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The criteria for searching for tSNPs were as follows: MAF (minor allele frequency) of CHB > 0.10, and a linkage disequilibrium value of r >0.8.
Furthermore, positions 106 and 237 were in linkage disequilibrium (D' value of 0.766) [ 26, 27]).
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The LD (linkage disequilibrium) values for the four pairs of SNPs and the probable haplotypes with their frequencies (Table 7) have been calculated.
The linkage disequilibrium D' value suggests only a negligible level of recombination in the population studied.
Sorting output of the linkage disequilibrium values between pairs of SNPs in ascending order by the position of SNP 1 or 2 produced linkages from the reference SNP in the upstream and downstream directions, respectively.
Linkage disequilibrium values between markers of lcyE and crtRB1 genes were low with R values ranging from 0.004 to 0.188.
Linkage disequilibrium values between sites of interest were evaluated by calculating the " D' " value associated with its Fisher and Chi-square statistical tests, using DnaSP v5 software [ 54].
Moreover, we have shown that, in our case, this correction mainly made it possible to eliminate a certain number of disequilibrium values between unlinked or very weak markers.
Because approximately 2.8 Mb separates these markers, a distance far in excess of typical linkage disequilibrium values in the Indian population [23], we conclude that these two SNPs are not independently linked to a separate single causative mutation.
A plot of the chromosome 1 linkage disequilibrium values, −log(p ) against R, showed that the most significant R values occurred for R > 0.8.
Linkage disequilibrium values are given by R. The haplotype blocks were estimated using the 'solid spine of LD' method, which defines haplotype blocks by the first and the last SNPs being in strong linkage disequilibrium with all intermediate markers.
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