国际人类基因组单体型图计划   首页 | 关于本计划 | 数据 | 出版物 | Tutorial

可获得《HapMap数据的可靠使用和发表的指导》

图形化数据浏览

窗体顶端

使用通用基因组浏览器查看HapMap数据中有关基因组的信息，以及检索特定基因组区域的基因型及其频率。可直接链接到染色体

窗体底端

数据打包下载

以下目录包括了本项目的已公开数据（更多信息请参考 HapMap 数据访问政策 ）。每个数据的细节可以在各相应目录的“READMEs”中找到：

• 批量数据
• 基因型数据 ：递交到数据协调中心（DCC）的单个基因分型数据（新用户需要先 注册）
• 连锁不平衡数据 ：使用D'、LOD、R² 对最新的基因分型数据进行连锁不平衡分析。
• phase数据：由第16次公布的数据（即第一阶段数据集）经软件PHASE运算产生
• SNPs 分类 ：根据若干标准（详见“ 如何挑选 SNPs ”）挑选出来优先进行分型的dbSNP库中的参考SNP组群。每条染色体上的SNP数目及更详细内容在名为“00README”的文件中。
• 频率：递交到数据协调中心的等位位点和基因型频率数据汇总。这些数据也已递交至 dbSNP 库，可在新版的dbSNP中检索到。
• 重组率和重组热点：通过基因分型数据计算的重组率和重组热点
• SNP 分析实验 ：递交到数据协调中心的详细实验内容。包括每个 SNP分型平台所有的 PCR引物序列，延伸探针等。


• 软件
• 通用基因组浏览器：基因组浏览器的配置文件、GFF文件、插件和其他用于本地安装基因组浏览器的文件的完全集，带有HapMap基因分型数据和等位基因频率。


• 文件
• 实验方案：包含项目中涉及的各种实验设计、基因分型方案等
• 样本／个体 ：本项目所使用的样本及提供该样本的个体信息。 （详情见“ 项目介绍 ：人群及样本”）。
• XML文档：HapMap项目使用的XML格式的文件。

ENCODE regions

For more information about the ENCODE Project see HapMap ENCODE Page

 

Population descriptors:    
   YRI     : Yoruba in Ibadan, Nigeria  
   JPT+CHB : Japanese in Tokyo, Japan + Han Chinese in Beijing, China (combined on one plate)
   CEU     : CEPH (Utah residents with ancestry from northern and western Europe)

Generated Fri Apr 13 13:44:05 EDT 2007

公布说明

 -HapMap data release #23a, March 2008, on NCBI B36 assembly, dbSNP b126 --

This release contains genotypes and frequencies from the HapMap project, and
includes all data from phases I+II of the project. In addition, it contains 
commercially available arrays, including the Affymetrix 6.0, 100k, 500k and 
nsSNP products, Illumina Infinium 100k and 300k genotyping arrays. For 
more details on those, please see release notes for previous HapMap releases.

Mapping errors for merged SNPs that were detected in rel23 have now been corrected 
by using BLAT software. Change in position affected 1,708 SNPs in CEU, 
2,636 in JPT+CHB, and 4,669 in YRI. Complete lists of these SNPs can be found in:

http://ftp.hapmap.org/genotypes/2008-03/rs_strand/unfiltered/Mapping_error_*_r23a.txt

Additional inconsistencies that were detected and fixed for this release are grouped 
under the following categories:

- 2,990 SNPs with multiple alleles were removed from the QC+ filtered sets. For a
complete list of SNPs and featured allele (dbSNP b126), see 
Multiple_allele_errorlist_r23a.txt in the above ftp directory.

- 232 SNPs with strand orientation inconsistencies were removed from the QC+
filtered sets. For a complete list, see strand_flipped_error.txt in the above ftp 
directory.

- 39 SNP pairs with identical positions in dbSNP b126. These fall into special 
categories and may have been removed from the QC+ filtered sets as explained
below. For a complete list, see special_redundancies_QC+_r23a.txt in the above 
ftp directory. 

NOT REMOVED:
24 SNP pairs later merged into a single refSNP cluster (or rsid) in dbSNP b128
7 SNP pairs not yet merged into a single rsid as of dbSNP b128

REMOVED:
8 SNP pairs inconsitently mapped (ie, one SNP maps to chrN_random)
4 SNP pairs with inconsistent allele entries (ie, one SNP with multiple alleles)

- 108 SNPs on chrX, chrY or chrMT failed HapMap QC criteria implemented using PLINK 
software. These SNPs were kept in the current release but will be removed from the 
QC+ filtered sets in future HapMap releases. For a complete list of SNPs, see 
PLINK_errors_chrX_chrY_chrMT.txt in the above ftp directory. 
HapMap 'QC-' fail flags used in this list:

p =>  passrate < 80%
d =>  >1 duplicate discrepancy
h =>  Hardy-Weinberg p-value < 0.001 (calculated seperately for Jap & Chi)
m =>  >1 Mendel inconsistencies
s =>  fail-flagged by submitter (but only if gt-set didn't fail any of the DCC-imposed thresholds above)
x =>  >= 1 heterozygous haplotype (male for chrX; either sex for chrMT)
y =>  >= 1 female genotype present on chrY


Genotyped SNPs (non-redundant set):

Chrom       CEU   JPT+CHB   YRI   
---------------------------------------------
chr1     307,691  311,854  305,929
chr10    209,342  211,862  204,146
chr11    204,228  205,538  195,110
chr12    191,979  193,071  187,294
chr13    155,905  158,406  152,674
chr14    123,071  123,764  118,518
chr15    106,814  107,363  102,431
chr16    109,692  109,734  104,530
chr17     89,701   89,576   85,541
chr18    119,118  120,025  115,768
chr19     56,607   56,687   53,766
chr2     326,231  327,180  318,602
chr20    119,921  119,989  115,921
chr21     50,165   51,900   49,154
chr22     54,786   56,716   54,840
chr3     255,391  255,618  250,155
chr4     244,849  245,102  238,922
chr5     247,632  248,154  242,186
chr6     268,348  272,814  265,955
chr7     213,023  213,891  208,708
chr8     213,095  216,811  212,014
chr9     181,445  183,433  180,147
chrMT        216      209      215
chrX     118,086  118,740  117,313
chrY         672      667      668
---------------------------------------------
Total    3,968,008  3,999,104  3,880,507

--------------------------------------- 
help@hapmap.org

关于 DCC

HapMap数据协调中心负责协调（DCC）和管理本项目的数据传递、存储，发放及对外公布。同时负责基因分型数据库和本网页的管理维护。DCC由 冷泉港实验室的Lincoln Stein小组(Lincoln Stein's group)运作。

最后更新： : index.html.zh,v 1.12 2005/09/29 20:17:47 krishnan Exp