This track shows locations of the Single Nucleotide Polymorphisms on the Affymetrix 120K SNP Genotyping Array. The SNPs in this track include all of the markers from the array that have been successfully mapped against the current assembly.
The SNPs were selected from public domain databases or the Perlegen SNP database. Genotypes for these markers were generated at Affymetrix using GeneChip(r) DNA analysis technology.
During sample preparation, an enzyme is used to fragment the genomic DNA into smaller pieces. The restriction endonucleases HindIII and XbaI have been used to generate this data.
Genotypes are reported as pairs of basecalls representing the two observed alleles. Individual genotypes for which no call was made are labeled 'NC'. A minimum of 46 genotype calls in the set of 54 individuals are included for each SNP.
Allele Frequency for the 'A' allele is two times the number of 'AA' calls plus the number of 'AB' calls, divided by two times the total number of calls. Allele Frequency for the 'B' allele is two times the number of 'BB' calls plus the number of 'AB' calls, divided by two times the total number of calls. The Minimum Allele Frequency is the lesser of these two values. Heterozygosity is two times the product of the two allele frequencies.
Thanks to dbSnp at the NCBI for providing the public SNPs, and thanks to Perlegen Sciences, Inc. for providing additional SNPs from their database. Additional information about the Perlegen SNP discovery process can be found in Science 294: 1719-1723 (2001):
Blocks of Limited Haplotype Diversity Revealed by High-Resolution
Scanning of Human Chromosome 21
N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett, J. M. Doshi,
C. R. Hacker, C. R. Kautzer, D. H. Lee, C. Marjoribanks,
D. P. McDonough, B. T. N. Nguyen, M. C. Norris, J. B. Sheehan,
N. Shen, D. Stern, R. P. Stokowski, D. J. Thomas, M. O. Trulson,
K. R. Vyas, K. A. Frazer, S. P. A. Fodor, and D. R. Cox.
Thanks to Affymetrix, Inc. for developing the genotyping array and providing the genotype data for 54 individuals. For more details on this genotyping assay, please see the supplemental information on the Affymetrix 120K SNP product.
Please see the Terms and Conditions for the use of this data at the Affymetrix, Inc. site.