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QC Report for Methylation Calling
Input parameters
| value | |
|---|---|
| Sample name | /data/Runs/415630/output/415630-20250125_0254/415630-L3453-Z0001-CAGCTCGAATGCGAT/415630-L3453-Z0001- CAGCTCGAATGCGAT.methyl_seq |
| h5 file | /data/Runs/415630/output/415630-20250125_0254/415630-L3453-Z0001-CAGCTCGAATGCGAT/415630-L3453-Z0001- CAGCTCGAATGCGAT.methyl_seq.applicationQC.h5 |
Human Genome: Global Methylation Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 71.16 |
| Percent Methylation: std | 12.21 |
| Percent Methylation: median | 72.00 |
| Total CpGs: | 740,142 |
| Coverage: mean | 52.63 |
| Coverage: std | 19.15 |
| Coverage: median | 53.00 |
Human Genome: Details of Per-Read Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 58.44 |
| Percent Methylation: std | 41.32 |
| Percent Methylation: median | 66.67 |
| Total CpGs: mean | 2.68 |
| Total CpGs: std | 2.98 |
| Total CpGs: median | 2.00 |
Human Genome: Cytosines in Other Contexts Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 72.65% |
| Percent Methylation: Std | 10.56% |
| Percent Methylation: Median | 73.00% |
| Coverage: Mean | 51.27 |
| Coverage: Std | 19.07 |
| Coverage: Median | 52.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.03% |
| Percent Methylation: Std | 13.92% |
| Percent Methylation: Median | 71.00% |
| Coverage: Mean | 28.46 |
| Coverage: Std | 13.15 |
| Coverage: Median | 27.00 |
Human Genome: M-bias plots of mean methylation along reads
M-bias Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 69.49% |
| Percent Methylation: Std | 10.08% |
| Percent Methylation: Median | 71.25% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 69.54% |
| Percent Methylation: Std | 8.94% |
| Percent Methylation: Median | 71.76% |
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 | 67.41% |
| Percent Methylation: Std | 9.32% |
| Percent Methylation: Median | 70.15% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.15% |
| Percent Methylation: Std | 5.81% |
| Percent Methylation: Median | 71.67% |
Control Genomes: Methylation and Coverage Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 0.49% |
| Percent Methylation: Std | 5.35% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 1,263 |
| Coverage: Mean | 16.41 |
| Coverage: Std | 16.02 |
| Coverage: Median | 12.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 0.52% |
| Percent Methylation: Std | 1.66% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 171 |
| Coverage: Mean | 60.19 |
| Coverage: Std | 63.56 |
| Coverage: Median | 35.00 |
Human Genome: Additional Details of CpG Methylation and Coverage
Human Genome: Values of CpG Methylation and Coverage
| value | |
|---|---|
| bin | |
| 10 | 2,170 |
| 20 | 747 |
| 30 | 3,091 |
| 40 | 6,570 |
| 50 | 16,923 |
| 60 | 70,065 |
| 70 | 192,343 |
| 80 | 266,738 |
| 90 | 156,178 |
| 100 | 25,317 |
| value | |
|---|---|
| bin | |
| 10 | 16,846 |
| 20 | 17,395 |
| 30 | 34,361 |
| 40 | 77,700 |
| 50 | 152,776 |
| 60 | 192,688 |
| 70 | 144,879 |
| 80 | 69,283 |
| 90 | 22,225 |
| 100 | 5,833 |
| 110 | 1,800 |
| 120 | 826 |
| 130 | 484 |
| 140 | 332 |
| 150 | 287 |
| 160 | 222 |
| 170 | 205 |
| 180 | 179 |
| 190 | 141 |
| 200 | 1,680 |
| value | |
|---|---|
| bin | |
| 10 | 2.28% |
| 20 | 4.63% |
| 30 | 9.27% |
| 40 | 19.77% |
| 50 | 40.41% |
| 60 | 66.44% |
| 70 | 86.02% |
| 80 | 95.38% |
| 90 | 98.38% |
| 100 | 99.17% |
| 110 | 99.41% |
| 120 | 99.52% |
| 130 | 99.59% |
| 140 | 99.63% |
| 150 | 99.67% |
| 160 | 99.70% |
| 170 | 99.73% |
| 180 | 99.75% |
| 190 | 99.77% |
| 200 | 100.00% |