how are alleles represented in the sequenced reads?

Question

[lait]

Suppose the following:

1. there exists gene X on chromosome Y. The wild type allele is 'A' and the recessive allele is 'a'
2. Allele 'a' is caused by a mutation in base T by substituting it with base A at position #12897
3. I sequenced a human genome which has the alleles 'A' and 'a' for gene X
4. In the reference genome, the allele present for gene X is 'A'

a- First, in the reference genome, do the two strands of the chromosomes exist ? so would we have two strands of chromosome Y and then have two alleles for gene X on each chromosome strand ? or is it just one strand?

b- so when mapping the reads to the reference genome, we would have (theoretically, and as an example) around 100 reads having nucleotide T at position #12897 and 100 reads having base A at position #12897, those represents the two alleles for gene X, is that correct ?

c- Speaking about SNPs, we consider a certain base to be a SNP if this base is different from the associated base in the same position in the reference genome. But what if this base in the sequenced genome is not a SNP, and the one in the reference genome should be the SNP ? is this possible? hope I was clear in this.

Answer 1

[JC]

a) the reference genome generally only shows one allele (the predominant or the one sequenced).

b) if the individual is heterozygous for the SNP and everything in sequencing is done correctly, yes, you expect 50%-50%

c) that's why we have several iterations over the human genome versions, the first time you have only the sequences "as sequenced", comparing with other individuals, you can define which positions are universal and shared and which are personal, then you patch the reference and release a new version.

I hope this helps with your homework.

more info: http://bfy.tw/Encx