About This Database
LD_bin Data (Phase II)
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Data name
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LD_bin Data (Phase II) | ||||||||||||||||||||
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DOI
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10.18908/lsdba.nbdc00036-007 |
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Description of data contents
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Results of LD bin calculations for D2 (Phase II) 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_2R80M5.gff.gz
File URL :
File size :
12.1MB
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Simple search URL
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Data acquisition method
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Genotype Data (Phase II) |
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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 ldSELECT (Carson et al., AJHG 74, 106-120, 2004) after the program was modified so that it can handle haploid data. 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: 541,686 entries
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