plink.assoc

The plink.assoc file contains the fields:

 CHR     Chromosome
 SNP     SNP ID
 BP      Physical position (base-pair)
 A1      Minor allele name (based on whole sample)
 F_A     Frequency of this allele in cases
 F_U     Frequency of this allele in controls
 A2      Major allele name
 CHISQ   Basic allelic test chi-square (1df)
 P       Asymptotic p-value for this test
 OR      Estimated odds ratio (for A1, i.e. A2 is reference)

Example:

CHR	SNP	BP	A1	F_A	F_U	A2	CHISQ	P	OR
1	rs3094315	742429	C	0.1509	0.1394	T	0.0759	0.782	1.097
1	rs4040617	769185	G	0.1509	0.1202	A	0.5849	0.444	1.301
1	rs2980300	775852	A	0.1961	0.1683	G	0.3576	0.549	1.205
1	rs4075116	993492	G	0.2547	0.2163	A	0.585	0.444	1.238
...	...	...	...	...	...	...	...	...	...