File name | Descriptions |
---|---|
GWASsummary_{TRAITNAME}_Japanese_SakaueKanai2020.auto.txt.gz | Summary results for autosomal variants |
GWASsummary_{TRAITNAME}_Japanese_SakaueKanai2020.chrX.txt.gz | Summary results for X-chromosomal variants |
We provide the output from SAIGE software.
Please also refer to the SAIGE website.
# | column name | Descriptions |
---|---|---|
1 | v | marker name (CHR:POS:REF:ALT) |
2 | CHR | chromosome |
3 | POS | position (hg19) |
4 | SNPID | rsID (if present) or equivalent ID |
5 | Allele1 | REF allele |
6 | Allele2 | ALT allele (This allele is the effect allele.) |
7 | AC_Allele2 | allele count of Allele2 (ALT) |
8 | AF_Allele2 | allele frequency of Allele2 (ALT) |
9 | imputationInfo | RSQ value in imputation |
10 | N | sample size |
11 | BETA | effect size of Allele2 |
12 | SE | standard error f BETA |
13 | Tstat | score statistic |
14 | p.value | P value with SPA (suddle point approximation) applied |
15 | p.value.NA | P value when SPA is not applied |
16 | Is.SPA.converge | whether SPA is converged or not |
17 | varT | estimated variance of score statistic with sample related incorporated |
18 | varTstar | variance of score statistic without sample related incorporated |
19 | AF.Cases | allele frequency of Allele2 in cases |
20 | AF.Controls | allele frequency of Allele2 in controls |
We provide the output from BOLT software.
Please also refer to the BOLT website.
# | column name | Descriptions |
---|---|---|
1 | v | marker name (CHR:POS:REF:ALT) |
2 | SNP | rsID (if present) or equivalent ID |
3 | CHR | chromosome |
4 | BP | position (hg19) |
5 | GENPOS | genetic position |
6 | ALLELE1 | the effect allele |
7 | ALLELE0 | the other allele |
8 | A1FREQ | the frequency of ALLELE1 |
9 | INFO | RSQ value in imputation |
10 | CHISQ_LINREG | chi-squared value in linear regression |
11 | P_LINREG | P value in linear regression |
12 | BETA | effect size from BOLT-LMM approximation to infinitesimal mixed model |
13 | SE | standard error of effect size |
14 | CHISQ_BOLT_LMM_INF | infinitesimal mixed model association test chi-squared value |
15 | P_BOLT_LMM_INF | infinitesimal mixed model association test P value |
If you use these summary statistics, please cite the following paper;
Sakaue S and Kanai M et al. A global atlas of genetic associations of 220 deep phenotypes. medRxiv 2020.