plink1_assoc_outputs
Union of common association columns across .assoc, .assoc.fisher, .assoc.linear, .assoc.logistic, and .assoc.dosage; see per-extension specs in formats/plink_*.json.
Overview
| Field |
Value |
| Format key |
plink |
| Spec file |
formats/plink.json |
| Cite name |
PLINK 1.9 |
| Version |
PLINK 1.9 (doc revision 19 Aug 2025) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/1.9/formats |
| Citation |
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| Header row |
yes |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
BETA |
BETA |
— |
BP |
POS |
— |
CHISQ |
CHISQ |
— |
CHR |
CHR |
— |
F_A |
EAF_CASE |
— |
F_U |
EAF_CONTROL |
— |
FRQ |
EAF |
— |
FRQ_A |
EAF_CASE |
— |
FRQ_U |
EAF_CONTROL |
— |
INFO |
INFO |
— |
NMISS |
N |
— |
OR |
OR |
— |
P |
P |
— |
SE |
SE |
— |
SNP |
SNPID |
rsID |
STAT |
T |
— |
| ## Coverage |
|
|
9/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
yes |
EA, NEA |
— |
| Effect size |
yes |
BETA, OR |
HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
|
|