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 |
|
| RA | USA300TCH1516_ALE | 6,838 | A→G | 5.9% | E593G (GAA→GGA) | gyrB → | DNA gyrase subunit B |
| RA | USA300TCH1516_ALE | 39,672 | C→A | 100% | V488F (GTT→TTT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 32.2% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 28.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 238,030 | T→C | 5.7% | L11L (TTA→CTA) | gsiD_2 → | Glutathione transport system permease protein GsiD |
| RA | USA300TCH1516_ALE | 307,880 | T→C | 7.6% | L43P (CTG→CCG) | lytR_1 → | Sensory transduction protein LytR |
| RA | USA300TCH1516_ALE | 348,452 | A→G | 5.7% | E130G (GAA→GGA) | yezG_5 → | putative antitoxin YezG |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 100% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 56.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 597,770 | A→T | 100% | V168V (GTA→GTT) | tuf → | Elongation factor Tu |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 100% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,005,078 | T→C | 6.0% | I508T (ATT→ACT) | pepF1_1 → | Oligoendopeptidase F, plasmid |
| RA | USA300TCH1516_ALE | 1,063,849 | C→T | 100% | D214N (GAC→AAC) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,103,793 | G→T | 8.6% | A67S (GCG→TCG) | pdhB → | Pyruvate dehydrogenase E1 component subunit beta |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 100% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,232,148 | G→T | 100% | G18V (GGC→GTC) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_RS07505 | Chorismate synthase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,672,412 | G→A | 66.0% | A194V (GCA→GTA) | sigA ← | RNA polymerase sigma factor SigA |
| RA | USA300TCH1516_ALE | 1,689,552 | A→G | 13.5% | F105S (TTC→TCC) | dnaJ ← | Chaperone protein DnaJ |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,746,458 | T→C | 6.3% | E170G (GAA→GGA) | recJ ← | Single‑stranded‑DNA‑specific exonuclease RecJ |
| MC JC | USA300TCH1516_ALE | 1,747,374 | Δ3 bp | 100% | coding (2073‑2075/2280 nt) | USA300HOU_RS08710 ← | Heme uptake protein MmpL11 |
| RA | USA300TCH1516_ALE | 1,775,841 | T→C | 85.2% | H228R (CAT→CGT) | clpX ← | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | USA300TCH1516_ALE | 1,979,300 | G→T | 6.3% | A89D (GCT→GAT) | USA300HOU_RS09860 ← | 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 | 2,027,751 | C→G | 100% | V66L (GTA→CTA) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,038,244 | T→A | 7.2% | T39S (ACA→TCA) | USA300HOU_RS10295 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,050,741 | C→T | 6.1% | E518K (GAG→AAG) | pcrA ← | ATP‑dependent DNA helicase PcrA |
| RA | USA300TCH1516_ALE | 2,095,255 | T→A | 5.9% | K222M (AAG→ATG) | USA300HOU_RS10605 ← | hypothetical protein |
| 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 | 12.7% | Q55H (CAG→CAT) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | 100% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,358,585 | G→C | 10.2% | D111E (GAC→GAG) | rpoA_1 ← | DNA‑directed RNA polymerase subunit alpha |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,632,393 | C→T | 7.9% | intergenic (‑184/+498) | fnbA_1 ← / ← fnbA_2 | Fibronectin‑binding protein A/Fibronectin‑binding protein A |
| RA | USA300TCH1516_ALE | 2,709,906 | C→A | 46.9% | E341* (GAA→TAA) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,841,601 | C→T | 11.0% | D170N (GAC→AAC) | USA300HOU_RS14555 ← | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 34173 = | 73 (1.250) | 9 (0.160) | 5/248 | NT | 12.1% | coding (462/480 nt) | rlmH | Ribosomal RNA large subunit methyltransferase H |
| ? | USA300TCH1516_ALE | = 57858 | 61 (1.090) | intergenic (+304/+613) | USA300HOU_RS00240/USA300TCH1516_00049 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 34173 = | 73 (1.250) | 4 (0.070) | 3/254 | NT | 5.1% | coding (462/480 nt) | rlmH | Ribosomal RNA large subunit methyltransferase H |
| ? | USA300TCH1516_ALE | = 88831 | 77 (1.350) | intergenic (+204/‑561) | nusG_1/USA300TCH1516_00080 | Transcription termination/antitermination protein NusG/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 45 (0.770) | 35 (0.870) +40 bp |
23/180 | NT | 53.0% | 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 | = 2870578 | 55 (0.940) | 4 (0.070) | 4/248 | NT | 7.0% | intergenic (‑46/+21) | mnmG/mnmE | tRNA uridine 5‑carboxymethylaminomethyl modification enzyme MnmG/tRNA modification GTPase MnmE |
| ? | USA300TCH1516_ALE | = 2870582 | 54 (0.970) | intergenic (‑50/+17) | mnmG/mnmE | tRNA uridine 5‑carboxymethylaminomethyl modification enzyme MnmG/tRNA modification GTPase MnmE | |||||