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  • SNPs statistics

    I have an excel file contatins called SNPs among ten different strains in relation to the reference genome- I would like to caluclate the unique SNPs to every strain and to know the excat snps difference among all the strains- how can I do this plaease?, thanks

  • #2
    You need khi-square or Fisher exact test. For every SNP you have to create a 2x2 contingency table like this:
    SNP in other strains SNP in other strains
    + -
    SNP in your strain + a b
    SNP in your strain - c d

    You can use a,b,c,d to calculate the association.

    Sorry, the table editing is not working.

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