Description of columns for the Averaged Methylation Information

SNP regions categorized as I or II are highlighted in blue.

 

(1) Calculation Type - This field is always Average ASM, which means that the methylation information of CpGs within this SNP regions are summed.

(2) Contains SNPs at CG Sites - Indicates whether there are SNP sites that overlap with CpGs in this region. "Y" means yes and "N" means no. If there is/are SNP(s) overlapping with CpG site(s), there is a second row that shows the statistics excluding CpGs that overlap with SNPs.

(3) Differential Methylation P-Value - This p-value represents the significance of ASM given the information in the proceeding columns.

(4) Group 1 C Count - The number of cytosines called across CpGs positions that are associated with the first base of the heterozygous SNP calls.

(5) Group 1 T Count - The number of thymines called across CpGs positions that are associated with the first base of the heterozygous SNP calls.

(6) Group 2 C Count - The number of cytosines called across CpGs positions that are associated with the second base of the heterozygous SNP calls.

(7) Group 2 T Count - The number of thymines called across CpGs positions that are associated with the second base of the heterozygous SNP calls.

(8) Allelic Methylation Frequency Difference - The averaged methylation frequency difference between the two alleles.

(9) CpG Specific Information - ASM calculations and information for each CpG is shown here.

*Note: SNPs highlighted in red are heterozygous SNP calls on chromosome X in male cell lines (i.e. false positives).