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["Supplementary Data S1: Quality metrics for MBD-seq data"]
[]
["A: Pair-wise Pearson correlation between samples (MEDIPS.correlation)"]
[]
[null,null,"Liver1","Liver2","Liver3","Liver4","Liver5","Liver6","Liver7","Liver8","Liver9","Liver10","Liver11"]
[null,"Liver1",1,0.90301354199999995,0.87481183900000004,0.87144952099999995,0.88488185699999999,0.86885084099999998,0.85943772699999998,0.78820123900000005,0.85370584299999996,0.85425539500000003,0.867218559]
[null,"Liver2",null,1,0.86803735400000004,0.864425059,0.88547068100000004,0.86126503399999998,0.85555476799999997,0.769077703,0.85282142299999997,0.84791408099999999,0.86642672200000004]
[null,"Liver3",null,null,1,0.87513434099999998,0.86691137399999996,0.87291792700000004,0.84389550599999996,0.80171877400000002,0.82263292499999996,0.84839538299999995,0.83930062100000002]
[null,"Liver4",null,null,null,1,0.86052229599999996,0.87184675199999995,0.83837625699999996,0.80700907799999999,0.81745966800000003,0.84307877600000003,0.833517116]
[null,"Liver5",{"$nulls":4},1,0.86343888199999996,0.844427869,0.77548037999999997,0.85168786500000004,0.84607194900000005,0.85742744800000004]
[null,"Liver6",{"$nulls":5},1,0.83751188600000004,0.81039288700000001,0.82205597600000002,0.84542347799999995,0.8371828]
[null,"Liver7",{"$nulls":6},1,0.80885923000000004,0.86665248299999997,0.87156543200000003,0.88049089300000005]
[null,"Liver8",{"$nulls":7},1,0.78016522700000002,0.81171418299999998,0.79258744599999997]
[null,"Liver9",{"$nulls":8},1,0.86692256700000003,0.891381902]
[null,"Liver10",{"$nulls":9},1,0.88172161599999999]
[null,"Liver11",{"$nulls":10},1]
[]
[]
["B: CpG enrichment in seqeunced fragments(MEDIPS.CpGenrich function)"]
["This shows CpG counts among the sequenced DNA fragments, and CpG enrichment (calculated as relevative frequency of CpG in read fragments divided by the relative frequency of CpG in the reference genome)"]
["Column annotations provided here:",null,"regions.CG = number of CpGs within regions covered by sequenced reads","regions.C = number of Cs within regions covered by sequenced reads","regions.G = number of Gs within regions covered by sequenced reads","regions.relH = relative frequency of CpGs within regions covered by sequenced reads","regions.GoGe = Observed/expected ratio  of CpGs within regions covered by sequenced reads","genome.C = number of Cs within reference genome","genome.G = number of Gs within reference genome","genome.CG = number of CGs within reference genome","genome.relH = relative frequency of CpGs within reference genome","genome.GoGe = observed/expected ratio  of CpGs within reference genome","enrichment.score.relH = enrichment in relative frequency in CpGs in the sequenced fragments (regions.relH/genome.relH)","enrichment.score.GoGe = ratio of observed vs expected CpHs in sequenced reads relative to reference (regions.GoGe/genome.GoGe)"]
["Sample","ReferenceGenome","regions.CG","regions.C","regions.G","regions.relH","regions.GoGe","genome.C","genome.G","genome.CG","genome.relH","genome.GoGe","enrichment.score.relH","enrichment.score.GoGe"]
["Liver1","Mmusculus.UCSC.mm10",61759183,753620416,755052447,1.92489421335247,0.34823020844771302,551559571,551598209,21867837,0.80233112345951596,0.19590374768253399,2.3991269403244,1.77755766577793]
["Liver2","Mmusculus.UCSC.mm10",54629881,631722915,632984664,2.0484664440000002,0.36434418000000002,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.5531434399999999,1.859812198]
["Liver3","Mmusculus.UCSC.mm10",54096571,732647802,734863854,1.716832248,0.31659895399999999,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.1398051229999999,1.616094422]
["Liver4","Mmusculus.UCSC.mm10",55404672,755853583,756607785,1.6984980780000001,0.31602339499999998,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.116953997,1.613156456]
["Liver5","Mmusculus.UCSC.mm10",47410522,600247988,601581248,1.8540701390000001,0.33573630900000001,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.3108540670000002,1.7137819599999999]
["Liver6","Mmusculus.UCSC.mm10",62821167,879226320,880818645,1.644448828,0.309887784,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.04958873,1.5818369370000001]
["Liver7","Mmusculus.UCSC.mm10",50829243,639634075,641380954,1.853783446,0.33971962300000003,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.3104967410000001,1.7341149760000001]
["Liver8","Mmusculus.UCSC.mm10",58004906,861016319,862365959,1.5337664740000001,0.29543859300000003,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,1.9116377630000001,1.5080803540000001]
["Liver9","Mmusculus.UCSC.mm10",56274066,705924413,707923022,1.858742492,0.34092050800000001,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.316677538,1.740244951]
["Liver10","Mmusculus.UCSC.mm10",58438914,777433594,779168485,1.7415983749999999,0.32371407400000002,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.170672836,1.652413889]
["Liver11","Mmusculus.UCSC.mm10",60889902,745561949,746730469,1.913586147,0.348012565,551559571,551598209,21867837,0.80233112299999998,0.19590374799999999,2.385032925,1.776446695]
[]
[]
["C: CpG coverage (MEDIPS.seqCoverage function)"]
[]
["Total number of CGs in the reference GRCm38/mm10 reference genome: 21867837"]
[]
["Number of reads that map to a CpG pattern","Liver1 (%)","Liver2 (%)","Liver3 (%)","Liver4 (%)","Liver5 (%)","Liver6 (%)","Liver7 (%)","Liver8 (%)","Liver9 (%)","Liver10 (%)","Liver11 (%)","Average (% coverage)"]
[0,46.22,52.07,47.08,44.15,50.75,39.659999999999997,48.49,36.79,44.74,43.05,45.09,45.280909090909091,"On average, 45% of CG patterns were not covered by a single short fragment"]
[1,15.39,14.62,14.62,15.38,15.64,15.8,15.59,15.58,17.34,16.13,16.309999999999999,15.672727272727274]
[2,8.8699999999999992,7.73,8.7100000000000009,9.52,8.7100000000000009,10.210000000000001,8.85,10.97,10.19,9.84,9.44,9.3672727272727272]
[3,5.82,4.9400000000000004,5.92,6.58,5.59,7.17,5.81,8.25,6.46,6.65,6.1,6.299090909090908]
[4,4.17,3.5,4.37,4.8499999999999996,3.92,5.3,4.13,6.36,4.32,4.7699999999999996,4.26,4.5409090909090901]
[5,3.14,2.67,3.39,3.72,2.89,4.07,3.11,5,3.07,3.59,3.15,3.436363636363637]
[">5",16.38,14.48,15.6,15.8,12.5,17.8,14.01,17.05,13.89,15.97,15.66,15.376363636363635,"On average, 15 % of CpG patterns were not covered by more than 5 reads"]
[]
["Summary:"]
[null,"Liver1","Liver2","Liver3","Liver4","Liver5","Liver6","Liver7","Liver8","Liver9","Liver10","Liver11","Average"]
["total aligned reads",10659297,8860034,10468283,10837155,8495368,12691701,9109375,12564343,10058270,11147770,10571366,10496632.909090908]
["Reads that do not cover CG pattern",279990,201150,375738,368240,267828,508395,260148,483469,320156,415034,324047,345835.90909090912]
["Reads that do not cover pattern (%)",2.63,2.27,3.59,3.4,3.15,4.01,2.86,3.85,3.18,3.72,3.07,3.2481818181818185,"On average, 3 % of reads did not map to a CG pattern"]
[]
[]
["D: Average coverage by CpG density"]
["CF (coupling factor) is the number of CpGs in a window."]
[]
["Total bins (500 bp windows)",5451088]
["Mean CF per bin",4.0119999999999996]
["Median CF per bin",3]
[]
[]
[null,"Total","CF=0","0<CF<3","CF>=3"]
["Number of bins",5451088,595064,1705811,3150213]
["Average reads counts",3.081,0.44109999999999999,1.026,4.6929999999999996]