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 |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| MC | CP000731 | 1 | Δ27,041 bp | 100% | repA–USA300HOU_pUSA300HOUMR0033 | 26 genes repA, USA300HOU_pUSA300HOUMR0003, USA300HOU_pUSA300HOUMR0004, USA300HOU_pUSA300HOUMR0005, USA300HOU_pUSA300HOUMR0006, cadR, cadX, USA300HOU_pUSA300HOUMR0010, blaZ, blaR, blaI, USA300HOU_pUSA300HOUMR0014, USA300HOU_pUSA300HOUMR0015, USA300HOU_pUSA300HOUMR0016, USA300HOU_pUSA300HOUMR0018, USA300HOU_pUSA300HOUMR0019, USA300HOU_pUSA300HOUMR0021, USA300HOU_pUSA300HOUMR0023, USA300HOU_pUSA300HOUMR0024, USA300HOU_pUSA300HOUMR0027, USA300HOU_pUSA300HOUMR0028, USA300HOU_pUSA300HOUMR0029, USA300HOU_pUSA300HOUMR0030, USA300HOU_pUSA300HOUMR0031, USA300HOU_pUSA300HOUMR0032, USA300HOU_pUSA300HOUMR0033 |
|
| MC | NC_012417 | 1 | Δ3,125 bp | 100% | USA300HOU_RS14890–USA300HOU_RS14900 | USA300HOU_RS14890, USA300HOU_RS15665, USA300HOU_RS14895, USA300HOU_RS14900 | |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 9.9% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 27.4% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 25.6% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 367,644 | G→T | 100% | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 406,961 | C→G | 60.0% | A353G (GCA→GGA) | USA300HOU_RS01880 → | putative acetyl‑CoA acyltransferase |
| RA | USA300TCH1516_ALE | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 41.8% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 535,044 | A→G | 15.3% | L2L (TTA→TTG) | prs → | Ribose‑phosphate pyrophosphokinase |
| RA | USA300TCH1516_ALE | 638,614 | G→T | 100% | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| RA | USA300TCH1516_ALE | 646,838 | G→A | 55.0% | intergenic (+192/‑395) | lipL → / → galK | Octanoyl‑[GcvH]:protein N‑octanoyltransferase/Galactokinase |
| RA | USA300TCH1516_ALE | 654,252 | C→T | 58.0% | S360L (TCG→TTG) | USA300HOU_RS03120 → | Ribonuclease |
| RA | USA300TCH1516_ALE | 707,879 | A→T | 100% | L11I (TTA→ATA) | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 790,778 | G→A | 100% | intergenic (+277/‑197) | kipA_1 → / → ltaS | KipI antagonist/Lipoteichoic acid synthase |
| RA | USA300TCH1516_ALE | 942,060 | C→G | 46.5% | intergenic (‑31/+218) | ptlE ← / ← mnhG1 | Neopentalenolactone D synthase/Na(+)/H(+) antiporter subunit G1 |
| RA | USA300TCH1516_ALE | 1,064,126 | G→C | 44.7% | Y121* (TAC→TAG) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,087,670 | A→T | 82.6% | L5I (TTA→ATA) | ykoE ← | Putative HMP/thiamine permease protein YkoE |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,274,212 | A→T | 58.8% | K205N (AAA→AAT) | codY → | GTP‑sensing transcriptional pleiotropic repressor CodY |
| RA | USA300TCH1516_ALE | 1,296,417 | C→T | 13.4% | A137V (GCG→GTG) | pnp → | Polyribonucleotide nucleotidyltransferase |
| RA | USA300TCH1516_ALE | 1,318,237 | T→A | 45.7% | F124Y (TTT→TAT) | miaB → | tRNA‑2‑methylthio‑N(6)‑dimethylallyladenosine synthase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA_2 ← | Cold shock protein CspA |
| RA | USA300TCH1516_ALE | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,530,723 | G→A | 58.5% | T184I (ACA→ATA) | bshA ← | N‑acetyl‑alpha‑D‑glucosaminyl L‑malate synthase |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,775,556 | G→A | 47.2% | P323L (CCT→CTT) | clpX ← | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 1,834,119 | G→T | 67.9% | intergenic (+68/‑46) | osmC → / → USA300HOU_RS09140 | Peroxiredoxin OsmC/Soluble hydrogenase 42 kDa subunit |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,027,561 | G→C | 49.8% | T129S (ACC→AGC) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,035,886 | T→C | 66.2% | intergenic (+386/‑3) | ftnA → / → polC_2 | Bacterial non‑heme ferritin/DNA polymerase III PolC‑type |
| RA | USA300TCH1516_ALE | 2,143,110 | G→A | 49.8% | V163V (GTG→GTA) | USA300HOU_RS10935 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,274,965 | G→C | 45.0% | E106D (GAG→GAC) | mtlR → | Transcriptional regulator MtlR |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,664,466 | G→A | 50.4% | A65T (GCG→ACG) | pitA_2 → | L‑methionine sulfoximine/L‑methionine sulfone acetyltransferase |
| RA | USA300TCH1516_ALE | 2,679,708 | G→A | 64.6% | W64* (TGG→TGA) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 25 (1.040) | 16 (0.970) +40 bp |
15/180 | NT | 46.2% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | 29 (1.210) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||