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QC Report for Methylation Calling
Input parameters
| value | |
|---|---|
| Sample name | /data/Runs/415630/output/415630-20250125_0254/415630-L3451-Z0011-CACGCACTGCCAGAT/415630-L3451-Z0011- CACGCACTGCCAGAT.methyl_seq |
| h5 file | /data/Runs/415630/output/415630-20250125_0254/415630-L3451-Z0011-CACGCACTGCCAGAT/415630-L3451-Z0011- CACGCACTGCCAGAT.methyl_seq.applicationQC.h5 |
Human Genome: Global Methylation Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 71.19 |
| Percent Methylation: std | 12.50 |
| Percent Methylation: median | 72.00 |
| Total CpGs: | 740,070 |
| Coverage: mean | 49.19 |
| Coverage: std | 18.14 |
| Coverage: median | 50.00 |
Human Genome: Details of Per-Read Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 58.21 |
| Percent Methylation: std | 41.45 |
| Percent Methylation: median | 66.67 |
| Total CpGs: mean | 2.64 |
| Total CpGs: std | 2.95 |
| Total CpGs: median | 2.00 |
Human Genome: Cytosines in Other Contexts Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 72.93% |
| Percent Methylation: Std | 10.85% |
| Percent Methylation: Median | 74.00% |
| Coverage: Mean | 48.00 |
| Coverage: Std | 18.06 |
| Coverage: Median | 49.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.23% |
| Percent Methylation: Std | 14.37% |
| Percent Methylation: Median | 71.00% |
| Coverage: Mean | 26.65 |
| Coverage: Std | 12.68 |
| Coverage: Median | 25.00 |
Human Genome: M-bias plots of mean methylation along reads
M-bias Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.84% |
| Percent Methylation: Std | 7.38% |
| Percent Methylation: Median | 71.16% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 69.44% |
| Percent Methylation: Std | 8.70% |
| Percent Methylation: Median | 71.77% |
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 | 68.36% |
| Percent Methylation: Std | 8.27% |
| Percent Methylation: Median | 70.19% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.88% |
| Percent Methylation: Std | 6.96% |
| Percent Methylation: Median | 71.72% |
Control Genomes: Methylation and Coverage Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 2.02% |
| Percent Methylation: Std | 12.92% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 815 |
| Coverage: Mean | 3.74 |
| Coverage: Std | 3.73 |
| Coverage: Median | 2.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 20.52% |
| Percent Methylation: Std | 24.74% |
| Percent Methylation: Median | 14.00% |
| Total CpGs: | 159 |
| Coverage: Mean | 13.56 |
| Coverage: Std | 18.01 |
| Coverage: Median | 7.00 |
Human Genome: Additional Details of CpG Methylation and Coverage
Human Genome: Values of CpG Methylation and Coverage
| value | |
|---|---|
| bin | |
| 10 | 2,209 |
| 20 | 847 |
| 30 | 3,019 |
| 40 | 6,993 |
| 50 | 18,021 |
| 60 | 73,111 |
| 70 | 189,670 |
| 80 | 257,961 |
| 90 | 158,859 |
| 100 | 29,380 |
| value | |
|---|---|
| bin | |
| 10 | 17,708 |
| 20 | 19,594 |
| 30 | 41,555 |
| 40 | 102,517 |
| 50 | 187,465 |
| 60 | 194,429 |
| 70 | 114,779 |
| 80 | 42,918 |
| 90 | 11,392 |
| 100 | 2,948 |
| 110 | 1,027 |
| 120 | 579 |
| 130 | 372 |
| 140 | 288 |
| 150 | 250 |
| 160 | 219 |
| 170 | 181 |
| 180 | 151 |
| 190 | 136 |
| 200 | 1,562 |
| value | |
|---|---|
| bin | |
| 10 | 2.39% |
| 20 | 5.04% |
| 30 | 10.66% |
| 40 | 24.51% |
| 50 | 49.84% |
| 60 | 76.11% |
| 70 | 91.62% |
| 80 | 97.42% |
| 90 | 98.96% |
| 100 | 99.36% |
| 110 | 99.49% |
| 120 | 99.57% |
| 130 | 99.62% |
| 140 | 99.66% |
| 150 | 99.70% |
| 160 | 99.73% |
| 170 | 99.75% |
| 180 | 99.77% |
| 190 | 99.79% |
| 200 | 100.00% |