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 |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 39,668 | C→G | 12.1% | G489A (GGT→GCT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 39,945 | T→A | 13.4% | I397F (ATT→TTT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 14.5% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 21.4% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 22.2% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 19.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 385,617 | G→A | 21.7% | H332Y (CAT→TAT) | licR ← | putative licABCH operon regulator |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 45.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,472 | G→A | 44.6% | A67V (GCT→GTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,981,418 | C→A | 42.3% | intergenic (‑17/+339) | USA300HOU_RS09870 ← / ← liaR | hypothetical protein/Transcriptional regulatory protein LiaR |
| RA | USA300TCH1516_ALE | 2,004,313 | G→A | 8.9% | H99Y (CAT→TAT) | perR ← | Peroxide‑responsive repressor PerR |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,028,622 | G→T | 32.7% | T8K (ACG→AAG) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,149,822 | G→T | 11.1% | G68C (GGT→TGT) | agrA → | Accessory gene regulator A |
| RA | USA300TCH1516_ALE | 2,245,923 | C→T | 6.3% | E29K (GAA→AAA) | rpoE ← | putative DNA‑directed RNA polymerase subunit delta |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,587,842 | C→T | 11.8% | intergenic (‑239/‑120) | relJ ← / → yehR | Antitoxin RelJ/putative lipoprotein YehR |
| RA | USA300TCH1516_ALE | 2,685,891 | A→T | 9.7% | E184V (GAA→GTA) | clpL → | ATP‑dependent Clp protease ATP‑binding subunit ClpL |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | 22032 = | 126 (0.990) | 6 (0.050) | 6/230 | NT | 5.2% | coding (489/1467 nt) | USA300HOU_pUSA300HOUMR0028 | macrolide transporter |
| ? | CP000731 | 22054 = | 100 (0.840) | coding (511/1467 nt) | USA300HOU_pUSA300HOUMR0028 | macrolide transporter | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 44 (0.950) | 25 (0.800) +40 bp |
21/166 | NT | 45.8% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | 895785 = | 54 (1.170) | 4 (0.100) | 3/212 | NT | 9.4% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 31 (0.780) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||