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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,744,362 | 0 | G | A | 79.0% | 74.1 / 15.5 | 38 | H104Y (CAC→TAC) | apt | adenine phosphoribosyltransferase |
| * | CP000730 | 2,405,489 | 0 | G | T | 77.8% | 78.1 / 25.7 | 45 | intergenic (‑127/‑124) | USA300HOU_2268/ureA | UT family urea transporter/urease gamma subunit |
| * | CP000730 | 707,910 | 0 | A | G | 75.6% | 81.9 / 20.0 | 45 | intergenic (‑1/‑121) | mntB/sirR | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| * | CP000730 | 2,679,725 | 0 | G | A | 75.0% | 56.6 / 19.5 | 36 | W70* (TGG→TAG) | cbpD | possible secretory antigen |
| * | CP000730 | 1,909,486 | 1 | . | T | 70.8% | 125.3 / 50.0 | 48 | coding (293/303 nt) | USA300HOU_1771 | hypothetical membrane protein |
| * | CP000730 | 512,643 | 0 | A | G | 48.4% | 8.5 / 126.9 | 91 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 2,026,655 | 0 | C | T | 40.0% | 14.4 / 37.6 | 35 | E87K (GAA→AAA) | vraR | response regulator VraR |
| * | CP000730 | 111,512 | 0 | A | G | 35.3% | 50.9 / 49.0 | 51 | S194S (TCA→TCG) | USA300HOU_0110 | possible staphylococcal tandem lipoprotein |
| * | CP000730 | 111,516 | 0 | C | A | 32.6% | 70.3 / 42.5 | 49 | Q196K (CAA→AAA) | USA300HOU_0110 | possible staphylococcal tandem lipoprotein |
| * | CP000730 | 1,797,772 | 0 | G | C | 30.0% | 27.8 / 16.3 | 21 | R7G (CGC→GGC) | phoR | sensor histidine kinase |
| * | CP000730 | 110,660 | 0 | T | A | 27.7% | 79.3 / 38.5 | 47 | I173I (ATT→ATA) | USA300HOU_0109 | staphylococcal tandem lipoprotein |
| * | CP000730 | 1,474,639 | 0 | C | G | 21.9% | 90.9 / 25.5 | 41 | A9129P (GCA→CCA) | ebh | extracellular matrix binding protein |
| * | CP000730 | 707,879 | 0 | A | T | 21.4% | 83.6 / 25.7 | 42 | L11I (TTA→ATA) | mntB | ABC superfamily ATP binding cassette transporter, ABC protein |
| * | CP000730 | 110,651 | 0 | C | T | 20.0% | 99.4 / 15.4 | 47 | D170D (GAC→GAT) | USA300HOU_0109 | staphylococcal tandem lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 2001795 = | NA (NA) | 11 (0.320) | 7/258 | 3.9 | NA | intergenic (‑18/+79) | USA300HOU_t0052/rrs3 | tRNA‑Ile/16S ribosomal RNA |
| ? | CP000730 | 2179784 = | NA (NA) | intergenic (‑228/+84) | rrl4/rrs4 | 23S ribosomal RNA/16S ribosomal RNA | |||||
| * | ? | CP000730 | = 558706 | 39 (1.040) | 11 (0.320) | 6/256 | 4.3 | 21.2% | intergenic (+95/‑5) | rrs2/USA300HOU_t0012 | 16S ribosomal RNA/tRNA‑Ile |
| ? | CP000730 | 2001806 = | 46 (1.330) | intergenic (‑29/+68) | USA300HOU_t0052/rrs3 | tRNA‑Ile/16S ribosomal RNA | |||||
| * | ? | CP000730 | 516988 = | NA (NA) | 6 (0.170) | 6/264 | 4.4 | NA | noncoding (2283/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | 517013 = | NA (NA) | noncoding (2308/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | = 1040370 | 23 (0.610) | 5 (0.150) | 4/250 | 5.1 | 19.7% | intergenic (‑6787/‑919) | USA300HOU_0983/USA300HOU_0984 | competence protein/glycosyltransferase |
| ? | CP000730 | = 1040397 | 20 (0.590) | intergenic (‑6814/‑892) | USA300HOU_0983/USA300HOU_0984 | competence protein/glycosyltransferase | |||||
| * | ? | CP000730 | = 2665491 | 46 (1.220) | 4 (0.120) | 4/256 | 5.3 | 8.5% | coding (43/99 nt) | USA300HOU_2520 | hypothetical protein |
| ? | CP000730 | = 2665513 | 44 (1.270) | coding (21/99 nt) | USA300HOU_2520 | hypothetical protein | |||||
| * | ? | CP000730 | 1980867 = | 37 (0.990) | 4 (0.110) | 4/258 | 5.3 | 10.6% | intergenic (‑38/+70) | USA300HOU_1840/yheA | hypothetical protein/transcriptional regulator |
| ? | CP000730 | 1980913 = | 33 (0.950) | intergenic (‑84/+24) | USA300HOU_1840/yheA | hypothetical protein/transcriptional regulator | |||||
| * | ? | CP000730 | 2687471 = | 58 (1.540) | 3 (0.090) | 3/256 | 5.8 | 5.4% | intergenic (+25/+44) | clp/USA300HOU_2543 | S14 family endopeptidase Clp/hypothetical protein |
| ? | CP000730 | 2687511 = | 52 (1.500) | intergenic (+65/+4) | clp/USA300HOU_2543 | S14 family endopeptidase Clp/hypothetical protein | |||||
| * | ? | CP000730 | = 811180 | 40 (1.070) | 3 (0.090) | 3/254 | 5.8 | 8.4% | intergenic (+22/‑111) | nrdF/USA300HOU_0757 | ribonucleoside‑diphosphate reductase subunit beta/hypothetical protein |
| ? | CP000730 | = 811226 | 29 (0.850) | intergenic (+68/‑65) | nrdF/USA300HOU_0757 | ribonucleoside‑diphosphate reductase subunit beta/hypothetical protein | |||||
| * | ? | CP000730 | 810097 = | 35 (0.930) | 3 (0.090) | 3/252 | 5.8 | 8.9% | intergenic (+28/‑90) | nrdE/nrdF | ribonuceloside diphosphate reductase subunit alpha/ribonucleoside‑diphosphate reductase subunit beta |
| ? | CP000730 | 810130 = | 30 (0.880) | intergenic (+61/‑57) | nrdE/nrdF | ribonuceloside diphosphate reductase subunit alpha/ribonucleoside‑diphosphate reductase subunit beta | |||||
| * | ? | CP000730 | 739788 = | 47 (1.250) | 4 (0.120) | 3/252 | 5.8 | 9.1% | intergenic (+15/+573) | pitA/sle1 | possible PiT family inorganic phosphate transporter/possible LysM domain protein |
| ? | CP000730 | 739837 = | 37 (1.090) | intergenic (+64/+524) | pitA/sle1 | possible PiT family inorganic phosphate transporter/possible LysM domain protein | |||||