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 | 512,643 | 0 | A | G | 54.4% | 50.1 / inf | 241 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 35.2% | 180.2 / 152.2 | 163 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 35.0% | 231.9 / 150.2 | 158 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 80 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 1333783 | 117 (1.030) | 23 (0.260) +30 bp |
20/218 | 7.3 | 20.5% | coding (184/1239 nt) | hflX | GTPase HflX |
| ? | USA300TCH1516_ALE | 1333814 = | 111 (0.970) | coding (215/1239 nt) | hflX | GTPase HflX | |||||
| * | ? | USA300TCH1516_ALE | 855629 = | 114 (1.000) | 7 (0.100) +57 bp |
4/164 | 12.7 | 9.9% | intergenic (+160/‑600) | zipA_1/cggR | Cell division protein ZipA/Central glycolytic genes regulator |
| ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||
| * | ? | USA300TCH1516_ALE | 2080726 = | 111 (0.970) | 16 (0.150) | 11/252 | 13.0 | 13.7% | intergenic (‑194/‑347) | USA300HOU_RS10505/aspC | hypothetical protein/Aspartate aminotransferase |
| ? | USA300TCH1516_ALE | 2080759 = | 101 (0.980) | intergenic (‑227/‑314) | USA300HOU_RS10505/aspC | hypothetical protein/Aspartate aminotransferase | |||||
| * | ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | 7 (0.100) +53 bp |
4/172 | 13.3 | 9.3% | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 |
| ? | USA300TCH1516_ALE | 2866774 = | 118 (1.030) | intergenic (‑173/+280) | USA300HOU_RS14695/noc_2 | hypothetical protein/Nucleoid occlusion protein | |||||
| * | ? | USA300TCH1516_ALE | 1695023 = | 115 (1.010) | 7 (0.100) +53 bp |
4/172 | 13.3 | 9.4% | intergenic (‑229/+301) | hemN_1/lepA | Oxygen‑independent coproporphyrinogen‑III oxidase‑like protein YqeR/Elongation factor 4 |
| ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||
| * | ? | USA300TCH1516_ALE | = 954748 | 106 (0.930) | 7 (0.100) +52 bp |
4/174 | 13.4 | 9.7% | intergenic (+402/+101) | gluD/glpQ_1 | NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase |
| ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||
| * | ? | USA300TCH1516_ALE | = 1380778 | 98 (0.860) | 7 (0.100) +51 bp |
4/176 | 13.5 | 9.9% | intergenic (+592/‑300) | opuD_1/acnA | Glycine betaine transporter OpuD/Aconitate hydratase A |
| ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||
| * | ? | USA300TCH1516_ALE | = 170067 | 117 (1.030) | 4 (0.060) +53 bp |
3/172 | 14.2 | 5.6% | intergenic (+614/‑363) | repE/USA300HOU_RS07235 | Replication initiation protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 2830190 = | 103 (0.900) | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 89 (0.780) | 57 (0.500) | 10/278 | 14.8 | 37.8% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1205383 = | 99 (0.870) | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase | |||||
| * | ? | USA300TCH1516_ALE | 431138 = | 122 (1.070) | 10 (0.090) | 8/258 | 15.2 | 8.2% | intergenic (+16/+65) | nfrA/tcyP | NADPH‑dependent oxidoreductase/L‑cystine uptake protein TcyP |
| ? | USA300TCH1516_ALE | 431188 = | 111 (1.050) | intergenic (+66/+15) | nfrA/tcyP | NADPH‑dependent oxidoreductase/L‑cystine uptake protein TcyP | |||||