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 | 31.8% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 35.2% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 38.9% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 41.9% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 49.3% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 23.9% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 27.8% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 62.5% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 29.1% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 28.8% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 61.6% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 32.1% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 59.8% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 30.5% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 29.0% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 28.7% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 58.3% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 59.1% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 88.2% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 54.9% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 50.2% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 18.3% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 12.6% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 27.3% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 24.6% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 9.9% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 30.9% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 60.9% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 59.7% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 58.7% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 6.8% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 8.4% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 28.8% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 27.2% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 9.6% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 455,181 | C→A | 11.2% | intergenic (+181/‑199) | set23 → / → set24 | staphylococcal exotoxin/staphylococcal exotoxin |
| RA | 512,643 | A→G | 52.9% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 873,632 | A→T | 6.0% | S179S (TCA→TCT) | clfA → | fibrinogen‑binding protein |
| RA | 984,359 | A→G | 5.9% | K101E (AAA→GAA) | eap → | possible extracellular adherence protein Eap |
| RA | 1,056,257 | C→A | 12.8% | intergenic (‑1758/+1909) | sspA ← / ← atl | S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase |
| RA | 1,081,153 | T→C | 6.6% | N295N (AAT→AAC) | purM → | phosphoribosylformylglycinamidine cyclo‑ligase |
| 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 | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,362 | G→A | 11.1% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,424 | A→G | 11.6% | L83S (TTA→TCA) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,473 | C→T | 7.7% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,644 | C→A | 22.8% | V10F (GTT→TTT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,857,839 | T→C | 6.6% | I179V (ATT→GTT) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,857,867 | C→T | 7.6% | L169L (TTG→TTA) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,929,796 | T→C | 35.9% | 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 | 35.2% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 36.1% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 50.9% | 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 | 58.6% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 59.6% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 61.9% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 43.2% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 19.0% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 43.5% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 12.5% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 58.4% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 61.0% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 61.3% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 59.9% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 60.4% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 61.0% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 52.9% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 52.4% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 51.0% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 50.2% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 50.7% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 38.9% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 34.6% | 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 | 2,233,544 | T→C | 6.4% | E174G (GAA→GGA) | prmC ← | HemK family methyltransferase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,386,969 | A→T | 6.9% | K117* (AAA→TAA) | marR → | MarR family transcriptional regulator |
| RA | 2,390,270 | T→C | 7.2% | E54G (GAA→GGA) | moaA ← | molybdenum (Mo2+) cofactor biosynthesis protein A |
| RA | 2,519,951 | T→G | 6.5% | P227P (CCA→CCC) | narG ← | nitrate reductase alpha subunit |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,680,105 | T→A | 6.5% | intergenic (+157/+375) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,132 | A→G | 8.1% | intergenic (+184/+348) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,184 | T→A | 6.3% | intergenic (+236/+296) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,185:1 | +T | 6.6% | intergenic (+237/+295) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,197:1 | +A | 6.2% | intergenic (+249/+283) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,198 | C→T | 7.5% | intergenic (+250/+282) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,680,214 | T→C | 6.8% | intergenic (+266/+266) | cbpD → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,774,969 | A→G | 10.1% | D739D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,774,981 | A→G | 10.1% | D735D (GAT→GAC) | clfB ← | clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 260294 | 50 (0.780) | 3 (0.050) | 3/238 | NT | 6.0% | intergenic (‑408/‑165) | USA300HOU_0232/pfl | iron (Fe3+) ABC superfamily ATP binding cassette transporter, membrane/binding protein/formate C‑acetyltransferase |
| ? | CP000730 | = 260312 | 49 (0.830) | intergenic (‑426/‑147) | USA300HOU_0232/pfl | iron (Fe3+) ABC superfamily ATP binding cassette transporter, membrane/binding protein/formate C‑acetyltransferase | |||||
| * | ? | CP000730 | 512620 = | 61 (0.950) | 54 (1.220) +40 bp |
45/180 | NT | 56.2% | 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 | = 1205323 | 63 (0.980) | 3 (0.050) +AGCGAA |
3/248 | NT | 6.2% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | = 1893309 | 33 (0.510) | intergenic (‑1303/+177) | rot/USA300HOU_1755 | repressor of toxins Rot/lysophospholipase | |||||
| * | ? | CP000730 | 2001491 = | 8 (0.120) | 6 (0.100) | 4/246 | NT | 44.2% | intergenic (‑100/+116) | rrl3/USA300HOU_t0051 | 23S ribosomal RNA/tRNA‑Ala |
| ? | CP000730 | 2179606 = | NA (NA) | intergenic (‑50/+262) | rrl4/rrs4 | 23S ribosomal RNA/16S ribosomal RNA | |||||