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 931 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,708,718 | 0 | G | A | 70.8% | 27.6 / 15.4 | 24 | A600A (GCG→GCA) | rsxC | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| * | NC_000913 | 357,880 | 0 | T | C | 54.4% | 23.6 / 64.5 | 46 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 357,890 | 0 | C | A | 53.1% | 24.1 / 75.7 | 49 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 1,825,056 | 0 | G | A | 48.6% | 54.3 / 58.1 | 70 | intergenic (‑119/+84) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| * | NC_000913 | 987,494 | 0 | T | G | 47.0% | 89.4 / 24.7 | 66 | intergenic (‑512/+91) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 46.6% | 97.7 / 33.7 | 73 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 357,873 | 0 | C | T | 45.1% | 36.7 / 28.9 | 51 | S273N (AGC→AAC) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 357,875 | 0 | A | T | 44.9% | 48.0 / 28.5 | 49 | N272K (AAT→AAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 3,026,941 | 0 | A | C | 44.6% | 135.8 / 18.2 | 83 | E392D (GAA→GAC) | guaD | guanine deaminase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 44.4% | 85.0 / 73.0 | 90 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 1,825,061 | 0 | G | A | 43.7% | 77.2 / 43.1 | 71 | intergenic (‑124/+79) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| * | NC_000913 | 2,676,106 | 0 | C | A | 43.2% | 118.8 / 37.9 | 74 | L240F (TTG→TTT) | yphD | putative sugar ABC transporter permease |
| * | NC_000913 | 2,001,918 | 0 | A | C | 43.2% | 185.7 / 27.4 | 96 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| * | NC_000913 | 802,118 | 0 | A | C | 43.0% | 140.8 / 18.6 | 86 | T78P (ACC→CCC) | ybhI | putative DASS family tricarboxylate or dicarboxylate transporter |
| * | NC_000913 | 3,423,294 | 0 | T | C | 42.9% | 153.6 / 42.0 | 112 | intergenic (+100/+129) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 523,335 | 0 | T | G | 42.7% | 123.7 / 19.0 | 82 | G25G (GGT→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 2,361,337 | 0 | A | C | 41.9% | 144.4 / 14.8 | 87 | G26G (GGT→GGG) | rhmD | L‑rhamnonate dehydratase |
| * | NC_000913 | 1,413,735 | 0 | A | T | 41.7% | 109.8 / 42.9 | 72 | Y2* (TAT→TAA) | ydaC | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| * | NC_000913 | 213,341 | 0 | A | G | 41.3% | 121.5 / 11.4 | 75 | G337G (GGA→GGG) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | NC_000913 | 3,177,748 | 0 | C | A | 41.2% | 153.0 / 61.8 | 114 | E55* (GAG→TAG) | nudF | ADP‑ribose pyrophosphatase |
| 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 = | 83 (0.780) | 27 (0.270) | 26/280 | 6.9 | 25.5% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 80 (0.800) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1207790 = | 69 (0.650) | 17 (0.180) | 16/266 | 9.8 | 24.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 46 (0.480) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4542690 | 78 (0.730) | 15 (0.150) | 15/280 | 10.7 | 16.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 79 (0.790) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1207805 | 77 (0.720) | 13 (0.140) | 10/266 | 12.6 | 18.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 45 (0.470) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||