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Table 2 Enrichment of genic and non-synonymous SNPs in genomic islands.

From: Evolutionary forces shaping genomic islands of population differentiation in humans

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+

  1. 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
  2. a subset of SNPs that are significant in the selection test at the 1% level
  3. 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
  4. 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
  5. d subset of SNPs that are located within HDIs or LDIs
  6. + enrichment of SNP category in SNP class
  7. - under-representation of SNP category in SNP class