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In addition, Hardy Weinberg equilibrium (HWE) and pairwise linkage disequilibrium (LD) were analyzed by Haploview 4.2 software.
Intra- and inter-locus LD were analyzed on nine markers flanking the Tvr1 gene.
Estimates did not change significantly when only those cases classified as definite LD were analyzed (Table 3).
For this reason, P. pastoris cells grown on glucose were harvested at the early stationary phase (26 h) and LD were analyzed.
Patterns of linkage disequilibrium (LD) were analyzed based on HapMap Phase II YRI for chromosome X (The International Hapmap Consortium 2005) and the 1000 Genome YRI for autosomal chromosomes (Durbin et al. 2010) via the LocusZoom software (Pruim et al. 2010).
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When linkage disequilibrium (LD) was analyzed for different human population cohorts, the prominence of low LD points (red colored on thermal scale) in the GE, US and JP cohorts in Figure 4A pointed to ongoing recombination events in these populations.
LD was analyzed with the squared correlation coefficient, r2, using Weir's method for estimating linkage disequilibrium from unphased diploid data [42]; R code was provided by S. Macdonald (U. Kansas).
Linkage disequilibrium (LD) was analyzed using CubeX software [ 19].
LD was analyzed and plotted using Haploview [ 32].
LD was analyzed within parents of the family cohorts and in the case-control cohort.
Linkage disequilibrium (LD) was analyzed using HaploView version 4.0 software (Broad Institute, Cambridge, MA, USA).
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