I am looking at LD between a SNP in one gene and three SNPS that are in the neighbouring gene and I am using Arlequin to do so..
This is what is confusing me...
SNPS 1 and 2 - derived alleles of SNP1 always occur with derived alleles of SNP2 (I can see this in the haplotypes) And..Arlequin tells me the following: D = 0.0135 D' = 0.8470 r2 = 0.0150 Chi squared = 6.1489 (P<0.005)
So this tells me that there is LD between them - and haplotypes observed are significantly different from those expected under Linkage equilibrium.
BUT for SNP1 and SNP 3 - which do not always occur together - haplotypes show the derived alleles of each never occur on the same haplotype background..
why then do I get these results?
D = 0.0050 D' = 1.00 r2 0.0059 Chi squared 2.475 (P>0.05 non significant)
I understand that this tells me the LD is not significant - but why do I get D' of 1.00?? In the 2x2 table there is also D' of -1.00 as shown below...
Table of standardized disequilibrium values (D'=D/Dmax)
Locus0\Locus1| C| T| 1| -1.0000| 1.0000| 2| 1.0000| -1.0000|
What does it mean?! Is this telling me that there is LD between the two ancestral alleles...but not between the two derived alleles (because they are not on the same haplotype background?)
I am so confused!!