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Old 03-27-2014, 10:38 PM   #1
bongbimit
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Default different between snp and point mutation in ngs data set

Hi all,
I 'm confusing about this 2 terms, i already know that in population if frequency >1% the alternative base is called snp and if <1% it called point mutation, but if i sequencing a blood sample and i have a reference genome to align my ngs dataset, how do i know the variant call from software ( e.g samtool ) is snp or point mutation.

Thanks all in advance.
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Old 03-28-2014, 01:29 AM   #2
dpryan
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You can't magically determine prevalence without sequencing a LOT of people and directly measuring its frequency.
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Old 03-28-2014, 01:44 AM   #3
rhinoceros
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The point mutation concept also includes indels, whereas SNPs are strictly substitutions. Hence, SNPs are a subtype of point mutations. The 1% SNP/point mutation divide isn't valid. A SNP is a SNP, no matter its frequency. A common SNP is a SNP that has ≥ 1% frequency..

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The HapMap project focuses only on common SNPs, those where each allele occurs in at least 1% of the population.
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