.psam
Sample table for .pgen. Last header line starts with '#FID' or '#IID'; FID may be omitted (then assumed '0'). Columns after SEX are phenotype/covariate names.
Overview
| Field |
Value |
| Format key |
plink_psam |
| Spec file |
formats/plink_psam.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#psam |
| 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 |
NA |
| Comment prefix |
# |
| Header row |
yes |
| Column order |
#FID, IID, #IID, SID, PAT, MAT, SEX |
| ## Column mapping |
|
| Raw header |
Canonical |
#FID |
FID |
#IID |
IID |
FID |
FID |
IID |
IID |
MAT |
MAT |
PAT |
PAT |
SEX |
SEX |
SID |
SID |
| ## Header descriptions |
|
| Column |
Description |
#FID |
Family ID (optional first column) |
#IID |
Individual ID (required) |
IID |
Individual ID |
MAT |
Maternal IID ('0' if unknown) |
PAT |
Paternal IID ('0' if unknown) |
SEX |
Sex (1=male, 2=female, NA/0=unknown) |
SID |
Source ID |
| ## Coverage |
|
0/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
no |
— |
SNPID, rsID |
| Genomic location |
no |
— |
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 |
no |
— |
INFO |
| ## See also |
|
|
|