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For the NRY data, cross-population comparisons were based either on UEP-defined haplogroups or on higher resolution haplotypes defined by a subset of 7 STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) common to all samples assembled in a database of about 5072 haplotypes from 72 populations (see Additional file 5).
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The structures of KIR haplotypes defined here prove this hypothesis to be true.
As these implausible results were likely to be due to the high similarity of haplogroup frequency profiles of West and West-Central Africa, both dominated by the E3a-M2 haplogroup, we performed a higher resolution analysis using the frequencies of haplotypes defined by a common set of 7 STR loci (see Additional file 5).
The potential value of haplotypes defined by several single nucleotide polymorphisms has attracted recent interest.
Six haplotypes, defined by six variable sites, were found.
f* - Number of haplotypes defined by the mutation.
rh is a measure of correlation between haplotypes defined by all SNPs and haplotypes defined by the selected htSNPs.
The haplo.glm function estimates haplotype frequencies with the EM algorithm and calculates for each haplotype linear regression coefficient and p-value, comparing each haplotype to a base haplotype, defined as the most common haplotype.
The G-A haplotype defined by SNP-420 and SNP-358 conferred the highest plasma resistin.
Haplotype analysis revealed a higher representation of the MIF haplotype defined by -173*C/-794 CATT5 (C5) in AOSD patients (P = 0.001).
Many haplotypes were defined common haplotypes because they were shared by at least two animal species in the study.
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