mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 3,652 | T→A | 17.4% | intergenic (+336/‑45) | dnaN → / → USA300HOU_0003 | DNA‑directed DNA polymerase beta subunit/hypothetical protein |
| RA | 35,814 | Δ1 bp | 35.6% | intergenic (+45/+63) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 35.8% | intergenic (+48/+60) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 40.6% | intergenic (+81/+27) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 42.6% | intergenic (+89/+19) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 52.7% | intergenic (+107/+1) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 24.2% | S213S (TCG→TCC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,940 | G→A | 28.7% | R204R (CGC→CGT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,970 | T→C | 61.0% | E194E (GAA→GAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,997 | T→C | 31.3% | T185T (ACA→ACG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,015 | C→T | 30.7% | R179R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,087 | A→G | 63.5% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,119 | C→T | 30.7% | V145I (GTA→ATA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,124 | G→A | 61.6% | A143V (GCT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,133 | A→G | 30.7% | V140A (GTA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,161 | T→C | 32.0% | I131V (ATT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,174 | T→C | 31.0% | K126K (AAA→AAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,269 | C→T | 60.0% | A95T (GCA→ACA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,315 | G→A | 61.7% | Y79Y (TAC→TAT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,378 | C→T | 90.7% | L58L (TTG→TTA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,413 | C→T | 59.7% | V47I (GTC→ATC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,444 | C→T | 54.8% | R36R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,471 | A→G | 35.7% | S27S (AGT→AGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,479 | T→C | 25.8% | T25A (ACA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,581 | C→T | 43.6% | intergenic (‑30/‑493) | USA300HOU_0026 ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 31.4% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 18.1% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 31.3% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 61.8% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 62.6% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 61.9% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 14.5% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 19.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 30.0% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 31.7% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 231,978 | T→C | 9.4% | M48T (ATG→ACG) | USA300HOU_0209 → | hypothetical protein |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → USA300HOU_0336 | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 58.6% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 547,929 | A→G | 13.4% | K191K (AAA→AAG) | ftsH → | cell division protein FtsH |
| RA | 624,924 | T→C | 11.1% | D395G (GAT→GGT) | USA300HOU_0559 ← | glycosyltransferase |
| RA | 635,184 | A→T | 9.5% | R455S (AGA→AGT) | vraA → | long‑chain‑fatty‑acid‑‑CoA ligase |
| RA | 638,614 | G→T | 100% | T14K (ACA→AAA) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 707,879 | A→T | 100% | L11I (TTA→ATA) | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 741,261 | C→A | 13.5% | intergenic (‑103/‑258) | USA300HOU_0686 ← / → USA300HOU_0687 | possible LysM domain protein/hypothetical membrane protein |
| RA | 790,778 | G→A | 100% | intergenic (+277/‑197) | USA300HOU_0741 → / → USA300HOU_0742 | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 905,331 | T→A | 5.6% | I58I (ATT→ATA) | USA300HOU_0864 → | hypothetical protein |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,277,850 | A→G | 11.4% | intergenic (+448/‑498) | USA300HOU_1191 → / → uppS | UMP kinase/di‑trans, poly‑cis‑decaprenylcistransferase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA ← | cold shock protein CspA |
| RA | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh ← | extracellular matrix binding protein |
| RA | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh ← | extracellular matrix binding protein |
| 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 | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,749,286 | C→T | 14.5% | D55N (GAC→AAC) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | USA300HOU_1679 ← | sensor histidine kinase |
| RA | 1,929,796 | T→C | 47.7% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 49.1% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 47.4% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 51.1% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 64.5% | intergenic (‑895/‑273) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,842 | Δ1 bp | 100% | intergenic (‑925/‑243) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,843 | Δ1 bp | 68.6% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 68.6% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 66.4% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,863:1 | +T | 52.4% | intergenic (‑946/‑222) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 11.3% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 56.1% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 5.6% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 65.7% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866:1 | +T | 4.0% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 67.7% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 68.9% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 67.5% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 65.8% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 66.2% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 57.2% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 57.5% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 55.8% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 55.5% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 55.0% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 50.4% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 37.8% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,021,817 | C→T | 76.5% | V139I (GTT→ATT) | USA300HOU_1873 ← | acyl‑CoA hydrolase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,340,892 | C→T | 13.8% | D230N (GAT→AAT) | USA300HOU_2198 ← | M23B subfamily peptidase |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | USA300HOU_2698 → | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 22 (0.690) | 20 (0.910) +40 bp |
15/180 | NT | 56.9% | 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 | 895785 = | 28 (0.880) | 42 (1.520) | 33/226 | NT | 65.5% | coding (806/822 nt) | USA300HOU_0849 | ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | = 909740 | 20 (0.720) | intergenic (‑663/‑371) | ear/USA300HOU_0868 | Ear protein/hypothetical protein | |||||
| * | ? | CP000730 | 2085296 = | 26 (0.820) | 30 (1.060) | 21/232 | NT | 56.5% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 23 (0.810) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||