breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
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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 |
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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 | 622,314 | C→A | S959R (AGC→AGA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
RA | USA300TCH1516_ALE | 632,405 | T→G | I177S (ATT→AGT) | proP → | Proline/betaine transporter |
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 |
RA | USA300TCH1516_ALE | 1,006,124 | A→T | S169R (AGT→AGA) | USA300HOU_RS04965 ← | hypothetical protein |
RA | USA300TCH1516_ALE | 1,058,293 | G→A | A1215V (GCA→GTA) | atl_1 ← | Bifunctional autolysin |
RA | USA300TCH1516_ALE | 1,232,465 | G→C | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
RA | USA300TCH1516_ALE | 1,329,645 | C→T | P265L (CCA→CTA) | glpD → | Aerobic glycerol‑3‑phosphate dehydrogenase |
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 | 1,646,189 | 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 | 1,797,772 | G→C | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
RA | USA300TCH1516_ALE | 1,834,119 | G→A | intergenic (+68/‑46) | osmC → / → USA300HOU_RS09140 | Peroxiredoxin OsmC/Soluble hydrogenase 42 kDa subunit |
RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
RA | USA300TCH1516_ALE | 2,143,110 | G→A | V163V (GTG→GTA) | USA300HOU_RS10935 → | hypothetical protein |
RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
RA | USA300TCH1516_ALE | 2,856,087 | T→A | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_012417 | 1 | 586 | 586 | NA [0] | [1] 2 | [USA300HOU_RS14890] | [USA300HOU_RS14890] |
* | * | ÷ | NC_012417 | 674 | 786 | 113 | 2 [1] | [1] 2 | USA300HOU_RS14890 | replication protein |
* | * | ÷ | NC_012417 | 928 | 1101 | 174 | 2 [1] | [1] 4 | [USA300HOU_RS14890]–[USA300HOU_RS15665] | [USA300HOU_RS14890],[USA300HOU_RS15665] |
* | * | ÷ | NC_012417 | 1537 | 1780 | 244 | 4 [1] | [0] 3 | USA300HOU_RS14895 | USA300HOU_RS14895 |
* | * | ÷ | NC_012417 | 2504 | 2619 | 116 | 3 [0] | [0] 2 | USA300HOU_RS14900 | hypothetical protein |
* | * | ÷ | NC_012417 | 2769 | 2809 | 41 | 3 [1] | [1] 3 | USA300HOU_RS14900/– | hypothetical protein/– |
* | * | ÷ | NC_012417 | 2959 | 3125 | 167 | 2 [0] | [0] NA | USA300HOU_RS14900/– | hypothetical protein/– |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | USA300TCH1516_ALE | 512620 = | 173 (1.020) | 129 (1.040) +40 bp |
56/216 | 0.4 | 50.6% | 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 |