I have files ‘cg.ped’ and ‘cg.map’.

I used plink --file cg --assoc --out data

to get data.assoc

Then I used plink --file cg --model --out data

to get data.model

However, in the data.model there are some missing values, like in lines 601-605 (0 in that A column, but missing values in that G column)

597 0 exm2270713 A G TREND 146/252 120/250 3.104e+00 1 7.811e-02

598 0 exm2270713 A G ALLELIC 146/252 120/250 1.531e+00 1 2.160e-01

599 0 exm2270713 A G DOM 145/54 119/66 NA NA NA

600 0 exm2270713 A G REC 1/198 1/184 NA NA NA

601 0 exm2277048 0 GENO 0/0/0 0/0/0 NA NA NA

602 0 exm2277048 0 TREND 0/0 0/0 NA NA NA

603 0 exm2277048 0 ALLELIC 0/0 0/0 NA NA NA

604 0 exm2277048 0 DOM 0/0 0/0 NA NA NA

605 0 exm2277048 0 REC 0/0 0/0 NA NA NA

606 0 exm2277076 A C GENO 1/0/207 1/0/190 NA NA NA

607 0 exm2277076 A C TREND 2/414 2/380 3.656e-03 1 9.518e-01

For these missing values, it causes that the follow-up work cannot continue.

Why and how to deal with this?

Thank you very much!