mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 6,838 | A→G | 5.9% | E593G (GAA→GGA) | gyrB → | DNA topoisomerase (ATP‑hydrolyzing) subunit B |
| RA | 39,672 | C→A | 100% | V488F (GTT→TTT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,660 | T→A | 6.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 31.5% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 29.3% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 238,030 | T→C | 5.7% | L11L (TTA→CTA) | USA300HOU_0214 → | oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 250,944 | C→A | 8.8% | Q109K (CAA→AAA) | USA300HOU_0224 → | possible dehydrogenase |
| RA | 307,880 | T→C | 7.5% | L43P (CTG→CCG) | lytR → | response regulator LytR |
| RA | 348,452 | A→G | 5.7% | E130G (GAA→GGA) | USA300HOU_0315 → | hypothetical protein |
| RA | 478,502 | C→A | 100% | D342E (GAC→GAA) | ndhF → | NADH dehydrogenase (ubiquinone) |
| RA | 512,643 | A→G | 56.3% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 597,770 | A→T | 100% | V168V (GTA→GTT) | tufA → | elongation factor EF1A |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,005,078 | T→C | 5.8% | I508T (ATT→ACT) | pepF → | M03 family oligopeptidase F |
| RA | 1,063,849 | C→T | 100% | D214N (GAC→AAC) | brpA ← | LytR family transcriptional regulator |
| RA | 1,103,793 | G→T | 8.5% | A67S (GCG→TCG) | phdB → | pyruvate dehydrogenase (acetyl‑transferring) beta subunit |
| RA | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,196,508 | C→A | 100% | intergenic (+2563/‑1229) | ftsQ → / → ylmE | cell division protein FtsQ/hypothetical protein |
| RA | 1,232,148 | G→T | 100% | G18V (GGC→GTC) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,672,412 | G→A | 66.5% | A194V (GCA→GTA) | rpoD ← | DNA‑directed RNA polymerase sigma subunit RpoD |
| RA | 1,689,552 | A→G | 13.0% | F105S (TTC→TCC) | dnaJ ← | chaperone DnaJ |
| RA | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,746,458 | T→C | 6.3% | E170G (GAA→GGA) | recJ ← | recombination protein RecJ |
| JC | 1,747,374 | Δ3 bp | 100% | coding (2073‑2075/2280 nt) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,775,841 | T→C | 85.3% | H228R (CAT→CGT) | clpX ← | S14 family endopeptidase ClpX |
| RA | 1,871,583 | G→A | 5.9% | P110L (CCA→CTA) | daaA ← | D‑alanine transaminase |
| RA | 1,979,300 | G→T | 6.2% | A89D (GCT→GAT) | yheA ← | hypothetical protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,027,751 | C→G | 100% | V66L (GTA→CTA) | vraS ← | sensor histidine kinase VraS |
| RA | 2,038,244 | T→A | 7.2% | T39S (ACA→TCA) | USA300HOU_1895 ← | hypothetical protein |
| RA | 2,050,741 | C→T | 6.1% | E518K (GAG→AAG) | pcrA ← | ATP‑dependent DNA helicase PcrA |
| RA | 2,095,255 | T→A | 5.9% | K222M (AAG→ATG) | hol ← | hypothetical bacteriophage protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,325 | C→A | 12.4% | Q55H (CAG→CAT) | ybbP ← | hypothetical membrane protein |
| RA | 2,337,959 | C→T | 100% | intergenic (‑125/‑119) | adhR ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,358,585 | G→C | 10.2% | D111E (GAC→GAG) | rpoA ← | DNA‑directed RNA polymerase alpha subunit |
| RA | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,632,393 | C→T | 7.7% | intergenic (‑184/+498) | fnbB ← / ← fnbA | fibronectin‑binding protein B/fibronectin‑binding protein A |
| RA | 2,709,906 | C→A | 46.2% | E341* (GAA→TAA) | oatA ← | possible acetyltransferase |
| RA | 2,841,601 | C→T | 11.9% | D170N (GAC→AAC) | USA300HOU_2683 ← | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 34173 = | 74 (1.250) | 9 (0.160) | 5/248 | NT | 12.0% | coding (462/480 nt) | orfX | hypothetical protein OrfX |
| ? | CP000730 | = 57858 | 62 (1.100) | intergenic (+304/+613) | USA300HOU_0048/USA300HOU_0049 | hypothetical membrane protein/hypothetical protein | |||||
| * | ? | CP000730 | 34173 = | 74 (1.250) | 4 (0.070) | 3/254 | NT | 5.0% | coding (462/480 nt) | orfX | hypothetical protein OrfX |
| ? | CP000730 | = 88831 | 79 (1.370) | coding (126/138 nt) | USA300HOU_0086 | hypothetical protein | |||||
| * | ? | CP000730 | 512620 = | 46 (0.780) | 36 (0.880) +40 bp |
24/180 | NT | 53.1% | 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 | = 2870578 | 55 (0.930) | 4 (0.070) | 4/248 | NT | 7.0% | intergenic (‑46/+21) | gidA/mnmE | glucose inhibited division protein A/GTP‑binding protein |
| ? | CP000730 | = 2870582 | 54 (0.960) | intergenic (‑50/+17) | gidA/mnmE | glucose inhibited division protein A/GTP‑binding protein | |||||