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
RA CP000731 81 N→G intergenic (–/‑151)  / → repA –/replication protein A
JC CP000731 6,552 +28 bp intergenic (+1069/‑419) cadX → / → USA300HOU_pUSA300HOUMR0010 cadmium efflux regulator/MarR family transcriptional regulator
RA CP000731 25,669 (A)7→6 coding (322/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein
RA USA300TCH1516_ALE 127,420 G→T L411F (TTG→TTT lctP_1 → L‑lactate permease
RA USA300TCH1516_ALE 733,536 G→T S207I (AGT→ATT)  graR_1 → Response regulator protein GraR
RA USA300TCH1516_ALE 1,054,623 G→A intergenic (‑124/+404) sspA ← / ← patA_2 Glutamyl endopeptidase/Putative N‑acetyl‑LL‑diaminopimelate aminotransferase
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 2,010,363 C→T C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,018,582 T→A K113* (AAA→TAA)  mgt ← Monofunctional glycosyltransferase
RA USA300TCH1516_ALE 2,279,705 G→A A943V (GCA→GTA)  ebh_3 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 2,373,531 G→T A82E (GCG→GAG)  pbuG ← Guanine/hypoxanthine permease PbuG
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 2176699–2181157 2181157 1–4459 3 [2] [2] 3 ilvA/USA300TCH1516_02069 L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 895785 =28 (1.520)12 (0.750) 10/234 0.5 35.6% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 19 (1.180)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD
* ? USA300TCH1516_ALE 2085296 =15 (0.810)9 (0.550) 9/240 0.7 37.2% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 17 (1.030)coding (1/825 nt) hlb_2 Phospholipase C