.pvar
Variant table for .pgen; VCF-style headers allowed. Last header line starts with '#CHROM'. Without headers, columns follow .bim order (CHROM, ID, CM, POS, ALT, REF or 5-column without CM).
Overview
| Field |
Value |
| Format key |
plink_pvar |
| Spec file |
formats/plink_pvar.json |
| Cite name |
PLINK 2.0 |
| Version |
PLINK 2.0 (doc revision 11 Mar 2026) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/2.0/formats#pvar |
| Citation |
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| NA value |
. |
| Comment prefix |
# |
| Header row |
yes |
| Column order |
#CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, CM |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
#CHROM |
CHR |
— |
ALT |
ALT |
— |
CHROM |
CHR |
— |
CM |
CM |
— |
FILTER |
FILTER |
— |
FORMAT |
FORMAT |
— |
ID |
SNPID |
rsID |
INFO |
INFO |
— |
POS |
POS |
— |
QUAL |
QUAL |
— |
REF |
REF |
— |
| ## Header descriptions |
|
|
| Column |
Description |
#CHROM |
Chromosome code |
ALT |
Alternate alleles (comma-separated) |
CM |
Centimorgan position (optional) |
FILTER |
FILTER field |
FORMAT |
FORMAT column when present |
ID |
Variant ID |
INFO |
INFO field |
POS |
Base-pair coordinate |
QUAL |
Phred-scaled locus quality |
REF |
Reference allele |
| ## Coverage |
|
3/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
no |
— |
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 |
yes |
INFO |
— |
| ## See also |
|
|
|