-- HapMap data release #14, December 2004, on NCBI B34 assembly, dbSNP b121 -- Summary of genotyped SNPs by chromosome: Genotyped SNPs Chrom CEU HCB JPT YRI --------------------------------------------- Chr1 69,587 55,651 55,626 54,688 Chr10 41,544 35,738 35,732 33,818 Chr11 41,936 26,119 26,116 24,957 Chr12 38,901 16,882 16,872 16,136 Chr13 31,053 25,843 25,827 26,575 Chr14 27,905 16,364 16,362 15,669 Chr15 25,369 15,659 15,660 14,919 Chr16 23,672 14,721 14,719 13,986 Chr17 23,340 14,959 14,959 14,298 Chr18 37,101 1,064 1,064 1,068 Chr19 16,337 10,088 10,087 9,625 Chr2 82,011 68,480 68,491 68,514 Chr20 16,970 10,075 10,066 11,316 Chr21 18,272 0 0 0 Chr22 17,561 6 6 1,242 Chr3 59,758 1,702 1,702 17,385 Chr4 56,243 18,048 18,050 18,067 Chr5 54,879 33,286 33,286 31,763 Chr6 58,220 40,244 40,245 45,341 Chr7 43,554 6,454 6,452 6,616 Chr8 66,833 746 746 5,991 Chr9 53,154 538 538 547 ChrX 52,528 1 1 0 --------------------------------------------- Total 956,730 412,669 412,608 432,523 New or changed in recent releases: -As of Dec 10th, it is no longer necessary to sign a clickwrap agreement in order to access HapMap genotype data. Users therefore no longer have to log on to hapmap.org to dump genotypes from GBrowse. Users can now also retrieve individual genotype data in bulk via anonymous FTP, previously not possible. -Raw LD-data now available via both a new GBrowse dumper plugin and for bulk-download (http://www.hapmap.org/downloads/ld_data/). This is the same dataset we use for generating the pairwise LD-plot in GBrowse. -Data for all 4x populations available -Small change in file format: new column 'qc_code'. Does not interfere with Haploview data import. -reference/other allele notation in frequency files, replaces major/minor notation -Bad sample: the plate with Japanese and Chinese samples turned out to have a bad well, so the unreliable genotypes from sample NA18996 were discarded from release data dumps. Therefore genotypes are available for only 44 samples from the JPT population, instead of the planned 45. This sample may be replaced by another for phase II of the project, in which case all SNPs done up to that point in time will simply be missing data for the new sample. The HapMap database is updated monthly with data submitted to the DCC by centers funded by agencies in the UK, Japan, US, China and Canada. New data are submitted to NCBI's dbSNP database within days and should become available also at http://www.ncbi.nih.gov/SNP/ soon thereafter, once NCBI has incorporated this submission into the next build of dbSNP. --------------------------------------- info@hapmap.org