Number of sites in .mafs.gz different from angsd

[bvaditi]

Hi, is the number of sites in .mafs.gz file supposed to be different from those in angsd log file? For one of my populations I get a different value when counted with wc -l of .mafs.gz. For all other populations the number of sites in angsd log file and .mafs.gz are same

[fgvieira]

The number of sites can be different between ngsF and angsd, but it should be quite similar. How many sites do you get for each case?