Table 1

Summary of Spearman's correlation coefficients between FST and ϕ as the discordance in replicabilities for the 37 associations from the Continental Set

ASSOCIATIONS

CATHEGORY

POOLINGa

VARIABLEb

N

P value


Full Set

All SNPs

By Gene

Average FST

33

0.496 *

0.003


Variance FST

32

0.636 *

7 × 10-5


Independently

Average FST

3710

0.155 *

2.58 × 10-21


tagSNPs

By Gene

Average FST

33

0.187

0.313


Independently

Average FST

538

0.16 *

2.02 × 10-4


Conservative Setc

All SNPs

By Gene

Average FST

26

0.666 *

0.0002


Variance FST

24

0.666 *

4.5 × 10-6


Independently

Average FST

2454

0.15 *

0.628


tagSNPs

By Gene

Average FST

24

0.453

0.280


Independently

Average FST

486

0.063 *

6.85 × 10-4


a Pooling by gene tests average genic FST, while in pooling independently each SNP has been assigned the replicability from the association it belongs to

b Variable indicates which parameter (either average or variance in FST) has been tested versus ϕ

c Conservative set contains those associations that have a replicability of ≥50% in at least one continent

Marigorta et al. BMC Genomics 2011 12:55   doi:10.1186/1471-2164-12-55

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