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 |
| Marginal read alignment evidence (highest frequency 20 of 57 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 35,970 | 0 | T | C | 61.0% | 407.0 / inf | 484 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,087 | 0 | A | G | 60.0% | 378.6 / inf | 672 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 36,124 | 0 | G | A | 59.4% | 196.0 / inf | 522 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 36,269 | 0 | C | T | 57.8% | 255.4 / inf | 921 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 76,295 | 0 | T | C | 56.7% | 305.2 / inf | 596 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 36,315 | 0 | G | A | 56.6% | 396.0 / inf | 1023 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 76,322 | 0 | G | A | 56.4% | 249.6 / inf | 566 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 512,643 | 0 | A | G | 55.4% | 21.4 / 96.1 | 74 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 76,353 | 0 | G | A | 55.0% | 184.2 / inf | 470 | intergenic (+411/‑723) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,861 | 0 | T | C | 54.5% | 28.6 / 112.1 | 88 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 54.5% | 19.6 / 120.8 | 88 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 54.5% | ‑2.6 / 152.4 | 88 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 54.5% | 22.7 / 114.8 | 88 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 53.9% | 17.3 / 190.2 | 89 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 53.9% | 17.3 / 188.6 | 89 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 53.9% | ‑1.5 / 156.1 | 89 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 53.9% | 58.3 / 120.1 | 89 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,876 | 0 | C | T | 53.8% | 38.8 / 105.8 | 78 | intergenic (+107/+1) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 1,929,866 | 0 | G | T | 52.4% | 4.7 / 150.0 | 89 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,413 | 0 | C | T | 52.4% | 89.6 / inf | 570 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 2440041 = | 66 (1.210) | 5 (0.100) | 5/244 | 2.8 | 7.2% | intergenic (+2/+64) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC |
| ? | CP000730 | 2440099 = | 69 (1.390) | intergenic (+60/+6) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC | |||||
| * | ? | CP000730 | 614104 = | 138 (2.520) | 9 (0.180) | 5/244 | 2.8 | 8.0% | coding (2416/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | = 618849 | 80 (1.610) | coding (3951/4146 nt) | sdrD | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD | |||||
| * | ? | CP000730 | 2736813 = | 39 (0.710) | 4 (0.080) | 4/246 | 3.1 | 11.0% | intergenic (+17/‑2697) | panE2/USA300HOU_2595 | 2‑dehydropantoate 2‑reductase/APC family amino acid‑polyamine‑organocation transporter |
| ? | CP000730 | 2736870 = | 29 (0.580) | intergenic (+74/‑2640) | panE2/USA300HOU_2595 | 2‑dehydropantoate 2‑reductase/APC family amino acid‑polyamine‑organocation transporter | |||||
| * | ? | CP000730 | 811169 = | 49 (0.900) | 5 (0.100) | 4/244 | 3.1 | 9.5% | intergenic (+11/‑122) | nrdF/USA300HOU_0757 | ribonucleoside‑diphosphate reductase subunit beta/hypothetical protein |
| ? | CP000730 | 811239 = | 51 (1.020) | intergenic (+81/‑52) | nrdF/USA300HOU_0757 | ribonucleoside‑diphosphate reductase subunit beta/hypothetical protein | |||||
| * | ? | CP000730 | = 2699153 | 40 (0.730) | 3 (0.060) | 3/254 | 3.4 | 10.2% | intergenic (+57/‑234) | copA/merP | P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter/MerTP family mercury (Hg2+) permease, binding protein MerP |
| ? | CP000730 | = 2699196 | 15 (0.290) | intergenic (+100/‑191) | copA/merP | P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter/MerTP family mercury (Hg2+) permease, binding protein MerP | |||||
| * | ? | CP000730 | 943914 = | 91 (1.660) | 3 (0.060) | 3/256 | 3.4 | 3.7% | coding (969/1497 nt) | mnhD2 | CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit D |
| ? | CP000730 | 943963 = | 71 (1.360) | coding (920/1497 nt) | mnhD2 | CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit D | |||||
| * | ? | CP000730 | 693013 = | 48 (0.880) | 3 (0.060) | 3/248 | 3.4 | 5.9% | intergenic (‑40/+135) | USA300HOU_0635/USA300HOU_0636 | possible replication initiation protein/hypothetical protein |
| ? | CP000730 | 693128 = | 52 (1.030) | intergenic (‑155/+20) | USA300HOU_0635/USA300HOU_0636 | possible replication initiation protein/hypothetical protein | |||||
| * | ? | CP000730 | = 613920 | 115 (2.130) | 5 (0.100) +GACTCA |
3/252 | 3.4 | 4.3% | coding (2232/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | 613921 = | 116 (2.120) | coding (2233/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC | |||||
| * | ? | CP000730 | = 516048 | NA (NA) | 3 (0.060) | 3/256 | 3.4 | NA | noncoding (1343/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | = 516079 | NA (NA) | noncoding (1374/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | 517222 = | NA (NA) | 3 (0.060) | 3/260 | 3.5 | NA | noncoding (2517/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | 517273 = | NA (NA) | noncoding (2568/2921 nt) | rrl1 | 23S ribosomal RNA | |||||