very low number of analyzed SNPs/var

[xbarvazx]

Hi,

I am using GEMMA with 'lmm 4' and for some reason I get a very low number of analyzed SNPs/var.

> GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
> Reading Files ... 
> ## number of total individuals = 323
> ## number of analyzed individuals = 299
> ## number of covariates = 1
> ## number of phenotypes = 1
> ## number of total SNPs/var        =  4172988
> ## number of analyzed SNPs         =    17264
> Start Eigen-Decomposition...
> pve estimate =0.573704
> se(pve) =0.163837
> ================================================== 100%

What could be the reason?