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Second, if the depth of coverage is increased, there is a greater likelihood of reads spanning both SNPs and revealing more underlying haplotypes.> -wrap-foot> *NA12878 has one block with 6 haplotypes.
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For blocks of linkage disequilibrium, we obtained ORs and 95% CIs for the underlying haplotypes under the assumption of an additive model (haplo.glm, minimum haplotype frequency 1%).
First, barring sequencing or mapping error, the number of observed haplotypes is less than or equal to the actual number of underlying haplotypes but is never greater.
Some patients had 2 or more underlying diseases or conditions.
Haplotype assembly has worked very well when the underlying haplotypes are long, such as those determined by sequencing a clonal source such as a cosmid or bacterial artificial chromosome (BAC) [ 14, 29].
The plot can accentuate LD by displaying specific geometrical shapes, and allowing for the underlying haplotype structure to be inferred without any haplotype-phasing algorithms.
Nevertheless, the textile plot allows for a deeper understanding of LD and the underlying haplotype structure among SNP genotypes.
However, because of the horizontalization criterion (see Methods for details), the textile plot can accentuate the underlying haplotype structure by displaying the diplotype configurations.
The direct presentation of the diplotype configurations in conjunction with such LD information allows for the simultaneous inference of the underlying haplotype structures in a single display.
Haploview 3.0 [ 45] was used to estimate and view the detailed blocks and their underlying haplotype structure.
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