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Table 2: Chromosome 1 cytosine counts and methylation

From: Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

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%
  1. 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.