Table 1.
Sources for SNPs Used To Build the Map
|
No. of SNPs in |
|||
| Sourcea | EntireDatabase | ValidatedMap of3,011 | ReducedMap of2,154 |
| TaqMan Assays-On-Demand SNP Genotyping Products database (De La Vega et al. 2002) | 177,781 | 1,913 | 1,316 |
| The SNP Consortium Allele Frequency Project (SNP Consortium Web site) | 54,824 | 759 | 592 |
| Applera Genomics Initiative exon resequencing database (Adams et al. 2002)b | 266,135 | 304 | 219 |
| Previously identified as informative for admixture analysis (Parra et al. 1998) | 18 | 14 | 13 |
| SNPs culled by D.R. from random published sources (especially Reich et al. 2003) and unpublished data | 1,348 | 14 | 9 |
| SeattleSNPs discovered by resequencing genes (UW-FHCRC Variation Discovery Resource Web site) | 6,305 |
7 |
5 |
| Totalb | ∼450,000 | 3,011 | 2,154 |
a
Many SNPs had allele frequency information submitted from multiple sources. To create a nonredundant entry, we included frequency data only from the source in which the most samples were genotyped.
b
Only 10,530 SNPs from the Applera gene resequencing database, those with SIC >0.1, were in the actual list from which SNPs were selected. This meant that the total number of SNPs in the list we analyzed was 250,806; however, the effective number used for choosing differentiated markers was thus larger, ∼450,000.