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
adult_liver_replicate_1 adult_liver_replicate_1 27743024 35.5955487044239 32 17 50 26110792 24111465 15014293 4403780
adult_liver_replicate_2 adult_liver_replicate_2 27977710 34.3992749942722 34 21 47 27024456 25489770 16375420 2397368
adult_sorted_CD4_replicate_1 adult_sorted_CD4_replicate_1 28017574 33.5423765098292 32 20 45 27226132 25732298 15712302 2252401
adult_sorted_CD4_replicate_2 adult_sorted_CD4_replicate_2 27941607 25.4422493308993 24 15 34 26635718 24254287 10099247 397136
adult_sorted_CD8_replicate_1 adult_sorted_CD8_replicate_1 28050449 35.9573194710716 35 22 48 27440369 26132555 16936099 3163865
adult_sorted_CD8_replicate_2 adult_sorted_CD8_replicate_2 28011739 28.3239666769707 27 17 38 27102260 25209769 12360633 722054
bcell_1 bcell_1 27258613 5.22612760964764 5 3 7 14372018 1787915 28980 12969
bcell_2 bcell_2 9359992 3.29600687692895 2 1 4 2005734 356421 11860 6131
Colon_Primary_Normal Colon_Primary_Normal 27381577 26.8242756434372 24 12 38 24928969 22065022 10728955 1588972
Colon_Tumor_Primary Colon_Tumor_Primary 27631247 25.9442399396596 24 13 36 25637104 22897514 10323017 988366
colonic_mucosa colonic_mucosa 27330768 21.8222219368296 20 11 30 24845374 21470969 7359642 307266
fetal_adrenal fetal_adrenal 27294063 14.3979837666528 13 7 20 23136327 17175913 1963993 80888
fetal_brain fetal_brain 27916781 22.8379878754646 23 16 29 27278477 25632913 6458473 60778
fetal_heart fetal_heart 28012996 32.2569757979475 32 21 42 27361601 26147397 15675420 1089497
fetal_muscle_leg fetal_muscle_leg 26971384 17.8703867031814 15 8 25 23304263 18739351 4621282 139986
fetal_thymus fetal_thymus 27508367 21.0591888278937 19 11 29 25157509 21520120 6591601 218856
Frontal_cortex_AD_1 Frontal_cortex_AD_1 27921892 29.4659171377069 29 20 38 27331639 26040229 13222738 485807
Frontal_cortex_AD_2 Frontal_cortex_AD_2 27942570 39.0943990119735 38 26 50 27559143 26793496 19060343 3482544
Frontal_cortex_normal_1 Frontal_cortex_normal_1 27982041 37.7186101971618 37 27 47 27850576 27449063 19389202 1902397
Frontal_cortex_normal_2 Frontal_cortex_normal_2 27914852 27.7622374641284 26 18 36 27286241 25787160 11356026 475483
H1_derived_mesenchymal_stem_cells H1_derived_mesenchymal_stem_cells 26054000 15.3320254087664 11 5 21 19616428 14086500 3375961 377418
H1_derived_neuronal_progenitor_cells H1_derived_neuronal_progenitor_cells 27955121 14.0681212218684 13 9 18 25757126 19647465 638709 64694
H1_BMP4_derived_mesendoderm_cells H1_BMP4_derived_mesendoderm_cells 27991294 16.6177273547982 15 10 21 26413128 21804662 1878179 54307
HepG2 HepG2 26720541 12.2217392604439 10 5 17 20456486 13714398 1304379 102889
hippocampus_middle_replicate_1 hippocampus_middle_replicate_1 28018508 41.354314976372 39 24 56 27375399 26214937 18572678 5810024
hippocampus_middle_replicate_2 hippocampus_middle_replicate_2 27870352 29.8252704163909 28 17 41 26702544 24778042 13061892 1466821
HSCP_1 HSCP_1 27515729 7.96832255471043 7 4 10 19481393 7525986 171356 24982
HSCP_2 HSCP_2 24273814 2.86089079367585 2 1 4 3295928 130773 18399 10076
HUES64_CD184plus_endoderm_replicate_1 HUES64_CD184plus_endoderm_replicate_1 28056602 24.1109654333764 23 16 31 27414418 25339607 8479078 132022
HUES64_CD184plus_endoderm_replicate_2 HUES64_CD184plus_endoderm_replicate_2 28072381 46.0670219601251 45 31 60 27811170 27225631 21639724 7244895
HUES64_derived_CD56plus_ectoderm_replicate_1 HUES64_derived_CD56plus_ectoderm_replicate_1 28072823 49.0702776845777 48 31 66 27682015 26852043 21424018 9331348
HUES64_derived_CD56plus_ectoderm_replicate_2 HUES64_derived_CD56plus_ectoderm_replicate_2 27970255 32.6407384201538 32 18 45 26794608 24958915 15109402 2208844
HUES64_derived_CD56plus_mesoderm_replicate_1 HUES64_derived_CD56plus_mesoderm_replicate_1 27984259 33.3711457216001 32 19 45 26903457 25172072 15286641 2580052
HUES64_derived_CD56plus_mesoderm_replicate_2 HUES64_derived_CD56plus_mesoderm_replicate_2 27937828 18.6238667515599 18 12 25 26245106 22736511 3396264 68879
HUES64_replicate_1 HUES64_replicate_1 27520417 24.4012571829853 22 12 34 25236294 22208965 9316237 711744
HUES64_replicate_2 HUES64_replicate_2 27869991 31.0455412777134 28 16 43 26469474 24359006 13294057 2426916
human_sperm human_sperm 26969609 5.50196000246055 5 3 7 13525098 2779194 76103 24924
IMR90 IMR90 26932769 10.3779901353626 9 5 14 21150496 13064433 257882 41912
mobilized_CD34 mobilized_CD34 27933050 30.6677836469702 30 20 40 27309281 25961367 14510352 680226
subcutaneous_adipocyte_nuclei subcutaneous_adipocyte_nuclei 26757606 11.2572921508748 10 5 15 20970169 13434431 688220 53912
substantia_nigra substantia_nigra 27528311 24.0420087160451 22 13 34 25580542 22735757 9030611 407439
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 28158385 methylation sites.

Sequencing Coverage Thresholds

In total, between 0.0 and 7.0 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.