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 | 39,378 | C→A | 100% | D586Y (GAT→TAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 7.5% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 31.2% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 31.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 188,567 | A→T | 5.0% | D143V (GAT→GTT) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | USA300TCH1516_ALE | 221,865 | C→A | 7.6% | G470V (GGC→GTC) | ptsG_1 ← | PTS system glucose‑specific EIICBA component |
| RA | USA300TCH1516_ALE | 367,644 | G→T | 100% | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 423,247 | A→G | 100% | V112V (GTA→GTG) | USA300HOU_RS01970 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 454,656 | G→A | 100% | V119I (GTT→ATT) | tst_3 → | Toxic shock syndrome toxin‑1 |
| RA | USA300TCH1516_ALE | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 49.3% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 583,939 | G→A | 7.0% | intergenic (+23/‑249) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 638,614 | G→T | 100% | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| 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 | 911,610 | G→A | 100% | intergenic (‑221/‑107) | USA300HOU_RS04510 ← / → sufC | hypothetical protein/Vegetative protein 296 |
| RA | USA300TCH1516_ALE | 1,199,222 | C→A | 11.0% | F80L (TTC→TTA) | USA300HOU_RS05980 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| MC JC | USA300TCH1516_ALE | 1,302,967 | Δ4 bp | 100% | coding (325‑328/714 nt) | phnF → | putative transcriptional regulator PhnF |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,419,527 | G→T | 100% | P7T (CCT→ACT) | USA300HOU_RS07040 ← | hypothetical protein |
| 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 | 1,551,783 | A→G | 7.4% | S231P (TCA→CCA) | ebpS ← | Elastin‑binding protein EbpS |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,672,434 | C→T | 72.4% | A187T (GCA→ACA) | sigA ← | RNA polymerase sigma factor SigA |
| RA | USA300TCH1516_ALE | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,784,962 | C→T | 5.0% | G40D (GGC→GAC) | thrS ← | Threonine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 1,802,628 | A→T | 7.8% | K321M (AAG→ATG) | cycA_1 → | D‑serine/D‑alanine/glycine transporter |
| RA | USA300TCH1516_ALE | 1,809,898 | A→G | 6.7% | F91F (TTT→TTC) | accD ← | Acetyl‑coenzyme A carboxylase carboxyl transferase subunit beta |
| RA | USA300TCH1516_ALE | 1,944,670 | G→A | 100% | intergenic (‑251/‑713) | splA ← / → USA300HOU_RS09665 | Serine protease SplA/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,026,655 | C→T | 100% | E87K (GAA→AAA) | vraR ← | Response regulator protein VraR |
| RA | USA300TCH1516_ALE | 2,261,772 | T→C | 5.7% | V185V (GTA→GTG) | yhfK ← | putative sugar epimerase YhfK |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,325 | C→A | 100% | Q55H (CAG→CAT) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,386,119 | G→A | 62.5% | P114L (CCG→CTG) | USA300HOU_RS12250 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,502,141 | C→A | 100% | A222D (GCC→GAC) | melR_2 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,679,455 | Δ1 bp | 100% | intergenic (+327/‑62) | USA300HOU_RS13790 → / → ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,710,893 | Δ1 bp | 100% | coding (34/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
| 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 | 34173 = | 71 (1.140) | 5 (0.080) | 5/246 | NT | 7.1% | coding (462/480 nt) | rlmH | Ribosomal RNA large subunit methyltransferase H |
| ? | USA300TCH1516_ALE | = 57858 | 64 (1.080) | intergenic (+304/+613) | USA300HOU_RS00240/USA300TCH1516_00049 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 83 (1.340) | 47 (1.100) +40 bp |
34/178 | NT | 45.2% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 62 (1.000) | 4 (0.070) | 4/244 | NT | 5.0% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 93 (1.580) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 2001491 = | 11 (0.180) | 3 (0.050) | 3/244 | NT | 22.4% | intergenic (‑3219/+116) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala |
| ? | USA300TCH1516_ALE | 2179606 = | NA (NA) | intergenic (+3368/+1927) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly | |||||
| * | ? | USA300TCH1516_ALE | = 2674542 | 69 (1.110) | 6 (0.100) | 3/238 | NT | 8.2% | intergenic (‑54/+247) | glcB/ydaP | PTS system glucoside‑specific EIICBA component/Putative thiamine pyrophosphate‑containing protein YdaP |
| ? | USA300TCH1516_ALE | = 2674577 | 71 (1.240) | intergenic (‑89/+212) | glcB/ydaP | PTS system glucoside‑specific EIICBA component/Putative thiamine pyrophosphate‑containing protein YdaP | |||||
| * | ? | USA300TCH1516_ALE | = 2777745 | 41 (0.660) | 3 (0.050) | 3/244 | NT | 6.9% | coding (495/705 nt) | arcR_2 | HTH‑type transcriptional regulator ArcR |
| ? | USA300TCH1516_ALE | = 2777785 | 42 (0.720) | coding (455/705 nt) | arcR_2 | HTH‑type transcriptional regulator ArcR | |||||