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QC Report for Methylation Calling



Input parameters


  value
Sample name /data/Runs/412410/output/412410-20250516_2212/412410-EL_7-Z0208-CATGCTCAATATCTGAT/412410-EL_7-Z0208- CATGCTCAATATCTGAT.methyl_seq
h5 file /data/Runs/412410/output/412410-20250516_2212/412410-EL_7-Z0208-CATGCTCAATATCTGAT/412410-EL_7-Z0208- CATGCTCAATATCTGAT.methyl_seq.applicationQC.h5

Human Genome: Global Methylation Statistics


value
metric
Percent Methylation: mean 74.12
Percent Methylation: std 28.69
Percent Methylation: median 86.00
Total CpGs: 736,875
Coverage: mean 68.04
Coverage: std 28.22
Coverage: median 70.00

Human Genome: Details of Per-Read Descriptive Statistics

value
metric
Percent Methylation: mean 55.25
Percent Methylation: std 46.87
Percent Methylation: median 75.00
Total CpGs: mean 1.91
Total CpGs: std 2.47
Total CpGs: median 1.00

Human Genome: Cytosines in Other Contexts Descriptive Statistics


CHG
  value
metric  
Percent Methylation: Mean 0.69%
Percent Methylation: Std 2.45%
Percent Methylation: Median 0.00%
Coverage: Mean 67.50
Coverage: Std 26.97
Coverage: Median 69.00
  
CHH
  value
metric  
Percent Methylation: Mean 0.67%
Percent Methylation: Std 2.88%
Percent Methylation: Median 0.00%
Coverage: Mean 33.90
Coverage: Std 15.77
Coverage: Median 34.00
  

Human Genome: M-bias plots of mean methylation along reads


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M-bias Descriptive Statistics

OT
  value
metric  
Percent Methylation: Mean 58.48%
Percent Methylation: Std 16.67%
Percent Methylation: Median 57.70%
  
OB
  value
metric  
Percent Methylation: Mean 60.77%
Percent Methylation: Std 15.66%
Percent Methylation: Median 63.19%
  

Human Genome: M-bias plots of mean methylation on CHH/CHG along reads


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M-bias of CHH/CHG Descriptive Statistics

OT
  value
metric  
Percent Methylation: Mean 4.05%
Percent Methylation: Std 7.13%
Percent Methylation: Median 1.26%
  
OB
  value
metric  
Percent Methylation: Mean 0.84%
Percent Methylation: Std 4.98%
Percent Methylation: Median 0.51%
  

Control Genomes: Methylation and Coverage Descriptive Statistics

Lambda
  value
metric  
Percent Methylation: Mean 0.07%
Percent Methylation: Std 0.39%
Percent Methylation: Median 0.00%
Total CpGs: 3,113
Coverage: Mean 200.00
Coverage: Std 0.00
Coverage: Median 200.00
  
pUC19
  value
metric  
Percent Methylation: Mean 97.18%
Percent Methylation: Std 0.89%
Percent Methylation: Median 97.00%
Total CpGs: 173
Coverage: Mean 200.00
Coverage: Std 0.00
Coverage: Median 200.00
  

Human Genome: Additional Details of CpG Methylation and Coverage


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No description has been provided for this image

Human Genome: Values of CpG Methylation and Coverage

Percent Methylation
  value
bin  
10 63,209
20 13,898
30 12,030
40 12,990
50 17,040
60 24,582
70 39,439
80 79,746
90 189,059
100 284,882
  
Coverage
  value
bin  
10 30,424
20 21,928
30 22,066
40 31,357
50 53,188
60 85,953
70 116,393
80 124,199
90 104,914
100 70,963
110 39,993
120 19,238
130 8,183
140 3,032
150 1,221
160 580
170 335
180 253
190 183
200 2,472
  
Cumulative Coverage
  value
bin  
10 4.13%
20 7.10%
30 10.10%
40 14.35%
50 21.57%
60 33.24%
70 49.03%
80 65.89%
90 80.13%
100 89.76%
110 95.18%
120 97.79%
130 98.90%
140 99.32%
150 99.48%
160 99.56%
170 99.61%
180 99.64%
190 99.66%
200 100.00%