Table 2

Enrichment of genic and non-synonymous SNPs in genomic islands.

SNP subset

Genic

Non-synonymous


High population differentiation

p-value(selection test) < = 0.01a

0.6576

0.1307


Most likely states (Viterbi)b

< 0.0001+

0.0002+


FDR < = 0.001c

< 0.0001+

0.0374+


Islandsd

< 0.0001+

0.0053+


Low population differentiation

p-value(selection test) < = 0.01a

0.2143

0.6402


Most likely states (Viterbi)b

0.0303-

0.5888


FDR < = 0.001c

0.0007-

0.6543


Islandsd

< 0.0001-

0.0083+


Fisher exact test for enrichment or depletion of genic and non-synonymous SNPs in genomic islands defined by the selection test or by the HMM approach

a subset of SNPs that are significant in the selection test at the 1% level

b subset of SNPs that belong to the high-differentiation or low-differentiation state as identified by the Viterbi algorithm in the first step of the HMM approach

c subset of SNPs that are assigned to the high-differentiation or low-differentiation state under a genome-wide FDR = 0.001 in the second step of the HMM approach

d subset of SNPs that are located within HDIs or LDIs

+ enrichment of SNP category in SNP class

- under-representation of SNP category in SNP class

Hofer et al. BMC Genomics 2012 13:107   doi:10.1186/1471-2164-13-107

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