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QC Report for Methylation Calling
Input parameters
| value | |
|---|---|
| Sample name | /data/Runs/415630/output/415630-20250125_0254/415630-L3455-Z0005-CATGTATCCTCTGAT/415630-L3455-Z0005- CATGTATCCTCTGAT.methyl_seq |
| h5 file | /data/Runs/415630/output/415630-20250125_0254/415630-L3455-Z0005-CATGTATCCTCTGAT/415630-L3455-Z0005- CATGTATCCTCTGAT.methyl_seq.applicationQC.h5 |
Human Genome: Global Methylation Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 71.99 |
| Percent Methylation: std | 12.60 |
| Percent Methylation: median | 73.00 |
| Total CpGs: | 739,329 |
| Coverage: mean | 42.10 |
| Coverage: std | 16.14 |
| Coverage: median | 42.00 |
Human Genome: Details of Per-Read Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 58.77 |
| Percent Methylation: std | 41.46 |
| Percent Methylation: median | 66.67 |
| Total CpGs: mean | 2.63 |
| Total CpGs: std | 2.93 |
| Total CpGs: median | 2.00 |
Human Genome: Cytosines in Other Contexts Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 73.51% |
| Percent Methylation: Std | 11.02% |
| Percent Methylation: Median | 75.00% |
| Coverage: Mean | 41.07 |
| Coverage: Std | 15.88 |
| Coverage: Median | 42.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.91% |
| Percent Methylation: Std | 14.60% |
| Percent Methylation: Median | 72.00% |
| Coverage: Mean | 22.81 |
| Coverage: Std | 11.26 |
| Coverage: Median | 22.00 |
Human Genome: M-bias plots of mean methylation along reads
M-bias Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.19% |
| Percent Methylation: Std | 9.39% |
| Percent Methylation: Median | 71.95% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.56% |
| Percent Methylation: Std | 7.83% |
| Percent Methylation: Median | 72.62% |
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 | 68.53% |
| Percent Methylation: Std | 11.50% |
| Percent Methylation: Median | 70.70% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.91% |
| Percent Methylation: Std | 5.19% |
| Percent Methylation: Median | 72.40% |
Control Genomes: Methylation and Coverage Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 0.28% |
| Percent Methylation: Std | 2.53% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 1,349 |
| Coverage: Mean | 13.77 |
| Coverage: Std | 14.65 |
| Coverage: Median | 8.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 3.63% |
| Percent Methylation: Std | 11.18% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 170 |
| Coverage: Mean | 55.51 |
| Coverage: Std | 61.53 |
| Coverage: Median | 30.00 |
Human Genome: Additional Details of CpG Methylation and Coverage
Human Genome: Values of CpG Methylation and Coverage
| value | |
|---|---|
| bin | |
| 10 | 2,203 |
| 20 | 903 |
| 30 | 3,000 |
| 40 | 6,838 |
| 50 | 16,272 |
| 60 | 65,326 |
| 70 | 176,499 |
| 80 | 258,804 |
| 90 | 173,952 |
| 100 | 35,532 |
| value | |
|---|---|
| bin | |
| 10 | 20,434 |
| 20 | 28,974 |
| 30 | 74,827 |
| 40 | 178,816 |
| 50 | 227,999 |
| 60 | 142,808 |
| 70 | 48,531 |
| 80 | 10,533 |
| 90 | 2,239 |
| 100 | 835 |
| 110 | 515 |
| 120 | 342 |
| 130 | 284 |
| 140 | 264 |
| 150 | 220 |
| 160 | 167 |
| 170 | 167 |
| 180 | 124 |
| 190 | 109 |
| 200 | 1,141 |
| value | |
|---|---|
| bin | |
| 10 | 2.76% |
| 20 | 6.68% |
| 30 | 16.80% |
| 40 | 40.99% |
| 50 | 71.83% |
| 60 | 91.14% |
| 70 | 97.71% |
| 80 | 99.13% |
| 90 | 99.44% |
| 100 | 99.55% |
| 110 | 99.62% |
| 120 | 99.67% |
| 130 | 99.70% |
| 140 | 99.74% |
| 150 | 99.77% |
| 160 | 99.79% |
| 170 | 99.81% |
| 180 | 99.83% |
| 190 | 99.85% |
| 200 | 100.00% |