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 563 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 357,880 | 0 | T | C | 50.0% | 58.6 / 23.2 | 58 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 4,378,802 | 0 | A | C | 46.8% | 124.6 / 18.5 | 79 | V48G (GTA→GGA) | ampC | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| * | NC_000913 | 1,222,233 | 0 | G | A | 46.5% | 36.4 / 22.0 | 43 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| * | NC_000913 | 659,940 | 0 | T | A | 45.9% | 70.0 / 44.0 | 61 | I93F (ATT→TTT) | lipA | lipoate synthase |
| * | NC_000913 | 354,288 | 0 | T | G | 45.4% | 125.1 / 24.5 | 86 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 357,890 | 0 | C | A | 45.0% | 57.8 / 33.3 | 60 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 606,612 | 0 | G | A | 44.6% | 106.7 / 32.2 | 74 | Q258* (CAG→TAG) | ybdK | weak gamma‑glutamyl:cysteine ligase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 44.0% | 98.9 / 30.2 | 75 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,200 | 0 | G | A | 43.8% | 97.1 / 42.5 | 80 | S217F (TCC→TTC) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,346,675 | 0 | T | G | 43.3% | 157.7 / 27.8 | 99 | T218P (ACC→CCC) | fumB | anaerobic class I fumarate hydratase (fumarase B) |
| * | NC_000913 | 1,487,163 | 0 | C | T | 42.6% | 62.1 / 29.2 | 54 | intergenic (+200/‑72) | hrpA/ydcF | putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding |
| * | NC_000913 | 4,112,578 | 0 | T | G | 42.3% | 140.6 / 14.4 | 81 | G88G (GGT→GGG) | yiiR | DUF805 family putative inner membrane protein |
| * | NC_000913 | 3,508,657 | 0 | A | G | 41.2% | 111.5 / 21.6 | 80 | F386S (TTC→TCC) | yhfW | phosphopentomutase‑related metalloenzyme superfamily protein |
| * | NC_000913 | 3,026,941 | 0 | A | C | 41.2% | 146.6 / 12.3 | 86 | E392D (GAA→GAC) | guaD | guanine deaminase |
| * | NC_000913 | 2,480,371 | 0 | T | G | 40.7% | 143.4 / 12.7 | 81 | G390G (GGT→GGG) | dsdA | D‑serine dehydratase |
| * | NC_000913 | 2,921,173 | 0 | T | C | 40.7% | 129.3 / 25.0 | 81 | I310V (ATT→GTT) | gudP | putative D‑glucarate transporter |
| * | NC_000913 | 3,035,757 | 0 | A | C | 40.7% | 147.1 / 19.6 | 81 | G150G (GGT→GGG) | prfB | peptide chain release factor RF‑2 |
| * | NC_000913 | 2,578,143 | 0 | A | C | 40.5% | 136.8 / 21.7 | 79 | L79V (TTA→GTA) | maeB | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| * | NC_000913 | 2,349,145 | 0 | A | C | 40.3% | 120.8 / 16.9 | 67 | F110V (TTC→GTC) | inaA | acid‑inducible Kdo/WaaP family putative kinase |
| * | NC_000913 | 2,151,589 | 0 | A | T | 40.0% | 68.5 / 24.4 | 50 | L135F (TTA→TTT) | yegJ | uncharacterized protein |
| 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 | = 257907 | 0 (0.000) | 17 (0.220) | 17/282 | 4.9 | 100% | intergenic (+8/‑769) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers | |||||
| * | ? | NC_000913 | = 1207805 | 59 (0.710) | 14 (0.190) | 14/266 | 5.3 | 21.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 49 (0.660) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207790 = | 58 (0.700) | 10 (0.140) | 10/266 | 6.5 | 16.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 52 (0.700) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 925901 = | 54 (0.650) | 13 (0.160) +C |
11/296 | 6.8 | 20.9% | noncoding (71/88 nt) | serW | tRNA‑Ser |
| ? | NC_000913 | = 1097399 | 45 (0.540) | intergenic (+570/+166) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||