Webb26 apr. 2024 · To ensure data quality, quality control (QC) was performed across the six goat populations by removing any SNPs with call rate <95%, MAF <0.05 and Hardy–Weinberg equilibrium (HWE) (p < 10 −5) using PLINK v. 1.07 . Moreover, samples with more than 10% missing genotypes were removed from the data set. WebbWe used PLINK 1.9 to conduct association tests and clumping procedures to identify asthma- and obesity-related SNPs. First, we identified asthma-associated SNPs from subset 1 (10,360 participants, 606,086 SNPs) by logistic regression models. BMI- and WHtR-associated SNPs were identified from subset 2 by linear regression models.

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Webb21 mars 2024 · VCF4.3官方文档 Variant Call Format，可以用来表示单核苷酸多态性（SNP）、插入缺失（InDel，也就是短片段的插入与缺失）、结构变异(SV: Structural Variant，也就是大片段的插入与缺失) 、拷贝数量变异（CNV：Copy Number Variant）【CNV：比如一个基因在染色体的一条染色单体上的数目为1，但是在染色体复制过程 ... Webbdeepvariant Link to section 'Introduction' of 'deepvariant' Introduction DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. csufresno football

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Webb28 mars 2024 · SNP loci (Supplemental Table 11), of which SNPs in the Chr05A2:49.644 − 50.146 Mb and Chr06A2:25.866 − 26.384 Mb regions are very strongly associated ( Figure 4B ). Webb17 feb. 2024 · SNP genotypes were clustered and scored using Illumina GenomeStudio v2.0, and were subject to quality control with the following parameters: SNP minor allele frequency (MAF) > 0.001, ID genotyping success >0.9, and SNP genotyping success >0.99. WebbPLINK will generate a number of standard summary statistics that are useful for quality control (e.g. missing genotype rate, minor allele frequency, Hardy-Weinberg equilibrium … csu fresno housing