Entering edit mode
8.0 years ago
sv91707
▴
10
Dear all,
Recently I came up with a task of Homozygosity mapping and a question came up in my mind. What makes a region homozygous ? I know its the region where markers/alleles are homozgous, but what percentage of them makes a region homozgous. For example, In sequence homology, say proteins, a minimum sequence identity is tend to be >40. Is there some kind of stat or criteria for homozygosity, or any other thing. Also, How do you define that particular region homozygous, like some score but what percentage of homozgous alleles makes that score out of total SNPs or any other polymorphic marker in that region.
Looking forward for answers.
A homozygous region would be 100% homozygous. The relevant metric, rather than identity, would be the length of the homozygous region, relative to the animal's normal het rate. For example, if the animal has a het rate of ~1/1000, then a 500bp homozygous would not be interesting, but a 20kbp homozygous region would be interesting. A apparent 200kb homozygous region would be very interesting and indicate a probable long deletion rather than true homozygousity.
What I got from that reply is that total number of heterozygous alleles/markers should be less than, lets say 5 percent of total markers in that region, for the region to be approx 100 percent homozygous ?
It depends on the reliability of your test. If your het-calling is 100% accurate, then a homozygous region would contain 0% heterozygous markers.