mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.1 revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 35,970 | T→C | 12.5% | E194E (GAA→GAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,087 | A→G | 8.5% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,119 | C→T | 11.4% | V145I (GTA→ATA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,315 | G→A | 12.1% | Y79Y (TAC→TAT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,378 | C→T | 12.2% | L58L (TTG→TTA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,413 | C→T | 8.1% | V47I (GTC→ATC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 76,265 | C→T | 10.4% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,969 | G→A | 20.7% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 9.2% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 12.3% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 28.0% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 27.7% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 9.8% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 195,286 | T→A | 20.7% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 340,387 | A→T | 15.0% | K19M (AAG→ATG) | esaC → | virulence protein EsaC |
| RA | 382,916 | C→A | 23.0% | G331C (GGT→TGT) | USA300HOU_0350 ← | PTS family porter component IIC |
| RA | 396,540 | G→A | 11.3% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 478,502 | C→A | 85.0% | D342E (GAC→GAA) | USA300HOU_0457 → | NADH dehydrogenase (ubiquinone) |
| RA | 512,643 | A→G | 35.7% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 554,989 | T→C | 8.2% | intergenic (+1956/‑1103) | folB → / → rrf2 | dihydroneopterin aldolase/5S ribosomal RNA |
| RA | 584,121 | G→T | 77.2% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 607,884 | G→A | 19.1% | R209* (CGA→TGA) | USA300HOU_0550 ← | deoxynucleoside kinase |
| RA | 665,392 | T→G | 18.3% | L79* (TTA→TGA) | USA300HOU_0608 → | possible acetytransferase |
| RA | 707,909 | A→T | 79.1% | M1M (TTG→ATG) † | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 707,910 | A→G | 19.5% | intergenic (‑1/‑121) | USA300HOU_0653 ← / → USA300HOU_0654 | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 832,706 | A→T | 5.7% | I488F (ATT→TTT) | secA1 → | Sec family Type I general secretory pathway preprotein translocase subunit SecA |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | USA300HOU_0930 ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 90.9% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,105,994 | T→C | 85.3% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,196,508 | C→A | 83.8% | intergenic (+2563/‑1229) | ftsQ → / → USA300HOU_1125 | cell division protein FtsQ/hypothetical protein |
| RA | 1,231,470 | A→C | 43.9% | M39L (ATG→CTG) | USA300HOU_1156 → | possible PP2C protein phosphatase |
| RA | 1,233,504 | T→A | 15.8% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,391,351 | G→A | 26.5% | G196S (GGT→AGT) | alsT → | AGCS family alanine or glycine:sodium (Na+) symporter |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,362 | G→A | 19.0% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,473 | C→T | 83.2% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,963,768 | C→G | 12.7% | V365L (GTA→CTA) | hemG ← | protoporphyrinogen oxidase |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,027,191 | A→C | 9.6% | H252Q (CAT→CAG) | vraS ← | sensor histidine kinase VraS |
| RA | 2,027,694 | A→T | 14.4% | S85T (TCA→ACA) | vraS ← | sensor histidine kinase VraS |
| RA | 2,162,009 | C→A | 7.6% | Q428K (CAA→AAA) | mutS2 → | possible DNA mismatch repair protein MutS |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,337,959 | C→T | 86.9% | intergenic (‑125/‑119) | USA300HOU_2195 ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,352,815 | G→A | 11.4% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | 12.0% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,692 | Δ1 bp | 70.3% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | C→A | 100% | H406N (CAT→AAT) ‡ | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,699 | A→T | 77.0% | H406L (CAT→CTT) ‡ | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,473,767 | T→C | 6.3% | I280V (ATA→GTA) | tcaB ← | MFS family major facilitator transporter, teicoplanin:cation symporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,628,458 | G→A | 7.3% | G250G (GGC→GGT) | galU ← | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 57 (1.090) | 31 (0.860) +40 bp |
26/180 | NT | 44.1% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 1998278 = | NA (NA) | intergenic (‑6/+5) | USA300HOU_t0050/rrf4 | tRNA‑Val/5S ribosomal RNA | |||||
| * | ? | CP000730 | = 907281 | 45 (0.860) | 5 (0.100) | 3/240 | NT | 10.5% | intergenic (+390/‑39) | USA300HOU_0865/USA300HOU_0866 | hypothetical protein/hypothetical protein |
| ? | CP000730 | = 907290 | 44 (0.910) | intergenic (+399/‑30) | USA300HOU_0865/USA300HOU_0866 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | 1030884 = | 57 (1.090) | 3 (0.060) | 3/234 | NT | 5.7% | intergenic (+7/‑132) | USA300HOU_0981/USA300HOU_0982 | Trk family potassium (K+) transporter, membrane protein/possible 5'‑nucleotidase |
| ? | CP000730 | 1030933 = | 48 (1.020) | intergenic (+56/‑83) | USA300HOU_0981/USA300HOU_0982 | Trk family potassium (K+) transporter, membrane protein/possible 5'‑nucleotidase | |||||
| * | ? | CP000730 | = 2442821 | 46 (0.880) | 5 (0.110) | 5/228 | NT | 11.3% | intergenic (+18/+40) | USA300HOU_2304/USA300HOU_2305 | transcriptional regulator/hypothetical protein |
| ? | CP000730 | = 2442838 | 38 (0.830) | intergenic (+35/+23) | USA300HOU_2304/USA300HOU_2305 | transcriptional regulator/hypothetical protein | |||||
| * | ? | CP000730 | 2561201 = | 55 (1.050) | 3 (0.060) | 3/232 | NT | 5.9% | intergenic (+30/+33) | USA300HOU_2422/USA300HOU_2423 | hypothetical protein/hypothetical protein |
| ? | CP000730 | 2561237 = | 47 (1.000) | coding (804/807 nt) | USA300HOU_2423 | hypothetical protein | |||||