## SGVP genotype and allele frequencies ##

This directory contains datafiles with genotype and allele frequencies on all unique SNPs genotyped on the AffymetrixSNP6.0 and Illumina1M combined. 

CHS: 96 unrelated Chinese,
MAS: 89 unrelated Malays,
INS: 83 unrelated Asian Indians.

Data for the above populations are available, descriptors shown with three-letter abbreviations used in filenames and throughout the website.

Alleles are expressed in the forward (+) strand of the reference human genome (NCBI build 36 or UCSC hg18), in lexical order. 

Each one of the below directories contains the following datasets, arranged by chromosome and population. The following datasets are available:
    
QC+/ 
SNPs in this dataset are QC+ and polymorphic in at least one population panel. This excludes SNPs which are monomorphic across all 3 ethnic groups
 
QC+mono/    
SNPs in this dataset are QC+, including SNPs which are monomorphic across all 3 ethnic groups

-File formats:
Files of each type (genotype-freqs & allele-freqs) in all dirs have the same format and can be concatenated together if desired and used as big table, or users can download data for just the chromosome they are interested in.

genotype_freqs*.txt:
Col1: refSNP rs# identifer in dbSNP
Col2: chromosome that SNP maps to
Col3: chromosome position of SNP, in basepairs on reference sequence
Col4: strand of reference sequence that SNP maps to
Col5: version of reference sequence assembly
Col6: genotype center that produced the genotypes
Col7: protocol used for genotyping
Col8: assay used for genotyping
Col9: panel of individuals genotyped
Col10: QC-code, QC+ or QC+mono 
Col11: genotype of homozygote for reference allele
Col12: frequency of ref-allele homozygotes
Col13: number of ref-allele homozygotes observed
Col14: genotype of heterozygote 
Col15: frequency of heterozygotes
Col16: number of heterozygotes observed
Col17: genotype of homozygote for other allele
Col18: frequency of other-allele homozygotes
Col19: number of other-allele homozygotes observed
Col20: total number of genotypes observed

allele_freqs*.txt:
Col1: refSNP rs# identifer in dbSNP
Col2: chromosome that SNP maps to
Col3: chromosome position of SNP, in basepairs on reference sequence
Col4: strand of reference sequence that SNP maps to
Col5: version of reference sequence assembly
Col6: genotype center that produced the genotypes
Col7: protocol used for genotyping
Col8: assay used for genotyping
Col9: panel of individuals genotyped
Col10: QC-code, QC+ or QC+mono 
Col11: reference allele
Col12: frequency of ref-allele
Col13: number of ref-alleles observed
Col14: other allele
Col15: frequency of other allele
Col16: number of other alleles observed
Col17: total number of chromosomes observed