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This is primarily due to redundancy in the genetic code, which translates similar codons into similar amino acids. Furthermore, mutating an amino acid to a residue with significantly different properties could affect the folding and/or activity of the protein.
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.
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]
In this case the odds ratio for allele T is A:B (meaning 'A to B', in standard odds terminology) divided by X:Y, which in mathematical notation is simply (A/B)/(X/Y). When the allele frequency in the case group is much higher than in the control group, the odds ratio is higher than 1, and vice versa for lower allele frequency.
In practice the odds ratio is commonly used for case-control studies, as the relative risk cannot be estimated. [1] In fact, the odds ratio has much more common use in statistics, since logistic regression, often associated with clinical trials, works with the log of the odds ratio, not relative risk. Because the (natural log of the) odds of a ...
In probability theory and computer science, a log probability is simply a logarithm of a probability. [1] The use of log probabilities means representing probabilities on a logarithmic scale ( − ∞ , 0 ] {\displaystyle (-\infty ,0]} , instead of the standard [ 0 , 1 ] {\displaystyle [0,1]} unit interval .
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For example, in a genetic association case-control study, such as Genome-wide association study, a point in a volcano plot represents a single-nucleotide polymorphism. Its x value can be the logarithm of the odds ratio and its y value can be -log 10 of the p value from a Chi-square test or a Chi-square test statistic. [4]