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Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
Allele frequency in   TGP
Sample 99.9%
AFR 100.0%
AMR 99.9%
EAS 99.5%
EUR 100.0%
SAS 100.0%
reference ← allele frequency → alternate
Age estimation summary Joint clock
Data source Mode Mean Median 95% confidence interval # pairs Quality score
 Genomes in TGP997.4988.6985.2760.9 – 1,229.55041.000
 in units of generations 
Age estimation profile Joint clock How to interpret this figure?

Click on pairwise TMRCA result to see the shared ancestry of the genome pair.

TMRCA filtering applies to the pairs shown.

Download this figure in PNG format
This feature is experimental! It is only provided to illustrate plausible variations in time scales. Note that pairwise TMRCA and allele age were estimated on the basis of shared haplotype segments that were previously inferred using a hidden Markov model (HMM), for which the default parameters were used. Any changes made here will only affect the scaling of TMRCA, but not allele age, which is displayed without change.
Coalescent rate prior:
Effective population size (Ne): (diploid)
Mutation rate (μ): ×10-8 per site per generation
Recombination rate (r): HapMap genetic map for Chromosome 2 was used; cannot be changed
Data shown in this figure can be downloaded from this page.
Allele age Time of the mutation event that gave rise to the focal allele; estimated from the distributions of pairwise TMRCA inferred for concordant and discordant pairs.
TMRCA Time to the most recent common ancestor; inferred from genetic information observed locally (around the focal genomic position) at the haplotype segment shared between a pair of genomes.
Concordant pair A pair of haplotypes (i.e. genomes) which both carry the focal allele. Concordant pairs are expected to share a most recent common ancestor more recently than the time of the focal mutation event.
Discordant pair A pair of haplotypes (i.e. genomes) where one carries the focal allele and the other does not. Discordant pairs are expected to share a most recent common ancestor further back in time than the time of the focal mutation event.