mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 707,910 | 0 | A | G | 74.2% | 98.5 / 40.5 | 62 | intergenic (‑1/‑121) | znuC_1/ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| * | USA300TCH1516_ALE | 1,233,504 | 0 | T | A | 73.1% | 99.8 / 38.7 | 52 | V470D (GTT→GAT) | prkC | Serine/threonine‑protein kinase PrkC |
| * | USA300TCH1516_ALE | 18,890 | 0 | C | G | 72.9% | 92.3 / 40.6 | 48 | N182K (AAC→AAG) | gdpP | Cyclic‑di‑AMP phosphodiesterase GdpP |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 51.1% | 1.9 / 212.1 | 137 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 39.4% | 103.4 / 103.7 | 94 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 39.0% | 87.2 / 103.7 | 96 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 2,026,655 | 0 | C | T | 29.5% | 82.1 / 49.0 | 61 | E87K (GAA→AAA) | vraR | Response regulator protein VraR |
| * | USA300TCH1516_ALE | 707,879 | 0 | A | T | 23.8% | 128.7 / 46.6 | 63 | L11I (TTA→ATA) | znuC_1 | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| * | USA300TCH1516_ALE | 479,553 | 0 | G | A | 23.7% | 111.1 / 35.8 | 59 | A194T (GCA→ACA) | USA300HOU_RS02280 | hypothetical protein |
| * | USA300TCH1516_ALE | 367,644 | 0 | G | T | 22.4% | 183.2 / 40.3 | 76 | intergenic (‑96/‑62) | nanA/bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| * | USA300TCH1516_ALE | 1,797,772 | 0 | G | C | 22.0% | 119.5 / 33.5 | 50 | R7G (CGC→GGC) | phoR | Alkaline phosphatase synthesis sensor protein PhoR |
| * | USA300TCH1516_ALE | 1,419,527 | 0 | G | T | 21.1% | 120.2 / 23.9 | 52 | P7T (CCT→ACT) | USA300HOU_RS07040 | hypothetical protein |
| * | USA300TCH1516_ALE | 1,744,454 | 0 | C | T | 21.1% | 114.1 / 25.9 | 57 | G73D (GGC→GAC) | apt | Adenine phosphoribosyltransferase |
| Marginal new junction evidence (lowest skew 10 of 106 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 4433 | 2 (0.610) | 13 (0.010) | 5/270 | 0.1 | 1.3% | intergenic (+398/‑67) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1931 | 1958 (0.870) | intergenic (+164/+162) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 4419 | 2 (0.610) | 30 (0.030) | 11/264 | 0.1 | 2.9% | intergenic (+384/‑81) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1946 | 1982 (0.900) | intergenic (+179/+147) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 4367 | 2 (0.610) | 42 (0.040) | 13/268 | 0.1 | 4.0% | intergenic (+332/‑133) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1991 | 2020 (0.900) | intergenic (+224/+102) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4323 = | 1 (0.310) | 19 (0.020) | 13/266 | 0.1 | 1.9% | intergenic (+288/‑177) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2035 = | 1948 (0.880) | intergenic (+268/+58) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4294 = | 4 (1.220) | 56 (0.050) | 21/264 | 0.1 | 5.7% | intergenic (+259/‑206) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2073 = | 1861 (0.840) | intergenic (+306/+20) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2031785 | 70 (1.120) | 4 (0.110) +59 bp |
3/162 | 7.2 | 9.9% | intergenic (+251/+239) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2866882 | 56 (0.890) | intergenic (‑281/+172) | USA300HOU_RS14695/noc_2 | hypothetical protein/Nucleoid occlusion protein | |||||
| * | ? | USA300TCH1516_ALE | = 2031785 | 70 (1.120) | 4 (0.110) +59 bp |
3/162 | 7.2 | 9.4% | intergenic (+251/+239) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2031834 | 63 (1.000) | intergenic (+300/+190) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1470058 | 69 (1.100) | 4 (0.110) +59 bp |
3/162 | 7.2 | 9.0% | intergenic (‑105/‑240) | USA300TCH1516_01369/rnhA | hypothetical protein/14.7 kDa ribonuclease H‑like protein |
| ? | USA300TCH1516_ALE | = 2031785 | 70 (1.120) | intergenic (+251/+239) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1380507 = | 54 (0.860) | 4 (0.110) +59 bp |
3/162 | 7.2 | 10.0% | intergenic (+321/‑571) | opuD_1/acnA | Glycine betaine transporter OpuD/Aconitate hydratase A |
| ? | USA300TCH1516_ALE | = 2031785 | 70 (1.120) | intergenic (+251/+239) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1098235 | 59 (0.940) | 4 (0.110) +59 bp |
3/162 | 7.2 | 9.7% | intergenic (+214/+135) | ktrA/rnj1 | Ktr system potassium uptake protein A/Ribonuclease J 1 |
| ? | USA300TCH1516_ALE | = 2031785 | 70 (1.120) | intergenic (+251/+239) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein | |||||