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QC Report for Methylation Calling
Input parameters
| value | |
|---|---|
| Sample name | /data/Runs/415630/output/415630-20250125_0254/415630-L3449-Z0007-CGATTCATGCTCGAT/415630-L3449-Z0007- CGATTCATGCTCGAT.methyl_seq |
| h5 file | /data/Runs/415630/output/415630-20250125_0254/415630-L3449-Z0007-CGATTCATGCTCGAT/415630-L3449-Z0007- CGATTCATGCTCGAT.methyl_seq.applicationQC.h5 |
Human Genome: Global Methylation Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 72.60 |
| Percent Methylation: std | 12.99 |
| Percent Methylation: median | 74.00 |
| Total CpGs: | 737,764 |
| Coverage: mean | 34.00 |
| Coverage: std | 13.84 |
| Coverage: median | 34.00 |
Human Genome: Details of Per-Read Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 59.88 |
| Percent Methylation: std | 41.08 |
| Percent Methylation: median | 71.43 |
| Total CpGs: mean | 2.70 |
| Total CpGs: std | 2.99 |
| Total CpGs: median | 2.00 |
Human Genome: Cytosines in Other Contexts Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 74.17% |
| Percent Methylation: Std | 11.52% |
| Percent Methylation: Median | 75.00% |
| Coverage: Mean | 32.77 |
| Coverage: Std | 13.33 |
| Coverage: Median | 33.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.69% |
| Percent Methylation: Std | 15.48% |
| Percent Methylation: Median | 73.00% |
| Coverage: Mean | 17.99 |
| Coverage: Std | 9.50 |
| Coverage: Median | 17.00 |
Human Genome: M-bias plots of mean methylation along reads
M-bias Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.11% |
| Percent Methylation: Std | 10.16% |
| Percent Methylation: Median | 72.39% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.44% |
| Percent Methylation: Std | 8.72% |
| Percent Methylation: Median | 73.37% |
Human Genome: M-bias plots of mean methylation on CHH/CHG along reads
M-bias of CHH/CHG Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 68.10% |
| Percent Methylation: Std | 12.64% |
| Percent Methylation: Median | 71.23% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 72.83% |
| Percent Methylation: Std | 4.09% |
| Percent Methylation: Median | 73.34% |
Control Genomes: Methylation and Coverage Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 1.82% |
| Percent Methylation: Std | 12.60% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 653 |
| Coverage: Mean | 3.40 |
| Coverage: Std | 2.93 |
| Coverage: Median | 2.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 12.73% |
| Percent Methylation: Std | 31.12% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 132 |
| Coverage: Mean | 13.33 |
| Coverage: Std | 18.40 |
| Coverage: Median | 5.00 |
Human Genome: Additional Details of CpG Methylation and Coverage
Human Genome: Values of CpG Methylation and Coverage
| value | |
|---|---|
| bin | |
| 10 | 2,233 |
| 20 | 852 |
| 30 | 3,046 |
| 40 | 6,927 |
| 50 | 16,461 |
| 60 | 64,130 |
| 70 | 164,120 |
| 80 | 247,521 |
| 90 | 185,482 |
| 100 | 46,992 |
| value | |
|---|---|
| bin | |
| 10 | 24,858 |
| 20 | 54,619 |
| 30 | 171,518 |
| 40 | 264,224 |
| 50 | 163,047 |
| 60 | 46,513 |
| 70 | 7,882 |
| 80 | 1,674 |
| 90 | 700 |
| 100 | 460 |
| 110 | 323 |
| 120 | 255 |
| 130 | 198 |
| 140 | 162 |
| 150 | 171 |
| 160 | 120 |
| 170 | 102 |
| 180 | 69 |
| 190 | 63 |
| 200 | 806 |
| value | |
|---|---|
| bin | |
| 10 | 3.37% |
| 20 | 10.77% |
| 30 | 34.02% |
| 40 | 69.84% |
| 50 | 91.94% |
| 60 | 98.24% |
| 70 | 99.31% |
| 80 | 99.54% |
| 90 | 99.63% |
| 100 | 99.69% |
| 110 | 99.74% |
| 120 | 99.77% |
| 130 | 99.80% |
| 140 | 99.82% |
| 150 | 99.84% |
| 160 | 99.86% |
| 170 | 99.87% |
| 180 | 99.88% |
| 190 | 99.89% |
| 200 | 100.00% |