Table 2:
Chromosome 1 cytosine counts and methylation
| Sample | Sample genotype | Reference Genotypes | % methylation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Reference CpG | Reference CpH | Reference DpN (D = A,T,G) | Ref CpG | Ref CpH | Ref DpN | |||||
| OTB normal colon | CpG | 3,758,803 | 99.39% | 12,540 | 0.02% | 11,838 | 0.01% | 73% | 80% | 82% |
| CpH | 7,773 | 0.21% | 78,427,918 | 99.95% | 18,804 | 0.01% | 1% | 1% | 1% | |
| DpN | 5,658 | 0.15% | 14,166 | 0.02% | 128,570,817 | 99.97% | NA | NA | NA | |
| CpG/CpH het | 7,218 | 0.19% | 8,998 | 0.01% | NA | NA | 39% | 39% | NA | |
| CpG/RpG het | 2,512 | 0.07% | NA | NA | 1,826 | 0.00% | 74% | NA | 77% | |
| TCGA Normal lung | CpG | 4,153,196 | 99.52% | 10,995 | 0.01% | 10,511 | 0.01% | 76% | 84% | 85% |
| CpH | 5,460 | 0.13% | 85,031,960 | 99.96% | 16,420 | 0.01% | 1% | 1% | 1% | |
| DpN | 5,310 | 0.13% | 13,725 | 0.02% | 133,490,905 | 99.98% | NA | NA | NA | |
| CpG/CpH het | 6,682 | 0.16% | 8,529 | 0.01% | NA | NA | 37% | 39% | NA | |
| CpG/RpG het | 2,476 | 0.06% | NA | NA | 1,993 | 0.00% | 80% | NA | 78% | |
| TCGA normal breast | CpG | 4,100,643 | 99.54% | 10,893 | 0.01% | 10,657 | 0.01% | 75% | 85% | 86% |
| CpH | 5,286 | 0.13% | 80,654,084 | 99.96% | 13,390 | 0.01% | 1% | 1% | 1% | |
| DpN | 4,954 | 0.12% | 13,310 | 0.02% | 136,180,779 | 99.98% | NA | NA | NA | |
| CpG/CpH het | 6,289 | 0.15% | 8,120 | 0.01% | NA | NA | 39% | 40% | NA | |
| CpG/RpG het | 2,413 | 0.06% | NA | NA | 1,854 | 0.00% | 78% | NA | 79% | |
| Xie 2012 Mouse F1i (chr1) | CpG | 2,125,320 | 97.51% | 10,990 | 0.02% | 11,757 | 0.01% | 76% | 83% | 84% |
| CpH | 4,314 | 0.20% | 57,706,841 | 99.87% | 20,312 | 0.02% | 3% | 3% | 3% | |
| DpN | 5,300 | 0.24% | 20,905 | 0.04% | 118,570,097 | 99.96% | NA | NA | NA | |
| CpG/CpH het | 28,896 | 1.33% | 36,735 | 0.06% | NA | NA | 43% | 42% | NA | |
| CpG/RpG het | 15,754 | 0.72% | NA | NA | 12,917 | 0.01% | 78% | NA | 82% | |
| Xie 2012 Mouse F1r (chr1) | CpG | 2,199,907 | 97.52% | 11,268 | 0.02% | 11,974 | 0.01% | 75% | 83% | 84% |
| CpH | 4,476 | 0.20% | 58,685,115 | 99.87% | 20,933 | 0.02% | 3% | 3% | 4% | |
| DpN | 5,171 | 0.23% | 20,765 | 0.04% | 117,647,445 | 99.96% | NA | NA | NA | |
| CpG/CpH het | 29,983 | 1.33% | 38,159 | 0.06% | NA | NA | 43% | 42% | NA | |
| CpG/RpG het | 16,371 | 0.73% | NA | NA | 13,147 | 0.01% | 78% | NA | 82% | |
Notes: 'het' signifies heterozygous. Two non-reference bases in a row automatically filtered out. CpH = C(A/C/T). DpN = (A/T/G)(A/C/T/G). RpG = (A/G)G. CpG/TpG heterozygous genotypes are filtered out because they can not be used for methylation calling.