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I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact.

I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20.

My primary question is: how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?

I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.

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2 Answers 2

up vote 9 down vote accepted

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and heterozygotes at this SNP-position.

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Yeah, its a human. That's a really great answer; I can't believe I didn't think of such an obvious explanation. –  Slavatron Aug 4 at 17:33
    
Just to ascertain this- check the quality scores (phred), sequencing lanes, replicates etc at the SNP region: to make sure that it is not an artifact. –  WYSIWYG Aug 5 at 17:08
    
@WYSIWYG: the probability of this being an artifact is negligible given the systematic nature of the phenomenon: it's not about two reads having one mismatch. –  har-wradim Aug 5 at 21:23
    
I totally agree.. If it is really half the reads sort of situation. However, it is always good to confirm that there are no other hidden patterns. –  WYSIWYG Aug 6 at 4:12

Also I don't know what kind of genetic input your given but if there is variation in origin ie some saliva some cheek skin then there could be a tissue based difference in the genome.

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If it's cancer good luck finding a consistent set of tissue. –  caseyr547 Aug 5 at 5:18

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