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 | position | mutation | freq | annotation | gene | description |
| RA | 39,378 | C→T | 100% | D586N (GAT→AAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,660 | T→A | 9.7% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 26.7% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 25.6% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → nagC | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 406,961 | C→G | 61.3% | A353G (GCA→GGA) | atoB → | acetyl‑CoA C‑acetyltransferase |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 41.8% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 535,044 | A→G | 15.3% | intergenic (+4615/‑1110) | veg → / → rplY | hypothetical protein/ribosomal protein L25 |
| RA | 638,614 | G→T | 100% | T14K (ACA→AAA) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 646,838 | G→A | 55.0% | intergenic (+192/‑395) | lplA2 → / → mvaK1 | lipoate‑‑protein ligase A/mevalonate kinase |
| RA | 654,252 | C→T | 58.0% | S362L (TCG→TTG) | USA300HOU_0591 → | hypothetical protein |
| RA | 707,879 | A→T | 100% | L11I (TTA→ATA) | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 790,778 | G→A | 100% | intergenic (+277/‑197) | kipA → / → ltaS | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 942,060 | C→G | 46.4% | intergenic (‑31/+218) | USA300HOU_0905 ← / ← mnhG2 | hypothetical protein/CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit G |
| RA | 1,064,126 | G→C | 44.7% | Y121* (TAC→TAG) | brpA ← | LytR family transcriptional regulator |
| RA | 1,087,670 | A→T | 79.2% | L5I (TTA→ATA) | USA300HOU_1021 ← | hypothetical membrane protein |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,274,212 | A→T | 58.8% | K205N (AAA→AAT) | codY → | CodY family transcriptional regulator |
| RA | 1,296,417 | C→T | 13.4% | A137V (GCG→GTG) | pnp → | polyribonucleotide nucleotidyltransferase |
| RA | 1,318,237 | T→A | 43.6% | F124Y (TTT→TAT) | miaB → | 2‑methylthioadenine synthetase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,420,434 | G→A | 100% | A229T (GCG→ACG) | oppD → | M3 family oligoendopeptidase F |
| RA | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA ← | cold shock protein CspA |
| RA | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh ← | extracellular matrix binding protein |
| RA | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh ← | extracellular matrix binding protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,530,723 | G→A | 58.5% | T188I (ACA→ATA) | bshA ← | glycosyltransferase |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,775,556 | G→A | 47.2% | P323L (CCT→CTT) | clpX ← | S14 family endopeptidase ClpX |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | phoR ← | sensor histidine kinase |
| RA | 1,834,119 | G→T | 67.9% | intergenic (+68/‑46) | ymaD → / → sgaA | hypothetical protein/class V aminotransferase |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,027,561 | G→C | 49.8% | T129S (ACC→AGC) | vraS ← | sensor histidine kinase VraS |
| RA | 2,035,886 | T→C | 66.2% | intergenic (‑212/‑3) | USA300HOU_1892 ← / → dnaQ | hypothetical protein/DNA‑directed DNA polymerase III |
| RA | 2,143,110 | G→A | 49.8% | V163V (GTG→GTA) | USA300HOU_2026 → | hypothetical membrane protein |
| RA | 2,274,965 | G→C | 45.0% | E106D (GAG→GAC) | bglG → | transcriptional antiterminator |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,664,466 | G→A | 52.7% | A65T (GCG→ACG) | pat → | acetyltransferase |
| RA | 2,679,708 | G→A | 64.6% | W64* (TGG→TGA) | cbpD → | possible secretory antigen |
| RA | 2,719,264:1 | +A | 100% | coding (208/705 nt) | USA300HOU_2573 → | dehydrogenase |
| RA | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | USA300HOU_2698 → | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 25 (1.030) | 16 (0.950) +40 bp |
15/180 | NT | 45.7% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 1998278 = | 30 (1.230) | intergenic (‑6/+5) | USA300HOU_t0050/rrf4 | tRNA‑Val/5S ribosomal RNA | |||||