4 results about "Genotype frequency" patented technology

The invention discloses an individual identification method and system based on whole genome single nucleotide polymorphism data, and relates to the technical field of forensic genetics, and the method specifically comprises the following steps: obtaining intersection SNP sites of a to-be-identified sample pair, and constructing an SNP site set with linkage balance; performing individual recognition capability evaluation on the linkage-balanced SNP site set based on the efficiency evaluation index to generate an optimal SNP site set; under the set mutual exclusion hypothesis, the probability value of each optimal SNP site is calculated based on the population genotype frequency and the prior typing error rate, and the total likelihood ratio is calculated based on the probability value of each optimal SNP site; a support hypothesis or hypothesis is selected based on a relationship between the total likelihood ratio and a preset threshold. The unavoidable typing errors in the whole genome sequencing data can be scientifically processed and explained by introducing the semi-continuous likelihood ratio calculation model integrating the typing error rate.

Embodiments of the present application provide a sample pollution detection method, device, system and related equipment, the method comprises: obtaining nucleic acid information of a sample; calculating the mutation genotype frequency value BAF of the sample at a preset site; wherein the preset site is multiple, and in a non-polluted sample, the proportion of homozygous sites in the preset site is greater than the first proportion; determining the homozygous site in the preset site according to the BAF of the preset site; calculating the proportion of the homozygous site in the preset site, if the proportion of the homozygous site is less than the first proportion, the sample is a contaminated sample. Embodiments of the present application can simply and directly judge whether the sample is contaminated.

The application provides a method for screening genetic lethal interval on the whole genome level of shellfish, and belongs to the technical field of shellfish breeding. The method obtains the genotype information of shellfish, locates ROH on the whole genome level, constructs the theoretical distribution of ROH, evaluates the actual distribution of ROH, defines the genetic lethal interval, and determines the genotype of the low survival rate individual by evaluating the genotype frequency and allele frequency distribution characteristics of the sites in the genetic lethal interval. The application can screen the genetic lethal interval on the whole genome level of shellfish, solves the problem that the survival and death of shellfish individuals cannot be converted into phenotype information suitable for traditional genetic analysis, and reveals the distribution characteristics and action mode of the genetic lethal interval on the whole genome level, thereby providing a theoretical basis for designing a shellfish breeding scheme, and providing a reliable standard for screening high-quality parent populations and high-quality breeding populations and improving breeding efficiency.

This invention discloses an individual identification method and system based on whole-genome single nucleotide polymorphism (SNP) data, belonging to the field of forensic genetics technology. The specific steps are as follows: obtaining the intersection SNP sites of the sample pairs to be identified, constructing a linkage-equilibrium SNP site set; evaluating the individual identification ability of the linkage-equilibrium SNP site set based on a power evaluation index, generating an optimal SNP site set; under the set mutual exclusion hypothesis, calculating the probability value of each optimal SNP site based on the population genotype frequency and the prior genotyping error rate, and calculating the total likelihood ratio based on the probability values ​​of each optimal SNP site; selecting a supporting hypothesis or hypothesis based on the relationship between the total likelihood ratio and a preset threshold. This invention, by introducing a semi-continuous likelihood ratio calculation model that integrates the genotyping error rate, can scientifically handle and explain the unavoidable genotyping errors in whole-genome sequencing data.