Hello Mostafa,

Here is what the plink manual states:

Allele frequency

• --freq < counts | case-control > < gz >
• --freqx <gz> (alias: --frqx)

By itself, --freq writes a minor allele frequency report to plink.frq. If you add the 'counts' modifier, an allele count report is written to plink.frq.count instead. Alternatively, you can use --freq with --within/--family to write a cluster-stratified frequency report to plink.frq.strat, or use the 'case-control' modifier to write a case/control phenotype-stratified report to plink.frq.cc.

--freqx writes a more informative genotype count report to plink.frqx.

For both flags, gzipped output can be requested with the 'gz' modifier.

Nonfounders are normally excluded from these counts/frequencies; use --nonfounders to change this.

All of these reports (except for --freq + --within/--family) are valid input for --read-freq; --freqx is the most powerful when used in that capacity, since it preserves deviation from Hardy-Weinberg equilibrium.

[source: https://www.cog-genomics.org/plink/1.9/basic_stats#freq]

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You used --freqx. Here is a description of the output:

.frqx (genotype count report)

Produced by --freqx. Valid input for --read-freq.

A text file with a header line, and then one line per variant with the following ten fields:

• CHR Chromosome code
• SNP Variant identifier
• A1 Allele 1 (usually minor)
• A2 Allele 2 (usually major)
• C(HOM A1) A1 homozygote count
• C(HET) Heterozygote count
• C(HOM A2) A2 homozygote count
• C(HAP A1) Haploid A1 count (includes male X chromosome)
• C(HAP A2) Haploid A2 count
• C(MISSING) Missing genotype count

[source: https://www.cog-genomics.org/plink/1.9/formats#frqx]

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Final piece of information: it looks like your bases are encoded in 1,2,3,4 format (A,C,G,T == 1,2,3,4).

So, now you should understand your output and, I believe, you will know whether or not you have chosen the correct program / command.

Kevin