I have just conducted a logistic conditional analysis by plink. The file shows two lines for a SNP. How to interpret this?
--allow-no-sex --bfile --condition rs3456 --dominant --logistic --out ***_rs3456 CHR SNP BP A1 TEST NMISS OR STAT P 1 rs1234 12345 C DOM 2000 1.03 0.1973 0.8436 1 rs1234 12345 C rs3456 2000 0.3986 -5.396 6e-08
As I wanted to do this analysis by
--dominant, the p-value for this analysis should be 0.8436 as above?
Also, if allelic/dom/rec models are all "NA", is it OK just to ignore those SNPs?
Thank you in advance!