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 | 35,814 | Δ1 bp | 41.0% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 38.8% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 51.3% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 51.5% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 46.4% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 15.6% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 19.2% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 63.8% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 28.7% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 29.1% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 56.6% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 30.2% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 58.6% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 29.5% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 28.1% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 25.2% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 59.8% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 57.8% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 93.0% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 51.8% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 49.2% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 28.0% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,501 | G→A | 15.0% | A17A (GCC→GCT) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 29.6% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 40,391 | G→T | 11.1% | A248E (GCG→GAG) | mecA ← | penicillin binding protein 2 prime |
| RA | 76,180 | C→T | 38.3% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 14.6% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 26.6% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 60.2% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 59.5% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 52.8% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 111,512 | A→G | 19.4% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 20.0% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 306,351 | C→A | 14.5% | A119E (GCG→GAG) | lytS → | sensor histidine kinase LytS |
| RA | 826,574 | C→T | 18.1% | D168N (GAT→AAT) | yvyE ← | hypothetical membrane protein |
| RA | 847,926 | T→C | 14.8% | A289A (GCT→GCC) | trxB1 → | thioredoxin‑disulfide reductase |
| RA | 1,009,940 | G→A | 14.2% | R73H (CGT→CAT) | rluA1 → | pseudouridylate synthase |
| RA | 1,221,684 | C→A | 19.6% | intergenic (+99/‑111) | rpoZ → / → rpoZ | DNA‑directed RNA polymerase subunit omega/bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase |
| RA | 1,223,605 | C→T | 22.3% | Y202Y (TAC→TAT) | priA → | primosomal protein N prime |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,459,907 | T→C | 13.8% | K21R (AAA→AGA) | USA300HOU_1356 ← | possible acetyltransferase |
| 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 | 1,929,796 | T→C | 33.3% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 34.1% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 33.9% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 33.1% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 40.4% | intergenic (‑895/‑273) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,843 | Δ1 bp | 56.5% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 56.2% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 54.7% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 43.8% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 44.0% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 52.9% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 52.1% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 54.7% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 54.7% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 54.7% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 53.9% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 46.5% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 44.9% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 36.6% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 36.6% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 37.1% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 32.9% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 32.8% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,096,684 | A→G | 22.1% | S246P (TCT→CCT) | USA300HOU_1958 ← | hypothetical bacteriophage protein |
| RA | 2,104,016 | T→C | 13.4% | K98K (AAA→AAG) | USA300HOU_1964 ← | hypothetical bacteriophage protein |
| RA | 2,138,686 | A→T | 14.5% | intergenic (‑34/+284) | USA300HOU_2020 ← / ← xtmA | hypothetical membrane protein/terminase small subunit |
| RA | 2,146,374 | T→C | 24.0% | L183S (TTA→TCA) | orf5 → | amidohydrolase |
| RA | 2,187,071 | C→T | 100% | R331K (AGA→AAA) | rsbU ← | sigma factor B regulator |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,306,533 | A→G | 13.8% | P368P (CCT→CCC) | lmrS ← | hypothetical membrane protein |
| RA | 2,391,573 | Δ1 bp | 16.0% | coding (169/447 nt) | moaE ← | molybdopterin synthase large subunit |
| RA | 2,391,574 | A→T | 16.0% | A56A (GCT→GCA) | moaE ← | molybdopterin synthase large subunit |
| RA | 2,403,678 | A→T | 16.0% | V185D (GTT→GAT) | USA300HOU_2267 ← | acyl‑CoA dehydrogenase |
| RA | 2,510,547 | G→A | 13.8% | intergenic (+669/‑404) | USA300HOU_2370 → / → USA300HOU_2372 | hypothetical protein/MerR family transcriptional regulator |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,566,074 | C→T | 9.5% | G20R (GGA→AGA) | USA300HOU_2426 ← | hypothetical protein |
| RA | 2,765,350 | T→C | 14.3% | intergenic (‑419/+276) | gpxA2 ← / ← USA300HOU_2620 | glutathione peroxidase/hypothetical protein |
| RA | 2,847,358 | C→T | 16.7% | N61N (AAC→AAT) | USA300HOU_2689 → | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 211704 = | 12 (0.550) | 5 (0.250) | 3/242 | NT | 28.4% | intergenic (+262/+66) | USA300HOU_0193/USA300HOU_0194 | possible holo‑[acyl‑carrier‑protein] synthase/hypothetical membrane protein |
| ? | CP000730 | 211755 = | 14 (0.690) | intergenic (+313/+15) | USA300HOU_0193/USA300HOU_0194 | possible holo‑[acyl‑carrier‑protein] synthase/hypothetical membrane protein | |||||
| * | ? | CP000730 | = 1873423 | 23 (1.060) | 5 (0.260) | 3/234 | NT | 19.0% | intergenic (‑99/+651) | USA300HOU_1742/USA300HOU_1743 | M20 family peptidase/hypothetical protein |
| ? | CP000730 | = 1873461 | 22 (1.120) | intergenic (‑137/+613) | USA300HOU_1742/USA300HOU_1743 | M20 family peptidase/hypothetical protein | |||||