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 | 110,660 | T→A | 17.4% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 36.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 37.0% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 63.6% | 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 | 73.6% | A67V (GCT→GTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,981,418 | C→A | 77.9% | 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 | 2,372,484 | A→T | 26.1% | L431* (TTA→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 | 2,774,855 | A→G | 17.8% | D777D (GAT→GAC) | clfB ← | Clumping factor B |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | USA300TCH1516_ALE | 2176681–2179433 | 2181135–2179437 | 5–4455 | 10 [9] | [9] 11 | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 27 (0.840) | 32 (1.440) +40 bp |
25/180 | NT | 63.2% | 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 | 848604 = | 19 (0.590) | 3 (0.100) | 3/244 | NT | 14.3% | intergenic (+609/‑271) | trxB/USA300HOU_RS04145 | Thioredoxin reductase/Nucleotide‑binding protein |
| ? | USA300TCH1516_ALE | 848625 = | 18 (0.600) | intergenic (+630/‑250) | trxB/USA300HOU_RS04145 | Thioredoxin reductase/Nucleotide‑binding protein | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 30 (0.930) | 6 (0.210) | 5/232 | NT | 18.8% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 25 (0.870) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||
| * | ? | USA300TCH1516_ALE | 2653484 = | 26 (0.810) | 3 (0.100) | 3/254 | NT | 11.0% | intergenic (+90/‑254) | fbp/USA300HOU_RS13650 | Fructose‑1,6‑bisphosphatase class 3/hypothetical protein |
| ? | USA300TCH1516_ALE | 2653543 = | 23 (0.730) | intergenic (+149/‑195) | fbp/USA300HOU_RS13650 | Fructose‑1,6‑bisphosphatase class 3/hypothetical protein | |||||