Description of R Data Matrix

 

Table Description

These columns describe the data related to the r2 calculations.

(1) and (2) CpG Pair 1 or 2 - The first two columns show the bp coordinate of the two CpGs involved in the r2 calculated.

(3) Distance - bp distance between CpG pairs.

(4) TT Count - the number of reads where both CpGs were all unmethylated. TT means the first CpG base is thymine and the second was thymine.

(5) TC Count - the number of reads where the first CpG was unemethylated and the second was methylation. TC means the first CpG base is thymine and the second is cytosine.

(6) T* Count - the number of reads where the first CpG was unmethylated. The methylation status of the second CpG was not considered.

(7) CT Count - the number of reads where the first CpG was methylated and the second CpG was unmethylated.

(8) CC Count - the number of reads where both CpGs are methylated.

(9) C* - the number of reads where the first CpG was methylated. The methylation status of the second CpG was not considered.

(10) *T - the number of reads where the second CpG was unmethylated. The methylation status of the first CpG was not considered.

(11) *C - the number of reads where the second CpG was methylated. The methylation status of the first CpG was not considered.

(12) R Value - the r value calculated based on the given data. This squared form of this value was used in additional analyses.

(13) Minor Allele Frequency A - The fraction of the least frequent allele in the first CpG site. In our methylation anlsysis, alleles represent methylation states (i.e. methylated or unmethylated).

(14) Minor Allele Frequency B - The fraction of the least frequent allele in the second CpG site. In our methylation anlsysis, alleles represent methylation states (i.e. methylated or unmethylated).