Gaps Size

Question

[ebgonzalezm]

What's the size of a gap in an alignment to be considered a deletion?

[Rm]

even one base...

Answer 1

[Pierre Lindenbaum]

One base: e.g: http://www.ncbi.nlm.nih.gov/pubmed/9621520 (not a ngs-related paper, but it shows that any deletion matters)

J Hum Genet. 1998;43(2):135-7. A one-base deletion (183delC) and a missense mutation (D276H) in the T-protein gene from a Japanese family with nonketotic hyperglycinemia.

[Niek De Klein]

why would it have to be ngs related?

Answer 2

[Geparada]

If you are aligning DNA-seq against a genome, all the gaps are candidates to be a deletion. But if you are aligning eukaryotic RNA-seq against a genome, gaps longer than 40 pb that have canonical boundaries (GT-AG, GC-AG or AT-AC) are introns. The smaller gaps are more likely to be a deletion than a intron, because the splicing machinery it's a very large RNA-protein complex that needs to fit on the splice junction sequences in order to process the intron.