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 69 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 567,389 | 0 | A | T | 78.1% | 62.1 / 15.1 | 32 | Q95L (CAA→CTA) | ctsR | CtsR family transcriptional regulator |
| * | CP000730 | 1,231,407 | 0 | G | A | 76.7% | 66.6 / 23.0 | 43 | E18K (GAA→AAA) | prpC | possible PP2C protein phosphatase |
| * | CP000730 | 587,957 | 0 | G | T | 74.2% | 38.5 / 22.6 | 31 | A621S (GCG→TCG) | rpoB | DNA‑directed RNA polymerase subunit beta |
| * | CP000730 | 2,159,426 | 0 | G | A | 73.1% | 34.2 / 14.4 | 26 | intergenic (‑2179/‑1302) | USA300HOU_2042/mutS2 | hypothetical membrane protein/possible DNA mismatch repair protein MutS |
| * | CP000730 | 1,744,443 | 0 | C | A | 72.7% | 43.6 / 20.4 | 33 | V77F (GTT→TTT) | apt | adenine phosphoribosyltransferase |
| * | CP000730 | 1,000,948 | 0 | C | T | 70.4% | 31.6 / 18.7 | 27 | T11I (ACA→ATA) | spxA | possible glutaredoxin |
| * | CP000730 | 36,269 | 0 | C | T | 59.5% | 188.7 / inf | 600 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 36,315 | 0 | G | A | 59.1% | 292.3 / inf | 652 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 36,124 | 0 | G | A | 58.8% | 184.8 / inf | 400 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 36,087 | 0 | A | G | 58.1% | 303.3 / inf | 505 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 57.9% | 227.0 / inf | 378 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,413 | 0 | C | T | 57.1% | 123.6 / inf | 368 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,861 | 0 | T | C | 56.8% | 35.0 / 85.1 | 74 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 76,295 | 0 | T | C | 56.1% | 165.1 / inf | 415 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,872 | 0 | G | A | 56.0% | 9.9 / 97.9 | 75 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 56.0% | ‑1.8 / 116.9 | 75 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 76,322 | 0 | G | A | 55.8% | 120.1 / inf | 392 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,867 | 0 | G | T | 55.4% | ‑4.0 / 121.2 | 75 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 512,643 | 0 | A | G | 55.0% | 27.8 / 94.8 | 80 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 1,929,866 | 0 | G | T | 54.8% | 5.6 / 121.7 | 75 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 2306157 | 48 (1.230) | 4 (0.120) | 4/244 | 4.9 | 9.1% | coding (78/108 nt) | USA300HOU_2165 | hypothetical protein |
| ? | CP000730 | = 2306167 | 38 (1.110) | coding (68/108 nt) | USA300HOU_2165 | hypothetical protein | |||||
| * | ? | CP000730 | = 2636366 | 48 (1.230) | 4 (0.110) | 4/256 | 5.2 | 9.2% | intergenic (‑419/+50) | fnbA/gntP | fibronectin‑binding protein A/GntP family gluconate:proton (H+) symporter |
| ? | CP000730 | = 2636392 | 35 (0.980) | intergenic (‑445/+24) | fnbA/gntP | fibronectin‑binding protein A/GntP family gluconate:proton (H+) symporter | |||||
| * | ? | CP000730 | 2181134 = | 18 (0.460) | 4 (0.110) | 4/262 | 5.3 | 19.1% | noncoding (274/1540 nt) | rrs4 | 16S ribosomal RNA |
| ? | CP000730 | 2297467 = | NA (NA) | noncoding (251/1540 nt) | rrs5 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | = 557330 | NA (NA) | 4 (0.110) | 4/262 | 5.3 | NA | noncoding (259/1540 nt) | rrs2 | 16S ribosomal RNA |
| ? | CP000730 | = 557337 | NA (NA) | noncoding (266/1540 nt) | rrs2 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | = 513066 | 9 (0.230) | 4 (0.110) | 4/262 | 5.3 | 32.1% | noncoding (274/1540 nt) | rrs1 | 16S ribosomal RNA |
| ? | CP000730 | = 557322 | NA (NA) | noncoding (251/1540 nt) | rrs2 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | = 263520 | 58 (1.490) | 4 (0.110) | 4/268 | 5.4 | 7.1% | intergenic (+19/‑85) | pflA/USA300HOU_0235 | [formate‑C‑acetyltransferase]‑activating enzyme/hypothetical protein |
| ? | CP000730 | = 263562 | 49 (1.310) | intergenic (+61/‑43) | pflA/USA300HOU_0235 | [formate‑C‑acetyltransferase]‑activating enzyme/hypothetical protein | |||||
| * | ? | CP000730 | = 2440052 | 42 (1.080) | 3 (0.080) | 3/254 | 5.7 | 6.7% | intergenic (+13/+53) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC |
| ? | CP000730 | = 2440086 | 45 (1.270) | intergenic (+47/+19) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC | |||||
| * | ? | CP000730 | = 2497335 | 47 (1.210) | 3 (0.080) | 3/258 | 5.8 | 6.3% | coding (385/945 nt) | corA | MIT family metal ion transporter CorA |
| ? | CP000730 | = 2497352 | 45 (1.250) | coding (402/945 nt) | corA | MIT family metal ion transporter CorA | |||||
| * | ? | CP000730 | 2030617 = | 43 (1.110) | 3 (0.080) | 3/262 | 5.8 | 7.2% | coding (70/987 nt) | USA300HOU_1885 | hypothetical membrane protein |
| ? | CP000730 | 2030676 = | 37 (1.010) | coding (129/987 nt) | USA300HOU_1885 | hypothetical membrane protein | |||||
| * | ? | CP000730 | = 1545880 | 33 (0.850) | 3 (0.080) | 3/258 | 5.8 | 8.7% | intergenic (‑183/+39) | engA/rpsA | GTP‑binding protein EngA/ribosomal protein S1 |
| ? | CP000730 | = 1545890 | 32 (0.890) | intergenic (‑193/+29) | engA/rpsA | GTP‑binding protein EngA/ribosomal protein S1 | |||||