Table 2: |
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|
Chromosome 1 cytosine counts and methylation |
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|
Sample |
Sample genotype |
Reference Genotypes |
% methylation |
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|
|
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|
Reference CpG |
Reference CpH |
Reference DpN (D = A,T,G) |
Ref CpG |
Ref CpH |
Ref DpN |
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|
|
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|
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% |
|
|
|
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|
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. |
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|
Liu et al. Genome Biology 2012 13:R61 doi:10.1186/gb-2012-13-7-r61 |
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