What does DNA phasing do to heterozygous and homozygous SNPs?

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)