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
AML_BM_B_UMCG_2007_229 AML_BM_B_UMCG_2007_229 25107202 29.3062735544964 27 14 41 23328219 21150362 11149162 1618286
AML_BM_B_UMCG_2009_052 AML_BM_B_UMCG_2009_052 25901732 29.3768953751819 27 15 41 24255640 22171960 11711913 1472059
AML_BM_B_UMCG_2012_082 AML_BM_B_UMCG_2012_082 25540641 29.3483627525245 28 16 40 24078518 22170363 11766846 1122539
AML_PBMC_V_UMCG_2003_180 AML_PBMC_V_UMCG_2003_180 25452676 30.3190954067069 28 16 42 23863602 21871302 11972114 1719725
AML_PBMC_V_UMCG_2004_152 AML_PBMC_V_UMCG_2004_152 25887176 27.7129779625248 26 15 38 24319612 22201410 10837406 861598
AML_PBMC_V_UMCG_2007_282 AML_PBMC_V_UMCG_2007_282 25247828 30.5275060096259 28 16 42 23675955 21710342 11986198 1783389
Bcell_gc_T_T14/10 Bcell_gc_T_T14/10 26132710 49.5147116774341 48 29 67 25288691 24394669 19321130 8915461
Bcell_mem_V_C003N3 Bcell_mem_V_C003N3 24495214 45.6681886102322 34 15 65 22391550 20345119 13442479 6891339
Bcell_mem_V_NC11/41 Bcell_mem_V_NC11/41 25989452 50.4815968801497 50 33 67 25375208 24739333 20475126 9200501
Bcell_mem_V_S004P1 Bcell_mem_V_S004P1 24548194 37.6019783369807 32 16 53 22800829 20866523 13000979 4909198
Bcell_naive_V_NC11/41 Bcell_naive_V_NC11/41 26580392 48.2925869189589 47 30 65 25826932 25031783 20013772 8513110
Bcell_naive_V_S001JP Bcell_naive_V_S001JP 25700247 31.2308824502737 28 15 44 23879654 21683276 11974401 2529360
Bcell_naive_V_S00DM8 Bcell_naive_V_S00DM8 25682545 34.2586558691905 28 14 48 23634260 21320684 12308345 4047624
Bcell_naive_C_C003K9 Bcell_naive_C_C003K9 26023517 32.1191376630607 29 16 44 24602482 22704496 12902189 2407874
Bcell_naive_C_C0068L Bcell_naive_C_C0068L 26174382 29.7077181039079 29 17 40 24933320 23222067 12491788 947618
Bcell_pre_B_F2012-2912 Bcell_pre_B_F2012-2912 26644451 52.8574554604259 51 30 72 25806797 24932296 20131916 10533218
DC_C_S00CP6 DC_C_S00CP6 25363524 32.7784624486724 27 13 46 23148375 20724571 11651097 3657941
DC_C_S00D71 DC_C_S00D71 25986887 33.3138599094228 30 17 47 24447778 22545736 13356805 2978268
Endo_prol_C_S00BJM Endo_prol_C_S00BJM 24722834 34.2545850932785 26 12 48 22240630 19699748 11172349 4272382
Endo_prol_C_S00DCS Endo_prol_C_S00DCS 25077572 32.3665392726218 28 14 46 23072116 20799794 11762698 3241439
Endo_rest_C_S00BJM Endo_rest_C_S00BJM 25778338 30.1845347826536 27 14 42 23998536 21667930 11537314 2064191
Endo_rest_C_S00DCS Endo_rest_C_S00DCS 24022513 30.6901830795138 23 10 43 21367217 18435523 9646368 3180131
Eosi_mat_V_S006XE Eosi_mat_V_S006XE 25616433 36.2724314895833 31 16 51 23860571 21870660 13499072 4507182
Eryth_C_S002R5 Eryth_C_S002R5 24375791 37.8735738257684 24 10 50 21289908 18398460 10353915 4903481
Eryth_C_S002S3 Eryth_C_S002S3 25429396 30.300025096939 27 14 42 23650090 21389189 11437045 2151660
Leuk_myel_B_pz284_ATRA Leuk_myel_B_pz284_ATRA 25218276 25.6162008457676 24 13 35 23479169 21078933 9260359 535538
Leuk_myel_B_pz284_CTR Leuk_myel_B_pz284_CTR 25191932 26.425574584752 24 13 37 23404659 21019214 9689064 785531
Leuk_myel_B_pz289_CTR Leuk_myel_B_pz289_CTR 23657658 21.3186995517477 13 6 28 18796260 14287299 5476150 1565031
Leuk_myel_B_pz290_CTR Leuk_myel_B_pz290_CTR 25482308 16.7865838133657 15 9 23 22926131 18642180 2608802 33275
MK_C_S004BT MK_C_S004BT 24149293 29.941471702712 20 8 42 20662999 17425762 8917617 3382752
MPP_B_F2012-2912 MPP_B_F2012-2912 26634910 49.3841042826876 48 28 67 25790820 24882803 19597634 9156443
Mac_f0_V_C005VG Mac_f0_V_C005VG 25768435 25.1763367856837 22 11 35 23438402 20446229 8923506 968490
Mac_f0_V_N000314138902_t6BG Mac_f0_V_N000314138902_t6BG 25946012 34.7130220628897 32 18 48 24558932 22898857 14323384 3268673
Mac_f0_V_N000314138902_t6 Mac_f0_V_N000314138902_t6 25316808 33.8710807460403 30 15 48 23382253 21287304 12670209 3727445
Mac_f0_V_S001S7 Mac_f0_V_S001S7 26021160 24.4603729810662 23 14 33 24416866 21937627 8658740 311986
Mac_f0_V_S0022I Mac_f0_V_S0022I 25770983 29.019635766319 27 15 40 24140630 22051080 11456868 1315559
Mac_f0_V_S00390 Mac_f0_V_S00390 25843423 25.7384065183625 24 14 35 24099698 21662230 9529239 499285
Mac_f0_C_S00BHQ Mac_f0_C_S00BHQ 25061969 32.615739170374 26 12 46 22640895 20031224 11083350 3788359
Mac_f0_C_S00DVR Mac_f0_C_S00DVR 24661473 31.6338895896445 21 9 43 21448843 18296861 9458464 3735610
Mac_f1_V_S001MJ Mac_f1_V_S001MJ 25627388 24.5887713956647 22 12 34 23644555 20968546 8624362 451047
Mac_f1_V_S001S7 Mac_f1_V_S001S7 26189375 25.1398240316922 24 14 34 24765749 22507830 9212417 307669
Mac_f1_V_S0022I Mac_f1_V_S0022I 26067006 27.7461727288512 26 15 38 24499038 22311981 10903011 904723
Mac_f1_V_S00H6O Mac_f1_V_S00H6O 26257331 34.5758630227878 33 19 47 25079915 23554224 14709214 2757004
Mac_f1_C_S0018A Mac_f1_C_S0018A 25248342 36.7926379086595 28 13 53 22929189 20530900 12278934 5085327
Mac_f1_C_S007SK Mac_f1_C_S007SK 25599479 38.2198274425819 32 15 55 23648337 21573136 13540142 5404243
Mac_f2_V_S00622 Mac_f2_V_S00622 26131000 24.2267548888294 23 15 32 24800690 22627424 8415626 129368
Mac_f2_V_S006VI Mac_f2_V_S006VI 25326737 27.842218245485 22 11 38 22956461 19845455 9356652 2144694
Mac_f2_V_S00BS4 Mac_f2_V_S00BS4 25954842 29.2919331198394 26 14 40 24106953 21665817 11059243 1764057
Mac_f2_V_S00FTN Mac_f2_V_S00FTN 26022633 33.6847652964248 32 18 46 24753289 23148168 14105676 2520991
Mac_f2_C_S00C1H Mac_f2_C_S00C1H 25100115 34.8266170095237 26 12 49 22602382 20035127 11416114 4473719
Mono_V_C000S5 Mono_V_C000S5 26735686 52.6520655950253 52 34 70 26085349 25452718 21286500 10423888
Mono_V_C0010K Mono_V_C0010K 26762320 42.6434993304019 42 30 54 26180415 25650913 20410225 4397548
Mono_V_C001UY Mono_V_C001UY 26720268 59.2419619069689 58 36 80 26052024 25413833 21651241 12751325
Mono_V_C004SQ Mono_V_C004SQ 25805136 87.4247031676175 85 52 119 25271424 24838505 22785851 17997865
Mono_V_N000314138902_t0 Mono_V_N000314138902_t0 25754294 32.3533992040318 30 16 45 24158636 22220927 12921360 2645245
Mono_V_S007G7 Mono_V_S007G7 25672838 33.966778390453 29 14 48 23633364 21394541 12542148 3899447
Mono_C_C005PS Mono_C_C005PS 25859653 96.4475333833753 95 60 129 25386497 25043465 23486554 19555418
Mono_C_S000RD Mono_C_S000RD 26756547 54.1582777852464 53 35 71 26168865 25623819 21776062 10868841
NK_V_C002CT NK_V_C002CT 26346026 41.2475276536962 39 23 56 25327800 24111597 17206725 5628614
NK_V_C006G5 NK_V_C006G5 25895683 30.046352977058 28 16 42 24419538 22498121 12283626 1385374
Neut_mat_V_C000S5 Neut_mat_V_C000S5 26806644 41.8281589817808 41 29 53 26244817 25712109 19838349 4185630
Neut_mat_V_C0010K Neut_mat_V_C0010K 26781467 49.4371356505601 49 34 63 26219801 25740274 21828431 8338783
Neut_mat_V_C0011I Neut_mat_V_C0011I 26376958 47.6567104515995 46 28 65 25533303 24623877 19242478 8216388
Neut_mat_V_C001UY Neut_mat_V_C001UY 26689925 63.7070768838803 62 38 86 26025810 25386884 21887203 14040602
Neut_mat_C_C00184 Neut_mat_C_C00184 26131179 61.6159850269289 53 27 88 24960838 23792386 18922884 11724455
Neut_mat_C_C004GD Neut_mat_C_C004GD 26445360 62.1480591680355 59 35 85 25690834 24959259 21161128 13140074
Plas_B_MO7071 Plas_B_MO7071 26223236 43.9559267208669 44 31 56 25674935 25169713 20487155 4957615
Plas_B_V156 Plas_B_V156 26282827 42.4420474251115 42 30 54 25739521 25187640 19922457 4278712
TCD4_V_S007DD TCD4_V_S007DD 25280628 35.3000224915299 27 12 50 22717780 20143049 11579536 4605109
TCD4_V_S008H1 TCD4_V_S008H1 25099962 34.8429073318916 24 10 49 22137554 19311950 10823667 4586866
TCD4_V_S009W4 TCD4_V_S009W4 25325735 35.137675333016 27 12 50 22888319 20412891 11853156 4557702
TCD4_cenM_V_S006YC TCD4_cenM_V_S006YC 25005543 35.4114424149877 29 14 50 22969193 20751990 12264335 4401247
TCD4_effM_V_S001U3 TCD4_effM_V_S001U3 25253878 39.3973166814222 35 18 55 23840609 22207317 14618567 5295001
TCD8_V_C00256 TCD8_V_C00256 26464766 37.8480486092339 36 22 51 25483171 24248990 16459434 3871088
TCD8_V_C003VO TCD8_V_C003VO 26221686 29.2646967094336 28 17 39 25029883 23356287 12226390 740281
TCD8_C_C0066P TCD8_C_C0066P 26133409 23.7095764658947 22 13 32 24488906 21954534 8071197 202423
TCD8_C_S00C2F TCD8_C_S00C2F 25079426 34.8303824018939 25 11 49 22166152 19389754 10949197 4589330
TCD8_cenM_V_C005UI TCD8_cenM_V_C005UI 26009778 27.7772870264406 27 16 38 24785039 22950146 11355906 442455
TCD8_effM_V_C00256 TCD8_effM_V_C00256 25581773 36.9493790754847 34 19 51 24332484 22775271 14725199 4077632
TCD8_term_V_S002ND TCD8_term_V_S002ND 24479237 36.8717319906662 29 14 52 22393905 20162268 12054814 4778190
Treg_V_S001U3 Treg_V_S001U3 25813847 35.256875234443 32 18 49 24383013 22653075 14064428 3617396
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 28571135 methylation sites.

Sequencing Coverage Thresholds

In total, between 8.9 and 14.0 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.