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 | ||
| * | CP000730 | 512,643 | 0 | A | G | 45.1% | 25.5 / 83.7 | 71 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 111,512 | 0 | A | G | 29.0% | 95.8 / 50.4 | 70 | S194S (TCA→TCG) | USA300HOU_0110 | possible staphylococcal tandem lipoprotein |
| * | CP000730 | 111,516 | 0 | C | A | 25.8% | 134.4 / 38.9 | 66 | Q196K (CAA→AAA) | USA300HOU_0110 | possible staphylococcal tandem lipoprotein |
| * | CP000730 | 110,660 | 0 | T | A | 24.5% | 90.8 / 33.0 | 49 | I173I (ATT→ATA) | USA300HOU_0109 | staphylococcal tandem lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 514402 = | 38 (1.000) | 24 (0.780) +26 bp |
4/218 | 4.2 | 39.5% | intergenic (+70/‑304) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | CP000730 | 514469 = | 53 (1.390) | intergenic (+137/‑237) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | CP000730 | 1966974 = | 32 (0.840) | 5 (0.140) | 5/252 | 4.3 | 12.8% | coding (29/111 nt) | USA300HOU_1826 | hypothetical protein |
| ? | CP000730 | 1966998 = | 38 (1.070) | coding (5/111 nt) | USA300HOU_1826 | hypothetical protein | |||||
| * | ? | CP000730 | = 1103184 | 40 (1.050) | 5 (0.140) | 5/260 | 4.4 | 11.8% | coding (706/1113 nt) | pdhA | pyruvate dehydrogenase (acetyl‑transferring) alpha subunit |
| ? | CP000730 | = 1103214 | 36 (0.980) | coding (736/1113 nt) | pdhA | pyruvate dehydrogenase (acetyl‑transferring) alpha subunit | |||||
| * | ? | CP000730 | 671622 = | 47 (1.240) | 5 (0.140) | 5/256 | 4.4 | 9.8% | intergenic (+247/‑141) | argS/USA300HOU_0614 | arginine‑‑tRNA ligase/deoxyribonuclease (pyrimidine dimer) |
| ? | CP000730 | = 1072271 | 47 (1.300) | intergenic (‑743/+62) | iraE/folD | possible chitinase/bifunctional methylenetetrahydrofolate dehydrogenase (NADP(+))/methenyltetrahydrofolate cyclohydrolase | |||||
| * | ? | CP000730 | 671577 = | 40 (1.050) | 5 (0.140) | 5/256 | 4.4 | 10.7% | intergenic (+202/‑186) | argS/USA300HOU_0614 | arginine‑‑tRNA ligase/deoxyribonuclease (pyrimidine dimer) |
| ? | CP000730 | 671629 = | 46 (1.280) | intergenic (+254/‑134) | argS/USA300HOU_0614 | arginine‑‑tRNA ligase/deoxyribonuclease (pyrimidine dimer) | |||||
| * | ? | CP000730 | 514469 = | 53 (1.390) | 24 (0.780) +26 bp |
3/218 | 4.7 | 35.9% | intergenic (+137/‑237) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | CP000730 | = 2179798 | NA (NA) | intergenic (‑242/+70) | rrl4/rrs4 | 23S ribosomal RNA/16S ribosomal RNA | |||||
| * | ? | CP000730 | = 365040 | 62 (1.630) | 4 (0.120) | 4/246 | 4.7 | 5.8% | intergenic (+50/+55) | nupC/USA300HOU_0334 | possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter |
| ? | CP000730 | = 365070 | 73 (2.110) | intergenic (+80/+25) | nupC/USA300HOU_0334 | possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter | |||||
| * | ? | CP000730 | 2494782 = | 24 (0.630) | 3 (0.090) | 3/248 | 5.2 | 10.7% | intergenic (+1/+62) | USA300HOU_2358/USA300HOU_2359 | hypothetical protein/hypothetical membrane protein |
| ? | CP000730 | 2494828 = | 28 (0.800) | intergenic (+47/+16) | USA300HOU_2358/USA300HOU_2359 | hypothetical protein/hypothetical membrane protein | |||||
| * | ? | CP000730 | 932460 = | 36 (0.950) | 3 (0.090) | 3/246 | 5.2 | 8.5% | intergenic (+6/+257) | dltD/nifU | D‑alanine transfer protein DltD/possible NifU family protein |
| ? | CP000730 | 932506 = | 32 (0.920) | intergenic (+52/+211) | dltD/nifU | D‑alanine transfer protein DltD/possible NifU family protein | |||||
| * | ? | CP000730 | 920680 = | 30 (0.790) | 3 (0.090) | 3/248 | 5.2 | 10.4% | coding (97/849 nt) | yunF | hypothetical protein |
| ? | CP000730 | 920729 = | 24 (0.690) | coding (146/849 nt) | yunF | hypothetical protein | |||||