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Mapping 500K HapMap Genotype Data Set

This dataset provides genotype calls for the Affymetrix 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 dataset 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
103096fc6e999060ceba4de25b27b91e
0b611e5d63ea09e05ac1986860c39ff4

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