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 |
| Marginal read alignment evidence (highest frequency 20 of 55 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 | 64.8% | 281.3 / 256.6 | 283 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,087 | 0 | A | G | 64.2% | 384.6 / inf | 393 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 36,124 | 0 | G | A | 63.9% | 218.9 / 295.0 | 297 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,875 | 0 | T | C | 61.1% | 41.9 / 50.0 | 54 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,269 | 0 | C | T | 61.0% | 193.3 / inf | 459 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 36,315 | 0 | G | A | 60.1% | 233.2 / inf | 512 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,873 | 0 | C | A | 60.0% | 15.0 / 67.8 | 55 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 76,295 | 0 | T | C | 60.0% | 187.0 / inf | 368 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 76,322 | 0 | G | A | 59.4% | 151.9 / inf | 357 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,872 | 0 | G | A | 57.9% | 26.9 / 62.0 | 57 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,861 | 0 | T | C | 55.9% | 26.3 / 66.6 | 59 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 55.9% | ‑3.6 / 87.0 | 59 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 55.9% | 55.9 / 62.1 | 59 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 76,353 | 0 | G | A | 55.5% | 78.2 / inf | 274 | intergenic (+411/‑723) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,917 | 0 | C | T | 55.3% | 9.6 / 57.2 | 47 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,918 | 0 | A | G | 55.3% | 13.2 / 54.8 | 47 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 55.0% | ‑4.9 / 92.0 | 60 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 54.1% | 7.1 / 125.3 | 61 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,413 | 0 | C | T | 52.5% | 14.1 / inf | 300 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,866 | 0 | G | T | 51.8% | 0.5 / 88.5 | 59 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 23 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 517681 | NA (NA) | 6 (0.190) | 6/260 | 3.7 | NA | intergenic (+55/‑20) | rrl1/rrf1 | 23S ribosomal RNA/5S ribosomal RNA |
| ? | CP000730 | = 517686 | NA (NA) | intergenic (+60/‑15) | rrl1/rrf1 | 23S ribosomal RNA/5S ribosomal RNA | |||||
| * | ? | CP000730 | 515911 = | NA (NA) | 7 (0.220) | 5/262 | 4.1 | NA | noncoding (1206/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | 515928 = | NA (NA) | noncoding (1223/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | = 2624439 | 3 (0.090) | 6 (0.180) | 4/268 | 4.7 | 75.4% | intergenic (‑1769/+2267) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T |
| ? | CP000730 | = 2624449 | 1 (0.030) | intergenic (‑1779/+2257) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T | |||||
| * | ? | CP000730 | = 2624069 | 3 (0.090) | 6 (0.180) | 4/268 | 4.7 | 67.0% | intergenic (‑1399/+2637) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T |
| ? | CP000730 | = 2624435 | 3 (0.090) | intergenic (‑1765/+2271) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T | |||||
| * | ? | CP000730 | = 2624055 | 5 (0.150) | 6 (0.180) | 4/268 | 4.7 | 67.2% | intergenic (‑1385/+2651) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T |
| ? | CP000730 | = 2624449 | 1 (0.030) | intergenic (‑1779/+2257) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T | |||||
| * | ? | CP000730 | = 2624055 | 5 (0.150) | 6 (0.180) | 4/268 | 4.7 | 60.4% | intergenic (‑1385/+2651) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T |
| ? | CP000730 | = 2624065 | 3 (0.090) | intergenic (‑1395/+2641) | USA300HOU_2485/sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T | |||||
| * | ? | CP000730 | 1172325 = | 23 (0.680) | 3 (0.100) | 3/246 | 4.9 | 12.9% | intergenic (+52/+393) | USA300HOU_1101/USA300HOU_1103 | hypothetical protein/exotoxin |
| ? | CP000730 | 1172364 = | 20 (0.670) | intergenic (+91/+354) | USA300HOU_1101/USA300HOU_1103 | hypothetical protein/exotoxin | |||||
| * | ? | CP000730 | 562451 = | 34 (1.010) | 4 (0.130) | 3/250 | 4.9 | 10.6% | intergenic (+386/+138) | rrf3/USA300HOU_0510 | 5S ribosomal RNA/GntR family transcriptional regulator |
| ? | CP000730 | 562497 = | 37 (1.220) | intergenic (+432/+92) | rrf3/USA300HOU_0510 | 5S ribosomal RNA/GntR family transcriptional regulator | |||||
| * | ? | CP000730 | 2538221 = | 40 (1.190) | 4 (0.130) | 3/262 | 5.1 | 9.6% | coding (266/687 nt) | gpmA2 | phosphoglycerate mutase |
| ? | CP000730 | 2538241 = | 37 (1.160) | coding (246/687 nt) | gpmA2 | phosphoglycerate mutase | |||||
| * | ? | CP000730 | 2125287 = | 41 (1.220) | 3 (0.090) | 3/260 | 5.1 | 7.5% | coding (686/933 nt) | dnaQ | possible exodeoxyribonuclease |
| ? | CP000730 | 2125322 = | 35 (1.110) | coding (721/933 nt) | dnaQ | possible exodeoxyribonuclease | |||||