The most commonly occurring haplotype was APD02 (found in 79% of individuals), which was found in all populations, except KUJ and WAD, in varying frequencies.
The algorithm used in THESIAS takes the most commonly observed haplotype in the population under investigation as the reference category and expresses the risk associated with the presence of each one of the other haplotypes as odds ratios (ORs) with 95% confidence intervals (CI) [(ORs (95% CI)].
The most commonly observed haplotype was that matching AB094593 ('haplotype 1'), and this was amplified from all onion populations surveyed.
However, in Tanzania, the microsatellite haplotype most commonly associated with SGEGA (haplotype 18 [131–104–125/4925/49 samples) was not identical to that most commonly associated with SGEAA (haplotype 11 [131–104–107]), because only 2 SGEAA samples were haplotype 18.
The AMY2 copy number-variant haplotypes most commonly found in European individuals are the duplication of AMY2A and AMY2B and the deletion of AMY2A.
The haplotypes being assembled may be derived from heterogeneous data sources but haplotype assembly is most commonly based on a set of molecular haplotypes [ 21- 23], so we will discuss this prior to the discussion of genetic and population-inferred haplotypes.
Additionally, the CCR5 haplotype most commonly found in African Pygmies is associated with delayed HIV-1 disease progression [ 66].
Susceptibility to RA is strongly associated with the expression of specific HLA class II alleles, and DRB1*0401 is the haplotype most commonly expressed in patients with RA [ 1, 2].
With detection of association in mind, we compared MATILDE and the most commonly used methods for haplotype block partitioning with respect to their ability to capture truly associated SNPs, rather than on boundary or membership agreement as in previous comparisons [ 18- 20].
In support of this notion, the B-region haplotype found associated with C11, B6, is also the one most commonly associated with C3; conversely 96% of C10 haplotypes are associated with B region haplotypes other than B6 (68% with B2; File S2).
