Data detail | |
 Data name | SNP List (Phase II) |
| DOI | 10.18908/lsdba.nbdc00036-001 |
| Description of data contents | A list of SNPs in D2 (Phase II). SNP genotypes in D1 (Phase I, Perlegen 281K SNPs) and those determined using Affymetrix 500K Array for overlapping 74 CHM samples were merged and QC'ed. LD bins were then determined. |
| Data file | |
| Simple search URL | http://togodb.biosciencedbc.jp/togodb/view/dhaplo_d2_snp_list#en |
| Data acquisition method | Perlegen 281K arrays, Affymetrix 500K arrays |
| Data analysis method | The analyses by Perlegen 281K arrays are described in Kukita et al. (2005). The analyses by Affymetrix 500K are described in Higasa et al. (2009). Affymetrix markers were mapped to NCBI Build 35 (Higasa mapping was on Build 36), and merged with Perlegen data. The original Affymetrix data contained a small fraction (< 1%) of SNPs that were genotyped heterozygote. These typings were judged to be errors because the materials were presumed to be homozygotes. Thus, all heterozygous calls (in Affymetrix data) were forced to be no calls. Many of the heterozygous calls were also low S/N calls and frequently irreproducible when tested. See "LD bin List" for the calculation of LD bins. |
| Number of data entries | 581,235 entries |
