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 | 15,413 | C→T | 7.3% | D68N (GAC→AAC) | USA300HOU_pUSA300HOUMR0019 ← | strepthothricin acetyltransferase |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 10.2% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 12.9% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 40.3% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 37.8% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 17.3% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 168,397 | G→C | 31.4% | P28R (CCC→CGC) | USA300TCH1516_00148 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 430,394 | A→G | 8.4% | K27E (AAA→GAA) | nfrA → | NADPH‑dependent oxidoreductase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 50.7% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 614,082 | G→A | 11.5% | S798S (TCG→TCA) | sdrC → | Serine‑aspartate repeat‑containing protein C |
| RA | USA300TCH1516_ALE | 975,902 | A→G | 8.6% | K400R (AAA→AGA) | oatA_1 → | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,435,068 | C→T | 22.7% | T142I (ACA→ATA) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| 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 | 1,744,428 | T→C | 27.0% | K82E (AAA→GAA) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,446 | G→T | 11.7% | P76T (CCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,494 | A→T | 27.7% | F60I (TTT→ATT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,891,158 | G→T | 10.0% | K112N (AAG→AAT) | vspIM → | Modification methylase VspI |
| RA | USA300TCH1516_ALE | 1,892,051 | A→T | 8.4% | intergenic (‑144/+376) | rot ← / ← USA300TCH1516_01749 | HTH‑type transcriptional regulator rot/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,811 | Δ1 bp | 8.9% | coding (108/810 nt) | mgt ← | Monofunctional glycosyltransferase |
| 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 | 6.6% | L342* (TTA→TAA) | 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 | 482715 = | 53 (0.860) | 3 (0.050) | 3/244 | NT | 6.2% | intergenic (+512/‑171) | USA300HOU_RS02285/USA300HOU_RS02295 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 482748 = | 41 (0.710) | intergenic (+545/‑138) | USA300HOU_RS02285/USA300HOU_RS02295 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 54 (0.870) | 48 (1.120) +40 bp |
37/180 | NT | 56.3% | 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 | 49 (0.790) | 7 (0.120) | 7/246 | NT | 11.9% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 57 (0.970) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 895785 = | 59 (0.950) | 12 (0.220) | 10/226 | NT | 18.7% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 53 (0.990) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 56 (0.900) | 99 (1.790) | 75/232 | NT | 67.4% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 46 (0.830) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||