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 447 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 1,097,580 | 0 | C | T | 46.5% | ‑3.1 / 134.4 | 87 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | protein YcdU/RtT sRNA |
| * | NC_007779 | 357,104 | 0 | T | C | 44.8% | 19.9 / 15.7 | 30 | K271E (AAA→GAA) | cynR | transcriptional regulator CynR |
| * | NC_007779 | 4,434,664 | 0 | T | G | 44.5% | 149.8 / 63.9 | 121 | L41V (TTG→GTG) | cycA | D‑serine/D‑alanine/glycine transporter |
| * | NC_007779 | 753,547 | 0 | T | A | 41.9% | 156.5 / 70.8 | 117 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NC_007779 | 344,552 | 0 | C | A | 41.3% | 169.8 / 49.8 | 93 | intergenic (+337/‑76) | Y75_RS01685/Y75_RS01690 | protein YahL/protein YahM |
| * | NC_007779 | 3,535,174 | 0 | A | C | 40.9% | 172.3 / 29.9 | 107 | intergenic (‑183/+77) | kdgT/sodA | 2‑keto‑3‑deoxygluconate transporter/superoxide dismutase [Mn] |
| * | NC_007779 | 1,555,714 | 0 | T | G | 40.4% | 126.4 / 36.7 | 114 | Y557S (TAC→TCC) | maeA | malate dehydrogenase |
| * | NC_007779 | 2,231,609 | 0 | T | C | 39.7% | 75.0 / 22.2 | 73 | pseudogene (484/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NC_007779 | 3,485,352 | 0 | A | C | 39.1% | 100.8 / 17.6 | 93 | A590A (GCA→GCC) | ppc | phosphoenolpyruvate carboxylase |
| * | NC_007779 | 2,391,532 | 0 | G | A | 37.1% | 110.8 / 67.4 | 90 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NC_007779 | 4,055,329 | 0 | T | G | 36.7% | 112.7 / 17.7 | 60 | Y580D (TAC→GAC) | ggt | gamma‑glutamyltransferase |
| * | NC_007779 | 4,609,024 | 0 | C | T | 36.0% | 165.2 / 44.8 | 112 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 357,099 | 0 | A | T | 35.7% | 22.5 / 10.5 | 30 | N272K (AAT→AAA) | cynR | transcriptional regulator CynR |
| * | NC_007779 | 3,205,100 | 0 | T | A | 35.6% | 114.2 / 49.3 | 104 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 3,895,018 | 0 | T | G | 35.6% | 113.9 / 17.4 | 91 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate transporter large permease YiaN |
| * | NC_007779 | 3,435,403 | 0 | T | G | 35.6% | 167.7 / 25.9 | 90 | G137G (GGT→GGG) | zraP | zinc resistance sensor/chaperone ZraP |
| * | NC_007779 | 3,205,091 | 0 | C | T | 35.2% | 119.3 / 66.2 | 106 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 3,131,958 | 0 | T | G | 35.1% | 164.6 / 17.0 | 77 | H219P (CAC→CCC) | yghS | dTMP kinase |
| * | NC_007779 | 1,273,399 | 0 | T | G | 34.9% | 208.8 / 32.2 | 104 | T10P (ACC→CCC) | chaA | sodium‑potassium/proton antiporter ChaA |
| * | NC_007779 | 121,507 | 0 | A | T | 34.9% | 141.2 / 41.5 | 83 | L15L (CTT→CTA) | aroP | aromatic amino acid transporter AroP |
| 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 | 1257888 = | 220 (1.350) | 12 (0.070) | 11/466 | 8.3 | 5.2% | intergenic (‑359/+410) | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
| ? | NC_007779 | = 2412225 | NA (NA) | intergenic (‑55/‑782) | Y75_RS12035/alaA | IS1‑like element IS1A family transposase/alanine transaminase AlaA | |||||
| * | ? | NC_007779 | = 1395641 | 143 (0.880) | 9 (0.060) | 8/466 | 9.5 | 5.9% | coding (701/1614 nt) | mppA | murein tripeptide ABC transporter substrate‑binding protein MppA |
| ? | NC_007779 | 2176983 = | NA (NA) | intergenic (‑3/‑68) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 4547362 = | 195 (1.200) | 8 (0.050) | 7/448 | 9.7 | 4.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_007779 | 4547676 = | 153 (0.980) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_007779 | = 290625 | NA (NA) | 7 (0.040) | 6/466 | 10.5 | 3.1% | intergenic (‑55/‑99) | Y75_RS01415/Y75_RS01420 | IS1‑like element IS1B family transposase/protein YagJ |
| ? | NC_007779 | 1257888 = | 220 (1.350) | intergenic (‑359/+410) | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF | |||||
| * | ? | NC_007779 | = 4547370 | 193 (1.190) | 5 (0.030) | 5/448 | 10.8 | 2.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_007779 | = 4547666 | 153 (0.980) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_007779 | = 4077000 | 159 (0.980) | 5 (0.030) | 4/452 | 11.5 | 3.1% | coding (1403/1506 nt) | glpD | glycerol‑3‑phosphate dehydrogenase |
| ? | NC_007779 | = 4077004 | 158 (1.000) | coding (1399/1506 nt) | glpD | glycerol‑3‑phosphate dehydrogenase | |||||
| * | ? | NC_007779 | 4521571 = | 197 (1.210) | 3 (0.020) | 3/448 | 12.1 | 1.6% | coding (827/954 nt) | fecR | fec operon regulator FecR |
| ? | NC_007779 | 4521605 = | 177 (1.130) | coding (793/954 nt) | fecR | fec operon regulator FecR | |||||
| * | ? | NC_007779 | 762245 = | 162 (1.000) | 3 (0.020) | 3/444 | 12.1 | 1.9% | coding (302/1218 nt) | odhB | 2‑oxoglutarate dehydrogenase complex dihydrolipoyllysine‑residue succinyltransferase |
| ? | NC_007779 | 762312 = | 150 (0.970) | coding (369/1218 nt) | odhB | 2‑oxoglutarate dehydrogenase complex dihydrolipoyllysine‑residue succinyltransferase | |||||
| * | ? | NC_007779 | = 2371153 | 191 (1.170) | 3 (0.020) | 3/458 | 12.3 | 1.6% | coding (556/1140 nt) | arnB | UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| ? | NC_007779 | = 2371160 | 176 (1.100) | coding (563/1140 nt) | arnB | UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase | |||||
| * | ? | NC_007779 | = 1241585 | 173 (1.060) | 3 (0.020) | 3/464 | 12.4 | 1.7% | intergenic (+59/+327) | dadX/cvrA | catabolic alanine racemase DadX/potassium/proton antiporter |
| ? | NC_007779 | 1241589 = | 169 (1.040) | intergenic (+63/+323) | dadX/cvrA | catabolic alanine racemase DadX/potassium/proton antiporter | |||||