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 | 62,645 | T→C | 8.2% | intergenic (‑112/+401) | USA300TCH1516_00053 ← / ← speG | hypothetical protein/Spermidine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 10.9% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 10.5% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 30.2% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 31.5% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 171,984 | A→G | 6.5% | E295G (GAA→GGA) | adhE → | Aldehyde‑alcohol dehydrogenase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 60.1% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 875,468 | G→C | 8.9% | S791S (TCG→TCC) | clfA → | Clumping factor A |
| RA | USA300TCH1516_ALE | 1,229,054 | A→G | 8.4% | N37S (AAT→AGT) | rsmB → | Ribosomal RNA small subunit methyltransferase B |
| RA | USA300TCH1516_ALE | 1,343,467 | T→A | 15.4% | A43A (GCT→GCA) | USA300HOU_RS06640 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,373,493 | A→T | 10.2% | I112I (ATA→ATT) | USA300TCH1516_01283 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| JC | USA300TCH1516_ALE | 1,441,097 | +TGTTG | 22.2% | coding (122/624 nt) | USA300HOU_RS07160 → | hypothetical protein |
| 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 | 100% | A67V (GCT→GTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,981,418 | C→A | 82.7% | intergenic (‑17/+339) | USA300HOU_RS09870 ← / ← liaR | hypothetical protein/Transcriptional regulatory protein LiaR |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,279,705 | 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 | 2,775,053 | A→G | 13.5% | D711D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,821,782 | A→G | 5.1% | intergenic (‑25/+54) | flr_2 ← / ← msrAB | Flavoredoxin/Peptide methionine sulfoxide reductase msrA/msrB |
| RA | USA300TCH1516_ALE | 2,827,037 | T→C | 7.0% | I94T (ATC→ACC) | icaA → | Poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 35 (0.780) | 30 (0.980) +40 bp |
24/178 | NT | 55.5% | 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 | = 800928 | 35 (0.780) | 3 (0.070) | 3/244 | NT | 7.0% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 47 (1.110) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 2007531 = | 45 (1.010) | 3 (0.070) | 3/238 | NT | 7.0% | intergenic (+46/‑196) | hemL2/USA300HOU_RS10115 | Glutamate‑1‑semialdehyde 2,1‑aminomutase 2/hypothetical protein |
| ? | USA300TCH1516_ALE | 2007597 = | 38 (0.920) | intergenic (+112/‑130) | hemL2/USA300HOU_RS10115 | Glutamate‑1‑semialdehyde 2,1‑aminomutase 2/hypothetical protein | |||||