Description of columns for CpG Specific Methylation Information
Proceeding the title for each SNP site is (ss) or (ds). "ss" indicates that this SNP was called on reads that mapped to a single strand. "ds" indicates that this SNP was called on reads that mapped to both strands.
Figure Information
The figure shows the allelic methylation frequencies for CpGs within this SNP region. The y-axis represents methylation frequencies, which vary from 0 (completely unmethylated) to 1 (completely methylated). The x-axis represents the bp position of the chromosome in which the SNP is located; the chromosome is shown in the title above the figure. Each point represents a CpG site and its methylation value in each allele is displayed separately. Alleles are distinguished by blue and red colors. The green vertical line represents the position of the SNP that is used to separate the alleles. If a CpG contains a SNP site, it is marked as an orange triangle. All other CpGs are shown as empty circles.
Table Information
Rows that are colored purple indicate CpGs that overlap with called SNPs.
(1) CpG Coordinate - This is the bp position of the CpG. The chromsome is shown in the title above the figure.
(2) Differential Methylation P-Value - This p-value represents the significance of ASM given the information in the proceeding columns.
(3) Group 1 C Count - The number of cytosines at this CpG's position that are associated with the first base of the heterozygous SNP calls.
(4) Group 1 T Count - The number of thymines at this CpG's position that are associated with the first base of the heterozygous SNP calls.
(5) Group 2 C Count - The number of cytosines at this CpG's position that are associated with the second base of the heterozygous SNP calls.
(6) Group 2 T Count - The number of thymines at this CpG's position that are associated with the second base of the heterozygous SNP calls.
(8) Allelic Methylation Frequency Difference - The methylation frequency difference between the two alleles at this CpG location.
*Note: Regions highlighted in red are associated with heterozygous SNP calls on chromosome X in male cell lines (i.e. false positive SNP calls).