Column |
Variable name |
Content |
Rang of variable |
Remark |
1 |
Population |
The population/group name |
CEU60, CHB45, JPT45, YRI60, Asian90, HapMap210, TWN367, Asian457, and Combination577 |
The number of samples (#samples) in a population/group is shown followed by the population/group name. |
2 |
Chr |
The chromosome index |
X = 1, 2, …, 23 |
1-22: autosomes, 23: X chromosome |
3 |
SNP_num |
The number of SNPs |
X = 1, 2, 3, …, #SNPs |
Affymetrix 100K: #SNPs = 116,204; |
4 |
Probe_set |
The probe sets of SNPs |
Nil |
|
5 |
Position |
The physical positions of SNPs |
X ≥ 0 |
|
6 |
Genotype |
The genotypes of SNPs |
AT, AC, AG, CT, CG, GT |
|
7 |
Location |
The gene location of SNPs |
INTRON, 3UTR, 5UTR, upstream, downstream, and CDS |
|
8 |
GCR |
The genotyping call rates of SNPs |
0 ≤ X ≤ 1 |
|
9 |
AF |
The allele frequencies of SNPs |
0 ≤ X ≤ 1 |
|
10 |
Heterozygosity |
The degree of locus heterozygosity of SNPs |
0 ≤ X ≤ 1 |
|
11 |
P_HWE |
P-value of HWE test w.o. adjusting multiple tests |
0 ≤ X ≤ 1 |
|
12 |
N_heterozygous |
The number of heterozygous individuals |
0 ≤ X ≤ #samples |
|
13 |
CPA(H) |
The arithmetic CPA |
X ≥ 0 |
Hoogendoorn et al (2000, HG) |
14 |
SE_CPA(H) |
The standard error of the arithmetic CPA estimate |
X ≥ 0 |
|
15 |
CPA(U) |
The unbiased CPA |
X ≥ 0 |
Yang et al (2005, Genetics) |
16 |
SE_CPA(U) |
The standard error of the unbiased CPA estimate |
X ≥ 0 |
|
17 |
CPA(G) |
The geometric CPA |
X ≥ 0 |
Yang et al (2005, Genetics) |
18 |
SE_CPA(G) |
The standard error of the geometric CPA estimate |
X ≥ 0 |
|