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 661,360 T→A L168M (TTG→ATG)  USA300HOU_RS03170 → hypothetical protein
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 1,744,607 T→C D22G (GAT→GGT)  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 2,028,191 C→A A152S (GCA→TCA)  USA300HOU_RS10230 ← 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

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =24 (0.860)25 (1.330)
+45 bp
19/190 0.1 57.8% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE 2176447 = 30 (1.080)intergenic (+209/+5086) ilvA/USA300TCH1516_02069 L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly
* ? USA300TCH1516_ALE 895785 =22 (0.790)39 (1.600) 25/246 0.1 63.8% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 25 (1.030)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD
* ? USA300TCH1516_ALE 2085296 =18 (0.650)21 (0.840) 17/252 0.4 53.7% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 20 (0.800)coding (1/825 nt) hlb_2 Phospholipase C