This data set provides genotype calls for the Mapping 500K chip set on the 270 samples that are used in the International HapMap Project. The 270 samples are comprised of 30 CEPH trios, 30 Yoruban trios, 45 unrelated Han Chinese samples and 45 unrelated Japanese samples.

As of HapMap phase 2 (release 19) about 365,000 or 73% of the Affymetrix 500K SNPs have also been typed by the HapMap Project. This excludes Affymetrix genotype submissions to HapMap.

The data set is available in two forms, with genotypes called by two different algorithms:

500K_HapMap270_DM (zip, 118 MB)

Contains genotypes and confidence scores determined by DM, the algorithm in the Mapping 500K Array Set
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500K_HapMap270_BRLMM (zip, 508 MB)

Contains genotypes and confidence scores determined by BRLMM, an improved genotyping algorithm.
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When unzipped, each zip will expand into five files, a file of genotype calls for each of the Nsp and Sty arrays, a file of confidence scores for each of the Nsp and Sty arrays, and a file documenting the format of the information. To verify the integrity of the downloaded data, please use the md5 checksums below.

File

md5 checksum

500K_HapMap270_DM

103096fc6e999060ceba4de25b27b91e

500K_HapMap270_BRLMM

0b611e5d63ea09e05ac1986860c39ff4

Additional information about the GeneChip™ Human Mapping 500K Array Set can be found on the product page.