.bim
Extended variant map with .bed: CHR, SNP, CM, BP, A1 (first/clear-bit allele, usually minor), A2 (second/set-bit allele, usually major). PLINK 2 .bim lists ALT before REF but encodes the same roles as 1.x A1/A2.
Overview
| Field |
Value |
| Format key |
plink_bim |
| Spec file |
formats/plink_bim.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#bim |
| 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 |
no |
| Column order |
0, 1, 2, 3, 4, 5 |
| ## Column mapping |
|
| Raw header |
Canonical |
0 |
CHR |
1 |
SNPID |
2 |
CM |
3 |
POS |
4 |
EA |
5 |
NEA |
| ## Header descriptions |
|
| Column |
Description |
0 |
Chromosome code |
1 |
Variant identifier |
2 |
Genetic distance in morgans (often 0) |
3 |
Base-pair coordinate (1-based) |
4 |
Allele 1 (minor in .bed; first allele) |
5 |
Allele 2 (major in .bed; second allele) |
| ## Coverage |
|
3/9 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 |
no |
— |
BETA, OR, HR, Z |
| Uncertainty |
no |
— |
SE |
| P-value |
no |
— |
P, MLOG10P |
| Sample size |
no |
— |
N, N_CASE |
| Allele frequency |
no |
— |
EAF, MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|