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 | 15,413 | C→T | 8.8% | 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 | 8.1% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 11.4% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 32.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 31.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 10.6% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| JC | USA300TCH1516_ALE | 130,854 | (T)5→1 | 9.9% | intergenic (‑94/+272) | sarS ← / ← yfhA | HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA |
| RA | USA300TCH1516_ALE | 252,626 | G→C | 9.2% | E301D (GAG→GAC) | gfo_2 → | Glucose‑‑fructose oxidoreductase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 53.2% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 618,567 | T→C | 13.0% | D1223D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 643,620 | G→A | 8.0% | intergenic (‑268/+281) | yjjP_1 ← / ← USA300HOU_RS03070 | Inner membrane protein YjjP/Putative heme‑dependent peroxidase |
| RA | USA300TCH1516_ALE | 888,887 | A→G | 7.6% | D137G (GAT→GGT) | nfnB → | Nitroreductase NfnB |
| RA | USA300TCH1516_ALE | 1,081,439 | G→T | 6.8% | R47I (AGA→ATA) | purN → | Phosphoribosylglycinamide formyltransferase |
| 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 | 1,744,446 | G→T | 9.7% | P76T (CCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,815,145 | C→T | 10.2% | D33N (GAT→AAT) | dnaE ← | DNA polymerase III subunit alpha |
| RA | USA300TCH1516_ALE | 1,892,051 | A→T | 8.5% | 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 | 2,028,508 | A→T | 14.3% | V46E (GTA→GAA) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,211,305 | A→G | 20.9% | intergenic (+298/+515) | USA300HOU_RS11275 → / ← yidC | hypothetical protein/Membrane protein insertase YidC |
| RA | USA300TCH1516_ALE | 2,217,285 | T→C | 5.3% | T97A (ACA→GCA) | ssbA_3 ← | Single‑stranded DNA‑binding protein A |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,645,589 | T→C | 5.3% | A233A (GCA→GCG) | sauU ← | putative sulfoacetate transporter SauU |
| RA | USA300TCH1516_ALE | 2,774,879 | A→G | 9.5% | D769D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,053 | A→G | 16.0% | D711D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,107 | A→G | 13.7% | D693D (GAT→GAC) | clfB ← | Clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 58 (0.930) | 58 (1.350) +40 bp |
42/178 | NT | 59.3% | 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 | = 557240 | NA (NA) | 3 (0.050) | 3/250 | NT | NA | intergenic (+298/‑1471) | USA300TCH1516_00504/USA300TCH1516_00505 | tRNA‑Ala/tRNA‑Ile |
| ? | USA300TCH1516_ALE | = 557277 | NA (NA) | intergenic (+335/‑1434) | USA300TCH1516_00504/USA300TCH1516_00505 | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | USA300TCH1516_ALE | 2179606 = | NA (NA) | 3 (0.050) | 3/244 | NT | 100% | intergenic (+3368/+1927) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
| ? | USA300TCH1516_ALE | 2179610 = | 0 (0.000) | intergenic (+3372/+1923) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly | |||||