Allele frequency visualization

Allele frequency visualization

2

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


snp


R


stacks


vcftools

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