Hello dears all,

Actually I have a .frq file (allele frequency file) which It is generated  from .vcf file through VCFtools and it is included by five populations (The vcf file is generated by Stacks pipeline). But the point is, I don't know how can I visual the allele frequency. I will be so grateful if anyone can help me to solve this issue. Here is a part of my .frq file.

Best regards.

    CHROM	POS	N_ALLELES	N_CHR	{ALLELE:FREQ}
    CM003279.1	116397	2	4	A:0.5	C:0.5
    CM003279.1	184945	2	4	C:0.5	G:0.5
    CM003279.1	185823	2	36	C:0.944444	T:0.0555556
    CM003279.1	408595	2	54	T:0.5	A:0.5
    CM003279.1	420946	2	10	A:0.5	T:0.5
    CM003279.1	420946	2	42	T:0.619048	A:0.380952
    CM003279.1	432468	2	4	A:0.5	T:0.5
    CM003279.1	432468	2	4	T:0.5	A:0.5
    CM003279.1	521247	2	6	A:0.5	C:0.5
    CM003279.1	521247	2	4	C:0.5	A:0.5
    CM003279.1	768668	2	46	T:0.978261	A:0.0217391
    CM003279.1	768678	2	50	A:0.84	G:0.16
    CM003279.1	768679	2	50	T:0.64	C:0.36
    CM003279.1	768685	2	50	G:0.84	C:0.16
    CM003279.1	768691	2	50	G:0.84	A:0.16
    CM003279.1	768705	2	50	C:0.84	T:0.16
    CM003279.1	768709	2	54	A:0.814815	T:0.185185
Perhaps you can use online VEP (Variant Effector Prediction) server  from ENSEMBL, just google it. I don't know whether your VCF file derived from  a plant species or animal species or prokaryotic species like bacteria. Depends on the species, you can choose the correct VEP-ENSEMBL server. Here, you could predict variants effect (with SIFT score) for each position of the SNPs from your VCF input file and you have to choose the correct species of interest when you give your input VCF file. For instance, here is the VEP ENSEMBL server for plants: https://plants.ensembl.org/Triticum_aestivum/Tools/VEP?db=core     you can read here for variant effects prediction/variant of alleles and annotations concerning VEP server: https://plants.ensembl.org/Help/View?id=484    Hope it may help. 