Quality Control

Quality Control

Sequencing Coverage Histograms

The sequencing coverage histograms show distribution of coverage across all chromosomes. In case certain samples seem to have significantly decreased coverage, they should be excluded from the analysis.

Sample labels

Figure 1

Open PDF Figure 1

Sequencing coverage histogram visualize the bulk distribution of read coverage for each sample.

Sample coverage summary

This section contains summary metrics on the number of sites and coverage can be found in the table below. The summary table below is also available as csv file.

sampleName sites_num sites_covgMean sites_covgMedian sites_covgPerc25 sites_covgPerc75 sites_numCovg5 sites_numCovg10 sites_numCovg30 sites_numCovg60
51_Hf03_BlCM_Ct_NOMe 51_Hf03_BlCM_Ct_NOMe 23538141 12.5552805550787 11 5 18 18787895 13049516 1259340 24395
51_Hf03_BlCM_Ct_WGBS 51_Hf03_BlCM_Ct_WGBS 26853792 23.96044621929 23 18 28 26481107 25702485 5855265 295704
51_Hf03_BlEM_Ct_NOMe 51_Hf03_BlEM_Ct_NOMe 23867132 13.0051286011239 11 6 18 19636037 13908346 1295118 18929
51_Hf03_BlEM_Ct_WGBS 51_Hf03_BlEM_Ct_WGBS 26846161 22.5827433203578 21 16 27 26443784 25377253 4660543 340422
51_Hf03_BlTN_Ct_NOMe 51_Hf03_BlTN_Ct_NOMe 24302066 16.9863098059235 15 8 24 21299479 17041379 3352716 78478
51_Hf03_BlTN_Ct_WGBS 51_Hf03_BlTN_Ct_WGBS 26862147 24.1014516449486 23 18 29 26506007 25654813 6194398 290728
51_Hf04_BlCM_Ct_NOMe 51_Hf04_BlCM_Ct_NOMe 22667399 9.09689192835931 8 4 13 15774568 8929334 281417 3762
51_Hf04_BlCM_Ct_WGBS 51_Hf04_BlCM_Ct_WGBS 26735394 26.2268208951774 26 19 33 26392921 25511254 9308918 187445
51_Hf04_BlEM_Ct_NOMe 51_Hf04_BlEM_Ct_NOMe 23742287 12.7810146933191 11 6 18 19294443 13697315 1152393 9338
51_Hf04_BlEM_Ct_WGBS 51_Hf04_BlEM_Ct_WGBS 26728501 24.125983009672 24 18 30 26376331 25501022 6827667 65721
51_Hf04_BlTN_Ct_NOMe 51_Hf04_BlTN_Ct_NOMe 23847680 12.8556335878375 11 6 18 19544517 13886348 1170193 8796
51_Hf04_BlTN_Ct_WGBS 51_Hf04_BlTN_Ct_WGBS 26795342 24.1090096554842 24 18 29 26461438 25696292 6598618 65728
51_Hf05_BlTA_Ct_NOMe 51_Hf05_BlTA_Ct_NOMe 23792105 12.6987186295622 11 6 18 19593475 13958010 926426 6845
Figure 2

Open PDF Figure 2

Covered sites and median coverages for each sample. Vertical bars depict 0.05 and 0.95 percentiles.

Sequencing Coverage Violin Plots

The plots below show an alternative approach to visualizing the coverage distribution.

Sample chunk

Figure 3

Open PDF Figure 3

Sequencing coverage histogram visualized as violin plots. Distributions are based on 27679670 methylation sites.

Sequencing Coverage Thresholds

In total, between 6.2 and 18.8 million sites are covered in all samples of the dataset. The figure below shows the change in supports for different coverage thresholds. The exact values are available in a dedicated comma-separated file accompanying this report.

Figure 4

Open PDF Figure 4

Line plot showing the number of CpG sites with a given support for different thresholds of minimal coverage. The support of a CpG site is the minimal number of samples that interrogate it.