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 | 39,378 | C→A | D586Y (GAT→TAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 367,644 | G→T | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 479,553 | G→A | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 638,614 | G→T | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| RA | USA300TCH1516_ALE | 707,879 | A→T | L11I (TTA→ATA) | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 790,778 | G→A | intergenic (+277/‑197) | kipA_1 → / → ltaS | KipI antagonist/Lipoteichoic acid synthase |
| MC JC | USA300TCH1516_ALE | 819,056 | Δ596 bp | [USA300HOU_RS04010] | [USA300HOU_RS04010] | |
| RA | USA300TCH1516_ALE | 1,064,126 | G→C | Y121* (TAC→TAG) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,238,307 | C→T | Q141* (CAA→TAA) | USA300HOU_RS06160 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,274,212 | A→T | K205N (AAA→AAT) | codY → | GTP‑sensing transcriptional pleiotropic repressor CodY |
| RA | USA300TCH1516_ALE | 1,318,237 | T→A | F124Y (TTT→TAT) | miaB → | tRNA‑2‑methylthio‑N(6)‑dimethylallyladenosine synthase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,007 | Δ1 bp | coding (34/201 nt) | cspA_2 ← | Cold shock protein CspA |
| RA | USA300TCH1516_ALE | 1,474,639 | C→G | A9129P (GCA→CCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,481,355 | G→T | A6890E (GCA→GAA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,607,132 | C→T | E275K (GAA→AAA) | frc ← | Formyl‑CoA:oxalate CoA‑transferase |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,454 | C→T | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,770,911 | T→A | S73C (AGT→TGT) | USA300HOU_RS08840 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 1,883,654 | C→T | G522D (GGT→GAT) | ebh_2 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,733 | (A)6→7 | coding (186/810 nt) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,143,110 | G→A | V163V (GTG→GTA) | USA300HOU_RS10935 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,274,965 | G→C | E106D (GAG→GAC) | mtlR → | Transcriptional regulator MtlR |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,315,088 | T→A | K61I (AAA→ATA) | ndhE ← | NAD(P)H‑quinone oxidoreductase subunit 4L, chloroplastic |
| RA | USA300TCH1516_ALE | 2,342,380 | A→C | L76V (TTG→GTG) | USA300HOU_RS11950 ← | putative hydrolase |
| RA | USA300TCH1516_ALE | 2,388,866 | A→G | intergenic (‑149/+542) | sarV ← / ← moaA | HTH‑type transcriptional regulator SarV/GTP 3',8‑cyclase |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,679,650 | G→A | C45Y (TGT→TAT) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,709,600 | (T)5→4 | coding (1327/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_012417 | 1 | 13 | 13 | NA [0] | [1] 2 | –/USA300HOU_RS14890 | –/replication protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 159 (1.260) | 123 (1.370) +40 bp |
75/196 | 0.0 | 52.1% | 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 | |||||