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muTect has good performance across a wide range of MAF levels.
muTect has the best FDR performance of the other algorithms we tested over a wide range of MAF and depths.
Larger samples of genotypes expand the number of possible combinations of lines that would allow a particular minor allele count, and thus confine rarity disequilibrium to a smaller range of MAF.
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In the case that a wider range of MAFs are of interest, NWDs can be used.
We generated receiver-operating characteristic curves (ROCs) for a range of median read depth and a range of MAFs.
Simulations were also performed over a range of MAFs for the causal variant between 1 and 50%.
These results provide support that each of the methods is able to find valid associations in SNP data over a range of MAFs and effect sizes.
Z-tests were implemented within each allele frequency bin to detect significant shifts in the proportion of SNPs exhibiting that particular range of MAFs between empirical and resampled neutral distributions.
This variant is one of the most ethnically stratified, exhibiting a wide range of MAFs: from 2 5% in Western European populations to 60 70% in North-East Asia (40), and alcohol intake is strongly culturally-dependent (41).
> -wrap-foot> Given the large number of variants associated at this locus with a broad range of allele frequencies (MAF 2 40%), we tested for the presence of multiple statistically independent signals at the AMH locus.
Summary of the results from the single nucleotide polymorphism (SNP) genotyping and diversity analysis Listed are sample size, total number of polymorphic SNP loci, range of minor-allele frequencies (MAF), average MAF, and total highly polymorphic SNP loci.
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