.assoc.dosage
Dosage association from --dosage. CHR/BP require --map. 'case-control-freqs' replaces FRQ with FRQ_A and FRQ_U.
Overview
| Field |
Value |
| Format key |
plink_dosage |
| Spec file |
formats/plink_dosage.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_dosage |
| 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, A2, FRQ, FRQ_A, FRQ_U, INFO, BETA, OR, SE, P |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
BETA |
BETA |
— |
BP |
POS |
— |
CHR |
CHR |
— |
FRQ |
EAF |
— |
FRQ_A |
EAF_CASE |
— |
FRQ_U |
EAF_CONTROL |
— |
INFO |
INFO |
— |
OR |
OR |
— |
P |
P |
— |
SE |
SE |
— |
SNP |
SNPID |
rsID |
| ## Header descriptions |
|
|
| Column |
Description |
A1 |
Allele 1 (usually minor) |
A2 |
Allele 2 (usually major) |
BETA |
Regression coefficient (quantitative trait) |
BP |
Base-pair coordinate |
CHR |
Chromosome code |
FRQ |
Allele 1 frequency (overall) |
FRQ_A |
Allele 1 frequency in cases ('case-control-freqs') |
FRQ_U |
Allele 1 frequency in controls ('case-control-freqs') |
INFO |
R-squared quality / information content |
OR |
Odds ratio (case/control) |
P |
Association p-value |
SE |
Standard error of effect (not OR SE) |
SNP |
Variant identifier |
| ## Coverage |
|
8/9 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 |
no |
— |
N, N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
|
|