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 | NC_012417 | 40 | G→T | 20.6% | intergenic (–/‑240) | – / → USA300HOU_RS14890 | –/replication protein |
| JC | USA300TCH1516_ALE | 62,817 | +TCAATT | 100% | intergenic (‑284/+229) | USA300TCH1516_00053 ← / ← speG | hypothetical protein/Spermidine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 10.5% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 39.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 36.0% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 171,052 | A→T | 5.9% | intergenic (+401/‑49) | USA300HOU_RS07235 → / → adhE | hypothetical protein/Aldehyde‑alcohol dehydrogenase |
| RA | USA300TCH1516_ALE | 197,615 | G→A | 6.1% | V214I (GTT→ATT) | cmpC → | Bicarbonate transport ATP‑binding protein CmpC |
| RA | USA300TCH1516_ALE | 465,678 | A→G | 6.0% | intergenic (+62/‑318) | lpl2_3 → / → lpl2_4 | putative lipoprotein/putative lipoprotein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 40.0% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| JC | USA300TCH1516_ALE | 643,716 | Δ21 bp | 7.4% | intergenic (‑364/+165) | yjjP_1 ← / ← USA300HOU_RS03070 | Inner membrane protein YjjP/Putative heme‑dependent peroxidase |
| 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 | 1,586,762 | T→C | 6.7% | E94G (GAA→GGA) | USA300HOU_RS07780 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,944,209 | Δ1 bp | 5.3% | coding (211/708 nt) | splA ← | Serine protease SplA |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,630 | Δ1 bp | 7.7% | coding (289/810 nt) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,018,634 | G→A | 8.9% | A95A (GCC→GCT) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,027,006 | G→A | 5.9% | A314V (GCT→GTT) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,028,049 | A→G | 54.2% | V199A (GTT→GCT) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,190,716 | A→G | 7.6% | Y128H (TAT→CAT) | USA300HOU_RS11190 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,373,525 | G→T | 50.0% | A84E (GCA→GAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,667 | G→A | 19.3% | Q37* (CAA→TAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,777,004 | G→A | 5.6% | A61V (GCA→GTA) | clfB ← | Clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 77 (1.210) | 43 (0.980) +40 bp |
33/180 | NT | 44.7% | 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 = | 71 (1.120) | 4 (0.070) | 4/226 | NT | 6.7% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 50 (0.910) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | = 1305129 | 76 (1.190) | 4 (0.070) | 3/236 | NT | 5.3% | coding (478/1287 nt) | albF | Putative zinc protease AlbF |
| ? | USA300TCH1516_ALE | = 1305131 | 75 (1.300) | coding (480/1287 nt) | albF | Putative zinc protease AlbF | |||||
| * | ? | USA300TCH1516_ALE | = 1801134 | 44 (0.690) | 4 (0.060) | 4/254 | NT | 8.2% | coding (186/1122 nt) | citZ | Citrate synthase 2 |
| ? | USA300TCH1516_ALE | = 1801146 | 47 (0.760) | coding (174/1122 nt) | citZ | Citrate synthase 2 | |||||