Exact(1)
In particular, for an individual i and a masked SNP j, we set the ancestry of the masked genotype g ij as the ancestry inferred in the most SNPs in a window of 10 un-masked SNPs centered on SNP j (five downstream and five upstream of SNPs j).
Similar(59)
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Although cultivars can be optimally clustered at the same value of K using the A- and D- genome SNP sets, the proportion of genetic ancestry of cultivars in these clusters was variable for different SNP sets, implying that the three wheat genomes have different degrees of genetic differentiation among breeding programs.
Although most of the data sets in our study define the deep ancestry of the phylogeny, they still shed some information to our interpretations of recent phenomena such as the current genetic diversity of the E haplogroup in an implication to the origin and spread of Afro-Asiatic languages and to the history of pastoralism.
To further assess the statistical confidence for these suspected instances of admixture, I performed a second clustering analysis, this time estimating the posterior probability that each individual had pure ancestry after first indicating the population of origin for each individual and setting the prior probability of pure ancestry to 0.95.
Second, I performed an additional round of admixture clustering after first indicating the population of origin for each individual and setting the prior probability of pure ancestry to 0.95.
A set of African ancestry DNA sequence variants comprising the E-1 haplotype, was significantly associated with ESKD.
The genetic ancestry of the sample set was examined by principal component analysis (PCA), Hopach clustering (van der Laan and Pollard 2002) and genetic distance Fst calculations (Supplementary Material 1, Supplementary Fig. 1 and 2, Supplementary Tables 2 and 3).
Theses adjustments were repeated with PC scores and the Northwest African ancestry estimates obtained from the full marker set and subsets of the markers ranking higher for ancestry informativeness.
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