About This Database
LD_bin Data (Phase III)
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Data name
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LD_bin Data (Phase III) | ||||||||||||||||||||
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DOI
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10.18908/lsdba.nbdc00036-008 |
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Description of data contents
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Results of LD bin calculations for D3 (Phase III) data sets. Files are in GFF format, and contains two kinds of lines, that are distinguishable by column# 3. - LD_BIN line: SNPs in LD bin. tagSNPs and best tagSNPs (*) are marked. - LD_BIN_BOUNDARIES: Limit of LD bin *SNP that shows the highest mean r<sup>2</sup> among the SNPs in the bin | ||||||||||||||||||||
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Data file
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File name :
bin_3R80M5Zb36.gff.gz
File URL :
File size :
12.8MB
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Simple search URL
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Data acquisition method
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Genotype Data (Phase III) |
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Data analysis method
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Common SNPs (MAF > 5%) were selected, and LDs (r2 values) between every SNP pairs within 300 kb were calculated. LD bins were collected so that SNP pairs within the bin shows r2 >0.8, by the greedy method of Tagzilla, which is based on the principle similar to ldSELECT (Carson et al., AJHG 74, 106-120, 2004). tagSNP is the SNP that shows r2 >0.8 for all other members of the bin. Best tagSNP is the SNP that shows the highest mean r2 for all other members of the bin. |
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Number of data entries
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SNP: 565,646 entries
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