mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
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 | 76,969 | G→A | 100% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 7.9% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 14.3% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 30.8% | 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 | 10.4% | 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 | 217,384 | A→G | 7.1% | M344T (ATG→ACG) | brnQ ← | possible LIVCS family branched chain amino acid:cation symporter |
| RA | 228,319 | T→C | 6.8% | intergenic (+165/‑523) | yleF → / → hsdR2 | RpiR family transcriptional regulator/type I site‑specific deoxyribonuclease restriction subunit |
| RA | 396,540 | G→A | 100% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 495,289 | G→A | 7.7% | Q277* (CAG→TAG) | yibE ← | hypothetical membrane protein |
| RA | 512,643 | A→G | 48.4% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 607,884 | G→A | 100% | R209* (CGA→TGA) | dck ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | 100% | L84I (CTA→ATA) | hxlA → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,392 | T→G | 100% | L79* (TTA→TGA) | iolS → | possible acetytransferase |
| RA | 678,888 | G→T | 11.2% | intergenic (+91/+160) | USA300HOU_0621 → / ← sarA | hydrolase/staphylococcal accessory regulator A |
| RA | 707,910 | A→G | 100% | intergenic (‑1/‑121) | mntB ← / → sirR | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 744,511 | G→C | 5.1% | intergenic (+2348/‑578) | yetJ → / → sarX | hypothetical membrane protein/possible staphylococcal accessory protein X |
| RA | 826,969 | G→T | 6.3% | A36D (GCT→GAT) | yvyE ← | hypothetical membrane protein |
| RA | 1,154,017 | C→A | 8.5% | A181E (GCA→GAA) | his2 → | MutS family DNA mismatch repair protein |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,243,307 | A→T | 5.0% | S249C (AGT→TGT) | plsX → | fatty acid/phospholipid synthesis protein |
| RA | 1,274,208 | C→T | 100% | S204L (TCA→TTA) | codY → | CodY family transcriptional regulator |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | 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) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,685,149 | T→A | 5.3% | intergenic (‑161/+59) | nfeD ← / ← rpsU | hypothetical membrane protein/ribosomal protein S21 |
| 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 | 9.0% | L169L (TTG→TTA) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,909,486:1 | +T | 100% | coding (293/303 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) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,028,269 | G→C | 100% | P126A (CCA→GCA) | yvqF ← | hypothetical membrane protein |
| RA | 2,077,013 | T→C | 9.8% | Y86C (TAT→TGT) | USA300HOU_1933 ← | hypothetical membrane protein |
| RA | 2,171,944 | A→G | 6.8% | N509D (AAT→GAT) | leuA2 → | 2‑isopropylmalate synthase |
| RA | 2,211,990 | C→T | 5.9% | V196I (GTC→ATC) | yidC ← | hypothetical membrane protein |
| RA | 2,235,173 | C→G | 8.3% | A185A (GCG→GCC) | tdk ← | thymidine kinase |
| 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 | 2,371,220 | C→T | 17.1% | intergenic (‑4337/+1221) | rpmC ← / ← pbuG | ribosomal protein L29/NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,384,414 | T→C | 7.3% | Y217C (TAT→TGT) | fmhB ← | peptidoglycan pentaglycine interpeptide biosynthesis protein FmhB |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,632,292 | C→A | 15.6% | intergenic (‑83/+599) | fnbB ← / ← fnbA | fibronectin‑binding protein B/fibronectin‑binding protein A |
| RA | 2,632,296 | G→A | 14.2% | intergenic (‑87/+595) | fnbB ← / ← fnbA | fibronectin‑binding protein B/fibronectin‑binding protein A |
| RA | 2,816,469 | G→C | 15.2% | Y620* (TAC→TAG) | sasA ← | serine‑threonine rich protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 73 (1.120) | 54 (1.200) +40 bp |
40/180 | NT | 51.7% | 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 | 68 (1.040) | 6 (0.100) | 5/246 | NT | 7.5% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 83 (1.340) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||