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 | 3,790 | G→A | 100% | A32T (GCA→ACA) | USA300HOU_0003 → | hypothetical protein |
| RA | 39,378 | C→A | 100% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 76,969 | G→A | 100% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 10.5% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 13.1% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 33.9% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 34.5% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 355,466 | G→A | 100% | P412S (CCA→TCA) | brnQ1 ← | LIVCS family branched chain amino acid:cation symporter |
| RA | 396,540 | G→A | 100% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 512,643 | A→G | 43.0% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 607,884 | G→A | 100% | R209* (CGA→TGA) | USA300HOU_0550 ← | deoxynucleoside kinase |
| RA | 618,567 | T→C | 10.3% | D1223D (GAT→GAC) | sdrD → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD |
| RA | 629,681 | C→A | 100% | L84I (CTA→ATA) | USA300HOU_0564 → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,392 | T→G | 100% | L79* (TTA→TGA) | USA300HOU_0608 → | possible acetytransferase |
| RA | 707,910 | A→G | 100% | intergenic (‑1/‑121) | USA300HOU_0653 ← / → USA300HOU_0654 | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 874,718 | A→C | 100% | K541N (AAA→AAC) | clfA → | fibrinogen‑binding protein |
| RA | 1,056,257 | C→A | 17.1% | intergenic (‑1758/+1909) | sspA ← / ← USA300HOU_0997 | S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase |
| RA | 1,064,254 | Δ1 bp | 100% | coding (235/1218 nt) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| RA | 1,217,669 | T→A | 10.1% | *71K (TAA→AAA) | USA300HOU_1144 → | hypothetical protein |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,440,085 | G→T | 100% | intergenic (‑45/‑891) | cspA ← / → xpaC | cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,662,436 | G→A | 9.6% | P657L (CCT→CTT) | pbp3 ← | penicillin‑binding protein 3 |
| RA | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| JC | 1,747,382 | (TAC)3→2 | 95.3% | coding (2065‑2067/2280 nt) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,963,768 | C→G | 100% | 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 | 2,027,672 | C→A | 100% | G92V (GGC→GTC) | vraS ← | sensor histidine kinase VraS |
| RA | 2,241,539 | T→C | 60.8% | intergenic (‑182/+284) | murZ ← / ← fbaA | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase/fructose‑bisphosphate aldolase |
| RA | 2,269,344 | A→G | 6.0% | V55A (GTA→GCA) | USA300HOU_2143 ← | possible HAD superfamily hydrolase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,262 | C→G | 100% | W76C (TGG→TGC) | USA300HOU_2153 ← | hypothetical membrane protein |
| RA | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,409,590 | A→G | 5.9% | Q127R (CAA→CGA) | ureG → | urease accessory protein UreG |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| JC | 2,501,544 | Δ108 bp | 9.8% | coding (68‑175/2106 nt) | USA300HOU_2364 → | AraC transcriptional regulator |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,544,276 | T→C | 8.5% | Y168Y (TAT→TAC) | hlgC → | gamma hemolysin component C |
| RA | 2,544,339 | C→T | 100% | V189V (GTC→GTT) | hlgC → | gamma hemolysin component C |
| RA | 2,614,662 | A→G | 7.8% | I3I (ATT→ATC) | USA300HOU_2478 ← | lipoprotein |
| RA | 2,709,576 | C→T | 93.7% | G451S (GGT→AGT) | USA300HOU_2562 ← | possible acetyltransferase |
| RA | 2,712,590 | A→G | 3.9% | S105P (TCA→CCA) | isaA ← | immunodominant antigen A |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 92 (1.430) | 50 (1.200) +45 bp |
35/168 | NT | 49.4% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 2176447 = | 66 (1.020) | noncoding (114/114 nt) | rrf5 | 5S ribosomal RNA | |||||