Data-Driven NGS Quality Control Guidelines

The data-driven guidelines detailed below for the quality control of next-generation sequencing (NGS) files were generated by comparing 47 quality features on 2000+ FastQ files manually labelled for quality. Guidelines have been generated for specific organisms and assays, and also for experimental conditions related to particular cell types or ChIP protein and antibody targets. Focus is given to the understanding of individual quality features and their effective combination.

Guideline Documents

  • Scientific publication (link to article): detailed motivations, methods, results and discussion.
  • Decision trees (link to PDF): methods summary and decision trees to classify NGS files by quality in a selection of data subsets
  • Interactive tables (below on this page): compare classification performance of the quality features in a selection of data subsets
  • Online interactive dashboard (external web site): compare values of the quality features in user-defined data subsets, including statistical test results on selected subsets

Data Subsets and Quality Features

Data: human, mouse, single-ended, paired-ended, RNA-seq (polyA+, total and small RNAs), ChIP-seq (transcription factor, histone and control), DNase-seq

Types of Quality Features

  • raw reads statistics from FastQC (RAW)
  • genome mapping statistics from Bowtie2 (MAP)
  • genomic localization of mapped reads (LOC)
  • TSS-relative localization of mapped reads (TSS)

Data subsets are defined by unique combinations of the following parameters:

  • Group 1 subsets: organism, run type, assay
  • Group 2 subsets: organism, run type, assay title
  • Group A subsets: organism, run type, assay title, biological sample
  • Group B subsets: organism, run type, assay title, ChIP protein target
  • Group C subsets: organism, run type, assay title, ChIP antibody target

Citations

Citing the scientific article and this web page:

Maximilian Sprang, Matteo Kr├╝ger, Miguel A Andrade-Navarro, Jean-Fred Fontaine
Statistical NGS quality control guidelines
Life Science Alliance Aug 2021, 4 (11) e202101113;
https://doi.org/10.26508/lsa.202101113

Our software to derive quality features and automatically classify NGS files by quality:

Albrecht, S., Sprang, M., Andrade-Navarro, M.A., Fontaine, J.F.
seqQscorer: automated quality control of next-generation sequencing data using machine learning.
Genome Biol 22, 75 (2021).
https://doi.org/10.1186/s13059-021-02294-2

Classification Performance of the Quality Features

Each table has 1 row per quality feature and 1 column per data subset. Performance is measured by area under ROC curve from 0.5 (random) to 1.0 (perfect classification)

Group 1 Subsets (High-Level)

Area under ROC curves for group 1 subsets in the NGS guidelines. The higher the area, the better the classification.
Featurehuman__ChIP-seq__single-endedhuman__RNA-seq__single-endedmouse__ChIP-seq__single-endedhuman__DNase-seq__paired-endedhuman__ChIP-seq__paired-endedmouse__DNase-seq__paired-ended
RAW_Basic_Statistics0.50.50.50.50.50.5
RAW_Per_base_sequence_quality0.70190569133950.572704081632650.866112418502370.514705882352940.503546099290780.53571428571429
RAW_Per_tile_sequence_quality0.505905571022260.504783163265310.548840708306010.665897731641680.554625018862230.59722222222222
RAW_Per_sequence_quality_scores0.744449531932530.510841836734690.881505343158060.514705882352940.50.5
RAW_Per_base_sequence_content0.603750221417140.571428571428570.555032599050960.627450980392160.624943413309190.66666666666667
RAW_Per_sequence_GC_content0.604487164490370.573660714285710.778635083523010.735294117647060.520295759770640.67318594104308
RAW_Per_base_N_content0.73306117128830.517857142857140.846649434821190.514657823913880.507092198581560.5
RAW_Sequence_Length_Distribution0.502742230347350.526785714285710.555900621118010.50.602836879432620.5
RAW_Sequence_Duplication_Levels0.505738463749420.64381377551020.51562439720690.677287581699350.50025149640360.61422902494331
RAW_Overrepresented_sequences0.679509974633120.691167091836730.893831256510170.680843906189930.505130526633470.59608843537415
RAW_Adapter_Content0.510958894953030.65003188775510.503105590062110.767925797770090.528368794326240.54166666666667
RAW_Kmer_Content0.546434097904810.526785714285710.560510782763010.50.515643076304010.5
MAP_SE_no_mapping0.725758583465070.750956632653060.9414567339223
MAP_SE_uniquely0.733485623761320.559948979591840.94465877088075
MAP_SE_multiple0.705127519559910.783163265306120.8724393349022
MAP_SE_overall0.725758583465070.750956632653060.9414567339223
MAP_MI_no_mapping0.725758583465070.750956632653060.94145673392230.795751633986930.616191338463860.74716553287982
MAP_MI_uniquely0.733485623761320.559948979591840.944658770880750.758602460592080.666465469543790.7624716553288
MAP_MI_multiple0.705127519559910.783163265306120.87243933490220.792195309496350.649564911221770.5890022675737
MAP_MI_overall0.725758583465070.750956632653060.94145673392230.811466743560170.64752779035260.74178004535147
MAP_PE_con_no_mapping0.795751633986930.616191338463860.74716553287982
MAP_PE_con_uniquely0.758602460592080.666465469543790.7624716553288
MAP_PE_con_multiple0.792195309496350.649564911221770.5890022675737
MAP_PE_dis_uniquely0.675413302575930.596297972938990.61507936507937
MAP_PE_cod_no_mapping0.78734140715110.546074141139780.58446712018141
MAP_PE_cod_uniquely0.819059976931950.670413963080330.61111111111111
MAP_PE_cod_multiple0.735390234525180.55950404909210.59467120181406
MAP_PE_overall0.811466743560170.64752779035260.74178004535147
LOC_Promoter0.535378280733530.725765306122450.575286447282130.773068050749710.61591469241990.96315192743764
LOC_5_UTR0.568148016937990.583227040816330.51340611859110.735101883890810.614556611840450.92687074829932
LOC_3_UTR0.55652069289360.71715561224490.571698622738320.540945790080740.701624666767270.7046485260771
LOC_1st_Exon0.588147415351810.508290816326530.514023378727670.708958093041140.600975806045970.8656462585034
LOC_Other_Exon0.634309128401890.536352040816330.728868485012150.647539407920030.656858306926210.83786848072562
LOC_1st_Intron0.576479985561930.501913265306120.53998688322210.571703191080350.607514712539610.84580498866213
LOC_Other_Intron0.536758586807210.72193877551020.590602214420740.737504805843910.561390272119110.79818594104308
LOC_Downstream0.552653830600020.674426020408160.521044712781140.677816224529030.67219958754590.74659863945578
LOC_Distal_Intergenic0.585640806259170.669323979591840.564175764823890.726066897347170.633921834917760.97108843537415
TSS_-45000.526322737618190.552295918367350.500887311446320.580738177623990.73605452442030.56349206349206
TSS_-35000.514994535592180.6406250.578604220516180.558102652825840.730773099944670.5391156462585
TSS_-25000.503246894311330.678571428571430.508101539292470.518502499038830.723731200643830.61904761904762
TSS_-15000.569708798866340.608099489795920.547548319895070.603517877739330.661812786077160.79365079365079
TSS_-5000.530345009675510.54846938775510.590582925041470.792099192618220.669030732860520.94784580498866
TSS_+5000.535829470370210.570790816326530.502796959993830.772106881968470.658719380312860.87471655328798
TSS_+15000.574606713033360.797831632653060.537479263917290.705113417916190.654293043609480.83786848072562
TSS_+25000.593275937555350.60618622448980.522067049882330.538831218762010.666742115587750.7375283446712
TSS_+35000.536765271098130.552136479591840.537537132055090.527297193387160.704416276847240.71003401360544
TSS_+45000.513216514209130.644132653061220.566355464681150.542243367935410.721090488406020.69387755102041

Group 2 Subsets (High-Level)

Area under ROC curves for group 2 subsets in the NGS guidelines. The higher the area, the better the classification.
Featurehuman__Control ChIP-seq__single-endedhuman__Histone ChIP-seq__single-endedhuman__TF ChIP-seq__single-endedhuman__polyA plus RNA-seq__single-endedhuman__small RNA-seq__single-endedmouse__Histone ChIP-seq__single-endedmouse__TF ChIP-seq__single-endedmouse__Control ChIP-seq__single-endedhuman__DNase-seq__paired-endedhuman__TF ChIP-seq__paired-endedhuman__Control ChIP-seq__paired-endedmouse__DNase-seq__paired-endedhuman__Histone ChIP-seq__paired-ended
RAW_Basic_Statistics0.50.50.50.50.50.50.50.50.50.50.50.50.5
RAW_Per_base_sequence_quality0.849527665317140.509201516263150.731783127997740.544994944388270.574380165289260.784914361001320.862822487485560.876050420168070.514705882352940.50.50.535714285714290.51388888888889
RAW_Per_tile_sequence_quality0.515182186234820.500672536072390.516745039029440.559150657229520.582644628099170.568511198945980.536869464767040.565826330532210.665897731641680.613402061855670.585470085470090.597222222222220.57777777777778
RAW_Per_sequence_quality_scores0.833333333333330.527237710931770.781656164770060.543478260869570.57024793388430.777338603425560.917404697728150.887955182072830.514705882352940.50.50.50.5
RAW_Per_base_sequence_content0.639507422402160.514184397163120.579046365089810.572800808897880.50.515151515151520.537350789372350.605042016806720.627450980392160.649885452462770.505128205128210.666666666666670.65
RAW_Per_sequence_GC_content0.67459514170040.638725849841040.560599078341010.678968655207280.515151515151520.751976284584980.819118213323070.66876750700280.735294117647060.51065292096220.531623931623930.673185941043080.62777777777778
RAW_Per_base_N_content0.827091767881240.567161897774520.763933038653250.541961577350860.515151515151520.726943346508560.92346938775510.786414565826330.514657823913880.505154639175260.50.50.6
RAW_Sequence_Length_Distribution0.514844804318490.50308755196870.503456221198160.565217391304350.50.598484848484850.50.559523809523810.50.655555555555560.525641025641030.50.54166666666667
RAW_Sequence_Duplication_Levels0.520917678812420.517761066275370.531764318630680.881193124368050.50.500658761528330.530997304582210.558123249299720.677287581699350.509106529209620.566666666666670.614229024943310.5
RAW_Overrepresented_sequences0.781713900134950.525525800929320.667948838521580.601112234580380.560606060606060.823616600790510.921447824412780.886554621848740.680843906189930.531615120274910.628205128205130.596088435374150.58333333333333
RAW_Adapter_Content0.513157894736840.505319148936170.516049092448040.645096056622850.893939393939390.50.505102040816330.50.767925797770090.550.512820512820510.541666666666670.5
RAW_Kmer_Content0.570850202429150.580520909757890.516335935295780.565217391304350.590909090909090.657279314888010.558240277242970.515406162464990.50.509507445589920.592307692307690.50.63888888888889
MAP_SE_no_mapping0.796221322537110.508131572511620.733358412489420.743174924165820.573002754820940.891633728590250.956873315363880.96778711484594
MAP_SE_uniquely0.776653171390010.549278552213260.7399840120380.796764408493430.603305785123970.913866930171280.958317289179820.97619047619048
MAP_SE_multiple0.840924426450740.571594521887990.750343270948930.979777553083920.564738292011020.702898550724640.926261070465920.89355742296919
MAP_SE_overall0.796221322537110.508131572511620.733358412489420.743174924165820.573002754820940.891633728590250.956873315363880.96778711484594
MAP_MI_no_mapping0.796221322537110.508131572511620.733358412489420.743174924165820.573002754820940.891633728590250.956873315363880.967787114845940.795751633986930.641008018327610.630769230769230.747165532879820.55
MAP_MI_uniquely0.776653171390010.549278552213260.7399840120380.796764408493430.603305785123970.913866930171280.958317289179820.976190476190480.758602460592080.692726231386030.735042735042730.76247165532880.53333333333333
MAP_MI_multiple0.840924426450740.571594521887990.750343270948930.979777553083920.564738292011020.702898550724640.926261070465920.893557422969190.792195309496350.678465063001150.675213675213680.58900226757370.78888888888889
MAP_MI_overall0.796221322537110.508131572511620.733358412489420.743174924165820.573002754820940.891633728590250.956873315363880.967787114845940.811466743560170.634879725085910.69743589743590.741780045351470.80833333333333
MAP_PE_con_no_mapping0.795751633986930.641008018327610.630769230769230.747165532879820.55
MAP_PE_con_uniquely0.758602460592080.692726231386030.735042735042730.76247165532880.53333333333333
MAP_PE_con_multiple0.792195309496350.678465063001150.675213675213680.58900226757370.78888888888889
MAP_PE_dis_uniquely0.675413302575930.548854524627720.80170940170940.615079365079370.88888888888889
MAP_PE_cod_no_mapping0.78734140715110.522680412371130.627350427350430.584467120181410.65
MAP_PE_cod_uniquely0.819059976931950.668384879725090.678632478632480.611111111111110.71666666666667
MAP_PE_cod_multiple0.735390234525180.601374570446740.533333333333330.594671201814060.65555555555556
MAP_PE_overall0.811466743560170.634879725085910.69743589743590.741780045351470.80833333333333
LOC_Promoter0.570850202429150.707569087796530.586767610269910.700707785642060.575757575757580.599143610013180.578167115902960.679271708683470.773068050749710.718213058419240.562393162393160.963151927437640.66111111111111
LOC_5_UTR0.535425101214570.715456101736370.602022006959470.840242669362990.647382920110190.658432147562580.540623796688490.570028011204480.735101883890810.699312714776630.617094017094020.926870748299320.65
LOC_3_UTR0.544197031039140.556065052580090.656898335371010.519716885743170.793388429752070.641304347826090.627069695802850.533613445378150.540945790080740.730355097365410.709401709401710.70464852607710.85
LOC_1st_Exon0.51383265856950.716984592809980.628298692748990.603640040444890.61983471074380.661396574440050.544859453215250.614845938375350.708958093041140.68361970217640.574358974358970.86564625850340.66111111111111
LOC_Other_Exon0.543522267206480.672474932746390.672293802313550.901921132457030.661157024793390.785902503293810.705044281863690.738095238095240.647539407920030.649255441008020.683760683760680.837868480725620.9
LOC_1st_Intron0.548245614035090.734348251406210.522232671870590.574317492416580.567493112947660.626152832674570.522718521370810.537815126050420.571703191080350.702290950744560.531623931623930.845804988662130.81111111111111
LOC_Other_Intron0.525978407557350.576363414037660.591432333301980.639029322548030.719008264462810.549407114624510.685598767809010.542016806722690.737504805843910.526918671248570.514529914529910.798185941043080.72222222222222
LOC_Downstream0.592780026990550.575996576180.619900310354560.623862487360970.716253443526170.622529644268770.601848286484410.561624649859940.677816224529030.705612829324170.545299145299150.746598639455780.63888888888889
LOC_Distal_Intergenic0.519905533063430.730496453900710.596896454434310.86855409504550.603305785123970.708498023715420.532730073161340.509803921568630.726066897347170.731386025200460.507692307692310.971088435374150.77777777777778
TSS_-45000.587719298245610.555881633651260.595189504373180.716885743174920.710743801652890.570322793148880.548517520215630.547619047619050.580738177623990.753665521191290.717094017094020.563492063492060.96666666666667
TSS_-35000.591093117408910.54074957202250.600352675632460.648129423660260.820936639118460.615612648221340.620908740854830.711484593837540.558102652825840.743928980526920.69572649572650.53911564625850.97777777777778
TSS_-25000.578947368421050.502659574468090.603216401768080.60465116279070.707988980716250.582345191040840.546110897189060.533613445378150.518502499038830.747594501718210.670085470085470.619047619047620.96111111111111
TSS_-15000.567476383265860.670212765957450.614502022006960.507583417593530.581267217630850.594202898550720.53051597997690.633053221288520.603517877739330.752290950744560.617094017094020.793650793650790.75
TSS_-5000.573549257759780.676510149180730.590139189316280.823053589484330.710743801652890.572793148880110.563919907585680.7030812324930.792099192618220.746391752577320.647863247863250.947845804988660.65555555555556
TSS_+5000.565452091767880.683449498654930.580612244897960.84327603640040.680440771349860.557971014492750.542549095109740.56722689075630.772106881968470.730927835051550.646153846153850.874716553287980.65
TSS_+15000.559379217273950.719002201027150.602736762907930.783619817997980.840220385674930.609354413702240.596264921062760.672268907563030.705113417916190.743528064146620.610256410256410.837868480725620.7
TSS_+25000.561403508771930.693384690633410.619194959089630.70980788675430.713498622589530.6169301712780.539468617635730.731092436974790.538831218762010.729209621993130.671794871794870.73752834467120.82222222222222
TSS_+35000.55819838056680.568629249205180.614553747766390.773003033367040.710743801652890.691040843214760.506738544474390.523109243697480.527297193387160.733390607101950.649572649572650.710034013605440.97222222222222
TSS_+45000.579284750337380.509384935191980.60232295683250.645096056622850.749311294765840.665513833992090.590392760877940.510504201680670.542243367935410.729324169530360.654700854700850.693877551020410.98333333333333

Group A Subsets (Biological Sample Specificity)

Area under ROC curves for group A subsets in the NGS guidelines. The higher the area, the better the classification.
Featurehuman__TF ChIP-seq__single-ended__H1human__TF ChIP-seq__single-ended__HeLa-S3human__TF ChIP-seq__single-ended__HepG2human__TF ChIP-seq__single-ended__K562human__polyA plus RNA-seq__single-ended__GM12878human__TF ChIP-seq__single-ended__A549human__TF ChIP-seq__single-ended__GM12878human__Control ChIP-seq__single-ended__GM12878human__TF ChIP-seq__single-ended__MCF-7human__TF ChIP-seq__single-ended__SK-N-SHhuman__Histone ChIP-seq__single-ended__MCF-7human__Control ChIP-seq__single-ended__HepG2human__TF ChIP-seq__single-ended__IMR-90human__TF ChIP-seq__single-ended__MCF_10Amouse__TF ChIP-seq__single-ended__MEL_cell_linemouse__Control ChIP-seq__single-ended__MEL_cell_linemouse__TF ChIP-seq__single-ended__CH12.LXhuman__TF ChIP-seq__paired-ended__HepG2human__TF ChIP-seq__paired-ended__K562human__TF ChIP-seq__paired-ended__MCF-7human__TF ChIP-seq__paired-ended__GM12878human__DNase-seq__paired-ended__transverse_colonhuman__DNase-seq__paired-ended__thyroid_glandhuman__TF ChIP-seq__paired-ended__HEK293human__Histone ChIP-seq__single-ended__gastrocnemius_medialishuman__DNase-seq__paired-ended__body_of_pancreasmouse__DNase-seq__paired-ended__limbmouse__DNase-seq__paired-ended__hindbrainmouse__DNase-seq__paired-ended__midbrainhuman__DNase-seq__paired-ended__limbhuman__Control ChIP-seq__paired-ended__PC-9human__DNase-seq__paired-ended__neural_progenitor_cell
RAW_Basic_Statistics0.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.5
RAW_Per_base_sequence_quality0.727158948685860.682539682539680.587662337662340.69846976401180.944444444444440.650.64843750.833333333333330.8181818181818210.80357142857143110.83750.955303030303030.954545454545450.884615384615380.50.50.50.50.550.520833333333330.50.50.538461538461540.538461538461540.50.6250.50.50.5
RAW_Per_tile_sequence_quality0.514392991239050.502976190476190.518398268398270.526456489675520.750.533928571428570.557904411764710.6250.712121212121210.566406250.589285714285710.833333333333330.6906250.66250.640909090909090.535353535353540.567873303167420.60.780487804878050.818181818181820.715909090909090.783333333333330.979166666666670.618037135278510.50.857142857142860.521978021978020.590909090909090.60.781250.666666666666670.5
RAW_Per_sequence_quality_scores0.747183979974970.769841269841270.675324675324680.702986725663720.750.7250.852941176470590.833333333333330.8181818181818210.92857142857143110.90.943939393939390.9545454545454510.50.50.50.50.550.520833333333330.50.50.50.50.50.50.50.50.5
RAW_Per_base_sequence_content0.522528160200250.68750.556818181818180.612278761061950.750.560714285714290.651654411764710.770833333333330.681818181818180.6250.50.888888888888890.5250.6656250.52196969696970.565656565656570.576923076923080.50.601626016260160.590909090909090.6250.850.93750.525198938992040.7510.642857142857140.580808080808080.70.56250.777777777777780.5
RAW_Per_sequence_GC_content0.523779724655820.593253968253970.715909090909090.55567846607670.555555555555560.522321428571430.631433823529410.583333333333330.520202020202020.52343750.7510.8250.71250.916666666666670.818181818181820.849547511312220.60.642276422764230.545454545454550.5568181818181810.895833333333330.516578249336870.550.961538461538460.648351648351650.777777777777780.80.6250.50.66666666666667
RAW_Per_base_N_content0.71714643304130.821428571428570.702380952380950.747418879056050.611111111111110.680357142857140.761029411764710.770833333333330.7222222222222210.642857142857141110.977272727272730.8181818181818210.50.512195121951220.50.50.550.520833333333330.50.50.50.50.50.50.50.50.5
RAW_Sequence_Length_Distribution0.50.50.523809523809520.50.50.50.50.50.50.50.50.50.50.50.50.555555555555560.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.5
RAW_Sequence_Duplication_Levels0.535043804755940.543650793650790.505411255411260.554203539823010.944444444444440.5250.501838235294120.50.535353535353540.531250.6250.50.66250.76250.545454545454550.636363636363640.576923076923080.50.536585365853660.545454545454550.50.583333333333330.770833333333330.50.70.807692307692310.560439560439560.707070707070710.8750.5781250.50.75
RAW_Overrepresented_sequences0.669586983729660.761904761904760.69913419913420.66039823008850.555555555555560.592857142857140.6112132352941210.757575757575760.8750.9107142857142910.93750.90.942424242424240.969696969696970.957013574660630.70.524390243902440.727272727272730.57954545454545110.547745358090190.7510.571428571428570.636363636363640.70.62510.5
RAW_Adapter_Content0.558823529411760.535714285714290.511904761904760.504424778761060.888888888888890.50.531250.50.50.56250.50.50.50.50.50.50.50.50.50.50.510.833333333333330.50.50.50.571428571428570.50.50.6250.50.5
RAW_Kmer_Content0.617647058823530.583333333333330.524350649350650.515025811209440.50.622321428571430.500919117647060.604166666666670.621212121212120.6718750.857142857142860.50.550.550.580303030303030.616161616161620.588235294117650.60.50.50.50.50.50.50.6750.50.50.50.50.50.611111111111110.5
MAP_SE_no_mapping0.704630788485610.835317460317460.60173160173160.645095870206490.888888888888890.622321428571430.691176470588240.750.9595959595959610.92857142857143110.956250.99393939393939110.55
MAP_SE_uniquely0.669586983729660.84523809523810.590909090909090.644358407079650.50.623214285714290.706801470588240.958333333333330.8484848484848511110.943750.99545454545455110.6
MAP_SE_multiple0.843554443053820.792658730158730.642857142857140.680955014749260.888888888888890.671428571428570.789522058823530.750.9797979797979810.85714285714286110.96250.9818181818181810.995475113122170.65
MAP_SE_overall0.704630788485610.835317460317460.60173160173160.645095870206490.888888888888890.622321428571430.691176470588240.750.9595959595959610.92857142857143110.956250.99393939393939110.55
MAP_MI_no_mapping0.704630788485610.835317460317460.60173160173160.645095870206490.888888888888890.622321428571430.691176470588240.750.9595959595959610.92857142857143110.956250.99393939393939110.760.756097560975610.681818181818180.90909090909091110.677718832891250.5510.637362637362640.9797979797979810.7187510.54166666666667
MAP_MI_uniquely0.669586983729660.84523809523810.590909090909090.644358407079650.50.623214285714290.706801470588240.958333333333330.8484848484848511110.943750.99545454545455110.720.845528455284550.727272727272730.75110.606100795755970.60.978021978021980.637362637362640.9797979797979810.687511
MAP_MI_multiple0.843554443053820.792658730158730.642857142857140.680955014749260.888888888888890.671428571428570.789522058823530.750.9797979797979810.85714285714286110.96250.9818181818181810.995475113122170.920.62601626016260.636363636363640.54545454545455110.562334217506630.6510.813186813186810.7727272727272710.7511
MAP_MI_overall0.704630788485610.835317460317460.60173160173160.645095870206490.888888888888890.622321428571430.691176470588240.750.9595959595959610.92857142857143110.956250.993939393939391110.853658536585370.772727272727270.84090909090909110.701591511936340.5510.549450549450550.9797979797979810.7510.5
LOC_Promoter0.727158948685860.565476190476190.505411255411260.5501474926253710.726785714285710.708639705882350.6250.676767676767680.5468750.785714285714290.611111111111110.70.5750.633333333333330.717171717171720.588235294117650.560.56097560975610.772727272727270.6818181818181810.833333333333330.549071618037140.80.648351648351650.857142857142860.95959595959596110.888888888888890.66666666666667
LOC_5_UTR0.640801001251560.553571428571430.531385281385280.5130899705014710.671428571428570.744485294117650.50.717171717171720.6093750.785714285714290.555555555555560.6250.5250.643939393939390.626262626262630.588235294117650.640.577235772357720.818181818181820.510.766666666666670.558355437665780.750.582417582417580.692307692307690.929292929292931110.95833333333333
LOC_3_UTR0.509386733416770.726190476190480.617965367965370.5119837758112110.71250.854779411764710.750.828282828282830.656250.7142857142857110.5750.80.580303030303030.707070707070710.631221719457010.80.617886178861790.590909090909090.8863636363636410.679166666666670.583554376657820.850.824175824175820.527472527472530.929292929292930.7750.5937511
LOC_1st_Exon0.667083854818520.619047619047620.536796536796540.502396755162240.666666666666670.66250.807904411764710.50.727272727272730.6093750.785714285714290.666666666666670.693750.531250.665151515151520.656565656565660.633484162895930.520.528455284552850.909090909090910.7045454545454510.766666666666670.591511936339520.80.516483516483520.527472527472530.919191919191921110.66666666666667
LOC_Other_Exon0.599499374217770.777777777777780.516233766233770.5547566371681410.694642857142860.841911764705880.666666666666670.727272727272730.68750.642857142857140.777777777777780.618750.681250.630303030303030.666666666666670.576923076923080.840.666666666666670.909090909090910.7727272727272710.770833333333330.541114058355440.750.648351648351650.560439560439560.9090909090909110.562510.875
LOC_1st_Intron0.558197747183980.547619047619050.659090909090910.502396755162240.777777777777780.632142857142860.766544117647060.541666666666670.69696969696970.640625110.66250.5750.550.515151515151520.53167420814480.60.87804878048780.50.50.783333333333330.5750.531830238726790.650.70329670329670.81318681318681110.7510.54166666666667
LOC_Other_Intron0.680851063829790.509920634920630.521645021645020.548856932153390.555555555555560.601785714285710.602022058823530.541666666666670.686868686868690.56250.642857142857140.611111111111110.693750.531250.731818181818180.828282828282830.592760180995480.560.56097560975610.909090909090910.5909090909090910.783333333333330.604774535809020.650.846153846153850.648351648351650.9090909090909110.7812510.66666666666667
LOC_Downstream0.722152690863580.541666666666670.508658008658010.508296460176990.888888888888890.6250.806985294117650.50.727272727272730.58593750.607142857142860.666666666666670.70.518750.551515151515150.535353535353540.622171945701360.520.544715447154470.909090909090910.7272727272727310.770833333333330.578249336870030.60.60439560439560.714285714285710.7878787878787910.93750.555555555555560.91666666666667
LOC_Distal_Intergenic0.657071339173970.519841269841270.579004329004330.575405604719760.777777777777780.76250.784007352941180.541666666666670.757575757575760.74218750.785714285714290.777777777777780.606250.550.525757575757580.616161616161620.524886877828050.680.731707317073170.681818181818180.7510.808333333333330.550397877984080.70.846153846153850.879120879120880.98989898989899110.888888888888890.66666666666667
TSS_-45000.516896120150190.613095238095240.501082251082250.527009587020650.666666666666670.717857142857140.747702205882350.541666666666670.747474747474750.52343750.785714285714290.611111111111110.7156250.606250.602272727272730.515151515151520.5067873303167410.739837398373980.727272727272730.6363636363636410.71250.531167108753320.750.692307692307690.70329670329670.5151515151515210.62511
TSS_-35000.501251564455570.644841269841270.521645021645020.523230088495580.555555555555560.685714285714290.795955882352940.6250.747474747474750.50781250.714285714285710.555555555555560.693750.506250.70.69696969696970.61312217194570.880.723577235772360.772727272727270.7272727272727310.754166666666670.522546419098140.70.60439560439560.747252747252750.666666666666670.950.62511
TSS_-25000.546933667083850.579365079365080.508658008658010.5168694690265510.684821428571430.819852941176470.583333333333330.767676767676770.5156250.535714285714290.611111111111110.73750.51250.631818181818180.575757575757580.549773755656110.720.682926829268290.590909090909090.5454545454545510.770833333333330.517241379310340.750.626373626373630.549450549450550.6868686868686910.70312511
TSS_-15000.620775969962450.581349206349210.535714285714290.536780973451330.777777777777780.719642857142860.801470588235290.50.757575757575760.57031250.678571428571430.611111111111110.71250.5406250.506060606060610.636363636363640.59728506787330.520.739837398373980.863636363636360.6818181818181810.791666666666670.572281167108750.70.582417582417580.571428571428570.757575757575761111
TSS_-5000.760951188986230.583333333333330.523809523809520.532448377581120.666666666666670.669642857142860.693014705882350.541666666666670.69696969696970.5468750.785714285714290.555555555555560.693750.550.604545454545450.676767676767680.554298642533940.60.569105691056910.545454545454550.6136363636363610.833333333333330.518567639257290.70.725274725274730.846153846153850.909090909090911111
TSS_+5000.703379224030040.55158730158730.530303030303030.531342182890860.777777777777780.683928571428570.727941176470590.541666666666670.686868686868690.5468750.821428571428570.555555555555560.693750.506250.610606060606060.555555555555560.561085972850680.560.552845528455280.727272727272730.5227272727272710.833333333333330.551724137931030.750.890109890109890.714285714285710.909090909090911111
TSS_+15000.638297872340430.543650793650790.536796536796540.524059734513270.777777777777780.655357142857140.779411764705880.6250.757575757575760.6406250.785714285714290.50.66250.543750.580303030303030.686868686868690.615384615384620.560.666666666666670.909090909090910.5227272727272710.766666666666670.578249336870030.650.516483516483520.527472527472530.727272727272731110.66666666666667
TSS_+25000.560700876095120.605158730158730.557900432900430.519911504424780.666666666666670.716071428571430.819852941176470.541666666666670.737373737373740.656250.714285714285710.611111111111110.7250.5750.516666666666670.666666666666670.524886877828050.720.674796747967480.727272727272730.5681818181818210.76250.538461538461540.80.516483516483520.593406593406590.7272727272727310.7812511
TSS_+35000.518147684605760.559523809523810.540043290043290.501014011799410.944444444444440.721428571428570.799632352941180.541666666666670.752525252525250.63281250.535714285714290.50.693750.6250.519696969696970.69696969696970.533936651583710.80.674796747967480.545454545454550.5227272727272710.768750.549071618037140.80.549450549450550.60439560439560.6868686868686910.5312511
TSS_+45000.529411764705880.597222222222220.516233766233770.519266224188790.777777777777780.739285714285710.840073529411760.541666666666670.747474747474750.57031250.571428571428570.666666666666670.63750.618750.542424242424240.626262626262630.570135746606330.840.674796747967480.636363636363640.6363636363636410.758333333333330.522546419098140.70.560439560439560.747252747252750.8080808080808110.62511
MAP_PE_con_no_mapping0.760.756097560975610.681818181818180.90909090909091110.6777188328912510.637362637362640.9797979797979810.7187510.54166666666667
MAP_PE_con_uniquely0.720.845528455284550.727272727272730.75110.606100795755970.978021978021980.637362637362640.9797979797979810.687511
MAP_PE_con_multiple0.920.62601626016260.636363636363640.54545454545455110.5623342175066310.813186813186810.7727272727272710.7511
MAP_PE_dis_uniquely0.720.983739837398370.545454545454550.6818181818181810.908333333333330.6259946949602110.549450549450550.676767676767680.80.750.888888888888890.66666666666667
MAP_PE_cod_no_mapping0.880.967479674796750.636363636363640.77272727272727110.7267904509283810.692307692307690.69696969696970.60.7511
MAP_PE_cod_uniquely0.640.967479674796750.681818181818180.75110.6976127320954910.593406593406590.737373737373740.750.750.666666666666670.58333333333333
MAP_PE_cod_multiple0.920.967479674796750.590909090909090.7727272727272710.966666666666670.7141909814323610.692307692307690.631313131313130.8750.7511
MAP_PE_overall10.853658536585370.772727272727270.84090909090909110.7015915119363410.549450549450550.9797979797979810.7510.5

Group B Subsets (ChIP Protein Specificity)

Area under ROC curves for group B subsets in the NGS guidelines. The higher the area, the better the classification.
 human__Control ChIP-seq__single-ended__Controlhuman__Histone ChIP-seq__single-ended__H3K4me1human__Histone ChIP-seq__single-ended__H3K36me3human__Histone ChIP-seq__single-ended__H3K27achuman__Histone ChIP-seq__single-ended__H3K27me3human__Histone ChIP-seq__single-ended__H3K4me3human__TF ChIP-seq__single-ended__POLR2Ahuman__Histone ChIP-seq__single-ended__H3K9me3human__Histone ChIP-seq__single-ended__H3K4me2human__TF ChIP-seq__single-ended__CTCFhuman__TF ChIP-seq__single-ended__EP300human__polyA plus RNA-seq__single-ended__nanhuman__small RNA-seq__single-ended__nanhuman__TF ChIP-seq__single-ended__NR3C1human__TF ChIP-seq__single-ended__MAXhuman__TF ChIP-seq__single-ended__MYChuman__Control ChIP-seq__single-ended__rabbit-IgG-controlhuman__TF ChIP-seq__single-ended__RELAhuman__TF ChIP-seq__single-ended__CHD1human__TF ChIP-seq__single-ended__RCOR1human__TF ChIP-seq__single-ended__ELK1human__TF ChIP-seq__single-ended__JUNDhuman__TF ChIP-seq__single-ended__MAZhuman__TF ChIP-seq__single-ended__MXI1human__TF ChIP-seq__single-ended__STAT3human__TF ChIP-seq__single-ended__BACH1human__TF ChIP-seq__single-ended__TCF7L2human__TF ChIP-seq__single-ended__FOSmouse__Histone ChIP-seq__single-ended__H3K27me3mouse__Control ChIP-seq__single-ended__Controlmouse__Histone ChIP-seq__single-ended__H3K27acmouse__Histone ChIP-seq__single-ended__H3K4me3mouse__Histone ChIP-seq__single-ended__H3K36me3mouse__Histone ChIP-seq__single-ended__H3K4me1mouse__TF ChIP-seq__single-ended__POLR2Amouse__TF ChIP-seq__single-ended__CTCFmouse__Histone ChIP-seq__single-ended__H3K9me3human__DNase-seq__paired-ended__nanhuman__Control ChIP-seq__paired-ended__Controlmouse__DNase-seq__paired-ended__nan
RAW_Basic_Statistics0.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.5
RAW_Per_base_sequence_quality0.773284313725490.583333333333330.517316017316020.60317460317460.539473684210530.555555555555560.830303030303030.555555555555560.70.951612903225810.821428571428570.544994944388270.574380165289260.666666666666670.916666666666670.7510.545454545454550.7142857142857110.81110.633333333333330.710.90.783333333333330.877192982456140.50.757142857142860.616666666666670.668831168831170.722222222222220.8615384615384610.514705882352940.50.53571428571429
RAW_Per_tile_sequence_quality0.54534313725490.509259259259260.647186147186150.549603174603170.517543859649120.533333333333330.609090909090910.515151515151520.90.604838709677420.642857142857140.559150657229520.582644628099170.583333333333330.604166666666670.555555555555560.597222222222220.772727272727270.785714285714290.8750.80.6250.90.727272727272730.533333333333330.80.916666666666670.650.850.644736842105260.911764705882350.514285714285710.766666666666670.642857142857140.638888888888890.628205128205130.805555555555560.665897731641680.611888111888110.59722222222222
RAW_Per_sequence_quality_scores0.735294117647060.604166666666670.508658008658010.583333333333330.513157894736840.555555555555560.775757575757580.592592592592590.633333333333330.967741935483870.821428571428570.543478260869570.57024793388430.50.979166666666670.9027777777777810.636363636363640.7142857142857110.81110.666666666666670.710.90.833333333333330.890350877192980.50.771428571428570.616666666666670.649350649350650.715277777777780.8128205128205110.514705882352940.50.5
RAW_Per_base_sequence_content0.575980392156860.67129629629630.590909090909090.50.570175438596490.774074074074070.560606060606060.577441077441080.80.808467741935480.535714285714290.572800808897880.50.666666666666670.531250.631944444444440.506944444444440.545454545454550.642857142857140.583333333333330.616666666666670.56250.550.50.80.60.666666666666670.50.80.607456140350880.764705882352940.542857142857140.691666666666670.59740259740260.750.741025641025640.50.627450980392160.637529137529140.66666666666667
RAW_Per_sequence_GC_content0.586703431372550.601851851851850.69913419913420.65476190476190.710526315789470.751851851851850.575757575757580.5286195286195310.542338709677420.535714285714290.678968655207280.515151515151520.583333333333330.531250.583333333333330.750.681818181818180.510.70.68750.850.636363636363640.80.650.583333333333330.950.733333333333330.645833333333330.833333333333330.80.750.688311688311690.729166666666670.623076923076920.750.735294117647060.59790209790210.67318594104308
RAW_Per_base_N_content0.726102941176470.666666666666670.681818181818180.710317460317460.548245614035090.555555555555560.70.508417508417510.60.959677419354840.750.541961577350860.515151515151520.50.916666666666670.9166666666666710.50.7142857142857110.80.93751110.70.916666666666670.90.833333333333330.782894736842110.558823529411760.642857142857140.60.818181818181820.750.692307692307690.833333333333330.514657823913880.50.5
RAW_Sequence_Length_Distribution0.526348039215690.50.50.535714285714290.50.50.50.50.533333333333330.50.50.565217391304350.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.70.565789473684210.558823529411760.60.650.50.50.50.666666666666670.50.525641025641030.5
RAW_Sequence_Duplication_Levels0.512254901960780.555555555555560.543290043290040.549603174603170.533625730994150.644444444444440.50.50.533333333333330.572580645161290.607142857142860.881193124368050.50.50.583333333333330.541666666666670.56250.50.50.541666666666670.50.510.666666666666670.633333333333330.550.50.50.583333333333330.517543859649120.833333333333330.50.708333333333330.545454545454550.513888888888890.50.930555555555560.677287581699350.50.61422902494331
RAW_Overrepresented_sequences0.671568627450980.590277777777780.567099567099570.60317460317460.596491228070180.625925925925930.615151515151520.592592592592590.70.693548387096770.785714285714290.601112234580380.560606060606060.729166666666670.770833333333330.895833333333330.944444444444440.681818181818180.8571428571428611110.984848484848480.70.80.833333333333330.90.90.872807017543860.745098039215690.721428571428570.916666666666670.876623376623380.708333333333330.674358974358970.986111111111110.680843906189930.552447552447550.59608843537415
RAW_Adapter_Content0.514705882352940.50.50.50.50.522222222222220.50.50.50.564516129032260.50.645096056622850.893939393939390.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.56250.50.50.767925797770090.512820512820510.54166666666667
RAW_Kmer_Content0.564338235294120.666666666666670.590909090909090.64682539682540.555555555555560.511111111111110.633333333333330.537037037037040.50.772177419354840.607142857142860.565217391304350.590909090909090.50.593750.50.6250.545454545454550.607142857142860.666666666666670.550.6250.50.590909090909090.50.50.50.50.550.525219298245610.637254901960780.757142857142860.508333333333330.616883116883120.50.558974358974360.583333333333330.50.672494172494170.5
MAP_SE_no_mapping0.680759803921570.555555555555560.582251082251080.65476190476190.654970760233920.592592592592590.781818181818180.525252525252530.666666666666670.9354838709677410.743174924165820.573002754820940.791666666666670.91666666666667110.818181818181820.6428571428571410.91110.533333333333330.5110.933333333333330.962719298245610.901960784313730.80.750.961038961038960.916666666666670.953846153846151
MAP_SE_uniquely0.64215686274510.527777777777780.60389610389610.678571428571430.672514619883040.60.812121212121210.649831649831650.666666666666670.9354838709677410.796764408493430.603305785123970.583333333333330.9375110.727272727272730.7142857142857110.666666666666671110.566666666666670.5110.90.973684210526320.980392156862750.928571428571430.883333333333330.961038961038960.916666666666670.933333333333331
MAP_SE_multiple0.738664215686270.736111111111110.543290043290040.599206349206350.88596491228070.60370370370370.624242424242420.712121212121210.533333333333330.923387096774190.785714285714290.979777553083920.564738292011020.833333333333330.875110.909090909090910.71428571428571111110.866666666666670.5510.80.750.866228070175440.705882352941180.578571428571430.650.740259740259740.833333333333330.892307692307691
MAP_SE_overall0.680759803921570.555555555555560.582251082251080.65476190476190.654970760233920.592592592592590.781818181818180.525252525252530.666666666666670.9354838709677410.743174924165820.573002754820940.791666666666670.91666666666667110.818181818181820.6428571428571410.91110.533333333333330.5110.933333333333330.962719298245610.901960784313730.80.750.961038961038960.916666666666670.953846153846151
MAP_MI_no_mapping0.680759803921570.555555555555560.582251082251080.65476190476190.654970760233920.592592592592590.781818181818180.525252525252530.666666666666670.9354838709677410.743174924165820.573002754820940.791666666666670.91666666666667110.818181818181820.6428571428571410.91110.533333333333330.5110.933333333333330.962719298245610.901960784313730.80.750.961038961038960.916666666666670.9538461538461510.795751633986930.589743589743590.74716553287982
MAP_MI_uniquely0.64215686274510.527777777777780.60389610389610.678571428571430.672514619883040.60.812121212121210.649831649831650.666666666666670.9354838709677410.796764408493430.603305785123970.583333333333330.9375110.727272727272730.7142857142857110.666666666666671110.566666666666670.5110.90.973684210526320.980392156862750.928571428571430.883333333333330.961038961038960.916666666666670.9333333333333310.758602460592080.794871794871790.7624716553288
MAP_MI_multiple0.738664215686270.736111111111110.543290043290040.599206349206350.88596491228070.60370370370370.624242424242420.712121212121210.533333333333330.923387096774190.785714285714290.979777553083920.564738292011020.833333333333330.875110.909090909090910.71428571428571111110.866666666666670.5510.80.750.866228070175440.705882352941180.578571428571430.650.740259740259740.833333333333330.8923076923076910.792195309496350.743589743589740.5890022675737
MAP_MI_overall0.680759803921570.555555555555560.582251082251080.65476190476190.654970760233920.592592592592590.781818181818180.525252525252530.666666666666670.9354838709677410.743174924165820.573002754820940.791666666666670.91666666666667110.818181818181820.6428571428571410.91110.533333333333330.5110.933333333333330.962719298245610.901960784313730.80.750.961038961038960.916666666666670.9538461538461510.811466743560170.617715617715620.74178004535147
LOC_Promoter0.523284313725490.509259259259260.523809523809520.89682539682540.576023391812870.518518518518520.939393939393940.740740740740740.80.633064516129030.785714285714290.700707785642060.575757575757580.708333333333330.750.50.6250.636363636363640.571428571428570.666666666666670.80.7510.666666666666670.80.70.50.80.966666666666670.6557017543859610.80.950.545454545454550.541666666666670.605128205128210.972222222222220.773068050749710.727272727272730.96315192743764
LOC_5_UTR0.525122549019610.532407407407410.536796536796540.89682539682540.576023391812870.525925925925930.89696969696970.69696969696970.80.556451612903230.714285714285710.840242669362990.647382920110190.750.729166666666670.555555555555560.569444444444440.545454545454550.642857142857140.50.80.81250.90.636363636363640.566666666666670.70.50.750.966666666666670.535087719298250.941176470588240.864285714285710.966666666666670.584415584415580.513888888888890.507692307692310.638888888888890.735101883890810.785547785547790.92687074829932
LOC_3_UTR0.531862745098040.597222222222220.727272727272730.59523809523810.687134502923980.659259259259260.551515151515150.7643097643097610.64919354838710.642857142857140.519716885743170.793388429752070.791666666666670.8750.652777777777780.666666666666670.818181818181820.7142857142857110.5333333333333310.60.8787878787878810.50.666666666666670.60.866666666666670.50.725490196078430.571428571428570.866666666666670.649350649350650.722222222222220.5384615384615410.540945790080740.741258741258740.7046485260771
LOC_1st_Exon0.549632352941180.560185185185190.532467532467530.876984126984130.511695906432750.533333333333330.933333333333330.680134680134680.733333333333330.588709677419350.714285714285710.603640040444890.61983471074380.541666666666670.770833333333330.583333333333330.50.727272727272730.642857142857140.666666666666670.633333333333330.81250.90.666666666666670.60.80.583333333333330.70.966666666666670.592105263157890.980392156862750.8857142857142910.584415584415580.513888888888890.507692307692310.638888888888890.708958093041140.708624708624710.8656462585034
LOC_Other_Exon0.551470588235290.574074074074070.623376623376620.746031746031750.602339181286550.555555555555560.618181818181820.737373737373740.866666666666670.786290322580650.571428571428570.901921132457030.661157024793390.6250.895833333333330.680555555555560.527777777777780.727272727272730.571428571428570.916666666666670.866666666666670.93750.70.515151515151520.70.80.666666666666670.60.966666666666670.745614035087720.862745098039220.950.966666666666670.70129870129870.791666666666670.605128205128210.611111111111110.647539407920030.757575757575760.83786848072562
LOC_1st_Intron0.553308823529410.611111111111110.523809523809520.829365079365080.701754385964910.607407407407410.854545454545450.6565656565656610.669354838709680.571428571428570.574317492416580.567493112947660.6250.729166666666670.680555555555560.652777777777780.818181818181820.785714285714290.750.766666666666670.93750.80.666666666666670.633333333333330.60.916666666666670.70.90.5087719298245610.80.733333333333330.70129870129870.750.5179487179487210.571703191080350.526806526806530.84580498866213
LOC_Other_Intron0.509191176470590.708333333333330.727272727272730.757936507936510.669590643274850.570370370370370.884848484848480.710437710437710.733333333333330.737903225806450.928571428571430.639029322548030.719008264462810.666666666666670.666666666666670.597222222222220.541666666666670.7272727272727310.583333333333330.566666666666670.7510.787878787878790.80.80.50.70.70.546052631578950.60784313725490.792857142857140.916666666666670.805194805194810.750.5230769230769210.737504805843910.50349650349650.79818594104308
LOC_Downstream0.507352941176470.504629629629630.50216450216450.623015873015870.587719298245610.681481481481480.739393939393940.79797979797980.866666666666670.516129032258060.857142857142860.623862487360970.716253443526170.6250.750.569444444444440.652777777777780.818181818181820.571428571428570.666666666666670.633333333333330.812510.666666666666670.566666666666670.80.750.8510.535087719298250.705882352941180.835714285714290.90.519480519480520.597222222222220.512820512820510.666666666666670.677816224529030.582750582750580.74659863945578
LOC_Distal_Intergenic0.54840686274510.518518518518520.645021645021650.916666666666670.690058479532160.511111111111110.830303030303030.734006734006730.866666666666670.681451612903230.785714285714290.86855409504550.603305785123970.666666666666670.81250.555555555555560.527777777777780.727272727272730.714285714285710.666666666666670.80.750.80.515151515151520.50.80.750.60.90.5197368421052610.8285714285714310.727272727272730.597222222222220.5128205128205110.726066897347170.594405594405590.97108843537415
TSS_-45000.537990196078430.569444444444440.515151515151520.57341269841270.70467836257310.50370370370370.706060606060610.717171717171720.80.588709677419350.857142857142860.716885743174920.710743801652890.916666666666670.68750.597222222222220.652777777777780.636363636363640.642857142857140.833333333333330.70.8750.90.666666666666670.80.60.750.650.750.51096491228070.637254901960780.832142857142860.883333333333330.558441558441560.722222222222220.548717948717950.972222222222220.580738177623990.708624708624710.56349206349206
TSS_-35000.551470588235290.564814814814810.530303030303030.511904761904760.660818713450290.50370370370370.684848484848480.713804713804710.933333333333330.572580645161290.857142857142860.648129423660260.820936639118460.8750.645833333333330.652777777777780.597222222222220.818181818181820.785714285714290.750.633333333333330.812510.666666666666670.90.60.916666666666670.60.883333333333330.787280701754390.60784313725490.785714285714290.783333333333330.558441558441560.680555555555560.5897435897435910.558102652825840.682983682983680.5391156462585
TSS_-25000.516544117647060.620370370370370.549783549783550.60317460317460.643274853801170.548148148148150.69696969696970.6801346801346810.5645161290322610.60465116279070.707988980716250.791666666666670.770833333333330.638888888888890.680555555555560.818181818181820.642857142857140.750.80.81250.90.757575757575760.80.60.833333333333330.60.883333333333330.515350877192980.647058823529410.80.733333333333330.623376623376620.652777777777780.553846153846150.583333333333330.518502499038830.678321678321680.61904761904762
TSS_-15000.512254901960780.694444444444440.575757575757580.769841269841270.619883040935670.540740740740740.690909090909090.6632996632996610.536290322580650.785714285714290.507583417593530.581267217630850.791666666666670.729166666666670.597222222222220.611111111111110.818181818181820.785714285714290.750.733333333333330.812510.727272727272730.80.70.750.60.90.598684210526320.803921568627450.50.60.610389610389610.555555555555560.533333333333330.527777777777780.603517877739330.70396270396270.79365079365079
TSS_-5000.518382352941180.652777777777780.658008658008660.892857142857140.543859649122810.562962962962960.951515151515150.707070707070710.80.681451612903230.785714285714290.823053589484330.710743801652890.750.750.50.569444444444440.727272727272730.642857142857140.583333333333330.866666666666670.7510.636363636363640.80.60.50.850.883333333333330.7127192982456110.785714285714290.716666666666670.662337662337660.597222222222220.5128205128205110.792099192618220.818181818181820.94784580498866
TSS_+5000.520833333333330.532407407407410.645021645021650.880952380952380.56725146198830.540740740740740.933333333333330.659932659932660.80.729838709677420.857142857142860.84327603640040.680440771349860.750.729166666666670.50.583333333333330.636363636363640.642857142857140.750.80.7510.666666666666670.60.60.50.850.616666666666670.611842105263160.901960784313730.842857142857140.70.740259740259740.638888888888890.6666666666666710.772106881968470.811188811188810.87471655328798
TSS_+15000.509803921568630.666666666666670.536796536796540.85317460317460.532163742690060.548148148148150.787878787878790.723905723905720.866666666666670.530241935483870.857142857142860.783619817997980.840220385674930.541666666666670.750.569444444444440.666666666666670.818181818181820.50.750.766666666666670.750.90.606060606060610.633333333333330.80.583333333333330.60.90.675438596491230.764705882352940.742857142857140.550.649350649350650.652777777777780.5948717948717910.705113417916190.729603729603730.83786848072562
TSS_+25000.500612745098040.685185185185190.541125541125540.742063492063490.584795321637430.592592592592590.636363636363640.7104377104377110.596774193548390.857142857142860.70980788675430.713498622589530.833333333333330.854166666666670.611111111111110.6250.818181818181820.642857142857140.833333333333330.766666666666670.93750.80.757575757575760.80.60.750.60.916666666666670.710526315789470.60784313725490.578571428571430.866666666666670.584415584415580.513888888888890.656410256410260.805555555555560.538831218762010.734265734265730.7375283446712
TSS_+35000.503982843137250.648148148148150.567099567099570.706349206349210.549707602339180.585185185185190.509090909090910.7138047138047110.637096774193550.714285714285710.773003033367040.710743801652890.8750.750.6250.708333333333330.818181818181820.928571428571430.833333333333330.733333333333330.93750.90.606060606060610.550.50.666666666666670.70.916666666666670.564692982456140.568627450980390.507142857142860.933333333333330.571428571428570.638888888888890.743589743589740.972222222222220.527297193387160.69696969696970.71003401360544
TSS_+45000.522671568627450.606481481481480.584415584415580.682539682539680.532163742690060.540740740740740.515151515151520.7272727272727310.620967741935480.642857142857140.645096056622850.749311294765840.916666666666670.68750.666666666666670.722222222222220.818181818181820.714285714285710.833333333333330.666666666666670.8750.80.727272727272730.60.50.583333333333330.70.90.517543859649120.705882352941180.614285714285710.966666666666670.675324675324680.777777777777780.635897435897440.805555555555560.542243367935410.666666666666670.69387755102041
MAP_PE_con_no_mapping0.795751633986930.589743589743590.74716553287982
MAP_PE_con_uniquely0.758602460592080.794871794871790.7624716553288
MAP_PE_con_multiple0.792195309496350.743589743589740.5890022675737
MAP_PE_dis_uniquely0.675413302575930.736596736596740.61507936507937
MAP_PE_cod_no_mapping0.78734140715110.505827505827510.58446712018141
MAP_PE_cod_uniquely0.819059976931950.589743589743590.61111111111111
MAP_PE_cod_multiple0.735390234525180.636363636363640.59467120181406
MAP_PE_overall0.811466743560170.617715617715620.74178004535147

Group C Subsets (ChIP Antibody Specificity)

Area under ROC curves for group C subsets in the NGS guidelines. The higher the area, the better the classification.
 human__Control ChIP-seq__single-ended__Control__nanhuman__Histone ChIP-seq__single-ended__H3K4me1__ENCAB000ADWhuman__Histone ChIP-seq__single-ended__H3K36me3__ENCAB000ADUhuman__Histone ChIP-seq__single-ended__H3K27me3__ENCAB000ANBhuman__polyA plus RNA-seq__single-ended__nan__nanhuman__small RNA-seq__single-ended__nan__nanhuman__TF ChIP-seq__single-ended__MAX__ENCAB000AILhuman__TF ChIP-seq__single-ended__POLR2A__ENCAB000AOChuman__TF ChIP-seq__single-ended__MYC__ENCAB000AEThuman__Control ChIP-seq__single-ended__rabbit-IgG-control__ENCAB000AOJhuman__TF ChIP-seq__single-ended__RELA__ENCAB000AJGhuman__TF ChIP-seq__single-ended__JUND__ENCAB000AIDhuman__TF ChIP-seq__single-ended__MAZ__ENCAB000AIMhuman__TF ChIP-seq__single-ended__MXI1__ENCAB000AIThuman__TF ChIP-seq__single-ended__STAT3__ENCAB000ALHhuman__TF ChIP-seq__single-ended__BACH1__ENCAB000AEAhuman__TF ChIP-seq__single-ended__TCF7L2__ENCAB000AOAhuman__TF ChIP-seq__single-ended__FOS__ENCAB000AEQmouse__Control ChIP-seq__single-ended__Control__nanmouse__TF ChIP-seq__single-ended__POLR2A__ENCAB281FBQmouse__TF ChIP-seq__single-ended__CTCF__ENCAB210NHKhuman__Histone ChIP-seq__single-ended__H3K27ac__ENCAB000AQNhuman__DNase-seq__paired-ended__nan__nanhuman__Control ChIP-seq__paired-ended__Control__nanmouse__DNase-seq__paired-ended__nan__nan
RAW_Basic_Statistics0.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.5
RAW_Per_base_sequence_quality0.773284313725490.550.547058823529410.70.544994944388270.574380165289260.916666666666670.933333333333330.7510.545454545454551110.633333333333330.710.90.858333333333330.68750.833333333333330.666666666666670.514705882352940.50.53571428571429
RAW_Per_tile_sequence_quality0.54534313725490.58750.605882352941180.650.559150657229520.582644628099170.604166666666670.650.555555555555560.597222222222220.772727272727270.6250.90.727272727272730.533333333333330.80.90.650.702777777777780.656250.753968253968250.619047619047620.665897731641680.611888111888110.59722222222222
RAW_Per_sequence_quality_scores0.735294117647060.63750.617647058823530.650.543478260869570.57024793388430.979166666666670.966666666666670.9027777777777810.636363636363641110.666666666666670.710.90.872222222222220.666666666666670.80158730158730.50.514705882352940.50.5
RAW_Per_base_sequence_content0.575980392156860.750.582352941176470.850.572800808897880.50.531250.666666666666670.631944444444440.506944444444440.545454545454550.56250.550.50.80.60.650.50.594444444444440.8854166666666710.511904761904760.627450980392160.637529137529140.66666666666667
RAW_Per_sequence_GC_content0.586703431372550.6750.535294117647060.650.678968655207280.515151515151520.531250.583333333333330.583333333333330.750.681818181818180.68750.850.636363636363640.80.650.550.950.605555555555560.6250.587301587301590.571428571428570.735294117647060.59790209790210.67318594104308
RAW_Per_base_N_content0.726102941176470.6250.641176470588240.60.541961577350860.515151515151520.916666666666670.983333333333330.9166666666666710.50.93751110.70.950.90.741666666666670.666666666666670.571428571428570.666666666666670.514657823913880.50.5
RAW_Sequence_Length_Distribution0.526348039215690.50.50.50.565217391304350.50.50.50.50.50.50.50.50.50.50.50.50.50.569444444444440.50.50.583333333333330.50.525641025641030.5
RAW_Sequence_Duplication_Levels0.512254901960780.50.5588235294117610.881193124368050.50.583333333333330.60.541666666666670.56250.50.510.666666666666670.633333333333330.550.50.50.558333333333330.531250.50.571428571428570.677287581699350.50.61422902494331
RAW_Overrepresented_sequences0.671568627450980.550.529411764705880.60.601112234580380.560606060606060.770833333333330.866666666666670.895833333333330.944444444444440.68181818181818110.984848484848480.70.80.80.90.855555555555560.6250.547619047619050.785714285714290.680843906189930.552447552447550.59608843537415
RAW_Adapter_Content0.514705882352940.50.50.50.645096056622850.893939393939390.50.50.50.50.50.50.50.50.50.50.50.50.50.583333333333330.50.50.767925797770090.512820512820510.54166666666667
RAW_Kmer_Content0.564338235294120.50.50.50.565217391304350.590909090909090.593750.633333333333330.50.6250.545454545454550.6250.50.590909090909090.50.50.50.50.554166666666670.50.666666666666670.50.50.672494172494170.5
MAP_SE_no_mapping0.680759803921570.8250.735294117647060.60.743174924165820.573002754820940.916666666666670.96666666666667110.818181818181821110.533333333333330.5110.955555555555560.9166666666666710.73809523809524
MAP_SE_uniquely0.64215686274510.8750.723529411764710.60.796764408493430.603305785123970.93750.96666666666667110.727272727272731110.566666666666670.5110.969444444444440.8958333333333310.9047619047619
MAP_SE_multiple0.738664215686270.60.523529411764710.90.979777553083920.564738292011020.8750.96666666666667110.909090909090911110.866666666666670.5510.80.841666666666670.812510.97619047619048
MAP_SE_overall0.680759803921570.8250.735294117647060.60.743174924165820.573002754820940.916666666666670.96666666666667110.818181818181821110.533333333333330.5110.955555555555560.9166666666666710.73809523809524
MAP_MI_no_mapping0.680759803921570.8250.735294117647060.60.743174924165820.573002754820940.916666666666670.96666666666667110.818181818181821110.533333333333330.5110.955555555555560.9166666666666710.738095238095240.795751633986930.589743589743590.74716553287982
MAP_MI_uniquely0.64215686274510.8750.723529411764710.60.796764408493430.603305785123970.93750.96666666666667110.727272727272731110.566666666666670.5110.969444444444440.8958333333333310.90476190476190.758602460592080.794871794871790.7624716553288
MAP_MI_multiple0.738664215686270.60.523529411764710.90.979777553083920.564738292011020.8750.96666666666667110.909090909090911110.866666666666670.5510.80.841666666666670.812510.976190476190480.792195309496350.743589743589740.5890022675737
MAP_MI_overall0.680759803921570.8250.735294117647060.60.743174924165820.573002754820940.916666666666670.96666666666667110.818181818181821110.533333333333330.5110.955555555555560.9166666666666710.738095238095240.811466743560170.617715617715620.74178004535147
LOC_Promoter0.523284313725490.70.7294117647058810.700707785642060.575757575757580.750.666666666666670.50.6250.636363636363640.7510.666666666666670.80.70.60.80.652777777777780.520833333333330.587301587301590.976190476190480.773068050749710.727272727272730.96315192743764
LOC_5_UTR0.525122549019610.50.6941176470588210.840242669362990.647382920110190.729166666666670.566666666666670.555555555555560.569444444444440.545454545454550.81250.90.636363636363640.566666666666670.70.60.750.533333333333330.56250.523809523809520.976190476190480.735101883890810.785547785547790.92687074829932
LOC_3_UTR0.531862745098040.80.7647058823529410.519716885743170.793388429752070.8750.766666666666670.652777777777780.666666666666670.8181818181818210.60.8787878787878810.50.60.60.527777777777780.770833333333330.555555555555560.928571428571430.540945790080740.741258741258740.7046485260771
LOC_1st_Exon0.549632352941180.8750.7294117647058810.603640040444890.61983471074380.770833333333330.666666666666670.583333333333330.50.727272727272730.81250.90.666666666666670.60.80.50.70.605555555555560.56250.507936507936510.976190476190480.708958093041140.708624708624710.8656462585034
LOC_Other_Exon0.551470588235290.7250.6823529411764710.901921132457030.661157024793390.895833333333330.833333333333330.680555555555560.527777777777780.727272727272730.93750.70.515151515151520.70.80.60.60.727777777777780.750.650793650793650.90476190476190.647539407920030.757575757575760.83786848072562
LOC_1st_Intron0.553308823529410.5750.6235294117647110.574317492416580.567493112947660.729166666666670.80.680555555555560.652777777777780.818181818181820.93750.80.666666666666670.633333333333330.610.70.572222222222220.729166666666670.523809523809520.952380952380950.571703191080350.526806526806530.84580498866213
LOC_Other_Intron0.509191176470590.7250.6823529411764710.639029322548030.719008264462810.666666666666670.60.597222222222220.541666666666670.727272727272730.7510.787878787878790.80.80.50.70.508333333333330.708333333333330.650793650793650.761904761904760.737504805843910.50349650349650.79818594104308
LOC_Downstream0.507352941176470.7750.6823529411764710.623862487360970.716253443526170.750.533333333333330.569444444444440.652777777777780.818181818181820.812510.666666666666670.566666666666670.80.70.850.527777777777780.708333333333330.619047619047620.547619047619050.677816224529030.582750582750580.74659863945578
LOC_Distal_Intergenic0.54840686274510.80.7058823529411810.86855409504550.603305785123970.81250.733333333333330.555555555555560.527777777777780.727272727272730.750.80.515151515151520.50.80.90.60.5250.68750.523809523809520.976190476190480.726066897347170.594405594405590.97108843537415
TSS_-45000.537990196078430.70.6705882352941210.716885743174920.710743801652890.68750.516666666666670.597222222222220.652777777777780.636363636363640.8750.90.666666666666670.80.60.70.650.586111111111110.729166666666670.507936507936510.59523809523810.580738177623990.708624708624710.56349206349206
TSS_-35000.551470588235290.6750.6529411764705910.648129423660260.820936639118460.645833333333330.566666666666670.652777777777780.597222222222220.818181818181820.812510.666666666666670.90.60.90.60.752777777777780.645833333333330.730158730158730.738095238095240.558102652825840.682983682983680.5391156462585
TSS_-25000.516544117647060.750.6235294117647110.60465116279070.707988980716250.770833333333330.60.638888888888890.680555555555560.818181818181820.81250.90.757575757575760.80.60.80.60.5250.666666666666670.682539682539680.809523809523810.518502499038830.678321678321680.61904761904762
TSS_-15000.512254901960780.7750.6352941176470610.507583417593530.581267217630850.729166666666670.566666666666670.597222222222220.611111111111110.818181818181820.812510.727272727272730.80.70.70.60.60.708333333333330.666666666666670.952380952380950.603517877739330.70396270396270.79365079365079
TSS_-5000.518382352941180.650.5058823529411810.823053589484330.710743801652890.750.733333333333330.50.569444444444440.727272727272730.7510.636363636363640.80.60.60.850.730555555555560.56250.523809523809520.976190476190480.792099192618220.818181818181820.94784580498866
TSS_+5000.520833333333330.650.5294117647058810.84327603640040.680440771349860.729166666666670.633333333333330.50.583333333333330.636363636363640.7510.666666666666670.60.60.60.850.686111111111110.6250.841269841269840.976190476190480.772106881968470.811188811188810.87471655328798
TSS_+15000.509803921568630.6750.6705882352941210.783619817997980.840220385674930.750.60.569444444444440.666666666666670.818181818181820.750.90.606060606060610.633333333333330.80.70.60.641666666666670.6250.730158730158730.952380952380950.705113417916190.729603729603730.83786848072562
TSS_+25000.500612745098040.7750.7058823529411810.70980788675430.713498622589530.854166666666670.533333333333330.611111111111110.6250.818181818181820.93750.80.757575757575760.80.60.70.60.680555555555560.541666666666670.857142857142860.928571428571430.538831218762010.734265734265730.7375283446712
TSS_+35000.503982843137250.80.7411764705882410.773003033367040.710743801652890.750.533333333333330.6250.708333333333330.818181818181820.93750.90.606060606060610.550.50.60.70.658333333333330.583333333333330.936507936507940.928571428571430.527297193387160.69696969696970.71003401360544
TSS_+45000.522671568627450.750.7294117647058810.645096056622850.749311294765840.68750.666666666666670.666666666666670.722222222222220.818181818181820.8750.80.727272727272730.60.50.50.70.505555555555560.770833333333330.746031746031750.928571428571430.542243367935410.666666666666670.69387755102041
MAP_PE_con_no_mapping0.795751633986930.589743589743590.74716553287982
MAP_PE_con_uniquely0.758602460592080.794871794871790.7624716553288
MAP_PE_con_multiple0.792195309496350.743589743589740.5890022675737
MAP_PE_dis_uniquely0.675413302575930.736596736596740.61507936507937
MAP_PE_cod_no_mapping0.78734140715110.505827505827510.58446712018141
MAP_PE_cod_uniquely0.819059976931950.589743589743590.61111111111111
MAP_PE_cod_multiple0.735390234525180.636363636363640.59467120181406
MAP_PE_overall0.811466743560170.617715617715620.74178004535147