DNA phasing affects heterozygous and homozygous SNPs differently:
Heterozygous SNPs:
These are positions where you have two different alleles (variants).
Before Phasing:
- You know you have A and G
- Unknown which came from which parent
- Represented as: AG or GA (unordered)
After Phasing:
- Maternal chromosome: A
- Paternal chromosome: G
- Clear parental assignment
Impact: Phasing is MOST useful for heterozygous SNPs because it resolves parental inheritance.
Homozygous SNPs:
These are positions where you have two identical alleles.
Before and After Phasing:
- Both chromosomes: A-A or G-G
- Phasing doesn't change anything
- Both alleles from same parent aren't distinguishable
- You inherited the same variant from both parents
Impact: Phasing has NO practical effect on homozygous SNPs since both copies are identical.
Why This Matters:
- Ancestry Analysis: Heterozygous SNPs reveal which parent contributed which ancestry
- DNA Matching: Helps identify which DNA segments match specific relatives
- Genetic Studies: Important for understanding compound heterozygosity
- Chromosome Mapping: Enables accurate chromosome painting
SNP Distribution:
In a typical human genome:
- ~3-4 million heterozygous SNPs (phasing helps here)
- ~1-2 million homozygous SNPs (phasing doesn't matter)