mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 110,651 | C→T | 13.4% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 16.8% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 32.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 31.6% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 452,493 | C→T | 14.6% | S116L (TCA→TTA) | USA300HOU_RS02140 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 44.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 619,116 | A→G | 9.0% | intergenic (+72/‑322) | sdrD → / → sdrE | Serine‑aspartate repeat‑containing protein D/Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 829,184 | G→A | 14.9% | V246I (GTT→ATT) | comFA → | ComF operon protein 1 |
| RA | USA300TCH1516_ALE | 842,690 | A→G | 7.4% | intergenic (+76/‑586) | uvrA → / → hprK | UvrABC system protein A/HPr kinase/phosphorylase |
| RA | USA300TCH1516_ALE | 882,089 | G→A | 8.0% | T11I (ACA→ATA) | USA300HOU_RS04300 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,324,247 | C→A | 12.8% | P340Q (CCA→CAA) | mutL → | DNA mismatch repair protein MutL |
| RA | USA300TCH1516_ALE | 1,402,143 | G→T | 7.8% | A175D (GCT→GAT) | tyrA ← | Prephenate dehydrogenase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,458,972 | T→C | 5.5% | D159G (GAT→GGT) | murG ← | UDP‑N‑acetylglucosamine‑‑N‑acetylmuramyl‑ (pentapeptide) pyrophosphoryl‑undecaprenol N‑acetylglucosamine transferase |
| 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 | 1,744,545 | A→T | 6.6% | Y43N (TAC→AAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,874,887 | G→A | 17.2% | L108F (CTT→TTT) | rsuA ← | Ribosomal small subunit pseudouridine synthase A |
| RA | USA300TCH1516_ALE | 1,974,657 | C→T | 8.3% | M869I (ATG→ATA) | smc_3 ← | Chromosome partition protein Smc |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,276 | G→A | 21.6% | Q215* (CAA→TAA) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,235,262 | G→A | 6.1% | Q156* (CAA→TAA) | tdk ← | Thymidine kinase |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,300,370 | C→G | 20.1% | A156P (GCT→CCT) | emrY ← | putative multidrug resistance protein EmrY |
| RA | USA300TCH1516_ALE | 2,372,557 | C→A | 18.4% | G407* (GGA→TGA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,429:1 | +C | 11.9% | coding (347/1335 nt) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,429:2 | +T | 11.9% | coding (347/1335 nt) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,697:1 | +T | 16.0% | coding (79/1335 nt) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 80 (1.220) | 46 (1.020) +40 bp |
35/178 | NT | 45.5% | 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 | 895785 = | 56 (0.850) | 11 (0.190) | 7/224 | NT | 17.8% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 53 (0.930) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | = 1299540 | 50 (0.760) | 4 (0.060) | 3/252 | NT | 7.1% | coding (1201/1674 nt) | rnj2 | Ribonuclease J 2 |
| ? | USA300TCH1516_ALE | = 1299564 | 56 (0.880) | coding (1225/1674 nt) | rnj2 | Ribonuclease J 2 | |||||
| * | ? | USA300TCH1516_ALE | = 1378545 | 59 (0.900) | 4 (0.060) | 4/248 | NT | 7.5% | coding (6/1647 nt) | opuD_1 | Glycine betaine transporter OpuD |
| ? | USA300TCH1516_ALE | = 1378579 | 42 (0.670) | coding (40/1647 nt) | opuD_1 | Glycine betaine transporter OpuD | |||||
| * | ? | USA300TCH1516_ALE | 1551802 = | 64 (0.980) | 4 (0.060) | 4/246 | NT | 6.2% | coding (672/1461 nt) | ebpS | Elastin‑binding protein EbpS |
| ? | USA300TCH1516_ALE | 1551860 = | 61 (0.980) | coding (614/1461 nt) | ebpS | Elastin‑binding protein EbpS | |||||
| * | ? | USA300TCH1516_ALE | 1980867 = | 59 (0.900) | 4 (0.070) | 4/238 | NT | 6.5% | intergenic (‑109/+70) | USA300HOU_RS09865/USA300HOU_RS09870 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1980913 = | 61 (1.010) | intergenic (‑155/+24) | USA300HOU_RS09865/USA300HOU_RS09870 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 72 (1.100) | 17 (0.290) | 15/230 | NT | 21.5% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 60 (1.030) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||
| * | ? | USA300TCH1516_ALE | = 2358790 | 76 (1.160) | 4 (0.060) | 3/248 | NT | 5.1% | coding (128/945 nt) | rpoA_1 | DNA‑directed RNA polymerase subunit alpha |
| ? | USA300TCH1516_ALE | = 2358806 | 77 (1.220) | coding (112/945 nt) | rpoA_1 | DNA‑directed RNA polymerase subunit alpha | |||||
| * | ? | USA300TCH1516_ALE | 2742800 = | 54 (0.820) | 4 (0.060) | 4/246 | NT | 7.5% | coding (167/417 nt) | USA300HOU_RS14120 | hypothetical protein |
| ? | USA300TCH1516_ALE | 2742840 = | 47 (0.750) | coding (207/417 nt) | USA300HOU_RS14120 | hypothetical protein | |||||