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Each setup of the concentrators or reflectors is evaluated by measuring the power output of the tested and the reference panels together throughout a day under the sun.
Sequencing using partial strands and limited markers, however, has its own limits, and its accuracy depends on the quality and number of the reference panels used for comparison.
Hence, we first evaluate the number of polymorphic sites in the reference panels selected.
Further study is warranted to compare the reference panels and related approaches exhaustively.
The magnitude of the divergence time affects the expected accuracies of the reference panels.
Aside from these modifications to the reference panels, we implemented the admixture HMM as described in Pool et al. (2012).
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The 221 filtered sequenced accessions passing quality control were used as the reference panel.
SNP positions in the 221 accessions of the reference panel were inserted by: dbmeister.py --db my_database.db --snp_pos my_snp_pos_file.
To construct the reference panel, we excluded structural variants and considered only SNPs with at least 90% information.
In order to use a much denser genetic map, we developed a Python script to infer the corresponding genetic positions of the 3,809,156 SNPs in the reference panel.
The reference panel used for imputation comprised of 90 known JPT + CHB haplotypes from the International HapMap Project data (Phase II Public Release #22 NCBI Build 36).
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