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PLINK currently supports following functionalities: data management; basic statistics (F ST, missing data, tests of Hardy–Weinberg equilibrium, inbreeding coefficient, etc.); Linkage disequilibrium (LD) calculation; Identity by descent (IBD) and identity by state (IBS) matrix calculation; population stratification, such as a Principal ...
The coefficient of inbreeding (COI) is a number measuring how inbred an individual is. Specifically, it is the probability that two alleles at any locus in an individual are identical by descent from a common ancestor of the two parents.
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals.
In population genetics, linkage disequilibrium (LD) is a measure of non-random association between segments of DNA at different positions on the chromosome in a given population based on a comparison between the frequency at which two alleles are detected together at the same loci versus the frequencies at which each allele is simply detected (alone or with the second allele) at that same loci.
F IT is the inbreeding coefficient of an individual (I) relative to the total (T) population, as above; F IS is the inbreeding coefficient of an individual (I) relative to the subpopulation (S), using the above for subpopulations and averaging them; and F ST is the effect of subpopulations (S) compared to the total population (T), and is ...
The coefficient of inbreeding, or the degree of inbreeding in an individual, is an estimate of the percent of homozygous alleles in the overall genome. [69] The more biologically related the parents are, the greater the coefficient of inbreeding, since their genomes have many similarities already.
Estimate the inbreeding coefficient from genome-wide SNPs; Estimate the variance explained by all the autosomal SNPs; Partition the genetic variance onto individual chromosomes; Estimate the genetic variance associated with the X-chromosome; Test the effect of dosage compensation on genetic variance on the X-chromosome;
The coefficient of relationship is a measure of the degree of consanguinity (or biological relationship) between two individuals. The term coefficient of relationship was defined by Sewall Wright in 1922, and was derived from his definition of the coefficient of inbreeding of 1921. The measure is most commonly used in genetics and genealogy.