Greetings and salutations,
I have somewhat simple question which I can not seem to get a consensus on based on literature. Long story short I have a whole bunch of whole exome sequencing data for cancer samples. I want to identify potential genes of interest in these samples, to do so I need a background mutation rate. My question is how does one calculate a simple background mutation rate (for now disregard differences in mutation rates between transversions, transitions, CpG islands etc). Is it simply the number of synonymous mutations / bp sequenced? Or does the number of non-synonymous mutations as well as location of synonymous mutations also come into calculating background mutation rate. Or am I way off?
Thank you in advance
-Dmitri
I have somewhat simple question which I can not seem to get a consensus on based on literature. Long story short I have a whole bunch of whole exome sequencing data for cancer samples. I want to identify potential genes of interest in these samples, to do so I need a background mutation rate. My question is how does one calculate a simple background mutation rate (for now disregard differences in mutation rates between transversions, transitions, CpG islands etc). Is it simply the number of synonymous mutations / bp sequenced? Or does the number of non-synonymous mutations as well as location of synonymous mutations also come into calculating background mutation rate. Or am I way off?
Thank you in advance
-Dmitri
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