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Minor allele frequency

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Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

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MAF: Minor allele frequency. The online version contains supplementary material available at https://doi.. org/10.1186/s . Details of the model underlying loimpute, the software used to impute the low-pass sequencing data analysed in this study.. Comparison of imputation r 2 across allele frequency bins for the 1000 Genomes panel.. Comparison of imputation r 2 across allele frequency bins for the HRC panel..

Analysis of functional variants in mitochondrial DNA of Finnish athletes

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The rate of common nonsynonymous variation was higher in haplogroups J and K than that in the remaining haplogroups, but rare nonsynonymous variation was simi- lar suggesting that the difference is due to nonsynon- ymous haplogroup-associated variants with minor allele frequency >.

Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

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Imputation accuracy depends on several factors in- cluding the size and composition of the reference panel [3, 7], the minor allele frequency (MAF) of imputed vari- ants [8], and correct placement of variants on the refer- ence genome assembly . The effect of the target panel size, on the other hand, has been barely studied.

The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population

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To consider the population minor allele frequency of the C >. T substitution rate (Methods), and the tendency of the Af-weighted rate was consistent with the above results (Fig. In addition, the protein-coding exons in the TSS-coding CGIs and the intragenic-coding CGIs had higher mutation rates than those of the non-coding re- gions (p <. chi-squared test), which were in con- trast to the trend at the CpGs not in the CGIs. Next, we assessed the CpG mutation dynamics in the vicinity of CGIs.

Population genomics and morphological features underlying the adaptive evolution of the eastern honey bee (Apis cerana)

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The ratio of the minor allele frequency (MAF) to the polymorphic SNP (Pic) was cal- culated using a custom Perl script. The Fis, Fst, and Fit values of the SNP locus in 243 samples were statistically analyzed using Genepop software (version . The Mantel test of the Fst matrix and distance matrix was performed using the ade4 package in R [37].

Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium

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The percentage of the membership of each country in the three sub- populations is presented in Table 2.. 1 The distribution of the 36,720 SNPs across the 21 chromosomes in the 103-spring wheat panel. 2 The distribution of polymorphic information content (PIC) (a), gene diversity (b), percentage of heterozygosity (c), and minor allele frequency (d) for the 37,295 SNP markers in the 103-spring wheat panel.

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

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Furthermore, across all three breeds, the Bayes fac- tor of CNVs was not different between the CNVs whose called copy number matched the imputed copy number and the CNVs whose called and imputed copy number did not match. one of the selection criteria for SNPs to be included on a genotype panel is high minor allele frequency (MAF . Successful imputation of CNVs from SNP genotype data may re- quire the use of SNPs which have a MAF similar to the MAF of the CNVs to be imputed..

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

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Quality control was performed using pre-imputation parameters, including 50% original call rate, 2.5% minor allele frequency, and a test of Men- delian inconsistencies (parent-offspring trio opposing homozygotes) determined using 16 (50%) of the families.. þ Accession þ SiteTree þ error ð2Þ where Accession is the tree effect modelled as the additive genetic effect of the individual, assumed random ~ N (0,G σ 2 g.

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

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Furthermore, approximately 65% of the single nucleotide polymorphisms (SNPs) were highly variable with a minor allele frequency (MAF) >. The total length of ROH in CKA sheep, in the range of <. 0.5 Mb, was lowest, suggesting CKA sheep have higher genetic diversity (Fig. 1c) was nearly consistent with those from the ROH profile, in which the lowest genetic diversity was found in the OLA breed. The effective population sizes of the four breeds 1000 years before present were OLA sheep >.

Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

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SNP genotyping of the association mapping collection After quality control, the genotyping data comprised a total of 10,739 polymorphic SNPs with imputed missing data and a minor allele frequency (MAF) greater than 5%.. In addition, the map of the 10,739 SNPs used for GWAS showed an average number of 28 SNPs mapped at the same genetic position..

Comparative analyses of copy number variations between Bos taurus and Bos indicus

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Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome- wide association studies. Guidelines for the nomenclature of the human heat shock proteins. Crystal structure of the MuSK tyrosine kinase: insights into receptor autoregulation

Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

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Chromosome, Pos (bp) physical position of the allelic variant, MAF Minor allele frequency, r 2 R squared value of the model with the SNP. All SNPs were physically positioned in the Wm82.a2 version of the Glycine max genome.

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

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The minor allele frequency (MAF) of the top SNP was 0.12 across all samples, whereas 0.05 in cases and 0.26 in controls. The odds ra- tio (OR) of the top SNP suggests that the associated locus is protective in this breed. 1), based on pairwise linkage disequilibrium (LD) estimates (r 2 ≥ 0.8) of the top SNP to the rest of the SNPs on CFA11. Conditional analysis confirmed the in- dependence of the association signal (Fig.

Genome-wide association studies for yield component traits in a macadamia breeding population

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MAF, minor allele frequency of the marker. For TC, 16 of the 44 significant markers were non- redundant, suggesting that there may be 16 QTLs con- trolling this trait. Multiple regression suggested that all of the the markers significantly associated with NW may have detected the same or linked QTLs, with the most significant SNP (s2204) being the only non-redundant marker. The location of scaffolds in linkage groups (Nock et al.

Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean

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For all of the mutant sites that were fil- tered (31,812 SNP loci, with a minor allele frequency (MAF) less than 0.05 per loci before filtering, and 21,783 SNP loci after filtering, including homozygous mutation loci and heterozygous mutation loci), a total of 1198 SNP loci were identified to be associated with virulence. A total of 18 genes in the secondary metabolism library were pre- dicted as Nonribosomal peptides (NRPs).

Validation of a novel associative transcriptomics pipeline in Brassica oleracea: Identifying candidates for vernalisation response

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Population structure was generated using both relaxed (all markers with a minor allele frequency (MAF) >. Linear regression was performed using RPKM as a predictor value to predict a quantitative outcome of the trait value. Additional file 4: Analysis of the smaller SNP data set with the Bayesian clustering algorithms implemented in the program STRUCTURE, identified four population clusters..

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

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MAF minor allele frequency, R 2 phenotypic contribution, Chr chromosome, RDW root dry weight, RDW/SDW root per shoot dry weight, TRL total root length, SUA surface area, ARD average root diameter, ROV root volume, RBN root branching number. 4 Manhattan plot of all potential significant SNPs associated with each root-related trait at each specific stage (V1, V2, and V3). Table 7 Candidate genes associated with potential SNPs and functional annotations.

Population analysis of the Korean native duck using whole-genome sequencing data

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After filtering out SNPs using various criteria such as minor allele frequency, genotype rate and the Hardy- Table 1 SNP statistics of 15 duck breeds. Korean native duck (KD . a Ti/Tv ratio is the ratio of the number of transitions to the number of transversions and standard deviations are in parentheses. Weinberg equilibrium (see Methods), we obtained a total of 8,769,869 SNPs from 123 individuals of 15 duck breeds.

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

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respectively, although the frequency of the minor allele was >. 5% in the array-called genotypes for most (>.

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

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Average frequency of minor allele for the 66,750 SNP loci was 0.21, and the proportion of heterozygotes was 0.05. Results from the PCA were consistent with clustering based on a neighbor-joining (NJ) phylogenetic analysis for the Capsicum population (Fig. Genetic diversity. Inbreeding coefficient for the Capsicum population was 0.54. Expected nucleotide diversity (θ) for the whole Capsicum panel was 0.18. baccatum and C.chacoense complex (0.55) (Additional file 2, Table S1).