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 freq annotation gene description
RA CP000731 81 N→G 100% intergenic (–/‑151)  / → repA –/replication protein A
JC CP000731 6,552 +28 bp 100% intergenic (+1069/‑419) cadX → / → USA300HOU_pUSA300HOUMR0010 cadmium efflux regulator/MarR family transcriptional regulator
RA CP000731 25,663 Δ1 bp 100% coding (316/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein
RA USA300TCH1516_ALE 111,512 A→G 30.8% S194S (TCA→TCG USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 111,516 C→A 30.1% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 512,643 A→G 30.2% intergenic (+711/‑6052) recR → / → speA_2 Recombination protein RecR/Arginine decarboxylase
RA USA300TCH1516_ALE 517,732 T→C 17.1% intergenic (+5800/‑963) recR → / → speA_2 Recombination protein RecR/Arginine decarboxylase
RA USA300TCH1516_ALE 1,084,916 C→T 16.1% V262I (GTT→ATT)  ykoC_1 ← Putative HMP/thiamine permease protein YkoC
RA USA300TCH1516_ALE 1,416,458 A→T 100% I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD
RA USA300TCH1516_ALE 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_RS07375 → hypothetical protein
RA USA300TCH1516_ALE 1,646,189 G→C 100% A155G (GCA→GGA)  ypdF ← Aminopeptidase YpdF
RA USA300TCH1516_ALE 1,744,607 T→C 100% D22G (GAT→GGT)  apt ← Adenine phosphoribosyltransferase
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,028,191 C→A 100% A152S (GCA→TCA)  USA300HOU_RS10230 ← hypothetical protein
RA USA300TCH1516_ALE 2,279,705 G→A 100% A943V (GCA→GTA)  ebh_3 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 2,393,232 A→G 19.7% S89P (TCA→CCA)  moeA ← Molybdopterin molybdenumtransferase
RA USA300TCH1516_ALE 2,532,298 A→T 100% 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 =48 (1.890)12 (0.730)
+45 bp
11/170 NT 31.5% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE = 517814 32 (1.260)intergenic (+5882/‑881) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
* ? USA300TCH1516_ALE 895785 =10 (0.390)6 (0.270) 6/226 NT 28.1% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 22 (1.000)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD
* ? USA300TCH1516_ALE 2085296 =26 (1.030)6 (0.270) 6/232 NT 23.0% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 17 (0.750)coding (1/825 nt) hlb_2 Phospholipase C