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 | annotation | gene | description |
| MC | CP000731 | 1 | Δ27,041 bp | 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 | 478,502 | C→A | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 584,121 | G→T | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 707,909 | A→T | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 973,213 | C→A | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,232,053 | A→T | D233V (GAT→GTT) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,257 | A→C | V78G (GTA→GGA) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | USA300TCH1516_ALE | 58811 | 58986 | 176 | 2 [1] | [1] 2 | USA300TCH1516_00049/USA300HOU_RS00245 | hypothetical protein/hypothetical protein |
| * | * | ÷ | USA300TCH1516_ALE | 1171580 | 1171700 | 121 | 2 [1] | [1] 2 | hly/USA300HOU_RS05830 | Alpha‑hemolysin/hypothetical protein |
| * | * | ÷ | USA300TCH1516_ALE | 1604567 | 1604652 | 86 | 2 [1] | [1] 2 | USA300HOU_RS07955/Int‑Tn_2 | hypothetical protein/Transposase from transposon Tn916 |
| * | * | ÷ | USA300TCH1516_ALE | 2055594 | 2055697 | 104 | 4 [1] | [1] 2 | purB/sspP | Adenylosuccinate lyase/Staphopain A |
| * | * | ÷ | USA300TCH1516_ALE | 2507017 | 2507091 | 75 | 2 [1] | [1] 2 | USA300HOU_RS12900/sarZ | hypothetical protein/HTH‑type transcriptional regulator SarZ |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 458102 = | NA (NA) | 3 (0.030) | 3/280 | 2.5 | NA | coding (712/1557 nt) | hsdM_1 | Type I restriction enzyme EcoKI M protein |
| ? | USA300TCH1516_ALE | 458161 = | NA (NA) | coding (771/1557 nt) | hsdM_1 | Type I restriction enzyme EcoKI M protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 23 (0.230) | 47 (0.650) +40 bp |
41/218 | 0.3 | 73.6% | 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 | = 513613 | NA (NA) | 122 (2.010) +57 bp |
57/184 | 0.1 | NA | intergenic (+1681/‑5082) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 513672 = | NA (NA) | intergenic (+1740/‑5023) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 514102 = | NA (NA) | 6 (0.060) | 5/284 | 2.2 | NA | intergenic (+2170/‑4593) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 514124 = | NA (NA) | intergenic (+2192/‑4571) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | = 514218 | NA (NA) | 4 (0.040) | 4/288 | 2.3 | NA | intergenic (+2286/‑4477) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 514270 | NA (NA) | intergenic (+2338/‑4425) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | = 515946 | NA (NA) | 3 (0.030) | 3/284 | 2.5 | NA | intergenic (+4014/‑2749) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 515981 | NA (NA) | intergenic (+4049/‑2714) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | = 517446 | NA (NA) | 16 (0.170) | 9/284 | 1.7 | NA | intergenic (+5514/‑1249) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 517450 | NA (NA) | intergenic (+5518/‑1245) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||