Quality control analysis of 1000 Genomes Project Omni2.5 genotypes
------------------------------------------------------------------

snpTable.txt is a tab-delimited text file.  There is one line for each of
the 2,458,861 markers in the vcf file obtained from 1000 Genomes.  The fields 
are as follows:

Chr = chromosome (1-22, 23 = X, 24 = Y, 26 = mitochondrion, 0 = unplaced)
SNP = marker name, as provided in the Broad dataset, or chr:bp if only present in the Sanger subset
cM = genetic position, based on the Rutgers map (http://compgen.rutgers.edu/rutgers_maps.shtml)
GRCh37 = physical position, based on hg19/GRCh37
A1 = less frequent allele in all samples
A2 = more frequent allele
CallRate = proportion of samples with non-missing genotypes
CallErr = number of heterozygous haploid genotypes, or non-missing calls for females on the Y chromosome, based on inferred sex
MendErr = number of observed errors in Mendelian transmission
MAF = minor allele frequency (frequency of A1)
Genotypes = counts of individuals with A1A1/A1A2/A2A2
P(HWE) = p-value from a test for Hardy-Weinberg equilibrium
FailedQC = did the SNP fail QC?  1 = yes, 0 = no

Note 1:  For markers not present in both the Broad and Sanger subsets, data
on CallRate, CallErr, MendErr, MAF, Genotypes, and P(HWE) are marked as NA.

Note2 :  A SNP failed QC if CallRate = NA, CallRate <0.97, CallErr >0, MAF = 0,
or MendErr >0.

Last modified 21 September 2016.