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Figure 3 | GigaScience

Figure 3

From: Second-generation PLINK: rising to the challenge of larger and richer datasets

Figure 3

Rapid classification of “recombination” variant pairs. This is a plot of 101 equally spaced D’ log-likelihoods for (rs58108140, rs140337953) in 1000 Genomes phase 1, used in Gabriel et al.’s method of identifying haplotype blocks. Whenever the upper end of the 90% confidence interval is smaller than 0.90 (i.e. the rightmost 11 likelihoods sum to less than 5% of the total), we have strong evidence for historical recombination between the two variants. After determining that L(D=x) has only one extreme value in [0, 1] and that it’s between 0.39 and 0.40, confirming L(D=0.90)<L(D=0.40)/220 is enough to finish classifying the variant pair (due to monotonicity: L(D=0.90)≥L(D=0.91)≥…≥L(D=1.00)); evaluation of the other 99 likelihoods is now skipped in this case. The dotted horizontal line is at L(D=0.40)/220.

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