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 | 9,085 | G→A | 50.3% | R685H (CGT→CAT) | gyrA → | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| RA | 18,890 | C→G | 93.9% | N182K (AAC→AAG) | USA300HOU_0014 → | DHH subfamily phosphodiesterase |
| 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 | 110,660 | T→A | 11.7% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 31.9% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 31.3% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 9.6% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 264,463 | G→A | 5.5% | W226* (TGG→TGA) | glpQ1 → | possible glycerophosphodiester phosphodiesterase |
| RA | 396,540 | G→A | 100% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 512,643 | A→G | 51.5% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 535,338 | A→T | 5.3% | intergenic (+4909/‑816) | USA300HOU_0494 → / → rplY | hypothetical protein/ribosomal protein L25 |
| RA | 607,884 | G→A | 100% | R209* (CGA→TGA) | USA300HOU_0550 ← | deoxynucleoside kinase |
| 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 | 702,669 | T→C | 3.7% | N154N (AAT→AAC) | USA300HOU_0650 → | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1 |
| 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 | 807,437:1 | +T | 10.5% | intergenic (‑635/‑166) | USA300HOU_0753 ← / → nrdI | DMT superfamily drug/metabolite transporter/ribonucleotide‑diphosphate reductase subunit gamma |
| RA | 1,100,582 | A→G | 6.2% | intergenic (‑146/+184) | USA300HOU_1033 ← / ← pdf1 | hypothetical protein/formylmethionine deformylase |
| RA | 1,120,712 | G→C | 7.5% | R67P (CGC→CCC) | USA300HOU_1050 → | hypothetical protein |
| RA | 1,218,732 | C→G | 4.6% | intergenic (+223/+40) | USA300HOU_1145 → / ← fbpA | possible 3‑demethylubiquinone‑9 3‑methyltransferase/fibrinogen‑binding protein |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,269,458 | G→T | 7.7% | D173Y (GAT→TAT) | gid → | glucose‑inhibited division protein Gid |
| RA | 1,274,208 | C→T | 100% | S204L (TCA→TTA) | USA300HOU_1186 → | CodY family transcriptional regulator |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,435,075 | T→A | 15.8% | G144G (GGT→GGA) | dapD → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑succinyltransferase |
| 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 | 1,679,145 | G→T | 12.4% | R4R (CGC→CGA) | recO ← | recombination protein RecO |
| RA | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,857,867 | C→T | 10.0% | L169L (TTG→TTA) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,909,490:1 | +T | 100% | coding (297/303 nt) | USA300HOU_1771 → | hypothetical membrane protein |
| 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 | 2,028,269 | G→C | 100% | P126A (CCA→GCA) | USA300HOU_1882 ← | hypothetical membrane protein |
| RA | 2,211,305 | A→G | 8.1% | intergenic (‑31/+515) | USA300HOU_2086 ← / ← USA300HOU_2087 | hypothetical protein/hypothetical membrane protein |
| RA | 2,240,343 | C→A | 5.8% | E339* (GAA→TAA) | murZ ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,695 | C→A | 7.0% | G298C (GGT→TGT) | arg ← | arginase |
| RA | 2,310,618 | A→T | 7.3% | G82G (GGT→GGA) | USA300HOU_2169 ← | possible iron (Fe3+) ABC superfamily ATP binding cassette transporter, binding protein |
| RA | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,405,489 | G→T | 94.8% | intergenic (‑127/‑124) | USA300HOU_2268 ← / → ureA | UT family urea transporter/urease gamma subunit |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,468,697 | C→T | 9.7% | E39K (GAA→AAA) | USA300HOU_2331 ← | possible esterase |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,589,376 | C→A | 4.3% | E263* (GAG→TAG) | gltB2 ← | glutamate synthase (NADPH) |
| RA | 2,604,421 | C→T | 6.5% | H430Y (CAT→TAT) | USA300HOU_2464 → | AbgT family p‑aminobenzoyl‑glutamate transporter |
| RA | 2,648,469 | T→A | 8.1% | G79G (GGA→GGT) | USA300HOU_2501 ← | MFS family major facilitator transporter |
| RA | 2,679,725 | G→A | 100% | W70* (TGG→TAG) | USA300HOU_2536 → | possible secretory antigen |
| JC | 2,709,677 | Δ12 bp | 94.7% | coding (1239‑1250/1812 nt) | USA300HOU_2562 ← | possible acetyltransferase |
| RA | 2,850,161 | A→G | 4.2% | intergenic (+150/‑2) | USA300HOU_2691 → / → pcp | rhodanese domain sulfurtransferase/C15 family pyroglutamyl‑peptidase I |
| RA | 2,852,714 | G→T | 8.4% | intergenic (+68/‑170) | USA300HOU_2695 → / → USA300HOU_2696 | hypothetical protein/DASS family divalent anion:sodium (Na+) symporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 92 (1.230) | 67 (1.300) +40 bp |
42/180 | NT | 51.4% | 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 | = 800928 | 82 (1.100) | 3 (0.040) | 3/246 | NT | 4.1% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 62 (0.880) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | = 1702267 | 59 (0.790) | 4 (0.060) | 4/238 | NT | 6.4% | intergenic (‑2/+38) | comEA/USA300HOU_1592 | possible competence protein comEA/hypothetical protein |
| ? | CP000730 | = 1702290 | 64 (0.940) | intergenic (‑25/+15) | comEA/USA300HOU_1592 | possible competence protein comEA/hypothetical protein | |||||
| * | ? | CP000730 | = 2097351 | 78 (1.050) | 3 (0.040) | 3/242 | NT | 3.8% | coding (69/1485 nt) | USA300HOU_1958 | hypothetical bacteriophage protein |
| ? | CP000730 | = 2097358 | 80 (1.150) | coding (62/1485 nt) | USA300HOU_1958 | hypothetical bacteriophage protein | |||||