Table 5

Comparison of the distribution of derived allele frequencies (DAF) for SNPs within several classes.

class

Perlegen population

class DAF median

ancestral repeats

genome


DAF median

p-value

DAF median

p-value


constrained elements

AFR

0.174

0.196

3.6 × 10-5

0.205

< 1 × 10-8


EUR

0.188

0.208

3.4 × 10-4

0.229

< 1 × 10-8


CHN

0.174

0.208

8.7 × 10-3

0.217

< 1 × 10-8


constrained elements 1 kb from genes

AFR

0.174

0.196

3.2 × 10-3

0.200

< 1 × 10-8


EUR

0.190

0.208

5.4 × 10-3

0.229

< 1 × 10-8


CHN

0.188

0.208

6.0 × 10-2

0.217

< 1 × 10-8


constrained elements 100 kb from genes

AFR

0.174

0.196

1.1 × 10-2

0.200

1.0 × 10-8


EUR

0.205

0.208

9.6 × 10-3

0.229

1.1 × 10-6


CHN

0.188

0.208

8.3 × 10-2

0.217

8.5 × 10-7


constrained elements outside of genes

AFR

0.174

0.196

3.0 × 10-3

0.196

< 1 × 10-8


EUR

0.188

0.208

5.3 × 10-3

0.229

< 1 × 10-8


CHN

0.188

0.208

6.1 × 10-2

0.217

< 1 × 10-8


H3K79me3

AFR

0.174

0.196

8.0 × 10-3

0.200

< 1 × 10-8


EUR

0.208

0.208

1.6 × 10-2

0.229

1.7 × 10-7


CHN

0.188

0.202

1.2 × 10-1

0.217

5.0 × 10-8


Classes presented are 1) constrained elements, 2) constrained elements at least 1 kb from the closest gene, and 3) constrained elements at least 100 kb from the closest gene, 4) constrained elements outside of genes, and 5) H3K79me3 regulatory attributes in comparison with the genome as a whole and ancestral repeats. We perform a Mann-Whitney U-test to compare the DAF distribution for SNPs in constrained elements, constrained elements outside of genes, and H3K79me3 regulatory attributes with that of the genome and that of ancestral repeats. We list the resulting p-values as well as the median DAF for each class.

Levenstien and Klein BMC Bioinformatics 2011 12:26   doi:10.1186/1471-2105-12-26

Open Data