | 9.6 | 8.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 71 (1.150) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 961903 = | 66 (1.000) | 9 (0.140) | 6/296 | 10.1 | 11.4% | intergenic (+19/‑92) | cmk/rpsA | cytidylate kinase/30S ribosomal subunit protein S1 |
| ? | NC_000913 | 2741203 = | 74 (1.130) | intergenic (‑53/‑157) | aroF/yfiL | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible/lipoprotein | |||||
| * | ? | NC_000913 | 1207790 = | 68 (1.030) | 4 (0.070) | 4/266 | 10.5 | 6.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 47 (0.800) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 66 (1.000) | 3 (0.050) | 3/266 | 11.3 | 5.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 47 (0.800) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||