Null Allele For Snp Data Set

Question

[714]

Hi all,

What is a null allele in the context of SNPs? As I understand it, in microsatellites a null allele occurs when the marker does not amplify via PCR. I was wondering if the same applies for SNPs? Does it simply mean a loci with missing data (i.e. ?/?; or ?/A due to low coverage, poor amplification) or does it mean something else too?

Thanks

[Fabio Marroni]

Theoretically, it is possible that when dealing with SNPs you have a NULL allele. Imagine if you have a SNP (or an indel) in the region where the prime should anneal. You might want to read the introduction of the paper I link. http://www.g3journal.org/content/early/2013/05/22/g3.113.006643