.assoc.fisher
Case/control allelic test with Fisher (or Fisher mid-p); same layout as .assoc but CHISQ is not written.
Overview
| Field |
Value |
| Format key |
plink_fisher |
| Spec file |
formats/plink_fisher.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#assoc |
| 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 order |
CHR, SNP, BP, A1, F_A, F_U, A2, P, OR, SE, L95, U95 |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
BP |
POS |
— |
C_A |
— |
— |
C_U |
— |
— |
CHISQ |
— |
— |
CHR |
CHR |
— |
F_A |
EAF_CASE |
— |
F_U |
EAF_CONTROL |
— |
L95 |
OR_95L |
— |
OR |
OR |
— |
P |
P |
— |
SE |
SE |
— |
SNP |
SNPID |
rsID |
U95 |
OR_95U |
— |
| ## Header descriptions |
|
|
| Column |
Description |
A1 |
Allele 1 (usually minor) |
A2 |
Allele 2 (usually major) |
BP |
Base-pair coordinate (1-based) |
C_A |
Allele 1 count among cases ('counts' modifier) |
C_U |
Allele 1 count among controls ('counts' modifier) |
CHR |
Chromosome code |
F_A |
Allele 1 frequency among cases |
F_U |
Allele 1 frequency among controls |
L95 |
Lower end of symmetric approx. CI for OR (--ci) |
OR |
odds(A1|case) / odds(A1|control) |
P |
Fisher (or mid-p) p-value |
SE |
Standard error of odds ratio estimate (--ci) |
SNP |
Variant identifier |
U95 |
Upper end of symmetric approx. CI for OR (--ci) |
| ## Coverage |
|
6/9 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 |
OR |
BETA, HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
no |
— |
N, N_CASE |
| Allele frequency |
no |
— |
EAF, MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|