SNPs statistics

mmmm · 07-26-2014, 11:55 AM

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

TiborNagy · 07-28-2014, 10:37 PM

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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07-26-2014, 11:55 AM	#1
mmmm Senior Member Location: UK Join Date: Jul 2013 Posts: 131	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

07-28-2014, 10:37 PM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	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.