SNP List (Phase III)
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Data name
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SNP List (Phase III) | ||||||||||||||||||||||
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DOI
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10.18908/lsdba.nbdc00036-002 |
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Description of data contents
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A list of SNPs in D3 (Phase III). The data is essentially the same as those described in Kukita et al. (2010) paper, but contains additional samples (CHM010 and CHM035) because their data were judged to be acceptable with regard to genotypes, though they were excluded at QC steps in the previous report. LD bins were then determined. | ||||||||||||||||||||||
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Data file
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File name :
dhaplo_d3_snp_list.zip
File URL :
File size :
23.9MB
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Simple search URL
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http://togodb.biosciencedbc.jp/togodb/view/dhaplo_d3_snp_list#en | ||||||||||||||||||||||
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Data acquisition method
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Affymetrix SNP 6.0 |
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Data analysis method
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A hundred complete hydatidiform moles (CHMs) were genotyped using Affymetrix SNP Array 6.0, and mapped on the human reference genome sequence, NCBI Build 36. Low log2R calls, calls judged to be in deleted regions (determined by CNV analysis), and heterozygous calls were forced to no calls, as described in the Kukita paper. After QCs by sample call rate and SNP call rate, the final data for 87 CHMs (876K SNPs) was obtained. See "LD bin List" for the calculation of LD bins. |
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Number of data entries
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876,399 entries |
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