Identity by Descent Calculator

Identity by Descent (IBD) vs Identity by State (IBS)

Two individuals share DNA segments that are either identical by descent (IBD) or identical by state (IBS). Understanding this distinction is fundamental to genetics, relatedness testing, and population genomics.

Identity by Descent (IBD)

Two DNA segments are IBD if they are inherited from a recent common ancestor through traceable genealogy. IBD segments reflect true genetic relatedness and are used to:

• Calculate kinship coefficients: The probability two alleles are IBD
• Detect relatives: Long IBD segments indicate close relationships
• Phase haplotypes: IBD segments help reconstruct chromosome inheritance
• Map disease genes: Affected relatives share IBD at causal loci

Identity by State (IBS)

Two DNA segments are IBS if they have the same alleles, regardless of whether they share a recent common ancestor. IBS includes both IBD segments and segments that happen to match by chance due to:

• Common alleles: Frequent variants appear identical without being IBD
• Ancient shared ancestry: All humans share ancestors, but distant IBD is undetectable
• Recurrent mutation: Same mutation arising independently (rare)

Kinship Coefficient

The kinship coefficient (φ) is the probability that two randomly sampled alleles, one from each individual at the same locus, are IBD. Key relationships:

• Full siblings: φ = 1/4 (share 0, 1, or 2 alleles IBD with probabilities 1/4, 1/2, 1/4)
• Half siblings: φ = 1/8 (share 0 or 1 alleles IBD with probabilities 1/2, 1/2)
• First cousins: φ = 1/16
• Parent-child: φ = 1/4 (always share exactly 1 allele IBD)
• Grandparent-grandchild: φ = 1/8

Detecting IBD Segments

In practice, IBD segments are inferred from genetic data by looking for long stretches of matching genotypes. The length of IBD segments depends on the number of meioses separating two individuals:

• Recent relatives: Long IBD segments (>5 cM) that survived recombination
• Distant relatives: Short IBD segments, harder to distinguish from IBS
• Recombination breaks IBD: Each meiosis introduces ~1 crossover per 100 cM

Applications

• Relatedness testing: Paternity tests, forensics, genealogy (23andMe, AncestryDNA)
• Genetic mapping: Linkage analysis uses IBD sharing among affected relatives
• Population genetics: IBD patterns reveal demographic history and migration
• Phasing: IBD helps infer which alleles are on the same chromosome
• Imputation: IBD segments can fill in missing genotypes

Simulating Meiosis and Recombination

This toy simulates the inheritance of chromosomes through a pedigree, modeling meiotic recombination that breaks and reshuffles ancestral chromosome segments. Each colored segment represents DNA inherited from a specific grandparent or great-grandparent. By comparing the genomes of two relatives, we can identify IBD segments and calculate the kinship coefficient.