Post Fst calculation analysis
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2.3 years ago
doodle ▴ 30

Hello,

I have calculated genome-wide Fst of SNP loci in 2 populations in Plink which uses VCF-tools's Fst estimator and got the following output :

CHR SNP POS NMISS FST 1 1:58460 58460 5732 -8.33795E-05 1 1:64904 64904 5732 -8.33795E-05 1 1:70728 70728 5731 0.000447608 1 1:77646 77646 5732 2.28393E-05 1 1:87734 87734 5732 0.000235296 1 1:530357 530357 5733 2.29353E-05

The 2 populations had 2059 and 3672 individuals and the output I got is for the total of 5733 individuals. I'm not sure of how to interpret the output. What do the positive and negative values mean? How can I identify genomic selection from the output? When and why do we do bootstrapping?

Any help on how to go about further analysis would be great!

Thank you.

Fst SNP loci population structure diveRsity • 495 views
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