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 | 111,512 | A→G | 37.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
RA | USA300TCH1516_ALE | 111,516 | C→A | 40.8% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
RA | USA300TCH1516_ALE | 512,643 | A→G | 57.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
RA | USA300TCH1516_ALE | 638,335 | A→G | 8.3% | V107A (GTC→GCC) | pdxK ← | Pyridoxine kinase |
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 | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
RA | USA300TCH1516_ALE | 2,028,124 | G→A | 72.5% | P174L (CCG→CTG) | USA300HOU_RS10230 ← | hypothetical protein |
RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
RA | USA300TCH1516_ALE | 2,372,751 | A→T | 83.9% | L342* (TTA→TAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
RA | USA300TCH1516_ALE | 2,462,758 | G→A | 48.4% | A70T (GCA→ACA) | USA300HOU_RS12680 → | Putative 3‑methyladenine DNA glycosylase |
RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | USA300TCH1516_ALE | 512620 = | 25 (0.770) | 28 (1.250) +40 bp |
23/180 | NT | 61.9% | 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 = | 27 (0.830) | 8 (0.280) | 8/226 | NT | 24.8% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
? | USA300TCH1516_ALE | = 909740 | 25 (0.890) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
* | ? | USA300TCH1516_ALE | 2085296 = | 29 (0.900) | 9 (0.310) | 8/232 | NT | 22.8% | coding (173/201 nt) | hlb_1 | Phospholipase C |
? | USA300TCH1516_ALE | = 2128343 | 35 (1.210) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||
* | ? | USA300TCH1516_ALE | = 2087015 | 25 (0.770) | 3 (0.100) | 3/242 | NT | 11.3% | intergenic (‑166/‑519) | scn_3/chp | Staphylococcal complement inhibitor/Chemotaxis inhibitory protein |
? | USA300TCH1516_ALE | = 2087021 | 24 (0.800) | intergenic (‑172/‑513) | scn_3/chp | Staphylococcal complement inhibitor/Chemotaxis inhibitory protein |