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Old 01-26-2011, 09:46 AM   #4
Location: cinci

Join Date: Apr 2010
Posts: 66

Referring to the cvs output results from the batch query I have a question and kind of request. The "dbSNP_Frequency" column values example 0.5 what does it represent? is it corresponding to minor allele frequency or average of some sort? Another question about "dbSNP_Frequency" and "1KG_Frequency" columns is that 0.5 frequency out of 1 sample (2n=2) may not be as significant as 0.5 out of 60 samples (2n=120) as the first one may be rare but second case it appears to be common snp. Is it possible to give count of samples this frequency is coming from. For example "0.5 (120)". the reason is I want to filter out >5% variants as common in at least 100 samples. Or can I safely use this frequency as such? Thank you

Last edited by husamia; 01-27-2011 at 03:31 AM.
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