mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 502 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 357,104 | 0 | T | C | 53.8% | 1.3 / 36.0 | 26 | K271E (AAA→GAA) | cynR | transcriptional regulator CynR |
| * | NC_007779 | 357,114 | 0 | C | A | 51.7% | 1.7 / 33.3 | 29 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| * | NC_007779 | 1,273,404 | 0 | A | T | 48.7% | 119.4 / 130.6 | 158 | V8E (GTA→GAA) | chaA | sodium‑potassium/proton antiporter ChaA |
| * | NC_007779 | 1,273,399 | 0 | T | G | 46.0% | 196.6 / 70.3 | 151 | T10P (ACC→CCC) | chaA | sodium‑potassium/proton antiporter ChaA |
| * | NC_007779 | 4,434,664 | 0 | T | G | 44.9% | 178.0 / 54.0 | 120 | L41V (TTG→GTG) | cycA | D‑serine/D‑alanine/glycine transporter |
| * | NC_007779 | 1,097,580 | 0 | C | T | 41.4% | 31.9 / 114.8 | 87 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | protein YcdU/RtT sRNA |
| * | NC_007779 | 1,273,410 | 0 | T | C | 40.8% | 240.5 / 53.2 | 165 | E6G (GAG→GGG) | chaA | sodium‑potassium/proton antiporter ChaA |
| * | NC_007779 | 2,391,532 | 0 | G | A | 40.6% | 128.0 / 108.0 | 123 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NC_007779 | 3,974,713 | 0 | G | T | 40.4% | 251.5 / 81.2 | 152 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NC_007779 | 344,552 | 0 | C | A | 40.4% | 207.7 / 71.8 | 114 | intergenic (+337/‑76) | Y75_RS01685/Y75_RS01690 | protein YahL/protein YahM |
| * | NC_007779 | 121,507 | 0 | A | T | 39.7% | 179.5 / 64.0 | 116 | L15L (CTT→CTA) | aroP | aromatic amino acid transporter AroP |
| * | NC_007779 | 3,880,031 | 0 | T | G | 39.0% | 108.0 / 40.7 | 95 | V289G (GTG→GGG) | selA | L‑seryl‑tRNA(Sec) selenium transferase |
| * | NC_007779 | 753,547 | 0 | T | A | 38.6% | 214.7 / 70.1 | 141 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NC_007779 | 357,099 | 0 | A | T | 38.5% | 11.5 / 10.4 | 26 | N272K (AAT→AAA) | cynR | transcriptional regulator CynR |
| * | NC_007779 | 3,205,091 | 0 | C | T | 37.5% | 144.7 / 100.4 | 147 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 3,777,754 | 0 | A | C | 37.0% | 78.8 / 29.2 | 93 | pseudogene (943/1617 nt) | Y75_RS18735 | PTS sugar transporter subunit IIB |
| * | NC_007779 | 1,273,422 | 0 | G | T | 36.2% | 329.3 / 61.7 | 160 | S2* (TCA→TAA) | chaA | sodium‑potassium/proton antiporter ChaA |
| * | NC_007779 | 1,555,714 | 0 | T | G | 36.1% | 216.3 / 30.4 | 146 | Y557S (TAC→TCC) | maeA | malate dehydrogenase |
| * | NC_007779 | 3,535,174 | 0 | A | C | 35.3% | 286.2 / 23.8 | 138 | intergenic (‑183/+77) | kdgT/sodA | 2‑keto‑3‑deoxygluconate transporter/superoxide dismutase [Mn] |
| * | NC_007779 | 3,796,196 | 0 | A | C | 35.0% | 242.0 / 30.3 | 120 | F86V (TTT→GTT) | adeD | adenine deaminase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 4547362 = | 194 (1.020) | 8 (0.040) | 8/448 | 10.4 | 4.3% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_007779 | 4547676 = | 169 (0.920) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_007779 | = 4547370 | 205 (1.080) | 5 (0.030) | 3/448 | 13.5 | 2.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_007779 | = 4547666 | 169 (0.920) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_007779 | = 2564595 | 171 (0.900) | 3 (0.020) | 3/450 | 13.5 | 1.8% | coding (946/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivating factor EutA |
| ? | NC_007779 | = 2564610 | 163 (0.890) | coding (931/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivating factor EutA | |||||
| * | ? | NC_007779 | = 1374998 | 240 (1.260) | 3 (0.020) | 3/450 | 13.5 | 1.3% | coding (63/882 nt) | ycjO | sugar ABC transporter permease |
| ? | NC_007779 | = 1375006 | 232 (1.260) | coding (71/882 nt) | ycjO | sugar ABC transporter permease | |||||
| * | ? | NC_007779 | 1544936 = | 235 (1.240) | 3 (0.020) | 3/466 | 13.8 | 1.7% | coding (839/1389 nt) | narU | nitrate/nitrite transporter NarU |
| ? | NC_007779 | = 3232082 | 110 (0.580) | coding (1762/2019 nt) | fadH | NADPH‑dependent 2,4‑dienoyl‑CoA reductase | |||||