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After the signs of the structure factors were assigned by using a direct phasing procedure, potential maps were made in order to determine atomic positions.
We employed the same parameters as described for the phasing procedure in build 37, and included autosomal and chromosome X markers.
The method may help to avoid a laborious phasing procedure when the component or the complex of interest is not present in the crystal.
The validity of the MC procedure is based on properly matching the null simulations with the observed data with regard to pedigree structure, missing data structure and phasing procedure (Curtis and Sham, 2006).
Here, the phasing procedure may incorrectly infer that an allele transmitted by the recipient was instead transmitted by his/her partner; thus the potential NCO allele is not necessarily observed in the grandchildren.
Using a phasing procedure (see methods), we could assign deletion locus haplotypes to 177 ORs, which in some cases harbor more than one event on a given chromosome, and in others create compound heterozygosity for two deletion types.
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Second, AlphaImpute implements some simple pedigree-based phasing rules that interact with the other phasing procedures to eliminate much of the phasing errors.
After quality control, 34,912 SNPs for Landrace, 36,578 SNPs for Large White, and 38,116 SNPs for Pietrain of the initial 64,232 SNPs were kept for phasing procedures.
For the phasing procedures BEAGLE was faster, than SHAPEIT2 which required around 52 hours to phase BTA29 for the 242 available animals, whereas BEAGLE performed the same job in less than 3 hours.
This two-phase procedure continues until there are no more features arriving.
First, we develop a generic exact approach which can be considered as a three-phase procedure.
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