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 | 10.4% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 35.4% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 35.6% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 13.0% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 46.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 728,366 | G→A | 6.6% | G79S (GGT→AGT) | USA300HOU_RS03535 → | hypothetical protein |
| 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 | 1,527,625 | A→G | 8.6% | C106C (TGT→TGC) | dinG_1 ← | putative ATP‑dependent helicase DinG |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,607 | T→C | 20.6% | D22G (GAT→GGT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,915,579 | T→C | 6.1% | T81T (ACA→ACG) | metK ← | S‑adenosylmethionine synthase |
| RA | USA300TCH1516_ALE | 1,952,639 | A→G | 11.4% | Y700Y (TAT→TAC) | nisB ← | Nisin biosynthesis protein NisB |
| 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 | 2,309,899 | G→T | 12.7% | S322* (TCA→TAA) | yfmC_2 ← | Fe(3+)‑citrate‑binding protein YfmC |
| RA | USA300TCH1516_ALE | 2,485,771 | A→C | 8.4% | intergenic (‑89/+292) | mqo1 ← / ← lctP_2 | putative malate:quinone oxidoreductase 1/L‑lactate permease |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,557,393 | A→G | 29.1% | D281G (GAT→GGT) | garK_2 → | Glycerate 2‑kinase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 499713 | 59 (1.080) | 5 (0.100) | 3/248 | NT | 8.0% | coding (2417/4500 nt) | gltA | Glutamate synthase [NADPH] large chain |
| ? | USA300TCH1516_ALE | = 499723 | 58 (1.100) | coding (2427/4500 nt) | gltA | Glutamate synthase [NADPH] large chain | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 63 (1.150) | 47 (1.250) +40 bp |
30/178 | NT | 52.0% | 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 | 1442900 = | NA (NA) | 4 (0.080) | 3/246 | NT | NA | intergenic (+133/+135) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1442915 = | NA (NA) | intergenic (+148/+120) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1766474 = | 48 (0.880) | 4 (0.080) | 3/240 | NT | 8.9% | coding (379/561 nt) | tag | DNA‑3‑methyladenine glycosylase 1 |
| ? | USA300TCH1516_ALE | 1766523 = | 37 (0.730) | coding (428/561 nt) | tag | DNA‑3‑methyladenine glycosylase 1 | |||||