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 37.6% S194S (TCA→TCG USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 111,516 C→A 40.8% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 512,643 A→G 57.4% intergenic (+711/‑6052) recR → / → speA_2 Recombination protein RecR/Arginine decarboxylase
RA USA300TCH1516_ALE 638,335 A→G 8.3% V107A (GTC→GCC)  pdxK ← Pyridoxine kinase
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 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,028,124 G→A 72.5% P174L (CCG→CTG)  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 2,372,751 A→T 83.9% L342* (TTA→TAA)  pbuG ← Guanine/hypoxanthine permease PbuG
RA USA300TCH1516_ALE 2,462,758 G→A 48.4% A70T (GCA→ACA)  USA300HOU_RS12680 → Putative 3‑methyladenine DNA glycosylase
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 =25 (0.770)28 (1.250)
+40 bp
23/180 NT 61.9% 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
* ? USA300TCH1516_ALE 895785 =27 (0.830)8 (0.280) 8/226 NT 24.8% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 25 (0.890)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD
* ? USA300TCH1516_ALE 2085296 =29 (0.900)9 (0.310) 8/232 NT 22.8% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 35 (1.210)coding (1/825 nt) hlb_2 Phospholipase C
* ? USA300TCH1516_ALE = 208701525 (0.770)3 (0.100) 3/242 NT 11.3% intergenic (‑166/‑519) scn_3/chp Staphylococcal complement inhibitor/Chemotaxis inhibitory protein
?USA300TCH1516_ALE = 2087021 24 (0.800)intergenic (‑172/‑513) scn_3/chp Staphylococcal complement inhibitor/Chemotaxis inhibitory protein