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 | 19,348 | G→A | 16.2% | G335D (GGT→GAT) | 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 | 110,651 | C→T | 12.1% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 13.8% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 32.2% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 31.2% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 22.0% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,572 | C→T | 10.2% | D214D (GAC→GAT) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 116,951 | T→C | 7.8% | G356G (GGT→GGC) | USA300HOU_0114 → | M20 family peptidase |
| RA | 178,003 | C→A | 12.6% | intergenic (+1811/‑23) | cap5C → / → cap5E | capsular polysaccharide biosynthesis protein Cap5C/capsular polysaccharide biosynthesis protein Cap5E |
| 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 | 54.9% | 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 | 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 | 861,896 | C→T | 6.6% | N459N (AAC→AAT) | pgm → | bisphosphoglycerate mutase |
| RA | 874,718 | A→C | 100% | K541N (AAA→AAC) | clfA → | fibrinogen‑binding protein |
| RA | 1,064,254 | Δ1 bp | 100% | coding (235/1218 nt) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,238,026 | T→A | 9.4% | L47H (CTT→CAT) | USA300HOU_1162 → | glycerone kinase |
| RA | 1,344,530 | G→A | 7.1% | intergenic (+266/‑163) | USA300HOU_1253 → / → USA300HOU_1255 | hypothetical protein/hypothetical protein |
| RA | 1,392,673 | A→G | 7.8% | intergenic (+447/‑47) | alsT → / → glcT | AGCS family alanine or glycine:sodium (Na+) symporter/transcriptional antiterminator |
| RA | 1,392,698 | C→T | 8.1% | intergenic (+472/‑22) | alsT → / → glcT | AGCS family alanine or glycine:sodium (Na+) symporter/transcriptional antiterminator |
| 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 | 1,525,990 | A→G | 7.8% | S651S (TCT→TCC) | dnaQ ← | DNA‑directed DNA polymerase III epsilon subunit |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| 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 | 1,776,114 | G→A | 29.8% | P137L (CCA→CTA) | clpX ← | S14 family endopeptidase ClpX |
| 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 | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,470,111 | G→A | 54.9% | S575L (TCA→TTA) | USA300HOU_2333 ← | MFS family major facilitator transporter, multidrug:cation symporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,656,349 | C→A | 10.5% | A53S (GCA→TCA) | USA300HOU_2509 ← | possible lactoylglutatione lyase |
| RA | 2,810,588 | T→C | 10.2% | S266G (AGC→GGC) | secY2 ← | Sec family Type I general secretory pathway protein SecY |
| RA | 2,836,655 | A→G | 6.4% | Y112H (TAC→CAC) | hisB ← | imidazoleglycerol‑phosphate dehydratase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 52495 = | 41 (0.840) | 52 (1.070) +T |
3/258 | NT | 58.3% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 34 (0.700) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 512620 = | 40 (0.820) | 43 (1.280) +40 bp |
32/180 | NT | 60.9% | 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 | = 1217693 | 45 (0.920) | 3 (0.070) | 3/228 | NT | 7.1% | intergenic (+22/‑415) | USA300HOU_1144/USA300HOU_1145 | hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase |
| ? | CP000730 | = 1217729 | 39 (0.910) | intergenic (+58/‑379) | USA300HOU_1144/USA300HOU_1145 | hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase | |||||
| * | ? | CP000730 | = 2476453 | 47 (0.960) | 3 (0.070) | 3/236 | NT | 6.3% | intergenic (‑198/+42) | tcaA/tcaR | teicoplanin resistance protein TcaA/transcriptional regulator TcaR |
| ? | CP000730 | = 2476476 | 46 (1.040) | intergenic (‑221/+19) | tcaA/tcaR | teicoplanin resistance protein TcaA/transcriptional regulator TcaR | |||||
| * | ? | CP000730 | = 2671420 | 45 (0.920) | 3 (0.060) | 3/250 | NT | 6.5% | coding (171/345 nt) | USA300HOU_2526 | possible thioredoxin |
| ? | CP000730 | = 2671462 | 43 (0.920) | coding (129/345 nt) | USA300HOU_2526 | possible thioredoxin | |||||