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These tables can be used to examine the genotypical outcome probabilities of the offspring of a single trait (allele), or when crossing multiple traits from the parents. The Punnett square is a visual representation of Mendelian inheritance , a fundamental concept in genetics discovered by Gregor Mendel . [ 10 ]
An odds ratio (OR) is a statistic that quantifies the strength of the association between two events, A and B. The odds ratio is defined as the ratio of the odds of event A taking place in the presence of B, and the odds of A in the absence of B. Due to symmetry, odds ratio reciprocally calculates the ratio of the odds of B occurring in the presence of A, and the odds of B in the absence of A.
It takes a combined log of odds ratio form, calculated from the contingency table of the variable set. The test inherits a chi-squared distribution with data-set adaptive degrees of freedom f, estimated from smaller bootstrapped samples of the data. The flexible and data-corrected probability distribution allows W-test to give relatively ...
In interval mapping, each locus is considered one at a time and the logarithm of the odds ratio is calculated for the model that the given locus is a true QTL. The odds ratio is related to the Pearson correlation coefficient between the phenotype and the marker genotype for each individual in the experimental cross. [18]
The information is often in the form of log odds of finding two specific character states aligned and depends on the assumed number of evolutionary changes or sequence dissimilarity between compared sequences.
After odds ratios and P-values have been calculated for all SNPs, a common approach is to create a Manhattan plot. In the context of GWA studies, this plot shows the negative logarithm of the P-value as a function of genomic location. Thus the SNPs with the most significant association stand out on the plot, usually as stacks of points because ...
Similarly, likelihoods are often transformed to the log scale, and the corresponding log-likelihood can be interpreted as the degree to which an event supports a statistical model. The log probability is widely used in implementations of computations with probability, and is studied as a concept in its own right in some applications of ...
In population genetics, the genotype frequency is the frequency or proportion (i.e., 0 < f < 1) of genotypes in a population. Although allele and genotype frequencies are related, it is important to clearly distinguish them.