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What is the difference between a putative and potential SNP?

Posted: Mon Feb 18, 2013 8:25 pm
by dpaetkau
Students were going through the Finishing Checklist and came upon putative and potential SNPs. What is the difference?

Re: What is the difference between a putative and potential

Posted: Tue Feb 19, 2013 12:35 am
by wleung
In most cases, we cannot confirm that a single nucleotide polymorphism (SNP) is genuine without doing additional sequencing on a population. However, we can often distinguish strong SNP candidates from weaker ones based on the number of high quality reads that shared the same allele.

For strong SNP candidates, we would expect to see multiple high quality reads that contain each allele. Furthermore, we expect about half of the reads to contain one allele while the other half of the reads will contain the other allele.

In contrast, if there is only one (or a few reads) that contain the other allele, then we are less confident that it is a SNP. These reads might have been misplaced or the discrepancy could be caused by "growth difference". Hence we might not be able to definitively resolve the high quality discrepancy.

The strong candidates would be classified as "putative" SNPs while the weaker candidates would be classified as "potential" SNPs.