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 | 39,378 | C→A | 100% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,660 | T→A | 19.4% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 36.1% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 34.1% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 198,135 | T→A | 39.0% | S63R (AGT→AGA) | USA300HOU_0187 → | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → USA300HOU_0336 | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 463,014 | C→A | 100% | E47* (GAA→TAA) | USA300HOU_0437 ← | hypothetical protein |
| RA | 469,786 | A→G | 100% | G118G (GGA→GGG) | USA300HOU_0445 → | hypothetical protein |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 57.8% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 638,614 | G→T | 100% | T14K (ACA→AAA) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 642,696 | T→A | 35.6% | Q219H (CAA→CAT) | USA300HOU_0579 ← | hypothetical membrane protein |
| RA | 707,879 | A→T | 100% | L11I (TTA→ATA) | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 790,778 | G→A | 100% | intergenic (+277/‑197) | USA300HOU_0741 → / → USA300HOU_0742 | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 990,149 | C→G | 33.0% | S14C (TCC→TGC) | oppD1 → | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | 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 | 1,440,007 | 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 | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | USA300HOU_1679 ← | sensor histidine kinase |
| RA | 1,909,155 | G→A | 29.5% | intergenic (‑221/‑39) | USA300HOU_1770 ← / → USA300HOU_1771 | transaldolase/hypothetical membrane protein |
| JC | 1,909,272 | Δ48 bp | 28.0% | coding (79‑126/303 nt) | USA300HOU_1771 → | hypothetical membrane protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| JC | 2,014,521:1 | (GTAAA)1→2 | 26.4% | coding (677/837 nt) | USA300HOU_1865 ← | teichoic acid ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,021,817 | C→T | 100% | V139I (GTT→ATT) | USA300HOU_1873 ← | acyl‑CoA hydrolase |
| RA | 2,027,751 | C→G | 100% | V66L (GTA→CTA) | vraS ← | sensor histidine kinase VraS |
| RA | 2,225,018 | C→G | 7.7% | V53L (GTA→CTA) | atpA ← | F‑ATPase superfamily proton(H+)‑ or sodium (Na+)‑translocating F‑type ATPase epsilon alpha subunit |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,252 | C→A | 100% | A80S (GCT→TCT) | USA300HOU_2153 ← | hypothetical membrane protein |
| RA | 2,360,799 | A→G | 100% | G66G (GGT→GGC) | adk ← | adenylate kinase |
| RA | 2,372,863 | C→G | 36.7% | G305R (GGA→CGA) | USA300HOU_2234 ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,503,491 | C→G | 32.3% | T672R (ACG→AGG) | USA300HOU_2364 → | AraC transcriptional regulator |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,679,710 | G→T | 100% | G65V (GGC→GTC) | USA300HOU_2536 → | possible secretory antigen |
| RA | 2,709,297 | T→A | 28.0% | K544* (AAA→TAA) | USA300HOU_2562 ← | possible acetyltransferase |
| RA | 2,709,919 | G→T | 32.9% | Y336* (TAC→TAA) | USA300HOU_2562 ← | possible acetyltransferase |
| RA | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | USA300HOU_2698 → | hypothetical protein |
| RA | 2,864,675 | G→T | 13.7% | intergenic (+439/+1110) | USA300HOU_2709 → / ← USA300HOU_2710 | hypothetical protein/hypothetical membrane protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 32 (1.040) | 28 (1.320) +40 bp |
22/178 | NT | 56.0% | 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 | 2085296 = | 15 (0.490) | 4 (0.150) | 4/230 | NT | 19.3% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 20 (0.730) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | = 2085309 | 13 (0.420) | 6 (0.220) | 6/230 | NT | 27.5% | intergenic (‑571/‑387) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | 2128358 = | 20 (0.730) | intergenic (+72/+1047) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | 2388283 = | 35 (1.140) | 3 (0.110) | 3/224 | NT | 10.1% | intergenic (+18/+84) | USA300HOU_2247/USA300HOU_2248 | MFS family major facilitator transporter/hypothetical protein |
| ? | CP000730 | 2388362 = | 23 (0.860) | intergenic (+97/+5) | USA300HOU_2247/USA300HOU_2248 | MFS family major facilitator transporter/hypothetical protein | |||||