Question about finding both alleles from sequencing and homozygous or heterozygous

[Thedy Veliz]

Hello, I have been teaching myself some very basic genetics to be able to understand my genes. This is my first time using IGV. Here is the set up for my questions:

I am looking for my genotype for rs1800497. I looked this up in SNPedia and found that the location is  113,400,106.

The attached image shows that I have a G at this location - as shown by the arrow.

Here are my questions:

1) How do I find out what my other allele is? Is G reference or my variant?

2) How do I know if it is homozygous or heterozygote - perhaps another way of asking #1

3) What is "Refseq Genes" at the bottom of the report? There are letters every three nucleotide in dark and light blueish color.

Thank you for your help!

[Jade Celis]

Hi,

Reading your post, I am assuming you have data from your own DNA? It seems that you haven't uploaded any files yet. The 'refseq genes' at the bottom is the 'reference sequence' (GRCh38), this is a standardized genome sequence with only one allele at each position. So you can't see the other allele because there only is one.

You need to upload your files to IGV to be able to compare the DNA from your samples to the reference sequence.

Kind regards,

Jade

Op maandag 13 mei 2024 om 19:04:46 UTC+2 schreef Thedy Veliz: