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.

Liu et al. Genome Biology 2012 13:R61   doi:10.1186/gb-2012-13-7-r61

Open Data